Starting phenix.real_space_refine on Fri Apr 5 15:46:23 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q8f_18253/04_2024/8q8f_18253.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q8f_18253/04_2024/8q8f_18253.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.93 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q8f_18253/04_2024/8q8f_18253.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q8f_18253/04_2024/8q8f_18253.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q8f_18253/04_2024/8q8f_18253.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q8f_18253/04_2024/8q8f_18253.pdb" } resolution = 2.93 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= 0.002 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: 4 Type Number sf(0) Gaussians S 6 5.16 5 C 2172 2.51 5 N 642 2.21 5 O 648 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 348": "OD1" <-> "OD2" Residue "A GLU 372": "OE1" <-> "OE2" Residue "A PHE 378": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 349": "NH1" <-> "NH2" Residue "B GLU 372": "OE1" <-> "OE2" Residue "B PHE 378": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 379": "NH1" <-> "NH2" Residue "C TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 349": "NH1" <-> "NH2" Residue "C GLU 372": "OE1" <-> "OE2" Residue "D TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 372": "OE1" <-> "OE2" Residue "D PHE 378": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 372": "OE1" <-> "OE2" Residue "F TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 349": "NH1" <-> "NH2" Residue "F GLU 372": "OE1" <-> "OE2" Residue "F PHE 378": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 3468 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 578 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 578 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 3, 'TRANS': 72} Chain: "B" Number of atoms: 578 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 578 Classifications: {'peptide': 76} Link IDs: {'CIS': 1, 'PTRANS': 3, 'TRANS': 71} Chain: "C" Number of atoms: 578 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 578 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 3, 'TRANS': 72} Chain: "D" Number of atoms: 578 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 578 Classifications: {'peptide': 76} Link IDs: {'CIS': 1, 'PTRANS': 3, 'TRANS': 71} Chain: "E" Number of atoms: 578 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 578 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 3, 'TRANS': 72} Chain: "F" Number of atoms: 578 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 578 Classifications: {'peptide': 76} Link IDs: {'CIS': 1, 'PTRANS': 3, 'TRANS': 71} Time building chain proxies: 2.36, per 1000 atoms: 0.68 Number of scatterers: 3468 At special positions: 0 Unit cell: (111.24, 124.424, 36.256, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 6 16.00 O 648 8.00 N 642 7.00 C 2172 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: 1.14 Conformation dependent library (CDL) restraints added in 721.3 milliseconds 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 792 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 19 sheets defined 0.0% alpha, 47.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.56 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'C' and resid 306 through 310 removed outlier: 6.520A pdb=" N GLN A 307 " --> pdb=" O ILE C 308 " (cutoff:3.500A) removed outlier: 7.752A pdb=" N TYR C 310 " --> pdb=" O GLN A 307 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N VAL A 309 " --> pdb=" O TYR C 310 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N VAL A 306 " --> pdb=" O GLN E 307 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N VAL E 309 " --> pdb=" O VAL A 306 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N ILE A 308 " --> pdb=" O VAL E 309 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'C' and resid 313 through 314 removed outlier: 6.853A pdb=" N VAL A 313 " --> pdb=" O ASP C 314 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 317 through 322 removed outlier: 6.441A pdb=" N LYS A 317 " --> pdb=" O VAL C 318 " (cutoff:3.500A) removed outlier: 7.906A pdb=" N SER C 320 " --> pdb=" O LYS A 317 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N THR A 319 " --> pdb=" O SER C 320 " (cutoff:3.500A) removed outlier: 8.537A pdb=" N CYS C 322 " --> pdb=" O THR A 319 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N LYS A 321 " --> pdb=" O CYS C 322 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 317 through 322 removed outlier: 6.441A pdb=" N LYS A 317 " --> pdb=" O VAL C 318 " (cutoff:3.500A) removed outlier: 7.906A pdb=" N SER C 320 " --> pdb=" O LYS A 317 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N THR A 319 " --> pdb=" O SER C 320 " (cutoff:3.500A) removed outlier: 8.537A pdb=" N CYS C 322 " --> pdb=" O THR A 319 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N LYS A 321 " --> pdb=" O CYS C 322 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 328 through 330 removed outlier: 6.302A pdb=" N ILE A 328 " --> pdb=" O HIS E 329 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 336 through 340 removed outlier: 6.614A pdb=" N VAL A 337 " --> pdb=" O GLU E 338 " (cutoff:3.500A) removed outlier: 7.806A pdb=" N LYS E 340 " --> pdb=" O VAL A 337 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N VAL A 339 " --> pdb=" O LYS E 340 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 343 through 346 removed outlier: 6.267A pdb=" N LYS A 343 " --> pdb=" O LEU C 344 " (cutoff:3.500A) removed outlier: 7.958A pdb=" N PHE C 346 " --> pdb=" O LYS A 343 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N ASP A 345 " --> pdb=" O PHE C 346 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 351 through 354 removed outlier: 6.409A pdb=" N GLN A 351 " --> pdb=" O SER C 352 " (cutoff:3.500A) removed outlier: 7.760A pdb=" N ILE C 354 " --> pdb=" O GLN A 351 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N LYS A 353 " --> pdb=" O ILE C 354 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 357 through 362 removed outlier: 6.357A pdb=" N ASP A 358 " --> pdb=" O ASN C 359 " (cutoff:3.500A) removed outlier: 7.982A pdb=" N THR C 361 " --> pdb=" O ASP A 358 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N ILE A 360 " --> pdb=" O THR C 361 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 369 through 378 removed outlier: 6.379A pdb=" N LYS A 369 " --> pdb=" O LYS C 370 " (cutoff:3.500A) removed outlier: 7.935A pdb=" N GLU C 372 " --> pdb=" O LYS A 369 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N ILE A 371 " --> pdb=" O GLU C 372 " (cutoff:3.500A) removed outlier: 7.976A pdb=" N HIS C 374 " --> pdb=" O ILE A 371 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N THR A 373 " --> pdb=" O HIS C 374 " (cutoff:3.500A) removed outlier: 8.010A pdb=" N LEU C 376 " --> pdb=" O THR A 373 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N LYS A 375 " --> pdb=" O LEU C 376 " (cutoff:3.500A) removed outlier: 7.902A pdb=" N PHE C 378 " --> pdb=" O LYS A 375 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N THR A 377 " --> pdb=" O PHE C 378 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N LYS A 370 " --> pdb=" O ILE E 371 " (cutoff:3.500A) removed outlier: 7.989A pdb=" N THR E 373 " --> pdb=" O LYS A 370 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N GLU A 372 " --> pdb=" O THR E 373 " (cutoff:3.500A) removed outlier: 8.383A pdb=" N LYS E 375 " --> pdb=" O GLU A 372 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N HIS A 374 " --> pdb=" O LYS E 375 " (cutoff:3.500A) removed outlier: 7.995A pdb=" N THR E 377 " --> pdb=" O HIS A 374 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N LEU A 376 " --> pdb=" O THR E 377 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'D' and resid 306 through 310 removed outlier: 6.492A pdb=" N GLN B 307 " --> pdb=" O ILE D 308 " (cutoff:3.500A) removed outlier: 7.638A pdb=" N TYR D 310 " --> pdb=" O GLN B 307 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N VAL B 309 " --> pdb=" O TYR D 310 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 313 through 314 removed outlier: 6.783A pdb=" N VAL B 313 " --> pdb=" O ASP D 314 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 317 through 321 removed outlier: 6.245A pdb=" N LYS B 317 " --> pdb=" O VAL D 318 " (cutoff:3.500A) removed outlier: 8.100A pdb=" N SER D 320 " --> pdb=" O LYS B 317 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N THR B 319 " --> pdb=" O SER D 320 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 328 through 330 removed outlier: 6.653A pdb=" N HIS B 329 " --> pdb=" O HIS F 330 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 336 through 340 removed outlier: 6.410A pdb=" N VAL B 337 " --> pdb=" O GLU F 338 " (cutoff:3.500A) removed outlier: 8.162A pdb=" N LYS F 340 " --> pdb=" O VAL B 337 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N VAL B 339 " --> pdb=" O LYS F 340 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 343 through 348 removed outlier: 6.831A pdb=" N ASP D 348 " --> pdb=" O LYS B 347 " (cutoff:3.500A) removed outlier: 8.998A pdb=" N LYS B 343 " --> pdb=" O LEU F 344 " (cutoff:3.500A) removed outlier: 10.105A pdb=" N PHE F 346 " --> pdb=" O LYS B 343 " (cutoff:3.500A) removed outlier: 9.035A pdb=" N ASP B 345 " --> pdb=" O PHE F 346 " (cutoff:3.500A) removed outlier: 9.309A pdb=" N ASP F 348 " --> pdb=" O ASP B 345 " (cutoff:3.500A) removed outlier: 5.934A pdb=" N LYS B 347 " --> pdb=" O ASP F 348 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 351 through 354 removed outlier: 6.744A pdb=" N GLN B 351 " --> pdb=" O SER D 352 " (cutoff:3.500A) removed outlier: 8.286A pdb=" N ILE D 354 " --> pdb=" O GLN B 351 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N LYS B 353 " --> pdb=" O ILE D 354 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 361 through 362 removed outlier: 6.580A pdb=" N THR B 361 " --> pdb=" O HIS F 362 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 368 through 378 removed outlier: 6.410A pdb=" N LYS B 369 " --> pdb=" O LYS D 370 " (cutoff:3.500A) removed outlier: 7.855A pdb=" N GLU D 372 " --> pdb=" O LYS B 369 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N ILE B 371 " --> pdb=" O GLU D 372 " (cutoff:3.500A) removed outlier: 7.747A pdb=" N HIS D 374 " --> pdb=" O ILE B 371 " (cutoff:3.500A) removed outlier: 5.959A pdb=" N THR B 373 " --> pdb=" O HIS D 374 " (cutoff:3.500A) removed outlier: 7.811A pdb=" N LEU D 376 " --> pdb=" O THR B 373 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N LYS B 375 " --> pdb=" O LEU D 376 " (cutoff:3.500A) removed outlier: 7.961A pdb=" N PHE D 378 " --> pdb=" O LYS B 375 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N THR B 377 " --> pdb=" O PHE D 378 " (cutoff:3.500A) 54 hydrogen bonds defined for protein. 159 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: 0.89 Time building geometry restraints manager: 1.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1030 1.33 - 1.45: 405 1.45 - 1.58: 2081 1.58 - 1.70: 0 1.70 - 1.82: 6 Bond restraints: 3522 Sorted by residual: bond pdb=" CZ ARG E 349 " pdb=" NH2 ARG E 349 " ideal model delta sigma weight residual 1.330 1.293 0.037 1.30e-02 5.92e+03 8.24e+00 bond pdb=" CZ ARG A 349 " pdb=" NH2 ARG A 349 " ideal model delta sigma weight residual 1.330 1.294 0.036 1.30e-02 5.92e+03 7.49e+00 bond pdb=" CZ ARG C 349 " pdb=" NH2 ARG C 349 " ideal model delta sigma weight residual 1.330 1.295 0.035 1.30e-02 5.92e+03 7.40e+00 bond pdb=" CZ ARG B 379 " pdb=" NH2 ARG B 379 " ideal model delta sigma weight residual 1.330 1.295 0.035 1.30e-02 5.92e+03 7.11e+00 bond pdb=" CZ ARG D 379 " pdb=" NH2 ARG D 379 " ideal model delta sigma weight residual 1.330 1.296 0.034 1.30e-02 5.92e+03 6.91e+00 ... (remaining 3517 not shown) Histogram of bond angle deviations from ideal: 101.77 - 107.51: 218 107.51 - 113.25: 1835 113.25 - 118.99: 873 118.99 - 124.73: 1595 124.73 - 130.47: 189 Bond angle restraints: 4710 Sorted by residual: angle pdb=" O CYS D 322 " pdb=" C CYS D 322 " pdb=" N GLY D 323 " ideal model delta sigma weight residual 123.25 115.67 7.58 1.14e+00 7.69e-01 4.43e+01 angle pdb=" O CYS B 322 " pdb=" C CYS B 322 " pdb=" N GLY B 323 " ideal model delta sigma weight residual 123.17 115.44 7.73 1.21e+00 6.83e-01 4.08e+01 angle pdb=" CA CYS D 322 " pdb=" C CYS D 322 " pdb=" N GLY D 323 " ideal model delta sigma weight residual 115.36 124.74 -9.38 1.48e+00 4.57e-01 4.01e+01 angle pdb=" CA CYS B 322 " pdb=" C CYS B 322 " pdb=" N GLY B 323 " ideal model delta sigma weight residual 115.36 124.94 -9.58 1.53e+00 4.27e-01 3.92e+01 angle pdb=" CA PHE E 346 " pdb=" CB PHE E 346 " pdb=" CG PHE E 346 " ideal model delta sigma weight residual 113.80 119.35 -5.55 1.00e+00 1.00e+00 3.08e+01 ... (remaining 4705 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 12.81: 1899 12.81 - 25.62: 176 25.62 - 38.43: 42 38.43 - 51.24: 12 51.24 - 64.05: 13 Dihedral angle restraints: 2142 sinusoidal: 894 harmonic: 1248 Sorted by residual: dihedral pdb=" CA SER A 341 " pdb=" C SER A 341 " pdb=" N GLU A 342 " pdb=" CA GLU A 342 " ideal model delta harmonic sigma weight residual 180.00 151.23 28.77 0 5.00e+00 4.00e-02 3.31e+01 dihedral pdb=" CA SER C 341 " pdb=" C SER C 341 " pdb=" N GLU C 342 " pdb=" CA GLU C 342 " ideal model delta harmonic sigma weight residual 180.00 151.61 28.39 0 5.00e+00 4.00e-02 3.22e+01 dihedral pdb=" CA LEU C 325 " pdb=" C LEU C 325 " pdb=" N GLY C 326 " pdb=" CA GLY C 326 " ideal model delta harmonic sigma weight residual -180.00 -151.64 -28.36 0 5.00e+00 4.00e-02 3.22e+01 ... (remaining 2139 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 275 0.061 - 0.122: 188 0.122 - 0.183: 52 0.183 - 0.243: 9 0.243 - 0.304: 4 Chirality restraints: 528 Sorted by residual: chirality pdb=" CA LYS B 347 " pdb=" N LYS B 347 " pdb=" C LYS B 347 " pdb=" CB LYS B 347 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.31e+00 chirality pdb=" CA LYS E 347 " pdb=" N LYS E 347 " pdb=" C LYS E 347 " pdb=" CB LYS E 347 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.05e+00 chirality pdb=" CA LYS F 331 " pdb=" N LYS F 331 " pdb=" C LYS F 331 " pdb=" CB LYS F 331 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.83e+00 ... (remaining 525 not shown) Planarity restraints: 600 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR E 310 " 0.161 2.00e-02 2.50e+03 9.29e-02 1.73e+02 pdb=" CG TYR E 310 " -0.038 2.00e-02 2.50e+03 pdb=" CD1 TYR E 310 " -0.063 2.00e-02 2.50e+03 pdb=" CD2 TYR E 310 " -0.075 2.00e-02 2.50e+03 pdb=" CE1 TYR E 310 " -0.064 2.00e-02 2.50e+03 pdb=" CE2 TYR E 310 " -0.059 2.00e-02 2.50e+03 pdb=" CZ TYR E 310 " -0.017 2.00e-02 2.50e+03 pdb=" OH TYR E 310 " 0.156 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 310 " 0.112 2.00e-02 2.50e+03 6.20e-02 7.69e+01 pdb=" CG TYR A 310 " -0.030 2.00e-02 2.50e+03 pdb=" CD1 TYR A 310 " -0.047 2.00e-02 2.50e+03 pdb=" CD2 TYR A 310 " -0.055 2.00e-02 2.50e+03 pdb=" CE1 TYR A 310 " -0.038 2.00e-02 2.50e+03 pdb=" CE2 TYR A 310 " -0.036 2.00e-02 2.50e+03 pdb=" CZ TYR A 310 " -0.003 2.00e-02 2.50e+03 pdb=" OH TYR A 310 " 0.097 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 310 " -0.085 2.00e-02 2.50e+03 4.92e-02 4.84e+01 pdb=" CG TYR B 310 " 0.019 2.00e-02 2.50e+03 pdb=" CD1 TYR B 310 " 0.032 2.00e-02 2.50e+03 pdb=" CD2 TYR B 310 " 0.043 2.00e-02 2.50e+03 pdb=" CE1 TYR B 310 " 0.037 2.00e-02 2.50e+03 pdb=" CE2 TYR B 310 " 0.028 2.00e-02 2.50e+03 pdb=" CZ TYR B 310 " 0.008 2.00e-02 2.50e+03 pdb=" OH TYR B 310 " -0.081 2.00e-02 2.50e+03 ... (remaining 597 not shown) Histogram of nonbonded interaction distances: 2.50 - 2.98: 1592 2.98 - 3.46: 2729 3.46 - 3.94: 5654 3.94 - 4.42: 5646 4.42 - 4.90: 10814 Nonbonded interactions: 26435 Sorted by model distance: nonbonded pdb=" OD1 ASP A 314 " pdb=" OG SER A 316 " model vdw 2.504 2.440 nonbonded pdb=" OD1 ASP C 314 " pdb=" OG SER C 316 " model vdw 2.505 2.440 nonbonded pdb=" OD1 ASP F 314 " pdb=" OG SER F 316 " model vdw 2.520 2.440 nonbonded pdb=" OD1 ASP B 314 " pdb=" OG SER B 316 " model vdw 2.528 2.440 nonbonded pdb=" OD1 ASP D 314 " pdb=" OG SER D 316 " model vdw 2.556 2.440 ... (remaining 26430 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = 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: 2.390 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: 0.000 Extract box with map and model: 10.970 Check model and map are aligned: 0.070 Set scattering table: 0.040 Process input model: 14.930 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.010 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:17.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7420 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 0.037 3522 Z= 0.745 Angle : 1.823 9.579 4710 Z= 1.219 Chirality : 0.082 0.304 528 Planarity : 0.010 0.093 600 Dihedral : 12.076 64.052 1350 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 0.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 0.76 % Allowed : 1.77 % Favored : 97.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.69 % 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: -1.60 (0.32), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.21 (0.24), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.018 0.003 HIS F 330 PHE 0.032 0.011 PHE B 346 TYR 0.161 0.039 TYR E 310 ARG 0.004 0.001 ARG E 349 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 139 time to evaluate : 0.400 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 316 SER cc_start: 0.8664 (p) cc_final: 0.8446 (p) REVERT: A 321 LYS cc_start: 0.7354 (mttt) cc_final: 0.6833 (tttm) REVERT: A 338 GLU cc_start: 0.7668 (tt0) cc_final: 0.7362 (mt-10) REVERT: A 343 LYS cc_start: 0.7701 (mtmt) cc_final: 0.7459 (mtpp) REVERT: A 375 LYS cc_start: 0.7863 (ttmt) cc_final: 0.7600 (tttt) REVERT: B 321 LYS cc_start: 0.7366 (mttt) cc_final: 0.7128 (mttm) REVERT: B 369 LYS cc_start: 0.7593 (tttt) cc_final: 0.7187 (tttt) REVERT: C 314 ASP cc_start: 0.8341 (t0) cc_final: 0.7734 (t0) REVERT: C 321 LYS cc_start: 0.8086 (mttt) cc_final: 0.7591 (tttm) REVERT: C 375 LYS cc_start: 0.8500 (ttmt) cc_final: 0.8156 (ttmt) REVERT: D 310 TYR cc_start: 0.8866 (t80) cc_final: 0.8620 (t80) REVERT: D 316 SER cc_start: 0.8442 (p) cc_final: 0.8225 (p) REVERT: D 321 LYS cc_start: 0.7992 (mttt) cc_final: 0.7697 (mttm) REVERT: E 321 LYS cc_start: 0.7487 (mttt) cc_final: 0.6983 (tttt) REVERT: E 370 LYS cc_start: 0.8138 (tttt) cc_final: 0.7936 (tttm) REVERT: E 372 GLU cc_start: 0.8334 (tt0) cc_final: 0.8110 (tt0) REVERT: F 321 LYS cc_start: 0.7752 (mttt) cc_final: 0.7520 (mtmm) outliers start: 3 outliers final: 0 residues processed: 139 average time/residue: 1.4083 time to fit residues: 200.3562 Evaluate side-chains 109 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 109 time to evaluate : 0.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 3.9990 chunk 31 optimal weight: 7.9990 chunk 17 optimal weight: 3.9990 chunk 10 optimal weight: 5.9990 chunk 21 optimal weight: 0.0670 chunk 32 optimal weight: 8.9990 chunk 12 optimal weight: 2.9990 chunk 20 optimal weight: 0.0270 chunk 24 optimal weight: 10.0000 chunk 38 optimal weight: 6.9990 chunk 11 optimal weight: 2.9990 overall best weight: 2.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 362 HIS C 359 ASN C 362 HIS E 362 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7535 moved from start: 0.3195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 3522 Z= 0.251 Angle : 0.655 7.162 4710 Z= 0.322 Chirality : 0.049 0.154 528 Planarity : 0.003 0.026 600 Dihedral : 5.873 20.263 468 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 1.77 % Allowed : 15.40 % Favored : 82.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.69 % 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: -1.67 (0.32), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.27 (0.25), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS F 330 PHE 0.015 0.002 PHE E 378 TYR 0.020 0.003 TYR F 310 ARG 0.003 0.000 ARG B 349 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 121 time to evaluate : 0.451 Fit side-chains REVERT: A 321 LYS cc_start: 0.7366 (mttt) cc_final: 0.6841 (tttm) REVERT: A 338 GLU cc_start: 0.7553 (tt0) cc_final: 0.7337 (mt-10) REVERT: A 343 LYS cc_start: 0.7692 (mtmt) cc_final: 0.7199 (ttmt) REVERT: A 375 LYS cc_start: 0.8003 (ttmt) cc_final: 0.7641 (tttt) REVERT: B 316 SER cc_start: 0.8957 (p) cc_final: 0.8644 (p) REVERT: B 356 SER cc_start: 0.8529 (OUTLIER) cc_final: 0.8205 (m) REVERT: B 369 LYS cc_start: 0.7741 (tttt) cc_final: 0.7364 (tttp) REVERT: C 321 LYS cc_start: 0.8146 (mttt) cc_final: 0.7599 (tttm) REVERT: C 343 LYS cc_start: 0.8112 (mtpp) cc_final: 0.7700 (tttt) REVERT: C 353 LYS cc_start: 0.8612 (mttt) cc_final: 0.8404 (mttt) REVERT: C 375 LYS cc_start: 0.8605 (ttmt) cc_final: 0.8315 (tppt) REVERT: D 321 LYS cc_start: 0.8228 (mttt) cc_final: 0.7800 (mttm) REVERT: E 321 LYS cc_start: 0.7394 (mttt) cc_final: 0.6939 (tttt) REVERT: E 343 LYS cc_start: 0.7842 (mtpp) cc_final: 0.7386 (tttt) REVERT: E 349 ARG cc_start: 0.6642 (mtm180) cc_final: 0.6278 (mpt90) REVERT: E 369 LYS cc_start: 0.7901 (mtmt) cc_final: 0.7317 (mttt) REVERT: E 375 LYS cc_start: 0.8014 (ttmt) cc_final: 0.7618 (tttt) REVERT: F 307 GLN cc_start: 0.8087 (tt0) cc_final: 0.7860 (tt0) REVERT: F 316 SER cc_start: 0.8763 (p) cc_final: 0.8448 (p) REVERT: F 356 SER cc_start: 0.7969 (m) cc_final: 0.7762 (m) outliers start: 7 outliers final: 2 residues processed: 122 average time/residue: 1.4954 time to fit residues: 186.3763 Evaluate side-chains 101 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 98 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 356 SER Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain D residue 379 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 31 optimal weight: 6.9990 chunk 25 optimal weight: 10.0000 chunk 10 optimal weight: 20.0000 chunk 38 optimal weight: 10.0000 chunk 41 optimal weight: 9.9990 chunk 34 optimal weight: 0.0040 chunk 37 optimal weight: 0.3980 chunk 13 optimal weight: 3.9990 chunk 30 optimal weight: 5.9990 chunk 28 optimal weight: 4.9990 chunk 19 optimal weight: 4.9990 overall best weight: 2.8798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 336 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7583 moved from start: 0.3935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 3522 Z= 0.294 Angle : 0.653 7.206 4710 Z= 0.321 Chirality : 0.049 0.135 528 Planarity : 0.003 0.026 600 Dihedral : 5.696 20.695 468 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 3.54 % Allowed : 20.71 % Favored : 75.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.69 % 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: -1.75 (0.32), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.32 (0.25), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS F 330 PHE 0.011 0.002 PHE C 378 TYR 0.018 0.003 TYR A 310 ARG 0.001 0.000 ARG C 379 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 104 time to evaluate : 0.408 Fit side-chains REVERT: A 321 LYS cc_start: 0.7429 (mttt) cc_final: 0.6832 (tttt) REVERT: A 338 GLU cc_start: 0.7690 (tt0) cc_final: 0.7386 (mt-10) REVERT: A 343 LYS cc_start: 0.7950 (mtmt) cc_final: 0.7239 (tttt) REVERT: A 375 LYS cc_start: 0.8043 (ttmt) cc_final: 0.7621 (tttt) REVERT: B 321 LYS cc_start: 0.7524 (mtmm) cc_final: 0.7253 (mttm) REVERT: B 369 LYS cc_start: 0.7704 (tttt) cc_final: 0.7384 (tttt) REVERT: C 321 LYS cc_start: 0.8111 (mttt) cc_final: 0.7575 (tttm) REVERT: C 343 LYS cc_start: 0.8030 (mtpp) cc_final: 0.7732 (tttt) REVERT: C 375 LYS cc_start: 0.8643 (ttmt) cc_final: 0.8343 (tppt) REVERT: D 321 LYS cc_start: 0.8260 (mttt) cc_final: 0.7862 (mttm) REVERT: D 369 LYS cc_start: 0.8538 (tttt) cc_final: 0.8159 (tttp) REVERT: D 379 ARG cc_start: 0.6083 (OUTLIER) cc_final: 0.4846 (mtm180) REVERT: E 321 LYS cc_start: 0.7408 (mttt) cc_final: 0.6893 (tttm) REVERT: E 343 LYS cc_start: 0.7841 (mtpp) cc_final: 0.7403 (tttt) REVERT: E 348 ASP cc_start: 0.7787 (OUTLIER) cc_final: 0.7561 (p0) REVERT: E 349 ARG cc_start: 0.6638 (mtm180) cc_final: 0.6349 (mpt180) REVERT: E 369 LYS cc_start: 0.7943 (mtmt) cc_final: 0.7375 (mtpt) REVERT: E 375 LYS cc_start: 0.8129 (ttmt) cc_final: 0.7734 (tttt) REVERT: F 316 SER cc_start: 0.8714 (p) cc_final: 0.8417 (p) REVERT: F 379 ARG cc_start: 0.5395 (mmp-170) cc_final: 0.5080 (mmp-170) outliers start: 14 outliers final: 8 residues processed: 107 average time/residue: 1.6075 time to fit residues: 175.6071 Evaluate side-chains 103 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 93 time to evaluate : 0.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain B residue 347 LYS Chi-restraints excluded: chain B residue 352 SER Chi-restraints excluded: chain B residue 356 SER Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain D residue 356 SER Chi-restraints excluded: chain D residue 379 ARG Chi-restraints excluded: chain E residue 319 THR Chi-restraints excluded: chain E residue 348 ASP Chi-restraints excluded: chain E residue 373 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 4 optimal weight: 9.9990 chunk 18 optimal weight: 1.9990 chunk 25 optimal weight: 9.9990 chunk 38 optimal weight: 1.9990 chunk 40 optimal weight: 6.9990 chunk 20 optimal weight: 3.9990 chunk 36 optimal weight: 8.9990 chunk 10 optimal weight: 3.9990 chunk 33 optimal weight: 6.9990 chunk 23 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 330 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7608 moved from start: 0.4261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 3522 Z= 0.376 Angle : 0.673 7.782 4710 Z= 0.330 Chirality : 0.048 0.139 528 Planarity : 0.003 0.041 600 Dihedral : 5.701 22.523 468 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 3.79 % Allowed : 20.96 % Favored : 75.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.69 % 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: -1.88 (0.32), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.43 (0.25), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS F 330 PHE 0.008 0.002 PHE E 378 TYR 0.020 0.003 TYR A 310 ARG 0.001 0.000 ARG F 379 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 90 time to evaluate : 0.396 Fit side-chains REVERT: A 321 LYS cc_start: 0.7456 (mttt) cc_final: 0.6817 (ttpt) REVERT: A 338 GLU cc_start: 0.7756 (tt0) cc_final: 0.7385 (mt-10) REVERT: A 343 LYS cc_start: 0.7971 (mtmt) cc_final: 0.7212 (tttt) REVERT: A 375 LYS cc_start: 0.8066 (ttmt) cc_final: 0.7616 (tttt) REVERT: B 369 LYS cc_start: 0.7710 (tttt) cc_final: 0.7433 (tttt) REVERT: C 321 LYS cc_start: 0.8147 (mttt) cc_final: 0.7540 (ttpp) REVERT: C 343 LYS cc_start: 0.8080 (mtpp) cc_final: 0.7751 (tttt) REVERT: C 375 LYS cc_start: 0.8692 (ttmt) cc_final: 0.8376 (tppt) REVERT: D 369 LYS cc_start: 0.8522 (tttt) cc_final: 0.8147 (tttp) REVERT: D 379 ARG cc_start: 0.6499 (OUTLIER) cc_final: 0.5587 (mtm-85) REVERT: E 321 LYS cc_start: 0.7451 (mttt) cc_final: 0.6873 (tttm) REVERT: E 343 LYS cc_start: 0.7908 (mtpp) cc_final: 0.7475 (tttt) REVERT: E 348 ASP cc_start: 0.7907 (OUTLIER) cc_final: 0.7588 (p0) REVERT: E 349 ARG cc_start: 0.6662 (mtm180) cc_final: 0.6287 (mpt90) REVERT: E 369 LYS cc_start: 0.7931 (mtmt) cc_final: 0.7371 (mtpt) REVERT: E 375 LYS cc_start: 0.8182 (ttmt) cc_final: 0.7752 (tttt) outliers start: 15 outliers final: 8 residues processed: 94 average time/residue: 1.5543 time to fit residues: 149.3046 Evaluate side-chains 97 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 87 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain B residue 356 SER Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain D residue 379 ARG Chi-restraints excluded: chain E residue 316 SER Chi-restraints excluded: chain E residue 319 THR Chi-restraints excluded: chain E residue 348 ASP Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain F residue 338 GLU Chi-restraints excluded: chain F residue 358 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 30 optimal weight: 4.9990 chunk 16 optimal weight: 1.9990 chunk 34 optimal weight: 6.9990 chunk 28 optimal weight: 2.9990 chunk 0 optimal weight: 1.9990 chunk 20 optimal weight: 4.9990 chunk 36 optimal weight: 6.9990 chunk 10 optimal weight: 10.0000 chunk 13 optimal weight: 9.9990 chunk 8 optimal weight: 3.9990 chunk 23 optimal weight: 1.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 307 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 moved from start: 0.4384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 3522 Z= 0.274 Angle : 0.630 7.751 4710 Z= 0.304 Chirality : 0.048 0.121 528 Planarity : 0.003 0.027 600 Dihedral : 5.344 19.762 468 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 4.04 % Allowed : 21.97 % Favored : 73.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.69 % 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: -1.87 (0.32), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.42 (0.25), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS F 330 PHE 0.008 0.001 PHE E 378 TYR 0.015 0.003 TYR A 310 ARG 0.002 0.000 ARG C 349 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 92 time to evaluate : 0.427 Fit side-chains REVERT: A 321 LYS cc_start: 0.7456 (mttt) cc_final: 0.6832 (ttpt) REVERT: A 338 GLU cc_start: 0.7749 (tt0) cc_final: 0.7357 (mt-10) REVERT: A 343 LYS cc_start: 0.7967 (mtmt) cc_final: 0.7222 (tttt) REVERT: A 375 LYS cc_start: 0.8062 (ttmt) cc_final: 0.7619 (tttt) REVERT: B 351 GLN cc_start: 0.7552 (tt0) cc_final: 0.6684 (mp10) REVERT: B 369 LYS cc_start: 0.7730 (tttt) cc_final: 0.7330 (tppt) REVERT: C 321 LYS cc_start: 0.8107 (mttt) cc_final: 0.7500 (tttm) REVERT: C 343 LYS cc_start: 0.8087 (mtpp) cc_final: 0.7779 (tttt) REVERT: C 375 LYS cc_start: 0.8655 (ttmt) cc_final: 0.8356 (tppt) REVERT: D 321 LYS cc_start: 0.8191 (mttt) cc_final: 0.7775 (mttm) REVERT: D 369 LYS cc_start: 0.8510 (tttt) cc_final: 0.8122 (tttp) REVERT: D 379 ARG cc_start: 0.6435 (OUTLIER) cc_final: 0.5821 (mtm-85) REVERT: E 321 LYS cc_start: 0.7469 (mttt) cc_final: 0.6918 (tttm) REVERT: E 343 LYS cc_start: 0.7901 (mtpp) cc_final: 0.7536 (tttt) REVERT: E 348 ASP cc_start: 0.7759 (OUTLIER) cc_final: 0.7521 (p0) REVERT: E 349 ARG cc_start: 0.6789 (mtm180) cc_final: 0.6319 (mpt90) REVERT: E 369 LYS cc_start: 0.7962 (mtmt) cc_final: 0.7287 (mttt) REVERT: E 375 LYS cc_start: 0.8248 (ttmt) cc_final: 0.7845 (tttt) REVERT: F 316 SER cc_start: 0.8802 (p) cc_final: 0.8520 (p) outliers start: 16 outliers final: 11 residues processed: 95 average time/residue: 1.4929 time to fit residues: 144.9882 Evaluate side-chains 104 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 91 time to evaluate : 0.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 311 LYS Chi-restraints excluded: chain B residue 347 LYS Chi-restraints excluded: chain B residue 352 SER Chi-restraints excluded: chain B residue 356 SER Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain D residue 356 SER Chi-restraints excluded: chain D residue 379 ARG Chi-restraints excluded: chain E residue 316 SER Chi-restraints excluded: chain E residue 319 THR Chi-restraints excluded: chain E residue 348 ASP Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain F residue 351 GLN Chi-restraints excluded: chain F residue 358 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 10 optimal weight: 20.0000 chunk 40 optimal weight: 8.9990 chunk 33 optimal weight: 10.0000 chunk 18 optimal weight: 2.9990 chunk 3 optimal weight: 9.9990 chunk 13 optimal weight: 10.0000 chunk 21 optimal weight: 0.0870 chunk 39 optimal weight: 4.9990 chunk 4 optimal weight: 0.9980 chunk 23 optimal weight: 0.9990 chunk 29 optimal weight: 9.9990 overall best weight: 2.0164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 307 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7586 moved from start: 0.4479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3522 Z= 0.223 Angle : 0.600 8.431 4710 Z= 0.286 Chirality : 0.047 0.117 528 Planarity : 0.003 0.021 600 Dihedral : 5.112 20.125 468 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 4.29 % Allowed : 22.73 % Favored : 72.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.69 % 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: -1.86 (0.33), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.41 (0.25), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS F 330 PHE 0.007 0.001 PHE E 378 TYR 0.013 0.002 TYR A 310 ARG 0.001 0.000 ARG C 349 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 88 time to evaluate : 0.433 Fit side-chains REVERT: A 321 LYS cc_start: 0.7472 (mttt) cc_final: 0.6830 (tttt) REVERT: A 338 GLU cc_start: 0.7779 (tt0) cc_final: 0.7382 (mt-10) REVERT: A 343 LYS cc_start: 0.7960 (mtmt) cc_final: 0.7222 (tttt) REVERT: A 375 LYS cc_start: 0.8057 (ttmt) cc_final: 0.7652 (tttt) REVERT: B 351 GLN cc_start: 0.7636 (tt0) cc_final: 0.6673 (mp10) REVERT: B 369 LYS cc_start: 0.7740 (tttt) cc_final: 0.7356 (tppt) REVERT: C 321 LYS cc_start: 0.8110 (mttt) cc_final: 0.7487 (tttt) REVERT: C 343 LYS cc_start: 0.8099 (mtpp) cc_final: 0.7811 (tttt) REVERT: C 375 LYS cc_start: 0.8666 (ttmt) cc_final: 0.8300 (ttmt) REVERT: D 369 LYS cc_start: 0.8500 (tttt) cc_final: 0.8148 (tttp) REVERT: D 379 ARG cc_start: 0.6376 (OUTLIER) cc_final: 0.5866 (mtm-85) REVERT: E 321 LYS cc_start: 0.7456 (mttt) cc_final: 0.6941 (tttm) REVERT: E 343 LYS cc_start: 0.7896 (mtpp) cc_final: 0.7559 (tttt) REVERT: E 349 ARG cc_start: 0.6814 (mtm180) cc_final: 0.6312 (mpt90) REVERT: E 369 LYS cc_start: 0.7969 (mtmt) cc_final: 0.7402 (mtpt) REVERT: E 375 LYS cc_start: 0.8196 (ttmt) cc_final: 0.7830 (tttt) REVERT: F 316 SER cc_start: 0.8780 (p) cc_final: 0.8502 (p) REVERT: F 375 LYS cc_start: 0.7905 (tttm) cc_final: 0.7683 (ttpp) outliers start: 17 outliers final: 10 residues processed: 92 average time/residue: 1.4469 time to fit residues: 136.3108 Evaluate side-chains 96 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 85 time to evaluate : 0.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 311 LYS Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain B residue 352 SER Chi-restraints excluded: chain B residue 356 SER Chi-restraints excluded: chain C residue 311 LYS Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain D residue 356 SER Chi-restraints excluded: chain D residue 379 ARG Chi-restraints excluded: chain E residue 316 SER Chi-restraints excluded: chain E residue 319 THR Chi-restraints excluded: chain F residue 338 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 22 optimal weight: 9.9990 chunk 34 optimal weight: 0.9990 chunk 40 optimal weight: 5.9990 chunk 25 optimal weight: 7.9990 chunk 24 optimal weight: 10.0000 chunk 18 optimal weight: 9.9990 chunk 16 optimal weight: 8.9990 chunk 12 optimal weight: 5.9990 chunk 7 optimal weight: 10.0000 chunk 27 optimal weight: 1.9990 chunk 20 optimal weight: 7.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7621 moved from start: 0.4591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.045 3522 Z= 0.445 Angle : 0.702 8.252 4710 Z= 0.344 Chirality : 0.048 0.138 528 Planarity : 0.004 0.051 600 Dihedral : 5.617 24.499 468 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 4.55 % Allowed : 22.47 % Favored : 72.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.69 % 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: -2.03 (0.33), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.54 (0.25), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS F 330 PHE 0.007 0.002 PHE F 378 TYR 0.019 0.003 TYR A 310 ARG 0.001 0.000 ARG B 379 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 86 time to evaluate : 0.433 Fit side-chains REVERT: A 321 LYS cc_start: 0.7420 (mttt) cc_final: 0.6910 (mtpm) REVERT: A 343 LYS cc_start: 0.7998 (mtmt) cc_final: 0.7161 (tttt) REVERT: A 375 LYS cc_start: 0.8115 (ttmt) cc_final: 0.7660 (tttt) REVERT: B 351 GLN cc_start: 0.7624 (tt0) cc_final: 0.6781 (mp10) REVERT: B 369 LYS cc_start: 0.7772 (tttt) cc_final: 0.7489 (tttt) REVERT: C 321 LYS cc_start: 0.8165 (mttt) cc_final: 0.7578 (mtpm) REVERT: C 343 LYS cc_start: 0.8159 (mtpp) cc_final: 0.7793 (tttt) REVERT: C 375 LYS cc_start: 0.8703 (ttmt) cc_final: 0.8299 (tppt) REVERT: D 321 LYS cc_start: 0.8337 (mttt) cc_final: 0.7939 (mttm) REVERT: D 369 LYS cc_start: 0.8514 (tttt) cc_final: 0.8145 (tttp) REVERT: D 379 ARG cc_start: 0.6421 (OUTLIER) cc_final: 0.5547 (mtm-85) REVERT: E 321 LYS cc_start: 0.7520 (mttt) cc_final: 0.6934 (tttm) REVERT: E 343 LYS cc_start: 0.7930 (mtpp) cc_final: 0.7519 (tttt) REVERT: E 349 ARG cc_start: 0.6900 (mtm180) cc_final: 0.6323 (mpt90) REVERT: E 369 LYS cc_start: 0.8018 (mtmt) cc_final: 0.7348 (mttt) REVERT: E 375 LYS cc_start: 0.8204 (ttmt) cc_final: 0.7796 (tttt) REVERT: F 369 LYS cc_start: 0.7931 (tttt) cc_final: 0.7664 (tttt) outliers start: 18 outliers final: 13 residues processed: 94 average time/residue: 1.6210 time to fit residues: 155.6951 Evaluate side-chains 99 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 85 time to evaluate : 0.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 311 LYS Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain B residue 352 SER Chi-restraints excluded: chain B residue 356 SER Chi-restraints excluded: chain C residue 311 LYS Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain D residue 356 SER Chi-restraints excluded: chain D residue 379 ARG Chi-restraints excluded: chain E residue 316 SER Chi-restraints excluded: chain E residue 319 THR Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain F residue 338 GLU Chi-restraints excluded: chain F residue 351 GLN Chi-restraints excluded: chain F residue 352 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 3 optimal weight: 9.9990 chunk 31 optimal weight: 0.9990 chunk 36 optimal weight: 5.9990 chunk 38 optimal weight: 9.9990 chunk 35 optimal weight: 2.9990 chunk 37 optimal weight: 0.7980 chunk 22 optimal weight: 3.9990 chunk 16 optimal weight: 5.9990 chunk 29 optimal weight: 8.9990 chunk 11 optimal weight: 10.0000 chunk 34 optimal weight: 0.9980 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7596 moved from start: 0.4683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3522 Z= 0.216 Angle : 0.600 8.927 4710 Z= 0.287 Chirality : 0.047 0.116 528 Planarity : 0.003 0.021 600 Dihedral : 5.112 20.568 468 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 4.29 % Allowed : 22.73 % Favored : 72.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.69 % 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: -1.99 (0.33), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.51 (0.25), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS F 330 PHE 0.007 0.001 PHE E 378 TYR 0.011 0.002 TYR A 310 ARG 0.001 0.000 ARG E 379 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 87 time to evaluate : 0.454 Fit side-chains REVERT: A 321 LYS cc_start: 0.7445 (mttt) cc_final: 0.6780 (tttt) REVERT: A 343 LYS cc_start: 0.8074 (mtmt) cc_final: 0.7219 (tttt) REVERT: A 375 LYS cc_start: 0.8062 (ttmt) cc_final: 0.7653 (tttt) REVERT: B 351 GLN cc_start: 0.7634 (tt0) cc_final: 0.6802 (mp10) REVERT: B 369 LYS cc_start: 0.7750 (tttt) cc_final: 0.7361 (tppt) REVERT: C 321 LYS cc_start: 0.8138 (mttt) cc_final: 0.7603 (mtpm) REVERT: C 343 LYS cc_start: 0.8136 (mtpp) cc_final: 0.7803 (tttt) REVERT: C 375 LYS cc_start: 0.8652 (ttmt) cc_final: 0.8300 (ttmt) REVERT: D 369 LYS cc_start: 0.8496 (tttt) cc_final: 0.8142 (tttp) REVERT: D 379 ARG cc_start: 0.6413 (OUTLIER) cc_final: 0.5967 (mtm-85) REVERT: E 321 LYS cc_start: 0.7489 (mttt) cc_final: 0.6956 (tttm) REVERT: E 343 LYS cc_start: 0.7902 (mtpp) cc_final: 0.7553 (tttt) REVERT: E 349 ARG cc_start: 0.6895 (mtm180) cc_final: 0.6246 (mpt90) REVERT: E 369 LYS cc_start: 0.8014 (mtmt) cc_final: 0.7329 (mttt) REVERT: E 375 LYS cc_start: 0.8221 (ttmt) cc_final: 0.7841 (tttt) outliers start: 17 outliers final: 9 residues processed: 89 average time/residue: 1.4775 time to fit residues: 134.5503 Evaluate side-chains 93 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 83 time to evaluate : 0.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 311 LYS Chi-restraints excluded: chain B residue 352 SER Chi-restraints excluded: chain B residue 356 SER Chi-restraints excluded: chain C residue 311 LYS Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain D residue 356 SER Chi-restraints excluded: chain D residue 379 ARG Chi-restraints excluded: chain E residue 311 LYS Chi-restraints excluded: chain E residue 316 SER Chi-restraints excluded: chain E residue 319 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 6.9990 chunk 37 optimal weight: 3.9990 chunk 24 optimal weight: 10.0000 chunk 39 optimal weight: 10.0000 chunk 18 optimal weight: 9.9990 chunk 27 optimal weight: 5.9990 chunk 41 optimal weight: 0.0770 chunk 38 optimal weight: 20.0000 chunk 33 optimal weight: 10.0000 chunk 3 optimal weight: 10.0000 chunk 25 optimal weight: 0.6980 overall best weight: 3.5544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 307 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7615 moved from start: 0.4741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 3522 Z= 0.352 Angle : 0.650 8.903 4710 Z= 0.312 Chirality : 0.047 0.121 528 Planarity : 0.003 0.039 600 Dihedral : 5.333 23.213 468 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 3.79 % Allowed : 24.49 % Favored : 71.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.69 % 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: -2.05 (0.33), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.56 (0.25), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS F 330 PHE 0.007 0.002 PHE F 378 TYR 0.016 0.003 TYR A 310 ARG 0.001 0.000 ARG B 379 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 88 time to evaluate : 0.414 Fit side-chains REVERT: A 321 LYS cc_start: 0.7461 (mttt) cc_final: 0.6936 (mtpm) REVERT: A 338 GLU cc_start: 0.7788 (tt0) cc_final: 0.7521 (mt-10) REVERT: A 343 LYS cc_start: 0.8063 (mtmt) cc_final: 0.7214 (tttt) REVERT: A 375 LYS cc_start: 0.8097 (ttmt) cc_final: 0.7673 (tttt) REVERT: B 351 GLN cc_start: 0.7621 (tt0) cc_final: 0.6782 (mp10) REVERT: B 369 LYS cc_start: 0.7734 (tttt) cc_final: 0.7529 (tttp) REVERT: C 321 LYS cc_start: 0.8139 (mttt) cc_final: 0.7569 (mtpm) REVERT: C 343 LYS cc_start: 0.8147 (mtpp) cc_final: 0.7813 (tttt) REVERT: C 375 LYS cc_start: 0.8698 (ttmt) cc_final: 0.8415 (tppt) REVERT: D 369 LYS cc_start: 0.8504 (tttt) cc_final: 0.8141 (tttp) REVERT: D 379 ARG cc_start: 0.6454 (OUTLIER) cc_final: 0.5726 (mtm-85) REVERT: E 321 LYS cc_start: 0.7531 (mttt) cc_final: 0.6982 (tttm) REVERT: E 343 LYS cc_start: 0.7941 (mtpp) cc_final: 0.7584 (tttt) REVERT: E 348 ASP cc_start: 0.7885 (p0) cc_final: 0.7663 (p0) REVERT: E 349 ARG cc_start: 0.7039 (mtm180) cc_final: 0.6340 (mmt-90) REVERT: E 369 LYS cc_start: 0.8020 (mtmt) cc_final: 0.7351 (mttt) REVERT: E 375 LYS cc_start: 0.8196 (ttmt) cc_final: 0.7793 (tttt) REVERT: F 369 LYS cc_start: 0.7936 (tttt) cc_final: 0.7612 (tttt) REVERT: F 379 ARG cc_start: 0.5306 (mmp-170) cc_final: 0.5060 (mmp-170) outliers start: 15 outliers final: 11 residues processed: 91 average time/residue: 1.5359 time to fit residues: 142.9177 Evaluate side-chains 100 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 88 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 311 LYS Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain B residue 352 SER Chi-restraints excluded: chain B residue 356 SER Chi-restraints excluded: chain C residue 311 LYS Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain D residue 356 SER Chi-restraints excluded: chain D residue 379 ARG Chi-restraints excluded: chain E residue 316 SER Chi-restraints excluded: chain E residue 319 THR Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain F residue 351 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 20 optimal weight: 7.9990 chunk 26 optimal weight: 10.0000 chunk 35 optimal weight: 5.9990 chunk 10 optimal weight: 20.0000 chunk 30 optimal weight: 2.9990 chunk 4 optimal weight: 9.9990 chunk 9 optimal weight: 5.9990 chunk 33 optimal weight: 7.9990 chunk 13 optimal weight: 9.9990 chunk 34 optimal weight: 0.0970 chunk 6 optimal weight: 1.9990 overall best weight: 3.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 307 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7616 moved from start: 0.4791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 3522 Z= 0.336 Angle : 0.651 9.166 4710 Z= 0.311 Chirality : 0.047 0.120 528 Planarity : 0.003 0.037 600 Dihedral : 5.301 22.971 468 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 3.28 % Allowed : 25.51 % Favored : 71.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.69 % 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: -2.06 (0.32), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.56 (0.25), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS F 330 PHE 0.007 0.002 PHE F 378 TYR 0.015 0.003 TYR A 310 ARG 0.001 0.000 ARG B 379 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 87 time to evaluate : 0.499 Fit side-chains REVERT: A 321 LYS cc_start: 0.7456 (mttt) cc_final: 0.6934 (mtpm) REVERT: A 338 GLU cc_start: 0.7815 (tt0) cc_final: 0.7551 (mt-10) REVERT: A 343 LYS cc_start: 0.8105 (mtmt) cc_final: 0.7219 (tttt) REVERT: A 369 LYS cc_start: 0.7905 (mtpt) cc_final: 0.7431 (mtmm) REVERT: A 375 LYS cc_start: 0.8103 (ttmt) cc_final: 0.7677 (tttt) REVERT: B 351 GLN cc_start: 0.7633 (tt0) cc_final: 0.6827 (mp10) REVERT: B 369 LYS cc_start: 0.7738 (tttt) cc_final: 0.7347 (tppt) REVERT: C 321 LYS cc_start: 0.8132 (mttt) cc_final: 0.7566 (mtpm) REVERT: C 343 LYS cc_start: 0.8177 (mtpp) cc_final: 0.7845 (tttt) REVERT: C 375 LYS cc_start: 0.8691 (ttmt) cc_final: 0.8412 (tppt) REVERT: D 369 LYS cc_start: 0.8503 (tttt) cc_final: 0.8144 (tttp) REVERT: D 379 ARG cc_start: 0.6465 (OUTLIER) cc_final: 0.5790 (mtm-85) REVERT: E 321 LYS cc_start: 0.7543 (mttt) cc_final: 0.6997 (tttm) REVERT: E 343 LYS cc_start: 0.7923 (mtpp) cc_final: 0.7524 (tttt) REVERT: E 348 ASP cc_start: 0.7891 (OUTLIER) cc_final: 0.7648 (p0) REVERT: E 349 ARG cc_start: 0.7077 (mtm180) cc_final: 0.6260 (mpt90) REVERT: E 369 LYS cc_start: 0.8025 (mtmt) cc_final: 0.7336 (mttt) REVERT: E 375 LYS cc_start: 0.8151 (ttmt) cc_final: 0.7721 (tttt) REVERT: F 369 LYS cc_start: 0.7927 (tttt) cc_final: 0.7666 (tttt) REVERT: F 379 ARG cc_start: 0.5436 (mmp-170) cc_final: 0.4998 (mmp-170) outliers start: 13 outliers final: 11 residues processed: 90 average time/residue: 1.6005 time to fit residues: 147.2330 Evaluate side-chains 100 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 87 time to evaluate : 0.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 311 LYS Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain B residue 347 LYS Chi-restraints excluded: chain B residue 356 SER Chi-restraints excluded: chain C residue 311 LYS Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain D residue 356 SER Chi-restraints excluded: chain D residue 379 ARG Chi-restraints excluded: chain E residue 316 SER Chi-restraints excluded: chain E residue 319 THR Chi-restraints excluded: chain E residue 348 ASP Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain F residue 351 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 29 optimal weight: 10.0000 chunk 1 optimal weight: 1.9990 chunk 24 optimal weight: 10.0000 chunk 38 optimal weight: 6.9990 chunk 22 optimal weight: 10.0000 chunk 28 optimal weight: 6.9990 chunk 26 optimal weight: 7.9990 chunk 25 optimal weight: 3.9990 chunk 16 optimal weight: 7.9990 chunk 15 optimal weight: 3.9990 chunk 41 optimal weight: 6.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 307 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.120488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.100364 restraints weight = 4811.289| |-----------------------------------------------------------------------------| r_work (start): 0.3546 rms_B_bonded: 1.89 r_work: 0.3457 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3362 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.3362 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8797 moved from start: 0.4814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.047 3522 Z= 0.457 Angle : 0.703 9.002 4710 Z= 0.340 Chirality : 0.048 0.134 528 Planarity : 0.004 0.054 600 Dihedral : 5.529 24.844 468 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 3.54 % Allowed : 25.76 % Favored : 70.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.69 % 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: -2.12 (0.32), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.60 (0.25), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS F 330 PHE 0.008 0.002 PHE F 378 TYR 0.019 0.003 TYR A 310 ARG 0.002 0.000 ARG B 379 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2736.29 seconds wall clock time: 49 minutes 11.43 seconds (2951.43 seconds total)