Starting phenix.real_space_refine on Sat Aug 3 04:33:54 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q8y_18265/08_2024/8q8y_18265.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q8y_18265/08_2024/8q8y_18265.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.88 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q8y_18265/08_2024/8q8y_18265.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q8y_18265/08_2024/8q8y_18265.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q8y_18265/08_2024/8q8y_18265.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q8y_18265/08_2024/8q8y_18265.cif" } resolution = 2.88 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: 5 Type Number sf(0) Gaussians S 6 5.16 5 C 2124 2.51 5 N 618 2.21 5 O 627 1.98 5 H 3521 0.53 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 "D GLU 338": "OE1" <-> "OE2" Residue "D GLU 342": "OE1" <-> "OE2" Residue "D PHE 378": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 338": "OE1" <-> "OE2" Residue "C GLU 342": "OE1" <-> "OE2" Residue "C PHE 378": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 338": "OE1" <-> "OE2" Residue "B ASP 348": "OD1" <-> "OD2" Residue "B GLU 372": "OE1" <-> "OE2" Residue "E GLU 338": "OE1" <-> "OE2" Residue "E ASP 348": "OD1" <-> "OD2" Residue "E GLU 372": "OE1" <-> "OE2" Residue "F GLU 338": "OE1" <-> "OE2" Residue "F ASP 348": "OD1" <-> "OD2" Residue "F GLU 372": "OE1" <-> "OE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 6896 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 1162 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 3, 'TRANS': 70} Chain: "D" Number of atoms: 1161 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 1161 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 3, 'TRANS': 70} Chain: "C" Number of atoms: 1161 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 1161 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 3, 'TRANS': 70} Chain: "B" Number of atoms: 1137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 1137 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 3, 'TRANS': 69} Chain: "E" Number of atoms: 1138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 1138 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 3, 'TRANS': 69} Chain: "F" Number of atoms: 1137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 1137 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 3, 'TRANS': 69} Time building chain proxies: 4.72, per 1000 atoms: 0.68 Number of scatterers: 6896 At special positions: 0 Unit cell: (127.952, 140.311, 53.071, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 6 16.00 O 627 8.00 N 618 7.00 C 2124 6.00 H 3521 1.00 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: 4.92 Conformation dependent library (CDL) restraints added in 830.3 milliseconds 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 774 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 17 sheets defined 0.0% alpha, 53.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.72 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'D' and resid 307 through 310 removed outlier: 6.461A pdb=" N GLN A 307 " --> pdb=" O ILE D 308 " (cutoff:3.500A) removed outlier: 7.743A pdb=" N TYR D 310 " --> pdb=" O GLN A 307 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N VAL A 309 " --> pdb=" O TYR D 310 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 313 through 314 removed outlier: 6.793A pdb=" N VAL A 313 " --> pdb=" O ASP D 314 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 317 through 325 removed outlier: 6.565A pdb=" N VAL A 318 " --> pdb=" O THR C 319 " (cutoff:3.500A) removed outlier: 8.019A pdb=" N LYS C 321 " --> pdb=" O VAL A 318 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N SER A 320 " --> pdb=" O LYS C 321 " (cutoff:3.500A) removed outlier: 7.737A pdb=" N GLY C 323 " --> pdb=" O SER A 320 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N CYS A 322 " --> pdb=" O GLY C 323 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N LEU C 325 " --> pdb=" O CYS A 322 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N SER A 324 " --> pdb=" O LEU C 325 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 328 through 330 removed outlier: 6.796A pdb=" N HIS A 329 " --> pdb=" O HIS C 330 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 336 through 346 removed outlier: 6.825A pdb=" N LEU A 344 " --> pdb=" O LYS D 343 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N ASP D 345 " --> pdb=" O LEU A 344 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N PHE A 346 " --> pdb=" O ASP D 345 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N VAL A 337 " --> pdb=" O GLU C 338 " (cutoff:3.500A) removed outlier: 7.783A 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) removed outlier: 7.935A pdb=" N GLU C 342 " --> pdb=" O VAL A 339 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N SER A 341 " --> pdb=" O GLU C 342 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N LEU C 344 " --> pdb=" O SER A 341 " (cutoff:3.500A) removed outlier: 7.365A pdb=" N LYS A 343 " --> pdb=" O LEU C 344 " (cutoff:3.500A) removed outlier: 10.247A pdb=" N PHE C 346 " --> pdb=" O LYS A 343 " (cutoff:3.500A) removed outlier: 9.275A pdb=" N ASP A 345 " --> pdb=" O PHE C 346 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 350 through 354 removed outlier: 6.467A pdb=" N GLN A 351 " --> pdb=" O SER D 352 " (cutoff:3.500A) removed outlier: 8.059A pdb=" N ILE D 354 " --> pdb=" O GLN A 351 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N LYS A 353 " --> pdb=" O ILE D 354 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 359 through 362 removed outlier: 6.471A pdb=" N ILE A 360 " --> pdb=" O THR D 361 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 368 through 378 removed outlier: 6.538A pdb=" N LYS A 369 " --> pdb=" O LYS D 370 " (cutoff:3.500A) removed outlier: 7.940A pdb=" N GLU D 372 " --> pdb=" O LYS A 369 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N ILE A 371 " --> pdb=" O GLU D 372 " (cutoff:3.500A) removed outlier: 7.484A pdb=" N HIS D 374 " --> pdb=" O ILE A 371 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N THR A 373 " --> pdb=" O HIS D 374 " (cutoff:3.500A) removed outlier: 7.934A pdb=" N LEU D 376 " --> pdb=" O THR A 373 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N LYS A 375 " --> pdb=" O LEU D 376 " (cutoff:3.500A) removed outlier: 8.063A pdb=" N PHE D 378 " --> pdb=" O LYS A 375 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N THR A 377 " --> pdb=" O PHE D 378 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 307 through 310 removed outlier: 6.865A pdb=" N ILE B 308 " --> pdb=" O VAL E 309 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N GLN B 307 " --> pdb=" O ILE F 308 " (cutoff:3.500A) removed outlier: 7.654A pdb=" N TYR F 310 " --> pdb=" O GLN B 307 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N VAL B 309 " --> pdb=" O TYR F 310 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'E' and resid 313 through 314 removed outlier: 6.757A pdb=" N VAL B 313 " --> pdb=" O ASP F 314 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 317 through 325 removed outlier: 6.608A pdb=" N VAL B 318 " --> pdb=" O THR E 319 " (cutoff:3.500A) removed outlier: 7.806A pdb=" N LYS E 321 " --> pdb=" O VAL B 318 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N SER B 320 " --> pdb=" O LYS E 321 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N GLY E 323 " --> pdb=" O SER B 320 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N CYS B 322 " --> pdb=" O GLY E 323 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N LEU E 325 " --> pdb=" O CYS B 322 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N SER B 324 " --> pdb=" O LEU E 325 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N LYS B 317 " --> pdb=" O VAL F 318 " (cutoff:3.500A) removed outlier: 8.029A pdb=" N SER F 320 " --> pdb=" O LYS B 317 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N THR B 319 " --> pdb=" O SER F 320 " (cutoff:3.500A) removed outlier: 7.901A pdb=" N CYS F 322 " --> pdb=" O THR B 319 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N LYS B 321 " --> pdb=" O CYS F 322 " (cutoff:3.500A) removed outlier: 7.274A pdb=" N SER F 324 " --> pdb=" O LYS B 321 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N GLY B 323 " --> pdb=" O SER F 324 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'E' and resid 328 through 330 removed outlier: 6.505A pdb=" N ILE B 328 " --> pdb=" O HIS F 329 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 336 through 340 removed outlier: 6.611A pdb=" N VAL B 337 " --> pdb=" O GLU E 338 " (cutoff:3.500A) removed outlier: 8.033A pdb=" N LYS E 340 " --> pdb=" O VAL B 337 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N VAL B 339 " --> pdb=" O LYS E 340 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 343 through 346 removed outlier: 6.569A pdb=" N LEU B 344 " --> pdb=" O ASP E 345 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 351 through 354 removed outlier: 6.436A pdb=" N GLN B 351 " --> pdb=" O SER F 352 " (cutoff:3.500A) removed outlier: 7.835A pdb=" N ILE F 354 " --> pdb=" O GLN B 351 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N LYS B 353 " --> pdb=" O ILE F 354 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 357 through 362 removed outlier: 6.433A pdb=" N ASP B 358 " --> pdb=" O ASN F 359 " (cutoff:3.500A) removed outlier: 7.680A pdb=" N THR F 361 " --> pdb=" O ASP B 358 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N ILE B 360 " --> pdb=" O THR F 361 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 368 through 377 74 hydrogen bonds defined for protein. 222 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.10 Time building geometry restraints manager: 5.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.95 - 1.12: 3515 1.12 - 1.29: 562 1.29 - 1.46: 1015 1.46 - 1.64: 1852 1.64 - 1.81: 6 Bond restraints: 6950 Sorted by residual: bond pdb=" N LYS E 340 " pdb=" H LYS E 340 " ideal model delta sigma weight residual 0.860 1.010 -0.150 2.00e-02 2.50e+03 5.65e+01 bond pdb=" CE2 TYR C 310 " pdb=" HE2 TYR C 310 " ideal model delta sigma weight residual 0.930 1.080 -0.150 2.00e-02 2.50e+03 5.65e+01 bond pdb=" N VAL F 337 " pdb=" H VAL F 337 " ideal model delta sigma weight residual 0.860 1.010 -0.150 2.00e-02 2.50e+03 5.64e+01 bond pdb=" CD1 PHE E 378 " pdb=" HD1 PHE E 378 " ideal model delta sigma weight residual 0.930 1.080 -0.150 2.00e-02 2.50e+03 5.64e+01 bond pdb=" N SER F 324 " pdb=" H SER F 324 " ideal model delta sigma weight residual 0.860 1.010 -0.150 2.00e-02 2.50e+03 5.64e+01 ... (remaining 6945 not shown) Histogram of bond angle deviations from ideal: 96.24 - 103.00: 26 103.00 - 109.76: 5824 109.76 - 116.52: 3303 116.52 - 123.28: 2964 123.28 - 130.04: 559 Bond angle restraints: 12676 Sorted by residual: angle pdb=" CA PHE F 346 " pdb=" CB PHE F 346 " pdb=" CG PHE F 346 " ideal model delta sigma weight residual 113.80 119.79 -5.99 1.00e+00 1.00e+00 3.59e+01 angle pdb=" CA PHE B 346 " pdb=" CB PHE B 346 " pdb=" CG PHE B 346 " ideal model delta sigma weight residual 113.80 119.65 -5.85 1.00e+00 1.00e+00 3.42e+01 angle pdb=" CA ASP B 358 " pdb=" CB ASP B 358 " pdb=" CG ASP B 358 " ideal model delta sigma weight residual 112.60 118.21 -5.61 1.00e+00 1.00e+00 3.15e+01 angle pdb=" CA PHE E 346 " pdb=" CB PHE E 346 " pdb=" CG PHE E 346 " ideal model delta sigma weight residual 113.80 119.22 -5.42 1.00e+00 1.00e+00 2.94e+01 angle pdb=" CA ASP E 358 " pdb=" CB ASP E 358 " pdb=" CG ASP E 358 " ideal model delta sigma weight residual 112.60 117.96 -5.36 1.00e+00 1.00e+00 2.88e+01 ... (remaining 12671 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.54: 2781 14.54 - 29.07: 213 29.07 - 43.61: 67 43.61 - 58.14: 64 58.14 - 72.68: 75 Dihedral angle restraints: 3200 sinusoidal: 1827 harmonic: 1373 Sorted by residual: dihedral pdb=" CA GLY C 335 " pdb=" C GLY C 335 " pdb=" N GLN C 336 " pdb=" CA GLN C 336 " ideal model delta harmonic sigma weight residual -180.00 -152.03 -27.97 0 5.00e+00 4.00e-02 3.13e+01 dihedral pdb=" CA GLY A 335 " pdb=" C GLY A 335 " pdb=" N GLN A 336 " pdb=" CA GLN A 336 " ideal model delta harmonic sigma weight residual 180.00 -153.06 -26.94 0 5.00e+00 4.00e-02 2.90e+01 dihedral pdb=" CA GLY D 335 " pdb=" C GLY D 335 " pdb=" N GLN D 336 " pdb=" CA GLN D 336 " ideal model delta harmonic sigma weight residual -180.00 -153.21 -26.79 0 5.00e+00 4.00e-02 2.87e+01 ... (remaining 3197 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.084: 331 0.084 - 0.167: 131 0.167 - 0.250: 37 0.250 - 0.333: 14 0.333 - 0.416: 6 Chirality restraints: 519 Sorted by residual: 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 2.09 0.42 2.00e-01 2.50e+01 4.33e+00 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 2.12 0.39 2.00e-01 2.50e+01 3.85e+00 chirality pdb=" CA LYS A 317 " pdb=" N LYS A 317 " pdb=" C LYS A 317 " pdb=" CB LYS A 317 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.76e+00 ... (remaining 516 not shown) Planarity restraints: 999 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB HIS D 374 " -0.092 2.00e-02 2.50e+03 5.69e-02 7.30e+01 pdb=" CG HIS D 374 " 0.037 2.00e-02 2.50e+03 pdb=" ND1 HIS D 374 " 0.017 2.00e-02 2.50e+03 pdb=" CD2 HIS D 374 " 0.065 2.00e-02 2.50e+03 pdb=" CE1 HIS D 374 " 0.033 2.00e-02 2.50e+03 pdb=" NE2 HIS D 374 " 0.037 2.00e-02 2.50e+03 pdb=" HD2 HIS D 374 " 0.026 2.00e-02 2.50e+03 pdb=" HE1 HIS D 374 " -0.015 2.00e-02 2.50e+03 pdb=" HE2 HIS D 374 " -0.108 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS C 374 " -0.077 2.00e-02 2.50e+03 5.18e-02 6.03e+01 pdb=" CG HIS C 374 " 0.027 2.00e-02 2.50e+03 pdb=" ND1 HIS C 374 " 0.008 2.00e-02 2.50e+03 pdb=" CD2 HIS C 374 " 0.055 2.00e-02 2.50e+03 pdb=" CE1 HIS C 374 " 0.035 2.00e-02 2.50e+03 pdb=" NE2 HIS C 374 " 0.041 2.00e-02 2.50e+03 pdb=" HD2 HIS C 374 " 0.026 2.00e-02 2.50e+03 pdb=" HE1 HIS C 374 " -0.011 2.00e-02 2.50e+03 pdb=" HE2 HIS C 374 " -0.104 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 368 " 0.059 2.00e-02 2.50e+03 6.19e-02 5.74e+01 pdb=" CG ASN A 368 " -0.008 2.00e-02 2.50e+03 pdb=" OD1 ASN A 368 " -0.066 2.00e-02 2.50e+03 pdb=" ND2 ASN A 368 " 0.027 2.00e-02 2.50e+03 pdb="HD21 ASN A 368 " -0.091 2.00e-02 2.50e+03 pdb="HD22 ASN A 368 " 0.078 2.00e-02 2.50e+03 ... (remaining 996 not shown) Histogram of nonbonded interaction distances: 1.56 - 2.17: 519 2.17 - 2.77: 11605 2.77 - 3.38: 17807 3.38 - 3.99: 24689 3.99 - 4.60: 33629 Nonbonded interactions: 88249 Sorted by model distance: nonbonded pdb=" OD1 ASP A 314 " pdb=" HG SER A 316 " model vdw 1.557 2.450 nonbonded pdb=" OD1 ASP F 314 " pdb=" HG SER F 316 " model vdw 1.567 2.450 nonbonded pdb=" OD1 ASP C 314 " pdb=" HG SER C 316 " model vdw 1.573 2.450 nonbonded pdb=" OD1 ASP D 314 " pdb=" HG SER D 316 " model vdw 1.594 2.450 nonbonded pdb=" OD1 ASP A 358 " pdb=" HG SER C 356 " model vdw 1.599 2.450 ... (remaining 88244 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 306 through 373 or (resid 374 and (name N or name CA or na \ me C or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name \ NE2 or name H or name HA or name HB2 or name HB3 or name HD2 or name HE1 or nam \ e HE2)) or resid 375 through 378)) selection = chain 'B' selection = (chain 'C' and resid 306 through 378) selection = (chain 'D' and resid 306 through 378) selection = (chain 'E' and (resid 306 through 373 or (resid 374 and (name N or name CA or na \ me C or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name \ NE2 or name H or name HA or name HB2 or name HB3 or name HD2 or name HE1 or nam \ e HE2)) or resid 375 through 378)) 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: 3.990 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: 0.100 Extract box with map and model: 0.300 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 26.100 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.020 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:11.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7335 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 0.040 3429 Z= 0.741 Angle : 1.885 7.881 4590 Z= 1.239 Chirality : 0.107 0.416 519 Planarity : 0.009 0.041 582 Dihedral : 12.931 72.680 1314 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 0.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Cbeta Deviations : 1.03 % 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: -1.68 (0.32), residues: 429 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.27 (0.25), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.010 0.003 HIS F 330 PHE 0.027 0.009 PHE F 378 TYR 0.053 0.011 TYR C 310 ARG 0.006 0.001 ARG E 349 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 387 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 129 time to evaluate : 0.584 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 317 LYS cc_start: 0.7065 (pttt) cc_final: 0.6515 (ptmm) REVERT: A 336 GLN cc_start: 0.6956 (tt0) cc_final: 0.6665 (mt0) REVERT: A 338 GLU cc_start: 0.7444 (mt-10) cc_final: 0.6748 (mt-10) REVERT: A 369 LYS cc_start: 0.7421 (ttmt) cc_final: 0.6797 (tttt) REVERT: A 372 GLU cc_start: 0.7872 (mm-30) cc_final: 0.7226 (mm-30) REVERT: D 317 LYS cc_start: 0.7823 (pttt) cc_final: 0.7507 (ptmm) REVERT: D 336 GLN cc_start: 0.7594 (tt0) cc_final: 0.7387 (mt0) REVERT: D 338 GLU cc_start: 0.7815 (mt-10) cc_final: 0.7267 (tt0) REVERT: D 369 LYS cc_start: 0.8009 (ttmt) cc_final: 0.7354 (tttt) REVERT: C 311 LYS cc_start: 0.8102 (ttmt) cc_final: 0.6814 (tppt) REVERT: C 338 GLU cc_start: 0.7547 (mt-10) cc_final: 0.6844 (tt0) REVERT: C 369 LYS cc_start: 0.7561 (ttmt) cc_final: 0.7050 (tttt) REVERT: C 372 GLU cc_start: 0.8113 (mm-30) cc_final: 0.7506 (mm-30) REVERT: C 379 ARG cc_start: 0.6719 (mtp180) cc_final: 0.6309 (tmm160) REVERT: B 314 ASP cc_start: 0.7623 (t0) cc_final: 0.7294 (t0) REVERT: B 319 THR cc_start: 0.7593 (p) cc_final: 0.7218 (m) REVERT: B 340 LYS cc_start: 0.7865 (tttt) cc_final: 0.7484 (tmtp) REVERT: B 342 GLU cc_start: 0.7418 (mt-10) cc_final: 0.6361 (tm-30) REVERT: B 343 LYS cc_start: 0.6474 (ttmt) cc_final: 0.6226 (ttpt) REVERT: B 369 LYS cc_start: 0.7043 (mtpt) cc_final: 0.5990 (mptp) REVERT: E 311 LYS cc_start: 0.8147 (pttt) cc_final: 0.6508 (tppt) REVERT: E 340 LYS cc_start: 0.7896 (tttt) cc_final: 0.7565 (tmtp) REVERT: E 342 GLU cc_start: 0.7498 (mt-10) cc_final: 0.7004 (mt-10) REVERT: E 343 LYS cc_start: 0.6875 (ttmt) cc_final: 0.6661 (ttpt) REVERT: E 360 ILE cc_start: 0.7696 (tt) cc_final: 0.7385 (mt) REVERT: E 369 LYS cc_start: 0.7109 (mtpt) cc_final: 0.5952 (mptt) REVERT: E 372 GLU cc_start: 0.7811 (mt-10) cc_final: 0.7553 (mt-10) REVERT: F 311 LYS cc_start: 0.8290 (pttt) cc_final: 0.7775 (pttm) REVERT: F 342 GLU cc_start: 0.7163 (mt-10) cc_final: 0.6542 (tm-30) REVERT: F 369 LYS cc_start: 0.7630 (mtpt) cc_final: 0.7317 (ttpt) REVERT: F 375 LYS cc_start: 0.7881 (tttt) cc_final: 0.7474 (tppp) outliers start: 0 outliers final: 0 residues processed: 129 average time/residue: 2.7473 time to fit residues: 362.7856 Evaluate side-chains 85 residues out of total 387 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 85 time to evaluate : 0.584 ------------------------------------------------------------------------------- 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: 0.9990 chunk 31 optimal weight: 2.9990 chunk 17 optimal weight: 5.9990 chunk 10 optimal weight: 1.9990 chunk 21 optimal weight: 0.9980 chunk 32 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 20 optimal weight: 5.9990 chunk 24 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 327 ASN A 368 ASN D 327 ASN D 368 ASN C 327 ASN C 368 ASN B 327 ASN E 327 ASN F 327 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7498 moved from start: 0.3606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3429 Z= 0.178 Angle : 0.606 5.009 4590 Z= 0.304 Chirality : 0.052 0.134 519 Planarity : 0.003 0.021 582 Dihedral : 6.031 18.788 450 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 2.33 % Allowed : 12.14 % Favored : 85.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.32 (0.34), residues: 429 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.99 (0.26), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS F 330 PHE 0.007 0.001 PHE E 346 TYR 0.009 0.002 TYR D 310 ARG 0.002 0.001 ARG D 349 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 387 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 108 time to evaluate : 0.584 Fit side-chains REVERT: A 336 GLN cc_start: 0.6930 (tt0) cc_final: 0.6682 (mt0) REVERT: A 338 GLU cc_start: 0.7490 (mt-10) cc_final: 0.6862 (mt-10) REVERT: A 358 ASP cc_start: 0.7512 (m-30) cc_final: 0.7208 (m-30) REVERT: A 369 LYS cc_start: 0.7485 (ttmt) cc_final: 0.6851 (tttt) REVERT: A 372 GLU cc_start: 0.7664 (mm-30) cc_final: 0.7380 (tt0) REVERT: D 314 ASP cc_start: 0.8269 (t70) cc_final: 0.7840 (t70) REVERT: D 317 LYS cc_start: 0.7800 (pttt) cc_final: 0.7537 (ptmm) REVERT: D 338 GLU cc_start: 0.7819 (mt-10) cc_final: 0.7229 (tt0) REVERT: D 340 LYS cc_start: 0.8178 (ttmm) cc_final: 0.7898 (ttmt) REVERT: D 349 ARG cc_start: 0.6180 (mtm180) cc_final: 0.5471 (mtt180) REVERT: D 369 LYS cc_start: 0.7933 (ttmt) cc_final: 0.7298 (tttt) REVERT: D 372 GLU cc_start: 0.7733 (mm-30) cc_final: 0.7142 (mm-30) REVERT: C 311 LYS cc_start: 0.8054 (ttmt) cc_final: 0.6650 (tppt) REVERT: C 338 GLU cc_start: 0.7531 (mt-10) cc_final: 0.6900 (tt0) REVERT: C 369 LYS cc_start: 0.7592 (ttmt) cc_final: 0.7085 (tttt) REVERT: C 372 GLU cc_start: 0.7944 (mm-30) cc_final: 0.7436 (mm-30) REVERT: C 379 ARG cc_start: 0.6826 (mtp180) cc_final: 0.6200 (tmm160) REVERT: B 314 ASP cc_start: 0.7678 (t0) cc_final: 0.7450 (t0) REVERT: B 319 THR cc_start: 0.7503 (p) cc_final: 0.7103 (t) REVERT: B 340 LYS cc_start: 0.7860 (tttt) cc_final: 0.7485 (tmtp) REVERT: B 343 LYS cc_start: 0.6628 (ttmt) cc_final: 0.6248 (ttpt) REVERT: B 369 LYS cc_start: 0.7147 (mtpt) cc_final: 0.6801 (ttmm) REVERT: B 370 LYS cc_start: 0.7817 (OUTLIER) cc_final: 0.7378 (tmtm) REVERT: B 375 LYS cc_start: 0.7249 (tttt) cc_final: 0.6728 (ttpt) REVERT: E 311 LYS cc_start: 0.8124 (pttt) cc_final: 0.6422 (tppt) REVERT: E 319 THR cc_start: 0.7819 (p) cc_final: 0.7467 (t) REVERT: E 340 LYS cc_start: 0.7976 (tttt) cc_final: 0.7595 (tmtp) REVERT: E 342 GLU cc_start: 0.7297 (mt-10) cc_final: 0.7091 (mt-10) REVERT: E 343 LYS cc_start: 0.7029 (ttmt) cc_final: 0.6754 (ttpt) REVERT: E 369 LYS cc_start: 0.7197 (mtpt) cc_final: 0.6916 (tttm) REVERT: E 370 LYS cc_start: 0.8286 (OUTLIER) cc_final: 0.7697 (tmtm) REVERT: E 375 LYS cc_start: 0.7544 (tttt) cc_final: 0.7000 (tppp) REVERT: F 311 LYS cc_start: 0.8257 (pttt) cc_final: 0.7669 (pttm) REVERT: F 314 ASP cc_start: 0.7311 (t0) cc_final: 0.7051 (t0) REVERT: F 316 SER cc_start: 0.8063 (m) cc_final: 0.7610 (p) REVERT: F 342 GLU cc_start: 0.7288 (mt-10) cc_final: 0.7025 (mp0) REVERT: F 343 LYS cc_start: 0.7234 (ttmm) cc_final: 0.6394 (mtmm) REVERT: F 351 GLN cc_start: 0.8488 (tt0) cc_final: 0.8221 (tt0) REVERT: F 369 LYS cc_start: 0.7711 (mtpt) cc_final: 0.7357 (tttm) REVERT: F 375 LYS cc_start: 0.8024 (tttt) cc_final: 0.7741 (ttpt) outliers start: 9 outliers final: 3 residues processed: 113 average time/residue: 2.7683 time to fit residues: 320.3668 Evaluate side-chains 88 residues out of total 387 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 83 time to evaluate : 0.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 375 LYS Chi-restraints excluded: chain D residue 324 SER Chi-restraints excluded: chain C residue 307 GLN Chi-restraints excluded: chain B residue 370 LYS Chi-restraints excluded: chain E residue 370 LYS 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: 6.9990 chunk 10 optimal weight: 6.9990 chunk 38 optimal weight: 7.9990 chunk 41 optimal weight: 10.0000 chunk 34 optimal weight: 6.9990 chunk 37 optimal weight: 0.9980 chunk 13 optimal weight: 6.9990 chunk 30 optimal weight: 3.9990 chunk 28 optimal weight: 0.0270 chunk 19 optimal weight: 5.9990 overall best weight: 3.6044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 351 GLN E 351 GLN F 359 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7575 moved from start: 0.4413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 3429 Z= 0.312 Angle : 0.644 4.944 4590 Z= 0.323 Chirality : 0.053 0.140 519 Planarity : 0.003 0.025 582 Dihedral : 5.629 18.446 450 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 1.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 5.17 % Allowed : 12.14 % Favored : 82.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.38 (0.34), residues: 429 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.05 (0.26), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS B 374 PHE 0.006 0.001 PHE D 378 TYR 0.014 0.003 TYR C 310 ARG 0.003 0.000 ARG C 379 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 387 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 83 time to evaluate : 0.591 Fit side-chains revert: symmetry clash REVERT: A 336 GLN cc_start: 0.7063 (tt0) cc_final: 0.6744 (mt0) REVERT: A 338 GLU cc_start: 0.7396 (mt-10) cc_final: 0.6889 (tt0) REVERT: A 340 LYS cc_start: 0.7524 (OUTLIER) cc_final: 0.7242 (mtmt) REVERT: A 369 LYS cc_start: 0.7417 (ttmt) cc_final: 0.6750 (tttt) REVERT: D 314 ASP cc_start: 0.8241 (t70) cc_final: 0.7786 (t70) REVERT: D 317 LYS cc_start: 0.7863 (pttt) cc_final: 0.7486 (ptmm) REVERT: D 338 GLU cc_start: 0.7824 (mt-10) cc_final: 0.7266 (tt0) REVERT: D 340 LYS cc_start: 0.8131 (ttmm) cc_final: 0.7870 (ttmt) REVERT: D 349 ARG cc_start: 0.6066 (mtm180) cc_final: 0.5369 (mtt180) REVERT: D 369 LYS cc_start: 0.7995 (ttmt) cc_final: 0.7348 (tttt) REVERT: D 372 GLU cc_start: 0.7688 (mm-30) cc_final: 0.7106 (mm-30) REVERT: C 338 GLU cc_start: 0.7618 (mt-10) cc_final: 0.6838 (tt0) REVERT: C 369 LYS cc_start: 0.7552 (ttmt) cc_final: 0.7009 (tttt) REVERT: C 372 GLU cc_start: 0.8134 (mm-30) cc_final: 0.7572 (mm-30) REVERT: C 379 ARG cc_start: 0.6975 (mtp180) cc_final: 0.6489 (tmm160) REVERT: B 319 THR cc_start: 0.7530 (p) cc_final: 0.7181 (m) REVERT: B 340 LYS cc_start: 0.7846 (tttt) cc_final: 0.7472 (tmtp) REVERT: B 369 LYS cc_start: 0.7129 (mtpt) cc_final: 0.6803 (ttpt) REVERT: B 375 LYS cc_start: 0.7352 (tttt) cc_final: 0.6862 (ttpt) REVERT: E 311 LYS cc_start: 0.8187 (pttt) cc_final: 0.6400 (tppt) REVERT: E 321 LYS cc_start: 0.7297 (mttt) cc_final: 0.7009 (mtmt) REVERT: E 340 LYS cc_start: 0.7950 (tttt) cc_final: 0.7556 (tmtp) REVERT: E 342 GLU cc_start: 0.7382 (mt-10) cc_final: 0.7109 (mt-10) REVERT: E 343 LYS cc_start: 0.7066 (ttmt) cc_final: 0.5679 (tppt) REVERT: E 369 LYS cc_start: 0.7175 (mtpt) cc_final: 0.6850 (tttt) REVERT: E 375 LYS cc_start: 0.7539 (tttt) cc_final: 0.6867 (ttpt) REVERT: F 314 ASP cc_start: 0.7531 (t0) cc_final: 0.7096 (t70) REVERT: F 316 SER cc_start: 0.8002 (m) cc_final: 0.7654 (p) REVERT: F 340 LYS cc_start: 0.8464 (OUTLIER) cc_final: 0.8015 (tmtp) REVERT: F 342 GLU cc_start: 0.7539 (mt-10) cc_final: 0.7316 (mp0) REVERT: F 351 GLN cc_start: 0.8492 (tt0) cc_final: 0.8259 (tt0) REVERT: F 369 LYS cc_start: 0.7652 (mtpt) cc_final: 0.7365 (ttpt) REVERT: F 375 LYS cc_start: 0.8027 (tttt) cc_final: 0.7750 (ttpt) outliers start: 20 outliers final: 6 residues processed: 93 average time/residue: 3.0790 time to fit residues: 292.8783 Evaluate side-chains 84 residues out of total 387 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 76 time to evaluate : 0.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 340 LYS Chi-restraints excluded: chain A residue 341 SER Chi-restraints excluded: chain C residue 307 GLN Chi-restraints excluded: chain C residue 375 LYS Chi-restraints excluded: chain C residue 377 THR Chi-restraints excluded: chain B residue 370 LYS Chi-restraints excluded: chain F residue 319 THR Chi-restraints excluded: chain F residue 340 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 4 optimal weight: 7.9990 chunk 18 optimal weight: 0.9990 chunk 25 optimal weight: 7.9990 chunk 38 optimal weight: 6.9990 chunk 40 optimal weight: 0.5980 chunk 20 optimal weight: 7.9990 chunk 36 optimal weight: 1.9990 chunk 10 optimal weight: 4.9990 chunk 33 optimal weight: 4.9990 chunk 23 optimal weight: 3.9990 chunk 0 optimal weight: 7.9990 overall best weight: 2.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 351 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7573 moved from start: 0.4787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3429 Z= 0.217 Angle : 0.566 4.717 4590 Z= 0.279 Chirality : 0.051 0.132 519 Planarity : 0.003 0.024 582 Dihedral : 5.149 16.163 450 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 0.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 3.62 % Allowed : 12.92 % Favored : 83.46 % 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: -1.47 (0.34), residues: 429 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.11 (0.26), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 374 PHE 0.005 0.001 PHE D 378 TYR 0.009 0.002 TYR F 310 ARG 0.001 0.000 ARG C 379 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 387 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 80 time to evaluate : 0.604 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 338 GLU cc_start: 0.7402 (mt-10) cc_final: 0.6914 (mt-10) REVERT: A 340 LYS cc_start: 0.7483 (OUTLIER) cc_final: 0.7193 (mtmt) REVERT: A 369 LYS cc_start: 0.7425 (ttmt) cc_final: 0.6746 (tttt) REVERT: D 314 ASP cc_start: 0.8293 (t70) cc_final: 0.7826 (t70) REVERT: D 317 LYS cc_start: 0.7893 (pttt) cc_final: 0.7508 (ptmm) REVERT: D 338 GLU cc_start: 0.7773 (mt-10) cc_final: 0.7218 (tt0) REVERT: D 340 LYS cc_start: 0.8100 (ttmm) cc_final: 0.7792 (ttmt) REVERT: D 349 ARG cc_start: 0.6105 (mtm180) cc_final: 0.5410 (mtt180) REVERT: D 369 LYS cc_start: 0.7978 (ttmt) cc_final: 0.7326 (tttt) REVERT: C 336 GLN cc_start: 0.7690 (mt0) cc_final: 0.7456 (mt0) REVERT: C 338 GLU cc_start: 0.7629 (mt-10) cc_final: 0.6863 (tt0) REVERT: C 340 LYS cc_start: 0.7618 (OUTLIER) cc_final: 0.7256 (mttt) REVERT: C 369 LYS cc_start: 0.7550 (ttmt) cc_final: 0.6997 (tttt) REVERT: C 372 GLU cc_start: 0.8012 (mm-30) cc_final: 0.7679 (mm-30) REVERT: C 379 ARG cc_start: 0.7046 (mtp180) cc_final: 0.6520 (tmm160) REVERT: B 319 THR cc_start: 0.7567 (p) cc_final: 0.7223 (m) REVERT: B 340 LYS cc_start: 0.7839 (tttt) cc_final: 0.7476 (tmtp) REVERT: B 369 LYS cc_start: 0.7126 (mtpt) cc_final: 0.6799 (ttpt) REVERT: B 375 LYS cc_start: 0.7396 (tttt) cc_final: 0.7036 (ttpt) REVERT: E 311 LYS cc_start: 0.8160 (pttt) cc_final: 0.6380 (tppt) REVERT: E 319 THR cc_start: 0.7828 (p) cc_final: 0.7333 (t) REVERT: E 340 LYS cc_start: 0.7967 (tttt) cc_final: 0.7578 (tmtp) REVERT: E 342 GLU cc_start: 0.7320 (mt-10) cc_final: 0.7116 (mt-10) REVERT: E 343 LYS cc_start: 0.7215 (ttmt) cc_final: 0.6876 (ttpt) REVERT: E 369 LYS cc_start: 0.7193 (mtpt) cc_final: 0.6875 (tttt) REVERT: E 375 LYS cc_start: 0.7568 (tttt) cc_final: 0.6905 (ttpt) REVERT: F 314 ASP cc_start: 0.7410 (t0) cc_final: 0.7019 (t70) REVERT: F 316 SER cc_start: 0.8079 (m) cc_final: 0.7821 (p) REVERT: F 340 LYS cc_start: 0.8451 (OUTLIER) cc_final: 0.7998 (tmtp) REVERT: F 342 GLU cc_start: 0.7597 (mt-10) cc_final: 0.7341 (mp0) REVERT: F 351 GLN cc_start: 0.8503 (tt0) cc_final: 0.8263 (tt0) REVERT: F 369 LYS cc_start: 0.7675 (mtpt) cc_final: 0.7400 (ttpt) REVERT: F 375 LYS cc_start: 0.8079 (tttt) cc_final: 0.7626 (ttpt) outliers start: 14 outliers final: 4 residues processed: 89 average time/residue: 3.0024 time to fit residues: 273.3192 Evaluate side-chains 88 residues out of total 387 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 81 time to evaluate : 0.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 340 LYS Chi-restraints excluded: chain A residue 341 SER Chi-restraints excluded: chain D residue 324 SER Chi-restraints excluded: chain C residue 307 GLN Chi-restraints excluded: chain C residue 340 LYS Chi-restraints excluded: chain B residue 370 LYS Chi-restraints excluded: chain F residue 340 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 30 optimal weight: 5.9990 chunk 16 optimal weight: 5.9990 chunk 34 optimal weight: 6.9990 chunk 28 optimal weight: 4.9990 chunk 0 optimal weight: 7.9990 chunk 20 optimal weight: 7.9990 chunk 36 optimal weight: 0.7980 chunk 10 optimal weight: 5.9990 chunk 13 optimal weight: 2.9990 chunk 8 optimal weight: 7.9990 chunk 23 optimal weight: 1.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 336 GLN E 351 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7586 moved from start: 0.4932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 3429 Z= 0.288 Angle : 0.593 4.658 4590 Z= 0.295 Chirality : 0.052 0.137 519 Planarity : 0.003 0.027 582 Dihedral : 5.256 16.938 450 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 1.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 3.10 % Allowed : 14.47 % Favored : 82.43 % 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 (0.34), residues: 429 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.17 (0.26), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 374 PHE 0.005 0.001 PHE D 378 TYR 0.011 0.003 TYR C 310 ARG 0.002 0.000 ARG C 379 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 387 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 74 time to evaluate : 0.582 Fit side-chains revert: symmetry clash REVERT: A 338 GLU cc_start: 0.7311 (mt-10) cc_final: 0.6890 (mt-10) REVERT: A 340 LYS cc_start: 0.7519 (OUTLIER) cc_final: 0.7191 (mtmt) REVERT: A 369 LYS cc_start: 0.7397 (ttmt) cc_final: 0.6660 (tttt) REVERT: D 314 ASP cc_start: 0.8260 (t70) cc_final: 0.7776 (t70) REVERT: D 317 LYS cc_start: 0.7904 (pttt) cc_final: 0.7497 (ptmm) REVERT: D 338 GLU cc_start: 0.7809 (mt-10) cc_final: 0.7180 (tt0) REVERT: D 340 LYS cc_start: 0.8126 (ttmm) cc_final: 0.7814 (ttmt) REVERT: D 349 ARG cc_start: 0.6002 (mtm180) cc_final: 0.5385 (mtt180) REVERT: D 369 LYS cc_start: 0.7998 (ttmt) cc_final: 0.7333 (tttt) REVERT: C 336 GLN cc_start: 0.7749 (mt0) cc_final: 0.7472 (mt0) REVERT: C 338 GLU cc_start: 0.7610 (mt-10) cc_final: 0.6848 (tt0) REVERT: C 340 LYS cc_start: 0.7562 (OUTLIER) cc_final: 0.7251 (mttt) REVERT: C 369 LYS cc_start: 0.7548 (ttmt) cc_final: 0.6977 (tttt) REVERT: C 372 GLU cc_start: 0.8097 (mm-30) cc_final: 0.7550 (mm-30) REVERT: C 379 ARG cc_start: 0.7072 (mtp180) cc_final: 0.6575 (tmm160) REVERT: B 319 THR cc_start: 0.7537 (p) cc_final: 0.7310 (m) REVERT: B 322 CYS cc_start: 0.7759 (p) cc_final: 0.7552 (m) REVERT: B 340 LYS cc_start: 0.7842 (tttt) cc_final: 0.7469 (tmtp) REVERT: B 369 LYS cc_start: 0.7142 (mtpt) cc_final: 0.6803 (ttpt) REVERT: E 311 LYS cc_start: 0.8198 (pttt) cc_final: 0.6418 (tppt) REVERT: E 340 LYS cc_start: 0.7929 (tttt) cc_final: 0.7546 (tmtp) REVERT: E 342 GLU cc_start: 0.7422 (mt-10) cc_final: 0.7126 (mt-10) REVERT: E 343 LYS cc_start: 0.7168 (ttmt) cc_final: 0.5716 (tppt) REVERT: E 369 LYS cc_start: 0.7168 (mtpt) cc_final: 0.6827 (tttt) REVERT: E 375 LYS cc_start: 0.7569 (tttt) cc_final: 0.6944 (mtpp) REVERT: F 314 ASP cc_start: 0.7470 (t0) cc_final: 0.7005 (t70) REVERT: F 316 SER cc_start: 0.8046 (m) cc_final: 0.7744 (p) REVERT: F 340 LYS cc_start: 0.8484 (OUTLIER) cc_final: 0.8033 (tmtp) REVERT: F 342 GLU cc_start: 0.7640 (mt-10) cc_final: 0.7341 (pm20) REVERT: F 369 LYS cc_start: 0.7641 (mtpt) cc_final: 0.7383 (ttpt) REVERT: F 375 LYS cc_start: 0.8192 (tttt) cc_final: 0.7521 (ttpt) outliers start: 12 outliers final: 3 residues processed: 81 average time/residue: 3.1860 time to fit residues: 263.6833 Evaluate side-chains 77 residues out of total 387 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 71 time to evaluate : 0.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 340 LYS Chi-restraints excluded: chain A residue 341 SER Chi-restraints excluded: chain C residue 307 GLN Chi-restraints excluded: chain C residue 340 LYS Chi-restraints excluded: chain B residue 370 LYS Chi-restraints excluded: chain F residue 340 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 10 optimal weight: 6.9990 chunk 40 optimal weight: 4.9990 chunk 33 optimal weight: 2.9990 chunk 18 optimal weight: 4.9990 chunk 3 optimal weight: 0.9990 chunk 13 optimal weight: 5.9990 chunk 21 optimal weight: 6.9990 chunk 39 optimal weight: 6.9990 chunk 4 optimal weight: 3.9990 chunk 23 optimal weight: 6.9990 chunk 29 optimal weight: 0.8980 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 351 GLN F 351 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7583 moved from start: 0.5078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 3429 Z= 0.241 Angle : 0.560 4.887 4590 Z= 0.277 Chirality : 0.051 0.134 519 Planarity : 0.003 0.027 582 Dihedral : 5.054 16.008 450 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 1.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 3.62 % Allowed : 14.99 % Favored : 81.40 % 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: -1.58 (0.34), residues: 429 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.20 (0.26), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 374 PHE 0.003 0.001 PHE D 378 TYR 0.010 0.002 TYR A 310 ARG 0.001 0.000 ARG C 379 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 387 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 77 time to evaluate : 0.478 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 338 GLU cc_start: 0.7266 (mt-10) cc_final: 0.6856 (mt-10) REVERT: A 340 LYS cc_start: 0.7488 (OUTLIER) cc_final: 0.7154 (mtmt) REVERT: A 369 LYS cc_start: 0.7425 (ttmt) cc_final: 0.6628 (tttt) REVERT: A 372 GLU cc_start: 0.7688 (OUTLIER) cc_final: 0.7383 (tt0) REVERT: D 314 ASP cc_start: 0.8281 (t70) cc_final: 0.7807 (t70) REVERT: D 317 LYS cc_start: 0.7905 (pttt) cc_final: 0.7482 (ptmm) REVERT: D 338 GLU cc_start: 0.7741 (mt-10) cc_final: 0.7075 (tt0) REVERT: D 340 LYS cc_start: 0.8112 (ttmm) cc_final: 0.7614 (mttt) REVERT: D 349 ARG cc_start: 0.5989 (mtm180) cc_final: 0.5371 (mtt180) REVERT: D 369 LYS cc_start: 0.7973 (ttmt) cc_final: 0.7297 (tttt) REVERT: C 338 GLU cc_start: 0.7618 (mt-10) cc_final: 0.6851 (tt0) REVERT: C 340 LYS cc_start: 0.7588 (OUTLIER) cc_final: 0.7241 (mttt) REVERT: C 369 LYS cc_start: 0.7541 (ttmt) cc_final: 0.6968 (tttt) REVERT: C 372 GLU cc_start: 0.8077 (mm-30) cc_final: 0.7599 (mm-30) REVERT: C 379 ARG cc_start: 0.7021 (mtp180) cc_final: 0.6444 (tmm160) REVERT: B 319 THR cc_start: 0.7547 (p) cc_final: 0.7336 (m) REVERT: B 340 LYS cc_start: 0.7834 (tttt) cc_final: 0.7483 (tmtp) REVERT: B 343 LYS cc_start: 0.6439 (ttmm) cc_final: 0.5547 (tttt) REVERT: B 369 LYS cc_start: 0.7126 (mtpt) cc_final: 0.6792 (ttpt) REVERT: E 311 LYS cc_start: 0.8176 (pttt) cc_final: 0.6422 (tppt) REVERT: E 340 LYS cc_start: 0.7950 (tttt) cc_final: 0.7569 (tmtp) REVERT: E 342 GLU cc_start: 0.7441 (mt-10) cc_final: 0.7151 (mt-10) REVERT: E 343 LYS cc_start: 0.7206 (ttmt) cc_final: 0.5754 (tppt) REVERT: E 369 LYS cc_start: 0.7151 (mtpt) cc_final: 0.6823 (tttt) REVERT: E 375 LYS cc_start: 0.7589 (tttt) cc_final: 0.6959 (mtpp) REVERT: F 314 ASP cc_start: 0.7351 (t0) cc_final: 0.6904 (t0) REVERT: F 316 SER cc_start: 0.7956 (m) cc_final: 0.7653 (p) REVERT: F 338 GLU cc_start: 0.7894 (OUTLIER) cc_final: 0.7628 (tt0) REVERT: F 340 LYS cc_start: 0.8458 (OUTLIER) cc_final: 0.7963 (tmtp) REVERT: F 342 GLU cc_start: 0.7699 (mt-10) cc_final: 0.7421 (pm20) REVERT: F 343 LYS cc_start: 0.7202 (ttmm) cc_final: 0.6383 (tttm) REVERT: F 369 LYS cc_start: 0.7654 (mtpt) cc_final: 0.7387 (ttpt) REVERT: F 375 LYS cc_start: 0.8172 (tttt) cc_final: 0.7528 (mtpp) outliers start: 14 outliers final: 3 residues processed: 85 average time/residue: 3.1038 time to fit residues: 270.1264 Evaluate side-chains 81 residues out of total 387 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 73 time to evaluate : 0.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 340 LYS Chi-restraints excluded: chain A residue 341 SER Chi-restraints excluded: chain A residue 372 GLU Chi-restraints excluded: chain C residue 307 GLN Chi-restraints excluded: chain C residue 340 LYS Chi-restraints excluded: chain E residue 372 GLU Chi-restraints excluded: chain F residue 338 GLU Chi-restraints excluded: chain F residue 340 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 22 optimal weight: 6.9990 chunk 34 optimal weight: 5.9990 chunk 40 optimal weight: 0.5980 chunk 25 optimal weight: 7.9990 chunk 24 optimal weight: 5.9990 chunk 18 optimal weight: 4.9990 chunk 16 optimal weight: 3.9990 chunk 12 optimal weight: 5.9990 chunk 7 optimal weight: 0.6980 chunk 27 optimal weight: 0.8980 chunk 20 optimal weight: 2.9990 overall best weight: 1.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 351 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7578 moved from start: 0.5211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3429 Z= 0.186 Angle : 0.517 4.584 4590 Z= 0.256 Chirality : 0.051 0.132 519 Planarity : 0.003 0.026 582 Dihedral : 4.772 15.093 450 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 0.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 3.36 % Allowed : 15.50 % Favored : 81.14 % 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: -1.58 (0.34), residues: 429 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.20 (0.26), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS D 374 PHE 0.002 0.001 PHE B 346 TYR 0.008 0.002 TYR B 310 ARG 0.001 0.000 ARG C 379 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 387 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 77 time to evaluate : 0.587 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 338 GLU cc_start: 0.7280 (mt-10) cc_final: 0.6884 (mt-10) REVERT: A 340 LYS cc_start: 0.7439 (OUTLIER) cc_final: 0.6658 (mtmt) REVERT: A 369 LYS cc_start: 0.7426 (ttmt) cc_final: 0.6670 (tttt) REVERT: A 372 GLU cc_start: 0.7677 (OUTLIER) cc_final: 0.7347 (tt0) REVERT: D 314 ASP cc_start: 0.8327 (t70) cc_final: 0.7881 (t70) REVERT: D 317 LYS cc_start: 0.7903 (pttt) cc_final: 0.7488 (ptmm) REVERT: D 338 GLU cc_start: 0.7733 (mt-10) cc_final: 0.7145 (tt0) REVERT: D 340 LYS cc_start: 0.8110 (ttmm) cc_final: 0.7524 (mttt) REVERT: D 349 ARG cc_start: 0.6107 (mtm180) cc_final: 0.5474 (mtt180) REVERT: D 369 LYS cc_start: 0.7979 (ttmt) cc_final: 0.7317 (tttt) REVERT: C 338 GLU cc_start: 0.7583 (mt-10) cc_final: 0.6843 (tt0) REVERT: C 340 LYS cc_start: 0.7600 (OUTLIER) cc_final: 0.7279 (mttt) REVERT: C 369 LYS cc_start: 0.7500 (ttmt) cc_final: 0.6924 (tttt) REVERT: C 372 GLU cc_start: 0.8073 (mm-30) cc_final: 0.7604 (mm-30) REVERT: C 379 ARG cc_start: 0.7035 (mtp180) cc_final: 0.6371 (tmm160) REVERT: B 340 LYS cc_start: 0.7833 (tttt) cc_final: 0.7466 (tmtp) REVERT: B 369 LYS cc_start: 0.7113 (mtpt) cc_final: 0.6796 (ttpt) REVERT: E 311 LYS cc_start: 0.8195 (pttt) cc_final: 0.6426 (tppt) REVERT: E 340 LYS cc_start: 0.8008 (tttt) cc_final: 0.7616 (tmtp) REVERT: E 342 GLU cc_start: 0.7421 (mt-10) cc_final: 0.7134 (mt-10) REVERT: E 343 LYS cc_start: 0.7199 (ttmt) cc_final: 0.5756 (tppt) REVERT: E 369 LYS cc_start: 0.7195 (mtpt) cc_final: 0.6896 (tttm) REVERT: E 375 LYS cc_start: 0.7591 (tttt) cc_final: 0.6959 (mtpp) REVERT: F 314 ASP cc_start: 0.7345 (t0) cc_final: 0.6876 (t0) REVERT: F 316 SER cc_start: 0.8001 (m) cc_final: 0.7702 (p) REVERT: F 338 GLU cc_start: 0.7887 (OUTLIER) cc_final: 0.7625 (tt0) REVERT: F 340 LYS cc_start: 0.8443 (OUTLIER) cc_final: 0.7932 (tmtp) REVERT: F 342 GLU cc_start: 0.7683 (mt-10) cc_final: 0.7441 (pm20) REVERT: F 343 LYS cc_start: 0.7207 (ttmm) cc_final: 0.6427 (tttt) REVERT: F 369 LYS cc_start: 0.7662 (mtpt) cc_final: 0.7373 (ttpt) REVERT: F 375 LYS cc_start: 0.8170 (tttt) cc_final: 0.7537 (mtpp) outliers start: 13 outliers final: 3 residues processed: 85 average time/residue: 3.0013 time to fit residues: 261.1672 Evaluate side-chains 80 residues out of total 387 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 72 time to evaluate : 0.687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 340 LYS Chi-restraints excluded: chain A residue 341 SER Chi-restraints excluded: chain A residue 372 GLU Chi-restraints excluded: chain D residue 324 SER Chi-restraints excluded: chain C residue 307 GLN Chi-restraints excluded: chain C residue 340 LYS Chi-restraints excluded: chain F residue 338 GLU Chi-restraints excluded: chain F residue 340 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 3 optimal weight: 8.9990 chunk 31 optimal weight: 6.9990 chunk 36 optimal weight: 4.9990 chunk 38 optimal weight: 6.9990 chunk 35 optimal weight: 3.9990 chunk 37 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 chunk 16 optimal weight: 0.4980 chunk 29 optimal weight: 1.9990 chunk 11 optimal weight: 0.8980 chunk 34 optimal weight: 5.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 362 HIS E 351 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7573 moved from start: 0.5335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 3429 Z= 0.155 Angle : 0.507 5.165 4590 Z= 0.248 Chirality : 0.051 0.127 519 Planarity : 0.003 0.025 582 Dihedral : 4.526 14.755 450 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 0.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 2.58 % Allowed : 15.25 % Favored : 82.17 % 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: -1.56 (0.35), residues: 429 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.18 (0.27), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 374 PHE 0.002 0.000 PHE B 346 TYR 0.007 0.001 TYR B 310 ARG 0.001 0.000 ARG A 379 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 387 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 83 time to evaluate : 0.609 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 338 GLU cc_start: 0.7271 (mt-10) cc_final: 0.6800 (mt-10) REVERT: A 369 LYS cc_start: 0.7454 (ttmt) cc_final: 0.6701 (tttt) REVERT: A 372 GLU cc_start: 0.7668 (OUTLIER) cc_final: 0.7341 (tt0) REVERT: D 314 ASP cc_start: 0.8338 (t70) cc_final: 0.7884 (t70) REVERT: D 317 LYS cc_start: 0.7884 (pttt) cc_final: 0.7492 (ptmm) REVERT: D 338 GLU cc_start: 0.7706 (mt-10) cc_final: 0.7124 (tt0) REVERT: D 340 LYS cc_start: 0.8074 (ttmm) cc_final: 0.7575 (mttt) REVERT: D 349 ARG cc_start: 0.6085 (mtm180) cc_final: 0.5446 (mtt180) REVERT: D 369 LYS cc_start: 0.7971 (ttmt) cc_final: 0.7315 (tttt) REVERT: C 336 GLN cc_start: 0.7765 (mt0) cc_final: 0.7037 (mp-120) REVERT: C 338 GLU cc_start: 0.7581 (mt-10) cc_final: 0.6854 (tt0) REVERT: C 340 LYS cc_start: 0.7645 (OUTLIER) cc_final: 0.7262 (mttt) REVERT: C 369 LYS cc_start: 0.7486 (ttmt) cc_final: 0.6929 (tttt) REVERT: C 372 GLU cc_start: 0.8024 (mm-30) cc_final: 0.7562 (mm-30) REVERT: C 379 ARG cc_start: 0.7047 (mtp180) cc_final: 0.6396 (tmm160) REVERT: B 340 LYS cc_start: 0.7834 (tttt) cc_final: 0.7400 (tmtp) REVERT: B 343 LYS cc_start: 0.6460 (ttmm) cc_final: 0.5588 (tttm) REVERT: B 369 LYS cc_start: 0.7138 (mtpt) cc_final: 0.6812 (ttpt) REVERT: E 311 LYS cc_start: 0.8179 (pttt) cc_final: 0.6404 (tppt) REVERT: E 340 LYS cc_start: 0.8028 (tttt) cc_final: 0.7595 (tmtp) REVERT: E 342 GLU cc_start: 0.7380 (mt-10) cc_final: 0.7091 (mt-10) REVERT: E 343 LYS cc_start: 0.7172 (ttmt) cc_final: 0.5754 (tppt) REVERT: E 369 LYS cc_start: 0.7190 (mtpt) cc_final: 0.6907 (tttm) REVERT: E 375 LYS cc_start: 0.7584 (tttt) cc_final: 0.6932 (mtpp) REVERT: F 314 ASP cc_start: 0.7275 (t0) cc_final: 0.6817 (t0) REVERT: F 316 SER cc_start: 0.8004 (m) cc_final: 0.7760 (p) REVERT: F 338 GLU cc_start: 0.7886 (OUTLIER) cc_final: 0.7616 (tt0) REVERT: F 340 LYS cc_start: 0.8404 (OUTLIER) cc_final: 0.7831 (tmtm) REVERT: F 342 GLU cc_start: 0.7750 (mt-10) cc_final: 0.7484 (pm20) REVERT: F 343 LYS cc_start: 0.7204 (ttmm) cc_final: 0.6447 (tttt) REVERT: F 369 LYS cc_start: 0.7644 (mtpt) cc_final: 0.7345 (ttpt) REVERT: F 375 LYS cc_start: 0.8178 (tttt) cc_final: 0.7547 (mtpp) outliers start: 10 outliers final: 3 residues processed: 88 average time/residue: 3.0122 time to fit residues: 271.1393 Evaluate side-chains 84 residues out of total 387 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 77 time to evaluate : 0.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 341 SER Chi-restraints excluded: chain A residue 372 GLU Chi-restraints excluded: chain D residue 324 SER Chi-restraints excluded: chain C residue 307 GLN Chi-restraints excluded: chain C residue 340 LYS Chi-restraints excluded: chain F residue 338 GLU Chi-restraints excluded: chain F residue 340 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 0.0970 chunk 37 optimal weight: 4.9990 chunk 24 optimal weight: 5.9990 chunk 39 optimal weight: 3.9990 chunk 18 optimal weight: 3.9990 chunk 27 optimal weight: 8.9990 chunk 41 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 33 optimal weight: 4.9990 chunk 3 optimal weight: 7.9990 chunk 25 optimal weight: 0.9980 overall best weight: 2.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 336 GLN E 351 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7581 moved from start: 0.5330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3429 Z= 0.194 Angle : 0.519 4.501 4590 Z= 0.257 Chirality : 0.051 0.129 519 Planarity : 0.003 0.025 582 Dihedral : 4.668 15.337 450 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 0.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 2.07 % Allowed : 16.54 % Favored : 81.40 % 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: -1.56 (0.35), residues: 429 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.18 (0.27), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 374 PHE 0.003 0.001 PHE D 378 TYR 0.008 0.002 TYR B 310 ARG 0.001 0.000 ARG C 379 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 387 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 78 time to evaluate : 0.568 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 338 GLU cc_start: 0.7276 (mt-10) cc_final: 0.6803 (mt-10) REVERT: D 314 ASP cc_start: 0.8307 (t70) cc_final: 0.7843 (t70) REVERT: D 317 LYS cc_start: 0.7921 (pttt) cc_final: 0.7522 (ptmm) REVERT: D 338 GLU cc_start: 0.7734 (mt-10) cc_final: 0.7107 (tt0) REVERT: D 340 LYS cc_start: 0.8066 (ttmm) cc_final: 0.7554 (mttt) REVERT: D 349 ARG cc_start: 0.6101 (mtm180) cc_final: 0.5453 (mtt180) REVERT: D 369 LYS cc_start: 0.7973 (ttmt) cc_final: 0.7311 (tttt) REVERT: C 336 GLN cc_start: 0.7783 (mt0) cc_final: 0.7038 (mp-120) REVERT: C 338 GLU cc_start: 0.7593 (mt-10) cc_final: 0.6837 (tt0) REVERT: C 340 LYS cc_start: 0.7589 (OUTLIER) cc_final: 0.7259 (mttt) REVERT: C 369 LYS cc_start: 0.7474 (ttmt) cc_final: 0.6906 (tttt) REVERT: C 372 GLU cc_start: 0.8085 (mm-30) cc_final: 0.7526 (mm-30) REVERT: C 379 ARG cc_start: 0.7027 (mtp180) cc_final: 0.6378 (tmm160) REVERT: B 340 LYS cc_start: 0.7857 (tttt) cc_final: 0.7383 (tmtp) REVERT: B 343 LYS cc_start: 0.6485 (ttmm) cc_final: 0.5671 (tttm) REVERT: B 369 LYS cc_start: 0.7130 (mtpt) cc_final: 0.6794 (ttpt) REVERT: E 311 LYS cc_start: 0.8201 (pttt) cc_final: 0.6413 (tppt) REVERT: E 340 LYS cc_start: 0.8023 (tttt) cc_final: 0.7603 (tmtp) REVERT: E 342 GLU cc_start: 0.7385 (mt-10) cc_final: 0.7124 (mt-10) REVERT: E 343 LYS cc_start: 0.7147 (ttmt) cc_final: 0.5791 (tppt) REVERT: E 369 LYS cc_start: 0.7203 (mtpt) cc_final: 0.6894 (tttm) REVERT: E 375 LYS cc_start: 0.7581 (tttt) cc_final: 0.6935 (mtpp) REVERT: F 314 ASP cc_start: 0.7289 (t0) cc_final: 0.6770 (t0) REVERT: F 316 SER cc_start: 0.7984 (m) cc_final: 0.7715 (p) REVERT: F 338 GLU cc_start: 0.7888 (OUTLIER) cc_final: 0.7628 (tt0) REVERT: F 340 LYS cc_start: 0.8424 (OUTLIER) cc_final: 0.7855 (tmtm) REVERT: F 342 GLU cc_start: 0.7742 (mt-10) cc_final: 0.7454 (pm20) REVERT: F 369 LYS cc_start: 0.7636 (mtpt) cc_final: 0.7334 (ttpt) REVERT: F 375 LYS cc_start: 0.8185 (tttt) cc_final: 0.7540 (mtpp) outliers start: 8 outliers final: 4 residues processed: 82 average time/residue: 3.1752 time to fit residues: 266.3830 Evaluate side-chains 82 residues out of total 387 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 75 time to evaluate : 0.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 341 SER Chi-restraints excluded: chain D residue 324 SER Chi-restraints excluded: chain C residue 307 GLN Chi-restraints excluded: chain C residue 340 LYS Chi-restraints excluded: chain E residue 372 GLU Chi-restraints excluded: chain F residue 338 GLU Chi-restraints excluded: chain F residue 340 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 20 optimal weight: 0.9980 chunk 26 optimal weight: 4.9990 chunk 35 optimal weight: 0.0870 chunk 10 optimal weight: 2.9990 chunk 30 optimal weight: 3.9990 chunk 4 optimal weight: 6.9990 chunk 9 optimal weight: 5.9990 chunk 33 optimal weight: 0.6980 chunk 13 optimal weight: 1.9990 chunk 34 optimal weight: 4.9990 chunk 6 optimal weight: 0.6980 overall best weight: 0.8960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 336 GLN E 351 GLN F 362 HIS F 368 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7562 moved from start: 0.5472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 3429 Z= 0.142 Angle : 0.498 5.886 4590 Z= 0.241 Chirality : 0.051 0.125 519 Planarity : 0.002 0.025 582 Dihedral : 4.329 14.489 450 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 1.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 1.55 % Allowed : 17.31 % Favored : 81.14 % 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: 429 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.16 (0.27), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS B 374 PHE 0.002 0.000 PHE B 346 TYR 0.007 0.001 TYR B 310 ARG 0.001 0.000 ARG D 349 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 387 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 82 time to evaluate : 0.572 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 338 GLU cc_start: 0.7265 (mt-10) cc_final: 0.6802 (mt-10) REVERT: A 369 LYS cc_start: 0.7473 (ttmt) cc_final: 0.6722 (tttt) REVERT: D 314 ASP cc_start: 0.8364 (t70) cc_final: 0.7899 (t70) REVERT: D 317 LYS cc_start: 0.7889 (pttt) cc_final: 0.7501 (ptmm) REVERT: D 336 GLN cc_start: 0.8175 (mt0) cc_final: 0.7675 (mp10) REVERT: D 338 GLU cc_start: 0.7692 (mt-10) cc_final: 0.7100 (tt0) REVERT: D 340 LYS cc_start: 0.8041 (ttmm) cc_final: 0.7566 (mttt) REVERT: D 349 ARG cc_start: 0.6123 (mtm180) cc_final: 0.5474 (mtt180) REVERT: D 369 LYS cc_start: 0.7961 (ttmt) cc_final: 0.7305 (tttt) REVERT: C 307 GLN cc_start: 0.7712 (OUTLIER) cc_final: 0.6792 (mm-40) REVERT: C 336 GLN cc_start: 0.7771 (mt0) cc_final: 0.6997 (mp-120) REVERT: C 338 GLU cc_start: 0.7546 (mt-10) cc_final: 0.6747 (tt0) REVERT: C 340 LYS cc_start: 0.7660 (mtmt) cc_final: 0.7254 (mttt) REVERT: C 369 LYS cc_start: 0.7465 (ttmt) cc_final: 0.6901 (tttt) REVERT: C 372 GLU cc_start: 0.8020 (mm-30) cc_final: 0.7556 (mm-30) REVERT: C 379 ARG cc_start: 0.6976 (mtp180) cc_final: 0.6337 (tmm160) REVERT: B 340 LYS cc_start: 0.7838 (tttt) cc_final: 0.7394 (tmtp) REVERT: B 343 LYS cc_start: 0.6540 (ttmm) cc_final: 0.5792 (tttm) REVERT: B 369 LYS cc_start: 0.7152 (mtpt) cc_final: 0.6833 (ttpt) REVERT: E 311 LYS cc_start: 0.8161 (pttt) cc_final: 0.6278 (tppt) REVERT: E 319 THR cc_start: 0.7788 (p) cc_final: 0.7487 (t) REVERT: E 340 LYS cc_start: 0.8036 (tttt) cc_final: 0.7615 (tmtp) REVERT: E 342 GLU cc_start: 0.7339 (mt-10) cc_final: 0.7072 (mt-10) REVERT: E 343 LYS cc_start: 0.7147 (ttmt) cc_final: 0.5741 (tppt) REVERT: E 369 LYS cc_start: 0.7213 (mtpt) cc_final: 0.6921 (tttm) REVERT: F 314 ASP cc_start: 0.7251 (t0) cc_final: 0.6797 (t0) REVERT: F 316 SER cc_start: 0.7939 (m) cc_final: 0.7692 (p) REVERT: F 338 GLU cc_start: 0.7887 (OUTLIER) cc_final: 0.7623 (tt0) REVERT: F 340 LYS cc_start: 0.8351 (OUTLIER) cc_final: 0.7791 (tmtm) REVERT: F 342 GLU cc_start: 0.7801 (mt-10) cc_final: 0.7498 (pm20) REVERT: F 343 LYS cc_start: 0.7206 (ttmm) cc_final: 0.6298 (tttm) REVERT: F 369 LYS cc_start: 0.7629 (mtpt) cc_final: 0.7326 (ttpt) REVERT: F 375 LYS cc_start: 0.8106 (tttt) cc_final: 0.7447 (ttpt) outliers start: 6 outliers final: 2 residues processed: 87 average time/residue: 2.8255 time to fit residues: 251.7389 Evaluate side-chains 84 residues out of total 387 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 79 time to evaluate : 0.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 341 SER Chi-restraints excluded: chain D residue 324 SER Chi-restraints excluded: chain C residue 307 GLN Chi-restraints excluded: chain F residue 338 GLU Chi-restraints excluded: chain F residue 340 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 29 optimal weight: 0.8980 chunk 1 optimal weight: 8.9990 chunk 24 optimal weight: 5.9990 chunk 38 optimal weight: 1.9990 chunk 22 optimal weight: 0.7980 chunk 28 optimal weight: 0.0770 chunk 26 optimal weight: 5.9990 chunk 25 optimal weight: 6.9990 chunk 16 optimal weight: 0.6980 chunk 15 optimal weight: 2.9990 chunk 41 optimal weight: 5.9990 overall best weight: 0.8940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 336 GLN E 351 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.131804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.120781 restraints weight = 13917.431| |-----------------------------------------------------------------------------| r_work (start): 0.3741 rms_B_bonded: 1.30 r_work: 0.3677 rms_B_bonded: 1.39 restraints_weight: 0.5000 r_work: 0.3611 rms_B_bonded: 2.45 restraints_weight: 0.2500 r_work (final): 0.3611 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8653 moved from start: 0.5534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 3429 Z= 0.143 Angle : 0.484 5.138 4590 Z= 0.236 Chirality : 0.051 0.126 519 Planarity : 0.002 0.024 582 Dihedral : 4.203 14.372 450 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 1.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 1.55 % Allowed : 17.83 % Favored : 80.62 % 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: -1.49 (0.35), residues: 429 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.13 (0.27), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS B 374 PHE 0.002 0.000 PHE B 346 TYR 0.006 0.001 TYR B 310 ARG 0.001 0.000 ARG A 349 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5394.68 seconds wall clock time: 93 minutes 21.23 seconds (5601.23 seconds total)