Starting phenix.real_space_refine on Tue Mar 3 11:45:05 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7qkl_14046/03_2026/7qkl_14046.cif Found real_map, /net/cci-nas-00/data/ceres_data/7qkl_14046/03_2026/7qkl_14046.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.07 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7qkl_14046/03_2026/7qkl_14046.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7qkl_14046/03_2026/7qkl_14046.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7qkl_14046/03_2026/7qkl_14046.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7qkl_14046/03_2026/7qkl_14046.map" } resolution = 2.07 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= 0.003 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 14 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/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: 0.72, per 1000 atoms: 0.21 Number of scatterers: 3468 At special positions: 0 Unit cell: (90.64, 135.136, 40.376, 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: 0.22 Conformation dependent library (CDL) restraints added in 144.2 milliseconds 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 16 sheets defined 0.0% alpha, 57.9% 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 306 through 310 removed outlier: 6.474A pdb=" N GLN A 307 " --> pdb=" O ILE C 308 " (cutoff:3.500A) removed outlier: 7.666A pdb=" N TYR C 310 " --> pdb=" O GLN A 307 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N VAL A 309 " --> pdb=" O TYR C 310 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 313 through 314 removed outlier: 6.771A pdb=" N VAL A 313 " --> pdb=" O ASP C 314 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 317 through 324 removed outlier: 6.431A pdb=" N LYS A 317 " --> pdb=" O VAL C 318 " (cutoff:3.500A) removed outlier: 8.089A pdb=" N SER C 320 " --> pdb=" O LYS A 317 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N THR A 319 " --> pdb=" O SER C 320 " (cutoff:3.500A) removed outlier: 8.166A pdb=" N CYS C 322 " --> pdb=" O THR A 319 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N LYS A 321 " --> pdb=" O CYS C 322 " (cutoff:3.500A) removed outlier: 7.729A pdb=" N SER C 324 " --> pdb=" O LYS A 321 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N GLY A 323 " --> pdb=" O SER C 324 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 328 through 330 removed outlier: 6.447A pdb=" N HIS A 329 " --> pdb=" O HIS C 330 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 336 through 347 removed outlier: 5.967A pdb=" N VAL A 337 " --> pdb=" O GLU C 338 " (cutoff:3.500A) removed outlier: 7.669A pdb=" N LYS C 340 " --> pdb=" O VAL A 337 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N VAL A 339 " --> pdb=" O LYS C 340 " (cutoff:3.500A) removed outlier: 7.939A pdb=" N GLU C 342 " --> pdb=" O VAL A 339 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N SER A 341 " --> pdb=" O GLU C 342 " (cutoff:3.500A) removed outlier: 7.921A pdb=" N LEU C 344 " --> pdb=" O SER A 341 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N LYS A 343 " --> pdb=" O LEU C 344 " (cutoff:3.500A) removed outlier: 7.662A pdb=" N PHE C 346 " --> pdb=" O LYS A 343 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N ASP A 345 " --> pdb=" O PHE C 346 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N VAL C 337 " --> pdb=" O GLN B 336 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N GLU B 338 " --> pdb=" O VAL C 337 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 350 through 354 removed outlier: 6.581A pdb=" N GLN A 351 " --> pdb=" O SER C 352 " (cutoff:3.500A) removed outlier: 8.080A pdb=" N ILE C 354 " --> pdb=" O GLN A 351 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N LYS A 353 " --> pdb=" O ILE C 354 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N VAL B 350 " --> pdb=" O GLN C 351 " (cutoff:3.500A) removed outlier: 7.929A pdb=" N LYS C 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N SER B 352 " --> pdb=" O LYS C 353 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 357 through 362 removed outlier: 6.615A pdb=" N ASP A 358 " --> pdb=" O ASN C 359 " (cutoff:3.500A) removed outlier: 7.848A pdb=" N THR C 361 " --> pdb=" O ASP A 358 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N ILE A 360 " --> pdb=" O THR C 361 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N LEU B 357 " --> pdb=" O ASP C 358 " (cutoff:3.500A) removed outlier: 7.722A pdb=" N ILE C 360 " --> pdb=" O LEU B 357 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N ASN B 359 " --> pdb=" O ILE C 360 " (cutoff:3.500A) removed outlier: 7.847A pdb=" N HIS C 362 " --> pdb=" O ASN B 359 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N THR B 361 " --> pdb=" O HIS C 362 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'A' and resid 368 through 378 removed outlier: 6.549A pdb=" N LYS A 369 " --> pdb=" O LYS C 370 " (cutoff:3.500A) removed outlier: 7.913A pdb=" N GLU C 372 " --> pdb=" O LYS A 369 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N ILE A 371 " --> pdb=" O GLU C 372 " (cutoff:3.500A) removed outlier: 8.025A pdb=" N HIS C 374 " --> pdb=" O ILE A 371 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N THR A 373 " --> pdb=" O HIS C 374 " (cutoff:3.500A) removed outlier: 7.963A pdb=" N LEU C 376 " --> pdb=" O THR A 373 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N LYS A 375 " --> pdb=" O LEU C 376 " (cutoff:3.500A) removed outlier: 7.889A pdb=" N PHE C 378 " --> pdb=" O LYS A 375 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N THR A 377 " --> pdb=" O PHE C 378 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 306 through 310 removed outlier: 6.410A pdb=" N GLN D 307 " --> pdb=" O ILE F 308 " (cutoff:3.500A) removed outlier: 7.610A pdb=" N TYR F 310 " --> pdb=" O GLN D 307 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N VAL D 309 " --> pdb=" O TYR F 310 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 313 through 314 removed outlier: 6.813A pdb=" N VAL D 313 " --> pdb=" O ASP F 314 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 317 through 324 removed outlier: 6.482A pdb=" N LYS D 317 " --> pdb=" O VAL F 318 " (cutoff:3.500A) removed outlier: 8.123A pdb=" N SER F 320 " --> pdb=" O LYS D 317 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N THR D 319 " --> pdb=" O SER F 320 " (cutoff:3.500A) removed outlier: 8.177A pdb=" N CYS F 322 " --> pdb=" O THR D 319 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N LYS D 321 " --> pdb=" O CYS F 322 " (cutoff:3.500A) removed outlier: 7.795A pdb=" N SER F 324 " --> pdb=" O LYS D 321 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N GLY D 323 " --> pdb=" O SER F 324 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N VAL E 318 " --> pdb=" O THR F 319 " (cutoff:3.500A) removed outlier: 8.009A pdb=" N LYS F 321 " --> pdb=" O VAL E 318 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N SER E 320 " --> pdb=" O LYS F 321 " (cutoff:3.500A) removed outlier: 7.902A pdb=" N GLY F 323 " --> pdb=" O SER E 320 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N CYS E 322 " --> pdb=" O GLY F 323 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'D' and resid 328 through 330 removed outlier: 6.467A pdb=" N HIS D 329 " --> pdb=" O HIS F 330 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N ILE E 328 " --> pdb=" O HIS F 329 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'D' and resid 336 through 347 removed outlier: 6.997A pdb=" N VAL D 337 " --> pdb=" O GLN F 336 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N GLU F 338 " --> pdb=" O VAL D 337 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N VAL F 337 " --> pdb=" O GLN E 336 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N GLU E 338 " --> pdb=" O VAL F 337 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 350 through 354 removed outlier: 6.212A pdb=" N VAL E 350 " --> pdb=" O GLN F 351 " (cutoff:3.500A) removed outlier: 7.926A pdb=" N LYS F 353 " --> pdb=" O VAL E 350 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N SER E 352 " --> pdb=" O LYS F 353 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 357 through 362 removed outlier: 6.580A pdb=" N ASP D 358 " --> pdb=" O ASN F 359 " (cutoff:3.500A) removed outlier: 7.781A pdb=" N THR F 361 " --> pdb=" O ASP D 358 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N ILE D 360 " --> pdb=" O THR F 361 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N LEU E 357 " --> pdb=" O ASP F 358 " (cutoff:3.500A) removed outlier: 7.734A pdb=" N ILE F 360 " --> pdb=" O LEU E 357 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N ASN E 359 " --> pdb=" O ILE F 360 " (cutoff:3.500A) removed outlier: 7.829A pdb=" N HIS F 362 " --> pdb=" O ASN E 359 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N THR E 361 " --> pdb=" O HIS F 362 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'D' and resid 368 through 378 removed outlier: 6.537A pdb=" N LYS D 369 " --> pdb=" O LYS F 370 " (cutoff:3.500A) removed outlier: 7.899A pdb=" N GLU F 372 " --> pdb=" O LYS D 369 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N ILE D 371 " --> pdb=" O GLU F 372 " (cutoff:3.500A) removed outlier: 7.996A pdb=" N HIS F 374 " --> pdb=" O ILE D 371 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N THR D 373 " --> pdb=" O HIS F 374 " (cutoff:3.500A) removed outlier: 7.971A pdb=" N LEU F 376 " --> pdb=" O THR D 373 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N LYS D 375 " --> pdb=" O LEU F 376 " (cutoff:3.500A) removed outlier: 7.761A pdb=" N PHE F 378 " --> pdb=" O LYS D 375 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N THR D 377 " --> pdb=" O PHE F 378 " (cutoff:3.500A) 70 hydrogen bonds defined for protein. 210 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: 0.36 Time building geometry restraints manager: 0.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 1064 1.34 - 1.46: 410 1.46 - 1.58: 2041 1.58 - 1.70: 1 1.70 - 1.82: 6 Bond restraints: 3522 Sorted by residual: bond pdb=" CB VAL C 339 " pdb=" CG2 VAL C 339 " ideal model delta sigma weight residual 1.521 1.618 -0.097 3.30e-02 9.18e+02 8.62e+00 bond pdb=" CZ ARG C 349 " pdb=" NH2 ARG C 349 " ideal model delta sigma weight residual 1.330 1.298 0.032 1.30e-02 5.92e+03 6.05e+00 bond pdb=" CZ ARG A 349 " pdb=" NH2 ARG A 349 " ideal model delta sigma weight residual 1.330 1.298 0.032 1.30e-02 5.92e+03 5.89e+00 bond pdb=" CZ ARG F 349 " pdb=" NH2 ARG F 349 " ideal model delta sigma weight residual 1.330 1.299 0.031 1.30e-02 5.92e+03 5.75e+00 bond pdb=" CZ ARG D 349 " pdb=" NH2 ARG D 349 " ideal model delta sigma weight residual 1.330 1.299 0.031 1.30e-02 5.92e+03 5.70e+00 ... (remaining 3517 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.41: 4575 4.41 - 8.83: 105 8.83 - 13.24: 1 13.24 - 17.66: 9 17.66 - 22.07: 20 Bond angle restraints: 4710 Sorted by residual: angle pdb=" CA VAL D 309 " pdb=" CB VAL D 309 " pdb=" CG1 VAL D 309 " ideal model delta sigma weight residual 110.40 132.47 -22.07 1.70e+00 3.46e-01 1.69e+02 angle pdb=" CA VAL A 313 " pdb=" CB VAL A 313 " pdb=" CG1 VAL A 313 " ideal model delta sigma weight residual 110.40 132.46 -22.06 1.70e+00 3.46e-01 1.68e+02 angle pdb=" CA VAL A 309 " pdb=" CB VAL A 309 " pdb=" CG1 VAL A 309 " ideal model delta sigma weight residual 110.40 132.43 -22.03 1.70e+00 3.46e-01 1.68e+02 angle pdb=" CA VAL D 318 " pdb=" CB VAL D 318 " pdb=" CG1 VAL D 318 " ideal model delta sigma weight residual 110.40 131.78 -21.38 1.70e+00 3.46e-01 1.58e+02 angle pdb=" CA VAL B 309 " pdb=" CB VAL B 309 " pdb=" CG1 VAL B 309 " ideal model delta sigma weight residual 110.40 131.71 -21.31 1.70e+00 3.46e-01 1.57e+02 ... (remaining 4705 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.14: 1994 17.14 - 34.27: 110 34.27 - 51.40: 21 51.40 - 68.53: 11 68.53 - 85.67: 6 Dihedral angle restraints: 2142 sinusoidal: 894 harmonic: 1248 Sorted by residual: dihedral pdb=" CA LYS C 347 " pdb=" C LYS C 347 " pdb=" N ASP C 348 " pdb=" CA ASP C 348 " ideal model delta harmonic sigma weight residual 180.00 159.93 20.07 0 5.00e+00 4.00e-02 1.61e+01 dihedral pdb=" CA LYS F 347 " pdb=" C LYS F 347 " pdb=" N ASP F 348 " pdb=" CA ASP F 348 " ideal model delta harmonic sigma weight residual 180.00 160.65 19.35 0 5.00e+00 4.00e-02 1.50e+01 dihedral pdb=" C VAL C 337 " pdb=" N VAL C 337 " pdb=" CA VAL C 337 " pdb=" CB VAL C 337 " ideal model delta harmonic sigma weight residual -122.00 -131.33 9.33 0 2.50e+00 1.60e-01 1.39e+01 ... (remaining 2139 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.249: 489 0.249 - 0.498: 9 0.498 - 0.747: 5 0.747 - 0.996: 14 0.996 - 1.246: 11 Chirality restraints: 528 Sorted by residual: chirality pdb=" CB VAL C 313 " pdb=" CA VAL C 313 " pdb=" CG1 VAL C 313 " pdb=" CG2 VAL C 313 " both_signs ideal model delta sigma weight residual False -2.63 -1.38 -1.25 2.00e-01 2.50e+01 3.88e+01 chirality pdb=" CB VAL C 318 " pdb=" CA VAL C 318 " pdb=" CG1 VAL C 318 " pdb=" CG2 VAL C 318 " both_signs ideal model delta sigma weight residual False -2.63 -1.42 -1.21 2.00e-01 2.50e+01 3.67e+01 chirality pdb=" CB VAL A 309 " pdb=" CA VAL A 309 " pdb=" CG1 VAL A 309 " pdb=" CG2 VAL A 309 " both_signs ideal model delta sigma weight residual False -2.63 -1.45 -1.18 2.00e-01 2.50e+01 3.46e+01 ... (remaining 525 not shown) Planarity restraints: 600 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR C 310 " -0.058 2.00e-02 2.50e+03 3.30e-02 2.17e+01 pdb=" CG TYR C 310 " 0.019 2.00e-02 2.50e+03 pdb=" CD1 TYR C 310 " 0.020 2.00e-02 2.50e+03 pdb=" CD2 TYR C 310 " 0.027 2.00e-02 2.50e+03 pdb=" CE1 TYR C 310 " 0.021 2.00e-02 2.50e+03 pdb=" CE2 TYR C 310 " 0.016 2.00e-02 2.50e+03 pdb=" CZ TYR C 310 " 0.010 2.00e-02 2.50e+03 pdb=" OH TYR C 310 " -0.055 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 310 " -0.038 2.00e-02 2.50e+03 2.41e-02 1.16e+01 pdb=" CG TYR A 310 " 0.007 2.00e-02 2.50e+03 pdb=" CD1 TYR A 310 " 0.014 2.00e-02 2.50e+03 pdb=" CD2 TYR A 310 " 0.014 2.00e-02 2.50e+03 pdb=" CE1 TYR A 310 " 0.017 2.00e-02 2.50e+03 pdb=" CE2 TYR A 310 " 0.018 2.00e-02 2.50e+03 pdb=" CZ TYR A 310 " 0.013 2.00e-02 2.50e+03 pdb=" OH TYR A 310 " -0.045 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS F 330 " 0.034 2.00e-02 2.50e+03 2.56e-02 9.80e+00 pdb=" CG HIS F 330 " -0.039 2.00e-02 2.50e+03 pdb=" ND1 HIS F 330 " -0.017 2.00e-02 2.50e+03 pdb=" CD2 HIS F 330 " -0.015 2.00e-02 2.50e+03 pdb=" CE1 HIS F 330 " 0.019 2.00e-02 2.50e+03 pdb=" NE2 HIS F 330 " 0.018 2.00e-02 2.50e+03 ... (remaining 597 not shown) Histogram of nonbonded interaction distances: 2.54 - 3.01: 1698 3.01 - 3.48: 2830 3.48 - 3.95: 5551 3.95 - 4.43: 5560 4.43 - 4.90: 10503 Nonbonded interactions: 26142 Sorted by model distance: nonbonded pdb=" OD1 ASP F 314 " pdb=" OG SER F 316 " model vdw 2.537 3.040 nonbonded pdb=" OD1 ASP A 314 " pdb=" OG SER A 316 " model vdw 2.545 3.040 nonbonded pdb=" OD1 ASP C 314 " pdb=" OG SER C 316 " model vdw 2.545 3.040 nonbonded pdb=" OD1 ASP D 314 " pdb=" OG SER D 316 " model vdw 2.555 3.040 nonbonded pdb=" OD1 ASP E 314 " pdb=" OG SER E 316 " model vdw 2.559 3.040 ... (remaining 26137 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: 5.110 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: 4.310 Find NCS groups from input model: 0.040 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:6.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 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 0.097 3522 Z= 0.675 Angle : 2.367 22.071 4710 Z= 1.491 Chirality : 0.248 1.246 528 Planarity : 0.009 0.050 600 Dihedral : 12.790 85.668 1350 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 0.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % 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 are not related in a simple way. whole: -1.75 (0.32), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.33 (0.25), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG C 349 TYR 0.058 0.012 TYR C 310 PHE 0.030 0.009 PHE B 378 HIS 0.008 0.002 HIS B 330 Details of bonding type rmsd covalent geometry : bond 0.01126 ( 3522) covalent geometry : angle 2.36723 ( 4710) hydrogen bonds : bond 0.05666 ( 70) hydrogen bonds : angle 8.18498 ( 210) *********************** 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 218 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 218 time to evaluate : 0.156 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 343 LYS cc_start: 0.6820 (tptm) cc_final: 0.6506 (mptp) REVERT: A 345 ASP cc_start: 0.7368 (t0) cc_final: 0.6655 (m-30) REVERT: A 349 ARG cc_start: 0.7184 (mtt-85) cc_final: 0.6708 (mtm180) REVERT: B 343 LYS cc_start: 0.7418 (tptm) cc_final: 0.7041 (mtmt) REVERT: C 343 LYS cc_start: 0.6950 (tptm) cc_final: 0.6334 (mptp) REVERT: C 349 ARG cc_start: 0.7092 (mtt-85) cc_final: 0.6874 (mtm180) REVERT: D 343 LYS cc_start: 0.6878 (tptm) cc_final: 0.6288 (tmmt) REVERT: D 360 ILE cc_start: 0.8825 (mp) cc_final: 0.8590 (mt) REVERT: E 320 SER cc_start: 0.8785 (t) cc_final: 0.8534 (p) REVERT: E 343 LYS cc_start: 0.7573 (tptm) cc_final: 0.6969 (mptt) REVERT: E 348 ASP cc_start: 0.7159 (t0) cc_final: 0.6875 (t0) REVERT: F 343 LYS cc_start: 0.6980 (tptm) cc_final: 0.6460 (mptp) REVERT: F 345 ASP cc_start: 0.7302 (t0) cc_final: 0.7054 (t0) REVERT: F 349 ARG cc_start: 0.7080 (mtt-85) cc_final: 0.6588 (mtm180) REVERT: F 353 LYS cc_start: 0.8307 (mttt) cc_final: 0.8020 (mttt) outliers start: 0 outliers final: 0 residues processed: 218 average time/residue: 0.5742 time to fit residues: 128.0404 Evaluate side-chains 149 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 149 time to evaluate : 0.153 ------------------------------------------------------------------------------- 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: 4.9990 chunk 26 optimal weight: 2.9990 chunk 2 optimal weight: 4.9990 chunk 16 optimal weight: 6.9990 chunk 32 optimal weight: 6.9990 chunk 31 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 30 optimal weight: 8.9990 chunk 22 optimal weight: 6.9990 chunk 37 optimal weight: 5.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 359 ASN B 307 GLN B 359 ASN C 351 GLN C 359 ASN D 359 ASN E 351 GLN E 359 ASN F 359 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.140534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.126783 restraints weight = 2954.538| |-----------------------------------------------------------------------------| r_work (start): 0.3768 rms_B_bonded: 1.00 r_work: 0.3678 rms_B_bonded: 1.15 restraints_weight: 0.5000 r_work: 0.3587 rms_B_bonded: 2.01 restraints_weight: 0.2500 r_work (final): 0.3587 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8793 moved from start: 0.2971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 3522 Z= 0.165 Angle : 0.670 7.002 4710 Z= 0.322 Chirality : 0.053 0.128 528 Planarity : 0.004 0.029 600 Dihedral : 4.831 18.390 468 Min Nonbonded Distance : 2.638 Molprobity Statistics. All-atom Clashscore : 2.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 0.76 % Allowed : 18.69 % Favored : 80.56 % 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 are not related in a simple way. whole: -1.20 (0.34), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.90 (0.26), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG F 379 TYR 0.006 0.001 TYR B 310 PHE 0.010 0.002 PHE E 346 HIS 0.003 0.001 HIS E 374 Details of bonding type rmsd covalent geometry : bond 0.00385 ( 3522) covalent geometry : angle 0.67036 ( 4710) hydrogen bonds : bond 0.02319 ( 70) hydrogen bonds : angle 6.01563 ( 210) *********************** 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 154 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 151 time to evaluate : 0.127 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 343 LYS cc_start: 0.7944 (tptm) cc_final: 0.7721 (tmmt) REVERT: D 307 GLN cc_start: 0.8484 (tt0) cc_final: 0.8266 (tt0) outliers start: 3 outliers final: 1 residues processed: 151 average time/residue: 0.7650 time to fit residues: 117.6852 Evaluate side-chains 119 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 118 time to evaluate : 0.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 337 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 12 optimal weight: 8.9990 chunk 6 optimal weight: 4.9990 chunk 22 optimal weight: 6.9990 chunk 31 optimal weight: 6.9990 chunk 17 optimal weight: 8.9990 chunk 34 optimal weight: 0.0980 chunk 37 optimal weight: 20.0000 chunk 18 optimal weight: 6.9990 chunk 13 optimal weight: 5.9990 chunk 35 optimal weight: 5.9990 chunk 25 optimal weight: 0.2980 overall best weight: 3.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 351 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.139352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.125775 restraints weight = 2980.178| |-----------------------------------------------------------------------------| r_work (start): 0.3741 rms_B_bonded: 1.03 r_work: 0.3646 rms_B_bonded: 1.17 restraints_weight: 0.5000 r_work: 0.3554 rms_B_bonded: 2.04 restraints_weight: 0.2500 r_work (final): 0.3554 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8830 moved from start: 0.3770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.022 3522 Z= 0.188 Angle : 0.638 6.466 4710 Z= 0.308 Chirality : 0.052 0.137 528 Planarity : 0.003 0.036 600 Dihedral : 4.838 18.136 468 Min Nonbonded Distance : 2.637 Molprobity Statistics. All-atom Clashscore : 3.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 1.01 % Allowed : 21.72 % Favored : 77.27 % 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 are not related in a simple way. whole: -1.22 (0.34), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.92 (0.26), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 379 TYR 0.008 0.002 TYR B 310 PHE 0.007 0.002 PHE E 346 HIS 0.002 0.001 HIS E 374 Details of bonding type rmsd covalent geometry : bond 0.00430 ( 3522) covalent geometry : angle 0.63774 ( 4710) hydrogen bonds : bond 0.02381 ( 70) hydrogen bonds : angle 5.81926 ( 210) *********************** 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 123 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 119 time to evaluate : 0.164 Fit side-chains revert: symmetry clash REVERT: D 307 GLN cc_start: 0.8507 (tt0) cc_final: 0.8303 (tt0) REVERT: D 343 LYS cc_start: 0.8230 (mptp) cc_final: 0.7784 (tmmt) outliers start: 4 outliers final: 1 residues processed: 119 average time/residue: 0.6899 time to fit residues: 83.8133 Evaluate side-chains 111 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 110 time to evaluate : 0.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 341 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 10.0000 chunk 1 optimal weight: 3.9990 chunk 36 optimal weight: 9.9990 chunk 17 optimal weight: 10.0000 chunk 20 optimal weight: 6.9990 chunk 15 optimal weight: 1.9990 chunk 3 optimal weight: 0.8980 chunk 2 optimal weight: 3.9990 chunk 14 optimal weight: 9.9990 chunk 7 optimal weight: 0.8980 chunk 40 optimal weight: 9.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 351 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.139493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.126116 restraints weight = 2962.521| |-----------------------------------------------------------------------------| r_work (start): 0.3747 rms_B_bonded: 1.02 r_work: 0.3652 rms_B_bonded: 1.16 restraints_weight: 0.5000 r_work: 0.3561 rms_B_bonded: 2.03 restraints_weight: 0.2500 r_work (final): 0.3561 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8826 moved from start: 0.3861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.017 3522 Z= 0.138 Angle : 0.572 5.776 4710 Z= 0.273 Chirality : 0.050 0.140 528 Planarity : 0.003 0.021 600 Dihedral : 4.681 17.405 468 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 2.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 1.01 % Allowed : 21.46 % Favored : 77.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.26 (0.35), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.95 (0.26), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 379 TYR 0.007 0.002 TYR B 310 PHE 0.005 0.002 PHE D 378 HIS 0.002 0.001 HIS A 362 Details of bonding type rmsd covalent geometry : bond 0.00309 ( 3522) covalent geometry : angle 0.57224 ( 4710) hydrogen bonds : bond 0.02027 ( 70) hydrogen bonds : angle 5.47772 ( 210) *********************** 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 109 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 105 time to evaluate : 0.161 Fit side-chains revert: symmetry clash REVERT: C 343 LYS cc_start: 0.8187 (OUTLIER) cc_final: 0.7942 (mptt) outliers start: 4 outliers final: 0 residues processed: 107 average time/residue: 0.6281 time to fit residues: 68.7090 Evaluate side-chains 103 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 102 time to evaluate : 0.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 343 LYS 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: 10.0000 chunk 19 optimal weight: 9.9990 chunk 39 optimal weight: 10.0000 chunk 6 optimal weight: 0.0970 chunk 0 optimal weight: 10.0000 chunk 31 optimal weight: 0.0050 chunk 40 optimal weight: 9.9990 chunk 3 optimal weight: 5.9990 chunk 1 optimal weight: 5.9990 chunk 9 optimal weight: 0.0030 overall best weight: 2.4206 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 351 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.140155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.127554 restraints weight = 3154.072| |-----------------------------------------------------------------------------| r_work (start): 0.3749 rms_B_bonded: 0.96 r_work: 0.3655 rms_B_bonded: 1.13 restraints_weight: 0.5000 r_work: 0.3566 rms_B_bonded: 1.98 restraints_weight: 0.2500 r_work (final): 0.3566 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8821 moved from start: 0.3956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 3522 Z= 0.140 Angle : 0.561 5.370 4710 Z= 0.269 Chirality : 0.050 0.130 528 Planarity : 0.003 0.020 600 Dihedral : 4.660 17.304 468 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 2.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 0.51 % Allowed : 21.46 % 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 are not related in a simple way. whole: -1.27 (0.35), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.95 (0.27), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 379 TYR 0.008 0.002 TYR B 310 PHE 0.008 0.002 PHE D 378 HIS 0.002 0.001 HIS A 362 Details of bonding type rmsd covalent geometry : bond 0.00315 ( 3522) covalent geometry : angle 0.56084 ( 4710) hydrogen bonds : bond 0.02036 ( 70) hydrogen bonds : angle 5.32376 ( 210) *********************** 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 101 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 99 time to evaluate : 0.105 Fit side-chains revert: symmetry clash REVERT: C 343 LYS cc_start: 0.8263 (OUTLIER) cc_final: 0.8015 (mptt) REVERT: F 343 LYS cc_start: 0.8210 (mptp) cc_final: 0.7930 (tmtm) outliers start: 2 outliers final: 1 residues processed: 100 average time/residue: 0.5994 time to fit residues: 61.3528 Evaluate side-chains 101 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 99 time to evaluate : 0.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 343 LYS Chi-restraints excluded: chain D residue 315 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 11 optimal weight: 1.9990 chunk 15 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 20 optimal weight: 10.0000 chunk 12 optimal weight: 4.9990 chunk 31 optimal weight: 0.0970 chunk 34 optimal weight: 0.0570 chunk 36 optimal weight: 3.9990 chunk 32 optimal weight: 3.9990 chunk 18 optimal weight: 5.9990 chunk 38 optimal weight: 2.9990 overall best weight: 1.8302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 307 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.140069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.126745 restraints weight = 2984.649| |-----------------------------------------------------------------------------| r_work (start): 0.3754 rms_B_bonded: 1.02 r_work: 0.3660 rms_B_bonded: 1.16 restraints_weight: 0.5000 r_work: 0.3570 rms_B_bonded: 2.04 restraints_weight: 0.2500 r_work (final): 0.3570 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8818 moved from start: 0.3969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.017 3522 Z= 0.115 Angle : 0.529 4.985 4710 Z= 0.252 Chirality : 0.049 0.124 528 Planarity : 0.002 0.020 600 Dihedral : 4.520 16.683 468 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 2.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 0.76 % Allowed : 20.71 % Favored : 78.54 % 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 are not related in a simple way. whole: -1.26 (0.35), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.95 (0.27), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 379 TYR 0.007 0.002 TYR B 310 PHE 0.006 0.001 PHE D 378 HIS 0.001 0.000 HIS A 362 Details of bonding type rmsd covalent geometry : bond 0.00256 ( 3522) covalent geometry : angle 0.52925 ( 4710) hydrogen bonds : bond 0.01832 ( 70) hydrogen bonds : angle 5.10002 ( 210) *********************** 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 103 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 100 time to evaluate : 0.126 Fit side-chains revert: symmetry clash REVERT: B 379 ARG cc_start: 0.6967 (mpt90) cc_final: 0.6657 (mpt-90) REVERT: C 343 LYS cc_start: 0.8223 (tmtm) cc_final: 0.7977 (mptt) REVERT: F 343 LYS cc_start: 0.8204 (OUTLIER) cc_final: 0.7899 (tmtm) outliers start: 3 outliers final: 0 residues processed: 101 average time/residue: 0.6330 time to fit residues: 65.3956 Evaluate side-chains 107 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 106 time to evaluate : 0.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 343 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 25 optimal weight: 7.9990 chunk 29 optimal weight: 9.9990 chunk 11 optimal weight: 2.9990 chunk 20 optimal weight: 10.0000 chunk 32 optimal weight: 6.9990 chunk 36 optimal weight: 3.9990 chunk 13 optimal weight: 0.9990 chunk 40 optimal weight: 10.0000 chunk 28 optimal weight: 10.0000 chunk 33 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 307 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.139267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.126615 restraints weight = 3144.396| |-----------------------------------------------------------------------------| r_work (start): 0.3739 rms_B_bonded: 0.96 r_work: 0.3644 rms_B_bonded: 1.13 restraints_weight: 0.5000 r_work: 0.3554 rms_B_bonded: 1.98 restraints_weight: 0.2500 r_work (final): 0.3554 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8830 moved from start: 0.3980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 3522 Z= 0.180 Angle : 0.582 5.224 4710 Z= 0.286 Chirality : 0.051 0.129 528 Planarity : 0.003 0.029 600 Dihedral : 4.787 17.396 468 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 2.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 0.51 % Allowed : 20.96 % Favored : 78.54 % 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 are not related in a simple way. whole: -1.28 (0.35), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.97 (0.27), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 379 TYR 0.009 0.002 TYR B 310 PHE 0.005 0.002 PHE F 346 HIS 0.003 0.001 HIS A 362 Details of bonding type rmsd covalent geometry : bond 0.00409 ( 3522) covalent geometry : angle 0.58245 ( 4710) hydrogen bonds : bond 0.02317 ( 70) hydrogen bonds : angle 5.33775 ( 210) *********************** 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 106 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 104 time to evaluate : 0.152 Fit side-chains revert: symmetry clash REVERT: B 379 ARG cc_start: 0.6850 (mpt90) cc_final: 0.6552 (mpt-90) REVERT: C 343 LYS cc_start: 0.8270 (OUTLIER) cc_final: 0.8033 (mptt) REVERT: F 343 LYS cc_start: 0.8262 (OUTLIER) cc_final: 0.7938 (tmtm) outliers start: 2 outliers final: 0 residues processed: 104 average time/residue: 0.6329 time to fit residues: 67.2690 Evaluate side-chains 106 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 104 time to evaluate : 0.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 343 LYS Chi-restraints excluded: chain F residue 343 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 39 optimal weight: 10.0000 chunk 12 optimal weight: 0.6980 chunk 33 optimal weight: 5.9990 chunk 10 optimal weight: 0.0020 chunk 34 optimal weight: 6.9990 chunk 19 optimal weight: 4.9990 chunk 40 optimal weight: 0.9990 chunk 29 optimal weight: 10.0000 chunk 15 optimal weight: 8.9990 chunk 41 optimal weight: 5.9990 chunk 5 optimal weight: 6.9990 overall best weight: 2.5394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 351 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.139258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.125855 restraints weight = 3030.824| |-----------------------------------------------------------------------------| r_work (start): 0.3743 rms_B_bonded: 1.03 r_work: 0.3647 rms_B_bonded: 1.17 restraints_weight: 0.5000 r_work: 0.3556 rms_B_bonded: 2.06 restraints_weight: 0.2500 r_work (final): 0.3556 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8829 moved from start: 0.3996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 3522 Z= 0.144 Angle : 0.551 4.905 4710 Z= 0.267 Chirality : 0.050 0.125 528 Planarity : 0.003 0.022 600 Dihedral : 4.686 17.466 468 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 2.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 0.51 % Allowed : 20.45 % Favored : 79.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.30 (0.35), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.99 (0.27), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 379 TYR 0.008 0.002 TYR B 310 PHE 0.005 0.002 PHE F 346 HIS 0.002 0.001 HIS A 362 Details of bonding type rmsd covalent geometry : bond 0.00324 ( 3522) covalent geometry : angle 0.55145 ( 4710) hydrogen bonds : bond 0.02079 ( 70) hydrogen bonds : angle 5.22524 ( 210) *********************** 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 106 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 104 time to evaluate : 0.127 Fit side-chains revert: symmetry clash REVERT: B 379 ARG cc_start: 0.6847 (mpt90) cc_final: 0.6543 (mpt-90) REVERT: C 343 LYS cc_start: 0.8274 (OUTLIER) cc_final: 0.8019 (mptt) REVERT: F 343 LYS cc_start: 0.8245 (OUTLIER) cc_final: 0.7914 (tmtm) outliers start: 2 outliers final: 0 residues processed: 104 average time/residue: 0.6282 time to fit residues: 66.7594 Evaluate side-chains 106 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 104 time to evaluate : 0.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 343 LYS Chi-restraints excluded: chain F residue 343 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 41 optimal weight: 9.9990 chunk 16 optimal weight: 4.9990 chunk 3 optimal weight: 3.9990 chunk 8 optimal weight: 2.9990 chunk 37 optimal weight: 20.0000 chunk 40 optimal weight: 0.9980 chunk 39 optimal weight: 9.9990 chunk 23 optimal weight: 0.5980 chunk 10 optimal weight: 0.0980 chunk 4 optimal weight: 8.9990 chunk 25 optimal weight: 4.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 351 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.140148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.126802 restraints weight = 2982.423| |-----------------------------------------------------------------------------| r_work (start): 0.3755 rms_B_bonded: 1.02 r_work: 0.3661 rms_B_bonded: 1.16 restraints_weight: 0.5000 r_work: 0.3570 rms_B_bonded: 2.05 restraints_weight: 0.2500 r_work (final): 0.3570 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8818 moved from start: 0.4025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.016 3522 Z= 0.112 Angle : 0.525 4.772 4710 Z= 0.251 Chirality : 0.049 0.122 528 Planarity : 0.002 0.022 600 Dihedral : 4.536 16.888 468 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 2.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 0.51 % Allowed : 20.45 % Favored : 79.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.29 (0.35), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.97 (0.27), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 379 TYR 0.007 0.002 TYR B 310 PHE 0.006 0.001 PHE D 378 HIS 0.002 0.001 HIS A 362 Details of bonding type rmsd covalent geometry : bond 0.00252 ( 3522) covalent geometry : angle 0.52534 ( 4710) hydrogen bonds : bond 0.01816 ( 70) hydrogen bonds : angle 5.02664 ( 210) *********************** 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 107 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 105 time to evaluate : 0.098 Fit side-chains revert: symmetry clash REVERT: B 379 ARG cc_start: 0.6911 (mpt90) cc_final: 0.6602 (mpt-90) REVERT: C 343 LYS cc_start: 0.8268 (OUTLIER) cc_final: 0.8006 (mptt) outliers start: 2 outliers final: 0 residues processed: 105 average time/residue: 0.6734 time to fit residues: 72.3108 Evaluate side-chains 106 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 105 time to evaluate : 0.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 343 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 19 optimal weight: 10.0000 chunk 11 optimal weight: 0.5980 chunk 34 optimal weight: 0.9990 chunk 6 optimal weight: 0.7980 chunk 36 optimal weight: 4.9990 chunk 35 optimal weight: 3.9990 chunk 7 optimal weight: 10.0000 chunk 27 optimal weight: 0.0470 chunk 20 optimal weight: 5.9990 chunk 17 optimal weight: 3.9990 chunk 38 optimal weight: 5.9990 overall best weight: 1.2882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 307 GLN F 307 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.139925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.126872 restraints weight = 3062.034| |-----------------------------------------------------------------------------| r_work (start): 0.3770 rms_B_bonded: 1.01 r_work: 0.3674 rms_B_bonded: 1.17 restraints_weight: 0.5000 r_work: 0.3585 rms_B_bonded: 2.05 restraints_weight: 0.2500 r_work (final): 0.3585 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8807 moved from start: 0.4046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 3522 Z= 0.095 Angle : 0.513 4.678 4710 Z= 0.243 Chirality : 0.049 0.121 528 Planarity : 0.002 0.025 600 Dihedral : 4.382 15.802 468 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 2.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 0.25 % Allowed : 20.71 % Favored : 79.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.30 (0.35), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.98 (0.27), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 379 TYR 0.007 0.001 TYR B 310 PHE 0.006 0.001 PHE D 378 HIS 0.001 0.000 HIS B 374 Details of bonding type rmsd covalent geometry : bond 0.00213 ( 3522) covalent geometry : angle 0.51331 ( 4710) hydrogen bonds : bond 0.01628 ( 70) hydrogen bonds : angle 4.84656 ( 210) ********************** 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 106 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 105 time to evaluate : 0.163 Fit side-chains revert: symmetry clash REVERT: B 379 ARG cc_start: 0.6883 (mpt90) cc_final: 0.6574 (mpt-90) REVERT: C 307 GLN cc_start: 0.8427 (tt0) cc_final: 0.8215 (tt0) REVERT: C 343 LYS cc_start: 0.8169 (OUTLIER) cc_final: 0.7940 (mptt) outliers start: 1 outliers final: 0 residues processed: 105 average time/residue: 0.6750 time to fit residues: 72.3965 Evaluate side-chains 106 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 105 time to evaluate : 0.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 343 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 1 optimal weight: 3.9990 chunk 33 optimal weight: 5.9990 chunk 34 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 3 optimal weight: 5.9990 chunk 29 optimal weight: 2.9990 chunk 16 optimal weight: 20.0000 chunk 7 optimal weight: 10.0000 chunk 6 optimal weight: 0.8980 chunk 35 optimal weight: 3.9990 chunk 5 optimal weight: 7.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 307 GLN F 307 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.138753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.125337 restraints weight = 2993.828| |-----------------------------------------------------------------------------| r_work (start): 0.3735 rms_B_bonded: 1.03 r_work: 0.3639 rms_B_bonded: 1.17 restraints_weight: 0.5000 r_work: 0.3548 rms_B_bonded: 2.05 restraints_weight: 0.2500 r_work (final): 0.3548 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8835 moved from start: 0.4004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 3522 Z= 0.187 Angle : 0.587 5.031 4710 Z= 0.290 Chirality : 0.050 0.133 528 Planarity : 0.003 0.029 600 Dihedral : 4.779 17.367 468 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 2.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 0.51 % Allowed : 20.45 % Favored : 79.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.31 (0.35), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.99 (0.27), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 379 TYR 0.008 0.002 TYR B 310 PHE 0.006 0.002 PHE F 346 HIS 0.002 0.001 HIS D 330 Details of bonding type rmsd covalent geometry : bond 0.00423 ( 3522) covalent geometry : angle 0.58696 ( 4710) hydrogen bonds : bond 0.02333 ( 70) hydrogen bonds : angle 5.27748 ( 210) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2228.31 seconds wall clock time: 38 minutes 37.22 seconds (2317.22 seconds total)