Starting phenix.real_space_refine on Fri Aug 22 19:04:55 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8q8z_18266/08_2025/8q8z_18266.cif Found real_map, /net/cci-nas-00/data/ceres_data/8q8z_18266/08_2025/8q8z_18266.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.16 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8q8z_18266/08_2025/8q8z_18266.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8q8z_18266/08_2025/8q8z_18266.map" model { file = "/net/cci-nas-00/data/ceres_data/8q8z_18266/08_2025/8q8z_18266.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8q8z_18266/08_2025/8q8z_18266.cif" } resolution = 3.16 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 6 5.16 5 C 2160 2.51 5 N 636 2.21 5 O 642 1.98 5 H 3588 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 7032 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1172 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "C" Number of atoms: 1172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1172 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "E" Number of atoms: 1172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1172 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "B" Number of atoms: 1172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1172 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "D" Number of atoms: 1172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1172 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "F" Number of atoms: 1172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1172 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Time building chain proxies: 1.18, per 1000 atoms: 0.17 Number of scatterers: 7032 At special positions: 0 Unit cell: (146.672, 113.712, 50.264, 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 6 16.00 O 642 8.00 N 636 7.00 C 2160 6.00 H 3588 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.43 Conformation dependent library (CDL) restraints added in 228.3 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 792 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 18 sheets defined 0.0% alpha, 51.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.23 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'C' and resid 306 through 310 removed outlier: 6.485A pdb=" N VAL A 306 " --> pdb=" O GLN E 307 " (cutoff:3.500A) removed outlier: 7.813A pdb=" N VAL E 309 " --> pdb=" O VAL A 306 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N ILE A 308 " --> pdb=" O VAL E 309 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 313 through 314 removed outlier: 6.855A pdb=" N VAL A 313 " --> pdb=" O ASP C 314 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 317 through 325 removed outlier: 6.288A pdb=" N LYS A 317 " --> pdb=" O VAL C 318 " (cutoff:3.500A) removed outlier: 8.047A pdb=" N SER C 320 " --> pdb=" O LYS A 317 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N THR A 319 " --> pdb=" O SER C 320 " (cutoff:3.500A) removed outlier: 8.069A pdb=" N CYS C 322 " --> pdb=" O THR A 319 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N LYS A 321 " --> pdb=" O CYS C 322 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N SER C 324 " --> pdb=" O LYS A 321 " (cutoff:3.500A) removed outlier: 5.977A pdb=" N GLY A 323 " --> pdb=" O SER C 324 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N VAL A 318 " --> pdb=" O THR E 319 " (cutoff:3.500A) removed outlier: 8.027A pdb=" N LYS E 321 " --> pdb=" O VAL A 318 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N SER A 320 " --> pdb=" O LYS E 321 " (cutoff:3.500A) removed outlier: 7.898A pdb=" N GLY E 323 " --> pdb=" O SER A 320 " (cutoff:3.500A) removed outlier: 5.955A pdb=" N CYS A 322 " --> pdb=" O GLY E 323 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N LEU E 325 " --> pdb=" O CYS A 322 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N SER A 324 " --> pdb=" O LEU E 325 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 328 through 330 removed outlier: 6.850A pdb=" N ILE A 328 " --> pdb=" O HIS C 329 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 333 through 334 removed outlier: 6.730A pdb=" N GLY A 333 " --> pdb=" O GLY C 334 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 337 through 342 removed outlier: 6.576A pdb=" N GLU A 338 " --> pdb=" O VAL C 339 " (cutoff:3.500A) removed outlier: 7.996A pdb=" N SER C 341 " --> pdb=" O GLU A 338 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N LYS A 340 " --> pdb=" O SER C 341 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N VAL A 337 " --> pdb=" O GLU E 338 " (cutoff:3.500A) removed outlier: 8.259A pdb=" N LYS E 340 " --> pdb=" O VAL A 337 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N VAL A 339 " --> pdb=" O LYS E 340 " (cutoff:3.500A) removed outlier: 7.953A pdb=" N GLU E 342 " --> pdb=" O VAL A 339 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N SER A 341 " --> pdb=" O GLU E 342 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'C' and resid 350 through 354 removed outlier: 6.375A pdb=" N VAL A 350 " --> pdb=" O GLN E 351 " (cutoff:3.500A) removed outlier: 8.056A pdb=" N LYS E 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N SER A 352 " --> pdb=" O LYS E 353 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 357 through 362 removed outlier: 6.226A pdb=" N ASP A 358 " --> pdb=" O ASN C 359 " (cutoff:3.500A) removed outlier: 7.956A pdb=" N THR C 361 " --> pdb=" O ASP A 358 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N ILE A 360 " --> pdb=" O THR C 361 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 368 through 378 removed outlier: 6.672A pdb=" N LYS A 369 " --> pdb=" O LYS C 370 " (cutoff:3.500A) removed outlier: 7.591A pdb=" N GLU C 372 " --> pdb=" O LYS A 369 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N ILE A 371 " --> pdb=" O GLU C 372 " (cutoff:3.500A) removed outlier: 8.073A pdb=" N HIS C 374 " --> pdb=" O ILE A 371 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N THR A 373 " --> pdb=" O HIS C 374 " (cutoff:3.500A) removed outlier: 7.612A pdb=" N LEU C 376 " --> pdb=" O THR A 373 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N LYS A 375 " --> pdb=" O LEU C 376 " (cutoff:3.500A) removed outlier: 7.935A pdb=" N PHE C 378 " --> pdb=" O LYS A 375 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N THR A 377 " --> pdb=" O PHE C 378 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 306 through 310 removed outlier: 6.508A pdb=" N GLN B 307 " --> pdb=" O ILE D 308 " (cutoff:3.500A) removed outlier: 7.750A pdb=" N TYR D 310 " --> pdb=" O GLN B 307 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N VAL B 309 " --> pdb=" O TYR D 310 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 313 through 314 removed outlier: 6.861A pdb=" N VAL B 313 " --> pdb=" O ASP D 314 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 317 through 325 removed outlier: 6.177A pdb=" N LYS B 317 " --> pdb=" O VAL D 318 " (cutoff:3.500A) removed outlier: 8.113A pdb=" N SER D 320 " --> pdb=" O LYS B 317 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N THR B 319 " --> pdb=" O SER D 320 " (cutoff:3.500A) removed outlier: 8.103A pdb=" N CYS D 322 " --> pdb=" O THR B 319 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N LYS B 321 " --> pdb=" O CYS D 322 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N SER D 324 " --> pdb=" O LYS B 321 " (cutoff:3.500A) removed outlier: 5.937A pdb=" N GLY B 323 " --> pdb=" O SER D 324 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 328 through 330 removed outlier: 6.745A pdb=" N ILE B 328 " --> pdb=" O HIS D 329 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 337 through 342 removed outlier: 6.542A pdb=" N VAL B 337 " --> pdb=" O GLU F 338 " (cutoff:3.500A) removed outlier: 7.994A pdb=" N LYS F 340 " --> pdb=" O VAL B 337 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N VAL B 339 " --> pdb=" O LYS F 340 " (cutoff:3.500A) removed outlier: 7.911A pdb=" N GLU F 342 " --> pdb=" O VAL B 339 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N SER B 341 " --> pdb=" O GLU F 342 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 345 through 346 removed outlier: 6.667A pdb=" N ASP B 345 " --> pdb=" O PHE D 346 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 350 through 354 removed outlier: 6.469A pdb=" N GLN B 351 " --> pdb=" O SER D 352 " (cutoff:3.500A) removed outlier: 7.938A pdb=" N ILE D 354 " --> pdb=" O GLN B 351 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N LYS B 353 " --> pdb=" O ILE D 354 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 359 through 362 Processing sheet with id=AB9, first strand: chain 'D' and resid 369 through 378 removed outlier: 6.473A pdb=" N LYS B 369 " --> pdb=" O LYS D 370 " (cutoff:3.500A) removed outlier: 7.943A pdb=" N GLU D 372 " --> pdb=" O LYS B 369 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N ILE B 371 " --> pdb=" O GLU D 372 " (cutoff:3.500A) removed outlier: 7.904A pdb=" N HIS D 374 " --> pdb=" O ILE B 371 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N THR B 373 " --> pdb=" O HIS D 374 " (cutoff:3.500A) removed outlier: 8.019A pdb=" N LEU D 376 " --> pdb=" O THR B 373 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N LYS B 375 " --> pdb=" O LEU D 376 " (cutoff:3.500A) removed outlier: 8.230A pdb=" N PHE D 378 " --> pdb=" O LYS B 375 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N THR B 377 " --> pdb=" O PHE D 378 " (cutoff:3.500A) 67 hydrogen bonds defined for protein. 201 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.35 Time building geometry restraints manager: 0.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.95 - 1.12: 3582 1.12 - 1.29: 570 1.29 - 1.47: 1140 1.47 - 1.64: 1788 1.64 - 1.81: 6 Bond restraints: 7086 Sorted by residual: bond pdb=" N SER A 305 " pdb=" H SER A 305 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.70e+01 bond pdb=" N SER E 305 " pdb=" H SER E 305 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.70e+01 bond pdb=" NE2 HIS D 330 " pdb=" HE2 HIS D 330 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.70e+01 bond pdb=" CD2 HIS E 362 " pdb=" HD2 HIS E 362 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.69e+01 bond pdb=" N LYS C 311 " pdb=" H LYS C 311 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.69e+01 ... (remaining 7081 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.36: 10591 2.36 - 4.71: 1720 4.71 - 7.07: 565 7.07 - 9.42: 30 9.42 - 11.78: 6 Bond angle restraints: 12912 Sorted by residual: angle pdb=" CA ASP B 358 " pdb=" CB ASP B 358 " pdb=" CG ASP B 358 " ideal model delta sigma weight residual 112.60 118.37 -5.77 1.00e+00 1.00e+00 3.33e+01 angle pdb=" CA ASP E 358 " pdb=" CB ASP E 358 " pdb=" CG ASP E 358 " ideal model delta sigma weight residual 112.60 117.10 -4.50 1.00e+00 1.00e+00 2.03e+01 angle pdb=" CA ASP C 358 " pdb=" CB ASP C 358 " pdb=" CG ASP C 358 " ideal model delta sigma weight residual 112.60 117.06 -4.46 1.00e+00 1.00e+00 1.99e+01 angle pdb=" CB HIS E 329 " pdb=" CG HIS E 329 " pdb=" CD2 HIS E 329 " ideal model delta sigma weight residual 131.20 125.44 5.76 1.30e+00 5.92e-01 1.96e+01 angle pdb=" CA ASP F 358 " pdb=" CB ASP F 358 " pdb=" CG ASP F 358 " ideal model delta sigma weight residual 112.60 117.03 -4.43 1.00e+00 1.00e+00 1.96e+01 ... (remaining 12907 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.39: 2936 17.39 - 34.77: 164 34.77 - 52.16: 71 52.16 - 69.54: 87 69.54 - 86.93: 6 Dihedral angle restraints: 3264 sinusoidal: 1866 harmonic: 1398 Sorted by residual: dihedral pdb=" C LYS F 331 " pdb=" N LYS F 331 " pdb=" CA LYS F 331 " pdb=" CB LYS F 331 " ideal model delta harmonic sigma weight residual -122.60 -132.47 9.87 0 2.50e+00 1.60e-01 1.56e+01 dihedral pdb=" C LYS B 331 " pdb=" N LYS B 331 " pdb=" CA LYS B 331 " pdb=" CB LYS B 331 " ideal model delta harmonic sigma weight residual -122.60 -131.81 9.21 0 2.50e+00 1.60e-01 1.36e+01 dihedral pdb=" C LYS E 331 " pdb=" N LYS E 331 " pdb=" CA LYS E 331 " pdb=" CB LYS E 331 " ideal model delta harmonic sigma weight residual -122.60 -131.71 9.11 0 2.50e+00 1.60e-01 1.33e+01 ... (remaining 3261 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.067: 314 0.067 - 0.133: 173 0.133 - 0.199: 29 0.199 - 0.265: 5 0.265 - 0.332: 7 Chirality restraints: 528 Sorted by residual: chirality pdb=" CA LYS F 331 " pdb=" N LYS F 331 " pdb=" C LYS F 331 " pdb=" CB LYS F 331 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.75e+00 chirality pdb=" CA LYS B 331 " pdb=" N LYS B 331 " pdb=" C LYS B 331 " pdb=" CB LYS B 331 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.66e+00 chirality pdb=" CA LYS E 331 " pdb=" N LYS E 331 " pdb=" C LYS E 331 " pdb=" CB LYS E 331 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.65e+00 ... (remaining 525 not shown) Planarity restraints: 1020 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR F 310 " 0.141 2.00e-02 2.50e+03 6.19e-02 1.15e+02 pdb=" CG TYR F 310 " -0.019 2.00e-02 2.50e+03 pdb=" CD1 TYR F 310 " -0.046 2.00e-02 2.50e+03 pdb=" CD2 TYR F 310 " -0.042 2.00e-02 2.50e+03 pdb=" CE1 TYR F 310 " -0.043 2.00e-02 2.50e+03 pdb=" CE2 TYR F 310 " -0.027 2.00e-02 2.50e+03 pdb=" CZ TYR F 310 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR F 310 " 0.129 2.00e-02 2.50e+03 pdb=" HD1 TYR F 310 " -0.013 2.00e-02 2.50e+03 pdb=" HD2 TYR F 310 " -0.040 2.00e-02 2.50e+03 pdb=" HE1 TYR F 310 " -0.027 2.00e-02 2.50e+03 pdb=" HE2 TYR F 310 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR D 310 " 0.123 2.00e-02 2.50e+03 5.16e-02 7.98e+01 pdb=" CG TYR D 310 " -0.031 2.00e-02 2.50e+03 pdb=" CD1 TYR D 310 " -0.042 2.00e-02 2.50e+03 pdb=" CD2 TYR D 310 " -0.045 2.00e-02 2.50e+03 pdb=" CE1 TYR D 310 " -0.035 2.00e-02 2.50e+03 pdb=" CE2 TYR D 310 " -0.021 2.00e-02 2.50e+03 pdb=" CZ TYR D 310 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR D 310 " 0.096 2.00e-02 2.50e+03 pdb=" HD1 TYR D 310 " -0.004 2.00e-02 2.50e+03 pdb=" HD2 TYR D 310 " -0.030 2.00e-02 2.50e+03 pdb=" HE1 TYR D 310 " -0.014 2.00e-02 2.50e+03 pdb=" HE2 TYR D 310 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN A 336 " 0.071 2.00e-02 2.50e+03 6.87e-02 7.08e+01 pdb=" CD GLN A 336 " -0.018 2.00e-02 2.50e+03 pdb=" OE1 GLN A 336 " -0.053 2.00e-02 2.50e+03 pdb=" NE2 GLN A 336 " -0.061 2.00e-02 2.50e+03 pdb="HE21 GLN A 336 " -0.056 2.00e-02 2.50e+03 pdb="HE22 GLN A 336 " 0.116 2.00e-02 2.50e+03 ... (remaining 1017 not shown) Histogram of nonbonded interaction distances: 1.56 - 2.17: 597 2.17 - 2.78: 12050 2.78 - 3.39: 18264 3.39 - 3.99: 25160 3.99 - 4.60: 34497 Nonbonded interactions: 90568 Sorted by model distance: nonbonded pdb=" OD1 ASP F 314 " pdb=" HG SER F 316 " model vdw 1.565 2.450 nonbonded pdb=" OD1 ASP B 314 " pdb=" HG SER B 316 " model vdw 1.583 2.450 nonbonded pdb=" OD1 ASP E 314 " pdb=" HG SER E 316 " model vdw 1.589 2.450 nonbonded pdb=" OD1 ASP A 314 " pdb=" HG SER A 316 " model vdw 1.615 2.450 nonbonded pdb=" OD1 ASP C 314 " pdb=" HG SER C 316 " model vdw 1.616 2.450 ... (remaining 90563 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.290 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: 0.040 Extract box with map and model: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 7.470 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.010 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:1.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7328 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 0.036 3498 Z= 0.689 Angle : 1.876 7.705 4680 Z= 1.233 Chirality : 0.083 0.332 528 Planarity : 0.010 0.072 594 Dihedral : 10.800 86.926 1344 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 0.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.15 (0.33), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.63 (0.26), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.002 ARG B 379 TYR 0.127 0.043 TYR F 310 PHE 0.033 0.009 PHE B 346 HIS 0.012 0.003 HIS B 362 Details of bonding type rmsd covalent geometry : bond 0.01098 ( 3498) covalent geometry : angle 1.87637 ( 4680) hydrogen bonds : bond 0.06474 ( 67) hydrogen bonds : angle 7.78214 ( 201) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 125 time to evaluate : 0.192 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: A 340 LYS cc_start: 0.7490 (tttt) cc_final: 0.7017 (ttmt) REVERT: A 375 LYS cc_start: 0.7480 (tttt) cc_final: 0.7116 (tttm) REVERT: C 311 LYS cc_start: 0.8435 (mttt) cc_final: 0.8025 (mtmt) REVERT: C 317 LYS cc_start: 0.7723 (mttt) cc_final: 0.7465 (mtpt) REVERT: C 327 ASN cc_start: 0.8060 (m-40) cc_final: 0.7756 (m110) REVERT: C 340 LYS cc_start: 0.8217 (tttt) cc_final: 0.7634 (ttmt) REVERT: C 370 LYS cc_start: 0.7845 (tttm) cc_final: 0.7622 (tttt) REVERT: C 372 GLU cc_start: 0.7660 (tt0) cc_final: 0.7373 (tt0) REVERT: C 375 LYS cc_start: 0.8195 (tttt) cc_final: 0.7883 (tttp) REVERT: E 311 LYS cc_start: 0.7968 (mttt) cc_final: 0.7280 (tppt) REVERT: E 349 ARG cc_start: 0.6304 (mtm180) cc_final: 0.5911 (mmm160) REVERT: B 348 ASP cc_start: 0.8291 (t0) cc_final: 0.8003 (t0) REVERT: B 351 GLN cc_start: 0.7106 (tt0) cc_final: 0.6608 (mt0) REVERT: B 375 LYS cc_start: 0.7659 (tttt) cc_final: 0.7362 (ttmt) REVERT: D 311 LYS cc_start: 0.8023 (mttt) cc_final: 0.7754 (pttp) REVERT: D 317 LYS cc_start: 0.7895 (mttt) cc_final: 0.7331 (mtmt) REVERT: D 340 LYS cc_start: 0.7997 (tttt) cc_final: 0.7583 (mtpt) REVERT: D 351 GLN cc_start: 0.8048 (tt0) cc_final: 0.7480 (mt0) REVERT: D 375 LYS cc_start: 0.8017 (tttt) cc_final: 0.7772 (ttmt) REVERT: F 311 LYS cc_start: 0.7765 (mttt) cc_final: 0.7269 (mmtm) REVERT: F 351 GLN cc_start: 0.7375 (tt0) cc_final: 0.6881 (mt0) REVERT: F 375 LYS cc_start: 0.7960 (tttt) cc_final: 0.7660 (ttmt) REVERT: F 378 PHE cc_start: 0.7745 (t80) cc_final: 0.7452 (t80) outliers start: 0 outliers final: 0 residues processed: 125 average time/residue: 0.2966 time to fit residues: 40.8496 Evaluate side-chains 88 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 88 time to evaluate : 0.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 24 optimal weight: 5.9990 chunk 26 optimal weight: 5.9990 chunk 2 optimal weight: 1.9990 chunk 16 optimal weight: 0.7980 chunk 32 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 chunk 22 optimal weight: 5.9990 chunk 37 optimal weight: 1.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 330 HIS B 327 ASN D 327 ASN F 327 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4210 r_free = 0.4210 target = 0.139356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.122405 restraints weight = 12779.627| |-----------------------------------------------------------------------------| r_work (start): 0.3959 rms_B_bonded: 2.00 r_work: 0.3863 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3770 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.3770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.3337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3498 Z= 0.114 Angle : 0.531 3.941 4680 Z= 0.270 Chirality : 0.052 0.137 528 Planarity : 0.004 0.036 594 Dihedral : 4.876 13.067 462 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 1.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.76 % Allowed : 4.29 % Favored : 94.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.34 (0.36), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.01 (0.28), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 349 TYR 0.011 0.002 TYR D 310 PHE 0.010 0.001 PHE F 346 HIS 0.002 0.001 HIS C 330 Details of bonding type rmsd covalent geometry : bond 0.00263 ( 3498) covalent geometry : angle 0.53110 ( 4680) hydrogen bonds : bond 0.01827 ( 67) hydrogen bonds : angle 5.13757 ( 201) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 79 time to evaluate : 0.201 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 342 GLU cc_start: 0.7385 (mp0) cc_final: 0.7180 (mp0) REVERT: A 375 LYS cc_start: 0.8062 (tttt) cc_final: 0.7703 (tttm) REVERT: C 311 LYS cc_start: 0.8668 (mttt) cc_final: 0.8214 (mtmt) REVERT: C 349 ARG cc_start: 0.7852 (mtt90) cc_final: 0.7624 (mtt90) REVERT: C 375 LYS cc_start: 0.8462 (tttt) cc_final: 0.8167 (tttp) REVERT: E 311 LYS cc_start: 0.8099 (mttt) cc_final: 0.7406 (tppt) REVERT: E 348 ASP cc_start: 0.8053 (t0) cc_final: 0.7789 (t0) REVERT: E 349 ARG cc_start: 0.6695 (mtm180) cc_final: 0.6342 (mmp-170) REVERT: B 348 ASP cc_start: 0.8789 (t0) cc_final: 0.8566 (t70) REVERT: B 351 GLN cc_start: 0.8140 (tt0) cc_final: 0.7862 (mt0) REVERT: B 375 LYS cc_start: 0.8272 (tttt) cc_final: 0.7951 (ttmt) REVERT: D 311 LYS cc_start: 0.8501 (mttt) cc_final: 0.7978 (pttp) REVERT: F 311 LYS cc_start: 0.8176 (mttt) cc_final: 0.7842 (mttm) outliers start: 3 outliers final: 2 residues processed: 81 average time/residue: 0.3140 time to fit residues: 28.0550 Evaluate side-chains 63 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 61 time to evaluate : 0.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain C residue 324 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 6 optimal weight: 6.9990 chunk 28 optimal weight: 0.5980 chunk 12 optimal weight: 4.9990 chunk 22 optimal weight: 7.9990 chunk 38 optimal weight: 7.9990 chunk 20 optimal weight: 1.9990 chunk 21 optimal weight: 3.9990 chunk 39 optimal weight: 4.9990 chunk 1 optimal weight: 6.9990 chunk 27 optimal weight: 2.9990 chunk 41 optimal weight: 0.9980 overall best weight: 2.1186 ------------------------------------------------------------------------------- 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 = 0.4106 r_free = 0.4106 target = 0.128701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.112986 restraints weight = 13709.171| |-----------------------------------------------------------------------------| r_work (start): 0.3865 rms_B_bonded: 1.87 r_work: 0.3760 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.3672 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.3672 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.4346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 3498 Z= 0.140 Angle : 0.498 3.934 4680 Z= 0.253 Chirality : 0.051 0.129 528 Planarity : 0.003 0.029 594 Dihedral : 4.549 11.855 462 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 2.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Rotamer: Outliers : 0.76 % Allowed : 7.07 % Favored : 92.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.28 (0.37), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.97 (0.28), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 379 TYR 0.014 0.002 TYR F 310 PHE 0.009 0.001 PHE F 346 HIS 0.002 0.001 HIS E 374 Details of bonding type rmsd covalent geometry : bond 0.00308 ( 3498) covalent geometry : angle 0.49803 ( 4680) hydrogen bonds : bond 0.01385 ( 67) hydrogen bonds : angle 4.27766 ( 201) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 62 time to evaluate : 0.206 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 340 LYS cc_start: 0.8141 (tttt) cc_final: 0.7715 (ttmt) REVERT: A 342 GLU cc_start: 0.7401 (mp0) cc_final: 0.7200 (mp0) REVERT: A 375 LYS cc_start: 0.8217 (tttt) cc_final: 0.7937 (tttm) REVERT: C 311 LYS cc_start: 0.8676 (mttt) cc_final: 0.8240 (ttpt) REVERT: C 375 LYS cc_start: 0.8561 (tttt) cc_final: 0.8281 (tttp) REVERT: E 311 LYS cc_start: 0.8169 (mttt) cc_final: 0.7514 (tppt) REVERT: E 348 ASP cc_start: 0.7991 (t0) cc_final: 0.7790 (t0) REVERT: E 349 ARG cc_start: 0.6711 (mtm180) cc_final: 0.6403 (mmp-170) REVERT: B 351 GLN cc_start: 0.8268 (tt0) cc_final: 0.8040 (mt0) REVERT: B 375 LYS cc_start: 0.8431 (tttt) cc_final: 0.8107 (ttmt) REVERT: D 311 LYS cc_start: 0.8547 (mttt) cc_final: 0.8047 (pttp) REVERT: F 311 LYS cc_start: 0.8236 (mttt) cc_final: 0.7842 (mmtm) REVERT: F 375 LYS cc_start: 0.8425 (tttt) cc_final: 0.8113 (ttmt) outliers start: 3 outliers final: 2 residues processed: 64 average time/residue: 0.4122 time to fit residues: 28.5187 Evaluate side-chains 62 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 60 time to evaluate : 0.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain C residue 324 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 21 optimal weight: 8.9990 chunk 2 optimal weight: 4.9990 chunk 27 optimal weight: 6.9990 chunk 0 optimal weight: 7.9990 chunk 32 optimal weight: 0.5980 chunk 38 optimal weight: 5.9990 chunk 39 optimal weight: 4.9990 chunk 3 optimal weight: 8.9990 chunk 14 optimal weight: 6.9990 chunk 18 optimal weight: 1.9990 chunk 40 optimal weight: 0.9990 overall best weight: 2.7188 ------------------------------------------------------------------------------- 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 = 0.4072 r_free = 0.4072 target = 0.127869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.111754 restraints weight = 13847.465| |-----------------------------------------------------------------------------| r_work (start): 0.3822 rms_B_bonded: 1.90 r_work: 0.3727 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.3638 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.3638 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.4729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 3498 Z= 0.176 Angle : 0.495 3.937 4680 Z= 0.251 Chirality : 0.051 0.124 528 Planarity : 0.003 0.030 594 Dihedral : 4.573 10.937 462 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 2.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Rotamer: Outliers : 1.26 % Allowed : 6.31 % Favored : 92.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.45 (0.36), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.10 (0.28), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 349 TYR 0.012 0.003 TYR F 310 PHE 0.008 0.001 PHE B 346 HIS 0.002 0.001 HIS E 374 Details of bonding type rmsd covalent geometry : bond 0.00387 ( 3498) covalent geometry : angle 0.49476 ( 4680) hydrogen bonds : bond 0.01323 ( 67) hydrogen bonds : angle 3.99948 ( 201) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 72 time to evaluate : 0.206 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 340 LYS cc_start: 0.8196 (tttt) cc_final: 0.7740 (ttmt) REVERT: A 349 ARG cc_start: 0.7617 (mtp85) cc_final: 0.7410 (mtp85) REVERT: A 375 LYS cc_start: 0.8284 (tttt) cc_final: 0.7992 (tttm) REVERT: C 311 LYS cc_start: 0.8686 (mttt) cc_final: 0.8266 (ttpt) REVERT: C 340 LYS cc_start: 0.8489 (tttt) cc_final: 0.8078 (ttmt) REVERT: E 311 LYS cc_start: 0.8138 (mttt) cc_final: 0.7491 (tppt) REVERT: E 348 ASP cc_start: 0.8045 (t0) cc_final: 0.7817 (t0) REVERT: E 349 ARG cc_start: 0.6656 (mtm180) cc_final: 0.6172 (mmm160) REVERT: B 375 LYS cc_start: 0.8458 (tttt) cc_final: 0.8096 (ttmt) REVERT: D 311 LYS cc_start: 0.8538 (mttt) cc_final: 0.8012 (pttp) REVERT: D 321 LYS cc_start: 0.8534 (mttt) cc_final: 0.7947 (mtpt) REVERT: D 340 LYS cc_start: 0.8219 (tttt) cc_final: 0.7861 (mtpt) REVERT: D 375 LYS cc_start: 0.8553 (tttt) cc_final: 0.8255 (ttmt) REVERT: F 311 LYS cc_start: 0.8268 (mttt) cc_final: 0.7800 (mmtt) REVERT: F 375 LYS cc_start: 0.8366 (tttt) cc_final: 0.8020 (ttmt) outliers start: 5 outliers final: 4 residues processed: 75 average time/residue: 0.4311 time to fit residues: 34.9678 Evaluate side-chains 71 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 67 time to evaluate : 0.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain C residue 324 SER Chi-restraints excluded: chain F residue 348 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 34 optimal weight: 0.6980 chunk 9 optimal weight: 3.9990 chunk 39 optimal weight: 4.9990 chunk 25 optimal weight: 1.9990 chunk 32 optimal weight: 0.3980 chunk 6 optimal weight: 5.9990 chunk 14 optimal weight: 7.9990 chunk 33 optimal weight: 1.9990 chunk 16 optimal weight: 0.9980 chunk 36 optimal weight: 3.9990 chunk 29 optimal weight: 0.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- 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 = 0.4131 r_free = 0.4131 target = 0.133104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.116585 restraints weight = 13335.980| |-----------------------------------------------------------------------------| r_work (start): 0.3880 rms_B_bonded: 1.90 r_work: 0.3782 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.3694 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.3694 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.5099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 3498 Z= 0.084 Angle : 0.438 3.698 4680 Z= 0.217 Chirality : 0.051 0.124 528 Planarity : 0.003 0.035 594 Dihedral : 4.166 9.939 462 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 2.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.46 % Favored : 99.54 % Rotamer: Outliers : 1.01 % Allowed : 6.57 % Favored : 92.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.39 (0.37), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.05 (0.28), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 349 TYR 0.006 0.001 TYR A 310 PHE 0.006 0.001 PHE B 378 HIS 0.002 0.000 HIS B 362 Details of bonding type rmsd covalent geometry : bond 0.00186 ( 3498) covalent geometry : angle 0.43806 ( 4680) hydrogen bonds : bond 0.01056 ( 67) hydrogen bonds : angle 3.76651 ( 201) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 59 time to evaluate : 0.209 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 375 LYS cc_start: 0.8294 (tttt) cc_final: 0.8023 (tttm) REVERT: C 311 LYS cc_start: 0.8606 (mttt) cc_final: 0.8218 (ttpt) REVERT: E 311 LYS cc_start: 0.8023 (mttt) cc_final: 0.7481 (tppt) REVERT: E 347 LYS cc_start: 0.8551 (mttm) cc_final: 0.8053 (mptt) REVERT: E 348 ASP cc_start: 0.7998 (t0) cc_final: 0.7758 (t0) REVERT: E 349 ARG cc_start: 0.6623 (mtm180) cc_final: 0.6319 (mmp-170) REVERT: B 349 ARG cc_start: 0.8393 (mtt180) cc_final: 0.8126 (mtp180) REVERT: B 375 LYS cc_start: 0.8455 (tttt) cc_final: 0.8110 (ttmt) REVERT: D 311 LYS cc_start: 0.8493 (mttt) cc_final: 0.8025 (pttp) REVERT: F 311 LYS cc_start: 0.8205 (mttt) cc_final: 0.7614 (mmtm) REVERT: F 375 LYS cc_start: 0.8315 (tttt) cc_final: 0.7971 (ttmt) outliers start: 4 outliers final: 3 residues processed: 61 average time/residue: 0.4155 time to fit residues: 27.5459 Evaluate side-chains 60 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 57 time to evaluate : 0.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain C residue 324 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 33 optimal weight: 5.9990 chunk 23 optimal weight: 5.9990 chunk 39 optimal weight: 4.9990 chunk 1 optimal weight: 7.9990 chunk 32 optimal weight: 1.9990 chunk 28 optimal weight: 0.0370 chunk 18 optimal weight: 5.9990 chunk 38 optimal weight: 3.9990 chunk 26 optimal weight: 0.9980 chunk 29 optimal weight: 0.9980 chunk 31 optimal weight: 4.9990 overall best weight: 1.6062 ------------------------------------------------------------------------------- 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 = 0.4101 r_free = 0.4101 target = 0.130773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.114157 restraints weight = 13562.185| |-----------------------------------------------------------------------------| r_work (start): 0.3847 rms_B_bonded: 1.94 r_work: 0.3753 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.3666 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.3666 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.5222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 3498 Z= 0.116 Angle : 0.444 3.736 4680 Z= 0.222 Chirality : 0.051 0.122 528 Planarity : 0.003 0.039 594 Dihedral : 4.110 9.975 462 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 2.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 1.26 % Allowed : 6.57 % Favored : 92.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.43 (0.37), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.08 (0.28), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 349 TYR 0.008 0.002 TYR F 310 PHE 0.005 0.001 PHE B 378 HIS 0.002 0.000 HIS E 374 Details of bonding type rmsd covalent geometry : bond 0.00255 ( 3498) covalent geometry : angle 0.44441 ( 4680) hydrogen bonds : bond 0.01052 ( 67) hydrogen bonds : angle 3.64779 ( 201) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 59 time to evaluate : 0.201 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 340 LYS cc_start: 0.8201 (tttt) cc_final: 0.7721 (ttmt) REVERT: A 375 LYS cc_start: 0.8350 (tttt) cc_final: 0.8045 (tttp) REVERT: C 311 LYS cc_start: 0.8630 (mttt) cc_final: 0.8226 (ttpt) REVERT: C 375 LYS cc_start: 0.8602 (tttt) cc_final: 0.8319 (tttp) REVERT: E 311 LYS cc_start: 0.8095 (mttt) cc_final: 0.7443 (tppt) REVERT: E 347 LYS cc_start: 0.8561 (mttm) cc_final: 0.8043 (mptt) REVERT: E 348 ASP cc_start: 0.7984 (t0) cc_final: 0.7744 (t0) REVERT: E 349 ARG cc_start: 0.6635 (mtm180) cc_final: 0.6119 (mmm160) REVERT: B 375 LYS cc_start: 0.8457 (tttt) cc_final: 0.8085 (ttmt) REVERT: D 311 LYS cc_start: 0.8517 (mttt) cc_final: 0.8026 (pttp) REVERT: F 311 LYS cc_start: 0.8248 (mttt) cc_final: 0.7780 (mmtt) REVERT: F 375 LYS cc_start: 0.8352 (tttt) cc_final: 0.8015 (ttmt) outliers start: 5 outliers final: 5 residues processed: 62 average time/residue: 0.4023 time to fit residues: 27.1236 Evaluate side-chains 64 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 59 time to evaluate : 0.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain C residue 324 SER Chi-restraints excluded: chain F residue 348 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 37 optimal weight: 6.9990 chunk 17 optimal weight: 7.9990 chunk 24 optimal weight: 8.9990 chunk 4 optimal weight: 6.9990 chunk 12 optimal weight: 5.9990 chunk 19 optimal weight: 3.9990 chunk 26 optimal weight: 4.9990 chunk 3 optimal weight: 2.9990 chunk 41 optimal weight: 6.9990 chunk 25 optimal weight: 3.9990 chunk 11 optimal weight: 0.7980 overall best weight: 3.3588 ------------------------------------------------------------------------------- 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 = 0.4029 r_free = 0.4029 target = 0.125351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.109084 restraints weight = 13852.014| |-----------------------------------------------------------------------------| r_work (start): 0.3781 rms_B_bonded: 1.89 r_work: 0.3673 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.3583 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.3583 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.5319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 3498 Z= 0.210 Angle : 0.490 3.913 4680 Z= 0.251 Chirality : 0.051 0.122 528 Planarity : 0.004 0.037 594 Dihedral : 4.391 11.057 462 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 2.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 1.52 % Allowed : 6.06 % Favored : 92.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.70 (0.36), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.29 (0.28), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 349 TYR 0.012 0.003 TYR F 310 PHE 0.008 0.001 PHE B 346 HIS 0.003 0.001 HIS E 374 Details of bonding type rmsd covalent geometry : bond 0.00463 ( 3498) covalent geometry : angle 0.49019 ( 4680) hydrogen bonds : bond 0.01253 ( 67) hydrogen bonds : angle 3.75685 ( 201) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 71 time to evaluate : 0.211 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 340 LYS cc_start: 0.8263 (tttt) cc_final: 0.7789 (ttmt) REVERT: A 375 LYS cc_start: 0.8376 (tttt) cc_final: 0.8071 (tttp) REVERT: C 311 LYS cc_start: 0.8671 (mttt) cc_final: 0.8289 (ttpt) REVERT: C 340 LYS cc_start: 0.8549 (tttt) cc_final: 0.8156 (ttmt) REVERT: C 375 LYS cc_start: 0.8633 (tttt) cc_final: 0.8352 (tttp) REVERT: E 311 LYS cc_start: 0.8084 (mttt) cc_final: 0.7450 (tppt) REVERT: E 348 ASP cc_start: 0.8078 (t0) cc_final: 0.7857 (t0) REVERT: E 349 ARG cc_start: 0.6698 (mtm180) cc_final: 0.6191 (mmm160) REVERT: B 315 LEU cc_start: 0.8902 (OUTLIER) cc_final: 0.8652 (mt) REVERT: B 375 LYS cc_start: 0.8508 (tttt) cc_final: 0.8149 (ttmt) REVERT: D 311 LYS cc_start: 0.8550 (mttt) cc_final: 0.8056 (pttp) REVERT: D 321 LYS cc_start: 0.8568 (mttt) cc_final: 0.8008 (mtpt) REVERT: D 340 LYS cc_start: 0.8280 (tttt) cc_final: 0.7931 (mtpt) REVERT: D 375 LYS cc_start: 0.8629 (tttt) cc_final: 0.8358 (ttmt) REVERT: F 311 LYS cc_start: 0.8316 (mttt) cc_final: 0.7839 (mmtt) REVERT: F 340 LYS cc_start: 0.8133 (tttt) cc_final: 0.7806 (mtpt) REVERT: F 375 LYS cc_start: 0.8411 (tttt) cc_final: 0.8047 (ttmt) outliers start: 6 outliers final: 5 residues processed: 75 average time/residue: 0.4560 time to fit residues: 36.7761 Evaluate side-chains 73 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 67 time to evaluate : 0.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain C residue 324 SER Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain F residue 348 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 21 optimal weight: 8.9990 chunk 26 optimal weight: 6.9990 chunk 30 optimal weight: 0.9980 chunk 20 optimal weight: 0.9980 chunk 18 optimal weight: 4.9990 chunk 13 optimal weight: 4.9990 chunk 33 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 14 optimal weight: 6.9990 chunk 6 optimal weight: 0.8980 chunk 23 optimal weight: 0.6980 overall best weight: 1.3182 ------------------------------------------------------------------------------- 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 = 0.4089 r_free = 0.4089 target = 0.129007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.112825 restraints weight = 13741.849| |-----------------------------------------------------------------------------| r_work (start): 0.3843 rms_B_bonded: 1.89 r_work: 0.3736 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3644 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.3644 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.5489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 3498 Z= 0.098 Angle : 0.441 3.672 4680 Z= 0.220 Chirality : 0.051 0.123 528 Planarity : 0.003 0.040 594 Dihedral : 4.139 11.283 462 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 2.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 1.01 % Allowed : 7.07 % Favored : 91.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.62 (0.37), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.23 (0.28), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 349 TYR 0.006 0.001 TYR D 310 PHE 0.005 0.001 PHE B 378 HIS 0.002 0.000 HIS B 362 Details of bonding type rmsd covalent geometry : bond 0.00214 ( 3498) covalent geometry : angle 0.44138 ( 4680) hydrogen bonds : bond 0.00935 ( 67) hydrogen bonds : angle 3.63596 ( 201) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 65 time to evaluate : 0.210 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 340 LYS cc_start: 0.8242 (tttt) cc_final: 0.7785 (ttmt) REVERT: A 349 ARG cc_start: 0.7651 (mtp85) cc_final: 0.7303 (mtm180) REVERT: A 375 LYS cc_start: 0.8433 (tttt) cc_final: 0.7922 (ttmm) REVERT: C 311 LYS cc_start: 0.8617 (mttt) cc_final: 0.8258 (ttpt) REVERT: C 349 ARG cc_start: 0.7670 (mtt90) cc_final: 0.5304 (pmt-80) REVERT: C 375 LYS cc_start: 0.8593 (tttt) cc_final: 0.8354 (tttp) REVERT: E 311 LYS cc_start: 0.8083 (mttt) cc_final: 0.7441 (tppt) REVERT: E 347 LYS cc_start: 0.8590 (mttm) cc_final: 0.8082 (mptt) REVERT: E 349 ARG cc_start: 0.6653 (mtm180) cc_final: 0.6200 (mmp-170) REVERT: B 321 LYS cc_start: 0.8174 (mttt) cc_final: 0.7715 (mtpt) REVERT: B 375 LYS cc_start: 0.8456 (tttt) cc_final: 0.8117 (ttmt) REVERT: D 311 LYS cc_start: 0.8526 (mttt) cc_final: 0.8045 (pttp) REVERT: F 311 LYS cc_start: 0.8295 (mttt) cc_final: 0.7813 (mmtt) REVERT: F 340 LYS cc_start: 0.8102 (tttt) cc_final: 0.7686 (mtpt) REVERT: F 375 LYS cc_start: 0.8395 (tttt) cc_final: 0.8043 (ttmt) outliers start: 4 outliers final: 3 residues processed: 67 average time/residue: 0.3906 time to fit residues: 28.4155 Evaluate side-chains 67 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 64 time to evaluate : 0.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain C residue 324 SER Chi-restraints excluded: chain F residue 348 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 24 optimal weight: 0.6980 chunk 41 optimal weight: 4.9990 chunk 11 optimal weight: 5.9990 chunk 39 optimal weight: 0.6980 chunk 13 optimal weight: 2.9990 chunk 17 optimal weight: 5.9990 chunk 4 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 1 optimal weight: 0.7980 chunk 19 optimal weight: 2.9990 chunk 30 optimal weight: 6.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- 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 = 0.4108 r_free = 0.4108 target = 0.130169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.114029 restraints weight = 13613.518| |-----------------------------------------------------------------------------| r_work (start): 0.3866 rms_B_bonded: 1.89 r_work: 0.3759 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3668 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.3668 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.5593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 3498 Z= 0.087 Angle : 0.438 4.368 4680 Z= 0.216 Chirality : 0.051 0.123 528 Planarity : 0.003 0.041 594 Dihedral : 3.965 11.156 462 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 2.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 0.76 % Allowed : 7.58 % Favored : 91.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.56 (0.38), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.18 (0.29), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 349 TYR 0.005 0.001 TYR F 310 PHE 0.007 0.001 PHE B 378 HIS 0.001 0.000 HIS B 362 Details of bonding type rmsd covalent geometry : bond 0.00199 ( 3498) covalent geometry : angle 0.43779 ( 4680) hydrogen bonds : bond 0.00800 ( 67) hydrogen bonds : angle 3.40490 ( 201) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 70 time to evaluate : 0.248 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 340 LYS cc_start: 0.8253 (tttt) cc_final: 0.7778 (ttmt) REVERT: A 375 LYS cc_start: 0.8437 (tttt) cc_final: 0.7928 (ttmm) REVERT: C 311 LYS cc_start: 0.8611 (mttt) cc_final: 0.8236 (ttpt) REVERT: C 340 LYS cc_start: 0.8530 (tttt) cc_final: 0.8125 (ttmt) REVERT: C 375 LYS cc_start: 0.8603 (tttt) cc_final: 0.8374 (tttp) REVERT: E 311 LYS cc_start: 0.8050 (mttt) cc_final: 0.7418 (tppt) REVERT: E 347 LYS cc_start: 0.8507 (mttm) cc_final: 0.8004 (mptt) REVERT: E 349 ARG cc_start: 0.6701 (mtm180) cc_final: 0.6297 (mmp-170) REVERT: B 321 LYS cc_start: 0.8157 (mttt) cc_final: 0.7701 (mtpt) REVERT: B 340 LYS cc_start: 0.7830 (tttt) cc_final: 0.7465 (mtpt) REVERT: B 375 LYS cc_start: 0.8449 (tttt) cc_final: 0.8118 (ttmt) REVERT: D 311 LYS cc_start: 0.8515 (mttt) cc_final: 0.8048 (pttp) REVERT: F 311 LYS cc_start: 0.8256 (mttt) cc_final: 0.7756 (mmtt) REVERT: F 340 LYS cc_start: 0.8143 (tttt) cc_final: 0.7691 (mtpt) REVERT: F 375 LYS cc_start: 0.8393 (tttt) cc_final: 0.8044 (ttmt) outliers start: 3 outliers final: 3 residues processed: 72 average time/residue: 0.3864 time to fit residues: 30.2312 Evaluate side-chains 73 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 70 time to evaluate : 0.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain C residue 324 SER Chi-restraints excluded: chain F residue 348 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 27 optimal weight: 7.9990 chunk 24 optimal weight: 8.9990 chunk 6 optimal weight: 7.9990 chunk 31 optimal weight: 0.9980 chunk 34 optimal weight: 3.9990 chunk 3 optimal weight: 3.9990 chunk 19 optimal weight: 4.9990 chunk 0 optimal weight: 7.9990 chunk 26 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 chunk 15 optimal weight: 3.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- 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 = 0.4032 r_free = 0.4032 target = 0.124636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.108473 restraints weight = 13966.333| |-----------------------------------------------------------------------------| r_work (start): 0.3783 rms_B_bonded: 1.88 r_work: 0.3675 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3583 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.3583 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 moved from start: 0.5637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 3498 Z= 0.188 Angle : 0.490 3.874 4680 Z= 0.250 Chirality : 0.051 0.122 528 Planarity : 0.004 0.039 594 Dihedral : 4.282 11.196 462 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 3.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 0.76 % Allowed : 7.83 % Favored : 91.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.80 (0.37), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.36 (0.28), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 349 TYR 0.011 0.002 TYR B 310 PHE 0.007 0.001 PHE B 346 HIS 0.002 0.001 HIS C 362 Details of bonding type rmsd covalent geometry : bond 0.00411 ( 3498) covalent geometry : angle 0.48955 ( 4680) hydrogen bonds : bond 0.01133 ( 67) hydrogen bonds : angle 3.42842 ( 201) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 75 time to evaluate : 0.122 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 340 LYS cc_start: 0.8268 (tttt) cc_final: 0.7798 (ttmt) REVERT: A 375 LYS cc_start: 0.8407 (tttt) cc_final: 0.7887 (ttmm) REVERT: C 311 LYS cc_start: 0.8657 (mttt) cc_final: 0.8286 (ttpt) REVERT: C 340 LYS cc_start: 0.8582 (tttt) cc_final: 0.8179 (ttmt) REVERT: C 375 LYS cc_start: 0.8632 (tttt) cc_final: 0.8390 (tttp) REVERT: E 311 LYS cc_start: 0.8115 (mttt) cc_final: 0.7426 (tppt) REVERT: E 349 ARG cc_start: 0.6707 (mtm180) cc_final: 0.6150 (mmm160) REVERT: B 321 LYS cc_start: 0.8196 (mttt) cc_final: 0.7716 (mtpt) REVERT: B 340 LYS cc_start: 0.7818 (tttt) cc_final: 0.7501 (mtpt) REVERT: B 375 LYS cc_start: 0.8463 (tttt) cc_final: 0.8111 (ttmt) REVERT: D 311 LYS cc_start: 0.8545 (mttt) cc_final: 0.8058 (pttp) REVERT: D 321 LYS cc_start: 0.8546 (mttt) cc_final: 0.8001 (mtpt) REVERT: D 340 LYS cc_start: 0.8274 (tttt) cc_final: 0.7942 (mtpt) REVERT: D 375 LYS cc_start: 0.8639 (tttt) cc_final: 0.8361 (ttmt) REVERT: F 311 LYS cc_start: 0.8309 (mttt) cc_final: 0.7827 (mmtt) REVERT: F 340 LYS cc_start: 0.8201 (tttt) cc_final: 0.7877 (mtpt) REVERT: F 375 LYS cc_start: 0.8397 (tttt) cc_final: 0.8046 (ttmt) outliers start: 3 outliers final: 3 residues processed: 77 average time/residue: 0.3930 time to fit residues: 32.4909 Evaluate side-chains 76 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 73 time to evaluate : 0.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain C residue 324 SER Chi-restraints excluded: chain F residue 348 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 39 optimal weight: 4.9990 chunk 7 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 21 optimal weight: 8.9990 chunk 28 optimal weight: 0.9990 chunk 35 optimal weight: 0.7980 chunk 3 optimal weight: 5.9990 chunk 8 optimal weight: 0.0570 chunk 9 optimal weight: 1.9990 chunk 4 optimal weight: 3.9990 chunk 11 optimal weight: 0.9980 overall best weight: 0.9702 ------------------------------------------------------------------------------- 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 = 0.4087 r_free = 0.4087 target = 0.129005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.112868 restraints weight = 13536.113| |-----------------------------------------------------------------------------| r_work (start): 0.3847 rms_B_bonded: 1.87 r_work: 0.3740 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.3651 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.3651 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.5712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 3498 Z= 0.088 Angle : 0.455 4.866 4680 Z= 0.225 Chirality : 0.051 0.121 528 Planarity : 0.003 0.044 594 Dihedral : 4.027 11.145 462 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 2.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 0.76 % Allowed : 8.33 % Favored : 90.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.65 (0.38), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.25 (0.29), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 349 TYR 0.005 0.001 TYR A 310 PHE 0.005 0.001 PHE B 378 HIS 0.002 0.000 HIS E 362 Details of bonding type rmsd covalent geometry : bond 0.00201 ( 3498) covalent geometry : angle 0.45547 ( 4680) hydrogen bonds : bond 0.00869 ( 67) hydrogen bonds : angle 3.26440 ( 201) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2417.86 seconds wall clock time: 41 minutes 40.26 seconds (2500.26 seconds total)