Starting phenix.real_space_refine on Mon Aug 25 01:43:46 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hh2_34749/08_2025/8hh2_34749.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hh2_34749/08_2025/8hh2_34749.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8hh2_34749/08_2025/8hh2_34749.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hh2_34749/08_2025/8hh2_34749.map" model { file = "/net/cci-nas-00/data/ceres_data/8hh2_34749/08_2025/8hh2_34749.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hh2_34749/08_2025/8hh2_34749.cif" } resolution = 3.0 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): 0.03s 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: 6.38, per 1000 atoms: 0.26 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: 2.27 Conformation dependent library (CDL) restraints added in 1.1 seconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.96 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: 4.75 Time building geometry restraints manager: 2.97 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.500 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.380 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 24.290 Find NCS groups from input model: 0.570 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8600 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 : 0.992 Fit side-chains revert: symmetry clash REVERT: A 262 ASP cc_start: 0.7503 (m-30) cc_final: 0.7297 (m-30) REVERT: A 390 ARG cc_start: 0.8527 (tpp-160) cc_final: 0.8241 (tpp80) REVERT: B 373 LYS cc_start: 0.8888 (ttpt) cc_final: 0.8652 (ttpp) REVERT: C 109 ASN cc_start: 0.8137 (t0) cc_final: 0.7932 (t0) REVERT: C 272 GLU cc_start: 0.8282 (tt0) cc_final: 0.7962 (tt0) REVERT: D 376 ARG cc_start: 0.7173 (mmm160) cc_final: 0.6868 (mmm160) REVERT: D 389 MET cc_start: 0.7809 (mmt) cc_final: 0.7430 (mmm) REVERT: E 56 ASP cc_start: 0.7798 (t0) cc_final: 0.7508 (t0) REVERT: E 213 MET cc_start: 0.8600 (mtp) cc_final: 0.8108 (mtt) REVERT: G 225 ILE cc_start: 0.8092 (OUTLIER) cc_final: 0.7839 (mp) outliers start: 13 outliers final: 4 residues processed: 237 average time/residue: 0.8005 time to fit residues: 213.5637 Evaluate side-chains 143 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 138 time to evaluate : 0.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 381 THR Chi-restraints excluded: chain B residue 385 ASP Chi-restraints excluded: chain E residue 341 TYR Chi-restraints excluded: chain E residue 386 ILE Chi-restraints excluded: chain G residue 225 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 197 optimal weight: 1.9990 chunk 215 optimal weight: 0.8980 chunk 20 optimal weight: 7.9990 chunk 132 optimal weight: 10.0000 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 8.9990 chunk 207 optimal weight: 4.9990 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 6.9990 chunk 183 optimal weight: 8.9990 chunk 298 optimal weight: 9.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 266 GLN B 467 ASN B 483 ASN C 113 GLN C 407 GLN D 365 GLN E 371 GLN E 381 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.090003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.069424 restraints weight = 48479.010| |-----------------------------------------------------------------------------| r_work (start): 0.2920 rms_B_bonded: 2.24 r_work: 0.2810 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2690 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8893 moved from start: 0.1134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 24688 Z= 0.234 Angle : 0.612 9.973 33485 Z= 0.322 Chirality : 0.048 0.325 3856 Planarity : 0.005 0.061 4363 Dihedral : 8.791 178.751 3589 Min Nonbonded Distance : 1.858 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.25 % Favored : 97.66 % Rotamer: Outliers : 1.67 % Allowed : 6.81 % Favored : 91.51 % 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: 0.78 (0.15), residues: 3115 helix: 1.30 (0.15), residues: 1242 sheet: 0.43 (0.22), residues: 532 loop : -0.08 (0.17), residues: 1341 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 333 TYR 0.022 0.002 TYR F 341 PHE 0.018 0.002 PHE D 257 HIS 0.007 0.001 HIS A 215 Details of bonding type rmsd covalent geometry : bond 0.00573 (24688) covalent geometry : angle 0.61202 (33485) hydrogen bonds : bond 0.05536 ( 1152) hydrogen bonds : angle 4.97774 ( 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 188 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 145 time to evaluate : 1.082 Fit side-chains revert: symmetry clash REVERT: B 60 MET cc_start: 0.9363 (mmt) cc_final: 0.9063 (mmt) REVERT: C 272 GLU cc_start: 0.8977 (tt0) cc_final: 0.8705 (tt0) REVERT: C 384 LEU cc_start: 0.7775 (pt) cc_final: 0.6962 (mm) REVERT: C 392 LEU cc_start: 0.7505 (mp) cc_final: 0.7190 (mp) REVERT: D 376 ARG cc_start: 0.7340 (mmm160) cc_final: 0.6741 (mmm160) REVERT: D 389 MET cc_start: 0.7593 (mmt) cc_final: 0.7197 (mmm) REVERT: E 56 ASP cc_start: 0.8573 (t0) cc_final: 0.8170 (t0) REVERT: E 389 MET cc_start: 0.7283 (OUTLIER) cc_final: 0.6683 (tmt) outliers start: 43 outliers final: 13 residues processed: 173 average time/residue: 0.6995 time to fit residues: 136.7756 Evaluate side-chains 142 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 128 time to evaluate : 0.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain C residue 144 GLU Chi-restraints excluded: chain C residue 191 MET Chi-restraints excluded: chain C residue 223 VAL Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain D residue 285 MET Chi-restraints excluded: chain E residue 341 TYR Chi-restraints excluded: chain E residue 386 ILE Chi-restraints excluded: chain E residue 389 MET Chi-restraints excluded: chain F residue 341 TYR Chi-restraints excluded: chain G residue 179 ILE Chi-restraints excluded: chain G residue 272 GLN Chi-restraints excluded: chain G residue 273 GLU Chi-restraints excluded: chain G residue 284 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 176 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 chunk 284 optimal weight: 10.0000 chunk 41 optimal weight: 0.7980 chunk 228 optimal weight: 5.9990 chunk 149 optimal weight: 1.9990 chunk 133 optimal weight: 0.8980 chunk 216 optimal weight: 4.9990 chunk 305 optimal weight: 9.9990 chunk 99 optimal weight: 2.9990 chunk 85 optimal weight: 5.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.092475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.072018 restraints weight = 48007.217| |-----------------------------------------------------------------------------| r_work (start): 0.2968 rms_B_bonded: 2.24 r_work: 0.2859 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2740 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8847 moved from start: 0.1207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 24688 Z= 0.117 Angle : 0.497 6.833 33485 Z= 0.262 Chirality : 0.044 0.180 3856 Planarity : 0.004 0.058 4363 Dihedral : 8.087 176.074 3584 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.10 % Allowed : 1.80 % Favored : 98.11 % Rotamer: Outliers : 1.64 % Allowed : 9.03 % Favored : 89.33 % 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: 1.08 (0.15), residues: 3115 helix: 1.63 (0.15), residues: 1237 sheet: 0.49 (0.22), residues: 542 loop : 0.04 (0.17), residues: 1336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 390 TYR 0.014 0.001 TYR F 341 PHE 0.018 0.001 PHE C 343 HIS 0.003 0.001 HIS D 363 Details of bonding type rmsd covalent geometry : bond 0.00267 (24688) covalent geometry : angle 0.49713 (33485) hydrogen bonds : bond 0.04239 ( 1152) hydrogen bonds : angle 4.64533 ( 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 183 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 141 time to evaluate : 1.028 Fit side-chains revert: symmetry clash REVERT: A 390 ARG cc_start: 0.8728 (OUTLIER) cc_final: 0.7824 (ttm110) REVERT: B 60 MET cc_start: 0.9345 (mmt) cc_final: 0.9035 (mmt) REVERT: B 89 ARG cc_start: 0.8586 (ptp-110) cc_final: 0.8305 (ptm160) REVERT: B 390 ARG cc_start: 0.9014 (OUTLIER) cc_final: 0.8645 (tpp-160) REVERT: C 48 MET cc_start: 0.8857 (ttp) cc_final: 0.8642 (mtm) REVERT: C 272 GLU cc_start: 0.8929 (tt0) cc_final: 0.8606 (tt0) REVERT: C 384 LEU cc_start: 0.7451 (pt) cc_final: 0.6784 (mm) REVERT: D 1 MET cc_start: 0.4008 (tpt) cc_final: 0.3365 (pmt) REVERT: D 376 ARG cc_start: 0.7301 (mmm160) cc_final: 0.6603 (mmm160) REVERT: E 56 ASP cc_start: 0.8547 (t0) cc_final: 0.8101 (t0) REVERT: E 389 MET cc_start: 0.7141 (OUTLIER) cc_final: 0.6607 (tmt) REVERT: F 1 MET cc_start: 0.7117 (OUTLIER) cc_final: 0.6582 (ttt) REVERT: F 389 MET cc_start: 0.8301 (ttm) cc_final: 0.8002 (ttp) outliers start: 42 outliers final: 10 residues processed: 167 average time/residue: 0.8348 time to fit residues: 157.6833 Evaluate side-chains 138 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 124 time to evaluate : 0.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 390 ARG Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 390 ARG Chi-restraints excluded: chain C residue 223 VAL Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain D residue 301 THR Chi-restraints excluded: chain E residue 341 TYR Chi-restraints excluded: chain E residue 389 MET Chi-restraints excluded: chain E residue 456 VAL Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 301 THR Chi-restraints excluded: chain G residue 179 ILE Chi-restraints excluded: chain G residue 273 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 235 optimal weight: 1.9990 chunk 8 optimal weight: 0.3980 chunk 22 optimal weight: 4.9990 chunk 107 optimal weight: 5.9990 chunk 67 optimal weight: 8.9990 chunk 128 optimal weight: 1.9990 chunk 144 optimal weight: 2.9990 chunk 300 optimal weight: 10.0000 chunk 203 optimal weight: 6.9990 chunk 241 optimal weight: 7.9990 chunk 245 optimal weight: 4.9990 overall best weight: 2.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 8 GLN D 179 HIS E 381 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.091130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.070687 restraints weight = 48158.884| |-----------------------------------------------------------------------------| r_work (start): 0.2940 rms_B_bonded: 2.23 r_work: 0.2830 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2710 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2710 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8876 moved from start: 0.1343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 24688 Z= 0.163 Angle : 0.530 6.756 33485 Z= 0.278 Chirality : 0.045 0.219 3856 Planarity : 0.004 0.056 4363 Dihedral : 7.977 177.288 3582 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.25 % Favored : 97.66 % Rotamer: Outliers : 2.14 % Allowed : 10.05 % Favored : 87.81 % 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: 1.64 (0.15), residues: 1229 sheet: 0.44 (0.22), residues: 539 loop : -0.00 (0.17), residues: 1347 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 333 TYR 0.015 0.001 TYR G 100 PHE 0.018 0.001 PHE C 343 HIS 0.004 0.001 HIS A 215 Details of bonding type rmsd covalent geometry : bond 0.00394 (24688) covalent geometry : angle 0.52979 (33485) hydrogen bonds : bond 0.04644 ( 1152) hydrogen bonds : angle 4.65357 ( 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 185 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 130 time to evaluate : 1.003 Fit side-chains revert: symmetry clash REVERT: A 87 GLU cc_start: 0.8767 (OUTLIER) cc_final: 0.8558 (tm-30) REVERT: A 390 ARG cc_start: 0.8779 (OUTLIER) cc_final: 0.7866 (ttm110) REVERT: B 89 ARG cc_start: 0.8576 (ptp-110) cc_final: 0.8285 (ptm160) REVERT: B 390 ARG cc_start: 0.9087 (OUTLIER) cc_final: 0.8718 (tpp-160) REVERT: C 384 LEU cc_start: 0.7277 (pt) cc_final: 0.6626 (mm) REVERT: C 392 LEU cc_start: 0.7397 (mp) cc_final: 0.6985 (mp) REVERT: D 10 MET cc_start: 0.8559 (OUTLIER) cc_final: 0.8329 (mmm) REVERT: E 56 ASP cc_start: 0.8549 (t0) cc_final: 0.8112 (t0) REVERT: E 389 MET cc_start: 0.7169 (OUTLIER) cc_final: 0.6710 (tmt) REVERT: E 397 LYS cc_start: 0.5097 (OUTLIER) cc_final: 0.4339 (mmpt) REVERT: E 469 MET cc_start: 0.7023 (OUTLIER) cc_final: 0.6566 (mtt) REVERT: F 1 MET cc_start: 0.7334 (ptt) cc_final: 0.6593 (ttt) outliers start: 55 outliers final: 17 residues processed: 164 average time/residue: 0.8463 time to fit residues: 156.6814 Evaluate side-chains 147 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 123 time to evaluate : 1.022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 GLU Chi-restraints excluded: chain A residue 390 ARG Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 390 ARG Chi-restraints excluded: chain B residue 496 LYS Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 144 GLU Chi-restraints excluded: chain C residue 223 VAL Chi-restraints excluded: chain D residue 10 MET Chi-restraints excluded: chain D residue 285 MET Chi-restraints excluded: chain D residue 301 THR Chi-restraints excluded: chain E residue 341 TYR Chi-restraints excluded: chain E residue 358 ILE Chi-restraints excluded: chain E residue 389 MET Chi-restraints excluded: chain E residue 395 GLU Chi-restraints excluded: chain E residue 397 LYS Chi-restraints excluded: chain E residue 469 MET Chi-restraints excluded: chain F residue 301 THR Chi-restraints excluded: chain G residue 179 ILE Chi-restraints excluded: chain G residue 224 LEU Chi-restraints excluded: chain G residue 272 GLN Chi-restraints excluded: chain G residue 273 GLU Chi-restraints excluded: chain G residue 284 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 118 optimal weight: 6.9990 chunk 35 optimal weight: 1.9990 chunk 190 optimal weight: 5.9990 chunk 200 optimal weight: 0.8980 chunk 156 optimal weight: 9.9990 chunk 284 optimal weight: 9.9990 chunk 137 optimal weight: 0.9990 chunk 101 optimal weight: 9.9990 chunk 209 optimal weight: 2.9990 chunk 232 optimal weight: 0.0050 chunk 197 optimal weight: 0.9980 overall best weight: 0.9798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 8 GLN D 371 GLN E 381 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.093079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.072690 restraints weight = 47565.639| |-----------------------------------------------------------------------------| r_work (start): 0.2983 rms_B_bonded: 2.24 r_work: 0.2875 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2757 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8828 moved from start: 0.1482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 24688 Z= 0.100 Angle : 0.474 6.994 33485 Z= 0.249 Chirality : 0.043 0.154 3856 Planarity : 0.004 0.053 4363 Dihedral : 7.591 173.315 3582 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.10 % Allowed : 1.70 % Favored : 98.20 % Rotamer: Outliers : 2.22 % Allowed : 10.20 % Favored : 87.58 % 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: 1.23 (0.15), residues: 3115 helix: 1.81 (0.15), residues: 1239 sheet: 0.49 (0.22), residues: 559 loop : 0.09 (0.17), residues: 1317 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 333 TYR 0.015 0.001 TYR G 100 PHE 0.017 0.001 PHE A 395 HIS 0.003 0.000 HIS D 363 Details of bonding type rmsd covalent geometry : bond 0.00219 (24688) covalent geometry : angle 0.47396 (33485) hydrogen bonds : bond 0.03723 ( 1152) hydrogen bonds : angle 4.44638 ( 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 198 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 141 time to evaluate : 1.057 Fit side-chains revert: symmetry clash REVERT: A 390 ARG cc_start: 0.8698 (OUTLIER) cc_final: 0.7819 (ttm110) REVERT: B 89 ARG cc_start: 0.8603 (ptp-110) cc_final: 0.8297 (ptm160) REVERT: B 390 ARG cc_start: 0.9068 (OUTLIER) cc_final: 0.8742 (tpp-160) REVERT: C 272 GLU cc_start: 0.8977 (tt0) cc_final: 0.8765 (tt0) REVERT: C 384 LEU cc_start: 0.7444 (pt) cc_final: 0.6810 (mm) REVERT: D 1 MET cc_start: 0.3786 (tpt) cc_final: 0.3556 (pmt) REVERT: D 376 ARG cc_start: 0.7248 (mmm160) cc_final: 0.6351 (mmm160) REVERT: E 56 ASP cc_start: 0.8494 (t0) cc_final: 0.8017 (OUTLIER) REVERT: E 389 MET cc_start: 0.7315 (OUTLIER) cc_final: 0.6957 (tpp) REVERT: E 395 GLU cc_start: 0.8005 (OUTLIER) cc_final: 0.7661 (mp0) REVERT: E 469 MET cc_start: 0.7041 (OUTLIER) cc_final: 0.6578 (mtt) REVERT: F 1 MET cc_start: 0.7248 (ptt) cc_final: 0.6655 (ttt) REVERT: F 389 MET cc_start: 0.8269 (ttm) cc_final: 0.8019 (ttp) outliers start: 57 outliers final: 21 residues processed: 178 average time/residue: 0.7723 time to fit residues: 156.3105 Evaluate side-chains 150 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 125 time to evaluate : 0.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 390 ARG Chi-restraints excluded: chain A residue 448 ILE Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain B residue 125 GLU Chi-restraints excluded: chain B residue 129 ILE Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 390 ARG Chi-restraints excluded: chain B residue 496 LYS Chi-restraints excluded: chain C residue 68 GLU Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 223 VAL Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain C residue 314 THR Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain D residue 285 MET Chi-restraints excluded: chain D residue 301 THR Chi-restraints excluded: chain E residue 341 TYR Chi-restraints excluded: chain E residue 389 MET Chi-restraints excluded: chain E residue 395 GLU Chi-restraints excluded: chain E residue 456 VAL Chi-restraints excluded: chain E residue 469 MET Chi-restraints excluded: chain F residue 301 THR Chi-restraints excluded: chain G residue 179 ILE Chi-restraints excluded: chain G residue 273 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 50 optimal weight: 5.9990 chunk 229 optimal weight: 10.0000 chunk 33 optimal weight: 6.9990 chunk 237 optimal weight: 10.0000 chunk 5 optimal weight: 0.9990 chunk 38 optimal weight: 8.9990 chunk 182 optimal weight: 0.5980 chunk 236 optimal weight: 1.9990 chunk 123 optimal weight: 8.9990 chunk 172 optimal weight: 0.3980 chunk 196 optimal weight: 0.3980 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 381 GLN F 330 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.093460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.073103 restraints weight = 48009.538| |-----------------------------------------------------------------------------| r_work (start): 0.2994 rms_B_bonded: 2.25 r_work: 0.2885 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2766 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.2766 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8824 moved from start: 0.1591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 24688 Z= 0.096 Angle : 0.472 8.141 33485 Z= 0.246 Chirality : 0.043 0.147 3856 Planarity : 0.004 0.065 4363 Dihedral : 7.437 169.956 3582 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.10 % Allowed : 1.93 % Favored : 97.98 % Rotamer: Outliers : 1.79 % Allowed : 11.10 % Favored : 87.11 % 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: 1.36 (0.15), residues: 3115 helix: 1.93 (0.15), residues: 1238 sheet: 0.57 (0.22), residues: 557 loop : 0.15 (0.17), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG E 333 TYR 0.028 0.001 TYR G 100 PHE 0.013 0.001 PHE B 444 HIS 0.003 0.000 HIS D 363 Details of bonding type rmsd covalent geometry : bond 0.00209 (24688) covalent geometry : angle 0.47189 (33485) hydrogen bonds : bond 0.03594 ( 1152) hydrogen bonds : angle 4.37452 ( 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 184 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 138 time to evaluate : 0.983 Fit side-chains revert: symmetry clash REVERT: A 390 ARG cc_start: 0.8676 (OUTLIER) cc_final: 0.7756 (ttm110) REVERT: B 60 MET cc_start: 0.9313 (mmt) cc_final: 0.9012 (mmt) REVERT: B 89 ARG cc_start: 0.8600 (ptp-110) cc_final: 0.8303 (ptm160) REVERT: C 272 GLU cc_start: 0.8983 (tt0) cc_final: 0.8756 (tt0) REVERT: C 384 LEU cc_start: 0.7480 (pt) cc_final: 0.6817 (mm) REVERT: D 376 ARG cc_start: 0.7181 (mmm160) cc_final: 0.6454 (mmm160) REVERT: E 56 ASP cc_start: 0.8485 (t0) cc_final: 0.8014 (OUTLIER) REVERT: E 378 LYS cc_start: 0.8930 (tptp) cc_final: 0.8631 (tptp) REVERT: E 389 MET cc_start: 0.7125 (OUTLIER) cc_final: 0.6751 (tpp) REVERT: E 395 GLU cc_start: 0.7916 (OUTLIER) cc_final: 0.7649 (mp0) REVERT: E 469 MET cc_start: 0.7052 (OUTLIER) cc_final: 0.6585 (mtt) REVERT: F 1 MET cc_start: 0.7219 (ptt) cc_final: 0.6633 (ttt) REVERT: F 213 MET cc_start: 0.9286 (mtp) cc_final: 0.8929 (mtt) REVERT: F 389 MET cc_start: 0.8297 (ttm) cc_final: 0.8000 (ttp) outliers start: 46 outliers final: 19 residues processed: 172 average time/residue: 0.8054 time to fit residues: 157.2280 Evaluate side-chains 151 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 129 time to evaluate : 1.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 390 ARG Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain B residue 125 GLU Chi-restraints excluded: chain B residue 129 ILE Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 496 LYS Chi-restraints excluded: chain C residue 68 GLU Chi-restraints excluded: chain C residue 223 VAL Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain C residue 314 THR Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain D residue 285 MET Chi-restraints excluded: chain D residue 301 THR Chi-restraints excluded: chain E residue 358 ILE Chi-restraints excluded: chain E residue 389 MET Chi-restraints excluded: chain E residue 395 GLU Chi-restraints excluded: chain E residue 456 VAL Chi-restraints excluded: chain E residue 469 MET Chi-restraints excluded: chain F residue 301 THR Chi-restraints excluded: chain G residue 179 ILE Chi-restraints excluded: chain G residue 273 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 123 optimal weight: 8.9990 chunk 3 optimal weight: 7.9990 chunk 304 optimal weight: 6.9990 chunk 253 optimal weight: 9.9990 chunk 161 optimal weight: 3.9990 chunk 20 optimal weight: 0.4980 chunk 105 optimal weight: 0.9990 chunk 163 optimal weight: 0.2980 chunk 91 optimal weight: 8.9990 chunk 226 optimal weight: 20.0000 chunk 217 optimal weight: 10.0000 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 407 GLN D 8 GLN E 381 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.091080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.070561 restraints weight = 48238.291| |-----------------------------------------------------------------------------| r_work (start): 0.2940 rms_B_bonded: 2.25 r_work: 0.2830 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2710 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2710 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8875 moved from start: 0.1587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 24688 Z= 0.166 Angle : 0.530 8.008 33485 Z= 0.277 Chirality : 0.045 0.208 3856 Planarity : 0.004 0.073 4363 Dihedral : 7.638 173.617 3580 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.22 % Favored : 97.75 % Rotamer: Outliers : 1.99 % Allowed : 11.33 % Favored : 86.68 % 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: 1.77 (0.15), residues: 1235 sheet: 0.44 (0.22), residues: 555 loop : 0.03 (0.17), residues: 1325 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.000 ARG E 333 TYR 0.036 0.001 TYR G 100 PHE 0.017 0.001 PHE A 395 HIS 0.004 0.001 HIS A 215 Details of bonding type rmsd covalent geometry : bond 0.00401 (24688) covalent geometry : angle 0.52989 (33485) hydrogen bonds : bond 0.04504 ( 1152) hydrogen bonds : angle 4.54293 ( 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 179 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 128 time to evaluate : 1.057 Fit side-chains REVERT: A 87 GLU cc_start: 0.8717 (OUTLIER) cc_final: 0.8462 (tm-30) REVERT: A 390 ARG cc_start: 0.8764 (OUTLIER) cc_final: 0.7892 (ttm110) REVERT: B 89 ARG cc_start: 0.8607 (ptp-110) cc_final: 0.8298 (ptm160) REVERT: B 392 LEU cc_start: 0.8187 (OUTLIER) cc_final: 0.7919 (tm) REVERT: C 384 LEU cc_start: 0.7538 (pt) cc_final: 0.6801 (mm) REVERT: C 392 LEU cc_start: 0.7452 (mp) cc_final: 0.7028 (mp) REVERT: D 376 ARG cc_start: 0.7198 (mmm160) cc_final: 0.6425 (mmm160) REVERT: E 56 ASP cc_start: 0.8523 (t0) cc_final: 0.8071 (t0) REVERT: E 389 MET cc_start: 0.7111 (OUTLIER) cc_final: 0.6617 (tmt) REVERT: E 395 GLU cc_start: 0.8064 (OUTLIER) cc_final: 0.7708 (mp0) REVERT: E 469 MET cc_start: 0.7063 (OUTLIER) cc_final: 0.6612 (mtt) REVERT: F 1 MET cc_start: 0.7303 (ptt) cc_final: 0.6680 (ttt) outliers start: 51 outliers final: 21 residues processed: 165 average time/residue: 0.8063 time to fit residues: 151.3865 Evaluate side-chains 152 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 125 time to evaluate : 1.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 GLU Chi-restraints excluded: chain A residue 390 ARG Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain B residue 125 GLU Chi-restraints excluded: chain B residue 129 ILE Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 392 LEU Chi-restraints excluded: chain B residue 496 LYS Chi-restraints excluded: chain C residue 68 GLU Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 223 VAL Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain C residue 314 THR Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain D residue 285 MET Chi-restraints excluded: chain D residue 301 THR Chi-restraints excluded: chain E residue 341 TYR Chi-restraints excluded: chain E residue 358 ILE Chi-restraints excluded: chain E residue 389 MET Chi-restraints excluded: chain E residue 395 GLU Chi-restraints excluded: chain E residue 456 VAL Chi-restraints excluded: chain E residue 469 MET Chi-restraints excluded: chain F residue 301 THR Chi-restraints excluded: chain G residue 179 ILE Chi-restraints excluded: chain G residue 273 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 29 optimal weight: 0.9990 chunk 144 optimal weight: 1.9990 chunk 8 optimal weight: 0.9990 chunk 245 optimal weight: 5.9990 chunk 22 optimal weight: 0.8980 chunk 215 optimal weight: 0.9980 chunk 165 optimal weight: 8.9990 chunk 10 optimal weight: 3.9990 chunk 70 optimal weight: 5.9990 chunk 272 optimal weight: 4.9990 chunk 13 optimal weight: 4.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 407 GLN D 330 ASN E 381 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.092862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.072427 restraints weight = 47918.952| |-----------------------------------------------------------------------------| r_work (start): 0.2979 rms_B_bonded: 2.24 r_work: 0.2869 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2750 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2750 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8839 moved from start: 0.1672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 24688 Z= 0.107 Angle : 0.485 8.166 33485 Z= 0.252 Chirality : 0.043 0.152 3856 Planarity : 0.004 0.075 4363 Dihedral : 7.324 165.977 3580 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.09 % Favored : 97.88 % Rotamer: Outliers : 1.52 % Allowed : 11.92 % Favored : 86.57 % 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: 1.28 (0.15), residues: 3115 helix: 1.86 (0.15), residues: 1244 sheet: 0.51 (0.22), residues: 545 loop : 0.12 (0.17), residues: 1326 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.000 ARG E 333 TYR 0.036 0.001 TYR G 100 PHE 0.025 0.001 PHE C 463 HIS 0.003 0.001 HIS D 363 Details of bonding type rmsd covalent geometry : bond 0.00242 (24688) covalent geometry : angle 0.48514 (33485) hydrogen bonds : bond 0.03739 ( 1152) hydrogen bonds : angle 4.41270 ( 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 175 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 136 time to evaluate : 1.116 Fit side-chains REVERT: A 390 ARG cc_start: 0.8727 (OUTLIER) cc_final: 0.7860 (ttm110) REVERT: B 89 ARG cc_start: 0.8611 (ptp-110) cc_final: 0.8309 (ptm160) REVERT: B 392 LEU cc_start: 0.8212 (OUTLIER) cc_final: 0.7953 (tm) REVERT: C 384 LEU cc_start: 0.7502 (pt) cc_final: 0.6745 (mm) REVERT: C 392 LEU cc_start: 0.7476 (mp) cc_final: 0.7056 (mp) REVERT: C 407 GLN cc_start: 0.7623 (OUTLIER) cc_final: 0.7193 (mp10) REVERT: D 376 ARG cc_start: 0.7183 (mmm160) cc_final: 0.6390 (mmm160) REVERT: E 56 ASP cc_start: 0.8509 (t0) cc_final: 0.8040 (OUTLIER) REVERT: E 378 LYS cc_start: 0.8926 (tptp) cc_final: 0.8612 (tptp) REVERT: E 389 MET cc_start: 0.7138 (OUTLIER) cc_final: 0.6680 (tmt) REVERT: E 395 GLU cc_start: 0.8057 (OUTLIER) cc_final: 0.7767 (mp0) REVERT: E 469 MET cc_start: 0.7042 (OUTLIER) cc_final: 0.6580 (mtt) REVERT: F 1 MET cc_start: 0.7277 (ptt) cc_final: 0.6696 (ttt) outliers start: 39 outliers final: 21 residues processed: 164 average time/residue: 0.8346 time to fit residues: 155.0263 Evaluate side-chains 154 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 128 time to evaluate : 1.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 390 ARG Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain B residue 125 GLU Chi-restraints excluded: chain B residue 129 ILE Chi-restraints excluded: chain B residue 392 LEU Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 144 GLU Chi-restraints excluded: chain C residue 223 VAL Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain C residue 314 THR Chi-restraints excluded: chain C residue 407 GLN Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain D residue 285 MET Chi-restraints excluded: chain D residue 301 THR Chi-restraints excluded: chain E residue 341 TYR Chi-restraints excluded: chain E residue 358 ILE Chi-restraints excluded: chain E residue 389 MET Chi-restraints excluded: chain E residue 395 GLU Chi-restraints excluded: chain E residue 456 VAL Chi-restraints excluded: chain E residue 469 MET Chi-restraints excluded: chain F residue 301 THR Chi-restraints excluded: chain G residue 179 ILE Chi-restraints excluded: chain G residue 272 GLN Chi-restraints excluded: chain G residue 273 GLU 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: 4.9990 chunk 45 optimal weight: 2.9990 chunk 200 optimal weight: 6.9990 chunk 103 optimal weight: 4.9990 chunk 150 optimal weight: 2.9990 chunk 308 optimal weight: 8.9990 chunk 207 optimal weight: 9.9990 chunk 136 optimal weight: 5.9990 chunk 250 optimal weight: 2.9990 chunk 184 optimal weight: 0.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 474 HIS C 407 GLN E 381 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.089896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.069783 restraints weight = 48187.471| |-----------------------------------------------------------------------------| r_work (start): 0.2933 rms_B_bonded: 2.23 r_work: 0.2823 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2703 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2703 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8877 moved from start: 0.1668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 24688 Z= 0.190 Angle : 0.561 10.158 33485 Z= 0.291 Chirality : 0.046 0.217 3856 Planarity : 0.005 0.085 4363 Dihedral : 7.537 167.169 3580 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.41 % Favored : 97.56 % Rotamer: Outliers : 1.64 % Allowed : 12.27 % Favored : 86.10 % 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: 1.05 (0.15), residues: 3115 helix: 1.69 (0.15), residues: 1234 sheet: 0.38 (0.22), residues: 537 loop : -0.01 (0.17), residues: 1344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.000 ARG E 333 TYR 0.037 0.001 TYR G 100 PHE 0.022 0.002 PHE C 463 HIS 0.005 0.001 HIS A 215 Details of bonding type rmsd covalent geometry : bond 0.00462 (24688) covalent geometry : angle 0.56050 (33485) hydrogen bonds : bond 0.04710 ( 1152) hydrogen bonds : angle 4.60379 ( 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 164 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 122 time to evaluate : 1.087 Fit side-chains REVERT: A 87 GLU cc_start: 0.8703 (OUTLIER) cc_final: 0.8449 (tm-30) REVERT: A 390 ARG cc_start: 0.8765 (OUTLIER) cc_final: 0.7907 (ttm110) REVERT: B 89 ARG cc_start: 0.8604 (ptp-110) cc_final: 0.8282 (ptm160) REVERT: B 392 LEU cc_start: 0.8140 (OUTLIER) cc_final: 0.7874 (tm) REVERT: C 392 LEU cc_start: 0.7469 (mp) cc_final: 0.7053 (mp) REVERT: D 376 ARG cc_start: 0.7178 (mmm160) cc_final: 0.6416 (mmm160) REVERT: E 56 ASP cc_start: 0.8535 (t0) cc_final: 0.8070 (t0) REVERT: E 378 LYS cc_start: 0.8948 (tptp) cc_final: 0.8662 (tptp) REVERT: E 389 MET cc_start: 0.7094 (OUTLIER) cc_final: 0.6609 (tmt) REVERT: E 469 MET cc_start: 0.7030 (OUTLIER) cc_final: 0.6575 (mtt) REVERT: F 1 MET cc_start: 0.7345 (ptt) cc_final: 0.6738 (ttt) REVERT: F 213 MET cc_start: 0.9219 (mtp) cc_final: 0.9015 (mtt) REVERT: F 341 TYR cc_start: 0.6605 (OUTLIER) cc_final: 0.5959 (t80) outliers start: 42 outliers final: 23 residues processed: 155 average time/residue: 0.8168 time to fit residues: 144.1291 Evaluate side-chains 149 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 120 time to evaluate : 1.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 GLU Chi-restraints excluded: chain A residue 390 ARG Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 125 GLU Chi-restraints excluded: chain B residue 129 ILE Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 392 LEU Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 144 GLU Chi-restraints excluded: chain C residue 223 VAL Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain C residue 314 THR Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain D residue 285 MET Chi-restraints excluded: chain D residue 301 THR Chi-restraints excluded: chain E residue 234 THR Chi-restraints excluded: chain E residue 341 TYR Chi-restraints excluded: chain E residue 358 ILE Chi-restraints excluded: chain E residue 389 MET Chi-restraints excluded: chain E residue 456 VAL Chi-restraints excluded: chain E residue 469 MET Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 301 THR Chi-restraints excluded: chain F residue 341 TYR Chi-restraints excluded: chain G residue 179 ILE Chi-restraints excluded: chain G residue 272 GLN Chi-restraints excluded: chain G residue 273 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 39 optimal weight: 0.9990 chunk 46 optimal weight: 0.9980 chunk 138 optimal weight: 6.9990 chunk 74 optimal weight: 4.9990 chunk 190 optimal weight: 5.9990 chunk 208 optimal weight: 5.9990 chunk 4 optimal weight: 6.9990 chunk 283 optimal weight: 0.2980 chunk 131 optimal weight: 9.9990 chunk 164 optimal weight: 2.9990 chunk 295 optimal weight: 7.9990 overall best weight: 2.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 407 GLN E 381 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.091081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.071054 restraints weight = 47854.559| |-----------------------------------------------------------------------------| r_work (start): 0.2953 rms_B_bonded: 2.21 r_work: 0.2842 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2723 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8861 moved from start: 0.1684 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= 0.144 Angle : 0.525 10.828 33485 Z= 0.273 Chirality : 0.045 0.190 3856 Planarity : 0.004 0.085 4363 Dihedral : 7.397 163.117 3580 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.15 % Favored : 97.82 % Rotamer: Outliers : 1.56 % Allowed : 12.19 % Favored : 86.25 % 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: 1.10 (0.15), residues: 3115 helix: 1.72 (0.15), residues: 1239 sheet: 0.46 (0.22), residues: 543 loop : -0.01 (0.17), residues: 1333 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.000 ARG E 333 TYR 0.033 0.001 TYR G 100 PHE 0.022 0.001 PHE C 463 HIS 0.003 0.001 HIS E 363 Details of bonding type rmsd covalent geometry : bond 0.00342 (24688) covalent geometry : angle 0.52510 (33485) hydrogen bonds : bond 0.04267 ( 1152) hydrogen bonds : angle 4.54065 ( 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 167 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 127 time to evaluate : 1.075 Fit side-chains REVERT: A 390 ARG cc_start: 0.8751 (OUTLIER) cc_final: 0.7915 (ttm110) REVERT: B 89 ARG cc_start: 0.8595 (ptp-110) cc_final: 0.8275 (ptm160) REVERT: B 392 LEU cc_start: 0.8100 (OUTLIER) cc_final: 0.7854 (tm) REVERT: C 384 LEU cc_start: 0.7594 (pt) cc_final: 0.6802 (mm) REVERT: C 392 LEU cc_start: 0.7480 (mp) cc_final: 0.7071 (mp) REVERT: D 376 ARG cc_start: 0.7160 (mmm160) cc_final: 0.6385 (mmm160) REVERT: E 56 ASP cc_start: 0.8517 (t0) cc_final: 0.8065 (t0) REVERT: E 378 LYS cc_start: 0.8970 (tptp) cc_final: 0.8686 (tptp) REVERT: E 389 MET cc_start: 0.7092 (OUTLIER) cc_final: 0.6611 (tmt) REVERT: E 469 MET cc_start: 0.7067 (OUTLIER) cc_final: 0.6617 (mtt) REVERT: F 1 MET cc_start: 0.7333 (ptt) cc_final: 0.6761 (ttt) REVERT: F 213 MET cc_start: 0.9182 (mtp) cc_final: 0.8969 (mtt) outliers start: 40 outliers final: 23 residues processed: 157 average time/residue: 0.8238 time to fit residues: 147.3486 Evaluate side-chains 149 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 122 time to evaluate : 1.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 390 ARG Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 125 GLU Chi-restraints excluded: chain B residue 129 ILE Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 392 LEU Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 144 GLU Chi-restraints excluded: chain C residue 223 VAL Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain C residue 314 THR Chi-restraints excluded: chain C residue 450 VAL Chi-restraints excluded: chain C residue 452 ASP Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain D residue 285 MET Chi-restraints excluded: chain D residue 301 THR Chi-restraints excluded: chain E residue 341 TYR Chi-restraints excluded: chain E residue 358 ILE Chi-restraints excluded: chain E residue 389 MET Chi-restraints excluded: chain E residue 456 VAL Chi-restraints excluded: chain E residue 469 MET Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 301 THR Chi-restraints excluded: chain G residue 179 ILE Chi-restraints excluded: chain G residue 273 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 64 optimal weight: 0.6980 chunk 212 optimal weight: 6.9990 chunk 271 optimal weight: 8.9990 chunk 280 optimal weight: 0.9990 chunk 174 optimal weight: 0.8980 chunk 122 optimal weight: 10.0000 chunk 266 optimal weight: 3.9990 chunk 276 optimal weight: 2.9990 chunk 172 optimal weight: 0.8980 chunk 137 optimal weight: 0.9990 chunk 269 optimal weight: 5.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- 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** C 407 GLN E 381 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.093330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.072933 restraints weight = 48032.386| |-----------------------------------------------------------------------------| r_work (start): 0.2987 rms_B_bonded: 2.25 r_work: 0.2878 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2759 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8829 moved from start: 0.1783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 24688 Z= 0.099 Angle : 0.487 10.353 33485 Z= 0.252 Chirality : 0.043 0.151 3856 Planarity : 0.004 0.080 4363 Dihedral : 7.112 159.197 3580 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.12 % Favored : 97.85 % Rotamer: Outliers : 1.01 % Allowed : 12.62 % Favored : 86.37 % 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: 1241 sheet: 0.54 (0.22), residues: 535 loop : 0.13 (0.17), residues: 1339 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.000 ARG E 333 TYR 0.025 0.001 TYR G 100 PHE 0.021 0.001 PHE C 463 HIS 0.003 0.001 HIS D 363 Details of bonding type rmsd covalent geometry : bond 0.00220 (24688) covalent geometry : angle 0.48673 (33485) hydrogen bonds : bond 0.03551 ( 1152) hydrogen bonds : angle 4.38452 ( 3276) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7407.62 seconds wall clock time: 127 minutes 14.99 seconds (7634.99 seconds total)