Starting phenix.real_space_refine on Fri Aug 22 13:45:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8q8r_18258/08_2025/8q8r_18258.cif Found real_map, /net/cci-nas-00/data/ceres_data/8q8r_18258/08_2025/8q8r_18258.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8q8r_18258/08_2025/8q8r_18258.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8q8r_18258/08_2025/8q8r_18258.map" model { file = "/net/cci-nas-00/data/ceres_data/8q8r_18258/08_2025/8q8r_18258.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8q8r_18258/08_2025/8q8r_18258.cif" } resolution = 2.1 write_initial_geo_file = False refinement { macro_cycles = 10 } 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: 4 Type Number sf(0) Gaussians S 6 5.16 5 C 2172 2.51 5 N 642 2.21 5 O 648 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 3468 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 578 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 578 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 3, 'TRANS': 72} Chain: "B" Number of atoms: 578 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 578 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 3, 'TRANS': 72} Chain: "C" Number of atoms: 578 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 578 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 3, 'TRANS': 72} Chain: "D" Number of atoms: 578 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 578 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 3, 'TRANS': 72} Chain: "E" Number of atoms: 578 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 578 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 3, 'TRANS': 72} Chain: "F" Number of atoms: 578 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 578 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 3, 'TRANS': 72} Time building chain proxies: 0.96, per 1000 atoms: 0.28 Number of scatterers: 3468 At special positions: 0 Unit cell: (87.967, 150.489, 36.35, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 6 16.00 O 648 8.00 N 642 7.00 C 2172 6.00 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: 0.25 Conformation dependent library (CDL) restraints added in 110.4 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 792 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 18 sheets defined 0.0% alpha, 51.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.11 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 307 through 310 Processing sheet with id=AA2, first strand: chain 'A' and resid 313 through 314 removed outlier: 6.740A pdb=" N VAL A 313 " --> pdb=" O ASP D 314 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 317 through 321 removed outlier: 6.342A pdb=" N VAL B 318 " --> pdb=" O THR D 319 " (cutoff:3.500A) removed outlier: 8.265A pdb=" N LYS D 321 " --> pdb=" O VAL B 318 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N SER B 320 " --> pdb=" O LYS D 321 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 325 through 330 removed outlier: 6.976A pdb=" N GLY D 326 " --> pdb=" O LEU A 325 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N ASN A 327 " --> pdb=" O GLY D 326 " (cutoff:3.500A) removed outlier: 5.731A pdb=" N GLY B 326 " --> pdb=" O ASN D 327 " (cutoff:3.500A) removed outlier: 8.519A pdb=" N HIS D 329 " --> pdb=" O GLY B 326 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N ILE B 328 " --> pdb=" O HIS D 329 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 336 through 340 removed outlier: 6.543A pdb=" N VAL B 337 " --> pdb=" O GLU D 338 " (cutoff:3.500A) removed outlier: 8.320A pdb=" N LYS D 340 " --> pdb=" O VAL B 337 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N VAL B 339 " --> pdb=" O LYS D 340 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 343 through 347 removed outlier: 6.172A pdb=" N LYS A 343 " --> pdb=" O LEU D 344 " (cutoff:3.500A) removed outlier: 7.748A pdb=" N PHE D 346 " --> pdb=" O LYS A 343 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N ASP A 345 " --> pdb=" O PHE D 346 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 350 through 356 removed outlier: 6.755A pdb=" N SER D 356 " --> pdb=" O GLY A 355 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N VAL B 350 " --> pdb=" O GLN D 351 " (cutoff:3.500A) removed outlier: 8.111A pdb=" N LYS D 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N SER B 352 " --> pdb=" O LYS D 353 " (cutoff:3.500A) removed outlier: 8.197A pdb=" N GLY D 355 " --> pdb=" O SER B 352 " (cutoff:3.500A) removed outlier: 8.168A pdb=" N ILE B 354 " --> pdb=" O GLY D 355 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 359 through 362 removed outlier: 6.595A pdb=" N ASN B 359 " --> pdb=" O ILE D 360 " (cutoff:3.500A) removed outlier: 7.807A pdb=" N HIS D 362 " --> pdb=" O ASN B 359 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N THR B 361 " --> pdb=" O HIS D 362 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 369 through 378 removed outlier: 6.520A pdb=" N LYS A 369 " --> pdb=" O LYS D 370 " (cutoff:3.500A) removed outlier: 7.926A pdb=" N GLU D 372 " --> pdb=" O LYS A 369 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N ILE A 371 " --> pdb=" O GLU D 372 " (cutoff:3.500A) removed outlier: 7.929A pdb=" N HIS D 374 " --> pdb=" O ILE A 371 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N THR A 373 " --> pdb=" O HIS D 374 " (cutoff:3.500A) removed outlier: 8.160A pdb=" N LEU D 376 " --> pdb=" O THR A 373 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N LYS A 375 " --> pdb=" O LEU D 376 " (cutoff:3.500A) removed outlier: 8.155A pdb=" N PHE D 378 " --> pdb=" O LYS A 375 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N THR A 377 " --> pdb=" O PHE D 378 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 307 through 310 removed outlier: 6.543A pdb=" N ILE C 308 " --> pdb=" O VAL E 309 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N ILE E 308 " --> pdb=" O VAL F 309 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'C' and resid 313 through 314 Processing sheet with id=AB3, first strand: chain 'C' and resid 317 through 321 removed outlier: 6.353A pdb=" N VAL C 318 " --> pdb=" O THR E 319 " (cutoff:3.500A) removed outlier: 8.250A pdb=" N LYS E 321 " --> pdb=" O VAL C 318 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N SER C 320 " --> pdb=" O LYS E 321 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N VAL E 318 " --> pdb=" O THR F 319 " (cutoff:3.500A) removed outlier: 8.273A pdb=" N LYS F 321 " --> pdb=" O VAL E 318 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N SER E 320 " --> pdb=" O LYS F 321 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'C' and resid 325 through 330 removed outlier: 5.764A pdb=" N GLY C 326 " --> pdb=" O ASN E 327 " (cutoff:3.500A) removed outlier: 8.518A pdb=" N HIS E 329 " --> pdb=" O GLY C 326 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N ILE C 328 " --> pdb=" O HIS E 329 " (cutoff:3.500A) removed outlier: 5.747A pdb=" N GLY E 326 " --> pdb=" O ASN F 327 " (cutoff:3.500A) removed outlier: 8.466A pdb=" N HIS F 329 " --> pdb=" O GLY E 326 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N ILE E 328 " --> pdb=" O HIS F 329 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'C' and resid 336 through 340 removed outlier: 6.535A pdb=" N VAL C 337 " --> pdb=" O GLU E 338 " (cutoff:3.500A) removed outlier: 8.305A pdb=" N LYS E 340 " --> pdb=" O VAL C 337 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N VAL C 339 " --> pdb=" O LYS E 340 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N VAL E 337 " --> pdb=" O GLU F 338 " (cutoff:3.500A) removed outlier: 8.318A pdb=" N LYS F 340 " --> pdb=" O VAL E 337 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N VAL E 339 " --> pdb=" O LYS F 340 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'C' and resid 343 through 347 Processing sheet with id=AB7, first strand: chain 'C' and resid 350 through 356 removed outlier: 6.358A pdb=" N VAL C 350 " --> pdb=" O GLN E 351 " (cutoff:3.500A) removed outlier: 8.138A pdb=" N LYS E 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N SER C 352 " --> pdb=" O LYS E 353 " (cutoff:3.500A) removed outlier: 8.170A pdb=" N GLY E 355 " --> pdb=" O SER C 352 " (cutoff:3.500A) removed outlier: 8.177A pdb=" N ILE C 354 " --> pdb=" O GLY E 355 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N VAL E 350 " --> pdb=" O GLN F 351 " (cutoff:3.500A) removed outlier: 8.092A pdb=" N LYS F 353 " --> pdb=" O VAL E 350 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N SER E 352 " --> pdb=" O LYS F 353 " (cutoff:3.500A) removed outlier: 8.148A pdb=" N GLY F 355 " --> pdb=" O SER E 352 " (cutoff:3.500A) removed outlier: 8.207A pdb=" N ILE E 354 " --> pdb=" O GLY F 355 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'C' and resid 359 through 362 removed outlier: 6.570A pdb=" N ASN C 359 " --> pdb=" O ILE E 360 " (cutoff:3.500A) removed outlier: 7.825A pdb=" N HIS E 362 " --> pdb=" O ASN C 359 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N THR C 361 " --> pdb=" O HIS E 362 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N ASN E 359 " --> pdb=" O ILE F 360 " (cutoff:3.500A) removed outlier: 7.855A pdb=" N HIS F 362 " --> pdb=" O ASN E 359 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N THR E 361 " --> pdb=" O HIS F 362 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'C' and resid 369 through 378 68 hydrogen bonds defined for protein. 204 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: 0.32 Time building geometry restraints manager: 0.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 950 1.33 - 1.45: 455 1.45 - 1.57: 2111 1.57 - 1.69: 0 1.69 - 1.81: 6 Bond restraints: 3522 Sorted by residual: bond pdb=" CZ ARG C 379 " pdb=" NH2 ARG C 379 " ideal model delta sigma weight residual 1.330 1.295 0.035 1.30e-02 5.92e+03 7.10e+00 bond pdb=" CZ ARG B 379 " pdb=" NH2 ARG B 379 " ideal model delta sigma weight residual 1.330 1.296 0.034 1.30e-02 5.92e+03 6.89e+00 bond pdb=" CZ ARG D 349 " pdb=" NH2 ARG D 349 " ideal model delta sigma weight residual 1.330 1.297 0.033 1.30e-02 5.92e+03 6.47e+00 bond pdb=" CZ ARG D 379 " pdb=" NH2 ARG D 379 " ideal model delta sigma weight residual 1.330 1.298 0.032 1.30e-02 5.92e+03 6.25e+00 bond pdb=" CZ ARG F 379 " pdb=" NH2 ARG F 379 " ideal model delta sigma weight residual 1.330 1.298 0.032 1.30e-02 5.92e+03 6.22e+00 ... (remaining 3517 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.68: 3165 1.68 - 3.36: 1208 3.36 - 5.03: 283 5.03 - 6.71: 47 6.71 - 8.39: 7 Bond angle restraints: 4710 Sorted by residual: angle pdb=" CB HIS B 374 " pdb=" CG HIS B 374 " pdb=" CD2 HIS B 374 " ideal model delta sigma weight residual 131.20 125.16 6.04 1.30e+00 5.92e-01 2.16e+01 angle pdb=" CB HIS E 362 " pdb=" CG HIS E 362 " pdb=" CD2 HIS E 362 " ideal model delta sigma weight residual 131.20 125.18 6.02 1.30e+00 5.92e-01 2.14e+01 angle pdb=" CB HIS A 362 " pdb=" CG HIS A 362 " pdb=" CD2 HIS A 362 " ideal model delta sigma weight residual 131.20 125.19 6.01 1.30e+00 5.92e-01 2.13e+01 angle pdb=" C LEU B 357 " pdb=" CA LEU B 357 " pdb=" CB LEU B 357 " ideal model delta sigma weight residual 111.74 119.08 -7.34 1.59e+00 3.96e-01 2.13e+01 angle pdb=" OE1 GLN D 336 " pdb=" CD GLN D 336 " pdb=" NE2 GLN D 336 " ideal model delta sigma weight residual 122.60 117.99 4.61 1.00e+00 1.00e+00 2.13e+01 ... (remaining 4705 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.49: 1949 13.49 - 26.98: 150 26.98 - 40.47: 28 40.47 - 53.96: 7 53.96 - 67.45: 8 Dihedral angle restraints: 2142 sinusoidal: 894 harmonic: 1248 Sorted by residual: dihedral pdb=" N ARG C 349 " pdb=" C ARG C 349 " pdb=" CA ARG C 349 " pdb=" CB ARG C 349 " ideal model delta harmonic sigma weight residual 122.80 135.29 -12.49 0 2.50e+00 1.60e-01 2.49e+01 dihedral pdb=" C ARG C 349 " pdb=" N ARG C 349 " pdb=" CA ARG C 349 " pdb=" CB ARG C 349 " ideal model delta harmonic sigma weight residual -122.60 -135.07 12.47 0 2.50e+00 1.60e-01 2.49e+01 dihedral pdb=" N ARG B 349 " pdb=" C ARG B 349 " pdb=" CA ARG B 349 " pdb=" CB ARG B 349 " ideal model delta harmonic sigma weight residual 122.80 134.85 -12.05 0 2.50e+00 1.60e-01 2.32e+01 ... (remaining 2139 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.092: 380 0.092 - 0.184: 124 0.184 - 0.275: 16 0.275 - 0.367: 2 0.367 - 0.459: 6 Chirality restraints: 528 Sorted by residual: chirality pdb=" CA ARG C 349 " pdb=" N ARG C 349 " pdb=" C ARG C 349 " pdb=" CB ARG C 349 " both_signs ideal model delta sigma weight residual False 2.51 2.05 0.46 2.00e-01 2.50e+01 5.26e+00 chirality pdb=" CA ARG B 349 " pdb=" N ARG B 349 " pdb=" C ARG B 349 " pdb=" CB ARG B 349 " both_signs ideal model delta sigma weight residual False 2.51 2.08 0.43 2.00e-01 2.50e+01 4.67e+00 chirality pdb=" CA GLU D 372 " pdb=" N GLU D 372 " pdb=" C GLU D 372 " pdb=" CB GLU D 372 " both_signs ideal model delta sigma weight residual False 2.51 2.08 0.43 2.00e-01 2.50e+01 4.59e+00 ... (remaining 525 not shown) Planarity restraints: 600 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR D 310 " 0.082 2.00e-02 2.50e+03 4.57e-02 4.17e+01 pdb=" CG TYR D 310 " -0.028 2.00e-02 2.50e+03 pdb=" CD1 TYR D 310 " -0.029 2.00e-02 2.50e+03 pdb=" CD2 TYR D 310 " -0.037 2.00e-02 2.50e+03 pdb=" CE1 TYR D 310 " -0.029 2.00e-02 2.50e+03 pdb=" CE2 TYR D 310 " -0.025 2.00e-02 2.50e+03 pdb=" CZ TYR D 310 " -0.009 2.00e-02 2.50e+03 pdb=" OH TYR D 310 " 0.074 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE E 378 " -0.064 2.00e-02 2.50e+03 4.81e-02 4.06e+01 pdb=" CG PHE E 378 " 0.008 2.00e-02 2.50e+03 pdb=" CD1 PHE E 378 " 0.051 2.00e-02 2.50e+03 pdb=" CD2 PHE E 378 " 0.069 2.00e-02 2.50e+03 pdb=" CE1 PHE E 378 " 0.011 2.00e-02 2.50e+03 pdb=" CE2 PHE E 378 " -0.007 2.00e-02 2.50e+03 pdb=" CZ PHE E 378 " -0.067 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR E 310 " -0.073 2.00e-02 2.50e+03 4.31e-02 3.72e+01 pdb=" CG TYR E 310 " 0.014 2.00e-02 2.50e+03 pdb=" CD1 TYR E 310 " 0.033 2.00e-02 2.50e+03 pdb=" CD2 TYR E 310 " 0.030 2.00e-02 2.50e+03 pdb=" CE1 TYR E 310 " 0.028 2.00e-02 2.50e+03 pdb=" CE2 TYR E 310 " 0.033 2.00e-02 2.50e+03 pdb=" CZ TYR E 310 " 0.010 2.00e-02 2.50e+03 pdb=" OH TYR E 310 " -0.074 2.00e-02 2.50e+03 ... (remaining 597 not shown) Histogram of nonbonded interaction distances: 2.51 - 2.98: 1551 2.98 - 3.46: 2879 3.46 - 3.94: 5435 3.94 - 4.42: 5766 4.42 - 4.90: 10964 Nonbonded interactions: 26595 Sorted by model distance: nonbonded pdb=" OD1 ASP A 314 " pdb=" OG SER A 316 " model vdw 2.505 3.040 nonbonded pdb=" OD1 ASP F 314 " pdb=" OG SER F 316 " model vdw 2.517 3.040 nonbonded pdb=" OD1 ASP E 314 " pdb=" OG SER E 316 " model vdw 2.519 3.040 nonbonded pdb=" OD1 ASP D 314 " pdb=" OG SER D 316 " model vdw 2.521 3.040 nonbonded pdb=" OD1 ASP B 314 " pdb=" OG SER B 316 " model vdw 2.532 3.040 ... (remaining 26590 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' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' 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: 3.880 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: 0.000 Extract box with map and model: 0.090 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 4.790 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.000 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:5.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 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 0.037 3522 Z= 0.703 Angle : 1.820 8.390 4710 Z= 1.198 Chirality : 0.098 0.459 528 Planarity : 0.013 0.122 600 Dihedral : 11.112 67.450 1350 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 0.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.04 % Favored : 88.96 % Rotamer: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Cbeta Deviations : 1.52 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.41 (0.31), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.06 (0.23), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG F 379 TYR 0.082 0.027 TYR D 310 PHE 0.069 0.022 PHE E 378 HIS 0.016 0.005 HIS E 330 Details of bonding type rmsd covalent geometry : bond 0.01130 ( 3522) covalent geometry : angle 1.81998 ( 4710) hydrogen bonds : bond 0.06912 ( 68) hydrogen bonds : angle 6.93175 ( 204) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 182 time to evaluate : 0.123 Fit side-chains REVERT: A 373 THR cc_start: 0.8478 (m) cc_final: 0.7846 (p) REVERT: B 314 ASP cc_start: 0.8131 (t0) cc_final: 0.7899 (t0) REVERT: B 315 LEU cc_start: 0.8638 (mp) cc_final: 0.8346 (mm) REVERT: B 370 LYS cc_start: 0.8283 (tttp) cc_final: 0.7660 (tttp) REVERT: B 373 THR cc_start: 0.8466 (m) cc_final: 0.8177 (p) REVERT: B 375 LYS cc_start: 0.8002 (ttmt) cc_final: 0.7546 (tttt) REVERT: C 373 THR cc_start: 0.8502 (m) cc_final: 0.8236 (p) REVERT: D 373 THR cc_start: 0.8470 (m) cc_final: 0.7991 (p) REVERT: E 373 THR cc_start: 0.8517 (m) cc_final: 0.7994 (p) REVERT: F 336 GLN cc_start: 0.8580 (tp40) cc_final: 0.8244 (mt0) outliers start: 0 outliers final: 0 residues processed: 182 average time/residue: 0.6029 time to fit residues: 112.2485 Evaluate side-chains 105 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 105 time to evaluate : 0.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 24 optimal weight: 5.9990 chunk 26 optimal weight: 2.9990 chunk 2 optimal weight: 0.8980 chunk 16 optimal weight: 1.9990 chunk 32 optimal weight: 3.9990 chunk 31 optimal weight: 9.9990 chunk 25 optimal weight: 3.9990 chunk 19 optimal weight: 8.9990 chunk 30 optimal weight: 7.9990 chunk 22 optimal weight: 5.9990 chunk 37 optimal weight: 2.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4206 r_free = 0.4206 target = 0.154845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.127335 restraints weight = 3270.390| |-----------------------------------------------------------------------------| r_work (start): 0.3845 rms_B_bonded: 1.48 r_work: 0.3763 rms_B_bonded: 1.60 restraints_weight: 0.5000 r_work: 0.3683 rms_B_bonded: 2.67 restraints_weight: 0.2500 r_work (final): 0.3683 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8503 moved from start: 0.3394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.020 3522 Z= 0.158 Angle : 0.747 9.036 4710 Z= 0.358 Chirality : 0.052 0.160 528 Planarity : 0.003 0.022 600 Dihedral : 6.222 17.961 468 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.76 % Favored : 93.24 % Rotamer: Outliers : 4.80 % Allowed : 17.17 % Favored : 78.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.34 (0.32), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.01 (0.24), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 379 TYR 0.010 0.002 TYR D 310 PHE 0.009 0.002 PHE C 378 HIS 0.006 0.002 HIS B 329 Details of bonding type rmsd covalent geometry : bond 0.00352 ( 3522) covalent geometry : angle 0.74749 ( 4710) hydrogen bonds : bond 0.02433 ( 68) hydrogen bonds : angle 5.30002 ( 204) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 125 time to evaluate : 0.118 Fit side-chains REVERT: A 311 LYS cc_start: 0.8231 (mttt) cc_final: 0.7631 (mmpt) REVERT: A 373 THR cc_start: 0.8798 (m) cc_final: 0.8457 (p) REVERT: B 375 LYS cc_start: 0.8306 (ttmt) cc_final: 0.8023 (tttt) REVERT: B 379 ARG cc_start: 0.6006 (mtm180) cc_final: 0.5775 (mpp-170) REVERT: C 372 GLU cc_start: 0.8104 (tt0) cc_final: 0.7772 (mm-30) REVERT: C 375 LYS cc_start: 0.8330 (ttmt) cc_final: 0.8063 (tttt) REVERT: E 372 GLU cc_start: 0.8094 (mt-10) cc_final: 0.7832 (mm-30) REVERT: F 378 PHE cc_start: 0.7879 (t80) cc_final: 0.7453 (t80) outliers start: 19 outliers final: 7 residues processed: 134 average time/residue: 0.5318 time to fit residues: 73.0623 Evaluate side-chains 125 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 118 time to evaluate : 0.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain B residue 356 SER Chi-restraints excluded: chain C residue 356 SER Chi-restraints excluded: chain D residue 356 SER Chi-restraints excluded: chain F residue 357 LEU Chi-restraints excluded: chain F residue 373 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 12 optimal weight: 3.9990 chunk 6 optimal weight: 3.9990 chunk 22 optimal weight: 9.9990 chunk 31 optimal weight: 10.0000 chunk 17 optimal weight: 1.9990 chunk 34 optimal weight: 0.0270 chunk 37 optimal weight: 7.9990 chunk 18 optimal weight: 0.0870 chunk 13 optimal weight: 6.9990 chunk 35 optimal weight: 10.0000 chunk 25 optimal weight: 9.9990 overall best weight: 2.0222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 307 GLN C 351 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4199 r_free = 0.4199 target = 0.154758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.127533 restraints weight = 3280.044| |-----------------------------------------------------------------------------| r_work (start): 0.3846 rms_B_bonded: 1.49 r_work: 0.3763 rms_B_bonded: 1.63 restraints_weight: 0.5000 r_work: 0.3679 rms_B_bonded: 2.72 restraints_weight: 0.2500 r_work (final): 0.3679 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8506 moved from start: 0.3675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 3522 Z= 0.131 Angle : 0.679 8.379 4710 Z= 0.321 Chirality : 0.051 0.147 528 Planarity : 0.003 0.022 600 Dihedral : 5.754 16.013 468 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.08 % Favored : 93.92 % Rotamer: Outliers : 4.80 % Allowed : 18.94 % Favored : 76.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.45 (0.32), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.10 (0.24), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 349 TYR 0.010 0.002 TYR D 310 PHE 0.006 0.002 PHE C 378 HIS 0.004 0.001 HIS B 329 Details of bonding type rmsd covalent geometry : bond 0.00286 ( 3522) covalent geometry : angle 0.67888 ( 4710) hydrogen bonds : bond 0.01994 ( 68) hydrogen bonds : angle 4.93834 ( 204) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 119 time to evaluate : 0.101 Fit side-chains revert: symmetry clash REVERT: A 311 LYS cc_start: 0.8203 (mttt) cc_final: 0.7629 (mmpt) REVERT: A 373 THR cc_start: 0.8813 (m) cc_final: 0.8541 (p) REVERT: B 343 LYS cc_start: 0.8201 (OUTLIER) cc_final: 0.7967 (mtpt) REVERT: B 375 LYS cc_start: 0.8338 (ttmt) cc_final: 0.8063 (tttt) REVERT: C 372 GLU cc_start: 0.8062 (tt0) cc_final: 0.7830 (mm-30) REVERT: C 375 LYS cc_start: 0.8326 (ttmt) cc_final: 0.8104 (tttt) REVERT: E 347 LYS cc_start: 0.8007 (OUTLIER) cc_final: 0.7782 (mtmt) REVERT: F 340 LYS cc_start: 0.8202 (mttt) cc_final: 0.7882 (mmmt) REVERT: F 343 LYS cc_start: 0.8232 (mmtt) cc_final: 0.7908 (mtpm) outliers start: 19 outliers final: 8 residues processed: 130 average time/residue: 0.5813 time to fit residues: 77.2971 Evaluate side-chains 117 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 107 time to evaluate : 0.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain B residue 343 LYS Chi-restraints excluded: chain B residue 356 SER Chi-restraints excluded: chain C residue 343 LYS Chi-restraints excluded: chain C residue 347 LYS Chi-restraints excluded: chain C residue 356 SER Chi-restraints excluded: chain D residue 356 SER Chi-restraints excluded: chain E residue 347 LYS Chi-restraints excluded: chain F residue 357 LEU Chi-restraints excluded: chain F residue 373 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 0.0010 chunk 1 optimal weight: 5.9990 chunk 36 optimal weight: 0.6980 chunk 17 optimal weight: 5.9990 chunk 20 optimal weight: 0.4980 chunk 15 optimal weight: 0.4980 chunk 3 optimal weight: 10.0000 chunk 2 optimal weight: 9.9990 chunk 14 optimal weight: 10.0000 chunk 7 optimal weight: 10.0000 chunk 40 optimal weight: 10.0000 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 307 GLN C 351 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4208 r_free = 0.4208 target = 0.156597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.129703 restraints weight = 3203.269| |-----------------------------------------------------------------------------| r_work (start): 0.3860 rms_B_bonded: 1.46 r_work: 0.3782 rms_B_bonded: 1.57 restraints_weight: 0.5000 r_work: 0.3703 rms_B_bonded: 2.62 restraints_weight: 0.2500 r_work (final): 0.3703 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.3776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.015 3522 Z= 0.110 Angle : 0.621 7.853 4710 Z= 0.291 Chirality : 0.050 0.136 528 Planarity : 0.003 0.020 600 Dihedral : 5.451 15.026 468 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.21 % Favored : 92.79 % Rotamer: Outliers : 4.55 % Allowed : 18.94 % Favored : 76.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.43 (0.32), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.08 (0.25), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 349 TYR 0.009 0.002 TYR D 310 PHE 0.011 0.002 PHE E 378 HIS 0.003 0.001 HIS D 362 Details of bonding type rmsd covalent geometry : bond 0.00238 ( 3522) covalent geometry : angle 0.62057 ( 4710) hydrogen bonds : bond 0.01721 ( 68) hydrogen bonds : angle 4.72789 ( 204) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 109 time to evaluate : 0.151 Fit side-chains revert: symmetry clash REVERT: A 373 THR cc_start: 0.8798 (m) cc_final: 0.8554 (p) REVERT: B 343 LYS cc_start: 0.8148 (OUTLIER) cc_final: 0.7899 (mtpt) REVERT: B 375 LYS cc_start: 0.8324 (ttmt) cc_final: 0.8061 (tttt) REVERT: C 372 GLU cc_start: 0.8052 (tt0) cc_final: 0.7747 (mm-30) REVERT: C 375 LYS cc_start: 0.8279 (ttmt) cc_final: 0.8076 (tttt) REVERT: E 347 LYS cc_start: 0.7955 (OUTLIER) cc_final: 0.7695 (mtmt) REVERT: F 319 THR cc_start: 0.8197 (m) cc_final: 0.7915 (p) REVERT: F 321 LYS cc_start: 0.8487 (tttp) cc_final: 0.8204 (tptt) REVERT: F 343 LYS cc_start: 0.8239 (mmtt) cc_final: 0.7972 (mtpm) outliers start: 18 outliers final: 7 residues processed: 119 average time/residue: 0.5558 time to fit residues: 67.7588 Evaluate side-chains 114 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 105 time to evaluate : 0.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 343 LYS Chi-restraints excluded: chain B residue 356 SER Chi-restraints excluded: chain C residue 343 LYS Chi-restraints excluded: chain C residue 347 LYS Chi-restraints excluded: chain C residue 356 SER Chi-restraints excluded: chain D residue 356 SER Chi-restraints excluded: chain E residue 347 LYS Chi-restraints excluded: chain F residue 357 LEU Chi-restraints excluded: chain F residue 373 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 28 optimal weight: 10.0000 chunk 15 optimal weight: 0.7980 chunk 19 optimal weight: 4.9990 chunk 39 optimal weight: 10.0000 chunk 6 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 31 optimal weight: 8.9990 chunk 40 optimal weight: 10.0000 chunk 3 optimal weight: 10.0000 chunk 1 optimal weight: 5.9990 chunk 9 optimal weight: 10.0000 overall best weight: 5.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 351 GLN F 351 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.152005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.127178 restraints weight = 3374.954| |-----------------------------------------------------------------------------| r_work (start): 0.3792 rms_B_bonded: 1.32 r_work: 0.3706 rms_B_bonded: 1.52 restraints_weight: 0.5000 r_work: 0.3625 rms_B_bonded: 2.54 restraints_weight: 0.2500 r_work (final): 0.3625 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8537 moved from start: 0.3579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.031 3522 Z= 0.290 Angle : 0.766 10.819 4710 Z= 0.389 Chirality : 0.056 0.259 528 Planarity : 0.004 0.026 600 Dihedral : 6.180 18.150 468 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.11 % Favored : 91.89 % Rotamer: Outliers : 6.06 % Allowed : 18.18 % Favored : 75.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.60 (0.32), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.21 (0.24), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 379 TYR 0.011 0.003 TYR D 310 PHE 0.011 0.003 PHE F 378 HIS 0.007 0.002 HIS B 329 Details of bonding type rmsd covalent geometry : bond 0.00639 ( 3522) covalent geometry : angle 0.76636 ( 4710) hydrogen bonds : bond 0.02498 ( 68) hydrogen bonds : angle 5.13481 ( 204) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 106 time to evaluate : 0.093 Fit side-chains revert: symmetry clash REVERT: A 307 GLN cc_start: 0.7570 (tt0) cc_final: 0.7181 (tt0) REVERT: A 373 THR cc_start: 0.8770 (m) cc_final: 0.8519 (p) REVERT: B 375 LYS cc_start: 0.8310 (ttmt) cc_final: 0.8064 (tttt) REVERT: C 342 GLU cc_start: 0.7600 (mm-30) cc_final: 0.7179 (mp0) REVERT: C 372 GLU cc_start: 0.7997 (tt0) cc_final: 0.7755 (mm-30) REVERT: C 375 LYS cc_start: 0.8312 (ttmt) cc_final: 0.8107 (tttt) REVERT: E 347 LYS cc_start: 0.8100 (OUTLIER) cc_final: 0.7871 (mtmt) REVERT: F 343 LYS cc_start: 0.8275 (mmtt) cc_final: 0.8015 (mtpm) outliers start: 24 outliers final: 13 residues processed: 118 average time/residue: 0.5931 time to fit residues: 71.7706 Evaluate side-chains 115 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 101 time to evaluate : 0.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain B residue 356 SER Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain C residue 343 LYS Chi-restraints excluded: chain C residue 347 LYS Chi-restraints excluded: chain C residue 356 SER Chi-restraints excluded: chain D residue 356 SER Chi-restraints excluded: chain E residue 319 THR Chi-restraints excluded: chain E residue 347 LYS Chi-restraints excluded: chain F residue 347 LYS Chi-restraints excluded: chain F residue 356 SER Chi-restraints excluded: chain F residue 357 LEU Chi-restraints excluded: chain F residue 373 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 11 optimal weight: 9.9990 chunk 15 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 20 optimal weight: 2.9990 chunk 12 optimal weight: 0.7980 chunk 31 optimal weight: 6.9990 chunk 34 optimal weight: 0.6980 chunk 36 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 chunk 18 optimal weight: 0.9990 chunk 38 optimal weight: 5.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 307 GLN C 307 GLN C 351 GLN F 307 GLN F 351 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4215 r_free = 0.4215 target = 0.157500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.132997 restraints weight = 3358.086| |-----------------------------------------------------------------------------| r_work (start): 0.3882 rms_B_bonded: 1.32 r_work: 0.3801 rms_B_bonded: 1.50 restraints_weight: 0.5000 r_work: 0.3723 rms_B_bonded: 2.51 restraints_weight: 0.2500 r_work (final): 0.3723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.3890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.014 3522 Z= 0.097 Angle : 0.592 6.985 4710 Z= 0.278 Chirality : 0.050 0.138 528 Planarity : 0.003 0.022 600 Dihedral : 5.349 14.977 468 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 2.27 % Allowed : 22.73 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.50 (0.33), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.13 (0.25), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 379 TYR 0.008 0.001 TYR D 310 PHE 0.015 0.001 PHE E 378 HIS 0.002 0.001 HIS E 362 Details of bonding type rmsd covalent geometry : bond 0.00208 ( 3522) covalent geometry : angle 0.59217 ( 4710) hydrogen bonds : bond 0.01586 ( 68) hydrogen bonds : angle 4.66740 ( 204) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 113 time to evaluate : 0.104 Fit side-chains revert: symmetry clash REVERT: A 307 GLN cc_start: 0.7506 (tt0) cc_final: 0.7117 (tt0) REVERT: A 373 THR cc_start: 0.8800 (m) cc_final: 0.8579 (p) REVERT: B 375 LYS cc_start: 0.8314 (ttmt) cc_final: 0.8062 (tttt) REVERT: C 319 THR cc_start: 0.8205 (m) cc_final: 0.7861 (p) REVERT: C 372 GLU cc_start: 0.7989 (tt0) cc_final: 0.7756 (mm-30) REVERT: E 373 THR cc_start: 0.8683 (m) cc_final: 0.8333 (p) REVERT: F 319 THR cc_start: 0.8209 (m) cc_final: 0.7943 (p) REVERT: F 343 LYS cc_start: 0.8228 (mmtt) cc_final: 0.8025 (mtpm) outliers start: 9 outliers final: 3 residues processed: 117 average time/residue: 0.5777 time to fit residues: 69.2311 Evaluate side-chains 109 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 106 time to evaluate : 0.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 343 LYS Chi-restraints excluded: chain C residue 347 LYS Chi-restraints excluded: chain F residue 357 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 25 optimal weight: 10.0000 chunk 29 optimal weight: 5.9990 chunk 11 optimal weight: 1.9990 chunk 20 optimal weight: 6.9990 chunk 32 optimal weight: 10.0000 chunk 36 optimal weight: 2.9990 chunk 13 optimal weight: 9.9990 chunk 40 optimal weight: 7.9990 chunk 28 optimal weight: 0.9980 chunk 33 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 351 GLN F 351 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4176 r_free = 0.4176 target = 0.154362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.129401 restraints weight = 3367.026| |-----------------------------------------------------------------------------| r_work (start): 0.3828 rms_B_bonded: 1.33 r_work: 0.3744 rms_B_bonded: 1.51 restraints_weight: 0.5000 r_work: 0.3663 rms_B_bonded: 2.53 restraints_weight: 0.2500 r_work (final): 0.3663 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8507 moved from start: 0.3777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 3522 Z= 0.154 Angle : 0.637 8.506 4710 Z= 0.309 Chirality : 0.051 0.165 528 Planarity : 0.003 0.023 600 Dihedral : 5.620 15.957 468 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.66 % Favored : 92.34 % Rotamer: Outliers : 5.05 % Allowed : 21.72 % Favored : 73.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.45 (0.33), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.10 (0.25), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 379 TYR 0.009 0.002 TYR D 310 PHE 0.013 0.002 PHE E 378 HIS 0.004 0.001 HIS B 329 Details of bonding type rmsd covalent geometry : bond 0.00336 ( 3522) covalent geometry : angle 0.63684 ( 4710) hydrogen bonds : bond 0.01878 ( 68) hydrogen bonds : angle 4.75041 ( 204) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 107 time to evaluate : 0.161 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 307 GLN cc_start: 0.7514 (tt0) cc_final: 0.7134 (tt0) REVERT: A 373 THR cc_start: 0.8782 (m) cc_final: 0.8545 (p) REVERT: B 375 LYS cc_start: 0.8339 (ttmt) cc_final: 0.8069 (tttt) REVERT: C 342 GLU cc_start: 0.7530 (OUTLIER) cc_final: 0.7131 (mp0) REVERT: C 372 GLU cc_start: 0.8009 (tt0) cc_final: 0.7769 (mm-30) REVERT: F 343 LYS cc_start: 0.8226 (mmtt) cc_final: 0.8001 (mtpm) outliers start: 20 outliers final: 9 residues processed: 118 average time/residue: 0.5713 time to fit residues: 68.9787 Evaluate side-chains 112 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 102 time to evaluate : 0.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain B residue 356 SER Chi-restraints excluded: chain C residue 342 GLU Chi-restraints excluded: chain C residue 343 LYS Chi-restraints excluded: chain C residue 347 LYS Chi-restraints excluded: chain C residue 356 SER Chi-restraints excluded: chain E residue 356 SER Chi-restraints excluded: chain F residue 347 LYS Chi-restraints excluded: chain F residue 357 LEU Chi-restraints excluded: chain F residue 373 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 39 optimal weight: 9.9990 chunk 12 optimal weight: 0.9980 chunk 33 optimal weight: 7.9990 chunk 10 optimal weight: 3.9990 chunk 34 optimal weight: 0.5980 chunk 19 optimal weight: 0.5980 chunk 40 optimal weight: 3.9990 chunk 29 optimal weight: 10.0000 chunk 15 optimal weight: 0.7980 chunk 41 optimal weight: 7.9990 chunk 5 optimal weight: 5.9990 overall best weight: 1.3982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 307 GLN C 351 GLN F 307 GLN F 351 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.156248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.129199 restraints weight = 3265.940| |-----------------------------------------------------------------------------| r_work (start): 0.3854 rms_B_bonded: 1.47 r_work: 0.3774 rms_B_bonded: 1.59 restraints_weight: 0.5000 r_work: 0.3690 rms_B_bonded: 2.67 restraints_weight: 0.2500 r_work (final): 0.3690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8498 moved from start: 0.3899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.016 3522 Z= 0.107 Angle : 0.600 7.526 4710 Z= 0.284 Chirality : 0.050 0.130 528 Planarity : 0.003 0.023 600 Dihedral : 5.365 15.111 468 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.08 % Favored : 93.92 % Rotamer: Outliers : 3.79 % Allowed : 22.73 % Favored : 73.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.50 (0.34), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.13 (0.26), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 379 TYR 0.008 0.001 TYR D 310 PHE 0.013 0.001 PHE E 378 HIS 0.002 0.001 HIS C 329 Details of bonding type rmsd covalent geometry : bond 0.00234 ( 3522) covalent geometry : angle 0.59980 ( 4710) hydrogen bonds : bond 0.01617 ( 68) hydrogen bonds : angle 4.59834 ( 204) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 106 time to evaluate : 0.147 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 307 GLN cc_start: 0.7491 (tt0) cc_final: 0.7054 (tt0) REVERT: A 373 THR cc_start: 0.8829 (m) cc_final: 0.8550 (p) REVERT: B 375 LYS cc_start: 0.8363 (ttmt) cc_final: 0.8068 (tttt) REVERT: C 372 GLU cc_start: 0.8043 (tt0) cc_final: 0.7768 (mm-30) REVERT: F 319 THR cc_start: 0.8255 (m) cc_final: 0.7986 (p) REVERT: F 343 LYS cc_start: 0.8249 (mmtt) cc_final: 0.7975 (mtpm) outliers start: 15 outliers final: 10 residues processed: 116 average time/residue: 0.6282 time to fit residues: 74.6100 Evaluate side-chains 114 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 104 time to evaluate : 0.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain B residue 356 SER Chi-restraints excluded: chain C residue 343 LYS Chi-restraints excluded: chain C residue 347 LYS Chi-restraints excluded: chain C residue 356 SER Chi-restraints excluded: chain D residue 356 SER Chi-restraints excluded: chain E residue 356 SER Chi-restraints excluded: chain F residue 347 LYS Chi-restraints excluded: chain F residue 357 LEU Chi-restraints excluded: chain F residue 373 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 41 optimal weight: 1.9990 chunk 16 optimal weight: 9.9990 chunk 3 optimal weight: 0.5980 chunk 8 optimal weight: 2.9990 chunk 37 optimal weight: 6.9990 chunk 40 optimal weight: 3.9990 chunk 39 optimal weight: 9.9990 chunk 23 optimal weight: 10.0000 chunk 10 optimal weight: 2.9990 chunk 4 optimal weight: 9.9990 chunk 25 optimal weight: 9.9990 overall best weight: 2.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 351 GLN F 307 GLN F 351 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.154576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.129648 restraints weight = 3331.499| |-----------------------------------------------------------------------------| r_work (start): 0.3831 rms_B_bonded: 1.32 r_work: 0.3747 rms_B_bonded: 1.50 restraints_weight: 0.5000 r_work: 0.3666 rms_B_bonded: 2.51 restraints_weight: 0.2500 r_work (final): 0.3666 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 moved from start: 0.3813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3522 Z= 0.154 Angle : 0.646 8.496 4710 Z= 0.312 Chirality : 0.053 0.188 528 Planarity : 0.003 0.024 600 Dihedral : 5.634 15.731 468 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.66 % Favored : 92.34 % Rotamer: Outliers : 4.04 % Allowed : 23.48 % Favored : 72.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.48 (0.34), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.12 (0.26), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 379 TYR 0.008 0.002 TYR D 310 PHE 0.013 0.002 PHE E 378 HIS 0.003 0.001 HIS B 329 Details of bonding type rmsd covalent geometry : bond 0.00345 ( 3522) covalent geometry : angle 0.64594 ( 4710) hydrogen bonds : bond 0.01889 ( 68) hydrogen bonds : angle 4.68218 ( 204) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 102 time to evaluate : 0.153 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 307 GLN cc_start: 0.7536 (tt0) cc_final: 0.7115 (tt0) REVERT: A 373 THR cc_start: 0.8756 (m) cc_final: 0.8549 (p) REVERT: B 375 LYS cc_start: 0.8332 (ttmt) cc_final: 0.8065 (tttt) REVERT: C 372 GLU cc_start: 0.8017 (tt0) cc_final: 0.7761 (mm-30) REVERT: E 373 THR cc_start: 0.8680 (m) cc_final: 0.8346 (p) REVERT: F 343 LYS cc_start: 0.8236 (mmtt) cc_final: 0.8003 (mtpm) outliers start: 16 outliers final: 11 residues processed: 111 average time/residue: 0.6493 time to fit residues: 73.7689 Evaluate side-chains 112 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 101 time to evaluate : 0.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 356 SER Chi-restraints excluded: chain C residue 343 LYS Chi-restraints excluded: chain C residue 347 LYS Chi-restraints excluded: chain C residue 356 SER Chi-restraints excluded: chain D residue 356 SER Chi-restraints excluded: chain E residue 356 SER Chi-restraints excluded: chain F residue 347 LYS Chi-restraints excluded: chain F residue 357 LEU Chi-restraints excluded: chain F residue 373 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 19 optimal weight: 4.9990 chunk 11 optimal weight: 9.9990 chunk 34 optimal weight: 10.0000 chunk 6 optimal weight: 0.3980 chunk 36 optimal weight: 7.9990 chunk 35 optimal weight: 2.9990 chunk 7 optimal weight: 10.0000 chunk 27 optimal weight: 7.9990 chunk 20 optimal weight: 4.9990 chunk 17 optimal weight: 3.9990 chunk 38 optimal weight: 7.9990 overall best weight: 3.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 351 GLN F 307 GLN F 351 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.152711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.125340 restraints weight = 3230.920| |-----------------------------------------------------------------------------| r_work (start): 0.3798 rms_B_bonded: 1.46 r_work: 0.3717 rms_B_bonded: 1.56 restraints_weight: 0.5000 r_work: 0.3636 rms_B_bonded: 2.58 restraints_weight: 0.2500 r_work (final): 0.3636 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8531 moved from start: 0.3767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 3522 Z= 0.196 Angle : 0.695 9.498 4710 Z= 0.342 Chirality : 0.054 0.193 528 Planarity : 0.004 0.025 600 Dihedral : 5.855 16.521 468 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.88 % Favored : 92.12 % Rotamer: Outliers : 3.79 % Allowed : 23.48 % Favored : 72.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.56 (0.33), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.18 (0.25), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 379 TYR 0.010 0.002 TYR D 310 PHE 0.012 0.002 PHE E 378 HIS 0.004 0.001 HIS B 329 Details of bonding type rmsd covalent geometry : bond 0.00436 ( 3522) covalent geometry : angle 0.69490 ( 4710) hydrogen bonds : bond 0.02063 ( 68) hydrogen bonds : angle 4.83186 ( 204) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 103 time to evaluate : 0.101 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 307 GLN cc_start: 0.7511 (tt0) cc_final: 0.7080 (tt0) REVERT: A 373 THR cc_start: 0.8795 (m) cc_final: 0.8561 (p) REVERT: B 375 LYS cc_start: 0.8353 (ttmt) cc_final: 0.8082 (tttt) REVERT: C 342 GLU cc_start: 0.7515 (OUTLIER) cc_final: 0.7108 (mp0) REVERT: C 372 GLU cc_start: 0.8034 (tt0) cc_final: 0.7782 (mm-30) REVERT: F 343 LYS cc_start: 0.8236 (mmtt) cc_final: 0.7968 (mtpm) outliers start: 15 outliers final: 11 residues processed: 114 average time/residue: 0.6126 time to fit residues: 71.5497 Evaluate side-chains 113 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 101 time to evaluate : 0.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 356 SER Chi-restraints excluded: chain C residue 342 GLU Chi-restraints excluded: chain C residue 343 LYS Chi-restraints excluded: chain C residue 347 LYS Chi-restraints excluded: chain C residue 356 SER Chi-restraints excluded: chain D residue 356 SER Chi-restraints excluded: chain E residue 356 SER Chi-restraints excluded: chain F residue 347 LYS Chi-restraints excluded: chain F residue 357 LEU Chi-restraints excluded: chain F residue 373 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 1 optimal weight: 9.9990 chunk 33 optimal weight: 7.9990 chunk 34 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 3 optimal weight: 9.9990 chunk 29 optimal weight: 5.9990 chunk 16 optimal weight: 0.8980 chunk 7 optimal weight: 10.0000 chunk 6 optimal weight: 5.9990 chunk 35 optimal weight: 0.0070 chunk 5 optimal weight: 5.9990 overall best weight: 3.7804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 307 GLN C 351 GLN F 307 GLN F 351 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.153359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.127765 restraints weight = 3338.455| |-----------------------------------------------------------------------------| r_work (start): 0.3806 rms_B_bonded: 1.36 r_work: 0.3722 rms_B_bonded: 1.52 restraints_weight: 0.5000 r_work: 0.3637 rms_B_bonded: 2.55 restraints_weight: 0.2500 r_work (final): 0.3637 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8533 moved from start: 0.3762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.029 3522 Z= 0.210 Angle : 0.714 9.662 4710 Z= 0.350 Chirality : 0.055 0.210 528 Planarity : 0.004 0.026 600 Dihedral : 5.919 16.772 468 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.88 % Favored : 92.12 % Rotamer: Outliers : 3.03 % Allowed : 23.74 % Favored : 73.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.62 (0.33), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.22 (0.25), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG F 379 TYR 0.009 0.002 TYR D 310 PHE 0.018 0.003 PHE D 378 HIS 0.005 0.001 HIS B 329 Details of bonding type rmsd covalent geometry : bond 0.00467 ( 3522) covalent geometry : angle 0.71382 ( 4710) hydrogen bonds : bond 0.02158 ( 68) hydrogen bonds : angle 4.90449 ( 204) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2203.30 seconds wall clock time: 38 minutes 17.68 seconds (2297.68 seconds total)