Starting phenix.real_space_refine on Tue Aug 6 04:55:19 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9emc_19817/08_2024/9emc_19817.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9emc_19817/08_2024/9emc_19817.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.26 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9emc_19817/08_2024/9emc_19817.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9emc_19817/08_2024/9emc_19817.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9emc_19817/08_2024/9emc_19817.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9emc_19817/08_2024/9emc_19817.cif" } resolution = 3.26 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 18 5.49 5 Mg 6 5.21 5 S 75 5.16 5 C 9672 2.51 5 N 2718 2.21 5 O 3000 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 278": "OE1" <-> "OE2" Residue "A GLU 370": "OE1" <-> "OE2" Residue "A GLU 396": "OE1" <-> "OE2" Residue "D GLU 300": "OE1" <-> "OE2" Residue "D GLU 376": "OE1" <-> "OE2" Residue "D GLU 377": "OE1" <-> "OE2" Residue "D GLU 378": "OE1" <-> "OE2" Residue "D GLU 445": "OE1" <-> "OE2" Residue "B GLU 278": "OE1" <-> "OE2" Residue "B GLU 370": "OE1" <-> "OE2" Residue "B GLU 396": "OE1" <-> "OE2" Residue "C GLU 278": "OE1" <-> "OE2" Residue "C GLU 370": "OE1" <-> "OE2" Residue "C GLU 396": "OE1" <-> "OE2" Residue "F GLU 300": "OE1" <-> "OE2" Residue "F GLU 376": "OE1" <-> "OE2" Residue "F GLU 377": "OE1" <-> "OE2" Residue "F GLU 378": "OE1" <-> "OE2" Residue "F GLU 445": "OE1" <-> "OE2" Residue "E GLU 300": "OE1" <-> "OE2" Residue "E GLU 376": "OE1" <-> "OE2" Residue "E GLU 377": "OE1" <-> "OE2" Residue "E GLU 378": "OE1" <-> "OE2" Residue "E GLU 445": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 15489 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2476 Number of conformers: 1 Conformer: "" Number of residues, atoms: 322, 2476 Classifications: {'peptide': 322} Link IDs: {'PTRANS': 11, 'TRANS': 310} Chain breaks: 2 Chain: "D" Number of atoms: 2623 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2623 Classifications: {'peptide': 337} Link IDs: {'PTRANS': 9, 'TRANS': 327} Chain breaks: 1 Chain: "B" Number of atoms: 2476 Number of conformers: 1 Conformer: "" Number of residues, atoms: 322, 2476 Classifications: {'peptide': 322} Link IDs: {'PTRANS': 11, 'TRANS': 310} Chain breaks: 2 Chain: "C" Number of atoms: 2476 Number of conformers: 1 Conformer: "" Number of residues, atoms: 322, 2476 Classifications: {'peptide': 322} Link IDs: {'PTRANS': 11, 'TRANS': 310} Chain breaks: 2 Chain: "F" Number of atoms: 2623 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2623 Classifications: {'peptide': 337} Link IDs: {'PTRANS': 9, 'TRANS': 327} Chain breaks: 1 Chain: "E" Number of atoms: 2623 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2623 Classifications: {'peptide': 337} Link IDs: {'PTRANS': 9, 'TRANS': 327} Chain breaks: 1 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 8.86, per 1000 atoms: 0.57 Number of scatterers: 15489 At special positions: 0 Unit cell: (129.043, 126.562, 87.6832, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 75 16.00 P 18 15.00 Mg 6 11.99 O 3000 8.00 N 2718 7.00 C 9672 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.62 Conformation dependent library (CDL) restraints added in 2.8 seconds 3894 Ramachandran restraints generated. 1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3666 Finding SS restraints... Secondary structure from input PDB file: 96 helices and 24 sheets defined 54.2% alpha, 11.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.96 Creating SS restraints... Processing helix chain 'A' and resid 42 through 59 removed outlier: 3.606A pdb=" N LYS A 59 " --> pdb=" O LEU A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 88 Processing helix chain 'A' and resid 99 through 102 removed outlier: 4.020A pdb=" N TYR A 102 " --> pdb=" O SER A 99 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 99 through 102' Processing helix chain 'A' and resid 107 through 119 Processing helix chain 'A' and resid 240 through 247 Processing helix chain 'A' and resid 272 through 289 removed outlier: 3.582A pdb=" N ARG A 276 " --> pdb=" O THR A 272 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N GLU A 278 " --> pdb=" O LYS A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 307 Processing helix chain 'A' and resid 308 through 320 removed outlier: 3.926A pdb=" N ARG A 317 " --> pdb=" O THR A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 347 through 350 Processing helix chain 'A' and resid 351 through 356 Processing helix chain 'A' and resid 367 through 382 Processing helix chain 'A' and resid 387 through 401 Processing helix chain 'A' and resid 402 through 408 removed outlier: 3.753A pdb=" N SER A 406 " --> pdb=" O THR A 402 " (cutoff:3.500A) Processing helix chain 'A' and resid 409 through 421 removed outlier: 3.582A pdb=" N ALA A 413 " --> pdb=" O LEU A 409 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 437 removed outlier: 3.581A pdb=" N VAL A 430 " --> pdb=" O GLU A 426 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 450 Processing helix chain 'D' and resid 49 through 66 Processing helix chain 'D' and resid 82 through 95 removed outlier: 3.873A pdb=" N GLY D 95 " --> pdb=" O ALA D 91 " (cutoff:3.500A) Processing helix chain 'D' and resid 114 through 125 Processing helix chain 'D' and resid 244 through 251 Processing helix chain 'D' and resid 255 through 259 removed outlier: 3.954A pdb=" N LEU D 258 " --> pdb=" O GLN D 255 " (cutoff:3.500A) Processing helix chain 'D' and resid 269 through 287 Processing helix chain 'D' and resid 300 through 304 Processing helix chain 'D' and resid 305 through 316 removed outlier: 3.730A pdb=" N ARG D 314 " --> pdb=" O SER D 310 " (cutoff:3.500A) Processing helix chain 'D' and resid 343 through 346 Processing helix chain 'D' and resid 347 through 352 Processing helix chain 'D' and resid 363 through 378 Processing helix chain 'D' and resid 383 through 397 Processing helix chain 'D' and resid 398 through 416 removed outlier: 3.742A pdb=" N ALA D 402 " --> pdb=" O SER D 398 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ILE D 406 " --> pdb=" O ALA D 402 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N THR D 407 " --> pdb=" O ILE D 403 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ALA D 408 " --> pdb=" O GLN D 404 " (cutoff:3.500A) Processing helix chain 'D' and resid 422 through 433 removed outlier: 3.538A pdb=" N ILE D 426 " --> pdb=" O GLN D 422 " (cutoff:3.500A) Processing helix chain 'D' and resid 435 through 446 removed outlier: 3.936A pdb=" N GLU D 445 " --> pdb=" O GLN D 441 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N TYR D 446 " --> pdb=" O TYR D 442 " (cutoff:3.500A) Processing helix chain 'D' and resid 447 through 449 No H-bonds generated for 'chain 'D' and resid 447 through 449' Processing helix chain 'B' and resid 42 through 59 removed outlier: 3.607A pdb=" N LYS B 59 " --> pdb=" O LEU B 55 " (cutoff:3.500A) Processing helix chain 'B' and resid 76 through 88 Processing helix chain 'B' and resid 99 through 102 removed outlier: 4.020A pdb=" N TYR B 102 " --> pdb=" O SER B 99 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 99 through 102' Processing helix chain 'B' and resid 107 through 119 Processing helix chain 'B' and resid 240 through 247 Processing helix chain 'B' and resid 272 through 289 removed outlier: 3.581A pdb=" N ARG B 276 " --> pdb=" O THR B 272 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N GLU B 278 " --> pdb=" O LYS B 274 " (cutoff:3.500A) Processing helix chain 'B' and resid 303 through 307 Processing helix chain 'B' and resid 308 through 320 removed outlier: 3.926A pdb=" N ARG B 317 " --> pdb=" O THR B 313 " (cutoff:3.500A) Processing helix chain 'B' and resid 347 through 350 Processing helix chain 'B' and resid 351 through 356 Processing helix chain 'B' and resid 367 through 382 Processing helix chain 'B' and resid 387 through 401 Processing helix chain 'B' and resid 402 through 408 removed outlier: 3.753A pdb=" N SER B 406 " --> pdb=" O THR B 402 " (cutoff:3.500A) Processing helix chain 'B' and resid 409 through 421 removed outlier: 3.582A pdb=" N ALA B 413 " --> pdb=" O LEU B 409 " (cutoff:3.500A) Processing helix chain 'B' and resid 426 through 437 removed outlier: 3.581A pdb=" N VAL B 430 " --> pdb=" O GLU B 426 " (cutoff:3.500A) Processing helix chain 'B' and resid 439 through 450 Processing helix chain 'C' and resid 42 through 59 removed outlier: 3.607A pdb=" N LYS C 59 " --> pdb=" O LEU C 55 " (cutoff:3.500A) Processing helix chain 'C' and resid 76 through 88 Processing helix chain 'C' and resid 99 through 102 removed outlier: 4.021A pdb=" N TYR C 102 " --> pdb=" O SER C 99 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 99 through 102' Processing helix chain 'C' and resid 107 through 119 Processing helix chain 'C' and resid 240 through 247 Processing helix chain 'C' and resid 272 through 289 removed outlier: 3.582A pdb=" N ARG C 276 " --> pdb=" O THR C 272 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N GLU C 278 " --> pdb=" O LYS C 274 " (cutoff:3.500A) Processing helix chain 'C' and resid 303 through 307 Processing helix chain 'C' and resid 308 through 320 removed outlier: 3.926A pdb=" N ARG C 317 " --> pdb=" O THR C 313 " (cutoff:3.500A) Processing helix chain 'C' and resid 347 through 350 Processing helix chain 'C' and resid 351 through 356 Processing helix chain 'C' and resid 367 through 382 Processing helix chain 'C' and resid 387 through 401 Processing helix chain 'C' and resid 402 through 408 removed outlier: 3.753A pdb=" N SER C 406 " --> pdb=" O THR C 402 " (cutoff:3.500A) Processing helix chain 'C' and resid 409 through 421 removed outlier: 3.582A pdb=" N ALA C 413 " --> pdb=" O LEU C 409 " (cutoff:3.500A) Processing helix chain 'C' and resid 426 through 437 removed outlier: 3.581A pdb=" N VAL C 430 " --> pdb=" O GLU C 426 " (cutoff:3.500A) Processing helix chain 'C' and resid 439 through 450 Processing helix chain 'F' and resid 49 through 66 Processing helix chain 'F' and resid 82 through 95 removed outlier: 3.872A pdb=" N GLY F 95 " --> pdb=" O ALA F 91 " (cutoff:3.500A) Processing helix chain 'F' and resid 114 through 125 Processing helix chain 'F' and resid 244 through 251 Processing helix chain 'F' and resid 255 through 259 removed outlier: 3.955A pdb=" N LEU F 258 " --> pdb=" O GLN F 255 " (cutoff:3.500A) Processing helix chain 'F' and resid 269 through 287 Processing helix chain 'F' and resid 300 through 304 Processing helix chain 'F' and resid 305 through 316 removed outlier: 3.730A pdb=" N ARG F 314 " --> pdb=" O SER F 310 " (cutoff:3.500A) Processing helix chain 'F' and resid 343 through 346 Processing helix chain 'F' and resid 347 through 352 Processing helix chain 'F' and resid 363 through 378 Processing helix chain 'F' and resid 383 through 397 Processing helix chain 'F' and resid 398 through 416 removed outlier: 3.743A pdb=" N ALA F 402 " --> pdb=" O SER F 398 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ILE F 406 " --> pdb=" O ALA F 402 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N THR F 407 " --> pdb=" O ILE F 403 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ALA F 408 " --> pdb=" O GLN F 404 " (cutoff:3.500A) Processing helix chain 'F' and resid 422 through 433 removed outlier: 3.537A pdb=" N ILE F 426 " --> pdb=" O GLN F 422 " (cutoff:3.500A) Processing helix chain 'F' and resid 435 through 446 removed outlier: 3.936A pdb=" N GLU F 445 " --> pdb=" O GLN F 441 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N TYR F 446 " --> pdb=" O TYR F 442 " (cutoff:3.500A) Processing helix chain 'F' and resid 447 through 449 No H-bonds generated for 'chain 'F' and resid 447 through 449' Processing helix chain 'E' and resid 49 through 66 Processing helix chain 'E' and resid 82 through 95 removed outlier: 3.872A pdb=" N GLY E 95 " --> pdb=" O ALA E 91 " (cutoff:3.500A) Processing helix chain 'E' and resid 114 through 125 Processing helix chain 'E' and resid 244 through 251 Processing helix chain 'E' and resid 255 through 259 removed outlier: 3.954A pdb=" N LEU E 258 " --> pdb=" O GLN E 255 " (cutoff:3.500A) Processing helix chain 'E' and resid 269 through 287 Processing helix chain 'E' and resid 300 through 304 Processing helix chain 'E' and resid 305 through 316 removed outlier: 3.730A pdb=" N ARG E 314 " --> pdb=" O SER E 310 " (cutoff:3.500A) Processing helix chain 'E' and resid 343 through 346 Processing helix chain 'E' and resid 347 through 352 Processing helix chain 'E' and resid 363 through 378 Processing helix chain 'E' and resid 383 through 397 Processing helix chain 'E' and resid 398 through 416 removed outlier: 3.742A pdb=" N ALA E 402 " --> pdb=" O SER E 398 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ILE E 406 " --> pdb=" O ALA E 402 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N THR E 407 " --> pdb=" O ILE E 403 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ALA E 408 " --> pdb=" O GLN E 404 " (cutoff:3.500A) Processing helix chain 'E' and resid 422 through 433 removed outlier: 3.538A pdb=" N ILE E 426 " --> pdb=" O GLN E 422 " (cutoff:3.500A) Processing helix chain 'E' and resid 435 through 446 removed outlier: 3.936A pdb=" N GLU E 445 " --> pdb=" O GLN E 441 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N TYR E 446 " --> pdb=" O TYR E 442 " (cutoff:3.500A) Processing helix chain 'E' and resid 447 through 449 No H-bonds generated for 'chain 'E' and resid 447 through 449' Processing sheet with id=AA1, first strand: chain 'A' and resid 35 through 36 Processing sheet with id=AA2, first strand: chain 'A' and resid 93 through 97 removed outlier: 6.514A pdb=" N CYS A 94 " --> pdb=" O PHE A 300 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N ASP A 302 " --> pdb=" O CYS A 94 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N MET A 96 " --> pdb=" O ASP A 302 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N LEU A 299 " --> pdb=" O ILE A 328 " (cutoff:3.500A) removed outlier: 7.730A pdb=" N ALA A 330 " --> pdb=" O LEU A 299 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N VAL A 301 " --> pdb=" O ALA A 330 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N VAL A 66 " --> pdb=" O PHE A 329 " (cutoff:3.500A) removed outlier: 7.862A pdb=" N SER A 331 " --> pdb=" O VAL A 66 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N LEU A 68 " --> pdb=" O SER A 331 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 236 through 239 Processing sheet with id=AA4, first strand: chain 'A' and resid 336 through 337 removed outlier: 3.516A pdb=" N CYS A 336 " --> pdb=" O SER A 346 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N SER A 346 " --> pdb=" O CYS A 336 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'D' and resid 42 through 43 Processing sheet with id=AA6, first strand: chain 'D' and resid 100 through 104 removed outlier: 6.664A pdb=" N THR D 101 " --> pdb=" O PHE D 297 " (cutoff:3.500A) removed outlier: 7.462A pdb=" N ASP D 299 " --> pdb=" O THR D 101 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N ILE D 103 " --> pdb=" O ASP D 299 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLY D 77 " --> pdb=" O THR D 328 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N ALA D 72 " --> pdb=" O LEU D 355 " (cutoff:3.500A) removed outlier: 8.040A pdb=" N VAL D 357 " --> pdb=" O ALA D 72 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N LEU D 74 " --> pdb=" O VAL D 357 " (cutoff:3.500A) removed outlier: 7.664A pdb=" N THR D 359 " --> pdb=" O LEU D 74 " (cutoff:3.500A) removed outlier: 7.313A pdb=" N ALA D 76 " --> pdb=" O THR D 359 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 238 through 243 Processing sheet with id=AA8, first strand: chain 'D' and resid 333 through 334 Processing sheet with id=AA9, first strand: chain 'B' and resid 35 through 36 Processing sheet with id=AB1, first strand: chain 'B' and resid 93 through 97 removed outlier: 6.514A pdb=" N CYS B 94 " --> pdb=" O PHE B 300 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N ASP B 302 " --> pdb=" O CYS B 94 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N MET B 96 " --> pdb=" O ASP B 302 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N LEU B 299 " --> pdb=" O ILE B 328 " (cutoff:3.500A) removed outlier: 7.730A pdb=" N ALA B 330 " --> pdb=" O LEU B 299 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N VAL B 301 " --> pdb=" O ALA B 330 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N VAL B 66 " --> pdb=" O PHE B 329 " (cutoff:3.500A) removed outlier: 7.863A pdb=" N SER B 331 " --> pdb=" O VAL B 66 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N LEU B 68 " --> pdb=" O SER B 331 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 236 through 239 Processing sheet with id=AB3, first strand: chain 'B' and resid 336 through 337 removed outlier: 3.515A pdb=" N CYS B 336 " --> pdb=" O SER B 346 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N SER B 346 " --> pdb=" O CYS B 336 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'C' and resid 35 through 36 Processing sheet with id=AB5, first strand: chain 'C' and resid 93 through 97 removed outlier: 6.515A pdb=" N CYS C 94 " --> pdb=" O PHE C 300 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N ASP C 302 " --> pdb=" O CYS C 94 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N MET C 96 " --> pdb=" O ASP C 302 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N LEU C 299 " --> pdb=" O ILE C 328 " (cutoff:3.500A) removed outlier: 7.730A pdb=" N ALA C 330 " --> pdb=" O LEU C 299 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N VAL C 301 " --> pdb=" O ALA C 330 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N VAL C 66 " --> pdb=" O PHE C 329 " (cutoff:3.500A) removed outlier: 7.863A pdb=" N SER C 331 " --> pdb=" O VAL C 66 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N LEU C 68 " --> pdb=" O SER C 331 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 236 through 239 Processing sheet with id=AB7, first strand: chain 'C' and resid 336 through 337 removed outlier: 3.516A pdb=" N CYS C 336 " --> pdb=" O SER C 346 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N SER C 346 " --> pdb=" O CYS C 336 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'F' and resid 42 through 43 Processing sheet with id=AB9, first strand: chain 'F' and resid 100 through 104 removed outlier: 6.665A pdb=" N THR F 101 " --> pdb=" O PHE F 297 " (cutoff:3.500A) removed outlier: 7.462A pdb=" N ASP F 299 " --> pdb=" O THR F 101 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N ILE F 103 " --> pdb=" O ASP F 299 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLY F 77 " --> pdb=" O THR F 328 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N ALA F 72 " --> pdb=" O LEU F 355 " (cutoff:3.500A) removed outlier: 8.040A pdb=" N VAL F 357 " --> pdb=" O ALA F 72 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N LEU F 74 " --> pdb=" O VAL F 357 " (cutoff:3.500A) removed outlier: 7.664A pdb=" N THR F 359 " --> pdb=" O LEU F 74 " (cutoff:3.500A) removed outlier: 7.314A pdb=" N ALA F 76 " --> pdb=" O THR F 359 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 238 through 243 Processing sheet with id=AC2, first strand: chain 'F' and resid 333 through 334 Processing sheet with id=AC3, first strand: chain 'E' and resid 42 through 43 Processing sheet with id=AC4, first strand: chain 'E' and resid 100 through 104 removed outlier: 6.664A pdb=" N THR E 101 " --> pdb=" O PHE E 297 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N ASP E 299 " --> pdb=" O THR E 101 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N ILE E 103 " --> pdb=" O ASP E 299 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLY E 77 " --> pdb=" O THR E 328 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N ALA E 72 " --> pdb=" O LEU E 355 " (cutoff:3.500A) removed outlier: 8.039A pdb=" N VAL E 357 " --> pdb=" O ALA E 72 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N LEU E 74 " --> pdb=" O VAL E 357 " (cutoff:3.500A) removed outlier: 7.664A pdb=" N THR E 359 " --> pdb=" O LEU E 74 " (cutoff:3.500A) removed outlier: 7.313A pdb=" N ALA E 76 " --> pdb=" O THR E 359 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 238 through 243 Processing sheet with id=AC6, first strand: chain 'E' and resid 333 through 334 762 hydrogen bonds defined for protein. 2178 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.94 Time building geometry restraints manager: 6.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 4362 1.33 - 1.45: 2348 1.45 - 1.57: 8818 1.57 - 1.69: 18 1.69 - 1.81: 132 Bond restraints: 15678 Sorted by residual: bond pdb=" N ILE B 52 " pdb=" CA ILE B 52 " ideal model delta sigma weight residual 1.460 1.501 -0.041 1.21e-02 6.83e+03 1.16e+01 bond pdb=" N ILE C 52 " pdb=" CA ILE C 52 " ideal model delta sigma weight residual 1.460 1.500 -0.040 1.21e-02 6.83e+03 1.11e+01 bond pdb=" N ILE A 52 " pdb=" CA ILE A 52 " ideal model delta sigma weight residual 1.460 1.499 -0.039 1.21e-02 6.83e+03 1.04e+01 bond pdb=" N VAL A 327 " pdb=" CA VAL A 327 " ideal model delta sigma weight residual 1.459 1.497 -0.038 1.20e-02 6.94e+03 1.03e+01 bond pdb=" N VAL B 327 " pdb=" CA VAL B 327 " ideal model delta sigma weight residual 1.459 1.496 -0.038 1.20e-02 6.94e+03 9.86e+00 ... (remaining 15673 not shown) Histogram of bond angle deviations from ideal: 98.60 - 106.80: 540 106.80 - 115.00: 9445 115.00 - 123.20: 9991 123.20 - 131.40: 1152 131.40 - 139.61: 31 Bond angle restraints: 21159 Sorted by residual: angle pdb=" CA GLY C 297 " pdb=" C GLY C 297 " pdb=" O GLY C 297 " ideal model delta sigma weight residual 121.78 117.41 4.37 9.10e-01 1.21e+00 2.30e+01 angle pdb=" CA GLY A 297 " pdb=" C GLY A 297 " pdb=" O GLY A 297 " ideal model delta sigma weight residual 121.78 117.44 4.34 9.10e-01 1.21e+00 2.27e+01 angle pdb=" CA GLY B 297 " pdb=" C GLY B 297 " pdb=" O GLY B 297 " ideal model delta sigma weight residual 121.78 117.46 4.32 9.10e-01 1.21e+00 2.26e+01 angle pdb=" N ILE B 323 " pdb=" CA ILE B 323 " pdb=" C ILE B 323 " ideal model delta sigma weight residual 113.43 108.40 5.03 1.09e+00 8.42e-01 2.13e+01 angle pdb=" N ILE A 323 " pdb=" CA ILE A 323 " pdb=" C ILE A 323 " ideal model delta sigma weight residual 113.43 108.45 4.98 1.09e+00 8.42e-01 2.08e+01 ... (remaining 21154 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 8268 17.93 - 35.87: 1121 35.87 - 53.80: 286 53.80 - 71.73: 90 71.73 - 89.67: 30 Dihedral angle restraints: 9795 sinusoidal: 4125 harmonic: 5670 Sorted by residual: dihedral pdb=" CA ASP C 343 " pdb=" C ASP C 343 " pdb=" N ILE C 344 " pdb=" CA ILE C 344 " ideal model delta harmonic sigma weight residual 180.00 160.28 19.72 0 5.00e+00 4.00e-02 1.56e+01 dihedral pdb=" CA ASP B 343 " pdb=" C ASP B 343 " pdb=" N ILE B 344 " pdb=" CA ILE B 344 " ideal model delta harmonic sigma weight residual 180.00 160.38 19.62 0 5.00e+00 4.00e-02 1.54e+01 dihedral pdb=" CA ASP A 343 " pdb=" C ASP A 343 " pdb=" N ILE A 344 " pdb=" CA ILE A 344 " ideal model delta harmonic sigma weight residual 180.00 160.39 19.61 0 5.00e+00 4.00e-02 1.54e+01 ... (remaining 9792 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.082: 1796 0.082 - 0.163: 570 0.163 - 0.245: 102 0.245 - 0.326: 13 0.326 - 0.408: 6 Chirality restraints: 2487 Sorted by residual: chirality pdb=" CB VAL A 238 " pdb=" CA VAL A 238 " pdb=" CG1 VAL A 238 " pdb=" CG2 VAL A 238 " both_signs ideal model delta sigma weight residual False -2.63 -2.22 -0.41 2.00e-01 2.50e+01 4.16e+00 chirality pdb=" CB VAL B 238 " pdb=" CA VAL B 238 " pdb=" CG1 VAL B 238 " pdb=" CG2 VAL B 238 " both_signs ideal model delta sigma weight residual False -2.63 -2.22 -0.41 2.00e-01 2.50e+01 4.14e+00 chirality pdb=" CB VAL C 238 " pdb=" CA VAL C 238 " pdb=" CG1 VAL C 238 " pdb=" CG2 VAL C 238 " both_signs ideal model delta sigma weight residual False -2.63 -2.22 -0.41 2.00e-01 2.50e+01 4.12e+00 ... (remaining 2484 not shown) Planarity restraints: 2679 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PRO B 72 " -0.021 2.00e-02 2.50e+03 4.20e-02 1.76e+01 pdb=" C PRO B 72 " 0.073 2.00e-02 2.50e+03 pdb=" O PRO B 72 " -0.028 2.00e-02 2.50e+03 pdb=" N GLY B 73 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO A 72 " 0.021 2.00e-02 2.50e+03 4.19e-02 1.75e+01 pdb=" C PRO A 72 " -0.072 2.00e-02 2.50e+03 pdb=" O PRO A 72 " 0.028 2.00e-02 2.50e+03 pdb=" N GLY A 73 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO C 72 " -0.021 2.00e-02 2.50e+03 4.16e-02 1.73e+01 pdb=" C PRO C 72 " 0.072 2.00e-02 2.50e+03 pdb=" O PRO C 72 " -0.028 2.00e-02 2.50e+03 pdb=" N GLY C 73 " -0.024 2.00e-02 2.50e+03 ... (remaining 2676 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 232 2.64 - 3.20: 12668 3.20 - 3.77: 24775 3.77 - 4.33: 35551 4.33 - 4.90: 56782 Nonbonded interactions: 130008 Sorted by model distance: nonbonded pdb=" O3G ATP A 501 " pdb="MG MG A 502 " model vdw 2.075 2.170 nonbonded pdb=" O3G ATP C 501 " pdb="MG MG C 502 " model vdw 2.076 2.170 nonbonded pdb=" O3G ATP B 501 " pdb="MG MG B 502 " model vdw 2.076 2.170 nonbonded pdb=" OG1 THR F 84 " pdb="MG MG F 502 " model vdw 2.088 2.170 nonbonded pdb=" OG1 THR D 84 " pdb="MG MG D 502 " model vdw 2.089 2.170 ... (remaining 130003 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' } 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: 2.310 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: 0.010 Extract box with map and model: 0.650 Check model and map are aligned: 0.110 Set scattering table: 0.150 Process input model: 44.330 Find NCS groups from input model: 0.610 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6761 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 : 0.011 0.111 15678 Z= 0.711 Angle : 1.344 9.972 21159 Z= 0.825 Chirality : 0.082 0.408 2487 Planarity : 0.009 0.058 2679 Dihedral : 18.595 89.668 6129 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 1.44 % Allowed : 18.65 % Favored : 79.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.73 (0.16), residues: 1947 helix: -3.87 (0.09), residues: 993 sheet: -1.79 (0.31), residues: 252 loop : 0.02 (0.23), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.005 TRP D 283 HIS 0.011 0.003 HIS B 241 PHE 0.018 0.004 PHE B 312 TYR 0.044 0.003 TYR A 314 ARG 0.023 0.002 ARG F 330 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3894 Ramachandran restraints generated. 1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3894 Ramachandran restraints generated. 1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 511 residues out of total 1662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 487 time to evaluate : 1.895 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 24 outliers final: 3 residues processed: 502 average time/residue: 0.2843 time to fit residues: 206.1187 Evaluate side-chains 264 residues out of total 1662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 261 time to evaluate : 1.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 371 MET Chi-restraints excluded: chain F residue 380 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 164 optimal weight: 9.9990 chunk 147 optimal weight: 0.7980 chunk 82 optimal weight: 0.8980 chunk 50 optimal weight: 1.9990 chunk 99 optimal weight: 7.9990 chunk 78 optimal weight: 3.9990 chunk 152 optimal weight: 0.9990 chunk 59 optimal weight: 4.9990 chunk 92 optimal weight: 0.9980 chunk 113 optimal weight: 0.7980 chunk 177 optimal weight: 5.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 HIS A 42 GLN A 316 HIS A 332 ASN A 420 ASN D 25 HIS D 277 ASN D 302 HIS D 341 GLN B 18 HIS B 42 GLN B 115 ASN B 289 GLN C 13 GLN C 18 HIS C 115 ASN C 332 ASN C 335 ASN C 373 GLN ** F 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 447 GLN E 25 HIS ** E 302 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 341 GLN E 404 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7438 moved from start: 0.4001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 15678 Z= 0.217 Angle : 0.600 8.494 21159 Z= 0.319 Chirality : 0.043 0.228 2487 Planarity : 0.005 0.039 2679 Dihedral : 9.929 89.665 2339 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 3.49 % Allowed : 22.98 % Favored : 73.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.33 (0.18), residues: 1947 helix: -1.18 (0.14), residues: 1029 sheet: -1.46 (0.29), residues: 288 loop : 0.48 (0.24), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP E 283 HIS 0.008 0.001 HIS F 302 PHE 0.018 0.002 PHE F 297 TYR 0.013 0.001 TYR E 430 ARG 0.007 0.001 ARG D 414 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3894 Ramachandran restraints generated. 1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3894 Ramachandran restraints generated. 1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 1662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 268 time to evaluate : 1.886 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 58 outliers final: 24 residues processed: 318 average time/residue: 0.2396 time to fit residues: 116.6207 Evaluate side-chains 236 residues out of total 1662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 212 time to evaluate : 1.848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 CYS Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 264 MET Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain D residue 86 ILE Chi-restraints excluded: chain D residue 101 THR Chi-restraints excluded: chain D residue 265 THR Chi-restraints excluded: chain D residue 365 LYS Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain C residue 17 SER Chi-restraints excluded: chain C residue 240 LEU Chi-restraints excluded: chain C residue 328 ILE Chi-restraints excluded: chain F residue 31 LEU Chi-restraints excluded: chain F residue 86 ILE Chi-restraints excluded: chain F residue 236 LYS Chi-restraints excluded: chain F residue 312 LEU Chi-restraints excluded: chain F residue 380 VAL Chi-restraints excluded: chain F residue 426 ILE Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 371 LEU Chi-restraints excluded: chain E residue 400 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 98 optimal weight: 6.9990 chunk 54 optimal weight: 9.9990 chunk 147 optimal weight: 0.9980 chunk 120 optimal weight: 4.9990 chunk 48 optimal weight: 4.9990 chunk 177 optimal weight: 1.9990 chunk 191 optimal weight: 10.0000 chunk 157 optimal weight: 6.9990 chunk 175 optimal weight: 0.9980 chunk 60 optimal weight: 3.9990 chunk 142 optimal weight: 3.9990 overall best weight: 2.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 280 ASN ** A 316 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 408 GLN A 420 ASN D 277 ASN C 42 GLN ** C 316 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 380 GLN C 408 GLN F 27 HIS F 240 HIS E 275 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.8036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 15678 Z= 0.319 Angle : 0.621 8.467 21159 Z= 0.331 Chirality : 0.044 0.167 2487 Planarity : 0.005 0.057 2679 Dihedral : 8.801 71.736 2336 Min Nonbonded Distance : 1.757 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 4.39 % Allowed : 20.70 % Favored : 74.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.18), residues: 1947 helix: 0.20 (0.16), residues: 1053 sheet: -0.92 (0.29), residues: 285 loop : 0.01 (0.23), residues: 609 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 283 HIS 0.005 0.001 HIS A 18 PHE 0.029 0.003 PHE D 297 TYR 0.016 0.002 TYR E 430 ARG 0.010 0.001 ARG E 284 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3894 Ramachandran restraints generated. 1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3894 Ramachandran restraints generated. 1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 154 time to evaluate : 1.951 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 313 ASN cc_start: 0.7105 (m110) cc_final: 0.6793 (m110) REVERT: F 313 ASN cc_start: 0.6868 (m-40) cc_final: 0.6666 (m-40) REVERT: F 378 GLU cc_start: 0.7138 (OUTLIER) cc_final: 0.6800 (mp0) REVERT: F 405 LEU cc_start: 0.8595 (OUTLIER) cc_final: 0.8393 (mp) outliers start: 73 outliers final: 27 residues processed: 221 average time/residue: 0.2586 time to fit residues: 86.0051 Evaluate side-chains 154 residues out of total 1662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 125 time to evaluate : 1.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain D residue 308 SER Chi-restraints excluded: chain D residue 318 SER Chi-restraints excluded: chain D residue 360 THR Chi-restraints excluded: chain B residue 18 HIS Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain C residue 409 LEU Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 75 ILE Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 127 ILE Chi-restraints excluded: chain F residue 236 LYS Chi-restraints excluded: chain F residue 260 LEU Chi-restraints excluded: chain F residue 265 THR Chi-restraints excluded: chain F residue 292 ILE Chi-restraints excluded: chain F residue 378 GLU Chi-restraints excluded: chain F residue 380 VAL Chi-restraints excluded: chain F residue 405 LEU Chi-restraints excluded: chain F residue 426 ILE Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 59 VAL Chi-restraints excluded: chain E residue 97 ASP Chi-restraints excluded: chain E residue 265 THR Chi-restraints excluded: chain E residue 400 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 175 optimal weight: 0.9980 chunk 133 optimal weight: 1.9990 chunk 92 optimal weight: 3.9990 chunk 19 optimal weight: 0.9990 chunk 84 optimal weight: 3.9990 chunk 119 optimal weight: 0.9980 chunk 178 optimal weight: 0.9990 chunk 188 optimal weight: 0.9990 chunk 93 optimal weight: 4.9990 chunk 168 optimal weight: 0.8980 chunk 50 optimal weight: 2.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 HIS C 42 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.8263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 15678 Z= 0.163 Angle : 0.481 8.362 21159 Z= 0.254 Chirality : 0.041 0.161 2487 Planarity : 0.003 0.034 2679 Dihedral : 8.377 64.025 2335 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 2.47 % Allowed : 21.84 % Favored : 75.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.19), residues: 1947 helix: 0.93 (0.16), residues: 1053 sheet: -0.59 (0.30), residues: 285 loop : 0.29 (0.24), residues: 609 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP E 283 HIS 0.003 0.001 HIS B 305 PHE 0.013 0.001 PHE F 297 TYR 0.011 0.001 TYR D 446 ARG 0.006 0.000 ARG B 333 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3894 Ramachandran restraints generated. 1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3894 Ramachandran restraints generated. 1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 143 time to evaluate : 1.845 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 116 PHE cc_start: 0.8482 (OUTLIER) cc_final: 0.8226 (t80) REVERT: A 264 MET cc_start: 0.6741 (pmm) cc_final: 0.6116 (pmm) REVERT: D 447 GLN cc_start: 0.4859 (tp-100) cc_final: 0.4623 (tp40) REVERT: F 261 PHE cc_start: 0.7687 (m-80) cc_final: 0.7433 (m-10) REVERT: F 378 GLU cc_start: 0.6993 (OUTLIER) cc_final: 0.6758 (mp0) REVERT: F 405 LEU cc_start: 0.8542 (OUTLIER) cc_final: 0.8310 (mp) outliers start: 41 outliers final: 20 residues processed: 179 average time/residue: 0.2492 time to fit residues: 68.9041 Evaluate side-chains 151 residues out of total 1662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 128 time to evaluate : 1.949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 PHE Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain C residue 264 MET Chi-restraints excluded: chain C residue 371 MET Chi-restraints excluded: chain C residue 409 LEU Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 75 ILE Chi-restraints excluded: chain F residue 127 ILE Chi-restraints excluded: chain F residue 236 LYS Chi-restraints excluded: chain F residue 238 VAL Chi-restraints excluded: chain F residue 260 LEU Chi-restraints excluded: chain F residue 265 THR Chi-restraints excluded: chain F residue 371 LEU Chi-restraints excluded: chain F residue 378 GLU Chi-restraints excluded: chain F residue 380 VAL Chi-restraints excluded: chain F residue 405 LEU Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 90 MET Chi-restraints excluded: chain E residue 265 THR Chi-restraints excluded: chain E residue 375 CYS Chi-restraints excluded: chain E residue 400 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 156 optimal weight: 5.9990 chunk 106 optimal weight: 0.6980 chunk 2 optimal weight: 6.9990 chunk 140 optimal weight: 9.9990 chunk 77 optimal weight: 1.9990 chunk 160 optimal weight: 0.9980 chunk 130 optimal weight: 0.0870 chunk 0 optimal weight: 10.0000 chunk 96 optimal weight: 9.9990 chunk 169 optimal weight: 0.7980 chunk 47 optimal weight: 5.9990 overall best weight: 0.9160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 313 ASN ** C 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 240 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.8562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 15678 Z= 0.153 Angle : 0.471 10.435 21159 Z= 0.247 Chirality : 0.041 0.216 2487 Planarity : 0.003 0.029 2679 Dihedral : 7.911 60.393 2335 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 2.53 % Allowed : 21.18 % Favored : 76.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.99 (0.19), residues: 1947 helix: 1.27 (0.16), residues: 1053 sheet: -0.33 (0.30), residues: 285 loop : 0.31 (0.24), residues: 609 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP E 283 HIS 0.003 0.001 HIS B 316 PHE 0.013 0.001 PHE F 297 TYR 0.013 0.001 TYR D 446 ARG 0.007 0.000 ARG B 333 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3894 Ramachandran restraints generated. 1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3894 Ramachandran restraints generated. 1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 136 time to evaluate : 1.830 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 116 PHE cc_start: 0.8447 (OUTLIER) cc_final: 0.8189 (t80) REVERT: A 264 MET cc_start: 0.6854 (pmm) cc_final: 0.6494 (pmm) REVERT: F 261 PHE cc_start: 0.7744 (m-80) cc_final: 0.7528 (m-10) REVERT: F 378 GLU cc_start: 0.6975 (OUTLIER) cc_final: 0.6692 (mp0) REVERT: F 405 LEU cc_start: 0.8570 (OUTLIER) cc_final: 0.8329 (mp) outliers start: 42 outliers final: 24 residues processed: 169 average time/residue: 0.2393 time to fit residues: 63.1740 Evaluate side-chains 151 residues out of total 1662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 124 time to evaluate : 1.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 116 PHE Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain B residue 18 HIS Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 359 MET Chi-restraints excluded: chain C residue 264 MET Chi-restraints excluded: chain C residue 364 MET Chi-restraints excluded: chain C residue 371 MET Chi-restraints excluded: chain C residue 409 LEU Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 60 LEU Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 127 ILE Chi-restraints excluded: chain F residue 265 THR Chi-restraints excluded: chain F residue 292 ILE Chi-restraints excluded: chain F residue 378 GLU Chi-restraints excluded: chain F residue 380 VAL Chi-restraints excluded: chain F residue 405 LEU Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 265 THR Chi-restraints excluded: chain E residue 292 ILE Chi-restraints excluded: chain E residue 326 MET Chi-restraints excluded: chain E residue 375 CYS Chi-restraints excluded: chain E residue 400 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 63 optimal weight: 0.9990 chunk 169 optimal weight: 0.7980 chunk 37 optimal weight: 7.9990 chunk 110 optimal weight: 0.0970 chunk 46 optimal weight: 7.9990 chunk 188 optimal weight: 5.9990 chunk 156 optimal weight: 0.9980 chunk 87 optimal weight: 1.9990 chunk 15 optimal weight: 0.8980 chunk 62 optimal weight: 9.9990 chunk 99 optimal weight: 9.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 240 HIS F 341 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.8780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 15678 Z= 0.142 Angle : 0.456 7.223 21159 Z= 0.240 Chirality : 0.040 0.210 2487 Planarity : 0.003 0.045 2679 Dihedral : 7.668 57.990 2335 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 2.41 % Allowed : 21.66 % Favored : 75.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.19 (0.19), residues: 1947 helix: 1.44 (0.17), residues: 1056 sheet: -0.19 (0.30), residues: 285 loop : 0.32 (0.24), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP E 283 HIS 0.003 0.001 HIS B 316 PHE 0.020 0.001 PHE E 257 TYR 0.009 0.001 TYR F 340 ARG 0.007 0.000 ARG D 353 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3894 Ramachandran restraints generated. 1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3894 Ramachandran restraints generated. 1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 134 time to evaluate : 1.858 Fit side-chains revert: symmetry clash REVERT: A 116 PHE cc_start: 0.8401 (OUTLIER) cc_final: 0.8139 (t80) REVERT: A 264 MET cc_start: 0.6900 (pmm) cc_final: 0.6596 (pmm) REVERT: F 261 PHE cc_start: 0.7689 (m-80) cc_final: 0.7485 (m-10) REVERT: F 378 GLU cc_start: 0.7021 (OUTLIER) cc_final: 0.6705 (mp0) REVERT: F 405 LEU cc_start: 0.8564 (OUTLIER) cc_final: 0.8342 (mp) outliers start: 40 outliers final: 23 residues processed: 164 average time/residue: 0.2584 time to fit residues: 64.5646 Evaluate side-chains 147 residues out of total 1662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 121 time to evaluate : 1.831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 116 PHE Chi-restraints excluded: chain D residue 62 MET Chi-restraints excluded: chain B residue 359 MET Chi-restraints excluded: chain C residue 264 MET Chi-restraints excluded: chain C residue 278 GLU Chi-restraints excluded: chain C residue 364 MET Chi-restraints excluded: chain C residue 371 MET Chi-restraints excluded: chain C residue 409 LEU Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 75 ILE Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 127 ILE Chi-restraints excluded: chain F residue 236 LYS Chi-restraints excluded: chain F residue 265 THR Chi-restraints excluded: chain F residue 292 ILE Chi-restraints excluded: chain F residue 371 LEU Chi-restraints excluded: chain F residue 378 GLU Chi-restraints excluded: chain F residue 380 VAL Chi-restraints excluded: chain F residue 405 LEU Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 265 THR Chi-restraints excluded: chain E residue 292 ILE Chi-restraints excluded: chain E residue 326 MET Chi-restraints excluded: chain E residue 400 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 181 optimal weight: 0.9980 chunk 21 optimal weight: 0.3980 chunk 107 optimal weight: 3.9990 chunk 137 optimal weight: 1.9990 chunk 106 optimal weight: 0.7980 chunk 158 optimal weight: 1.9990 chunk 105 optimal weight: 4.9990 chunk 187 optimal weight: 0.9990 chunk 117 optimal weight: 7.9990 chunk 114 optimal weight: 0.9990 chunk 86 optimal weight: 0.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 380 GLN ** A 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.8962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.057 15678 Z= 0.150 Angle : 0.465 8.424 21159 Z= 0.244 Chirality : 0.041 0.237 2487 Planarity : 0.003 0.031 2679 Dihedral : 7.477 60.494 2335 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 2.47 % Allowed : 21.18 % Favored : 76.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.34 (0.19), residues: 1947 helix: 1.57 (0.17), residues: 1056 sheet: -0.10 (0.30), residues: 285 loop : 0.35 (0.24), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP E 283 HIS 0.002 0.000 HIS A 348 PHE 0.017 0.001 PHE E 257 TYR 0.009 0.001 TYR E 387 ARG 0.005 0.000 ARG C 333 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3894 Ramachandran restraints generated. 1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3894 Ramachandran restraints generated. 1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 126 time to evaluate : 2.027 Fit side-chains revert: symmetry clash REVERT: A 124 ILE cc_start: 0.8641 (OUTLIER) cc_final: 0.8274 (mt) REVERT: A 264 MET cc_start: 0.6963 (pmm) cc_final: 0.6700 (pmm) REVERT: A 333 ARG cc_start: 0.6509 (tpt170) cc_final: 0.6185 (tpm170) REVERT: F 378 GLU cc_start: 0.7087 (OUTLIER) cc_final: 0.6723 (mp0) REVERT: F 405 LEU cc_start: 0.8607 (OUTLIER) cc_final: 0.8382 (mp) REVERT: E 244 LEU cc_start: 0.8646 (OUTLIER) cc_final: 0.8441 (mt) outliers start: 41 outliers final: 24 residues processed: 156 average time/residue: 0.2444 time to fit residues: 59.9468 Evaluate side-chains 149 residues out of total 1662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 121 time to evaluate : 1.804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 MET Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 116 PHE Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain D residue 258 LEU Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 359 MET Chi-restraints excluded: chain C residue 264 MET Chi-restraints excluded: chain C residue 278 GLU Chi-restraints excluded: chain C residue 364 MET Chi-restraints excluded: chain C residue 371 MET Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 127 ILE Chi-restraints excluded: chain F residue 265 THR Chi-restraints excluded: chain F residue 292 ILE Chi-restraints excluded: chain F residue 371 LEU Chi-restraints excluded: chain F residue 378 GLU Chi-restraints excluded: chain F residue 380 VAL Chi-restraints excluded: chain F residue 405 LEU Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 244 LEU Chi-restraints excluded: chain E residue 265 THR Chi-restraints excluded: chain E residue 292 ILE Chi-restraints excluded: chain E residue 375 CYS Chi-restraints excluded: chain E residue 400 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 116 optimal weight: 8.9990 chunk 75 optimal weight: 4.9990 chunk 112 optimal weight: 7.9990 chunk 56 optimal weight: 2.9990 chunk 36 optimal weight: 0.9980 chunk 119 optimal weight: 6.9990 chunk 128 optimal weight: 9.9990 chunk 92 optimal weight: 4.9990 chunk 17 optimal weight: 4.9990 chunk 147 optimal weight: 0.8980 chunk 170 optimal weight: 6.9990 overall best weight: 2.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 289 GLN B 335 ASN C 335 ASN ** C 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.9452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 15678 Z= 0.332 Angle : 0.543 10.483 21159 Z= 0.285 Chirality : 0.043 0.219 2487 Planarity : 0.004 0.034 2679 Dihedral : 7.788 74.719 2335 Min Nonbonded Distance : 1.843 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 2.29 % Allowed : 21.42 % Favored : 76.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.28 (0.19), residues: 1947 helix: 1.52 (0.17), residues: 1059 sheet: -0.08 (0.31), residues: 285 loop : 0.29 (0.24), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP F 283 HIS 0.005 0.001 HIS C 305 PHE 0.018 0.002 PHE F 297 TYR 0.017 0.001 TYR E 387 ARG 0.007 0.001 ARG A 333 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3894 Ramachandran restraints generated. 1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3894 Ramachandran restraints generated. 1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 124 time to evaluate : 1.736 Fit side-chains REVERT: B 264 MET cc_start: 0.6383 (pmm) cc_final: 0.5973 (pmm) REVERT: F 378 GLU cc_start: 0.7248 (OUTLIER) cc_final: 0.6788 (mp0) outliers start: 38 outliers final: 26 residues processed: 155 average time/residue: 0.2483 time to fit residues: 60.0205 Evaluate side-chains 139 residues out of total 1662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 112 time to evaluate : 1.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 MET Chi-restraints excluded: chain A residue 116 PHE Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain D residue 62 MET Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 359 MET Chi-restraints excluded: chain C residue 264 MET Chi-restraints excluded: chain C residue 278 GLU Chi-restraints excluded: chain C residue 364 MET Chi-restraints excluded: chain C residue 371 MET Chi-restraints excluded: chain C residue 391 LEU Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 127 ILE Chi-restraints excluded: chain F residue 265 THR Chi-restraints excluded: chain F residue 292 ILE Chi-restraints excluded: chain F residue 371 LEU Chi-restraints excluded: chain F residue 378 GLU Chi-restraints excluded: chain F residue 380 VAL Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 265 THR Chi-restraints excluded: chain E residue 292 ILE Chi-restraints excluded: chain E residue 375 CYS Chi-restraints excluded: chain E residue 400 ARG Chi-restraints excluded: chain E residue 436 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 180 optimal weight: 0.8980 chunk 164 optimal weight: 6.9990 chunk 175 optimal weight: 1.9990 chunk 105 optimal weight: 4.9990 chunk 76 optimal weight: 5.9990 chunk 137 optimal weight: 3.9990 chunk 53 optimal weight: 0.9980 chunk 158 optimal weight: 0.9990 chunk 165 optimal weight: 0.6980 chunk 174 optimal weight: 4.9990 chunk 115 optimal weight: 3.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 335 ASN ** C 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.9591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 15678 Z= 0.170 Angle : 0.490 9.820 21159 Z= 0.255 Chirality : 0.041 0.231 2487 Planarity : 0.003 0.029 2679 Dihedral : 7.669 73.453 2335 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 1.62 % Allowed : 22.26 % Favored : 76.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.42 (0.20), residues: 1947 helix: 1.67 (0.17), residues: 1056 sheet: -0.02 (0.31), residues: 285 loop : 0.29 (0.25), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP F 283 HIS 0.003 0.001 HIS D 302 PHE 0.015 0.001 PHE E 257 TYR 0.017 0.001 TYR D 446 ARG 0.005 0.000 ARG C 333 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3894 Ramachandran restraints generated. 1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3894 Ramachandran restraints generated. 1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 121 time to evaluate : 1.735 Fit side-chains REVERT: B 264 MET cc_start: 0.6464 (pmm) cc_final: 0.6147 (pmm) REVERT: F 135 THR cc_start: 0.6740 (p) cc_final: 0.6258 (p) REVERT: F 378 GLU cc_start: 0.7148 (OUTLIER) cc_final: 0.6749 (mp0) outliers start: 27 outliers final: 22 residues processed: 141 average time/residue: 0.2388 time to fit residues: 52.6299 Evaluate side-chains 139 residues out of total 1662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 116 time to evaluate : 1.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 MET Chi-restraints excluded: chain A residue 116 PHE Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 335 ASN Chi-restraints excluded: chain B residue 359 MET Chi-restraints excluded: chain C residue 264 MET Chi-restraints excluded: chain C residue 278 GLU Chi-restraints excluded: chain C residue 371 MET Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 127 ILE Chi-restraints excluded: chain F residue 265 THR Chi-restraints excluded: chain F residue 292 ILE Chi-restraints excluded: chain F residue 371 LEU Chi-restraints excluded: chain F residue 378 GLU Chi-restraints excluded: chain F residue 380 VAL Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 265 THR Chi-restraints excluded: chain E residue 292 ILE Chi-restraints excluded: chain E residue 375 CYS Chi-restraints excluded: chain E residue 400 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 185 optimal weight: 3.9990 chunk 113 optimal weight: 0.1980 chunk 87 optimal weight: 4.9990 chunk 128 optimal weight: 6.9990 chunk 194 optimal weight: 3.9990 chunk 178 optimal weight: 8.9990 chunk 154 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 119 optimal weight: 2.9990 chunk 94 optimal weight: 6.9990 chunk 122 optimal weight: 5.9990 overall best weight: 2.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 255 GLN B 335 ASN C 348 HIS ** C 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 302 HIS ** F 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.9579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.118 15678 Z= 0.253 Angle : 0.714 59.188 21159 Z= 0.410 Chirality : 0.042 0.235 2487 Planarity : 0.003 0.027 2679 Dihedral : 7.666 73.420 2335 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 1.56 % Allowed : 21.90 % Favored : 76.53 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.41 (0.20), residues: 1947 helix: 1.66 (0.17), residues: 1056 sheet: -0.00 (0.31), residues: 285 loop : 0.29 (0.25), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP F 283 HIS 0.006 0.001 HIS C 348 PHE 0.015 0.001 PHE E 257 TYR 0.015 0.001 TYR D 446 ARG 0.016 0.000 ARG F 336 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3894 Ramachandran restraints generated. 1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3894 Ramachandran restraints generated. 1947 Oldfield, 0 Emsley, 1947 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 117 time to evaluate : 1.976 Fit side-chains revert: symmetry clash REVERT: B 264 MET cc_start: 0.6475 (pmm) cc_final: 0.6151 (pmm) REVERT: F 135 THR cc_start: 0.6745 (p) cc_final: 0.6263 (p) REVERT: F 378 GLU cc_start: 0.7149 (OUTLIER) cc_final: 0.6730 (mp0) outliers start: 26 outliers final: 24 residues processed: 138 average time/residue: 0.2432 time to fit residues: 53.4205 Evaluate side-chains 141 residues out of total 1662 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 116 time to evaluate : 1.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 MET Chi-restraints excluded: chain A residue 116 PHE Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain D residue 258 LEU Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 359 MET Chi-restraints excluded: chain C residue 264 MET Chi-restraints excluded: chain C residue 278 GLU Chi-restraints excluded: chain C residue 371 MET Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 127 ILE Chi-restraints excluded: chain F residue 265 THR Chi-restraints excluded: chain F residue 292 ILE Chi-restraints excluded: chain F residue 371 LEU Chi-restraints excluded: chain F residue 378 GLU Chi-restraints excluded: chain F residue 380 VAL Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 265 THR Chi-restraints excluded: chain E residue 292 ILE Chi-restraints excluded: chain E residue 375 CYS Chi-restraints excluded: chain E residue 400 ARG Chi-restraints excluded: chain E residue 436 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 164 optimal weight: 4.9990 chunk 47 optimal weight: 5.9990 chunk 142 optimal weight: 3.9990 chunk 22 optimal weight: 4.9990 chunk 42 optimal weight: 0.9980 chunk 154 optimal weight: 1.9990 chunk 64 optimal weight: 3.9990 chunk 159 optimal weight: 8.9990 chunk 19 optimal weight: 0.9980 chunk 28 optimal weight: 9.9990 chunk 136 optimal weight: 0.8980 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 335 ASN ** C 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.063519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2759 r_free = 0.2759 target = 0.050485 restraints weight = 43356.222| |-----------------------------------------------------------------------------| r_work (start): 0.2758 rms_B_bonded: 3.65 r_work: 0.2591 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.2591 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8782 moved from start: 0.9593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.118 15678 Z= 0.253 Angle : 0.714 59.188 21159 Z= 0.410 Chirality : 0.042 0.235 2487 Planarity : 0.003 0.027 2679 Dihedral : 7.666 73.420 2335 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 1.56 % Allowed : 21.90 % Favored : 76.53 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.41 (0.20), residues: 1947 helix: 1.66 (0.17), residues: 1056 sheet: -0.00 (0.31), residues: 285 loop : 0.29 (0.25), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP F 283 HIS 0.006 0.001 HIS C 348 PHE 0.015 0.001 PHE E 257 TYR 0.015 0.001 TYR D 446 ARG 0.016 0.000 ARG F 336 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2955.54 seconds wall clock time: 54 minutes 12.41 seconds (3252.41 seconds total)