Starting phenix.real_space_refine on Sun Aug 24 06:09:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7yjk_33873/08_2025/7yjk_33873.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yjk_33873/08_2025/7yjk_33873.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7yjk_33873/08_2025/7yjk_33873.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yjk_33873/08_2025/7yjk_33873.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7yjk_33873/08_2025/7yjk_33873.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yjk_33873/08_2025/7yjk_33873.map" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 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: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 100 5.16 5 C 11390 2.51 5 N 2978 2.21 5 O 3188 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 174 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 17658 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 3424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 445, 3424 Classifications: {'peptide': 445} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 20, 'TRANS': 424} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'PHE:plan': 1, 'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 14 Chain: "B" Number of atoms: 3665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 470, 3665 Classifications: {'peptide': 470} Link IDs: {'PTRANS': 21, 'TRANS': 448} Chain breaks: 1 Chain: "D" Number of atoms: 1277 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1277 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 9, 'TRANS': 146} Chain: "C" Number of atoms: 402 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 402 Classifications: {'peptide': 47} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'TRANS': 46} Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 2, 'ARG:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 25 Chain: "E" Number of atoms: 3424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 445, 3424 Classifications: {'peptide': 445} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 20, 'TRANS': 424} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'PHE:plan': 1, 'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 14 Chain: "F" Number of atoms: 3665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 470, 3665 Classifications: {'peptide': 470} Link IDs: {'PTRANS': 21, 'TRANS': 448} Chain breaks: 1 Chain: "H" Number of atoms: 1277 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1277 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 9, 'TRANS': 146} Chain: "G" Number of atoms: 402 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 402 Classifications: {'peptide': 47} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'TRANS': 46} Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 2, 'ARG:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 25 Chain: "B" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 61 Unusual residues: {'PLP': 1, 'Z1T': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "F" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 61 Unusual residues: {'PLP': 1, 'Z1T': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Time building chain proxies: 4.00, per 1000 atoms: 0.23 Number of scatterers: 17658 At special positions: 0 Unit cell: (126.36, 145.8, 118.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 100 16.00 P 2 15.00 O 3188 8.00 N 2978 7.00 C 11390 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.53 Conformation dependent library (CDL) restraints added in 649.5 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 4432 Ramachandran restraints generated. 2216 Oldfield, 0 Emsley, 2216 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4140 Finding SS restraints... Secondary structure from input PDB file: 88 helices and 18 sheets defined 49.6% alpha, 8.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.42 Creating SS restraints... Processing helix chain 'A' and resid 37 through 52 removed outlier: 4.134A pdb=" N GLU A 41 " --> pdb=" O HIS A 37 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N GLY A 45 " --> pdb=" O GLU A 41 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N VAL A 46 " --> pdb=" O GLY A 42 " (cutoff:3.500A) Processing helix chain 'A' and resid 67 through 76 removed outlier: 3.662A pdb=" N GLU A 71 " --> pdb=" O GLN A 67 " (cutoff:3.500A) Processing helix chain 'A' and resid 127 through 137 removed outlier: 3.687A pdb=" N SER A 131 " --> pdb=" O LYS A 127 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N THR A 133 " --> pdb=" O LEU A 129 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 168 removed outlier: 3.910A pdb=" N LEU A 157 " --> pdb=" O ILE A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 182 removed outlier: 4.021A pdb=" N MET A 182 " --> pdb=" O LEU A 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 185 through 190 removed outlier: 3.653A pdb=" N PHE A 189 " --> pdb=" O THR A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 213 removed outlier: 3.528A pdb=" N GLY A 209 " --> pdb=" O GLY A 205 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N GLN A 211 " --> pdb=" O GLN A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 239 removed outlier: 3.534A pdb=" N LYS A 238 " --> pdb=" O LYS A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 275 removed outlier: 3.713A pdb=" N GLU A 272 " --> pdb=" O VAL A 268 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LYS A 273 " --> pdb=" O LYS A 269 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N TYR A 274 " --> pdb=" O LEU A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 301 Processing helix chain 'A' and resid 303 through 307 Processing helix chain 'A' and resid 328 through 335 Processing helix chain 'A' and resid 349 through 366 removed outlier: 3.716A pdb=" N ALA A 355 " --> pdb=" O TYR A 351 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ALA A 356 " --> pdb=" O LEU A 352 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N ILE A 357 " --> pdb=" O ALA A 353 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N THR A 358 " --> pdb=" O SER A 354 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 382 removed outlier: 4.119A pdb=" N VAL A 371 " --> pdb=" O PRO A 367 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU A 373 " --> pdb=" O MET A 369 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ASN A 376 " --> pdb=" O LYS A 372 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 429 removed outlier: 3.763A pdb=" N LEU A 417 " --> pdb=" O LYS A 413 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N LEU A 427 " --> pdb=" O ALA A 423 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLU A 429 " --> pdb=" O ARG A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 460 through 477 removed outlier: 3.722A pdb=" N LEU A 464 " --> pdb=" O SER A 460 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LEU A 465 " --> pdb=" O GLU A 461 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N SER A 468 " --> pdb=" O LEU A 464 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LEU A 471 " --> pdb=" O ALA A 467 " (cutoff:3.500A) Processing helix chain 'B' and resid 6 through 29 removed outlier: 3.649A pdb=" N SER B 11 " --> pdb=" O LEU B 7 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N TYR B 13 " --> pdb=" O ALA B 9 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N PHE B 29 " --> pdb=" O LEU B 25 " (cutoff:3.500A) Processing helix chain 'B' and resid 53 through 58 Processing helix chain 'B' and resid 60 through 67 removed outlier: 3.834A pdb=" N GLN B 64 " --> pdb=" O HIS B 61 " (cutoff:3.500A) removed outlier: 5.785A pdb=" N ASP B 65 " --> pdb=" O ARG B 62 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N PHE B 67 " --> pdb=" O GLN B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 120 through 129 Processing helix chain 'B' and resid 145 through 160 removed outlier: 3.738A pdb=" N GLU B 152 " --> pdb=" O HIS B 148 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N GLU B 153 " --> pdb=" O ALA B 149 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N THR B 156 " --> pdb=" O GLU B 152 " (cutoff:3.500A) Processing helix chain 'B' and resid 171 through 176 removed outlier: 3.688A pdb=" N SER B 175 " --> pdb=" O TYR B 171 " (cutoff:3.500A) Processing helix chain 'B' and resid 177 through 182 Processing helix chain 'B' and resid 195 through 205 removed outlier: 3.555A pdb=" N VAL B 199 " --> pdb=" O HIS B 195 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N SER B 205 " --> pdb=" O GLY B 201 " (cutoff:3.500A) Processing helix chain 'B' and resid 216 through 231 removed outlier: 3.551A pdb=" N LEU B 220 " --> pdb=" O THR B 216 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ARG B 222 " --> pdb=" O SER B 218 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLU B 226 " --> pdb=" O ARG B 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 258 through 269 removed outlier: 4.016A pdb=" N ILE B 265 " --> pdb=" O GLU B 261 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LYS B 268 " --> pdb=" O ALA B 264 " (cutoff:3.500A) Processing helix chain 'B' and resid 290 through 295 Processing helix chain 'B' and resid 298 through 302 removed outlier: 3.913A pdb=" N VAL B 302 " --> pdb=" O THR B 299 " (cutoff:3.500A) Processing helix chain 'B' and resid 323 through 334 removed outlier: 3.569A pdb=" N HIS B 332 " --> pdb=" O GLN B 328 " (cutoff:3.500A) Processing helix chain 'B' and resid 334 through 339 Processing helix chain 'B' and resid 345 through 359 removed outlier: 3.619A pdb=" N GLN B 350 " --> pdb=" O PRO B 346 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N ILE B 351 " --> pdb=" O SER B 347 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ALA B 354 " --> pdb=" O GLN B 350 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N VAL B 357 " --> pdb=" O SER B 353 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 388 removed outlier: 3.959A pdb=" N GLN B 369 " --> pdb=" O ASN B 365 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N LYS B 370 " --> pdb=" O ARG B 366 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N LEU B 371 " --> pdb=" O GLY B 367 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N ARG B 375 " --> pdb=" O LEU B 371 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N SER B 378 " --> pdb=" O ILE B 374 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N PHE B 380 " --> pdb=" O GLU B 376 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N MET B 388 " --> pdb=" O GLU B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 409 through 421 removed outlier: 3.796A pdb=" N ALA B 413 " --> pdb=" O ALA B 409 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N SER B 415 " --> pdb=" O ILE B 411 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLU B 417 " --> pdb=" O ALA B 413 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N CYS B 418 " --> pdb=" O PHE B 414 " (cutoff:3.500A) Processing helix chain 'B' and resid 449 through 468 removed outlier: 3.599A pdb=" N LYS B 458 " --> pdb=" O ILE B 454 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ASP B 465 " --> pdb=" O SER B 461 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N LEU B 466 " --> pdb=" O LYS B 462 " (cutoff:3.500A) Processing helix chain 'D' and resid 15 through 23 removed outlier: 3.952A pdb=" N GLU D 19 " --> pdb=" O ARG D 16 " (cutoff:3.500A) removed outlier: 5.062A pdb=" N TRP D 20 " --> pdb=" O ASN D 17 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N PHE D 21 " --> pdb=" O THR D 18 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N MET D 22 " --> pdb=" O GLU D 19 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N TYR D 23 " --> pdb=" O TRP D 20 " (cutoff:3.500A) Processing helix chain 'D' and resid 25 through 45 removed outlier: 3.511A pdb=" N LEU D 34 " --> pdb=" O TYR D 30 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LEU D 42 " --> pdb=" O TRP D 38 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N SER D 43 " --> pdb=" O LEU D 39 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N SER D 45 " --> pdb=" O VAL D 41 " (cutoff:3.500A) Processing helix chain 'D' and resid 48 through 69 removed outlier: 3.664A pdb=" N VAL D 62 " --> pdb=" O LEU D 58 " (cutoff:3.500A) Processing helix chain 'D' and resid 76 through 80 removed outlier: 4.188A pdb=" N ASP D 79 " --> pdb=" O PHE D 76 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLN D 80 " --> pdb=" O ALA D 77 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 76 through 80' Processing helix chain 'D' and resid 87 through 92 removed outlier: 3.505A pdb=" N MET D 92 " --> pdb=" O TRP D 88 " (cutoff:3.500A) Processing helix chain 'D' and resid 93 through 96 Processing helix chain 'D' and resid 99 through 119 Proline residue: D 109 - end of helix Processing helix chain 'D' and resid 126 through 141 Processing helix chain 'C' and resid 2 through 15 removed outlier: 3.557A pdb=" N THR C 14 " --> pdb=" O LEU C 10 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N PHE C 15 " --> pdb=" O TYR C 11 " (cutoff:3.500A) Processing helix chain 'C' and resid 21 through 46 removed outlier: 3.563A pdb=" N LEU C 27 " --> pdb=" O TRP C 23 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N PHE C 28 " --> pdb=" O GLU C 24 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N SER C 30 " --> pdb=" O TYR C 26 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N LEU C 31 " --> pdb=" O LEU C 27 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LEU C 35 " --> pdb=" O LEU C 31 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ARG C 45 " --> pdb=" O TYR C 41 " (cutoff:3.500A) Processing helix chain 'E' and resid 37 through 52 removed outlier: 4.135A pdb=" N GLU E 41 " --> pdb=" O HIS E 37 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N GLY E 45 " --> pdb=" O GLU E 41 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N VAL E 46 " --> pdb=" O GLY E 42 " (cutoff:3.500A) Processing helix chain 'E' and resid 67 through 76 removed outlier: 3.662A pdb=" N GLU E 71 " --> pdb=" O GLN E 67 " (cutoff:3.500A) Processing helix chain 'E' and resid 127 through 137 removed outlier: 3.689A pdb=" N SER E 131 " --> pdb=" O LYS E 127 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N THR E 133 " --> pdb=" O LEU E 129 " (cutoff:3.500A) Processing helix chain 'E' and resid 153 through 168 removed outlier: 3.909A pdb=" N LEU E 157 " --> pdb=" O ILE E 153 " (cutoff:3.500A) Processing helix chain 'E' and resid 177 through 182 removed outlier: 4.021A pdb=" N MET E 182 " --> pdb=" O LEU E 179 " (cutoff:3.500A) Processing helix chain 'E' and resid 185 through 190 removed outlier: 3.653A pdb=" N PHE E 189 " --> pdb=" O THR E 185 " (cutoff:3.500A) Processing helix chain 'E' and resid 203 through 213 removed outlier: 3.527A pdb=" N GLY E 209 " --> pdb=" O GLY E 205 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N GLN E 211 " --> pdb=" O GLN E 207 " (cutoff:3.500A) Processing helix chain 'E' and resid 224 through 239 removed outlier: 3.534A pdb=" N LYS E 238 " --> pdb=" O LYS E 234 " (cutoff:3.500A) Processing helix chain 'E' and resid 265 through 275 removed outlier: 3.713A pdb=" N GLU E 272 " --> pdb=" O VAL E 268 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LYS E 273 " --> pdb=" O LYS E 269 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N TYR E 274 " --> pdb=" O LEU E 270 " (cutoff:3.500A) Processing helix chain 'E' and resid 295 through 301 Processing helix chain 'E' and resid 303 through 307 Processing helix chain 'E' and resid 328 through 335 Processing helix chain 'E' and resid 349 through 366 removed outlier: 3.716A pdb=" N ALA E 355 " --> pdb=" O TYR E 351 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ALA E 356 " --> pdb=" O LEU E 352 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N ILE E 357 " --> pdb=" O ALA E 353 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N THR E 358 " --> pdb=" O SER E 354 " (cutoff:3.500A) Processing helix chain 'E' and resid 367 through 382 removed outlier: 4.119A pdb=" N VAL E 371 " --> pdb=" O PRO E 367 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LEU E 373 " --> pdb=" O MET E 369 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ASN E 376 " --> pdb=" O LYS E 372 " (cutoff:3.500A) Processing helix chain 'E' and resid 411 through 429 removed outlier: 3.763A pdb=" N LEU E 417 " --> pdb=" O LYS E 413 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N LEU E 427 " --> pdb=" O ALA E 423 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLU E 429 " --> pdb=" O ARG E 425 " (cutoff:3.500A) Processing helix chain 'E' and resid 460 through 477 removed outlier: 3.723A pdb=" N LEU E 464 " --> pdb=" O SER E 460 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N LEU E 465 " --> pdb=" O GLU E 461 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N SER E 468 " --> pdb=" O LEU E 464 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU E 471 " --> pdb=" O ALA E 467 " (cutoff:3.500A) Processing helix chain 'F' and resid 6 through 29 removed outlier: 3.649A pdb=" N SER F 11 " --> pdb=" O LEU F 7 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N TYR F 13 " --> pdb=" O ALA F 9 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N PHE F 29 " --> pdb=" O LEU F 25 " (cutoff:3.500A) Processing helix chain 'F' and resid 53 through 58 Processing helix chain 'F' and resid 60 through 67 removed outlier: 3.835A pdb=" N GLN F 64 " --> pdb=" O HIS F 61 " (cutoff:3.500A) removed outlier: 5.786A pdb=" N ASP F 65 " --> pdb=" O ARG F 62 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N PHE F 67 " --> pdb=" O GLN F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 120 through 129 Processing helix chain 'F' and resid 145 through 160 removed outlier: 3.738A pdb=" N GLU F 152 " --> pdb=" O HIS F 148 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N GLU F 153 " --> pdb=" O ALA F 149 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N THR F 156 " --> pdb=" O GLU F 152 " (cutoff:3.500A) Processing helix chain 'F' and resid 171 through 176 removed outlier: 3.687A pdb=" N SER F 175 " --> pdb=" O TYR F 171 " (cutoff:3.500A) Processing helix chain 'F' and resid 177 through 182 Processing helix chain 'F' and resid 195 through 205 removed outlier: 3.555A pdb=" N VAL F 199 " --> pdb=" O HIS F 195 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N SER F 205 " --> pdb=" O GLY F 201 " (cutoff:3.500A) Processing helix chain 'F' and resid 216 through 231 removed outlier: 3.550A pdb=" N LEU F 220 " --> pdb=" O THR F 216 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ARG F 222 " --> pdb=" O SER F 218 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLU F 226 " --> pdb=" O ARG F 222 " (cutoff:3.500A) Processing helix chain 'F' and resid 258 through 269 removed outlier: 4.015A pdb=" N ILE F 265 " --> pdb=" O GLU F 261 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LYS F 268 " --> pdb=" O ALA F 264 " (cutoff:3.500A) Processing helix chain 'F' and resid 290 through 295 Processing helix chain 'F' and resid 298 through 302 removed outlier: 3.913A pdb=" N VAL F 302 " --> pdb=" O THR F 299 " (cutoff:3.500A) Processing helix chain 'F' and resid 323 through 334 removed outlier: 3.568A pdb=" N HIS F 332 " --> pdb=" O GLN F 328 " (cutoff:3.500A) Processing helix chain 'F' and resid 334 through 339 Processing helix chain 'F' and resid 345 through 359 removed outlier: 3.620A pdb=" N GLN F 350 " --> pdb=" O PRO F 346 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N ILE F 351 " --> pdb=" O SER F 347 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ALA F 354 " --> pdb=" O GLN F 350 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N VAL F 357 " --> pdb=" O SER F 353 " (cutoff:3.500A) Processing helix chain 'F' and resid 365 through 388 removed outlier: 3.960A pdb=" N GLN F 369 " --> pdb=" O ASN F 365 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N LYS F 370 " --> pdb=" O ARG F 366 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N LEU F 371 " --> pdb=" O GLY F 367 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N ARG F 375 " --> pdb=" O LEU F 371 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N SER F 378 " --> pdb=" O ILE F 374 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N PHE F 380 " --> pdb=" O GLU F 376 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N MET F 388 " --> pdb=" O GLU F 384 " (cutoff:3.500A) Processing helix chain 'F' and resid 409 through 421 removed outlier: 3.796A pdb=" N ALA F 413 " --> pdb=" O ALA F 409 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N SER F 415 " --> pdb=" O ILE F 411 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLU F 417 " --> pdb=" O ALA F 413 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N CYS F 418 " --> pdb=" O PHE F 414 " (cutoff:3.500A) Processing helix chain 'F' and resid 449 through 468 removed outlier: 3.600A pdb=" N LYS F 458 " --> pdb=" O ILE F 454 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ASP F 465 " --> pdb=" O SER F 461 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N LEU F 466 " --> pdb=" O LYS F 462 " (cutoff:3.500A) Processing helix chain 'H' and resid 15 through 23 removed outlier: 3.952A pdb=" N GLU H 19 " --> pdb=" O ARG H 16 " (cutoff:3.500A) removed outlier: 5.062A pdb=" N TRP H 20 " --> pdb=" O ASN H 17 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N PHE H 21 " --> pdb=" O THR H 18 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N MET H 22 " --> pdb=" O GLU H 19 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N TYR H 23 " --> pdb=" O TRP H 20 " (cutoff:3.500A) Processing helix chain 'H' and resid 25 through 45 removed outlier: 3.511A pdb=" N LEU H 34 " --> pdb=" O TYR H 30 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LEU H 42 " --> pdb=" O TRP H 38 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N SER H 43 " --> pdb=" O LEU H 39 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N SER H 45 " --> pdb=" O VAL H 41 " (cutoff:3.500A) Processing helix chain 'H' and resid 48 through 69 removed outlier: 3.664A pdb=" N VAL H 62 " --> pdb=" O LEU H 58 " (cutoff:3.500A) Processing helix chain 'H' and resid 76 through 80 removed outlier: 4.188A pdb=" N ASP H 79 " --> pdb=" O PHE H 76 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLN H 80 " --> pdb=" O ALA H 77 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 76 through 80' Processing helix chain 'H' and resid 87 through 92 removed outlier: 3.506A pdb=" N MET H 92 " --> pdb=" O TRP H 88 " (cutoff:3.500A) Processing helix chain 'H' and resid 93 through 96 Processing helix chain 'H' and resid 99 through 119 Proline residue: H 109 - end of helix Processing helix chain 'H' and resid 126 through 141 Processing helix chain 'G' and resid 2 through 15 removed outlier: 3.557A pdb=" N THR G 14 " --> pdb=" O LEU G 10 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N PHE G 15 " --> pdb=" O TYR G 11 " (cutoff:3.500A) Processing helix chain 'G' and resid 21 through 46 removed outlier: 3.563A pdb=" N LEU G 27 " --> pdb=" O TRP G 23 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N PHE G 28 " --> pdb=" O GLU G 24 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N SER G 30 " --> pdb=" O TYR G 26 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N LEU G 31 " --> pdb=" O LEU G 27 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LEU G 35 " --> pdb=" O LEU G 31 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ARG G 45 " --> pdb=" O TYR G 41 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 96 through 97 removed outlier: 3.727A pdb=" N THR A 105 " --> pdb=" O GLU A 97 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N THR A 104 " --> pdb=" O VAL A 111 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N VAL A 111 " --> pdb=" O THR A 104 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 171 through 175 removed outlier: 3.643A pdb=" N ASP A 171 " --> pdb=" O GLY A 327 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLY A 327 " --> pdb=" O ASP A 171 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N VAL A 278 " --> pdb=" O VAL A 309 " (cutoff:3.500A) removed outlier: 8.002A pdb=" N THR A 311 " --> pdb=" O VAL A 278 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N LEU A 280 " --> pdb=" O THR A 311 " (cutoff:3.500A) removed outlier: 8.407A pdb=" N ALA A 313 " --> pdb=" O LEU A 280 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ASP A 281 " --> pdb=" O ALA A 251 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 390 through 391 Processing sheet with id=AA4, first strand: chain 'A' and resid 435 through 436 removed outlier: 3.663A pdb=" N VAL A 435 " --> pdb=" O LYS A 452 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 2 through 5 removed outlier: 3.732A pdb=" N ILE B 2 " --> pdb=" O ALA D 8 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 78 through 79 removed outlier: 3.504A pdb=" N PHE B 79 " --> pdb=" O CYS B 102 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N LEU B 103 " --> pdb=" O ALA B 424 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 82 through 85 removed outlier: 5.569A pdb=" N GLU B 83 " --> pdb=" O THR B 96 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 163 through 167 removed outlier: 3.829A pdb=" N GLY B 318 " --> pdb=" O PHE B 167 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N TYR B 319 " --> pdb=" O GLY B 307 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N THR B 308 " --> pdb=" O GLU B 277 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N VAL B 244 " --> pdb=" O TYR B 274 " (cutoff:3.500A) removed outlier: 7.779A pdb=" N ASP B 276 " --> pdb=" O VAL B 244 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 400 through 404 removed outlier: 3.680A pdb=" N ILE B 442 " --> pdb=" O MET B 401 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ARG B 439 " --> pdb=" O VAL B 428 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N VAL B 426 " --> pdb=" O ARG B 441 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 96 through 97 removed outlier: 3.727A pdb=" N THR E 105 " --> pdb=" O GLU E 97 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N THR E 104 " --> pdb=" O VAL E 111 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N VAL E 111 " --> pdb=" O THR E 104 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 171 through 175 removed outlier: 3.643A pdb=" N ASP E 171 " --> pdb=" O GLY E 327 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLY E 327 " --> pdb=" O ASP E 171 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N VAL E 278 " --> pdb=" O VAL E 309 " (cutoff:3.500A) removed outlier: 8.002A pdb=" N THR E 311 " --> pdb=" O VAL E 278 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N LEU E 280 " --> pdb=" O THR E 311 " (cutoff:3.500A) removed outlier: 8.408A pdb=" N ALA E 313 " --> pdb=" O LEU E 280 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ASP E 281 " --> pdb=" O ALA E 251 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 390 through 391 Processing sheet with id=AB4, first strand: chain 'E' and resid 435 through 436 removed outlier: 3.662A pdb=" N VAL E 435 " --> pdb=" O LYS E 452 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 2 through 5 removed outlier: 3.750A pdb=" N ILE F 2 " --> pdb=" O ALA H 8 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 78 through 79 removed outlier: 3.504A pdb=" N PHE F 79 " --> pdb=" O CYS F 102 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N LEU F 103 " --> pdb=" O ALA F 424 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 82 through 85 removed outlier: 5.569A pdb=" N GLU F 83 " --> pdb=" O THR F 96 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 163 through 167 removed outlier: 3.829A pdb=" N GLY F 318 " --> pdb=" O PHE F 167 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N TYR F 319 " --> pdb=" O GLY F 307 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N THR F 308 " --> pdb=" O GLU F 277 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N VAL F 244 " --> pdb=" O TYR F 274 " (cutoff:3.500A) removed outlier: 7.778A pdb=" N ASP F 276 " --> pdb=" O VAL F 244 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 400 through 404 removed outlier: 3.679A pdb=" N ILE F 442 " --> pdb=" O MET F 401 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ARG F 439 " --> pdb=" O VAL F 428 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N VAL F 426 " --> pdb=" O ARG F 441 " (cutoff:3.500A) 700 hydrogen bonds defined for protein. 1992 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: 2.64 Time building geometry restraints manager: 1.98 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: 5575 1.34 - 1.46: 3163 1.46 - 1.57: 9172 1.57 - 1.69: 4 1.69 - 1.81: 156 Bond restraints: 18070 Sorted by residual: bond pdb=" C ARG E 62 " pdb=" N PRO E 63 " ideal model delta sigma weight residual 1.332 1.589 -0.258 1.26e-02 6.30e+03 4.18e+02 bond pdb=" C ARG A 62 " pdb=" N PRO A 63 " ideal model delta sigma weight residual 1.332 1.589 -0.258 1.26e-02 6.30e+03 4.18e+02 bond pdb=" C14 Z1T F 502 " pdb=" C15 Z1T F 502 " ideal model delta sigma weight residual 1.329 1.525 -0.196 2.00e-02 2.50e+03 9.65e+01 bond pdb=" C14 Z1T B 502 " pdb=" C15 Z1T B 502 " ideal model delta sigma weight residual 1.329 1.525 -0.196 2.00e-02 2.50e+03 9.64e+01 bond pdb=" C13 Z1T B 502 " pdb=" C14 Z1T B 502 " ideal model delta sigma weight residual 1.494 1.525 -0.031 2.00e-02 2.50e+03 2.33e+00 ... (remaining 18065 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.12: 23659 2.12 - 4.24: 700 4.24 - 6.36: 103 6.36 - 8.48: 4 8.48 - 10.60: 8 Bond angle restraints: 24474 Sorted by residual: angle pdb=" N ARG B 30 " pdb=" CA ARG B 30 " pdb=" C ARG B 30 " ideal model delta sigma weight residual 113.55 106.70 6.85 1.26e+00 6.30e-01 2.95e+01 angle pdb=" N ARG F 30 " pdb=" CA ARG F 30 " pdb=" C ARG F 30 " ideal model delta sigma weight residual 113.55 106.71 6.84 1.26e+00 6.30e-01 2.95e+01 angle pdb=" N GLU F 253 " pdb=" CA GLU F 253 " pdb=" C GLU F 253 " ideal model delta sigma weight residual 114.75 108.80 5.95 1.26e+00 6.30e-01 2.23e+01 angle pdb=" N GLU B 253 " pdb=" CA GLU B 253 " pdb=" C GLU B 253 " ideal model delta sigma weight residual 114.75 108.85 5.90 1.26e+00 6.30e-01 2.19e+01 angle pdb=" C SER F 398 " pdb=" N PRO F 399 " pdb=" CA PRO F 399 " ideal model delta sigma weight residual 119.56 123.65 -4.09 1.01e+00 9.80e-01 1.64e+01 ... (remaining 24469 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.41: 9619 17.41 - 34.81: 906 34.81 - 52.22: 188 52.22 - 69.63: 32 69.63 - 87.04: 17 Dihedral angle restraints: 10762 sinusoidal: 4304 harmonic: 6458 Sorted by residual: dihedral pdb=" CA VAL E 288 " pdb=" C VAL E 288 " pdb=" N LEU E 289 " pdb=" CA LEU E 289 " ideal model delta harmonic sigma weight residual 180.00 -155.28 -24.72 0 5.00e+00 4.00e-02 2.44e+01 dihedral pdb=" CA VAL A 288 " pdb=" C VAL A 288 " pdb=" N LEU A 289 " pdb=" CA LEU A 289 " ideal model delta harmonic sigma weight residual -180.00 -155.36 -24.64 0 5.00e+00 4.00e-02 2.43e+01 dihedral pdb=" CA GLY F 50 " pdb=" C GLY F 50 " pdb=" N HIS F 51 " pdb=" CA HIS F 51 " ideal model delta harmonic sigma weight residual -180.00 -159.92 -20.08 0 5.00e+00 4.00e-02 1.61e+01 ... (remaining 10759 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 1841 0.050 - 0.100: 737 0.100 - 0.150: 154 0.150 - 0.200: 6 0.200 - 0.251: 2 Chirality restraints: 2740 Sorted by residual: chirality pdb=" CA TYR D 122 " pdb=" N TYR D 122 " pdb=" C TYR D 122 " pdb=" CB TYR D 122 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.57e+00 chirality pdb=" CA TYR H 122 " pdb=" N TYR H 122 " pdb=" C TYR H 122 " pdb=" CB TYR H 122 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.52e+00 chirality pdb=" CA GLU A 477 " pdb=" N GLU A 477 " pdb=" C GLU A 477 " pdb=" CB GLU A 477 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.18e-01 ... (remaining 2737 not shown) Planarity restraints: 3074 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR F 433 " 0.053 5.00e-02 4.00e+02 7.89e-02 9.96e+00 pdb=" N PRO F 434 " -0.136 5.00e-02 4.00e+02 pdb=" CA PRO F 434 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO F 434 " 0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR B 433 " -0.052 5.00e-02 4.00e+02 7.88e-02 9.93e+00 pdb=" N PRO B 434 " 0.136 5.00e-02 4.00e+02 pdb=" CA PRO B 434 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO B 434 " -0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 59 " -0.046 5.00e-02 4.00e+02 6.94e-02 7.72e+00 pdb=" N PRO A 60 " 0.120 5.00e-02 4.00e+02 pdb=" CA PRO A 60 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO A 60 " -0.038 5.00e-02 4.00e+02 ... (remaining 3071 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 3140 2.76 - 3.29: 16059 3.29 - 3.83: 26498 3.83 - 4.36: 32340 4.36 - 4.90: 58063 Nonbonded interactions: 136100 Sorted by model distance: nonbonded pdb=" O LEU A 43 " pdb=" CG2 VAL A 46 " model vdw 2.223 3.460 nonbonded pdb=" O LEU E 43 " pdb=" CG2 VAL E 46 " model vdw 2.223 3.460 nonbonded pdb=" ND1 HIS D 118 " pdb=" OE2 GLU E 41 " model vdw 2.234 3.120 nonbonded pdb=" OE2 GLU A 41 " pdb=" ND1 HIS H 118 " model vdw 2.239 3.120 nonbonded pdb=" OD2 ASP F 27 " pdb=" NH2 ARG F 57 " model vdw 2.245 3.120 ... (remaining 136095 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'F' } ncs_group { reference = chain 'D' selection = chain 'H' } ncs_group { reference = chain 'C' selection = chain 'G' } 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: 1.150 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: 0.270 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 15.590 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 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 : 0.008 0.258 18072 Z= 0.400 Angle : 0.892 10.604 24474 Z= 0.535 Chirality : 0.053 0.251 2740 Planarity : 0.006 0.079 3074 Dihedral : 14.225 87.037 6622 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.72 % Allowed : 7.13 % Favored : 92.15 % Rotamer: Outliers : 0.21 % Allowed : 1.05 % Favored : 98.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.10 (0.17), residues: 2216 helix: -1.76 (0.15), residues: 1046 sheet: -1.60 (0.33), residues: 238 loop : -2.40 (0.19), residues: 932 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 455 TYR 0.033 0.002 TYR E 177 PHE 0.024 0.002 PHE E 220 TRP 0.016 0.002 TRP C 23 HIS 0.008 0.001 HIS F 337 Details of bonding type rmsd covalent geometry : bond 0.00806 (18070) covalent geometry : angle 0.89207 (24474) hydrogen bonds : bond 0.26275 ( 700) hydrogen bonds : angle 7.49189 ( 1992) Misc. bond : bond 0.00622 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4432 Ramachandran restraints generated. 2216 Oldfield, 0 Emsley, 2216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4432 Ramachandran restraints generated. 2216 Oldfield, 0 Emsley, 2216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 207 time to evaluate : 0.701 Fit side-chains REVERT: A 52 LEU cc_start: 0.8478 (tt) cc_final: 0.8136 (mp) REVERT: A 246 ARG cc_start: 0.8204 (mtm180) cc_final: 0.7897 (mtt180) REVERT: B 28 PHE cc_start: 0.7619 (t80) cc_final: 0.7349 (t80) REVERT: B 30 ARG cc_start: 0.7817 (tpt170) cc_final: 0.7299 (mpt180) REVERT: D 1 MET cc_start: 0.4792 (ttm) cc_final: 0.4160 (ptm) REVERT: E 52 LEU cc_start: 0.8461 (tt) cc_final: 0.8116 (mp) REVERT: E 246 ARG cc_start: 0.8200 (mtm180) cc_final: 0.7892 (mtt180) REVERT: F 28 PHE cc_start: 0.7590 (t80) cc_final: 0.7232 (t80) REVERT: F 30 ARG cc_start: 0.7797 (tpt170) cc_final: 0.7250 (mpt180) REVERT: H 1 MET cc_start: 0.4822 (ttm) cc_final: 0.4140 (ptm) outliers start: 4 outliers final: 4 residues processed: 211 average time/residue: 0.1399 time to fit residues: 44.0157 Evaluate side-chains 183 residues out of total 1926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 179 time to evaluate : 0.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 428 LYS Chi-restraints excluded: chain E residue 51 LEU Chi-restraints excluded: chain E residue 428 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 216 optimal weight: 3.9990 chunk 98 optimal weight: 5.9990 chunk 194 optimal weight: 5.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 7.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 6.9990 chunk 200 optimal weight: 1.9990 chunk 212 optimal weight: 6.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 GLN A 223 ASN B 194 ASN ** B 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 379 ASN D 80 GLN D 96 GLN D 101 ASN E 207 GLN E 223 ASN F 194 ASN ** F 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 379 ASN H 80 GLN H 96 GLN H 101 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.121470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.093320 restraints weight = 24606.323| |-----------------------------------------------------------------------------| r_work (start): 0.3010 rms_B_bonded: 2.10 r_work: 0.2891 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2756 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 moved from start: 0.1161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 18072 Z= 0.178 Angle : 0.623 7.699 24474 Z= 0.325 Chirality : 0.046 0.163 2740 Planarity : 0.006 0.080 3074 Dihedral : 6.976 59.754 2536 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.27 % Allowed : 5.96 % Favored : 93.77 % Rotamer: Outliers : 0.63 % Allowed : 7.46 % Favored : 91.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.06 (0.17), residues: 2216 helix: -0.80 (0.16), residues: 1056 sheet: -0.85 (0.34), residues: 250 loop : -2.12 (0.19), residues: 910 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 373 TYR 0.016 0.002 TYR E 177 PHE 0.027 0.002 PHE B 79 TRP 0.015 0.001 TRP G 23 HIS 0.006 0.001 HIS F 214 Details of bonding type rmsd covalent geometry : bond 0.00435 (18070) covalent geometry : angle 0.62278 (24474) hydrogen bonds : bond 0.05878 ( 700) hydrogen bonds : angle 4.48284 ( 1992) Misc. bond : bond 0.00068 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4432 Ramachandran restraints generated. 2216 Oldfield, 0 Emsley, 2216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4432 Ramachandran restraints generated. 2216 Oldfield, 0 Emsley, 2216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 176 time to evaluate : 0.859 Fit side-chains REVERT: B 30 ARG cc_start: 0.8331 (tpt170) cc_final: 0.7261 (mpt180) REVERT: B 171 TYR cc_start: 0.7934 (t80) cc_final: 0.7575 (t80) REVERT: C 24 GLU cc_start: 0.9002 (mt-10) cc_final: 0.8764 (mt-10) REVERT: F 30 ARG cc_start: 0.8353 (tpt170) cc_final: 0.7253 (mpt180) REVERT: F 171 TYR cc_start: 0.8006 (t80) cc_final: 0.7590 (t80) outliers start: 12 outliers final: 5 residues processed: 182 average time/residue: 0.1326 time to fit residues: 36.7854 Evaluate side-chains 169 residues out of total 1926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 164 time to evaluate : 0.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 32 VAL Chi-restraints excluded: chain E residue 288 VAL Chi-restraints excluded: chain F residue 96 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 25 optimal weight: 0.0570 chunk 90 optimal weight: 4.9990 chunk 142 optimal weight: 3.9990 chunk 132 optimal weight: 3.9990 chunk 72 optimal weight: 3.9990 chunk 162 optimal weight: 0.5980 chunk 107 optimal weight: 0.9990 chunk 170 optimal weight: 4.9990 chunk 77 optimal weight: 4.9990 chunk 67 optimal weight: 0.4980 chunk 177 optimal weight: 4.9990 overall best weight: 1.2302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 214 HIS D 96 GLN F 214 HIS H 96 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.127731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.100539 restraints weight = 24202.167| |-----------------------------------------------------------------------------| r_work (start): 0.3066 rms_B_bonded: 2.02 r_work: 0.2948 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2813 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 moved from start: 0.1596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 18072 Z= 0.117 Angle : 0.528 8.481 24474 Z= 0.273 Chirality : 0.043 0.152 2740 Planarity : 0.005 0.077 3074 Dihedral : 6.063 58.886 2524 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.27 % Allowed : 4.42 % Favored : 95.31 % Rotamer: Outliers : 1.37 % Allowed : 9.19 % Favored : 89.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.53 (0.18), residues: 2216 helix: -0.26 (0.17), residues: 1040 sheet: -0.85 (0.35), residues: 238 loop : -1.88 (0.19), residues: 938 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 147 TYR 0.011 0.001 TYR E 177 PHE 0.021 0.001 PHE F 79 TRP 0.015 0.001 TRP G 23 HIS 0.005 0.001 HIS F 214 Details of bonding type rmsd covalent geometry : bond 0.00272 (18070) covalent geometry : angle 0.52823 (24474) hydrogen bonds : bond 0.04267 ( 700) hydrogen bonds : angle 4.01655 ( 1992) Misc. bond : bond 0.00033 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4432 Ramachandran restraints generated. 2216 Oldfield, 0 Emsley, 2216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4432 Ramachandran restraints generated. 2216 Oldfield, 0 Emsley, 2216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 189 time to evaluate : 0.521 Fit side-chains REVERT: A 96 LEU cc_start: 0.8598 (OUTLIER) cc_final: 0.8322 (pp) REVERT: B 30 ARG cc_start: 0.8408 (tpt170) cc_final: 0.7309 (mpt180) REVERT: B 171 TYR cc_start: 0.7950 (t80) cc_final: 0.7509 (t80) REVERT: C 24 GLU cc_start: 0.8973 (mt-10) cc_final: 0.8703 (mt-10) REVERT: E 96 LEU cc_start: 0.8595 (OUTLIER) cc_final: 0.8327 (pp) REVERT: F 30 ARG cc_start: 0.8420 (tpt170) cc_final: 0.7317 (mpt180) REVERT: F 171 TYR cc_start: 0.7931 (t80) cc_final: 0.7483 (t80) outliers start: 26 outliers final: 12 residues processed: 207 average time/residue: 0.1242 time to fit residues: 39.0041 Evaluate side-chains 187 residues out of total 1926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 173 time to evaluate : 0.771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 386 ASP Chi-restraints excluded: chain B residue 7 LEU Chi-restraints excluded: chain B residue 79 PHE Chi-restraints excluded: chain B residue 287 THR Chi-restraints excluded: chain D residue 51 MET Chi-restraints excluded: chain C residue 32 VAL Chi-restraints excluded: chain E residue 96 LEU Chi-restraints excluded: chain E residue 288 VAL Chi-restraints excluded: chain E residue 386 ASP Chi-restraints excluded: chain F residue 7 LEU Chi-restraints excluded: chain F residue 79 PHE Chi-restraints excluded: chain F residue 287 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 90 optimal weight: 3.9990 chunk 216 optimal weight: 2.9990 chunk 65 optimal weight: 8.9990 chunk 97 optimal weight: 5.9990 chunk 181 optimal weight: 2.9990 chunk 86 optimal weight: 1.9990 chunk 78 optimal weight: 4.9990 chunk 152 optimal weight: 6.9990 chunk 135 optimal weight: 0.9990 chunk 196 optimal weight: 0.0470 chunk 53 optimal weight: 7.9990 overall best weight: 1.8086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 96 GLN H 96 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.126869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.099725 restraints weight = 24203.578| |-----------------------------------------------------------------------------| r_work (start): 0.3056 rms_B_bonded: 2.01 r_work: 0.2934 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2801 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2801 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8506 moved from start: 0.1715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 18072 Z= 0.144 Angle : 0.546 6.819 24474 Z= 0.283 Chirality : 0.044 0.159 2740 Planarity : 0.005 0.075 3074 Dihedral : 5.911 59.950 2524 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.27 % Allowed : 4.69 % Favored : 95.04 % Rotamer: Outliers : 1.52 % Allowed : 10.56 % Favored : 87.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.34 (0.18), residues: 2216 helix: -0.03 (0.17), residues: 1026 sheet: -0.91 (0.33), residues: 264 loop : -1.81 (0.20), residues: 926 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 147 TYR 0.011 0.001 TYR E 177 PHE 0.024 0.002 PHE F 79 TRP 0.012 0.001 TRP G 23 HIS 0.004 0.001 HIS A 203 Details of bonding type rmsd covalent geometry : bond 0.00351 (18070) covalent geometry : angle 0.54589 (24474) hydrogen bonds : bond 0.04392 ( 700) hydrogen bonds : angle 3.88989 ( 1992) Misc. bond : bond 0.00038 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4432 Ramachandran restraints generated. 2216 Oldfield, 0 Emsley, 2216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4432 Ramachandran restraints generated. 2216 Oldfield, 0 Emsley, 2216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 173 time to evaluate : 0.661 Fit side-chains REVERT: B 30 ARG cc_start: 0.8467 (tpt170) cc_final: 0.7369 (mpt180) REVERT: B 171 TYR cc_start: 0.7997 (t80) cc_final: 0.7527 (t80) REVERT: B 306 MET cc_start: 0.8828 (tmm) cc_final: 0.8535 (ttp) REVERT: F 30 ARG cc_start: 0.8456 (tpt170) cc_final: 0.7382 (mpt180) REVERT: F 171 TYR cc_start: 0.7991 (t80) cc_final: 0.7533 (t80) outliers start: 29 outliers final: 14 residues processed: 187 average time/residue: 0.1220 time to fit residues: 34.8264 Evaluate side-chains 180 residues out of total 1926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 166 time to evaluate : 0.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 331 ILE Chi-restraints excluded: chain A residue 386 ASP Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain B residue 79 PHE Chi-restraints excluded: chain B residue 287 THR Chi-restraints excluded: chain D residue 51 MET Chi-restraints excluded: chain C residue 32 VAL Chi-restraints excluded: chain E residue 288 VAL Chi-restraints excluded: chain E residue 331 ILE Chi-restraints excluded: chain E residue 386 ASP Chi-restraints excluded: chain E residue 433 LEU Chi-restraints excluded: chain F residue 79 PHE Chi-restraints excluded: chain F residue 287 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 161 optimal weight: 0.8980 chunk 172 optimal weight: 4.9990 chunk 194 optimal weight: 0.9980 chunk 168 optimal weight: 1.9990 chunk 203 optimal weight: 4.9990 chunk 217 optimal weight: 2.9990 chunk 123 optimal weight: 3.9990 chunk 192 optimal weight: 2.9990 chunk 148 optimal weight: 5.9990 chunk 190 optimal weight: 1.9990 chunk 197 optimal weight: 2.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 300 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 96 GLN ** E 300 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 96 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.122511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.093999 restraints weight = 24705.285| |-----------------------------------------------------------------------------| r_work (start): 0.3022 rms_B_bonded: 2.13 r_work: 0.2901 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2764 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2764 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.1868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 18072 Z= 0.139 Angle : 0.535 7.733 24474 Z= 0.275 Chirality : 0.044 0.155 2740 Planarity : 0.005 0.066 3074 Dihedral : 5.779 58.625 2524 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.06 % Favored : 95.76 % Rotamer: Outliers : 1.42 % Allowed : 11.87 % Favored : 86.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.17 (0.18), residues: 2216 helix: 0.09 (0.17), residues: 1030 sheet: -0.89 (0.33), residues: 262 loop : -1.69 (0.20), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 147 TYR 0.011 0.001 TYR F 85 PHE 0.024 0.001 PHE B 79 TRP 0.011 0.001 TRP C 23 HIS 0.003 0.001 HIS D 60 Details of bonding type rmsd covalent geometry : bond 0.00340 (18070) covalent geometry : angle 0.53469 (24474) hydrogen bonds : bond 0.04207 ( 700) hydrogen bonds : angle 3.82482 ( 1992) Misc. bond : bond 0.00036 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4432 Ramachandran restraints generated. 2216 Oldfield, 0 Emsley, 2216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4432 Ramachandran restraints generated. 2216 Oldfield, 0 Emsley, 2216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 176 time to evaluate : 0.753 Fit side-chains REVERT: A 38 PHE cc_start: 0.6004 (m-80) cc_final: 0.5757 (m-80) REVERT: A 96 LEU cc_start: 0.8628 (OUTLIER) cc_final: 0.8306 (pp) REVERT: A 421 LYS cc_start: 0.8770 (ptmt) cc_final: 0.8273 (ptmm) REVERT: B 30 ARG cc_start: 0.8422 (tpt170) cc_final: 0.7249 (mpt180) REVERT: B 171 TYR cc_start: 0.7960 (t80) cc_final: 0.7504 (t80) REVERT: B 306 MET cc_start: 0.8875 (tmm) cc_final: 0.8488 (ttp) REVERT: C 24 GLU cc_start: 0.8931 (mt-10) cc_final: 0.8699 (mt-10) REVERT: E 96 LEU cc_start: 0.8624 (OUTLIER) cc_final: 0.8303 (pp) REVERT: E 421 LYS cc_start: 0.8780 (ptmt) cc_final: 0.8279 (ptmm) REVERT: F 30 ARG cc_start: 0.8424 (tpt170) cc_final: 0.7244 (mpt180) REVERT: F 171 TYR cc_start: 0.7960 (t80) cc_final: 0.7504 (t80) REVERT: F 306 MET cc_start: 0.8880 (tmm) cc_final: 0.8421 (ttp) outliers start: 27 outliers final: 19 residues processed: 194 average time/residue: 0.1143 time to fit residues: 34.6058 Evaluate side-chains 191 residues out of total 1926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 170 time to evaluate : 0.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 331 ILE Chi-restraints excluded: chain A residue 386 ASP Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain B residue 79 PHE Chi-restraints excluded: chain B residue 287 THR Chi-restraints excluded: chain B residue 388 MET Chi-restraints excluded: chain D residue 51 MET Chi-restraints excluded: chain C residue 32 VAL Chi-restraints excluded: chain C residue 36 MET Chi-restraints excluded: chain E residue 96 LEU Chi-restraints excluded: chain E residue 268 VAL Chi-restraints excluded: chain E residue 288 VAL Chi-restraints excluded: chain E residue 331 ILE Chi-restraints excluded: chain E residue 386 ASP Chi-restraints excluded: chain E residue 433 LEU Chi-restraints excluded: chain F residue 79 PHE Chi-restraints excluded: chain F residue 287 THR Chi-restraints excluded: chain F residue 388 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 38 optimal weight: 1.9990 chunk 68 optimal weight: 8.9990 chunk 212 optimal weight: 5.9990 chunk 48 optimal weight: 2.9990 chunk 12 optimal weight: 5.9990 chunk 131 optimal weight: 4.9990 chunk 11 optimal weight: 0.0070 chunk 206 optimal weight: 1.9990 chunk 201 optimal weight: 8.9990 chunk 132 optimal weight: 0.0470 chunk 106 optimal weight: 4.9990 overall best weight: 1.4102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 300 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 96 GLN ** E 300 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 96 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.123549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.095169 restraints weight = 24399.213| |-----------------------------------------------------------------------------| r_work (start): 0.3037 rms_B_bonded: 2.11 r_work: 0.2916 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2780 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2780 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.1986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 18072 Z= 0.119 Angle : 0.515 7.865 24474 Z= 0.264 Chirality : 0.043 0.153 2740 Planarity : 0.004 0.064 3074 Dihedral : 5.623 57.293 2524 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.24 % Favored : 95.58 % Rotamer: Outliers : 1.68 % Allowed : 12.24 % Favored : 86.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.96 (0.18), residues: 2216 helix: 0.26 (0.17), residues: 1032 sheet: -0.81 (0.33), residues: 260 loop : -1.57 (0.20), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 294 TYR 0.011 0.001 TYR F 85 PHE 0.022 0.001 PHE B 79 TRP 0.012 0.001 TRP G 23 HIS 0.003 0.001 HIS E 203 Details of bonding type rmsd covalent geometry : bond 0.00287 (18070) covalent geometry : angle 0.51525 (24474) hydrogen bonds : bond 0.03862 ( 700) hydrogen bonds : angle 3.74095 ( 1992) Misc. bond : bond 0.00028 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4432 Ramachandran restraints generated. 2216 Oldfield, 0 Emsley, 2216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4432 Ramachandran restraints generated. 2216 Oldfield, 0 Emsley, 2216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 182 time to evaluate : 0.599 Fit side-chains REVERT: A 38 PHE cc_start: 0.5984 (m-80) cc_final: 0.5733 (m-80) REVERT: A 96 LEU cc_start: 0.8614 (OUTLIER) cc_final: 0.8310 (pp) REVERT: A 421 LYS cc_start: 0.8729 (ptmt) cc_final: 0.8236 (ptmm) REVERT: B 30 ARG cc_start: 0.8412 (tpt170) cc_final: 0.7238 (mpt180) REVERT: B 171 TYR cc_start: 0.7949 (t80) cc_final: 0.7508 (t80) REVERT: B 256 ILE cc_start: 0.9133 (OUTLIER) cc_final: 0.8765 (mt) REVERT: B 306 MET cc_start: 0.8853 (tmm) cc_final: 0.8478 (ttp) REVERT: C 24 GLU cc_start: 0.8918 (mt-10) cc_final: 0.8656 (mt-10) REVERT: E 96 LEU cc_start: 0.8601 (OUTLIER) cc_final: 0.8291 (pp) REVERT: E 421 LYS cc_start: 0.8729 (ptmt) cc_final: 0.8238 (ptmm) REVERT: F 30 ARG cc_start: 0.8414 (tpt170) cc_final: 0.7262 (mpt180) REVERT: F 171 TYR cc_start: 0.7982 (t80) cc_final: 0.7520 (t80) REVERT: F 256 ILE cc_start: 0.9143 (OUTLIER) cc_final: 0.8719 (mt) REVERT: F 306 MET cc_start: 0.8868 (tmm) cc_final: 0.8508 (ttp) REVERT: F 373 ARG cc_start: 0.8651 (OUTLIER) cc_final: 0.8421 (mtm-85) outliers start: 32 outliers final: 17 residues processed: 204 average time/residue: 0.1240 time to fit residues: 38.9492 Evaluate side-chains 198 residues out of total 1926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 176 time to evaluate : 0.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 118 ASN Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 331 ILE Chi-restraints excluded: chain A residue 386 ASP Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain B residue 79 PHE Chi-restraints excluded: chain B residue 256 ILE Chi-restraints excluded: chain B residue 287 THR Chi-restraints excluded: chain D residue 51 MET Chi-restraints excluded: chain C residue 32 VAL Chi-restraints excluded: chain E residue 96 LEU Chi-restraints excluded: chain E residue 118 ASN Chi-restraints excluded: chain E residue 288 VAL Chi-restraints excluded: chain E residue 331 ILE Chi-restraints excluded: chain E residue 386 ASP Chi-restraints excluded: chain E residue 433 LEU Chi-restraints excluded: chain F residue 79 PHE Chi-restraints excluded: chain F residue 256 ILE Chi-restraints excluded: chain F residue 287 THR Chi-restraints excluded: chain F residue 373 ARG Chi-restraints excluded: chain F residue 388 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 147 optimal weight: 10.0000 chunk 110 optimal weight: 0.0070 chunk 97 optimal weight: 1.9990 chunk 104 optimal weight: 5.9990 chunk 154 optimal weight: 0.1980 chunk 218 optimal weight: 4.9990 chunk 173 optimal weight: 4.9990 chunk 63 optimal weight: 0.5980 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 0.9990 chunk 195 optimal weight: 2.9990 overall best weight: 0.7602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 300 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 96 GLN ** E 300 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 96 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.125917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.097878 restraints weight = 24609.575| |-----------------------------------------------------------------------------| r_work (start): 0.3072 rms_B_bonded: 2.10 r_work: 0.2952 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2815 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.2174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 18072 Z= 0.090 Angle : 0.485 7.639 24474 Z= 0.247 Chirality : 0.042 0.145 2740 Planarity : 0.004 0.062 3074 Dihedral : 5.421 56.228 2524 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.88 % Favored : 95.94 % Rotamer: Outliers : 1.52 % Allowed : 13.24 % Favored : 85.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.71 (0.18), residues: 2216 helix: 0.48 (0.17), residues: 1032 sheet: -0.68 (0.34), residues: 254 loop : -1.46 (0.20), residues: 930 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 425 TYR 0.010 0.001 TYR F 85 PHE 0.019 0.001 PHE F 79 TRP 0.014 0.001 TRP G 23 HIS 0.002 0.000 HIS E 203 Details of bonding type rmsd covalent geometry : bond 0.00205 (18070) covalent geometry : angle 0.48452 (24474) hydrogen bonds : bond 0.03329 ( 700) hydrogen bonds : angle 3.64099 ( 1992) Misc. bond : bond 0.00014 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4432 Ramachandran restraints generated. 2216 Oldfield, 0 Emsley, 2216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4432 Ramachandran restraints generated. 2216 Oldfield, 0 Emsley, 2216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 192 time to evaluate : 0.624 Fit side-chains REVERT: A 96 LEU cc_start: 0.8588 (OUTLIER) cc_final: 0.8285 (pp) REVERT: A 421 LYS cc_start: 0.8736 (ptmt) cc_final: 0.8260 (ptmm) REVERT: B 30 ARG cc_start: 0.8390 (tpt170) cc_final: 0.7240 (mpt180) REVERT: B 171 TYR cc_start: 0.7961 (t80) cc_final: 0.7470 (t80) REVERT: B 306 MET cc_start: 0.8830 (tmm) cc_final: 0.8465 (ttp) REVERT: C 24 GLU cc_start: 0.8895 (mt-10) cc_final: 0.8627 (mt-10) REVERT: E 96 LEU cc_start: 0.8563 (OUTLIER) cc_final: 0.8264 (pp) REVERT: E 421 LYS cc_start: 0.8727 (ptmt) cc_final: 0.8256 (ptmm) REVERT: F 30 ARG cc_start: 0.8416 (tpt170) cc_final: 0.7284 (mpt180) REVERT: F 171 TYR cc_start: 0.7971 (t80) cc_final: 0.7479 (t80) REVERT: F 306 MET cc_start: 0.8863 (tmm) cc_final: 0.8514 (ttp) outliers start: 29 outliers final: 11 residues processed: 213 average time/residue: 0.1445 time to fit residues: 46.7478 Evaluate side-chains 190 residues out of total 1926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 177 time to evaluate : 0.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 331 ILE Chi-restraints excluded: chain B residue 79 PHE Chi-restraints excluded: chain B residue 287 THR Chi-restraints excluded: chain D residue 51 MET Chi-restraints excluded: chain E residue 96 LEU Chi-restraints excluded: chain E residue 268 VAL Chi-restraints excluded: chain E residue 288 VAL Chi-restraints excluded: chain E residue 331 ILE Chi-restraints excluded: chain F residue 79 PHE Chi-restraints excluded: chain F residue 287 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 201 optimal weight: 1.9990 chunk 120 optimal weight: 4.9990 chunk 9 optimal weight: 4.9990 chunk 211 optimal weight: 0.7980 chunk 177 optimal weight: 4.9990 chunk 153 optimal weight: 1.9990 chunk 62 optimal weight: 5.9990 chunk 79 optimal weight: 0.6980 chunk 90 optimal weight: 0.9990 chunk 174 optimal weight: 6.9990 chunk 96 optimal weight: 2.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 300 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 96 GLN ** E 300 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 96 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.125298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.097360 restraints weight = 24361.443| |-----------------------------------------------------------------------------| r_work (start): 0.3040 rms_B_bonded: 2.08 r_work: 0.2926 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2792 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2792 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.2184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 18072 Z= 0.114 Angle : 0.515 10.507 24474 Z= 0.260 Chirality : 0.043 0.151 2740 Planarity : 0.004 0.062 3074 Dihedral : 5.384 53.316 2524 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.33 % Favored : 95.49 % Rotamer: Outliers : 1.73 % Allowed : 13.55 % Favored : 84.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.66 (0.18), residues: 2216 helix: 0.53 (0.17), residues: 1030 sheet: -0.65 (0.34), residues: 254 loop : -1.44 (0.20), residues: 932 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 373 TYR 0.011 0.001 TYR F 85 PHE 0.022 0.001 PHE F 79 TRP 0.011 0.001 TRP G 23 HIS 0.003 0.001 HIS E 203 Details of bonding type rmsd covalent geometry : bond 0.00272 (18070) covalent geometry : angle 0.51550 (24474) hydrogen bonds : bond 0.03665 ( 700) hydrogen bonds : angle 3.67473 ( 1992) Misc. bond : bond 0.00019 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4432 Ramachandran restraints generated. 2216 Oldfield, 0 Emsley, 2216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4432 Ramachandran restraints generated. 2216 Oldfield, 0 Emsley, 2216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 175 time to evaluate : 0.740 Fit side-chains REVERT: A 96 LEU cc_start: 0.8613 (OUTLIER) cc_final: 0.8267 (pp) REVERT: A 421 LYS cc_start: 0.8669 (ptmt) cc_final: 0.8204 (ptmm) REVERT: B 30 ARG cc_start: 0.8355 (tpt170) cc_final: 0.7187 (mpt180) REVERT: B 171 TYR cc_start: 0.7909 (t80) cc_final: 0.7458 (t80) REVERT: B 306 MET cc_start: 0.8833 (tmm) cc_final: 0.8510 (ttp) REVERT: C 24 GLU cc_start: 0.8896 (mt-10) cc_final: 0.8562 (mt-10) REVERT: E 96 LEU cc_start: 0.8588 (OUTLIER) cc_final: 0.8241 (pp) REVERT: E 421 LYS cc_start: 0.8664 (ptmt) cc_final: 0.8201 (ptmm) REVERT: F 30 ARG cc_start: 0.8365 (tpt170) cc_final: 0.7210 (mpt180) REVERT: F 171 TYR cc_start: 0.7909 (t80) cc_final: 0.7453 (t80) REVERT: F 306 MET cc_start: 0.8847 (tmm) cc_final: 0.8545 (ttp) outliers start: 33 outliers final: 18 residues processed: 202 average time/residue: 0.1408 time to fit residues: 43.4390 Evaluate side-chains 190 residues out of total 1926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 170 time to evaluate : 0.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 118 ASN Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 331 ILE Chi-restraints excluded: chain A residue 386 ASP Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain B residue 79 PHE Chi-restraints excluded: chain B residue 287 THR Chi-restraints excluded: chain D residue 51 MET Chi-restraints excluded: chain E residue 96 LEU Chi-restraints excluded: chain E residue 118 ASN Chi-restraints excluded: chain E residue 268 VAL Chi-restraints excluded: chain E residue 288 VAL Chi-restraints excluded: chain E residue 331 ILE Chi-restraints excluded: chain E residue 386 ASP Chi-restraints excluded: chain E residue 433 LEU Chi-restraints excluded: chain F residue 79 PHE Chi-restraints excluded: chain F residue 287 THR Chi-restraints excluded: chain G residue 31 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 208 optimal weight: 0.0970 chunk 62 optimal weight: 3.9990 chunk 58 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 chunk 136 optimal weight: 0.4980 chunk 91 optimal weight: 8.9990 chunk 129 optimal weight: 4.9990 chunk 174 optimal weight: 5.9990 chunk 133 optimal weight: 3.9990 chunk 166 optimal weight: 3.9990 chunk 115 optimal weight: 2.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 300 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 96 GLN ** E 300 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 96 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.124017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.095727 restraints weight = 24501.409| |-----------------------------------------------------------------------------| r_work (start): 0.3044 rms_B_bonded: 2.10 r_work: 0.2925 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2788 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8468 moved from start: 0.2205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 18072 Z= 0.124 Angle : 0.514 8.512 24474 Z= 0.262 Chirality : 0.043 0.153 2740 Planarity : 0.004 0.064 3074 Dihedral : 5.386 52.274 2524 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.11 % Favored : 95.71 % Rotamer: Outliers : 1.58 % Allowed : 13.81 % Favored : 84.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.60 (0.18), residues: 2216 helix: 0.55 (0.17), residues: 1030 sheet: -0.63 (0.33), residues: 276 loop : -1.38 (0.21), residues: 910 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 373 TYR 0.011 0.001 TYR F 85 PHE 0.023 0.001 PHE F 79 TRP 0.010 0.001 TRP G 23 HIS 0.003 0.001 HIS E 203 Details of bonding type rmsd covalent geometry : bond 0.00299 (18070) covalent geometry : angle 0.51383 (24474) hydrogen bonds : bond 0.03837 ( 700) hydrogen bonds : angle 3.69252 ( 1992) Misc. bond : bond 0.00027 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4432 Ramachandran restraints generated. 2216 Oldfield, 0 Emsley, 2216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4432 Ramachandran restraints generated. 2216 Oldfield, 0 Emsley, 2216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 169 time to evaluate : 0.760 Fit side-chains REVERT: A 38 PHE cc_start: 0.6048 (m-80) cc_final: 0.5541 (m-80) REVERT: A 96 LEU cc_start: 0.8615 (OUTLIER) cc_final: 0.8292 (pp) REVERT: A 421 LYS cc_start: 0.8750 (ptmt) cc_final: 0.8260 (ptmm) REVERT: B 30 ARG cc_start: 0.8393 (tpt170) cc_final: 0.7245 (mpt180) REVERT: B 171 TYR cc_start: 0.7999 (t80) cc_final: 0.7524 (t80) REVERT: B 306 MET cc_start: 0.8820 (tmm) cc_final: 0.8447 (ttp) REVERT: C 24 GLU cc_start: 0.8937 (mt-10) cc_final: 0.8700 (mt-10) REVERT: E 96 LEU cc_start: 0.8601 (OUTLIER) cc_final: 0.8289 (pp) REVERT: E 421 LYS cc_start: 0.8716 (ptmt) cc_final: 0.8245 (ptmm) REVERT: F 30 ARG cc_start: 0.8413 (tpt170) cc_final: 0.7267 (mpt180) REVERT: F 171 TYR cc_start: 0.8001 (t80) cc_final: 0.7521 (t80) REVERT: F 306 MET cc_start: 0.8842 (tmm) cc_final: 0.8483 (ttp) outliers start: 30 outliers final: 25 residues processed: 193 average time/residue: 0.1419 time to fit residues: 42.3004 Evaluate side-chains 191 residues out of total 1926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 164 time to evaluate : 0.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 118 ASN Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 331 ILE Chi-restraints excluded: chain A residue 386 ASP Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain A residue 437 SER Chi-restraints excluded: chain B residue 79 PHE Chi-restraints excluded: chain B residue 287 THR Chi-restraints excluded: chain B residue 407 ASN Chi-restraints excluded: chain D residue 51 MET Chi-restraints excluded: chain D residue 142 PHE Chi-restraints excluded: chain E residue 96 LEU Chi-restraints excluded: chain E residue 118 ASN Chi-restraints excluded: chain E residue 268 VAL Chi-restraints excluded: chain E residue 288 VAL Chi-restraints excluded: chain E residue 331 ILE Chi-restraints excluded: chain E residue 386 ASP Chi-restraints excluded: chain E residue 433 LEU Chi-restraints excluded: chain E residue 437 SER Chi-restraints excluded: chain F residue 79 PHE Chi-restraints excluded: chain F residue 287 THR Chi-restraints excluded: chain F residue 407 ASN Chi-restraints excluded: chain H residue 83 TYR Chi-restraints excluded: chain H residue 142 PHE Chi-restraints excluded: chain G residue 31 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 110 optimal weight: 6.9990 chunk 100 optimal weight: 6.9990 chunk 106 optimal weight: 0.9990 chunk 4 optimal weight: 3.9990 chunk 50 optimal weight: 0.2980 chunk 45 optimal weight: 0.8980 chunk 156 optimal weight: 5.9990 chunk 47 optimal weight: 9.9990 chunk 198 optimal weight: 5.9990 chunk 163 optimal weight: 3.9990 chunk 54 optimal weight: 2.9990 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 300 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 96 GLN ** E 300 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 96 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.123093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.094775 restraints weight = 24313.303| |-----------------------------------------------------------------------------| r_work (start): 0.3019 rms_B_bonded: 2.09 r_work: 0.2901 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2767 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 moved from start: 0.2179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 18072 Z= 0.142 Angle : 0.542 10.623 24474 Z= 0.274 Chirality : 0.044 0.153 2740 Planarity : 0.005 0.066 3074 Dihedral : 5.441 51.712 2524 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.65 % Favored : 95.17 % Rotamer: Outliers : 1.58 % Allowed : 13.71 % Favored : 84.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.66 (0.18), residues: 2216 helix: 0.51 (0.17), residues: 1030 sheet: -0.95 (0.33), residues: 270 loop : -1.31 (0.20), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 373 TYR 0.011 0.001 TYR F 85 PHE 0.025 0.002 PHE F 79 TRP 0.012 0.001 TRP C 22 HIS 0.004 0.001 HIS A 203 Details of bonding type rmsd covalent geometry : bond 0.00348 (18070) covalent geometry : angle 0.54214 (24474) hydrogen bonds : bond 0.04095 ( 700) hydrogen bonds : angle 3.74024 ( 1992) Misc. bond : bond 0.00032 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4432 Ramachandran restraints generated. 2216 Oldfield, 0 Emsley, 2216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4432 Ramachandran restraints generated. 2216 Oldfield, 0 Emsley, 2216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 167 time to evaluate : 0.699 Fit side-chains REVERT: A 38 PHE cc_start: 0.6050 (m-80) cc_final: 0.5543 (m-80) REVERT: A 96 LEU cc_start: 0.8640 (OUTLIER) cc_final: 0.8319 (pp) REVERT: A 421 LYS cc_start: 0.8719 (ptmt) cc_final: 0.8203 (ptmm) REVERT: B 30 ARG cc_start: 0.8421 (tpt170) cc_final: 0.7260 (mpt180) REVERT: B 171 TYR cc_start: 0.8043 (t80) cc_final: 0.7563 (t80) REVERT: B 306 MET cc_start: 0.8825 (tmm) cc_final: 0.8456 (ttp) REVERT: C 24 GLU cc_start: 0.8943 (mt-10) cc_final: 0.8689 (mt-10) REVERT: E 38 PHE cc_start: 0.6054 (m-80) cc_final: 0.5544 (m-80) REVERT: E 96 LEU cc_start: 0.8632 (OUTLIER) cc_final: 0.8313 (pp) REVERT: E 421 LYS cc_start: 0.8717 (ptmt) cc_final: 0.8211 (ptmm) REVERT: F 30 ARG cc_start: 0.8408 (tpt170) cc_final: 0.7256 (mpt180) REVERT: F 171 TYR cc_start: 0.8036 (t80) cc_final: 0.7551 (t80) REVERT: F 306 MET cc_start: 0.8866 (tmm) cc_final: 0.8509 (ttp) outliers start: 30 outliers final: 26 residues processed: 192 average time/residue: 0.1428 time to fit residues: 42.3177 Evaluate side-chains 190 residues out of total 1926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 162 time to evaluate : 0.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 118 ASN Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 331 ILE Chi-restraints excluded: chain A residue 386 ASP Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain A residue 437 SER Chi-restraints excluded: chain B residue 79 PHE Chi-restraints excluded: chain B residue 287 THR Chi-restraints excluded: chain B residue 407 ASN Chi-restraints excluded: chain D residue 51 MET Chi-restraints excluded: chain D residue 83 TYR Chi-restraints excluded: chain D residue 142 PHE Chi-restraints excluded: chain E residue 96 LEU Chi-restraints excluded: chain E residue 118 ASN Chi-restraints excluded: chain E residue 268 VAL Chi-restraints excluded: chain E residue 288 VAL Chi-restraints excluded: chain E residue 331 ILE Chi-restraints excluded: chain E residue 386 ASP Chi-restraints excluded: chain E residue 433 LEU Chi-restraints excluded: chain E residue 437 SER Chi-restraints excluded: chain F residue 79 PHE Chi-restraints excluded: chain F residue 287 THR Chi-restraints excluded: chain F residue 407 ASN Chi-restraints excluded: chain H residue 83 TYR Chi-restraints excluded: chain H residue 142 PHE Chi-restraints excluded: chain G residue 31 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 124 optimal weight: 0.7980 chunk 16 optimal weight: 6.9990 chunk 207 optimal weight: 2.9990 chunk 98 optimal weight: 5.9990 chunk 210 optimal weight: 6.9990 chunk 121 optimal weight: 3.9990 chunk 33 optimal weight: 4.9990 chunk 78 optimal weight: 4.9990 chunk 9 optimal weight: 4.9990 chunk 188 optimal weight: 1.9990 chunk 97 optimal weight: 0.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 300 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 96 GLN ** E 300 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 96 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.122111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.093604 restraints weight = 24564.341| |-----------------------------------------------------------------------------| r_work (start): 0.3006 rms_B_bonded: 2.11 r_work: 0.2889 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2754 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2754 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.2176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 18072 Z= 0.160 Angle : 0.548 9.353 24474 Z= 0.280 Chirality : 0.045 0.156 2740 Planarity : 0.005 0.068 3074 Dihedral : 5.518 50.968 2524 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.47 % Favored : 95.35 % Rotamer: Outliers : 1.52 % Allowed : 13.87 % Favored : 84.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.76 (0.18), residues: 2216 helix: 0.42 (0.17), residues: 1042 sheet: -0.95 (0.33), residues: 270 loop : -1.40 (0.20), residues: 904 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 373 TYR 0.012 0.001 TYR F 85 PHE 0.026 0.002 PHE F 79 TRP 0.013 0.001 TRP C 22 HIS 0.004 0.001 HIS A 203 Details of bonding type rmsd covalent geometry : bond 0.00395 (18070) covalent geometry : angle 0.54788 (24474) hydrogen bonds : bond 0.04312 ( 700) hydrogen bonds : angle 3.79935 ( 1992) Misc. bond : bond 0.00039 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4163.92 seconds wall clock time: 72 minutes 12.20 seconds (4332.20 seconds total)