Starting phenix.real_space_refine on Wed Mar 12 00:44:05 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8q8y_18265/03_2025/8q8y_18265.cif Found real_map, /net/cci-nas-00/data/ceres_data/8q8y_18265/03_2025/8q8y_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/cci-nas-00/data/ceres_data/8q8y_18265/03_2025/8q8y_18265.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8q8y_18265/03_2025/8q8y_18265.map" model { file = "/net/cci-nas-00/data/ceres_data/8q8y_18265/03_2025/8q8y_18265.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8q8y_18265/03_2025/8q8y_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. Time to flip 17 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/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: 4.79, per 1000 atoms: 0.69 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.54 Conformation dependent library (CDL) restraints added in 633.7 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: 0.64 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: 2.07 Time building geometry restraints manager: 1.92 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: 0.00 - 2.55: 10645 2.55 - 5.10: 1547 5.10 - 7.66: 464 7.66 - 10.21: 14 10.21 - 12.76: 6 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: 4.890 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: 0.120 Extract box with map and model: 0.310 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 19.120 Find NCS groups from input model: 0.230 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:15.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.130 ------------------------------------------------------------------------------- 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 to be fit. rotamer outliers: 0 poor density : 129 time to evaluate : 0.523 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: 2.8352 time to fit residues: 374.2586 Evaluate side-chains 85 residues out of total 387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 85 time to evaluate : 0.605 ------------------------------------------------------------------------------- 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: 0.9980 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 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.135354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.124105 restraints weight = 13674.315| |-----------------------------------------------------------------------------| r_work (start): 0.3785 rms_B_bonded: 1.34 r_work: 0.3714 rms_B_bonded: 1.48 restraints_weight: 0.5000 r_work: 0.3645 rms_B_bonded: 2.61 restraints_weight: 0.2500 r_work (final): 0.3645 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8595 moved from start: 0.3620 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= 0.179 Angle : 0.604 4.983 4590 Z= 0.303 Chirality : 0.052 0.135 519 Planarity : 0.003 0.021 582 Dihedral : 5.998 18.762 450 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % 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 0.003 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 to be fit. rotamer outliers: 9 poor density : 108 time to evaluate : 0.558 Fit side-chains REVERT: A 338 GLU cc_start: 0.8076 (mt-10) cc_final: 0.7808 (mt-10) REVERT: A 358 ASP cc_start: 0.8695 (m-30) cc_final: 0.8476 (m-30) REVERT: D 338 GLU cc_start: 0.8095 (mt-10) cc_final: 0.7821 (tt0) REVERT: D 340 LYS cc_start: 0.8676 (ttmm) cc_final: 0.8465 (ttmt) REVERT: C 311 LYS cc_start: 0.8570 (ttmt) cc_final: 0.7558 (tppt) REVERT: C 338 GLU cc_start: 0.8080 (mt-10) cc_final: 0.7815 (tt0) REVERT: C 379 ARG cc_start: 0.7254 (mtp180) cc_final: 0.6352 (tmm160) REVERT: B 319 THR cc_start: 0.8689 (p) cc_final: 0.8412 (t) REVERT: B 343 LYS cc_start: 0.7544 (ttmt) cc_final: 0.7281 (ttpt) REVERT: B 375 LYS cc_start: 0.8387 (tttt) cc_final: 0.8020 (ttpt) REVERT: E 311 LYS cc_start: 0.8492 (pttt) cc_final: 0.7416 (tppt) REVERT: E 370 LYS cc_start: 0.8591 (OUTLIER) cc_final: 0.8182 (tmtm) REVERT: E 375 LYS cc_start: 0.8505 (tttt) cc_final: 0.8242 (tppp) REVERT: F 311 LYS cc_start: 0.8686 (pttt) cc_final: 0.8263 (pttm) REVERT: F 343 LYS cc_start: 0.7799 (ttmm) cc_final: 0.7123 (mtmm) outliers start: 9 outliers final: 3 residues processed: 113 average time/residue: 2.8353 time to fit residues: 327.9421 Evaluate side-chains 66 residues out of total 387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 62 time to evaluate : 0.586 ------------------------------------------------------------------------------- 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 E residue 370 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 38 optimal weight: 6.9990 chunk 29 optimal weight: 3.9990 chunk 4 optimal weight: 7.9990 chunk 26 optimal weight: 6.9990 chunk 13 optimal weight: 8.9990 chunk 7 optimal weight: 2.9990 chunk 33 optimal weight: 0.9980 chunk 22 optimal weight: 0.8980 chunk 25 optimal weight: 7.9990 chunk 18 optimal weight: 1.9990 chunk 21 optimal weight: 5.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- 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 E 351 GLN F 351 GLN F 359 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.127938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.116359 restraints weight = 12943.033| |-----------------------------------------------------------------------------| r_work (start): 0.3647 rms_B_bonded: 1.29 r_work: 0.3567 rms_B_bonded: 1.43 restraints_weight: 0.5000 r_work: 0.3494 rms_B_bonded: 2.53 restraints_weight: 0.2500 r_work (final): 0.3494 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8696 moved from start: 0.5044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3429 Z= 0.205 Angle : 0.570 4.735 4590 Z= 0.283 Chirality : 0.052 0.136 519 Planarity : 0.003 0.020 582 Dihedral : 5.208 16.798 450 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 2.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 6.46 % Allowed : 14.99 % Favored : 78.55 % 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: -1.35 (0.34), residues: 429 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.02 (0.26), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS D 374 PHE 0.005 0.001 PHE D 378 TYR 0.010 0.002 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 93 residues out of total 387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 68 time to evaluate : 0.568 Fit side-chains REVERT: A 340 LYS cc_start: 0.8594 (OUTLIER) cc_final: 0.8346 (mtmt) REVERT: D 338 GLU cc_start: 0.8111 (mt-10) cc_final: 0.7889 (tt0) REVERT: D 340 LYS cc_start: 0.8629 (ttmm) cc_final: 0.8407 (ttmt) REVERT: C 311 LYS cc_start: 0.8602 (ttmt) cc_final: 0.7705 (tppt) REVERT: C 338 GLU cc_start: 0.8078 (mt-10) cc_final: 0.7784 (tt0) REVERT: C 379 ARG cc_start: 0.7417 (mtp180) cc_final: 0.6641 (tmm160) REVERT: B 375 LYS cc_start: 0.8431 (tttt) cc_final: 0.8108 (ttpt) REVERT: E 311 LYS cc_start: 0.8554 (pttt) cc_final: 0.7468 (tppt) REVERT: E 340 LYS cc_start: 0.8710 (OUTLIER) cc_final: 0.8024 (tmtp) REVERT: E 343 LYS cc_start: 0.7795 (OUTLIER) cc_final: 0.6555 (tppt) REVERT: E 370 LYS cc_start: 0.8716 (OUTLIER) cc_final: 0.8325 (tmtm) REVERT: E 375 LYS cc_start: 0.8468 (tttt) cc_final: 0.8127 (ttpt) REVERT: F 311 LYS cc_start: 0.8792 (pttt) cc_final: 0.8304 (pttm) REVERT: F 340 LYS cc_start: 0.8678 (OUTLIER) cc_final: 0.8321 (tmtp) outliers start: 25 outliers final: 6 residues processed: 83 average time/residue: 2.6867 time to fit residues: 228.7738 Evaluate side-chains 72 residues out of total 387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 61 time to evaluate : 0.577 ------------------------------------------------------------------------------- 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 375 LYS Chi-restraints excluded: chain E residue 319 THR Chi-restraints excluded: chain E residue 340 LYS Chi-restraints excluded: chain E residue 343 LYS Chi-restraints excluded: chain E 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 33 optimal weight: 4.9990 chunk 1 optimal weight: 7.9990 chunk 20 optimal weight: 3.9990 chunk 25 optimal weight: 7.9990 chunk 13 optimal weight: 6.9990 chunk 24 optimal weight: 5.9990 chunk 6 optimal weight: 1.9990 chunk 21 optimal weight: 6.9990 chunk 7 optimal weight: 3.9990 chunk 27 optimal weight: 5.9990 chunk 2 optimal weight: 4.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.122916 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.111215 restraints weight = 13077.576| |-----------------------------------------------------------------------------| r_work (start): 0.3571 rms_B_bonded: 1.27 r_work: 0.3491 rms_B_bonded: 1.42 restraints_weight: 0.5000 r_work: 0.3417 rms_B_bonded: 2.51 restraints_weight: 0.2500 r_work (final): 0.3417 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8751 moved from start: 0.5355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 3429 Z= 0.327 Angle : 0.631 4.875 4590 Z= 0.316 Chirality : 0.052 0.138 519 Planarity : 0.003 0.027 582 Dihedral : 5.543 18.004 450 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 1.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 5.17 % Allowed : 16.02 % Favored : 78.81 % 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: -1.48 (0.34), residues: 429 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.12 (0.26), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS B 374 PHE 0.008 0.001 PHE D 378 TYR 0.013 0.003 TYR C 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 71 residues out of total 387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 51 time to evaluate : 0.583 Fit side-chains REVERT: A 340 LYS cc_start: 0.8636 (OUTLIER) cc_final: 0.8275 (mtmt) REVERT: D 338 GLU cc_start: 0.8156 (mt-10) cc_final: 0.7848 (tt0) REVERT: D 340 LYS cc_start: 0.8622 (ttmm) cc_final: 0.8384 (ttmt) REVERT: C 338 GLU cc_start: 0.8112 (mt-10) cc_final: 0.7767 (tt0) REVERT: C 379 ARG cc_start: 0.7488 (mtp180) cc_final: 0.6727 (tmm160) REVERT: E 311 LYS cc_start: 0.8654 (pttt) cc_final: 0.7543 (tppt) REVERT: E 340 LYS cc_start: 0.8694 (OUTLIER) cc_final: 0.8088 (tmtp) REVERT: E 343 LYS cc_start: 0.7864 (OUTLIER) cc_final: 0.6622 (tppt) REVERT: F 319 THR cc_start: 0.8926 (OUTLIER) cc_final: 0.8709 (m) REVERT: F 342 GLU cc_start: 0.5609 (OUTLIER) cc_final: 0.3012 (mp0) outliers start: 20 outliers final: 6 residues processed: 63 average time/residue: 2.6128 time to fit residues: 169.2684 Evaluate side-chains 58 residues out of total 387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 47 time to evaluate : 0.609 ------------------------------------------------------------------------------- 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 372 GLU 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 E residue 319 THR Chi-restraints excluded: chain E residue 340 LYS Chi-restraints excluded: chain E residue 343 LYS Chi-restraints excluded: chain F residue 319 THR 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 31 optimal weight: 7.9990 chunk 1 optimal weight: 7.9990 chunk 35 optimal weight: 5.9990 chunk 39 optimal weight: 0.9990 chunk 21 optimal weight: 2.9990 chunk 10 optimal weight: 5.9990 chunk 37 optimal weight: 0.0170 chunk 20 optimal weight: 6.9990 chunk 33 optimal weight: 2.9990 chunk 25 optimal weight: 0.7980 chunk 38 optimal weight: 4.9990 overall best weight: 1.5624 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 351 GLN F 362 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.129078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.116615 restraints weight = 13338.021| |-----------------------------------------------------------------------------| r_work (start): 0.3645 rms_B_bonded: 1.38 r_work: 0.3564 rms_B_bonded: 1.50 restraints_weight: 0.5000 r_work: 0.3488 rms_B_bonded: 2.65 restraints_weight: 0.2500 r_work (final): 0.3488 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8688 moved from start: 0.5568 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= 0.157 Angle : 0.515 4.615 4590 Z= 0.255 Chirality : 0.051 0.129 519 Planarity : 0.003 0.024 582 Dihedral : 4.924 15.243 450 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 1.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 4.91 % Allowed : 17.31 % Favored : 77.78 % 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 : -1.17 (0.26), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS D 374 PHE 0.002 0.001 PHE D 378 TYR 0.006 0.002 TYR C 310 ARG 0.001 0.000 ARG D 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 80 residues out of total 387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 61 time to evaluate : 0.539 Fit side-chains revert: symmetry clash REVERT: A 340 LYS cc_start: 0.8533 (OUTLIER) cc_final: 0.8195 (mtmt) REVERT: A 342 GLU cc_start: 0.8288 (OUTLIER) cc_final: 0.7905 (pt0) REVERT: A 372 GLU cc_start: 0.8125 (OUTLIER) cc_final: 0.7902 (tt0) REVERT: D 338 GLU cc_start: 0.8040 (mt-10) cc_final: 0.7808 (tt0) REVERT: D 340 LYS cc_start: 0.8572 (ttmm) cc_final: 0.8347 (ttmt) REVERT: D 342 GLU cc_start: 0.8209 (pt0) cc_final: 0.7922 (tt0) REVERT: C 338 GLU cc_start: 0.8091 (mt-10) cc_final: 0.7709 (tt0) REVERT: C 340 LYS cc_start: 0.8547 (OUTLIER) cc_final: 0.8327 (mttt) REVERT: C 379 ARG cc_start: 0.7445 (mtp180) cc_final: 0.6645 (tmm160) REVERT: E 311 LYS cc_start: 0.8596 (pttt) cc_final: 0.7297 (tppt) REVERT: E 340 LYS cc_start: 0.8692 (OUTLIER) cc_final: 0.8049 (tmtp) REVERT: E 343 LYS cc_start: 0.7703 (OUTLIER) cc_final: 0.6325 (tppt) REVERT: E 370 LYS cc_start: 0.8889 (OUTLIER) cc_final: 0.8575 (tttm) REVERT: F 342 GLU cc_start: 0.5576 (OUTLIER) cc_final: 0.5372 (pm20) outliers start: 19 outliers final: 4 residues processed: 70 average time/residue: 2.4588 time to fit residues: 177.0960 Evaluate side-chains 68 residues out of total 387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 56 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 A residue 342 GLU 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 C residue 375 LYS Chi-restraints excluded: chain E residue 319 THR Chi-restraints excluded: chain E residue 340 LYS Chi-restraints excluded: chain E residue 343 LYS Chi-restraints excluded: chain E residue 370 LYS Chi-restraints excluded: chain F residue 342 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 19 optimal weight: 5.9990 chunk 6 optimal weight: 10.0000 chunk 36 optimal weight: 0.9990 chunk 23 optimal weight: 4.9990 chunk 8 optimal weight: 6.9990 chunk 2 optimal weight: 5.9990 chunk 12 optimal weight: 0.0050 chunk 21 optimal weight: 6.9990 chunk 17 optimal weight: 1.9990 chunk 28 optimal weight: 0.6980 chunk 24 optimal weight: 10.0000 overall best weight: 1.7400 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.127251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.115462 restraints weight = 12909.470| |-----------------------------------------------------------------------------| r_work (start): 0.3630 rms_B_bonded: 1.28 r_work: 0.3549 rms_B_bonded: 1.48 restraints_weight: 0.5000 r_work: 0.3475 rms_B_bonded: 2.61 restraints_weight: 0.2500 r_work (final): 0.3475 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8719 moved from start: 0.5658 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= 0.180 Angle : 0.512 4.568 4590 Z= 0.255 Chirality : 0.051 0.132 519 Planarity : 0.003 0.025 582 Dihedral : 4.764 14.672 450 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 1.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 4.39 % Allowed : 17.05 % Favored : 78.55 % 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: -1.60 (0.34), residues: 429 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.21 (0.26), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS D 374 PHE 0.003 0.001 PHE D 378 TYR 0.008 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 73 residues out of total 387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 56 time to evaluate : 0.624 Fit side-chains revert: symmetry clash REVERT: A 342 GLU cc_start: 0.8285 (OUTLIER) cc_final: 0.7978 (pt0) REVERT: D 338 GLU cc_start: 0.8073 (mt-10) cc_final: 0.7817 (tt0) REVERT: D 340 LYS cc_start: 0.8581 (ttmm) cc_final: 0.8282 (mttt) REVERT: C 338 GLU cc_start: 0.8065 (mt-10) cc_final: 0.7739 (tt0) REVERT: C 379 ARG cc_start: 0.7505 (mtp180) cc_final: 0.6636 (tmm160) REVERT: F 338 GLU cc_start: 0.8403 (OUTLIER) cc_final: 0.8095 (tt0) REVERT: F 340 LYS cc_start: 0.8643 (OUTLIER) cc_final: 0.8353 (tmtp) outliers start: 17 outliers final: 5 residues processed: 66 average time/residue: 2.4772 time to fit residues: 168.4462 Evaluate side-chains 62 residues out of total 387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 54 time to evaluate : 0.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 341 SER Chi-restraints excluded: chain A residue 342 GLU Chi-restraints excluded: chain D residue 324 SER Chi-restraints excluded: chain C residue 307 GLN Chi-restraints excluded: chain C residue 375 LYS Chi-restraints excluded: chain E residue 319 THR 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 9 optimal weight: 5.9990 chunk 31 optimal weight: 4.9990 chunk 0 optimal weight: 7.9990 chunk 38 optimal weight: 7.9990 chunk 5 optimal weight: 7.9990 chunk 22 optimal weight: 6.9990 chunk 13 optimal weight: 4.9990 chunk 18 optimal weight: 4.9990 chunk 6 optimal weight: 2.9990 chunk 24 optimal weight: 0.8980 chunk 10 optimal weight: 5.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.121860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.110018 restraints weight = 13087.471| |-----------------------------------------------------------------------------| r_work (start): 0.3555 rms_B_bonded: 1.31 r_work: 0.3473 rms_B_bonded: 1.46 restraints_weight: 0.5000 r_work: 0.3399 rms_B_bonded: 2.56 restraints_weight: 0.2500 r_work (final): 0.3399 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8763 moved from start: 0.5737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 3429 Z= 0.316 Angle : 0.594 5.656 4590 Z= 0.298 Chirality : 0.052 0.130 519 Planarity : 0.003 0.028 582 Dihedral : 5.274 17.306 450 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 1.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 3.88 % Allowed : 17.31 % Favored : 78.81 % 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: -1.65 (0.34), residues: 429 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.25 (0.26), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS B 374 PHE 0.005 0.001 PHE D 378 TYR 0.012 0.002 TYR A 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 65 residues out of total 387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 50 time to evaluate : 0.614 Fit side-chains REVERT: D 338 GLU cc_start: 0.8124 (mt-10) cc_final: 0.7804 (tt0) REVERT: D 340 LYS cc_start: 0.8613 (ttmm) cc_final: 0.8228 (mttt) REVERT: C 338 GLU cc_start: 0.8136 (mt-10) cc_final: 0.7789 (tt0) REVERT: C 379 ARG cc_start: 0.7496 (mtp180) cc_final: 0.6792 (tmm160) REVERT: E 340 LYS cc_start: 0.8684 (OUTLIER) cc_final: 0.8218 (tmtp) REVERT: E 343 LYS cc_start: 0.7870 (OUTLIER) cc_final: 0.6581 (tppt) REVERT: F 338 GLU cc_start: 0.8431 (OUTLIER) cc_final: 0.8149 (tt0) REVERT: F 340 LYS cc_start: 0.8703 (OUTLIER) cc_final: 0.8355 (tmtp) outliers start: 15 outliers final: 3 residues processed: 58 average time/residue: 2.5809 time to fit residues: 154.0930 Evaluate side-chains 56 residues out of total 387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 49 time to evaluate : 0.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 341 SER Chi-restraints excluded: chain C residue 307 GLN Chi-restraints excluded: chain E residue 319 THR Chi-restraints excluded: chain E residue 340 LYS Chi-restraints excluded: chain E residue 343 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 34 optimal weight: 3.9990 chunk 23 optimal weight: 4.9990 chunk 18 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 chunk 15 optimal weight: 8.9990 chunk 12 optimal weight: 3.9990 chunk 40 optimal weight: 2.9990 chunk 21 optimal weight: 5.9990 chunk 26 optimal weight: 0.8980 chunk 10 optimal weight: 1.9990 chunk 36 optimal weight: 4.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.122446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.111273 restraints weight = 14064.717| |-----------------------------------------------------------------------------| r_work (start): 0.3602 rms_B_bonded: 1.31 r_work: 0.3534 rms_B_bonded: 1.39 restraints_weight: 0.5000 r_work: 0.3466 rms_B_bonded: 2.44 restraints_weight: 0.2500 r_work (final): 0.3466 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8737 moved from start: 0.5791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3429 Z= 0.224 Angle : 0.540 4.630 4590 Z= 0.269 Chirality : 0.051 0.128 519 Planarity : 0.003 0.027 582 Dihedral : 5.019 15.404 450 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 1.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 1.55 % Allowed : 19.38 % Favored : 79.07 % 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: -1.64 (0.34), residues: 429 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.24 (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 0.008 0.002 TYR A 310 ARG 0.001 0.000 ARG D 349 *********************** 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 58 residues out of total 387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 52 time to evaluate : 0.615 Fit side-chains revert: symmetry clash REVERT: D 338 GLU cc_start: 0.8030 (mt-10) cc_final: 0.7753 (tt0) REVERT: D 340 LYS cc_start: 0.8582 (ttmm) cc_final: 0.8193 (mttt) REVERT: C 338 GLU cc_start: 0.8079 (mt-10) cc_final: 0.7735 (tt0) REVERT: C 379 ARG cc_start: 0.7458 (mtp180) cc_final: 0.6575 (tmm160) REVERT: F 338 GLU cc_start: 0.8400 (OUTLIER) cc_final: 0.8077 (tt0) REVERT: F 340 LYS cc_start: 0.8638 (OUTLIER) cc_final: 0.8289 (tmtp) outliers start: 6 outliers final: 3 residues processed: 56 average time/residue: 2.5120 time to fit residues: 145.3116 Evaluate side-chains 54 residues out of total 387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 49 time to evaluate : 0.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 341 SER Chi-restraints excluded: chain C residue 307 GLN Chi-restraints excluded: chain E residue 319 THR 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 20 optimal weight: 6.9990 chunk 27 optimal weight: 7.9990 chunk 10 optimal weight: 2.9990 chunk 11 optimal weight: 4.9990 chunk 21 optimal weight: 5.9990 chunk 29 optimal weight: 0.9980 chunk 17 optimal weight: 1.9990 chunk 32 optimal weight: 4.9990 chunk 2 optimal weight: 4.9990 chunk 6 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 351 GLN F 368 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.123145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.111923 restraints weight = 14287.134| |-----------------------------------------------------------------------------| r_work (start): 0.3608 rms_B_bonded: 1.31 r_work: 0.3541 rms_B_bonded: 1.41 restraints_weight: 0.5000 r_work: 0.3475 rms_B_bonded: 2.46 restraints_weight: 0.2500 r_work (final): 0.3475 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8734 moved from start: 0.5887 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= 0.202 Angle : 0.522 4.535 4590 Z= 0.260 Chirality : 0.051 0.128 519 Planarity : 0.003 0.027 582 Dihedral : 4.856 15.747 450 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 1.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 2.07 % Allowed : 19.38 % Favored : 78.55 % 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: -1.67 (0.35), residues: 429 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.26 (0.26), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 374 PHE 0.002 0.001 PHE B 346 TYR 0.008 0.002 TYR A 310 ARG 0.001 0.000 ARG D 349 *********************** 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 60 residues out of total 387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 52 time to evaluate : 0.556 Fit side-chains revert: symmetry clash REVERT: D 338 GLU cc_start: 0.8027 (mt-10) cc_final: 0.7741 (tt0) REVERT: D 340 LYS cc_start: 0.8580 (ttmm) cc_final: 0.8227 (mttt) REVERT: C 336 GLN cc_start: 0.8396 (mt0) cc_final: 0.8129 (mp-120) REVERT: C 338 GLU cc_start: 0.8081 (mt-10) cc_final: 0.7744 (tt0) REVERT: C 379 ARG cc_start: 0.7479 (mtp180) cc_final: 0.6563 (tmm160) REVERT: F 338 GLU cc_start: 0.8384 (OUTLIER) cc_final: 0.8057 (tt0) REVERT: F 340 LYS cc_start: 0.8640 (OUTLIER) cc_final: 0.8258 (tmtp) outliers start: 8 outliers final: 5 residues processed: 56 average time/residue: 2.3740 time to fit residues: 137.1680 Evaluate side-chains 56 residues out of total 387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 49 time to evaluate : 0.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 341 SER Chi-restraints excluded: chain A residue 342 GLU Chi-restraints excluded: chain C residue 307 GLN Chi-restraints excluded: chain B residue 372 GLU Chi-restraints excluded: chain E residue 319 THR 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 26 optimal weight: 4.9990 chunk 38 optimal weight: 7.9990 chunk 34 optimal weight: 3.9990 chunk 20 optimal weight: 6.9990 chunk 6 optimal weight: 0.9980 chunk 16 optimal weight: 2.9990 chunk 14 optimal weight: 4.9990 chunk 9 optimal weight: 6.9990 chunk 35 optimal weight: 2.9990 chunk 17 optimal weight: 0.9990 chunk 4 optimal weight: 6.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 351 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.122560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.111282 restraints weight = 14275.845| |-----------------------------------------------------------------------------| r_work (start): 0.3598 rms_B_bonded: 1.33 r_work: 0.3533 rms_B_bonded: 1.41 restraints_weight: 0.5000 r_work: 0.3465 rms_B_bonded: 2.47 restraints_weight: 0.2500 r_work (final): 0.3465 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8739 moved from start: 0.5902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3429 Z= 0.219 Angle : 0.532 4.945 4590 Z= 0.265 Chirality : 0.051 0.129 519 Planarity : 0.003 0.026 582 Dihedral : 4.888 15.021 450 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 1.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 2.58 % Allowed : 19.12 % Favored : 78.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.69 (0.35), residues: 429 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.28 (0.26), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS F 374 PHE 0.002 0.001 PHE E 346 TYR 0.008 0.002 TYR C 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 59 residues out of total 387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 49 time to evaluate : 0.615 Fit side-chains revert: symmetry clash REVERT: D 338 GLU cc_start: 0.8046 (mt-10) cc_final: 0.7746 (tt0) REVERT: D 340 LYS cc_start: 0.8585 (ttmm) cc_final: 0.8237 (mttt) REVERT: C 336 GLN cc_start: 0.8410 (mt0) cc_final: 0.8146 (mp-120) REVERT: C 338 GLU cc_start: 0.8092 (mt-10) cc_final: 0.7747 (tt0) REVERT: C 379 ARG cc_start: 0.7500 (mtp180) cc_final: 0.6567 (tmm160) REVERT: E 340 LYS cc_start: 0.8659 (OUTLIER) cc_final: 0.8249 (tmtp) REVERT: F 338 GLU cc_start: 0.8394 (OUTLIER) cc_final: 0.8072 (tt0) REVERT: F 340 LYS cc_start: 0.8652 (OUTLIER) cc_final: 0.8279 (tmtp) outliers start: 10 outliers final: 4 residues processed: 55 average time/residue: 2.6138 time to fit residues: 148.3184 Evaluate side-chains 55 residues out of total 387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 48 time to evaluate : 0.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 342 GLU Chi-restraints excluded: chain C residue 307 GLN Chi-restraints excluded: chain B residue 372 GLU Chi-restraints excluded: chain E residue 319 THR Chi-restraints excluded: chain E residue 340 LYS Chi-restraints excluded: chain F residue 338 GLU Chi-restraints excluded: chain F residue 340 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 4 optimal weight: 6.9990 chunk 9 optimal weight: 6.9990 chunk 18 optimal weight: 0.9980 chunk 3 optimal weight: 0.9990 chunk 20 optimal weight: 3.9990 chunk 15 optimal weight: 6.9990 chunk 30 optimal weight: 0.9980 chunk 1 optimal weight: 0.9980 chunk 33 optimal weight: 0.9990 chunk 27 optimal weight: 7.9990 chunk 12 optimal weight: 0.9980 overall best weight: 0.9982 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.128638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.116582 restraints weight = 13124.482| |-----------------------------------------------------------------------------| r_work (start): 0.3653 rms_B_bonded: 1.31 r_work: 0.3574 rms_B_bonded: 1.48 restraints_weight: 0.5000 r_work: 0.3501 rms_B_bonded: 2.62 restraints_weight: 0.2500 r_work (final): 0.3501 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8711 moved from start: 0.5985 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= 0.139 Angle : 0.481 4.462 4590 Z= 0.238 Chirality : 0.051 0.128 519 Planarity : 0.003 0.026 582 Dihedral : 4.487 14.150 450 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 1.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 2.07 % Allowed : 19.12 % Favored : 78.81 % 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: -1.67 (0.35), residues: 429 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.26 (0.27), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 374 PHE 0.002 0.000 PHE B 346 TYR 0.005 0.001 TYR B 310 ARG 0.001 0.000 ARG D 349 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6570.78 seconds wall clock time: 111 minutes 45.33 seconds (6705.33 seconds total)