Starting phenix.real_space_refine on Fri Aug 22 13:42:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8q8l_18254/08_2025/8q8l_18254.cif Found real_map, /net/cci-nas-00/data/ceres_data/8q8l_18254/08_2025/8q8l_18254.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.04 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8q8l_18254/08_2025/8q8l_18254.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8q8l_18254/08_2025/8q8l_18254.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8q8l_18254/08_2025/8q8l_18254.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8q8l_18254/08_2025/8q8l_18254.map" } resolution = 3.04 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 6 5.16 5 C 2139 2.51 5 N 624 2.21 5 O 636 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 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: 3405 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 578 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 578 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 3, 'TRANS': 72} Chain: "C" Number of atoms: 578 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 578 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 3, 'TRANS': 72} Chain: "E" Number of atoms: 578 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 578 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 3, 'TRANS': 72} Chain: "B" Number of atoms: 557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 557 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 3, 'TRANS': 69} Chain: "D" Number of atoms: 557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 557 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 3, 'TRANS': 69} Chain: "F" Number of atoms: 557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 557 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 3, 'TRANS': 69} Time building chain proxies: 0.96, per 1000 atoms: 0.28 Number of scatterers: 3405 At special positions: 0 Unit cell: (112.064, 116.184, 42.024, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 6 16.00 O 636 8.00 N 624 7.00 C 2139 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.32 Conformation dependent library (CDL) restraints added in 143.9 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 870 Ramachandran restraints generated. 435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 780 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 21 sheets defined 0.0% alpha, 44.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.17 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'C' and resid 306 through 310 removed outlier: 6.611A pdb=" N GLN A 307 " --> pdb=" O ILE C 308 " (cutoff:3.500A) removed outlier: 7.864A pdb=" N TYR C 310 " --> pdb=" O GLN A 307 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N VAL A 309 " --> pdb=" O TYR C 310 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 313 through 314 removed outlier: 6.688A 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 320 removed outlier: 6.586A pdb=" N LYS A 317 " --> pdb=" O VAL C 318 " (cutoff:3.500A) removed outlier: 8.145A pdb=" N SER C 320 " --> pdb=" O LYS A 317 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N THR A 319 " --> pdb=" O SER C 320 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 328 through 330 removed outlier: 6.505A pdb=" N ILE A 328 " --> pdb=" O HIS E 329 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 336 through 340 removed outlier: 6.490A pdb=" N GLN A 336 " --> pdb=" O VAL C 337 " (cutoff:3.500A) removed outlier: 8.209A pdb=" N VAL C 339 " --> pdb=" O GLN A 336 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N GLU A 338 " --> pdb=" O VAL C 339 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N VAL A 337 " --> pdb=" O GLU E 338 " (cutoff:3.500A) removed outlier: 8.124A pdb=" N LYS E 340 " --> pdb=" O VAL A 337 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N VAL A 339 " --> pdb=" O LYS E 340 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'C' and resid 343 through 346 removed outlier: 6.155A pdb=" N LYS A 343 " --> pdb=" O LEU C 344 " (cutoff:3.500A) removed outlier: 7.950A pdb=" N PHE C 346 " --> pdb=" O LYS A 343 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N ASP A 345 " --> pdb=" O PHE C 346 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 351 through 352 removed outlier: 6.210A pdb=" N GLN A 351 " --> pdb=" O SER C 352 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 357 through 362 removed outlier: 6.436A pdb=" N ASP A 358 " --> pdb=" O ASN C 359 " (cutoff:3.500A) removed outlier: 8.061A pdb=" N THR C 361 " --> pdb=" O ASP A 358 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N ILE A 360 " --> pdb=" O THR C 361 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 357 through 362 removed outlier: 6.436A pdb=" N ASP A 358 " --> pdb=" O ASN C 359 " (cutoff:3.500A) removed outlier: 8.061A pdb=" N THR C 361 " --> pdb=" O ASP A 358 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N ILE A 360 " --> pdb=" O THR C 361 " (cutoff:3.500A) removed outlier: 8.141A pdb=" N HIS E 362 " --> pdb=" O ASN A 359 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N THR A 361 " --> pdb=" O HIS E 362 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'C' and resid 369 through 378 removed outlier: 6.482A pdb=" N LYS A 369 " --> pdb=" O LYS C 370 " (cutoff:3.500A) removed outlier: 7.887A pdb=" N GLU C 372 " --> pdb=" O LYS A 369 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N ILE A 371 " --> pdb=" O GLU C 372 " (cutoff:3.500A) removed outlier: 7.908A pdb=" N HIS C 374 " --> pdb=" O ILE A 371 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N THR A 373 " --> pdb=" O HIS C 374 " (cutoff:3.500A) removed outlier: 8.196A pdb=" N LEU C 376 " --> pdb=" O THR A 373 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N LYS A 375 " --> pdb=" O LEU C 376 " (cutoff:3.500A) removed outlier: 8.652A pdb=" N PHE C 378 " --> pdb=" O LYS A 375 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N THR A 377 " --> pdb=" O PHE C 378 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N THR E 373 " --> pdb=" O GLU A 372 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 307 through 310 Processing sheet with id=AB3, first strand: chain 'D' and resid 313 through 314 removed outlier: 7.004A pdb=" N VAL B 313 " --> pdb=" O ASP F 314 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 317 through 325 removed outlier: 6.404A pdb=" N VAL B 318 " --> pdb=" O THR D 319 " (cutoff:3.500A) removed outlier: 7.806A pdb=" N LYS D 321 " --> pdb=" O VAL B 318 " (cutoff:3.500A) removed outlier: 5.854A pdb=" N SER B 320 " --> pdb=" O LYS D 321 " (cutoff:3.500A) removed outlier: 7.915A pdb=" N GLY D 323 " --> pdb=" O SER B 320 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N CYS B 322 " --> pdb=" O GLY D 323 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N LEU D 325 " --> pdb=" O CYS B 322 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N SER B 324 " --> pdb=" O LEU D 325 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 328 through 330 removed outlier: 6.374A pdb=" N ILE B 328 " --> pdb=" O HIS F 329 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'D' and resid 337 through 340 removed outlier: 6.551A pdb=" N GLU B 338 " --> pdb=" O VAL F 339 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 343 through 346 Processing sheet with id=AB8, first strand: chain 'D' and resid 351 through 354 removed outlier: 6.403A pdb=" N GLN B 351 " --> pdb=" O SER F 352 " (cutoff:3.500A) removed outlier: 7.806A pdb=" N ILE F 354 " --> pdb=" O GLN B 351 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N LYS B 353 " --> pdb=" O ILE F 354 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 357 through 358 removed outlier: 6.751A pdb=" N LEU B 357 " --> pdb=" O ASP D 358 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 361 through 362 removed outlier: 6.515A pdb=" N THR B 361 " --> pdb=" O HIS D 362 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 368 through 373 removed outlier: 6.417A pdb=" N ASN B 368 " --> pdb=" O LYS D 369 " (cutoff:3.500A) removed outlier: 8.331A pdb=" N ILE D 371 " --> pdb=" O ASN B 368 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N LYS B 370 " --> pdb=" O ILE D 371 " (cutoff:3.500A) removed outlier: 8.506A pdb=" N THR D 373 " --> pdb=" O LYS B 370 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N GLU B 372 " --> pdb=" O THR D 373 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N LYS B 369 " --> pdb=" O LYS F 370 " (cutoff:3.500A) removed outlier: 8.080A pdb=" N GLU F 372 " --> pdb=" O LYS B 369 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N ILE B 371 " --> pdb=" O GLU F 372 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'D' and resid 376 through 377 removed outlier: 6.697A pdb=" N LEU B 376 " --> pdb=" O THR D 377 " (cutoff:3.500A) 56 hydrogen bonds defined for protein. 168 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.44 Time building geometry restraints manager: 0.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 965 1.33 - 1.45: 417 1.45 - 1.57: 2071 1.57 - 1.69: 0 1.69 - 1.81: 6 Bond restraints: 3459 Sorted by residual: bond pdb=" CA GLY E 366 " pdb=" C GLY E 366 " ideal model delta sigma weight residual 1.510 1.563 -0.053 1.39e-02 5.18e+03 1.46e+01 bond pdb=" CA LYS B 331 " pdb=" C LYS B 331 " ideal model delta sigma weight residual 1.532 1.554 -0.022 6.50e-03 2.37e+04 1.17e+01 bond pdb=" CA LYS E 331 " pdb=" C LYS E 331 " ideal model delta sigma weight residual 1.524 1.564 -0.040 1.26e-02 6.30e+03 1.02e+01 bond pdb=" CZ ARG A 349 " pdb=" NH2 ARG A 349 " ideal model delta sigma weight residual 1.330 1.292 0.038 1.30e-02 5.92e+03 8.60e+00 bond pdb=" CZ ARG E 349 " pdb=" NH2 ARG E 349 " ideal model delta sigma weight residual 1.330 1.292 0.038 1.30e-02 5.92e+03 8.40e+00 ... (remaining 3454 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.29: 4149 3.29 - 6.59: 459 6.59 - 9.88: 17 9.88 - 13.18: 3 13.18 - 16.47: 1 Bond angle restraints: 4629 Sorted by residual: angle pdb=" N CYS E 322 " pdb=" CA CYS E 322 " pdb=" C CYS E 322 " ideal model delta sigma weight residual 108.32 124.79 -16.47 1.64e+00 3.72e-01 1.01e+02 angle pdb=" C GLY E 323 " pdb=" N SER E 324 " pdb=" CA SER E 324 " ideal model delta sigma weight residual 122.44 134.40 -11.96 1.45e+00 4.76e-01 6.80e+01 angle pdb=" C GLY E 366 " pdb=" N GLY E 367 " pdb=" CA GLY E 367 " ideal model delta sigma weight residual 120.64 130.18 -9.54 1.26e+00 6.30e-01 5.73e+01 angle pdb=" N GLY E 323 " pdb=" CA GLY E 323 " pdb=" C GLY E 323 " ideal model delta sigma weight residual 112.22 125.05 -12.83 1.74e+00 3.30e-01 5.44e+01 angle pdb=" C GLY E 326 " pdb=" N ASN E 327 " pdb=" CA ASN E 327 " ideal model delta sigma weight residual 121.24 111.22 10.02 1.44e+00 4.82e-01 4.84e+01 ... (remaining 4624 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.44: 1778 11.44 - 22.88: 253 22.88 - 34.31: 53 34.31 - 45.75: 11 45.75 - 57.19: 8 Dihedral angle restraints: 2103 sinusoidal: 876 harmonic: 1227 Sorted by residual: dihedral pdb=" C LYS E 347 " pdb=" N LYS E 347 " pdb=" CA LYS E 347 " pdb=" CB LYS E 347 " ideal model delta harmonic sigma weight residual -122.60 -143.32 20.72 0 2.50e+00 1.60e-01 6.87e+01 dihedral pdb=" N LYS E 347 " pdb=" C LYS E 347 " pdb=" CA LYS E 347 " pdb=" CB LYS E 347 " ideal model delta harmonic sigma weight residual 122.80 142.01 -19.21 0 2.50e+00 1.60e-01 5.91e+01 dihedral pdb=" CA CYS E 322 " pdb=" C CYS E 322 " pdb=" N GLY E 323 " pdb=" CA GLY E 323 " ideal model delta harmonic sigma weight residual 180.00 149.93 30.07 0 5.00e+00 4.00e-02 3.62e+01 ... (remaining 2100 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.173: 466 0.173 - 0.346: 52 0.346 - 0.519: 3 0.519 - 0.693: 0 0.693 - 0.866: 1 Chirality restraints: 522 Sorted by residual: chirality pdb=" CA LYS E 347 " pdb=" N LYS E 347 " pdb=" C LYS E 347 " pdb=" CB LYS E 347 " both_signs ideal model delta sigma weight residual False 2.51 1.64 0.87 2.00e-01 2.50e+01 1.87e+01 chirality pdb=" CA LYS D 347 " pdb=" N LYS D 347 " pdb=" C LYS D 347 " pdb=" CB LYS D 347 " both_signs ideal model delta sigma weight residual False 2.51 2.01 0.50 2.00e-01 2.50e+01 6.34e+00 chirality pdb=" CA LYS B 347 " pdb=" N LYS B 347 " pdb=" C LYS B 347 " pdb=" CB LYS B 347 " both_signs ideal model delta sigma weight residual False 2.51 2.09 0.42 2.00e-01 2.50e+01 4.36e+00 ... (remaining 519 not shown) Planarity restraints: 588 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 310 " 0.160 2.00e-02 2.50e+03 8.90e-02 1.58e+02 pdb=" CG TYR A 310 " -0.047 2.00e-02 2.50e+03 pdb=" CD1 TYR A 310 " -0.061 2.00e-02 2.50e+03 pdb=" CD2 TYR A 310 " -0.078 2.00e-02 2.50e+03 pdb=" CE1 TYR A 310 " -0.057 2.00e-02 2.50e+03 pdb=" CE2 TYR A 310 " -0.047 2.00e-02 2.50e+03 pdb=" CZ TYR A 310 " -0.012 2.00e-02 2.50e+03 pdb=" OH TYR A 310 " 0.142 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 310 " 0.144 2.00e-02 2.50e+03 8.01e-02 1.28e+02 pdb=" CG TYR C 310 " -0.042 2.00e-02 2.50e+03 pdb=" CD1 TYR C 310 " -0.057 2.00e-02 2.50e+03 pdb=" CD2 TYR C 310 " -0.070 2.00e-02 2.50e+03 pdb=" CE1 TYR C 310 " -0.050 2.00e-02 2.50e+03 pdb=" CE2 TYR C 310 " -0.045 2.00e-02 2.50e+03 pdb=" CZ TYR C 310 " -0.007 2.00e-02 2.50e+03 pdb=" OH TYR C 310 " 0.127 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS E 362 " -0.081 2.00e-02 2.50e+03 6.04e-02 5.46e+01 pdb=" CG HIS E 362 " 0.096 2.00e-02 2.50e+03 pdb=" ND1 HIS E 362 " 0.037 2.00e-02 2.50e+03 pdb=" CD2 HIS E 362 " 0.033 2.00e-02 2.50e+03 pdb=" CE1 HIS E 362 " -0.046 2.00e-02 2.50e+03 pdb=" NE2 HIS E 362 " -0.039 2.00e-02 2.50e+03 ... (remaining 585 not shown) Histogram of nonbonded interaction distances: 2.54 - 3.01: 1722 3.01 - 3.48: 2786 3.48 - 3.96: 5333 3.96 - 4.43: 5408 4.43 - 4.90: 10265 Nonbonded interactions: 25514 Sorted by model distance: nonbonded pdb=" OD1 ASP E 314 " pdb=" OG SER E 316 " model vdw 2.539 3.040 nonbonded pdb=" OD1 ASP B 314 " pdb=" OG SER B 316 " model vdw 2.544 3.040 nonbonded pdb=" OD1 ASP F 314 " pdb=" OG SER F 316 " model vdw 2.546 3.040 nonbonded pdb=" OD1 ASP D 314 " pdb=" OG SER D 316 " model vdw 2.554 3.040 nonbonded pdb=" OD1 ASP C 314 " pdb=" OG SER C 316 " model vdw 2.563 3.040 ... (remaining 25509 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 306 through 378) selection = chain 'B' selection = (chain 'C' and resid 306 through 378) selection = chain 'D' selection = (chain 'E' and resid 306 through 378) 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: 4.440 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: 0.010 Extract box with map and model: 0.100 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 5.730 Find NCS groups from input model: 0.070 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:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7028 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 0.053 3459 Z= 0.733 Angle : 2.075 16.473 4629 Z= 1.364 Chirality : 0.115 0.866 522 Planarity : 0.012 0.089 588 Dihedral : 11.489 57.185 1323 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 0.29 Ramachandran Plot: Outliers : 0.23 % Allowed : 5.29 % Favored : 94.48 % Rotamer: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Cbeta Deviations : 0.51 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.24 % 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: -2.17 (0.32), residues: 435 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.64 (0.25), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 349 TYR 0.160 0.039 TYR A 310 PHE 0.045 0.014 PHE E 378 HIS 0.040 0.004 HIS E 330 Details of bonding type rmsd covalent geometry : bond 0.01145 ( 3459) covalent geometry : angle 2.07467 ( 4629) hydrogen bonds : bond 0.11466 ( 56) hydrogen bonds : angle 7.64931 ( 168) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 870 Ramachandran restraints generated. 435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 870 Ramachandran restraints generated. 435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 61 time to evaluate : 0.105 Fit side-chains REVERT: C 321 LYS cc_start: 0.7785 (mttt) cc_final: 0.7209 (ttmm) REVERT: C 349 ARG cc_start: 0.7314 (mtm180) cc_final: 0.7041 (mtp-110) REVERT: C 358 ASP cc_start: 0.7265 (m-30) cc_final: 0.6335 (m-30) REVERT: E 311 LYS cc_start: 0.8214 (pttt) cc_final: 0.7736 (ptmm) REVERT: E 317 LYS cc_start: 0.7356 (pttt) cc_final: 0.6673 (ptmt) REVERT: B 375 LYS cc_start: 0.7998 (tttt) cc_final: 0.7628 (tttp) REVERT: D 322 CYS cc_start: 0.8257 (p) cc_final: 0.7470 (m) REVERT: D 347 LYS cc_start: 0.7106 (ptmt) cc_final: 0.6475 (tppt) REVERT: D 372 GLU cc_start: 0.8473 (mt-10) cc_final: 0.8258 (mt-10) REVERT: F 375 LYS cc_start: 0.8564 (tttt) cc_final: 0.8105 (ttmt) outliers start: 0 outliers final: 0 residues processed: 61 average time/residue: 0.1188 time to fit residues: 8.1276 Evaluate side-chains 44 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 44 time to evaluate : 0.086 ------------------------------------------------------------------------------- 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: 1.9990 chunk 2 optimal weight: 1.9990 chunk 16 optimal weight: 4.9990 chunk 32 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 19 optimal weight: 1.9990 chunk 30 optimal weight: 0.9980 chunk 22 optimal weight: 4.9990 chunk 37 optimal weight: 1.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 362 HIS C 362 HIS E 330 HIS E 362 HIS B 327 ASN B 362 HIS D 330 HIS D 362 HIS F 327 ASN ** F 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 362 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4752 r_free = 0.4752 target = 0.265326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.4999 r_free = 0.4999 target = 0.228133 restraints weight = 3832.158| |-----------------------------------------------------------------------------| r_work (start): 0.4687 rms_B_bonded: 0.96 r_work: 0.5005 rms_B_bonded: 0.50 restraints_weight: 0.5000 r_work: 0.4973 rms_B_bonded: 0.90 restraints_weight: 0.2500 r_work: 0.4783 rms_B_bonded: 3.23 restraints_weight: 0.1250 r_work (final): 0.4783 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7733 moved from start: 0.2478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3459 Z= 0.143 Angle : 0.761 9.554 4629 Z= 0.394 Chirality : 0.054 0.179 522 Planarity : 0.004 0.043 588 Dihedral : 7.722 39.418 456 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 0.26 % Allowed : 10.00 % Favored : 89.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.47 % 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: -1.91 (0.32), residues: 435 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.45 (0.25), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 349 TYR 0.017 0.003 TYR B 310 PHE 0.011 0.002 PHE E 378 HIS 0.004 0.001 HIS F 329 Details of bonding type rmsd covalent geometry : bond 0.00311 ( 3459) covalent geometry : angle 0.76128 ( 4629) hydrogen bonds : bond 0.02614 ( 56) hydrogen bonds : angle 5.96900 ( 168) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 870 Ramachandran restraints generated. 435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 870 Ramachandran restraints generated. 435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 49 time to evaluate : 0.133 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 49 average time/residue: 0.1292 time to fit residues: 6.9669 Evaluate side-chains 34 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 33 time to evaluate : 0.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 319 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 14 optimal weight: 0.3980 chunk 16 optimal weight: 0.8980 chunk 31 optimal weight: 9.9990 chunk 19 optimal weight: 7.9990 chunk 9 optimal weight: 10.0000 chunk 39 optimal weight: 9.9990 chunk 17 optimal weight: 6.9990 chunk 13 optimal weight: 10.0000 chunk 5 optimal weight: 5.9990 chunk 8 optimal weight: 0.9990 chunk 26 optimal weight: 8.9990 overall best weight: 3.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 330 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4690 r_free = 0.4690 target = 0.257942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4940 r_free = 0.4940 target = 0.220548 restraints weight = 3873.361| |-----------------------------------------------------------------------------| r_work (start): 0.4616 rms_B_bonded: 0.98 r_work: 0.4946 rms_B_bonded: 0.50 restraints_weight: 0.5000 r_work: 0.4910 rms_B_bonded: 0.91 restraints_weight: 0.2500 r_work: 0.4719 rms_B_bonded: 3.22 restraints_weight: 0.1250 r_work (final): 0.4719 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.3307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 3459 Z= 0.188 Angle : 0.746 10.122 4629 Z= 0.384 Chirality : 0.055 0.156 522 Planarity : 0.004 0.040 588 Dihedral : 6.934 28.415 456 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 1.79 % Allowed : 11.28 % Favored : 86.92 % 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: -1.93 (0.32), residues: 435 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.46 (0.25), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 349 TYR 0.022 0.004 TYR E 310 PHE 0.007 0.001 PHE E 346 HIS 0.004 0.001 HIS E 330 Details of bonding type rmsd covalent geometry : bond 0.00423 ( 3459) covalent geometry : angle 0.74611 ( 4629) hydrogen bonds : bond 0.02566 ( 56) hydrogen bonds : angle 5.54595 ( 168) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 870 Ramachandran restraints generated. 435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 870 Ramachandran restraints generated. 435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 40 time to evaluate : 0.088 Fit side-chains REVERT: D 317 LYS cc_start: 0.8120 (OUTLIER) cc_final: 0.7674 (ptmt) outliers start: 7 outliers final: 5 residues processed: 45 average time/residue: 0.1303 time to fit residues: 6.5497 Evaluate side-chains 36 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 30 time to evaluate : 0.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 358 ASP Chi-restraints excluded: chain A residue 359 ASN Chi-restraints excluded: chain E residue 306 VAL Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain D residue 317 LYS Chi-restraints excluded: chain D residue 319 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 30 optimal weight: 0.0570 chunk 23 optimal weight: 5.9990 chunk 4 optimal weight: 10.0000 chunk 16 optimal weight: 7.9990 chunk 41 optimal weight: 10.0000 chunk 36 optimal weight: 7.9990 chunk 13 optimal weight: 7.9990 chunk 37 optimal weight: 0.7980 chunk 8 optimal weight: 0.9990 chunk 33 optimal weight: 9.9990 chunk 18 optimal weight: 0.7980 overall best weight: 1.7302 ------------------------------------------------------------------------------- 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 = 0.4451 r_free = 0.4451 target = 0.126129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4273 r_free = 0.4273 target = 0.110033 restraints weight = 4569.772| |-----------------------------------------------------------------------------| r_work (start): 0.4247 rms_B_bonded: 2.54 r_work: 0.4127 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.4012 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.4012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 0.3578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3459 Z= 0.133 Angle : 0.664 8.428 4629 Z= 0.338 Chirality : 0.051 0.132 522 Planarity : 0.004 0.039 588 Dihedral : 6.432 30.425 456 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 2.31 % Allowed : 13.33 % Favored : 84.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.24 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.01 (0.32), residues: 435 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.52 (0.25), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 349 TYR 0.017 0.003 TYR B 310 PHE 0.005 0.001 PHE B 346 HIS 0.003 0.001 HIS E 362 Details of bonding type rmsd covalent geometry : bond 0.00297 ( 3459) covalent geometry : angle 0.66424 ( 4629) hydrogen bonds : bond 0.02351 ( 56) hydrogen bonds : angle 5.51321 ( 168) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 870 Ramachandran restraints generated. 435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 870 Ramachandran restraints generated. 435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 30 time to evaluate : 0.121 Fit side-chains REVERT: D 317 LYS cc_start: 0.7901 (OUTLIER) cc_final: 0.6998 (ptmt) outliers start: 9 outliers final: 6 residues processed: 35 average time/residue: 0.1473 time to fit residues: 5.7197 Evaluate side-chains 34 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 27 time to evaluate : 0.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 359 ASN Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain E residue 306 VAL Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain D residue 317 LYS Chi-restraints excluded: chain D residue 319 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 22 optimal weight: 10.0000 chunk 38 optimal weight: 5.9990 chunk 8 optimal weight: 10.0000 chunk 19 optimal weight: 10.0000 chunk 36 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 chunk 9 optimal weight: 3.9990 chunk 33 optimal weight: 6.9990 chunk 13 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 16 optimal weight: 10.0000 overall best weight: 2.3990 ------------------------------------------------------------------------------- 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 = 0.4677 r_free = 0.4677 target = 0.256275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4912 r_free = 0.4912 target = 0.220492 restraints weight = 3897.466| |-----------------------------------------------------------------------------| r_work (start): 0.4606 rms_B_bonded: 1.13 r_work: 0.4914 rms_B_bonded: 0.57 restraints_weight: 0.5000 r_work: 0.4871 rms_B_bonded: 1.04 restraints_weight: 0.2500 r_work: 0.4659 rms_B_bonded: 3.77 restraints_weight: 0.1250 r_work (final): 0.4659 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.3760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 3459 Z= 0.158 Angle : 0.662 7.782 4629 Z= 0.338 Chirality : 0.052 0.134 522 Planarity : 0.004 0.040 588 Dihedral : 6.300 30.209 456 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 2.05 % Allowed : 13.33 % Favored : 84.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.24 % 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: -2.07 (0.32), residues: 435 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.57 (0.25), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 349 TYR 0.019 0.004 TYR E 310 PHE 0.007 0.001 PHE E 346 HIS 0.003 0.001 HIS E 362 Details of bonding type rmsd covalent geometry : bond 0.00351 ( 3459) covalent geometry : angle 0.66211 ( 4629) hydrogen bonds : bond 0.02196 ( 56) hydrogen bonds : angle 5.30209 ( 168) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 870 Ramachandran restraints generated. 435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 870 Ramachandran restraints generated. 435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 36 time to evaluate : 0.144 Fit side-chains REVERT: D 317 LYS cc_start: 0.7945 (OUTLIER) cc_final: 0.7532 (ptmt) outliers start: 8 outliers final: 7 residues processed: 40 average time/residue: 0.1497 time to fit residues: 6.5658 Evaluate side-chains 34 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 26 time to evaluate : 0.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 358 ASP Chi-restraints excluded: chain A residue 359 ASN Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain E residue 306 VAL Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain D residue 317 LYS Chi-restraints excluded: chain D residue 319 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 17 optimal weight: 9.9990 chunk 12 optimal weight: 6.9990 chunk 10 optimal weight: 6.9990 chunk 35 optimal weight: 4.9990 chunk 31 optimal weight: 9.9990 chunk 4 optimal weight: 10.0000 chunk 29 optimal weight: 0.8980 chunk 36 optimal weight: 8.9990 chunk 18 optimal weight: 3.9990 chunk 2 optimal weight: 9.9990 chunk 25 optimal weight: 9.9990 overall best weight: 4.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 307 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4315 r_free = 0.4315 target = 0.116872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.100828 restraints weight = 4870.769| |-----------------------------------------------------------------------------| r_work (start): 0.4108 rms_B_bonded: 2.59 r_work: 0.3979 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3863 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3863 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.3999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 3459 Z= 0.281 Angle : 0.781 7.877 4629 Z= 0.404 Chirality : 0.055 0.162 522 Planarity : 0.004 0.041 588 Dihedral : 6.870 30.478 456 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 2.56 % Allowed : 13.85 % Favored : 83.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.24 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.25 (0.32), residues: 435 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.71 (0.25), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 349 TYR 0.030 0.006 TYR E 310 PHE 0.014 0.002 PHE E 346 HIS 0.005 0.001 HIS E 362 Details of bonding type rmsd covalent geometry : bond 0.00624 ( 3459) covalent geometry : angle 0.78107 ( 4629) hydrogen bonds : bond 0.02529 ( 56) hydrogen bonds : angle 5.48989 ( 168) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 870 Ramachandran restraints generated. 435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 870 Ramachandran restraints generated. 435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 32 time to evaluate : 0.149 Fit side-chains REVERT: A 321 LYS cc_start: 0.7730 (mttt) cc_final: 0.7471 (ttmm) REVERT: D 317 LYS cc_start: 0.7987 (OUTLIER) cc_final: 0.7045 (ptmt) REVERT: F 322 CYS cc_start: 0.8512 (p) cc_final: 0.8067 (m) REVERT: F 336 GLN cc_start: 0.7974 (mp10) cc_final: 0.7698 (tt0) outliers start: 10 outliers final: 8 residues processed: 37 average time/residue: 0.1370 time to fit residues: 5.7160 Evaluate side-chains 39 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 30 time to evaluate : 0.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 358 ASP Chi-restraints excluded: chain A residue 359 ASN Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain E residue 306 VAL Chi-restraints excluded: chain B residue 307 GLN Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain D residue 317 LYS Chi-restraints excluded: chain D residue 319 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 39 optimal weight: 9.9990 chunk 25 optimal weight: 2.9990 chunk 6 optimal weight: 7.9990 chunk 34 optimal weight: 7.9990 chunk 2 optimal weight: 6.9990 chunk 38 optimal weight: 0.1980 chunk 4 optimal weight: 10.0000 chunk 18 optimal weight: 0.5980 chunk 21 optimal weight: 7.9990 chunk 35 optimal weight: 2.9990 chunk 22 optimal weight: 6.9990 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 307 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4632 r_free = 0.4632 target = 0.253000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4872 r_free = 0.4872 target = 0.215835 restraints weight = 3992.319| |-----------------------------------------------------------------------------| r_work (start): 0.4554 rms_B_bonded: 1.00 r_work: 0.4879 rms_B_bonded: 0.48 restraints_weight: 0.5000 r_work: 0.4842 rms_B_bonded: 0.87 restraints_weight: 0.2500 r_work: 0.4649 rms_B_bonded: 3.17 restraints_weight: 0.1250 r_work (final): 0.4649 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.4064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 3459 Z= 0.179 Angle : 0.686 7.319 4629 Z= 0.352 Chirality : 0.052 0.143 522 Planarity : 0.004 0.039 588 Dihedral : 6.560 29.751 456 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 2.56 % Allowed : 13.85 % Favored : 83.59 % 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: -2.35 (0.32), residues: 435 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.78 (0.24), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 349 TYR 0.018 0.004 TYR E 310 PHE 0.007 0.001 PHE E 346 HIS 0.004 0.001 HIS E 362 Details of bonding type rmsd covalent geometry : bond 0.00400 ( 3459) covalent geometry : angle 0.68607 ( 4629) hydrogen bonds : bond 0.02277 ( 56) hydrogen bonds : angle 5.31302 ( 168) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 870 Ramachandran restraints generated. 435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 870 Ramachandran restraints generated. 435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 29 time to evaluate : 0.150 Fit side-chains REVERT: D 317 LYS cc_start: 0.7922 (OUTLIER) cc_final: 0.7500 (ptmt) outliers start: 10 outliers final: 8 residues processed: 33 average time/residue: 0.1743 time to fit residues: 6.4350 Evaluate side-chains 36 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 27 time to evaluate : 0.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 358 ASP Chi-restraints excluded: chain A residue 359 ASN Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain E residue 306 VAL Chi-restraints excluded: chain B residue 307 GLN Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain D residue 317 LYS Chi-restraints excluded: chain D residue 319 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 37 optimal weight: 5.9990 chunk 28 optimal weight: 7.9990 chunk 15 optimal weight: 9.9990 chunk 39 optimal weight: 0.9980 chunk 29 optimal weight: 0.5980 chunk 23 optimal weight: 7.9990 chunk 19 optimal weight: 8.9990 chunk 31 optimal weight: 4.9990 chunk 14 optimal weight: 4.9990 chunk 38 optimal weight: 0.0770 chunk 5 optimal weight: 6.9990 overall best weight: 2.3342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 307 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4645 r_free = 0.4645 target = 0.253878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4880 r_free = 0.4880 target = 0.216684 restraints weight = 3970.352| |-----------------------------------------------------------------------------| r_work (start): 0.4570 rms_B_bonded: 1.02 r_work: 0.4888 rms_B_bonded: 0.49 restraints_weight: 0.5000 r_work: 0.4852 rms_B_bonded: 0.89 restraints_weight: 0.2500 r_work: 0.4663 rms_B_bonded: 3.21 restraints_weight: 0.1250 r_work (final): 0.4663 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.4192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3459 Z= 0.156 Angle : 0.657 6.707 4629 Z= 0.336 Chirality : 0.051 0.138 522 Planarity : 0.004 0.040 588 Dihedral : 6.307 29.519 456 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 2.82 % Allowed : 14.10 % Favored : 83.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -2.38 (0.32), residues: 435 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.80 (0.24), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 349 TYR 0.016 0.004 TYR E 310 PHE 0.006 0.001 PHE E 346 HIS 0.004 0.001 HIS E 362 Details of bonding type rmsd covalent geometry : bond 0.00349 ( 3459) covalent geometry : angle 0.65688 ( 4629) hydrogen bonds : bond 0.02081 ( 56) hydrogen bonds : angle 5.20801 ( 168) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 870 Ramachandran restraints generated. 435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 870 Ramachandran restraints generated. 435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 29 time to evaluate : 0.138 Fit side-chains REVERT: D 317 LYS cc_start: 0.7855 (OUTLIER) cc_final: 0.7460 (ptmt) outliers start: 11 outliers final: 8 residues processed: 34 average time/residue: 0.1730 time to fit residues: 6.4926 Evaluate side-chains 39 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 30 time to evaluate : 0.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 358 ASP Chi-restraints excluded: chain A residue 359 ASN Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain E residue 306 VAL Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain D residue 317 LYS Chi-restraints excluded: chain D residue 319 THR Chi-restraints excluded: chain F residue 319 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 7 optimal weight: 10.0000 chunk 18 optimal weight: 9.9990 chunk 36 optimal weight: 10.0000 chunk 40 optimal weight: 9.9990 chunk 20 optimal weight: 1.9990 chunk 8 optimal weight: 0.9990 chunk 17 optimal weight: 9.9990 chunk 14 optimal weight: 4.9990 chunk 16 optimal weight: 7.9990 chunk 37 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- 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 = 0.4641 r_free = 0.4641 target = 0.253172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4877 r_free = 0.4877 target = 0.216142 restraints weight = 3960.005| |-----------------------------------------------------------------------------| r_work (start): 0.4566 rms_B_bonded: 1.01 r_work: 0.4889 rms_B_bonded: 0.49 restraints_weight: 0.5000 r_work: 0.4849 rms_B_bonded: 0.89 restraints_weight: 0.2500 r_work: 0.4662 rms_B_bonded: 3.18 restraints_weight: 0.1250 r_work (final): 0.4662 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.4300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 3459 Z= 0.166 Angle : 0.660 6.744 4629 Z= 0.336 Chirality : 0.051 0.138 522 Planarity : 0.004 0.040 588 Dihedral : 6.176 28.348 456 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 2.82 % Allowed : 14.62 % Favored : 82.56 % 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: -2.42 (0.32), residues: 435 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.83 (0.24), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 349 TYR 0.017 0.004 TYR E 310 PHE 0.007 0.001 PHE E 346 HIS 0.004 0.001 HIS E 362 Details of bonding type rmsd covalent geometry : bond 0.00370 ( 3459) covalent geometry : angle 0.65969 ( 4629) hydrogen bonds : bond 0.02067 ( 56) hydrogen bonds : angle 5.14769 ( 168) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 870 Ramachandran restraints generated. 435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 870 Ramachandran restraints generated. 435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 31 time to evaluate : 0.085 Fit side-chains REVERT: E 317 LYS cc_start: 0.7976 (ptmt) cc_final: 0.7749 (ptpp) REVERT: D 317 LYS cc_start: 0.7840 (OUTLIER) cc_final: 0.7481 (ptmt) REVERT: F 349 ARG cc_start: 0.7384 (mtp180) cc_final: 0.6820 (mtp180) outliers start: 11 outliers final: 9 residues processed: 37 average time/residue: 0.1644 time to fit residues: 6.8052 Evaluate side-chains 40 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 30 time to evaluate : 0.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 358 ASP Chi-restraints excluded: chain A residue 359 ASN Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain E residue 306 VAL Chi-restraints excluded: chain E residue 327 ASN Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain D residue 317 LYS Chi-restraints excluded: chain D residue 319 THR Chi-restraints excluded: chain F residue 319 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 5 optimal weight: 10.0000 chunk 38 optimal weight: 0.0370 chunk 3 optimal weight: 10.0000 chunk 1 optimal weight: 10.0000 chunk 27 optimal weight: 10.0000 chunk 37 optimal weight: 7.9990 chunk 6 optimal weight: 3.9990 chunk 24 optimal weight: 9.9990 chunk 35 optimal weight: 9.9990 chunk 22 optimal weight: 5.9990 chunk 10 optimal weight: 7.9990 overall best weight: 5.2066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 307 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4587 r_free = 0.4587 target = 0.248001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4827 r_free = 0.4827 target = 0.210476 restraints weight = 3994.150| |-----------------------------------------------------------------------------| r_work (start): 0.4201 rms_B_bonded: 0.99 r_work: 0.4132 rms_B_bonded: 1.09 restraints_weight: 0.5000 r_work: 0.4061 rms_B_bonded: 1.89 restraints_weight: 0.2500 r_work (final): 0.4061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.4381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.043 3459 Z= 0.298 Angle : 0.781 7.158 4629 Z= 0.403 Chirality : 0.056 0.171 522 Planarity : 0.004 0.038 588 Dihedral : 6.701 30.020 456 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 2.82 % Allowed : 14.87 % Favored : 82.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.24 % 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: -2.60 (0.32), residues: 435 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.97 (0.24), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 349 TYR 0.029 0.006 TYR E 310 PHE 0.015 0.002 PHE E 346 HIS 0.005 0.001 HIS E 329 Details of bonding type rmsd covalent geometry : bond 0.00659 ( 3459) covalent geometry : angle 0.78059 ( 4629) hydrogen bonds : bond 0.02506 ( 56) hydrogen bonds : angle 5.33018 ( 168) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 870 Ramachandran restraints generated. 435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 870 Ramachandran restraints generated. 435 Oldfield, 0 Emsley, 435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 36 time to evaluate : 0.141 Fit side-chains REVERT: A 321 LYS cc_start: 0.7862 (mttt) cc_final: 0.7619 (ttmm) REVERT: E 311 LYS cc_start: 0.8660 (ptmm) cc_final: 0.6731 (tppt) REVERT: E 317 LYS cc_start: 0.7773 (ptmt) cc_final: 0.7219 (ptpp) REVERT: B 317 LYS cc_start: 0.7556 (pttt) cc_final: 0.7057 (ptpp) REVERT: B 353 LYS cc_start: 0.7865 (mttt) cc_final: 0.7588 (mttp) REVERT: D 317 LYS cc_start: 0.8058 (OUTLIER) cc_final: 0.7131 (ptmt) REVERT: F 349 ARG cc_start: 0.7124 (mtp180) cc_final: 0.6500 (mtp180) outliers start: 11 outliers final: 10 residues processed: 42 average time/residue: 0.1969 time to fit residues: 9.0239 Evaluate side-chains 40 residues out of total 390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 29 time to evaluate : 0.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 358 ASP Chi-restraints excluded: chain A residue 359 ASN Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain E residue 306 VAL Chi-restraints excluded: chain B residue 307 GLN Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain D residue 317 LYS Chi-restraints excluded: chain D residue 319 THR Chi-restraints excluded: chain F residue 319 THR Chi-restraints excluded: chain F residue 360 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 39 optimal weight: 2.9990 chunk 12 optimal weight: 7.9990 chunk 10 optimal weight: 6.9990 chunk 29 optimal weight: 7.9990 chunk 3 optimal weight: 3.9990 chunk 22 optimal weight: 2.9990 chunk 24 optimal weight: 9.9990 chunk 26 optimal weight: 8.9990 chunk 15 optimal weight: 6.9990 chunk 41 optimal weight: 6.9990 chunk 5 optimal weight: 1.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 307 GLN F 351 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4596 r_free = 0.4596 target = 0.249206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4837 r_free = 0.4837 target = 0.211541 restraints weight = 3999.283| |-----------------------------------------------------------------------------| r_work (start): 0.4520 rms_B_bonded: 0.99 r_work: 0.4849 rms_B_bonded: 0.47 restraints_weight: 0.5000 r_work: 0.4814 rms_B_bonded: 0.84 restraints_weight: 0.2500 r_work: 0.4632 rms_B_bonded: 2.95 restraints_weight: 0.1250 r_work (final): 0.4632 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.4471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 3459 Z= 0.230 Angle : 0.731 7.265 4629 Z= 0.376 Chirality : 0.054 0.154 522 Planarity : 0.004 0.041 588 Dihedral : 6.584 30.260 456 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 3.33 % Allowed : 14.62 % Favored : 82.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.24 % 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: -2.65 (0.32), residues: 435 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.01 (0.24), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 349 TYR 0.022 0.005 TYR C 310 PHE 0.010 0.002 PHE E 346 HIS 0.005 0.001 HIS E 362 Details of bonding type rmsd covalent geometry : bond 0.00511 ( 3459) covalent geometry : angle 0.73124 ( 4629) hydrogen bonds : bond 0.02351 ( 56) hydrogen bonds : angle 5.28410 ( 168) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1154.73 seconds wall clock time: 20 minutes 37.30 seconds (1237.30 seconds total)