Starting phenix.real_space_refine on Mon Aug 25 01:44:30 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hh3_34750/08_2025/8hh3_34750.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hh3_34750/08_2025/8hh3_34750.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8hh3_34750/08_2025/8hh3_34750.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hh3_34750/08_2025/8hh3_34750.map" model { file = "/net/cci-nas-00/data/ceres_data/8hh3_34750/08_2025/8hh3_34750.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hh3_34750/08_2025/8hh3_34750.cif" } resolution = 4.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.002 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 19 5.49 5 Mg 5 5.21 5 S 77 5.16 5 C 15287 2.51 5 N 4219 2.21 5 O 4674 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 24281 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 3661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 478, 3661 Classifications: {'peptide': 478} Link IDs: {'PTRANS': 23, 'TRANS': 454} Chain: "B" Number of atoms: 3661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 478, 3661 Classifications: {'peptide': 478} Link IDs: {'PTRANS': 23, 'TRANS': 454} Chain: "C" Number of atoms: 3661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 478, 3661 Classifications: {'peptide': 478} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 454} Chain: "D" Number of atoms: 3630 Number of conformers: 1 Conformer: "" Number of residues, atoms: 471, 3630 Classifications: {'peptide': 471} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 447} Chain: "E" Number of atoms: 3623 Number of conformers: 1 Conformer: "" Number of residues, atoms: 470, 3623 Classifications: {'peptide': 470} Link IDs: {'PTRANS': 23, 'TRANS': 446} Chain: "F" Number of atoms: 3630 Number of conformers: 1 Conformer: "" Number of residues, atoms: 471, 3630 Classifications: {'peptide': 471} Link IDs: {'PTRANS': 23, 'TRANS': 447} Chain: "G" Number of atoms: 2218 Number of conformers: 1 Conformer: "" Number of residues, atoms: 283, 2218 Classifications: {'peptide': 283} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 272} 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: "D" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, 'ADP': 1, 'PO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 36 Unusual residues: {'ATP': 1, 'PO4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" 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} Time building chain proxies: 5.49, per 1000 atoms: 0.23 Number of scatterers: 24281 At special positions: 0 Unit cell: (125.84, 127.6, 157.52, 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 77 16.00 P 19 15.00 Mg 5 11.99 O 4674 8.00 N 4219 7.00 C 15287 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.72 Conformation dependent library (CDL) restraints added in 953.7 milliseconds Enol-peptide restraints added in 1.2 microseconds 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5712 Finding SS restraints... Secondary structure from input PDB file: 127 helices and 21 sheets defined 48.3% alpha, 15.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.91 Creating SS restraints... Processing helix chain 'A' and resid 78 through 82 removed outlier: 4.130A pdb=" N GLY A 81 " --> pdb=" O PRO A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 100 through 104 Processing helix chain 'A' and resid 150 through 157 Processing helix chain 'A' and resid 174 through 186 removed outlier: 3.660A pdb=" N GLN A 186 " --> pdb=" O THR A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 189 No H-bonds generated for 'chain 'A' and resid 187 through 189' Processing helix chain 'A' and resid 201 through 216 Processing helix chain 'A' and resid 217 through 219 No H-bonds generated for 'chain 'A' and resid 217 through 219' Processing helix chain 'A' and resid 231 through 251 removed outlier: 3.529A pdb=" N LEU A 235 " --> pdb=" O PRO A 231 " (cutoff:3.500A) Proline residue: A 239 - end of helix removed outlier: 3.617A pdb=" N TYR A 248 " --> pdb=" O ALA A 244 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N PHE A 249 " --> pdb=" O MET A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 277 removed outlier: 3.782A pdb=" N GLN A 266 " --> pdb=" O ASP A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 286 Processing helix chain 'A' and resid 289 through 299 Processing helix chain 'A' and resid 305 through 309 removed outlier: 3.607A pdb=" N GLY A 309 " --> pdb=" O ASP A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 338 Processing helix chain 'A' and resid 345 through 350 Processing helix chain 'A' and resid 372 through 391 removed outlier: 3.894A pdb=" N GLY A 380 " --> pdb=" O LYS A 376 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N THR A 381 " --> pdb=" O LYS A 377 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LEU A 384 " --> pdb=" O GLY A 380 " (cutoff:3.500A) Processing helix chain 'A' and resid 392 through 396 Processing helix chain 'A' and resid 403 through 420 Processing helix chain 'A' and resid 429 through 442 Processing helix chain 'A' and resid 449 through 451 No H-bonds generated for 'chain 'A' and resid 449 through 451' Processing helix chain 'A' and resid 452 through 468 removed outlier: 4.399A pdb=" N GLN A 466 " --> pdb=" O LEU A 462 " (cutoff:3.500A) Processing helix chain 'A' and resid 468 through 479 Processing helix chain 'A' and resid 483 through 496 Processing helix chain 'B' and resid 100 through 104 Processing helix chain 'B' and resid 150 through 157 Processing helix chain 'B' and resid 174 through 186 removed outlier: 3.743A pdb=" N GLN B 186 " --> pdb=" O THR B 182 " (cutoff:3.500A) Processing helix chain 'B' and resid 201 through 216 Processing helix chain 'B' and resid 217 through 219 No H-bonds generated for 'chain 'B' and resid 217 through 219' Processing helix chain 'B' and resid 231 through 251 removed outlier: 3.621A pdb=" N LEU B 235 " --> pdb=" O PRO B 231 " (cutoff:3.500A) Proline residue: B 239 - end of helix removed outlier: 3.623A pdb=" N TYR B 248 " --> pdb=" O ALA B 244 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N PHE B 249 " --> pdb=" O MET B 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 262 through 277 Processing helix chain 'B' and resid 282 through 286 Processing helix chain 'B' and resid 289 through 299 removed outlier: 3.686A pdb=" N HIS B 294 " --> pdb=" O ILE B 290 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N LEU B 297 " --> pdb=" O LEU B 293 " (cutoff:3.500A) Processing helix chain 'B' and resid 328 through 336 Processing helix chain 'B' and resid 345 through 351 Processing helix chain 'B' and resid 372 through 396 removed outlier: 3.712A pdb=" N LYS B 377 " --> pdb=" O LYS B 373 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N GLY B 380 " --> pdb=" O LYS B 376 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N THR B 381 " --> pdb=" O LYS B 377 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N GLU B 391 " --> pdb=" O ALA B 387 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N ALA B 394 " --> pdb=" O ARG B 390 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 421 Processing helix chain 'B' and resid 429 through 442 Processing helix chain 'B' and resid 452 through 468 Processing helix chain 'B' and resid 468 through 479 removed outlier: 3.804A pdb=" N HIS B 474 " --> pdb=" O HIS B 470 " (cutoff:3.500A) Processing helix chain 'B' and resid 483 through 498 removed outlier: 3.637A pdb=" N THR B 497 " --> pdb=" O ALA B 493 " (cutoff:3.500A) Processing helix chain 'C' and resid 100 through 104 removed outlier: 3.594A 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 Processing helix chain 'C' and resid 201 through 216 Processing helix chain 'C' and resid 217 through 219 No H-bonds generated for 'chain 'C' and resid 217 through 219' Processing helix chain 'C' and resid 231 through 252 removed outlier: 3.587A pdb=" N LEU C 235 " --> pdb=" O PRO C 231 " (cutoff:3.500A) Proline residue: C 239 - end of helix removed outlier: 3.562A pdb=" N TYR C 248 " --> pdb=" O ALA C 244 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N PHE C 249 " --> pdb=" O MET C 245 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LYS C 252 " --> pdb=" O TYR C 248 " (cutoff:3.500A) Processing helix chain 'C' and resid 262 through 277 Processing helix chain 'C' and resid 282 through 286 Processing helix chain 'C' and resid 287 through 288 No H-bonds generated for 'chain 'C' and resid 287 through 288' Processing helix chain 'C' and resid 289 through 300 removed outlier: 3.703A pdb=" N HIS C 294 " --> pdb=" O ILE C 290 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N ARG C 300 " --> pdb=" O ARG C 296 " (cutoff:3.500A) Processing helix chain 'C' and resid 328 through 338 removed outlier: 3.510A pdb=" N SER C 336 " --> pdb=" O THR C 332 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ILE C 337 " --> pdb=" O ASN C 333 " (cutoff:3.500A) Processing helix chain 'C' and resid 345 through 351 Processing helix chain 'C' and resid 372 through 397 removed outlier: 3.767A pdb=" N GLY C 380 " --> pdb=" O LYS C 376 " (cutoff:3.500A) removed outlier: 5.508A pdb=" N THR C 381 " --> pdb=" O LYS C 377 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N LEU C 382 " --> pdb=" O VAL C 378 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N ARG C 383 " --> pdb=" O ALA C 379 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N LEU C 384 " --> pdb=" O GLY C 380 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N TYR C 389 " --> pdb=" O ASP C 385 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLU C 391 " --> pdb=" O ALA C 387 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ALA C 394 " --> pdb=" O ARG C 390 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLN C 397 " --> pdb=" O GLU C 393 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 421 removed outlier: 3.614A pdb=" N LYS C 421 " --> pdb=" O VAL C 417 " (cutoff:3.500A) Processing helix chain 'C' and resid 429 through 442 removed outlier: 3.945A pdb=" N LEU C 435 " --> pdb=" O GLU C 431 " (cutoff:3.500A) Processing helix chain 'C' and resid 449 through 467 removed outlier: 4.484A pdb=" N ARG C 454 " --> pdb=" O VAL C 450 " (cutoff:3.500A) removed outlier: 5.475A pdb=" N ARG C 455 " --> pdb=" O GLU C 451 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LYS C 458 " --> pdb=" O ARG C 454 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LEU C 462 " --> pdb=" O LYS C 458 " (cutoff:3.500A) Processing helix chain 'C' and resid 468 through 478 Processing helix chain 'C' and resid 483 through 496 Processing helix chain 'D' and resid 88 through 92 Processing helix chain 'D' and resid 124 through 128 removed outlier: 3.846A pdb=" N LEU D 128 " --> pdb=" O PHE D 125 " (cutoff:3.500A) Processing helix chain 'D' and resid 139 through 145 Processing helix chain 'D' and resid 163 through 176 Processing helix chain 'D' and resid 191 through 206 Processing helix chain 'D' and resid 207 through 209 No H-bonds generated for 'chain 'D' and resid 207 through 209' Processing helix chain 'D' and resid 221 through 226 Processing helix chain 'D' and resid 227 through 242 removed outlier: 3.747A pdb=" N TYR D 238 " --> pdb=" O THR D 234 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N PHE D 239 " --> pdb=" O MET D 235 " (cutoff:3.500A) Processing helix chain 'D' and resid 254 through 269 removed outlier: 3.982A pdb=" N THR D 258 " --> pdb=" O ILE D 254 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N ALA D 266 " --> pdb=" O SER D 262 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N LEU D 267 " --> pdb=" O GLU D 263 " (cutoff:3.500A) Processing helix chain 'D' and resid 280 through 290 Processing helix chain 'D' and resid 309 through 312 Processing helix chain 'D' and resid 315 through 320 Processing helix chain 'D' and resid 321 through 325 Processing helix chain 'D' and resid 332 through 338 Processing helix chain 'D' and resid 355 through 360 Processing helix chain 'D' and resid 360 through 388 removed outlier: 3.710A pdb=" N GLN D 381 " --> pdb=" O TYR D 377 " (cutoff:3.500A) removed outlier: 5.060A pdb=" N ASP D 382 " --> pdb=" O LYS D 378 " (cutoff:3.500A) removed outlier: 5.132A pdb=" N ILE D 383 " --> pdb=" O GLU D 379 " (cutoff:3.500A) Processing helix chain 'D' and resid 389 through 392 Processing helix chain 'D' and resid 393 through 410 removed outlier: 3.646A pdb=" N ARG D 405 " --> pdb=" O HIS D 401 " (cutoff:3.500A) Processing helix chain 'D' and resid 417 through 422 Processing helix chain 'D' and resid 429 through 443 Processing helix chain 'D' and resid 449 through 454 Processing helix chain 'D' and resid 458 through 469 removed outlier: 3.596A pdb=" N GLU D 464 " --> pdb=" O GLU D 460 " (cutoff:3.500A) Processing helix chain 'E' and resid 88 through 92 Processing helix chain 'E' and resid 124 through 128 removed outlier: 3.575A pdb=" N LEU E 128 " --> pdb=" O PHE E 125 " (cutoff:3.500A) Processing helix chain 'E' and resid 139 through 146 Processing helix chain 'E' and resid 163 through 179 Processing helix chain 'E' and resid 191 through 206 Processing helix chain 'E' and resid 207 through 209 No H-bonds generated for 'chain 'E' and resid 207 through 209' Processing helix chain 'E' and resid 221 through 242 removed outlier: 5.287A pdb=" N ALA E 229 " --> pdb=" O ARG E 225 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N LEU E 230 " --> pdb=" O MET E 226 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N TYR E 238 " --> pdb=" O THR E 234 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N PHE E 239 " --> pdb=" O MET E 235 " (cutoff:3.500A) Processing helix chain 'E' and resid 253 through 269 removed outlier: 3.618A pdb=" N PHE E 257 " --> pdb=" O ASN E 253 " (cutoff:3.500A) Processing helix chain 'E' and resid 273 through 277 Processing helix chain 'E' and resid 280 through 290 Processing helix chain 'E' and resid 308 through 312 Processing helix chain 'E' and resid 315 through 323 removed outlier: 3.580A pdb=" N SER E 323 " --> pdb=" O ALA E 319 " (cutoff:3.500A) Processing helix chain 'E' and resid 332 through 339 Processing helix chain 'E' and resid 360 through 385 removed outlier: 4.046A pdb=" N ASP E 382 " --> pdb=" O LYS E 378 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N ILE E 383 " --> pdb=" O GLU E 379 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ALA E 385 " --> pdb=" O GLN E 381 " (cutoff:3.500A) Processing helix chain 'E' and resid 393 through 410 removed outlier: 3.676A pdb=" N ARG E 405 " --> pdb=" O HIS E 401 " (cutoff:3.500A) Processing helix chain 'E' and resid 414 through 416 No H-bonds generated for 'chain 'E' and resid 414 through 416' Processing helix chain 'E' and resid 417 through 422 Processing helix chain 'E' and resid 429 through 442 Processing helix chain 'E' and resid 449 through 454 Processing helix chain 'E' and resid 458 through 470 removed outlier: 3.697A pdb=" N VAL E 462 " --> pdb=" O ARG E 458 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N VAL E 463 " --> pdb=" O ILE E 459 " (cutoff:3.500A) Processing helix chain 'F' and resid 88 through 92 Processing helix chain 'F' and resid 124 through 128 removed outlier: 3.507A pdb=" N GLU F 127 " --> pdb=" O LYS F 124 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU F 128 " --> pdb=" O PHE F 125 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 124 through 128' Processing helix chain 'F' and resid 139 through 146 Processing helix chain 'F' and resid 163 through 180 removed outlier: 4.613A pdb=" N GLN F 177 " --> pdb=" O HIS F 173 " (cutoff:3.500A) removed outlier: 4.998A pdb=" N GLU F 178 " --> pdb=" O ASN F 174 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N GLY F 180 " --> pdb=" O ALA F 176 " (cutoff:3.500A) Processing helix chain 'F' and resid 191 through 204 Processing helix chain 'F' and resid 206 through 209 removed outlier: 3.525A pdb=" N SER F 209 " --> pdb=" O GLY F 206 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 206 through 209' Processing helix chain 'F' and resid 221 through 242 removed outlier: 3.684A pdb=" N ARG F 227 " --> pdb=" O GLY F 223 " (cutoff:3.500A) removed outlier: 4.894A pdb=" N ALA F 229 " --> pdb=" O ARG F 225 " (cutoff:3.500A) removed outlier: 4.920A pdb=" N LEU F 230 " --> pdb=" O MET F 226 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N TYR F 238 " --> pdb=" O THR F 234 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N PHE F 239 " --> pdb=" O MET F 235 " (cutoff:3.500A) Processing helix chain 'F' and resid 254 through 269 removed outlier: 3.934A pdb=" N THR F 258 " --> pdb=" O ILE F 254 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ALA F 266 " --> pdb=" O SER F 262 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N LEU F 267 " --> pdb=" O GLU F 263 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLY F 269 " --> pdb=" O SER F 265 " (cutoff:3.500A) Processing helix chain 'F' and resid 273 through 277 Processing helix chain 'F' and resid 280 through 290 removed outlier: 3.543A pdb=" N LEU F 288 " --> pdb=" O GLU F 284 " (cutoff:3.500A) Processing helix chain 'F' and resid 309 through 312 Processing helix chain 'F' and resid 315 through 321 removed outlier: 3.504A pdb=" N THR F 321 " --> pdb=" O ALA F 317 " (cutoff:3.500A) Processing helix chain 'F' and resid 322 through 325 removed outlier: 3.652A pdb=" N LEU F 325 " --> pdb=" O PHE F 322 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 322 through 325' Processing helix chain 'F' and resid 332 through 338 removed outlier: 3.641A pdb=" N MET F 338 " --> pdb=" O LYS F 334 " (cutoff:3.500A) Processing helix chain 'F' and resid 355 through 360 Processing helix chain 'F' and resid 360 through 388 removed outlier: 4.322A pdb=" N ASP F 382 " --> pdb=" O LYS F 378 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N ILE F 383 " --> pdb=" O GLU F 379 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ILE F 386 " --> pdb=" O ASP F 382 " (cutoff:3.500A) Processing helix chain 'F' and resid 393 through 410 removed outlier: 3.766A pdb=" N ARG F 405 " --> pdb=" O HIS F 401 " (cutoff:3.500A) Processing helix chain 'F' and resid 415 through 420 removed outlier: 3.675A pdb=" N GLN F 419 " --> pdb=" O VAL F 416 " (cutoff:3.500A) Processing helix chain 'F' and resid 429 through 442 Processing helix chain 'F' and resid 449 through 454 Processing helix chain 'F' and resid 458 through 470 removed outlier: 4.032A pdb=" N VAL F 462 " --> pdb=" O ARG F 458 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N VAL F 463 " --> pdb=" O ILE F 459 " (cutoff:3.500A) Processing helix chain 'G' and resid 3 through 42 removed outlier: 4.040A pdb=" N PHE G 42 " --> pdb=" O ASN G 38 " (cutoff:3.500A) Processing helix chain 'G' and resid 42 through 57 removed outlier: 3.522A pdb=" N MET G 46 " --> pdb=" O PHE G 42 " (cutoff:3.500A) Processing helix chain 'G' and resid 63 through 68 Processing helix chain 'G' and resid 90 through 107 removed outlier: 3.876A pdb=" N VAL G 95 " --> pdb=" O TYR G 91 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N LYS G 105 " --> pdb=" O GLN G 101 " (cutoff:3.500A) Processing helix chain 'G' and resid 119 through 129 Processing helix chain 'G' and resid 145 through 162 removed outlier: 4.112A pdb=" N ILE G 149 " --> pdb=" O SER G 145 " (cutoff:3.500A) removed outlier: 5.102A pdb=" N GLU G 151 " --> pdb=" O ALA G 147 " (cutoff:3.500A) removed outlier: 5.919A pdb=" N ILE G 152 " --> pdb=" O ASP G 148 " (cutoff:3.500A) Processing helix chain 'G' and resid 208 through 283 removed outlier: 3.936A pdb=" N ASP G 214 " --> pdb=" O GLU G 210 " (cutoff:3.500A) Proline residue: G 218 - end of helix removed outlier: 3.543A pdb=" N GLY G 227 " --> pdb=" O SER G 223 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N ASP G 231 " --> pdb=" O GLY G 227 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N ALA G 234 " --> pdb=" O LEU G 230 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 60 through 66 removed outlier: 4.069A pdb=" N GLU A 51 " --> pdb=" O ALA A 63 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N LEU A 52 " --> pdb=" O THR A 91 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N ARG A 40 " --> pdb=" O ILE A 32 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N VAL A 34 " --> pdb=" O ILE A 38 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N ILE A 38 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N ASN A 70 " --> pdb=" O LEU A 66 " (cutoff:3.500A) removed outlier: 5.241A pdb=" N LEU A 66 " --> pdb=" O ASN A 70 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N GLY A 72 " --> pdb=" O LEU A 64 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N GLU E 75 " --> pdb=" O GLN E 33 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N GLN E 33 " --> pdb=" O GLU E 75 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N ARG E 60 " --> pdb=" O ALA E 51 " (cutoff:3.500A) removed outlier: 5.022A pdb=" N HIS E 53 " --> pdb=" O THR E 58 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N THR E 58 " --> pdb=" O HIS E 53 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N LYS E 17 " --> pdb=" O VAL E 6 " (cutoff:3.500A) removed outlier: 5.689A pdb=" N VAL E 6 " --> pdb=" O LYS E 17 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 96 through 98 Processing sheet with id=AA3, first strand: chain 'A' and resid 107 through 108 removed outlier: 6.408A pdb=" N ILE A 192 " --> pdb=" O LEU A 257 " (cutoff:3.500A) removed outlier: 8.003A pdb=" N VAL A 259 " --> pdb=" O ILE A 192 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N ILE A 194 " --> pdb=" O VAL A 259 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 145 through 146 removed outlier: 4.716A pdb=" N ILE A 159 " --> pdb=" O LEU A 146 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 60 through 66 removed outlier: 4.161A pdb=" N GLU B 51 " --> pdb=" O ALA B 63 " (cutoff:3.500A) removed outlier: 5.063A pdb=" N ARG B 93 " --> pdb=" O LEU B 52 " (cutoff:3.500A) removed outlier: 8.387A pdb=" N GLU B 54 " --> pdb=" O THR B 91 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N THR B 91 " --> pdb=" O GLU B 54 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N ARG B 40 " --> pdb=" O ILE B 32 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N VAL B 34 " --> pdb=" O ILE B 38 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N ILE B 38 " --> pdb=" O VAL B 34 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N VAL B 74 " --> pdb=" O ALA B 63 " (cutoff:3.500A) removed outlier: 5.745A pdb=" N ALA B 63 " --> pdb=" O VAL B 74 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N GLU F 75 " --> pdb=" O GLN F 33 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N GLN F 33 " --> pdb=" O GLU F 75 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N ARG F 60 " --> pdb=" O ALA F 51 " (cutoff:3.500A) removed outlier: 5.169A pdb=" N HIS F 53 " --> pdb=" O THR F 58 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N THR F 58 " --> pdb=" O HIS F 53 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N VAL F 13 " --> pdb=" O VAL F 9 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N VAL F 9 " --> pdb=" O VAL F 13 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N ASP F 15 " --> pdb=" O ILE F 7 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 96 through 99 removed outlier: 4.073A pdb=" N GLU B 125 " --> pdb=" O VAL B 99 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 107 through 108 removed outlier: 6.371A pdb=" N ILE B 192 " --> pdb=" O LEU B 257 " (cutoff:3.500A) removed outlier: 7.954A pdb=" N VAL B 259 " --> pdb=" O ILE B 192 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N ILE B 194 " --> pdb=" O VAL B 259 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N LEU B 166 " --> pdb=" O ILE B 342 " (cutoff:3.500A) removed outlier: 7.604A pdb=" N LEU B 344 " --> pdb=" O LEU B 166 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N ILE B 168 " --> pdb=" O LEU B 344 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 60 through 66 removed outlier: 4.153A pdb=" N GLU C 51 " --> pdb=" O ALA C 63 " (cutoff:3.500A) removed outlier: 5.232A pdb=" N ARG C 93 " --> pdb=" O LEU C 52 " (cutoff:3.500A) removed outlier: 8.647A pdb=" N GLU C 54 " --> pdb=" O THR C 91 " (cutoff:3.500A) removed outlier: 7.242A pdb=" N THR C 91 " --> pdb=" O GLU C 54 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N ARG C 40 " --> pdb=" O ILE C 32 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N VAL C 34 " --> pdb=" O ILE C 38 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N ILE C 38 " --> pdb=" O VAL C 34 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N GLY C 72 " --> pdb=" O LEU C 64 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N ARG D 60 " --> pdb=" O ALA D 51 " (cutoff:3.500A) removed outlier: 5.093A pdb=" N HIS D 53 " --> pdb=" O THR D 58 " (cutoff:3.500A) removed outlier: 7.395A pdb=" N THR D 58 " --> pdb=" O HIS D 53 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLN D 8 " --> pdb=" O ASP D 15 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N LYS D 17 " --> pdb=" O VAL D 6 " (cutoff:3.500A) removed outlier: 5.550A pdb=" N VAL D 6 " --> pdb=" O LYS D 17 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 96 through 99 removed outlier: 3.854A pdb=" N GLU 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: 6.294A pdb=" N VAL C 108 " --> pdb=" O THR C 225 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 318 through 320 removed outlier: 8.326A pdb=" N VAL C 319 " --> pdb=" O GLU C 165 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N ILE C 167 " --> pdb=" O VAL C 319 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 84 through 86 Processing sheet with id=AB4, first strand: chain 'D' and resid 95 through 96 removed outlier: 6.034A pdb=" N VAL D 247 " --> pdb=" O THR D 301 " (cutoff:3.500A) removed outlier: 7.602A pdb=" N ILE D 303 " --> pdb=" O VAL D 247 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N LEU D 249 " --> pdb=" O ILE D 303 " (cutoff:3.500A) removed outlier: 7.750A pdb=" N ALA D 305 " --> pdb=" O LEU D 249 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N ILE D 251 " --> pdb=" O ALA D 305 " (cutoff:3.500A) removed outlier: 8.700A pdb=" N TYR D 307 " --> pdb=" O ILE D 251 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N ILE D 154 " --> pdb=" O GLN D 304 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N ILE D 306 " --> pdb=" O ILE D 154 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N LEU D 156 " --> pdb=" O ILE D 306 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 134 through 135 removed outlier: 4.151A pdb=" N TYR D 148 " --> pdb=" O LEU D 135 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 84 through 86 Processing sheet with id=AB7, first strand: chain 'E' and resid 95 through 96 removed outlier: 6.313A pdb=" N PHE E 96 " --> pdb=" O PHE E 215 " (cutoff:3.500A) removed outlier: 7.861A pdb=" N GLN E 217 " --> pdb=" O PHE E 96 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N VAL E 184 " --> pdb=" O PHE E 250 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N ILE E 154 " --> pdb=" O GLN E 304 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N LYS E 153 " --> pdb=" O ALA E 327 " (cutoff:3.500A) removed outlier: 8.007A pdb=" N THR E 329 " --> pdb=" O LYS E 153 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N GLY E 155 " --> pdb=" O THR E 329 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 134 through 135 removed outlier: 4.368A pdb=" N TYR E 148 " --> pdb=" O LEU E 135 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 84 through 86 Processing sheet with id=AC1, first strand: chain 'F' and resid 95 through 96 removed outlier: 6.833A pdb=" N SER F 183 " --> pdb=" O ALA F 212 " (cutoff:3.500A) removed outlier: 8.416A pdb=" N VAL F 214 " --> pdb=" O SER F 183 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N PHE F 185 " --> pdb=" O VAL F 214 " (cutoff:3.500A) removed outlier: 7.868A pdb=" N GLY F 216 " --> pdb=" O PHE F 185 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N GLY F 187 " --> pdb=" O GLY F 216 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N VAL F 247 " --> pdb=" O THR F 301 " (cutoff:3.500A) removed outlier: 7.841A pdb=" N ILE F 303 " --> pdb=" O VAL F 247 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N LEU F 249 " --> pdb=" O ILE F 303 " (cutoff:3.500A) removed outlier: 7.960A pdb=" N ALA F 305 " --> pdb=" O LEU F 249 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N ILE F 251 " --> pdb=" O ALA F 305 " (cutoff:3.500A) removed outlier: 8.473A pdb=" N TYR F 307 " --> pdb=" O ILE F 251 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N ILE F 154 " --> pdb=" O GLN F 304 " (cutoff:3.500A) removed outlier: 7.478A pdb=" N ILE F 306 " --> pdb=" O ILE F 154 " (cutoff:3.500A) removed outlier: 6.021A pdb=" N LEU F 156 " --> pdb=" O ILE F 306 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 134 through 135 removed outlier: 4.314A pdb=" N TYR F 148 " --> pdb=" O LEU F 135 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'G' and resid 133 through 137 removed outlier: 8.128A pdb=" N ILE G 134 " --> pdb=" O TYR G 113 " (cutoff:3.500A) removed outlier: 8.211A pdb=" N ILE G 115 " --> pdb=" O ILE G 134 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N ASP G 136 " --> pdb=" O ILE G 115 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N VAL G 117 " --> pdb=" O ASP G 136 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N THR G 76 " --> pdb=" O ALA G 114 " (cutoff:3.500A) removed outlier: 7.536A pdb=" N ILE G 116 " --> pdb=" O THR G 76 " (cutoff:3.500A) removed outlier: 5.975A pdb=" N TYR G 78 " --> pdb=" O ILE G 116 " (cutoff:3.500A) removed outlier: 7.542A pdb=" N ILE G 118 " --> pdb=" O TYR G 78 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N VAL G 80 " --> pdb=" O ILE G 118 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N GLY G 77 " --> pdb=" O TYR G 169 " (cutoff:3.500A) removed outlier: 7.843A pdb=" N TYR G 171 " --> pdb=" O GLY G 77 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N LEU G 79 " --> pdb=" O TYR G 171 " (cutoff:3.500A) removed outlier: 8.678A pdb=" N ASN G 173 " --> pdb=" O LEU G 79 " (cutoff:3.500A) removed outlier: 8.606A pdb=" N ILE G 81 " --> pdb=" O ASN G 173 " (cutoff:3.500A) removed outlier: 11.186A pdb=" N TYR G 175 " --> pdb=" O ILE G 81 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N LEU G 168 " --> pdb=" O LEU G 188 " (cutoff:3.500A) 1152 hydrogen bonds defined for protein. 3276 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: 4.27 Time building geometry restraints manager: 2.20 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 4187 1.32 - 1.44: 5900 1.44 - 1.56: 14417 1.56 - 1.68: 30 1.68 - 1.80: 154 Bond restraints: 24688 Sorted by residual: bond pdb=" C VAL B 378 " pdb=" O VAL B 378 " ideal model delta sigma weight residual 1.237 1.413 -0.176 1.23e-02 6.61e+03 2.05e+02 bond pdb=" C ALA B 374 " pdb=" O ALA B 374 " ideal model delta sigma weight residual 1.236 1.368 -0.132 1.22e-02 6.72e+03 1.16e+02 bond pdb=" C LYS B 377 " pdb=" O LYS B 377 " ideal model delta sigma weight residual 1.236 1.318 -0.082 1.15e-02 7.56e+03 5.06e+01 bond pdb=" CA ILE F 340 " pdb=" C ILE F 340 " ideal model delta sigma weight residual 1.524 1.448 0.076 1.16e-02 7.43e+03 4.25e+01 bond pdb=" C GLY B 380 " pdb=" O GLY B 380 " ideal model delta sigma weight residual 1.234 1.303 -0.070 1.21e-02 6.83e+03 3.34e+01 ... (remaining 24683 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.78: 33209 2.78 - 5.55: 243 5.55 - 8.33: 22 8.33 - 11.11: 7 11.11 - 13.88: 4 Bond angle restraints: 33485 Sorted by residual: angle pdb=" C TYR F 341 " pdb=" N PRO F 342 " pdb=" CA PRO F 342 " ideal model delta sigma weight residual 119.84 105.96 13.88 1.25e+00 6.40e-01 1.23e+02 angle pdb=" CA LYS B 377 " pdb=" C LYS B 377 " pdb=" N VAL B 378 " ideal model delta sigma weight residual 116.92 127.12 -10.20 1.16e+00 7.43e-01 7.73e+01 angle pdb=" C TYR E 341 " pdb=" N PRO E 342 " pdb=" CA PRO E 342 " ideal model delta sigma weight residual 119.32 109.44 9.88 1.14e+00 7.69e-01 7.52e+01 angle pdb=" O LYS B 377 " pdb=" C LYS B 377 " pdb=" N VAL B 378 " ideal model delta sigma weight residual 122.03 113.08 8.95 1.04e+00 9.25e-01 7.41e+01 angle pdb=" O LYS B 373 " pdb=" C LYS B 373 " pdb=" N ALA B 374 " ideal model delta sigma weight residual 122.22 114.00 8.22 1.17e+00 7.31e-01 4.94e+01 ... (remaining 33480 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.76: 14642 30.76 - 61.52: 386 61.52 - 92.28: 63 92.28 - 123.03: 0 123.03 - 153.79: 2 Dihedral angle restraints: 15093 sinusoidal: 6168 harmonic: 8925 Sorted by residual: dihedral pdb=" O2A ADP D 503 " pdb=" O3A ADP D 503 " pdb=" PA ADP D 503 " pdb=" PB ADP D 503 " ideal model delta sinusoidal sigma weight residual -60.00 93.79 -153.79 1 2.00e+01 2.50e-03 4.55e+01 dihedral pdb=" C THR B 381 " pdb=" N THR B 381 " pdb=" CA THR B 381 " pdb=" CB THR B 381 " ideal model delta harmonic sigma weight residual -122.00 -137.97 15.97 0 2.50e+00 1.60e-01 4.08e+01 dihedral pdb=" C5' ADP D 503 " pdb=" O5' ADP D 503 " pdb=" PA ADP D 503 " pdb=" O2A ADP D 503 " ideal model delta sinusoidal sigma weight residual -60.00 74.45 -134.45 1 2.00e+01 2.50e-03 4.08e+01 ... (remaining 15090 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.151: 3843 0.151 - 0.303: 8 0.303 - 0.454: 2 0.454 - 0.605: 2 0.605 - 0.757: 1 Chirality restraints: 3856 Sorted by residual: chirality pdb=" CA TYR F 341 " pdb=" N TYR F 341 " pdb=" C TYR F 341 " pdb=" CB TYR F 341 " both_signs ideal model delta sigma weight residual False 2.51 1.75 0.76 2.00e-01 2.50e+01 1.43e+01 chirality pdb=" CA TYR E 341 " pdb=" N TYR E 341 " pdb=" C TYR E 341 " pdb=" CB TYR E 341 " both_signs ideal model delta sigma weight residual False 2.51 1.94 0.57 2.00e-01 2.50e+01 8.13e+00 chirality pdb=" CA THR B 381 " pdb=" N THR B 381 " pdb=" C THR B 381 " pdb=" CB THR B 381 " both_signs ideal model delta sigma weight residual False 2.53 2.02 0.51 2.00e-01 2.50e+01 6.42e+00 ... (remaining 3853 not shown) Planarity restraints: 4363 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE E 340 " 0.020 2.00e-02 2.50e+03 4.01e-02 1.60e+01 pdb=" C ILE E 340 " -0.069 2.00e-02 2.50e+03 pdb=" O ILE E 340 " 0.026 2.00e-02 2.50e+03 pdb=" N TYR E 341 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE E 383 " -0.018 2.00e-02 2.50e+03 3.60e-02 1.29e+01 pdb=" C ILE E 383 " 0.062 2.00e-02 2.50e+03 pdb=" O ILE E 383 " -0.023 2.00e-02 2.50e+03 pdb=" N ILE E 384 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP B 385 " -0.017 2.00e-02 2.50e+03 3.40e-02 1.16e+01 pdb=" C ASP B 385 " 0.059 2.00e-02 2.50e+03 pdb=" O ASP B 385 " -0.022 2.00e-02 2.50e+03 pdb=" N LEU B 386 " -0.020 2.00e-02 2.50e+03 ... (remaining 4360 not shown) Histogram of nonbonded interaction distances: 1.69 - 2.33: 22 2.33 - 2.97: 11559 2.97 - 3.62: 35306 3.62 - 4.26: 55629 4.26 - 4.90: 95698 Nonbonded interactions: 198214 Sorted by model distance: nonbonded pdb=" OG1 THR D 165 " pdb="MG MG D 502 " model vdw 1.690 2.170 nonbonded pdb=" O2G ATP B 600 " pdb="MG MG B 601 " model vdw 1.992 2.170 nonbonded pdb=" OG1 THR F 165 " pdb="MG MG F 601 " model vdw 1.994 2.170 nonbonded pdb=" OG1 THR C 176 " pdb="MG MG C 601 " model vdw 1.994 2.170 nonbonded pdb=" OG1 THR B 176 " pdb="MG MG B 601 " model vdw 2.003 2.170 ... (remaining 198209 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 501) selection = (chain 'B' and resid 24 through 501) selection = (chain 'C' and resid 24 through 501) } ncs_group { reference = (chain 'D' and resid 1 through 470) selection = (chain 'E' and resid 1 through 470) selection = (chain 'F' and resid 1 through 470) } 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 group one per residue 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: 3.900 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.280 Check model and map are aligned: 0.090 Set scattering table: 0.060 Process input model: 20.820 Find NCS groups from input model: 0.550 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7721 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 : 0.004 0.176 24688 Z= 0.244 Angle : 0.643 13.884 33485 Z= 0.392 Chirality : 0.049 0.757 3856 Planarity : 0.004 0.063 4363 Dihedral : 14.209 153.792 9381 Min Nonbonded Distance : 1.690 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.05 % Favored : 97.88 % Rotamer: Outliers : 0.51 % Allowed : 0.39 % Favored : 99.10 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 2.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.96 (0.15), residues: 3115 helix: 1.41 (0.15), residues: 1242 sheet: 0.59 (0.22), residues: 526 loop : 0.04 (0.17), residues: 1347 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 405 TYR 0.033 0.001 TYR F 341 PHE 0.010 0.001 PHE F 257 HIS 0.004 0.001 HIS D 363 Details of bonding type rmsd covalent geometry : bond 0.00397 (24688) covalent geometry : angle 0.64290 (33485) hydrogen bonds : bond 0.15010 ( 1152) hydrogen bonds : angle 6.13327 ( 3276) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 226 time to evaluate : 0.876 Fit side-chains REVERT: A 87 GLU cc_start: 0.8252 (tt0) cc_final: 0.7689 (tt0) REVERT: B 60 MET cc_start: 0.8717 (mmt) cc_final: 0.8352 (mmt) REVERT: B 373 LYS cc_start: 0.8423 (ttpt) cc_final: 0.8069 (ttpp) REVERT: B 451 GLU cc_start: 0.7715 (tt0) cc_final: 0.7125 (tp30) REVERT: C 109 ASN cc_start: 0.8404 (t0) cc_final: 0.7986 (t0) REVERT: C 272 GLU cc_start: 0.7742 (tt0) cc_final: 0.7171 (tt0) REVERT: C 457 GLU cc_start: 0.7709 (tt0) cc_final: 0.7449 (tt0) REVERT: D 334 LYS cc_start: 0.8099 (ttmm) cc_final: 0.7896 (ttmt) REVERT: D 376 ARG cc_start: 0.7188 (mmm160) cc_final: 0.6743 (mmm160) REVERT: D 389 MET cc_start: 0.7395 (mmt) cc_final: 0.7019 (mmm) REVERT: E 56 ASP cc_start: 0.7588 (t0) cc_final: 0.7213 (t0) REVERT: F 389 MET cc_start: 0.6932 (ttm) cc_final: 0.6641 (ttp) REVERT: F 390 ASP cc_start: 0.8181 (m-30) cc_final: 0.7962 (m-30) REVERT: G 222 GLU cc_start: 0.7870 (OUTLIER) cc_final: 0.7660 (mm-30) REVERT: G 225 ILE cc_start: 0.7474 (OUTLIER) cc_final: 0.7254 (mp) outliers start: 13 outliers final: 5 residues processed: 237 average time/residue: 0.1674 time to fit residues: 61.1611 Evaluate side-chains 158 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 151 time to evaluate : 0.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 197 optimal weight: 2.9990 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 7.9990 chunk 132 optimal weight: 8.9990 chunk 261 optimal weight: 7.9990 chunk 248 optimal weight: 7.9990 chunk 207 optimal weight: 4.9990 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 6.9990 chunk 183 optimal weight: 0.0870 chunk 298 optimal weight: 9.9990 overall best weight: 4.0166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 467 ASN D 365 GLN E 371 GLN E 381 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2662 r_free = 0.2662 target = 0.064358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2409 r_free = 0.2409 target = 0.053151 restraints weight = 57310.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2404 r_free = 0.2404 target = 0.052965 restraints weight = 50542.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2406 r_free = 0.2406 target = 0.053052 restraints weight = 47341.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2408 r_free = 0.2408 target = 0.053145 restraints weight = 43382.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2410 r_free = 0.2410 target = 0.053235 restraints weight = 40696.607| |-----------------------------------------------------------------------------| r_work (final): 0.2400 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.1069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 24688 Z= 0.247 Angle : 0.610 7.210 33485 Z= 0.322 Chirality : 0.049 0.253 3856 Planarity : 0.005 0.052 4363 Dihedral : 8.736 177.861 3580 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.31 % Favored : 97.59 % Rotamer: Outliers : 0.12 % Allowed : 4.13 % Favored : 95.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.75 (0.15), residues: 3115 helix: 1.28 (0.15), residues: 1240 sheet: 0.41 (0.22), residues: 545 loop : -0.09 (0.17), residues: 1330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 193 TYR 0.015 0.002 TYR G 100 PHE 0.018 0.002 PHE D 257 HIS 0.006 0.001 HIS A 215 Details of bonding type rmsd covalent geometry : bond 0.00606 (24688) covalent geometry : angle 0.60994 (33485) hydrogen bonds : bond 0.05640 ( 1152) hydrogen bonds : angle 5.00922 ( 3276) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 177 time to evaluate : 0.595 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 68 GLU cc_start: 0.6769 (tm-30) cc_final: 0.6502 (tm-30) REVERT: A 87 GLU cc_start: 0.7879 (tt0) cc_final: 0.7207 (tt0) REVERT: B 381 THR cc_start: 0.6366 (m) cc_final: 0.5750 (m) REVERT: B 451 GLU cc_start: 0.7197 (tt0) cc_final: 0.6945 (tp30) REVERT: B 465 ASP cc_start: 0.7712 (t70) cc_final: 0.7468 (t0) REVERT: C 191 MET cc_start: 0.7642 (ttm) cc_final: 0.7281 (ttm) REVERT: C 272 GLU cc_start: 0.7947 (tt0) cc_final: 0.7489 (tt0) REVERT: E 56 ASP cc_start: 0.7387 (t0) cc_final: 0.6978 (t0) REVERT: E 387 LEU cc_start: 0.6281 (tt) cc_final: 0.5485 (mt) REVERT: G 136 ASP cc_start: 0.7169 (p0) cc_final: 0.6753 (p0) REVERT: G 167 GLU cc_start: 0.6654 (mt-10) cc_final: 0.6427 (mt-10) REVERT: G 249 ASP cc_start: 0.7506 (m-30) cc_final: 0.7274 (m-30) outliers start: 3 outliers final: 1 residues processed: 180 average time/residue: 0.1705 time to fit residues: 47.4938 Evaluate side-chains 138 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 137 time to evaluate : 0.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 176 optimal weight: 8.9990 chunk 23 optimal weight: 4.9990 chunk 284 optimal weight: 0.9980 chunk 41 optimal weight: 5.9990 chunk 228 optimal weight: 7.9990 chunk 149 optimal weight: 9.9990 chunk 133 optimal weight: 0.9980 chunk 216 optimal weight: 3.9990 chunk 305 optimal weight: 5.9990 chunk 99 optimal weight: 2.9990 chunk 85 optimal weight: 1.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 381 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2685 r_free = 0.2685 target = 0.065487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2432 r_free = 0.2432 target = 0.054097 restraints weight = 56793.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2425 r_free = 0.2425 target = 0.053835 restraints weight = 54803.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2431 r_free = 0.2431 target = 0.054118 restraints weight = 51416.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2434 r_free = 0.2434 target = 0.054265 restraints weight = 46548.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2437 r_free = 0.2437 target = 0.054367 restraints weight = 41051.968| |-----------------------------------------------------------------------------| r_work (final): 0.2428 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.1199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 24688 Z= 0.154 Angle : 0.532 6.226 33485 Z= 0.281 Chirality : 0.045 0.173 3856 Planarity : 0.004 0.067 4363 Dihedral : 8.276 179.577 3580 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.10 % Allowed : 1.93 % Favored : 97.98 % Rotamer: Outliers : 0.08 % Allowed : 2.61 % Favored : 97.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.88 (0.15), residues: 3115 helix: 1.43 (0.15), residues: 1245 sheet: 0.44 (0.22), residues: 533 loop : -0.06 (0.17), residues: 1337 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 454 TYR 0.012 0.001 TYR G 100 PHE 0.021 0.001 PHE F 322 HIS 0.004 0.001 HIS A 425 Details of bonding type rmsd covalent geometry : bond 0.00368 (24688) covalent geometry : angle 0.53223 (33485) hydrogen bonds : bond 0.04746 ( 1152) hydrogen bonds : angle 4.76788 ( 3276) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 175 time to evaluate : 1.004 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 68 GLU cc_start: 0.6849 (tm-30) cc_final: 0.6533 (tm-30) REVERT: A 87 GLU cc_start: 0.7832 (tt0) cc_final: 0.7167 (tt0) REVERT: B 451 GLU cc_start: 0.7213 (tt0) cc_final: 0.6976 (tp30) REVERT: B 465 ASP cc_start: 0.7613 (t70) cc_final: 0.7397 (t0) REVERT: C 191 MET cc_start: 0.7739 (ttm) cc_final: 0.7363 (ttm) REVERT: C 272 GLU cc_start: 0.7914 (tt0) cc_final: 0.7395 (tt0) REVERT: E 56 ASP cc_start: 0.7354 (t0) cc_final: 0.6981 (t0) REVERT: F 1 MET cc_start: 0.5961 (ptt) cc_final: 0.5649 (ttt) outliers start: 2 outliers final: 0 residues processed: 177 average time/residue: 0.1720 time to fit residues: 46.5928 Evaluate side-chains 139 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 139 time to evaluate : 0.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 235 optimal weight: 7.9990 chunk 8 optimal weight: 4.9990 chunk 22 optimal weight: 3.9990 chunk 107 optimal weight: 0.9980 chunk 67 optimal weight: 10.0000 chunk 128 optimal weight: 9.9990 chunk 144 optimal weight: 1.9990 chunk 300 optimal weight: 10.0000 chunk 203 optimal weight: 8.9990 chunk 241 optimal weight: 6.9990 chunk 245 optimal weight: 6.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 179 HIS E 381 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2664 r_free = 0.2664 target = 0.064492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2407 r_free = 0.2407 target = 0.053185 restraints weight = 56968.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2403 r_free = 0.2403 target = 0.053007 restraints weight = 51612.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2405 r_free = 0.2405 target = 0.053093 restraints weight = 47773.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2407 r_free = 0.2407 target = 0.053185 restraints weight = 42827.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2408 r_free = 0.2408 target = 0.053222 restraints weight = 41336.229| |-----------------------------------------------------------------------------| r_work (final): 0.2396 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.1389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 24688 Z= 0.234 Angle : 0.587 6.807 33485 Z= 0.309 Chirality : 0.048 0.201 3856 Planarity : 0.005 0.062 4363 Dihedral : 8.228 175.988 3580 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.47 % Favored : 97.43 % Rotamer: Outliers : 0.04 % Allowed : 3.00 % Favored : 96.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.68 (0.15), residues: 3115 helix: 1.32 (0.15), residues: 1230 sheet: 0.39 (0.22), residues: 539 loop : -0.24 (0.17), residues: 1346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 106 TYR 0.018 0.001 TYR G 100 PHE 0.016 0.002 PHE D 125 HIS 0.006 0.001 HIS A 215 Details of bonding type rmsd covalent geometry : bond 0.00573 (24688) covalent geometry : angle 0.58714 (33485) hydrogen bonds : bond 0.05318 ( 1152) hydrogen bonds : angle 4.84215 ( 3276) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 163 time to evaluate : 0.821 Fit side-chains revert: symmetry clash REVERT: A 68 GLU cc_start: 0.7013 (tm-30) cc_final: 0.6650 (tm-30) REVERT: A 87 GLU cc_start: 0.7818 (tt0) cc_final: 0.7151 (tt0) REVERT: B 62 MET cc_start: 0.7911 (ttm) cc_final: 0.7564 (ttm) REVERT: B 451 GLU cc_start: 0.7303 (tt0) cc_final: 0.7011 (tp30) REVERT: B 465 ASP cc_start: 0.7680 (t70) cc_final: 0.7452 (t0) REVERT: C 191 MET cc_start: 0.7747 (ttm) cc_final: 0.7359 (ttm) REVERT: C 272 GLU cc_start: 0.7978 (tt0) cc_final: 0.7529 (tt0) REVERT: E 56 ASP cc_start: 0.7405 (t0) cc_final: 0.6973 (t0) REVERT: E 334 LYS cc_start: 0.7909 (mmtt) cc_final: 0.7702 (mmtm) REVERT: E 418 GLU cc_start: 0.8357 (tt0) cc_final: 0.8114 (tt0) REVERT: F 1 MET cc_start: 0.6029 (ptt) cc_final: 0.5695 (ttt) outliers start: 1 outliers final: 0 residues processed: 164 average time/residue: 0.1773 time to fit residues: 43.6528 Evaluate side-chains 136 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 136 time to evaluate : 0.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 118 optimal weight: 1.9990 chunk 35 optimal weight: 0.8980 chunk 190 optimal weight: 7.9990 chunk 200 optimal weight: 0.7980 chunk 156 optimal weight: 2.9990 chunk 284 optimal weight: 5.9990 chunk 137 optimal weight: 0.8980 chunk 101 optimal weight: 6.9990 chunk 209 optimal weight: 3.9990 chunk 232 optimal weight: 10.0000 chunk 197 optimal weight: 0.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 109 ASN ** E 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 381 GLN G 174 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2709 r_free = 0.2709 target = 0.066670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2457 r_free = 0.2457 target = 0.055302 restraints weight = 55674.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2450 r_free = 0.2450 target = 0.055026 restraints weight = 52764.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2452 r_free = 0.2452 target = 0.055156 restraints weight = 50648.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2454 r_free = 0.2454 target = 0.055207 restraints weight = 46908.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2455 r_free = 0.2455 target = 0.055290 restraints weight = 44219.040| |-----------------------------------------------------------------------------| r_work (final): 0.2448 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.1405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 24688 Z= 0.109 Angle : 0.496 6.925 33485 Z= 0.261 Chirality : 0.044 0.146 3856 Planarity : 0.004 0.060 4363 Dihedral : 7.751 179.116 3580 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.10 % Allowed : 1.83 % Favored : 98.07 % Rotamer: Outliers : 0.04 % Allowed : 1.52 % Favored : 98.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.04 (0.15), residues: 3115 helix: 1.64 (0.15), residues: 1232 sheet: 0.55 (0.22), residues: 528 loop : -0.06 (0.17), residues: 1355 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 333 TYR 0.017 0.001 TYR G 100 PHE 0.020 0.001 PHE C 343 HIS 0.006 0.001 HIS A 425 Details of bonding type rmsd covalent geometry : bond 0.00241 (24688) covalent geometry : angle 0.49626 (33485) hydrogen bonds : bond 0.04058 ( 1152) hydrogen bonds : angle 4.59206 ( 3276) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 175 time to evaluate : 0.829 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 68 GLU cc_start: 0.7027 (tm-30) cc_final: 0.6662 (tm-30) REVERT: A 87 GLU cc_start: 0.7729 (tt0) cc_final: 0.7059 (tt0) REVERT: B 62 MET cc_start: 0.7669 (ttm) cc_final: 0.7456 (ttt) REVERT: B 89 ARG cc_start: 0.6284 (ptp-110) cc_final: 0.6066 (ptp-170) REVERT: B 465 ASP cc_start: 0.7541 (t70) cc_final: 0.7305 (t0) REVERT: C 191 MET cc_start: 0.7649 (ttm) cc_final: 0.7305 (ttm) REVERT: C 272 GLU cc_start: 0.7871 (tt0) cc_final: 0.7348 (tt0) REVERT: E 56 ASP cc_start: 0.7351 (t0) cc_final: 0.6901 (t0) REVERT: F 1 MET cc_start: 0.5961 (ptt) cc_final: 0.5563 (ttp) outliers start: 1 outliers final: 0 residues processed: 176 average time/residue: 0.1741 time to fit residues: 46.5193 Evaluate side-chains 135 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 135 time to evaluate : 0.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 50 optimal weight: 0.2980 chunk 229 optimal weight: 10.0000 chunk 33 optimal weight: 9.9990 chunk 237 optimal weight: 9.9990 chunk 5 optimal weight: 3.9990 chunk 38 optimal weight: 3.9990 chunk 182 optimal weight: 7.9990 chunk 236 optimal weight: 6.9990 chunk 123 optimal weight: 1.9990 chunk 172 optimal weight: 0.7980 chunk 196 optimal weight: 3.9990 overall best weight: 2.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 381 GLN F 8 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2690 r_free = 0.2690 target = 0.065816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2438 r_free = 0.2438 target = 0.054516 restraints weight = 56260.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2434 r_free = 0.2434 target = 0.054348 restraints weight = 51705.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2437 r_free = 0.2437 target = 0.054516 restraints weight = 47306.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2439 r_free = 0.2439 target = 0.054582 restraints weight = 43571.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2441 r_free = 0.2441 target = 0.054703 restraints weight = 40774.111| |-----------------------------------------------------------------------------| r_work (final): 0.2433 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.1458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 24688 Z= 0.152 Angle : 0.523 6.039 33485 Z= 0.275 Chirality : 0.045 0.151 3856 Planarity : 0.004 0.057 4363 Dihedral : 7.747 179.513 3580 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.05 % Favored : 97.85 % Rotamer: Outliers : 0.04 % Allowed : 1.21 % Favored : 98.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.03 (0.15), residues: 3115 helix: 1.66 (0.15), residues: 1228 sheet: 0.51 (0.22), residues: 530 loop : -0.06 (0.17), residues: 1357 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 333 TYR 0.025 0.001 TYR G 100 PHE 0.016 0.001 PHE C 343 HIS 0.004 0.001 HIS A 425 Details of bonding type rmsd covalent geometry : bond 0.00365 (24688) covalent geometry : angle 0.52251 (33485) hydrogen bonds : bond 0.04453 ( 1152) hydrogen bonds : angle 4.60016 ( 3276) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 162 time to evaluate : 0.762 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 68 GLU cc_start: 0.7018 (tm-30) cc_final: 0.6814 (tm-30) REVERT: A 87 GLU cc_start: 0.7801 (tt0) cc_final: 0.7133 (tt0) REVERT: B 89 ARG cc_start: 0.6290 (ptp-110) cc_final: 0.6078 (ptp-170) REVERT: B 465 ASP cc_start: 0.7573 (t70) cc_final: 0.7321 (t0) REVERT: C 191 MET cc_start: 0.7650 (ttm) cc_final: 0.7311 (ttm) REVERT: C 272 GLU cc_start: 0.7916 (tt0) cc_final: 0.7438 (tt0) REVERT: C 407 GLN cc_start: 0.7971 (mt0) cc_final: 0.6681 (tp40) REVERT: E 56 ASP cc_start: 0.7413 (t0) cc_final: 0.6943 (t0) REVERT: E 418 GLU cc_start: 0.8238 (tt0) cc_final: 0.7971 (tt0) REVERT: F 1 MET cc_start: 0.5938 (ptt) cc_final: 0.5523 (ttp) outliers start: 1 outliers final: 0 residues processed: 163 average time/residue: 0.1834 time to fit residues: 45.0727 Evaluate side-chains 135 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 135 time to evaluate : 0.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 123 optimal weight: 3.9990 chunk 3 optimal weight: 0.4980 chunk 304 optimal weight: 0.9990 chunk 253 optimal weight: 9.9990 chunk 161 optimal weight: 6.9990 chunk 20 optimal weight: 1.9990 chunk 105 optimal weight: 0.8980 chunk 163 optimal weight: 0.7980 chunk 91 optimal weight: 5.9990 chunk 226 optimal weight: 0.0670 chunk 217 optimal weight: 0.0170 overall best weight: 0.4556 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 8 GLN E 381 GLN F 245 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2730 r_free = 0.2730 target = 0.067839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2491 r_free = 0.2491 target = 0.056759 restraints weight = 55808.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2484 r_free = 0.2484 target = 0.056508 restraints weight = 51506.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2487 r_free = 0.2487 target = 0.056673 restraints weight = 48864.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2491 r_free = 0.2491 target = 0.056827 restraints weight = 43248.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2491 r_free = 0.2491 target = 0.056865 restraints weight = 40431.291| |-----------------------------------------------------------------------------| r_work (final): 0.2481 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.1635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 24688 Z= 0.091 Angle : 0.469 5.722 33485 Z= 0.246 Chirality : 0.043 0.133 3856 Planarity : 0.004 0.056 4363 Dihedral : 7.353 171.098 3580 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.10 % Allowed : 1.83 % Favored : 98.07 % Rotamer: Outliers : 0.04 % Allowed : 0.86 % Favored : 99.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.31 (0.15), residues: 3115 helix: 1.90 (0.15), residues: 1230 sheet: 0.64 (0.22), residues: 537 loop : 0.09 (0.17), residues: 1348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 333 TYR 0.028 0.001 TYR C 389 PHE 0.016 0.001 PHE C 343 HIS 0.004 0.000 HIS A 425 Details of bonding type rmsd covalent geometry : bond 0.00184 (24688) covalent geometry : angle 0.46894 (33485) hydrogen bonds : bond 0.03449 ( 1152) hydrogen bonds : angle 4.42710 ( 3276) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 187 time to evaluate : 0.865 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 68 GLU cc_start: 0.6959 (tm-30) cc_final: 0.6722 (tm-30) REVERT: A 87 GLU cc_start: 0.7642 (tt0) cc_final: 0.7006 (tt0) REVERT: B 451 GLU cc_start: 0.7319 (tm-30) cc_final: 0.6899 (tm-30) REVERT: B 465 ASP cc_start: 0.7495 (t70) cc_final: 0.7232 (t0) REVERT: C 191 MET cc_start: 0.7632 (ttm) cc_final: 0.7337 (ttm) REVERT: C 272 GLU cc_start: 0.7817 (tt0) cc_final: 0.7580 (tt0) REVERT: C 407 GLN cc_start: 0.7909 (mt0) cc_final: 0.6690 (tp40) REVERT: E 41 GLU cc_start: 0.7506 (mt-10) cc_final: 0.7199 (mt-10) REVERT: E 56 ASP cc_start: 0.7412 (t0) cc_final: 0.6953 (t0) REVERT: E 418 GLU cc_start: 0.8179 (tt0) cc_final: 0.7878 (tt0) REVERT: F 1 MET cc_start: 0.5872 (ptt) cc_final: 0.5559 (ttp) outliers start: 1 outliers final: 0 residues processed: 188 average time/residue: 0.1639 time to fit residues: 47.5471 Evaluate side-chains 145 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 145 time to evaluate : 0.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 29 optimal weight: 5.9990 chunk 144 optimal weight: 2.9990 chunk 8 optimal weight: 3.9990 chunk 245 optimal weight: 0.0670 chunk 22 optimal weight: 1.9990 chunk 215 optimal weight: 0.0060 chunk 165 optimal weight: 8.9990 chunk 10 optimal weight: 3.9990 chunk 70 optimal weight: 1.9990 chunk 272 optimal weight: 0.9980 chunk 13 optimal weight: 5.9990 overall best weight: 1.0138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 381 GLN F 245 GLN G 130 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2723 r_free = 0.2723 target = 0.067477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2466 r_free = 0.2466 target = 0.055521 restraints weight = 55827.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2465 r_free = 0.2465 target = 0.055534 restraints weight = 51537.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2477 r_free = 0.2477 target = 0.056113 restraints weight = 45001.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2483 r_free = 0.2483 target = 0.056401 restraints weight = 36660.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2485 r_free = 0.2485 target = 0.056476 restraints weight = 31460.351| |-----------------------------------------------------------------------------| r_work (final): 0.2479 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.1669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 24688 Z= 0.103 Angle : 0.482 5.983 33485 Z= 0.252 Chirality : 0.043 0.136 3856 Planarity : 0.004 0.054 4363 Dihedral : 7.322 168.938 3580 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.10 % Allowed : 1.93 % Favored : 97.98 % Rotamer: Outliers : 0.04 % Allowed : 0.82 % Favored : 99.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.35 (0.15), residues: 3115 helix: 1.90 (0.15), residues: 1235 sheet: 0.68 (0.22), residues: 540 loop : 0.12 (0.17), residues: 1340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 442 TYR 0.022 0.001 TYR C 389 PHE 0.016 0.001 PHE C 463 HIS 0.003 0.001 HIS D 363 Details of bonding type rmsd covalent geometry : bond 0.00230 (24688) covalent geometry : angle 0.48217 (33485) hydrogen bonds : bond 0.03640 ( 1152) hydrogen bonds : angle 4.40233 ( 3276) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 169 time to evaluate : 0.961 Fit side-chains REVERT: A 68 GLU cc_start: 0.6956 (tm-30) cc_final: 0.6742 (tm-30) REVERT: A 87 GLU cc_start: 0.7684 (tt0) cc_final: 0.7063 (tt0) REVERT: B 95 MET cc_start: 0.7567 (mtp) cc_final: 0.6403 (mtp) REVERT: B 451 GLU cc_start: 0.7302 (tm-30) cc_final: 0.6903 (tm-30) REVERT: B 465 ASP cc_start: 0.7527 (t70) cc_final: 0.7281 (t0) REVERT: C 191 MET cc_start: 0.7624 (ttm) cc_final: 0.7334 (ttm) REVERT: C 272 GLU cc_start: 0.7916 (tt0) cc_final: 0.7675 (tt0) REVERT: C 407 GLN cc_start: 0.7905 (mt0) cc_final: 0.6654 (tp40) REVERT: D 376 ARG cc_start: 0.6687 (mmm160) cc_final: 0.6362 (mmm160) REVERT: E 41 GLU cc_start: 0.7462 (mt-10) cc_final: 0.7208 (mt-10) REVERT: E 56 ASP cc_start: 0.7461 (t0) cc_final: 0.6984 (t0) REVERT: E 334 LYS cc_start: 0.7926 (mmtt) cc_final: 0.7676 (mmtm) REVERT: E 418 GLU cc_start: 0.8160 (tt0) cc_final: 0.7870 (tt0) REVERT: F 1 MET cc_start: 0.5896 (ptt) cc_final: 0.5583 (ttp) outliers start: 1 outliers final: 0 residues processed: 170 average time/residue: 0.1621 time to fit residues: 42.8271 Evaluate side-chains 139 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 139 time to evaluate : 0.821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 102 optimal weight: 6.9990 chunk 218 optimal weight: 0.9990 chunk 45 optimal weight: 6.9990 chunk 200 optimal weight: 4.9990 chunk 103 optimal weight: 5.9990 chunk 150 optimal weight: 0.9980 chunk 308 optimal weight: 6.9990 chunk 207 optimal weight: 9.9990 chunk 136 optimal weight: 4.9990 chunk 250 optimal weight: 3.9990 chunk 184 optimal weight: 0.7980 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 381 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2685 r_free = 0.2685 target = 0.065691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2436 r_free = 0.2436 target = 0.054532 restraints weight = 56717.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2431 r_free = 0.2431 target = 0.054297 restraints weight = 51355.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2434 r_free = 0.2434 target = 0.054458 restraints weight = 48703.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2438 r_free = 0.2438 target = 0.054618 restraints weight = 42526.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2443 r_free = 0.2443 target = 0.054850 restraints weight = 39231.472| |-----------------------------------------------------------------------------| r_work (final): 0.2431 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.1614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 24688 Z= 0.161 Angle : 0.538 7.689 33485 Z= 0.281 Chirality : 0.046 0.174 3856 Planarity : 0.004 0.055 4363 Dihedral : 7.514 169.283 3580 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.22 % Favored : 97.69 % Rotamer: Outliers : 0.04 % Allowed : 0.90 % Favored : 99.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.15 (0.15), residues: 3115 helix: 1.74 (0.15), residues: 1236 sheet: 0.59 (0.22), residues: 526 loop : -0.01 (0.17), residues: 1353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 333 TYR 0.023 0.001 TYR C 389 PHE 0.015 0.001 PHE C 463 HIS 0.004 0.001 HIS A 215 Details of bonding type rmsd covalent geometry : bond 0.00387 (24688) covalent geometry : angle 0.53819 (33485) hydrogen bonds : bond 0.04447 ( 1152) hydrogen bonds : angle 4.55908 ( 3276) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 159 time to evaluate : 0.581 Fit side-chains REVERT: A 87 GLU cc_start: 0.7720 (tt0) cc_final: 0.7050 (tt0) REVERT: B 451 GLU cc_start: 0.7335 (tm-30) cc_final: 0.6938 (tm-30) REVERT: B 465 ASP cc_start: 0.7565 (t70) cc_final: 0.7323 (t0) REVERT: C 272 GLU cc_start: 0.7969 (tt0) cc_final: 0.7493 (tt0) REVERT: E 56 ASP cc_start: 0.7456 (t0) cc_final: 0.7018 (t0) REVERT: E 334 LYS cc_start: 0.7897 (mmtt) cc_final: 0.7667 (mmtm) REVERT: E 418 GLU cc_start: 0.8201 (tt0) cc_final: 0.7892 (tt0) REVERT: F 1 MET cc_start: 0.5919 (ptt) cc_final: 0.5552 (ttp) REVERT: F 469 MET cc_start: 0.8053 (ptp) cc_final: 0.7786 (ptm) outliers start: 1 outliers final: 0 residues processed: 160 average time/residue: 0.1645 time to fit residues: 40.8336 Evaluate side-chains 136 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 136 time to evaluate : 0.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 39 optimal weight: 4.9990 chunk 46 optimal weight: 7.9990 chunk 138 optimal weight: 2.9990 chunk 74 optimal weight: 4.9990 chunk 190 optimal weight: 5.9990 chunk 208 optimal weight: 5.9990 chunk 4 optimal weight: 1.9990 chunk 283 optimal weight: 0.0870 chunk 131 optimal weight: 10.0000 chunk 164 optimal weight: 3.9990 chunk 295 optimal weight: 7.9990 overall best weight: 2.8166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 381 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2678 r_free = 0.2678 target = 0.065319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2426 r_free = 0.2426 target = 0.053949 restraints weight = 56632.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2420 r_free = 0.2420 target = 0.053720 restraints weight = 55843.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2424 r_free = 0.2424 target = 0.053891 restraints weight = 51228.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2425 r_free = 0.2425 target = 0.053941 restraints weight = 49351.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2430 r_free = 0.2430 target = 0.054154 restraints weight = 44807.786| |-----------------------------------------------------------------------------| r_work (final): 0.2420 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.1635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 24688 Z= 0.182 Angle : 0.553 7.732 33485 Z= 0.289 Chirality : 0.047 0.172 3856 Planarity : 0.004 0.055 4363 Dihedral : 7.565 166.506 3580 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.28 % Favored : 97.62 % Rotamer: Outliers : 0.04 % Allowed : 0.23 % Favored : 99.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.01 (0.15), residues: 3115 helix: 1.62 (0.15), residues: 1234 sheet: 0.55 (0.23), residues: 525 loop : -0.10 (0.17), residues: 1356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 333 TYR 0.023 0.001 TYR G 100 PHE 0.014 0.001 PHE C 343 HIS 0.004 0.001 HIS A 215 Details of bonding type rmsd covalent geometry : bond 0.00446 (24688) covalent geometry : angle 0.55324 (33485) hydrogen bonds : bond 0.04663 ( 1152) hydrogen bonds : angle 4.62722 ( 3276) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 162 time to evaluate : 0.882 Fit side-chains REVERT: A 87 GLU cc_start: 0.7815 (tt0) cc_final: 0.7168 (tt0) REVERT: B 444 PHE cc_start: 0.5103 (m-10) cc_final: 0.4740 (m-10) REVERT: B 451 GLU cc_start: 0.7365 (tm-30) cc_final: 0.7041 (tm-30) REVERT: B 465 ASP cc_start: 0.7572 (t70) cc_final: 0.7354 (t0) REVERT: C 272 GLU cc_start: 0.7975 (tt0) cc_final: 0.7535 (tt0) REVERT: C 407 GLN cc_start: 0.7851 (mt0) cc_final: 0.6582 (tp40) REVERT: D 376 ARG cc_start: 0.6726 (mmm160) cc_final: 0.6349 (mmm160) REVERT: E 56 ASP cc_start: 0.7466 (t0) cc_final: 0.7032 (t0) REVERT: E 334 LYS cc_start: 0.7917 (mmtt) cc_final: 0.7690 (mmtm) REVERT: F 469 MET cc_start: 0.8057 (ptp) cc_final: 0.7788 (ptm) outliers start: 1 outliers final: 0 residues processed: 163 average time/residue: 0.1641 time to fit residues: 41.5060 Evaluate side-chains 132 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 132 time to evaluate : 0.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 64 optimal weight: 7.9990 chunk 212 optimal weight: 4.9990 chunk 271 optimal weight: 8.9990 chunk 280 optimal weight: 1.9990 chunk 174 optimal weight: 4.9990 chunk 122 optimal weight: 7.9990 chunk 266 optimal weight: 4.9990 chunk 276 optimal weight: 1.9990 chunk 172 optimal weight: 0.4980 chunk 137 optimal weight: 0.3980 chunk 269 optimal weight: 4.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 330 ASN E 381 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2686 r_free = 0.2686 target = 0.065685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2435 r_free = 0.2435 target = 0.054397 restraints weight = 56708.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2433 r_free = 0.2433 target = 0.054373 restraints weight = 49859.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2436 r_free = 0.2436 target = 0.054496 restraints weight = 45778.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2439 r_free = 0.2439 target = 0.054642 restraints weight = 41429.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2441 r_free = 0.2441 target = 0.054708 restraints weight = 38976.161| |-----------------------------------------------------------------------------| r_work (final): 0.2430 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.1647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 24688 Z= 0.143 Angle : 0.525 6.949 33485 Z= 0.275 Chirality : 0.045 0.155 3856 Planarity : 0.004 0.055 4363 Dihedral : 7.428 162.923 3580 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.22 % Favored : 97.69 % Rotamer: Outliers : 0.04 % Allowed : 0.31 % Favored : 99.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.04 (0.15), residues: 3115 helix: 1.68 (0.15), residues: 1233 sheet: 0.50 (0.23), residues: 526 loop : -0.07 (0.17), residues: 1356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 333 TYR 0.021 0.001 TYR G 100 PHE 0.017 0.001 PHE C 463 HIS 0.003 0.001 HIS D 363 Details of bonding type rmsd covalent geometry : bond 0.00340 (24688) covalent geometry : angle 0.52546 (33485) hydrogen bonds : bond 0.04311 ( 1152) hydrogen bonds : angle 4.56792 ( 3276) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2483.84 seconds wall clock time: 44 minutes 11.56 seconds (2651.56 seconds total)