Starting phenix.real_space_refine on Sat Aug 23 06:16:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8q9l_18285/08_2025/8q9l_18285.cif Found real_map, /net/cci-nas-00/data/ceres_data/8q9l_18285/08_2025/8q9l_18285.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.76 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8q9l_18285/08_2025/8q9l_18285.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8q9l_18285/08_2025/8q9l_18285.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8q9l_18285/08_2025/8q9l_18285.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8q9l_18285/08_2025/8q9l_18285.map" } resolution = 2.76 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: 5 Type Number sf(0) Gaussians S 9 5.16 5 C 3159 2.51 5 N 909 2.21 5 O 936 1.98 5 H 5220 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 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: 10233 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 1137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 1137 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 3, 'TRANS': 69} Chain: "C" Number of atoms: 1137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 1137 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 3, 'TRANS': 69} Chain: "E" Number of atoms: 1137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 1137 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 3, 'TRANS': 69} Chain: "B" Number of atoms: 1137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 1137 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 3, 'TRANS': 69} Chain: "D" Number of atoms: 1137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 1137 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 3, 'TRANS': 69} Chain: "F" Number of atoms: 1137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 1137 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 3, 'TRANS': 69} Chain: "G" Number of atoms: 1137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 1137 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 3, 'TRANS': 69} Chain: "H" Number of atoms: 1137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 1137 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 3, 'TRANS': 69} Chain: "I" Number of atoms: 1137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 1137 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 3, 'TRANS': 69} Time building chain proxies: 1.71, per 1000 atoms: 0.17 Number of scatterers: 10233 At special positions: 0 Unit cell: (138.13, 136.676, 43.62, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 9 16.00 O 936 8.00 N 909 7.00 C 3159 6.00 H 5220 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.85 Conformation dependent library (CDL) restraints added in 227.7 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1152 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 24 sheets defined 0.0% alpha, 55.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.18 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'C' and resid 307 through 310 removed outlier: 6.400A pdb=" N ILE A 308 " --> pdb=" O VAL C 309 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 313 through 314 removed outlier: 6.818A pdb=" N VAL A 313 " --> pdb=" O ASP E 314 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 317 through 330 removed outlier: 6.399A pdb=" N VAL A 318 " --> pdb=" O THR C 319 " (cutoff:3.500A) removed outlier: 8.142A pdb=" N LYS C 321 " --> pdb=" O VAL A 318 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N SER A 320 " --> pdb=" O LYS C 321 " (cutoff:3.500A) removed outlier: 8.145A pdb=" N GLY C 323 " --> pdb=" O SER A 320 " (cutoff:3.500A) removed outlier: 8.870A pdb=" N CYS A 322 " --> pdb=" O GLY C 323 " (cutoff:3.500A) removed outlier: 7.528A pdb=" N LEU C 325 " --> pdb=" O CYS A 322 " (cutoff:3.500A) removed outlier: 9.483A pdb=" N SER A 324 " --> pdb=" O LEU C 325 " (cutoff:3.500A) removed outlier: 10.128A pdb=" N ASN C 327 " --> pdb=" O SER A 324 " (cutoff:3.500A) removed outlier: 6.006A pdb=" N GLY A 326 " --> pdb=" O ASN C 327 " (cutoff:3.500A) removed outlier: 8.547A pdb=" N HIS C 329 " --> pdb=" O GLY A 326 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N ILE A 328 " --> pdb=" O HIS C 329 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N SER E 324 " --> pdb=" O GLY A 323 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N LEU A 325 " --> pdb=" O SER E 324 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N GLY E 326 " --> pdb=" O LEU A 325 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N ASN A 327 " --> pdb=" O GLY E 326 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 336 through 342 removed outlier: 6.711A pdb=" N VAL A 337 " --> pdb=" O GLU C 338 " (cutoff:3.500A) removed outlier: 8.028A pdb=" N LYS C 340 " --> pdb=" O VAL A 337 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N VAL A 339 " --> pdb=" O LYS C 340 " (cutoff:3.500A) removed outlier: 7.906A pdb=" N GLU C 342 " --> pdb=" O VAL A 339 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N SER A 341 " --> pdb=" O GLU C 342 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 345 through 346 removed outlier: 6.540A pdb=" N ASP A 345 " --> pdb=" O PHE E 346 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 350 through 355 removed outlier: 6.368A pdb=" N VAL A 350 " --> pdb=" O GLN C 351 " (cutoff:3.500A) removed outlier: 8.051A pdb=" N LYS C 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N SER A 352 " --> pdb=" O LYS C 353 " (cutoff:3.500A) removed outlier: 8.153A pdb=" N GLY C 355 " --> pdb=" O SER A 352 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N ILE A 354 " --> pdb=" O GLY C 355 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 360 through 362 removed outlier: 6.323A pdb=" N THR A 361 " --> pdb=" O HIS C 362 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 369 through 377 removed outlier: 6.660A pdb=" N LYS A 369 " --> pdb=" O LYS E 370 " (cutoff:3.500A) removed outlier: 8.070A pdb=" N GLU E 372 " --> pdb=" O LYS A 369 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N ILE A 371 " --> pdb=" O GLU E 372 " (cutoff:3.500A) removed outlier: 7.758A pdb=" N HIS E 374 " --> pdb=" O ILE A 371 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N THR A 373 " --> pdb=" O HIS E 374 " (cutoff:3.500A) removed outlier: 7.538A pdb=" N LEU E 376 " --> pdb=" O THR A 373 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N LYS A 375 " --> pdb=" O LEU E 376 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 307 through 310 removed outlier: 6.695A pdb=" N GLN B 307 " --> pdb=" O ILE F 308 " (cutoff:3.500A) removed outlier: 7.833A pdb=" N TYR F 310 " --> pdb=" O GLN B 307 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N VAL B 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: 6.845A pdb=" N VAL B 313 " --> pdb=" O ASP F 314 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 317 through 330 removed outlier: 6.760A pdb=" N SER B 324 " --> pdb=" O GLY D 323 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N LEU D 325 " --> pdb=" O SER B 324 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N GLY B 326 " --> pdb=" O LEU D 325 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N ASN D 327 " --> pdb=" O GLY B 326 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N SER F 324 " --> pdb=" O GLY B 323 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N LEU B 325 " --> pdb=" O SER F 324 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N GLY F 326 " --> pdb=" O LEU B 325 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N ASN B 327 " --> pdb=" O GLY F 326 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 336 through 342 removed outlier: 6.418A pdb=" N GLN B 336 " --> pdb=" O VAL F 337 " (cutoff:3.500A) removed outlier: 7.881A pdb=" N VAL F 339 " --> pdb=" O GLN B 336 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N GLU B 338 " --> pdb=" O VAL F 339 " (cutoff:3.500A) removed outlier: 7.825A pdb=" N SER F 341 " --> pdb=" O GLU B 338 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N LYS B 340 " --> pdb=" O SER F 341 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 345 through 346 removed outlier: 6.489A pdb=" N ASP B 345 " --> pdb=" O PHE F 346 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 350 through 355 Processing sheet with id=AB6, first strand: chain 'D' and resid 360 through 362 removed outlier: 6.357A pdb=" N THR B 361 " --> pdb=" O HIS D 362 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 369 through 377 removed outlier: 6.641A pdb=" N LYS B 369 " --> pdb=" O LYS F 370 " (cutoff:3.500A) removed outlier: 8.078A pdb=" N GLU F 372 " --> pdb=" O LYS B 369 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N ILE B 371 " --> pdb=" O GLU F 372 " (cutoff:3.500A) removed outlier: 7.739A pdb=" N HIS F 374 " --> pdb=" O ILE B 371 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N THR B 373 " --> pdb=" O HIS F 374 " (cutoff:3.500A) removed outlier: 7.601A pdb=" N LEU F 376 " --> pdb=" O THR B 373 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N LYS B 375 " --> pdb=" O LEU F 376 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'H' and resid 307 through 310 removed outlier: 6.757A pdb=" N GLN G 307 " --> pdb=" O ILE I 308 " (cutoff:3.500A) removed outlier: 7.812A pdb=" N TYR I 310 " --> pdb=" O GLN G 307 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N VAL G 309 " --> pdb=" O TYR I 310 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'H' and resid 313 through 314 removed outlier: 6.862A pdb=" N VAL G 313 " --> pdb=" O ASP I 314 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'H' and resid 317 through 330 removed outlier: 6.725A pdb=" N SER G 324 " --> pdb=" O GLY H 323 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N LEU H 325 " --> pdb=" O SER G 324 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N GLY G 326 " --> pdb=" O LEU H 325 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N ASN H 327 " --> pdb=" O GLY G 326 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N SER I 324 " --> pdb=" O GLY G 323 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N LEU G 325 " --> pdb=" O SER I 324 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N GLY I 326 " --> pdb=" O LEU G 325 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N ASN G 327 " --> pdb=" O GLY I 326 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'H' and resid 336 through 342 removed outlier: 6.661A pdb=" N VAL G 337 " --> pdb=" O GLU H 338 " (cutoff:3.500A) removed outlier: 7.987A pdb=" N LYS H 340 " --> pdb=" O VAL G 337 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N VAL G 339 " --> pdb=" O LYS H 340 " (cutoff:3.500A) removed outlier: 7.990A pdb=" N GLU H 342 " --> pdb=" O VAL G 339 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N SER G 341 " --> pdb=" O GLU H 342 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'H' and resid 345 through 346 removed outlier: 6.520A pdb=" N ASP G 345 " --> pdb=" O PHE I 346 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'H' and resid 350 through 355 removed outlier: 6.333A pdb=" N VAL G 350 " --> pdb=" O GLN H 351 " (cutoff:3.500A) removed outlier: 8.040A pdb=" N LYS H 353 " --> pdb=" O VAL G 350 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N SER G 352 " --> pdb=" O LYS H 353 " (cutoff:3.500A) removed outlier: 8.116A pdb=" N GLY H 355 " --> pdb=" O SER G 352 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N ILE G 354 " --> pdb=" O GLY H 355 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N GLN G 351 " --> pdb=" O SER I 352 " (cutoff:3.500A) removed outlier: 8.070A pdb=" N ILE I 354 " --> pdb=" O GLN G 351 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N LYS G 353 " --> pdb=" O ILE I 354 " (cutoff:3.500A) removed outlier: 7.357A pdb=" N SER I 356 " --> pdb=" O LYS G 353 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N GLY G 355 " --> pdb=" O SER I 356 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'H' and resid 360 through 362 removed outlier: 6.362A pdb=" N THR G 361 " --> pdb=" O HIS H 362 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'H' and resid 369 through 377 removed outlier: 6.631A pdb=" N LYS G 369 " --> pdb=" O LYS I 370 " (cutoff:3.500A) removed outlier: 8.057A pdb=" N GLU I 372 " --> pdb=" O LYS G 369 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N ILE G 371 " --> pdb=" O GLU I 372 " (cutoff:3.500A) removed outlier: 7.769A pdb=" N HIS I 374 " --> pdb=" O ILE G 371 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N THR G 373 " --> pdb=" O HIS I 374 " (cutoff:3.500A) removed outlier: 7.564A pdb=" N LEU I 376 " --> pdb=" O THR G 373 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N LYS G 375 " --> pdb=" O LEU I 376 " (cutoff:3.500A) 128 hydrogen bonds defined for protein. 384 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: 1.63 Time building geometry restraints manager: 1.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.94 - 1.11: 5211 1.11 - 1.28: 837 1.28 - 1.46: 1329 1.46 - 1.63: 2928 1.63 - 1.81: 9 Bond restraints: 10314 Sorted by residual: bond pdb=" ND2 ASN H 359 " pdb="HD22 ASN H 359 " ideal model delta sigma weight residual 0.860 1.010 -0.150 2.00e-02 2.50e+03 5.66e+01 bond pdb=" N LYS A 340 " pdb=" H LYS A 340 " ideal model delta sigma weight residual 0.860 1.010 -0.150 2.00e-02 2.50e+03 5.65e+01 bond pdb=" N LYS I 347 " pdb=" H LYS I 347 " ideal model delta sigma weight residual 0.860 1.010 -0.150 2.00e-02 2.50e+03 5.65e+01 bond pdb=" N ILE C 360 " pdb=" H ILE C 360 " ideal model delta sigma weight residual 0.860 1.010 -0.150 2.00e-02 2.50e+03 5.64e+01 bond pdb=" N THR A 361 " pdb=" H THR A 361 " ideal model delta sigma weight residual 0.860 1.010 -0.150 2.00e-02 2.50e+03 5.64e+01 ... (remaining 10309 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.52: 15923 2.52 - 5.04: 2210 5.04 - 7.57: 662 7.57 - 10.09: 15 10.09 - 12.61: 9 Bond angle restraints: 18819 Sorted by residual: angle pdb=" CB HIS F 374 " pdb=" CG HIS F 374 " pdb=" CD2 HIS F 374 " ideal model delta sigma weight residual 131.20 124.93 6.27 1.30e+00 5.92e-01 2.33e+01 angle pdb=" CB HIS A 374 " pdb=" CG HIS A 374 " pdb=" CD2 HIS A 374 " ideal model delta sigma weight residual 131.20 124.93 6.27 1.30e+00 5.92e-01 2.32e+01 angle pdb=" CB HIS I 374 " pdb=" CG HIS I 374 " pdb=" CD2 HIS I 374 " ideal model delta sigma weight residual 131.20 124.97 6.23 1.30e+00 5.92e-01 2.29e+01 angle pdb=" CB HIS E 374 " pdb=" CG HIS E 374 " pdb=" CD2 HIS E 374 " ideal model delta sigma weight residual 131.20 125.02 6.18 1.30e+00 5.92e-01 2.26e+01 angle pdb=" CB HIS B 374 " pdb=" CG HIS B 374 " pdb=" CD2 HIS B 374 " ideal model delta sigma weight residual 131.20 125.10 6.10 1.30e+00 5.92e-01 2.20e+01 ... (remaining 18814 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.54: 4119 13.54 - 27.08: 294 27.08 - 40.62: 97 40.62 - 54.16: 123 54.16 - 67.70: 119 Dihedral angle restraints: 4752 sinusoidal: 2709 harmonic: 2043 Sorted by residual: dihedral pdb=" CA ILE G 371 " pdb=" C ILE G 371 " pdb=" N GLU G 372 " pdb=" CA GLU G 372 " ideal model delta harmonic sigma weight residual -180.00 -157.59 -22.41 0 5.00e+00 4.00e-02 2.01e+01 dihedral pdb=" CA SER H 316 " pdb=" C SER H 316 " pdb=" N LYS H 317 " pdb=" CA LYS H 317 " ideal model delta harmonic sigma weight residual 180.00 158.19 21.81 0 5.00e+00 4.00e-02 1.90e+01 dihedral pdb=" CA ILE A 371 " pdb=" C ILE A 371 " pdb=" N GLU A 372 " pdb=" CA GLU A 372 " ideal model delta harmonic sigma weight residual 180.00 -158.21 -21.79 0 5.00e+00 4.00e-02 1.90e+01 ... (remaining 4749 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 435 0.064 - 0.129: 243 0.129 - 0.193: 72 0.193 - 0.258: 18 0.258 - 0.322: 6 Chirality restraints: 774 Sorted by residual: chirality pdb=" CA LYS H 317 " pdb=" N LYS H 317 " pdb=" C LYS H 317 " pdb=" CB LYS H 317 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.59e+00 chirality pdb=" CA LYS C 317 " pdb=" N LYS C 317 " pdb=" C LYS C 317 " pdb=" CB LYS C 317 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.58e+00 chirality pdb=" CA LYS D 317 " pdb=" N LYS D 317 " pdb=" C LYS D 317 " pdb=" CB LYS D 317 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.19e+00 ... (remaining 771 not shown) Planarity restraints: 1485 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN F 368 " 0.073 2.00e-02 2.50e+03 6.46e-02 6.25e+01 pdb=" CG ASN F 368 " -0.028 2.00e-02 2.50e+03 pdb=" OD1 ASN F 368 " -0.047 2.00e-02 2.50e+03 pdb=" ND2 ASN F 368 " -0.042 2.00e-02 2.50e+03 pdb="HD21 ASN F 368 " -0.061 2.00e-02 2.50e+03 pdb="HD22 ASN F 368 " 0.106 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 368 " -0.070 2.00e-02 2.50e+03 6.41e-02 6.16e+01 pdb=" CG ASN A 368 " 0.015 2.00e-02 2.50e+03 pdb=" OD1 ASN A 368 " 0.056 2.00e-02 2.50e+03 pdb=" ND2 ASN A 368 " 0.031 2.00e-02 2.50e+03 pdb="HD21 ASN A 368 " 0.070 2.00e-02 2.50e+03 pdb="HD22 ASN A 368 " -0.102 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 310 " -0.090 2.00e-02 2.50e+03 4.17e-02 5.23e+01 pdb=" CG TYR B 310 " 0.014 2.00e-02 2.50e+03 pdb=" CD1 TYR B 310 " 0.025 2.00e-02 2.50e+03 pdb=" CD2 TYR B 310 " 0.034 2.00e-02 2.50e+03 pdb=" CE1 TYR B 310 " 0.036 2.00e-02 2.50e+03 pdb=" CE2 TYR B 310 " 0.012 2.00e-02 2.50e+03 pdb=" CZ TYR B 310 " 0.003 2.00e-02 2.50e+03 pdb=" OH TYR B 310 " -0.085 2.00e-02 2.50e+03 pdb=" HD1 TYR B 310 " -0.007 2.00e-02 2.50e+03 pdb=" HD2 TYR B 310 " 0.035 2.00e-02 2.50e+03 pdb=" HE1 TYR B 310 " 0.029 2.00e-02 2.50e+03 pdb=" HE2 TYR B 310 " -0.005 2.00e-02 2.50e+03 ... (remaining 1482 not shown) Histogram of nonbonded interaction distances: 1.58 - 2.18: 873 2.18 - 2.79: 18013 2.79 - 3.39: 26435 3.39 - 4.00: 37363 4.00 - 4.60: 50819 Nonbonded interactions: 133503 Sorted by model distance: nonbonded pdb=" OD1 ASP F 314 " pdb=" HG SER F 316 " model vdw 1.581 2.450 nonbonded pdb=" OD1 ASP E 314 " pdb=" HG SER E 316 " model vdw 1.581 2.450 nonbonded pdb=" OD1 ASP I 314 " pdb=" HG SER I 316 " model vdw 1.587 2.450 nonbonded pdb=" OD1 ASP A 314 " pdb=" HG SER A 316 " model vdw 1.602 2.450 nonbonded pdb=" OD1 ASP G 314 " pdb=" HG SER G 316 " model vdw 1.605 2.450 ... (remaining 133498 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' selection = chain 'G' selection = chain 'H' selection = chain 'I' } 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: 5.720 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: 0.060 Extract box with map and model: 0.200 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 9.820 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7528 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 0.034 5094 Z= 0.672 Angle : 1.762 8.654 6822 Z= 1.160 Chirality : 0.086 0.322 774 Planarity : 0.011 0.048 864 Dihedral : 11.628 51.205 1944 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 0.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 0.00 % Allowed : 0.35 % Favored : 99.65 % 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: -1.68 (0.27), residues: 639 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.27 (0.21), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.002 ARG I 349 TYR 0.083 0.026 TYR B 310 PHE 0.030 0.009 PHE A 346 HIS 0.013 0.003 HIS H 330 Details of bonding type rmsd covalent geometry : bond 0.01097 ( 5094) covalent geometry : angle 1.76236 ( 6822) hydrogen bonds : bond 0.07627 ( 128) hydrogen bonds : angle 8.17267 ( 384) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 272 time to evaluate : 0.253 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 309 VAL cc_start: 0.5819 (t) cc_final: 0.5518 (p) REVERT: A 324 SER cc_start: 0.8584 (p) cc_final: 0.8251 (m) REVERT: A 340 LYS cc_start: 0.8088 (mtpt) cc_final: 0.7686 (mttp) REVERT: A 342 GLU cc_start: 0.8057 (mt-10) cc_final: 0.7651 (mm-30) REVERT: A 372 GLU cc_start: 0.7135 (tt0) cc_final: 0.6586 (mm-30) REVERT: A 377 THR cc_start: 0.7169 (m) cc_final: 0.6629 (p) REVERT: C 324 SER cc_start: 0.8585 (p) cc_final: 0.8298 (m) REVERT: C 340 LYS cc_start: 0.7959 (mtpt) cc_final: 0.7541 (mttt) REVERT: C 342 GLU cc_start: 0.8028 (mt-10) cc_final: 0.7591 (mm-30) REVERT: C 343 LYS cc_start: 0.8730 (mttt) cc_final: 0.8508 (mttm) REVERT: C 345 ASP cc_start: 0.8195 (t0) cc_final: 0.7934 (t70) REVERT: C 372 GLU cc_start: 0.7988 (tt0) cc_final: 0.7520 (mm-30) REVERT: C 374 HIS cc_start: 0.8072 (m-70) cc_final: 0.7764 (m-70) REVERT: C 375 LYS cc_start: 0.5754 (tttt) cc_final: 0.5365 (tppt) REVERT: C 378 PHE cc_start: 0.5176 (t80) cc_final: 0.4857 (t80) REVERT: E 310 TYR cc_start: 0.4492 (t80) cc_final: 0.4178 (t80) REVERT: E 320 SER cc_start: 0.8155 (t) cc_final: 0.7583 (p) REVERT: E 324 SER cc_start: 0.8541 (p) cc_final: 0.8158 (m) REVERT: E 340 LYS cc_start: 0.8463 (mtpt) cc_final: 0.8166 (mttt) REVERT: E 342 GLU cc_start: 0.8369 (mt-10) cc_final: 0.7872 (mm-30) REVERT: E 347 LYS cc_start: 0.8562 (mttt) cc_final: 0.7886 (mppt) REVERT: E 349 ARG cc_start: 0.6815 (mtt180) cc_final: 0.5214 (pmt-80) REVERT: E 369 LYS cc_start: 0.8091 (mttt) cc_final: 0.7665 (ttmp) REVERT: E 375 LYS cc_start: 0.7341 (tttt) cc_final: 0.6139 (pptt) REVERT: E 378 PHE cc_start: 0.4387 (t80) cc_final: 0.4181 (t80) REVERT: B 309 VAL cc_start: 0.5755 (t) cc_final: 0.5427 (p) REVERT: B 320 SER cc_start: 0.8638 (t) cc_final: 0.8285 (p) REVERT: B 321 LYS cc_start: 0.7466 (mtpt) cc_final: 0.7080 (mtmt) REVERT: B 340 LYS cc_start: 0.7939 (mtpt) cc_final: 0.7590 (mttt) REVERT: B 342 GLU cc_start: 0.8063 (mt-10) cc_final: 0.7620 (mm-30) REVERT: B 345 ASP cc_start: 0.8410 (t0) cc_final: 0.8175 (OUTLIER) REVERT: B 372 GLU cc_start: 0.7352 (tt0) cc_final: 0.6539 (mm-30) REVERT: B 375 LYS cc_start: 0.6009 (tttt) cc_final: 0.5747 (tptt) REVERT: B 377 THR cc_start: 0.7037 (m) cc_final: 0.6703 (p) REVERT: D 342 GLU cc_start: 0.7968 (mt-10) cc_final: 0.7460 (mm-30) REVERT: D 345 ASP cc_start: 0.8153 (t0) cc_final: 0.7658 (t0) REVERT: D 347 LYS cc_start: 0.8490 (mttt) cc_final: 0.8270 (mtmt) REVERT: D 372 GLU cc_start: 0.8025 (tt0) cc_final: 0.7584 (mm-30) REVERT: D 373 THR cc_start: 0.5821 (m) cc_final: 0.5612 (m) REVERT: D 374 HIS cc_start: 0.8008 (m-70) cc_final: 0.7379 (m-70) REVERT: D 375 LYS cc_start: 0.5800 (tttt) cc_final: 0.5542 (tppt) REVERT: D 377 THR cc_start: 0.6655 (m) cc_final: 0.6017 (p) REVERT: F 310 TYR cc_start: 0.4497 (t80) cc_final: 0.4167 (t80) REVERT: F 340 LYS cc_start: 0.8470 (mtpt) cc_final: 0.8179 (mttt) REVERT: F 342 GLU cc_start: 0.8421 (mt-10) cc_final: 0.8005 (mm-30) REVERT: F 349 ARG cc_start: 0.6828 (mtt180) cc_final: 0.5349 (ppt90) REVERT: F 369 LYS cc_start: 0.7982 (mttt) cc_final: 0.7777 (mtmm) REVERT: F 375 LYS cc_start: 0.7226 (tttt) cc_final: 0.5927 (pptt) REVERT: F 378 PHE cc_start: 0.4768 (t80) cc_final: 0.4544 (t80) REVERT: G 309 VAL cc_start: 0.5700 (t) cc_final: 0.5434 (p) REVERT: G 310 TYR cc_start: 0.4789 (t80) cc_final: 0.4544 (t80) REVERT: G 342 GLU cc_start: 0.8134 (mt-10) cc_final: 0.7678 (mm-30) REVERT: G 345 ASP cc_start: 0.8364 (t0) cc_final: 0.8126 (t0) REVERT: G 372 GLU cc_start: 0.7231 (tt0) cc_final: 0.6864 (mm-30) REVERT: G 378 PHE cc_start: 0.4375 (t80) cc_final: 0.4156 (t80) REVERT: H 331 LYS cc_start: 0.8573 (mtmt) cc_final: 0.8355 (mtpt) REVERT: H 342 GLU cc_start: 0.8115 (mt-10) cc_final: 0.7672 (mm-30) REVERT: H 345 ASP cc_start: 0.8242 (t0) cc_final: 0.7739 (t0) REVERT: H 347 LYS cc_start: 0.8511 (mttt) cc_final: 0.8298 (mtmt) REVERT: H 372 GLU cc_start: 0.8020 (tt0) cc_final: 0.7632 (mm-30) REVERT: H 374 HIS cc_start: 0.7980 (m-70) cc_final: 0.7559 (m-70) REVERT: H 375 LYS cc_start: 0.5712 (tttt) cc_final: 0.5455 (tppt) REVERT: I 309 VAL cc_start: 0.7306 (t) cc_final: 0.7096 (p) REVERT: I 310 TYR cc_start: 0.4767 (t80) cc_final: 0.4418 (t80) REVERT: I 320 SER cc_start: 0.8304 (t) cc_final: 0.7840 (p) REVERT: I 340 LYS cc_start: 0.8512 (mtpt) cc_final: 0.8252 (mttt) REVERT: I 342 GLU cc_start: 0.8419 (mt-10) cc_final: 0.7930 (mm-30) REVERT: I 347 LYS cc_start: 0.8611 (mttt) cc_final: 0.7878 (mppt) REVERT: I 349 ARG cc_start: 0.6703 (mtt180) cc_final: 0.5239 (pmt-80) REVERT: I 369 LYS cc_start: 0.8060 (mttt) cc_final: 0.7825 (ttmt) REVERT: I 375 LYS cc_start: 0.7280 (tttt) cc_final: 0.6052 (pptt) REVERT: I 378 PHE cc_start: 0.4593 (t80) cc_final: 0.4387 (t80) outliers start: 0 outliers final: 1 residues processed: 272 average time/residue: 1.1923 time to fit residues: 336.3236 Evaluate side-chains 217 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 217 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 54 optimal weight: 4.9990 chunk 24 optimal weight: 5.9990 chunk 48 optimal weight: 5.9990 chunk 56 optimal weight: 3.9990 chunk 26 optimal weight: 5.9990 chunk 2 optimal weight: 5.9990 chunk 16 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 chunk 32 optimal weight: 5.9990 chunk 31 optimal weight: 6.9990 chunk 25 optimal weight: 5.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 374 HIS B 307 GLN B 374 HIS H 307 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4208 r_free = 0.4208 target = 0.169928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.146480 restraints weight = 17330.078| |-----------------------------------------------------------------------------| r_work (start): 0.3872 rms_B_bonded: 1.71 r_work: 0.3807 rms_B_bonded: 1.68 restraints_weight: 0.5000 r_work: 0.3733 rms_B_bonded: 2.87 restraints_weight: 0.2500 r_work (final): 0.3733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8468 moved from start: 0.3936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 5094 Z= 0.183 Angle : 0.602 4.550 6822 Z= 0.317 Chirality : 0.053 0.142 774 Planarity : 0.003 0.019 864 Dihedral : 6.261 16.995 666 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 0.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % Rotamer: Outliers : 2.26 % Allowed : 12.15 % Favored : 85.59 % 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 (0.28), residues: 639 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.15 (0.21), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG G 349 TYR 0.013 0.002 TYR D 310 PHE 0.005 0.001 PHE C 346 HIS 0.005 0.001 HIS C 374 Details of bonding type rmsd covalent geometry : bond 0.00414 ( 5094) covalent geometry : angle 0.60154 ( 6822) hydrogen bonds : bond 0.03110 ( 128) hydrogen bonds : angle 5.48326 ( 384) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 200 time to evaluate : 0.191 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 309 VAL cc_start: 0.8808 (t) cc_final: 0.8408 (p) REVERT: A 345 ASP cc_start: 0.8168 (t0) cc_final: 0.7930 (t0) REVERT: A 369 LYS cc_start: 0.8193 (OUTLIER) cc_final: 0.7942 (ttmm) REVERT: C 311 LYS cc_start: 0.8666 (mtpt) cc_final: 0.7781 (mmpt) REVERT: C 345 ASP cc_start: 0.8132 (t0) cc_final: 0.7821 (t0) REVERT: C 369 LYS cc_start: 0.8223 (OUTLIER) cc_final: 0.7970 (ttmm) REVERT: C 375 LYS cc_start: 0.8102 (tttt) cc_final: 0.7707 (tppt) REVERT: E 321 LYS cc_start: 0.8713 (mtpt) cc_final: 0.8378 (mtpt) REVERT: E 347 LYS cc_start: 0.8514 (mttt) cc_final: 0.7640 (ttpt) REVERT: E 349 ARG cc_start: 0.6909 (mtt180) cc_final: 0.5598 (pmt-80) REVERT: E 369 LYS cc_start: 0.8257 (mttt) cc_final: 0.8000 (ttmp) REVERT: E 375 LYS cc_start: 0.8287 (tttt) cc_final: 0.7722 (tmmt) REVERT: B 309 VAL cc_start: 0.8705 (t) cc_final: 0.8397 (p) REVERT: D 338 GLU cc_start: 0.7695 (tt0) cc_final: 0.7410 (tt0) REVERT: D 375 LYS cc_start: 0.7979 (tttt) cc_final: 0.7672 (tppt) REVERT: F 347 LYS cc_start: 0.8499 (mttt) cc_final: 0.7810 (mppt) REVERT: F 349 ARG cc_start: 0.6923 (mtt180) cc_final: 0.5634 (pmt-80) REVERT: F 375 LYS cc_start: 0.8276 (tttt) cc_final: 0.7669 (tmmt) REVERT: G 309 VAL cc_start: 0.8679 (t) cc_final: 0.8345 (p) REVERT: G 331 LYS cc_start: 0.8793 (mtmm) cc_final: 0.8581 (mtmt) REVERT: H 309 VAL cc_start: 0.8645 (t) cc_final: 0.8166 (p) REVERT: H 375 LYS cc_start: 0.8149 (tttt) cc_final: 0.7633 (tppt) REVERT: I 347 LYS cc_start: 0.8533 (mttt) cc_final: 0.7658 (ttpt) REVERT: I 349 ARG cc_start: 0.6837 (mtt180) cc_final: 0.5572 (pmt-80) REVERT: I 369 LYS cc_start: 0.8263 (mttt) cc_final: 0.8014 (ttmp) REVERT: I 375 LYS cc_start: 0.8294 (tttt) cc_final: 0.7190 (pptt) outliers start: 13 outliers final: 1 residues processed: 203 average time/residue: 1.4520 time to fit residues: 303.8089 Evaluate side-chains 161 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 158 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 369 LYS Chi-restraints excluded: chain C residue 369 LYS Chi-restraints excluded: chain F residue 320 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 26 optimal weight: 5.9990 chunk 18 optimal weight: 7.9990 chunk 38 optimal weight: 7.9990 chunk 53 optimal weight: 7.9990 chunk 28 optimal weight: 10.0000 chunk 58 optimal weight: 8.9990 chunk 36 optimal weight: 0.6980 chunk 37 optimal weight: 7.9990 chunk 30 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 43 optimal weight: 9.9990 overall best weight: 3.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 307 GLN B 307 GLN H 307 GLN I 374 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.161864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.137430 restraints weight = 18184.636| |-----------------------------------------------------------------------------| r_work (start): 0.3733 rms_B_bonded: 1.77 r_work: 0.3657 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.3583 rms_B_bonded: 2.99 restraints_weight: 0.2500 r_work (final): 0.3583 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8543 moved from start: 0.5240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 5094 Z= 0.183 Angle : 0.552 4.410 6822 Z= 0.290 Chirality : 0.052 0.143 774 Planarity : 0.003 0.018 864 Dihedral : 5.613 16.736 666 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 0.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Rotamer: Outliers : 1.91 % Allowed : 18.23 % Favored : 79.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -1.76 (0.27), residues: 639 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.33 (0.21), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG F 349 TYR 0.011 0.001 TYR B 310 PHE 0.006 0.001 PHE C 346 HIS 0.003 0.001 HIS C 374 Details of bonding type rmsd covalent geometry : bond 0.00397 ( 5094) covalent geometry : angle 0.55152 ( 6822) hydrogen bonds : bond 0.02666 ( 128) hydrogen bonds : angle 4.93462 ( 384) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 158 time to evaluate : 0.346 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 309 VAL cc_start: 0.8662 (t) cc_final: 0.8214 (p) REVERT: A 345 ASP cc_start: 0.8262 (t0) cc_final: 0.7974 (t0) REVERT: A 369 LYS cc_start: 0.8233 (OUTLIER) cc_final: 0.7980 (ttmm) REVERT: C 331 LYS cc_start: 0.8813 (OUTLIER) cc_final: 0.8608 (mtmt) REVERT: C 347 LYS cc_start: 0.8247 (mtmt) cc_final: 0.8041 (mtmt) REVERT: C 375 LYS cc_start: 0.8022 (tttt) cc_final: 0.7521 (tppt) REVERT: E 321 LYS cc_start: 0.8792 (mtpt) cc_final: 0.8440 (mtpt) REVERT: E 347 LYS cc_start: 0.8562 (mttt) cc_final: 0.7608 (ttpt) REVERT: E 349 ARG cc_start: 0.7120 (mtt180) cc_final: 0.5469 (pmt-80) REVERT: E 369 LYS cc_start: 0.8331 (mttt) cc_final: 0.8069 (ttmp) REVERT: E 375 LYS cc_start: 0.8332 (tttt) cc_final: 0.7684 (tmmt) REVERT: E 378 PHE cc_start: 0.6996 (t80) cc_final: 0.6732 (t80) REVERT: D 375 LYS cc_start: 0.7916 (tttt) cc_final: 0.7620 (tppt) REVERT: F 347 LYS cc_start: 0.8544 (mttt) cc_final: 0.7796 (mppt) REVERT: F 349 ARG cc_start: 0.7064 (mtt180) cc_final: 0.5478 (pmt-80) REVERT: F 375 LYS cc_start: 0.8350 (tttt) cc_final: 0.7638 (tmmt) REVERT: G 309 VAL cc_start: 0.8669 (t) cc_final: 0.8288 (p) REVERT: H 375 LYS cc_start: 0.8053 (tttt) cc_final: 0.7559 (tppt) REVERT: I 347 LYS cc_start: 0.8587 (mttt) cc_final: 0.7837 (mppt) REVERT: I 349 ARG cc_start: 0.7046 (mtt180) cc_final: 0.5441 (pmt-80) REVERT: I 369 LYS cc_start: 0.8363 (mttt) cc_final: 0.8064 (ttmp) REVERT: I 375 LYS cc_start: 0.8266 (tttt) cc_final: 0.7665 (tmmt) outliers start: 11 outliers final: 4 residues processed: 158 average time/residue: 1.4808 time to fit residues: 241.2010 Evaluate side-chains 153 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 147 time to evaluate : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 369 LYS Chi-restraints excluded: chain C residue 331 LYS Chi-restraints excluded: chain B residue 345 ASP Chi-restraints excluded: chain D residue 309 VAL Chi-restraints excluded: chain G residue 345 ASP Chi-restraints excluded: chain H residue 345 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 0 optimal weight: 10.0000 chunk 46 optimal weight: 9.9990 chunk 50 optimal weight: 8.9990 chunk 21 optimal weight: 10.0000 chunk 34 optimal weight: 7.9990 chunk 17 optimal weight: 5.9990 chunk 20 optimal weight: 7.9990 chunk 62 optimal weight: 7.9990 chunk 12 optimal weight: 4.9990 chunk 44 optimal weight: 8.9990 chunk 57 optimal weight: 4.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 307 GLN B 307 GLN H 307 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.161225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.137995 restraints weight = 18722.980| |-----------------------------------------------------------------------------| r_work (start): 0.3705 rms_B_bonded: 1.71 r_work: 0.3631 rms_B_bonded: 1.71 restraints_weight: 0.5000 r_work: 0.3558 rms_B_bonded: 2.87 restraints_weight: 0.2500 r_work (final): 0.3558 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8573 moved from start: 0.5586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 5094 Z= 0.283 Angle : 0.600 4.425 6822 Z= 0.316 Chirality : 0.052 0.146 774 Planarity : 0.003 0.021 864 Dihedral : 5.722 17.916 666 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 1.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 3.12 % Allowed : 18.23 % Favored : 78.65 % 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: -2.13 (0.27), residues: 639 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.61 (0.20), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG F 349 TYR 0.013 0.002 TYR G 310 PHE 0.007 0.001 PHE C 346 HIS 0.004 0.001 HIS C 374 Details of bonding type rmsd covalent geometry : bond 0.00605 ( 5094) covalent geometry : angle 0.60000 ( 6822) hydrogen bonds : bond 0.02949 ( 128) hydrogen bonds : angle 4.95969 ( 384) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 141 time to evaluate : 0.315 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 369 LYS cc_start: 0.8272 (OUTLIER) cc_final: 0.8018 (ttmm) REVERT: C 331 LYS cc_start: 0.8820 (OUTLIER) cc_final: 0.8569 (mmmm) REVERT: C 369 LYS cc_start: 0.8249 (OUTLIER) cc_final: 0.7970 (ttmm) REVERT: C 375 LYS cc_start: 0.8060 (tttt) cc_final: 0.7653 (tppt) REVERT: E 347 LYS cc_start: 0.8587 (mttt) cc_final: 0.7932 (mppt) REVERT: E 369 LYS cc_start: 0.8389 (mttt) cc_final: 0.8070 (ttmp) REVERT: E 375 LYS cc_start: 0.8334 (tttt) cc_final: 0.7663 (tmmt) REVERT: B 369 LYS cc_start: 0.8321 (OUTLIER) cc_final: 0.7845 (ttmm) REVERT: D 375 LYS cc_start: 0.7956 (tttt) cc_final: 0.7654 (tppt) REVERT: F 347 LYS cc_start: 0.8603 (mttt) cc_final: 0.7824 (mppt) REVERT: F 375 LYS cc_start: 0.8425 (tttt) cc_final: 0.7734 (tmmt) REVERT: G 309 VAL cc_start: 0.8660 (t) cc_final: 0.8336 (p) REVERT: G 331 LYS cc_start: 0.8721 (OUTLIER) cc_final: 0.8470 (mmmm) REVERT: H 375 LYS cc_start: 0.8016 (tttt) cc_final: 0.7532 (tppt) REVERT: I 309 VAL cc_start: 0.8610 (OUTLIER) cc_final: 0.8268 (p) REVERT: I 347 LYS cc_start: 0.8591 (mttt) cc_final: 0.7809 (mppt) REVERT: I 369 LYS cc_start: 0.8432 (mttt) cc_final: 0.8099 (ttmp) REVERT: I 375 LYS cc_start: 0.8337 (tttt) cc_final: 0.7672 (tmmt) outliers start: 18 outliers final: 7 residues processed: 145 average time/residue: 1.3550 time to fit residues: 202.8906 Evaluate side-chains 147 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 134 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 345 ASP Chi-restraints excluded: chain A residue 369 LYS Chi-restraints excluded: chain C residue 331 LYS Chi-restraints excluded: chain C residue 369 LYS Chi-restraints excluded: chain B residue 309 VAL Chi-restraints excluded: chain B residue 345 ASP Chi-restraints excluded: chain B residue 369 LYS Chi-restraints excluded: chain D residue 309 VAL Chi-restraints excluded: chain F residue 320 SER Chi-restraints excluded: chain G residue 331 LYS Chi-restraints excluded: chain G residue 345 ASP Chi-restraints excluded: chain H residue 345 ASP Chi-restraints excluded: chain I residue 309 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 46 optimal weight: 9.9990 chunk 27 optimal weight: 9.9990 chunk 17 optimal weight: 7.9990 chunk 31 optimal weight: 9.9990 chunk 26 optimal weight: 4.9990 chunk 59 optimal weight: 8.9990 chunk 3 optimal weight: 4.9990 chunk 54 optimal weight: 5.9990 chunk 9 optimal weight: 9.9990 chunk 20 optimal weight: 10.0000 chunk 32 optimal weight: 4.9990 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 307 GLN H 307 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.157282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.133046 restraints weight = 18128.632| |-----------------------------------------------------------------------------| r_work (start): 0.3690 rms_B_bonded: 1.76 r_work: 0.3617 rms_B_bonded: 1.75 restraints_weight: 0.5000 r_work: 0.3542 rms_B_bonded: 2.94 restraints_weight: 0.2500 r_work (final): 0.3542 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8580 moved from start: 0.5716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 5094 Z= 0.259 Angle : 0.569 4.843 6822 Z= 0.299 Chirality : 0.051 0.145 774 Planarity : 0.003 0.019 864 Dihedral : 5.574 17.591 666 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 1.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 3.47 % Allowed : 19.62 % Favored : 76.91 % 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: -2.28 (0.27), residues: 639 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.73 (0.20), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 349 TYR 0.009 0.002 TYR B 310 PHE 0.006 0.001 PHE C 346 HIS 0.003 0.001 HIS D 374 Details of bonding type rmsd covalent geometry : bond 0.00542 ( 5094) covalent geometry : angle 0.56896 ( 6822) hydrogen bonds : bond 0.02796 ( 128) hydrogen bonds : angle 4.81726 ( 384) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 137 time to evaluate : 0.323 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 375 LYS cc_start: 0.8374 (tptp) cc_final: 0.8172 (tptt) REVERT: C 331 LYS cc_start: 0.8828 (OUTLIER) cc_final: 0.8617 (mtmt) REVERT: C 369 LYS cc_start: 0.8241 (OUTLIER) cc_final: 0.7967 (ttmm) REVERT: C 375 LYS cc_start: 0.8042 (tttt) cc_final: 0.7653 (tppt) REVERT: E 347 LYS cc_start: 0.8622 (mttt) cc_final: 0.7814 (mtmt) REVERT: E 369 LYS cc_start: 0.8406 (mttt) cc_final: 0.8117 (ttmp) REVERT: E 375 LYS cc_start: 0.8347 (tttt) cc_final: 0.7681 (tmmt) REVERT: B 340 LYS cc_start: 0.8160 (mtpt) cc_final: 0.7927 (mttt) REVERT: B 369 LYS cc_start: 0.8324 (OUTLIER) cc_final: 0.7854 (ttmm) REVERT: D 375 LYS cc_start: 0.7953 (tttt) cc_final: 0.7735 (tppt) REVERT: F 347 LYS cc_start: 0.8616 (mttt) cc_final: 0.7922 (mppt) REVERT: F 375 LYS cc_start: 0.8442 (tttt) cc_final: 0.7771 (tmmt) REVERT: G 309 VAL cc_start: 0.8652 (t) cc_final: 0.8325 (p) REVERT: G 372 GLU cc_start: 0.8205 (OUTLIER) cc_final: 0.7875 (mt-10) REVERT: H 375 LYS cc_start: 0.8096 (tttt) cc_final: 0.7626 (tppt) REVERT: I 309 VAL cc_start: 0.8596 (OUTLIER) cc_final: 0.8208 (p) REVERT: I 347 LYS cc_start: 0.8577 (mttt) cc_final: 0.7807 (mppt) REVERT: I 369 LYS cc_start: 0.8438 (mttt) cc_final: 0.8132 (ttmp) REVERT: I 375 LYS cc_start: 0.8379 (tttt) cc_final: 0.7734 (tmmt) outliers start: 20 outliers final: 10 residues processed: 144 average time/residue: 1.3584 time to fit residues: 201.9678 Evaluate side-chains 149 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 134 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain C residue 331 LYS Chi-restraints excluded: chain C residue 347 LYS Chi-restraints excluded: chain C residue 369 LYS Chi-restraints excluded: chain E residue 306 VAL Chi-restraints excluded: chain B residue 309 VAL Chi-restraints excluded: chain B residue 345 ASP Chi-restraints excluded: chain B residue 369 LYS Chi-restraints excluded: chain D residue 309 VAL Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain F residue 320 SER Chi-restraints excluded: chain G residue 345 ASP Chi-restraints excluded: chain G residue 372 GLU Chi-restraints excluded: chain H residue 345 ASP Chi-restraints excluded: chain I residue 309 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 59 optimal weight: 6.9990 chunk 11 optimal weight: 8.9990 chunk 39 optimal weight: 9.9990 chunk 14 optimal weight: 2.9990 chunk 2 optimal weight: 6.9990 chunk 25 optimal weight: 3.9990 chunk 37 optimal weight: 6.9990 chunk 26 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 8 optimal weight: 6.9990 chunk 56 optimal weight: 1.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 307 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.159796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.135530 restraints weight = 18277.039| |-----------------------------------------------------------------------------| r_work (start): 0.3743 rms_B_bonded: 1.79 r_work: 0.3669 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.3591 rms_B_bonded: 3.02 restraints_weight: 0.2500 r_work (final): 0.3591 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8552 moved from start: 0.5815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5094 Z= 0.139 Angle : 0.502 5.018 6822 Z= 0.261 Chirality : 0.051 0.140 774 Planarity : 0.002 0.018 864 Dihedral : 5.115 16.036 666 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 1.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 1.56 % Allowed : 21.70 % Favored : 76.74 % 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: -2.24 (0.27), residues: 639 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.70 (0.21), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 349 TYR 0.013 0.002 TYR D 310 PHE 0.004 0.001 PHE C 346 HIS 0.002 0.000 HIS C 374 Details of bonding type rmsd covalent geometry : bond 0.00294 ( 5094) covalent geometry : angle 0.50182 ( 6822) hydrogen bonds : bond 0.02161 ( 128) hydrogen bonds : angle 4.35403 ( 384) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 142 time to evaluate : 0.319 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 369 LYS cc_start: 0.8214 (OUTLIER) cc_final: 0.7928 (ttmm) REVERT: C 375 LYS cc_start: 0.8019 (tttt) cc_final: 0.7653 (tppt) REVERT: E 347 LYS cc_start: 0.8658 (mttt) cc_final: 0.7977 (mppt) REVERT: E 369 LYS cc_start: 0.8362 (mttt) cc_final: 0.8095 (ttmp) REVERT: E 375 LYS cc_start: 0.8326 (tttt) cc_final: 0.7691 (tmmt) REVERT: D 375 LYS cc_start: 0.7890 (tttt) cc_final: 0.7572 (tppt) REVERT: F 347 LYS cc_start: 0.8585 (mttt) cc_final: 0.7868 (mppt) REVERT: F 375 LYS cc_start: 0.8394 (tttt) cc_final: 0.7744 (tmmt) REVERT: G 309 VAL cc_start: 0.8657 (t) cc_final: 0.8343 (p) REVERT: H 375 LYS cc_start: 0.8073 (tttt) cc_final: 0.7624 (tppt) REVERT: I 309 VAL cc_start: 0.8573 (t) cc_final: 0.8201 (p) REVERT: I 347 LYS cc_start: 0.8583 (mttt) cc_final: 0.7821 (mppt) REVERT: I 369 LYS cc_start: 0.8364 (mttt) cc_final: 0.8101 (ttmp) REVERT: I 375 LYS cc_start: 0.8340 (tttt) cc_final: 0.7683 (tmmt) outliers start: 9 outliers final: 5 residues processed: 148 average time/residue: 1.4047 time to fit residues: 214.8157 Evaluate side-chains 132 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 126 time to evaluate : 0.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain C residue 369 LYS Chi-restraints excluded: chain B residue 309 VAL Chi-restraints excluded: chain D residue 309 VAL Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain G residue 345 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 8 optimal weight: 7.9990 chunk 47 optimal weight: 3.9990 chunk 43 optimal weight: 0.7980 chunk 58 optimal weight: 8.9990 chunk 35 optimal weight: 8.9990 chunk 48 optimal weight: 0.9980 chunk 1 optimal weight: 0.8980 chunk 37 optimal weight: 5.9990 chunk 26 optimal weight: 5.9990 chunk 49 optimal weight: 4.9990 chunk 51 optimal weight: 3.9990 overall best weight: 2.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 307 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.160097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.136471 restraints weight = 18409.384| |-----------------------------------------------------------------------------| r_work (start): 0.3749 rms_B_bonded: 1.75 r_work: 0.3674 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.3598 rms_B_bonded: 3.00 restraints_weight: 0.2500 r_work (final): 0.3598 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8535 moved from start: 0.5857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5094 Z= 0.121 Angle : 0.487 4.815 6822 Z= 0.252 Chirality : 0.051 0.138 774 Planarity : 0.002 0.018 864 Dihedral : 4.861 15.220 666 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 1.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Rotamer: Outliers : 1.22 % Allowed : 23.44 % Favored : 75.35 % 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: -2.21 (0.27), residues: 639 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.68 (0.21), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 349 TYR 0.010 0.001 TYR B 310 PHE 0.004 0.001 PHE G 346 HIS 0.001 0.000 HIS C 374 Details of bonding type rmsd covalent geometry : bond 0.00267 ( 5094) covalent geometry : angle 0.48653 ( 6822) hydrogen bonds : bond 0.01994 ( 128) hydrogen bonds : angle 4.16015 ( 384) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 131 time to evaluate : 0.296 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 372 GLU cc_start: 0.8176 (mm-30) cc_final: 0.7964 (mt-10) REVERT: C 369 LYS cc_start: 0.8202 (OUTLIER) cc_final: 0.7914 (ttmm) REVERT: C 375 LYS cc_start: 0.7958 (tttt) cc_final: 0.7553 (tppt) REVERT: E 347 LYS cc_start: 0.8659 (mttt) cc_final: 0.7976 (mppt) REVERT: E 369 LYS cc_start: 0.8340 (mttt) cc_final: 0.8063 (ttmp) REVERT: E 375 LYS cc_start: 0.8307 (tttt) cc_final: 0.7657 (tmmt) REVERT: F 347 LYS cc_start: 0.8566 (mttt) cc_final: 0.7847 (mppt) REVERT: F 375 LYS cc_start: 0.8417 (tttt) cc_final: 0.7734 (tmmt) REVERT: G 309 VAL cc_start: 0.8625 (t) cc_final: 0.8296 (p) REVERT: G 372 GLU cc_start: 0.8176 (mm-30) cc_final: 0.7961 (mt-10) REVERT: H 375 LYS cc_start: 0.8044 (tttt) cc_final: 0.7591 (tppt) REVERT: I 347 LYS cc_start: 0.8535 (mttt) cc_final: 0.7772 (mppt) REVERT: I 369 LYS cc_start: 0.8358 (mttt) cc_final: 0.8090 (ttmp) REVERT: I 375 LYS cc_start: 0.8328 (tttt) cc_final: 0.7678 (tmmt) outliers start: 7 outliers final: 4 residues processed: 136 average time/residue: 1.3461 time to fit residues: 189.1040 Evaluate side-chains 132 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 127 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain C residue 369 LYS Chi-restraints excluded: chain B residue 309 VAL Chi-restraints excluded: chain D residue 309 VAL Chi-restraints excluded: chain D residue 315 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 7 optimal weight: 7.9990 chunk 3 optimal weight: 10.0000 chunk 25 optimal weight: 9.9990 chunk 21 optimal weight: 10.0000 chunk 44 optimal weight: 8.9990 chunk 48 optimal weight: 9.9990 chunk 10 optimal weight: 3.9990 chunk 33 optimal weight: 4.9990 chunk 55 optimal weight: 0.9990 chunk 54 optimal weight: 6.9990 chunk 4 optimal weight: 0.6980 overall best weight: 3.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 307 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.159160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.135620 restraints weight = 18540.694| |-----------------------------------------------------------------------------| r_work (start): 0.3723 rms_B_bonded: 1.75 r_work: 0.3649 rms_B_bonded: 1.75 restraints_weight: 0.5000 r_work: 0.3573 rms_B_bonded: 2.96 restraints_weight: 0.2500 r_work (final): 0.3573 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8555 moved from start: 0.5922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 5094 Z= 0.170 Angle : 0.516 5.679 6822 Z= 0.269 Chirality : 0.051 0.141 774 Planarity : 0.002 0.018 864 Dihedral : 5.014 15.943 666 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 1.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Rotamer: Outliers : 1.39 % Allowed : 23.78 % Favored : 74.83 % 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: -2.25 (0.27), residues: 639 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.71 (0.21), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 349 TYR 0.011 0.002 TYR G 310 PHE 0.004 0.001 PHE G 346 HIS 0.002 0.001 HIS C 374 Details of bonding type rmsd covalent geometry : bond 0.00362 ( 5094) covalent geometry : angle 0.51618 ( 6822) hydrogen bonds : bond 0.02233 ( 128) hydrogen bonds : angle 4.28750 ( 384) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 126 time to evaluate : 0.212 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 369 LYS cc_start: 0.8226 (OUTLIER) cc_final: 0.7941 (ttmm) REVERT: C 375 LYS cc_start: 0.7989 (tttt) cc_final: 0.7594 (tppt) REVERT: E 347 LYS cc_start: 0.8639 (mttt) cc_final: 0.7802 (mtmt) REVERT: E 369 LYS cc_start: 0.8391 (mttt) cc_final: 0.8103 (ttmp) REVERT: E 375 LYS cc_start: 0.8296 (tttt) cc_final: 0.7652 (tmmt) REVERT: D 375 LYS cc_start: 0.7991 (tptt) cc_final: 0.7390 (tppt) REVERT: F 347 LYS cc_start: 0.8533 (mttt) cc_final: 0.7830 (mppt) REVERT: F 375 LYS cc_start: 0.8414 (tttt) cc_final: 0.7733 (tmmt) REVERT: G 309 VAL cc_start: 0.8628 (t) cc_final: 0.8315 (p) REVERT: G 372 GLU cc_start: 0.8178 (mm-30) cc_final: 0.7965 (mt-10) REVERT: H 375 LYS cc_start: 0.8027 (tttt) cc_final: 0.7566 (tppt) REVERT: I 347 LYS cc_start: 0.8540 (mttt) cc_final: 0.7773 (mppt) REVERT: I 369 LYS cc_start: 0.8417 (mttt) cc_final: 0.8130 (ttmp) REVERT: I 375 LYS cc_start: 0.8320 (tttt) cc_final: 0.7669 (tmmt) outliers start: 8 outliers final: 8 residues processed: 129 average time/residue: 1.1579 time to fit residues: 154.4530 Evaluate side-chains 131 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 122 time to evaluate : 0.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 345 ASP Chi-restraints excluded: chain C residue 369 LYS Chi-restraints excluded: chain B residue 309 VAL Chi-restraints excluded: chain B residue 345 ASP Chi-restraints excluded: chain D residue 309 VAL Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain F residue 377 THR Chi-restraints excluded: chain I residue 309 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 43 optimal weight: 3.9990 chunk 2 optimal weight: 6.9990 chunk 40 optimal weight: 0.0050 chunk 58 optimal weight: 5.9990 chunk 46 optimal weight: 4.9990 chunk 31 optimal weight: 5.9990 chunk 38 optimal weight: 5.9990 chunk 20 optimal weight: 3.9990 chunk 60 optimal weight: 1.9990 chunk 22 optimal weight: 9.9990 chunk 42 optimal weight: 9.9990 overall best weight: 3.0002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 307 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.158848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.135192 restraints weight = 18603.740| |-----------------------------------------------------------------------------| r_work (start): 0.3734 rms_B_bonded: 1.76 r_work: 0.3658 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.3581 rms_B_bonded: 2.99 restraints_weight: 0.2500 r_work (final): 0.3581 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8548 moved from start: 0.5941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5094 Z= 0.150 Angle : 0.503 5.789 6822 Z= 0.262 Chirality : 0.051 0.140 774 Planarity : 0.002 0.018 864 Dihedral : 4.920 15.575 666 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 1.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Rotamer: Outliers : 1.56 % Allowed : 23.09 % Favored : 75.35 % 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: -2.25 (0.27), residues: 639 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.70 (0.21), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 349 TYR 0.008 0.001 TYR B 310 PHE 0.004 0.001 PHE C 346 HIS 0.002 0.000 HIS C 374 Details of bonding type rmsd covalent geometry : bond 0.00322 ( 5094) covalent geometry : angle 0.50347 ( 6822) hydrogen bonds : bond 0.02124 ( 128) hydrogen bonds : angle 4.21419 ( 384) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 128 time to evaluate : 0.263 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 369 LYS cc_start: 0.8211 (OUTLIER) cc_final: 0.7927 (ttmm) REVERT: C 375 LYS cc_start: 0.7973 (tttt) cc_final: 0.7594 (tppt) REVERT: E 347 LYS cc_start: 0.8634 (mttt) cc_final: 0.7923 (mppt) REVERT: E 369 LYS cc_start: 0.8394 (mttt) cc_final: 0.8102 (ttmp) REVERT: E 375 LYS cc_start: 0.8300 (tttt) cc_final: 0.7655 (tmmt) REVERT: F 347 LYS cc_start: 0.8540 (mttt) cc_final: 0.7832 (mppt) REVERT: F 375 LYS cc_start: 0.8418 (tttt) cc_final: 0.7734 (tmmt) REVERT: G 309 VAL cc_start: 0.8618 (t) cc_final: 0.8297 (p) REVERT: G 372 GLU cc_start: 0.8158 (mm-30) cc_final: 0.7950 (mt-10) REVERT: H 375 LYS cc_start: 0.8031 (tttt) cc_final: 0.7570 (tppt) REVERT: I 347 LYS cc_start: 0.8530 (mttt) cc_final: 0.7760 (mppt) REVERT: I 369 LYS cc_start: 0.8415 (mttt) cc_final: 0.8131 (ttmp) REVERT: I 375 LYS cc_start: 0.8345 (tttt) cc_final: 0.7673 (tmmt) outliers start: 9 outliers final: 7 residues processed: 132 average time/residue: 1.1176 time to fit residues: 152.7765 Evaluate side-chains 133 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 125 time to evaluate : 0.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 345 ASP Chi-restraints excluded: chain C residue 369 LYS Chi-restraints excluded: chain B residue 309 VAL Chi-restraints excluded: chain B residue 345 ASP Chi-restraints excluded: chain D residue 309 VAL Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain F residue 377 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 36 optimal weight: 9.9990 chunk 29 optimal weight: 10.0000 chunk 23 optimal weight: 7.9990 chunk 59 optimal weight: 6.9990 chunk 20 optimal weight: 3.9990 chunk 22 optimal weight: 0.9990 chunk 31 optimal weight: 5.9990 chunk 28 optimal weight: 4.9990 chunk 52 optimal weight: 7.9990 chunk 62 optimal weight: 2.9990 chunk 48 optimal weight: 3.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 307 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.159419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.135876 restraints weight = 18588.926| |-----------------------------------------------------------------------------| r_work (start): 0.3746 rms_B_bonded: 1.75 r_work: 0.3673 rms_B_bonded: 1.74 restraints_weight: 0.5000 r_work: 0.3597 rms_B_bonded: 2.94 restraints_weight: 0.2500 r_work (final): 0.3597 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8555 moved from start: 0.6019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 5094 Z= 0.166 Angle : 0.517 5.958 6822 Z= 0.269 Chirality : 0.051 0.141 774 Planarity : 0.002 0.018 864 Dihedral : 4.965 15.617 666 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 1.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Rotamer: Outliers : 1.56 % Allowed : 22.92 % Favored : 75.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.28 (0.27), residues: 639 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.73 (0.20), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 349 TYR 0.014 0.002 TYR D 310 PHE 0.004 0.001 PHE C 346 HIS 0.002 0.000 HIS F 374 Details of bonding type rmsd covalent geometry : bond 0.00355 ( 5094) covalent geometry : angle 0.51664 ( 6822) hydrogen bonds : bond 0.02202 ( 128) hydrogen bonds : angle 4.27215 ( 384) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 124 time to evaluate : 0.332 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 369 LYS cc_start: 0.8214 (OUTLIER) cc_final: 0.7933 (ttmm) REVERT: C 375 LYS cc_start: 0.7951 (tttt) cc_final: 0.7618 (tppt) REVERT: E 347 LYS cc_start: 0.8619 (mttt) cc_final: 0.7902 (mppt) REVERT: E 369 LYS cc_start: 0.8409 (mttt) cc_final: 0.8127 (ttmp) REVERT: E 375 LYS cc_start: 0.8288 (tttt) cc_final: 0.7647 (tmmt) REVERT: D 375 LYS cc_start: 0.8022 (tptt) cc_final: 0.7382 (tppt) REVERT: F 347 LYS cc_start: 0.8543 (mttt) cc_final: 0.7845 (mppt) REVERT: F 375 LYS cc_start: 0.8434 (tttt) cc_final: 0.7757 (tmmt) REVERT: G 309 VAL cc_start: 0.8632 (t) cc_final: 0.8348 (p) REVERT: H 375 LYS cc_start: 0.8039 (tttt) cc_final: 0.7593 (tppt) REVERT: I 347 LYS cc_start: 0.8539 (mttt) cc_final: 0.7791 (mppt) REVERT: I 369 LYS cc_start: 0.8406 (mttt) cc_final: 0.8122 (ttmp) REVERT: I 375 LYS cc_start: 0.8330 (tttt) cc_final: 0.7688 (tmmt) outliers start: 9 outliers final: 8 residues processed: 127 average time/residue: 1.2024 time to fit residues: 157.7582 Evaluate side-chains 133 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 124 time to evaluate : 0.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 345 ASP Chi-restraints excluded: chain C residue 369 LYS Chi-restraints excluded: chain B residue 309 VAL Chi-restraints excluded: chain B residue 345 ASP Chi-restraints excluded: chain D residue 309 VAL Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain F residue 377 THR Chi-restraints excluded: chain I residue 309 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 23 optimal weight: 7.9990 chunk 54 optimal weight: 6.9990 chunk 49 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 28 optimal weight: 8.9990 chunk 50 optimal weight: 10.0000 chunk 53 optimal weight: 5.9990 chunk 56 optimal weight: 0.8980 chunk 8 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 45 optimal weight: 9.9990 overall best weight: 3.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 307 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.157455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.133821 restraints weight = 18740.899| |-----------------------------------------------------------------------------| r_work (start): 0.3714 rms_B_bonded: 1.77 r_work: 0.3638 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.3562 rms_B_bonded: 2.99 restraints_weight: 0.2500 r_work (final): 0.3562 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8563 moved from start: 0.5985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 5094 Z= 0.187 Angle : 0.530 6.011 6822 Z= 0.277 Chirality : 0.051 0.141 774 Planarity : 0.003 0.018 864 Dihedral : 5.072 16.088 666 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 1.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Rotamer: Outliers : 1.56 % Allowed : 22.92 % Favored : 75.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.29 (0.27), residues: 639 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.73 (0.20), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 349 TYR 0.013 0.002 TYR C 310 PHE 0.004 0.001 PHE C 346 HIS 0.002 0.001 HIS C 374 Details of bonding type rmsd covalent geometry : bond 0.00396 ( 5094) covalent geometry : angle 0.53038 ( 6822) hydrogen bonds : bond 0.02324 ( 128) hydrogen bonds : angle 4.32695 ( 384) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4682.81 seconds wall clock time: 80 minutes 2.03 seconds (4802.03 seconds total)