Starting phenix.real_space_refine on Sun Mar 10 16:09:19 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qk2_14029/03_2024/7qk2_14029.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qk2_14029/03_2024/7qk2_14029.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.61 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qk2_14029/03_2024/7qk2_14029.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qk2_14029/03_2024/7qk2_14029.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qk2_14029/03_2024/7qk2_14029.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qk2_14029/03_2024/7qk2_14029.pdb" } resolution = 2.61 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= 0.004 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 2046 2.51 5 N 588 2.21 5 O 606 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 338": "OE1" <-> "OE2" Residue "A GLU 342": "OE1" <-> "OE2" Residue "A PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 349": "NH1" <-> "NH2" Residue "A GLU 372": "OE1" <-> "OE2" Residue "B GLU 338": "OE1" <-> "OE2" Residue "B GLU 342": "OE1" <-> "OE2" Residue "B PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 349": "NH1" <-> "NH2" Residue "B GLU 372": "OE1" <-> "OE2" Residue "C GLU 338": "OE1" <-> "OE2" Residue "C GLU 342": "OE1" <-> "OE2" Residue "C PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 349": "NH1" <-> "NH2" Residue "C GLU 372": "OE1" <-> "OE2" Residue "D GLU 338": "OE1" <-> "OE2" Residue "D GLU 342": "OE1" <-> "OE2" Residue "D PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 349": "NH1" <-> "NH2" Residue "D GLU 372": "OE1" <-> "OE2" Residue "D PHE 378": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 338": "OE1" <-> "OE2" Residue "E GLU 342": "OE1" <-> "OE2" Residue "E PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 349": "NH1" <-> "NH2" Residue "E GLU 372": "OE1" <-> "OE2" Residue "F GLU 338": "OE1" <-> "OE2" Residue "F GLU 342": "OE1" <-> "OE2" Residue "F PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 349": "NH1" <-> "NH2" Residue "F GLU 372": "OE1" <-> "OE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 3246 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 541 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 541 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 3, 'TRANS': 67} Chain: "B" Number of atoms: 541 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 541 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 3, 'TRANS': 67} Chain: "C" Number of atoms: 541 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 541 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 3, 'TRANS': 67} Chain: "D" Number of atoms: 541 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 541 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 3, 'TRANS': 67} Chain: "E" Number of atoms: 541 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 541 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 3, 'TRANS': 67} Chain: "F" Number of atoms: 541 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 541 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 3, 'TRANS': 67} Time building chain proxies: 2.34, per 1000 atoms: 0.72 Number of scatterers: 3246 At special positions: 0 Unit cell: (114.502, 110.14, 49.0725, 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 606 8.00 N 588 7.00 C 2046 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: 1.12 Conformation dependent library (CDL) restraints added in 644.7 milliseconds 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 744 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 18 sheets defined 0.0% alpha, 47.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.49 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'B' and resid 309 through 310 removed outlier: 6.556A pdb=" N VAL A 309 " --> pdb=" O TYR B 310 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 313 through 314 removed outlier: 6.804A pdb=" N VAL A 313 " --> pdb=" O ASP B 314 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 317 through 325 removed outlier: 6.418A pdb=" N LYS A 317 " --> pdb=" O VAL B 318 " (cutoff:3.500A) removed outlier: 8.099A pdb=" N SER B 320 " --> pdb=" O LYS A 317 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N THR A 319 " --> pdb=" O SER B 320 " (cutoff:3.500A) removed outlier: 7.955A pdb=" N CYS B 322 " --> pdb=" O THR A 319 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N LYS A 321 " --> pdb=" O CYS B 322 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N SER B 324 " --> pdb=" O LYS A 321 " (cutoff:3.500A) removed outlier: 5.906A pdb=" N GLY A 323 " --> pdb=" O SER B 324 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 328 through 330 removed outlier: 6.403A pdb=" N ILE A 328 " --> pdb=" O HIS B 329 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 336 through 341 removed outlier: 6.495A pdb=" N VAL A 337 " --> pdb=" O GLU C 338 " (cutoff:3.500A) removed outlier: 7.906A pdb=" N LYS C 340 " --> pdb=" O VAL A 337 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N VAL A 339 " --> pdb=" O LYS C 340 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 345 through 346 removed outlier: 6.699A pdb=" N ASP A 345 " --> pdb=" O PHE B 346 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 350 through 354 removed outlier: 6.571A pdb=" N GLN A 351 " --> pdb=" O SER B 352 " (cutoff:3.500A) removed outlier: 8.143A pdb=" N ILE B 354 " --> pdb=" O GLN A 351 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N LYS A 353 " --> pdb=" O ILE B 354 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 359 through 362 removed outlier: 6.676A pdb=" N ASN A 359 " --> pdb=" O ILE C 360 " (cutoff:3.500A) removed outlier: 8.235A pdb=" N HIS C 362 " --> pdb=" O ASN A 359 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N THR A 361 " --> pdb=" O HIS C 362 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 368 through 377 removed outlier: 6.404A pdb=" N LYS A 369 " --> pdb=" O LYS B 370 " (cutoff:3.500A) removed outlier: 7.873A pdb=" N GLU B 372 " --> pdb=" O LYS A 369 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N ILE A 371 " --> pdb=" O GLU B 372 " (cutoff:3.500A) removed outlier: 8.135A pdb=" N HIS B 374 " --> pdb=" O ILE A 371 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N THR A 373 " --> pdb=" O HIS B 374 " (cutoff:3.500A) removed outlier: 8.115A pdb=" N LEU B 376 " --> pdb=" O THR A 373 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N LYS A 375 " --> pdb=" O LEU B 376 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N ASN A 368 " --> pdb=" O LYS C 369 " (cutoff:3.500A) removed outlier: 7.938A pdb=" N ILE C 371 " --> pdb=" O ASN A 368 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N LYS A 370 " --> pdb=" O ILE C 371 " (cutoff:3.500A) removed outlier: 8.131A pdb=" N THR C 373 " --> pdb=" O LYS A 370 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N GLU A 372 " --> pdb=" O THR C 373 " (cutoff:3.500A) removed outlier: 8.483A pdb=" N LYS C 375 " --> pdb=" O GLU A 372 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N HIS A 374 " --> pdb=" O LYS C 375 " (cutoff:3.500A) removed outlier: 8.138A pdb=" N THR C 377 " --> pdb=" O HIS A 374 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N LEU A 376 " --> pdb=" O THR C 377 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'E' and resid 309 through 310 removed outlier: 6.589A pdb=" N VAL D 309 " --> pdb=" O TYR E 310 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 313 through 314 removed outlier: 6.834A pdb=" N VAL D 313 " --> pdb=" O ASP E 314 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 317 through 325 removed outlier: 6.533A pdb=" N LYS D 317 " --> pdb=" O VAL E 318 " (cutoff:3.500A) removed outlier: 8.259A pdb=" N SER E 320 " --> pdb=" O LYS D 317 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N THR D 319 " --> pdb=" O SER E 320 " (cutoff:3.500A) removed outlier: 8.069A pdb=" N CYS E 322 " --> pdb=" O THR D 319 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N LYS D 321 " --> pdb=" O CYS E 322 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N SER E 324 " --> pdb=" O LYS D 321 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N GLY D 323 " --> pdb=" O SER E 324 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 328 through 330 removed outlier: 6.371A pdb=" N ILE D 328 " --> pdb=" O HIS E 329 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 336 through 341 removed outlier: 6.494A pdb=" N VAL D 337 " --> pdb=" O GLU F 338 " (cutoff:3.500A) removed outlier: 7.916A pdb=" N LYS F 340 " --> pdb=" O VAL D 337 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N VAL D 339 " --> pdb=" O LYS F 340 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 345 through 346 removed outlier: 6.675A pdb=" N ASP D 345 " --> pdb=" O PHE E 346 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 350 through 354 removed outlier: 6.622A pdb=" N GLN D 351 " --> pdb=" O SER E 352 " (cutoff:3.500A) removed outlier: 8.143A pdb=" N ILE E 354 " --> pdb=" O GLN D 351 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N LYS D 353 " --> pdb=" O ILE E 354 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 359 through 362 Processing sheet with id=AB9, first strand: chain 'E' and resid 368 through 377 removed outlier: 6.440A pdb=" N ASN D 368 " --> pdb=" O LYS F 369 " (cutoff:3.500A) removed outlier: 7.813A pdb=" N ILE F 371 " --> pdb=" O ASN D 368 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N LYS D 370 " --> pdb=" O ILE F 371 " (cutoff:3.500A) removed outlier: 8.135A pdb=" N THR F 373 " --> pdb=" O LYS D 370 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N GLU D 372 " --> pdb=" O THR F 373 " (cutoff:3.500A) removed outlier: 8.368A pdb=" N LYS F 375 " --> pdb=" O GLU D 372 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N HIS D 374 " --> pdb=" O LYS F 375 " (cutoff:3.500A) removed outlier: 8.095A pdb=" N THR F 377 " --> pdb=" O HIS D 374 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N LEU D 376 " --> pdb=" O THR F 377 " (cutoff:3.500A) 62 hydrogen bonds defined for protein. 186 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: 0.83 Time building geometry restraints manager: 1.25 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: 937 1.33 - 1.45: 377 1.45 - 1.57: 1980 1.57 - 1.69: 0 1.69 - 1.81: 6 Bond restraints: 3300 Sorted by residual: bond pdb=" CZ ARG B 349 " pdb=" NH2 ARG B 349 " ideal model delta sigma weight residual 1.330 1.296 0.034 1.30e-02 5.92e+03 7.00e+00 bond pdb=" CZ ARG E 349 " pdb=" NH2 ARG E 349 " ideal model delta sigma weight residual 1.330 1.296 0.034 1.30e-02 5.92e+03 6.93e+00 bond pdb=" CZ ARG D 349 " pdb=" NH2 ARG D 349 " ideal model delta sigma weight residual 1.330 1.296 0.034 1.30e-02 5.92e+03 6.87e+00 bond pdb=" CZ ARG F 349 " pdb=" NH2 ARG F 349 " ideal model delta sigma weight residual 1.330 1.297 0.033 1.30e-02 5.92e+03 6.62e+00 bond pdb=" CZ ARG A 349 " pdb=" NH2 ARG A 349 " ideal model delta sigma weight residual 1.330 1.297 0.033 1.30e-02 5.92e+03 6.57e+00 ... (remaining 3295 not shown) Histogram of bond angle deviations from ideal: 101.76 - 107.22: 186 107.22 - 112.67: 1548 112.67 - 118.13: 848 118.13 - 123.58: 1462 123.58 - 129.04: 372 Bond angle restraints: 4416 Sorted by residual: angle pdb=" CA ASP E 358 " pdb=" CB ASP E 358 " pdb=" CG ASP E 358 " ideal model delta sigma weight residual 112.60 118.08 -5.48 1.00e+00 1.00e+00 3.00e+01 angle pdb=" OE1 GLN F 351 " pdb=" CD GLN F 351 " pdb=" NE2 GLN F 351 " ideal model delta sigma weight residual 122.60 117.24 5.36 1.00e+00 1.00e+00 2.87e+01 angle pdb=" N SER D 356 " pdb=" CA SER D 356 " pdb=" C SER D 356 " ideal model delta sigma weight residual 111.14 116.87 -5.73 1.08e+00 8.57e-01 2.81e+01 angle pdb=" OE1 GLN D 351 " pdb=" CD GLN D 351 " pdb=" NE2 GLN D 351 " ideal model delta sigma weight residual 122.60 117.41 5.19 1.00e+00 1.00e+00 2.69e+01 angle pdb=" N SER A 356 " pdb=" CA SER A 356 " pdb=" C SER A 356 " ideal model delta sigma weight residual 111.07 116.46 -5.39 1.07e+00 8.73e-01 2.54e+01 ... (remaining 4411 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 10.68: 1726 10.68 - 21.36: 208 21.36 - 32.04: 42 32.04 - 42.71: 18 42.71 - 53.39: 10 Dihedral angle restraints: 2004 sinusoidal: 834 harmonic: 1170 Sorted by residual: dihedral pdb=" CA HIS C 374 " pdb=" C HIS C 374 " pdb=" N LYS C 375 " pdb=" CA LYS C 375 " ideal model delta harmonic sigma weight residual 180.00 153.77 26.23 0 5.00e+00 4.00e-02 2.75e+01 dihedral pdb=" CA LYS D 369 " pdb=" C LYS D 369 " pdb=" N LYS D 370 " pdb=" CA LYS D 370 " ideal model delta harmonic sigma weight residual 180.00 154.62 25.38 0 5.00e+00 4.00e-02 2.58e+01 dihedral pdb=" CA LYS E 369 " pdb=" C LYS E 369 " pdb=" N LYS E 370 " pdb=" CA LYS E 370 " ideal model delta harmonic sigma weight residual 180.00 156.69 23.31 0 5.00e+00 4.00e-02 2.17e+01 ... (remaining 2001 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 310 0.077 - 0.153: 129 0.153 - 0.230: 32 0.230 - 0.307: 21 0.307 - 0.383: 6 Chirality restraints: 498 Sorted by residual: chirality pdb=" CA LYS A 375 " pdb=" N LYS A 375 " pdb=" C LYS A 375 " pdb=" CB LYS A 375 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.68e+00 chirality pdb=" CA LYS F 347 " pdb=" N LYS F 347 " pdb=" C LYS F 347 " pdb=" CB LYS F 347 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.49e+00 chirality pdb=" CA GLN A 351 " pdb=" N GLN A 351 " pdb=" C GLN A 351 " pdb=" CB GLN A 351 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.22e+00 ... (remaining 495 not shown) Planarity restraints: 558 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE F 346 " -0.048 2.00e-02 2.50e+03 2.92e-02 1.50e+01 pdb=" CG PHE F 346 " 0.036 2.00e-02 2.50e+03 pdb=" CD1 PHE F 346 " 0.028 2.00e-02 2.50e+03 pdb=" CD2 PHE F 346 " 0.028 2.00e-02 2.50e+03 pdb=" CE1 PHE F 346 " -0.008 2.00e-02 2.50e+03 pdb=" CE2 PHE F 346 " -0.008 2.00e-02 2.50e+03 pdb=" CZ PHE F 346 " -0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR F 310 " -0.050 2.00e-02 2.50e+03 2.66e-02 1.42e+01 pdb=" CG TYR F 310 " 0.019 2.00e-02 2.50e+03 pdb=" CD1 TYR F 310 " 0.016 2.00e-02 2.50e+03 pdb=" CD2 TYR F 310 " 0.028 2.00e-02 2.50e+03 pdb=" CE1 TYR F 310 " 0.017 2.00e-02 2.50e+03 pdb=" CE2 TYR F 310 " 0.007 2.00e-02 2.50e+03 pdb=" CZ TYR F 310 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR F 310 " -0.038 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE D 346 " -0.044 2.00e-02 2.50e+03 2.70e-02 1.28e+01 pdb=" CG PHE D 346 " 0.033 2.00e-02 2.50e+03 pdb=" CD1 PHE D 346 " 0.026 2.00e-02 2.50e+03 pdb=" CD2 PHE D 346 " 0.025 2.00e-02 2.50e+03 pdb=" CE1 PHE D 346 " -0.007 2.00e-02 2.50e+03 pdb=" CE2 PHE D 346 " -0.007 2.00e-02 2.50e+03 pdb=" CZ PHE D 346 " -0.026 2.00e-02 2.50e+03 ... (remaining 555 not shown) Histogram of nonbonded interaction distances: 2.50 - 2.98: 1431 2.98 - 3.46: 2496 3.46 - 3.94: 5222 3.94 - 4.42: 5015 4.42 - 4.90: 9837 Nonbonded interactions: 24001 Sorted by model distance: nonbonded pdb=" OD1 ASP A 314 " pdb=" OG SER A 316 " model vdw 2.499 2.440 nonbonded pdb=" OD1 ASP D 314 " pdb=" OG SER D 316 " model vdw 2.508 2.440 nonbonded pdb=" OD1 ASP F 314 " pdb=" OG SER F 316 " model vdw 2.508 2.440 nonbonded pdb=" OD1 ASP C 314 " pdb=" OG SER C 316 " model vdw 2.514 2.440 nonbonded pdb=" OD1 ASP B 314 " pdb=" OG SER B 316 " model vdw 2.531 2.440 ... (remaining 23996 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: 1.090 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: 3.550 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 14.080 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 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 0.034 3300 Z= 0.740 Angle : 1.864 6.853 4416 Z= 1.222 Chirality : 0.106 0.383 498 Planarity : 0.009 0.062 558 Dihedral : 10.807 53.393 1260 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 0.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Cbeta Deviations : 2.69 % 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: -1.51 (0.33), residues: 414 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.14 (0.26), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.018 0.003 HIS E 374 PHE 0.048 0.013 PHE F 346 TYR 0.050 0.011 TYR F 310 ARG 0.007 0.001 ARG E 349 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 153 time to evaluate : 0.424 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 338 GLU cc_start: 0.8252 (mt-10) cc_final: 0.8051 (mt-10) REVERT: B 347 LYS cc_start: 0.8626 (mttp) cc_final: 0.7982 (pptt) REVERT: C 311 LYS cc_start: 0.7880 (mttt) cc_final: 0.7629 (mttm) REVERT: C 349 ARG cc_start: 0.8493 (mtt180) cc_final: 0.7029 (mmp-170) REVERT: D 340 LYS cc_start: 0.8417 (mmmm) cc_final: 0.8141 (mptp) REVERT: E 336 GLN cc_start: 0.8745 (tt0) cc_final: 0.8500 (tt0) REVERT: F 336 GLN cc_start: 0.8542 (tt0) cc_final: 0.8279 (tt0) outliers start: 0 outliers final: 0 residues processed: 153 average time/residue: 1.4427 time to fit residues: 225.2301 Evaluate side-chains 109 residues out of total 372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 109 time to evaluate : 0.419 ------------------------------------------------------------------------------- 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: 0.9980 chunk 31 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 21 optimal weight: 0.8980 chunk 32 optimal weight: 0.8980 chunk 12 optimal weight: 6.9990 chunk 20 optimal weight: 9.9990 chunk 24 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 327 ASN C 336 GLN D 359 ASN E 327 ASN E 330 HIS E 359 ASN F 351 GLN F 359 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.3060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 3300 Z= 0.159 Angle : 0.593 5.191 4416 Z= 0.292 Chirality : 0.049 0.125 498 Planarity : 0.003 0.019 558 Dihedral : 5.269 12.614 432 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 3.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 4.84 % Allowed : 18.82 % Favored : 76.34 % 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: -1.32 (0.36), residues: 414 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.00 (0.27), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS E 330 PHE 0.010 0.002 PHE D 346 TYR 0.007 0.001 TYR D 310 ARG 0.002 0.001 ARG F 349 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 139 time to evaluate : 0.453 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 340 LYS cc_start: 0.8149 (mptm) cc_final: 0.7905 (mtpt) REVERT: A 351 GLN cc_start: 0.8737 (pt0) cc_final: 0.8532 (mt0) REVERT: B 347 LYS cc_start: 0.8484 (mttp) cc_final: 0.7892 (pptt) REVERT: B 359 ASN cc_start: 0.9089 (m110) cc_final: 0.8852 (m-40) REVERT: C 311 LYS cc_start: 0.7793 (mttt) cc_final: 0.7528 (mtpp) REVERT: C 345 ASP cc_start: 0.8749 (t0) cc_final: 0.8521 (t70) REVERT: C 349 ARG cc_start: 0.8510 (mtt180) cc_final: 0.6917 (mmp-170) REVERT: C 351 GLN cc_start: 0.8767 (pt0) cc_final: 0.8525 (pt0) REVERT: D 308 ILE cc_start: 0.7848 (mt) cc_final: 0.7639 (mt) REVERT: E 340 LYS cc_start: 0.8328 (tppt) cc_final: 0.7986 (mmtp) REVERT: F 336 GLN cc_start: 0.8550 (tt0) cc_final: 0.8263 (mt0) REVERT: F 338 GLU cc_start: 0.8345 (tt0) cc_final: 0.7934 (tm-30) outliers start: 18 outliers final: 3 residues processed: 145 average time/residue: 1.3798 time to fit residues: 204.2965 Evaluate side-chains 106 residues out of total 372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 103 time to evaluate : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 341 SER Chi-restraints excluded: chain E residue 363 VAL Chi-restraints excluded: chain F residue 341 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 31 optimal weight: 2.9990 chunk 25 optimal weight: 9.9990 chunk 10 optimal weight: 9.9990 chunk 38 optimal weight: 4.9990 chunk 41 optimal weight: 8.9990 chunk 34 optimal weight: 6.9990 chunk 37 optimal weight: 9.9990 chunk 13 optimal weight: 7.9990 chunk 30 optimal weight: 6.9990 chunk 28 optimal weight: 0.1980 chunk 19 optimal weight: 9.9990 overall best weight: 4.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 336 GLN D 359 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.3290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.036 3300 Z= 0.379 Angle : 0.667 5.916 4416 Z= 0.331 Chirality : 0.050 0.122 498 Planarity : 0.003 0.029 558 Dihedral : 5.702 15.476 432 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 5.91 % Allowed : 20.43 % Favored : 73.66 % 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: -1.54 (0.35), residues: 414 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.17 (0.27), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS E 329 PHE 0.014 0.003 PHE D 346 TYR 0.014 0.003 TYR F 310 ARG 0.003 0.000 ARG E 349 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 108 time to evaluate : 0.411 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 338 GLU cc_start: 0.8206 (mt-10) cc_final: 0.7897 (mt-10) REVERT: A 340 LYS cc_start: 0.8231 (mptm) cc_final: 0.8017 (mtpt) REVERT: A 351 GLN cc_start: 0.8872 (pt0) cc_final: 0.8628 (mt0) REVERT: B 347 LYS cc_start: 0.8789 (mttp) cc_final: 0.8169 (pptt) REVERT: B 359 ASN cc_start: 0.9222 (m110) cc_final: 0.8963 (m-40) REVERT: C 311 LYS cc_start: 0.8000 (mttt) cc_final: 0.7672 (mttm) REVERT: C 349 ARG cc_start: 0.8499 (mtt180) cc_final: 0.6987 (mmp-170) REVERT: C 351 GLN cc_start: 0.8844 (pt0) cc_final: 0.8520 (pt0) REVERT: D 369 LYS cc_start: 0.8182 (mtpm) cc_final: 0.7942 (tttt) REVERT: F 336 GLN cc_start: 0.8656 (tt0) cc_final: 0.8334 (mt0) REVERT: F 338 GLU cc_start: 0.8394 (tt0) cc_final: 0.7958 (tm-30) outliers start: 22 outliers final: 12 residues processed: 121 average time/residue: 1.3465 time to fit residues: 166.4833 Evaluate side-chains 116 residues out of total 372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 104 time to evaluate : 0.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain C residue 343 LYS Chi-restraints excluded: chain C residue 352 SER Chi-restraints excluded: chain D residue 324 SER Chi-restraints excluded: chain D residue 341 SER Chi-restraints excluded: chain D residue 357 LEU Chi-restraints excluded: chain E residue 341 SER Chi-restraints excluded: chain E residue 343 LYS Chi-restraints excluded: chain E residue 363 VAL Chi-restraints excluded: chain F residue 341 SER Chi-restraints excluded: chain F residue 375 LYS 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: 0.5980 chunk 25 optimal weight: 8.9990 chunk 38 optimal weight: 6.9990 chunk 40 optimal weight: 3.9990 chunk 20 optimal weight: 9.9990 chunk 36 optimal weight: 2.9990 chunk 10 optimal weight: 0.9990 chunk 33 optimal weight: 2.9990 chunk 23 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 overall best weight: 2.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 336 GLN C 336 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.3497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3300 Z= 0.224 Angle : 0.574 4.558 4416 Z= 0.278 Chirality : 0.047 0.118 498 Planarity : 0.003 0.027 558 Dihedral : 5.154 12.868 432 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 4.57 % Allowed : 22.04 % Favored : 73.39 % 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: -1.62 (0.35), residues: 414 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.22 (0.27), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS E 329 PHE 0.013 0.002 PHE F 378 TYR 0.011 0.002 TYR F 310 ARG 0.002 0.000 ARG E 349 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 105 time to evaluate : 0.417 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 340 LYS cc_start: 0.8259 (mptm) cc_final: 0.8044 (mtpt) REVERT: B 347 LYS cc_start: 0.8855 (mttp) cc_final: 0.8181 (pptt) REVERT: B 359 ASN cc_start: 0.9214 (m110) cc_final: 0.8941 (m-40) REVERT: C 311 LYS cc_start: 0.7947 (mttt) cc_final: 0.7638 (mttm) REVERT: C 349 ARG cc_start: 0.8488 (mtt180) cc_final: 0.6949 (mmp-170) REVERT: F 336 GLN cc_start: 0.8606 (tt0) cc_final: 0.8345 (mt0) REVERT: F 338 GLU cc_start: 0.8391 (tt0) cc_final: 0.7968 (tm-30) outliers start: 17 outliers final: 9 residues processed: 116 average time/residue: 1.3313 time to fit residues: 158.0368 Evaluate side-chains 106 residues out of total 372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 97 time to evaluate : 0.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 343 LYS Chi-restraints excluded: chain D residue 324 SER Chi-restraints excluded: chain D residue 341 SER Chi-restraints excluded: chain D residue 343 LYS Chi-restraints excluded: chain D residue 357 LEU Chi-restraints excluded: chain E residue 341 SER Chi-restraints excluded: chain E residue 363 VAL Chi-restraints excluded: chain F residue 341 SER Chi-restraints excluded: chain F residue 375 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 30 optimal weight: 8.9990 chunk 16 optimal weight: 5.9990 chunk 34 optimal weight: 2.9990 chunk 28 optimal weight: 0.0770 chunk 0 optimal weight: 10.0000 chunk 20 optimal weight: 10.0000 chunk 36 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 13 optimal weight: 7.9990 chunk 8 optimal weight: 8.9990 chunk 23 optimal weight: 5.9990 overall best weight: 3.2146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 336 GLN C 336 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 moved from start: 0.3568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 3300 Z= 0.287 Angle : 0.593 5.711 4416 Z= 0.290 Chirality : 0.048 0.117 498 Planarity : 0.003 0.027 558 Dihedral : 5.233 14.084 432 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 5.11 % Allowed : 22.58 % Favored : 72.31 % 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: -1.73 (0.35), residues: 414 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.31 (0.27), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS E 329 PHE 0.015 0.002 PHE F 378 TYR 0.013 0.002 TYR F 310 ARG 0.001 0.000 ARG E 349 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 105 time to evaluate : 0.426 Fit side-chains revert: symmetry clash REVERT: A 340 LYS cc_start: 0.8316 (mptm) cc_final: 0.8085 (mtpt) REVERT: B 347 LYS cc_start: 0.8886 (mttp) cc_final: 0.8208 (pptt) REVERT: C 311 LYS cc_start: 0.8017 (mttt) cc_final: 0.7693 (mttm) REVERT: C 349 ARG cc_start: 0.8490 (mtt180) cc_final: 0.7055 (mmp-170) REVERT: F 336 GLN cc_start: 0.8572 (tt0) cc_final: 0.8304 (mt0) REVERT: F 338 GLU cc_start: 0.8397 (tt0) cc_final: 0.7893 (tm-30) outliers start: 19 outliers final: 12 residues processed: 116 average time/residue: 1.4392 time to fit residues: 170.4817 Evaluate side-chains 97 residues out of total 372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 85 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain B residue 343 LYS Chi-restraints excluded: chain C residue 352 SER Chi-restraints excluded: chain D residue 324 SER Chi-restraints excluded: chain D residue 341 SER Chi-restraints excluded: chain D residue 343 LYS Chi-restraints excluded: chain D residue 357 LEU Chi-restraints excluded: chain E residue 341 SER Chi-restraints excluded: chain E residue 343 LYS Chi-restraints excluded: chain E residue 363 VAL Chi-restraints excluded: chain F residue 341 SER Chi-restraints excluded: chain F residue 375 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 10 optimal weight: 5.9990 chunk 40 optimal weight: 4.9990 chunk 33 optimal weight: 9.9990 chunk 18 optimal weight: 7.9990 chunk 3 optimal weight: 4.9990 chunk 13 optimal weight: 10.0000 chunk 21 optimal weight: 10.0000 chunk 39 optimal weight: 7.9990 chunk 4 optimal weight: 5.9990 chunk 23 optimal weight: 8.9990 chunk 29 optimal weight: 8.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 336 GLN D 351 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.3592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.043 3300 Z= 0.503 Angle : 0.689 6.585 4416 Z= 0.344 Chirality : 0.050 0.136 498 Planarity : 0.004 0.034 558 Dihedral : 5.711 17.141 432 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 4.57 % Allowed : 22.85 % Favored : 72.58 % 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: -1.93 (0.35), residues: 414 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.46 (0.27), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS E 329 PHE 0.020 0.003 PHE F 378 TYR 0.017 0.003 TYR F 310 ARG 0.005 0.001 ARG E 349 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 88 time to evaluate : 0.507 Fit side-chains revert: symmetry clash REVERT: A 338 GLU cc_start: 0.8325 (mt-10) cc_final: 0.8043 (mt-10) REVERT: A 340 LYS cc_start: 0.8381 (mptm) cc_final: 0.8113 (mtpt) REVERT: B 340 LYS cc_start: 0.8626 (mtpm) cc_final: 0.8390 (mtpt) REVERT: B 347 LYS cc_start: 0.8941 (mttp) cc_final: 0.8310 (pptt) REVERT: C 311 LYS cc_start: 0.8049 (mttt) cc_final: 0.7647 (mtpp) REVERT: C 349 ARG cc_start: 0.8495 (mtt180) cc_final: 0.7068 (mmp-170) REVERT: D 336 GLN cc_start: 0.8588 (mt0) cc_final: 0.8302 (mt0) REVERT: F 336 GLN cc_start: 0.8636 (tt0) cc_final: 0.8297 (mt0) REVERT: F 338 GLU cc_start: 0.8412 (tt0) cc_final: 0.8013 (tm-30) REVERT: F 348 ASP cc_start: 0.8883 (OUTLIER) cc_final: 0.8590 (t70) outliers start: 17 outliers final: 14 residues processed: 100 average time/residue: 1.2230 time to fit residues: 125.3421 Evaluate side-chains 99 residues out of total 372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 84 time to evaluate : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain B residue 343 LYS Chi-restraints excluded: chain C residue 352 SER Chi-restraints excluded: chain D residue 324 SER Chi-restraints excluded: chain D residue 341 SER Chi-restraints excluded: chain D residue 343 LYS Chi-restraints excluded: chain D residue 357 LEU Chi-restraints excluded: chain E residue 341 SER Chi-restraints excluded: chain E residue 343 LYS Chi-restraints excluded: chain E residue 363 VAL Chi-restraints excluded: chain F residue 341 SER Chi-restraints excluded: chain F residue 348 ASP Chi-restraints excluded: chain F residue 352 SER Chi-restraints excluded: chain F residue 375 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 22 optimal weight: 0.9980 chunk 34 optimal weight: 5.9990 chunk 40 optimal weight: 3.9990 chunk 25 optimal weight: 4.9990 chunk 24 optimal weight: 0.9990 chunk 18 optimal weight: 6.9990 chunk 16 optimal weight: 3.9990 chunk 12 optimal weight: 5.9990 chunk 7 optimal weight: 4.9990 chunk 27 optimal weight: 6.9990 chunk 20 optimal weight: 4.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 336 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.3705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 3300 Z= 0.275 Angle : 0.599 7.454 4416 Z= 0.289 Chirality : 0.047 0.116 498 Planarity : 0.003 0.033 558 Dihedral : 5.223 14.414 432 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 4.30 % Allowed : 23.66 % Favored : 72.04 % 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: -1.86 (0.35), residues: 414 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.41 (0.27), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS D 330 PHE 0.016 0.002 PHE D 378 TYR 0.013 0.002 TYR F 310 ARG 0.003 0.001 ARG A 349 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 96 time to evaluate : 0.424 Fit side-chains revert: symmetry clash REVERT: A 340 LYS cc_start: 0.8287 (mptm) cc_final: 0.8079 (mtpt) REVERT: B 340 LYS cc_start: 0.8578 (mtpm) cc_final: 0.8355 (mtpt) REVERT: B 347 LYS cc_start: 0.8948 (mttp) cc_final: 0.8250 (pptt) REVERT: B 369 LYS cc_start: 0.8488 (tttt) cc_final: 0.8272 (tttt) REVERT: C 311 LYS cc_start: 0.8016 (mttt) cc_final: 0.7681 (mttm) REVERT: C 349 ARG cc_start: 0.8477 (mtt180) cc_final: 0.6966 (mmp-170) REVERT: D 336 GLN cc_start: 0.8607 (mt0) cc_final: 0.8331 (mt0) REVERT: F 336 GLN cc_start: 0.8597 (tt0) cc_final: 0.8307 (mt0) REVERT: F 338 GLU cc_start: 0.8450 (tt0) cc_final: 0.8048 (tm-30) REVERT: F 348 ASP cc_start: 0.8881 (OUTLIER) cc_final: 0.8611 (t0) outliers start: 16 outliers final: 13 residues processed: 107 average time/residue: 1.2919 time to fit residues: 141.7057 Evaluate side-chains 100 residues out of total 372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 86 time to evaluate : 0.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain B residue 343 LYS Chi-restraints excluded: chain C residue 352 SER Chi-restraints excluded: chain D residue 324 SER Chi-restraints excluded: chain D residue 341 SER Chi-restraints excluded: chain D residue 343 LYS Chi-restraints excluded: chain D residue 357 LEU Chi-restraints excluded: chain E residue 341 SER Chi-restraints excluded: chain E residue 343 LYS Chi-restraints excluded: chain E residue 363 VAL Chi-restraints excluded: chain F residue 341 SER Chi-restraints excluded: chain F residue 348 ASP 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: 10.0000 chunk 31 optimal weight: 7.9990 chunk 36 optimal weight: 4.9990 chunk 38 optimal weight: 9.9990 chunk 35 optimal weight: 8.9990 chunk 37 optimal weight: 7.9990 chunk 22 optimal weight: 3.9990 chunk 16 optimal weight: 3.9990 chunk 29 optimal weight: 0.9990 chunk 11 optimal weight: 0.4980 chunk 34 optimal weight: 9.9990 overall best weight: 2.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 336 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.3732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 3300 Z= 0.266 Angle : 0.603 8.079 4416 Z= 0.289 Chirality : 0.047 0.117 498 Planarity : 0.003 0.033 558 Dihedral : 5.132 14.339 432 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 4.03 % Allowed : 23.39 % Favored : 72.58 % 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: -1.86 (0.35), residues: 414 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.41 (0.27), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 329 PHE 0.016 0.002 PHE D 378 TYR 0.014 0.002 TYR D 310 ARG 0.003 0.001 ARG A 349 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 95 time to evaluate : 0.447 Fit side-chains revert: symmetry clash REVERT: A 340 LYS cc_start: 0.8289 (mptm) cc_final: 0.8084 (mtpt) REVERT: A 349 ARG cc_start: 0.8726 (mtt90) cc_final: 0.8289 (mmt90) REVERT: B 340 LYS cc_start: 0.8593 (mtpm) cc_final: 0.8359 (mtpt) REVERT: B 347 LYS cc_start: 0.9041 (mttp) cc_final: 0.8294 (pptt) REVERT: B 369 LYS cc_start: 0.8504 (tttt) cc_final: 0.8282 (tttt) REVERT: C 311 LYS cc_start: 0.8007 (mttt) cc_final: 0.7671 (mttm) REVERT: C 345 ASP cc_start: 0.8799 (t0) cc_final: 0.8368 (m-30) REVERT: C 349 ARG cc_start: 0.8474 (mtt180) cc_final: 0.6895 (mmp-170) REVERT: D 336 GLN cc_start: 0.8605 (mt0) cc_final: 0.8340 (mt0) REVERT: F 336 GLN cc_start: 0.8556 (tt0) cc_final: 0.8287 (mt0) REVERT: F 338 GLU cc_start: 0.8461 (tt0) cc_final: 0.8044 (tm-30) REVERT: F 348 ASP cc_start: 0.8868 (OUTLIER) cc_final: 0.8610 (t0) outliers start: 15 outliers final: 10 residues processed: 104 average time/residue: 1.2182 time to fit residues: 129.9003 Evaluate side-chains 105 residues out of total 372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 94 time to evaluate : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 343 LYS Chi-restraints excluded: chain C residue 352 SER Chi-restraints excluded: chain D residue 324 SER Chi-restraints excluded: chain D residue 341 SER Chi-restraints excluded: chain D residue 343 LYS Chi-restraints excluded: chain D residue 357 LEU Chi-restraints excluded: chain E residue 341 SER Chi-restraints excluded: chain E residue 343 LYS Chi-restraints excluded: chain E residue 363 VAL Chi-restraints excluded: chain F residue 348 ASP Chi-restraints excluded: chain F residue 352 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 8.9990 chunk 37 optimal weight: 6.9990 chunk 24 optimal weight: 9.9990 chunk 39 optimal weight: 5.9990 chunk 18 optimal weight: 3.9990 chunk 27 optimal weight: 10.0000 chunk 41 optimal weight: 7.9990 chunk 38 optimal weight: 3.9990 chunk 33 optimal weight: 9.9990 chunk 3 optimal weight: 10.0000 chunk 25 optimal weight: 1.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 336 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.3726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.038 3300 Z= 0.394 Angle : 0.659 8.206 4416 Z= 0.322 Chirality : 0.048 0.124 498 Planarity : 0.003 0.035 558 Dihedral : 5.422 16.228 432 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 4.03 % Allowed : 23.12 % Favored : 72.85 % 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: -1.95 (0.35), residues: 414 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.48 (0.27), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS E 329 PHE 0.018 0.003 PHE D 378 TYR 0.015 0.003 TYR F 310 ARG 0.004 0.001 ARG E 349 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 95 time to evaluate : 0.431 Fit side-chains revert: symmetry clash REVERT: A 340 LYS cc_start: 0.8351 (mptm) cc_final: 0.8124 (mtpt) REVERT: A 349 ARG cc_start: 0.8727 (mtt90) cc_final: 0.8309 (mmt90) REVERT: B 340 LYS cc_start: 0.8591 (mtpm) cc_final: 0.8375 (mtpt) REVERT: B 347 LYS cc_start: 0.9047 (mttp) cc_final: 0.8369 (pptt) REVERT: C 311 LYS cc_start: 0.8050 (mttt) cc_final: 0.7703 (mttm) REVERT: C 340 LYS cc_start: 0.8584 (mtpp) cc_final: 0.8217 (mtpt) REVERT: C 349 ARG cc_start: 0.8464 (mtt180) cc_final: 0.6982 (mmp-170) REVERT: D 336 GLN cc_start: 0.8602 (mt0) cc_final: 0.8348 (mt0) REVERT: F 336 GLN cc_start: 0.8630 (tt0) cc_final: 0.8340 (mt0) REVERT: F 338 GLU cc_start: 0.8483 (tt0) cc_final: 0.8076 (tm-30) REVERT: F 348 ASP cc_start: 0.8870 (OUTLIER) cc_final: 0.8589 (t70) REVERT: F 349 ARG cc_start: 0.8305 (mtp180) cc_final: 0.8053 (mtt180) outliers start: 15 outliers final: 13 residues processed: 106 average time/residue: 1.2821 time to fit residues: 139.1667 Evaluate side-chains 103 residues out of total 372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 89 time to evaluate : 0.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain B residue 343 LYS Chi-restraints excluded: chain C residue 352 SER Chi-restraints excluded: chain D residue 324 SER Chi-restraints excluded: chain D residue 341 SER Chi-restraints excluded: chain D residue 343 LYS Chi-restraints excluded: chain D residue 357 LEU Chi-restraints excluded: chain E residue 341 SER Chi-restraints excluded: chain E residue 343 LYS Chi-restraints excluded: chain E residue 363 VAL Chi-restraints excluded: chain F residue 341 SER Chi-restraints excluded: chain F residue 348 ASP Chi-restraints excluded: chain F residue 352 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 20 optimal weight: 3.9990 chunk 26 optimal weight: 5.9990 chunk 35 optimal weight: 7.9990 chunk 10 optimal weight: 10.0000 chunk 30 optimal weight: 8.9990 chunk 4 optimal weight: 10.0000 chunk 9 optimal weight: 0.7980 chunk 33 optimal weight: 0.7980 chunk 13 optimal weight: 0.7980 chunk 34 optimal weight: 7.9990 chunk 6 optimal weight: 1.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 336 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.3771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 3300 Z= 0.183 Angle : 0.576 8.104 4416 Z= 0.271 Chirality : 0.047 0.119 498 Planarity : 0.003 0.033 558 Dihedral : 4.814 13.682 432 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 2.96 % Allowed : 23.92 % Favored : 73.12 % 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: -1.81 (0.36), residues: 414 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.37 (0.27), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS B 329 PHE 0.017 0.002 PHE D 378 TYR 0.012 0.002 TYR F 310 ARG 0.004 0.001 ARG A 349 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 101 time to evaluate : 0.387 Fit side-chains revert: symmetry clash REVERT: B 340 LYS cc_start: 0.8533 (mtpm) cc_final: 0.8301 (mtpt) REVERT: B 347 LYS cc_start: 0.9033 (mttp) cc_final: 0.8395 (pptt) REVERT: C 311 LYS cc_start: 0.7970 (mttt) cc_final: 0.7661 (mttm) REVERT: C 345 ASP cc_start: 0.8788 (t0) cc_final: 0.8354 (m-30) REVERT: C 349 ARG cc_start: 0.8442 (mtt180) cc_final: 0.6954 (mmp-170) REVERT: F 336 GLN cc_start: 0.8542 (tt0) cc_final: 0.8317 (mt0) REVERT: F 338 GLU cc_start: 0.8445 (tt0) cc_final: 0.8047 (tm-30) REVERT: F 348 ASP cc_start: 0.8839 (OUTLIER) cc_final: 0.8580 (t0) outliers start: 11 outliers final: 9 residues processed: 110 average time/residue: 1.3802 time to fit residues: 155.5818 Evaluate side-chains 101 residues out of total 372 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 91 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain C residue 352 SER Chi-restraints excluded: chain D residue 324 SER Chi-restraints excluded: chain D residue 341 SER Chi-restraints excluded: chain D residue 343 LYS Chi-restraints excluded: chain E residue 341 SER Chi-restraints excluded: chain E residue 343 LYS Chi-restraints excluded: chain E residue 363 VAL Chi-restraints excluded: chain F residue 348 ASP Chi-restraints excluded: chain F residue 352 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 29 optimal weight: 9.9990 chunk 1 optimal weight: 8.9990 chunk 24 optimal weight: 7.9990 chunk 38 optimal weight: 5.9990 chunk 22 optimal weight: 4.9990 chunk 28 optimal weight: 5.9990 chunk 26 optimal weight: 10.0000 chunk 25 optimal weight: 2.9990 chunk 16 optimal weight: 0.9990 chunk 15 optimal weight: 0.8980 chunk 41 optimal weight: 9.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.112453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.100207 restraints weight = 4348.850| |-----------------------------------------------------------------------------| r_work (start): 0.3408 rms_B_bonded: 1.59 r_work: 0.3315 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.3231 rms_B_bonded: 3.07 restraints_weight: 0.2500 r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8535 moved from start: 0.3776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 3300 Z= 0.289 Angle : 0.631 8.240 4416 Z= 0.302 Chirality : 0.048 0.127 498 Planarity : 0.003 0.033 558 Dihedral : 5.140 15.671 432 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 2.96 % Allowed : 24.46 % Favored : 72.58 % 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: -1.86 (0.36), residues: 414 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.41 (0.27), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS D 330 PHE 0.018 0.002 PHE D 378 TYR 0.016 0.002 TYR F 310 ARG 0.006 0.001 ARG A 349 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2579.81 seconds wall clock time: 46 minutes 11.09 seconds (2771.09 seconds total)