Starting phenix.real_space_refine on Thu May 1 04:12:30 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8q9l_18285/05_2025/8q9l_18285.cif Found real_map, /net/cci-nas-00/data/ceres_data/8q9l_18285/05_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8q9l_18285/05_2025/8q9l_18285.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8q9l_18285/05_2025/8q9l_18285.map" model { file = "/net/cci-nas-00/data/ceres_data/8q9l_18285/05_2025/8q9l_18285.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8q9l_18285/05_2025/8q9l_18285.cif" } resolution = 2.76 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 9 5.16 5 C 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/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: 7.07, per 1000 atoms: 0.69 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: 2.91 Conformation dependent library (CDL) restraints added in 772.5 milliseconds 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: 1.18 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: 3.69 Time building geometry restraints manager: 3.53 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: 0.01 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: 3.410 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: 0.200 Extract box with map and model: 0.480 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 29.350 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.040 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:13.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.390 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 HIS 0.013 0.003 HIS H 330 PHE 0.030 0.009 PHE A 346 TYR 0.083 0.026 TYR B 310 ARG 0.006 0.002 ARG I 349 Details of bonding type rmsd hydrogen bonds : bond 0.07627 ( 128) hydrogen bonds : angle 8.17267 ( 384) covalent geometry : bond 0.01097 ( 5094) covalent geometry : angle 1.76236 ( 6822) *********************** 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 : 0.920 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: A 309 VAL cc_start: 0.5819 (t) cc_final: 0.5517 (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 347 LYS cc_start: 0.8284 (mttt) cc_final: 0.8012 (mttp) 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: 0.7933 (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: 0.7760 (m-70) REVERT: C 375 LYS cc_start: 0.5754 (tttt) cc_final: 0.5384 (tppt) REVERT: C 376 LEU cc_start: 0.7456 (tt) cc_final: 0.7253 (tt) 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: 0.4177 (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: 0.7879 (mppt) REVERT: E 349 ARG cc_start: 0.6815 (mtt180) cc_final: 0.5220 (pmt-80) REVERT: E 369 LYS cc_start: 0.8091 (mttt) cc_final: 0.7664 (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: 0.8286 (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: 0.7622 (mm-30) REVERT: B 372 GLU cc_start: 0.7352 (tt0) cc_final: 0.6542 (mm-30) REVERT: B 375 LYS cc_start: 0.6009 (tttt) cc_final: 0.5746 (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: 0.7459 (mm-30) REVERT: D 345 ASP cc_start: 0.8153 (t0) cc_final: 0.7628 (t0) 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: 0.5615 (m) REVERT: D 374 HIS cc_start: 0.8008 (m-70) cc_final: 0.7372 (m-70) REVERT: D 375 LYS cc_start: 0.5800 (tttt) cc_final: 0.5569 (tppt) REVERT: D 377 THR cc_start: 0.6655 (m) cc_final: 0.6015 (p) REVERT: F 310 TYR cc_start: 0.4497 (t80) cc_final: 0.4165 (t80) REVERT: F 340 LYS cc_start: 0.8470 (mtpt) cc_final: 0.8178 (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: 0.7778 (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: 0.4545 (t80) REVERT: G 309 VAL cc_start: 0.5700 (t) cc_final: 0.5433 (p) REVERT: G 310 TYR cc_start: 0.4789 (t80) cc_final: 0.4543 (t80) REVERT: G 342 GLU cc_start: 0.8134 (mt-10) cc_final: 0.7671 (mm-30) REVERT: G 345 ASP cc_start: 0.8364 (t0) cc_final: 0.8116 (t0) REVERT: G 372 GLU cc_start: 0.7231 (tt0) cc_final: 0.6863 (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: 0.7738 (t0) REVERT: H 347 LYS cc_start: 0.8511 (mttt) cc_final: 0.8299 (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: 0.7551 (m-70) REVERT: H 375 LYS cc_start: 0.5712 (tttt) cc_final: 0.5417 (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: 0.7929 (mm-30) REVERT: I 347 LYS cc_start: 0.8611 (mttt) cc_final: 0.7850 (mppt) REVERT: I 349 ARG cc_start: 0.6703 (mtt180) cc_final: 0.5267 (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: 2.5459 time to fit residues: 718.7039 Evaluate side-chains 220 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 219 time to evaluate : 0.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 345 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 53 optimal weight: 5.9990 chunk 47 optimal weight: 6.9990 chunk 26 optimal weight: 5.9990 chunk 16 optimal weight: 0.9990 chunk 32 optimal weight: 5.9990 chunk 25 optimal weight: 5.9990 chunk 49 optimal weight: 6.9990 chunk 19 optimal weight: 1.9990 chunk 30 optimal weight: 5.9990 chunk 36 optimal weight: 5.9990 chunk 57 optimal weight: 5.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- 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 I 374 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4197 r_free = 0.4197 target = 0.168770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.145331 restraints weight = 17339.860| |-----------------------------------------------------------------------------| r_work (start): 0.3826 rms_B_bonded: 1.72 r_work: 0.3760 rms_B_bonded: 1.70 restraints_weight: 0.5000 r_work: 0.3686 rms_B_bonded: 2.89 restraints_weight: 0.2500 r_work (final): 0.3686 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.3907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 5094 Z= 0.182 Angle : 0.610 4.468 6822 Z= 0.324 Chirality : 0.052 0.142 774 Planarity : 0.003 0.020 864 Dihedral : 7.864 120.248 668 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 0.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % Rotamer: Outliers : 2.08 % Allowed : 12.50 % Favored : 85.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 HIS 0.005 0.001 HIS C 374 PHE 0.005 0.001 PHE D 346 TYR 0.011 0.002 TYR D 310 ARG 0.002 0.001 ARG F 349 Details of bonding type rmsd hydrogen bonds : bond 0.03195 ( 128) hydrogen bonds : angle 5.54787 ( 384) covalent geometry : bond 0.00398 ( 5094) covalent geometry : angle 0.60981 ( 6822) *********************** 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 215 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 203 time to evaluate : 0.914 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: 0.8416 (p) REVERT: A 338 GLU cc_start: 0.7508 (tt0) cc_final: 0.7301 (tt0) REVERT: A 345 ASP cc_start: 0.8181 (t0) cc_final: 0.7927 (t0) REVERT: A 369 LYS cc_start: 0.8191 (OUTLIER) cc_final: 0.7952 (ttmm) REVERT: C 311 LYS cc_start: 0.8680 (mtpt) cc_final: 0.7791 (mmpt) REVERT: C 345 ASP cc_start: 0.8131 (t0) cc_final: 0.7827 (t0) REVERT: C 369 LYS cc_start: 0.8231 (OUTLIER) cc_final: 0.7982 (ttmm) REVERT: C 375 LYS cc_start: 0.8116 (tttt) cc_final: 0.7639 (tppt) REVERT: E 347 LYS cc_start: 0.8510 (mttt) cc_final: 0.7905 (mppt) REVERT: E 349 ARG cc_start: 0.6923 (mtt180) cc_final: 0.5591 (pmt-80) REVERT: E 369 LYS cc_start: 0.8265 (mttt) cc_final: 0.8007 (ttmp) REVERT: E 375 LYS cc_start: 0.8281 (tttt) cc_final: 0.7744 (tmmt) REVERT: B 309 VAL cc_start: 0.8706 (t) cc_final: 0.8400 (p) REVERT: B 331 LYS cc_start: 0.8760 (mtmt) cc_final: 0.8532 (mtmt) REVERT: D 331 LYS cc_start: 0.8844 (OUTLIER) cc_final: 0.8556 (mtmm) REVERT: D 345 ASP cc_start: 0.8073 (t0) cc_final: 0.7732 (t0) REVERT: D 375 LYS cc_start: 0.7972 (tttt) cc_final: 0.7578 (tppt) REVERT: F 347 LYS cc_start: 0.8502 (mttt) cc_final: 0.7813 (mppt) REVERT: F 349 ARG cc_start: 0.6935 (mtt180) cc_final: 0.5643 (pmt-80) REVERT: F 375 LYS cc_start: 0.8268 (tttt) cc_final: 0.7678 (tmmt) REVERT: G 309 VAL cc_start: 0.8674 (t) cc_final: 0.8326 (p) REVERT: G 331 LYS cc_start: 0.8783 (mtmm) cc_final: 0.8530 (mmmm) REVERT: G 349 ARG cc_start: 0.7065 (mtm180) cc_final: 0.6645 (mtp85) REVERT: H 309 VAL cc_start: 0.8641 (t) cc_final: 0.8159 (p) REVERT: H 375 LYS cc_start: 0.8119 (tttt) cc_final: 0.7576 (tppt) REVERT: I 347 LYS cc_start: 0.8522 (mttt) cc_final: 0.7800 (mppt) REVERT: I 349 ARG cc_start: 0.6884 (mtt180) cc_final: 0.5529 (pmt-80) REVERT: I 369 LYS cc_start: 0.8271 (mttt) cc_final: 0.8003 (ttmp) REVERT: I 375 LYS cc_start: 0.8280 (tttt) cc_final: 0.7212 (pptt) outliers start: 12 outliers final: 2 residues processed: 205 average time/residue: 3.0962 time to fit residues: 655.8113 Evaluate side-chains 164 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 159 time to evaluate : 0.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 369 LYS Chi-restraints excluded: chain C residue 369 LYS Chi-restraints excluded: chain B residue 308 ILE Chi-restraints excluded: chain D residue 331 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 6 optimal weight: 9.9990 chunk 49 optimal weight: 0.1980 chunk 8 optimal weight: 0.9990 chunk 15 optimal weight: 0.9980 chunk 56 optimal weight: 6.9990 chunk 54 optimal weight: 7.9990 chunk 22 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 14 optimal weight: 2.9990 chunk 27 optimal weight: 8.9990 chunk 29 optimal weight: 0.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- 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 336 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.167222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.142973 restraints weight = 17917.905| |-----------------------------------------------------------------------------| r_work (start): 0.3812 rms_B_bonded: 1.76 r_work: 0.3750 rms_B_bonded: 1.72 restraints_weight: 0.5000 r_work: 0.3678 rms_B_bonded: 2.92 restraints_weight: 0.2500 r_work (final): 0.3678 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8491 moved from start: 0.5297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 5094 Z= 0.095 Angle : 0.497 4.206 6822 Z= 0.260 Chirality : 0.052 0.139 774 Planarity : 0.002 0.017 864 Dihedral : 5.265 14.999 666 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 0.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.63 % Favored : 99.37 % Rotamer: Outliers : 1.22 % Allowed : 19.79 % Favored : 78.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.64 (0.27), residues: 639 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.24 (0.21), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS C 374 PHE 0.005 0.001 PHE C 346 TYR 0.010 0.001 TYR B 310 ARG 0.000 0.000 ARG G 349 Details of bonding type rmsd hydrogen bonds : bond 0.02236 ( 128) hydrogen bonds : angle 4.63433 ( 384) covalent geometry : bond 0.00222 ( 5094) covalent geometry : angle 0.49746 ( 6822) *********************** 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 171 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 164 time to evaluate : 0.833 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 309 VAL cc_start: 0.8693 (t) cc_final: 0.8261 (p) REVERT: A 345 ASP cc_start: 0.8234 (t0) cc_final: 0.7906 (t70) REVERT: C 345 ASP cc_start: 0.8141 (t0) cc_final: 0.7927 (t0) REVERT: C 347 LYS cc_start: 0.8157 (mtmt) cc_final: 0.7891 (mtmt) REVERT: C 375 LYS cc_start: 0.7997 (tttt) cc_final: 0.7521 (tppt) REVERT: E 347 LYS cc_start: 0.8491 (mttt) cc_final: 0.7564 (ttpt) REVERT: E 349 ARG cc_start: 0.6916 (mtt180) cc_final: 0.5513 (pmt-80) REVERT: E 369 LYS cc_start: 0.8182 (mttt) cc_final: 0.7934 (ttmp) REVERT: E 375 LYS cc_start: 0.8237 (tttt) cc_final: 0.7683 (tmmt) REVERT: E 378 PHE cc_start: 0.7046 (t80) cc_final: 0.6811 (t80) REVERT: D 338 GLU cc_start: 0.7690 (tt0) cc_final: 0.7460 (tt0) REVERT: D 345 ASP cc_start: 0.8126 (t0) cc_final: 0.7917 (t0) REVERT: D 347 LYS cc_start: 0.8161 (mttp) cc_final: 0.7844 (mttp) REVERT: D 375 LYS cc_start: 0.7937 (tttt) cc_final: 0.7644 (tppt) REVERT: F 347 LYS cc_start: 0.8445 (mttt) cc_final: 0.7522 (ttpt) REVERT: F 349 ARG cc_start: 0.6981 (mtt180) cc_final: 0.5516 (pmt-80) REVERT: F 375 LYS cc_start: 0.8267 (tttt) cc_final: 0.7631 (tmmt) REVERT: G 309 VAL cc_start: 0.8664 (t) cc_final: 0.8324 (p) REVERT: G 349 ARG cc_start: 0.7113 (mtm180) cc_final: 0.6563 (mtp85) REVERT: H 375 LYS cc_start: 0.8067 (tttt) cc_final: 0.7638 (tppt) REVERT: I 347 LYS cc_start: 0.8395 (mttt) cc_final: 0.7765 (mppt) REVERT: I 349 ARG cc_start: 0.6917 (mtt180) cc_final: 0.5533 (pmt-80) REVERT: I 369 LYS cc_start: 0.8116 (mttt) cc_final: 0.7860 (ttmp) REVERT: I 375 LYS cc_start: 0.8200 (tttt) cc_final: 0.7677 (tmmt) outliers start: 7 outliers final: 2 residues processed: 167 average time/residue: 3.3273 time to fit residues: 574.4447 Evaluate side-chains 151 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 149 time to evaluate : 0.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 309 VAL Chi-restraints excluded: chain G residue 345 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 34 optimal weight: 9.9990 chunk 40 optimal weight: 0.6980 chunk 39 optimal weight: 7.9990 chunk 7 optimal weight: 8.9990 chunk 46 optimal weight: 9.9990 chunk 15 optimal weight: 4.9990 chunk 54 optimal weight: 5.9990 chunk 28 optimal weight: 7.9990 chunk 23 optimal weight: 6.9990 chunk 56 optimal weight: 8.9990 chunk 43 optimal weight: 10.0000 overall best weight: 5.3388 ------------------------------------------------------------------------------- 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 = 0.4086 r_free = 0.4086 target = 0.158707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.134987 restraints weight = 18655.672| |-----------------------------------------------------------------------------| r_work (start): 0.3714 rms_B_bonded: 1.73 r_work: 0.3639 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.3565 rms_B_bonded: 2.95 restraints_weight: 0.2500 r_work (final): 0.3565 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8565 moved from start: 0.5568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 5094 Z= 0.240 Angle : 0.574 4.271 6822 Z= 0.302 Chirality : 0.052 0.144 774 Planarity : 0.003 0.020 864 Dihedral : 5.553 17.634 666 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 1.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 1.56 % Allowed : 20.49 % Favored : 77.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.91 (0.27), residues: 639 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.45 (0.21), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS D 374 PHE 0.005 0.001 PHE D 346 TYR 0.012 0.002 TYR G 310 ARG 0.002 0.001 ARG F 349 Details of bonding type rmsd hydrogen bonds : bond 0.02658 ( 128) hydrogen bonds : angle 4.80135 ( 384) covalent geometry : bond 0.00515 ( 5094) covalent geometry : angle 0.57358 ( 6822) *********************** 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 153 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 144 time to evaluate : 1.269 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 345 ASP cc_start: 0.8220 (t0) cc_final: 0.7977 (OUTLIER) REVERT: C 331 LYS cc_start: 0.8819 (OUTLIER) cc_final: 0.8615 (mtmt) REVERT: C 375 LYS cc_start: 0.7991 (tttt) cc_final: 0.7470 (tppt) REVERT: E 347 LYS cc_start: 0.8549 (mttt) cc_final: 0.7856 (mppt) REVERT: E 349 ARG cc_start: 0.7270 (mtt180) cc_final: 0.5461 (pmt-80) REVERT: E 369 LYS cc_start: 0.8384 (mttt) cc_final: 0.8090 (ttmp) REVERT: E 375 LYS cc_start: 0.8319 (tttt) cc_final: 0.7657 (tmmt) REVERT: E 378 PHE cc_start: 0.7012 (t80) cc_final: 0.6801 (t80) REVERT: D 345 ASP cc_start: 0.8143 (t0) cc_final: 0.7832 (t0) REVERT: D 375 LYS cc_start: 0.7939 (tttt) cc_final: 0.7583 (tppt) REVERT: F 347 LYS cc_start: 0.8552 (mttt) cc_final: 0.7796 (mppt) REVERT: F 375 LYS cc_start: 0.8344 (tttt) cc_final: 0.7684 (tmmt) REVERT: G 309 VAL cc_start: 0.8642 (t) cc_final: 0.8304 (p) REVERT: H 375 LYS cc_start: 0.8033 (tttt) cc_final: 0.7569 (tppt) REVERT: I 309 VAL cc_start: 0.8675 (OUTLIER) cc_final: 0.8357 (p) REVERT: I 347 LYS cc_start: 0.8580 (mttt) cc_final: 0.7871 (mppt) REVERT: I 349 ARG cc_start: 0.7191 (mtt180) cc_final: 0.5362 (pmt-80) REVERT: I 369 LYS cc_start: 0.8408 (mttt) cc_final: 0.8106 (ttmp) REVERT: I 375 LYS cc_start: 0.8272 (tttt) cc_final: 0.7141 (pptt) outliers start: 9 outliers final: 4 residues processed: 145 average time/residue: 3.4952 time to fit residues: 524.4365 Evaluate side-chains 140 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 135 time to evaluate : 1.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 331 LYS Chi-restraints excluded: chain B residue 309 VAL Chi-restraints excluded: chain D residue 309 VAL Chi-restraints excluded: chain G 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 20 optimal weight: 10.0000 chunk 7 optimal weight: 3.9990 chunk 49 optimal weight: 0.3980 chunk 60 optimal weight: 8.9990 chunk 5 optimal weight: 5.9990 chunk 11 optimal weight: 2.9990 chunk 21 optimal weight: 10.0000 chunk 23 optimal weight: 7.9990 chunk 28 optimal weight: 0.9980 chunk 38 optimal weight: 7.9990 chunk 13 optimal weight: 3.9990 overall best weight: 2.4786 ------------------------------------------------------------------------------- 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 = 0.4114 r_free = 0.4114 target = 0.161463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.138101 restraints weight = 18760.142| |-----------------------------------------------------------------------------| r_work (start): 0.3754 rms_B_bonded: 1.75 r_work: 0.3678 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.3605 rms_B_bonded: 2.99 restraints_weight: 0.2500 r_work (final): 0.3605 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8535 moved from start: 0.5628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5094 Z= 0.135 Angle : 0.502 4.603 6822 Z= 0.261 Chirality : 0.051 0.139 774 Planarity : 0.002 0.020 864 Dihedral : 5.113 16.218 666 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 1.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Rotamer: Outliers : 1.39 % Allowed : 21.53 % Favored : 77.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.01 (0.27), residues: 639 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.52 (0.21), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS H 374 PHE 0.007 0.001 PHE C 346 TYR 0.013 0.001 TYR E 310 ARG 0.002 0.000 ARG F 349 Details of bonding type rmsd hydrogen bonds : bond 0.02108 ( 128) hydrogen bonds : angle 4.38967 ( 384) covalent geometry : bond 0.00288 ( 5094) covalent geometry : angle 0.50199 ( 6822) *********************** 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 149 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 141 time to evaluate : 0.943 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: C 347 LYS cc_start: 0.8179 (mtmt) cc_final: 0.7974 (mttp) REVERT: C 375 LYS cc_start: 0.7961 (tttt) cc_final: 0.7489 (tppt) REVERT: E 347 LYS cc_start: 0.8528 (mttt) cc_final: 0.7552 (ttpt) REVERT: E 349 ARG cc_start: 0.7273 (mtt180) cc_final: 0.5360 (pmt-80) REVERT: E 369 LYS cc_start: 0.8333 (mttt) cc_final: 0.8045 (ttmp) REVERT: E 375 LYS cc_start: 0.8253 (tttt) cc_final: 0.7621 (tmmt) REVERT: E 378 PHE cc_start: 0.6956 (t80) cc_final: 0.6748 (t80) REVERT: D 345 ASP cc_start: 0.8116 (t0) cc_final: 0.7794 (t0) REVERT: D 375 LYS cc_start: 0.7934 (tttt) cc_final: 0.7562 (tppt) REVERT: F 347 LYS cc_start: 0.8520 (mttt) cc_final: 0.7743 (mppt) REVERT: F 375 LYS cc_start: 0.8293 (tttt) cc_final: 0.7659 (tmmt) REVERT: G 309 VAL cc_start: 0.8631 (t) cc_final: 0.8282 (p) REVERT: H 375 LYS cc_start: 0.8032 (tttt) cc_final: 0.7555 (tppt) REVERT: I 309 VAL cc_start: 0.8612 (OUTLIER) cc_final: 0.8279 (p) REVERT: I 347 LYS cc_start: 0.8540 (mttt) cc_final: 0.7827 (mppt) REVERT: I 349 ARG cc_start: 0.7246 (mtt180) cc_final: 0.5344 (pmt-80) REVERT: I 369 LYS cc_start: 0.8321 (mttt) cc_final: 0.8045 (ttmp) REVERT: I 375 LYS cc_start: 0.8260 (tttt) cc_final: 0.7637 (tmmt) REVERT: I 378 PHE cc_start: 0.6922 (t80) cc_final: 0.6706 (t80) outliers start: 8 outliers final: 4 residues processed: 144 average time/residue: 2.9406 time to fit residues: 437.7373 Evaluate side-chains 137 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 132 time to evaluate : 0.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain B residue 309 VAL Chi-restraints excluded: chain D residue 309 VAL Chi-restraints excluded: chain G 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 33 optimal weight: 4.9990 chunk 8 optimal weight: 8.9990 chunk 54 optimal weight: 3.9990 chunk 59 optimal weight: 8.9990 chunk 38 optimal weight: 7.9990 chunk 50 optimal weight: 9.9990 chunk 20 optimal weight: 9.9990 chunk 12 optimal weight: 5.9990 chunk 42 optimal weight: 10.0000 chunk 36 optimal weight: 5.9990 chunk 52 optimal weight: 4.9990 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 307 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.159940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.136693 restraints weight = 18908.342| |-----------------------------------------------------------------------------| r_work (start): 0.3714 rms_B_bonded: 1.74 r_work: 0.3635 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.3561 rms_B_bonded: 2.97 restraints_weight: 0.2500 r_work (final): 0.3561 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8571 moved from start: 0.5724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 5094 Z= 0.236 Angle : 0.555 4.760 6822 Z= 0.292 Chirality : 0.051 0.144 774 Planarity : 0.003 0.029 864 Dihedral : 5.359 17.267 666 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 1.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 2.08 % Allowed : 21.53 % Favored : 76.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.17 (0.27), residues: 639 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.64 (0.20), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS C 374 PHE 0.005 0.001 PHE C 346 TYR 0.011 0.002 TYR G 310 ARG 0.003 0.001 ARG F 349 Details of bonding type rmsd hydrogen bonds : bond 0.02536 ( 128) hydrogen bonds : angle 4.64333 ( 384) covalent geometry : bond 0.00501 ( 5094) covalent geometry : angle 0.55467 ( 6822) *********************** 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 143 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 131 time to evaluate : 0.962 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 331 LYS cc_start: 0.8856 (OUTLIER) cc_final: 0.8648 (mtmt) REVERT: C 369 LYS cc_start: 0.8237 (OUTLIER) cc_final: 0.7960 (ttmm) REVERT: C 375 LYS cc_start: 0.7980 (tttt) cc_final: 0.7518 (tppt) REVERT: E 347 LYS cc_start: 0.8555 (mttt) cc_final: 0.7834 (mppt) REVERT: E 369 LYS cc_start: 0.8432 (mttt) cc_final: 0.8111 (ttmp) REVERT: E 375 LYS cc_start: 0.8295 (tttt) cc_final: 0.7614 (tmmt) REVERT: D 345 ASP cc_start: 0.8082 (t0) cc_final: 0.7758 (t0) REVERT: D 375 LYS cc_start: 0.7946 (tttt) cc_final: 0.7614 (tppt) REVERT: F 347 LYS cc_start: 0.8589 (mttt) cc_final: 0.7856 (mppt) REVERT: F 375 LYS cc_start: 0.8400 (tttt) cc_final: 0.7733 (tmmt) REVERT: G 309 VAL cc_start: 0.8626 (t) cc_final: 0.8288 (p) REVERT: G 372 GLU cc_start: 0.8245 (OUTLIER) cc_final: 0.7929 (mt-10) REVERT: H 375 LYS cc_start: 0.8038 (tttt) cc_final: 0.7568 (tppt) REVERT: I 347 LYS cc_start: 0.8573 (mttt) cc_final: 0.7821 (mppt) REVERT: I 369 LYS cc_start: 0.8420 (mttt) cc_final: 0.8118 (ttmp) REVERT: I 375 LYS cc_start: 0.8327 (tttt) cc_final: 0.7691 (tmmt) outliers start: 12 outliers final: 5 residues processed: 137 average time/residue: 2.9513 time to fit residues: 418.2895 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 : 0.860 ------------------------------------------------------------------------------- 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 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 Chi-restraints excluded: chain G residue 372 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 27 optimal weight: 9.9990 chunk 2 optimal weight: 6.9990 chunk 42 optimal weight: 10.0000 chunk 37 optimal weight: 6.9990 chunk 31 optimal weight: 4.9990 chunk 16 optimal weight: 1.9990 chunk 55 optimal weight: 8.9990 chunk 13 optimal weight: 5.9990 chunk 36 optimal weight: 6.9990 chunk 50 optimal weight: 5.9990 chunk 26 optimal weight: 5.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- 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 = 0.4090 r_free = 0.4090 target = 0.158417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.134215 restraints weight = 18368.553| |-----------------------------------------------------------------------------| r_work (start): 0.3695 rms_B_bonded: 1.79 r_work: 0.3621 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.3545 rms_B_bonded: 2.99 restraints_weight: 0.2500 r_work (final): 0.3545 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8567 moved from start: 0.5830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 5094 Z= 0.227 Angle : 0.552 5.427 6822 Z= 0.290 Chirality : 0.051 0.143 774 Planarity : 0.003 0.026 864 Dihedral : 5.347 17.227 666 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 1.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 2.43 % Allowed : 21.53 % Favored : 76.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.27 (0.27), residues: 639 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.72 (0.20), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS C 374 PHE 0.005 0.001 PHE C 346 TYR 0.010 0.002 TYR G 310 ARG 0.004 0.001 ARG E 349 Details of bonding type rmsd hydrogen bonds : bond 0.02487 ( 128) hydrogen bonds : angle 4.60492 ( 384) covalent geometry : bond 0.00475 ( 5094) covalent geometry : angle 0.55200 ( 6822) *********************** 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 145 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 131 time to evaluate : 0.812 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 331 LYS cc_start: 0.8835 (OUTLIER) cc_final: 0.8626 (mtmt) REVERT: C 369 LYS cc_start: 0.8221 (OUTLIER) cc_final: 0.7945 (ttmm) REVERT: C 375 LYS cc_start: 0.7974 (tttt) cc_final: 0.7541 (tppt) REVERT: E 347 LYS cc_start: 0.8592 (mttt) cc_final: 0.7864 (mppt) REVERT: E 369 LYS cc_start: 0.8456 (mttt) cc_final: 0.8157 (ttmp) REVERT: E 375 LYS cc_start: 0.8323 (tttt) cc_final: 0.7650 (tmmt) REVERT: D 345 ASP cc_start: 0.8055 (t0) cc_final: 0.7740 (t0) REVERT: D 375 LYS cc_start: 0.7970 (tttt) cc_final: 0.7628 (tppt) REVERT: F 347 LYS cc_start: 0.8552 (mttt) cc_final: 0.7826 (mppt) REVERT: F 375 LYS cc_start: 0.8409 (tttt) cc_final: 0.7745 (tmmt) REVERT: G 309 VAL cc_start: 0.8621 (t) cc_final: 0.8250 (p) REVERT: G 372 GLU cc_start: 0.8227 (OUTLIER) cc_final: 0.7929 (mt-10) REVERT: H 375 LYS cc_start: 0.8084 (tttt) cc_final: 0.7604 (tppt) REVERT: I 309 VAL cc_start: 0.8650 (OUTLIER) cc_final: 0.8327 (p) REVERT: I 347 LYS cc_start: 0.8532 (mttt) cc_final: 0.7771 (mppt) REVERT: I 369 LYS cc_start: 0.8427 (mttt) cc_final: 0.8134 (ttmp) REVERT: I 375 LYS cc_start: 0.8387 (tttt) cc_final: 0.7715 (tmmt) outliers start: 14 outliers final: 7 residues processed: 139 average time/residue: 2.7487 time to fit residues: 395.7290 Evaluate side-chains 135 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 124 time to evaluate : 0.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 331 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 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 I residue 309 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 61 optimal weight: 0.5980 chunk 50 optimal weight: 10.0000 chunk 20 optimal weight: 10.0000 chunk 62 optimal weight: 5.9990 chunk 46 optimal weight: 0.5980 chunk 52 optimal weight: 5.9990 chunk 4 optimal weight: 5.9990 chunk 39 optimal weight: 5.9990 chunk 23 optimal weight: 7.9990 chunk 48 optimal weight: 4.9990 chunk 27 optimal weight: 9.9990 overall best weight: 3.6386 ------------------------------------------------------------------------------- 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 = 0.4102 r_free = 0.4102 target = 0.159162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.134966 restraints weight = 18305.877| |-----------------------------------------------------------------------------| r_work (start): 0.3710 rms_B_bonded: 1.79 r_work: 0.3636 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.3562 rms_B_bonded: 2.97 restraints_weight: 0.2500 r_work (final): 0.3562 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8556 moved from start: 0.5944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 5094 Z= 0.178 Angle : 0.525 5.616 6822 Z= 0.275 Chirality : 0.051 0.142 774 Planarity : 0.003 0.021 864 Dihedral : 5.169 16.439 666 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 1.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 1.91 % Allowed : 22.74 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.27 (0.27), residues: 639 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.72 (0.20), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS H 374 PHE 0.006 0.001 PHE C 346 TYR 0.012 0.002 TYR D 310 ARG 0.003 0.000 ARG E 349 Details of bonding type rmsd hydrogen bonds : bond 0.02272 ( 128) hydrogen bonds : angle 4.46218 ( 384) covalent geometry : bond 0.00375 ( 5094) covalent geometry : angle 0.52525 ( 6822) *********************** 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 141 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 130 time to evaluate : 0.955 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 369 LYS cc_start: 0.8219 (OUTLIER) cc_final: 0.7919 (ttmm) REVERT: C 375 LYS cc_start: 0.7921 (tttt) cc_final: 0.7504 (tppt) REVERT: E 347 LYS cc_start: 0.8574 (mttt) cc_final: 0.7840 (mppt) REVERT: E 369 LYS cc_start: 0.8445 (mttt) cc_final: 0.8144 (ttmp) REVERT: E 375 LYS cc_start: 0.8322 (tttt) cc_final: 0.7661 (tmmt) REVERT: B 369 LYS cc_start: 0.8293 (OUTLIER) cc_final: 0.7799 (ttmm) REVERT: D 345 ASP cc_start: 0.8051 (t0) cc_final: 0.7740 (t0) REVERT: D 375 LYS cc_start: 0.7950 (tttt) cc_final: 0.7630 (tppt) REVERT: F 347 LYS cc_start: 0.8548 (mttt) cc_final: 0.7838 (mppt) REVERT: F 375 LYS cc_start: 0.8398 (tttt) cc_final: 0.7747 (tmmt) REVERT: G 309 VAL cc_start: 0.8616 (t) cc_final: 0.8236 (p) REVERT: G 372 GLU cc_start: 0.8208 (mm-30) cc_final: 0.7932 (mt-10) REVERT: H 375 LYS cc_start: 0.8061 (tttt) cc_final: 0.7581 (tppt) REVERT: I 309 VAL cc_start: 0.8615 (t) cc_final: 0.8268 (p) REVERT: I 347 LYS cc_start: 0.8536 (mttt) cc_final: 0.7780 (mppt) REVERT: I 369 LYS cc_start: 0.8420 (mttt) cc_final: 0.8138 (ttmp) REVERT: I 375 LYS cc_start: 0.8352 (tttt) cc_final: 0.7697 (tmmt) outliers start: 11 outliers final: 7 residues processed: 136 average time/residue: 2.8798 time to fit residues: 405.3380 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 : 0.943 ------------------------------------------------------------------------------- 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 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 7 optimal weight: 6.9990 chunk 39 optimal weight: 3.9990 chunk 15 optimal weight: 4.9990 chunk 21 optimal weight: 10.0000 chunk 25 optimal weight: 2.9990 chunk 13 optimal weight: 0.8980 chunk 49 optimal weight: 6.9990 chunk 55 optimal weight: 5.9990 chunk 59 optimal weight: 1.9990 chunk 10 optimal weight: 9.9990 chunk 14 optimal weight: 0.8980 overall best weight: 2.1586 ------------------------------------------------------------------------------- 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 = 0.4127 r_free = 0.4127 target = 0.160790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.136690 restraints weight = 18165.919| |-----------------------------------------------------------------------------| r_work (start): 0.3745 rms_B_bonded: 1.78 r_work: 0.3672 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.3597 rms_B_bonded: 2.97 restraints_weight: 0.2500 r_work (final): 0.3597 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8536 moved from start: 0.5984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5094 Z= 0.125 Angle : 0.497 5.782 6822 Z= 0.259 Chirality : 0.051 0.140 774 Planarity : 0.002 0.018 864 Dihedral : 4.896 15.111 666 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 1.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Rotamer: Outliers : 1.74 % Allowed : 24.13 % Favored : 74.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.20 (0.27), residues: 639 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.67 (0.21), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS H 374 PHE 0.007 0.001 PHE C 346 TYR 0.009 0.001 TYR G 310 ARG 0.002 0.000 ARG E 349 Details of bonding type rmsd hydrogen bonds : bond 0.01999 ( 128) hydrogen bonds : angle 4.19784 ( 384) covalent geometry : bond 0.00274 ( 5094) covalent geometry : angle 0.49730 ( 6822) *********************** 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 141 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 131 time to evaluate : 1.090 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 369 LYS cc_start: 0.8187 (OUTLIER) cc_final: 0.7889 (ttmm) REVERT: C 375 LYS cc_start: 0.7916 (tttt) cc_final: 0.7483 (tppt) REVERT: E 347 LYS cc_start: 0.8566 (mttt) cc_final: 0.7630 (ttpt) REVERT: E 369 LYS cc_start: 0.8361 (mttt) cc_final: 0.8066 (ttmp) REVERT: E 375 LYS cc_start: 0.8309 (tttt) cc_final: 0.7654 (tmmt) REVERT: D 345 ASP cc_start: 0.8056 (t0) cc_final: 0.7765 (t0) REVERT: D 375 LYS cc_start: 0.7973 (tttt) cc_final: 0.7688 (tppt) REVERT: F 347 LYS cc_start: 0.8525 (mttt) cc_final: 0.7812 (mppt) REVERT: F 375 LYS cc_start: 0.8414 (tttt) cc_final: 0.7740 (tmmt) REVERT: G 372 GLU cc_start: 0.8142 (OUTLIER) cc_final: 0.7940 (mt-10) REVERT: H 375 LYS cc_start: 0.8046 (tttt) cc_final: 0.7569 (tppt) REVERT: I 309 VAL cc_start: 0.8661 (OUTLIER) cc_final: 0.8260 (p) REVERT: I 347 LYS cc_start: 0.8526 (mttt) cc_final: 0.7766 (mppt) REVERT: I 369 LYS cc_start: 0.8355 (mttt) cc_final: 0.8087 (ttmp) REVERT: I 375 LYS cc_start: 0.8302 (tttt) cc_final: 0.7653 (tmmt) outliers start: 10 outliers final: 5 residues processed: 134 average time/residue: 2.8882 time to fit residues: 402.5316 Evaluate side-chains 132 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 124 time to evaluate : 0.861 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain G residue 372 GLU 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 28 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 59 optimal weight: 0.8980 chunk 45 optimal weight: 0.9980 chunk 7 optimal weight: 3.9990 chunk 57 optimal weight: 8.9990 chunk 51 optimal weight: 4.9990 chunk 11 optimal weight: 4.9990 chunk 10 optimal weight: 5.9990 chunk 27 optimal weight: 10.0000 chunk 23 optimal weight: 7.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.160375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.136213 restraints weight = 18292.503| |-----------------------------------------------------------------------------| r_work (start): 0.3738 rms_B_bonded: 1.79 r_work: 0.3665 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.3590 rms_B_bonded: 2.98 restraints_weight: 0.2500 r_work (final): 0.3590 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8539 moved from start: 0.5967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 5094 Z= 0.130 Angle : 0.501 5.840 6822 Z= 0.261 Chirality : 0.051 0.140 774 Planarity : 0.002 0.018 864 Dihedral : 4.831 14.744 666 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 1.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Rotamer: Outliers : 1.74 % Allowed : 24.13 % Favored : 74.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.18 (0.27), residues: 639 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.65 (0.21), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS C 374 PHE 0.007 0.001 PHE H 346 TYR 0.009 0.001 TYR H 310 ARG 0.002 0.000 ARG E 349 Details of bonding type rmsd hydrogen bonds : bond 0.02016 ( 128) hydrogen bonds : angle 4.15148 ( 384) covalent geometry : bond 0.00287 ( 5094) covalent geometry : angle 0.50097 ( 6822) ********************** 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 139 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 129 time to evaluate : 0.920 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 369 LYS cc_start: 0.8202 (OUTLIER) cc_final: 0.7904 (ttmm) REVERT: C 375 LYS cc_start: 0.7910 (tttt) cc_final: 0.7498 (tppt) REVERT: E 347 LYS cc_start: 0.8569 (mttt) cc_final: 0.7625 (ttpt) REVERT: E 369 LYS cc_start: 0.8394 (mttt) cc_final: 0.8100 (ttmp) REVERT: E 375 LYS cc_start: 0.8299 (tttt) cc_final: 0.7653 (tmmt) REVERT: D 345 ASP cc_start: 0.8054 (t0) cc_final: 0.7762 (t0) REVERT: D 375 LYS cc_start: 0.7972 (tttt) cc_final: 0.7679 (tppt) REVERT: F 347 LYS cc_start: 0.8531 (mttt) cc_final: 0.7818 (mppt) REVERT: F 375 LYS cc_start: 0.8424 (tttt) cc_final: 0.7735 (tmmt) REVERT: G 372 GLU cc_start: 0.8139 (OUTLIER) cc_final: 0.7937 (mt-10) REVERT: H 375 LYS cc_start: 0.8035 (tttt) cc_final: 0.7564 (tppt) REVERT: I 347 LYS cc_start: 0.8527 (mttt) cc_final: 0.7770 (mppt) REVERT: I 369 LYS cc_start: 0.8373 (mttt) cc_final: 0.8103 (ttmp) REVERT: I 375 LYS cc_start: 0.8303 (tttt) cc_final: 0.7630 (tmmt) outliers start: 10 outliers final: 5 residues processed: 133 average time/residue: 2.8103 time to fit residues: 387.1378 Evaluate side-chains 134 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 127 time to evaluate : 0.809 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain G residue 372 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 0 optimal weight: 10.0000 chunk 41 optimal weight: 4.9990 chunk 25 optimal weight: 0.6980 chunk 23 optimal weight: 7.9990 chunk 17 optimal weight: 7.9990 chunk 39 optimal weight: 0.9990 chunk 57 optimal weight: 7.9990 chunk 34 optimal weight: 6.9990 chunk 20 optimal weight: 0.9990 chunk 7 optimal weight: 0.9980 chunk 46 optimal weight: 9.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- 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 = 0.4144 r_free = 0.4144 target = 0.162398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.138402 restraints weight = 18233.903| |-----------------------------------------------------------------------------| r_work (start): 0.3760 rms_B_bonded: 1.78 r_work: 0.3686 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.3612 rms_B_bonded: 3.00 restraints_weight: 0.2500 r_work (final): 0.3612 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8526 moved from start: 0.6065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 5094 Z= 0.109 Angle : 0.487 5.837 6822 Z= 0.253 Chirality : 0.051 0.139 774 Planarity : 0.002 0.018 864 Dihedral : 4.680 13.787 666 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 1.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Rotamer: Outliers : 1.22 % Allowed : 24.65 % Favored : 74.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.16 (0.27), residues: 639 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.63 (0.21), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS H 374 PHE 0.005 0.001 PHE H 346 TYR 0.007 0.001 TYR H 310 ARG 0.002 0.000 ARG E 349 Details of bonding type rmsd hydrogen bonds : bond 0.01885 ( 128) hydrogen bonds : angle 4.02734 ( 384) covalent geometry : bond 0.00250 ( 5094) covalent geometry : angle 0.48673 ( 6822) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10896.47 seconds wall clock time: 188 minutes 22.95 seconds (11302.95 seconds total)