Starting phenix.real_space_refine on Sun Jul 5 00:21:27 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8hh3_34750/07_2026/8hh3_34750.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hh3_34750/07_2026/8hh3_34750.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8hh3_34750/07_2026/8hh3_34750.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hh3_34750/07_2026/8hh3_34750.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8hh3_34750/07_2026/8hh3_34750.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8hh3_34750/07_2026/8hh3_34750.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8hh3_34750/07_2026/8hh3_34750.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hh3_34750/07_2026/8hh3_34750.map" } resolution = 4.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 19 5.49 5 Mg 5 5.21 5 S 77 5.16 5 C 15287 2.51 5 N 4219 2.21 5 O 4674 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.08s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 24281 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 3661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 478, 3661 Classifications: {'peptide': 478} Link IDs: {'PTRANS': 23, 'TRANS': 454} Chain: "B" Number of atoms: 3661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 478, 3661 Classifications: {'peptide': 478} Link IDs: {'PTRANS': 23, 'TRANS': 454} Chain: "C" Number of atoms: 3661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 478, 3661 Classifications: {'peptide': 478} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 454} Chain: "D" Number of atoms: 3630 Number of conformers: 1 Conformer: "" Number of residues, atoms: 471, 3630 Classifications: {'peptide': 471} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 447} Chain: "E" Number of atoms: 3623 Number of conformers: 1 Conformer: "" Number of residues, atoms: 470, 3623 Classifications: {'peptide': 470} Link IDs: {'PTRANS': 23, 'TRANS': 446} Chain: "F" Number of atoms: 3630 Number of conformers: 1 Conformer: "" Number of residues, atoms: 471, 3630 Classifications: {'peptide': 471} Link IDs: {'PTRANS': 23, 'TRANS': 447} Chain: "G" Number of atoms: 2218 Number of conformers: 1 Conformer: "" Number of residues, atoms: 283, 2218 Classifications: {'peptide': 283} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 272} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, 'ADP': 1, 'PO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 36 Unusual residues: {'ATP': 1, 'PO4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 5.66, per 1000 atoms: 0.23 Number of scatterers: 24281 At special positions: 0 Unit cell: (125.84, 127.6, 157.52, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 77 16.00 P 19 15.00 Mg 5 11.99 O 4674 8.00 N 4219 7.00 C 15287 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.93 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 0.73 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: 4.65 Time building geometry restraints manager: 2.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 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: 14571 30.76 - 61.52: 309 61.52 - 92.28: 56 92.28 - 123.03: 0 123.03 - 153.79: 2 Dihedral angle restraints: 14938 sinusoidal: 6013 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 14935 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.151: 3843 0.151 - 0.303: 8 0.303 - 0.454: 2 0.454 - 0.605: 2 0.605 - 0.757: 1 Chirality restraints: 3856 Sorted by residual: chirality pdb=" CA TYR F 341 " pdb=" N TYR F 341 " pdb=" C TYR F 341 " pdb=" CB TYR F 341 " both_signs ideal model delta sigma weight residual False 2.51 1.75 0.76 2.00e-01 2.50e+01 1.43e+01 chirality pdb=" CA TYR E 341 " pdb=" N TYR E 341 " pdb=" C TYR E 341 " pdb=" CB TYR E 341 " both_signs ideal model delta sigma weight residual False 2.51 1.94 0.57 2.00e-01 2.50e+01 8.13e+00 chirality pdb=" CA THR B 381 " pdb=" N THR B 381 " pdb=" C THR B 381 " pdb=" CB THR B 381 " both_signs ideal model delta sigma weight residual False 2.53 2.02 0.51 2.00e-01 2.50e+01 6.42e+00 ... (remaining 3853 not shown) Planarity restraints: 4363 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE E 340 " 0.020 2.00e-02 2.50e+03 4.01e-02 1.60e+01 pdb=" C ILE E 340 " -0.069 2.00e-02 2.50e+03 pdb=" O ILE E 340 " 0.026 2.00e-02 2.50e+03 pdb=" N TYR E 341 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE E 383 " -0.018 2.00e-02 2.50e+03 3.60e-02 1.29e+01 pdb=" C ILE E 383 " 0.062 2.00e-02 2.50e+03 pdb=" O ILE E 383 " -0.023 2.00e-02 2.50e+03 pdb=" N ILE E 384 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP B 385 " -0.017 2.00e-02 2.50e+03 3.40e-02 1.16e+01 pdb=" C ASP B 385 " 0.059 2.00e-02 2.50e+03 pdb=" O ASP B 385 " -0.022 2.00e-02 2.50e+03 pdb=" N LEU B 386 " -0.020 2.00e-02 2.50e+03 ... (remaining 4360 not shown) Histogram of nonbonded interaction distances: 1.69 - 2.33: 22 2.33 - 2.97: 11559 2.97 - 3.62: 35306 3.62 - 4.26: 55629 4.26 - 4.90: 95698 Nonbonded interactions: 198214 Sorted by model distance: nonbonded pdb=" OG1 THR D 165 " pdb="MG MG D 502 " model vdw 1.690 2.170 nonbonded pdb=" O2G ATP B 600 " pdb="MG MG B 601 " model vdw 1.992 2.170 nonbonded pdb=" OG1 THR F 165 " pdb="MG MG F 601 " model vdw 1.994 2.170 nonbonded pdb=" OG1 THR C 176 " pdb="MG MG C 601 " model vdw 1.994 2.170 nonbonded pdb=" OG1 THR B 176 " pdb="MG MG B 601 " model vdw 2.003 2.170 ... (remaining 198209 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 24 through 501) selection = (chain 'B' and resid 24 through 501) selection = (chain 'C' and resid 24 through 501) } ncs_group { reference = (chain 'D' and resid 1 through 470) selection = (chain 'E' and resid 1 through 470) selection = (chain 'F' and resid 1 through 470) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.380 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.460 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 22.740 Find NCS groups from input model: 0.720 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 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 : 13.555 153.792 9226 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 are 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/Z covalent geometry : bond 0.00397 / 0.24 (24688) covalent geometry : angle 0.64290 / 0.39 (33485) hydrogen bonds : bond 0.15010 / 10.21 ( 1152) hydrogen bonds : angle 6.13327 / 4.30 ( 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 : 1.016 Fit side-chains REVERT: A 87 GLU cc_start: 0.8252 (tt0) cc_final: 0.7689 (tt0) REVERT: B 60 MET cc_start: 0.8717 (mmt) cc_final: 0.8352 (mmt) REVERT: B 373 LYS cc_start: 0.8423 (ttpt) cc_final: 0.8069 (ttpp) REVERT: B 451 GLU cc_start: 0.7715 (tt0) cc_final: 0.7125 (tp30) REVERT: C 109 ASN cc_start: 0.8404 (t0) cc_final: 0.7986 (t0) REVERT: C 272 GLU cc_start: 0.7742 (tt0) cc_final: 0.7172 (tt0) REVERT: C 457 GLU cc_start: 0.7709 (tt0) cc_final: 0.7449 (tt0) REVERT: D 334 LYS cc_start: 0.8099 (ttmm) cc_final: 0.7896 (ttmt) REVERT: D 376 ARG cc_start: 0.7188 (mmm160) cc_final: 0.6743 (mmm160) REVERT: D 389 MET cc_start: 0.7395 (mmt) cc_final: 0.7019 (mmm) REVERT: E 56 ASP cc_start: 0.7588 (t0) cc_final: 0.7213 (t0) REVERT: F 389 MET cc_start: 0.6932 (ttm) cc_final: 0.6641 (ttp) REVERT: F 390 ASP cc_start: 0.8181 (m-30) cc_final: 0.7961 (m-30) REVERT: G 222 GLU cc_start: 0.7870 (OUTLIER) cc_final: 0.7660 (mm-30) REVERT: G 225 ILE cc_start: 0.7474 (OUTLIER) cc_final: 0.7254 (mp) outliers start: 13 outliers final: 5 residues processed: 237 average time/residue: 0.1880 time to fit residues: 68.2310 Evaluate side-chains 158 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 151 time to evaluate : 0.907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 197 optimal weight: 2.9990 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 7.9990 chunk 132 optimal weight: 8.9990 chunk 261 optimal weight: 7.9990 chunk 248 optimal weight: 7.9990 chunk 207 optimal weight: 4.9990 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 6.9990 chunk 183 optimal weight: 0.0870 chunk 298 optimal weight: 9.9990 overall best weight: 4.0166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 467 ASN D 365 GLN E 371 GLN E 381 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2661 r_free = 0.2661 target = 0.064284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2405 r_free = 0.2405 target = 0.052953 restraints weight = 57334.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2400 r_free = 0.2400 target = 0.052777 restraints weight = 53687.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2402 r_free = 0.2402 target = 0.052895 restraints weight = 49609.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2403 r_free = 0.2403 target = 0.052945 restraints weight = 47352.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2404 r_free = 0.2404 target = 0.052994 restraints weight = 44049.515| |-----------------------------------------------------------------------------| r_work (final): 0.2394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.1126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 24688 Z= 0.247 Angle : 0.613 7.552 33485 Z= 0.323 Chirality : 0.049 0.239 3856 Planarity : 0.005 0.060 4363 Dihedral : 6.395 179.886 3425 Min Nonbonded Distance : 1.856 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.34 % Favored : 97.56 % Rotamer: Outliers : 0.16 % Allowed : 4.32 % Favored : 95.52 % 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 are not related in a simple way. whole: 0.73 (0.15), residues: 3115 helix: 1.26 (0.15), residues: 1239 sheet: 0.40 (0.22), residues: 545 loop : -0.11 (0.17), residues: 1331 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 193 TYR 0.016 0.002 TYR G 100 PHE 0.019 0.002 PHE D 257 HIS 0.007 0.001 HIS A 215 Details of bonding type rmsd/Z covalent geometry : bond 0.00608 / 0.25 (24688) covalent geometry : angle 0.61346 / 0.32 (33485) hydrogen bonds : bond 0.05630 / 3.76 ( 1152) hydrogen bonds : angle 4.98884 / 3.50 ( 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 179 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 175 time to evaluate : 0.911 Fit side-chains revert: symmetry clash REVERT: A 68 GLU cc_start: 0.6719 (tm-30) cc_final: 0.6370 (tm-30) REVERT: A 87 GLU cc_start: 0.7877 (tt0) cc_final: 0.7206 (tt0) REVERT: B 381 THR cc_start: 0.6298 (m) cc_final: 0.5719 (m) REVERT: B 383 ARG cc_start: 0.6488 (tpt-90) cc_final: 0.6213 (tpt170) REVERT: B 451 GLU cc_start: 0.7221 (tt0) cc_final: 0.6960 (tp30) REVERT: B 465 ASP cc_start: 0.7741 (t70) cc_final: 0.7487 (t0) REVERT: C 191 MET cc_start: 0.7651 (ttm) cc_final: 0.7293 (ttm) REVERT: C 272 GLU cc_start: 0.7949 (tt0) cc_final: 0.7492 (tt0) REVERT: D 338 MET cc_start: 0.7011 (mtp) cc_final: 0.6802 (mtp) REVERT: E 56 ASP cc_start: 0.7400 (t0) cc_final: 0.6972 (t0) REVERT: E 334 LYS cc_start: 0.7878 (mmtt) cc_final: 0.7652 (mmtm) REVERT: E 387 LEU cc_start: 0.6254 (tt) cc_final: 0.5483 (mt) REVERT: G 136 ASP cc_start: 0.7165 (p0) cc_final: 0.6745 (p0) REVERT: G 167 GLU cc_start: 0.6567 (mt-10) cc_final: 0.6343 (mt-10) REVERT: G 249 ASP cc_start: 0.7513 (m-30) cc_final: 0.7303 (m-30) outliers start: 4 outliers final: 2 residues processed: 179 average time/residue: 0.1916 time to fit residues: 52.9126 Evaluate side-chains 141 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 139 time to evaluate : 0.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 176 optimal weight: 6.9990 chunk 23 optimal weight: 4.9990 chunk 284 optimal weight: 0.9990 chunk 41 optimal weight: 5.9990 chunk 228 optimal weight: 7.9990 chunk 149 optimal weight: 0.0270 chunk 133 optimal weight: 0.9980 chunk 216 optimal weight: 3.9990 chunk 305 optimal weight: 4.9990 chunk 99 optimal weight: 0.9980 chunk 85 optimal weight: 0.1980 overall best weight: 0.6440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.2720 r_free = 0.2720 target = 0.067210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2474 r_free = 0.2474 target = 0.056005 restraints weight = 56165.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2471 r_free = 0.2471 target = 0.055910 restraints weight = 48985.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2474 r_free = 0.2474 target = 0.056075 restraints weight = 44845.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2479 r_free = 0.2479 target = 0.056286 restraints weight = 41498.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2480 r_free = 0.2480 target = 0.056315 restraints weight = 37934.561| |-----------------------------------------------------------------------------| r_work (final): 0.2468 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.1235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 24688 Z= 0.100 Angle : 0.484 5.791 33485 Z= 0.254 Chirality : 0.043 0.139 3856 Planarity : 0.004 0.068 4363 Dihedral : 5.947 174.591 3425 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.10 % Allowed : 1.54 % Favored : 98.36 % Rotamer: Outliers : 0.08 % Allowed : 2.22 % Favored : 97.70 % 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 are not related in a simple way. whole: 1.14 (0.15), residues: 3115 helix: 1.63 (0.15), residues: 1243 sheet: 0.55 (0.22), residues: 533 loop : 0.11 (0.17), residues: 1339 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 405 TYR 0.014 0.001 TYR G 100 PHE 0.019 0.001 PHE F 322 HIS 0.006 0.001 HIS A 425 Details of bonding type rmsd/Z covalent geometry : bond 0.00210 / 0.10 (24688) covalent geometry : angle 0.48428 / 0.25 (33485) hydrogen bonds : bond 0.03986 / 2.67 ( 1152) hydrogen bonds : angle 4.63198 / 3.25 ( 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 200 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 198 time to evaluate : 0.967 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 68 GLU cc_start: 0.6826 (tm-30) cc_final: 0.6467 (tm-30) REVERT: A 87 GLU cc_start: 0.7812 (tt0) cc_final: 0.7205 (tt0) REVERT: B 32 ILE cc_start: 0.8761 (mt) cc_final: 0.8438 (mm) REVERT: B 89 ARG cc_start: 0.6302 (ptp-110) cc_final: 0.6043 (ptp-170) REVERT: B 465 ASP cc_start: 0.7555 (t70) cc_final: 0.7347 (t0) REVERT: C 191 MET cc_start: 0.7669 (ttm) cc_final: 0.7345 (ttm) REVERT: C 272 GLU cc_start: 0.7802 (tt0) cc_final: 0.7224 (tt0) REVERT: D 376 ARG cc_start: 0.6616 (mmm160) cc_final: 0.6128 (mmm160) REVERT: E 56 ASP cc_start: 0.7349 (t0) cc_final: 0.6883 (t0) outliers start: 2 outliers final: 0 residues processed: 200 average time/residue: 0.1999 time to fit residues: 60.2466 Evaluate side-chains 140 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 140 time to evaluate : 0.884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 235 optimal weight: 7.9990 chunk 8 optimal weight: 2.9990 chunk 22 optimal weight: 3.9990 chunk 107 optimal weight: 9.9990 chunk 67 optimal weight: 10.0000 chunk 128 optimal weight: 9.9990 chunk 144 optimal weight: 2.9990 chunk 300 optimal weight: 8.9990 chunk 203 optimal weight: 9.9990 chunk 241 optimal weight: 9.9990 chunk 245 optimal weight: 9.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 179 HIS E 381 GLN E 401 HIS G 174 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2644 r_free = 0.2644 target = 0.063521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2385 r_free = 0.2385 target = 0.052340 restraints weight = 57417.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2380 r_free = 0.2380 target = 0.052146 restraints weight = 52331.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2382 r_free = 0.2382 target = 0.052214 restraints weight = 48594.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2383 r_free = 0.2383 target = 0.052256 restraints weight = 43556.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2384 r_free = 0.2384 target = 0.052318 restraints weight = 42226.052| |-----------------------------------------------------------------------------| r_work (final): 0.2374 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.1529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.053 24688 Z= 0.318 Angle : 0.655 7.290 33485 Z= 0.343 Chirality : 0.051 0.237 3856 Planarity : 0.005 0.063 4363 Dihedral : 6.446 173.497 3425 Min Nonbonded Distance : 1.854 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.73 % Favored : 97.17 % Rotamer: Outliers : 0.08 % Allowed : 3.23 % Favored : 96.69 % 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 are not related in a simple way. whole: 0.58 (0.15), residues: 3115 helix: 1.18 (0.15), residues: 1234 sheet: 0.32 (0.22), residues: 542 loop : -0.24 (0.17), residues: 1339 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 106 TYR 0.019 0.002 TYR G 100 PHE 0.017 0.002 PHE A 395 HIS 0.006 0.001 HIS A 215 Details of bonding type rmsd/Z covalent geometry : bond 0.00779 / 0.32 (24688) covalent geometry : angle 0.65508 / 0.34 (33485) hydrogen bonds : bond 0.06000 / 4.00 ( 1152) hydrogen bonds : angle 4.97636 / 3.50 ( 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 157 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 155 time to evaluate : 0.995 Fit side-chains revert: symmetry clash REVERT: A 68 GLU cc_start: 0.7019 (tm-30) cc_final: 0.6650 (tm-30) REVERT: A 87 GLU cc_start: 0.7866 (tt0) cc_final: 0.7126 (tt0) REVERT: B 465 ASP cc_start: 0.7681 (t70) cc_final: 0.7456 (t0) REVERT: C 191 MET cc_start: 0.7861 (ttm) cc_final: 0.7507 (ttm) REVERT: C 272 GLU cc_start: 0.7976 (tt0) cc_final: 0.7562 (tt0) REVERT: E 56 ASP cc_start: 0.7432 (t0) cc_final: 0.6988 (t0) REVERT: E 395 GLU cc_start: 0.7680 (mp0) cc_final: 0.7464 (mp0) REVERT: G 166 ASP cc_start: 0.6928 (p0) cc_final: 0.6674 (p0) outliers start: 2 outliers final: 1 residues processed: 157 average time/residue: 0.1848 time to fit residues: 44.9717 Evaluate side-chains 133 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 132 time to evaluate : 0.978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 118 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 chunk 190 optimal weight: 5.9990 chunk 200 optimal weight: 0.9990 chunk 156 optimal weight: 0.9990 chunk 284 optimal weight: 4.9990 chunk 137 optimal weight: 4.9990 chunk 101 optimal weight: 0.9990 chunk 209 optimal weight: 2.9990 chunk 232 optimal weight: 4.9990 chunk 197 optimal weight: 0.5980 overall best weight: 1.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 196 ASN ** E 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 381 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2707 r_free = 0.2707 target = 0.066628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2460 r_free = 0.2460 target = 0.055634 restraints weight = 55675.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2452 r_free = 0.2452 target = 0.055309 restraints weight = 52347.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2454 r_free = 0.2454 target = 0.055377 restraints weight = 48713.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2456 r_free = 0.2456 target = 0.055489 restraints weight = 43548.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2457 r_free = 0.2457 target = 0.055537 restraints weight = 41212.705| |-----------------------------------------------------------------------------| r_work (final): 0.2447 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.1461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 24688 Z= 0.110 Angle : 0.497 5.978 33485 Z= 0.261 Chirality : 0.044 0.154 3856 Planarity : 0.004 0.060 4363 Dihedral : 6.051 179.318 3425 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.10 % Allowed : 1.83 % Favored : 98.07 % Rotamer: Outliers : 0.04 % Allowed : 1.60 % Favored : 98.36 % 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 are not related in a simple way. whole: 0.95 (0.15), residues: 3115 helix: 1.57 (0.15), residues: 1234 sheet: 0.44 (0.22), residues: 540 loop : -0.08 (0.17), residues: 1341 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 333 TYR 0.015 0.001 TYR G 100 PHE 0.019 0.001 PHE C 343 HIS 0.005 0.001 HIS A 425 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.11 (24688) covalent geometry : angle 0.49653 / 0.26 (33485) hydrogen bonds : bond 0.04062 / 2.72 ( 1152) hydrogen bonds : angle 4.63078 / 3.26 ( 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 178 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 177 time to evaluate : 0.957 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 68 GLU cc_start: 0.7073 (tm-30) cc_final: 0.6704 (tm-30) REVERT: A 87 GLU cc_start: 0.7797 (tt0) cc_final: 0.7147 (tt0) REVERT: B 465 ASP cc_start: 0.7587 (t70) cc_final: 0.7337 (t0) REVERT: C 191 MET cc_start: 0.7678 (ttm) cc_final: 0.7328 (ttm) REVERT: C 272 GLU cc_start: 0.7856 (tt0) cc_final: 0.7312 (tt0) REVERT: E 56 ASP cc_start: 0.7389 (t0) cc_final: 0.6953 (t0) REVERT: E 334 LYS cc_start: 0.7884 (mmtt) cc_final: 0.7645 (mmtm) REVERT: E 395 GLU cc_start: 0.7694 (mp0) cc_final: 0.7446 (mp0) REVERT: F 469 MET cc_start: 0.7978 (ptp) cc_final: 0.7650 (ptm) outliers start: 1 outliers final: 0 residues processed: 178 average time/residue: 0.1596 time to fit residues: 44.0746 Evaluate side-chains 134 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 134 time to evaluate : 0.802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 50 optimal weight: 3.9990 chunk 229 optimal weight: 8.9990 chunk 33 optimal weight: 8.9990 chunk 237 optimal weight: 10.0000 chunk 5 optimal weight: 0.9980 chunk 38 optimal weight: 6.9990 chunk 182 optimal weight: 7.9990 chunk 236 optimal weight: 7.9990 chunk 123 optimal weight: 7.9990 chunk 172 optimal weight: 4.9990 chunk 196 optimal weight: 0.7980 overall best weight: 3.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 330 ASN E 381 GLN F 8 GLN ** G 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2662 r_free = 0.2662 target = 0.064396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2407 r_free = 0.2407 target = 0.053212 restraints weight = 56976.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2402 r_free = 0.2402 target = 0.052978 restraints weight = 49569.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2404 r_free = 0.2404 target = 0.053081 restraints weight = 48376.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2406 r_free = 0.2406 target = 0.053205 restraints weight = 43462.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2410 r_free = 0.2410 target = 0.053367 restraints weight = 40301.304| |-----------------------------------------------------------------------------| r_work (final): 0.2399 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.1543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 24688 Z= 0.221 Angle : 0.580 6.346 33485 Z= 0.303 Chirality : 0.048 0.186 3856 Planarity : 0.005 0.058 4363 Dihedral : 6.219 176.973 3425 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.57 % Favored : 97.34 % Rotamer: Outliers : 0.04 % Allowed : 1.91 % Favored : 98.05 % 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 are not related in a simple way. whole: 0.75 (0.15), residues: 3115 helix: 1.41 (0.15), residues: 1234 sheet: 0.36 (0.23), residues: 530 loop : -0.21 (0.17), residues: 1351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 390 TYR 0.014 0.001 TYR G 100 PHE 0.016 0.002 PHE D 257 HIS 0.005 0.001 HIS A 215 Details of bonding type rmsd/Z covalent geometry : bond 0.00544 / 0.22 (24688) covalent geometry : angle 0.57964 / 0.30 (33485) hydrogen bonds : bond 0.05168 / 3.44 ( 1152) hydrogen bonds : angle 4.76215 / 3.35 ( 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 158 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 157 time to evaluate : 0.970 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 87 GLU cc_start: 0.7829 (tt0) cc_final: 0.7172 (tt0) REVERT: B 465 ASP cc_start: 0.7620 (t70) cc_final: 0.7385 (t0) REVERT: C 191 MET cc_start: 0.7733 (ttm) cc_final: 0.7342 (ttm) REVERT: C 272 GLU cc_start: 0.8020 (tt0) cc_final: 0.7554 (tt0) REVERT: E 56 ASP cc_start: 0.7401 (t0) cc_final: 0.6991 (t0) REVERT: E 334 LYS cc_start: 0.7905 (mmtt) cc_final: 0.7690 (mmtm) REVERT: E 395 GLU cc_start: 0.7751 (mp0) cc_final: 0.7476 (mp0) REVERT: F 469 MET cc_start: 0.7960 (ptp) cc_final: 0.7621 (ptm) outliers start: 1 outliers final: 0 residues processed: 158 average time/residue: 0.1769 time to fit residues: 43.3950 Evaluate side-chains 133 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 133 time to evaluate : 0.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 123 optimal weight: 2.9990 chunk 3 optimal weight: 6.9990 chunk 304 optimal weight: 6.9990 chunk 253 optimal weight: 7.9990 chunk 161 optimal weight: 0.0470 chunk 20 optimal weight: 0.9990 chunk 105 optimal weight: 1.9990 chunk 163 optimal weight: 0.8980 chunk 91 optimal weight: 4.9990 chunk 226 optimal weight: 2.9990 chunk 217 optimal weight: 0.4980 overall best weight: 0.8882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 381 GLN F 245 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2709 r_free = 0.2709 target = 0.066821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2462 r_free = 0.2462 target = 0.055646 restraints weight = 56045.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2459 r_free = 0.2459 target = 0.055571 restraints weight = 49075.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2460 r_free = 0.2460 target = 0.055617 restraints weight = 47415.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2461 r_free = 0.2461 target = 0.055662 restraints weight = 43080.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2462 r_free = 0.2462 target = 0.055736 restraints weight = 40535.008| |-----------------------------------------------------------------------------| r_work (final): 0.2453 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.1573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 24688 Z= 0.104 Angle : 0.492 6.211 33485 Z= 0.257 Chirality : 0.043 0.147 3856 Planarity : 0.004 0.058 4363 Dihedral : 5.877 174.454 3425 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.10 % Allowed : 1.73 % Favored : 98.17 % Rotamer: Outliers : 0.04 % Allowed : 0.93 % Favored : 99.03 % 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 are not related in a simple way. whole: 1.07 (0.15), residues: 3115 helix: 1.70 (0.15), residues: 1235 sheet: 0.53 (0.23), residues: 518 loop : -0.06 (0.17), residues: 1362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 333 TYR 0.017 0.001 TYR G 100 PHE 0.016 0.001 PHE C 343 HIS 0.003 0.001 HIS A 425 Details of bonding type rmsd/Z covalent geometry : bond 0.00226 / 0.10 (24688) covalent geometry : angle 0.49153 / 0.26 (33485) hydrogen bonds : bond 0.03874 / 2.59 ( 1152) hydrogen bonds : angle 4.55640 / 3.21 ( 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 167 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 166 time to evaluate : 0.957 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 GLU cc_start: 0.6595 (tm-30) cc_final: 0.6303 (tm-30) REVERT: A 87 GLU cc_start: 0.7677 (tt0) cc_final: 0.7009 (tt0) REVERT: B 465 ASP cc_start: 0.7549 (t70) cc_final: 0.7305 (t0) REVERT: C 191 MET cc_start: 0.7666 (ttm) cc_final: 0.7328 (ttm) REVERT: C 272 GLU cc_start: 0.7927 (tt0) cc_final: 0.7386 (tt0) REVERT: C 407 GLN cc_start: 0.7911 (mt0) cc_final: 0.6689 (tp40) REVERT: E 56 ASP cc_start: 0.7384 (t0) cc_final: 0.7001 (t0) REVERT: E 395 GLU cc_start: 0.7773 (mp0) cc_final: 0.7482 (mp0) outliers start: 1 outliers final: 0 residues processed: 167 average time/residue: 0.1815 time to fit residues: 47.1542 Evaluate side-chains 139 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 139 time to evaluate : 0.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 29 optimal weight: 5.9990 chunk 144 optimal weight: 1.9990 chunk 8 optimal weight: 0.9980 chunk 245 optimal weight: 2.9990 chunk 22 optimal weight: 0.2980 chunk 215 optimal weight: 0.5980 chunk 165 optimal weight: 7.9990 chunk 10 optimal weight: 0.6980 chunk 70 optimal weight: 2.9990 chunk 272 optimal weight: 1.9990 chunk 13 optimal weight: 4.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 381 GLN G 130 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2719 r_free = 0.2719 target = 0.067263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2474 r_free = 0.2474 target = 0.056136 restraints weight = 55820.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2472 r_free = 0.2472 target = 0.056030 restraints weight = 46897.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2474 r_free = 0.2474 target = 0.056141 restraints weight = 42529.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2476 r_free = 0.2476 target = 0.056220 restraints weight = 39786.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2480 r_free = 0.2480 target = 0.056414 restraints weight = 37007.462| |-----------------------------------------------------------------------------| r_work (final): 0.2472 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.1642 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= 0.101 Angle : 0.490 7.616 33485 Z= 0.254 Chirality : 0.044 0.146 3856 Planarity : 0.004 0.056 4363 Dihedral : 5.722 170.509 3425 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.10 % Allowed : 1.86 % Favored : 98.04 % Rotamer: Outliers : 0.04 % Allowed : 0.74 % Favored : 99.22 % 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 are not related in a simple way. whole: 1.25 (0.15), residues: 3115 helix: 1.85 (0.15), residues: 1233 sheet: 0.59 (0.22), residues: 526 loop : 0.06 (0.17), residues: 1356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 390 TYR 0.012 0.001 TYR G 100 PHE 0.016 0.001 PHE C 463 HIS 0.003 0.001 HIS A 425 Details of bonding type rmsd/Z covalent geometry : bond 0.00223 / 0.10 (24688) covalent geometry : angle 0.49000 / 0.25 (33485) hydrogen bonds : bond 0.03708 / 2.48 ( 1152) hydrogen bonds : angle 4.44030 / 3.13 ( 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 174 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 173 time to evaluate : 0.963 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 68 GLU cc_start: 0.6514 (tm-30) cc_final: 0.6056 (tm-30) REVERT: A 87 GLU cc_start: 0.7666 (tt0) cc_final: 0.7056 (tt0) REVERT: B 465 ASP cc_start: 0.7519 (t70) cc_final: 0.7276 (t0) REVERT: C 191 MET cc_start: 0.7698 (ttm) cc_final: 0.7488 (ttm) REVERT: C 272 GLU cc_start: 0.7860 (tt0) cc_final: 0.7401 (tt0) REVERT: C 407 GLN cc_start: 0.7889 (mt0) cc_final: 0.7582 (mp10) REVERT: E 41 GLU cc_start: 0.7426 (mt-10) cc_final: 0.7187 (mt-10) REVERT: E 56 ASP cc_start: 0.7424 (t0) cc_final: 0.6924 (t0) REVERT: E 395 GLU cc_start: 0.7760 (mp0) cc_final: 0.7469 (mp0) REVERT: F 1 MET cc_start: 0.5956 (ptt) cc_final: 0.5601 (ttt) outliers start: 1 outliers final: 0 residues processed: 174 average time/residue: 0.1733 time to fit residues: 47.2721 Evaluate side-chains 142 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 142 time to evaluate : 0.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 102 optimal weight: 0.9980 chunk 218 optimal weight: 0.7980 chunk 45 optimal weight: 5.9990 chunk 200 optimal weight: 6.9990 chunk 103 optimal weight: 0.7980 chunk 150 optimal weight: 5.9990 chunk 308 optimal weight: 4.9990 chunk 207 optimal weight: 4.9990 chunk 136 optimal weight: 4.9990 chunk 250 optimal weight: 3.9990 chunk 184 optimal weight: 0.8980 overall best weight: 1.4982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 381 GLN F 245 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2706 r_free = 0.2706 target = 0.066620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2458 r_free = 0.2458 target = 0.055407 restraints weight = 56219.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2449 r_free = 0.2449 target = 0.055068 restraints weight = 52912.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2455 r_free = 0.2455 target = 0.055361 restraints weight = 51989.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2459 r_free = 0.2459 target = 0.055539 restraints weight = 44360.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2465 r_free = 0.2465 target = 0.055788 restraints weight = 39430.846| |-----------------------------------------------------------------------------| r_work (final): 0.2456 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.1655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 24688 Z= 0.118 Angle : 0.498 6.612 33485 Z= 0.258 Chirality : 0.044 0.161 3856 Planarity : 0.004 0.056 4363 Dihedral : 5.658 168.037 3425 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.10 % Allowed : 1.89 % Favored : 98.01 % Rotamer: Outliers : 0.04 % Allowed : 0.66 % Favored : 99.30 % 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 are not related in a simple way. whole: 1.23 (0.15), residues: 3115 helix: 1.83 (0.15), residues: 1236 sheet: 0.61 (0.22), residues: 535 loop : 0.03 (0.17), residues: 1344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 333 TYR 0.011 0.001 TYR G 100 PHE 0.014 0.001 PHE C 343 HIS 0.006 0.001 HIS A 425 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.12 (24688) covalent geometry : angle 0.49801 / 0.26 (33485) hydrogen bonds : bond 0.03916 / 2.61 ( 1152) hydrogen bonds : angle 4.44367 / 3.12 ( 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 165 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 164 time to evaluate : 1.027 Fit side-chains revert: symmetry clash REVERT: A 68 GLU cc_start: 0.6560 (tm-30) cc_final: 0.6193 (tm-30) REVERT: A 87 GLU cc_start: 0.7676 (tt0) cc_final: 0.7029 (tt0) REVERT: B 465 ASP cc_start: 0.7516 (t70) cc_final: 0.7281 (t0) REVERT: C 191 MET cc_start: 0.7771 (ttm) cc_final: 0.7487 (ttm) REVERT: C 272 GLU cc_start: 0.7917 (tt0) cc_final: 0.7424 (tt0) REVERT: C 407 GLN cc_start: 0.7886 (mt0) cc_final: 0.7577 (mp10) REVERT: D 376 ARG cc_start: 0.6632 (mmm160) cc_final: 0.6340 (mmm160) REVERT: E 41 GLU cc_start: 0.7454 (mt-10) cc_final: 0.7217 (mt-10) REVERT: E 56 ASP cc_start: 0.7438 (t0) cc_final: 0.6984 (t0) REVERT: E 395 GLU cc_start: 0.7709 (mp0) cc_final: 0.7410 (mp0) REVERT: F 1 MET cc_start: 0.5883 (ptt) cc_final: 0.5567 (ttt) REVERT: G 191 LEU cc_start: 0.7791 (tp) cc_final: 0.7571 (tt) outliers start: 1 outliers final: 0 residues processed: 165 average time/residue: 0.1776 time to fit residues: 46.1316 Evaluate side-chains 142 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 142 time to evaluate : 1.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 39 optimal weight: 4.9990 chunk 46 optimal weight: 1.9990 chunk 138 optimal weight: 2.9990 chunk 74 optimal weight: 4.9990 chunk 190 optimal weight: 10.0000 chunk 208 optimal weight: 5.9990 chunk 4 optimal weight: 0.9990 chunk 283 optimal weight: 1.9990 chunk 131 optimal weight: 20.0000 chunk 164 optimal weight: 6.9990 chunk 295 optimal weight: 4.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 381 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2683 r_free = 0.2683 target = 0.065485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2432 r_free = 0.2432 target = 0.054348 restraints weight = 56568.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2431 r_free = 0.2431 target = 0.054271 restraints weight = 47671.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2432 r_free = 0.2432 target = 0.054337 restraints weight = 42371.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2433 r_free = 0.2433 target = 0.054397 restraints weight = 39335.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2434 r_free = 0.2434 target = 0.054433 restraints weight = 38295.334| |-----------------------------------------------------------------------------| r_work (final): 0.2425 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.1640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 24688 Z= 0.170 Angle : 0.546 7.477 33485 Z= 0.283 Chirality : 0.046 0.164 3856 Planarity : 0.004 0.056 4363 Dihedral : 5.796 167.546 3425 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.28 % Favored : 97.62 % Rotamer: Outliers : 0.04 % Allowed : 0.19 % Favored : 99.77 % 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 are not related in a simple way. whole: 1.05 (0.15), residues: 3115 helix: 1.69 (0.15), residues: 1236 sheet: 0.55 (0.22), residues: 524 loop : -0.10 (0.17), residues: 1355 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 442 TYR 0.022 0.001 TYR G 100 PHE 0.018 0.001 PHE F 322 HIS 0.006 0.001 HIS A 425 Details of bonding type rmsd/Z covalent geometry : bond 0.00416 / 0.17 (24688) covalent geometry : angle 0.54572 / 0.28 (33485) hydrogen bonds : bond 0.04519 / 3.01 ( 1152) hydrogen bonds : angle 4.57068 / 3.22 ( 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 158 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 157 time to evaluate : 0.767 Fit side-chains revert: symmetry clash REVERT: A 68 GLU cc_start: 0.6632 (tm-30) cc_final: 0.6323 (tm-30) REVERT: A 87 GLU cc_start: 0.7758 (tt0) cc_final: 0.7104 (tt0) REVERT: B 465 ASP cc_start: 0.7584 (t70) cc_final: 0.7345 (t0) REVERT: C 272 GLU cc_start: 0.7938 (tt0) cc_final: 0.7500 (tt0) REVERT: C 407 GLN cc_start: 0.7908 (mt0) cc_final: 0.6692 (tp40) REVERT: E 56 ASP cc_start: 0.7483 (t0) cc_final: 0.7009 (t0) REVERT: E 334 LYS cc_start: 0.7912 (mmtt) cc_final: 0.7711 (mmtm) REVERT: F 1 MET cc_start: 0.5896 (ptt) cc_final: 0.5587 (ttt) outliers start: 1 outliers final: 0 residues processed: 158 average time/residue: 0.1764 time to fit residues: 44.0001 Evaluate side-chains 136 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 136 time to evaluate : 0.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 64 optimal weight: 1.9990 chunk 212 optimal weight: 0.9980 chunk 271 optimal weight: 8.9990 chunk 280 optimal weight: 4.9990 chunk 174 optimal weight: 0.9980 chunk 122 optimal weight: 9.9990 chunk 266 optimal weight: 0.0270 chunk 276 optimal weight: 0.9980 chunk 172 optimal weight: 0.9980 chunk 137 optimal weight: 0.6980 chunk 269 optimal weight: 4.9990 overall best weight: 0.7438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 266 GLN E 381 GLN G 174 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2720 r_free = 0.2720 target = 0.067304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2480 r_free = 0.2480 target = 0.056473 restraints weight = 56183.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2480 r_free = 0.2480 target = 0.056467 restraints weight = 47030.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2480 r_free = 0.2480 target = 0.056489 restraints weight = 42507.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2482 r_free = 0.2482 target = 0.056559 restraints weight = 38710.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2483 r_free = 0.2483 target = 0.056623 restraints weight = 37384.614| |-----------------------------------------------------------------------------| r_work (final): 0.2471 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.1750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 24688 Z= 0.095 Angle : 0.485 6.509 33485 Z= 0.251 Chirality : 0.043 0.136 3856 Planarity : 0.004 0.055 4363 Dihedral : 5.426 158.701 3425 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.10 % Allowed : 1.70 % Favored : 98.20 % Rotamer: Outliers : 0.08 % Allowed : 0.19 % Favored : 99.73 % 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 are not related in a simple way. whole: 1.26 (0.15), residues: 3115 helix: 1.88 (0.15), residues: 1234 sheet: 0.62 (0.22), residues: 531 loop : 0.02 (0.17), residues: 1350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 333 TYR 0.019 0.001 TYR G 100 PHE 0.015 0.001 PHE C 343 HIS 0.006 0.001 HIS A 425 Details of bonding type rmsd/Z covalent geometry : bond 0.00205 / 0.10 (24688) covalent geometry : angle 0.48546 / 0.25 (33485) hydrogen bonds : bond 0.03561 / 2.38 ( 1152) hydrogen bonds : angle 4.38573 / 3.09 ( 3276) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2807.12 seconds wall clock time: 49 minutes 47.05 seconds (2987.05 seconds total)