Starting phenix.real_space_refine on Sat Mar 7 14:43:02 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7nkh_12439/03_2026/7nkh_12439_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7nkh_12439/03_2026/7nkh_12439.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.78 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7nkh_12439/03_2026/7nkh_12439.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7nkh_12439/03_2026/7nkh_12439.map" model { file = "/net/cci-nas-00/data/ceres_data/7nkh_12439/03_2026/7nkh_12439_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7nkh_12439/03_2026/7nkh_12439_trim.cif" } resolution = 2.78 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= 0.001 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: 7 Type Number sf(0) Gaussians P 16 5.49 5 Mg 5 5.21 5 S 71 5.16 5 C 14224 2.51 5 N 3941 2.21 5 O 4455 1.98 5 H 22565 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 45277 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 7470 Number of conformers: 1 Conformer: "" Number of residues, atoms: 493, 7470 Classifications: {'peptide': 493} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 19, 'TRANS': 471} Chain: "B" Number of atoms: 7377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 486, 7377 Classifications: {'peptide': 486} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 19, 'TRANS': 464} Chain breaks: 1 Chain: "C" Number of atoms: 7476 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 492, 7455 Classifications: {'peptide': 492} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 19, 'TRANS': 470} Conformer: "B" Number of residues, atoms: 492, 7455 Classifications: {'peptide': 492} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 19, 'TRANS': 470} bond proxies already assigned to first conformer: 7491 Chain: "D" Number of atoms: 7143 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 467, 7125 Classifications: {'peptide': 467} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 22, 'TRANS': 442} Conformer: "B" Number of residues, atoms: 467, 7125 Classifications: {'peptide': 467} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 22, 'TRANS': 442} bond proxies already assigned to first conformer: 7171 Chain: "E" Number of atoms: 7087 Number of conformers: 1 Conformer: "" Number of residues, atoms: 464, 7087 Classifications: {'peptide': 464} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 22, 'TRANS': 439} Chain: "F" Number of atoms: 7147 Number of conformers: 1 Conformer: "" Number of residues, atoms: 468, 7147 Classifications: {'peptide': 468} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 22, 'TRANS': 443} Chain: "G" Number of atoms: 1378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 1378 Classifications: {'peptide': 89} Link IDs: {'TRANS': 88} Chain breaks: 2 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 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} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "F" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N AGLN D 453 " occ=0.50 ... (32 atoms not shown) pdb="HE22BGLN D 453 " occ=0.50 Time building chain proxies: 9.60, per 1000 atoms: 0.21 Number of scatterers: 45277 At special positions: 0 Unit cell: (122.84, 126.16, 112.05, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 71 16.00 P 16 15.00 Mg 5 11.99 O 4455 8.00 N 3941 7.00 C 14224 6.00 H 22565 1.00 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: 3.50 Conformation dependent library (CDL) restraints added in 1.4 seconds 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5366 Finding SS restraints... Secondary structure from input PDB file: 125 helices and 0 sheets defined 42.8% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.92 Creating SS restraints... Processing helix chain 'A' and resid 82 through 84 No H-bonds generated for 'chain 'A' and resid 82 through 84' Processing helix chain 'A' and resid 104 through 106 No H-bonds generated for 'chain 'A' and resid 104 through 106' Processing helix chain 'A' and resid 139 through 141 No H-bonds generated for 'chain 'A' and resid 139 through 141' Processing helix chain 'A' and resid 154 through 159 Processing helix chain 'A' and resid 178 through 195 removed outlier: 4.264A pdb=" N ARG A 190 " --> pdb=" O ILE A 186 " (cutoff:3.500A) removed outlier: 5.060A pdb=" N GLU A 191 " --> pdb=" O LEU A 187 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N ALA A 192 " --> pdb=" O ASN A 188 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 225 Processing helix chain 'A' and resid 243 through 263 Proline residue: A 250 - end of helix removed outlier: 3.671A pdb=" N TRP A 260 " --> pdb=" O ILE A 256 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ASN A 263 " --> pdb=" O HIS A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 287 Processing helix chain 'A' and resid 294 through 296 No H-bonds generated for 'chain 'A' and resid 294 through 296' Processing helix chain 'A' and resid 301 through 311 removed outlier: 4.106A pdb=" N ARG A 311 " --> pdb=" O ARG A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 319 No H-bonds generated for 'chain 'A' and resid 317 through 319' Processing helix chain 'A' and resid 340 through 348 Processing helix chain 'A' and resid 357 through 361 Processing helix chain 'A' and resid 378 through 381 Processing helix chain 'A' and resid 384 through 390 Processing helix chain 'A' and resid 393 through 406 removed outlier: 5.139A pdb=" N ALA A 405 " --> pdb=" O ARG A 401 " (cutoff:3.500A) removed outlier: 5.834A pdb=" N PHE A 406 " --> pdb=" O GLU A 402 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 430 Processing helix chain 'A' and resid 441 through 452 Processing helix chain 'A' and resid 461 through 478 removed outlier: 4.792A pdb=" N GLN A 465 " --> pdb=" O GLU A 462 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N SER A 478 " --> pdb=" O VAL A 475 " (cutoff:3.500A) Processing helix chain 'A' and resid 481 through 489 Processing helix chain 'A' and resid 494 through 510 Processing helix chain 'B' and resid 82 through 84 No H-bonds generated for 'chain 'B' and resid 82 through 84' Processing helix chain 'B' and resid 104 through 106 No H-bonds generated for 'chain 'B' and resid 104 through 106' Processing helix chain 'B' and resid 154 through 159 Processing helix chain 'B' and resid 178 through 195 removed outlier: 3.745A pdb=" N GLN B 189 " --> pdb=" O THR B 185 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N ARG B 190 " --> pdb=" O ILE B 186 " (cutoff:3.500A) removed outlier: 5.293A pdb=" N GLU B 191 " --> pdb=" O LEU B 187 " (cutoff:3.500A) removed outlier: 4.911A pdb=" N ALA B 192 " --> pdb=" O ASN B 188 " (cutoff:3.500A) Processing helix chain 'B' and resid 213 through 225 Processing helix chain 'B' and resid 228 through 231 Processing helix chain 'B' and resid 243 through 263 Proline residue: B 250 - end of helix removed outlier: 3.689A pdb=" N TRP B 260 " --> pdb=" O ILE B 256 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ASN B 263 " --> pdb=" O HIS B 259 " (cutoff:3.500A) Processing helix chain 'B' and resid 274 through 287 Processing helix chain 'B' and resid 294 through 296 No H-bonds generated for 'chain 'B' and resid 294 through 296' Processing helix chain 'B' and resid 301 through 311 removed outlier: 4.180A pdb=" N ARG B 311 " --> pdb=" O ARG B 307 " (cutoff:3.500A) Processing helix chain 'B' and resid 317 through 319 No H-bonds generated for 'chain 'B' and resid 317 through 319' Processing helix chain 'B' and resid 340 through 348 Processing helix chain 'B' and resid 357 through 362 Processing helix chain 'B' and resid 384 through 405 removed outlier: 5.460A pdb=" N SER B 392 " --> pdb=" O GLU B 388 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N LEU B 393 " --> pdb=" O VAL B 389 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N LEU B 395 " --> pdb=" O GLY B 391 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N GLU B 402 " --> pdb=" O SER B 398 " (cutoff:3.500A) Processing helix chain 'B' and resid 415 through 431 Processing helix chain 'B' and resid 441 through 452 Processing helix chain 'B' and resid 461 through 477 removed outlier: 5.158A pdb=" N GLN B 465 " --> pdb=" O GLU B 462 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N VAL B 475 " --> pdb=" O LEU B 472 " (cutoff:3.500A) Processing helix chain 'B' and resid 480 through 489 Processing helix chain 'B' and resid 494 through 510 Processing helix chain 'C' and resid 82 through 84 No H-bonds generated for 'chain 'C' and resid 82 through 84' Processing helix chain 'C' and resid 104 through 106 No H-bonds generated for 'chain 'C' and resid 104 through 106' Processing helix chain 'C' and resid 154 through 159 Processing helix chain 'C' and resid 178 through 195 removed outlier: 3.754A pdb=" N GLN C 189 " --> pdb=" O THR C 185 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N ARG C 190 " --> pdb=" O ILE C 186 " (cutoff:3.500A) removed outlier: 5.258A pdb=" N GLU C 191 " --> pdb=" O LEU C 187 " (cutoff:3.500A) removed outlier: 4.960A pdb=" N ALA C 192 " --> pdb=" O ASN C 188 " (cutoff:3.500A) Processing helix chain 'C' and resid 213 through 225 Processing helix chain 'C' and resid 229 through 231 No H-bonds generated for 'chain 'C' and resid 229 through 231' Processing helix chain 'C' and resid 243 through 263 Proline residue: C 250 - end of helix removed outlier: 3.664A pdb=" N TRP C 260 " --> pdb=" O ILE C 256 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ASN C 263 " --> pdb=" O HIS C 259 " (cutoff:3.500A) Processing helix chain 'C' and resid 274 through 288 Processing helix chain 'C' and resid 294 through 296 No H-bonds generated for 'chain 'C' and resid 294 through 296' Processing helix chain 'C' and resid 301 through 311 removed outlier: 4.196A pdb=" N ARG C 311 " --> pdb=" O ARG C 307 " (cutoff:3.500A) Processing helix chain 'C' and resid 317 through 319 No H-bonds generated for 'chain 'C' and resid 317 through 319' Processing helix chain 'C' and resid 333 through 335 No H-bonds generated for 'chain 'C' and resid 333 through 335' Processing helix chain 'C' and resid 340 through 348 Processing helix chain 'C' and resid 357 through 361 Processing helix chain 'C' and resid 378 through 381 Processing helix chain 'C' and resid 384 through 389 Processing helix chain 'C' and resid 393 through 406 Processing helix chain 'C' and resid 415 through 431 Processing helix chain 'C' and resid 441 through 452 Processing helix chain 'C' and resid 461 through 477 removed outlier: 5.106A pdb=" N GLN C 465 " --> pdb=" O GLU C 462 " (cutoff:3.500A) Processing helix chain 'C' and resid 481 through 489 Processing helix chain 'C' and resid 494 through 510 removed outlier: 3.650A pdb=" N GLY C 510 " --> pdb=" O GLU C 506 " (cutoff:3.500A) Processing helix chain 'D' and resid 92 through 94 No H-bonds generated for 'chain 'D' and resid 92 through 94' Processing helix chain 'D' and resid 142 through 147 Processing helix chain 'D' and resid 166 through 177 Processing helix chain 'D' and resid 194 through 206 Processing helix chain 'D' and resid 210 through 212 No H-bonds generated for 'chain 'D' and resid 210 through 212' Processing helix chain 'D' and resid 224 through 243 removed outlier: 4.701A pdb=" N ALA D 231 " --> pdb=" O ARG D 227 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N LEU D 232 " --> pdb=" O MET D 228 " (cutoff:3.500A) Processing helix chain 'D' and resid 256 through 265 Processing helix chain 'D' and resid 268 through 270 No H-bonds generated for 'chain 'D' and resid 268 through 270' Processing helix chain 'D' and resid 276 through 278 No H-bonds generated for 'chain 'D' and resid 276 through 278' Processing helix chain 'D' and resid 283 through 293 Processing helix chain 'D' and resid 311 through 313 No H-bonds generated for 'chain 'D' and resid 311 through 313' Processing helix chain 'D' and resid 318 through 326 removed outlier: 4.263A pdb=" N ALA D 325 " --> pdb=" O ALA D 321 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N HIS D 326 " --> pdb=" O THR D 322 " (cutoff:3.500A) Processing helix chain 'D' and resid 335 through 339 Processing helix chain 'D' and resid 358 through 361 No H-bonds generated for 'chain 'D' and resid 358 through 361' Processing helix chain 'D' and resid 363 through 389 removed outlier: 4.606A pdb=" N ASP D 384 " --> pdb=" O LYS D 380 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N ILE D 385 " --> pdb=" O ASP D 381 " (cutoff:3.500A) Processing helix chain 'D' and resid 391 through 393 No H-bonds generated for 'chain 'D' and resid 391 through 393' Processing helix chain 'D' and resid 396 through 412 Processing helix chain 'D' and resid 417 through 423 removed outlier: 4.548A pdb=" N GLN D 421 " --> pdb=" O ALA D 418 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N THR D 423 " --> pdb=" O GLU D 420 " (cutoff:3.500A) Processing helix chain 'D' and resid 432 through 443 Processing helix chain 'D' and resid 452 through 455 Processing helix chain 'D' and resid 461 through 471 Processing helix chain 'E' and resid 92 through 94 No H-bonds generated for 'chain 'E' and resid 92 through 94' Processing helix chain 'E' and resid 142 through 146 Processing helix chain 'E' and resid 166 through 179 Processing helix chain 'E' and resid 194 through 207 Processing helix chain 'E' and resid 210 through 212 No H-bonds generated for 'chain 'E' and resid 210 through 212' Processing helix chain 'E' and resid 224 through 244 removed outlier: 5.045A pdb=" N ALA E 231 " --> pdb=" O ARG E 227 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N LEU E 232 " --> pdb=" O MET E 228 " (cutoff:3.500A) Processing helix chain 'E' and resid 256 through 270 Processing helix chain 'E' and resid 276 through 278 No H-bonds generated for 'chain 'E' and resid 276 through 278' Processing helix chain 'E' and resid 283 through 292 Processing helix chain 'E' and resid 311 through 313 No H-bonds generated for 'chain 'E' and resid 311 through 313' Processing helix chain 'E' and resid 318 through 326 removed outlier: 3.601A pdb=" N ALA E 325 " --> pdb=" O ALA E 321 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N HIS E 326 " --> pdb=" O THR E 322 " (cutoff:3.500A) Processing helix chain 'E' and resid 335 through 339 Processing helix chain 'E' and resid 358 through 361 No H-bonds generated for 'chain 'E' and resid 358 through 361' Processing helix chain 'E' and resid 363 through 389 removed outlier: 4.359A pdb=" N ASP E 384 " --> pdb=" O LYS E 380 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N ILE E 385 " --> pdb=" O ASP E 381 " (cutoff:3.500A) Processing helix chain 'E' and resid 391 through 393 No H-bonds generated for 'chain 'E' and resid 391 through 393' Processing helix chain 'E' and resid 396 through 411 Processing helix chain 'E' and resid 417 through 420 Processing helix chain 'E' and resid 432 through 444 Processing helix chain 'E' and resid 452 through 455 Processing helix chain 'E' and resid 461 through 470 Processing helix chain 'F' and resid 92 through 94 No H-bonds generated for 'chain 'F' and resid 92 through 94' Processing helix chain 'F' and resid 127 through 129 No H-bonds generated for 'chain 'F' and resid 127 through 129' Processing helix chain 'F' and resid 142 through 147 Processing helix chain 'F' and resid 166 through 177 Processing helix chain 'F' and resid 194 through 206 Processing helix chain 'F' and resid 210 through 212 No H-bonds generated for 'chain 'F' and resid 210 through 212' Processing helix chain 'F' and resid 224 through 243 removed outlier: 4.803A pdb=" N ALA F 231 " --> pdb=" O ARG F 227 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N LEU F 232 " --> pdb=" O MET F 228 " (cutoff:3.500A) Processing helix chain 'F' and resid 256 through 269 Processing helix chain 'F' and resid 276 through 278 No H-bonds generated for 'chain 'F' and resid 276 through 278' Processing helix chain 'F' and resid 283 through 294 removed outlier: 3.536A pdb=" N ILE F 294 " --> pdb=" O LEU F 290 " (cutoff:3.500A) Processing helix chain 'F' and resid 311 through 313 No H-bonds generated for 'chain 'F' and resid 311 through 313' Processing helix chain 'F' and resid 318 through 326 removed outlier: 4.520A pdb=" N ALA F 325 " --> pdb=" O ALA F 321 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N HIS F 326 " --> pdb=" O THR F 322 " (cutoff:3.500A) Processing helix chain 'F' and resid 335 through 339 Processing helix chain 'F' and resid 358 through 361 No H-bonds generated for 'chain 'F' and resid 358 through 361' Processing helix chain 'F' and resid 363 through 389 removed outlier: 4.332A pdb=" N ASP F 384 " --> pdb=" O LYS F 380 " (cutoff:3.500A) removed outlier: 4.939A pdb=" N ILE F 385 " --> pdb=" O ASP F 381 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ILE F 388 " --> pdb=" O ASP F 384 " (cutoff:3.500A) Processing helix chain 'F' and resid 396 through 412 Processing helix chain 'F' and resid 417 through 423 removed outlier: 4.086A pdb=" N GLN F 421 " --> pdb=" O ALA F 418 " (cutoff:3.500A) Processing helix chain 'F' and resid 432 through 444 Processing helix chain 'F' and resid 452 through 455 Processing helix chain 'F' and resid 461 through 470 Processing helix chain 'G' and resid 4 through 34 Processing helix chain 'G' and resid 259 through 303 746 hydrogen bonds defined for protein. 2067 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 9.93 Time building geometry restraints manager: 4.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 22546 1.03 - 1.22: 19 1.22 - 1.42: 9311 1.42 - 1.61: 13634 1.61 - 1.81: 125 Bond restraints: 45635 Sorted by residual: bond pdb=" C4 ADP D 600 " pdb=" C5 ADP D 600 " ideal model delta sigma weight residual 1.490 1.467 0.023 2.00e-02 2.50e+03 1.34e+00 bond pdb=" C4 ADP E 600 " pdb=" C5 ADP E 600 " ideal model delta sigma weight residual 1.490 1.467 0.023 2.00e-02 2.50e+03 1.27e+00 bond pdb=" CB GLN A 420 " pdb=" CG GLN A 420 " ideal model delta sigma weight residual 1.520 1.488 0.032 3.00e-02 1.11e+03 1.11e+00 bond pdb=" CG PRO F 344 " pdb=" CD PRO F 344 " ideal model delta sigma weight residual 1.512 1.484 0.028 2.70e-02 1.37e+03 1.11e+00 bond pdb=" C ALA B 390 " pdb=" O ALA B 390 " ideal model delta sigma weight residual 1.236 1.248 -0.012 1.34e-02 5.57e+03 8.40e-01 ... (remaining 45630 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.37: 80813 1.37 - 2.73: 1655 2.73 - 4.10: 165 4.10 - 5.47: 23 5.47 - 6.83: 21 Bond angle restraints: 82677 Sorted by residual: angle pdb=" C ASP E 254 " pdb=" N ASN E 255 " pdb=" CA ASN E 255 " ideal model delta sigma weight residual 121.70 127.43 -5.73 1.80e+00 3.09e-01 1.01e+01 angle pdb=" C ASP F 254 " pdb=" N ASN F 255 " pdb=" CA ASN F 255 " ideal model delta sigma weight residual 121.70 127.10 -5.40 1.80e+00 3.09e-01 8.98e+00 angle pdb=" N GLY E 218 " pdb=" CA GLY E 218 " pdb=" C GLY E 218 " ideal model delta sigma weight residual 113.18 106.35 6.83 2.37e+00 1.78e-01 8.31e+00 angle pdb=" C ASP D 254 " pdb=" N ASN D 255 " pdb=" CA ASN D 255 " ideal model delta sigma weight residual 121.70 126.86 -5.16 1.80e+00 3.09e-01 8.21e+00 angle pdb=" C ASP C 272 " pdb=" N ASP C 273 " pdb=" CA ASP C 273 " ideal model delta sigma weight residual 121.70 126.72 -5.02 1.80e+00 3.09e-01 7.79e+00 ... (remaining 82672 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.52: 20751 35.52 - 71.05: 564 71.05 - 106.57: 50 106.57 - 142.10: 0 142.10 - 177.62: 2 Dihedral angle restraints: 21367 sinusoidal: 11974 harmonic: 9393 Sorted by residual: dihedral pdb=" C5' ADP D 600 " pdb=" O5' ADP D 600 " pdb=" PA ADP D 600 " pdb=" O2A ADP D 600 " ideal model delta sinusoidal sigma weight residual -60.00 117.62 -177.62 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" C5' ADP E 600 " pdb=" O5' ADP E 600 " pdb=" PA ADP E 600 " pdb=" O2A ADP E 600 " ideal model delta sinusoidal sigma weight residual 300.00 144.50 155.50 1 2.00e+01 2.50e-03 4.58e+01 dihedral pdb=" O2A ADP E 600 " pdb=" O3A ADP E 600 " pdb=" PA ADP E 600 " pdb=" PB ADP E 600 " ideal model delta sinusoidal sigma weight residual -60.00 -156.26 96.26 1 2.00e+01 2.50e-03 2.66e+01 ... (remaining 21364 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 3166 0.060 - 0.121: 381 0.121 - 0.181: 32 0.181 - 0.241: 2 0.241 - 0.301: 10 Chirality restraints: 3591 Sorted by residual: chirality pdb=" C2' ATP B 600 " pdb=" C1' ATP B 600 " pdb=" C3' ATP B 600 " pdb=" O2' ATP B 600 " both_signs ideal model delta sigma weight residual False -2.68 -2.98 0.30 2.00e-01 2.50e+01 2.27e+00 chirality pdb=" C2' ATP C 600 " pdb=" C1' ATP C 600 " pdb=" C3' ATP C 600 " pdb=" O2' ATP C 600 " both_signs ideal model delta sigma weight residual False -2.68 -2.97 0.29 2.00e-01 2.50e+01 2.13e+00 chirality pdb=" C2' ATP F 600 " pdb=" C1' ATP F 600 " pdb=" C3' ATP F 600 " pdb=" O2' ATP F 600 " both_signs ideal model delta sigma weight residual False -2.68 -2.97 0.29 2.00e-01 2.50e+01 2.10e+00 ... (remaining 3588 not shown) Planarity restraints: 6921 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG E 374 " 0.158 9.50e-02 1.11e+02 5.27e-02 3.13e+00 pdb=" NE ARG E 374 " -0.010 2.00e-02 2.50e+03 pdb=" CZ ARG E 374 " 0.005 2.00e-02 2.50e+03 pdb=" NH1 ARG E 374 " 0.000 2.00e-02 2.50e+03 pdb=" NH2 ARG E 374 " 0.000 2.00e-02 2.50e+03 pdb="HH11 ARG E 374 " -0.005 2.00e-02 2.50e+03 pdb="HH12 ARG E 374 " 0.002 2.00e-02 2.50e+03 pdb="HH21 ARG E 374 " -0.000 2.00e-02 2.50e+03 pdb="HH22 ARG E 374 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY F 17 " -0.026 5.00e-02 4.00e+02 4.01e-02 2.57e+00 pdb=" N PRO F 18 " 0.069 5.00e-02 4.00e+02 pdb=" CA PRO F 18 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO F 18 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLY B 485 " 0.007 2.00e-02 2.50e+03 1.39e-02 1.93e+00 pdb=" C GLY B 485 " -0.024 2.00e-02 2.50e+03 pdb=" O GLY B 485 " 0.009 2.00e-02 2.50e+03 pdb=" N ILE B 486 " 0.008 2.00e-02 2.50e+03 ... (remaining 6918 not shown) Histogram of nonbonded interaction distances: 1.57 - 2.18: 2386 2.18 - 2.78: 93664 2.78 - 3.39: 134727 3.39 - 3.99: 181502 3.99 - 4.60: 281215 Nonbonded interactions: 693494 Sorted by model distance: nonbonded pdb=" H VAL D 277 " pdb=" OE2 GLU G 292 " model vdw 1.572 2.450 nonbonded pdb=" H GLY D 165 " pdb=" O1B ADP D 600 " model vdw 1.580 2.450 nonbonded pdb=" O ALA C 192 " pdb=" HG1 THR C 195 " model vdw 1.603 2.450 nonbonded pdb=" O PRO B 161 " pdb=" HG SER B 375 " model vdw 1.604 2.450 nonbonded pdb=" OE2 GLU F 52 " pdb=" HE2 HIS F 121 " model vdw 1.605 2.450 ... (remaining 693489 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 30 and (name N or name CA or name C or name O or name CB \ or name CG or name CD or name OE1 or name OE2 or name HA or name HB2 or name HB3 \ or name HG2 or name HG3)) or resid 31 through 173 or resid 175 through 406 or ( \ resid 414 and (name N or name CA or name C or name O or name CB or name CG or na \ me OD1 or name OD2 or name HA or name HB2 or name HB3)) or resid 415 through 601 \ )) selection = (chain 'B' and ((resid 30 and (name N or name CA or name C or name O or name CB \ or name CG or name CD or name OE1 or name OE2 or name HA or name HB2 or name HB3 \ or name HG2 or name HG3)) or resid 31 through 173 or resid 175 through 601)) selection = (chain 'C' and (resid 30 through 173 or resid 175 through 406 or (resid 414 and \ (name N or name CA or name C or name O or name CB or name CG or name OD1 or name \ OD2 or name HA or name HB2 or name HB3)) or resid 415 through 601)) } ncs_group { reference = (chain 'D' and (resid 8 through 452 or resid 455 through 471)) selection = (chain 'E' and (resid 8 through 166 or (resid 167 and (name N or name CA or name \ C or name O or name CB or name OG1 or name CG2 or name H or name HA or name HB \ or name HG21 or name HG22 or name HG23)) or resid 168 through 452 or resid 455 t \ hrough 471)) selection = (chain 'F' and ((resid 8 and (name N or name CA or name C or name O or name CB o \ r name OG1 or name CG2 or name HA or name HB or name HG1 or name HG21 or name HG \ 22 or name HG23)) or resid 9 through 452 or resid 455 through 471)) } 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.820 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.180 Extract box with map and model: 0.520 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 41.220 Find NCS groups from input model: 0.860 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8684 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 : 0.002 0.032 23070 Z= 0.116 Angle : 0.502 6.832 31280 Z= 0.260 Chirality : 0.043 0.301 3591 Planarity : 0.003 0.068 4098 Dihedral : 15.097 177.620 8644 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.11 % Favored : 97.82 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.21 % 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: 1.32 (0.16), residues: 2943 helix: 1.59 (0.15), residues: 1205 sheet: -0.03 (0.24), residues: 432 loop : 0.70 (0.19), residues: 1306 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 378 TYR 0.006 0.001 TYR E 366 PHE 0.011 0.001 PHE F 257 TRP 0.006 0.001 TRP B 247 HIS 0.002 0.001 HIS D 121 Details of bonding type rmsd covalent geometry : bond 0.00246 (23070) covalent geometry : angle 0.50150 (31280) hydrogen bonds : bond 0.06464 ( 746) hydrogen bonds : angle 3.68514 ( 2067) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 179 is missing expected H atoms. Skipping. Residue THR 179 is missing expected H atoms. Skipping. Residue THR 179 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Evaluate side-chains 165 residues out of total 2393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 165 time to evaluate : 1.098 Fit side-chains REVERT: B 418 LYS cc_start: 0.6441 (mptt) cc_final: 0.6126 (mptt) REVERT: D 173 MET cc_start: 0.9020 (mmt) cc_final: 0.8720 (mmt) outliers start: 0 outliers final: 0 residues processed: 165 average time/residue: 1.6657 time to fit residues: 310.4549 Evaluate side-chains 108 residues out of total 2393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 108 time to evaluate : 1.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 197 optimal weight: 1.9990 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 0.2980 chunk 132 optimal weight: 0.6980 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 1.9990 chunk 111 optimal weight: 1.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 277 GLN E 171 GLN F 245 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.074889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2806 r_free = 0.2806 target = 0.062744 restraints weight = 148447.482| |-----------------------------------------------------------------------------| r_work (start): 0.2802 rms_B_bonded: 1.86 r_work: 0.2713 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.2606 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.2606 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2611 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2611 r_free = 0.2611 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2611 r_free = 0.2611 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2611 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8914 moved from start: 0.0640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 23070 Z= 0.220 Angle : 0.521 7.674 31280 Z= 0.271 Chirality : 0.042 0.143 3591 Planarity : 0.004 0.058 4098 Dihedral : 8.612 157.141 3328 Min Nonbonded Distance : 1.714 Molprobity Statistics. All-atom Clashscore : 2.36 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.28 % Favored : 97.65 % Rotamer: Outliers : 0.25 % Allowed : 4.05 % Favored : 95.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.21 % 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: 1.12 (0.16), residues: 2943 helix: 1.48 (0.15), residues: 1206 sheet: -0.32 (0.24), residues: 436 loop : 0.60 (0.19), residues: 1301 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 374 TYR 0.011 0.001 TYR C 251 PHE 0.012 0.001 PHE B 467 TRP 0.005 0.001 TRP B 193 HIS 0.004 0.001 HIS D 121 Details of bonding type rmsd covalent geometry : bond 0.00501 (23070) covalent geometry : angle 0.52087 (31280) hydrogen bonds : bond 0.04842 ( 746) hydrogen bonds : angle 3.67328 ( 2067) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 179 is missing expected H atoms. Skipping. Residue THR 179 is missing expected H atoms. Skipping. Residue THR 179 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Evaluate side-chains 118 residues out of total 2393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 112 time to evaluate : 1.433 Fit side-chains REVERT: C 36 ASP cc_start: 0.8766 (p0) cc_final: 0.8503 (p0) REVERT: C 273 ASP cc_start: 0.8699 (OUTLIER) cc_final: 0.8222 (m-30) REVERT: D 173 MET cc_start: 0.9395 (mmt) cc_final: 0.9125 (mmt) outliers start: 6 outliers final: 1 residues processed: 116 average time/residue: 1.5666 time to fit residues: 207.2574 Evaluate side-chains 109 residues out of total 2393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 107 time to evaluate : 1.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 279 ASP Chi-restraints excluded: chain C residue 273 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 99 optimal weight: 1.9990 chunk 272 optimal weight: 1.9990 chunk 139 optimal weight: 1.9990 chunk 11 optimal weight: 0.4980 chunk 149 optimal weight: 1.9990 chunk 224 optimal weight: 3.9990 chunk 142 optimal weight: 2.9990 chunk 133 optimal weight: 1.9990 chunk 183 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 166 optimal weight: 0.9990 overall best weight: 1.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 171 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 = 0.3036 r_free = 0.3036 target = 0.074318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2793 r_free = 0.2793 target = 0.062070 restraints weight = 154691.925| |-----------------------------------------------------------------------------| r_work (start): 0.2788 rms_B_bonded: 1.90 r_work: 0.2697 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.2589 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.2589 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2597 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2597 r_free = 0.2597 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2597 r_free = 0.2597 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2597 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8928 moved from start: 0.0825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.082 23070 Z= 0.227 Angle : 0.517 6.912 31280 Z= 0.269 Chirality : 0.042 0.143 3591 Planarity : 0.004 0.044 4098 Dihedral : 8.377 126.990 3328 Min Nonbonded Distance : 1.709 Molprobity Statistics. All-atom Clashscore : 2.03 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.48 % Favored : 97.41 % Rotamer: Outliers : 0.42 % Allowed : 5.05 % Favored : 94.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.21 % 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 (0.16), residues: 2943 helix: 1.37 (0.15), residues: 1208 sheet: -0.58 (0.24), residues: 435 loop : 0.55 (0.19), residues: 1300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 335 TYR 0.012 0.001 TYR C 251 PHE 0.012 0.001 PHE C 245 TRP 0.005 0.001 TRP B 193 HIS 0.004 0.001 HIS D 121 Details of bonding type rmsd covalent geometry : bond 0.00517 (23070) covalent geometry : angle 0.51714 (31280) hydrogen bonds : bond 0.04999 ( 746) hydrogen bonds : angle 3.71877 ( 2067) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 179 is missing expected H atoms. Skipping. Residue THR 179 is missing expected H atoms. Skipping. Residue THR 179 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Evaluate side-chains 119 residues out of total 2393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 109 time to evaluate : 1.000 Fit side-chains REVERT: C 273 ASP cc_start: 0.8754 (OUTLIER) cc_final: 0.8249 (m-30) REVERT: D 173 MET cc_start: 0.9381 (mmt) cc_final: 0.9115 (mmt) REVERT: F 11 ARG cc_start: 0.8959 (OUTLIER) cc_final: 0.8745 (ptt-90) outliers start: 10 outliers final: 2 residues processed: 115 average time/residue: 1.4551 time to fit residues: 192.9179 Evaluate side-chains 104 residues out of total 2393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 100 time to evaluate : 1.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 279 ASP Chi-restraints excluded: chain C residue 273 ASP Chi-restraints excluded: chain F residue 11 ARG Chi-restraints excluded: chain F residue 248 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 146 optimal weight: 1.9990 chunk 103 optimal weight: 0.0060 chunk 61 optimal weight: 0.9990 chunk 0 optimal weight: 2.9990 chunk 84 optimal weight: 2.9990 chunk 221 optimal weight: 1.9990 chunk 162 optimal weight: 0.9990 chunk 33 optimal weight: 0.9990 chunk 205 optimal weight: 2.9990 chunk 106 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 overall best weight: 1.0004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 171 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 = 0.3046 r_free = 0.3046 target = 0.074761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2811 r_free = 0.2811 target = 0.062758 restraints weight = 146409.495| |-----------------------------------------------------------------------------| r_work (start): 0.2806 rms_B_bonded: 1.84 r_work: 0.2717 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.2613 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.2613 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2614 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2614 r_free = 0.2614 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2614 r_free = 0.2614 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2614 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8910 moved from start: 0.0857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 23070 Z= 0.163 Angle : 0.487 6.875 31280 Z= 0.252 Chirality : 0.041 0.139 3591 Planarity : 0.003 0.042 4098 Dihedral : 8.118 120.717 3328 Min Nonbonded Distance : 1.777 Molprobity Statistics. All-atom Clashscore : 2.05 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.28 % Favored : 97.62 % Rotamer: Outliers : 0.38 % Allowed : 5.34 % Favored : 94.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.02 (0.16), residues: 2943 helix: 1.48 (0.15), residues: 1207 sheet: -0.79 (0.24), residues: 426 loop : 0.62 (0.19), residues: 1310 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 335 TYR 0.010 0.001 TYR C 251 PHE 0.013 0.001 PHE F 257 TRP 0.005 0.001 TRP E 201 HIS 0.003 0.001 HIS D 121 Details of bonding type rmsd covalent geometry : bond 0.00368 (23070) covalent geometry : angle 0.48725 (31280) hydrogen bonds : bond 0.04630 ( 746) hydrogen bonds : angle 3.63280 ( 2067) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 179 is missing expected H atoms. Skipping. Residue THR 179 is missing expected H atoms. Skipping. Residue THR 179 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Evaluate side-chains 115 residues out of total 2393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 106 time to evaluate : 1.123 Fit side-chains revert: symmetry clash REVERT: D 173 MET cc_start: 0.9368 (mmt) cc_final: 0.9126 (mmt) REVERT: F 11 ARG cc_start: 0.8902 (OUTLIER) cc_final: 0.8487 (ptt-90) outliers start: 9 outliers final: 3 residues processed: 113 average time/residue: 1.4968 time to fit residues: 193.3505 Evaluate side-chains 106 residues out of total 2393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 102 time to evaluate : 1.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 279 ASP Chi-restraints excluded: chain F residue 11 ARG Chi-restraints excluded: chain F residue 208 ASN Chi-restraints excluded: chain F residue 410 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 216 optimal weight: 0.8980 chunk 126 optimal weight: 1.9990 chunk 129 optimal weight: 0.8980 chunk 4 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 102 optimal weight: 2.9990 chunk 31 optimal weight: 0.9990 chunk 90 optimal weight: 0.9990 chunk 119 optimal weight: 0.9980 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 171 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 = 0.3051 r_free = 0.3051 target = 0.074998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2810 r_free = 0.2810 target = 0.062798 restraints weight = 153433.963| |-----------------------------------------------------------------------------| r_work (start): 0.2805 rms_B_bonded: 1.90 r_work: 0.2714 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.2608 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.2608 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2612 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2612 r_free = 0.2612 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2612 r_free = 0.2612 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2612 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8913 moved from start: 0.0899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 23070 Z= 0.161 Angle : 0.481 6.689 31280 Z= 0.249 Chirality : 0.041 0.138 3591 Planarity : 0.003 0.044 4098 Dihedral : 7.940 111.959 3328 Min Nonbonded Distance : 1.768 Molprobity Statistics. All-atom Clashscore : 1.88 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.35 % Favored : 97.58 % Rotamer: Outliers : 0.33 % Allowed : 5.97 % Favored : 93.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.21 % 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 (0.16), residues: 2943 helix: 1.54 (0.15), residues: 1207 sheet: -0.88 (0.24), residues: 425 loop : 0.64 (0.19), residues: 1311 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 335 TYR 0.010 0.001 TYR C 251 PHE 0.012 0.001 PHE F 257 TRP 0.005 0.001 TRP E 201 HIS 0.003 0.001 HIS D 121 Details of bonding type rmsd covalent geometry : bond 0.00365 (23070) covalent geometry : angle 0.48136 (31280) hydrogen bonds : bond 0.04566 ( 746) hydrogen bonds : angle 3.60418 ( 2067) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 179 is missing expected H atoms. Skipping. Residue THR 179 is missing expected H atoms. Skipping. Residue THR 179 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Evaluate side-chains 119 residues out of total 2393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 111 time to evaluate : 1.163 Fit side-chains revert: symmetry clash REVERT: C 273 ASP cc_start: 0.8663 (OUTLIER) cc_final: 0.8164 (m-30) REVERT: D 173 MET cc_start: 0.9347 (mmt) cc_final: 0.9122 (mmt) outliers start: 8 outliers final: 4 residues processed: 117 average time/residue: 1.4822 time to fit residues: 199.9997 Evaluate side-chains 109 residues out of total 2393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 104 time to evaluate : 1.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 279 ASP Chi-restraints excluded: chain C residue 273 ASP Chi-restraints excluded: chain F residue 208 ASN Chi-restraints excluded: chain F residue 248 ASP Chi-restraints excluded: chain F residue 410 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 247 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 149 optimal weight: 0.6980 chunk 258 optimal weight: 1.9990 chunk 195 optimal weight: 2.9990 chunk 127 optimal weight: 1.9990 chunk 270 optimal weight: 1.9990 chunk 34 optimal weight: 0.5980 chunk 211 optimal weight: 1.9990 chunk 267 optimal weight: 3.9990 chunk 168 optimal weight: 1.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 171 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 = 0.3030 r_free = 0.3030 target = 0.073869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2789 r_free = 0.2789 target = 0.061608 restraints weight = 158000.555| |-----------------------------------------------------------------------------| r_work (start): 0.2789 rms_B_bonded: 1.92 r_work: 0.2697 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.2591 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.2591 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2595 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2595 r_free = 0.2595 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2595 r_free = 0.2595 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2595 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8930 moved from start: 0.0969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.086 23070 Z= 0.225 Angle : 0.509 7.077 31280 Z= 0.265 Chirality : 0.042 0.142 3591 Planarity : 0.004 0.046 4098 Dihedral : 7.992 111.392 3328 Min Nonbonded Distance : 1.751 Molprobity Statistics. All-atom Clashscore : 1.85 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.59 % Favored : 97.31 % Rotamer: Outliers : 0.29 % Allowed : 6.30 % Favored : 93.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.21 % 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: 0.94 (0.16), residues: 2943 helix: 1.42 (0.15), residues: 1207 sheet: -0.92 (0.24), residues: 427 loop : 0.60 (0.19), residues: 1309 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 335 TYR 0.012 0.001 TYR C 251 PHE 0.012 0.001 PHE F 257 TRP 0.005 0.001 TRP E 201 HIS 0.004 0.001 HIS D 121 Details of bonding type rmsd covalent geometry : bond 0.00513 (23070) covalent geometry : angle 0.50858 (31280) hydrogen bonds : bond 0.04933 ( 746) hydrogen bonds : angle 3.68610 ( 2067) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 179 is missing expected H atoms. Skipping. Residue THR 179 is missing expected H atoms. Skipping. Residue THR 179 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Evaluate side-chains 115 residues out of total 2393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 108 time to evaluate : 1.209 Fit side-chains revert: symmetry clash REVERT: C 273 ASP cc_start: 0.8702 (OUTLIER) cc_final: 0.8231 (m-30) REVERT: D 173 MET cc_start: 0.9364 (mmt) cc_final: 0.9127 (mmt) outliers start: 7 outliers final: 3 residues processed: 112 average time/residue: 1.3824 time to fit residues: 177.7346 Evaluate side-chains 106 residues out of total 2393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 102 time to evaluate : 1.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 279 ASP Chi-restraints excluded: chain C residue 273 ASP Chi-restraints excluded: chain F residue 248 ASP Chi-restraints excluded: chain F residue 410 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 91 optimal weight: 3.9990 chunk 60 optimal weight: 0.0670 chunk 120 optimal weight: 1.9990 chunk 93 optimal weight: 0.9990 chunk 229 optimal weight: 2.9990 chunk 165 optimal weight: 0.5980 chunk 116 optimal weight: 0.7980 chunk 49 optimal weight: 2.9990 chunk 246 optimal weight: 0.0670 chunk 52 optimal weight: 0.7980 chunk 181 optimal weight: 1.9990 overall best weight: 0.4656 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 171 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 = 0.3066 r_free = 0.3066 target = 0.075839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2824 r_free = 0.2824 target = 0.063463 restraints weight = 167680.576| |-----------------------------------------------------------------------------| r_work (start): 0.2820 rms_B_bonded: 2.00 r_work: 0.2726 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2618 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.2618 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2623 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2623 r_free = 0.2623 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2623 r_free = 0.2623 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2623 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8902 moved from start: 0.0964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 23070 Z= 0.107 Angle : 0.462 6.219 31280 Z= 0.237 Chirality : 0.040 0.138 3591 Planarity : 0.003 0.043 4098 Dihedral : 7.645 99.655 3328 Min Nonbonded Distance : 1.826 Molprobity Statistics. All-atom Clashscore : 2.03 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.38 % Favored : 97.55 % Rotamer: Outliers : 0.33 % Allowed : 6.42 % Favored : 93.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.21 % 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: 1.12 (0.16), residues: 2943 helix: 1.64 (0.15), residues: 1207 sheet: -1.01 (0.24), residues: 423 loop : 0.70 (0.19), residues: 1313 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 335 TYR 0.006 0.001 TYR E 366 PHE 0.013 0.001 PHE F 257 TRP 0.005 0.001 TRP E 201 HIS 0.002 0.001 HIS C 259 Details of bonding type rmsd covalent geometry : bond 0.00234 (23070) covalent geometry : angle 0.46212 (31280) hydrogen bonds : bond 0.04220 ( 746) hydrogen bonds : angle 3.51590 ( 2067) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 179 is missing expected H atoms. Skipping. Residue THR 179 is missing expected H atoms. Skipping. Residue THR 179 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Evaluate side-chains 119 residues out of total 2393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 111 time to evaluate : 1.217 Fit side-chains revert: symmetry clash outliers start: 8 outliers final: 4 residues processed: 116 average time/residue: 1.2552 time to fit residues: 167.9390 Evaluate side-chains 110 residues out of total 2393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 106 time to evaluate : 1.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 279 ASP Chi-restraints excluded: chain D residue 384 ASP Chi-restraints excluded: chain F residue 248 ASP Chi-restraints excluded: chain F residue 410 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 246 optimal weight: 1.9990 chunk 10 optimal weight: 0.1980 chunk 47 optimal weight: 2.9990 chunk 231 optimal weight: 4.9990 chunk 115 optimal weight: 0.9990 chunk 255 optimal weight: 0.9990 chunk 66 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 87 optimal weight: 5.9990 chunk 207 optimal weight: 2.9990 overall best weight: 1.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 420 GLN E 171 GLN F 245 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.074493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2802 r_free = 0.2802 target = 0.062183 restraints weight = 161111.599| |-----------------------------------------------------------------------------| r_work (start): 0.2801 rms_B_bonded: 1.95 r_work: 0.2709 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.2602 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.2602 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2606 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2606 r_free = 0.2606 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2606 r_free = 0.2606 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2606 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8920 moved from start: 0.0988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 23070 Z= 0.193 Angle : 0.490 6.700 31280 Z= 0.253 Chirality : 0.041 0.138 3591 Planarity : 0.003 0.044 4098 Dihedral : 7.684 98.378 3328 Min Nonbonded Distance : 1.765 Molprobity Statistics. All-atom Clashscore : 2.05 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.21 % Favored : 97.72 % Rotamer: Outliers : 0.29 % Allowed : 6.63 % Favored : 93.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.21 % 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: 1.09 (0.16), residues: 2943 helix: 1.58 (0.15), residues: 1206 sheet: -0.99 (0.24), residues: 425 loop : 0.70 (0.19), residues: 1312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 335 TYR 0.010 0.001 TYR C 251 PHE 0.012 0.001 PHE F 257 TRP 0.005 0.001 TRP E 201 HIS 0.003 0.001 HIS D 121 Details of bonding type rmsd covalent geometry : bond 0.00441 (23070) covalent geometry : angle 0.48984 (31280) hydrogen bonds : bond 0.04618 ( 746) hydrogen bonds : angle 3.56807 ( 2067) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 179 is missing expected H atoms. Skipping. Residue THR 179 is missing expected H atoms. Skipping. Residue THR 179 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Evaluate side-chains 115 residues out of total 2393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 108 time to evaluate : 0.936 Fit side-chains revert: symmetry clash outliers start: 7 outliers final: 3 residues processed: 112 average time/residue: 1.1007 time to fit residues: 144.3266 Evaluate side-chains 107 residues out of total 2393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 104 time to evaluate : 0.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 279 ASP Chi-restraints excluded: chain F residue 248 ASP Chi-restraints excluded: chain F residue 410 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 201 optimal weight: 1.9990 chunk 22 optimal weight: 0.9990 chunk 261 optimal weight: 1.9990 chunk 286 optimal weight: 2.9990 chunk 238 optimal weight: 0.9980 chunk 71 optimal weight: 0.9980 chunk 100 optimal weight: 1.9990 chunk 191 optimal weight: 0.5980 chunk 31 optimal weight: 0.9990 chunk 29 optimal weight: 2.9990 chunk 75 optimal weight: 0.7980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 420 GLN E 171 GLN F 245 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.075237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2813 r_free = 0.2813 target = 0.062934 restraints weight = 161735.827| |-----------------------------------------------------------------------------| r_work (start): 0.2810 rms_B_bonded: 1.96 r_work: 0.2718 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.2610 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.2610 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2613 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2613 r_free = 0.2613 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2613 r_free = 0.2613 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2613 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8911 moved from start: 0.0993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 23070 Z= 0.146 Angle : 0.475 6.480 31280 Z= 0.245 Chirality : 0.040 0.138 3591 Planarity : 0.003 0.043 4098 Dihedral : 7.615 93.635 3328 Min Nonbonded Distance : 1.786 Molprobity Statistics. All-atom Clashscore : 2.05 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.48 % Favored : 97.45 % Rotamer: Outliers : 0.25 % Allowed : 6.88 % Favored : 92.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.21 % 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: 1.11 (0.16), residues: 2943 helix: 1.61 (0.15), residues: 1208 sheet: -1.03 (0.24), residues: 425 loop : 0.73 (0.19), residues: 1310 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 335 TYR 0.009 0.001 TYR C 251 PHE 0.012 0.001 PHE F 257 TRP 0.005 0.001 TRP E 201 HIS 0.002 0.001 HIS C 259 Details of bonding type rmsd covalent geometry : bond 0.00327 (23070) covalent geometry : angle 0.47454 (31280) hydrogen bonds : bond 0.04434 ( 746) hydrogen bonds : angle 3.53426 ( 2067) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 179 is missing expected H atoms. Skipping. Residue THR 179 is missing expected H atoms. Skipping. Residue THR 179 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Evaluate side-chains 116 residues out of total 2393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 110 time to evaluate : 0.774 Fit side-chains revert: symmetry clash REVERT: D 173 MET cc_start: 0.9418 (mmt) cc_final: 0.9186 (mmt) outliers start: 6 outliers final: 3 residues processed: 114 average time/residue: 1.0008 time to fit residues: 133.8074 Evaluate side-chains 111 residues out of total 2393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 108 time to evaluate : 0.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 279 ASP Chi-restraints excluded: chain F residue 248 ASP Chi-restraints excluded: chain F residue 410 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 99 optimal weight: 2.9990 chunk 89 optimal weight: 0.9990 chunk 287 optimal weight: 3.9990 chunk 101 optimal weight: 0.4980 chunk 183 optimal weight: 0.4980 chunk 253 optimal weight: 0.9980 chunk 214 optimal weight: 1.9990 chunk 202 optimal weight: 1.9990 chunk 43 optimal weight: 0.3980 chunk 234 optimal weight: 2.9990 chunk 82 optimal weight: 0.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 171 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 = 0.3058 r_free = 0.3058 target = 0.075299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2823 r_free = 0.2823 target = 0.063126 restraints weight = 153427.748| |-----------------------------------------------------------------------------| r_work (start): 0.2824 rms_B_bonded: 1.90 r_work: 0.2733 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.2625 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.2625 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2628 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2628 r_free = 0.2628 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2628 r_free = 0.2628 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2628 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8902 moved from start: 0.1025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 23070 Z= 0.125 Angle : 0.463 6.162 31280 Z= 0.237 Chirality : 0.040 0.137 3591 Planarity : 0.003 0.042 4098 Dihedral : 7.447 89.273 3328 Min Nonbonded Distance : 1.803 Molprobity Statistics. All-atom Clashscore : 2.12 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.38 % Favored : 97.55 % Rotamer: Outliers : 0.17 % Allowed : 6.93 % Favored : 92.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.21 % 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: 1.19 (0.16), residues: 2943 helix: 1.70 (0.15), residues: 1208 sheet: -1.05 (0.24), residues: 425 loop : 0.77 (0.19), residues: 1310 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 335 TYR 0.009 0.001 TYR E 366 PHE 0.012 0.001 PHE F 257 TRP 0.005 0.001 TRP E 201 HIS 0.002 0.001 HIS D 121 Details of bonding type rmsd covalent geometry : bond 0.00279 (23070) covalent geometry : angle 0.46256 (31280) hydrogen bonds : bond 0.04237 ( 746) hydrogen bonds : angle 3.47351 ( 2067) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 179 is missing expected H atoms. Skipping. Residue THR 179 is missing expected H atoms. Skipping. Residue THR 179 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Evaluate side-chains 117 residues out of total 2393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 113 time to evaluate : 0.711 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 3 residues processed: 116 average time/residue: 0.8841 time to fit residues: 118.6772 Evaluate side-chains 111 residues out of total 2393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 108 time to evaluate : 0.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 279 ASP Chi-restraints excluded: chain F residue 248 ASP Chi-restraints excluded: chain F residue 410 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 292 random chunks: chunk 156 optimal weight: 0.9980 chunk 137 optimal weight: 0.8980 chunk 68 optimal weight: 1.9990 chunk 180 optimal weight: 0.3980 chunk 168 optimal weight: 1.9990 chunk 40 optimal weight: 0.9990 chunk 1 optimal weight: 0.9980 chunk 103 optimal weight: 1.9990 chunk 161 optimal weight: 0.9990 chunk 190 optimal weight: 0.8980 chunk 219 optimal weight: 0.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 171 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.075505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2823 r_free = 0.2823 target = 0.063470 restraints weight = 148244.091| |-----------------------------------------------------------------------------| r_work (start): 0.2819 rms_B_bonded: 1.85 r_work: 0.2728 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.2622 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.2622 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2631 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2631 r_free = 0.2631 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2631 r_free = 0.2631 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2631 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8906 moved from start: 0.1042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 23070 Z= 0.144 Angle : 0.469 6.154 31280 Z= 0.241 Chirality : 0.040 0.136 3591 Planarity : 0.003 0.045 4098 Dihedral : 7.406 89.752 3328 Min Nonbonded Distance : 1.789 Molprobity Statistics. All-atom Clashscore : 2.03 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.42 % Favored : 97.52 % Rotamer: Outliers : 0.29 % Allowed : 6.93 % Favored : 92.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.21 % 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: 1.19 (0.16), residues: 2943 helix: 1.70 (0.15), residues: 1208 sheet: -1.05 (0.24), residues: 425 loop : 0.77 (0.19), residues: 1310 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 407 TYR 0.009 0.001 TYR C 251 PHE 0.012 0.001 PHE F 257 TRP 0.005 0.001 TRP E 201 HIS 0.003 0.001 HIS D 121 Details of bonding type rmsd covalent geometry : bond 0.00326 (23070) covalent geometry : angle 0.46940 (31280) hydrogen bonds : bond 0.04325 ( 746) hydrogen bonds : angle 3.48241 ( 2067) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10338.55 seconds wall clock time: 175 minutes 36.40 seconds (10536.40 seconds total)