Starting phenix.real_space_refine on Fri May 23 14:48:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8h9e_34564/05_2025/8h9e_34564.cif Found real_map, /net/cci-nas-00/data/ceres_data/8h9e_34564/05_2025/8h9e_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8h9e_34564/05_2025/8h9e_34564.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8h9e_34564/05_2025/8h9e_34564.map" model { file = "/net/cci-nas-00/data/ceres_data/8h9e_34564/05_2025/8h9e_34564.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8h9e_34564/05_2025/8h9e_34564.cif" } resolution = 2.53 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.029 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): 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 15.60, per 1000 atoms: 0.64 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: 5.64 Conformation dependent library (CDL) restraints added in 2.9 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: 2.73 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: 9.23 Time building geometry restraints manager: 6.62 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: 14750 35.15 - 70.30: 283 70.30 - 105.45: 40 105.45 - 140.60: 0 140.60 - 175.75: 3 Dihedral angle restraints: 15076 sinusoidal: 6097 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 15073 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 508 or resid 601 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: 5.650 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.850 Check model and map are aligned: 0.170 Set scattering table: 0.220 Process input model: 54.930 Find NCS groups from input model: 1.910 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 75.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8497 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 : 14.539 175.753 9336 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.86 (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 HIS 0.004 0.001 HIS D 180 PHE 0.015 0.002 PHE F 444 TYR 0.012 0.002 TYR A 446 ARG 0.005 0.001 ARG F 298 Details of bonding type rmsd hydrogen bonds : bond 0.15719 ( 1225) hydrogen bonds : angle 6.92485 ( 3489) covalent geometry : bond 0.00821 (24557) covalent geometry : angle 0.80267 (33213) *********************** 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 : 2.642 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: 0.8511 (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: 1.7514 time to fit residues: 829.5330 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 : 2.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 263 optimal weight: 3.9990 chunk 236 optimal weight: 4.9990 chunk 131 optimal weight: 0.9990 chunk 80 optimal weight: 0.9980 chunk 159 optimal weight: 1.9990 chunk 126 optimal weight: 0.7980 chunk 244 optimal weight: 0.5980 chunk 94 optimal weight: 5.9990 chunk 148 optimal weight: 0.9980 chunk 182 optimal weight: 2.9990 chunk 283 optimal weight: 0.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 396 GLN A 405 GLN A 416 GLN A 492 GLN A 503 ASN B 48 GLN B 78 ASN 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: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.124296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.091640 restraints weight = 29332.703| |-----------------------------------------------------------------------------| r_work (start): 0.3040 rms_B_bonded: 1.76 r_work: 0.2933 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2819 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.2819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.1299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 24557 Z= 0.127 Angle : 0.539 7.063 33213 Z= 0.279 Chirality : 0.043 0.157 3871 Planarity : 0.004 0.046 4292 Dihedral : 8.273 157.627 3541 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.10 % Allowed : 1.75 % Favored : 98.15 % Rotamer: Outliers : 1.40 % Allowed : 10.71 % Favored : 87.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.15), residues: 3134 helix: 0.64 (0.14), residues: 1361 sheet: -0.58 (0.21), residues: 533 loop : -0.74 (0.17), residues: 1240 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS B 476 PHE 0.015 0.001 PHE J 34 TYR 0.012 0.001 TYR E 284 ARG 0.008 0.000 ARG F 15 Details of bonding type rmsd hydrogen bonds : bond 0.04658 ( 1225) hydrogen bonds : angle 5.29650 ( 3489) covalent geometry : bond 0.00279 (24557) covalent geometry : angle 0.53864 (33213) *********************** 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 374 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 338 time to evaluate : 3.045 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 359 LYS cc_start: 0.7948 (mttt) cc_final: 0.7681 (mttm) REVERT: A 475 GLN cc_start: 0.7782 (mt0) cc_final: 0.7547 (mt0) REVERT: A 488 LYS cc_start: 0.8254 (pttt) cc_final: 0.7761 (ptpt) REVERT: A 499 GLU cc_start: 0.8210 (tm-30) cc_final: 0.7920 (tm-30) REVERT: B 455 LYS cc_start: 0.8165 (mmtp) cc_final: 0.7534 (mmpt) REVERT: C 8 MET cc_start: 0.3606 (ptt) cc_final: 0.3112 (ptp) REVERT: C 45 ARG cc_start: 0.7890 (mmm160) cc_final: 0.7387 (ptm-80) REVERT: C 499 GLU cc_start: 0.6277 (OUTLIER) cc_final: 0.5883 (mt-10) REVERT: E 15 ARG cc_start: 0.8332 (ptt-90) cc_final: 0.7618 (ptp90) REVERT: E 112 LYS cc_start: 0.8540 (OUTLIER) cc_final: 0.8277 (mtpt) REVERT: E 249 GLN cc_start: 0.8950 (OUTLIER) cc_final: 0.7827 (mp10) REVERT: E 409 ARG cc_start: 0.7886 (mtm-85) cc_final: 0.7549 (mtt180) REVERT: E 415 ARG cc_start: 0.7564 (OUTLIER) cc_final: 0.6319 (mpt180) REVERT: F 422 GLN cc_start: 0.7827 (OUTLIER) cc_final: 0.7348 (mt0) REVERT: D 170 MET cc_start: 0.7933 (mmm) cc_final: 0.7645 (mmm) REVERT: D 203 MET cc_start: 0.8350 (mtt) cc_final: 0.7971 (mtt) REVERT: D 210 ASN cc_start: 0.8740 (t0) cc_final: 0.8234 (t0) REVERT: D 212 LYS cc_start: 0.7700 (ptpp) cc_final: 0.6865 (ptpp) REVERT: D 359 ARG cc_start: 0.7869 (mtm110) cc_final: 0.7321 (mtt-85) REVERT: D 414 GLN cc_start: 0.7197 (tt0) cc_final: 0.6953 (tt0) REVERT: D 458 GLN cc_start: 0.7168 (pm20) cc_final: 0.5844 (tp40) REVERT: G 18 LYS cc_start: 0.8027 (OUTLIER) cc_final: 0.7356 (tptt) REVERT: G 229 MET cc_start: 0.8309 (ttp) cc_final: 0.8055 (ttp) REVERT: O 33 GLU cc_start: 0.5649 (mp0) cc_final: 0.5326 (mm-30) REVERT: O 69 LEU cc_start: 0.6077 (mm) cc_final: 0.5540 (mm) outliers start: 36 outliers final: 10 residues processed: 355 average time/residue: 1.6675 time to fit residues: 663.8015 Evaluate side-chains 317 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 301 time to evaluate : 2.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 349 GLN Chi-restraints excluded: chain B residue 470 SER Chi-restraints excluded: chain C residue 124 LYS Chi-restraints excluded: chain C residue 180 ILE 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 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 Chi-restraints excluded: chain O residue 39 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 280 optimal weight: 5.9990 chunk 95 optimal weight: 10.0000 chunk 58 optimal weight: 0.0270 chunk 137 optimal weight: 9.9990 chunk 20 optimal weight: 3.9990 chunk 272 optimal weight: 6.9990 chunk 262 optimal weight: 4.9990 chunk 219 optimal weight: 0.0870 chunk 65 optimal weight: 6.9990 chunk 265 optimal weight: 6.9990 chunk 230 optimal weight: 3.9990 overall best weight: 2.6222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3404 r_free = 0.3404 target = 0.120766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.087429 restraints weight = 29325.397| |-----------------------------------------------------------------------------| r_work (start): 0.2989 rms_B_bonded: 1.84 r_work: 0.2879 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2764 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.2764 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8545 moved from start: 0.1301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 24557 Z= 0.237 Angle : 0.596 10.464 33213 Z= 0.308 Chirality : 0.047 0.149 3871 Planarity : 0.004 0.047 4292 Dihedral : 8.157 141.437 3541 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.27 % Favored : 97.64 % Rotamer: Outliers : 2.34 % Allowed : 12.15 % Favored : 85.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.15), residues: 3134 helix: 0.89 (0.14), residues: 1360 sheet: -0.45 (0.22), residues: 517 loop : -0.57 (0.17), residues: 1257 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS B 476 PHE 0.019 0.002 PHE B 468 TYR 0.019 0.002 TYR B 446 ARG 0.004 0.000 ARG F 15 Details of bonding type rmsd hydrogen bonds : bond 0.05476 ( 1225) hydrogen bonds : angle 5.25706 ( 3489) covalent geometry : bond 0.00573 (24557) covalent geometry : angle 0.59565 (33213) *********************** 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 367 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 307 time to evaluate : 2.569 Fit side-chains revert: symmetry clash REVERT: A 359 LYS cc_start: 0.8025 (mttt) cc_final: 0.7755 (mttm) REVERT: A 455 LYS cc_start: 0.8289 (mttp) cc_final: 0.8053 (mttt) REVERT: A 475 GLN cc_start: 0.7756 (mt0) cc_final: 0.7533 (mt0) REVERT: A 488 LYS cc_start: 0.8338 (pttt) cc_final: 0.7847 (ptpt) REVERT: A 499 GLU cc_start: 0.8269 (tm-30) cc_final: 0.7967 (tm-30) REVERT: B 426 GLU cc_start: 0.7876 (mm-30) cc_final: 0.7515 (tp30) REVERT: B 455 LYS cc_start: 0.8194 (mmtp) cc_final: 0.7597 (mmpt) REVERT: C 8 MET cc_start: 0.3754 (ptt) cc_final: 0.3231 (ptp) REVERT: C 45 ARG cc_start: 0.7963 (mmm160) cc_final: 0.7453 (ptm-80) REVERT: C 489 ILE cc_start: 0.6991 (OUTLIER) cc_final: 0.6786 (pp) REVERT: C 498 LYS cc_start: 0.7374 (OUTLIER) cc_final: 0.7043 (ttpp) REVERT: E 15 ARG cc_start: 0.8376 (ptt-90) cc_final: 0.7680 (ptp90) REVERT: E 112 LYS cc_start: 0.8616 (OUTLIER) cc_final: 0.8338 (mtpt) REVERT: E 409 ARG cc_start: 0.7968 (mtm-85) cc_final: 0.7394 (mtt-85) REVERT: E 415 ARG cc_start: 0.7775 (OUTLIER) cc_final: 0.6386 (mpt180) REVERT: F 27 GLN cc_start: 0.8863 (OUTLIER) cc_final: 0.8555 (tt0) REVERT: F 215 THR cc_start: 0.9017 (m) cc_final: 0.8749 (p) REVERT: F 422 GLN cc_start: 0.7877 (OUTLIER) cc_final: 0.7413 (mt0) REVERT: D 170 MET cc_start: 0.7991 (mmm) cc_final: 0.7767 (mmp) REVERT: D 203 MET cc_start: 0.8329 (mtt) cc_final: 0.7962 (mtt) REVERT: D 210 ASN cc_start: 0.8756 (t0) cc_final: 0.8324 (t0) REVERT: D 212 LYS cc_start: 0.7741 (ptpp) cc_final: 0.6939 (ptpp) REVERT: D 252 GLN cc_start: 0.7455 (mm-40) cc_final: 0.7035 (mm-40) REVERT: D 359 ARG cc_start: 0.7886 (mtm110) cc_final: 0.7327 (mtt-85) REVERT: D 414 GLN cc_start: 0.7310 (tt0) cc_final: 0.7078 (tt0) REVERT: D 458 GLN cc_start: 0.7186 (pm20) cc_final: 0.6044 (tp40) REVERT: G 229 MET cc_start: 0.8340 (ttp) cc_final: 0.8028 (ttp) REVERT: O 69 LEU cc_start: 0.6230 (mm) cc_final: 0.5832 (mm) REVERT: O 126 LEU cc_start: 0.7516 (OUTLIER) cc_final: 0.7285 (mt) outliers start: 60 outliers final: 14 residues processed: 341 average time/residue: 1.6791 time to fit residues: 643.4759 Evaluate side-chains 312 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 291 time to evaluate : 2.994 ------------------------------------------------------------------------------- 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 125 THR 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 489 ILE Chi-restraints excluded: chain C residue 498 LYS 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 335 THR Chi-restraints excluded: chain E residue 390 ILE Chi-restraints excluded: chain E residue 415 ARG Chi-restraints excluded: chain F residue 27 GLN 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 O residue 126 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 1 optimal weight: 10.0000 chunk 144 optimal weight: 10.0000 chunk 190 optimal weight: 3.9990 chunk 141 optimal weight: 6.9990 chunk 105 optimal weight: 1.9990 chunk 102 optimal weight: 0.7980 chunk 3 optimal weight: 1.9990 chunk 121 optimal weight: 0.8980 chunk 230 optimal weight: 0.8980 chunk 77 optimal weight: 0.5980 chunk 162 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 492 GLN B 78 ASN C 385 GLN C 503 ASN E 388 GLN D 180 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.124693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.091433 restraints weight = 29488.781| |-----------------------------------------------------------------------------| r_work (start): 0.3047 rms_B_bonded: 1.86 r_work: 0.2939 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2824 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.1678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 24557 Z= 0.114 Angle : 0.507 9.988 33213 Z= 0.259 Chirality : 0.043 0.141 3871 Planarity : 0.004 0.047 4292 Dihedral : 7.340 140.788 3541 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.50 % Favored : 98.47 % Rotamer: Outliers : 2.14 % Allowed : 13.01 % Favored : 84.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.15), residues: 3134 helix: 1.40 (0.14), residues: 1351 sheet: -0.32 (0.22), residues: 532 loop : -0.33 (0.17), residues: 1251 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.001 HIS B 476 PHE 0.012 0.001 PHE J 34 TYR 0.010 0.001 TYR O 12 ARG 0.006 0.000 ARG A 373 Details of bonding type rmsd hydrogen bonds : bond 0.04113 ( 1225) hydrogen bonds : angle 4.92413 ( 3489) covalent geometry : bond 0.00253 (24557) covalent geometry : angle 0.50660 (33213) *********************** 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 386 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 331 time to evaluate : 2.605 Fit side-chains revert: symmetry clash REVERT: A 8 MET cc_start: 0.5813 (mtp) cc_final: 0.4949 (mmt) REVERT: A 196 LYS cc_start: 0.8524 (ptmt) cc_final: 0.7611 (mmtp) REVERT: A 359 LYS cc_start: 0.7947 (mttt) cc_final: 0.7700 (mttm) REVERT: A 455 LYS cc_start: 0.8289 (mttp) cc_final: 0.8077 (mttt) REVERT: A 488 LYS cc_start: 0.8308 (pttt) cc_final: 0.7834 (ptpt) REVERT: A 491 GLU cc_start: 0.7737 (mm-30) cc_final: 0.7077 (mt-10) REVERT: A 499 GLU cc_start: 0.8318 (tm-30) cc_final: 0.8008 (tm-30) REVERT: B 54 GLU cc_start: 0.8047 (OUTLIER) cc_final: 0.7381 (tm-30) REVERT: B 226 MET cc_start: 0.8957 (tpt) cc_final: 0.8333 (tpt) REVERT: B 355 GLU cc_start: 0.7627 (OUTLIER) cc_final: 0.7126 (tt0) REVERT: B 455 LYS cc_start: 0.8153 (mmtp) cc_final: 0.7534 (mmpt) REVERT: B 475 GLN cc_start: 0.7183 (OUTLIER) cc_final: 0.6501 (mp-120) REVERT: B 476 HIS cc_start: 0.7665 (m-70) cc_final: 0.7407 (m-70) REVERT: B 477 GLN cc_start: 0.7378 (mm-40) cc_final: 0.7045 (mp10) REVERT: C 8 MET cc_start: 0.3676 (ptt) cc_final: 0.3169 (ptp) REVERT: C 45 ARG cc_start: 0.7833 (mmm160) cc_final: 0.7329 (ptm-80) REVERT: C 128 ARG cc_start: 0.7951 (mtt180) cc_final: 0.7744 (mtp180) REVERT: C 426 GLU cc_start: 0.7583 (OUTLIER) cc_final: 0.7246 (mp0) REVERT: C 489 ILE cc_start: 0.6752 (OUTLIER) cc_final: 0.6525 (pp) REVERT: C 498 LYS cc_start: 0.7389 (OUTLIER) cc_final: 0.7065 (ttpp) REVERT: C 499 GLU cc_start: 0.6266 (OUTLIER) cc_final: 0.5842 (mt-10) REVERT: E 15 ARG cc_start: 0.8330 (ptt-90) cc_final: 0.7692 (ptp90) REVERT: E 112 LYS cc_start: 0.8497 (OUTLIER) cc_final: 0.8288 (mtpt) REVERT: E 249 GLN cc_start: 0.8922 (OUTLIER) cc_final: 0.7847 (mp10) REVERT: E 409 ARG cc_start: 0.7897 (mtm-85) cc_final: 0.7489 (mtt-85) REVERT: E 415 ARG cc_start: 0.7530 (OUTLIER) cc_final: 0.6382 (mpt180) REVERT: D 132 GLU cc_start: 0.7941 (OUTLIER) cc_final: 0.7202 (mp0) REVERT: D 170 MET cc_start: 0.7889 (mmm) cc_final: 0.7678 (mmp) REVERT: D 203 MET cc_start: 0.8302 (mtt) cc_final: 0.7873 (mtt) REVERT: D 210 ASN cc_start: 0.8739 (t0) cc_final: 0.8201 (t0) REVERT: D 212 LYS cc_start: 0.7686 (ptpp) cc_final: 0.6864 (ptpp) REVERT: D 252 GLN cc_start: 0.7474 (mm-40) cc_final: 0.7018 (mt0) REVERT: D 359 ARG cc_start: 0.7774 (mtm110) cc_final: 0.7172 (mtt-85) REVERT: D 414 GLN cc_start: 0.7094 (tt0) cc_final: 0.6892 (tt0) REVERT: D 458 GLN cc_start: 0.7146 (pm20) cc_final: 0.5932 (mm-40) REVERT: G 229 MET cc_start: 0.8268 (ttp) cc_final: 0.8009 (ttp) REVERT: G 262 LEU cc_start: 0.8649 (OUTLIER) cc_final: 0.8423 (tt) REVERT: G 264 GLU cc_start: 0.8447 (mt-10) cc_final: 0.8220 (mt-10) REVERT: O 46 LEU cc_start: 0.5660 (OUTLIER) cc_final: 0.5452 (mp) REVERT: O 69 LEU cc_start: 0.6186 (mm) cc_final: 0.5810 (mm) REVERT: J 35 ARG cc_start: 0.5419 (mtt-85) cc_final: 0.5096 (ptm160) outliers start: 55 outliers final: 12 residues processed: 369 average time/residue: 1.6194 time to fit residues: 671.7669 Evaluate side-chains 331 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 306 time to evaluate : 2.657 ------------------------------------------------------------------------------- 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 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 301 LEU Chi-restraints excluded: chain C residue 426 GLU Chi-restraints excluded: chain C residue 489 ILE 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 415 ARG 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 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 289 optimal weight: 4.9990 chunk 59 optimal weight: 0.9980 chunk 53 optimal weight: 2.9990 chunk 181 optimal weight: 1.9990 chunk 293 optimal weight: 9.9990 chunk 221 optimal weight: 0.9990 chunk 48 optimal weight: 1.9990 chunk 54 optimal weight: 3.9990 chunk 249 optimal weight: 0.1980 chunk 193 optimal weight: 1.9990 chunk 162 optimal weight: 7.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 492 GLN B 78 ASN B 492 GLN 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: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.123675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.090252 restraints weight = 29504.563| |-----------------------------------------------------------------------------| r_work (start): 0.3031 rms_B_bonded: 1.86 r_work: 0.2922 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2807 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.1729 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= 0.138 Angle : 0.517 10.346 33213 Z= 0.264 Chirality : 0.043 0.145 3871 Planarity : 0.004 0.046 4292 Dihedral : 7.291 142.580 3541 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.60 % Favored : 98.37 % Rotamer: Outliers : 2.34 % Allowed : 13.90 % Favored : 83.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.15), residues: 3134 helix: 1.52 (0.14), residues: 1358 sheet: -0.25 (0.22), residues: 525 loop : -0.24 (0.17), residues: 1251 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS B 476 PHE 0.019 0.001 PHE B 468 TYR 0.010 0.001 TYR O 12 ARG 0.005 0.000 ARG F 15 Details of bonding type rmsd hydrogen bonds : bond 0.04319 ( 1225) hydrogen bonds : angle 4.88698 ( 3489) covalent geometry : bond 0.00321 (24557) covalent geometry : angle 0.51743 (33213) *********************** 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 368 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 308 time to evaluate : 3.037 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 MET cc_start: 0.5818 (mtp) cc_final: 0.4944 (mmt) REVERT: A 101 GLU cc_start: 0.8804 (OUTLIER) cc_final: 0.8592 (mt-10) REVERT: A 196 LYS cc_start: 0.8476 (ptmt) cc_final: 0.7607 (mmtp) REVERT: A 347 ASP cc_start: 0.8957 (m-30) cc_final: 0.8727 (m-30) REVERT: A 359 LYS cc_start: 0.7955 (mttt) cc_final: 0.7723 (mttm) REVERT: A 455 LYS cc_start: 0.8284 (mttp) cc_final: 0.8069 (mttt) REVERT: A 488 LYS cc_start: 0.8325 (pttt) cc_final: 0.7808 (ptpt) REVERT: A 491 GLU cc_start: 0.7815 (mm-30) cc_final: 0.7123 (mt-10) REVERT: A 499 GLU cc_start: 0.8290 (tm-30) cc_final: 0.7943 (tm-30) REVERT: B 54 GLU cc_start: 0.8039 (OUTLIER) cc_final: 0.7370 (tm-30) REVERT: B 355 GLU cc_start: 0.7641 (OUTLIER) cc_final: 0.7149 (tt0) REVERT: B 392 LEU cc_start: 0.8241 (OUTLIER) cc_final: 0.7997 (tm) REVERT: B 455 LYS cc_start: 0.8131 (mmtp) cc_final: 0.7515 (mmpt) REVERT: B 475 GLN cc_start: 0.7172 (OUTLIER) cc_final: 0.6482 (mp-120) REVERT: B 476 HIS cc_start: 0.7587 (m-70) cc_final: 0.7362 (m-70) REVERT: B 477 GLN cc_start: 0.7348 (mm-40) cc_final: 0.7006 (mp10) REVERT: C 8 MET cc_start: 0.3652 (ptt) cc_final: 0.2705 (mmt) REVERT: C 45 ARG cc_start: 0.7838 (mmm160) cc_final: 0.7339 (ptm-80) REVERT: C 489 ILE cc_start: 0.6691 (OUTLIER) cc_final: 0.6456 (pp) REVERT: C 498 LYS cc_start: 0.7388 (OUTLIER) cc_final: 0.7074 (ttpp) REVERT: C 499 GLU cc_start: 0.6316 (OUTLIER) cc_final: 0.5922 (mt-10) REVERT: E 15 ARG cc_start: 0.8302 (ptt-90) cc_final: 0.7693 (ptp90) REVERT: E 112 LYS cc_start: 0.8508 (OUTLIER) cc_final: 0.8259 (mtpt) REVERT: E 409 ARG cc_start: 0.7903 (mtm-85) cc_final: 0.7308 (mtt-85) REVERT: E 411 ARG cc_start: 0.7560 (mtt-85) cc_final: 0.7095 (mtp-110) REVERT: E 415 ARG cc_start: 0.7554 (OUTLIER) cc_final: 0.6290 (mpt180) REVERT: F 27 GLN cc_start: 0.8788 (OUTLIER) cc_final: 0.8546 (tt0) REVERT: D 132 GLU cc_start: 0.7941 (OUTLIER) cc_final: 0.7192 (mp0) REVERT: D 170 MET cc_start: 0.7895 (mmm) cc_final: 0.7610 (mmp) REVERT: D 203 MET cc_start: 0.8276 (mtt) cc_final: 0.7854 (mtt) REVERT: D 210 ASN cc_start: 0.8722 (t0) cc_final: 0.8182 (t0) REVERT: D 212 LYS cc_start: 0.7682 (ptpp) cc_final: 0.6905 (ptpp) REVERT: D 252 GLN cc_start: 0.7467 (mm-40) cc_final: 0.7048 (mt0) REVERT: D 359 ARG cc_start: 0.7831 (mtm110) cc_final: 0.7259 (mtt-85) REVERT: D 458 GLN cc_start: 0.7123 (pm20) cc_final: 0.5940 (mm-40) REVERT: G 18 LYS cc_start: 0.8116 (OUTLIER) cc_final: 0.7450 (tptt) REVERT: G 229 MET cc_start: 0.8253 (ttp) cc_final: 0.7984 (ttp) REVERT: G 262 LEU cc_start: 0.8665 (OUTLIER) cc_final: 0.8408 (tt) REVERT: O 69 LEU cc_start: 0.6226 (mm) cc_final: 0.5864 (mm) REVERT: J 35 ARG cc_start: 0.5405 (mtt-85) cc_final: 0.5095 (ptm160) outliers start: 60 outliers final: 19 residues processed: 347 average time/residue: 1.6807 time to fit residues: 654.7823 Evaluate side-chains 326 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 293 time to evaluate : 2.931 ------------------------------------------------------------------------------- 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 474 SER Chi-restraints excluded: chain B residue 38 ILE Chi-restraints excluded: chain B residue 54 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 489 ILE 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 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 415 ARG Chi-restraints excluded: chain F residue 27 GLN Chi-restraints excluded: chain F residue 205 GLU Chi-restraints excluded: chain F residue 345 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 18 LYS 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 234 optimal weight: 1.9990 chunk 227 optimal weight: 0.8980 chunk 247 optimal weight: 3.9990 chunk 8 optimal weight: 3.9990 chunk 82 optimal weight: 5.9990 chunk 137 optimal weight: 1.9990 chunk 301 optimal weight: 5.9990 chunk 187 optimal weight: 0.6980 chunk 228 optimal weight: 0.7980 chunk 233 optimal weight: 3.9990 chunk 46 optimal weight: 4.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 477 GLN A 492 GLN B 78 ASN B 492 GLN C 503 ASN E 388 GLN E 445 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.123786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.090772 restraints weight = 29242.537| |-----------------------------------------------------------------------------| r_work (start): 0.3039 rms_B_bonded: 1.76 r_work: 0.2933 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2820 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.2820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 moved from start: 0.1777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 24557 Z= 0.140 Angle : 0.521 10.897 33213 Z= 0.266 Chirality : 0.043 0.145 3871 Planarity : 0.004 0.045 4292 Dihedral : 7.261 144.108 3541 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.60 % Favored : 98.37 % Rotamer: Outliers : 2.26 % Allowed : 14.29 % Favored : 83.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.15), residues: 3134 helix: 1.61 (0.14), residues: 1358 sheet: -0.19 (0.22), residues: 515 loop : -0.23 (0.17), residues: 1261 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS B 476 PHE 0.014 0.001 PHE J 34 TYR 0.010 0.001 TYR E 461 ARG 0.006 0.000 ARG F 15 Details of bonding type rmsd hydrogen bonds : bond 0.04295 ( 1225) hydrogen bonds : angle 4.85904 ( 3489) covalent geometry : bond 0.00326 (24557) covalent geometry : angle 0.52058 (33213) *********************** 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 362 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 304 time to evaluate : 2.988 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 8 MET cc_start: 0.5802 (mtp) cc_final: 0.4929 (mmt) REVERT: A 101 GLU cc_start: 0.8790 (OUTLIER) cc_final: 0.8575 (mt-10) REVERT: A 143 ARG cc_start: 0.8289 (ptp-170) cc_final: 0.8085 (ptp-110) REVERT: A 196 LYS cc_start: 0.8454 (ptmt) cc_final: 0.7605 (mmtp) REVERT: A 347 ASP cc_start: 0.8927 (m-30) cc_final: 0.8662 (m-30) REVERT: A 359 LYS cc_start: 0.7935 (mttt) cc_final: 0.7696 (mttm) REVERT: A 455 LYS cc_start: 0.8280 (mttp) cc_final: 0.8060 (mttt) REVERT: A 488 LYS cc_start: 0.8322 (pttt) cc_final: 0.7800 (ptpt) REVERT: A 491 GLU cc_start: 0.7786 (mm-30) cc_final: 0.7025 (mt-10) REVERT: A 499 GLU cc_start: 0.8269 (tm-30) cc_final: 0.7969 (tm-30) REVERT: B 54 GLU cc_start: 0.7996 (OUTLIER) cc_final: 0.7302 (tm-30) REVERT: B 80 LYS cc_start: 0.8687 (OUTLIER) cc_final: 0.8464 (pttt) REVERT: B 226 MET cc_start: 0.8956 (tpt) cc_final: 0.8301 (tpt) REVERT: B 355 GLU cc_start: 0.7601 (OUTLIER) cc_final: 0.7116 (tt0) REVERT: B 455 LYS cc_start: 0.8134 (mmtp) cc_final: 0.7512 (mmpt) REVERT: B 475 GLN cc_start: 0.7159 (OUTLIER) cc_final: 0.6487 (mp-120) REVERT: B 476 HIS cc_start: 0.7550 (m-70) cc_final: 0.7253 (m-70) REVERT: B 477 GLN cc_start: 0.7327 (mm-40) cc_final: 0.6983 (mp10) REVERT: C 8 MET cc_start: 0.3727 (ptt) cc_final: 0.2749 (mmt) REVERT: C 45 ARG cc_start: 0.7771 (mmm160) cc_final: 0.7300 (ptm-80) REVERT: C 426 GLU cc_start: 0.7504 (OUTLIER) cc_final: 0.7153 (mp0) REVERT: C 489 ILE cc_start: 0.6672 (OUTLIER) cc_final: 0.6420 (pp) REVERT: C 498 LYS cc_start: 0.7375 (OUTLIER) cc_final: 0.7062 (ttpp) REVERT: C 499 GLU cc_start: 0.6290 (OUTLIER) cc_final: 0.5897 (mt-10) REVERT: E 112 LYS cc_start: 0.8495 (OUTLIER) cc_final: 0.8242 (mtpt) REVERT: E 409 ARG cc_start: 0.7889 (mtm-85) cc_final: 0.7305 (mtt-85) REVERT: E 411 ARG cc_start: 0.7526 (mtt-85) cc_final: 0.7069 (mtp-110) REVERT: E 415 ARG cc_start: 0.7524 (OUTLIER) cc_final: 0.6241 (mpt180) REVERT: F 27 GLN cc_start: 0.8757 (OUTLIER) cc_final: 0.8519 (tt0) REVERT: F 347 ILE cc_start: 0.8751 (mt) cc_final: 0.8509 (mm) REVERT: F 422 GLN cc_start: 0.7784 (OUTLIER) cc_final: 0.7307 (mt0) REVERT: D 132 GLU cc_start: 0.7938 (OUTLIER) cc_final: 0.7163 (mp0) REVERT: D 170 MET cc_start: 0.7836 (mmm) cc_final: 0.7580 (mmp) REVERT: D 203 MET cc_start: 0.8213 (mtt) cc_final: 0.7783 (mtt) REVERT: D 210 ASN cc_start: 0.8703 (t0) cc_final: 0.8152 (t0) REVERT: D 212 LYS cc_start: 0.7696 (ptpp) cc_final: 0.6917 (ptpp) REVERT: D 252 GLN cc_start: 0.7467 (mm-40) cc_final: 0.7019 (mt0) REVERT: D 458 GLN cc_start: 0.7097 (pm20) cc_final: 0.5925 (mm110) REVERT: G 229 MET cc_start: 0.8222 (ttp) cc_final: 0.7966 (ttp) REVERT: G 262 LEU cc_start: 0.8632 (OUTLIER) cc_final: 0.8392 (tt) REVERT: O 69 LEU cc_start: 0.6190 (mm) cc_final: 0.5832 (mm) REVERT: J 35 ARG cc_start: 0.5439 (mtt-85) cc_final: 0.5060 (ptm160) outliers start: 58 outliers final: 27 residues processed: 340 average time/residue: 1.6346 time to fit residues: 625.7575 Evaluate side-chains 336 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 294 time to evaluate : 2.744 ------------------------------------------------------------------------------- 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 474 SER 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 80 LYS Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 143 ARG 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 301 LEU Chi-restraints excluded: chain C residue 426 GLU Chi-restraints excluded: chain C residue 489 ILE 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 335 THR Chi-restraints excluded: chain E residue 415 ARG Chi-restraints excluded: chain F residue 27 GLN Chi-restraints excluded: chain F residue 205 GLU Chi-restraints excluded: chain F residue 345 LEU 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 434 LEU Chi-restraints excluded: chain G residue 18 LYS 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 214 optimal weight: 0.9990 chunk 272 optimal weight: 0.7980 chunk 126 optimal weight: 1.9990 chunk 94 optimal weight: 5.9990 chunk 133 optimal weight: 0.9980 chunk 30 optimal weight: 3.9990 chunk 237 optimal weight: 0.9980 chunk 251 optimal weight: 4.9990 chunk 208 optimal weight: 4.9990 chunk 179 optimal weight: 0.0470 chunk 35 optimal weight: 0.7980 overall best weight: 0.7278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 477 GLN A 492 GLN B 78 ASN B 492 GLN C 503 ASN E 388 GLN E 445 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.125520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.092126 restraints weight = 29440.521| |-----------------------------------------------------------------------------| r_work (start): 0.3058 rms_B_bonded: 1.86 r_work: 0.2949 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2834 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.2834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.1955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 24557 Z= 0.109 Angle : 0.497 11.279 33213 Z= 0.252 Chirality : 0.042 0.142 3871 Planarity : 0.004 0.045 4292 Dihedral : 7.012 143.702 3541 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.69 % Favored : 98.28 % Rotamer: Outliers : 2.22 % Allowed : 14.68 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.15), residues: 3134 helix: 1.76 (0.14), residues: 1358 sheet: -0.14 (0.23), residues: 509 loop : -0.17 (0.17), residues: 1267 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS B 476 PHE 0.022 0.001 PHE B 468 TYR 0.023 0.001 TYR B 446 ARG 0.006 0.000 ARG F 15 Details of bonding type rmsd hydrogen bonds : bond 0.03891 ( 1225) hydrogen bonds : angle 4.75484 ( 3489) covalent geometry : bond 0.00240 (24557) covalent geometry : angle 0.49725 (33213) *********************** 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 363 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 306 time to evaluate : 2.947 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 8 MET cc_start: 0.5756 (mtp) cc_final: 0.4868 (mmt) REVERT: A 196 LYS cc_start: 0.8407 (ptmt) cc_final: 0.7595 (mmtp) REVERT: A 347 ASP cc_start: 0.8820 (m-30) cc_final: 0.8510 (m-30) REVERT: A 359 LYS cc_start: 0.7921 (mttt) cc_final: 0.7690 (mttm) REVERT: A 455 LYS cc_start: 0.8318 (mttp) cc_final: 0.8099 (mttt) REVERT: A 484 ARG cc_start: 0.7328 (ttp80) cc_final: 0.7114 (ttp80) REVERT: A 488 LYS cc_start: 0.8296 (pttt) cc_final: 0.7766 (ptpt) REVERT: A 491 GLU cc_start: 0.7893 (mm-30) cc_final: 0.7058 (mt-10) REVERT: A 499 GLU cc_start: 0.8265 (tm-30) cc_final: 0.7956 (tm-30) REVERT: B 54 GLU cc_start: 0.8001 (OUTLIER) cc_final: 0.7318 (tm-30) REVERT: B 80 LYS cc_start: 0.8700 (OUTLIER) cc_final: 0.8479 (pttt) REVERT: B 226 MET cc_start: 0.8970 (tpt) cc_final: 0.8376 (tpt) REVERT: B 355 GLU cc_start: 0.7625 (OUTLIER) cc_final: 0.7152 (tt0) REVERT: B 392 LEU cc_start: 0.8181 (OUTLIER) cc_final: 0.7868 (tt) REVERT: B 455 LYS cc_start: 0.8135 (mmtp) cc_final: 0.7521 (mmpt) REVERT: B 475 GLN cc_start: 0.7177 (OUTLIER) cc_final: 0.6498 (mp-120) REVERT: B 476 HIS cc_start: 0.7523 (m-70) cc_final: 0.7283 (m-70) REVERT: B 477 GLN cc_start: 0.7318 (mm-40) cc_final: 0.6982 (mp10) REVERT: C 8 MET cc_start: 0.3651 (ptt) cc_final: 0.2718 (mmt) REVERT: C 45 ARG cc_start: 0.7724 (mmm160) cc_final: 0.7296 (ptm160) REVERT: C 128 ARG cc_start: 0.7937 (mtt180) cc_final: 0.7687 (mtp180) REVERT: C 426 GLU cc_start: 0.7520 (OUTLIER) cc_final: 0.7159 (mp0) REVERT: C 489 ILE cc_start: 0.6579 (OUTLIER) cc_final: 0.6318 (pp) REVERT: C 498 LYS cc_start: 0.7395 (OUTLIER) cc_final: 0.7077 (ttpp) REVERT: C 499 GLU cc_start: 0.6262 (OUTLIER) cc_final: 0.5905 (mt-10) REVERT: E 112 LYS cc_start: 0.8492 (OUTLIER) cc_final: 0.8264 (mtpt) REVERT: E 249 GLN cc_start: 0.8911 (OUTLIER) cc_final: 0.7848 (mp10) REVERT: E 409 ARG cc_start: 0.7853 (mtm-85) cc_final: 0.7297 (mtt-85) REVERT: E 411 ARG cc_start: 0.7567 (mtt-85) cc_final: 0.7104 (mtp-110) REVERT: E 415 ARG cc_start: 0.7485 (OUTLIER) cc_final: 0.6227 (mpt180) REVERT: F 30 GLU cc_start: 0.7512 (pm20) cc_final: 0.7175 (pp20) REVERT: F 347 ILE cc_start: 0.8760 (mt) cc_final: 0.8526 (mm) REVERT: D 132 GLU cc_start: 0.7968 (OUTLIER) cc_final: 0.7260 (mp0) REVERT: D 170 MET cc_start: 0.7841 (mmm) cc_final: 0.7587 (mmp) REVERT: D 203 MET cc_start: 0.8245 (mtt) cc_final: 0.7815 (mtt) REVERT: D 210 ASN cc_start: 0.8718 (t0) cc_final: 0.8159 (t0) REVERT: D 212 LYS cc_start: 0.7673 (ptpp) cc_final: 0.6882 (ptpp) REVERT: D 252 GLN cc_start: 0.7500 (mm-40) cc_final: 0.7079 (mt0) REVERT: D 359 ARG cc_start: 0.8373 (ttm170) cc_final: 0.8156 (ttm170) REVERT: D 458 GLN cc_start: 0.7069 (pm20) cc_final: 0.5909 (mm110) REVERT: G 229 MET cc_start: 0.8204 (ttp) cc_final: 0.7934 (ttp) REVERT: G 262 LEU cc_start: 0.8624 (OUTLIER) cc_final: 0.8418 (tt) REVERT: O 36 GLU cc_start: 0.6435 (tt0) cc_final: 0.5673 (mt-10) REVERT: O 69 LEU cc_start: 0.6232 (mm) cc_final: 0.5866 (mm) REVERT: O 153 LYS cc_start: 0.7448 (OUTLIER) cc_final: 0.6505 (pttt) REVERT: J 35 ARG cc_start: 0.5406 (mtt-85) cc_final: 0.5062 (ptm160) outliers start: 57 outliers final: 20 residues processed: 342 average time/residue: 1.6589 time to fit residues: 637.7825 Evaluate side-chains 335 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 300 time to evaluate : 2.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 349 GLN Chi-restraints excluded: chain A residue 474 SER Chi-restraints excluded: chain A residue 497 LEU Chi-restraints excluded: chain B residue 54 GLU 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 157 VAL Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain C residue 426 GLU Chi-restraints excluded: chain C residue 489 ILE 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 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 434 LEU 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 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 144 optimal weight: 2.9990 chunk 61 optimal weight: 5.9990 chunk 62 optimal weight: 4.9990 chunk 278 optimal weight: 0.7980 chunk 14 optimal weight: 5.9990 chunk 284 optimal weight: 0.9990 chunk 249 optimal weight: 0.1980 chunk 41 optimal weight: 8.9990 chunk 46 optimal weight: 0.9990 chunk 56 optimal weight: 6.9990 chunk 121 optimal weight: 0.9990 overall best weight: 0.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 477 GLN A 492 GLN B 78 ASN C 503 ASN E 388 GLN E 445 GLN F 27 GLN D 260 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.125949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.092877 restraints weight = 29283.454| |-----------------------------------------------------------------------------| r_work (start): 0.3067 rms_B_bonded: 1.77 r_work: 0.2962 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2848 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.2848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.2032 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= 0.111 Angle : 0.501 11.872 33213 Z= 0.254 Chirality : 0.042 0.143 3871 Planarity : 0.004 0.044 4292 Dihedral : 6.886 144.085 3541 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.63 % Favored : 98.34 % Rotamer: Outliers : 2.02 % Allowed : 15.11 % Favored : 82.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.06 (0.15), residues: 3134 helix: 1.81 (0.14), residues: 1360 sheet: -0.09 (0.23), residues: 509 loop : -0.09 (0.17), residues: 1265 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS B 476 PHE 0.014 0.001 PHE J 34 TYR 0.014 0.001 TYR E 384 ARG 0.004 0.000 ARG D 359 Details of bonding type rmsd hydrogen bonds : bond 0.03857 ( 1225) hydrogen bonds : angle 4.71151 ( 3489) covalent geometry : bond 0.00249 (24557) covalent geometry : angle 0.50137 (33213) *********************** 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 361 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 309 time to evaluate : 2.617 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 8 MET cc_start: 0.5723 (mtp) cc_final: 0.4841 (mmt) REVERT: A 196 LYS cc_start: 0.8352 (ptmt) cc_final: 0.7568 (mmtp) REVERT: A 347 ASP cc_start: 0.8745 (m-30) cc_final: 0.8539 (m-30) REVERT: A 359 LYS cc_start: 0.7893 (mttt) cc_final: 0.7664 (mttm) REVERT: A 455 LYS cc_start: 0.8316 (mttp) cc_final: 0.8097 (mttt) REVERT: A 477 GLN cc_start: 0.7994 (mm-40) cc_final: 0.7688 (tp40) REVERT: A 488 LYS cc_start: 0.8268 (pttt) cc_final: 0.7746 (ptpt) REVERT: A 491 GLU cc_start: 0.7893 (mm-30) cc_final: 0.7137 (mt-10) REVERT: A 499 GLU cc_start: 0.8254 (tm-30) cc_final: 0.7940 (tm-30) REVERT: B 54 GLU cc_start: 0.7978 (OUTLIER) cc_final: 0.7302 (tm-30) REVERT: B 80 LYS cc_start: 0.8685 (OUTLIER) cc_final: 0.8454 (pttt) REVERT: B 125 THR cc_start: 0.8397 (OUTLIER) cc_final: 0.8148 (p) REVERT: B 195 GLU cc_start: 0.7273 (tp30) cc_final: 0.7020 (tp30) REVERT: B 226 MET cc_start: 0.8957 (tpt) cc_final: 0.8326 (tpt) REVERT: B 355 GLU cc_start: 0.7596 (OUTLIER) cc_final: 0.7125 (tt0) REVERT: B 392 LEU cc_start: 0.8143 (OUTLIER) cc_final: 0.7861 (tt) REVERT: B 415 GLN cc_start: 0.7336 (mm-40) cc_final: 0.6906 (tp40) REVERT: B 426 GLU cc_start: 0.7892 (tp30) cc_final: 0.7515 (mm-30) REVERT: B 455 LYS cc_start: 0.8135 (mmtp) cc_final: 0.7517 (mmpt) REVERT: B 463 LYS cc_start: 0.7548 (ttmt) cc_final: 0.6966 (ptmm) REVERT: B 475 GLN cc_start: 0.7142 (OUTLIER) cc_final: 0.6472 (mp-120) REVERT: B 477 GLN cc_start: 0.7317 (mm-40) cc_final: 0.6987 (mp10) REVERT: C 8 MET cc_start: 0.3662 (ptt) cc_final: 0.2723 (mmt) REVERT: C 45 ARG cc_start: 0.7698 (mmm160) cc_final: 0.7279 (ptm160) REVERT: C 128 ARG cc_start: 0.7930 (mtt180) cc_final: 0.7675 (mtp180) REVERT: C 426 GLU cc_start: 0.7467 (OUTLIER) cc_final: 0.7132 (mp0) REVERT: C 489 ILE cc_start: 0.6515 (OUTLIER) cc_final: 0.6236 (pp) REVERT: C 498 LYS cc_start: 0.7392 (OUTLIER) cc_final: 0.7102 (ttpp) REVERT: C 499 GLU cc_start: 0.6222 (OUTLIER) cc_final: 0.5861 (mt-10) REVERT: E 112 LYS cc_start: 0.8479 (OUTLIER) cc_final: 0.8249 (mtpt) REVERT: E 249 GLN cc_start: 0.8894 (OUTLIER) cc_final: 0.7832 (mp10) REVERT: E 340 ARG cc_start: 0.7871 (ttp-170) cc_final: 0.7655 (tpp80) REVERT: E 382 GLN cc_start: 0.7778 (mt0) cc_final: 0.7488 (mt0) REVERT: E 409 ARG cc_start: 0.7828 (mtm-85) cc_final: 0.7431 (mtt-85) REVERT: E 411 ARG cc_start: 0.7567 (mtt-85) cc_final: 0.7101 (mtp-110) REVERT: E 415 ARG cc_start: 0.7449 (OUTLIER) cc_final: 0.6189 (mpt180) REVERT: F 30 GLU cc_start: 0.7528 (pm20) cc_final: 0.7152 (pp20) REVERT: F 347 ILE cc_start: 0.8740 (mt) cc_final: 0.8510 (mm) REVERT: D 132 GLU cc_start: 0.7951 (OUTLIER) cc_final: 0.7234 (mp0) REVERT: D 170 MET cc_start: 0.7761 (mmm) cc_final: 0.7509 (mmp) REVERT: D 203 MET cc_start: 0.8192 (mtt) cc_final: 0.7761 (mtt) REVERT: D 210 ASN cc_start: 0.8684 (t0) cc_final: 0.8134 (t0) REVERT: D 212 LYS cc_start: 0.7624 (ptpp) cc_final: 0.6840 (ptpp) REVERT: D 252 GLN cc_start: 0.7407 (mm-40) cc_final: 0.6846 (mt0) REVERT: D 458 GLN cc_start: 0.7034 (pm20) cc_final: 0.5886 (mm110) REVERT: G 229 MET cc_start: 0.8127 (ttp) cc_final: 0.7874 (ttp) REVERT: G 262 LEU cc_start: 0.8611 (OUTLIER) cc_final: 0.8399 (tt) REVERT: O 36 GLU cc_start: 0.6410 (tt0) cc_final: 0.5596 (mt-10) REVERT: O 69 LEU cc_start: 0.6246 (mm) cc_final: 0.5875 (mm) REVERT: O 153 LYS cc_start: 0.7522 (OUTLIER) cc_final: 0.6560 (pttt) REVERT: J 35 ARG cc_start: 0.5360 (mtt-85) cc_final: 0.5071 (ptm160) outliers start: 52 outliers final: 21 residues processed: 342 average time/residue: 1.7023 time to fit residues: 656.9284 Evaluate side-chains 339 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 302 time to evaluate : 2.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 474 SER Chi-restraints excluded: chain A residue 497 LEU Chi-restraints excluded: chain B residue 54 GLU 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 157 VAL Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain C residue 426 GLU Chi-restraints excluded: chain C residue 489 ILE Chi-restraints excluded: chain C residue 498 LYS Chi-restraints excluded: chain C residue 499 GLU Chi-restraints excluded: chain E residue 37 ASN 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 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 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 169 ILE 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 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 258 optimal weight: 3.9990 chunk 148 optimal weight: 0.7980 chunk 263 optimal weight: 0.0370 chunk 216 optimal weight: 1.9990 chunk 293 optimal weight: 5.9990 chunk 255 optimal weight: 2.9990 chunk 72 optimal weight: 0.6980 chunk 18 optimal weight: 4.9990 chunk 213 optimal weight: 2.9990 chunk 89 optimal weight: 5.9990 chunk 182 optimal weight: 0.6980 overall best weight: 0.8460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 492 GLN B 78 ASN C 503 ASN E 445 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.125981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.092479 restraints weight = 29371.518| |-----------------------------------------------------------------------------| r_work (start): 0.3063 rms_B_bonded: 1.86 r_work: 0.2955 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2840 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8472 moved from start: 0.2076 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= 0.113 Angle : 0.505 11.864 33213 Z= 0.255 Chirality : 0.042 0.143 3871 Planarity : 0.004 0.044 4292 Dihedral : 6.837 144.378 3541 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.75 % Favored : 98.21 % Rotamer: Outliers : 1.75 % Allowed : 15.62 % Favored : 82.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.09 (0.15), residues: 3134 helix: 1.84 (0.14), residues: 1360 sheet: -0.09 (0.23), residues: 509 loop : -0.07 (0.17), residues: 1265 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.010 0.001 HIS B 476 PHE 0.027 0.001 PHE B 468 TYR 0.014 0.001 TYR E 384 ARG 0.009 0.000 ARG C 30 Details of bonding type rmsd hydrogen bonds : bond 0.03859 ( 1225) hydrogen bonds : angle 4.70509 ( 3489) covalent geometry : bond 0.00257 (24557) covalent geometry : angle 0.50540 (33213) *********************** 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 354 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 309 time to evaluate : 2.783 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 8 MET cc_start: 0.5789 (mtp) cc_final: 0.4885 (mmt) REVERT: A 196 LYS cc_start: 0.8328 (ptmt) cc_final: 0.7582 (mmtp) REVERT: A 347 ASP cc_start: 0.8756 (m-30) cc_final: 0.8544 (m-30) REVERT: A 359 LYS cc_start: 0.7922 (mttt) cc_final: 0.7698 (mttm) REVERT: A 455 LYS cc_start: 0.8330 (mttp) cc_final: 0.8112 (mttt) REVERT: A 488 LYS cc_start: 0.8314 (pttt) cc_final: 0.7781 (ptpt) REVERT: A 491 GLU cc_start: 0.7878 (mm-30) cc_final: 0.7137 (mt-10) REVERT: A 499 GLU cc_start: 0.8268 (tm-30) cc_final: 0.7951 (tm-30) REVERT: B 54 GLU cc_start: 0.7997 (OUTLIER) cc_final: 0.7315 (tm-30) REVERT: B 80 LYS cc_start: 0.8704 (OUTLIER) cc_final: 0.8480 (pttt) REVERT: B 125 THR cc_start: 0.8417 (OUTLIER) cc_final: 0.8175 (p) REVERT: B 195 GLU cc_start: 0.7256 (tp30) cc_final: 0.7039 (tp30) REVERT: B 226 MET cc_start: 0.8973 (tpt) cc_final: 0.8345 (tpt) REVERT: B 355 GLU cc_start: 0.7644 (OUTLIER) cc_final: 0.7178 (tt0) REVERT: B 392 LEU cc_start: 0.8116 (OUTLIER) cc_final: 0.7847 (tt) REVERT: B 415 GLN cc_start: 0.7393 (mm-40) cc_final: 0.6954 (tp40) REVERT: B 426 GLU cc_start: 0.7909 (tp30) cc_final: 0.7476 (mm-30) REVERT: B 455 LYS cc_start: 0.8143 (mmtp) cc_final: 0.7526 (mmpt) REVERT: B 463 LYS cc_start: 0.7576 (ttmt) cc_final: 0.7049 (ptmm) REVERT: B 477 GLN cc_start: 0.7442 (mm-40) cc_final: 0.7093 (mp10) REVERT: C 8 MET cc_start: 0.3661 (ptt) cc_final: 0.2716 (mmt) REVERT: C 45 ARG cc_start: 0.7725 (mmm160) cc_final: 0.7312 (ptm160) REVERT: C 128 ARG cc_start: 0.7960 (mtt180) cc_final: 0.7721 (mtp180) REVERT: C 426 GLU cc_start: 0.7470 (OUTLIER) cc_final: 0.7147 (mp0) REVERT: C 498 LYS cc_start: 0.7425 (OUTLIER) cc_final: 0.7140 (ttpp) REVERT: C 499 GLU cc_start: 0.6263 (OUTLIER) cc_final: 0.5937 (mt-10) REVERT: E 112 LYS cc_start: 0.8505 (OUTLIER) cc_final: 0.8301 (mtpt) REVERT: E 249 GLN cc_start: 0.8907 (OUTLIER) cc_final: 0.7855 (mp10) REVERT: E 340 ARG cc_start: 0.7910 (ttp-170) cc_final: 0.7700 (tpp80) REVERT: E 409 ARG cc_start: 0.7865 (mtm-85) cc_final: 0.7505 (mtt-85) REVERT: E 411 ARG cc_start: 0.7649 (mtt-85) cc_final: 0.7163 (mtp-110) REVERT: E 415 ARG cc_start: 0.7479 (OUTLIER) cc_final: 0.6221 (mpt180) REVERT: F 347 ILE cc_start: 0.8781 (mt) cc_final: 0.8550 (mm) REVERT: F 422 GLN cc_start: 0.7784 (OUTLIER) cc_final: 0.7318 (mt0) REVERT: D 170 MET cc_start: 0.7825 (mmm) cc_final: 0.7567 (mmp) REVERT: D 203 MET cc_start: 0.8218 (mtt) cc_final: 0.7783 (mtt) REVERT: D 210 ASN cc_start: 0.8689 (t0) cc_final: 0.8138 (t0) REVERT: D 212 LYS cc_start: 0.7626 (ptpp) cc_final: 0.6839 (ptpp) REVERT: D 252 GLN cc_start: 0.7402 (mm-40) cc_final: 0.6869 (mt0) REVERT: D 359 ARG cc_start: 0.8325 (OUTLIER) cc_final: 0.7858 (ttm170) REVERT: D 458 GLN cc_start: 0.7056 (pm20) cc_final: 0.5921 (mm110) REVERT: G 229 MET cc_start: 0.8139 (ttp) cc_final: 0.7902 (ttp) REVERT: G 262 LEU cc_start: 0.8637 (OUTLIER) cc_final: 0.8429 (tt) REVERT: O 69 LEU cc_start: 0.6245 (mm) cc_final: 0.5886 (mm) REVERT: O 153 LYS cc_start: 0.7517 (OUTLIER) cc_final: 0.6568 (pttt) REVERT: J 35 ARG cc_start: 0.5432 (mtt-85) cc_final: 0.5152 (ptm160) outliers start: 45 outliers final: 20 residues processed: 336 average time/residue: 1.6479 time to fit residues: 621.7046 Evaluate side-chains 338 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 303 time to evaluate : 2.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 474 SER Chi-restraints excluded: chain A residue 497 LEU Chi-restraints excluded: chain B residue 54 GLU 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 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 112 LYS Chi-restraints excluded: chain E residue 249 GLN Chi-restraints excluded: chain E residue 263 ARG 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 169 ILE Chi-restraints excluded: chain D residue 359 ARG 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 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 212 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 234 optimal weight: 0.0570 chunk 242 optimal weight: 2.9990 chunk 272 optimal weight: 5.9990 chunk 140 optimal weight: 3.9990 chunk 233 optimal weight: 1.9990 chunk 2 optimal weight: 9.9990 chunk 122 optimal weight: 3.9990 chunk 171 optimal weight: 1.9990 chunk 137 optimal weight: 0.7980 overall best weight: 1.5704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 477 GLN A 492 GLN B 78 ASN C 366 ASN C 503 ASN E 445 GLN F 27 GLN D 260 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.123738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.090542 restraints weight = 29327.816| |-----------------------------------------------------------------------------| r_work (start): 0.3033 rms_B_bonded: 1.77 r_work: 0.2927 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2813 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.2813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8478 moved from start: 0.1908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 24557 Z= 0.160 Angle : 0.545 13.037 33213 Z= 0.277 Chirality : 0.044 0.153 3871 Planarity : 0.004 0.043 4292 Dihedral : 7.180 148.080 3541 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.95 % Favored : 98.02 % Rotamer: Outliers : 1.56 % Allowed : 16.04 % Favored : 82.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.98 (0.15), residues: 3134 helix: 1.71 (0.14), residues: 1358 sheet: -0.09 (0.23), residues: 515 loop : -0.10 (0.17), residues: 1261 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.013 0.001 HIS B 476 PHE 0.019 0.001 PHE E 427 TYR 0.017 0.001 TYR E 384 ARG 0.009 0.000 ARG F 15 Details of bonding type rmsd hydrogen bonds : bond 0.04429 ( 1225) hydrogen bonds : angle 4.84493 ( 3489) covalent geometry : bond 0.00380 (24557) covalent geometry : angle 0.54476 (33213) ********************** 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 342 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 302 time to evaluate : 2.907 Fit side-chains revert: symmetry clash REVERT: A 8 MET cc_start: 0.5876 (mtp) cc_final: 0.4982 (mmt) REVERT: A 101 GLU cc_start: 0.8802 (OUTLIER) cc_final: 0.8577 (mt-10) REVERT: A 143 ARG cc_start: 0.8180 (ptp90) cc_final: 0.7699 (mtt90) REVERT: A 196 LYS cc_start: 0.8352 (ptmt) cc_final: 0.7616 (mmtp) REVERT: A 347 ASP cc_start: 0.8932 (m-30) cc_final: 0.8643 (m-30) REVERT: A 359 LYS cc_start: 0.7929 (mttt) cc_final: 0.7697 (mttm) REVERT: A 416 GLN cc_start: 0.7597 (tp40) cc_final: 0.7333 (tp-100) REVERT: A 455 LYS cc_start: 0.8268 (mttp) cc_final: 0.8037 (mttt) REVERT: A 477 GLN cc_start: 0.7921 (mm-40) cc_final: 0.7625 (tp40) REVERT: A 488 LYS cc_start: 0.8309 (pttt) cc_final: 0.7933 (ptpt) REVERT: A 491 GLU cc_start: 0.7866 (mm-30) cc_final: 0.7098 (mt-10) REVERT: A 499 GLU cc_start: 0.8254 (tm-30) cc_final: 0.7941 (tm-30) REVERT: B 54 GLU cc_start: 0.7996 (OUTLIER) cc_final: 0.7292 (tm-30) REVERT: B 195 GLU cc_start: 0.7295 (tp30) cc_final: 0.7013 (tp30) REVERT: B 355 GLU cc_start: 0.7628 (OUTLIER) cc_final: 0.7151 (tt0) REVERT: B 392 LEU cc_start: 0.8179 (OUTLIER) cc_final: 0.7885 (tt) REVERT: B 455 LYS cc_start: 0.8132 (mmtp) cc_final: 0.7515 (mmpt) REVERT: B 477 GLN cc_start: 0.7473 (mm-40) cc_final: 0.7077 (mp10) REVERT: C 8 MET cc_start: 0.3721 (ptt) cc_final: 0.2743 (mmt) REVERT: C 45 ARG cc_start: 0.7768 (mmm160) cc_final: 0.7317 (ptm160) REVERT: C 128 ARG cc_start: 0.7961 (mtt180) cc_final: 0.7709 (mtp180) REVERT: C 426 GLU cc_start: 0.7460 (OUTLIER) cc_final: 0.7132 (mp0) REVERT: C 498 LYS cc_start: 0.7379 (OUTLIER) cc_final: 0.7082 (ttpp) REVERT: C 499 GLU cc_start: 0.6278 (OUTLIER) cc_final: 0.5956 (mt-10) REVERT: E 15 ARG cc_start: 0.8346 (mtm-85) cc_final: 0.8013 (mtm-85) REVERT: E 112 LYS cc_start: 0.8511 (OUTLIER) cc_final: 0.8265 (mtpt) REVERT: E 249 GLN cc_start: 0.8922 (OUTLIER) cc_final: 0.7863 (mp10) REVERT: E 340 ARG cc_start: 0.7919 (ttp-170) cc_final: 0.7715 (tpp80) REVERT: E 409 ARG cc_start: 0.7827 (mtm-85) cc_final: 0.7270 (mtt-85) REVERT: E 411 ARG cc_start: 0.7606 (mtt-85) cc_final: 0.7055 (mtp85) REVERT: E 415 ARG cc_start: 0.7559 (OUTLIER) cc_final: 0.6265 (mpt180) REVERT: F 30 GLU cc_start: 0.7579 (pm20) cc_final: 0.7181 (pp20) REVERT: F 347 ILE cc_start: 0.8778 (mt) cc_final: 0.8538 (mm) REVERT: F 422 GLN cc_start: 0.7801 (OUTLIER) cc_final: 0.7339 (mt0) REVERT: D 170 MET cc_start: 0.7805 (mmm) cc_final: 0.7538 (mmp) REVERT: D 203 MET cc_start: 0.8200 (mtt) cc_final: 0.7750 (mtt) REVERT: D 210 ASN cc_start: 0.8710 (t0) cc_final: 0.8174 (t0) REVERT: D 212 LYS cc_start: 0.7701 (ptpp) cc_final: 0.6921 (ptpp) REVERT: D 252 GLN cc_start: 0.7396 (mm-40) cc_final: 0.6853 (mt0) REVERT: D 458 GLN cc_start: 0.7028 (pm20) cc_final: 0.5951 (mm110) REVERT: G 229 MET cc_start: 0.8208 (ttp) cc_final: 0.7923 (ttp) REVERT: G 262 LEU cc_start: 0.8653 (OUTLIER) cc_final: 0.8397 (tt) REVERT: O 36 GLU cc_start: 0.6370 (tt0) cc_final: 0.5692 (mt-10) REVERT: O 69 LEU cc_start: 0.6248 (mm) cc_final: 0.5882 (mm) REVERT: O 153 LYS cc_start: 0.7518 (OUTLIER) cc_final: 0.6523 (pttt) REVERT: J 35 ARG cc_start: 0.5401 (mtt-85) cc_final: 0.5064 (ptm160) outliers start: 40 outliers final: 21 residues processed: 326 average time/residue: 1.7060 time to fit residues: 629.4371 Evaluate side-chains 331 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 297 time to evaluate : 2.571 ------------------------------------------------------------------------------- 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 474 SER Chi-restraints excluded: chain A residue 497 LEU Chi-restraints excluded: chain B residue 54 GLU Chi-restraints excluded: chain B residue 80 LYS Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 143 ARG 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 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 112 LYS Chi-restraints excluded: chain E residue 249 GLN Chi-restraints excluded: chain E residue 263 ARG 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 D residue 46 THR Chi-restraints excluded: chain D residue 127 MET 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 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 201 optimal weight: 0.6980 chunk 81 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 151 optimal weight: 6.9990 chunk 224 optimal weight: 4.9990 chunk 296 optimal weight: 20.0000 chunk 306 optimal weight: 10.0000 chunk 141 optimal weight: 3.9990 chunk 39 optimal weight: 0.9980 chunk 274 optimal weight: 5.9990 chunk 51 optimal weight: 0.7980 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 492 GLN B 78 ASN C 366 ASN C 503 ASN E 445 GLN F 27 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.123811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.090606 restraints weight = 29320.477| |-----------------------------------------------------------------------------| r_work (start): 0.3032 rms_B_bonded: 1.77 r_work: 0.2927 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2814 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.2814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8472 moved from start: 0.1921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 24557 Z= 0.154 Angle : 0.544 12.829 33213 Z= 0.276 Chirality : 0.044 0.147 3871 Planarity : 0.004 0.042 4292 Dihedral : 7.238 150.512 3541 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.91 % Favored : 98.05 % Rotamer: Outliers : 1.60 % Allowed : 15.93 % Favored : 82.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.20 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.97 (0.15), residues: 3134 helix: 1.67 (0.14), residues: 1364 sheet: -0.08 (0.23), residues: 515 loop : -0.08 (0.17), residues: 1255 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.014 0.001 HIS B 476 PHE 0.018 0.001 PHE E 427 TYR 0.018 0.001 TYR E 384 ARG 0.009 0.000 ARG F 15 Details of bonding type rmsd hydrogen bonds : bond 0.04381 ( 1225) hydrogen bonds : angle 4.86006 ( 3489) covalent geometry : bond 0.00365 (24557) covalent geometry : angle 0.54421 (33213) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 20489.94 seconds wall clock time: 352 minutes 55.98 seconds (21175.98 seconds total)