Starting phenix.real_space_refine on Fri Aug 22 17:07:58 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8q9k_18284/08_2025/8q9k_18284.cif Found real_map, /net/cci-nas-00/data/ceres_data/8q9k_18284/08_2025/8q9k_18284.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8q9k_18284/08_2025/8q9k_18284.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8q9k_18284/08_2025/8q9k_18284.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8q9k_18284/08_2025/8q9k_18284.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8q9k_18284/08_2025/8q9k_18284.map" } resolution = 3.2 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= 0.001 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 1932 2.51 5 N 570 2.21 5 O 582 1.98 5 H 3216 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 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: 6306 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1051 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 1051 Classifications: {'peptide': 68} Link IDs: {'PTRANS': 3, 'TRANS': 64} Chain: "E" Number of atoms: 1051 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 1051 Classifications: {'peptide': 68} Link IDs: {'PTRANS': 3, 'TRANS': 64} Chain: "C" Number of atoms: 1051 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 1051 Classifications: {'peptide': 68} Link IDs: {'PTRANS': 3, 'TRANS': 64} Chain: "D" Number of atoms: 1051 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 1051 Classifications: {'peptide': 68} Link IDs: {'PTRANS': 3, 'TRANS': 64} Chain: "B" Number of atoms: 1051 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 1051 Classifications: {'peptide': 68} Link IDs: {'PTRANS': 3, 'TRANS': 64} Chain: "F" Number of atoms: 1051 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 1051 Classifications: {'peptide': 68} Link IDs: {'PTRANS': 3, 'TRANS': 64} Time building chain proxies: 1.13, per 1000 atoms: 0.18 Number of scatterers: 6306 At special positions: 0 Unit cell: (139.256, 84.048, 41.2, 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 582 8.00 N 570 7.00 C 1932 6.00 H 3216 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: 0.34 Conformation dependent library (CDL) restraints added in 103.4 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 708 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 18 sheets defined 0.0% alpha, 45.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.13 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'E' and resid 309 through 310 removed outlier: 6.552A pdb=" N VAL A 309 " --> pdb=" O TYR F 310 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'E' and resid 313 through 314 removed outlier: 6.837A pdb=" N VAL A 313 " --> pdb=" O ASP F 314 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 317 through 322 removed outlier: 6.415A pdb=" N LYS A 317 " --> pdb=" O VAL F 318 " (cutoff:3.500A) removed outlier: 8.334A pdb=" N SER F 320 " --> pdb=" O LYS A 317 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N THR A 319 " --> pdb=" O SER F 320 " (cutoff:3.500A) removed outlier: 8.456A pdb=" N CYS F 322 " --> pdb=" O THR A 319 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N LYS A 321 " --> pdb=" O CYS F 322 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 325 through 330 removed outlier: 6.913A pdb=" N GLY A 326 " --> pdb=" O LEU E 325 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N ASN E 327 " --> pdb=" O GLY A 326 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N GLY F 326 " --> pdb=" O LEU A 325 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N ASN A 327 " --> pdb=" O GLY F 326 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 337 through 341 removed outlier: 6.613A pdb=" N VAL A 337 " --> pdb=" O GLU E 338 " (cutoff:3.500A) removed outlier: 8.198A pdb=" N LYS E 340 " --> pdb=" O VAL A 337 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N VAL A 339 " --> pdb=" O LYS E 340 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 345 through 346 removed outlier: 6.648A pdb=" N ASP A 345 " --> pdb=" O PHE F 346 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 350 through 354 removed outlier: 6.381A pdb=" N VAL A 350 " --> pdb=" O GLN E 351 " (cutoff:3.500A) removed outlier: 8.299A pdb=" N LYS E 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N SER A 352 " --> pdb=" O LYS E 353 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 357 through 362 removed outlier: 6.440A pdb=" N ASP A 358 " --> pdb=" O ASN F 359 " (cutoff:3.500A) removed outlier: 8.061A pdb=" N THR F 361 " --> pdb=" O ASP A 358 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N ILE A 360 " --> pdb=" O THR F 361 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 369 through 374 removed outlier: 6.568A pdb=" N LYS A 369 " --> pdb=" O LYS F 370 " (cutoff:3.500A) removed outlier: 8.080A pdb=" N GLU F 372 " --> pdb=" O LYS A 369 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N ILE A 371 " --> pdb=" O GLU F 372 " (cutoff:3.500A) removed outlier: 8.130A pdb=" N HIS F 374 " --> pdb=" O ILE A 371 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N THR A 373 " --> pdb=" O HIS F 374 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 309 through 310 removed outlier: 6.488A pdb=" N VAL C 309 " --> pdb=" O TYR D 310 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N VAL D 309 " --> pdb=" O TYR B 310 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'C' and resid 313 through 314 removed outlier: 6.753A pdb=" N VAL C 313 " --> pdb=" O ASP D 314 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N VAL D 313 " --> pdb=" O ASP B 314 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'C' and resid 317 through 322 removed outlier: 6.424A pdb=" N LYS C 317 " --> pdb=" O VAL D 318 " (cutoff:3.500A) removed outlier: 8.295A pdb=" N SER D 320 " --> pdb=" O LYS C 317 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N THR C 319 " --> pdb=" O SER D 320 " (cutoff:3.500A) removed outlier: 8.444A pdb=" N CYS D 322 " --> pdb=" O THR C 319 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N LYS C 321 " --> pdb=" O CYS D 322 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N LYS D 317 " --> pdb=" O VAL B 318 " (cutoff:3.500A) removed outlier: 8.336A pdb=" N SER B 320 " --> pdb=" O LYS D 317 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N THR D 319 " --> pdb=" O SER B 320 " (cutoff:3.500A) removed outlier: 8.501A pdb=" N CYS B 322 " --> pdb=" O THR D 319 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N LYS D 321 " --> pdb=" O CYS B 322 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'C' and resid 325 through 330 removed outlier: 8.850A pdb=" N LEU C 325 " --> pdb=" O GLY D 326 " (cutoff:3.500A) removed outlier: 9.832A pdb=" N ILE D 328 " --> pdb=" O LEU C 325 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N ASN C 327 " --> pdb=" O ILE D 328 " (cutoff:3.500A) removed outlier: 7.893A pdb=" N HIS D 330 " --> pdb=" O ASN C 327 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N HIS C 329 " --> pdb=" O HIS D 330 " (cutoff:3.500A) removed outlier: 8.894A pdb=" N LEU D 325 " --> pdb=" O GLY B 326 " (cutoff:3.500A) removed outlier: 9.761A pdb=" N ILE B 328 " --> pdb=" O LEU D 325 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N ASN D 327 " --> pdb=" O ILE B 328 " (cutoff:3.500A) removed outlier: 7.921A pdb=" N HIS B 330 " --> pdb=" O ASN D 327 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N HIS D 329 " --> pdb=" O HIS B 330 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'C' and resid 337 through 340 Processing sheet with id=AB6, first strand: chain 'C' and resid 345 through 346 removed outlier: 6.564A pdb=" N ASP C 345 " --> pdb=" O PHE D 346 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N ASP D 345 " --> pdb=" O PHE B 346 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'C' and resid 350 through 354 Processing sheet with id=AB8, first strand: chain 'C' and resid 357 through 362 removed outlier: 6.440A pdb=" N ASP C 358 " --> pdb=" O ASN D 359 " (cutoff:3.500A) removed outlier: 8.112A pdb=" N THR D 361 " --> pdb=" O ASP C 358 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N ILE C 360 " --> pdb=" O THR D 361 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N ASP D 358 " --> pdb=" O ASN B 359 " (cutoff:3.500A) removed outlier: 8.042A pdb=" N THR B 361 " --> pdb=" O ASP D 358 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N ILE D 360 " --> pdb=" O THR B 361 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'C' and resid 369 through 374 removed outlier: 6.501A pdb=" N LYS C 369 " --> pdb=" O LYS D 370 " (cutoff:3.500A) removed outlier: 7.998A pdb=" N GLU D 372 " --> pdb=" O LYS C 369 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N ILE C 371 " --> pdb=" O GLU D 372 " (cutoff:3.500A) removed outlier: 8.098A pdb=" N HIS D 374 " --> pdb=" O ILE C 371 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N THR C 373 " --> pdb=" O HIS D 374 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N LYS D 369 " --> pdb=" O LYS B 370 " (cutoff:3.500A) removed outlier: 8.092A pdb=" N GLU B 372 " --> pdb=" O LYS D 369 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N ILE D 371 " --> pdb=" O GLU B 372 " (cutoff:3.500A) removed outlier: 8.104A pdb=" N HIS B 374 " --> pdb=" O ILE D 371 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N THR D 373 " --> pdb=" O HIS B 374 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 47 hydrogen bonds defined for protein. 141 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: 1.10 Time building geometry restraints manager: 0.51 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: 3210 1.12 - 1.29: 522 1.29 - 1.46: 891 1.46 - 1.63: 1725 1.63 - 1.81: 6 Bond restraints: 6354 Sorted by residual: bond pdb=" N SER C 324 " pdb=" H SER C 324 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.70e+01 bond pdb=" NE ARG A 349 " pdb=" HE ARG A 349 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.70e+01 bond pdb=" CD2 PHE E 346 " pdb=" HD2 PHE E 346 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.69e+01 bond pdb=" N GLU F 338 " pdb=" H GLU F 338 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.68e+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 5.68e+01 ... (remaining 6349 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.10: 10214 3.10 - 6.19: 1247 6.19 - 9.29: 133 9.29 - 12.38: 6 12.38 - 15.48: 4 Bond angle restraints: 11604 Sorted by residual: angle pdb=" N GLY D 326 " pdb=" CA GLY D 326 " pdb=" C GLY D 326 " ideal model delta sigma weight residual 110.69 117.98 -7.29 1.33e+00 5.65e-01 3.00e+01 angle pdb=" C LYS C 340 " pdb=" N SER C 341 " pdb=" H SER C 341 " ideal model delta sigma weight residual 123.83 108.35 15.48 3.00e+00 1.11e-01 2.66e+01 angle pdb=" C LYS B 340 " pdb=" N SER B 341 " pdb=" H SER B 341 " ideal model delta sigma weight residual 123.83 108.63 15.20 3.00e+00 1.11e-01 2.57e+01 angle pdb=" N ARG D 349 " pdb=" CA ARG D 349 " pdb=" C ARG D 349 " ideal model delta sigma weight residual 110.35 117.23 -6.88 1.36e+00 5.41e-01 2.56e+01 angle pdb=" C LYS D 340 " pdb=" N SER D 341 " pdb=" H SER D 341 " ideal model delta sigma weight residual 123.83 108.95 14.88 3.00e+00 1.11e-01 2.46e+01 ... (remaining 11599 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.63: 2579 13.63 - 27.26: 156 27.26 - 40.89: 58 40.89 - 54.52: 42 54.52 - 68.15: 87 Dihedral angle restraints: 2922 sinusoidal: 1680 harmonic: 1242 Sorted by residual: dihedral pdb=" C ARG B 349 " pdb=" N ARG B 349 " pdb=" CA ARG B 349 " pdb=" CB ARG B 349 " ideal model delta harmonic sigma weight residual -122.60 -133.04 10.44 0 2.50e+00 1.60e-01 1.75e+01 dihedral pdb=" C ARG F 349 " pdb=" N ARG F 349 " pdb=" CA ARG F 349 " pdb=" CB ARG F 349 " ideal model delta harmonic sigma weight residual -122.60 -132.63 10.03 0 2.50e+00 1.60e-01 1.61e+01 dihedral pdb=" N ARG B 349 " pdb=" C ARG B 349 " pdb=" CA ARG B 349 " pdb=" CB ARG B 349 " ideal model delta harmonic sigma weight residual 122.80 131.83 -9.03 0 2.50e+00 1.60e-01 1.31e+01 ... (remaining 2919 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.085: 323 0.085 - 0.169: 124 0.169 - 0.254: 16 0.254 - 0.338: 2 0.338 - 0.423: 3 Chirality restraints: 468 Sorted by residual: chirality pdb=" CA ARG B 349 " pdb=" N ARG B 349 " pdb=" C ARG B 349 " pdb=" CB ARG B 349 " both_signs ideal model delta sigma weight residual False 2.51 2.09 0.42 2.00e-01 2.50e+01 4.47e+00 chirality pdb=" CA ARG F 349 " pdb=" N ARG F 349 " pdb=" C ARG F 349 " pdb=" CB ARG F 349 " both_signs ideal model delta sigma weight residual False 2.51 2.11 0.40 2.00e-01 2.50e+01 4.02e+00 chirality pdb=" CA ARG D 349 " pdb=" N ARG D 349 " pdb=" C ARG D 349 " pdb=" CB ARG D 349 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.38 2.00e-01 2.50e+01 3.52e+00 ... (remaining 465 not shown) Planarity restraints: 918 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS B 340 " 0.046 2.00e-02 2.50e+03 8.41e-02 7.07e+01 pdb=" N SER B 341 " -0.145 2.00e-02 2.50e+03 pdb=" CA SER B 341 " 0.045 2.00e-02 2.50e+03 pdb=" H SER B 341 " 0.055 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS C 340 " 0.044 2.00e-02 2.50e+03 7.88e-02 6.21e+01 pdb=" N SER C 341 " -0.136 2.00e-02 2.50e+03 pdb=" CA SER C 341 " 0.042 2.00e-02 2.50e+03 pdb=" H SER C 341 " 0.051 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS D 340 " 0.041 2.00e-02 2.50e+03 7.42e-02 5.51e+01 pdb=" N SER D 341 " -0.128 2.00e-02 2.50e+03 pdb=" CA SER D 341 " 0.039 2.00e-02 2.50e+03 pdb=" H SER D 341 " 0.048 2.00e-02 2.50e+03 ... (remaining 915 not shown) Histogram of nonbonded interaction distances: 1.57 - 2.18: 475 2.18 - 2.78: 10985 2.78 - 3.39: 16438 3.39 - 3.99: 21542 3.99 - 4.60: 30268 Nonbonded interactions: 79708 Sorted by model distance: nonbonded pdb=" OD1 ASP E 314 " pdb=" HG SER E 316 " model vdw 1.571 2.450 nonbonded pdb=" OD1 ASP C 314 " pdb=" HG SER C 316 " model vdw 1.573 2.450 nonbonded pdb=" OD1 ASP D 314 " pdb=" HG SER D 316 " model vdw 1.579 2.450 nonbonded pdb=" OD1 ASP A 314 " pdb=" HG SER A 316 " model vdw 1.583 2.450 nonbonded pdb=" OD1 ASP F 314 " pdb=" HG SER F 316 " model vdw 1.597 2.450 ... (remaining 79703 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: 3.640 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: 0.030 Extract box with map and model: 0.090 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 6.490 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.038 3138 Z= 0.690 Angle : 1.997 7.291 4194 Z= 1.327 Chirality : 0.088 0.423 468 Planarity : 0.011 0.092 534 Dihedral : 9.094 65.306 1212 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 0.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.94 (0.34), residues: 396 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.47 (0.26), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 349 TYR 0.049 0.014 TYR D 310 PHE 0.037 0.018 PHE D 346 HIS 0.016 0.003 HIS B 330 Details of bonding type rmsd covalent geometry : bond 0.01082 ( 3138) covalent geometry : angle 1.99672 ( 4194) hydrogen bonds : bond 0.09986 ( 47) hydrogen bonds : angle 6.26540 ( 141) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 151 time to evaluate : 0.145 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: E 317 LYS cc_start: 0.8756 (pttt) cc_final: 0.7914 (mmmt) REVERT: C 317 LYS cc_start: 0.8615 (pttt) cc_final: 0.7747 (mmtt) REVERT: C 345 ASP cc_start: 0.7730 (t0) cc_final: 0.7441 (t70) REVERT: F 340 LYS cc_start: 0.7983 (ttmt) cc_final: 0.7594 (tttm) outliers start: 0 outliers final: 0 residues processed: 151 average time/residue: 0.2673 time to fit residues: 44.4075 Evaluate side-chains 95 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 95 time to evaluate : 0.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 24 optimal weight: 20.0000 chunk 26 optimal weight: 4.9990 chunk 2 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 32 optimal weight: 3.9990 chunk 31 optimal weight: 5.9990 chunk 25 optimal weight: 5.9990 chunk 19 optimal weight: 6.9990 chunk 30 optimal weight: 7.9990 chunk 22 optimal weight: 0.9990 chunk 13 optimal weight: 5.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- 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 = 0.4377 r_free = 0.4377 target = 0.163435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.126940 restraints weight = 11026.069| |-----------------------------------------------------------------------------| r_work (start): 0.4118 rms_B_bonded: 2.46 r_work: 0.4022 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3922 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.5100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 3138 Z= 0.172 Angle : 0.586 4.380 4194 Z= 0.314 Chirality : 0.053 0.133 468 Planarity : 0.004 0.031 534 Dihedral : 5.710 19.403 414 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 1.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 1.41 % Allowed : 7.34 % Favored : 91.24 % 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: -1.89 (0.33), residues: 396 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.43 (0.25), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 349 TYR 0.004 0.001 TYR E 310 PHE 0.008 0.002 PHE D 346 HIS 0.003 0.001 HIS F 329 Details of bonding type rmsd covalent geometry : bond 0.00387 ( 3138) covalent geometry : angle 0.58626 ( 4194) hydrogen bonds : bond 0.03068 ( 47) hydrogen bonds : angle 4.68071 ( 141) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 110 time to evaluate : 0.200 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 319 THR cc_start: 0.8699 (m) cc_final: 0.8450 (p) REVERT: A 373 THR cc_start: 0.8898 (m) cc_final: 0.8438 (p) REVERT: E 317 LYS cc_start: 0.8861 (pttt) cc_final: 0.7088 (mmmt) REVERT: E 340 LYS cc_start: 0.8271 (ttmt) cc_final: 0.8011 (tttt) REVERT: E 345 ASP cc_start: 0.8269 (t0) cc_final: 0.8047 (t0) REVERT: E 369 LYS cc_start: 0.8780 (mtpt) cc_final: 0.8348 (mtmt) REVERT: C 317 LYS cc_start: 0.8810 (pttt) cc_final: 0.7026 (mmmt) REVERT: C 345 ASP cc_start: 0.8366 (t0) cc_final: 0.7987 (t0) REVERT: C 347 LYS cc_start: 0.8718 (mmtt) cc_final: 0.8336 (mmtm) REVERT: C 356 SER cc_start: 0.8745 (m) cc_final: 0.8492 (t) REVERT: D 331 LYS cc_start: 0.8246 (mtpt) cc_final: 0.7449 (tptt) REVERT: D 345 ASP cc_start: 0.8368 (t70) cc_final: 0.7670 (t0) REVERT: D 347 LYS cc_start: 0.8779 (mmtp) cc_final: 0.8251 (mmtt) REVERT: D 372 GLU cc_start: 0.8286 (tt0) cc_final: 0.7762 (tp30) REVERT: B 345 ASP cc_start: 0.8317 (t70) cc_final: 0.8092 (t0) outliers start: 5 outliers final: 5 residues processed: 112 average time/residue: 0.2506 time to fit residues: 31.2383 Evaluate side-chains 101 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 96 time to evaluate : 0.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 313 VAL Chi-restraints excluded: chain D residue 356 SER Chi-restraints excluded: chain B residue 356 SER Chi-restraints excluded: chain F residue 309 VAL Chi-restraints excluded: chain F residue 356 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 13 optimal weight: 9.9990 chunk 26 optimal weight: 2.9990 chunk 17 optimal weight: 0.9980 chunk 6 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 7 optimal weight: 5.9990 chunk 9 optimal weight: 1.9990 chunk 35 optimal weight: 0.3980 chunk 15 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 30 optimal weight: 10.0000 overall best weight: 1.6786 ------------------------------------------------------------------------------- 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 = 0.4408 r_free = 0.4408 target = 0.166549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4161 r_free = 0.4161 target = 0.130450 restraints weight = 10790.272| |-----------------------------------------------------------------------------| r_work (start): 0.4166 rms_B_bonded: 2.47 r_work: 0.4061 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3962 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.5594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3138 Z= 0.120 Angle : 0.514 4.279 4194 Z= 0.266 Chirality : 0.052 0.133 468 Planarity : 0.004 0.035 534 Dihedral : 5.183 19.276 414 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 1.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 2.82 % Allowed : 7.34 % Favored : 89.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.75 (0.34), residues: 396 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.32 (0.26), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 349 TYR 0.005 0.001 TYR E 310 PHE 0.004 0.001 PHE E 346 HIS 0.003 0.001 HIS F 329 Details of bonding type rmsd covalent geometry : bond 0.00277 ( 3138) covalent geometry : angle 0.51431 ( 4194) hydrogen bonds : bond 0.02309 ( 47) hydrogen bonds : angle 4.11586 ( 141) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 100 time to evaluate : 0.188 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 319 THR cc_start: 0.8593 (m) cc_final: 0.8375 (p) REVERT: A 372 GLU cc_start: 0.8362 (tt0) cc_final: 0.7932 (tp30) REVERT: E 317 LYS cc_start: 0.8751 (pttt) cc_final: 0.6954 (mmmt) REVERT: E 340 LYS cc_start: 0.8230 (ttmt) cc_final: 0.7953 (tttt) REVERT: E 369 LYS cc_start: 0.8779 (mtpt) cc_final: 0.8276 (mtmt) REVERT: C 317 LYS cc_start: 0.8715 (pttt) cc_final: 0.6912 (mmmt) REVERT: C 345 ASP cc_start: 0.8321 (t0) cc_final: 0.7905 (t0) REVERT: C 347 LYS cc_start: 0.8687 (mmtt) cc_final: 0.8257 (mmtm) REVERT: C 356 SER cc_start: 0.8698 (m) cc_final: 0.8439 (t) REVERT: C 369 LYS cc_start: 0.8921 (mtmt) cc_final: 0.8599 (mtmt) REVERT: D 345 ASP cc_start: 0.8349 (t70) cc_final: 0.7646 (t0) REVERT: D 347 LYS cc_start: 0.8782 (mmtp) cc_final: 0.8182 (mmtt) REVERT: D 369 LYS cc_start: 0.8918 (mtmt) cc_final: 0.8323 (mtmm) REVERT: D 372 GLU cc_start: 0.8330 (tt0) cc_final: 0.7756 (tp30) REVERT: B 345 ASP cc_start: 0.8371 (t70) cc_final: 0.8091 (t0) REVERT: F 369 LYS cc_start: 0.8946 (mtmt) cc_final: 0.8420 (mtmm) outliers start: 10 outliers final: 10 residues processed: 103 average time/residue: 0.2682 time to fit residues: 30.6474 Evaluate side-chains 105 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 95 time to evaluate : 0.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 356 SER Chi-restraints excluded: chain E residue 309 VAL Chi-restraints excluded: chain C residue 309 VAL Chi-restraints excluded: chain D residue 308 ILE Chi-restraints excluded: chain D residue 348 ASP Chi-restraints excluded: chain D residue 356 SER Chi-restraints excluded: chain B residue 356 SER Chi-restraints excluded: chain F residue 309 VAL Chi-restraints excluded: chain F residue 356 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 29 optimal weight: 3.9990 chunk 2 optimal weight: 3.9990 chunk 28 optimal weight: 0.0980 chunk 14 optimal weight: 4.9990 chunk 34 optimal weight: 4.9990 chunk 25 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 15 optimal weight: 3.9990 chunk 30 optimal weight: 3.9990 chunk 13 optimal weight: 9.9990 chunk 32 optimal weight: 2.9990 overall best weight: 3.0188 ------------------------------------------------------------------------------- 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 = 0.4365 r_free = 0.4365 target = 0.162367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.126367 restraints weight = 11040.651| |-----------------------------------------------------------------------------| r_work (start): 0.4098 rms_B_bonded: 2.39 r_work: 0.3997 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3899 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.5840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 3138 Z= 0.197 Angle : 0.537 4.196 4194 Z= 0.283 Chirality : 0.052 0.131 468 Planarity : 0.004 0.037 534 Dihedral : 5.360 17.520 414 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 2.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 1.98 % Allowed : 10.45 % Favored : 87.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.87 (0.33), residues: 396 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.42 (0.25), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 349 TYR 0.005 0.001 TYR A 310 PHE 0.006 0.002 PHE D 346 HIS 0.005 0.001 HIS A 329 Details of bonding type rmsd covalent geometry : bond 0.00437 ( 3138) covalent geometry : angle 0.53696 ( 4194) hydrogen bonds : bond 0.02259 ( 47) hydrogen bonds : angle 3.96992 ( 141) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 98 time to evaluate : 0.197 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 319 THR cc_start: 0.8633 (m) cc_final: 0.8409 (p) REVERT: A 372 GLU cc_start: 0.8334 (tt0) cc_final: 0.7933 (tp30) REVERT: E 317 LYS cc_start: 0.8789 (pttt) cc_final: 0.7005 (mmmt) REVERT: E 348 ASP cc_start: 0.8809 (t0) cc_final: 0.8491 (t0) REVERT: E 349 ARG cc_start: 0.7957 (ptp-170) cc_final: 0.5291 (mmm160) REVERT: E 369 LYS cc_start: 0.8794 (mtpt) cc_final: 0.8241 (mtmt) REVERT: C 317 LYS cc_start: 0.8823 (pttt) cc_final: 0.6998 (mmmt) REVERT: C 345 ASP cc_start: 0.8268 (t0) cc_final: 0.7840 (t0) REVERT: C 347 LYS cc_start: 0.8719 (mmtt) cc_final: 0.8387 (mmtt) REVERT: C 349 ARG cc_start: 0.7933 (ptp-170) cc_final: 0.5483 (mmm160) REVERT: C 356 SER cc_start: 0.8676 (OUTLIER) cc_final: 0.8372 (t) REVERT: D 345 ASP cc_start: 0.8355 (t70) cc_final: 0.7651 (t0) REVERT: D 347 LYS cc_start: 0.8812 (mmtp) cc_final: 0.8218 (mmtt) REVERT: D 349 ARG cc_start: 0.7646 (ptp-170) cc_final: 0.7442 (ptp-110) REVERT: D 372 GLU cc_start: 0.8331 (tt0) cc_final: 0.7788 (tp30) REVERT: B 345 ASP cc_start: 0.8400 (t70) cc_final: 0.8156 (t0) REVERT: B 349 ARG cc_start: 0.8104 (ptp90) cc_final: 0.7901 (ptp-170) outliers start: 7 outliers final: 6 residues processed: 101 average time/residue: 0.2804 time to fit residues: 31.2241 Evaluate side-chains 100 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 93 time to evaluate : 0.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 356 SER Chi-restraints excluded: chain E residue 356 SER Chi-restraints excluded: chain C residue 356 SER Chi-restraints excluded: chain D residue 356 SER Chi-restraints excluded: chain B residue 356 SER Chi-restraints excluded: chain F residue 309 VAL Chi-restraints excluded: chain F residue 356 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 22 optimal weight: 6.9990 chunk 32 optimal weight: 2.9990 chunk 12 optimal weight: 10.0000 chunk 14 optimal weight: 0.5980 chunk 33 optimal weight: 1.9990 chunk 34 optimal weight: 3.9990 chunk 5 optimal weight: 4.9990 chunk 13 optimal weight: 10.0000 chunk 9 optimal weight: 5.9990 chunk 8 optimal weight: 0.9990 chunk 24 optimal weight: 9.9990 overall best weight: 2.1188 ------------------------------------------------------------------------------- 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 = 0.4400 r_free = 0.4400 target = 0.164565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.128596 restraints weight = 11162.945| |-----------------------------------------------------------------------------| r_work (start): 0.4137 rms_B_bonded: 2.45 r_work: 0.4031 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3932 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.5975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3138 Z= 0.143 Angle : 0.498 3.950 4194 Z= 0.258 Chirality : 0.051 0.130 468 Planarity : 0.004 0.037 534 Dihedral : 5.081 17.506 414 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 2.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 2.82 % Allowed : 10.45 % Favored : 86.72 % 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: -1.84 (0.33), residues: 396 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.39 (0.25), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG F 349 TYR 0.004 0.001 TYR A 310 PHE 0.004 0.001 PHE E 346 HIS 0.003 0.001 HIS B 329 Details of bonding type rmsd covalent geometry : bond 0.00322 ( 3138) covalent geometry : angle 0.49805 ( 4194) hydrogen bonds : bond 0.01948 ( 47) hydrogen bonds : angle 3.92305 ( 141) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 94 time to evaluate : 0.184 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 319 THR cc_start: 0.8630 (m) cc_final: 0.8414 (p) REVERT: E 317 LYS cc_start: 0.8784 (pttt) cc_final: 0.6985 (mmmt) REVERT: E 348 ASP cc_start: 0.8741 (t0) cc_final: 0.8484 (t0) REVERT: E 349 ARG cc_start: 0.7921 (ptp-170) cc_final: 0.5145 (mmm-85) REVERT: E 369 LYS cc_start: 0.8763 (mtpt) cc_final: 0.8149 (mtmm) REVERT: C 317 LYS cc_start: 0.8766 (pttt) cc_final: 0.6922 (mmmt) REVERT: C 345 ASP cc_start: 0.8256 (t0) cc_final: 0.7840 (t0) REVERT: C 347 LYS cc_start: 0.8719 (mmtt) cc_final: 0.8405 (mmtt) REVERT: C 349 ARG cc_start: 0.7997 (ptp-170) cc_final: 0.5459 (mmm160) REVERT: C 356 SER cc_start: 0.8661 (OUTLIER) cc_final: 0.8353 (t) REVERT: D 345 ASP cc_start: 0.8324 (t70) cc_final: 0.7621 (t0) REVERT: D 347 LYS cc_start: 0.8804 (mmtp) cc_final: 0.8187 (mmtt) REVERT: D 349 ARG cc_start: 0.7642 (ptp-170) cc_final: 0.7414 (ptp-110) REVERT: D 372 GLU cc_start: 0.8319 (tt0) cc_final: 0.7783 (tp30) REVERT: B 345 ASP cc_start: 0.8388 (t70) cc_final: 0.8126 (t0) REVERT: B 349 ARG cc_start: 0.8033 (ptp90) cc_final: 0.7682 (ptp-170) REVERT: F 345 ASP cc_start: 0.8401 (t0) cc_final: 0.8003 (t0) REVERT: F 347 LYS cc_start: 0.8845 (mmtt) cc_final: 0.8601 (mmtt) outliers start: 10 outliers final: 9 residues processed: 99 average time/residue: 0.2703 time to fit residues: 29.4311 Evaluate side-chains 100 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 90 time to evaluate : 0.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 356 SER Chi-restraints excluded: chain E residue 309 VAL Chi-restraints excluded: chain E residue 356 SER Chi-restraints excluded: chain C residue 309 VAL Chi-restraints excluded: chain C residue 356 SER Chi-restraints excluded: chain D residue 348 ASP Chi-restraints excluded: chain D residue 356 SER Chi-restraints excluded: chain B residue 356 SER Chi-restraints excluded: chain F residue 309 VAL Chi-restraints excluded: chain F residue 356 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 10 optimal weight: 5.9990 chunk 32 optimal weight: 0.3980 chunk 21 optimal weight: 5.9990 chunk 20 optimal weight: 3.9990 chunk 6 optimal weight: 0.0980 chunk 28 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 16 optimal weight: 4.9990 chunk 27 optimal weight: 1.9990 chunk 18 optimal weight: 9.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- 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 = 0.4429 r_free = 0.4429 target = 0.167299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.131066 restraints weight = 10923.102| |-----------------------------------------------------------------------------| r_work (start): 0.4169 rms_B_bonded: 2.46 r_work: 0.4063 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3963 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.6095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 3138 Z= 0.103 Angle : 0.473 4.003 4194 Z= 0.243 Chirality : 0.051 0.133 468 Planarity : 0.004 0.038 534 Dihedral : 4.764 16.656 414 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 2.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 2.54 % Allowed : 10.45 % Favored : 87.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.76 (0.34), residues: 396 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.33 (0.26), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG A 349 TYR 0.004 0.001 TYR A 310 PHE 0.002 0.001 PHE E 346 HIS 0.002 0.001 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00242 ( 3138) covalent geometry : angle 0.47295 ( 4194) hydrogen bonds : bond 0.01763 ( 47) hydrogen bonds : angle 3.80971 ( 141) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 97 time to evaluate : 0.140 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 372 GLU cc_start: 0.8354 (tt0) cc_final: 0.8015 (tp30) REVERT: E 317 LYS cc_start: 0.8774 (pttt) cc_final: 0.6991 (mmmt) REVERT: E 340 LYS cc_start: 0.8229 (ttmt) cc_final: 0.7986 (tttt) REVERT: E 348 ASP cc_start: 0.8670 (t0) cc_final: 0.8466 (t0) REVERT: E 349 ARG cc_start: 0.7938 (ptp-170) cc_final: 0.5173 (mmm-85) REVERT: E 369 LYS cc_start: 0.8766 (mtpt) cc_final: 0.8173 (mtmm) REVERT: C 317 LYS cc_start: 0.8767 (pttt) cc_final: 0.6926 (mmmt) REVERT: C 345 ASP cc_start: 0.8259 (t0) cc_final: 0.7852 (t0) REVERT: C 347 LYS cc_start: 0.8762 (mmtt) cc_final: 0.8464 (mmtt) REVERT: C 349 ARG cc_start: 0.8030 (ptp-170) cc_final: 0.5404 (mmm160) REVERT: C 356 SER cc_start: 0.8652 (m) cc_final: 0.8413 (t) REVERT: D 345 ASP cc_start: 0.8307 (t70) cc_final: 0.7667 (t0) REVERT: D 347 LYS cc_start: 0.8802 (mmtp) cc_final: 0.8197 (mmtt) REVERT: D 349 ARG cc_start: 0.7584 (ptp-170) cc_final: 0.7329 (ptp-110) REVERT: D 372 GLU cc_start: 0.8287 (tt0) cc_final: 0.7800 (tp30) REVERT: B 345 ASP cc_start: 0.8369 (t70) cc_final: 0.8097 (t0) REVERT: B 349 ARG cc_start: 0.8030 (ptp90) cc_final: 0.7648 (ptp90) outliers start: 9 outliers final: 8 residues processed: 101 average time/residue: 0.2734 time to fit residues: 30.5313 Evaluate side-chains 101 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 93 time to evaluate : 0.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 356 SER Chi-restraints excluded: chain E residue 309 VAL Chi-restraints excluded: chain E residue 356 SER Chi-restraints excluded: chain C residue 309 VAL Chi-restraints excluded: chain D residue 348 ASP Chi-restraints excluded: chain D residue 356 SER Chi-restraints excluded: chain B residue 356 SER Chi-restraints excluded: chain F residue 356 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 14 optimal weight: 0.4980 chunk 25 optimal weight: 9.9990 chunk 35 optimal weight: 2.9990 chunk 8 optimal weight: 5.9990 chunk 19 optimal weight: 5.9990 chunk 5 optimal weight: 0.9980 chunk 27 optimal weight: 3.9990 chunk 22 optimal weight: 6.9990 chunk 2 optimal weight: 0.8980 chunk 13 optimal weight: 3.9990 chunk 16 optimal weight: 0.6980 overall best weight: 1.2182 ------------------------------------------------------------------------------- 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 = 0.4449 r_free = 0.4449 target = 0.168747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.132595 restraints weight = 10782.149| |-----------------------------------------------------------------------------| r_work (start): 0.4185 rms_B_bonded: 2.48 r_work: 0.4083 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3984 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.6200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 3138 Z= 0.099 Angle : 0.470 4.349 4194 Z= 0.239 Chirality : 0.051 0.132 468 Planarity : 0.004 0.036 534 Dihedral : 4.600 16.092 414 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 2.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 2.82 % Allowed : 11.02 % Favored : 86.16 % 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: -1.66 (0.34), residues: 396 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.26 (0.26), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG E 349 TYR 0.004 0.001 TYR E 310 PHE 0.003 0.001 PHE E 346 HIS 0.002 0.000 HIS B 329 Details of bonding type rmsd covalent geometry : bond 0.00237 ( 3138) covalent geometry : angle 0.46964 ( 4194) hydrogen bonds : bond 0.01737 ( 47) hydrogen bonds : angle 3.73421 ( 141) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 99 time to evaluate : 0.185 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 372 GLU cc_start: 0.8285 (tt0) cc_final: 0.8012 (tp30) REVERT: E 317 LYS cc_start: 0.8769 (pttt) cc_final: 0.6956 (mmmt) REVERT: E 340 LYS cc_start: 0.8255 (ttmt) cc_final: 0.8036 (tttt) REVERT: E 348 ASP cc_start: 0.8667 (t0) cc_final: 0.8420 (t0) REVERT: E 349 ARG cc_start: 0.7886 (ptp-170) cc_final: 0.5030 (mmm-85) REVERT: E 369 LYS cc_start: 0.8762 (mtpt) cc_final: 0.8169 (mtmm) REVERT: C 317 LYS cc_start: 0.8775 (pttt) cc_final: 0.6943 (mmmt) REVERT: C 345 ASP cc_start: 0.8250 (t0) cc_final: 0.7847 (t0) REVERT: C 347 LYS cc_start: 0.8764 (mmtt) cc_final: 0.8464 (mmtt) REVERT: C 349 ARG cc_start: 0.8004 (ptp-170) cc_final: 0.5423 (mmm160) REVERT: C 356 SER cc_start: 0.8661 (m) cc_final: 0.8415 (t) REVERT: D 345 ASP cc_start: 0.8281 (t70) cc_final: 0.7646 (t0) REVERT: D 347 LYS cc_start: 0.8831 (mmtp) cc_final: 0.8230 (mmtt) REVERT: D 349 ARG cc_start: 0.7567 (ptp-170) cc_final: 0.7324 (ptp-110) REVERT: D 372 GLU cc_start: 0.8287 (tt0) cc_final: 0.7738 (tp30) REVERT: B 345 ASP cc_start: 0.8369 (t70) cc_final: 0.8100 (t0) REVERT: B 349 ARG cc_start: 0.8001 (ptp90) cc_final: 0.7664 (ptp90) REVERT: B 372 GLU cc_start: 0.7914 (mm-30) cc_final: 0.6714 (mm-30) REVERT: F 319 THR cc_start: 0.8795 (p) cc_final: 0.8583 (m) outliers start: 10 outliers final: 9 residues processed: 104 average time/residue: 0.2749 time to fit residues: 31.7122 Evaluate side-chains 109 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 100 time to evaluate : 0.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 348 ASP Chi-restraints excluded: chain A residue 356 SER Chi-restraints excluded: chain E residue 309 VAL Chi-restraints excluded: chain E residue 356 SER Chi-restraints excluded: chain C residue 309 VAL Chi-restraints excluded: chain D residue 348 ASP Chi-restraints excluded: chain D residue 356 SER Chi-restraints excluded: chain B residue 356 SER Chi-restraints excluded: chain F residue 356 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 32 optimal weight: 4.9990 chunk 28 optimal weight: 3.9990 chunk 34 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 29 optimal weight: 0.8980 chunk 5 optimal weight: 4.9990 chunk 13 optimal weight: 10.0000 chunk 33 optimal weight: 0.9990 chunk 19 optimal weight: 4.9990 chunk 30 optimal weight: 2.9990 chunk 12 optimal weight: 9.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- 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 = 0.4402 r_free = 0.4402 target = 0.164881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.128609 restraints weight = 10968.667| |-----------------------------------------------------------------------------| r_work (start): 0.4136 rms_B_bonded: 2.44 r_work: 0.4030 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3931 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.6279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3138 Z= 0.147 Angle : 0.499 4.552 4194 Z= 0.257 Chirality : 0.051 0.131 468 Planarity : 0.004 0.035 534 Dihedral : 4.812 15.702 414 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 3.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 2.54 % Allowed : 11.02 % Favored : 86.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.67 (0.34), residues: 396 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.27 (0.26), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG F 349 TYR 0.004 0.001 TYR E 310 PHE 0.004 0.001 PHE D 346 HIS 0.003 0.001 HIS A 329 Details of bonding type rmsd covalent geometry : bond 0.00334 ( 3138) covalent geometry : angle 0.49942 ( 4194) hydrogen bonds : bond 0.01818 ( 47) hydrogen bonds : angle 3.74998 ( 141) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 96 time to evaluate : 0.142 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: E 317 LYS cc_start: 0.8823 (pttt) cc_final: 0.7068 (mmmt) REVERT: E 348 ASP cc_start: 0.8800 (t0) cc_final: 0.8576 (t0) REVERT: E 349 ARG cc_start: 0.8001 (ptp-170) cc_final: 0.5180 (mmm-85) REVERT: E 369 LYS cc_start: 0.8785 (mtpt) cc_final: 0.8220 (mtmt) REVERT: C 317 LYS cc_start: 0.8833 (pttt) cc_final: 0.7069 (mmmt) REVERT: C 345 ASP cc_start: 0.8249 (t0) cc_final: 0.7839 (t0) REVERT: C 347 LYS cc_start: 0.8747 (mmtt) cc_final: 0.8451 (mmtt) REVERT: C 349 ARG cc_start: 0.8082 (ptp-170) cc_final: 0.5695 (mmm160) REVERT: C 356 SER cc_start: 0.8673 (m) cc_final: 0.8405 (t) REVERT: D 345 ASP cc_start: 0.8289 (t70) cc_final: 0.7649 (t0) REVERT: D 347 LYS cc_start: 0.8846 (mmtp) cc_final: 0.8249 (mmtt) REVERT: D 349 ARG cc_start: 0.7713 (ptp-170) cc_final: 0.7471 (ptp-110) REVERT: D 372 GLU cc_start: 0.8263 (tt0) cc_final: 0.7779 (tp30) REVERT: B 345 ASP cc_start: 0.8375 (t70) cc_final: 0.8128 (t0) REVERT: B 349 ARG cc_start: 0.8019 (ptp90) cc_final: 0.7719 (ptp90) REVERT: B 372 GLU cc_start: 0.7917 (mm-30) cc_final: 0.6787 (mm-30) REVERT: F 358 ASP cc_start: 0.8460 (t0) cc_final: 0.8254 (t0) outliers start: 9 outliers final: 9 residues processed: 101 average time/residue: 0.2781 time to fit residues: 30.9859 Evaluate side-chains 101 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 92 time to evaluate : 0.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 348 ASP Chi-restraints excluded: chain A residue 356 SER Chi-restraints excluded: chain E residue 309 VAL Chi-restraints excluded: chain E residue 356 SER Chi-restraints excluded: chain C residue 309 VAL Chi-restraints excluded: chain D residue 348 ASP Chi-restraints excluded: chain D residue 356 SER Chi-restraints excluded: chain B residue 356 SER Chi-restraints excluded: chain F residue 356 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 4 optimal weight: 5.9990 chunk 32 optimal weight: 2.9990 chunk 10 optimal weight: 0.7980 chunk 22 optimal weight: 5.9990 chunk 20 optimal weight: 2.9990 chunk 33 optimal weight: 0.9990 chunk 21 optimal weight: 0.9990 chunk 19 optimal weight: 7.9990 chunk 29 optimal weight: 1.9990 chunk 5 optimal weight: 4.9990 chunk 23 optimal weight: 0.9980 overall best weight: 1.1586 ------------------------------------------------------------------------------- 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 = 0.4443 r_free = 0.4443 target = 0.168294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4185 r_free = 0.4185 target = 0.131824 restraints weight = 11018.125| |-----------------------------------------------------------------------------| r_work (start): 0.4181 rms_B_bonded: 2.50 r_work: 0.4073 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3973 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.6330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 3138 Z= 0.098 Angle : 0.472 4.302 4194 Z= 0.240 Chirality : 0.051 0.131 468 Planarity : 0.004 0.039 534 Dihedral : 4.563 15.768 414 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 2.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 2.26 % Allowed : 11.30 % Favored : 86.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.61 (0.34), residues: 396 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.22 (0.26), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG F 349 TYR 0.004 0.001 TYR A 310 PHE 0.002 0.001 PHE C 346 HIS 0.001 0.000 HIS C 374 Details of bonding type rmsd covalent geometry : bond 0.00234 ( 3138) covalent geometry : angle 0.47230 ( 4194) hydrogen bonds : bond 0.01742 ( 47) hydrogen bonds : angle 3.63581 ( 141) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 99 time to evaluate : 0.186 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: E 317 LYS cc_start: 0.8793 (pttt) cc_final: 0.7026 (mmmt) REVERT: E 348 ASP cc_start: 0.8678 (t0) cc_final: 0.8463 (t0) REVERT: E 349 ARG cc_start: 0.7933 (ptp-170) cc_final: 0.5100 (mmm-85) REVERT: E 369 LYS cc_start: 0.8747 (mtpt) cc_final: 0.8141 (mtmm) REVERT: C 317 LYS cc_start: 0.8780 (pttt) cc_final: 0.7017 (mmmt) REVERT: C 345 ASP cc_start: 0.8236 (t0) cc_final: 0.7826 (t0) REVERT: C 347 LYS cc_start: 0.8726 (mmtt) cc_final: 0.8418 (mmtt) REVERT: C 349 ARG cc_start: 0.8051 (ptp-170) cc_final: 0.5486 (mmm160) REVERT: C 356 SER cc_start: 0.8627 (m) cc_final: 0.8371 (t) REVERT: D 345 ASP cc_start: 0.8221 (t70) cc_final: 0.7636 (t0) REVERT: D 347 LYS cc_start: 0.8826 (mmtp) cc_final: 0.8210 (mmtt) REVERT: D 349 ARG cc_start: 0.7601 (ptp-170) cc_final: 0.7375 (ptp-110) REVERT: D 372 GLU cc_start: 0.8295 (tt0) cc_final: 0.7765 (tp30) REVERT: B 345 ASP cc_start: 0.8366 (t70) cc_final: 0.8092 (t0) REVERT: B 349 ARG cc_start: 0.7924 (ptp90) cc_final: 0.7629 (ptp90) REVERT: B 372 GLU cc_start: 0.7921 (mm-30) cc_final: 0.6758 (mm-30) REVERT: F 358 ASP cc_start: 0.8444 (t0) cc_final: 0.8215 (t0) outliers start: 8 outliers final: 8 residues processed: 103 average time/residue: 0.2883 time to fit residues: 32.9121 Evaluate side-chains 104 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 96 time to evaluate : 0.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 348 ASP Chi-restraints excluded: chain A residue 356 SER Chi-restraints excluded: chain E residue 309 VAL Chi-restraints excluded: chain E residue 356 SER Chi-restraints excluded: chain D residue 348 ASP Chi-restraints excluded: chain D residue 356 SER Chi-restraints excluded: chain B residue 356 SER Chi-restraints excluded: chain F residue 356 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 6 optimal weight: 1.9990 chunk 16 optimal weight: 4.9990 chunk 5 optimal weight: 3.9990 chunk 1 optimal weight: 10.0000 chunk 13 optimal weight: 10.0000 chunk 29 optimal weight: 3.9990 chunk 25 optimal weight: 0.8980 chunk 30 optimal weight: 0.5980 chunk 34 optimal weight: 3.9990 chunk 4 optimal weight: 0.9990 chunk 7 optimal weight: 1.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- 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 = 0.4448 r_free = 0.4448 target = 0.168302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.131537 restraints weight = 10828.114| |-----------------------------------------------------------------------------| r_work (start): 0.4178 rms_B_bonded: 2.49 r_work: 0.4074 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3976 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.6419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 3138 Z= 0.106 Angle : 0.479 4.528 4194 Z= 0.244 Chirality : 0.051 0.132 468 Planarity : 0.004 0.034 534 Dihedral : 4.498 15.266 414 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 2.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 2.26 % Allowed : 12.15 % Favored : 85.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.61 (0.34), residues: 396 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.22 (0.26), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG E 349 TYR 0.004 0.001 TYR A 310 PHE 0.002 0.001 PHE E 346 HIS 0.002 0.000 HIS A 329 Details of bonding type rmsd covalent geometry : bond 0.00254 ( 3138) covalent geometry : angle 0.47869 ( 4194) hydrogen bonds : bond 0.01681 ( 47) hydrogen bonds : angle 3.53986 ( 141) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 95 time to evaluate : 0.182 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: E 317 LYS cc_start: 0.8764 (pttt) cc_final: 0.7008 (mmmt) REVERT: E 348 ASP cc_start: 0.8673 (t0) cc_final: 0.8465 (t0) REVERT: E 349 ARG cc_start: 0.7954 (ptp-170) cc_final: 0.5115 (mmm-85) REVERT: E 369 LYS cc_start: 0.8756 (mtpt) cc_final: 0.8154 (mtmm) REVERT: C 317 LYS cc_start: 0.8798 (pttt) cc_final: 0.7074 (mmmt) REVERT: C 345 ASP cc_start: 0.8277 (t0) cc_final: 0.7886 (t0) REVERT: C 347 LYS cc_start: 0.8721 (mmtt) cc_final: 0.8423 (mmtt) REVERT: C 349 ARG cc_start: 0.8061 (ptp-170) cc_final: 0.5488 (mmm160) REVERT: C 356 SER cc_start: 0.8650 (m) cc_final: 0.8411 (t) REVERT: D 345 ASP cc_start: 0.8220 (t70) cc_final: 0.7657 (t0) REVERT: D 347 LYS cc_start: 0.8823 (mmtp) cc_final: 0.8244 (mmtt) REVERT: D 349 ARG cc_start: 0.7616 (ptp-170) cc_final: 0.7401 (ptp-110) REVERT: B 345 ASP cc_start: 0.8352 (t70) cc_final: 0.8079 (t0) REVERT: B 349 ARG cc_start: 0.7918 (ptp90) cc_final: 0.7648 (ptp90) REVERT: B 372 GLU cc_start: 0.7905 (mm-30) cc_final: 0.7693 (tt0) REVERT: F 358 ASP cc_start: 0.8432 (t0) cc_final: 0.8200 (t0) outliers start: 8 outliers final: 8 residues processed: 99 average time/residue: 0.2701 time to fit residues: 29.6450 Evaluate side-chains 102 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 94 time to evaluate : 0.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 348 ASP Chi-restraints excluded: chain A residue 356 SER Chi-restraints excluded: chain E residue 309 VAL Chi-restraints excluded: chain E residue 356 SER Chi-restraints excluded: chain D residue 348 ASP Chi-restraints excluded: chain D residue 356 SER Chi-restraints excluded: chain B residue 356 SER Chi-restraints excluded: chain F residue 356 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 11 optimal weight: 3.9990 chunk 29 optimal weight: 3.9990 chunk 4 optimal weight: 5.9990 chunk 25 optimal weight: 8.9990 chunk 20 optimal weight: 2.9990 chunk 7 optimal weight: 7.9990 chunk 14 optimal weight: 2.9990 chunk 15 optimal weight: 0.8980 chunk 6 optimal weight: 0.9980 chunk 18 optimal weight: 10.0000 chunk 8 optimal weight: 0.9980 overall best weight: 1.7784 ------------------------------------------------------------------------------- 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 = 0.4444 r_free = 0.4444 target = 0.167431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.130904 restraints weight = 10884.139| |-----------------------------------------------------------------------------| r_work (start): 0.4173 rms_B_bonded: 2.47 r_work: 0.4070 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3969 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.6429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 3138 Z= 0.125 Angle : 0.484 4.385 4194 Z= 0.246 Chirality : 0.051 0.130 468 Planarity : 0.004 0.035 534 Dihedral : 4.609 15.321 414 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 2.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 2.54 % Allowed : 11.58 % Favored : 85.88 % 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: -1.63 (0.34), residues: 396 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.23 (0.26), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 349 TYR 0.004 0.001 TYR A 310 PHE 0.003 0.001 PHE A 346 HIS 0.002 0.001 HIS B 329 Details of bonding type rmsd covalent geometry : bond 0.00290 ( 3138) covalent geometry : angle 0.48388 ( 4194) hydrogen bonds : bond 0.01723 ( 47) hydrogen bonds : angle 3.53628 ( 141) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2320.57 seconds wall clock time: 40 minutes 4.64 seconds (2404.64 seconds total)