Starting phenix.real_space_refine on Fri Aug 22 13:51:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8q2j_18109/08_2025/8q2j_18109.cif Found real_map, /net/cci-nas-00/data/ceres_data/8q2j_18109/08_2025/8q2j_18109.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.23 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8q2j_18109/08_2025/8q2j_18109.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8q2j_18109/08_2025/8q2j_18109.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8q2j_18109/08_2025/8q2j_18109.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8q2j_18109/08_2025/8q2j_18109.map" } resolution = 2.23 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 2193 2.51 5 N 648 2.21 5 O 660 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 22 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: 3507 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 582 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 582 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "B" Number of atoms: 587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 587 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "C" Number of atoms: 582 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 582 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "D" Number of atoms: 587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 587 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "E" Number of atoms: 582 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 582 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "F" Number of atoms: 587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 587 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Time building chain proxies: 0.97, per 1000 atoms: 0.28 Number of scatterers: 3507 At special positions: 0 Unit cell: (117.047, 119.228, 37.804, 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 660 8.00 N 648 7.00 C 2193 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: 0.16 Conformation dependent library (CDL) restraints added in 136.8 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 798 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 18 sheets defined 0.0% alpha, 51.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.16 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'C' and resid 306 through 310 removed outlier: 6.518A pdb=" N GLN A 307 " --> pdb=" O ILE C 308 " (cutoff:3.500A) removed outlier: 7.748A pdb=" N TYR C 310 " --> pdb=" O GLN A 307 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N VAL A 309 " --> pdb=" O TYR C 310 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 313 through 314 removed outlier: 6.781A pdb=" N VAL A 313 " --> pdb=" O ASP C 314 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 317 through 322 removed outlier: 6.543A pdb=" N LYS A 317 " --> pdb=" O VAL C 318 " (cutoff:3.500A) removed outlier: 8.004A pdb=" N SER C 320 " --> pdb=" O LYS A 317 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N THR A 319 " --> pdb=" O SER C 320 " (cutoff:3.500A) removed outlier: 8.387A pdb=" N CYS C 322 " --> pdb=" O THR A 319 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N LYS A 321 " --> pdb=" O CYS C 322 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 325 through 330 removed outlier: 6.872A pdb=" N GLY C 326 " --> pdb=" O LEU A 325 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N ASN A 327 " --> pdb=" O GLY C 326 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N GLY A 326 " --> pdb=" O LEU E 325 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N ASN E 327 " --> pdb=" O GLY A 326 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 337 through 342 removed outlier: 6.537A pdb=" N VAL A 337 " --> pdb=" O GLU E 338 " (cutoff:3.500A) removed outlier: 7.816A pdb=" N LYS E 340 " --> pdb=" O VAL A 337 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N VAL A 339 " --> pdb=" O LYS E 340 " (cutoff:3.500A) removed outlier: 8.013A pdb=" N GLU E 342 " --> pdb=" O VAL A 339 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N SER A 341 " --> pdb=" O GLU E 342 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 345 through 346 removed outlier: 6.504A pdb=" N ASP A 345 " --> pdb=" O PHE C 346 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 350 through 354 removed outlier: 6.261A pdb=" N VAL A 350 " --> pdb=" O GLN E 351 " (cutoff:3.500A) removed outlier: 7.961A pdb=" N LYS E 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N SER A 352 " --> pdb=" O LYS E 353 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 357 through 362 removed outlier: 6.419A pdb=" N LEU A 357 " --> pdb=" O ASP E 358 " (cutoff:3.500A) removed outlier: 7.979A pdb=" N ILE E 360 " --> pdb=" O LEU A 357 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N ASN A 359 " --> pdb=" O ILE E 360 " (cutoff:3.500A) removed outlier: 7.947A pdb=" N HIS E 362 " --> pdb=" O ASN A 359 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N THR A 361 " --> pdb=" O HIS E 362 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 369 through 378 removed outlier: 6.423A pdb=" N LYS A 369 " --> pdb=" O LYS C 370 " (cutoff:3.500A) removed outlier: 8.095A pdb=" N GLU C 372 " --> pdb=" O LYS A 369 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N ILE A 371 " --> pdb=" O GLU C 372 " (cutoff:3.500A) removed outlier: 8.063A pdb=" N HIS C 374 " --> pdb=" O ILE A 371 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N THR A 373 " --> pdb=" O HIS C 374 " (cutoff:3.500A) removed outlier: 7.972A pdb=" N LEU C 376 " --> pdb=" O THR A 373 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N LYS A 375 " --> pdb=" O LEU C 376 " (cutoff:3.500A) removed outlier: 7.914A pdb=" N PHE C 378 " --> pdb=" O LYS A 375 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N THR A 377 " --> pdb=" O PHE C 378 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 306 through 310 removed outlier: 6.580A pdb=" N SER B 305 " --> pdb=" O VAL D 306 " (cutoff:3.500A) removed outlier: 8.076A pdb=" N ILE D 308 " --> pdb=" O SER B 305 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N GLN B 307 " --> pdb=" O ILE D 308 " (cutoff:3.500A) removed outlier: 7.655A pdb=" N TYR D 310 " --> pdb=" O GLN B 307 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N VAL B 309 " --> pdb=" O TYR D 310 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 313 through 314 removed outlier: 6.935A pdb=" N VAL B 313 " --> pdb=" O ASP D 314 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 317 through 325 removed outlier: 6.525A pdb=" N LYS B 317 " --> pdb=" O VAL D 318 " (cutoff:3.500A) removed outlier: 7.930A pdb=" N SER D 320 " --> pdb=" O LYS B 317 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N THR B 319 " --> pdb=" O SER D 320 " (cutoff:3.500A) removed outlier: 8.123A pdb=" N CYS D 322 " --> pdb=" O THR B 319 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N LYS B 321 " --> pdb=" O CYS D 322 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N SER D 324 " --> pdb=" O LYS B 321 " (cutoff:3.500A) removed outlier: 5.910A pdb=" N GLY B 323 " --> pdb=" O SER D 324 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 328 through 330 removed outlier: 6.720A pdb=" N ILE B 328 " --> pdb=" O HIS D 329 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 337 through 342 removed outlier: 6.684A pdb=" N VAL B 337 " --> pdb=" O GLU F 338 " (cutoff:3.500A) removed outlier: 7.768A pdb=" N LYS F 340 " --> pdb=" O VAL B 337 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N VAL B 339 " --> pdb=" O LYS F 340 " (cutoff:3.500A) removed outlier: 7.882A pdb=" N GLU F 342 " --> pdb=" O VAL B 339 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N SER B 341 " --> pdb=" O GLU F 342 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 345 through 346 removed outlier: 6.358A pdb=" N ASP B 345 " --> pdb=" O PHE D 346 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 350 through 354 removed outlier: 6.190A pdb=" N VAL B 350 " --> pdb=" O GLN F 351 " (cutoff:3.500A) removed outlier: 7.912A pdb=" N LYS F 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N SER B 352 " --> pdb=" O LYS F 353 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 357 through 362 removed outlier: 6.733A pdb=" N ASP B 358 " --> pdb=" O ASN D 359 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N THR D 361 " --> pdb=" O ASP B 358 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N ILE B 360 " --> pdb=" O THR D 361 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N LEU B 357 " --> pdb=" O ASP F 358 " (cutoff:3.500A) removed outlier: 7.992A pdb=" N ILE F 360 " --> pdb=" O LEU B 357 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N ASN B 359 " --> pdb=" O ILE F 360 " (cutoff:3.500A) removed outlier: 7.859A pdb=" N HIS F 362 " --> pdb=" O ASN B 359 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N THR B 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 'D' and resid 368 through 378 removed outlier: 6.486A pdb=" N LYS B 369 " --> pdb=" O LYS D 370 " (cutoff:3.500A) removed outlier: 7.961A pdb=" N GLU D 372 " --> pdb=" O LYS B 369 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N ILE B 371 " --> pdb=" O GLU D 372 " (cutoff:3.500A) removed outlier: 7.903A pdb=" N HIS D 374 " --> pdb=" O ILE B 371 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N THR B 373 " --> pdb=" O HIS D 374 " (cutoff:3.500A) removed outlier: 7.988A pdb=" N LEU D 376 " --> pdb=" O THR B 373 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N LYS B 375 " --> pdb=" O LEU D 376 " (cutoff:3.500A) removed outlier: 7.916A pdb=" N PHE D 378 " --> pdb=" O LYS B 375 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N THR B 377 " --> pdb=" O PHE D 378 " (cutoff:3.500A) 76 hydrogen bonds defined for protein. 228 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: 0.47 Time building geometry restraints manager: 0.21 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: 1074 1.33 - 1.45: 374 1.45 - 1.57: 2107 1.57 - 1.69: 0 1.69 - 1.81: 6 Bond restraints: 3561 Sorted by residual: bond pdb=" CA LYS F 331 " pdb=" C LYS F 331 " ideal model delta sigma weight residual 1.532 1.555 -0.023 6.50e-03 2.37e+04 1.26e+01 bond pdb=" CZ ARG F 349 " pdb=" NH2 ARG F 349 " ideal model delta sigma weight residual 1.330 1.292 0.038 1.30e-02 5.92e+03 8.64e+00 bond pdb=" CA LYS F 331 " pdb=" CB LYS F 331 " ideal model delta sigma weight residual 1.522 1.548 -0.026 8.90e-03 1.26e+04 8.32e+00 bond pdb=" CA LYS D 331 " pdb=" CB LYS D 331 " ideal model delta sigma weight residual 1.522 1.547 -0.025 8.90e-03 1.26e+04 7.63e+00 bond pdb=" CZ ARG D 349 " pdb=" NH2 ARG D 349 " ideal model delta sigma weight residual 1.330 1.295 0.035 1.30e-02 5.92e+03 7.17e+00 ... (remaining 3556 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.36: 2822 1.36 - 2.73: 1367 2.73 - 4.09: 472 4.09 - 5.46: 86 5.46 - 6.82: 14 Bond angle restraints: 4761 Sorted by residual: angle pdb=" N GLY A 326 " pdb=" CA GLY A 326 " pdb=" C GLY A 326 " ideal model delta sigma weight residual 110.69 117.51 -6.82 1.33e+00 5.65e-01 2.63e+01 angle pdb=" CA ASP B 358 " pdb=" CB ASP B 358 " pdb=" CG ASP B 358 " ideal model delta sigma weight residual 112.60 117.65 -5.05 1.00e+00 1.00e+00 2.55e+01 angle pdb=" OE1 GLN B 336 " pdb=" CD GLN B 336 " pdb=" NE2 GLN B 336 " ideal model delta sigma weight residual 122.60 117.74 4.86 1.00e+00 1.00e+00 2.37e+01 angle pdb=" C ASP F 348 " pdb=" N ARG F 349 " pdb=" CA ARG F 349 " ideal model delta sigma weight residual 121.05 127.81 -6.76 1.43e+00 4.89e-01 2.24e+01 angle pdb=" CB HIS B 374 " pdb=" CG HIS B 374 " pdb=" CD2 HIS B 374 " ideal model delta sigma weight residual 131.20 125.06 6.14 1.30e+00 5.92e-01 2.23e+01 ... (remaining 4756 not shown) Histogram of dihedral angle deviations from ideal: 0.01 - 17.74: 2053 17.74 - 35.48: 92 35.48 - 53.22: 13 53.22 - 70.96: 3 70.96 - 88.69: 2 Dihedral angle restraints: 2163 sinusoidal: 903 harmonic: 1260 Sorted by residual: dihedral pdb=" CA GLY A 355 " pdb=" C GLY A 355 " pdb=" N SER A 356 " pdb=" CA SER A 356 " ideal model delta harmonic sigma weight residual 180.00 151.73 28.27 0 5.00e+00 4.00e-02 3.20e+01 dihedral pdb=" CA LEU E 357 " pdb=" C LEU E 357 " pdb=" N ASP E 358 " pdb=" CA ASP E 358 " ideal model delta harmonic sigma weight residual 180.00 154.60 25.40 0 5.00e+00 4.00e-02 2.58e+01 dihedral pdb=" CA GLY B 355 " pdb=" C GLY B 355 " pdb=" N SER B 356 " pdb=" CA SER B 356 " ideal model delta harmonic sigma weight residual 180.00 154.81 25.19 0 5.00e+00 4.00e-02 2.54e+01 ... (remaining 2160 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 301 0.062 - 0.124: 175 0.124 - 0.186: 42 0.186 - 0.248: 9 0.248 - 0.311: 4 Chirality restraints: 531 Sorted by residual: chirality pdb=" CA GLU A 372 " pdb=" N GLU A 372 " pdb=" C GLU A 372 " pdb=" CB GLU A 372 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.41e+00 chirality pdb=" CA GLU E 372 " pdb=" N GLU E 372 " pdb=" C GLU E 372 " pdb=" CB GLU E 372 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.05e+00 chirality pdb=" CA THR B 319 " pdb=" N THR B 319 " pdb=" C THR B 319 " pdb=" CB THR B 319 " both_signs ideal model delta sigma weight residual False 2.53 2.25 0.28 2.00e-01 2.50e+01 1.94e+00 ... (remaining 528 not shown) Planarity restraints: 609 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR F 310 " 0.091 2.00e-02 2.50e+03 5.23e-02 5.48e+01 pdb=" CG TYR F 310 " -0.021 2.00e-02 2.50e+03 pdb=" CD1 TYR F 310 " -0.036 2.00e-02 2.50e+03 pdb=" CD2 TYR F 310 " -0.045 2.00e-02 2.50e+03 pdb=" CE1 TYR F 310 " -0.036 2.00e-02 2.50e+03 pdb=" CE2 TYR F 310 " -0.029 2.00e-02 2.50e+03 pdb=" CZ TYR F 310 " -0.011 2.00e-02 2.50e+03 pdb=" OH TYR F 310 " 0.087 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR E 310 " 0.083 2.00e-02 2.50e+03 4.63e-02 4.29e+01 pdb=" CG TYR E 310 " -0.026 2.00e-02 2.50e+03 pdb=" CD1 TYR E 310 " -0.030 2.00e-02 2.50e+03 pdb=" CD2 TYR E 310 " -0.039 2.00e-02 2.50e+03 pdb=" CE1 TYR E 310 " -0.029 2.00e-02 2.50e+03 pdb=" CE2 TYR E 310 " -0.023 2.00e-02 2.50e+03 pdb=" CZ TYR E 310 " -0.012 2.00e-02 2.50e+03 pdb=" OH TYR E 310 " 0.076 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 310 " 0.072 2.00e-02 2.50e+03 4.13e-02 3.41e+01 pdb=" CG TYR A 310 " -0.020 2.00e-02 2.50e+03 pdb=" CD1 TYR A 310 " -0.025 2.00e-02 2.50e+03 pdb=" CD2 TYR A 310 " -0.035 2.00e-02 2.50e+03 pdb=" CE1 TYR A 310 " -0.028 2.00e-02 2.50e+03 pdb=" CE2 TYR A 310 " -0.021 2.00e-02 2.50e+03 pdb=" CZ TYR A 310 " -0.013 2.00e-02 2.50e+03 pdb=" OH TYR A 310 " 0.070 2.00e-02 2.50e+03 ... (remaining 606 not shown) Histogram of nonbonded interaction distances: 2.49 - 2.97: 1505 2.97 - 3.45: 2687 3.45 - 3.94: 5705 3.94 - 4.42: 5591 4.42 - 4.90: 10696 Nonbonded interactions: 26184 Sorted by model distance: nonbonded pdb=" OD1 ASP F 314 " pdb=" OG SER F 316 " model vdw 2.490 3.040 nonbonded pdb=" OD1 ASP D 314 " pdb=" OG SER D 316 " model vdw 2.499 3.040 nonbonded pdb=" OD1 ASP B 314 " pdb=" OG SER B 316 " model vdw 2.519 3.040 nonbonded pdb=" OD1 ASP E 314 " pdb=" OG SER E 316 " model vdw 2.535 3.040 nonbonded pdb=" OD1 ASP C 314 " pdb=" OG SER C 316 " model vdw 2.535 3.040 ... (remaining 26179 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 304 through 379) selection = (chain 'B' and resid 304 through 379) selection = (chain 'C' and resid 304 through 379) selection = (chain 'D' and resid 304 through 379) selection = (chain 'E' and resid 304 through 379) selection = (chain 'F' and resid 304 through 379) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.330 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.100 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 4.600 Find NCS groups from input model: 0.080 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:6.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7200 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 0.038 3561 Z= 0.674 Angle : 1.720 6.824 4761 Z= 1.160 Chirality : 0.079 0.311 531 Planarity : 0.010 0.071 609 Dihedral : 11.078 88.693 1365 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 0.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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 (0.31), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.23 (0.24), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 349 TYR 0.091 0.026 TYR F 310 PHE 0.035 0.012 PHE A 346 HIS 0.012 0.004 HIS A 330 Details of bonding type rmsd covalent geometry : bond 0.01082 ( 3561) covalent geometry : angle 1.71966 ( 4761) hydrogen bonds : bond 0.06753 ( 76) hydrogen bonds : angle 7.77198 ( 228) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 204 time to evaluate : 0.130 Fit side-chains revert: symmetry clash REVERT: A 311 LYS cc_start: 0.7818 (mttt) cc_final: 0.7530 (mttm) REVERT: A 317 LYS cc_start: 0.7043 (mtmt) cc_final: 0.6683 (mtpt) REVERT: A 338 GLU cc_start: 0.6921 (tt0) cc_final: 0.5878 (mt-10) REVERT: A 342 GLU cc_start: 0.7074 (mt-10) cc_final: 0.6604 (mt-10) REVERT: A 343 LYS cc_start: 0.7881 (mttt) cc_final: 0.7614 (mtpp) REVERT: A 353 LYS cc_start: 0.7411 (tttt) cc_final: 0.5931 (tptt) REVERT: A 358 ASP cc_start: 0.7242 (m-30) cc_final: 0.6818 (m-30) REVERT: A 369 LYS cc_start: 0.6714 (mttt) cc_final: 0.6034 (mtpp) REVERT: A 370 LYS cc_start: 0.7418 (tttp) cc_final: 0.6913 (ttmt) REVERT: A 373 THR cc_start: 0.7803 (m) cc_final: 0.7345 (p) REVERT: A 375 LYS cc_start: 0.7255 (tttt) cc_final: 0.7052 (tttt) REVERT: B 345 ASP cc_start: 0.6846 (m-30) cc_final: 0.6221 (t70) REVERT: B 348 ASP cc_start: 0.8206 (t70) cc_final: 0.7992 (t0) REVERT: B 353 LYS cc_start: 0.7015 (tttt) cc_final: 0.6591 (tttm) REVERT: B 375 LYS cc_start: 0.7608 (tttt) cc_final: 0.7061 (ttpp) REVERT: C 307 GLN cc_start: 0.8278 (tt0) cc_final: 0.7880 (tt0) REVERT: C 311 LYS cc_start: 0.8232 (mttt) cc_final: 0.7978 (mttm) REVERT: C 320 SER cc_start: 0.7604 (t) cc_final: 0.7339 (p) REVERT: C 336 GLN cc_start: 0.8206 (tt0) cc_final: 0.7923 (tt0) REVERT: C 338 GLU cc_start: 0.7444 (tt0) cc_final: 0.7002 (tm-30) REVERT: C 340 LYS cc_start: 0.7880 (mttt) cc_final: 0.7504 (mtmm) REVERT: C 342 GLU cc_start: 0.7536 (mt-10) cc_final: 0.7127 (mt-10) REVERT: C 343 LYS cc_start: 0.8064 (mttt) cc_final: 0.7772 (mttm) REVERT: C 349 ARG cc_start: 0.6452 (mtm180) cc_final: 0.6051 (mtt180) REVERT: C 353 LYS cc_start: 0.7737 (tttt) cc_final: 0.6777 (tptt) REVERT: C 369 LYS cc_start: 0.7617 (mttt) cc_final: 0.6980 (mtpp) REVERT: C 370 LYS cc_start: 0.7871 (tttp) cc_final: 0.7520 (ttmt) REVERT: C 371 ILE cc_start: 0.8166 (mt) cc_final: 0.7738 (mp) REVERT: C 372 GLU cc_start: 0.7364 (mt-10) cc_final: 0.6269 (mm-30) REVERT: C 373 THR cc_start: 0.8235 (m) cc_final: 0.7848 (p) REVERT: C 375 LYS cc_start: 0.8036 (tttt) cc_final: 0.7709 (tttt) REVERT: D 314 ASP cc_start: 0.7230 (t0) cc_final: 0.6917 (t0) REVERT: D 315 LEU cc_start: 0.8312 (mt) cc_final: 0.7971 (mm) REVERT: D 317 LYS cc_start: 0.7720 (mttt) cc_final: 0.7358 (mtpt) REVERT: D 321 LYS cc_start: 0.7725 (mttt) cc_final: 0.7197 (mttp) REVERT: D 338 GLU cc_start: 0.7798 (tt0) cc_final: 0.7137 (tt0) REVERT: D 345 ASP cc_start: 0.7255 (m-30) cc_final: 0.6768 (t70) REVERT: D 347 LYS cc_start: 0.7951 (mttt) cc_final: 0.7634 (mmtm) REVERT: D 353 LYS cc_start: 0.7856 (tttt) cc_final: 0.7582 (tttm) REVERT: D 373 THR cc_start: 0.8328 (m) cc_final: 0.7952 (p) REVERT: D 375 LYS cc_start: 0.8246 (tttt) cc_final: 0.7726 (ttpp) REVERT: D 379 ARG cc_start: 0.6720 (mtt-85) cc_final: 0.6292 (mmp-170) REVERT: E 311 LYS cc_start: 0.7813 (mttt) cc_final: 0.6878 (mttm) REVERT: E 336 GLN cc_start: 0.7688 (tt0) cc_final: 0.7391 (tt0) REVERT: E 338 GLU cc_start: 0.6808 (tt0) cc_final: 0.6077 (mt-10) REVERT: E 342 GLU cc_start: 0.7377 (mt-10) cc_final: 0.7128 (mt-10) REVERT: E 343 LYS cc_start: 0.8105 (mttt) cc_final: 0.7855 (mtpp) REVERT: E 347 LYS cc_start: 0.8048 (mttt) cc_final: 0.7808 (mttm) REVERT: E 348 ASP cc_start: 0.7897 (t0) cc_final: 0.7658 (t0) REVERT: E 349 ARG cc_start: 0.6798 (mtm180) cc_final: 0.5746 (mtp180) REVERT: E 353 LYS cc_start: 0.7295 (tttt) cc_final: 0.5997 (tptt) REVERT: E 356 SER cc_start: 0.7331 (p) cc_final: 0.7005 (t) REVERT: E 369 LYS cc_start: 0.6882 (mttt) cc_final: 0.6240 (mtpp) REVERT: E 373 THR cc_start: 0.7841 (m) cc_final: 0.7121 (p) REVERT: E 375 LYS cc_start: 0.7191 (tttt) cc_final: 0.6686 (tttp) REVERT: F 311 LYS cc_start: 0.7444 (mttt) cc_final: 0.6550 (mttm) REVERT: F 317 LYS cc_start: 0.7056 (mttt) cc_final: 0.6837 (mtpt) REVERT: F 321 LYS cc_start: 0.6984 (mttt) cc_final: 0.6605 (mttm) REVERT: F 336 GLN cc_start: 0.7452 (tt0) cc_final: 0.7223 (tt0) REVERT: F 338 GLU cc_start: 0.7380 (tt0) cc_final: 0.6342 (tt0) REVERT: F 340 LYS cc_start: 0.6749 (mttt) cc_final: 0.6081 (mmtt) REVERT: F 347 LYS cc_start: 0.7897 (mttt) cc_final: 0.7408 (mmtp) REVERT: F 348 ASP cc_start: 0.7818 (t0) cc_final: 0.7552 (t0) REVERT: F 353 LYS cc_start: 0.7234 (tttt) cc_final: 0.6750 (tttm) REVERT: F 356 SER cc_start: 0.7261 (p) cc_final: 0.7023 (t) REVERT: F 375 LYS cc_start: 0.7658 (tttt) cc_final: 0.7126 (ttpp) outliers start: 0 outliers final: 0 residues processed: 204 average time/residue: 0.5409 time to fit residues: 112.9918 Evaluate side-chains 187 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 187 time to evaluate : 0.093 ------------------------------------------------------------------------------- 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: 4.9990 chunk 2 optimal weight: 0.9990 chunk 16 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 chunk 31 optimal weight: 8.9990 chunk 25 optimal weight: 0.9980 chunk 19 optimal weight: 0.9980 chunk 30 optimal weight: 0.9980 chunk 22 optimal weight: 6.9990 chunk 37 optimal weight: 7.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 336 GLN A 362 HIS B 351 GLN D 307 GLN D 327 ASN F 351 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.128608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.114147 restraints weight = 3926.785| |-----------------------------------------------------------------------------| r_work (start): 0.3677 rms_B_bonded: 1.46 r_work: 0.3580 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.3490 rms_B_bonded: 2.98 restraints_weight: 0.2500 r_work (final): 0.3490 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8669 moved from start: 0.2024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 3561 Z= 0.112 Angle : 0.572 5.529 4761 Z= 0.291 Chirality : 0.049 0.130 531 Planarity : 0.003 0.020 609 Dihedral : 5.203 18.492 474 Min Nonbonded Distance : 2.628 Molprobity Statistics. All-atom Clashscore : 1.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.89 % Favored : 99.11 % Rotamer: Outliers : 1.75 % Allowed : 10.03 % Favored : 88.22 % 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: -1.52 (0.32), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.15 (0.25), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 379 TYR 0.008 0.002 TYR B 310 PHE 0.013 0.002 PHE C 378 HIS 0.003 0.001 HIS C 329 Details of bonding type rmsd covalent geometry : bond 0.00247 ( 3561) covalent geometry : angle 0.57234 ( 4761) hydrogen bonds : bond 0.02375 ( 76) hydrogen bonds : angle 5.56665 ( 228) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 188 time to evaluate : 0.094 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 342 GLU cc_start: 0.7800 (mt-10) cc_final: 0.7442 (mt-10) REVERT: A 353 LYS cc_start: 0.8652 (tttt) cc_final: 0.8325 (tptt) REVERT: C 342 GLU cc_start: 0.7969 (mt-10) cc_final: 0.7678 (mt-10) REVERT: C 345 ASP cc_start: 0.8396 (m-30) cc_final: 0.8007 (t70) REVERT: C 353 LYS cc_start: 0.8618 (tttt) cc_final: 0.8376 (tptt) REVERT: C 372 GLU cc_start: 0.8114 (mt-10) cc_final: 0.7742 (mm-30) REVERT: D 324 SER cc_start: 0.9005 (t) cc_final: 0.8748 (m) REVERT: D 338 GLU cc_start: 0.8525 (tt0) cc_final: 0.8237 (tt0) REVERT: D 379 ARG cc_start: 0.7426 (mtt-85) cc_final: 0.6873 (mmp-170) REVERT: E 311 LYS cc_start: 0.8512 (mttt) cc_final: 0.7975 (mttm) REVERT: E 349 ARG cc_start: 0.7784 (mtm180) cc_final: 0.6849 (mtp180) REVERT: E 353 LYS cc_start: 0.8637 (tttt) cc_final: 0.8276 (tptt) REVERT: E 375 LYS cc_start: 0.8565 (tttt) cc_final: 0.8312 (tttp) REVERT: F 311 LYS cc_start: 0.8237 (mttt) cc_final: 0.7741 (mttm) REVERT: F 338 GLU cc_start: 0.8318 (tt0) cc_final: 0.7959 (tt0) REVERT: F 340 LYS cc_start: 0.8208 (mttt) cc_final: 0.7923 (mmtt) outliers start: 7 outliers final: 2 residues processed: 189 average time/residue: 0.5605 time to fit residues: 108.3045 Evaluate side-chains 157 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 155 time to evaluate : 0.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 341 SER Chi-restraints excluded: chain F residue 319 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 22 optimal weight: 5.9990 chunk 24 optimal weight: 9.9990 chunk 35 optimal weight: 8.9990 chunk 8 optimal weight: 2.9990 chunk 34 optimal weight: 4.9990 chunk 36 optimal weight: 1.9990 chunk 9 optimal weight: 7.9990 chunk 41 optimal weight: 9.9990 chunk 2 optimal weight: 10.0000 chunk 19 optimal weight: 10.0000 chunk 39 optimal weight: 6.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 336 GLN B 307 GLN C 307 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.121028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.106381 restraints weight = 3955.688| |-----------------------------------------------------------------------------| r_work (start): 0.3566 rms_B_bonded: 1.46 r_work: 0.3469 rms_B_bonded: 1.68 restraints_weight: 0.5000 r_work: 0.3382 rms_B_bonded: 2.83 restraints_weight: 0.2500 r_work (final): 0.3382 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8758 moved from start: 0.2960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.035 3561 Z= 0.254 Angle : 0.667 4.935 4761 Z= 0.339 Chirality : 0.051 0.126 531 Planarity : 0.004 0.023 609 Dihedral : 5.192 17.984 474 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.89 % Favored : 99.11 % Rotamer: Outliers : 1.75 % Allowed : 20.05 % Favored : 78.20 % 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: -1.74 (0.32), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.32 (0.25), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 379 TYR 0.013 0.003 TYR E 310 PHE 0.016 0.003 PHE F 346 HIS 0.005 0.001 HIS D 329 Details of bonding type rmsd covalent geometry : bond 0.00559 ( 3561) covalent geometry : angle 0.66727 ( 4761) hydrogen bonds : bond 0.02800 ( 76) hydrogen bonds : angle 5.39557 ( 228) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 154 time to evaluate : 0.166 Fit side-chains revert: symmetry clash REVERT: A 321 LYS cc_start: 0.8691 (mtmt) cc_final: 0.8467 (mtpp) REVERT: A 353 LYS cc_start: 0.8585 (tttt) cc_final: 0.8195 (tptt) REVERT: C 342 GLU cc_start: 0.8045 (mt-10) cc_final: 0.7778 (mt-10) REVERT: C 347 LYS cc_start: 0.8673 (mmtt) cc_final: 0.7353 (pmtt) REVERT: C 353 LYS cc_start: 0.8664 (tttt) cc_final: 0.8360 (tptt) REVERT: C 372 GLU cc_start: 0.8269 (mt-10) cc_final: 0.7831 (mm-30) REVERT: D 338 GLU cc_start: 0.8481 (tt0) cc_final: 0.8152 (tt0) REVERT: D 379 ARG cc_start: 0.7539 (mtt-85) cc_final: 0.7316 (mtt-85) REVERT: E 311 LYS cc_start: 0.8722 (mttt) cc_final: 0.8117 (mttm) REVERT: E 349 ARG cc_start: 0.7809 (mtm180) cc_final: 0.6770 (mmp-170) REVERT: E 353 LYS cc_start: 0.8631 (tttt) cc_final: 0.8264 (tptt) REVERT: E 375 LYS cc_start: 0.8589 (tttt) cc_final: 0.8325 (tttp) REVERT: F 338 GLU cc_start: 0.8359 (tt0) cc_final: 0.7950 (tt0) outliers start: 7 outliers final: 3 residues processed: 156 average time/residue: 0.5975 time to fit residues: 95.2687 Evaluate side-chains 145 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 142 time to evaluate : 0.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 375 LYS Chi-restraints excluded: chain E residue 341 SER Chi-restraints excluded: chain F residue 319 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 29 optimal weight: 2.9990 chunk 32 optimal weight: 10.0000 chunk 6 optimal weight: 10.0000 chunk 28 optimal weight: 6.9990 chunk 12 optimal weight: 9.9990 chunk 22 optimal weight: 5.9990 chunk 38 optimal weight: 8.9990 chunk 20 optimal weight: 5.9990 chunk 21 optimal weight: 7.9990 chunk 39 optimal weight: 3.9990 chunk 1 optimal weight: 6.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 336 GLN B 307 GLN C 307 GLN C 330 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.120282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.105604 restraints weight = 3946.158| |-----------------------------------------------------------------------------| r_work (start): 0.3544 rms_B_bonded: 1.45 r_work: 0.3449 rms_B_bonded: 1.67 restraints_weight: 0.5000 r_work: 0.3363 rms_B_bonded: 2.80 restraints_weight: 0.2500 r_work (final): 0.3363 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8765 moved from start: 0.3144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.037 3561 Z= 0.284 Angle : 0.682 8.107 4761 Z= 0.345 Chirality : 0.051 0.136 531 Planarity : 0.004 0.026 609 Dihedral : 5.239 17.603 474 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.67 % Favored : 99.33 % Rotamer: Outliers : 2.76 % Allowed : 18.30 % Favored : 78.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -1.96 (0.31), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.49 (0.24), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 379 TYR 0.014 0.003 TYR E 310 PHE 0.015 0.003 PHE B 346 HIS 0.005 0.001 HIS B 329 Details of bonding type rmsd covalent geometry : bond 0.00617 ( 3561) covalent geometry : angle 0.68247 ( 4761) hydrogen bonds : bond 0.02820 ( 76) hydrogen bonds : angle 5.32702 ( 228) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 147 time to evaluate : 0.127 Fit side-chains revert: symmetry clash REVERT: A 353 LYS cc_start: 0.8608 (tttt) cc_final: 0.8285 (tptt) REVERT: C 342 GLU cc_start: 0.8027 (mt-10) cc_final: 0.7789 (mt-10) REVERT: C 347 LYS cc_start: 0.8671 (mmtt) cc_final: 0.7419 (pmtt) REVERT: C 353 LYS cc_start: 0.8665 (tttt) cc_final: 0.8399 (tptp) REVERT: C 372 GLU cc_start: 0.8321 (mt-10) cc_final: 0.7885 (mm-30) REVERT: D 338 GLU cc_start: 0.8434 (tt0) cc_final: 0.8084 (tt0) REVERT: D 379 ARG cc_start: 0.7540 (mtt-85) cc_final: 0.6892 (mmp-170) REVERT: E 311 LYS cc_start: 0.8732 (mttt) cc_final: 0.8163 (mttm) REVERT: E 349 ARG cc_start: 0.7868 (mtm180) cc_final: 0.6757 (mmp-170) REVERT: E 353 LYS cc_start: 0.8644 (tttt) cc_final: 0.8296 (tptt) REVERT: E 375 LYS cc_start: 0.8604 (tttt) cc_final: 0.8348 (tttp) REVERT: F 338 GLU cc_start: 0.8314 (tt0) cc_final: 0.7889 (tt0) outliers start: 11 outliers final: 5 residues processed: 152 average time/residue: 0.6122 time to fit residues: 94.9516 Evaluate side-chains 144 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 139 time to evaluate : 0.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain B residue 375 LYS Chi-restraints excluded: chain D residue 317 LYS Chi-restraints excluded: chain E residue 341 SER Chi-restraints excluded: chain F residue 319 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 8 optimal weight: 10.0000 chunk 1 optimal weight: 7.9990 chunk 15 optimal weight: 0.8980 chunk 39 optimal weight: 6.9990 chunk 31 optimal weight: 5.9990 chunk 13 optimal weight: 10.0000 chunk 35 optimal weight: 1.9990 chunk 3 optimal weight: 4.9990 chunk 30 optimal weight: 8.9990 chunk 2 optimal weight: 0.9990 chunk 6 optimal weight: 0.9980 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 336 GLN B 307 GLN C 307 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.122872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.108310 restraints weight = 3958.457| |-----------------------------------------------------------------------------| r_work (start): 0.3586 rms_B_bonded: 1.46 r_work: 0.3494 rms_B_bonded: 1.68 restraints_weight: 0.5000 r_work: 0.3407 rms_B_bonded: 2.84 restraints_weight: 0.2500 r_work (final): 0.3407 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8736 moved from start: 0.3196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3561 Z= 0.141 Angle : 0.560 4.533 4761 Z= 0.281 Chirality : 0.049 0.123 531 Planarity : 0.003 0.024 609 Dihedral : 4.788 16.860 474 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.67 % Favored : 99.33 % Rotamer: Outliers : 1.25 % Allowed : 20.05 % Favored : 78.70 % 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 aren not related in a simple way. whole: -1.90 (0.32), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.44 (0.25), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 379 TYR 0.011 0.002 TYR F 310 PHE 0.012 0.002 PHE F 346 HIS 0.002 0.001 HIS C 329 Details of bonding type rmsd covalent geometry : bond 0.00306 ( 3561) covalent geometry : angle 0.56044 ( 4761) hydrogen bonds : bond 0.02112 ( 76) hydrogen bonds : angle 4.94351 ( 228) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 152 time to evaluate : 0.154 Fit side-chains revert: symmetry clash REVERT: A 321 LYS cc_start: 0.8664 (mtmt) cc_final: 0.8459 (mtpp) REVERT: A 353 LYS cc_start: 0.8599 (tttt) cc_final: 0.8290 (tptt) REVERT: C 342 GLU cc_start: 0.7963 (mt-10) cc_final: 0.7707 (mt-10) REVERT: C 347 LYS cc_start: 0.8652 (mmtt) cc_final: 0.7339 (pmtt) REVERT: C 353 LYS cc_start: 0.8644 (tttt) cc_final: 0.8330 (tptt) REVERT: C 372 GLU cc_start: 0.8274 (mt-10) cc_final: 0.7864 (mm-30) REVERT: D 324 SER cc_start: 0.8996 (t) cc_final: 0.8779 (m) REVERT: D 338 GLU cc_start: 0.8460 (tt0) cc_final: 0.8120 (tt0) REVERT: D 379 ARG cc_start: 0.7516 (mtt-85) cc_final: 0.6881 (mmp-170) REVERT: E 311 LYS cc_start: 0.8666 (mttt) cc_final: 0.8089 (mttm) REVERT: E 349 ARG cc_start: 0.7782 (mtm180) cc_final: 0.6694 (mmp-170) REVERT: E 353 LYS cc_start: 0.8657 (tttt) cc_final: 0.8315 (tptt) REVERT: E 375 LYS cc_start: 0.8609 (tttt) cc_final: 0.8358 (tttp) REVERT: F 338 GLU cc_start: 0.8314 (tt0) cc_final: 0.7900 (tt0) outliers start: 5 outliers final: 3 residues processed: 155 average time/residue: 0.5950 time to fit residues: 94.2057 Evaluate side-chains 150 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 147 time to evaluate : 0.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 317 LYS Chi-restraints excluded: chain E residue 341 SER Chi-restraints excluded: chain F residue 319 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 0 optimal weight: 10.0000 chunk 27 optimal weight: 0.0070 chunk 32 optimal weight: 0.2980 chunk 38 optimal weight: 9.9990 chunk 39 optimal weight: 0.9980 chunk 3 optimal weight: 10.0000 chunk 14 optimal weight: 4.9990 chunk 18 optimal weight: 0.2980 chunk 40 optimal weight: 4.9990 chunk 13 optimal weight: 5.9990 chunk 1 optimal weight: 8.9990 overall best weight: 1.3200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 336 GLN B 307 GLN C 307 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.124736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.110241 restraints weight = 3997.321| |-----------------------------------------------------------------------------| r_work (start): 0.3621 rms_B_bonded: 1.48 r_work: 0.3532 rms_B_bonded: 1.71 restraints_weight: 0.5000 r_work: 0.3448 rms_B_bonded: 2.88 restraints_weight: 0.2500 r_work (final): 0.3448 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8719 moved from start: 0.3291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 3561 Z= 0.110 Angle : 0.536 6.062 4761 Z= 0.265 Chirality : 0.048 0.120 531 Planarity : 0.003 0.023 609 Dihedral : 4.549 16.184 474 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.89 % Favored : 99.11 % Rotamer: Outliers : 0.75 % Allowed : 20.80 % Favored : 78.45 % 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: -1.87 (0.32), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.42 (0.25), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 379 TYR 0.010 0.002 TYR F 310 PHE 0.010 0.002 PHE C 378 HIS 0.002 0.000 HIS C 329 Details of bonding type rmsd covalent geometry : bond 0.00238 ( 3561) covalent geometry : angle 0.53606 ( 4761) hydrogen bonds : bond 0.01829 ( 76) hydrogen bonds : angle 4.70982 ( 228) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 152 time to evaluate : 0.121 Fit side-chains revert: symmetry clash REVERT: A 353 LYS cc_start: 0.8638 (tttt) cc_final: 0.8373 (tptt) REVERT: C 340 LYS cc_start: 0.8373 (mtmm) cc_final: 0.8130 (mttm) REVERT: C 342 GLU cc_start: 0.7905 (mt-10) cc_final: 0.7667 (mt-10) REVERT: C 347 LYS cc_start: 0.8636 (mmtt) cc_final: 0.7383 (pmtt) REVERT: C 353 LYS cc_start: 0.8622 (tttt) cc_final: 0.8342 (tptt) REVERT: C 372 GLU cc_start: 0.8252 (mt-10) cc_final: 0.7832 (mm-30) REVERT: D 338 GLU cc_start: 0.8442 (tt0) cc_final: 0.8110 (tt0) REVERT: D 379 ARG cc_start: 0.7426 (mtt-85) cc_final: 0.6814 (mmp-170) REVERT: E 311 LYS cc_start: 0.8618 (mttt) cc_final: 0.8048 (mttm) REVERT: E 349 ARG cc_start: 0.7739 (mtm180) cc_final: 0.6816 (mtp180) REVERT: E 353 LYS cc_start: 0.8659 (tttt) cc_final: 0.8329 (tptt) REVERT: E 375 LYS cc_start: 0.8606 (tttt) cc_final: 0.8357 (tttp) REVERT: F 338 GLU cc_start: 0.8322 (tt0) cc_final: 0.7923 (tt0) outliers start: 3 outliers final: 3 residues processed: 153 average time/residue: 0.6515 time to fit residues: 101.8192 Evaluate side-chains 146 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 143 time to evaluate : 0.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 317 LYS Chi-restraints excluded: chain E residue 315 LEU Chi-restraints excluded: chain F residue 319 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 41 optimal weight: 9.9990 chunk 36 optimal weight: 10.0000 chunk 35 optimal weight: 6.9990 chunk 18 optimal weight: 7.9990 chunk 33 optimal weight: 7.9990 chunk 29 optimal weight: 7.9990 chunk 25 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 8 optimal weight: 6.9990 chunk 14 optimal weight: 2.9990 chunk 13 optimal weight: 3.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 336 GLN B 307 GLN C 307 GLN C 330 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.118188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.103939 restraints weight = 4204.537| |-----------------------------------------------------------------------------| r_work (start): 0.3542 rms_B_bonded: 1.43 r_work: 0.3446 rms_B_bonded: 1.67 restraints_weight: 0.5000 r_work: 0.3357 rms_B_bonded: 2.82 restraints_weight: 0.2500 r_work (final): 0.3357 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8771 moved from start: 0.3277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.040 3561 Z= 0.314 Angle : 0.696 5.332 4761 Z= 0.355 Chirality : 0.052 0.138 531 Planarity : 0.004 0.024 609 Dihedral : 5.161 17.602 474 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 2.26 % Allowed : 19.80 % Favored : 77.94 % 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: -2.01 (0.32), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.52 (0.24), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG D 349 TYR 0.015 0.004 TYR A 310 PHE 0.017 0.003 PHE F 346 HIS 0.005 0.001 HIS B 329 Details of bonding type rmsd covalent geometry : bond 0.00688 ( 3561) covalent geometry : angle 0.69563 ( 4761) hydrogen bonds : bond 0.02837 ( 76) hydrogen bonds : angle 5.19876 ( 228) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 142 time to evaluate : 0.099 Fit side-chains revert: symmetry clash REVERT: A 321 LYS cc_start: 0.8722 (mtpp) cc_final: 0.8449 (mtpt) REVERT: A 353 LYS cc_start: 0.8635 (tttt) cc_final: 0.8285 (tptt) REVERT: B 373 THR cc_start: 0.8908 (m) cc_final: 0.8630 (p) REVERT: C 342 GLU cc_start: 0.8010 (mt-10) cc_final: 0.7780 (mt-10) REVERT: C 353 LYS cc_start: 0.8661 (tttt) cc_final: 0.8402 (tptt) REVERT: D 338 GLU cc_start: 0.8476 (tt0) cc_final: 0.8131 (tt0) REVERT: D 379 ARG cc_start: 0.7555 (mtt-85) cc_final: 0.6856 (mmp-170) REVERT: E 311 LYS cc_start: 0.8729 (mttt) cc_final: 0.8184 (mttm) REVERT: E 349 ARG cc_start: 0.7890 (mtm180) cc_final: 0.6739 (mmp-170) REVERT: E 353 LYS cc_start: 0.8683 (tttt) cc_final: 0.8326 (tptt) REVERT: E 375 LYS cc_start: 0.8596 (tttt) cc_final: 0.8343 (tttp) REVERT: F 338 GLU cc_start: 0.8329 (tt0) cc_final: 0.7948 (tt0) outliers start: 9 outliers final: 3 residues processed: 146 average time/residue: 0.6458 time to fit residues: 96.2378 Evaluate side-chains 144 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 141 time to evaluate : 0.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain D residue 317 LYS Chi-restraints excluded: chain F residue 319 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 33 optimal weight: 0.9980 chunk 23 optimal weight: 5.9990 chunk 28 optimal weight: 3.9990 chunk 7 optimal weight: 1.9990 chunk 34 optimal weight: 3.9990 chunk 9 optimal weight: 5.9990 chunk 39 optimal weight: 0.9980 chunk 25 optimal weight: 4.9990 chunk 32 optimal weight: 0.7980 chunk 6 optimal weight: 6.9990 chunk 14 optimal weight: 1.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 336 GLN B 307 GLN C 307 GLN C 330 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.123569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.109240 restraints weight = 4006.443| |-----------------------------------------------------------------------------| r_work (start): 0.3594 rms_B_bonded: 1.46 r_work: 0.3503 rms_B_bonded: 1.68 restraints_weight: 0.5000 r_work: 0.3417 rms_B_bonded: 2.83 restraints_weight: 0.2500 r_work (final): 0.3417 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8728 moved from start: 0.3382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 3561 Z= 0.117 Angle : 0.569 6.823 4761 Z= 0.279 Chirality : 0.049 0.121 531 Planarity : 0.003 0.023 609 Dihedral : 4.702 16.513 474 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.89 % Favored : 99.11 % Rotamer: Outliers : 0.50 % Allowed : 21.80 % Favored : 77.69 % 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: -1.94 (0.32), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.47 (0.24), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 379 TYR 0.010 0.002 TYR F 310 PHE 0.009 0.002 PHE C 378 HIS 0.002 0.000 HIS A 330 Details of bonding type rmsd covalent geometry : bond 0.00256 ( 3561) covalent geometry : angle 0.56885 ( 4761) hydrogen bonds : bond 0.01911 ( 76) hydrogen bonds : angle 4.79231 ( 228) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 154 time to evaluate : 0.117 Fit side-chains revert: symmetry clash REVERT: A 321 LYS cc_start: 0.8702 (mtpp) cc_final: 0.8437 (mtpt) REVERT: A 349 ARG cc_start: 0.8209 (mtt180) cc_final: 0.7980 (mtt180) REVERT: A 353 LYS cc_start: 0.8635 (tttt) cc_final: 0.8320 (tptt) REVERT: B 373 THR cc_start: 0.8892 (m) cc_final: 0.8586 (p) REVERT: C 342 GLU cc_start: 0.7970 (mt-10) cc_final: 0.7729 (mt-10) REVERT: C 347 LYS cc_start: 0.8647 (mmtt) cc_final: 0.7396 (pmtt) REVERT: C 353 LYS cc_start: 0.8635 (tttt) cc_final: 0.8391 (tptt) REVERT: C 372 GLU cc_start: 0.8290 (mm-30) cc_final: 0.7935 (mm-30) REVERT: D 338 GLU cc_start: 0.8442 (tt0) cc_final: 0.8099 (tt0) REVERT: D 353 LYS cc_start: 0.8603 (tttm) cc_final: 0.8317 (tttt) REVERT: D 379 ARG cc_start: 0.7455 (mtt-85) cc_final: 0.6850 (mmp-170) REVERT: E 311 LYS cc_start: 0.8624 (mttt) cc_final: 0.8059 (mttm) REVERT: E 349 ARG cc_start: 0.7791 (mtm180) cc_final: 0.6672 (mmp-170) REVERT: E 353 LYS cc_start: 0.8682 (tttt) cc_final: 0.8329 (tptt) REVERT: E 369 LYS cc_start: 0.8495 (mtpp) cc_final: 0.8249 (mtpp) REVERT: E 375 LYS cc_start: 0.8608 (tttt) cc_final: 0.8360 (tttp) REVERT: F 338 GLU cc_start: 0.8291 (tt0) cc_final: 0.7909 (tt0) outliers start: 2 outliers final: 2 residues processed: 155 average time/residue: 0.6452 time to fit residues: 101.9776 Evaluate side-chains 150 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 148 time to evaluate : 0.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 317 LYS Chi-restraints excluded: chain F residue 319 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 18 optimal weight: 6.9990 chunk 8 optimal weight: 10.0000 chunk 20 optimal weight: 0.0060 chunk 2 optimal weight: 10.0000 chunk 30 optimal weight: 6.9990 chunk 4 optimal weight: 2.9990 chunk 24 optimal weight: 6.9990 chunk 25 optimal weight: 9.9990 chunk 5 optimal weight: 10.0000 chunk 31 optimal weight: 2.9990 chunk 32 optimal weight: 8.9990 overall best weight: 4.0004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 336 GLN B 307 GLN C 307 GLN E 336 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.118893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.104939 restraints weight = 4113.668| |-----------------------------------------------------------------------------| r_work (start): 0.3575 rms_B_bonded: 1.40 r_work: 0.3481 rms_B_bonded: 1.64 restraints_weight: 0.5000 r_work: 0.3394 rms_B_bonded: 2.78 restraints_weight: 0.2500 r_work (final): 0.3394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8758 moved from start: 0.3355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 3561 Z= 0.230 Angle : 0.648 5.401 4761 Z= 0.327 Chirality : 0.050 0.125 531 Planarity : 0.003 0.023 609 Dihedral : 4.968 17.454 474 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.00 % Allowed : 21.55 % Favored : 77.44 % 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: -1.97 (0.32), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.49 (0.24), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 349 TYR 0.014 0.003 TYR A 310 PHE 0.016 0.002 PHE F 346 HIS 0.003 0.001 HIS C 329 Details of bonding type rmsd covalent geometry : bond 0.00501 ( 3561) covalent geometry : angle 0.64799 ( 4761) hydrogen bonds : bond 0.02463 ( 76) hydrogen bonds : angle 5.01983 ( 228) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 143 time to evaluate : 0.132 Fit side-chains REVERT: A 321 LYS cc_start: 0.8691 (mtpp) cc_final: 0.8433 (mtmt) REVERT: A 353 LYS cc_start: 0.8632 (tttt) cc_final: 0.8282 (tptt) REVERT: B 373 THR cc_start: 0.8892 (m) cc_final: 0.8604 (p) REVERT: C 342 GLU cc_start: 0.7975 (mt-10) cc_final: 0.7732 (mt-10) REVERT: C 347 LYS cc_start: 0.8670 (mmtt) cc_final: 0.7410 (pmtt) REVERT: C 353 LYS cc_start: 0.8650 (tttt) cc_final: 0.8392 (tptt) REVERT: D 338 GLU cc_start: 0.8456 (tt0) cc_final: 0.8107 (tt0) REVERT: D 379 ARG cc_start: 0.7571 (mtt-85) cc_final: 0.6874 (mmp-170) REVERT: E 311 LYS cc_start: 0.8716 (mttt) cc_final: 0.8164 (mttm) REVERT: E 349 ARG cc_start: 0.7897 (mtm180) cc_final: 0.6738 (mmp-170) REVERT: E 353 LYS cc_start: 0.8690 (tttt) cc_final: 0.8322 (tptt) REVERT: F 338 GLU cc_start: 0.8311 (tt0) cc_final: 0.7924 (tt0) outliers start: 4 outliers final: 2 residues processed: 145 average time/residue: 0.6567 time to fit residues: 97.1432 Evaluate side-chains 135 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 133 time to evaluate : 0.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 317 LYS Chi-restraints excluded: chain F residue 319 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 32 optimal weight: 5.9990 chunk 40 optimal weight: 6.9990 chunk 41 optimal weight: 9.9990 chunk 13 optimal weight: 0.9980 chunk 33 optimal weight: 5.9990 chunk 8 optimal weight: 10.0000 chunk 31 optimal weight: 7.9990 chunk 28 optimal weight: 4.9990 chunk 23 optimal weight: 2.9990 chunk 39 optimal weight: 3.9990 chunk 1 optimal weight: 7.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 336 GLN B 307 GLN C 307 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.120594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.106143 restraints weight = 4013.326| |-----------------------------------------------------------------------------| r_work (start): 0.3564 rms_B_bonded: 1.45 r_work: 0.3473 rms_B_bonded: 1.65 restraints_weight: 0.5000 r_work: 0.3389 rms_B_bonded: 2.78 restraints_weight: 0.2500 r_work (final): 0.3389 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8755 moved from start: 0.3400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 3561 Z= 0.224 Angle : 0.655 5.373 4761 Z= 0.331 Chirality : 0.050 0.128 531 Planarity : 0.003 0.024 609 Dihedral : 4.995 17.445 474 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.89 % Favored : 99.11 % Rotamer: Outliers : 0.50 % Allowed : 22.31 % Favored : 77.19 % 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: -2.02 (0.32), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.53 (0.24), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 349 TYR 0.013 0.003 TYR A 310 PHE 0.013 0.002 PHE F 346 HIS 0.003 0.001 HIS C 329 Details of bonding type rmsd covalent geometry : bond 0.00488 ( 3561) covalent geometry : angle 0.65470 ( 4761) hydrogen bonds : bond 0.02442 ( 76) hydrogen bonds : angle 5.05941 ( 228) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 134 time to evaluate : 0.160 Fit side-chains REVERT: A 321 LYS cc_start: 0.8691 (mtpp) cc_final: 0.8423 (mtmt) REVERT: A 353 LYS cc_start: 0.8637 (tttt) cc_final: 0.8272 (tptt) REVERT: B 373 THR cc_start: 0.8896 (m) cc_final: 0.8609 (p) REVERT: C 342 GLU cc_start: 0.7989 (mt-10) cc_final: 0.7756 (mt-10) REVERT: C 347 LYS cc_start: 0.8663 (mmtt) cc_final: 0.7410 (pmtt) REVERT: C 353 LYS cc_start: 0.8640 (tttt) cc_final: 0.8391 (tptt) REVERT: D 338 GLU cc_start: 0.8455 (tt0) cc_final: 0.8111 (tt0) REVERT: D 353 LYS cc_start: 0.8627 (tttm) cc_final: 0.8380 (tttt) REVERT: D 379 ARG cc_start: 0.7551 (mtt-85) cc_final: 0.6884 (mmp-170) REVERT: E 311 LYS cc_start: 0.8701 (mttt) cc_final: 0.8164 (mttm) REVERT: E 349 ARG cc_start: 0.7859 (mtm180) cc_final: 0.6738 (mmp-170) REVERT: E 353 LYS cc_start: 0.8683 (tttt) cc_final: 0.8325 (tptt) REVERT: E 369 LYS cc_start: 0.8566 (mtpp) cc_final: 0.8307 (mtpp) REVERT: F 338 GLU cc_start: 0.8307 (tt0) cc_final: 0.7931 (tt0) outliers start: 2 outliers final: 2 residues processed: 136 average time/residue: 0.6267 time to fit residues: 87.1096 Evaluate side-chains 136 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 134 time to evaluate : 0.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 317 LYS Chi-restraints excluded: chain F residue 319 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 33 optimal weight: 0.4980 chunk 22 optimal weight: 6.9990 chunk 25 optimal weight: 0.9990 chunk 30 optimal weight: 9.9990 chunk 41 optimal weight: 7.9990 chunk 10 optimal weight: 5.9990 chunk 28 optimal weight: 4.9990 chunk 40 optimal weight: 9.9990 chunk 15 optimal weight: 7.9990 chunk 24 optimal weight: 8.9990 chunk 11 optimal weight: 0.8980 overall best weight: 2.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 336 GLN B 307 GLN C 307 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.121568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.107096 restraints weight = 3991.908| |-----------------------------------------------------------------------------| r_work (start): 0.3583 rms_B_bonded: 1.46 r_work: 0.3490 rms_B_bonded: 1.67 restraints_weight: 0.5000 r_work: 0.3403 rms_B_bonded: 2.83 restraints_weight: 0.2500 r_work (final): 0.3403 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8749 moved from start: 0.3423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 3561 Z= 0.172 Angle : 0.618 5.214 4761 Z= 0.310 Chirality : 0.049 0.125 531 Planarity : 0.003 0.023 609 Dihedral : 4.861 17.047 474 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.89 % Favored : 99.11 % Rotamer: Outliers : 0.75 % Allowed : 22.31 % Favored : 76.94 % 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: -1.98 (0.32), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.50 (0.24), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 349 TYR 0.011 0.003 TYR A 310 PHE 0.011 0.002 PHE B 346 HIS 0.003 0.001 HIS C 329 Details of bonding type rmsd covalent geometry : bond 0.00373 ( 3561) covalent geometry : angle 0.61758 ( 4761) hydrogen bonds : bond 0.02213 ( 76) hydrogen bonds : angle 4.92350 ( 228) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2290.38 seconds wall clock time: 39 minutes 45.95 seconds (2385.95 seconds total)