Starting phenix.real_space_refine on Sat Jun 21 03:57:21 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hh5_34752/06_2025/8hh5_34752.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hh5_34752/06_2025/8hh5_34752.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8hh5_34752/06_2025/8hh5_34752.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hh5_34752/06_2025/8hh5_34752.map" model { file = "/net/cci-nas-00/data/ceres_data/8hh5_34752/06_2025/8hh5_34752.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hh5_34752/06_2025/8hh5_34752.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.001 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: 6 Type Number sf(0) Gaussians P 18 5.49 5 Mg 6 5.21 5 S 77 5.16 5 C 15287 2.51 5 N 4219 2.21 5 O 4670 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 30 residue(s): 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 24277 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: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 446} Chain: "F" 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: "G" Number of atoms: 2218 Number of conformers: 1 Conformer: "" Number of residues, atoms: 283, 2218 Classifications: {'peptide': 283} Link IDs: {'PTRANS': 10, '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: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 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: 14.45, per 1000 atoms: 0.60 Number of scatterers: 24277 At special positions: 0 Unit cell: (125.84, 124.96, 152.24, 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 18 15.00 Mg 6 11.99 O 4670 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: 6.04 Conformation dependent library (CDL) restraints added in 3.0 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: 136 helices and 21 sheets defined 48.4% alpha, 15.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.15 Creating SS restraints... Processing helix chain 'A' and resid 78 through 82 removed outlier: 4.076A 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 135 through 139 removed outlier: 3.863A pdb=" N ARG A 139 " --> pdb=" O VAL A 136 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 157 Processing helix chain 'A' and resid 174 through 186 removed outlier: 3.579A pdb=" N GLN A 186 " --> pdb=" O THR A 182 " (cutoff:3.500A) 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 252 removed outlier: 3.565A 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: 4.022A pdb=" N PHE A 249 " --> pdb=" O MET A 245 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LYS A 252 " --> pdb=" O TYR A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 277 Processing helix chain 'A' and resid 282 through 286 Processing helix chain 'A' and resid 287 through 288 No H-bonds generated for 'chain 'A' and resid 287 through 288' Processing helix chain 'A' and resid 289 through 299 removed outlier: 3.582A pdb=" N HIS A 294 " --> pdb=" O ILE A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 309 Processing helix chain 'A' and resid 328 through 338 Processing helix chain 'A' and resid 345 through 351 Processing helix chain 'A' and resid 372 through 392 removed outlier: 3.886A pdb=" N VAL A 378 " --> pdb=" O ALA A 374 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N GLY A 380 " --> pdb=" O LYS A 376 " (cutoff:3.500A) removed outlier: 6.084A pdb=" N THR A 381 " --> pdb=" O LYS A 377 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N LEU A 382 " --> pdb=" O VAL A 378 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N ARG A 390 " --> pdb=" O LEU A 386 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N GLU A 391 " --> pdb=" O ALA A 387 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LEU A 392 " --> pdb=" O ALA A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 393 through 397 removed outlier: 3.522A pdb=" N ALA A 396 " --> pdb=" O GLU A 393 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N GLN A 397 " --> pdb=" O ALA A 394 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 393 through 397' Processing helix chain 'A' and resid 406 through 421 Processing helix chain 'A' and resid 429 through 443 removed outlier: 3.550A pdb=" N GLY A 443 " --> pdb=" O ALA A 439 " (cutoff:3.500A) 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 Processing helix chain 'A' and resid 468 through 479 Processing helix chain 'A' and resid 483 through 498 removed outlier: 3.668A pdb=" N THR A 497 " --> pdb=" O ALA A 493 " (cutoff:3.500A) Processing helix chain 'B' and resid 100 through 104 Processing helix chain 'B' and resid 135 through 139 removed outlier: 3.684A pdb=" N ARG B 139 " --> pdb=" O VAL B 136 " (cutoff:3.500A) Processing helix chain 'B' and resid 150 through 155 Processing helix chain 'B' and resid 174 through 186 removed outlier: 3.576A 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: 3.615A pdb=" N LEU B 235 " --> pdb=" O PRO B 231 " (cutoff:3.500A) Proline residue: B 239 - end of helix removed outlier: 3.779A pdb=" N TYR B 248 " --> pdb=" O ALA B 244 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N PHE B 249 " --> pdb=" O MET B 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 263 through 277 Processing helix chain 'B' and resid 282 through 286 Processing helix chain 'B' and resid 287 through 288 No H-bonds generated for 'chain 'B' and resid 287 through 288' Processing helix chain 'B' and resid 289 through 299 removed outlier: 3.720A pdb=" N HIS B 294 " --> pdb=" O ILE B 290 " (cutoff:3.500A) Processing helix chain 'B' and resid 328 through 336 Processing helix chain 'B' and resid 345 through 350 Processing helix chain 'B' and resid 372 through 379 Processing helix chain 'B' and resid 381 through 396 Processing helix chain 'B' and resid 397 through 399 No H-bonds generated for 'chain 'B' and resid 397 through 399' Processing helix chain 'B' and resid 402 through 411 Processing helix chain 'B' and resid 412 through 421 Processing helix chain 'B' and resid 429 through 442 removed outlier: 3.642A pdb=" N ILE B 436 " --> pdb=" O LYS B 432 " (cutoff:3.500A) Processing helix chain 'B' and resid 449 through 451 No H-bonds generated for 'chain 'B' and resid 449 through 451' Processing helix chain 'B' and resid 452 through 468 removed outlier: 3.837A pdb=" N LEU B 462 " --> pdb=" O LYS B 458 " (cutoff:3.500A) Processing helix chain 'B' and resid 468 through 479 Processing helix chain 'B' and resid 486 through 498 removed outlier: 4.038A pdb=" N ALA B 490 " --> pdb=" O ASP B 486 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N THR B 497 " --> pdb=" O ALA B 493 " (cutoff:3.500A) Processing helix chain 'C' and resid 100 through 104 removed outlier: 3.526A 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 251 removed outlier: 3.665A pdb=" N LEU C 235 " --> pdb=" O PRO C 231 " (cutoff:3.500A) Proline residue: C 239 - end of helix removed outlier: 3.683A 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) Processing helix chain 'C' and resid 262 through 277 Processing helix chain 'C' and resid 282 through 286 Processing helix chain 'C' and resid 289 through 299 Processing helix chain 'C' and resid 328 through 336 Processing helix chain 'C' and resid 345 through 351 Processing helix chain 'C' and resid 372 through 393 removed outlier: 4.565A pdb=" N THR C 381 " --> pdb=" O LYS C 377 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LEU C 382 " --> pdb=" O VAL C 378 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N LEU C 384 " --> pdb=" O GLY C 380 " (cutoff:3.500A) Processing helix chain 'C' and resid 394 through 399 removed outlier: 4.182A pdb=" N GLN C 397 " --> pdb=" O ALA C 394 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 421 Processing helix chain 'C' and resid 429 through 442 Processing helix chain 'C' and resid 449 through 451 No H-bonds generated for 'chain 'C' and resid 449 through 451' Processing helix chain 'C' and resid 452 through 467 removed outlier: 3.517A pdb=" N LEU C 462 " --> pdb=" O LYS C 458 " (cutoff:3.500A) Processing helix chain 'C' and resid 468 through 479 removed outlier: 3.647A pdb=" N LEU C 472 " --> pdb=" O GLY C 468 " (cutoff:3.500A) Processing helix chain 'C' and resid 483 through 496 Processing helix chain 'D' and resid 88 through 92 removed outlier: 3.609A pdb=" N LEU D 92 " --> pdb=" O GLU D 89 " (cutoff:3.500A) Processing helix chain 'D' and resid 124 through 128 removed outlier: 3.597A pdb=" N LEU D 128 " --> pdb=" O PHE D 125 " (cutoff:3.500A) Processing helix chain 'D' and resid 139 through 146 Processing helix chain 'D' and resid 163 through 180 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 242 removed outlier: 3.598A pdb=" N VAL D 228 " --> pdb=" O ALA D 224 " (cutoff:3.500A) removed outlier: 5.030A pdb=" N ALA D 229 " --> pdb=" O ARG D 225 " (cutoff:3.500A) removed outlier: 4.807A pdb=" N LEU D 230 " --> pdb=" O MET D 226 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N TYR D 238 " --> pdb=" O THR D 234 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N PHE D 239 " --> pdb=" O MET D 235 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ARG D 240 " --> pdb=" O ALA D 236 " (cutoff:3.500A) Processing helix chain 'D' and resid 253 through 269 removed outlier: 3.656A pdb=" N PHE D 257 " --> pdb=" O ASN D 253 " (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 323 removed outlier: 4.173A pdb=" N SER D 323 " --> pdb=" O ALA D 319 " (cutoff:3.500A) Processing helix chain 'D' and resid 332 through 339 removed outlier: 3.536A pdb=" N MET D 338 " --> pdb=" O LYS D 334 " (cutoff:3.500A) Processing helix chain 'D' and resid 355 through 360 Processing helix chain 'D' and resid 360 through 378 Processing helix chain 'D' and resid 380 through 387 removed outlier: 3.627A pdb=" N ILE D 386 " --> pdb=" O ASP D 382 " (cutoff:3.500A) Processing helix chain 'D' and resid 388 through 392 Processing helix chain 'D' and resid 393 through 410 removed outlier: 3.947A pdb=" N ARG D 405 " --> pdb=" O HIS D 401 " (cutoff:3.500A) Processing helix chain 'D' and resid 414 through 416 No H-bonds generated for 'chain 'D' and resid 414 through 416' Processing helix chain 'D' and resid 417 through 422 Processing helix chain 'D' and resid 429 through 443 removed outlier: 3.563A pdb=" N ARG D 435 " --> pdb=" O LYS D 431 " (cutoff:3.500A) Processing helix chain 'D' and resid 449 through 454 Processing helix chain 'D' and resid 458 through 470 removed outlier: 3.980A pdb=" N VAL D 462 " --> pdb=" O ARG D 458 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N VAL D 463 " --> pdb=" O ILE D 459 " (cutoff:3.500A) Processing helix chain 'E' and resid 88 through 92 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 226 Processing helix chain 'E' and resid 227 through 243 removed outlier: 3.842A pdb=" N TYR E 238 " --> pdb=" O THR E 234 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N PHE E 239 " --> pdb=" O MET E 235 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ARG E 240 " --> pdb=" O ALA E 236 " (cutoff:3.500A) Processing helix chain 'E' and resid 253 through 269 removed outlier: 4.036A pdb=" N PHE E 257 " --> pdb=" O ASN E 253 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N THR E 258 " --> pdb=" O ILE E 254 " (cutoff:3.500A) 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: 3.576A 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 387 removed outlier: 4.051A pdb=" N ASP E 382 " --> pdb=" O LYS E 378 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ILE E 383 " --> pdb=" O GLU E 379 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ALA E 385 " --> pdb=" O GLN E 381 " (cutoff:3.500A) Processing helix chain 'E' and resid 393 through 410 removed outlier: 3.695A pdb=" N ARG E 405 " --> pdb=" O HIS E 401 " (cutoff:3.500A) Processing helix chain 'E' and resid 417 through 422 Processing helix chain 'E' and resid 429 through 443 Processing helix chain 'E' and resid 449 through 454 Processing helix chain 'E' and resid 458 through 470 removed outlier: 3.686A pdb=" N VAL E 462 " --> pdb=" O ARG E 458 " (cutoff:3.500A) Processing helix chain 'F' and resid 88 through 92 Processing helix chain 'F' and resid 139 through 146 Processing helix chain 'F' and resid 163 through 176 Processing helix chain 'F' and resid 191 through 206 Processing helix chain 'F' and resid 207 through 209 No H-bonds generated for 'chain 'F' and resid 207 through 209' Processing helix chain 'F' and resid 221 through 226 Processing helix chain 'F' and resid 227 through 242 removed outlier: 3.543A pdb=" N TYR F 238 " --> pdb=" O THR F 234 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N PHE F 239 " --> pdb=" O MET F 235 " (cutoff:3.500A) Processing helix chain 'F' and resid 254 through 266 removed outlier: 4.061A pdb=" N THR F 258 " --> pdb=" O ILE F 254 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N ALA F 266 " --> pdb=" O SER F 262 " (cutoff:3.500A) Processing helix chain 'F' and resid 267 through 269 No H-bonds generated for 'chain 'F' and resid 267 through 269' Processing helix chain 'F' and resid 273 through 277 Processing helix chain 'F' and resid 280 through 290 removed outlier: 3.504A 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 322 removed outlier: 3.633A pdb=" N PHE F 322 " --> pdb=" O PRO F 318 " (cutoff:3.500A) Processing helix chain 'F' and resid 323 through 325 No H-bonds generated for 'chain 'F' and resid 323 through 325' Processing helix chain 'F' and resid 332 through 339 removed outlier: 3.509A pdb=" N GLY F 339 " --> pdb=" O LEU F 335 " (cutoff:3.500A) Processing helix chain 'F' and resid 355 through 360 Processing helix chain 'F' and resid 360 through 380 Processing helix chain 'F' and resid 380 through 388 Processing helix chain 'F' and resid 389 through 392 removed outlier: 3.509A pdb=" N LEU F 392 " --> pdb=" O MET F 389 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 389 through 392' Processing helix chain 'F' and resid 393 through 410 removed outlier: 3.675A pdb=" N ARG F 405 " --> pdb=" O HIS F 401 " (cutoff:3.500A) Processing helix chain 'F' and resid 415 through 420 removed outlier: 3.863A 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 removed outlier: 3.543A pdb=" N ARG F 454 " --> pdb=" O ASP F 451 " (cutoff:3.500A) Processing helix chain 'F' and resid 458 through 470 removed outlier: 3.928A pdb=" N VAL F 462 " --> pdb=" O ARG F 458 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N VAL F 463 " --> pdb=" O ILE F 459 " (cutoff:3.500A) Processing helix chain 'G' and resid 3 through 42 removed outlier: 4.172A pdb=" N GLN G 37 " --> pdb=" O ASN G 33 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N ASN G 38 " --> pdb=" O ARG G 34 " (cutoff:3.500A) Processing helix chain 'G' and resid 42 through 57 removed outlier: 3.534A pdb=" N MET G 46 " --> pdb=" O PHE G 42 " (cutoff:3.500A) Processing helix chain 'G' and resid 90 through 107 removed outlier: 3.624A pdb=" N LEU G 96 " --> pdb=" O ASN G 92 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N VAL G 99 " --> pdb=" O VAL G 95 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N THR G 102 " --> pdb=" O LEU G 98 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N LYS G 105 " --> pdb=" O GLN G 101 " (cutoff:3.500A) Processing helix chain 'G' and resid 119 through 127 removed outlier: 4.144A pdb=" N LEU G 123 " --> pdb=" O GLY G 119 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N SER G 124 " --> pdb=" O ARG G 120 " (cutoff:3.500A) Processing helix chain 'G' and resid 145 through 161 removed outlier: 3.995A pdb=" N GLU G 151 " --> pdb=" O ALA G 147 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N ILE G 152 " --> pdb=" O ASP G 148 " (cutoff:3.500A) Processing helix chain 'G' and resid 162 through 164 No H-bonds generated for 'chain 'G' and resid 162 through 164' Processing helix chain 'G' and resid 208 through 284 Proline residue: G 218 - end of helix removed outlier: 3.979A pdb=" N GLN G 267 " --> pdb=" O ASN G 263 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N ALA G 268 " --> pdb=" O ARG G 264 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ALA G 269 " --> pdb=" O ALA G 265 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N LEU G 284 " --> pdb=" O GLY G 280 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 60 through 66 removed outlier: 3.986A pdb=" N GLU A 51 " --> pdb=" O ALA A 63 " (cutoff:3.500A) removed outlier: 7.344A pdb=" N LEU A 52 " --> pdb=" O THR A 91 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N THR A 91 " --> pdb=" O LEU A 52 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N ARG A 40 " --> pdb=" O ILE A 32 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N VAL A 34 " --> pdb=" O ILE A 38 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N ILE A 38 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N VAL A 74 " --> pdb=" O ALA A 63 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N ALA A 63 " --> pdb=" O VAL A 74 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N GLU E 75 " --> pdb=" O GLN E 33 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N GLN E 33 " --> pdb=" O GLU E 75 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N ARG E 60 " --> pdb=" O ALA E 51 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N HIS E 53 " --> pdb=" O THR E 58 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N THR E 58 " --> pdb=" O HIS E 53 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N LYS E 17 " --> pdb=" O VAL E 6 " (cutoff:3.500A) removed outlier: 5.723A 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 99 removed outlier: 4.074A pdb=" N GLU A 125 " --> pdb=" O VAL A 99 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 107 through 108 removed outlier: 6.324A pdb=" N ILE A 192 " --> pdb=" O LEU A 257 " (cutoff:3.500A) removed outlier: 7.948A pdb=" N VAL A 259 " --> pdb=" O ILE A 192 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N ILE A 194 " --> pdb=" O VAL A 259 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N TYR A 260 " --> pdb=" O LEU A 316 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 60 through 66 removed outlier: 4.182A pdb=" N GLU B 51 " --> pdb=" O ALA B 63 " (cutoff:3.500A) removed outlier: 5.111A pdb=" N ARG B 93 " --> pdb=" O LEU B 52 " (cutoff:3.500A) removed outlier: 8.359A pdb=" N GLU B 54 " --> pdb=" O THR B 91 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N THR B 91 " --> pdb=" O GLU B 54 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N ARG B 40 " --> pdb=" O ILE B 32 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N VAL B 34 " --> pdb=" O ILE B 38 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N ILE B 38 " --> pdb=" O VAL B 34 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N ASN B 70 " --> pdb=" O LEU B 66 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N LEU B 66 " --> pdb=" O ASN B 70 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N GLY B 72 " --> pdb=" O LEU B 64 " (cutoff:3.500A) removed outlier: 5.770A pdb=" N GLU F 75 " --> pdb=" O GLN F 33 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N GLN F 33 " --> pdb=" O GLU F 75 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N ARG F 60 " --> pdb=" O ALA F 51 " (cutoff:3.500A) removed outlier: 5.132A pdb=" N HIS F 53 " --> pdb=" O THR F 58 " (cutoff:3.500A) removed outlier: 7.382A pdb=" N THR F 58 " --> pdb=" O HIS F 53 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N VAL F 13 " --> pdb=" O VAL F 9 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N VAL F 9 " --> pdb=" O VAL F 13 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N ASP F 15 " --> pdb=" O ILE F 7 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 96 through 99 removed outlier: 3.910A pdb=" N GLU B 125 " --> pdb=" O VAL B 99 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 107 through 108 removed outlier: 3.619A pdb=" N TYR B 260 " --> pdb=" O LEU B 316 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N LEU B 166 " --> pdb=" O ILE B 342 " (cutoff:3.500A) removed outlier: 7.545A pdb=" N LEU B 344 " --> pdb=" O LEU B 166 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N ILE B 168 " --> pdb=" O LEU B 344 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 28 through 35 removed outlier: 6.475A pdb=" N ARG C 40 " --> pdb=" O ILE C 32 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N VAL C 34 " --> pdb=" O ILE C 38 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N ILE C 38 " --> pdb=" O VAL C 34 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N GLY C 72 " --> pdb=" O LEU C 64 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 96 through 99 removed outlier: 3.904A pdb=" N GLU C 125 " --> pdb=" O VAL C 99 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 107 through 108 removed outlier: 6.556A pdb=" N LEU C 166 " --> pdb=" O ILE C 342 " (cutoff:3.500A) removed outlier: 7.647A pdb=" N LEU C 344 " --> pdb=" O LEU C 166 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N ILE C 168 " --> pdb=" O LEU C 344 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 4 through 9 removed outlier: 6.497A pdb=" N ASP D 15 " --> pdb=" O ILE D 7 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N VAL D 9 " --> pdb=" O VAL D 13 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N VAL D 13 " --> pdb=" O VAL D 9 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N THR D 58 " --> pdb=" O HIS D 53 " (cutoff:3.500A) removed outlier: 5.043A pdb=" N HIS D 53 " --> pdb=" O THR D 58 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N ARG D 60 " --> pdb=" O ALA D 51 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N ASN D 28 " --> pdb=" O VAL D 50 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N ALA D 29 " --> pdb=" O THR D 79 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N GLN D 33 " --> pdb=" O GLU D 75 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N GLU D 75 " --> pdb=" O GLN D 33 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 84 through 86 Processing sheet with id=AB3, first strand: chain 'D' and resid 95 through 96 removed outlier: 6.332A pdb=" N PHE D 96 " --> pdb=" O PHE D 215 " (cutoff:3.500A) removed outlier: 7.896A pdb=" N GLN D 217 " --> pdb=" O PHE D 96 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N ILE D 182 " --> pdb=" O ASP D 246 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N ILE D 154 " --> pdb=" O GLN D 304 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N ILE D 306 " --> pdb=" O ILE D 154 " (cutoff:3.500A) removed outlier: 5.972A pdb=" N LEU D 156 " --> pdb=" O ILE D 306 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ALA D 327 " --> pdb=" O LYS D 153 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 134 through 135 removed outlier: 4.399A pdb=" N TYR D 148 " --> pdb=" O LEU D 135 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 84 through 86 Processing sheet with id=AB6, first strand: chain 'E' and resid 95 through 96 removed outlier: 6.186A pdb=" N VAL E 247 " --> pdb=" O THR E 301 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N ILE E 303 " --> pdb=" O VAL E 247 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N LEU E 249 " --> pdb=" O ILE E 303 " (cutoff:3.500A) removed outlier: 7.772A pdb=" N ALA E 305 " --> pdb=" O LEU E 249 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N ILE E 251 " --> pdb=" O ALA E 305 " (cutoff:3.500A) removed outlier: 6.062A pdb=" N ILE E 154 " --> pdb=" O GLN E 304 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N LYS E 153 " --> pdb=" O ALA E 327 " (cutoff:3.500A) removed outlier: 8.230A pdb=" N THR E 329 " --> pdb=" O LYS E 153 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N GLY E 155 " --> pdb=" O THR E 329 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 134 through 135 removed outlier: 4.518A pdb=" N TYR E 148 " --> pdb=" O LEU E 135 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 84 through 86 Processing sheet with id=AB9, first strand: chain 'F' and resid 95 through 96 removed outlier: 6.667A pdb=" N SER F 183 " --> pdb=" O ALA F 212 " (cutoff:3.500A) removed outlier: 8.271A pdb=" N VAL F 214 " --> pdb=" O SER F 183 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N PHE F 185 " --> pdb=" O VAL F 214 " (cutoff:3.500A) removed outlier: 7.847A pdb=" N GLY F 216 " --> pdb=" O PHE F 185 " (cutoff:3.500A) removed outlier: 5.768A pdb=" N GLY F 187 " --> pdb=" O GLY F 216 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N VAL F 247 " --> pdb=" O THR F 301 " (cutoff:3.500A) removed outlier: 7.725A pdb=" N ILE F 303 " --> pdb=" O VAL F 247 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N LEU F 249 " --> pdb=" O ILE F 303 " (cutoff:3.500A) removed outlier: 8.040A pdb=" N ALA F 305 " --> pdb=" O LEU F 249 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N ILE F 251 " --> pdb=" O ALA F 305 " (cutoff:3.500A) removed outlier: 8.408A pdb=" N TYR F 307 " --> pdb=" O ILE F 251 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 134 through 135 removed outlier: 4.305A pdb=" N TYR F 148 " --> pdb=" O LEU F 135 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'G' and resid 133 through 137 removed outlier: 9.189A pdb=" N ILE G 115 " --> pdb=" O ILE G 134 " (cutoff:3.500A) removed outlier: 7.656A pdb=" N ASP G 136 " --> pdb=" O ILE G 115 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N VAL G 117 " --> pdb=" O ASP G 136 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N TYR G 78 " --> pdb=" O ILE G 116 " (cutoff:3.500A) removed outlier: 7.734A pdb=" N ILE G 118 " --> pdb=" O TYR G 78 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N VAL G 80 " --> pdb=" O ILE G 118 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N GLY G 77 " --> pdb=" O TYR G 169 " (cutoff:3.500A) removed outlier: 8.069A pdb=" N TYR G 171 " --> pdb=" O GLY G 77 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N LEU G 79 " --> pdb=" O TYR G 171 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'G' and resid 173 through 175 1157 hydrogen bonds defined for protein. 3291 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: 9.74 Time building geometry restraints manager: 7.07 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8233 1.34 - 1.46: 3836 1.46 - 1.58: 12434 1.58 - 1.69: 27 1.69 - 1.81: 154 Bond restraints: 24684 Sorted by residual: bond pdb=" O3 PO4 D 602 " pdb=" P PO4 D 602 " ideal model delta sigma weight residual 1.569 1.507 0.062 2.00e-02 2.50e+03 9.68e+00 bond pdb=" O2 PO4 D 602 " pdb=" P PO4 D 602 " ideal model delta sigma weight residual 1.567 1.506 0.061 2.00e-02 2.50e+03 9.41e+00 bond pdb=" O4 PO4 D 602 " pdb=" P PO4 D 602 " ideal model delta sigma weight residual 1.568 1.509 0.059 2.00e-02 2.50e+03 8.56e+00 bond pdb=" O1 PO4 D 602 " pdb=" P PO4 D 602 " ideal model delta sigma weight residual 1.565 1.506 0.059 2.00e-02 2.50e+03 8.56e+00 bond pdb=" CA VAL G 73 " pdb=" CB VAL G 73 " ideal model delta sigma weight residual 1.527 1.546 -0.019 1.31e-02 5.83e+03 2.18e+00 ... (remaining 24679 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.03: 32972 2.03 - 4.05: 453 4.05 - 6.08: 50 6.08 - 8.10: 3 8.10 - 10.13: 1 Bond angle restraints: 33479 Sorted by residual: angle pdb=" N VAL C 366 " pdb=" CA VAL C 366 " pdb=" C VAL C 366 " ideal model delta sigma weight residual 111.91 106.58 5.33 8.90e-01 1.26e+00 3.59e+01 angle pdb=" C ASN E 97 " pdb=" N VAL E 98 " pdb=" CA VAL E 98 " ideal model delta sigma weight residual 121.97 132.10 -10.13 1.80e+00 3.09e-01 3.16e+01 angle pdb=" N VAL B 366 " pdb=" CA VAL B 366 " pdb=" C VAL B 366 " ideal model delta sigma weight residual 113.42 108.65 4.77 1.17e+00 7.31e-01 1.66e+01 angle pdb=" N VAL E 98 " pdb=" CA VAL E 98 " pdb=" CB VAL E 98 " ideal model delta sigma weight residual 111.23 116.95 -5.72 1.65e+00 3.67e-01 1.20e+01 angle pdb=" N ASP A 262 " pdb=" CA ASP A 262 " pdb=" C ASP A 262 " ideal model delta sigma weight residual 107.32 112.98 -5.66 1.65e+00 3.67e-01 1.18e+01 ... (remaining 33474 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.41: 14710 33.41 - 66.82: 332 66.82 - 100.23: 49 100.23 - 133.64: 0 133.64 - 167.05: 2 Dihedral angle restraints: 15093 sinusoidal: 6168 harmonic: 8925 Sorted by residual: dihedral pdb=" O2A ADP D 603 " pdb=" O3A ADP D 603 " pdb=" PA ADP D 603 " pdb=" PB ADP D 603 " ideal model delta sinusoidal sigma weight residual -60.00 107.05 -167.05 1 2.00e+01 2.50e-03 4.74e+01 dihedral pdb=" C5' ADP D 603 " pdb=" O5' ADP D 603 " pdb=" PA ADP D 603 " pdb=" O2A ADP D 603 " ideal model delta sinusoidal sigma weight residual 300.00 133.97 166.03 1 2.00e+01 2.50e-03 4.73e+01 dihedral pdb=" CA LEU G 159 " pdb=" C LEU G 159 " pdb=" N PHE G 160 " pdb=" CA PHE G 160 " ideal model delta harmonic sigma weight residual 180.00 154.15 25.85 0 5.00e+00 4.00e-02 2.67e+01 ... (remaining 15090 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 2279 0.031 - 0.063: 998 0.063 - 0.094: 341 0.094 - 0.126: 208 0.126 - 0.157: 30 Chirality restraints: 3856 Sorted by residual: chirality pdb=" CA VAL E 214 " pdb=" N VAL E 214 " pdb=" C VAL E 214 " pdb=" CB VAL E 214 " both_signs ideal model delta sigma weight residual False 2.44 2.60 -0.16 2.00e-01 2.50e+01 6.19e-01 chirality pdb=" CB THR F 301 " pdb=" CA THR F 301 " pdb=" OG1 THR F 301 " pdb=" CG2 THR F 301 " both_signs ideal model delta sigma weight residual False 2.55 2.40 0.15 2.00e-01 2.50e+01 5.57e-01 chirality pdb=" CA VAL E 456 " pdb=" N VAL E 456 " pdb=" C VAL E 456 " pdb=" CB VAL E 456 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.53e-01 ... (remaining 3853 not shown) Planarity restraints: 4363 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL G 43 " 0.067 5.00e-02 4.00e+02 9.97e-02 1.59e+01 pdb=" N PRO G 44 " -0.172 5.00e-02 4.00e+02 pdb=" CA PRO G 44 " 0.051 5.00e-02 4.00e+02 pdb=" CD PRO G 44 " 0.055 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU F 220 " 0.027 5.00e-02 4.00e+02 4.08e-02 2.66e+00 pdb=" N PRO F 221 " -0.071 5.00e-02 4.00e+02 pdb=" CA PRO F 221 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO F 221 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP E 315 " 0.027 5.00e-02 4.00e+02 4.07e-02 2.66e+00 pdb=" N PRO E 316 " -0.070 5.00e-02 4.00e+02 pdb=" CA PRO E 316 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO E 316 " 0.023 5.00e-02 4.00e+02 ... (remaining 4360 not shown) Histogram of nonbonded interaction distances: 1.88 - 2.48: 91 2.48 - 3.09: 17027 3.09 - 3.69: 35678 3.69 - 4.30: 53451 4.30 - 4.90: 90894 Nonbonded interactions: 197141 Sorted by model distance: nonbonded pdb="MG MG D 601 " pdb=" O4 PO4 D 602 " model vdw 1.881 2.170 nonbonded pdb=" O1G ATP C 600 " pdb="MG MG C 601 " model vdw 1.943 2.170 nonbonded pdb="MG MG F 601 " pdb=" O3G ATP F 602 " model vdw 1.984 2.170 nonbonded pdb=" OG1 THR B 176 " pdb="MG MG B 601 " model vdw 2.005 2.170 nonbonded pdb=" OG1 THR F 165 " pdb="MG MG F 601 " model vdw 2.008 2.170 ... (remaining 197136 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 24 through 501) selection = (chain 'B' and resid 24 through 501) selection = (chain 'C' and resid 24 through 501) } ncs_group { reference = (chain 'D' and resid 1 through 470) selection = (chain 'E' and resid 1 through 470) selection = (chain 'F' and resid 1 through 470) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.130 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.890 Check model and map are aligned: 0.180 Set scattering table: 0.200 Process input model: 54.680 Find NCS groups from input model: 1.550 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:23.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 84.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8544 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 0.062 24684 Z= 0.163 Angle : 0.603 10.126 33479 Z= 0.346 Chirality : 0.045 0.157 3856 Planarity : 0.005 0.100 4363 Dihedral : 14.432 167.050 9381 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.18 % Favored : 97.78 % Rotamer: Outliers : 0.00 % Allowed : 0.27 % Favored : 99.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.95 (0.15), residues: 3115 helix: 1.28 (0.15), residues: 1277 sheet: 0.82 (0.22), residues: 511 loop : 0.03 (0.17), residues: 1327 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.001 HIS D 363 PHE 0.011 0.001 PHE E 125 TYR 0.025 0.001 TYR G 175 ARG 0.014 0.000 ARG G 264 Details of bonding type rmsd hydrogen bonds : bond 0.14982 ( 1157) hydrogen bonds : angle 6.16509 ( 3291) covalent geometry : bond 0.00359 (24684) covalent geometry : angle 0.60300 (33479) *********************** 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 201 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 201 time to evaluate : 2.855 Fit side-chains REVERT: B 418 GLU cc_start: 0.8319 (tp30) cc_final: 0.8068 (mp0) REVERT: D 56 ASP cc_start: 0.7984 (t0) cc_final: 0.7749 (t0) REVERT: D 311 ASP cc_start: 0.7999 (t70) cc_final: 0.7732 (t0) REVERT: D 469 MET cc_start: 0.8388 (mtm) cc_final: 0.8177 (mtp) REVERT: E 407 GLN cc_start: 0.8732 (tt0) cc_final: 0.8398 (tt0) REVERT: G 26 MET cc_start: 0.7575 (mmm) cc_final: 0.6866 (mmm) outliers start: 0 outliers final: 1 residues processed: 201 average time/residue: 1.5048 time to fit residues: 350.7850 Evaluate side-chains 143 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 142 time to evaluate : 2.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 136 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 261 optimal weight: 7.9990 chunk 234 optimal weight: 0.7980 chunk 130 optimal weight: 6.9990 chunk 80 optimal weight: 0.0030 chunk 158 optimal weight: 10.0000 chunk 125 optimal weight: 2.9990 chunk 242 optimal weight: 8.9990 chunk 94 optimal weight: 8.9990 chunk 147 optimal weight: 10.0000 chunk 180 optimal weight: 9.9990 chunk 281 optimal weight: 0.9990 overall best weight: 2.3596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 381 GLN E 169 GLN ** G 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 181 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.098840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.076278 restraints weight = 46670.797| |-----------------------------------------------------------------------------| r_work (start): 0.3063 rms_B_bonded: 2.48 r_work: 0.2946 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2824 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8733 moved from start: 0.0818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 24684 Z= 0.159 Angle : 0.555 7.733 33479 Z= 0.292 Chirality : 0.046 0.155 3856 Planarity : 0.004 0.041 4363 Dihedral : 8.961 155.858 3582 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.73 % Favored : 97.24 % Rotamer: Outliers : 1.05 % Allowed : 5.88 % Favored : 93.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.15), residues: 3115 helix: 1.30 (0.15), residues: 1284 sheet: 0.66 (0.22), residues: 538 loop : 0.04 (0.18), residues: 1293 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.001 HIS D 363 PHE 0.028 0.001 PHE B 350 TYR 0.015 0.001 TYR G 91 ARG 0.006 0.000 ARG G 264 Details of bonding type rmsd hydrogen bonds : bond 0.04454 ( 1157) hydrogen bonds : angle 5.06713 ( 3291) covalent geometry : bond 0.00380 (24684) covalent geometry : angle 0.55458 (33479) *********************** 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 187 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 160 time to evaluate : 2.685 Fit side-chains REVERT: A 189 GLN cc_start: 0.8074 (OUTLIER) cc_final: 0.7851 (mp10) REVERT: B 418 GLU cc_start: 0.8772 (tp30) cc_final: 0.8448 (mp0) REVERT: D 56 ASP cc_start: 0.8544 (t0) cc_final: 0.8199 (t0) REVERT: D 311 ASP cc_start: 0.8364 (t70) cc_final: 0.8021 (t0) REVERT: D 469 MET cc_start: 0.8615 (mtm) cc_final: 0.8339 (mtp) REVERT: E 407 GLN cc_start: 0.8889 (tt0) cc_final: 0.8524 (tt0) REVERT: G 26 MET cc_start: 0.7309 (mmm) cc_final: 0.6517 (mmm) REVERT: G 126 PHE cc_start: 0.5833 (m-80) cc_final: 0.5375 (m-80) outliers start: 27 outliers final: 8 residues processed: 173 average time/residue: 1.3052 time to fit residues: 263.0644 Evaluate side-chains 149 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 140 time to evaluate : 2.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 GLN Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 347 ASP Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 265 SER Chi-restraints excluded: chain E residue 98 VAL Chi-restraints excluded: chain F residue 431 LYS Chi-restraints excluded: chain G residue 271 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 129 optimal weight: 7.9990 chunk 166 optimal weight: 3.9990 chunk 30 optimal weight: 6.9990 chunk 297 optimal weight: 9.9990 chunk 81 optimal weight: 7.9990 chunk 239 optimal weight: 8.9990 chunk 126 optimal weight: 6.9990 chunk 283 optimal weight: 6.9990 chunk 128 optimal weight: 7.9990 chunk 21 optimal weight: 0.0770 chunk 51 optimal weight: 0.9980 overall best weight: 3.8144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.097098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.074630 restraints weight = 46856.223| |-----------------------------------------------------------------------------| r_work (start): 0.3032 rms_B_bonded: 2.46 r_work: 0.2916 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2793 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.2793 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8767 moved from start: 0.1073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 24684 Z= 0.226 Angle : 0.599 7.420 33479 Z= 0.314 Chirality : 0.048 0.169 3856 Planarity : 0.005 0.043 4363 Dihedral : 8.863 150.406 3580 Min Nonbonded Distance : 1.848 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.79 % Favored : 97.17 % Rotamer: Outliers : 1.29 % Allowed : 9.35 % Favored : 89.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.15), residues: 3115 helix: 1.21 (0.15), residues: 1274 sheet: 0.53 (0.22), residues: 531 loop : -0.13 (0.17), residues: 1310 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.001 HIS D 363 PHE 0.021 0.002 PHE B 350 TYR 0.019 0.002 TYR G 91 ARG 0.007 0.000 ARG E 333 Details of bonding type rmsd hydrogen bonds : bond 0.04906 ( 1157) hydrogen bonds : angle 5.06421 ( 3291) covalent geometry : bond 0.00554 (24684) covalent geometry : angle 0.59857 (33479) *********************** 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 185 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 152 time to evaluate : 2.533 Fit side-chains REVERT: B 191 MET cc_start: 0.8736 (OUTLIER) cc_final: 0.8422 (ttp) REVERT: B 418 GLU cc_start: 0.8792 (tp30) cc_final: 0.8453 (mp0) REVERT: D 56 ASP cc_start: 0.8626 (t0) cc_final: 0.8301 (t0) REVERT: D 311 ASP cc_start: 0.8444 (t70) cc_final: 0.8023 (t0) REVERT: D 469 MET cc_start: 0.8620 (mtm) cc_final: 0.8373 (mtp) REVERT: E 333 ARG cc_start: 0.8732 (tpp80) cc_final: 0.8362 (tpp-160) REVERT: E 407 GLN cc_start: 0.8902 (tt0) cc_final: 0.8547 (tt0) REVERT: G 26 MET cc_start: 0.7312 (mmm) cc_final: 0.6494 (mmm) outliers start: 33 outliers final: 14 residues processed: 171 average time/residue: 1.4109 time to fit residues: 281.1562 Evaluate side-chains 156 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 141 time to evaluate : 2.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 MET Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 485 ASP Chi-restraints excluded: chain B residue 191 MET Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 347 ASP Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 265 SER Chi-restraints excluded: chain D residue 338 MET Chi-restraints excluded: chain E residue 98 VAL Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain F residue 228 VAL Chi-restraints excluded: chain G residue 249 ASP Chi-restraints excluded: chain G residue 271 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 203 optimal weight: 6.9990 chunk 247 optimal weight: 7.9990 chunk 36 optimal weight: 10.0000 chunk 145 optimal weight: 3.9990 chunk 278 optimal weight: 4.9990 chunk 3 optimal weight: 0.9990 chunk 56 optimal weight: 7.9990 chunk 134 optimal weight: 6.9990 chunk 137 optimal weight: 6.9990 chunk 38 optimal weight: 7.9990 chunk 105 optimal weight: 0.0970 overall best weight: 3.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 196 ASN ** G 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.097161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.074615 restraints weight = 47184.686| |-----------------------------------------------------------------------------| r_work (start): 0.3031 rms_B_bonded: 2.49 r_work: 0.2918 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2797 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8765 moved from start: 0.1201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 24684 Z= 0.206 Angle : 0.579 7.367 33479 Z= 0.303 Chirality : 0.047 0.156 3856 Planarity : 0.005 0.043 4363 Dihedral : 8.634 146.543 3580 Min Nonbonded Distance : 1.861 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.89 % Favored : 97.08 % Rotamer: Outliers : 1.75 % Allowed : 10.09 % Favored : 88.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.15), residues: 3115 helix: 1.21 (0.15), residues: 1275 sheet: 0.48 (0.22), residues: 516 loop : -0.21 (0.17), residues: 1324 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.001 HIS D 363 PHE 0.018 0.002 PHE G 125 TYR 0.018 0.001 TYR G 91 ARG 0.005 0.000 ARG E 333 Details of bonding type rmsd hydrogen bonds : bond 0.04666 ( 1157) hydrogen bonds : angle 4.98151 ( 3291) covalent geometry : bond 0.00505 (24684) covalent geometry : angle 0.57919 (33479) *********************** 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 198 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 153 time to evaluate : 4.406 Fit side-chains REVERT: B 191 MET cc_start: 0.8715 (OUTLIER) cc_final: 0.8467 (ttp) REVERT: B 418 GLU cc_start: 0.8753 (tp30) cc_final: 0.8424 (mp0) REVERT: B 435 LEU cc_start: 0.9085 (OUTLIER) cc_final: 0.8847 (mm) REVERT: C 499 VAL cc_start: 0.9107 (OUTLIER) cc_final: 0.8877 (m) REVERT: D 56 ASP cc_start: 0.8662 (t0) cc_final: 0.8323 (t0) REVERT: D 311 ASP cc_start: 0.8459 (t70) cc_final: 0.8020 (t0) REVERT: D 469 MET cc_start: 0.8559 (mtm) cc_final: 0.8096 (mtm) REVERT: E 2 THR cc_start: 0.6761 (OUTLIER) cc_final: 0.6205 (t) REVERT: E 333 ARG cc_start: 0.8691 (tpp80) cc_final: 0.8332 (tpp-160) REVERT: E 407 GLN cc_start: 0.8897 (tt0) cc_final: 0.8574 (tt0) REVERT: G 26 MET cc_start: 0.7331 (mmm) cc_final: 0.6516 (mmm) REVERT: G 74 LYS cc_start: 0.3303 (tptt) cc_final: 0.3044 (tptt) REVERT: G 167 GLU cc_start: 0.6562 (OUTLIER) cc_final: 0.5907 (pp20) REVERT: G 175 TYR cc_start: 0.3775 (p90) cc_final: 0.3167 (p90) REVERT: G 191 LEU cc_start: 0.6127 (OUTLIER) cc_final: 0.5920 (tm) REVERT: G 200 ARG cc_start: 0.2636 (mpt180) cc_final: 0.1666 (tmt170) REVERT: G 267 GLN cc_start: 0.7383 (OUTLIER) cc_final: 0.6750 (pt0) REVERT: G 270 ILE cc_start: 0.7366 (OUTLIER) cc_final: 0.6859 (tp) outliers start: 45 outliers final: 23 residues processed: 186 average time/residue: 1.6299 time to fit residues: 354.0455 Evaluate side-chains 175 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 144 time to evaluate : 2.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 MET Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 320 GLU Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 485 ASP Chi-restraints excluded: chain B residue 191 MET Chi-restraints excluded: chain B residue 435 LEU Chi-restraints excluded: chain C residue 38 ILE Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 347 ASP Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain D residue 265 SER Chi-restraints excluded: chain D residue 301 THR Chi-restraints excluded: chain D residue 338 MET Chi-restraints excluded: chain E residue 2 THR Chi-restraints excluded: chain E residue 99 LEU Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain F residue 10 MET Chi-restraints excluded: chain F residue 228 VAL Chi-restraints excluded: chain F residue 301 THR Chi-restraints excluded: chain G residue 34 ARG Chi-restraints excluded: chain G residue 133 VAL Chi-restraints excluded: chain G residue 167 GLU Chi-restraints excluded: chain G residue 191 LEU Chi-restraints excluded: chain G residue 267 GLN Chi-restraints excluded: chain G residue 270 ILE Chi-restraints excluded: chain G residue 271 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 197 optimal weight: 6.9990 chunk 125 optimal weight: 6.9990 chunk 7 optimal weight: 1.9990 chunk 58 optimal weight: 0.6980 chunk 247 optimal weight: 6.9990 chunk 178 optimal weight: 8.9990 chunk 237 optimal weight: 8.9990 chunk 292 optimal weight: 0.9990 chunk 114 optimal weight: 9.9990 chunk 176 optimal weight: 8.9990 chunk 279 optimal weight: 5.9990 overall best weight: 3.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 180 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.097096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.074572 restraints weight = 47136.692| |-----------------------------------------------------------------------------| r_work (start): 0.3030 rms_B_bonded: 2.48 r_work: 0.2914 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2794 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2794 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8768 moved from start: 0.1311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 24684 Z= 0.202 Angle : 0.579 7.694 33479 Z= 0.301 Chirality : 0.047 0.156 3856 Planarity : 0.005 0.045 4363 Dihedral : 8.507 147.693 3580 Min Nonbonded Distance : 1.863 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.99 % Favored : 96.98 % Rotamer: Outliers : 2.22 % Allowed : 10.86 % Favored : 86.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.15), residues: 3115 helix: 1.25 (0.15), residues: 1268 sheet: 0.45 (0.23), residues: 517 loop : -0.24 (0.17), residues: 1330 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS D 363 PHE 0.038 0.002 PHE G 126 TYR 0.019 0.001 TYR G 91 ARG 0.005 0.000 ARG E 333 Details of bonding type rmsd hydrogen bonds : bond 0.04600 ( 1157) hydrogen bonds : angle 4.94643 ( 3291) covalent geometry : bond 0.00494 (24684) covalent geometry : angle 0.57875 (33479) *********************** 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 207 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 150 time to evaluate : 3.072 Fit side-chains REVERT: B 191 MET cc_start: 0.8692 (OUTLIER) cc_final: 0.8439 (ttp) REVERT: B 435 LEU cc_start: 0.9078 (OUTLIER) cc_final: 0.8864 (mm) REVERT: C 499 VAL cc_start: 0.9094 (OUTLIER) cc_final: 0.8880 (m) REVERT: D 56 ASP cc_start: 0.8681 (t0) cc_final: 0.8329 (t0) REVERT: D 311 ASP cc_start: 0.8438 (t70) cc_final: 0.7975 (t0) REVERT: D 469 MET cc_start: 0.8465 (mtm) cc_final: 0.8254 (mtp) REVERT: E 2 THR cc_start: 0.6655 (OUTLIER) cc_final: 0.6070 (t) REVERT: E 333 ARG cc_start: 0.8669 (tpp80) cc_final: 0.8319 (tpp-160) REVERT: E 389 MET cc_start: 0.7424 (tpt) cc_final: 0.7120 (tpp) REVERT: E 407 GLN cc_start: 0.8892 (tt0) cc_final: 0.8566 (tt0) REVERT: G 26 MET cc_start: 0.7300 (mmm) cc_final: 0.6510 (mmm) REVERT: G 167 GLU cc_start: 0.6594 (OUTLIER) cc_final: 0.5909 (pp20) REVERT: G 175 TYR cc_start: 0.3894 (p90) cc_final: 0.3325 (p90) REVERT: G 200 ARG cc_start: 0.2436 (mpt180) cc_final: 0.1477 (tmt170) REVERT: G 267 GLN cc_start: 0.7550 (OUTLIER) cc_final: 0.7076 (pt0) REVERT: G 270 ILE cc_start: 0.7250 (OUTLIER) cc_final: 0.6710 (tp) outliers start: 57 outliers final: 33 residues processed: 195 average time/residue: 1.2697 time to fit residues: 292.2587 Evaluate side-chains 179 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 139 time to evaluate : 3.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 MET Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 320 GLU Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 485 ASP Chi-restraints excluded: chain B residue 191 MET Chi-restraints excluded: chain B residue 435 LEU Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain C residue 38 ILE Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 314 THR Chi-restraints excluded: chain C residue 347 ASP Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain D residue 265 SER Chi-restraints excluded: chain D residue 301 THR Chi-restraints excluded: chain D residue 314 THR Chi-restraints excluded: chain D residue 338 MET Chi-restraints excluded: chain E residue 2 THR Chi-restraints excluded: chain E residue 99 LEU Chi-restraints excluded: chain E residue 258 THR Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain E residue 359 VAL Chi-restraints excluded: chain E residue 392 LEU Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 228 VAL Chi-restraints excluded: chain F residue 301 THR Chi-restraints excluded: chain F residue 421 THR Chi-restraints excluded: chain F residue 440 ILE Chi-restraints excluded: chain G residue 34 ARG Chi-restraints excluded: chain G residue 133 VAL Chi-restraints excluded: chain G residue 167 GLU Chi-restraints excluded: chain G residue 267 GLN Chi-restraints excluded: chain G residue 270 ILE Chi-restraints excluded: chain G residue 271 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 265 optimal weight: 6.9990 chunk 207 optimal weight: 7.9990 chunk 61 optimal weight: 3.9990 chunk 239 optimal weight: 0.8980 chunk 150 optimal weight: 3.9990 chunk 196 optimal weight: 0.8980 chunk 99 optimal weight: 0.9990 chunk 72 optimal weight: 3.9990 chunk 149 optimal weight: 7.9990 chunk 186 optimal weight: 2.9990 chunk 176 optimal weight: 4.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.098670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.075941 restraints weight = 46730.334| |-----------------------------------------------------------------------------| r_work (start): 0.3054 rms_B_bonded: 2.48 r_work: 0.2939 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2817 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8747 moved from start: 0.1353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 24684 Z= 0.138 Angle : 0.544 9.933 33479 Z= 0.280 Chirality : 0.045 0.150 3856 Planarity : 0.004 0.043 4363 Dihedral : 8.163 153.564 3580 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.76 % Favored : 97.21 % Rotamer: Outliers : 1.91 % Allowed : 11.49 % Favored : 86.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.88 (0.15), residues: 3115 helix: 1.42 (0.15), residues: 1271 sheet: 0.56 (0.23), residues: 508 loop : -0.12 (0.17), residues: 1336 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS D 363 PHE 0.015 0.001 PHE A 350 TYR 0.016 0.001 TYR G 91 ARG 0.006 0.000 ARG G 34 Details of bonding type rmsd hydrogen bonds : bond 0.04005 ( 1157) hydrogen bonds : angle 4.78940 ( 3291) covalent geometry : bond 0.00328 (24684) covalent geometry : angle 0.54425 (33479) *********************** 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 203 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 154 time to evaluate : 3.407 Fit side-chains REVERT: A 189 GLN cc_start: 0.8131 (OUTLIER) cc_final: 0.7915 (mp10) REVERT: B 191 MET cc_start: 0.8629 (OUTLIER) cc_final: 0.8323 (ttp) REVERT: B 435 LEU cc_start: 0.9059 (OUTLIER) cc_final: 0.8843 (mm) REVERT: C 499 VAL cc_start: 0.9098 (OUTLIER) cc_final: 0.8886 (m) REVERT: D 56 ASP cc_start: 0.8665 (t0) cc_final: 0.8273 (t0) REVERT: D 311 ASP cc_start: 0.8424 (t70) cc_final: 0.7918 (t0) REVERT: D 469 MET cc_start: 0.8449 (mtm) cc_final: 0.8017 (mtm) REVERT: E 2 THR cc_start: 0.6624 (OUTLIER) cc_final: 0.6063 (t) REVERT: E 333 ARG cc_start: 0.8652 (tpp80) cc_final: 0.8314 (tpp-160) REVERT: E 407 GLN cc_start: 0.8868 (tt0) cc_final: 0.8521 (tt0) REVERT: G 26 MET cc_start: 0.7327 (mmm) cc_final: 0.6533 (mmm) REVERT: G 126 PHE cc_start: 0.6014 (m-80) cc_final: 0.5602 (m-80) REVERT: G 143 GLN cc_start: 0.5814 (pp30) cc_final: 0.5546 (pp30) REVERT: G 167 GLU cc_start: 0.6473 (OUTLIER) cc_final: 0.5901 (pp20) REVERT: G 175 TYR cc_start: 0.3844 (p90) cc_final: 0.3218 (p90) REVERT: G 267 GLN cc_start: 0.7467 (OUTLIER) cc_final: 0.7000 (pt0) REVERT: G 270 ILE cc_start: 0.7140 (OUTLIER) cc_final: 0.6652 (tp) REVERT: G 273 GLU cc_start: 0.8735 (OUTLIER) cc_final: 0.8407 (pp20) outliers start: 49 outliers final: 29 residues processed: 191 average time/residue: 1.5294 time to fit residues: 344.6045 Evaluate side-chains 181 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 143 time to evaluate : 3.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 189 GLN Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 320 GLU Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 485 ASP Chi-restraints excluded: chain B residue 129 ILE Chi-restraints excluded: chain B residue 191 MET Chi-restraints excluded: chain B residue 262 ASP Chi-restraints excluded: chain B residue 435 LEU Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain C residue 38 ILE Chi-restraints excluded: chain C residue 314 THR Chi-restraints excluded: chain C residue 347 ASP Chi-restraints excluded: chain C residue 366 VAL Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain D residue 265 SER Chi-restraints excluded: chain D residue 301 THR Chi-restraints excluded: chain D residue 338 MET Chi-restraints excluded: chain E residue 2 THR Chi-restraints excluded: chain E residue 99 LEU Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain E residue 392 LEU Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 301 THR Chi-restraints excluded: chain F residue 387 LEU Chi-restraints excluded: chain F residue 421 THR Chi-restraints excluded: chain G residue 34 ARG Chi-restraints excluded: chain G residue 133 VAL Chi-restraints excluded: chain G residue 167 GLU Chi-restraints excluded: chain G residue 267 GLN Chi-restraints excluded: chain G residue 270 ILE Chi-restraints excluded: chain G residue 271 THR Chi-restraints excluded: chain G residue 273 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 281 optimal weight: 2.9990 chunk 264 optimal weight: 9.9990 chunk 114 optimal weight: 5.9990 chunk 45 optimal weight: 6.9990 chunk 131 optimal weight: 7.9990 chunk 240 optimal weight: 0.5980 chunk 254 optimal weight: 10.0000 chunk 29 optimal weight: 1.9990 chunk 200 optimal weight: 0.9990 chunk 182 optimal weight: 8.9990 chunk 271 optimal weight: 5.9990 overall best weight: 2.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 55 ASN ** G 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.097859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.075282 restraints weight = 47313.580| |-----------------------------------------------------------------------------| r_work (start): 0.3042 rms_B_bonded: 2.50 r_work: 0.2926 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2803 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2803 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8750 moved from start: 0.1412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 24684 Z= 0.163 Angle : 0.556 10.280 33479 Z= 0.286 Chirality : 0.045 0.153 3856 Planarity : 0.004 0.043 4363 Dihedral : 8.174 163.086 3580 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.92 % Favored : 97.05 % Rotamer: Outliers : 2.10 % Allowed : 11.76 % Favored : 86.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.88 (0.15), residues: 3115 helix: 1.45 (0.15), residues: 1262 sheet: 0.57 (0.23), residues: 500 loop : -0.15 (0.17), residues: 1353 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS D 363 PHE 0.014 0.001 PHE A 350 TYR 0.017 0.001 TYR G 91 ARG 0.006 0.000 ARG G 34 Details of bonding type rmsd hydrogen bonds : bond 0.04184 ( 1157) hydrogen bonds : angle 4.78196 ( 3291) covalent geometry : bond 0.00395 (24684) covalent geometry : angle 0.55596 (33479) *********************** 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 205 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 151 time to evaluate : 3.466 Fit side-chains REVERT: A 189 GLN cc_start: 0.8149 (OUTLIER) cc_final: 0.7923 (mp10) REVERT: B 191 MET cc_start: 0.8648 (OUTLIER) cc_final: 0.8335 (ttp) REVERT: B 435 LEU cc_start: 0.9054 (OUTLIER) cc_final: 0.8838 (mm) REVERT: D 56 ASP cc_start: 0.8618 (t0) cc_final: 0.8233 (t0) REVERT: D 311 ASP cc_start: 0.8460 (t70) cc_final: 0.7960 (t0) REVERT: D 469 MET cc_start: 0.8424 (mtm) cc_final: 0.8206 (mtp) REVERT: E 2 THR cc_start: 0.6629 (OUTLIER) cc_final: 0.6054 (t) REVERT: E 333 ARG cc_start: 0.8673 (tpp80) cc_final: 0.8327 (tpp-160) REVERT: E 389 MET cc_start: 0.7480 (tpt) cc_final: 0.7175 (tpp) REVERT: G 26 MET cc_start: 0.7245 (mmm) cc_final: 0.6424 (mmm) REVERT: G 125 PHE cc_start: 0.6535 (t80) cc_final: 0.6319 (t80) REVERT: G 126 PHE cc_start: 0.6181 (m-80) cc_final: 0.5718 (m-80) REVERT: G 143 GLN cc_start: 0.5757 (pp30) cc_final: 0.5474 (pp30) REVERT: G 167 GLU cc_start: 0.6491 (OUTLIER) cc_final: 0.5905 (pp20) REVERT: G 175 TYR cc_start: 0.3847 (p90) cc_final: 0.3216 (p90) REVERT: G 267 GLN cc_start: 0.7439 (OUTLIER) cc_final: 0.6949 (pt0) REVERT: G 270 ILE cc_start: 0.7212 (OUTLIER) cc_final: 0.6690 (tp) REVERT: G 273 GLU cc_start: 0.8735 (OUTLIER) cc_final: 0.8330 (pp20) outliers start: 54 outliers final: 35 residues processed: 192 average time/residue: 1.8003 time to fit residues: 404.4597 Evaluate side-chains 185 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 142 time to evaluate : 2.884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 189 GLN Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 320 GLU Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 485 ASP Chi-restraints excluded: chain B residue 129 ILE Chi-restraints excluded: chain B residue 191 MET Chi-restraints excluded: chain B residue 262 ASP Chi-restraints excluded: chain B residue 435 LEU Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain C residue 38 ILE Chi-restraints excluded: chain C residue 314 THR Chi-restraints excluded: chain C residue 347 ASP Chi-restraints excluded: chain C residue 366 VAL Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain D residue 265 SER Chi-restraints excluded: chain D residue 301 THR Chi-restraints excluded: chain D residue 338 MET Chi-restraints excluded: chain E residue 2 THR Chi-restraints excluded: chain E residue 10 MET Chi-restraints excluded: chain E residue 99 LEU Chi-restraints excluded: chain E residue 258 THR Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain E residue 359 VAL Chi-restraints excluded: chain E residue 392 LEU Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 228 VAL Chi-restraints excluded: chain F residue 301 THR Chi-restraints excluded: chain F residue 387 LEU Chi-restraints excluded: chain F residue 421 THR Chi-restraints excluded: chain F residue 440 ILE Chi-restraints excluded: chain G residue 34 ARG Chi-restraints excluded: chain G residue 133 VAL Chi-restraints excluded: chain G residue 167 GLU Chi-restraints excluded: chain G residue 267 GLN Chi-restraints excluded: chain G residue 270 ILE Chi-restraints excluded: chain G residue 271 THR Chi-restraints excluded: chain G residue 273 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 256 optimal weight: 8.9990 chunk 245 optimal weight: 5.9990 chunk 250 optimal weight: 4.9990 chunk 299 optimal weight: 30.0000 chunk 67 optimal weight: 0.0370 chunk 159 optimal weight: 8.9990 chunk 173 optimal weight: 10.0000 chunk 109 optimal weight: 1.9990 chunk 70 optimal weight: 3.9990 chunk 274 optimal weight: 6.9990 chunk 306 optimal weight: 6.9990 overall best weight: 3.4066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.096619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.074367 restraints weight = 47423.543| |-----------------------------------------------------------------------------| r_work (start): 0.3023 rms_B_bonded: 2.45 r_work: 0.2910 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2789 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8765 moved from start: 0.1456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 24684 Z= 0.206 Angle : 0.594 11.103 33479 Z= 0.304 Chirality : 0.047 0.156 3856 Planarity : 0.005 0.043 4363 Dihedral : 8.364 173.002 3580 Min Nonbonded Distance : 1.858 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.99 % Favored : 96.98 % Rotamer: Outliers : 2.10 % Allowed : 12.31 % Favored : 85.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.15), residues: 3115 helix: 1.36 (0.15), residues: 1262 sheet: 0.49 (0.23), residues: 501 loop : -0.21 (0.17), residues: 1352 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS D 363 PHE 0.015 0.001 PHE E 125 TYR 0.018 0.001 TYR G 91 ARG 0.011 0.000 ARG G 154 Details of bonding type rmsd hydrogen bonds : bond 0.04521 ( 1157) hydrogen bonds : angle 4.84344 ( 3291) covalent geometry : bond 0.00505 (24684) covalent geometry : angle 0.59373 (33479) *********************** 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 195 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 141 time to evaluate : 3.810 Fit side-chains REVERT: B 191 MET cc_start: 0.8637 (OUTLIER) cc_final: 0.8374 (ttp) REVERT: B 435 LEU cc_start: 0.9065 (OUTLIER) cc_final: 0.8838 (mm) REVERT: D 56 ASP cc_start: 0.8628 (t0) cc_final: 0.8219 (t0) REVERT: D 311 ASP cc_start: 0.8478 (t70) cc_final: 0.7992 (t0) REVERT: D 469 MET cc_start: 0.8411 (mtm) cc_final: 0.8200 (mtp) REVERT: E 2 THR cc_start: 0.6674 (OUTLIER) cc_final: 0.6116 (t) REVERT: E 45 ASP cc_start: 0.8870 (t0) cc_final: 0.8638 (m-30) REVERT: E 333 ARG cc_start: 0.8676 (tpp80) cc_final: 0.8333 (tpp-160) REVERT: E 407 GLN cc_start: 0.8719 (tt0) cc_final: 0.8472 (tt0) REVERT: G 5 ARG cc_start: 0.6758 (OUTLIER) cc_final: 0.6243 (ttm-80) REVERT: G 26 MET cc_start: 0.7225 (mmm) cc_final: 0.6430 (mmm) REVERT: G 125 PHE cc_start: 0.6639 (t80) cc_final: 0.6393 (t80) REVERT: G 126 PHE cc_start: 0.6329 (m-80) cc_final: 0.5893 (m-80) REVERT: G 143 GLN cc_start: 0.5523 (pp30) cc_final: 0.5321 (pp30) REVERT: G 167 GLU cc_start: 0.6630 (OUTLIER) cc_final: 0.5961 (pp20) REVERT: G 175 TYR cc_start: 0.3889 (p90) cc_final: 0.3252 (p90) REVERT: G 267 GLN cc_start: 0.7511 (OUTLIER) cc_final: 0.7019 (pt0) REVERT: G 270 ILE cc_start: 0.7166 (OUTLIER) cc_final: 0.6631 (tp) REVERT: G 273 GLU cc_start: 0.8772 (OUTLIER) cc_final: 0.8393 (pp20) outliers start: 54 outliers final: 39 residues processed: 184 average time/residue: 1.3469 time to fit residues: 295.3286 Evaluate side-chains 187 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 140 time to evaluate : 2.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 320 GLU Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 485 ASP Chi-restraints excluded: chain B residue 129 ILE Chi-restraints excluded: chain B residue 191 MET Chi-restraints excluded: chain B residue 262 ASP Chi-restraints excluded: chain B residue 435 LEU Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 38 ILE Chi-restraints excluded: chain C residue 314 THR Chi-restraints excluded: chain C residue 347 ASP Chi-restraints excluded: chain C residue 366 VAL Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain D residue 265 SER Chi-restraints excluded: chain D residue 301 THR Chi-restraints excluded: chain D residue 314 THR Chi-restraints excluded: chain D residue 338 MET Chi-restraints excluded: chain E residue 2 THR Chi-restraints excluded: chain E residue 10 MET Chi-restraints excluded: chain E residue 99 LEU Chi-restraints excluded: chain E residue 258 THR Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain E residue 359 VAL Chi-restraints excluded: chain E residue 392 LEU Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 228 VAL Chi-restraints excluded: chain F residue 301 THR Chi-restraints excluded: chain F residue 386 ILE Chi-restraints excluded: chain F residue 387 LEU Chi-restraints excluded: chain F residue 421 THR Chi-restraints excluded: chain F residue 440 ILE Chi-restraints excluded: chain G residue 5 ARG Chi-restraints excluded: chain G residue 34 ARG Chi-restraints excluded: chain G residue 133 VAL Chi-restraints excluded: chain G residue 167 GLU Chi-restraints excluded: chain G residue 267 GLN Chi-restraints excluded: chain G residue 270 ILE Chi-restraints excluded: chain G residue 271 THR Chi-restraints excluded: chain G residue 273 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 278 optimal weight: 3.9990 chunk 247 optimal weight: 3.9990 chunk 193 optimal weight: 7.9990 chunk 75 optimal weight: 0.9990 chunk 194 optimal weight: 3.9990 chunk 16 optimal weight: 2.9990 chunk 135 optimal weight: 2.9990 chunk 61 optimal weight: 4.9990 chunk 230 optimal weight: 8.9990 chunk 210 optimal weight: 0.5980 chunk 149 optimal weight: 5.9990 overall best weight: 2.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 107 HIS ** G 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.097488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.075268 restraints weight = 47369.071| |-----------------------------------------------------------------------------| r_work (start): 0.3039 rms_B_bonded: 2.46 r_work: 0.2926 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2805 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8746 moved from start: 0.1479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 24684 Z= 0.154 Angle : 0.561 11.631 33479 Z= 0.287 Chirality : 0.045 0.151 3856 Planarity : 0.004 0.043 4363 Dihedral : 8.240 177.710 3580 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.95 % Favored : 97.01 % Rotamer: Outliers : 1.95 % Allowed : 12.69 % Favored : 85.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.15), residues: 3115 helix: 1.44 (0.15), residues: 1263 sheet: 0.61 (0.24), residues: 481 loop : -0.17 (0.17), residues: 1371 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS D 363 PHE 0.013 0.001 PHE B 350 TYR 0.017 0.001 TYR G 91 ARG 0.009 0.000 ARG G 154 Details of bonding type rmsd hydrogen bonds : bond 0.04142 ( 1157) hydrogen bonds : angle 4.75164 ( 3291) covalent geometry : bond 0.00369 (24684) covalent geometry : angle 0.56147 (33479) *********************** 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 200 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 150 time to evaluate : 2.990 Fit side-chains REVERT: B 191 MET cc_start: 0.8619 (OUTLIER) cc_final: 0.8298 (ttp) REVERT: B 435 LEU cc_start: 0.9035 (OUTLIER) cc_final: 0.8833 (mm) REVERT: D 56 ASP cc_start: 0.8601 (t0) cc_final: 0.8197 (t0) REVERT: D 311 ASP cc_start: 0.8484 (t70) cc_final: 0.7993 (t0) REVERT: D 469 MET cc_start: 0.8382 (mtm) cc_final: 0.8178 (mtp) REVERT: E 2 THR cc_start: 0.6675 (OUTLIER) cc_final: 0.6119 (t) REVERT: E 45 ASP cc_start: 0.8861 (t0) cc_final: 0.8628 (m-30) REVERT: E 333 ARG cc_start: 0.8656 (tpp80) cc_final: 0.8320 (tpp-160) REVERT: E 407 GLN cc_start: 0.8708 (tt0) cc_final: 0.8463 (tt0) REVERT: G 26 MET cc_start: 0.7209 (mmm) cc_final: 0.6433 (mmm) REVERT: G 125 PHE cc_start: 0.6627 (t80) cc_final: 0.6359 (t80) REVERT: G 126 PHE cc_start: 0.6238 (m-80) cc_final: 0.5758 (m-80) REVERT: G 167 GLU cc_start: 0.6572 (OUTLIER) cc_final: 0.5938 (pp20) REVERT: G 175 TYR cc_start: 0.3908 (p90) cc_final: 0.3242 (p90) REVERT: G 267 GLN cc_start: 0.7441 (OUTLIER) cc_final: 0.6952 (pt0) REVERT: G 270 ILE cc_start: 0.7127 (OUTLIER) cc_final: 0.6600 (tp) REVERT: G 273 GLU cc_start: 0.8759 (OUTLIER) cc_final: 0.8379 (pp20) outliers start: 50 outliers final: 38 residues processed: 189 average time/residue: 1.7245 time to fit residues: 384.2461 Evaluate side-chains 188 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 143 time to evaluate : 3.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 MET Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 320 GLU Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain B residue 129 ILE Chi-restraints excluded: chain B residue 191 MET Chi-restraints excluded: chain B residue 262 ASP Chi-restraints excluded: chain B residue 435 LEU Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 38 ILE Chi-restraints excluded: chain C residue 80 THR Chi-restraints excluded: chain C residue 314 THR Chi-restraints excluded: chain C residue 347 ASP Chi-restraints excluded: chain C residue 366 VAL Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain D residue 265 SER Chi-restraints excluded: chain D residue 314 THR Chi-restraints excluded: chain D residue 338 MET Chi-restraints excluded: chain E residue 2 THR Chi-restraints excluded: chain E residue 10 MET Chi-restraints excluded: chain E residue 99 LEU Chi-restraints excluded: chain E residue 258 THR Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain E residue 359 VAL Chi-restraints excluded: chain E residue 392 LEU Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 228 VAL Chi-restraints excluded: chain F residue 301 THR Chi-restraints excluded: chain F residue 386 ILE Chi-restraints excluded: chain F residue 387 LEU Chi-restraints excluded: chain F residue 421 THR Chi-restraints excluded: chain F residue 440 ILE Chi-restraints excluded: chain G residue 34 ARG Chi-restraints excluded: chain G residue 133 VAL Chi-restraints excluded: chain G residue 167 GLU Chi-restraints excluded: chain G residue 267 GLN Chi-restraints excluded: chain G residue 270 ILE Chi-restraints excluded: chain G residue 271 THR Chi-restraints excluded: chain G residue 273 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 220 optimal weight: 4.9990 chunk 52 optimal weight: 2.9990 chunk 179 optimal weight: 7.9990 chunk 253 optimal weight: 9.9990 chunk 113 optimal weight: 1.9990 chunk 109 optimal weight: 1.9990 chunk 224 optimal weight: 10.0000 chunk 134 optimal weight: 2.9990 chunk 159 optimal weight: 9.9990 chunk 130 optimal weight: 6.9990 chunk 9 optimal weight: 0.0030 overall best weight: 1.9998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 219 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.097982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.075778 restraints weight = 47091.284| |-----------------------------------------------------------------------------| r_work (start): 0.3048 rms_B_bonded: 2.45 r_work: 0.2935 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2814 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8739 moved from start: 0.1506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 24684 Z= 0.142 Angle : 0.562 12.036 33479 Z= 0.287 Chirality : 0.045 0.163 3856 Planarity : 0.004 0.043 4363 Dihedral : 8.115 177.643 3580 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.83 % Favored : 97.14 % Rotamer: Outliers : 1.87 % Allowed : 13.01 % Favored : 85.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.93 (0.15), residues: 3115 helix: 1.50 (0.15), residues: 1265 sheet: 0.61 (0.23), residues: 500 loop : -0.14 (0.17), residues: 1350 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS D 363 PHE 0.012 0.001 PHE A 350 TYR 0.016 0.001 TYR G 91 ARG 0.009 0.000 ARG G 154 Details of bonding type rmsd hydrogen bonds : bond 0.03986 ( 1157) hydrogen bonds : angle 4.70655 ( 3291) covalent geometry : bond 0.00339 (24684) covalent geometry : angle 0.56247 (33479) ********************** 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 199 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 151 time to evaluate : 2.606 Fit side-chains REVERT: B 191 MET cc_start: 0.8599 (OUTLIER) cc_final: 0.8284 (ttp) REVERT: D 56 ASP cc_start: 0.8591 (t0) cc_final: 0.8193 (t0) REVERT: D 311 ASP cc_start: 0.8467 (t70) cc_final: 0.7978 (t0) REVERT: D 469 MET cc_start: 0.8390 (mtm) cc_final: 0.8174 (mtp) REVERT: E 2 THR cc_start: 0.6665 (OUTLIER) cc_final: 0.6097 (t) REVERT: E 45 ASP cc_start: 0.8841 (t0) cc_final: 0.8581 (m-30) REVERT: E 333 ARG cc_start: 0.8653 (tpp80) cc_final: 0.8321 (tpp-160) REVERT: E 389 MET cc_start: 0.7462 (tpt) cc_final: 0.7151 (tpp) REVERT: E 407 GLN cc_start: 0.8686 (tt0) cc_final: 0.8440 (tt0) REVERT: G 5 ARG cc_start: 0.6731 (OUTLIER) cc_final: 0.6168 (ttm-80) REVERT: G 26 MET cc_start: 0.7207 (mmm) cc_final: 0.6441 (mmm) REVERT: G 125 PHE cc_start: 0.6634 (t80) cc_final: 0.6386 (t80) REVERT: G 126 PHE cc_start: 0.6224 (m-80) cc_final: 0.5793 (m-80) REVERT: G 167 GLU cc_start: 0.6589 (OUTLIER) cc_final: 0.5945 (pp20) REVERT: G 175 TYR cc_start: 0.3935 (p90) cc_final: 0.3318 (p90) REVERT: G 270 ILE cc_start: 0.7193 (OUTLIER) cc_final: 0.6683 (tp) REVERT: G 273 GLU cc_start: 0.8756 (OUTLIER) cc_final: 0.8362 (pp20) outliers start: 48 outliers final: 35 residues processed: 187 average time/residue: 1.2111 time to fit residues: 266.1652 Evaluate side-chains 187 residues out of total 2568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 146 time to evaluate : 2.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain B residue 129 ILE Chi-restraints excluded: chain B residue 191 MET Chi-restraints excluded: chain B residue 262 ASP Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 38 ILE Chi-restraints excluded: chain C residue 80 THR Chi-restraints excluded: chain C residue 314 THR Chi-restraints excluded: chain C residue 347 ASP Chi-restraints excluded: chain C residue 366 VAL Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain D residue 265 SER Chi-restraints excluded: chain D residue 301 THR Chi-restraints excluded: chain D residue 338 MET Chi-restraints excluded: chain E residue 2 THR Chi-restraints excluded: chain E residue 10 MET Chi-restraints excluded: chain E residue 99 LEU Chi-restraints excluded: chain E residue 258 THR Chi-restraints excluded: chain E residue 301 THR Chi-restraints excluded: chain E residue 359 VAL Chi-restraints excluded: chain E residue 392 LEU Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 228 VAL Chi-restraints excluded: chain F residue 301 THR Chi-restraints excluded: chain F residue 386 ILE Chi-restraints excluded: chain F residue 421 THR Chi-restraints excluded: chain F residue 440 ILE Chi-restraints excluded: chain G residue 5 ARG Chi-restraints excluded: chain G residue 34 ARG Chi-restraints excluded: chain G residue 133 VAL Chi-restraints excluded: chain G residue 167 GLU Chi-restraints excluded: chain G residue 270 ILE Chi-restraints excluded: chain G residue 271 THR Chi-restraints excluded: chain G residue 273 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 64 optimal weight: 0.9990 chunk 17 optimal weight: 8.9990 chunk 198 optimal weight: 5.9990 chunk 47 optimal weight: 10.0000 chunk 51 optimal weight: 6.9990 chunk 15 optimal weight: 0.9980 chunk 136 optimal weight: 4.9990 chunk 94 optimal weight: 10.0000 chunk 239 optimal weight: 1.9990 chunk 75 optimal weight: 7.9990 chunk 93 optimal weight: 10.0000 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 219 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.097021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.074741 restraints weight = 47277.945| |-----------------------------------------------------------------------------| r_work (start): 0.3030 rms_B_bonded: 2.46 r_work: 0.2917 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2796 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8757 moved from start: 0.1540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 24684 Z= 0.188 Angle : 0.596 12.166 33479 Z= 0.305 Chirality : 0.046 0.155 3856 Planarity : 0.004 0.043 4363 Dihedral : 8.245 171.461 3580 Min Nonbonded Distance : 1.867 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.02 % Favored : 96.95 % Rotamer: Outliers : 1.75 % Allowed : 13.32 % Favored : 84.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.15), residues: 3115 helix: 1.41 (0.15), residues: 1261 sheet: 0.59 (0.23), residues: 497 loop : -0.21 (0.17), residues: 1357 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS D 363 PHE 0.017 0.001 PHE G 42 TYR 0.018 0.001 TYR G 91 ARG 0.009 0.000 ARG G 154 Details of bonding type rmsd hydrogen bonds : bond 0.04407 ( 1157) hydrogen bonds : angle 4.80364 ( 3291) covalent geometry : bond 0.00458 (24684) covalent geometry : angle 0.59564 (33479) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16432.50 seconds wall clock time: 292 minutes 13.18 seconds (17533.18 seconds total)