Starting phenix.real_space_refine on Mon Sep 30 04:51:07 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hh8_34755/09_2024/8hh8_34755.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hh8_34755/09_2024/8hh8_34755.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hh8_34755/09_2024/8hh8_34755.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hh8_34755/09_2024/8hh8_34755.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hh8_34755/09_2024/8hh8_34755.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hh8_34755/09_2024/8hh8_34755.cif" } resolution = 2.8 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 16 5.49 5 Mg 5 5.21 5 S 77 5.16 5 C 15277 2.51 5 N 4214 2.21 5 O 4661 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 24250 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 3661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 478, 3661 Classifications: {'peptide': 478} Link IDs: {'PTRANS': 23, 'TRANS': 454} Chain: "B" Number of atoms: 3661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 478, 3661 Classifications: {'peptide': 478} Link IDs: {'PTRANS': 23, 'TRANS': 454} Chain: "C" Number of atoms: 3661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 478, 3661 Classifications: {'peptide': 478} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 454} Chain: "D" Number of atoms: 3630 Number of conformers: 1 Conformer: "" Number of residues, atoms: 471, 3630 Classifications: {'peptide': 471} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 447} Chain: "E" Number of atoms: 3623 Number of conformers: 1 Conformer: "" Number of residues, atoms: 470, 3623 Classifications: {'peptide': 470} Link IDs: {'PTRANS': 23, 'TRANS': 446} Chain: "F" Number of atoms: 3630 Number of conformers: 1 Conformer: "" Number of residues, atoms: 471, 3630 Classifications: {'peptide': 471} Link IDs: {'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: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 272} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, 'ADP': 1, 'PO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Unusual residues: {'PO4': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 15.38, per 1000 atoms: 0.63 Number of scatterers: 24250 At special positions: 0 Unit cell: (127.6, 122.32, 154.88, 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 16 15.00 Mg 5 11.99 O 4661 8.00 N 4214 7.00 C 15277 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: 6.27 Conformation dependent library (CDL) restraints added in 3.1 seconds 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5712 Finding SS restraints... Secondary structure from input PDB file: 131 helices and 20 sheets defined 48.1% alpha, 16.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.20 Creating SS restraints... Processing helix chain 'A' and resid 100 through 104 Processing helix chain 'A' and resid 150 through 157 Processing helix chain 'A' and resid 174 through 186 removed outlier: 3.605A 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: 3.590A pdb=" N LEU A 235 " --> pdb=" O PRO A 231 " (cutoff:3.500A) Proline residue: A 239 - end of helix removed outlier: 3.645A pdb=" N TYR A 248 " --> pdb=" O ALA A 244 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N PHE A 249 " --> pdb=" O MET A 245 " (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 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 391 removed outlier: 3.803A pdb=" N VAL A 378 " --> pdb=" O ALA A 374 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N GLY A 380 " --> pdb=" O LYS A 376 " (cutoff:3.500A) removed outlier: 5.438A pdb=" N THR A 381 " --> pdb=" O LYS A 377 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLU A 391 " --> pdb=" O ALA A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 393 through 397 removed outlier: 4.030A pdb=" N GLN A 397 " --> pdb=" O ALA A 394 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 421 removed outlier: 3.550A pdb=" N LYS A 421 " --> pdb=" O VAL A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 442 removed outlier: 3.623A pdb=" N LEU A 435 " --> pdb=" O GLU A 431 " (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 removed outlier: 3.550A pdb=" N ASP A 465 " --> pdb=" O TYR A 461 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLN A 466 " --> pdb=" O LEU A 462 " (cutoff:3.500A) Processing helix chain 'A' and resid 468 through 479 Processing helix chain 'A' and resid 483 through 498 removed outlier: 3.572A pdb=" N THR A 497 " --> pdb=" O ALA A 493 " (cutoff:3.500A) Processing helix chain 'B' and resid 100 through 104 removed outlier: 3.569A pdb=" N LEU B 103 " --> pdb=" O GLY B 100 " (cutoff:3.500A) Processing helix chain 'B' and resid 135 through 139 removed outlier: 3.741A pdb=" N ARG B 139 " --> pdb=" O VAL B 136 " (cutoff:3.500A) Processing helix chain 'B' and resid 150 through 157 Processing helix chain 'B' and resid 174 through 186 removed outlier: 3.602A 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 252 removed outlier: 3.645A pdb=" N LEU B 235 " --> pdb=" O PRO B 231 " (cutoff:3.500A) Proline residue: B 239 - end of helix removed outlier: 3.668A pdb=" N TYR B 248 " --> pdb=" O ALA B 244 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N PHE B 249 " --> pdb=" O MET B 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 262 through 277 Processing helix chain 'B' and resid 282 through 286 Processing helix chain 'B' and resid 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: 3.700A pdb=" N HIS B 294 " --> pdb=" O ILE B 290 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LEU B 297 " --> pdb=" O LEU B 293 " (cutoff:3.500A) Processing helix chain 'B' and resid 328 through 336 Processing helix chain 'B' and resid 345 through 350 Processing helix chain 'B' and resid 372 through 399 removed outlier: 3.979A pdb=" N GLY B 380 " --> pdb=" O LYS B 376 " (cutoff:3.500A) removed outlier: 5.560A pdb=" N THR B 381 " --> pdb=" O LYS B 377 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N LEU B 382 " --> pdb=" O VAL B 378 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LEU B 392 " --> pdb=" O ALA B 388 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N ALA B 394 " --> pdb=" O ARG B 390 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N PHE B 395 " --> pdb=" O GLU B 391 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N PHE B 398 " --> pdb=" O ALA B 394 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 420 removed outlier: 3.543A pdb=" N ARG B 415 " --> pdb=" O ALA B 411 " (cutoff:3.500A) Processing helix chain 'B' and resid 429 through 442 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: 3.610A 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 483 through 498 Processing helix chain 'C' and resid 100 through 104 removed outlier: 3.678A 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 removed outlier: 3.586A pdb=" N GLN C 186 " --> pdb=" O THR C 182 " (cutoff:3.500A) Processing helix chain 'C' and resid 201 through 215 Processing helix chain 'C' and resid 216 through 219 removed outlier: 3.551A pdb=" N ASP C 219 " --> pdb=" O GLY C 216 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 216 through 219' Processing helix chain 'C' and resid 231 through 251 removed outlier: 3.567A pdb=" N LEU C 235 " --> pdb=" O PRO C 231 " (cutoff:3.500A) Proline residue: C 239 - end of helix removed outlier: 3.768A 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 287 through 288 No H-bonds generated for 'chain 'C' and resid 287 through 288' Processing helix chain 'C' and resid 289 through 299 removed outlier: 3.599A pdb=" N HIS C 294 " --> pdb=" O ILE C 290 " (cutoff:3.500A) Processing helix chain 'C' and resid 305 through 309 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 396 removed outlier: 3.702A pdb=" N GLY C 380 " --> pdb=" O LYS C 376 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N THR C 381 " --> pdb=" O LYS C 377 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLU C 393 " --> pdb=" O TYR C 389 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N PHE C 395 " --> pdb=" O GLU C 391 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N ALA C 396 " --> pdb=" O LEU C 392 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 421 removed outlier: 3.539A pdb=" N LYS C 421 " --> pdb=" O VAL C 417 " (cutoff:3.500A) 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 Processing helix chain 'C' and resid 468 through 479 removed outlier: 3.512A pdb=" N LEU C 472 " --> pdb=" O GLY C 468 " (cutoff:3.500A) Processing helix chain 'C' and resid 483 through 498 removed outlier: 3.509A pdb=" N THR C 497 " --> pdb=" O ALA C 493 " (cutoff:3.500A) Processing helix chain 'D' and resid 88 through 92 Processing helix chain 'D' and resid 139 through 146 Processing helix chain 'D' and resid 163 through 176 Processing helix chain 'D' and resid 191 through 206 Processing helix chain 'D' and resid 207 through 209 No H-bonds generated for 'chain 'D' and resid 207 through 209' Processing helix chain 'D' and resid 221 through 242 removed outlier: 4.970A pdb=" N ALA D 229 " --> pdb=" O ARG D 225 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N LEU D 230 " --> pdb=" O MET D 226 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N TYR D 238 " --> pdb=" O THR D 234 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N PHE D 239 " --> pdb=" O MET D 235 " (cutoff:3.500A) Processing helix chain 'D' and resid 254 through 269 removed outlier: 3.604A pdb=" N THR D 258 " --> pdb=" O ILE D 254 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N ALA D 266 " --> pdb=" O SER D 262 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N LEU D 267 " --> pdb=" O GLU D 263 " (cutoff:3.500A) Processing helix chain 'D' and resid 280 through 290 Processing helix chain 'D' and resid 309 through 312 Processing helix chain 'D' and resid 315 through 322 Processing helix chain 'D' and resid 323 through 325 No H-bonds generated for 'chain 'D' and resid 323 through 325' Processing helix chain 'D' and resid 332 through 339 Processing helix chain 'D' and resid 355 through 360 Processing helix chain 'D' and resid 360 through 388 removed outlier: 4.179A pdb=" N ASP D 382 " --> pdb=" O LYS D 378 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N ILE D 383 " --> pdb=" O GLU D 379 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ILE D 386 " --> pdb=" O ASP D 382 " (cutoff:3.500A) Processing helix chain 'D' and resid 395 through 410 removed outlier: 3.831A pdb=" N ARG D 405 " --> pdb=" O HIS D 401 " (cutoff:3.500A) Processing helix chain 'D' and resid 417 through 422 Processing helix chain 'D' and resid 429 through 443 Processing helix chain 'D' and resid 449 through 454 removed outlier: 3.592A pdb=" N ARG D 454 " --> pdb=" O ASP D 451 " (cutoff:3.500A) Processing helix chain 'D' and resid 458 through 469 removed outlier: 4.038A pdb=" N VAL D 462 " --> pdb=" O ARG D 458 " (cutoff:3.500A) removed outlier: 3.843A 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 124 through 128 Processing helix chain 'E' and resid 139 through 146 Processing helix chain 'E' and resid 163 through 180 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 243 removed outlier: 5.142A pdb=" N ALA E 229 " --> pdb=" O ARG E 225 " (cutoff:3.500A) removed outlier: 4.889A pdb=" N LEU E 230 " --> pdb=" O MET E 226 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N PHE E 239 " --> pdb=" O MET E 235 " (cutoff:3.500A) Processing helix chain 'E' and resid 253 through 269 removed outlier: 3.824A pdb=" N PHE E 257 " --> pdb=" O ASN E 253 " (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: 3.530A 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 355 through 360 Processing helix chain 'E' and resid 360 through 380 removed outlier: 3.598A pdb=" N LEU E 380 " --> pdb=" O ARG E 376 " (cutoff:3.500A) Processing helix chain 'E' and resid 380 through 388 Processing helix chain 'E' and resid 389 through 392 Processing helix chain 'E' and resid 393 through 410 removed outlier: 3.523A pdb=" N ARG E 405 " --> pdb=" O HIS E 401 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N PHE E 408 " --> pdb=" O ARG E 404 " (cutoff:3.500A) Processing helix chain 'E' and resid 417 through 422 Processing helix chain 'E' and resid 429 through 442 Processing helix chain 'E' and resid 449 through 454 Processing helix chain 'E' and resid 458 through 470 removed outlier: 3.933A pdb=" N VAL E 462 " --> pdb=" O ARG E 458 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N VAL E 463 " --> pdb=" O ILE E 459 " (cutoff:3.500A) Processing helix chain 'F' and resid 88 through 92 Processing helix chain 'F' and resid 124 through 128 removed outlier: 3.577A pdb=" N LEU F 128 " --> pdb=" O PHE F 125 " (cutoff:3.500A) Processing helix chain 'F' and resid 139 through 146 Processing helix chain 'F' and resid 163 through 176 Processing helix chain 'F' and resid 177 through 179 No H-bonds generated for 'chain 'F' and resid 177 through 179' 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 242 removed outlier: 5.199A pdb=" N ALA F 229 " --> pdb=" O ARG F 225 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N LEU F 230 " --> pdb=" O MET F 226 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N TYR F 238 " --> pdb=" O THR F 234 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N PHE F 239 " --> pdb=" O MET F 235 " (cutoff:3.500A) Processing helix chain 'F' and resid 254 through 269 removed outlier: 3.964A pdb=" N THR F 258 " --> pdb=" O ILE F 254 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ALA F 266 " --> pdb=" O SER F 262 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N LEU F 267 " --> pdb=" O GLU F 263 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLY F 269 " --> pdb=" O SER F 265 " (cutoff:3.500A) Processing helix chain 'F' and resid 280 through 290 Processing helix chain 'F' and resid 309 through 312 Processing helix chain 'F' and resid 315 through 322 removed outlier: 3.639A 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 338 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 Processing helix chain 'F' and resid 393 through 410 removed outlier: 3.710A pdb=" N ARG F 405 " --> pdb=" O HIS F 401 " (cutoff:3.500A) Processing helix chain 'F' and resid 415 through 419 removed outlier: 3.936A pdb=" N GLN F 419 " --> pdb=" O VAL F 416 " (cutoff:3.500A) Processing helix chain 'F' and resid 429 through 443 Processing helix chain 'F' and resid 449 through 454 removed outlier: 3.613A pdb=" N ARG F 454 " --> pdb=" O ASP F 451 " (cutoff:3.500A) Processing helix chain 'F' and resid 458 through 465 removed outlier: 3.527A pdb=" N VAL F 462 " --> pdb=" O ARG F 458 " (cutoff:3.500A) Processing helix chain 'G' and resid 3 through 57 removed outlier: 3.711A pdb=" N SER G 30 " --> pdb=" O MET G 26 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N VAL G 43 " --> pdb=" O ALA G 39 " (cutoff:3.500A) Proline residue: G 44 - end of helix Processing helix chain 'G' and resid 90 through 107 removed outlier: 3.972A pdb=" N VAL G 95 " --> pdb=" O TYR G 91 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU G 98 " --> pdb=" O ASN G 94 " (cutoff:3.500A) Processing helix chain 'G' and resid 119 through 129 removed outlier: 3.562A pdb=" N LEU G 123 " --> pdb=" O GLY G 119 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ARG G 129 " --> pdb=" O PHE G 125 " (cutoff:3.500A) Processing helix chain 'G' and resid 149 through 162 removed outlier: 3.550A pdb=" N PHE G 160 " --> pdb=" O THR G 156 " (cutoff:3.500A) Processing helix chain 'G' and resid 210 through 221 removed outlier: 3.941A pdb=" N ASP G 214 " --> pdb=" O GLU G 210 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N VAL G 215 " --> pdb=" O GLU G 211 " (cutoff:3.500A) Proline residue: G 218 - end of helix Processing helix chain 'G' and resid 222 through 227 Processing helix chain 'G' and resid 228 through 283 Processing sheet with id=AA1, first strand: chain 'A' and resid 60 through 66 removed outlier: 3.892A pdb=" N GLU A 51 " --> pdb=" O ALA A 63 " (cutoff:3.500A) removed outlier: 7.357A pdb=" N LEU A 52 " --> pdb=" O THR A 91 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N THR A 91 " --> pdb=" O LEU A 52 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N ARG A 40 " --> pdb=" O ILE A 32 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N VAL A 34 " --> pdb=" O ILE A 38 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N ILE A 38 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N VAL A 74 " --> pdb=" O ALA A 63 " (cutoff:3.500A) removed outlier: 5.478A pdb=" N ALA A 63 " --> pdb=" O VAL A 74 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N GLU E 75 " --> pdb=" O GLN E 33 " (cutoff:3.500A) removed outlier: 4.989A pdb=" N GLN E 33 " --> pdb=" O GLU E 75 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N ARG E 60 " --> pdb=" O ALA E 51 " (cutoff:3.500A) removed outlier: 5.093A pdb=" N HIS E 53 " --> pdb=" O THR E 58 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N THR E 58 " --> pdb=" O HIS E 53 " (cutoff:3.500A) removed outlier: 6.069A pdb=" N LYS E 17 " --> pdb=" O VAL E 6 " (cutoff:3.500A) removed outlier: 5.648A 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: 4.050A 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: 6.486A pdb=" N VAL A 108 " --> pdb=" O THR A 225 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N ILE A 192 " --> pdb=" O LEU A 257 " (cutoff:3.500A) removed outlier: 8.064A pdb=" N VAL A 259 " --> pdb=" O ILE A 192 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N ILE A 194 " --> pdb=" O VAL A 259 " (cutoff:3.500A) removed outlier: 3.620A 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: 4.404A pdb=" N GLU B 51 " --> pdb=" O ALA B 63 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N LEU B 52 " --> pdb=" O THR B 91 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N ARG B 40 " --> pdb=" O ILE B 32 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N VAL B 34 " --> pdb=" O ILE B 38 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N ILE B 38 " --> pdb=" O VAL B 34 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N VAL B 74 " --> pdb=" O ALA B 63 " (cutoff:3.500A) removed outlier: 5.774A pdb=" N ALA B 63 " --> pdb=" O VAL B 74 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N LEU B 76 " --> pdb=" O GLY B 61 " (cutoff:3.500A) removed outlier: 5.873A pdb=" N GLY B 61 " --> pdb=" O LEU B 76 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N GLU F 75 " --> pdb=" O GLN F 33 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N GLN F 33 " --> pdb=" O GLU F 75 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N ARG F 60 " --> pdb=" O ALA F 51 " (cutoff:3.500A) removed outlier: 5.117A pdb=" N HIS F 53 " --> pdb=" O THR F 58 " (cutoff:3.500A) removed outlier: 7.332A pdb=" N THR F 58 " --> pdb=" O HIS F 53 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLN F 8 " --> pdb=" O ASP F 15 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N LYS F 17 " --> pdb=" O VAL F 6 " (cutoff:3.500A) removed outlier: 5.774A pdb=" N VAL F 6 " --> pdb=" O LYS F 17 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 96 through 99 removed outlier: 4.198A 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: 6.400A pdb=" N ILE B 192 " --> pdb=" O LEU B 257 " (cutoff:3.500A) removed outlier: 8.021A pdb=" N VAL B 259 " --> pdb=" O ILE B 192 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N ILE B 194 " --> pdb=" O VAL B 259 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N TYR B 260 " --> pdb=" O LEU B 316 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N LEU B 166 " --> pdb=" O ILE B 342 " (cutoff:3.500A) removed outlier: 7.510A pdb=" N LEU B 344 " --> pdb=" O LEU B 166 " (cutoff:3.500A) removed outlier: 6.847A 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: 6.310A pdb=" N ARG C 40 " --> pdb=" O ILE C 32 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N VAL C 34 " --> pdb=" O ILE C 38 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N ILE C 38 " --> pdb=" O VAL C 34 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N VAL C 74 " --> pdb=" O ALA C 63 " (cutoff:3.500A) removed outlier: 5.674A pdb=" N ALA C 63 " --> pdb=" O VAL C 74 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N GLU C 51 " --> pdb=" O ALA C 63 " (cutoff:3.500A) removed outlier: 7.231A pdb=" N LEU C 52 " --> pdb=" O THR C 91 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 96 through 99 removed outlier: 3.875A 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: 6.519A pdb=" N ILE C 192 " --> pdb=" O LEU C 257 " (cutoff:3.500A) removed outlier: 8.162A pdb=" N VAL C 259 " --> pdb=" O ILE C 192 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N ILE C 194 " --> pdb=" O VAL C 259 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N TYR C 260 " --> pdb=" O LEU C 316 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 4 through 10 removed outlier: 5.741A pdb=" N VAL D 6 " --> pdb=" O LYS D 17 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N LYS D 17 " --> pdb=" O VAL D 6 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLN D 8 " --> pdb=" O ASP D 15 " (cutoff:3.500A) removed outlier: 7.309A pdb=" N THR D 58 " --> pdb=" O HIS D 53 " (cutoff:3.500A) removed outlier: 5.085A pdb=" N HIS D 53 " --> pdb=" O THR D 58 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N ARG D 60 " --> pdb=" O ALA D 51 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N GLN D 33 " --> pdb=" O GLU D 75 " (cutoff:3.500A) removed outlier: 6.936A 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: 3.513A pdb=" N ILE D 182 " --> pdb=" O ASP D 246 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N ILE D 154 " --> pdb=" O GLN D 304 " (cutoff:3.500A) removed outlier: 7.499A pdb=" N ILE D 306 " --> pdb=" O ILE D 154 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N LEU D 156 " --> pdb=" O ILE D 306 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 134 through 135 removed outlier: 4.219A 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: 6.371A pdb=" N PHE E 96 " --> pdb=" O PHE E 215 " (cutoff:3.500A) removed outlier: 7.473A pdb=" N GLN E 217 " --> pdb=" O PHE E 96 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N VAL E 247 " --> pdb=" O THR E 301 " (cutoff:3.500A) removed outlier: 7.897A pdb=" N ILE E 303 " --> pdb=" O VAL E 247 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N LEU E 249 " --> pdb=" O ILE E 303 " (cutoff:3.500A) removed outlier: 7.860A pdb=" N ALA E 305 " --> pdb=" O LEU E 249 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N ILE E 251 " --> pdb=" O ALA E 305 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA E 327 " --> pdb=" O LYS E 153 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 134 through 135 removed outlier: 4.372A 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: 6.327A pdb=" N VAL F 247 " --> pdb=" O THR F 301 " (cutoff:3.500A) removed outlier: 7.744A pdb=" N ILE F 303 " --> pdb=" O VAL F 247 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N LEU F 249 " --> pdb=" O ILE F 303 " (cutoff:3.500A) removed outlier: 7.897A pdb=" N ALA F 305 " --> pdb=" O LEU F 249 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N ILE F 251 " --> pdb=" O ALA F 305 " (cutoff:3.500A) removed outlier: 8.559A pdb=" N TYR F 307 " --> pdb=" O ILE F 251 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N ILE F 154 " --> pdb=" O GLN F 304 " (cutoff:3.500A) removed outlier: 7.395A pdb=" N ILE F 306 " --> pdb=" O ILE F 154 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N LEU F 156 " --> pdb=" O ILE F 306 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 134 through 135 removed outlier: 4.201A 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: 8.070A pdb=" N ILE G 134 " --> pdb=" O TYR G 113 " (cutoff:3.500A) removed outlier: 8.033A pdb=" N ILE G 115 " --> pdb=" O ILE G 134 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N ASP G 136 " --> pdb=" O ILE G 115 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N VAL G 117 " --> pdb=" O ASP G 136 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N THR G 76 " --> pdb=" O ALA G 114 " (cutoff:3.500A) removed outlier: 7.681A pdb=" N ILE G 116 " --> pdb=" O THR G 76 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N TYR G 78 " --> pdb=" O ILE G 116 " (cutoff:3.500A) removed outlier: 7.846A pdb=" N ILE G 118 " --> pdb=" O TYR G 78 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N VAL G 80 " --> pdb=" O ILE G 118 " (cutoff:3.500A) removed outlier: 5.274A pdb=" N ASN G 173 " --> pdb=" O ILE G 81 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N MET G 170 " --> pdb=" O LYS G 187 " (cutoff:3.500A) removed outlier: 5.645A pdb=" N LYS G 187 " --> pdb=" O MET G 170 " (cutoff:3.500A) removed outlier: 7.665A pdb=" N TYR G 172 " --> pdb=" O GLU G 185 " (cutoff:3.500A) removed outlier: 5.474A pdb=" N GLU G 185 " --> pdb=" O TYR G 172 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N HIS G 174 " --> pdb=" O VAL G 183 " (cutoff:3.500A) removed outlier: 5.601A pdb=" N VAL G 183 " --> pdb=" O HIS G 174 " (cutoff:3.500A) 1163 hydrogen bonds defined for protein. 3315 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: 10.11 Time building geometry restraints manager: 7.00 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: 8226 1.34 - 1.46: 4591 1.46 - 1.58: 11666 1.58 - 1.70: 18 1.70 - 1.82: 154 Bond restraints: 24655 Sorted by residual: bond pdb=" N THR C 406 " pdb=" CA THR C 406 " ideal model delta sigma weight residual 1.459 1.498 -0.039 1.21e-02 6.83e+03 1.05e+01 bond pdb=" O3 PO4 D 603 " pdb=" P PO4 D 603 " ideal model delta sigma weight residual 1.569 1.509 0.060 2.00e-02 2.50e+03 9.02e+00 bond pdb=" O3 PO4 E 501 " pdb=" P PO4 E 501 " ideal model delta sigma weight residual 1.569 1.510 0.059 2.00e-02 2.50e+03 8.80e+00 bond pdb=" O4 PO4 E 501 " pdb=" P PO4 E 501 " ideal model delta sigma weight residual 1.568 1.510 0.058 2.00e-02 2.50e+03 8.51e+00 bond pdb=" O4 PO4 D 603 " pdb=" P PO4 D 603 " ideal model delta sigma weight residual 1.568 1.510 0.058 2.00e-02 2.50e+03 8.45e+00 ... (remaining 24650 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.85: 32920 1.85 - 3.70: 458 3.70 - 5.55: 46 5.55 - 7.40: 7 7.40 - 9.25: 2 Bond angle restraints: 33433 Sorted by residual: angle pdb=" C LYS C 409 " pdb=" CA LYS C 409 " pdb=" CB LYS C 409 " ideal model delta sigma weight residual 110.79 103.92 6.87 1.66e+00 3.63e-01 1.71e+01 angle pdb=" N LYS C 409 " pdb=" CA LYS C 409 " pdb=" C LYS C 409 " ideal model delta sigma weight residual 111.28 107.40 3.88 1.09e+00 8.42e-01 1.27e+01 angle pdb=" N GLN C 407 " pdb=" CA GLN C 407 " pdb=" C GLN C 407 " ideal model delta sigma weight residual 111.28 107.45 3.83 1.09e+00 8.42e-01 1.23e+01 angle pdb=" C LEU D 455 " pdb=" N VAL D 456 " pdb=" CA VAL D 456 " ideal model delta sigma weight residual 123.08 119.89 3.19 1.01e+00 9.80e-01 9.97e+00 angle pdb=" C ILE G 225 " pdb=" N TYR G 226 " pdb=" CA TYR G 226 " ideal model delta sigma weight residual 122.79 117.44 5.35 1.70e+00 3.46e-01 9.90e+00 ... (remaining 33428 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.31: 14195 22.31 - 44.63: 689 44.63 - 66.94: 129 66.94 - 89.26: 44 89.26 - 111.57: 2 Dihedral angle restraints: 15059 sinusoidal: 6134 harmonic: 8925 Sorted by residual: dihedral pdb=" O1B ADP D 602 " pdb=" O3A ADP D 602 " pdb=" PB ADP D 602 " pdb=" PA ADP D 602 " ideal model delta sinusoidal sigma weight residual -60.00 -171.57 111.57 1 2.00e+01 2.50e-03 3.28e+01 dihedral pdb=" CA GLU G 222 " pdb=" C GLU G 222 " pdb=" N SER G 223 " pdb=" CA SER G 223 " ideal model delta harmonic sigma weight residual 180.00 159.72 20.28 0 5.00e+00 4.00e-02 1.65e+01 dihedral pdb=" C LYS C 409 " pdb=" N LYS C 409 " pdb=" CA LYS C 409 " pdb=" CB LYS C 409 " ideal model delta harmonic sigma weight residual -122.60 -112.97 -9.63 0 2.50e+00 1.60e-01 1.48e+01 ... (remaining 15056 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 3248 0.059 - 0.117: 552 0.117 - 0.176: 49 0.176 - 0.234: 2 0.234 - 0.293: 1 Chirality restraints: 3852 Sorted by residual: chirality pdb=" CA LYS C 409 " pdb=" N LYS C 409 " pdb=" C LYS C 409 " pdb=" CB LYS C 409 " both_signs ideal model delta sigma weight residual False 2.51 2.80 -0.29 2.00e-01 2.50e+01 2.15e+00 chirality pdb=" CG LEU G 194 " pdb=" CB LEU G 194 " pdb=" CD1 LEU G 194 " pdb=" CD2 LEU G 194 " both_signs ideal model delta sigma weight residual False -2.59 -2.37 -0.22 2.00e-01 2.50e+01 1.20e+00 chirality pdb=" CA TYR G 226 " pdb=" N TYR G 226 " pdb=" C TYR G 226 " pdb=" CB TYR G 226 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.99e-01 ... (remaining 3849 not shown) Planarity restraints: 4362 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN C 109 " -0.039 5.00e-02 4.00e+02 5.83e-02 5.44e+00 pdb=" N PRO C 110 " 0.101 5.00e-02 4.00e+02 pdb=" CA PRO C 110 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO C 110 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU D 220 " 0.032 5.00e-02 4.00e+02 4.77e-02 3.64e+00 pdb=" N PRO D 221 " -0.082 5.00e-02 4.00e+02 pdb=" CA PRO D 221 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO D 221 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU F 220 " -0.029 5.00e-02 4.00e+02 4.41e-02 3.11e+00 pdb=" N PRO F 221 " 0.076 5.00e-02 4.00e+02 pdb=" CA PRO F 221 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO F 221 " -0.024 5.00e-02 4.00e+02 ... (remaining 4359 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.57: 113 2.57 - 3.15: 19253 3.15 - 3.73: 36384 3.73 - 4.32: 52466 4.32 - 4.90: 89186 Nonbonded interactions: 197402 Sorted by model distance: nonbonded pdb="MG MG F 601 " pdb=" O3G ATP F 602 " model vdw 1.983 2.170 nonbonded pdb=" OG1 THR F 165 " pdb="MG MG F 601 " model vdw 2.010 2.170 nonbonded pdb=" O1G ATP C 600 " pdb="MG MG C 601 " model vdw 2.016 2.170 nonbonded pdb=" OG1 THR C 176 " pdb="MG MG C 601 " model vdw 2.020 2.170 nonbonded pdb=" OG1 THR B 176 " pdb="MG MG B 601 " model vdw 2.058 2.170 ... (remaining 197397 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' selection = chain 'B' selection = chain 'C' } 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: 3.450 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: 1.030 Check model and map are aligned: 0.190 Set scattering table: 0.240 Process input model: 57.450 Find NCS groups from input model: 1.650 Set up NCS constraints: 0.140 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:13.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 77.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8727 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 : 0.003 0.060 24655 Z= 0.195 Angle : 0.556 9.254 33433 Z= 0.319 Chirality : 0.044 0.293 3852 Planarity : 0.004 0.058 4362 Dihedral : 14.033 111.572 9347 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 0.08 % Allowed : 0.39 % Favored : 99.53 % 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: 1.14 (0.15), residues: 3115 helix: 1.63 (0.15), residues: 1260 sheet: 0.96 (0.23), residues: 536 loop : -0.12 (0.17), residues: 1319 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS E 363 PHE 0.014 0.001 PHE A 463 TYR 0.025 0.001 TYR G 226 ARG 0.003 0.000 ARG A 164 *********************** 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 140 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 138 time to evaluate : 2.737 Fit side-chains revert: symmetry clash REVERT: B 465 ASP cc_start: 0.8126 (m-30) cc_final: 0.7835 (m-30) REVERT: E 1 MET cc_start: 0.5116 (ptm) cc_final: 0.4567 (ptm) outliers start: 2 outliers final: 0 residues processed: 140 average time/residue: 1.4555 time to fit residues: 234.2538 Evaluate side-chains 98 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 98 time to evaluate : 2.687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 261 optimal weight: 2.9990 chunk 234 optimal weight: 9.9990 chunk 130 optimal weight: 8.9990 chunk 80 optimal weight: 9.9990 chunk 158 optimal weight: 4.9990 chunk 125 optimal weight: 2.9990 chunk 242 optimal weight: 5.9990 chunk 94 optimal weight: 9.9990 chunk 147 optimal weight: 9.9990 chunk 180 optimal weight: 0.0970 chunk 281 optimal weight: 2.9990 overall best weight: 2.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 46 ASN A 266 GLN C 189 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8848 moved from start: 0.1570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 24655 Z= 0.309 Angle : 0.576 9.158 33433 Z= 0.301 Chirality : 0.046 0.285 3852 Planarity : 0.005 0.053 4362 Dihedral : 7.583 83.066 3546 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 2.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 0.78 % Allowed : 5.33 % Favored : 93.89 % 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: 0.97 (0.15), residues: 3115 helix: 1.52 (0.15), residues: 1266 sheet: 0.63 (0.22), residues: 550 loop : -0.14 (0.17), residues: 1299 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS G 107 PHE 0.019 0.002 PHE D 257 TYR 0.021 0.001 TYR A 329 ARG 0.004 0.000 ARG G 240 *********************** 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 123 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 103 time to evaluate : 2.821 Fit side-chains revert: symmetry clash REVERT: B 465 ASP cc_start: 0.8169 (m-30) cc_final: 0.7861 (m-30) REVERT: E 1 MET cc_start: 0.5267 (ptm) cc_final: 0.4733 (ptm) outliers start: 20 outliers final: 5 residues processed: 115 average time/residue: 1.3806 time to fit residues: 184.7018 Evaluate side-chains 97 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 92 time to evaluate : 2.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 384 LEU Chi-restraints excluded: chain D residue 10 MET Chi-restraints excluded: chain D residue 301 THR Chi-restraints excluded: chain D residue 456 VAL Chi-restraints excluded: chain D residue 467 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 156 optimal weight: 7.9990 chunk 87 optimal weight: 3.9990 chunk 234 optimal weight: 4.9990 chunk 191 optimal weight: 8.9990 chunk 77 optimal weight: 0.4980 chunk 282 optimal weight: 6.9990 chunk 304 optimal weight: 5.9990 chunk 251 optimal weight: 4.9990 chunk 279 optimal weight: 5.9990 chunk 96 optimal weight: 4.9990 chunk 226 optimal weight: 9.9990 overall best weight: 3.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 470 HIS D 217 GLN G 143 GLN G 174 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8885 moved from start: 0.1950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 24655 Z= 0.402 Angle : 0.594 9.398 33433 Z= 0.310 Chirality : 0.047 0.229 3852 Planarity : 0.005 0.050 4362 Dihedral : 7.623 86.490 3546 Min Nonbonded Distance : 1.852 Molprobity Statistics. All-atom Clashscore : 3.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 1.21 % Allowed : 6.93 % Favored : 91.86 % 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: 0.79 (0.15), residues: 3115 helix: 1.39 (0.15), residues: 1274 sheet: 0.54 (0.22), residues: 549 loop : -0.27 (0.17), residues: 1292 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS F 363 PHE 0.020 0.002 PHE D 257 TYR 0.022 0.001 TYR A 329 ARG 0.004 0.000 ARG F 193 *********************** 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 126 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 95 time to evaluate : 3.016 Fit side-chains REVERT: B 465 ASP cc_start: 0.8337 (m-30) cc_final: 0.7965 (m-30) REVERT: E 1 MET cc_start: 0.5250 (ptm) cc_final: 0.4751 (ptm) REVERT: G 48 LYS cc_start: 0.5432 (OUTLIER) cc_final: 0.4840 (tmtt) outliers start: 31 outliers final: 12 residues processed: 118 average time/residue: 1.3249 time to fit residues: 183.0665 Evaluate side-chains 107 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 94 time to evaluate : 2.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain C residue 384 LEU Chi-restraints excluded: chain C residue 392 LEU Chi-restraints excluded: chain D residue 10 MET Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 218 MET Chi-restraints excluded: chain D residue 301 THR Chi-restraints excluded: chain D residue 383 ILE Chi-restraints excluded: chain D residue 392 LEU Chi-restraints excluded: chain D residue 456 VAL Chi-restraints excluded: chain G residue 48 LYS Chi-restraints excluded: chain G residue 191 LEU Chi-restraints excluded: chain G residue 224 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 278 optimal weight: 5.9990 chunk 212 optimal weight: 1.9990 chunk 146 optimal weight: 6.9990 chunk 31 optimal weight: 5.9990 chunk 134 optimal weight: 6.9990 chunk 189 optimal weight: 4.9990 chunk 283 optimal weight: 4.9990 chunk 299 optimal weight: 6.9990 chunk 147 optimal weight: 5.9990 chunk 268 optimal weight: 6.9990 chunk 80 optimal weight: 0.0980 overall best weight: 3.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8885 moved from start: 0.2111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 24655 Z= 0.373 Angle : 0.573 9.298 33433 Z= 0.299 Chirality : 0.047 0.210 3852 Planarity : 0.004 0.049 4362 Dihedral : 7.420 93.568 3546 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 3.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 1.48 % Allowed : 8.10 % Favored : 90.42 % 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: 0.75 (0.15), residues: 3115 helix: 1.39 (0.15), residues: 1274 sheet: 0.49 (0.22), residues: 544 loop : -0.32 (0.17), residues: 1297 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.001 HIS E 363 PHE 0.020 0.002 PHE D 257 TYR 0.018 0.001 TYR A 329 ARG 0.005 0.000 ARG C 412 *********************** 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 137 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 99 time to evaluate : 3.068 Fit side-chains REVERT: A 492 GLU cc_start: 0.7936 (OUTLIER) cc_final: 0.7493 (mt-10) REVERT: B 465 ASP cc_start: 0.8361 (m-30) cc_final: 0.7985 (m-30) REVERT: E 1 MET cc_start: 0.5303 (ptm) cc_final: 0.4839 (ptm) REVERT: G 48 LYS cc_start: 0.5364 (OUTLIER) cc_final: 0.4753 (tmtt) REVERT: G 226 TYR cc_start: 0.8077 (OUTLIER) cc_final: 0.7298 (m-80) outliers start: 38 outliers final: 15 residues processed: 128 average time/residue: 1.2349 time to fit residues: 186.5204 Evaluate side-chains 114 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 96 time to evaluate : 2.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 492 GLU Chi-restraints excluded: chain B residue 381 THR Chi-restraints excluded: chain C residue 321 THR Chi-restraints excluded: chain C residue 384 LEU Chi-restraints excluded: chain C residue 500 VAL Chi-restraints excluded: chain D residue 10 MET Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 210 LYS Chi-restraints excluded: chain D residue 218 MET Chi-restraints excluded: chain D residue 301 THR Chi-restraints excluded: chain D residue 383 ILE Chi-restraints excluded: chain D residue 456 VAL Chi-restraints excluded: chain E residue 359 VAL Chi-restraints excluded: chain E residue 462 VAL Chi-restraints excluded: chain G residue 48 LYS Chi-restraints excluded: chain G residue 226 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 249 optimal weight: 1.9990 chunk 170 optimal weight: 6.9990 chunk 4 optimal weight: 0.8980 chunk 223 optimal weight: 1.9990 chunk 123 optimal weight: 5.9990 chunk 255 optimal weight: 3.9990 chunk 207 optimal weight: 7.9990 chunk 0 optimal weight: 8.9990 chunk 153 optimal weight: 6.9990 chunk 268 optimal weight: 6.9990 chunk 75 optimal weight: 8.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 474 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8876 moved from start: 0.2167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 24655 Z= 0.314 Angle : 0.549 9.465 33433 Z= 0.286 Chirality : 0.045 0.190 3852 Planarity : 0.004 0.049 4362 Dihedral : 7.285 95.428 3546 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 3.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 1.56 % Allowed : 9.27 % Favored : 89.17 % 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: 1.47 (0.15), residues: 1276 sheet: 0.48 (0.22), residues: 543 loop : -0.29 (0.17), residues: 1296 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS E 363 PHE 0.019 0.002 PHE D 257 TYR 0.016 0.001 TYR G 226 ARG 0.003 0.000 ARG C 412 *********************** 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 138 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 98 time to evaluate : 3.101 Fit side-chains REVERT: A 492 GLU cc_start: 0.7926 (OUTLIER) cc_final: 0.7499 (mt-10) REVERT: B 465 ASP cc_start: 0.8360 (m-30) cc_final: 0.7970 (m-30) REVERT: E 1 MET cc_start: 0.5278 (ptm) cc_final: 0.4846 (ptm) REVERT: F 387 LEU cc_start: 0.8883 (OUTLIER) cc_final: 0.8623 (pp) REVERT: G 48 LYS cc_start: 0.5457 (OUTLIER) cc_final: 0.4881 (tmtt) REVERT: G 68 LEU cc_start: 0.8162 (mm) cc_final: 0.7898 (tm) REVERT: G 226 TYR cc_start: 0.7942 (OUTLIER) cc_final: 0.7411 (m-80) outliers start: 40 outliers final: 21 residues processed: 127 average time/residue: 1.2580 time to fit residues: 189.1851 Evaluate side-chains 122 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 97 time to evaluate : 3.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 492 GLU Chi-restraints excluded: chain B residue 250 MET Chi-restraints excluded: chain B residue 381 THR Chi-restraints excluded: chain B residue 404 LYS Chi-restraints excluded: chain B residue 500 VAL Chi-restraints excluded: chain C residue 321 THR Chi-restraints excluded: chain C residue 384 LEU Chi-restraints excluded: chain C residue 500 VAL Chi-restraints excluded: chain D residue 10 MET Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 218 MET Chi-restraints excluded: chain D residue 383 ILE Chi-restraints excluded: chain D residue 392 LEU Chi-restraints excluded: chain D residue 456 VAL Chi-restraints excluded: chain E residue 359 VAL Chi-restraints excluded: chain E residue 462 VAL Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 168 ILE Chi-restraints excluded: chain F residue 387 LEU Chi-restraints excluded: chain G residue 48 LYS Chi-restraints excluded: chain G residue 191 LEU Chi-restraints excluded: chain G residue 226 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 100 optimal weight: 5.9990 chunk 269 optimal weight: 3.9990 chunk 59 optimal weight: 3.9990 chunk 175 optimal weight: 2.9990 chunk 73 optimal weight: 5.9990 chunk 299 optimal weight: 9.9990 chunk 248 optimal weight: 5.9990 chunk 138 optimal weight: 9.9990 chunk 24 optimal weight: 4.9990 chunk 99 optimal weight: 4.9990 chunk 157 optimal weight: 2.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 196 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8892 moved from start: 0.2266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 24655 Z= 0.392 Angle : 0.583 9.422 33433 Z= 0.303 Chirality : 0.047 0.178 3852 Planarity : 0.004 0.050 4362 Dihedral : 7.372 97.730 3546 Min Nonbonded Distance : 1.861 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 1.67 % Allowed : 9.58 % Favored : 88.75 % 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: 0.71 (0.15), residues: 3115 helix: 1.41 (0.15), residues: 1270 sheet: 0.43 (0.22), residues: 543 loop : -0.38 (0.17), residues: 1302 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS E 363 PHE 0.021 0.002 PHE D 257 TYR 0.018 0.001 TYR G 226 ARG 0.003 0.000 ARG F 193 *********************** 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 138 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 95 time to evaluate : 3.041 Fit side-chains REVERT: A 492 GLU cc_start: 0.7913 (OUTLIER) cc_final: 0.7503 (mt-10) REVERT: B 465 ASP cc_start: 0.8371 (m-30) cc_final: 0.7983 (m-30) REVERT: E 1 MET cc_start: 0.5254 (ptm) cc_final: 0.4849 (ptm) REVERT: F 387 LEU cc_start: 0.8941 (OUTLIER) cc_final: 0.8666 (pp) REVERT: G 46 MET cc_start: 0.8184 (tpt) cc_final: 0.7937 (tpp) REVERT: G 48 LYS cc_start: 0.5467 (OUTLIER) cc_final: 0.4884 (tmtt) REVERT: G 68 LEU cc_start: 0.8142 (mm) cc_final: 0.7927 (tm) REVERT: G 226 TYR cc_start: 0.8028 (OUTLIER) cc_final: 0.7433 (m-80) outliers start: 43 outliers final: 30 residues processed: 128 average time/residue: 1.2128 time to fit residues: 184.2078 Evaluate side-chains 129 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 95 time to evaluate : 3.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 48 MET Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 492 GLU Chi-restraints excluded: chain B residue 250 MET Chi-restraints excluded: chain B residue 381 THR Chi-restraints excluded: chain B residue 404 LYS Chi-restraints excluded: chain B residue 500 VAL Chi-restraints excluded: chain C residue 25 VAL Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 191 MET Chi-restraints excluded: chain C residue 321 THR Chi-restraints excluded: chain C residue 384 LEU Chi-restraints excluded: chain C residue 500 VAL Chi-restraints excluded: chain D residue 10 MET Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 210 LYS Chi-restraints excluded: chain D residue 301 THR Chi-restraints excluded: chain D residue 383 ILE Chi-restraints excluded: chain D residue 392 LEU Chi-restraints excluded: chain D residue 394 ASP Chi-restraints excluded: chain D residue 456 VAL Chi-restraints excluded: chain E residue 359 VAL Chi-restraints excluded: chain E residue 462 VAL Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 168 ILE Chi-restraints excluded: chain F residue 387 LEU Chi-restraints excluded: chain G residue 48 LYS Chi-restraints excluded: chain G residue 191 LEU Chi-restraints excluded: chain G residue 224 LEU Chi-restraints excluded: chain G residue 226 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 289 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 170 optimal weight: 8.9990 chunk 219 optimal weight: 2.9990 chunk 169 optimal weight: 0.9980 chunk 252 optimal weight: 7.9990 chunk 167 optimal weight: 2.9990 chunk 298 optimal weight: 1.9990 chunk 186 optimal weight: 4.9990 chunk 182 optimal weight: 0.9990 chunk 137 optimal weight: 7.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8860 moved from start: 0.2253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 24655 Z= 0.224 Angle : 0.517 9.289 33433 Z= 0.268 Chirality : 0.044 0.148 3852 Planarity : 0.004 0.048 4362 Dihedral : 7.113 95.410 3546 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 1.25 % Allowed : 10.12 % Favored : 88.63 % 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: 1.63 (0.15), residues: 1271 sheet: 0.56 (0.22), residues: 528 loop : -0.29 (0.17), residues: 1316 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS E 363 PHE 0.018 0.001 PHE D 257 TYR 0.014 0.001 TYR G 226 ARG 0.002 0.000 ARG C 412 *********************** 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 131 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 99 time to evaluate : 3.228 Fit side-chains REVERT: B 465 ASP cc_start: 0.8319 (m-30) cc_final: 0.7937 (m-30) REVERT: C 404 LYS cc_start: 0.8483 (mmmt) cc_final: 0.8223 (mtpp) REVERT: E 1 MET cc_start: 0.5210 (ptm) cc_final: 0.4792 (ptm) REVERT: F 387 LEU cc_start: 0.8870 (OUTLIER) cc_final: 0.8603 (pp) REVERT: G 46 MET cc_start: 0.8158 (tpt) cc_final: 0.7910 (tpp) outliers start: 32 outliers final: 20 residues processed: 123 average time/residue: 1.3331 time to fit residues: 191.9580 Evaluate side-chains 119 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 98 time to evaluate : 3.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 48 MET Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain B residue 250 MET Chi-restraints excluded: chain B residue 404 LYS Chi-restraints excluded: chain B residue 500 VAL Chi-restraints excluded: chain C residue 384 LEU Chi-restraints excluded: chain D residue 10 MET Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 301 THR Chi-restraints excluded: chain D residue 383 ILE Chi-restraints excluded: chain D residue 394 ASP Chi-restraints excluded: chain D residue 456 VAL Chi-restraints excluded: chain E residue 359 VAL Chi-restraints excluded: chain E residue 462 VAL Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 387 LEU Chi-restraints excluded: chain G residue 191 LEU Chi-restraints excluded: chain G residue 245 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 184 optimal weight: 10.0000 chunk 119 optimal weight: 0.0570 chunk 178 optimal weight: 2.9990 chunk 90 optimal weight: 0.9990 chunk 58 optimal weight: 2.9990 chunk 57 optimal weight: 0.6980 chunk 189 optimal weight: 5.9990 chunk 203 optimal weight: 5.9990 chunk 147 optimal weight: 10.0000 chunk 27 optimal weight: 2.9990 chunk 234 optimal weight: 5.9990 overall best weight: 1.5504 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 8 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8844 moved from start: 0.2280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 24655 Z= 0.188 Angle : 0.500 10.964 33433 Z= 0.259 Chirality : 0.043 0.173 3852 Planarity : 0.004 0.048 4362 Dihedral : 6.915 89.757 3546 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 1.13 % Allowed : 10.24 % Favored : 88.63 % 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: 1.07 (0.15), residues: 3115 helix: 1.77 (0.15), residues: 1271 sheet: 0.58 (0.22), residues: 528 loop : -0.24 (0.17), residues: 1316 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS E 363 PHE 0.015 0.001 PHE D 257 TYR 0.011 0.001 TYR G 226 ARG 0.002 0.000 ARG C 412 *********************** 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 129 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 100 time to evaluate : 2.820 Fit side-chains REVERT: B 465 ASP cc_start: 0.8328 (m-30) cc_final: 0.7949 (m-30) REVERT: C 404 LYS cc_start: 0.8447 (mmmt) cc_final: 0.8209 (mtpp) REVERT: E 1 MET cc_start: 0.5167 (ptm) cc_final: 0.4737 (ptm) REVERT: G 46 MET cc_start: 0.8162 (tpt) cc_final: 0.7930 (tpp) REVERT: G 226 TYR cc_start: 0.7609 (OUTLIER) cc_final: 0.7123 (m-80) outliers start: 29 outliers final: 21 residues processed: 121 average time/residue: 1.1966 time to fit residues: 171.5658 Evaluate side-chains 120 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 98 time to evaluate : 2.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 MET Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 500 VAL Chi-restraints excluded: chain B residue 250 MET Chi-restraints excluded: chain B residue 404 LYS Chi-restraints excluded: chain B residue 500 VAL Chi-restraints excluded: chain C residue 321 THR Chi-restraints excluded: chain C residue 384 LEU Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 301 THR Chi-restraints excluded: chain D residue 383 ILE Chi-restraints excluded: chain D residue 394 ASP Chi-restraints excluded: chain D residue 456 VAL Chi-restraints excluded: chain E residue 359 VAL Chi-restraints excluded: chain E residue 462 VAL Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 168 ILE Chi-restraints excluded: chain G residue 191 LEU Chi-restraints excluded: chain G residue 226 TYR Chi-restraints excluded: chain G residue 245 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 271 optimal weight: 6.9990 chunk 286 optimal weight: 6.9990 chunk 261 optimal weight: 0.0970 chunk 278 optimal weight: 6.9990 chunk 167 optimal weight: 0.7980 chunk 121 optimal weight: 7.9990 chunk 218 optimal weight: 2.9990 chunk 85 optimal weight: 8.9990 chunk 251 optimal weight: 6.9990 chunk 263 optimal weight: 3.9990 chunk 277 optimal weight: 6.9990 overall best weight: 2.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 8 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8874 moved from start: 0.2322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 24655 Z= 0.315 Angle : 0.552 12.090 33433 Z= 0.285 Chirality : 0.045 0.160 3852 Planarity : 0.004 0.049 4362 Dihedral : 7.076 92.223 3546 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 1.17 % Allowed : 10.40 % Favored : 88.43 % 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: 0.92 (0.15), residues: 3115 helix: 1.62 (0.15), residues: 1271 sheet: 0.50 (0.22), residues: 519 loop : -0.27 (0.17), residues: 1325 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS E 363 PHE 0.019 0.002 PHE D 257 TYR 0.014 0.001 TYR G 226 ARG 0.002 0.000 ARG F 193 *********************** 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 128 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 98 time to evaluate : 2.777 Fit side-chains REVERT: B 465 ASP cc_start: 0.8376 (m-30) cc_final: 0.7974 (m-30) REVERT: E 1 MET cc_start: 0.5209 (ptm) cc_final: 0.4786 (ptm) REVERT: F 387 LEU cc_start: 0.8808 (OUTLIER) cc_final: 0.8554 (pp) outliers start: 30 outliers final: 22 residues processed: 121 average time/residue: 1.2644 time to fit residues: 179.9705 Evaluate side-chains 120 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 97 time to evaluate : 2.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 48 MET Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain B residue 250 MET Chi-restraints excluded: chain B residue 404 LYS Chi-restraints excluded: chain B residue 500 VAL Chi-restraints excluded: chain C residue 321 THR Chi-restraints excluded: chain C residue 384 LEU Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 301 THR Chi-restraints excluded: chain D residue 383 ILE Chi-restraints excluded: chain D residue 392 LEU Chi-restraints excluded: chain D residue 394 ASP Chi-restraints excluded: chain D residue 456 VAL Chi-restraints excluded: chain E residue 359 VAL Chi-restraints excluded: chain E residue 462 VAL Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 168 ILE Chi-restraints excluded: chain F residue 387 LEU Chi-restraints excluded: chain G residue 191 LEU Chi-restraints excluded: chain G residue 245 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 182 optimal weight: 0.9980 chunk 294 optimal weight: 7.9990 chunk 179 optimal weight: 3.9990 chunk 139 optimal weight: 1.9990 chunk 204 optimal weight: 5.9990 chunk 308 optimal weight: 3.9990 chunk 284 optimal weight: 8.9990 chunk 245 optimal weight: 0.9990 chunk 25 optimal weight: 0.0980 chunk 189 optimal weight: 0.9980 chunk 150 optimal weight: 3.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 8 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8825 moved from start: 0.2331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 24655 Z= 0.145 Angle : 0.487 12.465 33433 Z= 0.250 Chirality : 0.043 0.164 3852 Planarity : 0.004 0.047 4362 Dihedral : 6.753 89.615 3546 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 0.82 % Allowed : 10.86 % Favored : 88.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.68 % 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: 1.18 (0.15), residues: 3115 helix: 1.90 (0.15), residues: 1259 sheet: 0.62 (0.23), residues: 519 loop : -0.18 (0.17), residues: 1337 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS E 363 PHE 0.014 0.001 PHE D 125 TYR 0.012 0.001 TYR G 226 ARG 0.002 0.000 ARG C 412 ********************** 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 120 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 99 time to evaluate : 3.111 Fit side-chains REVERT: B 465 ASP cc_start: 0.8295 (m-30) cc_final: 0.7924 (m-30) REVERT: E 1 MET cc_start: 0.5190 (ptm) cc_final: 0.4768 (ptm) REVERT: G 46 MET cc_start: 0.8147 (tpt) cc_final: 0.7927 (tpp) REVERT: G 226 TYR cc_start: 0.7433 (OUTLIER) cc_final: 0.6778 (m-80) outliers start: 21 outliers final: 12 residues processed: 114 average time/residue: 1.4003 time to fit residues: 188.7684 Evaluate side-chains 110 residues out of total 2568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 97 time to evaluate : 3.020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain B residue 500 VAL Chi-restraints excluded: chain C residue 321 THR Chi-restraints excluded: chain C residue 384 LEU Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 301 THR Chi-restraints excluded: chain D residue 383 ILE Chi-restraints excluded: chain E residue 359 VAL Chi-restraints excluded: chain E residue 462 VAL Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain G residue 191 LEU Chi-restraints excluded: chain G residue 226 TYR Chi-restraints excluded: chain G residue 245 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: chunk 195 optimal weight: 0.1980 chunk 261 optimal weight: 4.9990 chunk 75 optimal weight: 10.0000 chunk 226 optimal weight: 9.9990 chunk 36 optimal weight: 7.9990 chunk 68 optimal weight: 5.9990 chunk 246 optimal weight: 1.9990 chunk 103 optimal weight: 3.9990 chunk 252 optimal weight: 2.9990 chunk 31 optimal weight: 5.9990 chunk 45 optimal weight: 1.9990 overall best weight: 2.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 65 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.071596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2803 r_free = 0.2803 target = 0.053482 restraints weight = 53861.846| |-----------------------------------------------------------------------------| r_work (start): 0.2782 rms_B_bonded: 2.33 r_work: 0.2664 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2540 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2540 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9089 moved from start: 0.2341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 24655 Z= 0.245 Angle : 0.516 12.512 33433 Z= 0.266 Chirality : 0.044 0.164 3852 Planarity : 0.004 0.048 4362 Dihedral : 6.815 88.620 3546 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 0.70 % Allowed : 11.02 % Favored : 88.28 % 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: 1.10 (0.15), residues: 3115 helix: 1.81 (0.15), residues: 1265 sheet: 0.60 (0.23), residues: 519 loop : -0.21 (0.17), residues: 1331 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS E 363 PHE 0.018 0.001 PHE D 257 TYR 0.014 0.001 TYR G 226 ARG 0.002 0.000 ARG C 412 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5347.99 seconds wall clock time: 95 minutes 38.62 seconds (5738.62 seconds total)