Starting phenix.real_space_refine on Sat Jul 4 23:56:48 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8h9e_34564/07_2026/8h9e_34564.cif Found real_map, /net/cci-nas-00/data/ceres_data/8h9e_34564/07_2026/8h9e_34564.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.53 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/8h9e_34564/07_2026/8h9e_34564.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8h9e_34564/07_2026/8h9e_34564.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8h9e_34564/07_2026/8h9e_34564.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8h9e_34564/07_2026/8h9e_34564.map" model { file = "/net/cci-nas-00/data/ceres_data/8h9e_34564/07_2026/8h9e_34564.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8h9e_34564/07_2026/8h9e_34564.cif" } resolution = 2.53 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.029 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 87 5.16 5 C 15234 2.51 5 N 4210 2.21 5 O 4665 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 212 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 24214 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 3830 Number of conformers: 1 Conformer: "" Number of residues, atoms: 503, 3830 Classifications: {'peptide': 503} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 484} Chain breaks: 1 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: 3714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 487, 3714 Classifications: {'peptide': 487} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 468} 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: "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: "J" Number of atoms: 270 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 270 Classifications: {'peptide': 35} Link IDs: {'TRANS': 34} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 5.53, per 1000 atoms: 0.23 Number of scatterers: 24214 At special positions: 0 Unit cell: (132.86, 124.1, 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 87 16.00 P 13 15.00 Mg 5 11.99 O 4665 8.00 N 4210 7.00 C 15234 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.11 Conformation dependent library (CDL) restraints added in 1.4 seconds 6268 Ramachandran restraints generated. 3134 Oldfield, 0 Emsley, 3134 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5740 Finding SS restraints... Secondary structure from input PDB file: 146 helices and 20 sheets defined 51.5% alpha, 14.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.81 Creating SS restraints... Processing helix chain 'A' and resid 8 through 18 Processing helix chain 'A' and resid 78 through 82 removed outlier: 3.858A pdb=" N LEU A 81 " --> pdb=" O ASN A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 100 through 104 removed outlier: 3.508A 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: 3.806A pdb=" N GLN A 186 " --> pdb=" O THR A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 192 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: 3.993A pdb=" N PHE A 257 " --> pdb=" O MET A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 285 removed outlier: 3.661A 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 removed outlier: 3.520A pdb=" N GLY A 317 " --> pdb=" O ASP A 314 " (cutoff:3.500A) 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: 3.589A pdb=" N ALA A 377 " --> pdb=" O VAL A 374 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 401 removed outlier: 3.994A 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 428 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 508 Processing helix chain 'B' and resid 78 through 82 Processing helix chain 'B' and resid 100 through 104 removed outlier: 3.638A 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 removed outlier: 3.625A pdb=" N LYS B 198 " --> pdb=" O GLU B 195 " (cutoff:3.500A) 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 260 Proline residue: B 247 - end of helix removed outlier: 3.990A pdb=" N PHE B 257 " --> pdb=" O MET B 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 270 through 285 Processing helix chain 'B' and resid 290 through 294 Processing helix chain 'B' and resid 297 through 307 removed outlier: 3.743A pdb=" N HIS B 302 " --> pdb=" O VAL B 298 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N LEU B 305 " --> pdb=" O LEU B 301 " (cutoff:3.500A) Processing helix chain 'B' and resid 313 through 317 Processing helix chain 'B' and resid 336 through 346 Processing helix chain 'B' and resid 353 through 359 Processing helix chain 'B' and resid 380 through 401 removed outlier: 4.384A pdb=" N THR B 389 " --> pdb=" O GLN B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 413 through 429 removed outlier: 3.631A 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 451 through 455 removed outlier: 3.680A pdb=" N LYS B 455 " --> pdb=" O TYR B 452 " (cutoff:3.500A) 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 476 Processing helix chain 'B' and resid 476 through 487 Processing helix chain 'B' and resid 490 through 507 Processing helix chain 'C' and resid 78 through 82 removed outlier: 3.758A pdb=" N LEU C 81 " --> pdb=" O ASN C 78 " (cutoff:3.500A) Processing helix chain 'C' and resid 100 through 104 removed outlier: 3.556A pdb=" N LEU C 103 " --> pdb=" O GLY C 100 " (cutoff:3.500A) Processing helix chain 'C' and resid 150 through 157 Processing helix chain 'C' and resid 174 through 186 removed outlier: 3.738A 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 194 through 197 removed outlier: 3.543A pdb=" N LYS C 197 " --> pdb=" O ASP C 194 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 194 through 197' 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 260 Proline residue: C 247 - end of helix removed outlier: 4.128A pdb=" N PHE C 257 " --> pdb=" O MET C 253 " (cutoff:3.500A) Processing helix chain 'C' and resid 270 through 285 removed outlier: 3.651A 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: 3.788A pdb=" N LEU C 305 " --> pdb=" O LEU C 301 " (cutoff:3.500A) Processing helix chain 'C' and resid 313 through 317 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 Processing helix chain 'C' and resid 380 through 400 removed outlier: 4.031A pdb=" N THR C 389 " --> pdb=" O GLN C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 418 through 429 Processing helix chain 'C' and resid 437 through 450 Processing helix chain 'C' and resid 457 through 459 No H-bonds generated for 'chain 'C' and resid 457 through 459' Processing helix chain 'C' and resid 460 through 476 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 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: 4.897A pdb=" N ALA E 236 " --> pdb=" O ARG E 232 " (cutoff:3.500A) removed outlier: 5.046A pdb=" N LEU E 237 " --> pdb=" O ALA E 233 " (cutoff:3.500A) Processing helix chain 'E' and resid 260 through 275 removed outlier: 3.601A pdb=" N PHE E 264 " --> pdb=" O ASN E 260 " (cutoff:3.500A) Processing helix chain 'E' and resid 280 through 284 removed outlier: 3.518A pdb=" N TYR E 284 " --> pdb=" O ALA E 281 " (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 344 Processing helix chain 'E' and resid 362 through 367 Processing helix chain 'E' and resid 367 through 391 removed outlier: 3.582A pdb=" N ILE E 390 " --> pdb=" O SER E 386 " (cutoff:3.500A) Processing helix chain 'E' and resid 402 through 418 removed outlier: 3.940A 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 450 Processing helix chain 'E' and resid 456 through 460 removed outlier: 3.533A pdb=" N PHE E 460 " --> pdb=" O GLU E 457 " (cutoff:3.500A) Processing helix chain 'E' and resid 465 through 475 removed outlier: 3.716A 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 Processing helix chain 'F' and resid 140 through 147 Processing helix chain 'F' and resid 164 through 177 Processing helix chain 'F' and resid 192 through 206 Processing helix chain 'F' and resid 228 through 249 removed outlier: 4.939A pdb=" N ALA F 236 " --> pdb=" O ARG F 232 " (cutoff:3.500A) removed outlier: 5.023A pdb=" N LEU F 237 " --> pdb=" O ALA F 233 " (cutoff:3.500A) Processing helix chain 'F' and resid 261 through 275 removed outlier: 4.021A pdb=" N THR F 265 " --> pdb=" O ILE F 261 " (cutoff:3.500A) removed outlier: 4.190A 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 Processing helix chain 'F' and resid 362 through 394 removed outlier: 7.794A pdb=" N SER F 368 " --> pdb=" O ASN F 364 " (cutoff:3.500A) removed outlier: 9.402A pdb=" N GLU F 369 " --> pdb=" O ILE F 365 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N HIS F 370 " --> pdb=" O VAL F 366 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N ASP F 389 " --> pdb=" O LYS F 385 " (cutoff:3.500A) removed outlier: 5.359A pdb=" N ILE F 390 " --> pdb=" O SER F 386 " (cutoff:3.500A) Processing helix chain 'F' and resid 395 through 399 removed outlier: 3.895A pdb=" N GLU F 398 " --> pdb=" O GLY F 395 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LEU F 399 " --> pdb=" O MET F 396 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 395 through 399' Processing helix chain 'F' and resid 400 through 418 removed outlier: 3.786A pdb=" N SER F 418 " --> pdb=" O GLN F 414 " (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 Processing helix chain 'D' and resid 90 through 94 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 206 Processing helix chain 'D' and resid 228 through 249 removed outlier: 4.872A pdb=" N ALA D 236 " --> pdb=" O ARG D 232 " (cutoff:3.500A) removed outlier: 5.037A pdb=" N LEU D 237 " --> pdb=" O ALA D 233 " (cutoff:3.500A) Processing helix chain 'D' and resid 261 through 273 removed outlier: 4.038A pdb=" N THR D 265 " --> pdb=" O ILE D 261 " (cutoff:3.500A) removed outlier: 4.550A 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: 3.724A 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 345 Processing helix chain 'D' and resid 367 through 395 removed outlier: 4.177A pdb=" N ASP D 389 " --> pdb=" O LYS D 385 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N ILE D 390 " --> pdb=" O SER D 386 " (cutoff:3.500A) Processing helix chain 'D' and resid 396 through 399 removed outlier: 3.856A pdb=" N LEU D 399 " --> pdb=" O MET D 396 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 396 through 399' Processing helix chain 'D' and resid 400 through 418 removed outlier: 3.666A pdb=" N SER D 418 " --> pdb=" O GLN D 414 " (cutoff:3.500A) Processing helix chain 'D' and resid 421 through 423 No H-bonds generated for 'chain 'D' and resid 421 through 423' Processing helix chain 'D' and resid 424 through 429 Processing helix chain 'D' and resid 436 through 450 Processing helix chain 'D' and resid 456 through 461 Processing helix chain 'D' and resid 465 through 480 Processing helix chain 'G' and resid 3 through 32 removed outlier: 3.683A pdb=" N ALA G 32 " --> pdb=" O ALA G 28 " (cutoff:3.500A) Processing helix chain 'G' and resid 224 through 271 Processing helix chain 'O' and resid 12 through 28 Processing helix chain 'O' and resid 31 through 48 removed outlier: 3.748A pdb=" N GLU O 48 " --> pdb=" O GLN O 44 " (cutoff:3.500A) Processing helix chain 'O' and resid 48 through 56 Processing helix chain 'O' and resid 61 through 76 removed outlier: 3.715A pdb=" N GLU O 76 " --> pdb=" O ILE O 72 " (cutoff:3.500A) Processing helix chain 'O' and resid 79 through 92 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 155 through 159 removed outlier: 3.663A pdb=" N ILE O 158 " --> pdb=" O ASP O 155 " (cutoff:3.500A) Processing helix chain 'O' and resid 174 through 188 removed outlier: 3.749A pdb=" N LYS O 178 " --> pdb=" O SER O 174 " (cutoff:3.500A) Processing helix chain 'J' and resid 13 through 18 Processing helix chain 'J' and resid 20 through 45 removed outlier: 3.948A pdb=" N ALA J 44 " --> pdb=" O GLU J 40 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 60 through 66 removed outlier: 3.920A pdb=" N GLU A 51 " --> pdb=" O SER A 63 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N MET A 52 " --> pdb=" O THR A 91 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N ARG A 40 " --> pdb=" O LEU A 32 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N ILE A 34 " --> pdb=" O ILE A 38 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N ILE A 38 " --> pdb=" O ILE A 34 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N VAL A 74 " --> pdb=" O SER A 63 " (cutoff:3.500A) removed outlier: 5.929A pdb=" N SER A 63 " --> pdb=" O VAL A 74 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N ARG E 62 " --> pdb=" O ALA E 53 " (cutoff:3.500A) removed outlier: 4.949A pdb=" N HIS E 55 " --> pdb=" O THR E 60 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N THR E 60 " --> pdb=" O HIS E 55 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N VAL E 23 " --> pdb=" O VAL E 19 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N VAL E 19 " --> pdb=" O VAL E 23 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N ASP E 25 " --> pdb=" O VAL E 17 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 96 through 99 removed outlier: 4.087A 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: 6.522A pdb=" N ALA A 264 " --> pdb=" O THR A 322 " (cutoff:3.500A) removed outlier: 8.017A pdb=" N LEU A 324 " --> pdb=" O ALA A 264 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N ILE A 266 " --> pdb=" O LEU A 324 " (cutoff:3.500A) removed outlier: 7.430A pdb=" N VAL A 326 " --> pdb=" O ILE A 266 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N TYR A 268 " --> pdb=" O VAL A 326 " (cutoff:3.500A) removed outlier: 8.058A pdb=" N GLU A 328 " --> pdb=" O TYR A 268 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N LEU A 166 " --> pdb=" O ILE A 350 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N LEU A 352 " --> pdb=" O LEU A 166 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N ILE A 168 " --> pdb=" O LEU A 352 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 60 through 66 removed outlier: 4.117A pdb=" N GLU B 51 " --> pdb=" O SER B 63 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N MET B 52 " --> pdb=" O THR B 91 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N ARG B 40 " --> pdb=" O LEU B 32 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N ILE B 34 " --> pdb=" O ILE B 38 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N ILE B 38 " --> pdb=" O ILE B 34 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N GLY B 72 " --> pdb=" O LEU B 64 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N LYS B 60 " --> pdb=" O PHE B 76 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N ARG F 62 " --> pdb=" O ALA F 53 " (cutoff:3.500A) removed outlier: 5.060A pdb=" N HIS F 55 " --> pdb=" O THR F 60 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N THR F 60 " --> pdb=" O HIS F 55 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N VAL F 23 " --> pdb=" O VAL F 19 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N VAL F 19 " --> pdb=" O VAL F 23 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N ASP F 25 " --> pdb=" O VAL F 17 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 96 through 99 removed outlier: 4.138A pdb=" N THR B 125 " --> pdb=" O VAL B 99 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 107 through 109 removed outlier: 6.515A pdb=" N ALA B 264 " --> pdb=" O THR B 322 " (cutoff:3.500A) removed outlier: 7.966A pdb=" N LEU B 324 " --> pdb=" O ALA B 264 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N ILE B 266 " --> pdb=" O LEU B 324 " (cutoff:3.500A) removed outlier: 7.465A pdb=" N VAL B 326 " --> pdb=" O ILE B 266 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N TYR B 268 " --> pdb=" O VAL B 326 " (cutoff:3.500A) removed outlier: 8.108A pdb=" N GLU B 328 " --> pdb=" O TYR B 268 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N LEU B 166 " --> pdb=" O ILE B 350 " (cutoff:3.500A) removed outlier: 7.492A pdb=" N LEU B 352 " --> pdb=" O LEU B 166 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N ILE B 168 " --> pdb=" O LEU B 352 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 145 through 146 removed outlier: 4.472A pdb=" N ILE B 159 " --> pdb=" O MET B 146 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 26 through 35 removed outlier: 6.622A pdb=" N ARG C 40 " --> pdb=" O LEU C 32 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N ILE C 34 " --> pdb=" O ILE C 38 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N ILE C 38 " --> pdb=" O ILE C 34 " (cutoff:3.500A) 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: 5.751A pdb=" N SER C 63 " --> pdb=" O VAL C 74 " (cutoff:3.500A) removed outlier: 6.947A 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 '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: 6.592A pdb=" N ARG D 62 " --> pdb=" O ALA D 53 " (cutoff:3.500A) removed outlier: 5.010A pdb=" N HIS D 55 " --> pdb=" O THR D 60 " (cutoff:3.500A) removed outlier: 7.181A 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=AA9, first strand: chain 'C' and resid 96 through 99 removed outlier: 4.089A pdb=" N THR C 125 " --> pdb=" O VAL C 99 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 107 through 108 removed outlier: 6.505A pdb=" N VAL C 108 " --> pdb=" O SER C 233 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N ALA C 264 " --> pdb=" O THR C 322 " (cutoff:3.500A) removed outlier: 8.178A pdb=" N LEU C 324 " --> pdb=" O ALA C 264 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N ILE C 266 " --> pdb=" O LEU C 324 " (cutoff:3.500A) removed outlier: 7.603A pdb=" N VAL C 326 " --> pdb=" O ILE C 266 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N TYR C 268 " --> pdb=" O VAL C 326 " (cutoff:3.500A) removed outlier: 8.028A pdb=" N GLU C 328 " --> pdb=" O TYR C 268 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N LEU C 166 " --> pdb=" O ILE C 350 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 145 through 146 removed outlier: 4.458A pdb=" N ILE C 159 " --> pdb=" O MET C 146 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 86 through 89 removed outlier: 4.548A pdb=" N GLN E 115 " --> pdb=" O VAL E 89 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 97 through 98 removed outlier: 6.417A pdb=" N MET E 98 " --> pdb=" O TYR E 222 " (cutoff:3.500A) removed outlier: 7.959A pdb=" N GLN E 224 " --> pdb=" O MET E 98 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N VAL E 185 " --> pdb=" O PHE E 257 " (cutoff:3.500A) removed outlier: 7.757A pdb=" N ASP E 259 " --> pdb=" O VAL E 185 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N ALA E 187 " --> pdb=" O ASP E 259 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N VAL E 254 " --> pdb=" O THR E 308 " (cutoff:3.500A) removed outlier: 7.473A pdb=" N VAL E 310 " --> pdb=" O VAL E 254 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N LEU E 256 " --> pdb=" O VAL E 310 " (cutoff:3.500A) removed outlier: 7.706A pdb=" N ALA E 312 " --> pdb=" O LEU E 256 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N ILE E 258 " --> pdb=" O ALA E 312 " (cutoff:3.500A) removed outlier: 5.977A pdb=" N ILE E 155 " --> pdb=" O GLN E 311 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N LYS E 154 " --> pdb=" O ALA E 334 " (cutoff:3.500A) removed outlier: 7.896A pdb=" N THR E 336 " --> pdb=" O LYS E 154 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N GLY E 156 " --> pdb=" O THR E 336 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 135 through 136 removed outlier: 4.372A pdb=" N TYR E 149 " --> pdb=" O LEU E 136 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 86 through 89 removed outlier: 4.337A pdb=" N GLN F 115 " --> pdb=" O VAL F 89 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 97 through 98 removed outlier: 6.400A pdb=" N MET F 98 " --> pdb=" O TYR F 222 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N VAL F 254 " --> pdb=" O THR F 308 " (cutoff:3.500A) removed outlier: 7.886A pdb=" N VAL F 310 " --> pdb=" O VAL F 254 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N LEU F 256 " --> pdb=" O VAL F 310 " (cutoff:3.500A) removed outlier: 7.783A pdb=" N ALA F 312 " --> pdb=" O LEU F 256 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N ILE F 258 " --> pdb=" O ALA F 312 " (cutoff:3.500A) removed outlier: 8.074A pdb=" N TYR F 314 " --> pdb=" O ILE F 258 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N LYS F 154 " --> pdb=" O ALA F 334 " (cutoff:3.500A) removed outlier: 7.786A pdb=" N THR F 336 " --> pdb=" O LYS F 154 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N GLY F 156 " --> pdb=" O THR F 336 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 135 through 136 removed outlier: 4.218A pdb=" N TYR F 149 " --> pdb=" O LEU F 136 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 86 through 89 removed outlier: 4.398A pdb=" N GLN D 115 " --> pdb=" O VAL D 89 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 97 through 98 removed outlier: 6.316A pdb=" N MET D 98 " --> pdb=" O TYR D 222 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N VAL D 254 " --> pdb=" O THR D 308 " (cutoff:3.500A) removed outlier: 7.697A pdb=" N VAL D 310 " --> pdb=" O VAL D 254 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N LEU D 256 " --> pdb=" O VAL D 310 " (cutoff:3.500A) removed outlier: 7.522A pdb=" N ALA D 312 " --> pdb=" O LEU D 256 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N ILE D 258 " --> pdb=" O ALA D 312 " (cutoff:3.500A) removed outlier: 7.865A pdb=" N TYR D 314 " --> pdb=" O ILE D 258 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N PHE D 158 " --> pdb=" O LEU D 338 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 135 through 136 removed outlier: 4.238A pdb=" N TYR D 149 " --> pdb=" O LEU D 136 " (cutoff:3.500A) 1225 hydrogen bonds defined for protein. 3489 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.44 Time building geometry restraints manager: 2.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 5119 1.33 - 1.45: 4927 1.45 - 1.57: 14323 1.57 - 1.69: 21 1.69 - 1.81: 167 Bond restraints: 24557 Sorted by residual: bond pdb=" C6 ATP B 601 " pdb=" N6 ATP B 601 " ideal model delta sigma weight residual 1.337 1.459 -0.122 1.10e-02 8.26e+03 1.23e+02 bond pdb=" C6 ATP C 601 " pdb=" N6 ATP C 601 " ideal model delta sigma weight residual 1.337 1.459 -0.122 1.10e-02 8.26e+03 1.23e+02 bond pdb=" C6 ATP A 601 " pdb=" N6 ATP A 601 " ideal model delta sigma weight residual 1.337 1.457 -0.120 1.10e-02 8.26e+03 1.20e+02 bond pdb=" C4 ATP C 601 " pdb=" N9 ATP C 601 " ideal model delta sigma weight residual 1.374 1.284 0.090 1.00e-02 1.00e+04 8.01e+01 bond pdb=" C8 ATP C 601 " pdb=" N9 ATP C 601 " ideal model delta sigma weight residual 1.370 1.263 0.107 1.20e-02 6.94e+03 7.98e+01 ... (remaining 24552 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.45: 32993 3.45 - 6.90: 185 6.90 - 10.35: 26 10.35 - 13.80: 6 13.80 - 17.26: 3 Bond angle restraints: 33213 Sorted by residual: angle pdb=" PB ATP B 601 " pdb=" O3B ATP B 601 " pdb=" PG ATP B 601 " ideal model delta sigma weight residual 139.87 122.61 17.26 1.00e+00 1.00e+00 2.98e+02 angle pdb=" PB ATP A 601 " pdb=" O3B ATP A 601 " pdb=" PG ATP A 601 " ideal model delta sigma weight residual 139.87 123.58 16.29 1.00e+00 1.00e+00 2.65e+02 angle pdb=" PB ATP C 601 " pdb=" O3B ATP C 601 " pdb=" PG ATP C 601 " ideal model delta sigma weight residual 139.87 124.89 14.98 1.00e+00 1.00e+00 2.24e+02 angle pdb=" PA ATP C 601 " pdb=" O3A ATP C 601 " pdb=" PB ATP C 601 " ideal model delta sigma weight residual 136.83 125.71 11.12 1.00e+00 1.00e+00 1.24e+02 angle pdb=" PA ATP A 601 " pdb=" O3A ATP A 601 " pdb=" PB ATP A 601 " ideal model delta sigma weight residual 136.83 125.74 11.09 1.00e+00 1.00e+00 1.23e+02 ... (remaining 33208 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.15: 14682 35.15 - 70.30: 261 70.30 - 105.45: 37 105.45 - 140.60: 0 140.60 - 175.75: 3 Dihedral angle restraints: 14983 sinusoidal: 6004 harmonic: 8979 Sorted by residual: dihedral pdb=" C5' ADP F 501 " pdb=" O5' ADP F 501 " pdb=" PA ADP F 501 " pdb=" O2A ADP F 501 " ideal model delta sinusoidal sigma weight residual -60.00 115.76 -175.75 1 2.00e+01 2.50e-03 4.79e+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 -60.00 109.33 -169.33 1 2.00e+01 2.50e-03 4.76e+01 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 86.99 -146.98 1 2.00e+01 2.50e-03 4.41e+01 ... (remaining 14980 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 2824 0.050 - 0.101: 848 0.101 - 0.151: 188 0.151 - 0.202: 7 0.202 - 0.252: 4 Chirality restraints: 3871 Sorted by residual: 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 -2.43 -0.25 2.00e-01 2.50e+01 1.59e+00 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 -2.44 -0.24 2.00e-01 2.50e+01 1.45e+00 chirality pdb=" CA ILE D 278 " pdb=" N ILE D 278 " pdb=" C ILE D 278 " pdb=" CB ILE D 278 " both_signs ideal model delta sigma weight residual False 2.43 2.66 -0.22 2.00e-01 2.50e+01 1.25e+00 ... (remaining 3868 not shown) Planarity restraints: 4292 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 188 " 0.630 9.50e-02 1.11e+02 2.82e-01 4.87e+01 pdb=" NE ARG A 188 " -0.039 2.00e-02 2.50e+03 pdb=" CZ ARG A 188 " -0.002 2.00e-02 2.50e+03 pdb=" NH1 ARG A 188 " -0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG A 188 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG J 16 " -0.584 9.50e-02 1.11e+02 2.62e-01 4.18e+01 pdb=" NE ARG J 16 " 0.035 2.00e-02 2.50e+03 pdb=" CZ ARG J 16 " 0.005 2.00e-02 2.50e+03 pdb=" NH1 ARG J 16 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG J 16 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG J 25 " -0.270 9.50e-02 1.11e+02 1.21e-01 9.02e+00 pdb=" NE ARG J 25 " 0.017 2.00e-02 2.50e+03 pdb=" CZ ARG J 25 " 0.001 2.00e-02 2.50e+03 pdb=" NH1 ARG J 25 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG J 25 " -0.009 2.00e-02 2.50e+03 ... (remaining 4289 not shown) Histogram of nonbonded interaction distances: 1.96 - 2.54: 147 2.54 - 3.13: 18858 3.13 - 3.72: 37674 3.72 - 4.31: 58276 4.31 - 4.90: 94733 Nonbonded interactions: 209688 Sorted by model distance: nonbonded pdb=" OG1 THR B 176 " pdb="MG MG B 602 " model vdw 1.956 2.170 nonbonded pdb=" O1B ADP F 501 " pdb="MG MG F 502 " model vdw 2.048 2.170 nonbonded pdb=" O3G ATP B 601 " pdb="MG MG B 602 " model vdw 2.084 2.170 nonbonded pdb=" OG1 THR A 176 " pdb="MG MG A 602 " model vdw 2.086 2.170 nonbonded pdb=" OG1 THR D 166 " pdb="MG MG D 502 " model vdw 2.097 2.170 ... (remaining 209683 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' and resid 24 through 602) } 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: 13.790 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 0.490 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 24.690 Find NCS groups from input model: 1.000 Set up NCS constraints: 0.060 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: 0.000 Load rotamer database and sin/cos tables:9.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8873 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 : 0.008 0.145 24557 Z= 0.439 Angle : 0.803 17.256 33213 Z= 0.515 Chirality : 0.049 0.252 3871 Planarity : 0.008 0.282 4292 Dihedral : 14.237 175.753 9243 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.68 % Favored : 97.22 % Rotamer: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.86 (0.13), residues: 3134 helix: -0.92 (0.12), residues: 1361 sheet: -0.96 (0.22), residues: 479 loop : -1.52 (0.15), residues: 1294 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG F 298 TYR 0.012 0.002 TYR A 446 PHE 0.015 0.002 PHE F 444 HIS 0.004 0.001 HIS D 180 Details of bonding type rmsd/Z covalent geometry : bond 0.00821 / 0.44 (24557) covalent geometry : angle 0.80267 / 0.51 (33213) hydrogen bonds : bond 0.15719 / 10.72 ( 1225) hydrogen bonds : angle 6.92485 / 4.82 ( 3489) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6268 Ramachandran restraints generated. 3134 Oldfield, 0 Emsley, 3134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6268 Ramachandran restraints generated. 3134 Oldfield, 0 Emsley, 3134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 425 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 425 time to evaluate : 0.939 Fit side-chains REVERT: A 359 LYS cc_start: 0.8232 (mttt) cc_final: 0.7955 (mttm) REVERT: A 399 GLU cc_start: 0.7727 (mm-30) cc_final: 0.7438 (tp30) REVERT: A 419 SER cc_start: 0.8512 (m) cc_final: 0.8303 (m) REVERT: A 488 LYS cc_start: 0.8627 (pttt) cc_final: 0.8295 (ptpt) REVERT: C 8 MET cc_start: 0.4229 (ptt) cc_final: 0.3757 (ptp) REVERT: D 212 LYS cc_start: 0.7863 (ptpp) cc_final: 0.7655 (ptpp) REVERT: D 470 VAL cc_start: 0.7787 (m) cc_final: 0.7579 (t) REVERT: O 69 LEU cc_start: 0.6587 (mm) cc_final: 0.6218 (mm) outliers start: 0 outliers final: 0 residues processed: 425 average time/residue: 0.8737 time to fit residues: 413.2448 Evaluate side-chains 303 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 303 time to evaluate : 0.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 197 optimal weight: 3.9990 chunk 215 optimal weight: 0.6980 chunk 20 optimal weight: 0.6980 chunk 132 optimal weight: 0.5980 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 0.9980 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 0.5980 chunk 183 optimal weight: 6.9990 chunk 298 optimal weight: 5.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 396 GLN A 405 GLN A 416 GLN A 492 GLN A 503 ASN B 48 GLN B 466 ASN C 208 GLN C 503 ASN F 224 GLN F 249 GLN F 296 GLN F 331 HIS D 252 GLN D 266 GLN D 446 GLN O 87 ASN O 99 GLN J 41 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.124956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.092335 restraints weight = 29541.202| |-----------------------------------------------------------------------------| r_work (start): 0.3050 rms_B_bonded: 1.78 r_work: 0.2945 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2832 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.2832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8754 moved from start: 0.1410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 24557 Z= 0.119 Angle : 0.526 7.206 33213 Z= 0.272 Chirality : 0.043 0.143 3871 Planarity : 0.004 0.046 4292 Dihedral : 6.969 152.690 3448 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.10 % Allowed : 1.66 % Favored : 98.25 % Rotamer: Outliers : 1.48 % Allowed : 10.55 % Favored : 87.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.19 (0.15), residues: 3134 helix: 0.68 (0.14), residues: 1358 sheet: -0.56 (0.21), residues: 530 loop : -0.70 (0.17), residues: 1246 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 15 TYR 0.012 0.001 TYR F 245 PHE 0.016 0.001 PHE J 34 HIS 0.004 0.001 HIS B 476 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.12 (24557) covalent geometry : angle 0.52636 / 0.27 (33213) hydrogen bonds : bond 0.04483 / 3.07 ( 1225) hydrogen bonds : angle 5.23752 / 3.64 ( 3489) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6268 Ramachandran restraints generated. 3134 Oldfield, 0 Emsley, 3134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6268 Ramachandran restraints generated. 3134 Oldfield, 0 Emsley, 3134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 341 time to evaluate : 0.971 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 359 LYS cc_start: 0.7912 (mttt) cc_final: 0.7648 (mttm) REVERT: A 488 LYS cc_start: 0.8230 (pttt) cc_final: 0.7779 (ptpt) REVERT: A 499 GLU cc_start: 0.8200 (tm-30) cc_final: 0.7957 (tm-30) REVERT: B 455 LYS cc_start: 0.8152 (mmtp) cc_final: 0.7523 (mmpt) REVERT: C 8 MET cc_start: 0.3663 (ptt) cc_final: 0.3154 (ptp) REVERT: C 45 ARG cc_start: 0.7862 (mmm160) cc_final: 0.7367 (ptm-80) REVERT: C 128 ARG cc_start: 0.7941 (mtt180) cc_final: 0.7714 (mtp180) REVERT: E 15 ARG cc_start: 0.8306 (ptt-90) cc_final: 0.7628 (ptp90) REVERT: E 112 LYS cc_start: 0.8521 (OUTLIER) cc_final: 0.8284 (mtpt) REVERT: E 249 GLN cc_start: 0.8913 (OUTLIER) cc_final: 0.7784 (mp10) REVERT: E 409 ARG cc_start: 0.7879 (mtm-85) cc_final: 0.7557 (mtt180) REVERT: E 415 ARG cc_start: 0.7512 (OUTLIER) cc_final: 0.6378 (mpt180) REVERT: F 344 GLU cc_start: 0.8092 (mm-30) cc_final: 0.7785 (mm-30) REVERT: F 422 GLN cc_start: 0.7808 (OUTLIER) cc_final: 0.7317 (mt0) REVERT: D 170 MET cc_start: 0.7911 (mmm) cc_final: 0.7585 (mmm) REVERT: D 203 MET cc_start: 0.8366 (mtt) cc_final: 0.8016 (mtt) REVERT: D 210 ASN cc_start: 0.8705 (t0) cc_final: 0.8207 (t0) REVERT: D 212 LYS cc_start: 0.7700 (ptpp) cc_final: 0.6867 (ptpp) REVERT: D 359 ARG cc_start: 0.7880 (mtm110) cc_final: 0.7254 (mtt-85) REVERT: D 414 GLN cc_start: 0.7184 (tt0) cc_final: 0.6927 (tt0) REVERT: D 458 GLN cc_start: 0.7184 (pm20) cc_final: 0.6703 (pm20) REVERT: G 18 LYS cc_start: 0.8021 (OUTLIER) cc_final: 0.7355 (tptt) REVERT: G 229 MET cc_start: 0.8304 (ttp) cc_final: 0.8018 (ttp) REVERT: O 33 GLU cc_start: 0.5626 (mp0) cc_final: 0.5316 (mm-30) outliers start: 38 outliers final: 7 residues processed: 359 average time/residue: 0.8070 time to fit residues: 325.1334 Evaluate side-chains 309 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 297 time to evaluate : 0.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 470 SER Chi-restraints excluded: chain C residue 124 LYS Chi-restraints excluded: chain E residue 112 LYS Chi-restraints excluded: chain E residue 205 GLU Chi-restraints excluded: chain E residue 249 GLN Chi-restraints excluded: chain E residue 415 ARG Chi-restraints excluded: chain F residue 282 VAL Chi-restraints excluded: chain F residue 422 GLN Chi-restraints excluded: chain D residue 46 THR Chi-restraints excluded: chain D residue 386 SER Chi-restraints excluded: chain D residue 434 LEU Chi-restraints excluded: chain G residue 18 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 242 optimal weight: 4.9990 chunk 297 optimal weight: 8.9990 chunk 162 optimal weight: 5.9990 chunk 72 optimal weight: 2.9990 chunk 187 optimal weight: 5.9990 chunk 62 optimal weight: 0.5980 chunk 209 optimal weight: 2.9990 chunk 258 optimal weight: 3.9990 chunk 273 optimal weight: 4.9990 chunk 17 optimal weight: 0.7980 chunk 44 optimal weight: 0.2980 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 492 GLN B 78 ASN E 388 GLN E 445 GLN D 252 GLN O 97 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.122923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.089606 restraints weight = 29614.325| |-----------------------------------------------------------------------------| r_work (start): 0.3019 rms_B_bonded: 1.86 r_work: 0.2911 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2796 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.2796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8803 moved from start: 0.1477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 24557 Z= 0.160 Angle : 0.534 10.231 33213 Z= 0.275 Chirality : 0.044 0.145 3871 Planarity : 0.004 0.047 4292 Dihedral : 6.617 139.681 3448 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.10 % Allowed : 1.85 % Favored : 98.05 % Rotamer: Outliers : 2.30 % Allowed : 12.23 % Favored : 85.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.28 (0.15), residues: 3134 helix: 1.13 (0.14), residues: 1351 sheet: -0.42 (0.22), residues: 533 loop : -0.48 (0.17), residues: 1250 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 9 TYR 0.020 0.001 TYR B 446 PHE 0.014 0.001 PHE J 34 HIS 0.008 0.001 HIS B 476 Details of bonding type rmsd/Z covalent geometry : bond 0.00376 / 0.16 (24557) covalent geometry : angle 0.53391 / 0.27 (33213) hydrogen bonds : bond 0.04743 / 3.22 ( 1225) hydrogen bonds : angle 5.08126 / 3.54 ( 3489) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6268 Ramachandran restraints generated. 3134 Oldfield, 0 Emsley, 3134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6268 Ramachandran restraints generated. 3134 Oldfield, 0 Emsley, 3134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 305 time to evaluate : 0.881 Fit side-chains revert: symmetry clash REVERT: A 8 MET cc_start: 0.5842 (mtp) cc_final: 0.4970 (mmt) REVERT: A 196 LYS cc_start: 0.8508 (ptmt) cc_final: 0.7584 (mmtp) REVERT: A 349 GLN cc_start: 0.8364 (OUTLIER) cc_final: 0.7728 (pt0) REVERT: A 359 LYS cc_start: 0.7985 (mttt) cc_final: 0.7732 (mttm) REVERT: A 381 ARG cc_start: 0.6989 (mmm160) cc_final: 0.6718 (mmp80) REVERT: A 455 LYS cc_start: 0.8362 (mttp) cc_final: 0.8107 (mttt) REVERT: A 488 LYS cc_start: 0.8330 (pttt) cc_final: 0.7821 (ptpt) REVERT: A 499 GLU cc_start: 0.8270 (tm-30) cc_final: 0.7952 (tm-30) REVERT: B 426 GLU cc_start: 0.7858 (mm-30) cc_final: 0.7621 (tp30) REVERT: B 455 LYS cc_start: 0.8193 (mmtp) cc_final: 0.7589 (mmpt) REVERT: C 8 MET cc_start: 0.3659 (ptt) cc_final: 0.3143 (ptp) REVERT: C 45 ARG cc_start: 0.7888 (mmm160) cc_final: 0.7365 (ptm-80) REVERT: C 498 LYS cc_start: 0.7350 (OUTLIER) cc_final: 0.7041 (ttpp) REVERT: C 499 GLU cc_start: 0.6378 (OUTLIER) cc_final: 0.5792 (mt-10) REVERT: E 15 ARG cc_start: 0.8310 (ptt-90) cc_final: 0.7667 (ptp90) REVERT: E 112 LYS cc_start: 0.8530 (OUTLIER) cc_final: 0.8277 (mtpt) REVERT: E 409 ARG cc_start: 0.7951 (mtm-85) cc_final: 0.7391 (mtt-85) REVERT: E 415 ARG cc_start: 0.7640 (OUTLIER) cc_final: 0.6383 (mpt180) REVERT: F 215 THR cc_start: 0.9005 (m) cc_final: 0.8738 (p) REVERT: F 344 GLU cc_start: 0.8119 (mm-30) cc_final: 0.7873 (mm-30) REVERT: D 132 GLU cc_start: 0.7965 (OUTLIER) cc_final: 0.7236 (mp0) REVERT: D 170 MET cc_start: 0.7960 (mmm) cc_final: 0.7742 (mmp) REVERT: D 203 MET cc_start: 0.8348 (mtt) cc_final: 0.7936 (mtt) REVERT: D 210 ASN cc_start: 0.8721 (t0) cc_final: 0.8228 (t0) REVERT: D 212 LYS cc_start: 0.7684 (ptpp) cc_final: 0.6866 (ptpp) REVERT: D 252 GLN cc_start: 0.7473 (mm-40) cc_final: 0.7079 (mm-40) REVERT: D 359 ARG cc_start: 0.7863 (mtm110) cc_final: 0.7293 (mtt-85) REVERT: D 422 GLN cc_start: 0.7572 (tp40) cc_final: 0.7125 (tp40) REVERT: D 458 GLN cc_start: 0.7186 (pm20) cc_final: 0.5978 (tp40) REVERT: G 229 MET cc_start: 0.8311 (ttp) cc_final: 0.8072 (ttp) REVERT: O 69 LEU cc_start: 0.6160 (mm) cc_final: 0.5783 (mm) outliers start: 59 outliers final: 11 residues processed: 340 average time/residue: 0.7673 time to fit residues: 292.4536 Evaluate side-chains 308 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 291 time to evaluate : 0.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 349 GLN Chi-restraints excluded: chain B residue 65 ASN Chi-restraints excluded: chain B residue 459 SER Chi-restraints excluded: chain B residue 470 SER Chi-restraints excluded: chain C residue 124 LYS Chi-restraints excluded: chain C residue 498 LYS Chi-restraints excluded: chain C residue 499 GLU Chi-restraints excluded: chain E residue 112 LYS Chi-restraints excluded: chain E residue 205 GLU Chi-restraints excluded: chain E residue 294 THR Chi-restraints excluded: chain E residue 335 THR Chi-restraints excluded: chain E residue 415 ARG Chi-restraints excluded: chain F residue 46 THR Chi-restraints excluded: chain D residue 46 THR Chi-restraints excluded: chain D residue 132 GLU Chi-restraints excluded: chain D residue 434 LEU Chi-restraints excluded: chain O residue 166 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 182 optimal weight: 0.9980 chunk 163 optimal weight: 1.9990 chunk 208 optimal weight: 2.9990 chunk 210 optimal weight: 0.7980 chunk 29 optimal weight: 2.9990 chunk 190 optimal weight: 6.9990 chunk 47 optimal weight: 4.9990 chunk 261 optimal weight: 3.9990 chunk 92 optimal weight: 20.0000 chunk 133 optimal weight: 2.9990 chunk 126 optimal weight: 1.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 492 GLN B 78 ASN C 503 ASN E 388 GLN E 445 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.122555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.089164 restraints weight = 29484.813| |-----------------------------------------------------------------------------| r_work (start): 0.3014 rms_B_bonded: 1.85 r_work: 0.2905 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2790 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.2790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8809 moved from start: 0.1543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 24557 Z= 0.172 Angle : 0.542 10.349 33213 Z= 0.279 Chirality : 0.044 0.146 3871 Planarity : 0.004 0.046 4292 Dihedral : 6.544 141.695 3448 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.72 % Favored : 98.25 % Rotamer: Outliers : 2.18 % Allowed : 13.28 % Favored : 84.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.48 (0.15), residues: 3134 helix: 1.31 (0.14), residues: 1353 sheet: -0.35 (0.22), residues: 539 loop : -0.37 (0.17), residues: 1242 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 15 TYR 0.011 0.001 TYR A 446 PHE 0.019 0.002 PHE B 468 HIS 0.011 0.001 HIS B 476 Details of bonding type rmsd/Z covalent geometry : bond 0.00410 / 0.17 (24557) covalent geometry : angle 0.54238 / 0.28 (33213) hydrogen bonds : bond 0.04755 / 3.23 ( 1225) hydrogen bonds : angle 5.03196 / 3.50 ( 3489) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6268 Ramachandran restraints generated. 3134 Oldfield, 0 Emsley, 3134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6268 Ramachandran restraints generated. 3134 Oldfield, 0 Emsley, 3134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 363 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 307 time to evaluate : 0.852 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 8 MET cc_start: 0.5861 (mtp) cc_final: 0.5005 (mmt) REVERT: A 196 LYS cc_start: 0.8527 (ptmt) cc_final: 0.7621 (mmtp) REVERT: A 349 GLN cc_start: 0.8374 (OUTLIER) cc_final: 0.7757 (pt0) REVERT: A 359 LYS cc_start: 0.7993 (mttt) cc_final: 0.7748 (mttm) REVERT: A 381 ARG cc_start: 0.6992 (mmm160) cc_final: 0.6747 (mmp80) REVERT: A 455 LYS cc_start: 0.8348 (mttp) cc_final: 0.8092 (mttt) REVERT: A 488 LYS cc_start: 0.8358 (pttt) cc_final: 0.7854 (ptpt) REVERT: A 499 GLU cc_start: 0.8298 (tm-30) cc_final: 0.7992 (tm-30) REVERT: B 54 GLU cc_start: 0.8061 (OUTLIER) cc_final: 0.7391 (tm-30) REVERT: B 426 GLU cc_start: 0.7830 (mm-30) cc_final: 0.7601 (tp30) REVERT: B 455 LYS cc_start: 0.8145 (mmtp) cc_final: 0.7524 (mmpt) REVERT: B 475 GLN cc_start: 0.7236 (OUTLIER) cc_final: 0.6535 (mp-120) REVERT: C 8 MET cc_start: 0.3719 (ptt) cc_final: 0.3210 (ptp) REVERT: C 45 ARG cc_start: 0.7891 (mmm160) cc_final: 0.7383 (ptm-80) REVERT: C 498 LYS cc_start: 0.7392 (OUTLIER) cc_final: 0.7108 (ttpp) REVERT: C 499 GLU cc_start: 0.6359 (OUTLIER) cc_final: 0.5835 (mt-10) REVERT: E 15 ARG cc_start: 0.8335 (ptt-90) cc_final: 0.7679 (ptp90) REVERT: E 112 LYS cc_start: 0.8552 (OUTLIER) cc_final: 0.8297 (mtpt) REVERT: E 249 GLN cc_start: 0.8945 (OUTLIER) cc_final: 0.7859 (mp10) REVERT: E 409 ARG cc_start: 0.7912 (mtm-85) cc_final: 0.7351 (mtt-85) REVERT: E 415 ARG cc_start: 0.7681 (OUTLIER) cc_final: 0.6404 (mpt180) REVERT: F 27 GLN cc_start: 0.8843 (OUTLIER) cc_final: 0.8594 (tt0) REVERT: F 344 GLU cc_start: 0.8142 (mm-30) cc_final: 0.7908 (mm-30) REVERT: D 132 GLU cc_start: 0.7949 (OUTLIER) cc_final: 0.7220 (mp0) REVERT: D 170 MET cc_start: 0.7925 (mmm) cc_final: 0.7647 (mmp) REVERT: D 203 MET cc_start: 0.8325 (mtt) cc_final: 0.7891 (mtt) REVERT: D 210 ASN cc_start: 0.8735 (t0) cc_final: 0.8226 (t0) REVERT: D 212 LYS cc_start: 0.7683 (ptpp) cc_final: 0.6906 (ptpp) REVERT: D 252 GLN cc_start: 0.7434 (mm-40) cc_final: 0.7004 (mt0) REVERT: D 359 ARG cc_start: 0.7806 (mtm110) cc_final: 0.7254 (mtt-85) REVERT: D 458 GLN cc_start: 0.7165 (pm20) cc_final: 0.5991 (mm-40) REVERT: G 229 MET cc_start: 0.8322 (ttp) cc_final: 0.8044 (ttp) REVERT: G 262 LEU cc_start: 0.8696 (OUTLIER) cc_final: 0.8405 (tt) REVERT: G 264 GLU cc_start: 0.8472 (mt-10) cc_final: 0.8229 (mt-10) REVERT: O 46 LEU cc_start: 0.5700 (OUTLIER) cc_final: 0.5465 (mp) REVERT: O 69 LEU cc_start: 0.6244 (mm) cc_final: 0.5884 (mm) REVERT: J 35 ARG cc_start: 0.5459 (mtt-85) cc_final: 0.5104 (ptm160) outliers start: 56 outliers final: 15 residues processed: 343 average time/residue: 0.7576 time to fit residues: 291.4373 Evaluate side-chains 322 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 295 time to evaluate : 0.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 LYS Chi-restraints excluded: chain A residue 349 GLN Chi-restraints excluded: chain B residue 54 GLU Chi-restraints excluded: chain B residue 65 ASN Chi-restraints excluded: chain B residue 80 LYS Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 459 SER Chi-restraints excluded: chain B residue 470 SER Chi-restraints excluded: chain B residue 475 GLN Chi-restraints excluded: chain C residue 498 LYS Chi-restraints excluded: chain C residue 499 GLU Chi-restraints excluded: chain E residue 112 LYS Chi-restraints excluded: chain E residue 205 GLU Chi-restraints excluded: chain E residue 249 GLN Chi-restraints excluded: chain E residue 266 GLN Chi-restraints excluded: chain E residue 294 THR Chi-restraints excluded: chain E residue 335 THR Chi-restraints excluded: chain E residue 415 ARG Chi-restraints excluded: chain F residue 27 GLN Chi-restraints excluded: chain D residue 46 THR Chi-restraints excluded: chain D residue 132 GLU Chi-restraints excluded: chain D residue 292 MET Chi-restraints excluded: chain D residue 434 LEU Chi-restraints excluded: chain G residue 262 LEU Chi-restraints excluded: chain O residue 46 LEU Chi-restraints excluded: chain O residue 116 VAL Chi-restraints excluded: chain O residue 166 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 111 optimal weight: 3.9990 chunk 205 optimal weight: 0.9980 chunk 122 optimal weight: 3.9990 chunk 47 optimal weight: 4.9990 chunk 124 optimal weight: 0.9990 chunk 112 optimal weight: 0.9980 chunk 179 optimal weight: 0.1980 chunk 263 optimal weight: 0.9990 chunk 87 optimal weight: 2.9990 chunk 78 optimal weight: 2.9990 chunk 110 optimal weight: 1.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 492 GLN B 78 ASN C 503 ASN E 388 GLN E 445 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.125299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.091984 restraints weight = 29159.295| |-----------------------------------------------------------------------------| r_work (start): 0.3055 rms_B_bonded: 1.85 r_work: 0.2947 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2832 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8769 moved from start: 0.1824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 24557 Z= 0.112 Angle : 0.495 10.157 33213 Z= 0.252 Chirality : 0.042 0.140 3871 Planarity : 0.004 0.046 4292 Dihedral : 6.241 140.877 3448 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.60 % Favored : 98.37 % Rotamer: Outliers : 1.87 % Allowed : 14.14 % Favored : 84.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.79 (0.15), residues: 3134 helix: 1.59 (0.14), residues: 1359 sheet: -0.18 (0.22), residues: 522 loop : -0.25 (0.17), residues: 1253 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 15 TYR 0.010 0.001 TYR O 12 PHE 0.012 0.001 PHE J 34 HIS 0.012 0.001 HIS B 476 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.11 (24557) covalent geometry : angle 0.49518 / 0.25 (33213) hydrogen bonds : bond 0.03976 / 2.72 ( 1225) hydrogen bonds : angle 4.82429 / 3.36 ( 3489) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6268 Ramachandran restraints generated. 3134 Oldfield, 0 Emsley, 3134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6268 Ramachandran restraints generated. 3134 Oldfield, 0 Emsley, 3134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 319 time to evaluate : 0.943 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 196 LYS cc_start: 0.8463 (ptmt) cc_final: 0.7603 (mmtp) REVERT: A 347 ASP cc_start: 0.8866 (m-30) cc_final: 0.8582 (m-30) REVERT: A 349 GLN cc_start: 0.8332 (OUTLIER) cc_final: 0.7713 (pt0) REVERT: A 359 LYS cc_start: 0.7938 (mttt) cc_final: 0.7702 (mttm) REVERT: A 381 ARG cc_start: 0.6892 (mmm160) cc_final: 0.6635 (mmp80) REVERT: A 455 LYS cc_start: 0.8318 (mttp) cc_final: 0.8036 (mttt) REVERT: A 488 LYS cc_start: 0.8312 (pttt) cc_final: 0.7792 (ptpt) REVERT: A 499 GLU cc_start: 0.8293 (tm-30) cc_final: 0.7933 (tm-30) REVERT: B 54 GLU cc_start: 0.8008 (OUTLIER) cc_final: 0.7344 (tm-30) REVERT: B 80 LYS cc_start: 0.8731 (OUTLIER) cc_final: 0.8504 (pttt) REVERT: B 355 GLU cc_start: 0.7633 (OUTLIER) cc_final: 0.7135 (tt0) REVERT: B 392 LEU cc_start: 0.8231 (OUTLIER) cc_final: 0.7974 (tm) REVERT: B 426 GLU cc_start: 0.7784 (mm-30) cc_final: 0.7579 (tp30) REVERT: B 455 LYS cc_start: 0.8138 (mmtp) cc_final: 0.7507 (mmpt) REVERT: B 475 GLN cc_start: 0.7244 (OUTLIER) cc_final: 0.6455 (mp-120) REVERT: B 477 GLN cc_start: 0.7366 (mm-40) cc_final: 0.7011 (mp10) REVERT: C 8 MET cc_start: 0.3604 (ptt) cc_final: 0.2705 (mmt) REVERT: C 45 ARG cc_start: 0.7748 (mmm160) cc_final: 0.7291 (ptm-80) REVERT: C 197 LYS cc_start: 0.8443 (mtpt) cc_final: 0.7668 (mmmt) REVERT: C 426 GLU cc_start: 0.7581 (OUTLIER) cc_final: 0.7220 (mp0) REVERT: C 498 LYS cc_start: 0.7388 (OUTLIER) cc_final: 0.7082 (ttpp) REVERT: C 499 GLU cc_start: 0.6266 (OUTLIER) cc_final: 0.5853 (mt-10) REVERT: E 112 LYS cc_start: 0.8488 (OUTLIER) cc_final: 0.8257 (mtpt) REVERT: E 249 GLN cc_start: 0.8898 (OUTLIER) cc_final: 0.7875 (mp10) REVERT: E 409 ARG cc_start: 0.7890 (mtm-85) cc_final: 0.7324 (mtt-85) REVERT: E 415 ARG cc_start: 0.7512 (OUTLIER) cc_final: 0.6260 (mpt180) REVERT: F 344 GLU cc_start: 0.8118 (mm-30) cc_final: 0.7914 (mm-30) REVERT: D 170 MET cc_start: 0.7886 (mmm) cc_final: 0.7668 (mmp) REVERT: D 203 MET cc_start: 0.8278 (mtt) cc_final: 0.7861 (mtt) REVERT: D 210 ASN cc_start: 0.8710 (t0) cc_final: 0.8175 (t0) REVERT: D 212 LYS cc_start: 0.7675 (ptpp) cc_final: 0.6894 (ptpp) REVERT: D 252 GLN cc_start: 0.7461 (mm-40) cc_final: 0.7042 (mt0) REVERT: D 359 ARG cc_start: 0.7749 (mtm110) cc_final: 0.7179 (mtt-85) REVERT: D 422 GLN cc_start: 0.7490 (tp40) cc_final: 0.7040 (tp40) REVERT: D 458 GLN cc_start: 0.7113 (pm20) cc_final: 0.5908 (mm110) REVERT: G 229 MET cc_start: 0.8210 (ttp) cc_final: 0.7937 (ttp) REVERT: G 262 LEU cc_start: 0.8641 (OUTLIER) cc_final: 0.8410 (tt) REVERT: O 69 LEU cc_start: 0.6199 (mm) cc_final: 0.5834 (mm) REVERT: J 35 ARG cc_start: 0.5427 (mtt-85) cc_final: 0.5068 (ptm160) outliers start: 48 outliers final: 18 residues processed: 347 average time/residue: 0.8005 time to fit residues: 310.5474 Evaluate side-chains 330 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 299 time to evaluate : 0.855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 349 GLN Chi-restraints excluded: chain B residue 54 GLU Chi-restraints excluded: chain B residue 65 ASN Chi-restraints excluded: chain B residue 80 LYS Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 355 GLU Chi-restraints excluded: chain B residue 392 LEU Chi-restraints excluded: chain B residue 459 SER Chi-restraints excluded: chain B residue 470 SER Chi-restraints excluded: chain B residue 475 GLN Chi-restraints excluded: chain C residue 124 LYS Chi-restraints excluded: chain C residue 132 LYS Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain C residue 426 GLU Chi-restraints excluded: chain C residue 498 LYS Chi-restraints excluded: chain C residue 499 GLU Chi-restraints excluded: chain E residue 29 ASP Chi-restraints excluded: chain E residue 112 LYS Chi-restraints excluded: chain E residue 205 GLU Chi-restraints excluded: chain E residue 249 GLN Chi-restraints excluded: chain E residue 266 GLN Chi-restraints excluded: chain E residue 294 THR Chi-restraints excluded: chain E residue 415 ARG Chi-restraints excluded: chain F residue 434 LEU Chi-restraints excluded: chain D residue 292 MET Chi-restraints excluded: chain D residue 434 LEU Chi-restraints excluded: chain G residue 262 LEU Chi-restraints excluded: chain O residue 4 LEU Chi-restraints excluded: chain O residue 116 VAL Chi-restraints excluded: chain O residue 166 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 15 optimal weight: 0.9980 chunk 63 optimal weight: 0.9990 chunk 154 optimal weight: 0.0970 chunk 295 optimal weight: 10.0000 chunk 256 optimal weight: 9.9990 chunk 1 optimal weight: 6.9990 chunk 171 optimal weight: 0.8980 chunk 280 optimal weight: 3.9990 chunk 39 optimal weight: 8.9990 chunk 8 optimal weight: 4.9990 chunk 64 optimal weight: 6.9990 overall best weight: 1.3982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 475 GLN A 477 GLN A 492 GLN B 78 ASN C 503 ASN E 388 GLN E 445 GLN F 42 GLN D 260 ASN D 446 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.123773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.090247 restraints weight = 29410.227| |-----------------------------------------------------------------------------| r_work (start): 0.3030 rms_B_bonded: 1.85 r_work: 0.2922 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2807 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.2807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8787 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 : 0.003 0.039 24557 Z= 0.147 Angle : 0.524 10.214 33213 Z= 0.267 Chirality : 0.044 0.144 3871 Planarity : 0.004 0.044 4292 Dihedral : 6.312 142.902 3448 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.66 % Favored : 98.31 % Rotamer: Outliers : 2.26 % Allowed : 14.52 % Favored : 83.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.83 (0.15), residues: 3134 helix: 1.60 (0.14), residues: 1359 sheet: -0.21 (0.22), residues: 528 loop : -0.17 (0.17), residues: 1247 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 15 TYR 0.012 0.001 TYR E 384 PHE 0.020 0.001 PHE B 468 HIS 0.013 0.001 HIS B 476 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.15 (24557) covalent geometry : angle 0.52437 / 0.27 (33213) hydrogen bonds : bond 0.04345 / 2.96 ( 1225) hydrogen bonds : angle 4.86472 / 3.38 ( 3489) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6268 Ramachandran restraints generated. 3134 Oldfield, 0 Emsley, 3134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6268 Ramachandran restraints generated. 3134 Oldfield, 0 Emsley, 3134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 306 time to evaluate : 1.032 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 MET cc_start: 0.5848 (mtp) cc_final: 0.4963 (mmt) REVERT: A 196 LYS cc_start: 0.8456 (ptmt) cc_final: 0.7605 (mmtp) REVERT: A 347 ASP cc_start: 0.8948 (m-30) cc_final: 0.8639 (m-30) REVERT: A 349 GLN cc_start: 0.8350 (OUTLIER) cc_final: 0.7734 (pt0) REVERT: A 359 LYS cc_start: 0.7969 (mttt) cc_final: 0.7737 (mttm) REVERT: A 381 ARG cc_start: 0.6932 (mmm160) cc_final: 0.6678 (mmp80) REVERT: A 455 LYS cc_start: 0.8338 (mttp) cc_final: 0.8061 (mttt) REVERT: A 488 LYS cc_start: 0.8331 (pttt) cc_final: 0.7808 (ptpt) REVERT: A 499 GLU cc_start: 0.8302 (tm-30) cc_final: 0.8007 (tm-30) REVERT: B 54 GLU cc_start: 0.8006 (OUTLIER) cc_final: 0.7313 (tm-30) REVERT: B 355 GLU cc_start: 0.7641 (OUTLIER) cc_final: 0.7157 (tt0) REVERT: B 426 GLU cc_start: 0.7785 (mm-30) cc_final: 0.7579 (tp30) REVERT: B 455 LYS cc_start: 0.8133 (mmtp) cc_final: 0.7513 (mmpt) REVERT: B 475 GLN cc_start: 0.7459 (OUTLIER) cc_final: 0.6636 (mp-120) REVERT: B 477 GLN cc_start: 0.7378 (mm-40) cc_final: 0.7039 (mp10) REVERT: C 8 MET cc_start: 0.3667 (ptt) cc_final: 0.2693 (mmt) REVERT: C 45 ARG cc_start: 0.7797 (mmm160) cc_final: 0.7315 (ptm-80) REVERT: C 426 GLU cc_start: 0.7530 (OUTLIER) cc_final: 0.7163 (mp0) REVERT: C 498 LYS cc_start: 0.7377 (OUTLIER) cc_final: 0.7095 (ttpp) REVERT: C 499 GLU cc_start: 0.6291 (OUTLIER) cc_final: 0.5859 (mt-10) REVERT: E 112 LYS cc_start: 0.8517 (OUTLIER) cc_final: 0.8280 (mtpt) REVERT: E 249 GLN cc_start: 0.8919 (OUTLIER) cc_final: 0.7840 (mp10) REVERT: E 405 LEU cc_start: 0.8136 (tp) cc_final: 0.7935 (tt) REVERT: E 409 ARG cc_start: 0.7870 (mtm-85) cc_final: 0.7297 (mtt-85) REVERT: E 411 ARG cc_start: 0.7589 (mtt-85) cc_final: 0.7026 (mtp85) REVERT: E 415 ARG cc_start: 0.7626 (OUTLIER) cc_final: 0.6350 (mpt180) REVERT: F 344 GLU cc_start: 0.8109 (mm-30) cc_final: 0.7902 (mm-30) REVERT: F 347 ILE cc_start: 0.8783 (mt) cc_final: 0.8541 (mm) REVERT: F 422 GLN cc_start: 0.7808 (OUTLIER) cc_final: 0.7332 (mt0) REVERT: D 132 GLU cc_start: 0.7947 (OUTLIER) cc_final: 0.7206 (mp0) REVERT: D 170 MET cc_start: 0.7892 (mmm) cc_final: 0.7617 (mmp) REVERT: D 203 MET cc_start: 0.8250 (mtt) cc_final: 0.7824 (mtt) REVERT: D 210 ASN cc_start: 0.8719 (t0) cc_final: 0.8184 (t0) REVERT: D 212 LYS cc_start: 0.7699 (ptpp) cc_final: 0.6931 (ptpp) REVERT: D 252 GLN cc_start: 0.7456 (mm-40) cc_final: 0.7034 (mt0) REVERT: D 359 ARG cc_start: 0.7745 (mtm110) cc_final: 0.7220 (mtt-85) REVERT: D 458 GLN cc_start: 0.7109 (pm20) cc_final: 0.5950 (mm110) REVERT: G 229 MET cc_start: 0.8245 (ttp) cc_final: 0.7989 (ttp) REVERT: G 262 LEU cc_start: 0.8675 (OUTLIER) cc_final: 0.8403 (tt) REVERT: O 69 LEU cc_start: 0.6232 (mm) cc_final: 0.5812 (mm) REVERT: J 35 ARG cc_start: 0.5392 (mtt-85) cc_final: 0.5036 (ptm160) outliers start: 58 outliers final: 24 residues processed: 342 average time/residue: 0.8454 time to fit residues: 324.2546 Evaluate side-chains 332 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 295 time to evaluate : 0.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 349 GLN Chi-restraints excluded: chain B residue 54 GLU Chi-restraints excluded: chain B residue 65 ASN Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 355 GLU Chi-restraints excluded: chain B residue 459 SER Chi-restraints excluded: chain B residue 470 SER Chi-restraints excluded: chain B residue 475 GLN Chi-restraints excluded: chain C residue 124 LYS Chi-restraints excluded: chain C residue 132 LYS Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain C residue 426 GLU Chi-restraints excluded: chain C residue 498 LYS Chi-restraints excluded: chain C residue 499 GLU Chi-restraints excluded: chain E residue 29 ASP Chi-restraints excluded: chain E residue 112 LYS Chi-restraints excluded: chain E residue 205 GLU Chi-restraints excluded: chain E residue 249 GLN Chi-restraints excluded: chain E residue 263 ARG Chi-restraints excluded: chain E residue 266 GLN Chi-restraints excluded: chain E residue 294 THR Chi-restraints excluded: chain E residue 335 THR Chi-restraints excluded: chain E residue 355 ASP Chi-restraints excluded: chain E residue 415 ARG Chi-restraints excluded: chain F residue 205 GLU Chi-restraints excluded: chain F residue 422 GLN Chi-restraints excluded: chain F residue 434 LEU Chi-restraints excluded: chain D residue 46 THR Chi-restraints excluded: chain D residue 132 GLU Chi-restraints excluded: chain D residue 386 SER Chi-restraints excluded: chain D residue 434 LEU Chi-restraints excluded: chain G residue 262 LEU Chi-restraints excluded: chain O residue 4 LEU Chi-restraints excluded: chain O residue 116 VAL Chi-restraints excluded: chain O residue 148 LEU Chi-restraints excluded: chain O residue 166 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 1 optimal weight: 0.9990 chunk 238 optimal weight: 1.9990 chunk 95 optimal weight: 0.9990 chunk 99 optimal weight: 4.9990 chunk 209 optimal weight: 0.7980 chunk 254 optimal weight: 3.9990 chunk 199 optimal weight: 2.9990 chunk 128 optimal weight: 5.9990 chunk 157 optimal weight: 4.9990 chunk 136 optimal weight: 4.9990 chunk 53 optimal weight: 1.9990 overall best weight: 1.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 477 GLN A 492 GLN C 503 ASN E 388 GLN E 445 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.123905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.090348 restraints weight = 29410.535| |-----------------------------------------------------------------------------| r_work (start): 0.3031 rms_B_bonded: 1.85 r_work: 0.2923 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2808 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8787 moved from start: 0.1825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 24557 Z= 0.144 Angle : 0.521 10.534 33213 Z= 0.266 Chirality : 0.043 0.144 3871 Planarity : 0.004 0.044 4292 Dihedral : 6.319 144.626 3448 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.63 % Favored : 98.34 % Rotamer: Outliers : 2.10 % Allowed : 14.80 % Favored : 83.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.88 (0.15), residues: 3134 helix: 1.64 (0.14), residues: 1359 sheet: -0.15 (0.23), residues: 517 loop : -0.17 (0.17), residues: 1258 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 373 TYR 0.023 0.001 TYR B 446 PHE 0.014 0.001 PHE J 34 HIS 0.012 0.001 HIS B 476 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.14 (24557) covalent geometry : angle 0.52133 / 0.27 (33213) hydrogen bonds : bond 0.04321 / 2.94 ( 1225) hydrogen bonds : angle 4.86876 / 3.38 ( 3489) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6268 Ramachandran restraints generated. 3134 Oldfield, 0 Emsley, 3134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6268 Ramachandran restraints generated. 3134 Oldfield, 0 Emsley, 3134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 302 time to evaluate : 0.739 Fit side-chains revert: symmetry clash REVERT: A 101 GLU cc_start: 0.8799 (OUTLIER) cc_final: 0.8588 (mt-10) REVERT: A 196 LYS cc_start: 0.8413 (ptmt) cc_final: 0.7587 (mmtp) REVERT: A 349 GLN cc_start: 0.8399 (OUTLIER) cc_final: 0.7721 (pt0) REVERT: A 359 LYS cc_start: 0.7962 (mttt) cc_final: 0.7727 (mttm) REVERT: A 381 ARG cc_start: 0.6910 (mmm160) cc_final: 0.6659 (mmp80) REVERT: A 455 LYS cc_start: 0.8256 (mttp) cc_final: 0.8011 (mttt) REVERT: A 477 GLN cc_start: 0.7962 (mm-40) cc_final: 0.7694 (tp40) REVERT: A 488 LYS cc_start: 0.8331 (pttt) cc_final: 0.7804 (ptpt) REVERT: A 499 GLU cc_start: 0.8288 (tm-30) cc_final: 0.7993 (tm-30) REVERT: B 54 GLU cc_start: 0.8004 (OUTLIER) cc_final: 0.7296 (tm-30) REVERT: B 144 GLU cc_start: 0.8820 (OUTLIER) cc_final: 0.8581 (mt-10) REVERT: B 195 GLU cc_start: 0.7316 (tp30) cc_final: 0.7077 (tp30) REVERT: B 226 MET cc_start: 0.8967 (tpt) cc_final: 0.8337 (tpt) REVERT: B 355 GLU cc_start: 0.7633 (OUTLIER) cc_final: 0.7149 (tt0) REVERT: B 392 LEU cc_start: 0.8223 (OUTLIER) cc_final: 0.7995 (tm) REVERT: B 426 GLU cc_start: 0.7778 (mm-30) cc_final: 0.7569 (tp30) REVERT: B 455 LYS cc_start: 0.8140 (mmtp) cc_final: 0.7521 (mmpt) REVERT: B 475 GLN cc_start: 0.7482 (OUTLIER) cc_final: 0.6659 (mp-120) REVERT: B 477 GLN cc_start: 0.7406 (mm-40) cc_final: 0.7050 (mp10) REVERT: C 8 MET cc_start: 0.3682 (ptt) cc_final: 0.2724 (mmt) REVERT: C 45 ARG cc_start: 0.7782 (mmm160) cc_final: 0.7304 (ptm-80) REVERT: C 426 GLU cc_start: 0.7529 (OUTLIER) cc_final: 0.7191 (mp0) REVERT: C 498 LYS cc_start: 0.7387 (OUTLIER) cc_final: 0.7110 (ttpp) REVERT: C 499 GLU cc_start: 0.6237 (OUTLIER) cc_final: 0.5813 (mt-10) REVERT: E 112 LYS cc_start: 0.8498 (OUTLIER) cc_final: 0.8252 (mtpt) REVERT: E 249 GLN cc_start: 0.8930 (OUTLIER) cc_final: 0.7868 (mp10) REVERT: E 409 ARG cc_start: 0.7864 (mtm-85) cc_final: 0.7289 (mtt-85) REVERT: E 411 ARG cc_start: 0.7628 (mtt-85) cc_final: 0.7108 (mtp85) REVERT: E 415 ARG cc_start: 0.7609 (OUTLIER) cc_final: 0.6326 (mpt180) REVERT: F 30 GLU cc_start: 0.7529 (pm20) cc_final: 0.7198 (pp20) REVERT: F 344 GLU cc_start: 0.8128 (mm-30) cc_final: 0.7927 (mm-30) REVERT: F 347 ILE cc_start: 0.8785 (mt) cc_final: 0.8536 (mm) REVERT: F 422 GLN cc_start: 0.7803 (OUTLIER) cc_final: 0.7322 (mt0) REVERT: D 132 GLU cc_start: 0.7960 (OUTLIER) cc_final: 0.7241 (mp0) REVERT: D 170 MET cc_start: 0.7852 (mmm) cc_final: 0.7574 (mmp) REVERT: D 203 MET cc_start: 0.8233 (mtt) cc_final: 0.7810 (mtt) REVERT: D 210 ASN cc_start: 0.8734 (t0) cc_final: 0.8179 (t0) REVERT: D 212 LYS cc_start: 0.7702 (ptpp) cc_final: 0.6913 (ptpp) REVERT: D 252 GLN cc_start: 0.7482 (mm-40) cc_final: 0.6889 (mt0) REVERT: D 344 GLU cc_start: 0.7848 (OUTLIER) cc_final: 0.7585 (mt-10) REVERT: D 359 ARG cc_start: 0.7740 (mtm110) cc_final: 0.7217 (mtt-85) REVERT: D 422 GLN cc_start: 0.7451 (tp40) cc_final: 0.7005 (tp40) REVERT: D 458 GLN cc_start: 0.7102 (pm20) cc_final: 0.5949 (mm110) REVERT: G 229 MET cc_start: 0.8251 (ttp) cc_final: 0.7979 (ttp) REVERT: G 262 LEU cc_start: 0.8679 (OUTLIER) cc_final: 0.8411 (tt) REVERT: O 36 GLU cc_start: 0.6433 (tt0) cc_final: 0.5977 (mt-10) REVERT: O 69 LEU cc_start: 0.6210 (mm) cc_final: 0.5825 (mm) REVERT: O 153 LYS cc_start: 0.7458 (OUTLIER) cc_final: 0.6510 (pttt) REVERT: J 35 ARG cc_start: 0.5442 (mtt-85) cc_final: 0.5085 (ptm160) outliers start: 54 outliers final: 27 residues processed: 336 average time/residue: 0.7801 time to fit residues: 294.0100 Evaluate side-chains 338 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 293 time to evaluate : 0.974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 GLU Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 349 GLN Chi-restraints excluded: chain A residue 497 LEU Chi-restraints excluded: chain B residue 38 ILE Chi-restraints excluded: chain B residue 54 GLU Chi-restraints excluded: chain B residue 65 ASN Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 143 ARG Chi-restraints excluded: chain B residue 144 GLU Chi-restraints excluded: chain B residue 355 GLU Chi-restraints excluded: chain B residue 392 LEU Chi-restraints excluded: chain B residue 459 SER Chi-restraints excluded: chain B residue 470 SER Chi-restraints excluded: chain B residue 475 GLN Chi-restraints excluded: chain C residue 124 LYS Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain C residue 426 GLU Chi-restraints excluded: chain C residue 498 LYS Chi-restraints excluded: chain C residue 499 GLU Chi-restraints excluded: chain E residue 29 ASP Chi-restraints excluded: chain E residue 112 LYS Chi-restraints excluded: chain E residue 249 GLN Chi-restraints excluded: chain E residue 263 ARG Chi-restraints excluded: chain E residue 266 GLN Chi-restraints excluded: chain E residue 294 THR Chi-restraints excluded: chain E residue 335 THR Chi-restraints excluded: chain E residue 355 ASP Chi-restraints excluded: chain E residue 415 ARG Chi-restraints excluded: chain F residue 205 GLU Chi-restraints excluded: chain F residue 422 GLN Chi-restraints excluded: chain F residue 434 LEU Chi-restraints excluded: chain D residue 46 THR Chi-restraints excluded: chain D residue 127 MET Chi-restraints excluded: chain D residue 132 GLU Chi-restraints excluded: chain D residue 292 MET Chi-restraints excluded: chain D residue 344 GLU Chi-restraints excluded: chain D residue 434 LEU Chi-restraints excluded: chain G residue 262 LEU Chi-restraints excluded: chain O residue 4 LEU Chi-restraints excluded: chain O residue 116 VAL Chi-restraints excluded: chain O residue 148 LEU Chi-restraints excluded: chain O residue 153 LYS Chi-restraints excluded: chain O residue 166 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 104 optimal weight: 3.9990 chunk 15 optimal weight: 0.7980 chunk 255 optimal weight: 1.9990 chunk 125 optimal weight: 0.5980 chunk 264 optimal weight: 3.9990 chunk 275 optimal weight: 2.9990 chunk 297 optimal weight: 2.9990 chunk 220 optimal weight: 0.6980 chunk 272 optimal weight: 5.9990 chunk 227 optimal weight: 0.9990 chunk 130 optimal weight: 0.6980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 492 GLN B 492 GLN C 503 ASN E 388 GLN E 445 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.125580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.092203 restraints weight = 29238.856| |-----------------------------------------------------------------------------| r_work (start): 0.3059 rms_B_bonded: 1.85 r_work: 0.2951 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2836 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8767 moved from start: 0.1999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 24557 Z= 0.110 Angle : 0.506 10.799 33213 Z= 0.256 Chirality : 0.042 0.141 3871 Planarity : 0.004 0.044 4292 Dihedral : 6.164 144.189 3448 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.72 % Favored : 98.25 % Rotamer: Outliers : 1.99 % Allowed : 15.34 % Favored : 82.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.02 (0.15), residues: 3134 helix: 1.78 (0.14), residues: 1358 sheet: -0.11 (0.23), residues: 509 loop : -0.10 (0.18), residues: 1267 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 373 TYR 0.014 0.001 TYR E 384 PHE 0.024 0.001 PHE B 468 HIS 0.012 0.001 HIS B 476 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.11 (24557) covalent geometry : angle 0.50640 / 0.26 (33213) hydrogen bonds : bond 0.03878 / 2.65 ( 1225) hydrogen bonds : angle 4.76732 / 3.31 ( 3489) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6268 Ramachandran restraints generated. 3134 Oldfield, 0 Emsley, 3134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6268 Ramachandran restraints generated. 3134 Oldfield, 0 Emsley, 3134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 306 time to evaluate : 0.914 Fit side-chains revert: symmetry clash REVERT: A 8 MET cc_start: 0.5798 (mtp) cc_final: 0.4903 (mmt) REVERT: A 101 GLU cc_start: 0.8762 (OUTLIER) cc_final: 0.8551 (mt-10) REVERT: A 196 LYS cc_start: 0.8384 (ptmt) cc_final: 0.7586 (mmtp) REVERT: A 347 ASP cc_start: 0.8822 (m-30) cc_final: 0.8598 (m-30) REVERT: A 349 GLN cc_start: 0.8376 (OUTLIER) cc_final: 0.7705 (pt0) REVERT: A 359 LYS cc_start: 0.7931 (mttt) cc_final: 0.7701 (mttm) REVERT: A 381 ARG cc_start: 0.6867 (mmm160) cc_final: 0.6623 (mmp80) REVERT: A 455 LYS cc_start: 0.8269 (mttp) cc_final: 0.7992 (mttt) REVERT: A 488 LYS cc_start: 0.8320 (pttt) cc_final: 0.7795 (ptpt) REVERT: A 499 GLU cc_start: 0.8276 (tm-30) cc_final: 0.7975 (tm-30) REVERT: B 54 GLU cc_start: 0.7994 (OUTLIER) cc_final: 0.7291 (tm-30) REVERT: B 144 GLU cc_start: 0.8791 (OUTLIER) cc_final: 0.8591 (mt-10) REVERT: B 226 MET cc_start: 0.8953 (tpt) cc_final: 0.8363 (tpt) REVERT: B 355 GLU cc_start: 0.7627 (OUTLIER) cc_final: 0.7158 (tt0) REVERT: B 392 LEU cc_start: 0.8194 (OUTLIER) cc_final: 0.7879 (tt) REVERT: B 415 GLN cc_start: 0.7367 (mm-40) cc_final: 0.6933 (tp40) REVERT: B 455 LYS cc_start: 0.8113 (mmtp) cc_final: 0.7507 (mmpt) REVERT: B 463 LYS cc_start: 0.7583 (ttmt) cc_final: 0.6996 (ptmm) REVERT: B 475 GLN cc_start: 0.7578 (OUTLIER) cc_final: 0.6726 (mp-120) REVERT: B 477 GLN cc_start: 0.7487 (mm-40) cc_final: 0.7122 (mp10) REVERT: C 8 MET cc_start: 0.3592 (ptt) cc_final: 0.2651 (mmt) REVERT: C 45 ARG cc_start: 0.7756 (mmm160) cc_final: 0.7327 (ptm160) REVERT: C 426 GLU cc_start: 0.7481 (OUTLIER) cc_final: 0.7143 (mp0) REVERT: C 498 LYS cc_start: 0.7384 (OUTLIER) cc_final: 0.7109 (ttpp) REVERT: C 499 GLU cc_start: 0.6192 (OUTLIER) cc_final: 0.5806 (mt-10) REVERT: E 112 LYS cc_start: 0.8503 (OUTLIER) cc_final: 0.8298 (mtpt) REVERT: E 249 GLN cc_start: 0.8925 (OUTLIER) cc_final: 0.7925 (mp10) REVERT: E 340 ARG cc_start: 0.7924 (ttp-170) cc_final: 0.7680 (tpp80) REVERT: E 409 ARG cc_start: 0.7842 (mtm-85) cc_final: 0.7290 (mtt-85) REVERT: E 411 ARG cc_start: 0.7639 (mtt-85) cc_final: 0.7115 (mtp85) REVERT: E 415 ARG cc_start: 0.7511 (OUTLIER) cc_final: 0.6252 (mpt180) REVERT: F 30 GLU cc_start: 0.7566 (pm20) cc_final: 0.7157 (pp20) REVERT: F 347 ILE cc_start: 0.8782 (mt) cc_final: 0.8539 (mm) REVERT: D 132 GLU cc_start: 0.7962 (OUTLIER) cc_final: 0.7224 (mp0) REVERT: D 170 MET cc_start: 0.7852 (mmm) cc_final: 0.7619 (mmp) REVERT: D 203 MET cc_start: 0.8236 (mtt) cc_final: 0.7831 (mtt) REVERT: D 210 ASN cc_start: 0.8709 (t0) cc_final: 0.8147 (t0) REVERT: D 212 LYS cc_start: 0.7689 (ptpp) cc_final: 0.6892 (ptpp) REVERT: D 252 GLN cc_start: 0.7407 (mm-40) cc_final: 0.6857 (mt0) REVERT: D 359 ARG cc_start: 0.7635 (mtm110) cc_final: 0.7076 (mtt-85) REVERT: D 422 GLN cc_start: 0.7433 (tp40) cc_final: 0.6980 (tp40) REVERT: D 458 GLN cc_start: 0.7090 (pm20) cc_final: 0.5900 (mm110) REVERT: G 229 MET cc_start: 0.8200 (ttp) cc_final: 0.7932 (ttp) REVERT: G 262 LEU cc_start: 0.8636 (OUTLIER) cc_final: 0.8402 (tt) REVERT: O 36 GLU cc_start: 0.6456 (tt0) cc_final: 0.5651 (mt-10) REVERT: O 69 LEU cc_start: 0.6174 (mm) cc_final: 0.5785 (mm) REVERT: O 153 LYS cc_start: 0.7489 (OUTLIER) cc_final: 0.6541 (pttt) REVERT: J 35 ARG cc_start: 0.5424 (mtt-85) cc_final: 0.5099 (ptm160) outliers start: 51 outliers final: 22 residues processed: 338 average time/residue: 0.7937 time to fit residues: 301.4210 Evaluate side-chains 332 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 294 time to evaluate : 0.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 GLU Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 349 GLN Chi-restraints excluded: chain A residue 497 LEU Chi-restraints excluded: chain B residue 54 GLU Chi-restraints excluded: chain B residue 65 ASN Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 143 ARG Chi-restraints excluded: chain B residue 144 GLU Chi-restraints excluded: chain B residue 355 GLU Chi-restraints excluded: chain B residue 392 LEU Chi-restraints excluded: chain B residue 459 SER Chi-restraints excluded: chain B residue 470 SER Chi-restraints excluded: chain B residue 475 GLN Chi-restraints excluded: chain C residue 124 LYS Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain C residue 426 GLU Chi-restraints excluded: chain C residue 498 LYS Chi-restraints excluded: chain C residue 499 GLU Chi-restraints excluded: chain E residue 29 ASP Chi-restraints excluded: chain E residue 112 LYS Chi-restraints excluded: chain E residue 249 GLN Chi-restraints excluded: chain E residue 263 ARG Chi-restraints excluded: chain E residue 266 GLN Chi-restraints excluded: chain E residue 294 THR Chi-restraints excluded: chain E residue 355 ASP Chi-restraints excluded: chain E residue 415 ARG Chi-restraints excluded: chain F residue 205 GLU Chi-restraints excluded: chain F residue 434 LEU Chi-restraints excluded: chain D residue 46 THR Chi-restraints excluded: chain D residue 127 MET Chi-restraints excluded: chain D residue 132 GLU Chi-restraints excluded: chain D residue 434 LEU Chi-restraints excluded: chain G residue 262 LEU Chi-restraints excluded: chain O residue 116 VAL Chi-restraints excluded: chain O residue 148 LEU Chi-restraints excluded: chain O residue 153 LYS Chi-restraints excluded: chain O residue 166 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 113 optimal weight: 3.9990 chunk 157 optimal weight: 3.9990 chunk 128 optimal weight: 4.9990 chunk 198 optimal weight: 3.9990 chunk 250 optimal weight: 5.9990 chunk 186 optimal weight: 0.9990 chunk 268 optimal weight: 3.9990 chunk 80 optimal weight: 2.9990 chunk 168 optimal weight: 0.0970 chunk 297 optimal weight: 2.9990 chunk 108 optimal weight: 0.0980 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 477 GLN A 492 GLN C 503 ASN E 445 GLN D 260 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.123868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.090285 restraints weight = 29312.847| |-----------------------------------------------------------------------------| r_work (start): 0.3032 rms_B_bonded: 1.86 r_work: 0.2922 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2808 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8791 moved from start: 0.1901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 24557 Z= 0.150 Angle : 0.533 11.712 33213 Z= 0.270 Chirality : 0.044 0.145 3871 Planarity : 0.004 0.042 4292 Dihedral : 6.299 147.112 3448 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.75 % Favored : 98.21 % Rotamer: Outliers : 1.75 % Allowed : 15.58 % Favored : 82.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.96 (0.15), residues: 3134 helix: 1.68 (0.14), residues: 1364 sheet: -0.11 (0.23), residues: 517 loop : -0.09 (0.18), residues: 1253 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 15 TYR 0.016 0.001 TYR E 384 PHE 0.015 0.001 PHE J 34 HIS 0.013 0.001 HIS B 476 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.15 (24557) covalent geometry : angle 0.53264 / 0.27 (33213) hydrogen bonds : bond 0.04331 / 2.94 ( 1225) hydrogen bonds : angle 4.84472 / 3.37 ( 3489) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6268 Ramachandran restraints generated. 3134 Oldfield, 0 Emsley, 3134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6268 Ramachandran restraints generated. 3134 Oldfield, 0 Emsley, 3134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 293 time to evaluate : 1.018 Fit side-chains revert: symmetry clash REVERT: A 101 GLU cc_start: 0.8812 (OUTLIER) cc_final: 0.8600 (mt-10) REVERT: A 196 LYS cc_start: 0.8396 (ptmt) cc_final: 0.7624 (mmtp) REVERT: A 349 GLN cc_start: 0.8408 (OUTLIER) cc_final: 0.7737 (pt0) REVERT: A 359 LYS cc_start: 0.7967 (mttt) cc_final: 0.7735 (mttm) REVERT: A 381 ARG cc_start: 0.6936 (mmm160) cc_final: 0.6705 (mmp80) REVERT: A 455 LYS cc_start: 0.8280 (mttp) cc_final: 0.8032 (mttt) REVERT: A 477 GLN cc_start: 0.8007 (mm-40) cc_final: 0.7703 (tp40) REVERT: A 488 LYS cc_start: 0.8334 (pttt) cc_final: 0.7957 (ptpt) REVERT: A 499 GLU cc_start: 0.8272 (tm-30) cc_final: 0.7972 (tm-30) REVERT: B 54 GLU cc_start: 0.8011 (OUTLIER) cc_final: 0.7299 (tm-30) REVERT: B 144 GLU cc_start: 0.8822 (OUTLIER) cc_final: 0.8572 (mt-10) REVERT: B 355 GLU cc_start: 0.7632 (OUTLIER) cc_final: 0.7157 (tt0) REVERT: B 392 LEU cc_start: 0.8242 (OUTLIER) cc_final: 0.7937 (tt) REVERT: B 455 LYS cc_start: 0.8146 (mmtp) cc_final: 0.7528 (mmpt) REVERT: B 475 GLN cc_start: 0.7623 (OUTLIER) cc_final: 0.6830 (mp-120) REVERT: B 477 GLN cc_start: 0.7516 (mm-40) cc_final: 0.7125 (mp10) REVERT: C 8 MET cc_start: 0.3698 (ptt) cc_final: 0.2727 (mmt) REVERT: C 45 ARG cc_start: 0.7788 (mmm160) cc_final: 0.7346 (ptm160) REVERT: C 426 GLU cc_start: 0.7513 (OUTLIER) cc_final: 0.7189 (mp0) REVERT: C 498 LYS cc_start: 0.7407 (OUTLIER) cc_final: 0.7126 (ttpp) REVERT: C 499 GLU cc_start: 0.6233 (OUTLIER) cc_final: 0.5866 (mt-10) REVERT: E 112 LYS cc_start: 0.8526 (OUTLIER) cc_final: 0.8273 (mtpt) REVERT: E 249 GLN cc_start: 0.8933 (OUTLIER) cc_final: 0.7883 (mp10) REVERT: E 340 ARG cc_start: 0.7964 (ttp-170) cc_final: 0.7713 (tpp80) REVERT: E 409 ARG cc_start: 0.7858 (mtm-85) cc_final: 0.7289 (mtt-85) REVERT: E 411 ARG cc_start: 0.7654 (mtt-85) cc_final: 0.7171 (mtt-85) REVERT: E 415 ARG cc_start: 0.7611 (OUTLIER) cc_final: 0.6306 (mpt180) REVERT: F 15 ARG cc_start: 0.8459 (mtm110) cc_final: 0.8238 (mtm-85) REVERT: F 347 ILE cc_start: 0.8812 (mt) cc_final: 0.8574 (mm) REVERT: D 132 GLU cc_start: 0.7968 (OUTLIER) cc_final: 0.7222 (mp0) REVERT: D 170 MET cc_start: 0.7875 (mmm) cc_final: 0.7586 (mmp) REVERT: D 203 MET cc_start: 0.8237 (mtt) cc_final: 0.7803 (mtt) REVERT: D 210 ASN cc_start: 0.8737 (t0) cc_final: 0.8197 (t0) REVERT: D 212 LYS cc_start: 0.7711 (ptpp) cc_final: 0.6939 (ptpp) REVERT: D 252 GLN cc_start: 0.7391 (mm-40) cc_final: 0.6851 (mt0) REVERT: D 344 GLU cc_start: 0.7848 (OUTLIER) cc_final: 0.7582 (mt-10) REVERT: D 359 ARG cc_start: 0.7742 (mtm110) cc_final: 0.7219 (mtt-85) REVERT: D 458 GLN cc_start: 0.7075 (pm20) cc_final: 0.5956 (mm110) REVERT: G 229 MET cc_start: 0.8242 (ttp) cc_final: 0.7972 (ttp) REVERT: G 262 LEU cc_start: 0.8691 (OUTLIER) cc_final: 0.8416 (tt) REVERT: O 36 GLU cc_start: 0.6373 (tt0) cc_final: 0.5675 (mt-10) REVERT: O 69 LEU cc_start: 0.6209 (mm) cc_final: 0.5824 (mm) REVERT: O 153 LYS cc_start: 0.7496 (OUTLIER) cc_final: 0.6498 (pttt) REVERT: J 35 ARG cc_start: 0.5449 (mtt-85) cc_final: 0.5106 (ptm160) outliers start: 45 outliers final: 23 residues processed: 324 average time/residue: 0.8004 time to fit residues: 290.7023 Evaluate side-chains 328 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 288 time to evaluate : 0.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 GLU Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 349 GLN Chi-restraints excluded: chain A residue 497 LEU Chi-restraints excluded: chain B residue 54 GLU Chi-restraints excluded: chain B residue 65 ASN Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 143 ARG Chi-restraints excluded: chain B residue 144 GLU Chi-restraints excluded: chain B residue 355 GLU Chi-restraints excluded: chain B residue 392 LEU Chi-restraints excluded: chain B residue 459 SER Chi-restraints excluded: chain B residue 470 SER Chi-restraints excluded: chain B residue 475 GLN Chi-restraints excluded: chain C residue 124 LYS Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain C residue 426 GLU Chi-restraints excluded: chain C residue 498 LYS Chi-restraints excluded: chain C residue 499 GLU Chi-restraints excluded: chain E residue 29 ASP Chi-restraints excluded: chain E residue 112 LYS Chi-restraints excluded: chain E residue 249 GLN Chi-restraints excluded: chain E residue 263 ARG Chi-restraints excluded: chain E residue 266 GLN Chi-restraints excluded: chain E residue 294 THR Chi-restraints excluded: chain E residue 335 THR Chi-restraints excluded: chain E residue 355 ASP Chi-restraints excluded: chain E residue 415 ARG Chi-restraints excluded: chain F residue 205 GLU Chi-restraints excluded: chain D residue 46 THR Chi-restraints excluded: chain D residue 127 MET Chi-restraints excluded: chain D residue 132 GLU Chi-restraints excluded: chain D residue 344 GLU Chi-restraints excluded: chain D residue 434 LEU Chi-restraints excluded: chain G residue 262 LEU Chi-restraints excluded: chain O residue 116 VAL Chi-restraints excluded: chain O residue 148 LEU Chi-restraints excluded: chain O residue 153 LYS Chi-restraints excluded: chain O residue 166 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 138 optimal weight: 1.9990 chunk 127 optimal weight: 3.9990 chunk 69 optimal weight: 0.9990 chunk 3 optimal weight: 4.9990 chunk 225 optimal weight: 0.0010 chunk 135 optimal weight: 1.9990 chunk 145 optimal weight: 0.7980 chunk 252 optimal weight: 5.9990 chunk 85 optimal weight: 8.9990 chunk 237 optimal weight: 0.9980 chunk 174 optimal weight: 8.9990 overall best weight: 0.9590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 492 GLN C 503 ASN E 445 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.125053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.091559 restraints weight = 29287.785| |-----------------------------------------------------------------------------| r_work (start): 0.3050 rms_B_bonded: 1.85 r_work: 0.2941 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2826 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8774 moved from start: 0.1996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 24557 Z= 0.122 Angle : 0.523 11.914 33213 Z= 0.264 Chirality : 0.043 0.143 3871 Planarity : 0.004 0.042 4292 Dihedral : 6.217 147.583 3448 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.75 % Favored : 98.21 % Rotamer: Outliers : 1.71 % Allowed : 15.85 % Favored : 82.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.06 (0.15), residues: 3134 helix: 1.78 (0.14), residues: 1357 sheet: -0.09 (0.23), residues: 509 loop : -0.04 (0.18), residues: 1268 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 15 TYR 0.017 0.001 TYR E 384 PHE 0.030 0.001 PHE B 468 HIS 0.012 0.001 HIS B 476 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.12 (24557) covalent geometry : angle 0.52275 / 0.26 (33213) hydrogen bonds : bond 0.04028 / 2.74 ( 1225) hydrogen bonds : angle 4.79328 / 3.33 ( 3489) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6268 Ramachandran restraints generated. 3134 Oldfield, 0 Emsley, 3134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6268 Ramachandran restraints generated. 3134 Oldfield, 0 Emsley, 3134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 299 time to evaluate : 1.158 Fit side-chains revert: symmetry clash REVERT: A 8 MET cc_start: 0.5862 (mtp) cc_final: 0.4966 (mmt) REVERT: A 101 GLU cc_start: 0.8784 (OUTLIER) cc_final: 0.8573 (mt-10) REVERT: A 196 LYS cc_start: 0.8391 (ptmt) cc_final: 0.7626 (mmtp) REVERT: A 347 ASP cc_start: 0.8856 (m-30) cc_final: 0.8599 (m-30) REVERT: A 349 GLN cc_start: 0.8392 (OUTLIER) cc_final: 0.7719 (pt0) REVERT: A 359 LYS cc_start: 0.7937 (mttt) cc_final: 0.7707 (mttm) REVERT: A 381 ARG cc_start: 0.6892 (mmm160) cc_final: 0.6657 (mmp80) REVERT: A 455 LYS cc_start: 0.8274 (mttp) cc_final: 0.8026 (mttt) REVERT: A 488 LYS cc_start: 0.8317 (pttt) cc_final: 0.7933 (ptpt) REVERT: A 491 GLU cc_start: 0.7855 (mm-30) cc_final: 0.7117 (mt-10) REVERT: A 499 GLU cc_start: 0.8278 (tm-30) cc_final: 0.7974 (tm-30) REVERT: B 54 GLU cc_start: 0.7993 (OUTLIER) cc_final: 0.7286 (tm-30) REVERT: B 144 GLU cc_start: 0.8807 (OUTLIER) cc_final: 0.8594 (mt-10) REVERT: B 195 GLU cc_start: 0.7178 (tp30) cc_final: 0.6923 (tp30) REVERT: B 226 MET cc_start: 0.8967 (tpt) cc_final: 0.8342 (tpt) REVERT: B 355 GLU cc_start: 0.7616 (OUTLIER) cc_final: 0.7147 (tt0) REVERT: B 392 LEU cc_start: 0.8133 (OUTLIER) cc_final: 0.7861 (tt) REVERT: B 415 GLN cc_start: 0.7374 (mm-40) cc_final: 0.6960 (tp40) REVERT: B 455 LYS cc_start: 0.8121 (mmtp) cc_final: 0.7514 (mmpt) REVERT: B 465 GLU cc_start: 0.8035 (OUTLIER) cc_final: 0.7561 (tm-30) REVERT: B 475 GLN cc_start: 0.7637 (OUTLIER) cc_final: 0.6896 (mp-120) REVERT: B 477 GLN cc_start: 0.7482 (mm-40) cc_final: 0.7080 (mp10) REVERT: C 8 MET cc_start: 0.3705 (ptt) cc_final: 0.2725 (mmt) REVERT: C 45 ARG cc_start: 0.7774 (mmm160) cc_final: 0.7348 (ptm160) REVERT: C 426 GLU cc_start: 0.7502 (OUTLIER) cc_final: 0.7177 (mp0) REVERT: C 498 LYS cc_start: 0.7406 (OUTLIER) cc_final: 0.7126 (ttpp) REVERT: C 499 GLU cc_start: 0.6236 (OUTLIER) cc_final: 0.5880 (mt-10) REVERT: E 112 LYS cc_start: 0.8510 (OUTLIER) cc_final: 0.8297 (mtpt) REVERT: E 205 GLU cc_start: 0.8344 (tt0) cc_final: 0.8138 (pp20) REVERT: E 340 ARG cc_start: 0.7926 (ttp-170) cc_final: 0.7676 (tpp80) REVERT: E 409 ARG cc_start: 0.7857 (mtm-85) cc_final: 0.7277 (mtt-85) REVERT: E 411 ARG cc_start: 0.7638 (mtt-85) cc_final: 0.7106 (mtp85) REVERT: E 415 ARG cc_start: 0.7523 (OUTLIER) cc_final: 0.6253 (mpt180) REVERT: F 15 ARG cc_start: 0.8421 (mtm110) cc_final: 0.8210 (mtm-85) REVERT: F 30 GLU cc_start: 0.7602 (pm20) cc_final: 0.7230 (pp20) REVERT: F 347 ILE cc_start: 0.8788 (mt) cc_final: 0.8548 (mm) REVERT: D 132 GLU cc_start: 0.7979 (OUTLIER) cc_final: 0.7227 (mp0) REVERT: D 170 MET cc_start: 0.7832 (mmm) cc_final: 0.7565 (mmp) REVERT: D 203 MET cc_start: 0.8226 (mtt) cc_final: 0.7789 (mtt) REVERT: D 210 ASN cc_start: 0.8708 (t0) cc_final: 0.8149 (t0) REVERT: D 212 LYS cc_start: 0.7693 (ptpp) cc_final: 0.6906 (ptpp) REVERT: D 252 GLN cc_start: 0.7377 (mm-40) cc_final: 0.6969 (mt0) REVERT: D 344 GLU cc_start: 0.7823 (OUTLIER) cc_final: 0.7538 (mt-10) REVERT: D 359 ARG cc_start: 0.7681 (mtm110) cc_final: 0.7123 (mtt-85) REVERT: D 458 GLN cc_start: 0.7068 (pm20) cc_final: 0.5953 (mm110) REVERT: G 229 MET cc_start: 0.8212 (ttp) cc_final: 0.7950 (ttp) REVERT: G 262 LEU cc_start: 0.8661 (OUTLIER) cc_final: 0.8413 (tt) REVERT: O 36 GLU cc_start: 0.6382 (tt0) cc_final: 0.5677 (mt-10) REVERT: O 69 LEU cc_start: 0.6223 (mm) cc_final: 0.5837 (mm) REVERT: O 153 LYS cc_start: 0.7492 (OUTLIER) cc_final: 0.6501 (pttt) REVERT: J 35 ARG cc_start: 0.5418 (mtt-85) cc_final: 0.5119 (ptm160) outliers start: 44 outliers final: 23 residues processed: 327 average time/residue: 0.7733 time to fit residues: 283.8784 Evaluate side-chains 334 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 294 time to evaluate : 1.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 GLU Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 349 GLN Chi-restraints excluded: chain A residue 497 LEU Chi-restraints excluded: chain B residue 54 GLU Chi-restraints excluded: chain B residue 65 ASN Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 143 ARG Chi-restraints excluded: chain B residue 144 GLU Chi-restraints excluded: chain B residue 355 GLU Chi-restraints excluded: chain B residue 392 LEU Chi-restraints excluded: chain B residue 459 SER Chi-restraints excluded: chain B residue 465 GLU Chi-restraints excluded: chain B residue 470 SER Chi-restraints excluded: chain B residue 475 GLN Chi-restraints excluded: chain C residue 124 LYS Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain C residue 426 GLU Chi-restraints excluded: chain C residue 498 LYS Chi-restraints excluded: chain C residue 499 GLU Chi-restraints excluded: chain E residue 29 ASP Chi-restraints excluded: chain E residue 112 LYS Chi-restraints excluded: chain E residue 263 ARG Chi-restraints excluded: chain E residue 266 GLN Chi-restraints excluded: chain E residue 294 THR Chi-restraints excluded: chain E residue 355 ASP Chi-restraints excluded: chain E residue 415 ARG Chi-restraints excluded: chain F residue 205 GLU Chi-restraints excluded: chain F residue 434 LEU Chi-restraints excluded: chain D residue 46 THR Chi-restraints excluded: chain D residue 127 MET Chi-restraints excluded: chain D residue 132 GLU Chi-restraints excluded: chain D residue 344 GLU Chi-restraints excluded: chain D residue 434 LEU Chi-restraints excluded: chain G residue 262 LEU Chi-restraints excluded: chain O residue 116 VAL Chi-restraints excluded: chain O residue 148 LEU Chi-restraints excluded: chain O residue 153 LYS Chi-restraints excluded: chain O residue 166 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 126 optimal weight: 0.7980 chunk 181 optimal weight: 1.9990 chunk 7 optimal weight: 4.9990 chunk 241 optimal weight: 5.9990 chunk 198 optimal weight: 2.9990 chunk 308 optimal weight: 0.9980 chunk 37 optimal weight: 0.9980 chunk 161 optimal weight: 1.9990 chunk 73 optimal weight: 2.9990 chunk 46 optimal weight: 0.8980 chunk 140 optimal weight: 0.5980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 477 GLN A 492 GLN C 366 ASN C 503 ASN E 445 GLN F 197 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.125740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.092277 restraints weight = 29201.832| |-----------------------------------------------------------------------------| r_work (start): 0.3061 rms_B_bonded: 1.85 r_work: 0.2952 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2838 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8765 moved from start: 0.2083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 24557 Z= 0.115 Angle : 0.513 11.752 33213 Z= 0.258 Chirality : 0.042 0.141 3871 Planarity : 0.004 0.042 4292 Dihedral : 6.136 148.388 3448 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.69 % Favored : 98.28 % Rotamer: Outliers : 1.71 % Allowed : 15.85 % Favored : 82.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.08 (0.15), residues: 3134 helix: 1.81 (0.14), residues: 1360 sheet: -0.10 (0.23), residues: 502 loop : -0.05 (0.18), residues: 1272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 15 TYR 0.018 0.001 TYR E 384 PHE 0.017 0.001 PHE J 34 HIS 0.011 0.001 HIS B 476 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.11 (24557) covalent geometry : angle 0.51254 / 0.26 (33213) hydrogen bonds : bond 0.03895 / 2.66 ( 1225) hydrogen bonds : angle 4.73454 / 3.29 ( 3489) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9593.59 seconds wall clock time: 164 minutes 0.94 seconds (9840.94 seconds total)