Starting phenix.real_space_refine on Wed Feb 12 01:07:02 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8q8y_18265/02_2025/8q8y_18265.cif Found real_map, /net/cci-nas-00/data/ceres_data/8q8y_18265/02_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_18265/02_2025/8q8y_18265.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8q8y_18265/02_2025/8q8y_18265.map" model { file = "/net/cci-nas-00/data/ceres_data/8q8y_18265/02_2025/8q8y_18265.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8q8y_18265/02_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-5592/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: 5.04, per 1000 atoms: 0.73 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: 1.58 Conformation dependent library (CDL) restraints added in 606.0 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: 0.67 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: 2.33 Time building geometry restraints manager: 1.95 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: 3.330 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: 0.060 Set scattering table: 0.060 Process input model: 19.680 Find NCS groups from input model: 0.220 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:12.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.780 ------------------------------------------------------------------------------- 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 : 0.539 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: 2.9303 time to fit residues: 386.7325 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 : 0.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 0.9990 chunk 31 optimal weight: 2.9990 chunk 17 optimal weight: 5.9990 chunk 10 optimal weight: 1.9990 chunk 21 optimal weight: 0.9980 chunk 32 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 20 optimal weight: 5.9990 chunk 24 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 327 ASN A 368 ASN D 327 ASN D 368 ASN C 327 ASN C 368 ASN B 327 ASN E 327 ASN F 327 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.135144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.123878 restraints weight = 13682.029| |-----------------------------------------------------------------------------| r_work (start): 0.3782 rms_B_bonded: 1.33 r_work: 0.3713 rms_B_bonded: 1.46 restraints_weight: 0.5000 r_work: 0.3645 rms_B_bonded: 2.57 restraints_weight: 0.2500 r_work (final): 0.3645 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8593 moved from start: 0.3606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3429 Z= 0.178 Angle : 0.606 5.009 4590 Z= 0.304 Chirality : 0.052 0.134 519 Planarity : 0.003 0.021 582 Dihedral : 6.031 18.788 450 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 2.33 % Allowed : 12.14 % Favored : 85.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.32 (0.34), residues: 429 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.99 (0.26), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS F 330 PHE 0.007 0.001 PHE E 346 TYR 0.009 0.002 TYR D 310 ARG 0.002 0.001 ARG D 349 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 108 time to evaluate : 0.563 Fit side-chains REVERT: A 338 GLU cc_start: 0.8066 (mt-10) cc_final: 0.7800 (mt-10) REVERT: A 358 ASP cc_start: 0.8696 (m-30) cc_final: 0.8484 (m-30) REVERT: D 338 GLU cc_start: 0.8087 (mt-10) cc_final: 0.7814 (tt0) REVERT: D 340 LYS cc_start: 0.8670 (ttmm) cc_final: 0.8458 (ttmt) REVERT: C 311 LYS cc_start: 0.8569 (ttmt) cc_final: 0.7556 (tppt) REVERT: C 338 GLU cc_start: 0.8079 (mt-10) cc_final: 0.7841 (tt0) REVERT: C 379 ARG cc_start: 0.7254 (mtp180) cc_final: 0.6348 (tmm160) REVERT: B 319 THR cc_start: 0.8687 (p) cc_final: 0.8406 (t) REVERT: B 343 LYS cc_start: 0.7537 (ttmt) cc_final: 0.7274 (ttpt) REVERT: B 375 LYS cc_start: 0.8392 (tttt) cc_final: 0.8022 (ttpt) REVERT: E 311 LYS cc_start: 0.8497 (pttt) cc_final: 0.7419 (tppt) REVERT: E 370 LYS cc_start: 0.8602 (OUTLIER) cc_final: 0.8177 (tmtm) REVERT: E 375 LYS cc_start: 0.8500 (tttt) cc_final: 0.8236 (tppp) REVERT: F 311 LYS cc_start: 0.8683 (pttt) cc_final: 0.8257 (pttm) REVERT: F 343 LYS cc_start: 0.7794 (ttmm) cc_final: 0.7117 (mtmm) outliers start: 9 outliers final: 3 residues processed: 113 average time/residue: 2.9542 time to fit residues: 341.6915 Evaluate side-chains 65 residues out of total 387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 61 time to evaluate : 0.567 ------------------------------------------------------------------------------- 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: 5.9990 chunk 29 optimal weight: 0.4980 chunk 4 optimal weight: 7.9990 chunk 26 optimal weight: 5.9990 chunk 13 optimal weight: 10.0000 chunk 7 optimal weight: 0.9990 chunk 33 optimal weight: 4.9990 chunk 22 optimal weight: 2.9990 chunk 25 optimal weight: 6.9990 chunk 18 optimal weight: 2.9990 chunk 21 optimal weight: 5.9990 overall best weight: 2.4988 ------------------------------------------------------------------------------- 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 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 = 0.3810 r_free = 0.3810 target = 0.127131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.115486 restraints weight = 12782.971| |-----------------------------------------------------------------------------| r_work (start): 0.3633 rms_B_bonded: 1.27 r_work: 0.3551 rms_B_bonded: 1.42 restraints_weight: 0.5000 r_work: 0.3479 rms_B_bonded: 2.50 restraints_weight: 0.2500 r_work (final): 0.3479 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8706 moved from start: 0.5018 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= 0.227 Angle : 0.585 4.737 4590 Z= 0.292 Chirality : 0.053 0.140 519 Planarity : 0.003 0.022 582 Dihedral : 5.303 17.009 450 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 2.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 6.46 % Allowed : 15.25 % 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: -1.35 (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 0.003 0.001 HIS D 374 PHE 0.005 0.001 PHE D 378 TYR 0.011 0.003 TYR C 310 ARG 0.002 0.000 ARG C 379 *********************** REFINEMENT MACRO_CYCLE 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 91 residues out of total 387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 66 time to evaluate : 0.633 Fit side-chains REVERT: A 340 LYS cc_start: 0.8599 (OUTLIER) cc_final: 0.8340 (mtmt) REVERT: A 372 GLU cc_start: 0.8076 (OUTLIER) cc_final: 0.7870 (tt0) REVERT: D 338 GLU cc_start: 0.8135 (mt-10) cc_final: 0.7904 (tt0) REVERT: D 340 LYS cc_start: 0.8629 (ttmm) cc_final: 0.8413 (ttmt) REVERT: C 311 LYS cc_start: 0.8609 (ttmt) cc_final: 0.7706 (tppt) REVERT: C 336 GLN cc_start: 0.8092 (mt0) cc_final: 0.7884 (mt0) REVERT: C 338 GLU cc_start: 0.8116 (mt-10) cc_final: 0.7833 (tt0) REVERT: C 379 ARG cc_start: 0.7408 (mtp180) cc_final: 0.6649 (tmm160) REVERT: B 375 LYS cc_start: 0.8435 (tttt) cc_final: 0.8114 (ttpt) REVERT: E 311 LYS cc_start: 0.8594 (pttt) cc_final: 0.7309 (tppt) REVERT: E 340 LYS cc_start: 0.8700 (OUTLIER) cc_final: 0.8049 (tmtp) REVERT: E 370 LYS cc_start: 0.8752 (OUTLIER) cc_final: 0.8354 (tmtm) REVERT: E 375 LYS cc_start: 0.8459 (tttt) cc_final: 0.8114 (ttpt) REVERT: F 311 LYS cc_start: 0.8794 (pttt) cc_final: 0.8338 (pttm) REVERT: F 340 LYS cc_start: 0.8699 (OUTLIER) cc_final: 0.8340 (tmtp) outliers start: 25 outliers final: 6 residues processed: 81 average time/residue: 2.8914 time to fit residues: 240.1638 Evaluate side-chains 71 residues out of total 387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 60 time to evaluate : 0.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 340 LYS Chi-restraints excluded: chain A residue 341 SER Chi-restraints excluded: chain A residue 372 GLU Chi-restraints excluded: chain D residue 324 SER Chi-restraints excluded: chain C residue 307 GLN Chi-restraints excluded: chain C residue 375 LYS Chi-restraints excluded: chain E residue 319 THR Chi-restraints excluded: chain E residue 340 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: 2.9990 chunk 25 optimal weight: 6.9990 chunk 13 optimal weight: 6.9990 chunk 24 optimal weight: 4.9990 chunk 6 optimal weight: 0.9990 chunk 21 optimal weight: 6.9990 chunk 7 optimal weight: 5.9990 chunk 27 optimal weight: 4.9990 chunk 2 optimal weight: 4.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- 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 = 0.3756 r_free = 0.3756 target = 0.122785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.110962 restraints weight = 13043.857| |-----------------------------------------------------------------------------| r_work (start): 0.3575 rms_B_bonded: 1.29 r_work: 0.3493 rms_B_bonded: 1.44 restraints_weight: 0.5000 r_work: 0.3420 rms_B_bonded: 2.54 restraints_weight: 0.2500 r_work (final): 0.3420 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8753 moved from start: 0.5317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 3429 Z= 0.312 Angle : 0.627 4.967 4590 Z= 0.313 Chirality : 0.052 0.138 519 Planarity : 0.003 0.026 582 Dihedral : 5.549 18.439 450 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 2.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 5.17 % Allowed : 16.80 % Favored : 78.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.50 (0.34), residues: 429 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.13 (0.26), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS C 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 : 0.550 Fit side-chains revert: symmetry clash REVERT: A 340 LYS cc_start: 0.8638 (OUTLIER) cc_final: 0.8276 (mtmt) REVERT: D 338 GLU cc_start: 0.8163 (mt-10) cc_final: 0.7854 (tt0) REVERT: D 340 LYS cc_start: 0.8627 (ttmm) cc_final: 0.8388 (ttmt) REVERT: C 338 GLU cc_start: 0.8124 (mt-10) cc_final: 0.7772 (tt0) REVERT: C 379 ARG cc_start: 0.7478 (mtp180) cc_final: 0.6715 (tmm160) REVERT: E 311 LYS cc_start: 0.8653 (pttt) cc_final: 0.7503 (tppt) REVERT: E 340 LYS cc_start: 0.8706 (OUTLIER) cc_final: 0.8127 (tmtp) REVERT: F 319 THR cc_start: 0.8935 (OUTLIER) cc_final: 0.8725 (m) REVERT: F 342 GLU cc_start: 0.5684 (OUTLIER) cc_final: 0.3111 (mp0) outliers start: 20 outliers final: 7 residues processed: 63 average time/residue: 2.7668 time to fit residues: 179.0304 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 : 0.629 ------------------------------------------------------------------------------- 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 351 GLN 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: 0.8980 chunk 1 optimal weight: 7.9990 chunk 35 optimal weight: 0.0980 chunk 39 optimal weight: 0.3980 chunk 21 optimal weight: 2.9990 chunk 10 optimal weight: 5.9990 chunk 37 optimal weight: 3.9990 chunk 20 optimal weight: 6.9990 chunk 33 optimal weight: 3.9990 chunk 25 optimal weight: 2.9990 chunk 38 optimal weight: 4.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 362 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.128215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.116542 restraints weight = 12728.579| |-----------------------------------------------------------------------------| r_work (start): 0.3651 rms_B_bonded: 1.25 r_work: 0.3569 rms_B_bonded: 1.44 restraints_weight: 0.5000 r_work: 0.3497 rms_B_bonded: 2.53 restraints_weight: 0.2500 r_work (final): 0.3497 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8706 moved from start: 0.5557 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= 0.154 Angle : 0.511 4.619 4590 Z= 0.252 Chirality : 0.051 0.129 519 Planarity : 0.003 0.024 582 Dihedral : 4.874 15.123 450 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 1.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 3.62 % Allowed : 18.35 % Favored : 78.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.51 (0.35), residues: 429 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.14 (0.26), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS D 374 PHE 0.002 0.000 PHE B 346 TYR 0.006 0.002 TYR A 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 77 residues out of total 387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 63 time to evaluate : 0.584 Fit side-chains revert: symmetry clash REVERT: A 340 LYS cc_start: 0.8597 (OUTLIER) cc_final: 0.8217 (mtmt) REVERT: D 338 GLU cc_start: 0.8027 (mt-10) cc_final: 0.7772 (tt0) REVERT: D 340 LYS cc_start: 0.8578 (ttmm) cc_final: 0.8256 (mttt) REVERT: C 338 GLU cc_start: 0.8063 (mt-10) cc_final: 0.7730 (tt0) REVERT: C 379 ARG cc_start: 0.7478 (mtp180) cc_final: 0.6677 (tmm160) REVERT: E 310 TYR cc_start: 0.8907 (t80) cc_final: 0.8701 (t80) REVERT: E 370 LYS cc_start: 0.8852 (OUTLIER) cc_final: 0.8544 (tttm) REVERT: F 342 GLU cc_start: 0.5792 (mp0) cc_final: 0.5478 (pm20) outliers start: 14 outliers final: 5 residues processed: 70 average time/residue: 2.3164 time to fit residues: 167.2401 Evaluate side-chains 63 residues out of total 387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 56 time to evaluate : 0.637 ------------------------------------------------------------------------------- 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 370 LYS 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: 7.9990 chunk 36 optimal weight: 6.9990 chunk 23 optimal weight: 4.9990 chunk 8 optimal weight: 6.9990 chunk 2 optimal weight: 5.9990 chunk 12 optimal weight: 5.9990 chunk 21 optimal weight: 6.9990 chunk 17 optimal weight: 0.0980 chunk 28 optimal weight: 0.9990 chunk 24 optimal weight: 7.9990 overall best weight: 3.6188 ------------------------------------------------------------------------------- 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 = 0.3743 r_free = 0.3743 target = 0.121923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.109967 restraints weight = 13189.132| |-----------------------------------------------------------------------------| r_work (start): 0.3561 rms_B_bonded: 1.30 r_work: 0.3479 rms_B_bonded: 1.47 restraints_weight: 0.5000 r_work: 0.3406 rms_B_bonded: 2.57 restraints_weight: 0.2500 r_work (final): 0.3406 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8759 moved from start: 0.5614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 3429 Z= 0.311 Angle : 0.594 5.358 4590 Z= 0.298 Chirality : 0.052 0.137 519 Planarity : 0.003 0.028 582 Dihedral : 5.311 17.403 450 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 2.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 3.88 % Allowed : 17.57 % 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: -1.62 (0.34), residues: 429 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.22 (0.26), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS C 374 PHE 0.005 0.001 PHE D 378 TYR 0.011 0.003 TYR A 310 ARG 0.002 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 64 residues out of total 387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 49 time to evaluate : 0.705 Fit side-chains revert: symmetry clash REVERT: A 340 LYS cc_start: 0.8608 (OUTLIER) cc_final: 0.7951 (mtmt) REVERT: D 338 GLU cc_start: 0.8141 (mt-10) cc_final: 0.7847 (tt0) REVERT: D 340 LYS cc_start: 0.8608 (ttmm) cc_final: 0.8217 (mttt) REVERT: C 338 GLU cc_start: 0.8126 (mt-10) cc_final: 0.7769 (tt0) REVERT: C 379 ARG cc_start: 0.7555 (mtp180) cc_final: 0.6703 (tmm160) REVERT: E 340 LYS cc_start: 0.8694 (OUTLIER) cc_final: 0.8231 (tmtp) REVERT: F 338 GLU cc_start: 0.8425 (OUTLIER) cc_final: 0.8146 (tt0) REVERT: F 340 LYS cc_start: 0.8718 (OUTLIER) cc_final: 0.8395 (tmtp) REVERT: F 342 GLU cc_start: 0.5852 (OUTLIER) cc_final: 0.5511 (pm20) outliers start: 15 outliers final: 6 residues processed: 58 average time/residue: 2.7662 time to fit residues: 165.1846 Evaluate side-chains 61 residues out of total 387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 50 time to evaluate : 0.592 ------------------------------------------------------------------------------- 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 372 GLU Chi-restraints excluded: chain C residue 375 LYS 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 Chi-restraints excluded: chain F residue 342 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 9 optimal weight: 3.9990 chunk 31 optimal weight: 7.9990 chunk 0 optimal weight: 7.9990 chunk 38 optimal weight: 0.9980 chunk 5 optimal weight: 7.9990 chunk 22 optimal weight: 6.9990 chunk 13 optimal weight: 5.9990 chunk 18 optimal weight: 1.9990 chunk 6 optimal weight: 6.9990 chunk 24 optimal weight: 0.8980 chunk 10 optimal weight: 5.9990 overall best weight: 2.7786 ------------------------------------------------------------------------------- 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 = 0.3773 r_free = 0.3773 target = 0.124075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.112194 restraints weight = 12965.770| |-----------------------------------------------------------------------------| r_work (start): 0.3588 rms_B_bonded: 1.28 r_work: 0.3507 rms_B_bonded: 1.46 restraints_weight: 0.5000 r_work: 0.3433 rms_B_bonded: 2.56 restraints_weight: 0.2500 r_work (final): 0.3433 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8747 moved from start: 0.5685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 3429 Z= 0.234 Angle : 0.549 4.645 4590 Z= 0.274 Chirality : 0.051 0.133 519 Planarity : 0.003 0.027 582 Dihedral : 5.098 16.530 450 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 1.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % 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: -1.64 (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 0.009 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 66 residues out of total 387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 51 time to evaluate : 0.628 Fit side-chains revert: symmetry clash REVERT: A 340 LYS cc_start: 0.8596 (OUTLIER) cc_final: 0.7942 (mtmt) REVERT: D 338 GLU cc_start: 0.8092 (mt-10) cc_final: 0.7823 (tt0) REVERT: D 340 LYS cc_start: 0.8596 (ttmm) cc_final: 0.8217 (mttt) REVERT: C 338 GLU cc_start: 0.8092 (mt-10) cc_final: 0.7752 (tt0) REVERT: C 379 ARG cc_start: 0.7497 (mtp180) cc_final: 0.6586 (tmm160) REVERT: E 340 LYS cc_start: 0.8694 (OUTLIER) cc_final: 0.8260 (tmtp) REVERT: F 338 GLU cc_start: 0.8406 (OUTLIER) cc_final: 0.8107 (tt0) REVERT: F 340 LYS cc_start: 0.8674 (OUTLIER) cc_final: 0.8325 (tmtp) REVERT: F 342 GLU cc_start: 0.5933 (OUTLIER) cc_final: 0.5666 (pm20) outliers start: 15 outliers final: 4 residues processed: 59 average time/residue: 2.6296 time to fit residues: 159.8194 Evaluate side-chains 60 residues out of total 387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 51 time to evaluate : 0.613 ------------------------------------------------------------------------------- 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 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 Chi-restraints excluded: chain F residue 342 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 34 optimal weight: 6.9990 chunk 23 optimal weight: 5.9990 chunk 18 optimal weight: 4.9990 chunk 27 optimal weight: 1.9990 chunk 15 optimal weight: 6.9990 chunk 12 optimal weight: 3.9990 chunk 40 optimal weight: 0.9980 chunk 21 optimal weight: 6.9990 chunk 26 optimal weight: 0.8980 chunk 10 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- 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 = 0.3806 r_free = 0.3806 target = 0.126346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.114527 restraints weight = 12938.555| |-----------------------------------------------------------------------------| r_work (start): 0.3617 rms_B_bonded: 1.28 r_work: 0.3535 rms_B_bonded: 1.47 restraints_weight: 0.5000 r_work: 0.3461 rms_B_bonded: 2.59 restraints_weight: 0.2500 r_work (final): 0.3461 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8729 moved from start: 0.5769 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 : 0.510 4.525 4590 Z= 0.253 Chirality : 0.051 0.132 519 Planarity : 0.003 0.026 582 Dihedral : 4.762 14.848 450 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 1.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 2.33 % Allowed : 19.12 % 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: -1.62 (0.35), residues: 429 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.23 (0.27), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS D 374 PHE 0.002 0.000 PHE B 346 TYR 0.007 0.001 TYR C 310 ARG 0.001 0.000 ARG A 379 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 56 time to evaluate : 0.586 Fit side-chains revert: symmetry clash REVERT: A 340 LYS cc_start: 0.8568 (OUTLIER) cc_final: 0.8160 (mtpt) REVERT: C 336 GLN cc_start: 0.8373 (mt0) cc_final: 0.8130 (mp-120) REVERT: C 338 GLU cc_start: 0.8063 (mt-10) cc_final: 0.7743 (tt0) REVERT: C 379 ARG cc_start: 0.7506 (mtp180) cc_final: 0.6595 (tmm160) REVERT: F 338 GLU cc_start: 0.8410 (OUTLIER) cc_final: 0.8090 (tt0) REVERT: F 342 GLU cc_start: 0.5949 (OUTLIER) cc_final: 0.5728 (pm20) outliers start: 9 outliers final: 4 residues processed: 59 average time/residue: 2.2427 time to fit residues: 137.1784 Evaluate side-chains 58 residues out of total 387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 51 time to evaluate : 0.629 ------------------------------------------------------------------------------- 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 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 342 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 20 optimal weight: 5.9990 chunk 27 optimal weight: 7.9990 chunk 10 optimal weight: 3.9990 chunk 11 optimal weight: 2.9990 chunk 21 optimal weight: 5.9990 chunk 29 optimal weight: 0.8980 chunk 17 optimal weight: 5.9990 chunk 32 optimal weight: 5.9990 chunk 2 optimal weight: 4.9990 chunk 6 optimal weight: 0.9990 chunk 33 optimal weight: 0.6980 overall best weight: 1.9186 ------------------------------------------------------------------------------- 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 = 0.3811 r_free = 0.3811 target = 0.126631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.114050 restraints weight = 13639.719| |-----------------------------------------------------------------------------| r_work (start): 0.3607 rms_B_bonded: 1.39 r_work: 0.3526 rms_B_bonded: 1.51 restraints_weight: 0.5000 r_work: 0.3451 rms_B_bonded: 2.66 restraints_weight: 0.2500 r_work (final): 0.3451 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8711 moved from start: 0.5851 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= 0.188 Angle : 0.517 4.490 4590 Z= 0.257 Chirality : 0.051 0.128 519 Planarity : 0.003 0.026 582 Dihedral : 4.747 14.694 450 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 1.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 1.81 % Allowed : 19.64 % 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: -1.65 (0.35), residues: 429 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.25 (0.27), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 374 PHE 0.003 0.001 PHE D 378 TYR 0.007 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 58 residues out of total 387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 51 time to evaluate : 0.569 Fit side-chains revert: symmetry clash REVERT: A 340 LYS cc_start: 0.8508 (OUTLIER) cc_final: 0.8061 (mtpt) REVERT: A 342 GLU cc_start: 0.8158 (pt0) cc_final: 0.7836 (pt0) REVERT: C 336 GLN cc_start: 0.8397 (mt0) cc_final: 0.8101 (mp-120) REVERT: C 338 GLU cc_start: 0.8129 (mt-10) cc_final: 0.7736 (tt0) REVERT: C 379 ARG cc_start: 0.7502 (mtp180) cc_final: 0.6508 (tmm160) REVERT: F 338 GLU cc_start: 0.8446 (OUTLIER) cc_final: 0.8114 (tt0) REVERT: F 342 GLU cc_start: 0.5871 (OUTLIER) cc_final: 0.5668 (pm20) outliers start: 7 outliers final: 3 residues processed: 55 average time/residue: 2.3776 time to fit residues: 135.2103 Evaluate side-chains 56 residues out of total 387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 50 time to evaluate : 0.603 ------------------------------------------------------------------------------- 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 E residue 319 THR Chi-restraints excluded: chain F residue 338 GLU Chi-restraints excluded: chain F residue 342 GLU 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: 4.9990 chunk 20 optimal weight: 0.8980 chunk 6 optimal weight: 3.9990 chunk 16 optimal weight: 2.9990 chunk 14 optimal weight: 0.5980 chunk 9 optimal weight: 6.9990 chunk 35 optimal weight: 4.9990 chunk 17 optimal weight: 0.9990 chunk 4 optimal weight: 6.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- 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 = 0.3801 r_free = 0.3801 target = 0.125745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.113756 restraints weight = 13034.473| |-----------------------------------------------------------------------------| r_work (start): 0.3607 rms_B_bonded: 1.29 r_work: 0.3526 rms_B_bonded: 1.48 restraints_weight: 0.5000 r_work: 0.3453 rms_B_bonded: 2.60 restraints_weight: 0.2500 r_work (final): 0.3453 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8735 moved from start: 0.5878 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= 0.184 Angle : 0.509 4.493 4590 Z= 0.253 Chirality : 0.051 0.128 519 Planarity : 0.003 0.026 582 Dihedral : 4.701 14.495 450 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 1.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % 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: -1.65 (0.35), residues: 429 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.25 (0.27), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 374 PHE 0.003 0.001 PHE D 378 TYR 0.007 0.001 TYR A 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 61 residues out of total 387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 53 time to evaluate : 0.558 Fit side-chains revert: symmetry clash REVERT: A 340 LYS cc_start: 0.8556 (OUTLIER) cc_final: 0.8165 (mtpt) REVERT: A 342 GLU cc_start: 0.8121 (pt0) cc_final: 0.7847 (pt0) REVERT: C 336 GLN cc_start: 0.8372 (mt0) cc_final: 0.8160 (mp-120) REVERT: C 338 GLU cc_start: 0.8084 (mt-10) cc_final: 0.7744 (tt0) REVERT: C 379 ARG cc_start: 0.7521 (mtp180) cc_final: 0.6603 (tmm160) REVERT: E 340 LYS cc_start: 0.8706 (OUTLIER) cc_final: 0.8303 (tmtp) REVERT: F 338 GLU cc_start: 0.8391 (OUTLIER) cc_final: 0.8074 (tt0) REVERT: F 340 LYS cc_start: 0.8601 (OUTLIER) cc_final: 0.8263 (tmtp) outliers start: 8 outliers final: 3 residues processed: 58 average time/residue: 2.3780 time to fit residues: 142.2529 Evaluate side-chains 59 residues out of total 387 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 52 time to evaluate : 0.638 ------------------------------------------------------------------------------- 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 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: 1.9990 chunk 3 optimal weight: 4.9990 chunk 20 optimal weight: 0.8980 chunk 15 optimal weight: 6.9990 chunk 30 optimal weight: 4.9990 chunk 1 optimal weight: 0.9980 chunk 33 optimal weight: 0.9980 chunk 27 optimal weight: 7.9990 chunk 12 optimal weight: 2.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.125785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.114644 restraints weight = 14251.723| |-----------------------------------------------------------------------------| r_work (start): 0.3654 rms_B_bonded: 1.31 r_work: 0.3587 rms_B_bonded: 1.42 restraints_weight: 0.5000 r_work: 0.3519 rms_B_bonded: 2.49 restraints_weight: 0.2500 r_work (final): 0.3519 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8717 moved from start: 0.5918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 3429 Z= 0.166 Angle : 0.499 4.464 4590 Z= 0.247 Chirality : 0.051 0.127 519 Planarity : 0.003 0.025 582 Dihedral : 4.600 14.158 450 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 1.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 2.07 % Allowed : 19.90 % Favored : 78.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.65 (0.35), residues: 429 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.25 (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 D 378 TYR 0.006 0.001 TYR A 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: 6567.57 seconds wall clock time: 115 minutes 55.35 seconds (6955.35 seconds total)