Starting phenix.real_space_refine on Fri Jan 17 06:40:08 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bbl_44421/01_2025/9bbl_44421_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bbl_44421/01_2025/9bbl_44421.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9bbl_44421/01_2025/9bbl_44421.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bbl_44421/01_2025/9bbl_44421.map" model { file = "/net/cci-nas-00/data/ceres_data/9bbl_44421/01_2025/9bbl_44421_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bbl_44421/01_2025/9bbl_44421_neut.cif" } resolution = 2.5 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= 0.002 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 9 5.16 5 C 3198 2.51 5 N 936 2.21 5 O 951 1.98 5 H 5301 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 10395 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 1121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 1121 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 3, 'TRANS': 68} Chain: "B" Number of atoms: 1172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1172 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "C" Number of atoms: 1172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1172 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "D" Number of atoms: 1121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 1121 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 3, 'TRANS': 68} Chain: "E" Number of atoms: 1172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1172 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "F" Number of atoms: 1172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1172 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "G" Number of atoms: 1121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 1121 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 3, 'TRANS': 68} Chain: "H" Number of atoms: 1172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1172 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "I" Number of atoms: 1172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1172 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Time building chain proxies: 6.10, per 1000 atoms: 0.59 Number of scatterers: 10395 At special positions: 0 Unit cell: (151.58, 134.62, 41.34, 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 9 16.00 O 951 8.00 N 936 7.00 C 3198 6.00 H 5301 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: 2.53 Conformation dependent library (CDL) restraints added in 741.8 milliseconds 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1170 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 25 sheets defined 0.0% alpha, 42.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.04 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 313 through 314 removed outlier: 6.823A pdb=" N VAL A 313 " --> pdb=" O ASP G 314 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 317 through 321 removed outlier: 6.359A pdb=" N LYS A 317 " --> pdb=" O VAL G 318 " (cutoff:3.500A) removed outlier: 7.922A pdb=" N SER G 320 " --> pdb=" O LYS A 317 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N THR A 319 " --> pdb=" O SER G 320 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 328 through 330 removed outlier: 6.561A pdb=" N HIS A 329 " --> pdb=" O HIS G 330 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 336 through 339 removed outlier: 6.437A pdb=" N GLN A 336 " --> pdb=" O VAL G 337 " (cutoff:3.500A) removed outlier: 8.136A pdb=" N VAL G 339 " --> pdb=" O GLN A 336 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N GLU A 338 " --> pdb=" O VAL G 339 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 345 through 347 removed outlier: 6.431A pdb=" N PHE D 346 " --> pdb=" O LYS G 347 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 351 through 356 removed outlier: 6.836A pdb=" N SER G 356 " --> pdb=" O GLY A 355 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N SER D 352 " --> pdb=" O LYS G 353 " (cutoff:3.500A) removed outlier: 8.169A pdb=" N GLY G 355 " --> pdb=" O SER D 352 " (cutoff:3.500A) removed outlier: 7.953A pdb=" N ILE D 354 " --> pdb=" O GLY G 355 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 359 through 362 removed outlier: 6.252A pdb=" N ILE A 360 " --> pdb=" O THR G 361 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N ASN D 359 " --> pdb=" O ILE G 360 " (cutoff:3.500A) removed outlier: 7.981A pdb=" N HIS G 362 " --> pdb=" O ASN D 359 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N THR D 361 " --> pdb=" O HIS G 362 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'A' and resid 369 through 372 removed outlier: 6.737A pdb=" N LYS A 369 " --> pdb=" O LYS G 370 " (cutoff:3.500A) removed outlier: 8.235A pdb=" N GLU G 372 " --> pdb=" O LYS A 369 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N ILE A 371 " --> pdb=" O GLU G 372 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 306 through 308 Processing sheet with id=AB1, first strand: chain 'B' and resid 317 through 322 removed outlier: 6.377A pdb=" N LYS B 317 " --> pdb=" O VAL H 318 " (cutoff:3.500A) removed outlier: 8.012A pdb=" N SER H 320 " --> pdb=" O LYS B 317 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N THR B 319 " --> pdb=" O SER H 320 " (cutoff:3.500A) removed outlier: 8.611A pdb=" N CYS H 322 " --> pdb=" O THR B 319 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N LYS B 321 " --> pdb=" O CYS H 322 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 325 through 330 removed outlier: 8.725A pdb=" N LEU B 325 " --> pdb=" O GLY H 326 " (cutoff:3.500A) removed outlier: 9.780A pdb=" N ILE H 328 " --> pdb=" O LEU B 325 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N ASN B 327 " --> pdb=" O ILE H 328 " (cutoff:3.500A) removed outlier: 8.050A pdb=" N HIS H 330 " --> pdb=" O ASN B 327 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N HIS B 329 " --> pdb=" O HIS H 330 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N GLY E 326 " --> pdb=" O LEU H 325 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N ASN H 327 " --> pdb=" O GLY E 326 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 336 through 340 removed outlier: 6.338A pdb=" N VAL E 337 " --> pdb=" O GLU H 338 " (cutoff:3.500A) removed outlier: 7.845A pdb=" N LYS H 340 " --> pdb=" O VAL E 337 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N VAL E 339 " --> pdb=" O LYS H 340 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 344 through 347 removed outlier: 6.695A pdb=" N LEU E 344 " --> pdb=" O ASP H 345 " (cutoff:3.500A) removed outlier: 7.693A pdb=" N LYS H 347 " --> pdb=" O LEU E 344 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N PHE E 346 " --> pdb=" O LYS H 347 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 351 through 354 removed outlier: 6.448A pdb=" N GLN B 351 " --> pdb=" O SER H 352 " (cutoff:3.500A) removed outlier: 8.088A pdb=" N ILE H 354 " --> pdb=" O GLN B 351 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N LYS B 353 " --> pdb=" O ILE H 354 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 357 through 362 removed outlier: 6.501A pdb=" N ASP B 358 " --> pdb=" O ASN H 359 " (cutoff:3.500A) removed outlier: 7.931A pdb=" N THR H 361 " --> pdb=" O ASP B 358 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N ILE B 360 " --> pdb=" O THR H 361 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 369 through 374 removed outlier: 6.634A pdb=" N LYS B 369 " --> pdb=" O LYS H 370 " (cutoff:3.500A) removed outlier: 8.134A pdb=" N GLU H 372 " --> pdb=" O LYS B 369 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N ILE B 371 " --> pdb=" O GLU H 372 " (cutoff:3.500A) removed outlier: 7.936A pdb=" N HIS H 374 " --> pdb=" O ILE B 371 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N THR B 373 " --> pdb=" O HIS H 374 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 377 through 378 removed outlier: 6.394A pdb=" N THR B 377 " --> pdb=" O PHE H 378 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 306 through 310 removed outlier: 6.567A pdb=" N GLN C 307 " --> pdb=" O ILE I 308 " (cutoff:3.500A) removed outlier: 7.683A pdb=" N TYR I 310 " --> pdb=" O GLN C 307 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N VAL C 309 " --> pdb=" O TYR I 310 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N VAL F 306 " --> pdb=" O GLN I 307 " (cutoff:3.500A) removed outlier: 8.396A pdb=" N VAL I 309 " --> pdb=" O VAL F 306 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N ILE F 308 " --> pdb=" O VAL I 309 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'C' and resid 317 through 322 removed outlier: 6.399A pdb=" N LYS C 317 " --> pdb=" O VAL I 318 " (cutoff:3.500A) removed outlier: 8.034A pdb=" N SER I 320 " --> pdb=" O LYS C 317 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N THR C 319 " --> pdb=" O SER I 320 " (cutoff:3.500A) removed outlier: 8.445A pdb=" N CYS I 322 " --> pdb=" O THR C 319 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N LYS C 321 " --> pdb=" O CYS I 322 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 325 through 330 removed outlier: 8.706A pdb=" N LEU C 325 " --> pdb=" O GLY I 326 " (cutoff:3.500A) removed outlier: 9.917A pdb=" N ILE I 328 " --> pdb=" O LEU C 325 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N ASN C 327 " --> pdb=" O ILE I 328 " (cutoff:3.500A) removed outlier: 7.909A pdb=" N HIS I 330 " --> pdb=" O ASN C 327 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N HIS C 329 " --> pdb=" O HIS I 330 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N GLY F 326 " --> pdb=" O LEU I 325 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N ASN I 327 " --> pdb=" O GLY F 326 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 336 through 340 removed outlier: 6.430A pdb=" N VAL F 337 " --> pdb=" O GLU I 338 " (cutoff:3.500A) removed outlier: 7.992A pdb=" N LYS I 340 " --> pdb=" O VAL F 337 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N VAL F 339 " --> pdb=" O LYS I 340 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 344 through 347 removed outlier: 6.483A pdb=" N LEU F 344 " --> pdb=" O ASP I 345 " (cutoff:3.500A) removed outlier: 7.872A pdb=" N LYS I 347 " --> pdb=" O LEU F 344 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N PHE F 346 " --> pdb=" O LYS I 347 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 350 through 356 removed outlier: 6.829A pdb=" N SER I 356 " --> pdb=" O GLY C 355 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N VAL F 350 " --> pdb=" O GLN I 351 " (cutoff:3.500A) removed outlier: 8.008A pdb=" N LYS I 353 " --> pdb=" O VAL F 350 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N SER F 352 " --> pdb=" O LYS I 353 " (cutoff:3.500A) removed outlier: 8.645A pdb=" N GLY I 355 " --> pdb=" O SER F 352 " (cutoff:3.500A) removed outlier: 8.457A pdb=" N ILE F 354 " --> pdb=" O GLY I 355 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 359 through 362 removed outlier: 6.553A pdb=" N ASN F 359 " --> pdb=" O ILE I 360 " (cutoff:3.500A) removed outlier: 7.785A pdb=" N HIS I 362 " --> pdb=" O ASN F 359 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N THR F 361 " --> pdb=" O HIS I 362 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 369 through 377 91 hydrogen bonds defined for protein. 273 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: 3.18 Time building geometry restraints manager: 3.05 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.91 - 1.09: 5292 1.09 - 1.27: 846 1.27 - 1.45: 1242 1.45 - 1.63: 3087 1.63 - 1.81: 9 Bond restraints: 10476 Sorted by residual: bond pdb=" N THR G 361 " pdb=" H THR G 361 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.69e+01 bond pdb=" ND1 HIS D 330 " pdb=" HD1 HIS D 330 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.68e+01 bond pdb=" CE2 PHE D 378 " pdb=" HE2 PHE D 378 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.67e+01 bond pdb=" CD1 PHE D 378 " pdb=" HD1 PHE D 378 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.67e+01 bond pdb=" N SER D 324 " pdb=" H SER D 324 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.67e+01 ... (remaining 10471 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.46: 15638 2.46 - 4.93: 2586 4.93 - 7.39: 807 7.39 - 9.86: 52 9.86 - 12.32: 12 Bond angle restraints: 19095 Sorted by residual: angle pdb=" CA ASP D 358 " pdb=" CB ASP D 358 " pdb=" CG ASP D 358 " ideal model delta sigma weight residual 112.60 118.26 -5.66 1.00e+00 1.00e+00 3.20e+01 angle pdb=" C GLU C 342 " pdb=" CA GLU C 342 " pdb=" CB GLU C 342 " ideal model delta sigma weight residual 110.42 121.14 -10.72 1.99e+00 2.53e-01 2.90e+01 angle pdb=" CA PHE D 346 " pdb=" CB PHE D 346 " pdb=" CG PHE D 346 " ideal model delta sigma weight residual 113.80 119.17 -5.37 1.00e+00 1.00e+00 2.89e+01 angle pdb=" CA ASP G 358 " pdb=" CB ASP G 358 " pdb=" CG ASP G 358 " ideal model delta sigma weight residual 112.60 117.77 -5.17 1.00e+00 1.00e+00 2.67e+01 angle pdb=" CB HIS G 329 " pdb=" CG HIS G 329 " pdb=" CD2 HIS G 329 " ideal model delta sigma weight residual 131.20 124.51 6.69 1.30e+00 5.92e-01 2.65e+01 ... (remaining 19090 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.30: 4344 17.30 - 34.61: 233 34.61 - 51.91: 101 51.91 - 69.22: 143 69.22 - 86.52: 6 Dihedral angle restraints: 4827 sinusoidal: 2757 harmonic: 2070 Sorted by residual: dihedral pdb=" C GLU C 342 " pdb=" N GLU C 342 " pdb=" CA GLU C 342 " pdb=" CB GLU C 342 " ideal model delta harmonic sigma weight residual -122.60 -134.00 11.40 0 2.50e+00 1.60e-01 2.08e+01 dihedral pdb=" C GLU I 342 " pdb=" N GLU I 342 " pdb=" CA GLU I 342 " pdb=" CB GLU I 342 " ideal model delta harmonic sigma weight residual -122.60 -132.42 9.82 0 2.50e+00 1.60e-01 1.54e+01 dihedral pdb=" C ARG B 349 " pdb=" N ARG B 349 " pdb=" CA ARG B 349 " pdb=" CB ARG B 349 " ideal model delta harmonic sigma weight residual -122.60 -131.72 9.12 0 2.50e+00 1.60e-01 1.33e+01 ... (remaining 4824 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.081: 463 0.081 - 0.161: 238 0.161 - 0.242: 63 0.242 - 0.323: 11 0.323 - 0.403: 5 Chirality restraints: 780 Sorted by residual: chirality pdb=" CA PRO I 332 " pdb=" N PRO I 332 " pdb=" C PRO I 332 " pdb=" CB PRO I 332 " both_signs ideal model delta sigma weight residual False 2.72 2.32 0.40 2.00e-01 2.50e+01 4.06e+00 chirality pdb=" CA LEU A 325 " pdb=" N LEU A 325 " pdb=" C LEU A 325 " pdb=" CB LEU A 325 " both_signs ideal model delta sigma weight residual False 2.51 2.87 -0.36 2.00e-01 2.50e+01 3.30e+00 chirality pdb=" CG LEU C 357 " pdb=" CB LEU C 357 " pdb=" CD1 LEU C 357 " pdb=" CD2 LEU C 357 " both_signs ideal model delta sigma weight residual False -2.59 -2.93 0.34 2.00e-01 2.50e+01 2.93e+00 ... (remaining 777 not shown) Planarity restraints: 1509 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB HIS B 329 " 0.040 2.00e-02 2.50e+03 6.00e-02 8.11e+01 pdb=" CG HIS B 329 " -0.118 2.00e-02 2.50e+03 pdb=" ND1 HIS B 329 " -0.032 2.00e-02 2.50e+03 pdb=" CD2 HIS B 329 " -0.043 2.00e-02 2.50e+03 pdb=" CE1 HIS B 329 " -0.013 2.00e-02 2.50e+03 pdb=" NE2 HIS B 329 " -0.022 2.00e-02 2.50e+03 pdb=" HD1 HIS B 329 " 0.058 2.00e-02 2.50e+03 pdb=" HD2 HIS B 329 " 0.091 2.00e-02 2.50e+03 pdb=" HE1 HIS B 329 " 0.041 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS H 329 " 0.045 2.00e-02 2.50e+03 5.67e-02 7.23e+01 pdb=" CG HIS H 329 " -0.131 2.00e-02 2.50e+03 pdb=" ND1 HIS H 329 " 0.010 2.00e-02 2.50e+03 pdb=" CD2 HIS H 329 " -0.043 2.00e-02 2.50e+03 pdb=" CE1 HIS H 329 " 0.002 2.00e-02 2.50e+03 pdb=" NE2 HIS H 329 " -0.015 2.00e-02 2.50e+03 pdb=" HD1 HIS H 329 " 0.032 2.00e-02 2.50e+03 pdb=" HD2 HIS H 329 " 0.077 2.00e-02 2.50e+03 pdb=" HE1 HIS H 329 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS C 329 " -0.058 2.00e-02 2.50e+03 5.00e-02 5.62e+01 pdb=" CG HIS C 329 " 0.101 2.00e-02 2.50e+03 pdb=" ND1 HIS C 329 " 0.041 2.00e-02 2.50e+03 pdb=" CD2 HIS C 329 " 0.033 2.00e-02 2.50e+03 pdb=" CE1 HIS C 329 " 0.009 2.00e-02 2.50e+03 pdb=" NE2 HIS C 329 " 0.006 2.00e-02 2.50e+03 pdb=" HD1 HIS C 329 " -0.032 2.00e-02 2.50e+03 pdb=" HD2 HIS C 329 " -0.054 2.00e-02 2.50e+03 pdb=" HE1 HIS C 329 " -0.045 2.00e-02 2.50e+03 ... (remaining 1506 not shown) Histogram of nonbonded interaction distances: 1.53 - 2.15: 542 2.15 - 2.76: 17211 2.76 - 3.37: 28116 3.37 - 3.99: 36273 3.99 - 4.60: 52416 Nonbonded interactions: 134558 Sorted by model distance: nonbonded pdb=" OD1 ASP G 314 " pdb=" HG SER G 316 " model vdw 1.532 2.450 nonbonded pdb=" OD1 ASP A 314 " pdb=" HG SER A 316 " model vdw 1.539 2.450 nonbonded pdb=" OD1 ASP I 314 " pdb=" HG SER I 316 " model vdw 1.543 2.450 nonbonded pdb=" OD1 ASP C 314 " pdb=" HG SER C 316 " model vdw 1.548 2.450 nonbonded pdb=" OD1 ASP D 314 " pdb=" HG SER D 316 " model vdw 1.552 2.450 ... (remaining 134553 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and resid 307 through 378) selection = (chain 'C' and resid 307 through 378) selection = chain 'D' selection = (chain 'E' and resid 307 through 378) selection = (chain 'F' and resid 307 through 378) selection = chain 'G' selection = (chain 'H' and resid 307 through 378) selection = (chain 'I' and resid 307 through 378) } 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: 4.940 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: 0.170 Extract box with map and model: 0.360 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 25.230 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.030 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:12.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6397 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 0.045 5175 Z= 0.738 Angle : 2.112 10.719 6924 Z= 1.371 Chirality : 0.102 0.403 780 Planarity : 0.013 0.110 879 Dihedral : 10.019 86.521 1986 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 0.19 Ramachandran Plot: Outliers : 1.39 % Allowed : 9.72 % Favored : 88.89 % Rotamer: Outliers : 0.00 % Allowed : 0.68 % Favored : 99.32 % Cbeta Deviations : 0.34 % 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: -2.48 (0.26), residues: 648 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.88 (0.20), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.043 0.008 HIS H 329 PHE 0.027 0.010 PHE I 346 TYR 0.059 0.014 TYR B 310 ARG 0.009 0.002 ARG H 349 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 260 time to evaluate : 0.933 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 331 LYS cc_start: 0.8083 (mtmt) cc_final: 0.6036 (tptp) REVERT: A 342 GLU cc_start: 0.7620 (mt-10) cc_final: 0.6624 (mp0) REVERT: A 343 LYS cc_start: 0.8253 (mttt) cc_final: 0.8044 (mtmt) REVERT: A 356 SER cc_start: 0.7966 (p) cc_final: 0.7681 (t) REVERT: A 358 ASP cc_start: 0.7916 (m-30) cc_final: 0.7523 (m-30) REVERT: B 307 GLN cc_start: 0.7736 (pt0) cc_final: 0.7487 (pt0) REVERT: B 311 LYS cc_start: 0.7880 (mttt) cc_final: 0.6900 (mmtm) REVERT: B 317 LYS cc_start: 0.7429 (mtmt) cc_final: 0.6527 (tttp) REVERT: B 321 LYS cc_start: 0.7563 (tttt) cc_final: 0.7139 (tmmm) REVERT: B 336 GLN cc_start: 0.7656 (mt0) cc_final: 0.7398 (mt0) REVERT: B 338 GLU cc_start: 0.7211 (mt-10) cc_final: 0.6766 (mt-10) REVERT: B 340 LYS cc_start: 0.7572 (tttt) cc_final: 0.7152 (mtpp) REVERT: B 345 ASP cc_start: 0.7816 (t0) cc_final: 0.7469 (t0) REVERT: B 347 LYS cc_start: 0.7145 (mttp) cc_final: 0.6716 (mttp) REVERT: B 348 ASP cc_start: 0.7527 (t0) cc_final: 0.7217 (t0) REVERT: C 311 LYS cc_start: 0.7807 (mttt) cc_final: 0.6969 (mmtm) REVERT: C 321 LYS cc_start: 0.7327 (ttmt) cc_final: 0.6426 (tmtm) REVERT: C 331 LYS cc_start: 0.7388 (mttt) cc_final: 0.6965 (mtpt) REVERT: C 338 GLU cc_start: 0.7151 (tt0) cc_final: 0.6913 (tt0) REVERT: C 345 ASP cc_start: 0.8198 (t0) cc_final: 0.7530 (t0) REVERT: C 347 LYS cc_start: 0.7187 (mttt) cc_final: 0.6769 (mtpp) REVERT: C 348 ASP cc_start: 0.7867 (t0) cc_final: 0.7647 (t0) REVERT: C 372 GLU cc_start: 0.8161 (tt0) cc_final: 0.7899 (tt0) REVERT: D 311 LYS cc_start: 0.8118 (tttt) cc_final: 0.7580 (ttmp) REVERT: D 317 LYS cc_start: 0.8165 (mttt) cc_final: 0.7523 (mtpt) REVERT: D 321 LYS cc_start: 0.8220 (mttt) cc_final: 0.7463 (tptp) REVERT: D 331 LYS cc_start: 0.8116 (mtmt) cc_final: 0.7851 (mtpt) REVERT: D 340 LYS cc_start: 0.8093 (mttt) cc_final: 0.7431 (mttm) REVERT: D 341 SER cc_start: 0.8729 (m) cc_final: 0.8525 (m) REVERT: D 342 GLU cc_start: 0.7791 (mt-10) cc_final: 0.6985 (mp0) REVERT: D 343 LYS cc_start: 0.8306 (mttt) cc_final: 0.7838 (mttm) REVERT: D 347 LYS cc_start: 0.7821 (mttt) cc_final: 0.7319 (mtmm) REVERT: D 356 SER cc_start: 0.8138 (p) cc_final: 0.7878 (t) REVERT: D 358 ASP cc_start: 0.7682 (m-30) cc_final: 0.7250 (m-30) REVERT: D 369 LYS cc_start: 0.8145 (mttt) cc_final: 0.7845 (mttp) REVERT: D 372 GLU cc_start: 0.7934 (mt-10) cc_final: 0.7603 (mt-10) REVERT: D 375 LYS cc_start: 0.8076 (ttpt) cc_final: 0.7831 (ttmt) REVERT: E 317 LYS cc_start: 0.7738 (mtmt) cc_final: 0.7509 (mtpm) REVERT: E 320 SER cc_start: 0.7993 (t) cc_final: 0.7773 (p) REVERT: E 321 LYS cc_start: 0.7950 (tttt) cc_final: 0.7587 (tmmt) REVERT: E 331 LYS cc_start: 0.8589 (mttt) cc_final: 0.8358 (mttp) REVERT: E 336 GLN cc_start: 0.8036 (mt0) cc_final: 0.7421 (mt0) REVERT: E 338 GLU cc_start: 0.7510 (mt-10) cc_final: 0.7235 (tt0) REVERT: E 340 LYS cc_start: 0.7734 (tttt) cc_final: 0.7431 (tptp) REVERT: E 341 SER cc_start: 0.8173 (m) cc_final: 0.7835 (t) REVERT: E 342 GLU cc_start: 0.7662 (mt-10) cc_final: 0.6370 (mp0) REVERT: E 347 LYS cc_start: 0.7662 (mttp) cc_final: 0.7173 (mmtm) REVERT: E 369 LYS cc_start: 0.8492 (mttt) cc_final: 0.8172 (mttp) REVERT: F 311 LYS cc_start: 0.8344 (mttt) cc_final: 0.7480 (ttpp) REVERT: F 317 LYS cc_start: 0.7870 (pttt) cc_final: 0.7669 (ptmt) REVERT: F 342 GLU cc_start: 0.7678 (mt-10) cc_final: 0.6057 (mp0) REVERT: F 345 ASP cc_start: 0.8372 (t0) cc_final: 0.7979 (t0) REVERT: F 347 LYS cc_start: 0.7694 (mttt) cc_final: 0.6913 (mtmm) REVERT: F 349 ARG cc_start: 0.7266 (mtt180) cc_final: 0.6836 (mtp180) REVERT: F 353 LYS cc_start: 0.8380 (tttt) cc_final: 0.8022 (tttp) REVERT: F 369 LYS cc_start: 0.7983 (mttt) cc_final: 0.7404 (mtpp) REVERT: F 375 LYS cc_start: 0.8054 (tttt) cc_final: 0.7849 (ttmt) REVERT: G 311 LYS cc_start: 0.7831 (tttt) cc_final: 0.7403 (tppp) REVERT: G 317 LYS cc_start: 0.7457 (mttt) cc_final: 0.7166 (mtpm) REVERT: G 321 LYS cc_start: 0.7936 (mttt) cc_final: 0.7362 (mptt) REVERT: G 340 LYS cc_start: 0.7876 (mttt) cc_final: 0.6960 (mtpp) REVERT: G 342 GLU cc_start: 0.7607 (mt-10) cc_final: 0.6768 (mp0) REVERT: G 343 LYS cc_start: 0.8061 (mttt) cc_final: 0.7729 (mttp) REVERT: G 345 ASP cc_start: 0.7417 (m-30) cc_final: 0.7113 (m-30) REVERT: G 353 LYS cc_start: 0.7471 (mttt) cc_final: 0.7243 (mtmt) REVERT: G 356 SER cc_start: 0.8045 (p) cc_final: 0.7759 (p) REVERT: G 358 ASP cc_start: 0.7738 (m-30) cc_final: 0.7379 (m-30) REVERT: G 369 LYS cc_start: 0.7434 (mttt) cc_final: 0.7052 (mttp) REVERT: G 371 ILE cc_start: 0.8054 (mt) cc_final: 0.7747 (mp) REVERT: H 317 LYS cc_start: 0.7620 (mtmt) cc_final: 0.7378 (ttmm) REVERT: H 321 LYS cc_start: 0.7702 (tttt) cc_final: 0.7142 (mttp) REVERT: H 331 LYS cc_start: 0.8066 (mttt) cc_final: 0.7774 (mttp) REVERT: H 336 GLN cc_start: 0.7517 (mt0) cc_final: 0.6995 (mt0) REVERT: H 347 LYS cc_start: 0.7097 (mttp) cc_final: 0.6517 (mmtm) REVERT: H 356 SER cc_start: 0.8112 (m) cc_final: 0.7533 (p) REVERT: H 375 LYS cc_start: 0.7688 (tttt) cc_final: 0.7232 (tttm) REVERT: I 317 LYS cc_start: 0.7575 (pttt) cc_final: 0.7242 (pttt) REVERT: I 321 LYS cc_start: 0.7401 (ttmt) cc_final: 0.6922 (ttmm) REVERT: I 331 LYS cc_start: 0.7229 (mttt) cc_final: 0.6750 (mtpt) REVERT: I 338 GLU cc_start: 0.7508 (tt0) cc_final: 0.6791 (tt0) REVERT: I 347 LYS cc_start: 0.7326 (mttt) cc_final: 0.6226 (mmtm) REVERT: I 349 ARG cc_start: 0.7024 (mtt180) cc_final: 0.6545 (mtm180) REVERT: I 369 LYS cc_start: 0.7510 (mttt) cc_final: 0.6963 (mtpm) outliers start: 0 outliers final: 0 residues processed: 260 average time/residue: 2.9008 time to fit residues: 780.6008 Evaluate side-chains 206 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 206 time to evaluate : 1.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 53 optimal weight: 0.7980 chunk 47 optimal weight: 0.9990 chunk 26 optimal weight: 0.8980 chunk 16 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 chunk 25 optimal weight: 0.8980 chunk 49 optimal weight: 0.9990 chunk 19 optimal weight: 0.8980 chunk 30 optimal weight: 0.8980 chunk 36 optimal weight: 1.9990 chunk 57 optimal weight: 0.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 351 GLN I 307 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.144726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.129647 restraints weight = 19137.415| |-----------------------------------------------------------------------------| r_work (start): 0.3956 rms_B_bonded: 1.42 r_work: 0.3884 rms_B_bonded: 1.56 restraints_weight: 0.5000 r_work: 0.3812 rms_B_bonded: 2.75 restraints_weight: 0.2500 r_work (final): 0.3812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.3114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 5175 Z= 0.232 Angle : 0.714 5.357 6924 Z= 0.369 Chirality : 0.051 0.151 780 Planarity : 0.004 0.040 879 Dihedral : 6.450 18.856 681 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 2.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.10 % Favored : 92.90 % Rotamer: Outliers : 0.34 % Allowed : 11.79 % Favored : 87.86 % 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: -2.68 (0.25), residues: 648 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.03 (0.19), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.003 HIS B 362 PHE 0.016 0.002 PHE E 378 TYR 0.007 0.001 TYR F 310 ARG 0.004 0.000 ARG A 349 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 202 time to evaluate : 0.846 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: symmetry clash revert: symmetry clash REVERT: A 342 GLU cc_start: 0.8016 (mt-10) cc_final: 0.7541 (mp0) REVERT: B 311 LYS cc_start: 0.8203 (mttt) cc_final: 0.7597 (mmtm) REVERT: B 338 GLU cc_start: 0.8158 (mt-10) cc_final: 0.7937 (tt0) REVERT: B 348 ASP cc_start: 0.8437 (t0) cc_final: 0.8125 (t0) REVERT: C 311 LYS cc_start: 0.8391 (mttt) cc_final: 0.7924 (mmtm) REVERT: C 321 LYS cc_start: 0.8320 (ttmt) cc_final: 0.8084 (tmtm) REVERT: C 345 ASP cc_start: 0.8383 (t0) cc_final: 0.8084 (t0) REVERT: D 317 LYS cc_start: 0.8229 (mttt) cc_final: 0.7930 (mtpt) REVERT: D 342 GLU cc_start: 0.7780 (mt-10) cc_final: 0.7486 (mp0) REVERT: D 343 LYS cc_start: 0.8551 (mttt) cc_final: 0.8336 (mttm) REVERT: E 336 GLN cc_start: 0.8546 (mt0) cc_final: 0.8207 (mt0) REVERT: E 379 ARG cc_start: 0.5515 (pmt170) cc_final: 0.5013 (pmt-80) REVERT: F 311 LYS cc_start: 0.8640 (mttt) cc_final: 0.8182 (ttpp) REVERT: F 345 ASP cc_start: 0.8597 (t0) cc_final: 0.8363 (t0) REVERT: F 373 THR cc_start: 0.8802 (m) cc_final: 0.8522 (p) REVERT: G 340 LYS cc_start: 0.8700 (mttt) cc_final: 0.8422 (mttm) REVERT: G 342 GLU cc_start: 0.8071 (mt-10) cc_final: 0.7743 (mp0) REVERT: H 336 GLN cc_start: 0.8493 (mt0) cc_final: 0.8233 (mt0) REVERT: H 338 GLU cc_start: 0.8270 (mt-10) cc_final: 0.7929 (mt-10) REVERT: I 311 LYS cc_start: 0.8366 (mtpt) cc_final: 0.7739 (tttp) REVERT: I 347 LYS cc_start: 0.8537 (mttt) cc_final: 0.7993 (mmtm) outliers start: 2 outliers final: 1 residues processed: 203 average time/residue: 3.0631 time to fit residues: 641.6496 Evaluate side-chains 153 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 152 time to evaluate : 0.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 315 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 2 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 29 optimal weight: 3.9990 chunk 26 optimal weight: 0.0870 chunk 7 optimal weight: 2.9990 chunk 25 optimal weight: 0.3980 chunk 52 optimal weight: 1.9990 chunk 49 optimal weight: 0.6980 chunk 0 optimal weight: 2.9990 overall best weight: 1.0362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 351 GLN B 351 GLN C 336 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.141959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.126263 restraints weight = 19428.564| |-----------------------------------------------------------------------------| r_work (start): 0.3923 rms_B_bonded: 1.44 r_work: 0.3855 rms_B_bonded: 1.56 restraints_weight: 0.5000 r_work: 0.3785 rms_B_bonded: 2.71 restraints_weight: 0.2500 r_work (final): 0.3785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.4577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5175 Z= 0.225 Angle : 0.600 4.195 6924 Z= 0.306 Chirality : 0.050 0.137 780 Planarity : 0.004 0.033 879 Dihedral : 6.181 18.299 681 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 2.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.94 % Favored : 93.06 % Rotamer: Outliers : 1.54 % Allowed : 17.09 % Favored : 81.37 % 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: -2.64 (0.25), residues: 648 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.01 (0.19), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.002 HIS H 329 PHE 0.005 0.001 PHE D 346 TYR 0.008 0.002 TYR F 310 ARG 0.003 0.001 ARG A 349 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 161 time to evaluate : 0.923 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 342 GLU cc_start: 0.8026 (mt-10) cc_final: 0.7533 (mp0) REVERT: B 311 LYS cc_start: 0.8212 (mttt) cc_final: 0.7628 (mmtm) REVERT: B 321 LYS cc_start: 0.8532 (OUTLIER) cc_final: 0.8263 (tmmt) REVERT: B 338 GLU cc_start: 0.8241 (mt-10) cc_final: 0.8040 (tt0) REVERT: B 348 ASP cc_start: 0.8313 (t0) cc_final: 0.8033 (t70) REVERT: C 311 LYS cc_start: 0.8316 (mttt) cc_final: 0.7845 (mmtm) REVERT: C 321 LYS cc_start: 0.8252 (ttmt) cc_final: 0.8044 (tmtm) REVERT: C 345 ASP cc_start: 0.8295 (t0) cc_final: 0.8027 (t0) REVERT: D 314 ASP cc_start: 0.8758 (t0) cc_final: 0.8552 (t0) REVERT: D 317 LYS cc_start: 0.8190 (mttt) cc_final: 0.7919 (mtpt) REVERT: D 342 GLU cc_start: 0.7866 (mt-10) cc_final: 0.7473 (mp0) REVERT: E 336 GLN cc_start: 0.8544 (mt0) cc_final: 0.8204 (mt0) REVERT: E 342 GLU cc_start: 0.7995 (mt-10) cc_final: 0.7121 (mp0) REVERT: F 311 LYS cc_start: 0.8679 (mttt) cc_final: 0.7530 (pmtt) REVERT: F 345 ASP cc_start: 0.8550 (t0) cc_final: 0.8266 (t0) REVERT: F 373 THR cc_start: 0.8816 (m) cc_final: 0.8526 (p) REVERT: G 340 LYS cc_start: 0.8651 (mttt) cc_final: 0.8255 (mtpp) REVERT: G 342 GLU cc_start: 0.8061 (mt-10) cc_final: 0.7678 (mp0) REVERT: G 349 ARG cc_start: 0.7766 (mtm180) cc_final: 0.7085 (mtm180) REVERT: H 336 GLN cc_start: 0.8487 (mt0) cc_final: 0.8222 (mt0) REVERT: H 375 LYS cc_start: 0.8286 (tttt) cc_final: 0.8008 (tttm) REVERT: I 311 LYS cc_start: 0.8216 (mtpt) cc_final: 0.7702 (tttp) REVERT: I 347 LYS cc_start: 0.8492 (mttt) cc_final: 0.7924 (mmtm) outliers start: 9 outliers final: 3 residues processed: 165 average time/residue: 2.9524 time to fit residues: 504.6528 Evaluate side-chains 158 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 154 time to evaluate : 0.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 345 ASP Chi-restraints excluded: chain B residue 321 LYS Chi-restraints excluded: chain E residue 356 SER Chi-restraints excluded: chain G residue 356 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 45 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 55 optimal weight: 0.3980 chunk 58 optimal weight: 0.9990 chunk 33 optimal weight: 0.9980 chunk 7 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 351 GLN B 351 GLN C 336 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.139750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.123434 restraints weight = 18747.717| |-----------------------------------------------------------------------------| r_work (start): 0.3895 rms_B_bonded: 1.46 r_work: 0.3825 rms_B_bonded: 1.57 restraints_weight: 0.5000 r_work: 0.3753 rms_B_bonded: 2.73 restraints_weight: 0.2500 r_work (final): 0.3753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.4927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 5175 Z= 0.281 Angle : 0.600 5.324 6924 Z= 0.306 Chirality : 0.050 0.142 780 Planarity : 0.004 0.038 879 Dihedral : 6.189 18.227 681 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 2.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.56 % Favored : 92.44 % Rotamer: Outliers : 2.74 % Allowed : 17.26 % Favored : 80.00 % 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: -2.72 (0.26), residues: 648 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.06 (0.19), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.003 HIS B 362 PHE 0.007 0.001 PHE D 378 TYR 0.009 0.002 TYR E 310 ARG 0.003 0.001 ARG E 379 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 159 time to evaluate : 0.847 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 315 LEU cc_start: 0.8953 (mp) cc_final: 0.8641 (mp) REVERT: A 342 GLU cc_start: 0.8064 (mt-10) cc_final: 0.7547 (mp0) REVERT: B 311 LYS cc_start: 0.8321 (mttt) cc_final: 0.7721 (mmtm) REVERT: B 315 LEU cc_start: 0.9219 (OUTLIER) cc_final: 0.9015 (mp) REVERT: B 338 GLU cc_start: 0.8239 (mt-10) cc_final: 0.8036 (tt0) REVERT: B 348 ASP cc_start: 0.8294 (t0) cc_final: 0.7995 (t70) REVERT: B 379 ARG cc_start: 0.7100 (ttp-110) cc_final: 0.6498 (mtt90) REVERT: C 311 LYS cc_start: 0.8415 (mttt) cc_final: 0.7953 (mmtm) REVERT: C 321 LYS cc_start: 0.8348 (ttmt) cc_final: 0.8119 (tmtm) REVERT: C 345 ASP cc_start: 0.8304 (t0) cc_final: 0.7969 (t70) REVERT: D 314 ASP cc_start: 0.8747 (t0) cc_final: 0.8487 (t0) REVERT: E 336 GLN cc_start: 0.8542 (mt0) cc_final: 0.8295 (mt0) REVERT: E 342 GLU cc_start: 0.8036 (mt-10) cc_final: 0.7143 (mp0) REVERT: E 379 ARG cc_start: 0.6080 (OUTLIER) cc_final: 0.3564 (ptt90) REVERT: F 311 LYS cc_start: 0.8688 (mttt) cc_final: 0.7692 (pmtt) REVERT: G 321 LYS cc_start: 0.8815 (OUTLIER) cc_final: 0.8329 (mttt) REVERT: G 340 LYS cc_start: 0.8618 (mttt) cc_final: 0.8367 (mtmp) REVERT: G 342 GLU cc_start: 0.8083 (mt-10) cc_final: 0.7707 (mp0) REVERT: G 349 ARG cc_start: 0.7847 (mtm180) cc_final: 0.7120 (mtm180) REVERT: H 336 GLN cc_start: 0.8560 (mt0) cc_final: 0.8295 (mt0) REVERT: H 375 LYS cc_start: 0.8341 (tttt) cc_final: 0.8037 (tttm) REVERT: I 311 LYS cc_start: 0.8261 (mtpt) cc_final: 0.7774 (tttp) REVERT: I 347 LYS cc_start: 0.8454 (mttt) cc_final: 0.7895 (mmtm) outliers start: 16 outliers final: 5 residues processed: 164 average time/residue: 2.7334 time to fit residues: 464.8236 Evaluate side-chains 154 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 146 time to evaluate : 0.915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 345 ASP Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 358 ASP Chi-restraints excluded: chain D residue 345 ASP Chi-restraints excluded: chain E residue 356 SER Chi-restraints excluded: chain E residue 379 ARG Chi-restraints excluded: chain G residue 321 LYS Chi-restraints excluded: chain G residue 356 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 21 optimal weight: 2.9990 chunk 4 optimal weight: 0.7980 chunk 12 optimal weight: 3.9990 chunk 14 optimal weight: 2.9990 chunk 56 optimal weight: 0.8980 chunk 25 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 35 optimal weight: 0.7980 chunk 26 optimal weight: 0.9990 chunk 40 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 351 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.140530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.124453 restraints weight = 18718.259| |-----------------------------------------------------------------------------| r_work (start): 0.3902 rms_B_bonded: 1.47 r_work: 0.3833 rms_B_bonded: 1.57 restraints_weight: 0.5000 r_work: 0.3762 rms_B_bonded: 2.74 restraints_weight: 0.2500 r_work (final): 0.3762 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.5092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 5175 Z= 0.216 Angle : 0.561 4.912 6924 Z= 0.286 Chirality : 0.050 0.132 780 Planarity : 0.004 0.036 879 Dihedral : 6.041 18.495 681 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 2.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.10 % Favored : 92.90 % Rotamer: Outliers : 2.05 % Allowed : 18.46 % Favored : 79.49 % 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: -2.71 (0.26), residues: 648 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.06 (0.20), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS B 362 PHE 0.009 0.001 PHE G 378 TYR 0.008 0.002 TYR E 310 ARG 0.001 0.000 ARG H 379 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 155 time to evaluate : 0.870 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 315 LEU cc_start: 0.8974 (mp) cc_final: 0.8662 (mp) REVERT: A 342 GLU cc_start: 0.8023 (mt-10) cc_final: 0.7478 (mp0) REVERT: B 311 LYS cc_start: 0.8325 (mttt) cc_final: 0.7711 (mmtm) REVERT: B 321 LYS cc_start: 0.8536 (OUTLIER) cc_final: 0.8296 (tmmt) REVERT: B 338 GLU cc_start: 0.8220 (mt-10) cc_final: 0.8017 (tt0) REVERT: B 348 ASP cc_start: 0.8170 (t0) cc_final: 0.7848 (t70) REVERT: B 379 ARG cc_start: 0.7059 (ttp-110) cc_final: 0.6447 (mtt90) REVERT: C 311 LYS cc_start: 0.8420 (mttt) cc_final: 0.7928 (mmtm) REVERT: C 321 LYS cc_start: 0.8327 (ttmt) cc_final: 0.8112 (tmtm) REVERT: C 345 ASP cc_start: 0.8295 (t0) cc_final: 0.7962 (t70) REVERT: E 336 GLN cc_start: 0.8540 (mt0) cc_final: 0.8274 (mt0) REVERT: E 342 GLU cc_start: 0.8011 (mt-10) cc_final: 0.7142 (mp0) REVERT: F 311 LYS cc_start: 0.8647 (mttt) cc_final: 0.7645 (pmtt) REVERT: F 349 ARG cc_start: 0.8281 (mtp180) cc_final: 0.8075 (mtm180) REVERT: G 321 LYS cc_start: 0.8822 (OUTLIER) cc_final: 0.8369 (mttt) REVERT: G 340 LYS cc_start: 0.8610 (mttt) cc_final: 0.8300 (mtpp) REVERT: G 342 GLU cc_start: 0.8040 (mt-10) cc_final: 0.7661 (mp0) REVERT: G 349 ARG cc_start: 0.7843 (mtm180) cc_final: 0.7133 (mtm180) REVERT: G 378 PHE cc_start: 0.6293 (OUTLIER) cc_final: 0.6084 (t80) REVERT: H 336 GLN cc_start: 0.8542 (mt0) cc_final: 0.8274 (mt0) REVERT: H 375 LYS cc_start: 0.8380 (tttt) cc_final: 0.8074 (tttm) REVERT: I 311 LYS cc_start: 0.8240 (mtpt) cc_final: 0.7702 (tttp) REVERT: I 347 LYS cc_start: 0.8407 (mttt) cc_final: 0.7806 (mmtm) outliers start: 12 outliers final: 4 residues processed: 157 average time/residue: 2.7394 time to fit residues: 446.2958 Evaluate side-chains 152 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 145 time to evaluate : 0.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 345 ASP Chi-restraints excluded: chain B residue 321 LYS Chi-restraints excluded: chain B residue 358 ASP Chi-restraints excluded: chain E residue 356 SER Chi-restraints excluded: chain G residue 321 LYS Chi-restraints excluded: chain G residue 356 SER Chi-restraints excluded: chain G residue 378 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 4 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 60 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 57 optimal weight: 3.9990 chunk 6 optimal weight: 2.9990 chunk 48 optimal weight: 0.9990 chunk 50 optimal weight: 4.9990 chunk 30 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 351 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.136853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.121023 restraints weight = 19595.973| |-----------------------------------------------------------------------------| r_work (start): 0.3851 rms_B_bonded: 1.45 r_work: 0.3780 rms_B_bonded: 1.54 restraints_weight: 0.5000 r_work: 0.3707 rms_B_bonded: 2.68 restraints_weight: 0.2500 r_work (final): 0.3707 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.5264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 5175 Z= 0.332 Angle : 0.610 5.229 6924 Z= 0.310 Chirality : 0.050 0.135 780 Planarity : 0.005 0.064 879 Dihedral : 6.211 18.638 681 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 3.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.33 % Favored : 91.67 % Rotamer: Outliers : 1.71 % Allowed : 20.34 % Favored : 77.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.86 (0.26), residues: 648 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.17 (0.20), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.002 HIS G 330 PHE 0.011 0.001 PHE A 378 TYR 0.010 0.002 TYR E 310 ARG 0.005 0.001 ARG F 379 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 152 time to evaluate : 0.804 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 315 LEU cc_start: 0.8987 (mp) cc_final: 0.8703 (mp) REVERT: A 340 LYS cc_start: 0.8552 (mttt) cc_final: 0.8332 (mttp) REVERT: A 342 GLU cc_start: 0.7947 (mt-10) cc_final: 0.7355 (mp0) REVERT: B 311 LYS cc_start: 0.8453 (mttt) cc_final: 0.7737 (mmtm) REVERT: B 338 GLU cc_start: 0.8245 (mt-10) cc_final: 0.8027 (tt0) REVERT: C 311 LYS cc_start: 0.8488 (mttt) cc_final: 0.7976 (mmtm) REVERT: C 321 LYS cc_start: 0.8407 (ttmt) cc_final: 0.8150 (tmtm) REVERT: C 345 ASP cc_start: 0.8334 (t0) cc_final: 0.8038 (t70) REVERT: D 342 GLU cc_start: 0.8039 (mt-10) cc_final: 0.7670 (mp0) REVERT: E 336 GLN cc_start: 0.8574 (mt0) cc_final: 0.8294 (mt0) REVERT: E 342 GLU cc_start: 0.8082 (mt-10) cc_final: 0.7135 (mp0) REVERT: E 379 ARG cc_start: 0.6190 (OUTLIER) cc_final: 0.3442 (ptt90) REVERT: F 311 LYS cc_start: 0.8686 (mttt) cc_final: 0.7742 (pmtt) REVERT: F 349 ARG cc_start: 0.8295 (mtp180) cc_final: 0.8088 (mtm180) REVERT: G 321 LYS cc_start: 0.8812 (OUTLIER) cc_final: 0.8139 (tptm) REVERT: G 340 LYS cc_start: 0.8599 (mttt) cc_final: 0.8206 (mtpp) REVERT: G 342 GLU cc_start: 0.8063 (mt-10) cc_final: 0.7452 (mp0) REVERT: G 349 ARG cc_start: 0.7808 (mtm180) cc_final: 0.7100 (mtm180) REVERT: H 375 LYS cc_start: 0.8480 (tttt) cc_final: 0.8152 (tttm) REVERT: I 311 LYS cc_start: 0.8267 (mtpt) cc_final: 0.7696 (tttp) REVERT: I 347 LYS cc_start: 0.8416 (mttt) cc_final: 0.7821 (mptp) outliers start: 10 outliers final: 4 residues processed: 154 average time/residue: 2.9116 time to fit residues: 464.2907 Evaluate side-chains 142 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 136 time to evaluate : 0.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 345 ASP Chi-restraints excluded: chain D residue 345 ASP Chi-restraints excluded: chain E residue 356 SER Chi-restraints excluded: chain E residue 379 ARG Chi-restraints excluded: chain G residue 321 LYS Chi-restraints excluded: chain G residue 356 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 39 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 12 optimal weight: 0.6980 chunk 22 optimal weight: 0.9990 chunk 37 optimal weight: 0.9980 chunk 47 optimal weight: 1.9990 chunk 60 optimal weight: 0.9980 chunk 18 optimal weight: 0.7980 chunk 0 optimal weight: 2.9990 chunk 42 optimal weight: 0.7980 chunk 25 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 351 GLN H 336 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.140278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.124586 restraints weight = 18901.812| |-----------------------------------------------------------------------------| r_work (start): 0.3906 rms_B_bonded: 1.45 r_work: 0.3838 rms_B_bonded: 1.53 restraints_weight: 0.5000 r_work: 0.3766 rms_B_bonded: 2.68 restraints_weight: 0.2500 r_work (final): 0.3766 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.5380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 5175 Z= 0.186 Angle : 0.549 5.688 6924 Z= 0.278 Chirality : 0.050 0.131 780 Planarity : 0.004 0.045 879 Dihedral : 5.925 18.932 681 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 2.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.41 % Favored : 92.59 % Rotamer: Outliers : 1.54 % Allowed : 20.85 % Favored : 77.61 % 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: -2.88 (0.26), residues: 648 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.19 (0.20), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS I 329 PHE 0.017 0.001 PHE G 378 TYR 0.007 0.001 TYR E 310 ARG 0.006 0.001 ARG B 379 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 142 time to evaluate : 0.922 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 315 LEU cc_start: 0.8962 (mp) cc_final: 0.8667 (mp) REVERT: A 340 LYS cc_start: 0.8575 (mttt) cc_final: 0.8363 (mttp) REVERT: A 342 GLU cc_start: 0.7957 (mt-10) cc_final: 0.7461 (mp0) REVERT: B 311 LYS cc_start: 0.8414 (mttt) cc_final: 0.7593 (mmtm) REVERT: B 338 GLU cc_start: 0.8222 (mt-10) cc_final: 0.7992 (tt0) REVERT: B 348 ASP cc_start: 0.8080 (t0) cc_final: 0.7784 (t70) REVERT: C 311 LYS cc_start: 0.8461 (mttt) cc_final: 0.7901 (mmtm) REVERT: C 321 LYS cc_start: 0.8384 (ttmt) cc_final: 0.8119 (tmtm) REVERT: C 345 ASP cc_start: 0.8282 (t0) cc_final: 0.8007 (t70) REVERT: D 342 GLU cc_start: 0.7983 (mt-10) cc_final: 0.7733 (tt0) REVERT: E 336 GLN cc_start: 0.8491 (mt0) cc_final: 0.8216 (mt0) REVERT: E 342 GLU cc_start: 0.7938 (mt-10) cc_final: 0.7105 (mp0) REVERT: G 321 LYS cc_start: 0.8810 (OUTLIER) cc_final: 0.8133 (tptm) REVERT: G 340 LYS cc_start: 0.8583 (mttt) cc_final: 0.8237 (mtpp) REVERT: G 342 GLU cc_start: 0.8003 (mt-10) cc_final: 0.7581 (mp0) REVERT: G 349 ARG cc_start: 0.7775 (mtm180) cc_final: 0.7064 (mtm180) REVERT: H 336 GLN cc_start: 0.8547 (mt0) cc_final: 0.8259 (mt0) REVERT: H 375 LYS cc_start: 0.8447 (tttt) cc_final: 0.8127 (tttm) REVERT: I 311 LYS cc_start: 0.8247 (mtpt) cc_final: 0.7679 (tttp) REVERT: I 347 LYS cc_start: 0.8332 (mttt) cc_final: 0.7789 (mptp) outliers start: 9 outliers final: 5 residues processed: 145 average time/residue: 2.7587 time to fit residues: 415.8968 Evaluate side-chains 143 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 137 time to evaluate : 1.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 345 ASP Chi-restraints excluded: chain B residue 358 ASP Chi-restraints excluded: chain D residue 345 ASP Chi-restraints excluded: chain E residue 356 SER Chi-restraints excluded: chain G residue 321 LYS Chi-restraints excluded: chain G residue 356 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 22 optimal weight: 0.9990 chunk 42 optimal weight: 1.9990 chunk 51 optimal weight: 0.5980 chunk 62 optimal weight: 1.9990 chunk 33 optimal weight: 0.7980 chunk 35 optimal weight: 0.0030 chunk 11 optimal weight: 0.9990 chunk 3 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 59 optimal weight: 3.9990 chunk 26 optimal weight: 1.9990 overall best weight: 0.6794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 351 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.141416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.125845 restraints weight = 18786.561| |-----------------------------------------------------------------------------| r_work (start): 0.3942 rms_B_bonded: 1.44 r_work: 0.3874 rms_B_bonded: 1.56 restraints_weight: 0.5000 r_work: 0.3802 rms_B_bonded: 2.73 restraints_weight: 0.2500 r_work (final): 0.3802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.5491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 5175 Z= 0.166 Angle : 0.523 4.867 6924 Z= 0.265 Chirality : 0.050 0.131 780 Planarity : 0.004 0.038 879 Dihedral : 5.699 18.371 681 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 2.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.72 % Favored : 92.28 % Rotamer: Outliers : 1.37 % Allowed : 21.03 % Favored : 77.61 % 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: -2.87 (0.26), residues: 648 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.18 (0.19), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS I 329 PHE 0.005 0.001 PHE G 378 TYR 0.006 0.001 TYR E 310 ARG 0.005 0.000 ARG B 379 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 142 time to evaluate : 0.816 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 315 LEU cc_start: 0.8953 (mp) cc_final: 0.8665 (mp) REVERT: A 340 LYS cc_start: 0.8519 (mttt) cc_final: 0.8319 (mttp) REVERT: A 342 GLU cc_start: 0.7931 (mt-10) cc_final: 0.7469 (mp0) REVERT: B 311 LYS cc_start: 0.8431 (mttt) cc_final: 0.7665 (mmtm) REVERT: C 311 LYS cc_start: 0.8417 (mttt) cc_final: 0.7919 (mmtm) REVERT: C 321 LYS cc_start: 0.8406 (ttmt) cc_final: 0.8198 (tmtm) REVERT: C 345 ASP cc_start: 0.8266 (t0) cc_final: 0.8022 (t0) REVERT: E 336 GLN cc_start: 0.8467 (mt0) cc_final: 0.8139 (mt0) REVERT: E 342 GLU cc_start: 0.7865 (mt-10) cc_final: 0.7059 (mp0) REVERT: F 347 LYS cc_start: 0.8388 (mtmm) cc_final: 0.8116 (mtmm) REVERT: G 321 LYS cc_start: 0.8785 (OUTLIER) cc_final: 0.8157 (tptm) REVERT: G 340 LYS cc_start: 0.8567 (mttt) cc_final: 0.8251 (mtpp) REVERT: G 342 GLU cc_start: 0.7967 (mt-10) cc_final: 0.7569 (mp0) REVERT: G 349 ARG cc_start: 0.7776 (mtm180) cc_final: 0.7215 (mtm180) REVERT: H 375 LYS cc_start: 0.8395 (tttt) cc_final: 0.8101 (tttm) REVERT: I 311 LYS cc_start: 0.8235 (mtpt) cc_final: 0.7733 (tttp) REVERT: I 347 LYS cc_start: 0.8302 (mttt) cc_final: 0.7793 (mptp) outliers start: 8 outliers final: 6 residues processed: 144 average time/residue: 2.6289 time to fit residues: 393.1756 Evaluate side-chains 147 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 140 time to evaluate : 1.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 345 ASP Chi-restraints excluded: chain B residue 358 ASP Chi-restraints excluded: chain D residue 345 ASP Chi-restraints excluded: chain E residue 356 SER Chi-restraints excluded: chain G residue 321 LYS Chi-restraints excluded: chain G residue 345 ASP Chi-restraints excluded: chain G residue 356 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 53 optimal weight: 2.9990 chunk 38 optimal weight: 0.9980 chunk 0 optimal weight: 2.9990 chunk 50 optimal weight: 6.9990 chunk 15 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 chunk 52 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 46 optimal weight: 0.9980 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 351 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.137286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.121272 restraints weight = 19057.491| |-----------------------------------------------------------------------------| r_work (start): 0.3869 rms_B_bonded: 1.44 r_work: 0.3801 rms_B_bonded: 1.54 restraints_weight: 0.5000 r_work: 0.3729 rms_B_bonded: 2.69 restraints_weight: 0.2500 r_work (final): 0.3729 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.5587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 5175 Z= 0.327 Angle : 0.600 5.684 6924 Z= 0.306 Chirality : 0.049 0.134 780 Planarity : 0.005 0.060 879 Dihedral : 6.037 18.408 681 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 3.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.10 % Favored : 90.90 % Rotamer: Outliers : 1.37 % Allowed : 21.54 % Favored : 77.09 % 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: -2.97 (0.26), residues: 648 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.26 (0.20), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS G 330 PHE 0.006 0.001 PHE F 346 TYR 0.010 0.002 TYR B 310 ARG 0.008 0.001 ARG F 379 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 136 time to evaluate : 0.801 Fit side-chains revert: symmetry clash REVERT: A 315 LEU cc_start: 0.8978 (mp) cc_final: 0.8702 (mp) REVERT: A 340 LYS cc_start: 0.8517 (mttt) cc_final: 0.8298 (mttp) REVERT: A 342 GLU cc_start: 0.7965 (mt-10) cc_final: 0.7431 (mp0) REVERT: B 311 LYS cc_start: 0.8533 (mttt) cc_final: 0.7864 (mmtt) REVERT: C 311 LYS cc_start: 0.8548 (mttt) cc_final: 0.8046 (mmtm) REVERT: C 321 LYS cc_start: 0.8469 (ttmt) cc_final: 0.8222 (ttmm) REVERT: C 345 ASP cc_start: 0.8303 (t0) cc_final: 0.8043 (t70) REVERT: E 336 GLN cc_start: 0.8477 (mt0) cc_final: 0.8246 (mt0) REVERT: E 342 GLU cc_start: 0.7950 (mt-10) cc_final: 0.7114 (mp0) REVERT: F 347 LYS cc_start: 0.8486 (mtmm) cc_final: 0.8221 (mtmm) REVERT: G 321 LYS cc_start: 0.8827 (OUTLIER) cc_final: 0.8134 (tptm) REVERT: G 340 LYS cc_start: 0.8555 (mttt) cc_final: 0.8243 (mtpp) REVERT: G 342 GLU cc_start: 0.8001 (mt-10) cc_final: 0.7518 (mp0) REVERT: G 349 ARG cc_start: 0.7805 (mtm180) cc_final: 0.7116 (mtm180) REVERT: H 375 LYS cc_start: 0.8456 (tttt) cc_final: 0.8160 (tttm) REVERT: I 311 LYS cc_start: 0.8291 (mtpt) cc_final: 0.7734 (tttp) REVERT: I 347 LYS cc_start: 0.8372 (mttt) cc_final: 0.7845 (mptp) outliers start: 8 outliers final: 5 residues processed: 138 average time/residue: 2.8441 time to fit residues: 407.1055 Evaluate side-chains 142 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 136 time to evaluate : 0.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 345 ASP Chi-restraints excluded: chain D residue 345 ASP Chi-restraints excluded: chain E residue 356 SER Chi-restraints excluded: chain F residue 372 GLU Chi-restraints excluded: chain G residue 321 LYS Chi-restraints excluded: chain G residue 356 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 10 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 55 optimal weight: 0.8980 chunk 35 optimal weight: 0.3980 chunk 37 optimal weight: 0.9980 chunk 60 optimal weight: 2.9990 chunk 20 optimal weight: 0.9980 chunk 48 optimal weight: 2.9990 chunk 12 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 351 GLN H 336 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.140059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.124340 restraints weight = 18792.143| |-----------------------------------------------------------------------------| r_work (start): 0.3913 rms_B_bonded: 1.44 r_work: 0.3847 rms_B_bonded: 1.54 restraints_weight: 0.5000 r_work: 0.3775 rms_B_bonded: 2.70 restraints_weight: 0.2500 r_work (final): 0.3775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.5624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 5175 Z= 0.184 Angle : 0.539 5.765 6924 Z= 0.274 Chirality : 0.050 0.132 780 Planarity : 0.004 0.038 879 Dihedral : 5.763 18.389 681 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 2.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.87 % Favored : 92.13 % Rotamer: Outliers : 1.03 % Allowed : 22.22 % Favored : 76.75 % 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: -2.97 (0.26), residues: 648 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.25 (0.19), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS I 329 PHE 0.008 0.001 PHE G 378 TYR 0.006 0.001 TYR E 310 ARG 0.008 0.001 ARG B 379 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1296 Ramachandran restraints generated. 648 Oldfield, 0 Emsley, 648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 139 time to evaluate : 0.975 Fit side-chains revert: symmetry clash REVERT: A 315 LEU cc_start: 0.8962 (mp) cc_final: 0.8674 (mp) REVERT: A 342 GLU cc_start: 0.7929 (mt-10) cc_final: 0.7473 (mp0) REVERT: B 311 LYS cc_start: 0.8480 (mttt) cc_final: 0.7846 (mmtt) REVERT: C 311 LYS cc_start: 0.8483 (mttt) cc_final: 0.7953 (mmtm) REVERT: C 321 LYS cc_start: 0.8450 (ttmt) cc_final: 0.8220 (tmtm) REVERT: C 345 ASP cc_start: 0.8262 (t0) cc_final: 0.8004 (t70) REVERT: E 336 GLN cc_start: 0.8487 (mt0) cc_final: 0.8242 (mt0) REVERT: E 342 GLU cc_start: 0.7873 (mt-10) cc_final: 0.7078 (mp0) REVERT: F 347 LYS cc_start: 0.8376 (mtmm) cc_final: 0.8103 (mtmm) REVERT: G 321 LYS cc_start: 0.8832 (OUTLIER) cc_final: 0.8199 (tptm) REVERT: G 340 LYS cc_start: 0.8554 (mttt) cc_final: 0.8237 (mtpp) REVERT: G 342 GLU cc_start: 0.7946 (mt-10) cc_final: 0.7589 (mp0) REVERT: G 349 ARG cc_start: 0.7772 (mtm180) cc_final: 0.7206 (mtm180) REVERT: H 375 LYS cc_start: 0.8460 (tttt) cc_final: 0.8092 (tttt) REVERT: I 311 LYS cc_start: 0.8244 (mtpt) cc_final: 0.7723 (tttp) REVERT: I 347 LYS cc_start: 0.8323 (mttt) cc_final: 0.7802 (mptp) outliers start: 6 outliers final: 4 residues processed: 141 average time/residue: 2.7104 time to fit residues: 396.7754 Evaluate side-chains 137 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 132 time to evaluate : 0.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 345 ASP Chi-restraints excluded: chain D residue 345 ASP Chi-restraints excluded: chain E residue 356 SER Chi-restraints excluded: chain G residue 321 LYS Chi-restraints excluded: chain G residue 356 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 46 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 44 optimal weight: 0.7980 chunk 62 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 351 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.137238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.121189 restraints weight = 18786.280| |-----------------------------------------------------------------------------| r_work (start): 0.3865 rms_B_bonded: 1.42 r_work: 0.3799 rms_B_bonded: 1.51 restraints_weight: 0.5000 r_work: 0.3727 rms_B_bonded: 2.65 restraints_weight: 0.2500 r_work (final): 0.3727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.5691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 5175 Z= 0.331 Angle : 0.607 6.747 6924 Z= 0.307 Chirality : 0.050 0.134 780 Planarity : 0.004 0.039 879 Dihedral : 5.975 18.003 681 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.80 % Favored : 91.20 % Rotamer: Outliers : 0.85 % Allowed : 22.74 % Favored : 76.41 % 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: -3.01 (0.25), residues: 648 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.29 (0.19), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS G 330 PHE 0.006 0.001 PHE F 346 TYR 0.010 0.002 TYR B 310 ARG 0.008 0.001 ARG B 379 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10461.49 seconds wall clock time: 184 minutes 55.07 seconds (11095.07 seconds total)