Starting phenix.real_space_refine on Mon Mar 11 03:52:06 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q8y_18265/03_2024/8q8y_18265.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q8y_18265/03_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_18265/03_2024/8q8y_18265.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q8y_18265/03_2024/8q8y_18265.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q8y_18265/03_2024/8q8y_18265.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q8y_18265/03_2024/8q8y_18265.pdb" } 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-5265/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: 3.32, per 1000 atoms: 0.48 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: 5.03 Conformation dependent library (CDL) restraints added in 735.7 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: 0.66 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: 2.23 Time building geometry restraints manager: 5.30 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 1.850 nonbonded pdb=" OD1 ASP F 314 " pdb=" HG SER F 316 " model vdw 1.567 1.850 nonbonded pdb=" OD1 ASP C 314 " pdb=" HG SER C 316 " model vdw 1.573 1.850 nonbonded pdb=" OD1 ASP D 314 " pdb=" HG SER D 316 " model vdw 1.594 1.850 nonbonded pdb=" OD1 ASP A 358 " pdb=" HG SER C 356 " model vdw 1.599 1.850 ... (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 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: 2.400 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: 11.540 Check model and map are aligned: 0.110 Set scattering table: 0.080 Process input model: 25.560 Find NCS groups from input model: 0.350 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:15.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.110 ------------------------------------------------------------------------------- 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 : 0.628 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: 2.8970 time to fit residues: 382.2871 Evaluate side-chains 85 residues out of total 387 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 85 time to evaluate : 0.587 ------------------------------------------------------------------------------- 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: 3.9990 chunk 17 optimal weight: 6.9990 chunk 10 optimal weight: 1.9990 chunk 21 optimal weight: 0.9980 chunk 32 optimal weight: 1.9990 chunk 12 optimal weight: 0.9980 chunk 20 optimal weight: 5.9990 chunk 24 optimal weight: 5.9990 chunk 38 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 368 ASN D 327 ASN D 368 ASN C 368 ASN F 327 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7474 moved from start: 0.3451 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= 0.178 Angle : 0.600 4.870 4590 Z= 0.302 Chirality : 0.052 0.129 519 Planarity : 0.003 0.021 582 Dihedral : 5.980 18.345 450 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 2.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % 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: -1.31 (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 0.003 0.001 HIS B 330 PHE 0.007 0.001 PHE E 346 TYR 0.007 0.001 TYR C 310 ARG 0.002 0.001 ARG C 379 *********************** 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 110 residues out of total 387 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 101 time to evaluate : 0.664 Fit side-chains REVERT: A 338 GLU cc_start: 0.7382 (mt-10) cc_final: 0.6813 (tt0) REVERT: A 369 LYS cc_start: 0.7398 (ttmt) cc_final: 0.6768 (tttt) REVERT: A 372 GLU cc_start: 0.7784 (mm-30) cc_final: 0.7046 (mm-30) REVERT: D 314 ASP cc_start: 0.8210 (t70) cc_final: 0.7763 (t70) REVERT: D 317 LYS cc_start: 0.7770 (pttt) cc_final: 0.7520 (ptmm) REVERT: D 338 GLU cc_start: 0.7663 (mt-10) cc_final: 0.7183 (tt0) REVERT: D 340 LYS cc_start: 0.8194 (ttmm) cc_final: 0.7916 (ttmt) REVERT: D 349 ARG cc_start: 0.6230 (mtm180) cc_final: 0.5487 (mtt180) REVERT: D 369 LYS cc_start: 0.7943 (ttmt) cc_final: 0.7301 (tttt) REVERT: D 372 GLU cc_start: 0.7501 (mm-30) cc_final: 0.6850 (mm-30) REVERT: C 311 LYS cc_start: 0.8108 (ttmt) cc_final: 0.6741 (tppt) REVERT: C 338 GLU cc_start: 0.7330 (mt-10) cc_final: 0.6737 (tt0) REVERT: C 369 LYS cc_start: 0.7606 (ttmt) cc_final: 0.7089 (tttt) REVERT: C 372 GLU cc_start: 0.8007 (mm-30) cc_final: 0.7416 (mm-30) REVERT: C 379 ARG cc_start: 0.6855 (mtp180) cc_final: 0.6291 (tmm160) REVERT: B 319 THR cc_start: 0.7493 (p) cc_final: 0.7121 (t) REVERT: B 340 LYS cc_start: 0.7832 (tttt) cc_final: 0.7457 (tmtp) REVERT: B 369 LYS cc_start: 0.7133 (mtpt) cc_final: 0.6748 (ttmm) REVERT: B 370 LYS cc_start: 0.7821 (OUTLIER) cc_final: 0.7417 (tmtm) REVERT: B 375 LYS cc_start: 0.7224 (tttt) cc_final: 0.6710 (ttpt) REVERT: E 311 LYS cc_start: 0.8125 (pttt) cc_final: 0.6408 (tppt) REVERT: E 319 THR cc_start: 0.7781 (p) cc_final: 0.7453 (t) REVERT: E 340 LYS cc_start: 0.7900 (tttt) cc_final: 0.7533 (tmtp) REVERT: E 342 GLU cc_start: 0.7342 (mt-10) cc_final: 0.7129 (mt-10) REVERT: E 343 LYS cc_start: 0.6943 (ttmt) cc_final: 0.6669 (ttpt) REVERT: E 369 LYS cc_start: 0.7194 (mtpt) cc_final: 0.6925 (tttm) REVERT: E 370 LYS cc_start: 0.8282 (OUTLIER) cc_final: 0.7718 (tmtm) REVERT: E 375 LYS cc_start: 0.7517 (tttt) cc_final: 0.6978 (tppp) REVERT: F 311 LYS cc_start: 0.8247 (pttt) cc_final: 0.7700 (pttm) REVERT: F 314 ASP cc_start: 0.7045 (t70) cc_final: 0.6724 (t0) REVERT: F 316 SER cc_start: 0.7937 (m) cc_final: 0.7451 (p) REVERT: F 342 GLU cc_start: 0.7266 (mt-10) cc_final: 0.7032 (pm20) REVERT: F 369 LYS cc_start: 0.7678 (mtpt) cc_final: 0.6665 (mptt) REVERT: F 372 GLU cc_start: 0.7480 (mm-30) cc_final: 0.7216 (mm-30) REVERT: F 375 LYS cc_start: 0.8008 (tttt) cc_final: 0.7698 (ttpt) outliers start: 9 outliers final: 2 residues processed: 105 average time/residue: 3.2221 time to fit residues: 345.9954 Evaluate side-chains 85 residues out of total 387 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 81 time to evaluate : 0.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 8.9990 chunk 10 optimal weight: 4.9990 chunk 38 optimal weight: 0.4980 chunk 41 optimal weight: 6.9990 chunk 34 optimal weight: 6.9990 chunk 37 optimal weight: 4.9990 chunk 13 optimal weight: 8.9990 chunk 30 optimal weight: 4.9990 chunk 28 optimal weight: 1.9990 chunk 19 optimal weight: 5.9990 overall best weight: 3.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 351 GLN C 336 GLN E 330 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7559 moved from start: 0.4419 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= 0.291 Angle : 0.634 4.797 4590 Z= 0.317 Chirality : 0.052 0.140 519 Planarity : 0.003 0.023 582 Dihedral : 5.640 18.319 450 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 2.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 4.39 % Allowed : 12.66 % Favored : 82.95 % 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: -1.37 (0.34), residues: 429 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.03 (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 0.002 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 97 residues out of total 387 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 80 time to evaluate : 0.566 Fit side-chains revert: symmetry clash REVERT: A 338 GLU cc_start: 0.7400 (mt-10) cc_final: 0.6902 (tt0) REVERT: A 340 LYS cc_start: 0.7556 (OUTLIER) cc_final: 0.7250 (mtmt) REVERT: A 369 LYS cc_start: 0.7332 (ttmt) cc_final: 0.6647 (tttt) REVERT: D 314 ASP cc_start: 0.8178 (t70) cc_final: 0.7702 (t70) REVERT: D 317 LYS cc_start: 0.7863 (pttt) cc_final: 0.7497 (ptmm) REVERT: D 338 GLU cc_start: 0.7770 (mt-10) cc_final: 0.7232 (tt0) REVERT: D 340 LYS cc_start: 0.8114 (ttmm) cc_final: 0.7860 (ttmt) REVERT: D 349 ARG cc_start: 0.6057 (mtm180) cc_final: 0.5368 (mtt180) REVERT: D 369 LYS cc_start: 0.8002 (ttmt) cc_final: 0.7356 (tttt) REVERT: D 372 GLU cc_start: 0.7565 (mm-30) cc_final: 0.7055 (mm-30) REVERT: C 338 GLU cc_start: 0.7469 (mt-10) cc_final: 0.6740 (tt0) REVERT: C 369 LYS cc_start: 0.7548 (ttmt) cc_final: 0.7003 (tttt) REVERT: C 372 GLU cc_start: 0.8116 (mm-30) cc_final: 0.7586 (mm-30) REVERT: C 379 ARG cc_start: 0.6979 (mtp180) cc_final: 0.6505 (tmm160) REVERT: B 319 THR cc_start: 0.7455 (p) cc_final: 0.7219 (m) REVERT: B 340 LYS cc_start: 0.7804 (tttt) cc_final: 0.7433 (tmtp) REVERT: B 369 LYS cc_start: 0.7171 (mtpt) cc_final: 0.6818 (ttpt) REVERT: B 372 GLU cc_start: 0.7892 (mt-10) cc_final: 0.7578 (mm-30) REVERT: B 375 LYS cc_start: 0.7373 (tttt) cc_final: 0.6877 (ttpt) REVERT: E 311 LYS cc_start: 0.8178 (pttt) cc_final: 0.6415 (tppt) REVERT: E 340 LYS cc_start: 0.7889 (tttt) cc_final: 0.7488 (tmtp) REVERT: E 342 GLU cc_start: 0.7378 (mt-10) cc_final: 0.7165 (mt-10) REVERT: E 343 LYS cc_start: 0.7057 (ttmt) cc_final: 0.6736 (ttpp) REVERT: E 369 LYS cc_start: 0.7197 (mtpt) cc_final: 0.6856 (tttm) REVERT: E 375 LYS cc_start: 0.7548 (tttt) cc_final: 0.6861 (ttpt) REVERT: F 314 ASP cc_start: 0.7254 (t0) cc_final: 0.6664 (t70) REVERT: F 316 SER cc_start: 0.8006 (m) cc_final: 0.7577 (p) REVERT: F 340 LYS cc_start: 0.8481 (OUTLIER) cc_final: 0.8035 (tmtp) REVERT: F 369 LYS cc_start: 0.7657 (mtpt) cc_final: 0.7382 (ttpt) REVERT: F 375 LYS cc_start: 0.8038 (tttt) cc_final: 0.7788 (ttpt) outliers start: 17 outliers final: 4 residues processed: 88 average time/residue: 3.1703 time to fit residues: 285.4362 Evaluate side-chains 81 residues out of total 387 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 75 time to evaluate : 0.601 ------------------------------------------------------------------------------- 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 B residue 370 LYS 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: 8.9990 chunk 38 optimal weight: 5.9990 chunk 40 optimal weight: 0.8980 chunk 20 optimal weight: 7.9990 chunk 36 optimal weight: 5.9990 chunk 10 optimal weight: 4.9990 chunk 33 optimal weight: 4.9990 chunk 23 optimal weight: 5.9990 chunk 0 optimal weight: 7.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 327 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7566 moved from start: 0.4774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 3429 Z= 0.287 Angle : 0.598 4.688 4590 Z= 0.299 Chirality : 0.051 0.132 519 Planarity : 0.003 0.025 582 Dihedral : 5.477 17.386 450 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 2.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 3.62 % Allowed : 13.70 % 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: -1.41 (0.34), residues: 429 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.07 (0.26), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS C 374 PHE 0.006 0.001 PHE D 378 TYR 0.011 0.002 TYR A 310 ARG 0.002 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 86 residues out of total 387 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 72 time to evaluate : 0.635 Fit side-chains revert: symmetry clash REVERT: A 338 GLU cc_start: 0.7382 (mt-10) cc_final: 0.6850 (tt0) REVERT: A 340 LYS cc_start: 0.7518 (OUTLIER) cc_final: 0.7185 (mtmt) REVERT: A 369 LYS cc_start: 0.7322 (ttmt) cc_final: 0.6597 (tttt) REVERT: D 314 ASP cc_start: 0.8182 (t70) cc_final: 0.7706 (t70) REVERT: D 317 LYS cc_start: 0.7872 (pttt) cc_final: 0.7472 (ptmm) REVERT: D 338 GLU cc_start: 0.7798 (mt-10) cc_final: 0.7250 (tt0) REVERT: D 340 LYS cc_start: 0.8133 (ttmm) cc_final: 0.7805 (ttmt) REVERT: D 349 ARG cc_start: 0.6046 (mtm180) cc_final: 0.5387 (mtt180) REVERT: D 369 LYS cc_start: 0.7976 (ttmt) cc_final: 0.7313 (tttt) REVERT: D 372 GLU cc_start: 0.7571 (mm-30) cc_final: 0.6968 (mm-30) REVERT: C 338 GLU cc_start: 0.7471 (mt-10) cc_final: 0.6822 (tt0) REVERT: C 369 LYS cc_start: 0.7537 (ttmt) cc_final: 0.6958 (tttt) REVERT: C 372 GLU cc_start: 0.8092 (mm-30) cc_final: 0.7529 (mm-30) REVERT: C 379 ARG cc_start: 0.6919 (mtp180) cc_final: 0.6378 (tmm160) REVERT: B 319 THR cc_start: 0.7494 (p) cc_final: 0.7244 (m) REVERT: B 322 CYS cc_start: 0.7924 (p) cc_final: 0.7572 (m) REVERT: B 340 LYS cc_start: 0.7843 (tttt) cc_final: 0.7472 (tmtp) REVERT: B 369 LYS cc_start: 0.7159 (mtpt) cc_final: 0.6821 (ttpt) REVERT: B 372 GLU cc_start: 0.7881 (OUTLIER) cc_final: 0.7588 (mm-30) REVERT: E 311 LYS cc_start: 0.8215 (pttt) cc_final: 0.6427 (tppt) REVERT: E 340 LYS cc_start: 0.7868 (tttt) cc_final: 0.7496 (tmtp) REVERT: E 343 LYS cc_start: 0.7116 (ttmt) cc_final: 0.6765 (ttpt) REVERT: E 369 LYS cc_start: 0.7175 (mtpt) cc_final: 0.6847 (tttt) REVERT: E 375 LYS cc_start: 0.7571 (tttt) cc_final: 0.6871 (ttpt) REVERT: F 314 ASP cc_start: 0.7250 (t0) cc_final: 0.6630 (t70) REVERT: F 316 SER cc_start: 0.8024 (m) cc_final: 0.7610 (p) REVERT: F 340 LYS cc_start: 0.8514 (OUTLIER) cc_final: 0.8063 (tmtp) REVERT: F 342 GLU cc_start: 0.4815 (OUTLIER) cc_final: 0.2699 (mp0) REVERT: F 369 LYS cc_start: 0.7685 (mtpt) cc_final: 0.7412 (ttpt) REVERT: F 375 LYS cc_start: 0.8092 (tttt) cc_final: 0.7437 (ttpt) outliers start: 14 outliers final: 3 residues processed: 81 average time/residue: 3.2031 time to fit residues: 265.1444 Evaluate side-chains 74 residues out of total 387 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 67 time to evaluate : 0.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 340 LYS Chi-restraints excluded: chain C residue 307 GLN Chi-restraints excluded: chain C residue 377 THR Chi-restraints excluded: chain B residue 370 LYS Chi-restraints excluded: chain B residue 372 GLU Chi-restraints excluded: chain F residue 340 LYS Chi-restraints excluded: chain F residue 342 GLU 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: 4.9990 chunk 34 optimal weight: 6.9990 chunk 28 optimal weight: 3.9990 chunk 0 optimal weight: 7.9990 chunk 20 optimal weight: 3.9990 chunk 36 optimal weight: 6.9990 chunk 10 optimal weight: 5.9990 chunk 13 optimal weight: 0.0370 chunk 8 optimal weight: 5.9990 chunk 23 optimal weight: 0.9980 overall best weight: 2.8064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7565 moved from start: 0.4976 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= 0.245 Angle : 0.560 4.543 4590 Z= 0.277 Chirality : 0.050 0.132 519 Planarity : 0.003 0.026 582 Dihedral : 5.208 15.803 450 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 1.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 2.84 % Allowed : 15.25 % Favored : 81.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.45 (0.34), residues: 429 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.09 (0.26), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS C 374 PHE 0.003 0.001 PHE A 346 TYR 0.009 0.002 TYR C 310 ARG 0.001 0.000 ARG E 349 *********************** 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 83 residues out of total 387 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 72 time to evaluate : 0.612 Fit side-chains revert: symmetry clash REVERT: A 338 GLU cc_start: 0.7375 (mt-10) cc_final: 0.6844 (tt0) REVERT: A 340 LYS cc_start: 0.7477 (OUTLIER) cc_final: 0.7167 (mtmt) REVERT: D 314 ASP cc_start: 0.8191 (t70) cc_final: 0.7704 (t70) REVERT: D 317 LYS cc_start: 0.7880 (pttt) cc_final: 0.7459 (ptmm) REVERT: D 338 GLU cc_start: 0.7764 (mt-10) cc_final: 0.7267 (tt0) REVERT: D 340 LYS cc_start: 0.8123 (ttmm) cc_final: 0.7813 (ttmt) REVERT: D 349 ARG cc_start: 0.6037 (mtm180) cc_final: 0.5403 (mtt180) REVERT: D 369 LYS cc_start: 0.7955 (ttmt) cc_final: 0.7306 (tttt) REVERT: C 338 GLU cc_start: 0.7428 (mt-10) cc_final: 0.6809 (tt0) REVERT: C 369 LYS cc_start: 0.7538 (ttmt) cc_final: 0.6967 (tttt) REVERT: C 372 GLU cc_start: 0.8096 (mm-30) cc_final: 0.7521 (mm-30) REVERT: C 379 ARG cc_start: 0.6856 (mtp180) cc_final: 0.6307 (tmm160) REVERT: B 319 THR cc_start: 0.7600 (p) cc_final: 0.7170 (t) REVERT: B 322 CYS cc_start: 0.7840 (p) cc_final: 0.7620 (m) REVERT: B 340 LYS cc_start: 0.7823 (tttt) cc_final: 0.7491 (tmtp) REVERT: B 369 LYS cc_start: 0.7134 (mtpt) cc_final: 0.6799 (ttpt) REVERT: B 372 GLU cc_start: 0.7897 (OUTLIER) cc_final: 0.7594 (mm-30) REVERT: E 311 LYS cc_start: 0.8172 (pttt) cc_final: 0.6400 (tppt) REVERT: E 340 LYS cc_start: 0.7910 (tttt) cc_final: 0.7542 (tmtp) REVERT: E 343 LYS cc_start: 0.7159 (ttmt) cc_final: 0.6813 (ttpp) REVERT: E 369 LYS cc_start: 0.7178 (mtpt) cc_final: 0.6841 (tttt) REVERT: E 375 LYS cc_start: 0.7582 (tttt) cc_final: 0.6945 (mtpp) REVERT: F 314 ASP cc_start: 0.7249 (t70) cc_final: 0.6643 (t70) REVERT: F 316 SER cc_start: 0.8044 (m) cc_final: 0.7642 (p) REVERT: F 340 LYS cc_start: 0.8504 (OUTLIER) cc_final: 0.8019 (tmtp) REVERT: F 369 LYS cc_start: 0.7668 (mtpt) cc_final: 0.7407 (ttpt) REVERT: F 375 LYS cc_start: 0.8123 (tttt) cc_final: 0.7441 (ttpt) outliers start: 11 outliers final: 4 residues processed: 78 average time/residue: 3.0894 time to fit residues: 246.4874 Evaluate side-chains 78 residues out of total 387 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 71 time to evaluate : 0.564 ------------------------------------------------------------------------------- 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 377 THR Chi-restraints excluded: chain B residue 370 LYS Chi-restraints excluded: chain B residue 372 GLU 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: 1.9990 chunk 18 optimal weight: 5.9990 chunk 3 optimal weight: 0.9980 chunk 13 optimal weight: 0.7980 chunk 21 optimal weight: 6.9990 chunk 39 optimal weight: 2.9990 chunk 4 optimal weight: 0.9980 chunk 23 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 362 HIS F 368 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7546 moved from start: 0.5138 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= 0.164 Angle : 0.506 4.574 4590 Z= 0.247 Chirality : 0.050 0.127 519 Planarity : 0.003 0.025 582 Dihedral : 4.778 14.833 450 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 2.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 2.58 % Allowed : 14.99 % 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: -1.44 (0.34), residues: 429 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.09 (0.26), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 374 PHE 0.002 0.001 PHE D 378 TYR 0.006 0.001 TYR A 310 ARG 0.001 0.000 ARG D 349 *********************** 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 86 residues out of total 387 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 76 time to evaluate : 0.608 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 338 GLU cc_start: 0.7351 (mt-10) cc_final: 0.6765 (tt0) REVERT: D 314 ASP cc_start: 0.8247 (t70) cc_final: 0.7755 (t70) REVERT: D 317 LYS cc_start: 0.7888 (pttt) cc_final: 0.7494 (ptmm) REVERT: D 338 GLU cc_start: 0.7720 (mt-10) cc_final: 0.7128 (tt0) REVERT: D 340 LYS cc_start: 0.8107 (ttmm) cc_final: 0.7540 (mttt) REVERT: D 349 ARG cc_start: 0.5967 (mtm180) cc_final: 0.5346 (mtt180) REVERT: D 369 LYS cc_start: 0.7944 (ttmt) cc_final: 0.7304 (tttt) REVERT: C 338 GLU cc_start: 0.7383 (mt-10) cc_final: 0.6788 (tt0) REVERT: C 369 LYS cc_start: 0.7471 (ttmt) cc_final: 0.6899 (tttt) REVERT: C 372 GLU cc_start: 0.8104 (mm-30) cc_final: 0.7770 (mm-30) REVERT: C 379 ARG cc_start: 0.6944 (mtp180) cc_final: 0.6355 (tmm160) REVERT: B 319 THR cc_start: 0.7556 (p) cc_final: 0.7254 (m) REVERT: B 340 LYS cc_start: 0.7823 (tttt) cc_final: 0.7469 (tmtp) REVERT: B 343 LYS cc_start: 0.6567 (ttmm) cc_final: 0.5689 (tttm) REVERT: B 369 LYS cc_start: 0.7183 (mtpt) cc_final: 0.6832 (ttpt) REVERT: B 372 GLU cc_start: 0.7837 (OUTLIER) cc_final: 0.7613 (mm-30) REVERT: E 311 LYS cc_start: 0.8155 (pttt) cc_final: 0.6410 (tppt) REVERT: E 340 LYS cc_start: 0.7957 (tttt) cc_final: 0.7558 (tmtp) REVERT: E 343 LYS cc_start: 0.7214 (ttmt) cc_final: 0.5748 (tppt) REVERT: E 369 LYS cc_start: 0.7210 (mtpt) cc_final: 0.6904 (tttm) REVERT: F 314 ASP cc_start: 0.7229 (t70) cc_final: 0.6606 (t70) REVERT: F 316 SER cc_start: 0.8026 (m) cc_final: 0.7651 (p) REVERT: F 340 LYS cc_start: 0.8433 (OUTLIER) cc_final: 0.7966 (tmtp) REVERT: F 369 LYS cc_start: 0.7667 (mtpt) cc_final: 0.7392 (ttpt) REVERT: F 375 LYS cc_start: 0.8112 (tttt) cc_final: 0.7438 (ttpt) outliers start: 10 outliers final: 2 residues processed: 81 average time/residue: 3.0166 time to fit residues: 250.0221 Evaluate side-chains 77 residues out of total 387 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 73 time to evaluate : 0.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 341 SER Chi-restraints excluded: chain C residue 307 GLN Chi-restraints excluded: chain B residue 372 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: 5.9990 chunk 34 optimal weight: 6.9990 chunk 40 optimal weight: 2.9990 chunk 25 optimal weight: 8.9990 chunk 24 optimal weight: 7.9990 chunk 18 optimal weight: 6.9990 chunk 16 optimal weight: 3.9990 chunk 12 optimal weight: 3.9990 chunk 7 optimal weight: 6.9990 chunk 27 optimal weight: 4.9990 chunk 20 optimal weight: 3.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 336 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7579 moved from start: 0.5189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 3429 Z= 0.331 Angle : 0.590 5.231 4590 Z= 0.296 Chirality : 0.051 0.134 519 Planarity : 0.003 0.028 582 Dihedral : 5.298 15.908 450 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 2.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 2.33 % Allowed : 15.25 % 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: -1.47 (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 0.012 0.002 TYR C 310 ARG 0.002 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 81 residues out of total 387 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 72 time to evaluate : 0.563 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 336 GLN cc_start: 0.7636 (mt0) cc_final: 0.7341 (mt0) REVERT: A 338 GLU cc_start: 0.7367 (mt-10) cc_final: 0.6722 (tt0) REVERT: D 314 ASP cc_start: 0.8172 (t70) cc_final: 0.7668 (t70) REVERT: D 317 LYS cc_start: 0.7903 (pttt) cc_final: 0.7453 (ptmm) REVERT: D 338 GLU cc_start: 0.7786 (mt-10) cc_final: 0.7132 (tt0) REVERT: D 340 LYS cc_start: 0.8116 (ttmm) cc_final: 0.7551 (mttt) REVERT: D 349 ARG cc_start: 0.5994 (mtm180) cc_final: 0.5346 (mtt180) REVERT: D 369 LYS cc_start: 0.7946 (ttmt) cc_final: 0.7289 (tttt) REVERT: C 338 GLU cc_start: 0.7446 (mt-10) cc_final: 0.6791 (tt0) REVERT: C 369 LYS cc_start: 0.7528 (ttmt) cc_final: 0.6924 (tttt) REVERT: C 372 GLU cc_start: 0.8102 (mm-30) cc_final: 0.7714 (mm-30) REVERT: C 379 ARG cc_start: 0.6968 (mtp180) cc_final: 0.6360 (tmm160) REVERT: B 340 LYS cc_start: 0.7860 (tttt) cc_final: 0.7493 (tmtp) REVERT: B 369 LYS cc_start: 0.7150 (mtpt) cc_final: 0.6804 (ttpt) REVERT: B 372 GLU cc_start: 0.7941 (OUTLIER) cc_final: 0.7639 (mm-30) REVERT: E 311 LYS cc_start: 0.8166 (pttt) cc_final: 0.6419 (tppt) REVERT: E 340 LYS cc_start: 0.7927 (tttt) cc_final: 0.7548 (tmtp) REVERT: E 343 LYS cc_start: 0.7164 (ttmt) cc_final: 0.5708 (tppt) REVERT: E 369 LYS cc_start: 0.7109 (mtpt) cc_final: 0.6763 (tttt) REVERT: E 375 LYS cc_start: 0.7573 (tttt) cc_final: 0.6915 (mtpp) REVERT: F 314 ASP cc_start: 0.7223 (t70) cc_final: 0.6573 (t70) REVERT: F 316 SER cc_start: 0.7960 (m) cc_final: 0.7544 (p) REVERT: F 340 LYS cc_start: 0.8475 (OUTLIER) cc_final: 0.8019 (tmtp) REVERT: F 369 LYS cc_start: 0.7695 (mtpt) cc_final: 0.7401 (ttpt) REVERT: F 375 LYS cc_start: 0.8138 (tttt) cc_final: 0.7463 (ttpt) outliers start: 9 outliers final: 1 residues processed: 76 average time/residue: 3.1777 time to fit residues: 247.0892 Evaluate side-chains 71 residues out of total 387 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 68 time to evaluate : 0.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 307 GLN Chi-restraints excluded: chain B residue 372 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: 0.8980 chunk 31 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 38 optimal weight: 6.9990 chunk 35 optimal weight: 0.9990 chunk 37 optimal weight: 3.9990 chunk 22 optimal weight: 0.9980 chunk 16 optimal weight: 4.9990 chunk 29 optimal weight: 0.7980 chunk 11 optimal weight: 4.9990 chunk 34 optimal weight: 0.9980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 368 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7548 moved from start: 0.5305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 3429 Z= 0.141 Angle : 0.492 4.982 4590 Z= 0.240 Chirality : 0.050 0.125 519 Planarity : 0.003 0.028 582 Dihedral : 4.643 14.366 450 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 1.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 1.03 % Allowed : 16.28 % 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: -1.43 (0.35), residues: 429 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.08 (0.26), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS D 374 PHE 0.002 0.000 PHE B 346 TYR 0.005 0.001 TYR A 310 ARG 0.001 0.000 ARG D 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 83 residues out of total 387 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 79 time to evaluate : 0.595 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 338 GLU cc_start: 0.7359 (mt-10) cc_final: 0.6768 (tt0) REVERT: D 314 ASP cc_start: 0.8260 (t70) cc_final: 0.7769 (t70) REVERT: D 317 LYS cc_start: 0.7900 (pttt) cc_final: 0.7490 (ptmm) REVERT: D 338 GLU cc_start: 0.7727 (mt-10) cc_final: 0.7173 (tt0) REVERT: D 340 LYS cc_start: 0.8086 (ttmm) cc_final: 0.7544 (mttt) REVERT: D 349 ARG cc_start: 0.5969 (mtm180) cc_final: 0.5354 (mtt180) REVERT: D 369 LYS cc_start: 0.7936 (ttmt) cc_final: 0.7311 (tttt) REVERT: C 336 GLN cc_start: 0.7773 (mt0) cc_final: 0.7006 (mp-120) REVERT: C 338 GLU cc_start: 0.7355 (mt-10) cc_final: 0.6791 (tt0) REVERT: C 369 LYS cc_start: 0.7457 (ttmt) cc_final: 0.6883 (tttt) REVERT: C 372 GLU cc_start: 0.8074 (mm-30) cc_final: 0.7747 (mm-30) REVERT: C 379 ARG cc_start: 0.6949 (mtp180) cc_final: 0.6328 (tmm160) REVERT: B 340 LYS cc_start: 0.7885 (tttt) cc_final: 0.7503 (tmtp) REVERT: B 343 LYS cc_start: 0.6549 (ttmm) cc_final: 0.5671 (tttm) REVERT: B 369 LYS cc_start: 0.7158 (mtpt) cc_final: 0.6826 (ttpt) REVERT: B 372 GLU cc_start: 0.7789 (OUTLIER) cc_final: 0.7546 (mm-30) REVERT: E 311 LYS cc_start: 0.8160 (pttt) cc_final: 0.6422 (tppt) REVERT: E 340 LYS cc_start: 0.7984 (tttt) cc_final: 0.7569 (tmtp) REVERT: E 343 LYS cc_start: 0.7196 (ttmt) cc_final: 0.5721 (tppt) REVERT: E 369 LYS cc_start: 0.7204 (mtpt) cc_final: 0.6923 (tttm) REVERT: E 375 LYS cc_start: 0.7573 (tttt) cc_final: 0.6949 (mtpp) REVERT: F 314 ASP cc_start: 0.7222 (t70) cc_final: 0.6633 (t70) REVERT: F 316 SER cc_start: 0.8073 (m) cc_final: 0.7672 (p) REVERT: F 340 LYS cc_start: 0.8368 (OUTLIER) cc_final: 0.7938 (tmtp) REVERT: F 369 LYS cc_start: 0.7656 (mtpt) cc_final: 0.7348 (ttpt) REVERT: F 375 LYS cc_start: 0.8113 (tttt) cc_final: 0.7467 (mtpp) outliers start: 4 outliers final: 1 residues processed: 81 average time/residue: 3.0486 time to fit residues: 252.6396 Evaluate side-chains 79 residues out of total 387 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 76 time to evaluate : 0.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 307 GLN Chi-restraints excluded: chain B residue 372 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: 0.8980 chunk 37 optimal weight: 5.9990 chunk 24 optimal weight: 6.9990 chunk 39 optimal weight: 2.9990 chunk 18 optimal weight: 4.9990 chunk 27 optimal weight: 8.9990 chunk 41 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 33 optimal weight: 5.9990 chunk 3 optimal weight: 0.7980 chunk 25 optimal weight: 0.8980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 327 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7554 moved from start: 0.5380 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= 0.160 Angle : 0.487 4.395 4590 Z= 0.240 Chirality : 0.050 0.125 519 Planarity : 0.003 0.028 582 Dihedral : 4.551 13.944 450 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 2.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 1.29 % Allowed : 16.54 % 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: -1.41 (0.35), residues: 429 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.07 (0.27), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 374 PHE 0.002 0.000 PHE B 346 TYR 0.006 0.001 TYR C 310 ARG 0.001 0.000 ARG D 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 83 residues out of total 387 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 78 time to evaluate : 0.591 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 338 GLU cc_start: 0.7370 (mt-10) cc_final: 0.6779 (tt0) REVERT: A 372 GLU cc_start: 0.7720 (OUTLIER) cc_final: 0.7364 (tt0) REVERT: D 314 ASP cc_start: 0.8265 (t70) cc_final: 0.7739 (t70) REVERT: D 317 LYS cc_start: 0.7887 (pttt) cc_final: 0.7521 (ptmm) REVERT: D 338 GLU cc_start: 0.7733 (mt-10) cc_final: 0.7172 (tt0) REVERT: D 340 LYS cc_start: 0.8060 (ttmm) cc_final: 0.7538 (mttt) REVERT: D 349 ARG cc_start: 0.5957 (mtm180) cc_final: 0.5347 (mtt180) REVERT: D 369 LYS cc_start: 0.7931 (ttmt) cc_final: 0.7295 (tttt) REVERT: C 336 GLN cc_start: 0.7789 (mt0) cc_final: 0.7035 (mp-120) REVERT: C 338 GLU cc_start: 0.7390 (mt-10) cc_final: 0.6803 (tt0) REVERT: C 369 LYS cc_start: 0.7462 (ttmt) cc_final: 0.6890 (tttt) REVERT: C 372 GLU cc_start: 0.8086 (mm-30) cc_final: 0.7561 (mm-30) REVERT: C 379 ARG cc_start: 0.6956 (mtp180) cc_final: 0.6325 (tmm160) REVERT: B 340 LYS cc_start: 0.7871 (tttt) cc_final: 0.7497 (tmtp) REVERT: B 343 LYS cc_start: 0.6592 (ttmm) cc_final: 0.5755 (tttm) REVERT: B 369 LYS cc_start: 0.7154 (mtpt) cc_final: 0.6821 (ttpt) REVERT: B 372 GLU cc_start: 0.7861 (OUTLIER) cc_final: 0.7580 (mm-30) REVERT: E 311 LYS cc_start: 0.8193 (pttt) cc_final: 0.6402 (tppt) REVERT: E 340 LYS cc_start: 0.7987 (tttt) cc_final: 0.7575 (tmtp) REVERT: E 343 LYS cc_start: 0.7227 (ttmt) cc_final: 0.5756 (tppt) REVERT: E 369 LYS cc_start: 0.7195 (mtpt) cc_final: 0.6908 (tttm) REVERT: E 375 LYS cc_start: 0.7604 (tttt) cc_final: 0.6958 (mtpp) REVERT: F 314 ASP cc_start: 0.7218 (t70) cc_final: 0.6614 (t70) REVERT: F 316 SER cc_start: 0.8057 (m) cc_final: 0.7656 (p) REVERT: F 340 LYS cc_start: 0.8375 (OUTLIER) cc_final: 0.7914 (tmtp) REVERT: F 369 LYS cc_start: 0.7657 (mtpt) cc_final: 0.7360 (ttpt) REVERT: F 375 LYS cc_start: 0.8125 (tttt) cc_final: 0.7474 (mtpp) outliers start: 5 outliers final: 2 residues processed: 80 average time/residue: 3.1932 time to fit residues: 261.2577 Evaluate side-chains 82 residues out of total 387 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 77 time to evaluate : 0.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 B residue 372 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: 6.9990 chunk 26 optimal weight: 5.9990 chunk 35 optimal weight: 0.9980 chunk 10 optimal weight: 3.9990 chunk 30 optimal weight: 4.9990 chunk 4 optimal weight: 6.9990 chunk 9 optimal weight: 4.9990 chunk 33 optimal weight: 1.9990 chunk 13 optimal weight: 6.9990 chunk 34 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 336 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7570 moved from start: 0.5377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3429 Z= 0.220 Angle : 0.520 4.480 4590 Z= 0.258 Chirality : 0.050 0.127 519 Planarity : 0.003 0.028 582 Dihedral : 4.864 14.748 450 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 2.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 1.29 % Allowed : 17.31 % 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: -1.42 (0.35), residues: 429 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.07 (0.27), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 374 PHE 0.004 0.001 PHE D 378 TYR 0.008 0.002 TYR C 310 ARG 0.001 0.000 ARG D 379 ********************** 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 77 residues out of total 387 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 72 time to evaluate : 0.618 Fit side-chains revert: symmetry clash REVERT: A 338 GLU cc_start: 0.7357 (mt-10) cc_final: 0.6754 (tt0) REVERT: D 314 ASP cc_start: 0.8233 (t70) cc_final: 0.7691 (t70) REVERT: D 317 LYS cc_start: 0.7953 (pttt) cc_final: 0.7529 (ptmm) REVERT: D 338 GLU cc_start: 0.7731 (mt-10) cc_final: 0.7133 (tt0) REVERT: D 340 LYS cc_start: 0.8079 (ttmm) cc_final: 0.7556 (mttt) REVERT: D 349 ARG cc_start: 0.6023 (mtm180) cc_final: 0.5395 (mtt180) REVERT: D 369 LYS cc_start: 0.7939 (ttmt) cc_final: 0.7294 (tttt) REVERT: C 338 GLU cc_start: 0.7431 (mt-10) cc_final: 0.6827 (tt0) REVERT: C 369 LYS cc_start: 0.7472 (ttmt) cc_final: 0.6872 (tttt) REVERT: C 372 GLU cc_start: 0.8100 (mm-30) cc_final: 0.7696 (mm-30) REVERT: C 379 ARG cc_start: 0.6928 (mtp180) cc_final: 0.6247 (tmm160) REVERT: B 340 LYS cc_start: 0.7852 (tttt) cc_final: 0.7477 (tmtp) REVERT: B 343 LYS cc_start: 0.6589 (ttmm) cc_final: 0.5788 (tttm) REVERT: B 369 LYS cc_start: 0.7142 (mtpt) cc_final: 0.6805 (ttpt) REVERT: B 372 GLU cc_start: 0.7883 (OUTLIER) cc_final: 0.7648 (mm-30) REVERT: E 311 LYS cc_start: 0.8225 (pttt) cc_final: 0.6416 (tppt) REVERT: E 340 LYS cc_start: 0.7963 (tttt) cc_final: 0.7551 (tmtp) REVERT: E 343 LYS cc_start: 0.7201 (ttmt) cc_final: 0.5746 (tppt) REVERT: E 369 LYS cc_start: 0.7158 (mtpt) cc_final: 0.6827 (tttt) REVERT: E 375 LYS cc_start: 0.7595 (tttt) cc_final: 0.6947 (mtpp) REVERT: F 314 ASP cc_start: 0.7216 (t70) cc_final: 0.6553 (t70) REVERT: F 316 SER cc_start: 0.8055 (m) cc_final: 0.7644 (p) REVERT: F 340 LYS cc_start: 0.8398 (OUTLIER) cc_final: 0.7946 (tmtp) REVERT: F 369 LYS cc_start: 0.7656 (mtpt) cc_final: 0.7390 (ttpt) REVERT: F 375 LYS cc_start: 0.8138 (tttt) cc_final: 0.7481 (mtpp) outliers start: 5 outliers final: 1 residues processed: 74 average time/residue: 3.2789 time to fit residues: 247.9175 Evaluate side-chains 75 residues out of total 387 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 72 time to evaluate : 0.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 307 GLN Chi-restraints excluded: chain B residue 372 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: 3.9990 chunk 1 optimal weight: 7.9990 chunk 24 optimal weight: 6.9990 chunk 38 optimal weight: 2.9990 chunk 22 optimal weight: 0.9990 chunk 28 optimal weight: 0.9980 chunk 26 optimal weight: 2.9990 chunk 25 optimal weight: 5.9990 chunk 16 optimal weight: 1.9990 chunk 15 optimal weight: 0.8980 chunk 41 optimal weight: 0.7980 overall best weight: 1.1384 ------------------------------------------------------------------------------- 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 = 0.3804 r_free = 0.3804 target = 0.126121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.114475 restraints weight = 14217.045| |-----------------------------------------------------------------------------| r_work (start): 0.3648 rms_B_bonded: 1.35 r_work: 0.3582 rms_B_bonded: 1.43 restraints_weight: 0.5000 r_work: 0.3513 rms_B_bonded: 2.50 restraints_weight: 0.2500 r_work (final): 0.3513 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8681 moved from start: 0.5445 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= 0.148 Angle : 0.473 4.399 4590 Z= 0.232 Chirality : 0.050 0.123 519 Planarity : 0.003 0.028 582 Dihedral : 4.474 13.813 450 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 2.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 1.55 % Allowed : 16.54 % Favored : 81.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.41 (0.35), residues: 429 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.07 (0.27), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS C 374 PHE 0.002 0.000 PHE B 346 TYR 0.005 0.001 TYR C 310 ARG 0.001 0.000 ARG D 379 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5364.29 seconds wall clock time: 93 minutes 59.54 seconds (5639.54 seconds total)