Starting phenix.real_space_refine on Fri Oct 10 11:07:21 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8q88_18249/10_2025/8q88_18249.cif Found real_map, /net/cci-nas-00/data/ceres_data/8q88_18249/10_2025/8q88_18249.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.95 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8q88_18249/10_2025/8q88_18249.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8q88_18249/10_2025/8q88_18249.map" model { file = "/net/cci-nas-00/data/ceres_data/8q88_18249/10_2025/8q88_18249.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8q88_18249/10_2025/8q88_18249.cif" } resolution = 2.95 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= 0.003 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 2172 2.51 5 N 642 2.21 5 O 648 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 3468 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: "B" 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: "D" 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: "F" Number of atoms: 578 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 578 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 3, 'TRANS': 72} Time building chain proxies: 1.10, per 1000 atoms: 0.32 Number of scatterers: 3468 At special positions: 0 Unit cell: (137.608, 88.168, 39.552, 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 648 8.00 N 642 7.00 C 2172 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: 0.26 Conformation dependent library (CDL) restraints added in 134.7 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 792 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 18 sheets defined 0.0% alpha, 50.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.15 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 306 through 310 removed outlier: 6.547A pdb=" N GLN A 307 " --> pdb=" O ILE D 308 " (cutoff:3.500A) removed outlier: 7.678A pdb=" N TYR D 310 " --> pdb=" O GLN A 307 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N VAL A 309 " --> pdb=" O TYR D 310 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 313 through 314 removed outlier: 6.826A pdb=" N VAL A 313 " --> pdb=" O ASP D 314 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 317 through 322 removed outlier: 6.386A pdb=" N VAL B 318 " --> pdb=" O THR D 319 " (cutoff:3.500A) removed outlier: 8.128A pdb=" N LYS D 321 " --> pdb=" O VAL B 318 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N SER B 320 " --> pdb=" O LYS D 321 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 325 through 330 removed outlier: 7.010A pdb=" N GLY D 326 " --> pdb=" O LEU A 325 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N ASN A 327 " --> pdb=" O GLY D 326 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N GLY B 326 " --> pdb=" O ASN D 327 " (cutoff:3.500A) removed outlier: 8.440A pdb=" N HIS D 329 " --> pdb=" O GLY B 326 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N ILE B 328 " --> pdb=" O HIS D 329 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 336 through 340 removed outlier: 6.473A pdb=" N VAL B 337 " --> pdb=" O GLU D 338 " (cutoff:3.500A) removed outlier: 8.235A pdb=" N LYS D 340 " --> pdb=" O VAL B 337 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N VAL B 339 " --> pdb=" O LYS D 340 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 343 through 348 removed outlier: 7.027A pdb=" N LEU A 344 " --> pdb=" O LYS D 343 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N ASP D 345 " --> pdb=" O LEU A 344 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N PHE A 346 " --> pdb=" O ASP D 345 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N LYS D 347 " --> pdb=" O PHE A 346 " (cutoff:3.500A) removed outlier: 9.256A pdb=" N LYS B 343 " --> pdb=" O LEU D 344 " (cutoff:3.500A) removed outlier: 9.816A pdb=" N PHE D 346 " --> pdb=" O LYS B 343 " (cutoff:3.500A) removed outlier: 8.727A pdb=" N ASP B 345 " --> pdb=" O PHE D 346 " (cutoff:3.500A) removed outlier: 9.188A pdb=" N ASP D 348 " --> pdb=" O ASP B 345 " (cutoff:3.500A) removed outlier: 5.759A pdb=" N LYS B 347 " --> pdb=" O ASP D 348 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 353 through 354 removed outlier: 6.607A pdb=" N LYS A 353 " --> pdb=" O ILE D 354 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 357 through 362 Processing sheet with id=AA9, first strand: chain 'A' and resid 369 through 378 removed outlier: 6.509A pdb=" N LYS A 369 " --> pdb=" O LYS D 370 " (cutoff:3.500A) removed outlier: 7.938A pdb=" N GLU D 372 " --> pdb=" O LYS A 369 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N ILE A 371 " --> pdb=" O GLU D 372 " (cutoff:3.500A) removed outlier: 7.833A pdb=" N HIS D 374 " --> pdb=" O ILE A 371 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N THR A 373 " --> pdb=" O HIS D 374 " (cutoff:3.500A) removed outlier: 8.008A pdb=" N LEU D 376 " --> pdb=" O THR A 373 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N LYS A 375 " --> pdb=" O LEU D 376 " (cutoff:3.500A) removed outlier: 7.852A pdb=" N PHE D 378 " --> pdb=" O LYS A 375 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N THR A 377 " --> pdb=" O PHE D 378 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 306 through 310 removed outlier: 6.557A pdb=" N GLN C 307 " --> pdb=" O ILE F 308 " (cutoff:3.500A) removed outlier: 7.761A pdb=" N TYR F 310 " --> pdb=" O GLN C 307 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N VAL C 309 " --> pdb=" O TYR F 310 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 313 through 314 removed outlier: 6.910A pdb=" N VAL C 313 " --> pdb=" O ASP F 314 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 317 through 322 removed outlier: 6.390A pdb=" N VAL C 318 " --> pdb=" O THR E 319 " (cutoff:3.500A) removed outlier: 8.027A pdb=" N LYS E 321 " --> pdb=" O VAL C 318 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N SER C 320 " --> pdb=" O LYS E 321 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 325 through 330 removed outlier: 5.859A pdb=" N GLY C 326 " --> pdb=" O ASN E 327 " (cutoff:3.500A) removed outlier: 8.355A pdb=" N HIS E 329 " --> pdb=" O GLY C 326 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N ILE C 328 " --> pdb=" O HIS E 329 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N GLY F 326 " --> pdb=" O LEU C 325 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N ASN C 327 " --> pdb=" O GLY F 326 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 336 through 340 removed outlier: 6.502A pdb=" N VAL C 337 " --> pdb=" O GLU E 338 " (cutoff:3.500A) removed outlier: 8.313A pdb=" N LYS E 340 " --> pdb=" O VAL C 337 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N VAL C 339 " --> pdb=" O LYS E 340 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 343 through 348 removed outlier: 9.132A pdb=" N LYS C 343 " --> pdb=" O LEU E 344 " (cutoff:3.500A) removed outlier: 9.856A pdb=" N PHE E 346 " --> pdb=" O LYS C 343 " (cutoff:3.500A) removed outlier: 8.710A pdb=" N ASP C 345 " --> pdb=" O PHE E 346 " (cutoff:3.500A) removed outlier: 9.362A pdb=" N ASP E 348 " --> pdb=" O ASP C 345 " (cutoff:3.500A) removed outlier: 5.817A pdb=" N LYS C 347 " --> pdb=" O ASP E 348 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N LEU C 344 " --> pdb=" O LYS F 343 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N ASP F 345 " --> pdb=" O LEU C 344 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N PHE C 346 " --> pdb=" O ASP F 345 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N LYS F 347 " --> pdb=" O PHE C 346 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 353 through 354 removed outlier: 6.576A pdb=" N LYS C 353 " --> pdb=" O ILE F 354 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 357 through 362 removed outlier: 6.260A pdb=" N ASP C 358 " --> pdb=" O ASN F 359 " (cutoff:3.500A) removed outlier: 7.827A pdb=" N THR F 361 " --> pdb=" O ASP C 358 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N ILE C 360 " --> pdb=" O THR F 361 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 369 through 378 removed outlier: 7.730A pdb=" N GLU F 372 " --> pdb=" O LYS C 369 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N ILE C 371 " --> pdb=" O GLU F 372 " (cutoff:3.500A) removed outlier: 7.805A pdb=" N HIS F 374 " --> pdb=" O ILE C 371 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N THR C 373 " --> pdb=" O HIS F 374 " (cutoff:3.500A) removed outlier: 7.990A pdb=" N LEU F 376 " --> pdb=" O THR C 373 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N LYS C 375 " --> pdb=" O LEU F 376 " (cutoff:3.500A) 71 hydrogen bonds defined for protein. 213 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: 0.43 Time building geometry restraints manager: 0.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 1044 1.33 - 1.45: 390 1.45 - 1.57: 2082 1.57 - 1.69: 0 1.69 - 1.81: 6 Bond restraints: 3522 Sorted by residual: bond pdb=" N LYS F 370 " pdb=" CA LYS F 370 " ideal model delta sigma weight residual 1.458 1.491 -0.032 1.19e-02 7.06e+03 7.43e+00 bond pdb=" CZ ARG C 349 " pdb=" NH2 ARG C 349 " ideal model delta sigma weight residual 1.330 1.295 0.035 1.30e-02 5.92e+03 7.32e+00 bond pdb=" CZ ARG B 349 " pdb=" NH2 ARG B 349 " ideal model delta sigma weight residual 1.330 1.295 0.035 1.30e-02 5.92e+03 7.30e+00 bond pdb=" CZ ARG F 349 " pdb=" NH2 ARG F 349 " ideal model delta sigma weight residual 1.330 1.295 0.035 1.30e-02 5.92e+03 7.27e+00 bond pdb=" CZ ARG D 349 " pdb=" NH2 ARG D 349 " ideal model delta sigma weight residual 1.330 1.296 0.034 1.30e-02 5.92e+03 6.99e+00 ... (remaining 3517 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.22: 3710 2.22 - 4.44: 905 4.44 - 6.67: 91 6.67 - 8.89: 3 8.89 - 11.11: 1 Bond angle restraints: 4710 Sorted by residual: angle pdb=" N HIS E 362 " pdb=" CA HIS E 362 " pdb=" C HIS E 362 " ideal model delta sigma weight residual 108.52 119.63 -11.11 1.63e+00 3.76e-01 4.65e+01 angle pdb=" CB HIS F 362 " pdb=" CG HIS F 362 " pdb=" CD2 HIS F 362 " ideal model delta sigma weight residual 131.20 125.05 6.15 1.30e+00 5.92e-01 2.24e+01 angle pdb=" CA PHE D 346 " pdb=" CB PHE D 346 " pdb=" CG PHE D 346 " ideal model delta sigma weight residual 113.80 118.44 -4.64 1.00e+00 1.00e+00 2.15e+01 angle pdb=" CB HIS C 362 " pdb=" CG HIS C 362 " pdb=" CD2 HIS C 362 " ideal model delta sigma weight residual 131.20 125.24 5.96 1.30e+00 5.92e-01 2.10e+01 angle pdb=" CA ASP A 358 " pdb=" CB ASP A 358 " pdb=" CG ASP A 358 " ideal model delta sigma weight residual 112.60 117.19 -4.59 1.00e+00 1.00e+00 2.10e+01 ... (remaining 4705 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.32: 1953 13.32 - 26.65: 167 26.65 - 39.97: 15 39.97 - 53.29: 4 53.29 - 66.61: 3 Dihedral angle restraints: 2142 sinusoidal: 894 harmonic: 1248 Sorted by residual: dihedral pdb=" C HIS E 362 " pdb=" N HIS E 362 " pdb=" CA HIS E 362 " pdb=" CB HIS E 362 " ideal model delta harmonic sigma weight residual -122.60 -136.32 13.72 0 2.50e+00 1.60e-01 3.01e+01 dihedral pdb=" CA SER D 324 " pdb=" C SER D 324 " pdb=" N LEU D 325 " pdb=" CA LEU D 325 " ideal model delta harmonic sigma weight residual 180.00 154.39 25.61 0 5.00e+00 4.00e-02 2.62e+01 dihedral pdb=" CA SER B 324 " pdb=" C SER B 324 " pdb=" N LEU B 325 " pdb=" CA LEU B 325 " ideal model delta harmonic sigma weight residual 180.00 154.45 25.55 0 5.00e+00 4.00e-02 2.61e+01 ... (remaining 2139 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.102: 404 0.102 - 0.203: 110 0.203 - 0.305: 9 0.305 - 0.406: 4 0.406 - 0.508: 1 Chirality restraints: 528 Sorted by residual: chirality pdb=" CA HIS E 362 " pdb=" N HIS E 362 " pdb=" C HIS E 362 " pdb=" CB HIS E 362 " both_signs ideal model delta sigma weight residual False 2.51 2.00 0.51 2.00e-01 2.50e+01 6.44e+00 chirality pdb=" CA LYS A 317 " pdb=" N LYS A 317 " pdb=" C LYS A 317 " pdb=" CB LYS A 317 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.25e+00 chirality pdb=" CA LYS A 347 " pdb=" N LYS A 347 " pdb=" C LYS A 347 " pdb=" CB LYS A 347 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.72e+00 ... (remaining 525 not shown) Planarity restraints: 600 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR E 310 " -0.106 2.00e-02 2.50e+03 5.84e-02 6.83e+01 pdb=" CG TYR E 310 " 0.034 2.00e-02 2.50e+03 pdb=" CD1 TYR E 310 " 0.041 2.00e-02 2.50e+03 pdb=" CD2 TYR E 310 " 0.052 2.00e-02 2.50e+03 pdb=" CE1 TYR E 310 " 0.037 2.00e-02 2.50e+03 pdb=" CE2 TYR E 310 " 0.029 2.00e-02 2.50e+03 pdb=" CZ TYR E 310 " 0.005 2.00e-02 2.50e+03 pdb=" OH TYR E 310 " -0.091 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR D 310 " 0.081 2.00e-02 2.50e+03 4.50e-02 4.05e+01 pdb=" CG TYR D 310 " -0.022 2.00e-02 2.50e+03 pdb=" CD1 TYR D 310 " -0.031 2.00e-02 2.50e+03 pdb=" CD2 TYR D 310 " -0.040 2.00e-02 2.50e+03 pdb=" CE1 TYR D 310 " -0.030 2.00e-02 2.50e+03 pdb=" CE2 TYR D 310 " -0.023 2.00e-02 2.50e+03 pdb=" CZ TYR D 310 " -0.005 2.00e-02 2.50e+03 pdb=" OH TYR D 310 " 0.072 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 310 " 0.080 2.00e-02 2.50e+03 4.45e-02 3.95e+01 pdb=" CG TYR A 310 " -0.021 2.00e-02 2.50e+03 pdb=" CD1 TYR A 310 " -0.031 2.00e-02 2.50e+03 pdb=" CD2 TYR A 310 " -0.041 2.00e-02 2.50e+03 pdb=" CE1 TYR A 310 " -0.031 2.00e-02 2.50e+03 pdb=" CE2 TYR A 310 " -0.022 2.00e-02 2.50e+03 pdb=" CZ TYR A 310 " -0.004 2.00e-02 2.50e+03 pdb=" OH TYR A 310 " 0.070 2.00e-02 2.50e+03 ... (remaining 597 not shown) Histogram of nonbonded interaction distances: 2.49 - 2.97: 1526 2.97 - 3.45: 2703 3.45 - 3.94: 5461 3.94 - 4.42: 5453 4.42 - 4.90: 10569 Nonbonded interactions: 25712 Sorted by model distance: nonbonded pdb=" OD1 ASP E 314 " pdb=" OG SER E 316 " model vdw 2.489 3.040 nonbonded pdb=" OD1 ASP A 314 " pdb=" OG SER A 316 " model vdw 2.510 3.040 nonbonded pdb=" OD1 ASP C 314 " pdb=" OG SER C 316 " model vdw 2.513 3.040 nonbonded pdb=" OD1 ASP D 314 " pdb=" OG SER D 316 " model vdw 2.528 3.040 nonbonded pdb=" OD1 ASP B 314 " pdb=" OG SER B 316 " model vdw 2.550 3.040 ... (remaining 25707 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.080 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: 0.000 Extract box with map and model: 0.080 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 5.470 Find NCS groups from input model: 0.050 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:7.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.036 3522 Z= 0.685 Angle : 1.818 11.109 4710 Z= 1.210 Chirality : 0.092 0.508 528 Planarity : 0.010 0.058 600 Dihedral : 9.882 66.611 1350 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 0.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 0.25 % Allowed : 0.00 % Favored : 99.75 % Cbeta Deviations : 0.25 % 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: -1.51 (0.32), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.14 (0.25), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 349 TYR 0.106 0.028 TYR E 310 PHE 0.060 0.012 PHE B 378 HIS 0.024 0.005 HIS F 330 Details of bonding type rmsd covalent geometry : bond 0.01081 ( 3522) covalent geometry : angle 1.81847 ( 4710) hydrogen bonds : bond 0.06942 ( 71) hydrogen bonds : angle 7.61421 ( 213) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 79 time to evaluate : 0.150 Fit side-chains REVERT: A 340 LYS cc_start: 0.7710 (ttmt) cc_final: 0.7312 (mtmt) REVERT: C 356 SER cc_start: 0.8736 (p) cc_final: 0.8515 (m) REVERT: E 317 LYS cc_start: 0.8012 (pttt) cc_final: 0.7706 (ptpt) REVERT: E 356 SER cc_start: 0.8812 (p) cc_final: 0.8606 (m) outliers start: 1 outliers final: 0 residues processed: 79 average time/residue: 0.5805 time to fit residues: 47.1610 Evaluate side-chains 41 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 41 time to evaluate : 0.143 ------------------------------------------------------------------------------- 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: 4.9990 chunk 26 optimal weight: 4.9990 chunk 2 optimal weight: 3.9990 chunk 16 optimal weight: 0.8980 chunk 32 optimal weight: 0.9980 chunk 31 optimal weight: 5.9990 chunk 25 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 22 optimal weight: 5.9990 chunk 37 optimal weight: 3.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 368 ASN ** C 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 368 ASN ** E 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 351 GLN E 368 ASN F 330 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4354 r_free = 0.4354 target = 0.150823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.135234 restraints weight = 3923.289| |-----------------------------------------------------------------------------| r_work (start): 0.4169 rms_B_bonded: 2.25 r_work: 0.4034 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3908 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3908 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.2505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3522 Z= 0.145 Angle : 0.709 6.117 4710 Z= 0.363 Chirality : 0.052 0.139 528 Planarity : 0.003 0.018 600 Dihedral : 6.307 17.098 468 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 2.78 % Allowed : 8.08 % Favored : 89.14 % 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: -1.26 (0.32), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.95 (0.24), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG F 349 TYR 0.017 0.003 TYR D 310 PHE 0.015 0.002 PHE E 378 HIS 0.011 0.002 HIS D 330 Details of bonding type rmsd covalent geometry : bond 0.00337 ( 3522) covalent geometry : angle 0.70918 ( 4710) hydrogen bonds : bond 0.01964 ( 71) hydrogen bonds : angle 5.18436 ( 213) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 50 time to evaluate : 0.135 Fit side-chains REVERT: A 340 LYS cc_start: 0.7717 (ttmt) cc_final: 0.7099 (mttt) REVERT: B 305 SER cc_start: 0.7991 (OUTLIER) cc_final: 0.7625 (p) REVERT: E 317 LYS cc_start: 0.8001 (pttt) cc_final: 0.7419 (ptpt) REVERT: E 369 LYS cc_start: 0.8248 (mtmt) cc_final: 0.8038 (mttp) REVERT: F 331 LYS cc_start: 0.8186 (OUTLIER) cc_final: 0.7904 (mptt) REVERT: F 356 SER cc_start: 0.8962 (p) cc_final: 0.8738 (m) outliers start: 11 outliers final: 3 residues processed: 59 average time/residue: 0.4042 time to fit residues: 24.7086 Evaluate side-chains 43 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 38 time to evaluate : 0.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 317 LYS Chi-restraints excluded: chain B residue 341 SER Chi-restraints excluded: chain D residue 305 SER Chi-restraints excluded: chain F residue 331 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 12 optimal weight: 8.9990 chunk 6 optimal weight: 2.9990 chunk 22 optimal weight: 7.9990 chunk 31 optimal weight: 10.0000 chunk 17 optimal weight: 5.9990 chunk 34 optimal weight: 0.0870 chunk 37 optimal weight: 2.9990 chunk 18 optimal weight: 0.8980 chunk 13 optimal weight: 3.9990 chunk 35 optimal weight: 10.0000 chunk 25 optimal weight: 10.0000 overall best weight: 2.1964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 330 HIS A 351 GLN C 330 HIS E 330 HIS E 351 GLN F 351 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4284 r_free = 0.4284 target = 0.146249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.130448 restraints weight = 4038.610| |-----------------------------------------------------------------------------| r_work (start): 0.4110 rms_B_bonded: 2.31 r_work: 0.3976 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3852 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3852 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.3244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 3522 Z= 0.155 Angle : 0.651 5.548 4710 Z= 0.330 Chirality : 0.050 0.132 528 Planarity : 0.003 0.022 600 Dihedral : 5.556 14.973 468 Min Nonbonded Distance : 2.628 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 1.26 % Allowed : 11.62 % Favored : 87.12 % 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: -1.47 (0.32), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.11 (0.25), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 379 TYR 0.025 0.003 TYR F 310 PHE 0.016 0.002 PHE E 378 HIS 0.008 0.002 HIS D 330 Details of bonding type rmsd covalent geometry : bond 0.00357 ( 3522) covalent geometry : angle 0.65072 ( 4710) hydrogen bonds : bond 0.01558 ( 71) hydrogen bonds : angle 4.66852 ( 213) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 50 time to evaluate : 0.153 Fit side-chains REVERT: B 342 GLU cc_start: 0.8159 (mm-30) cc_final: 0.6235 (mp0) REVERT: C 320 SER cc_start: 0.8535 (m) cc_final: 0.8200 (t) REVERT: D 340 LYS cc_start: 0.7734 (ttmt) cc_final: 0.7391 (ttmt) REVERT: E 317 LYS cc_start: 0.8127 (pttt) cc_final: 0.7543 (ptpt) outliers start: 5 outliers final: 1 residues processed: 52 average time/residue: 0.6070 time to fit residues: 32.5474 Evaluate side-chains 41 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 40 time to evaluate : 0.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 317 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 10.0000 chunk 1 optimal weight: 8.9990 chunk 36 optimal weight: 9.9990 chunk 17 optimal weight: 6.9990 chunk 20 optimal weight: 3.9990 chunk 15 optimal weight: 10.0000 chunk 3 optimal weight: 8.9990 chunk 2 optimal weight: 1.9990 chunk 14 optimal weight: 8.9990 chunk 7 optimal weight: 10.0000 chunk 40 optimal weight: 7.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 351 GLN E 351 GLN F 351 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.129406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.115665 restraints weight = 4493.007| |-----------------------------------------------------------------------------| r_work (start): 0.3919 rms_B_bonded: 2.20 r_work: 0.3792 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3671 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3671 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.3882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.046 3522 Z= 0.369 Angle : 0.820 6.814 4710 Z= 0.425 Chirality : 0.056 0.176 528 Planarity : 0.004 0.022 600 Dihedral : 6.166 17.814 468 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 3.79 % Allowed : 13.64 % Favored : 82.58 % 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: -2.01 (0.32), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.52 (0.24), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 379 TYR 0.027 0.005 TYR A 310 PHE 0.024 0.004 PHE E 378 HIS 0.008 0.002 HIS A 330 Details of bonding type rmsd covalent geometry : bond 0.00854 ( 3522) covalent geometry : angle 0.81969 ( 4710) hydrogen bonds : bond 0.02091 ( 71) hydrogen bonds : angle 4.89970 ( 213) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 45 time to evaluate : 0.154 Fit side-chains REVERT: B 342 GLU cc_start: 0.8379 (OUTLIER) cc_final: 0.6236 (mp0) REVERT: C 320 SER cc_start: 0.8629 (m) cc_final: 0.8394 (t) REVERT: C 369 LYS cc_start: 0.8708 (mtpt) cc_final: 0.8361 (mttt) REVERT: D 340 LYS cc_start: 0.7726 (ttmt) cc_final: 0.7477 (ttmm) REVERT: E 317 LYS cc_start: 0.8224 (pttt) cc_final: 0.7671 (ptpt) outliers start: 15 outliers final: 8 residues processed: 55 average time/residue: 0.6558 time to fit residues: 37.0455 Evaluate side-chains 44 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 35 time to evaluate : 0.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 317 LYS Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain B residue 341 SER Chi-restraints excluded: chain B residue 342 GLU Chi-restraints excluded: chain B residue 356 SER Chi-restraints excluded: chain C residue 331 LYS Chi-restraints excluded: chain E residue 331 LYS Chi-restraints excluded: chain F residue 305 SER Chi-restraints excluded: chain F residue 311 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 28 optimal weight: 0.4980 chunk 15 optimal weight: 10.0000 chunk 19 optimal weight: 6.9990 chunk 39 optimal weight: 2.9990 chunk 6 optimal weight: 5.9990 chunk 0 optimal weight: 8.9990 chunk 31 optimal weight: 7.9990 chunk 40 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 1 optimal weight: 0.7980 chunk 9 optimal weight: 5.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 351 GLN C 368 ASN D 368 ASN F 351 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4227 r_free = 0.4227 target = 0.141991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.126637 restraints weight = 4049.117| |-----------------------------------------------------------------------------| r_work (start): 0.4054 rms_B_bonded: 2.28 r_work: 0.3925 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3808 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.3996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3522 Z= 0.137 Angle : 0.647 6.956 4710 Z= 0.323 Chirality : 0.050 0.149 528 Planarity : 0.004 0.029 600 Dihedral : 5.548 15.548 468 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 3.03 % Allowed : 15.91 % Favored : 81.06 % 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: -2.04 (0.34), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.55 (0.26), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 379 TYR 0.019 0.003 TYR B 310 PHE 0.015 0.002 PHE F 378 HIS 0.008 0.001 HIS A 330 Details of bonding type rmsd covalent geometry : bond 0.00310 ( 3522) covalent geometry : angle 0.64660 ( 4710) hydrogen bonds : bond 0.01315 ( 71) hydrogen bonds : angle 4.57927 ( 213) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 45 time to evaluate : 0.148 Fit side-chains REVERT: B 342 GLU cc_start: 0.8242 (OUTLIER) cc_final: 0.6215 (mp0) REVERT: C 320 SER cc_start: 0.8656 (m) cc_final: 0.8342 (t) REVERT: C 369 LYS cc_start: 0.8632 (mtpt) cc_final: 0.8207 (mttp) REVERT: D 340 LYS cc_start: 0.7750 (ttmt) cc_final: 0.7444 (ttmt) REVERT: E 317 LYS cc_start: 0.8218 (pttt) cc_final: 0.7645 (ptpt) REVERT: F 331 LYS cc_start: 0.8066 (mttt) cc_final: 0.7737 (mptt) outliers start: 12 outliers final: 5 residues processed: 52 average time/residue: 0.8133 time to fit residues: 43.1981 Evaluate side-chains 45 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 39 time to evaluate : 0.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 356 SER Chi-restraints excluded: chain B residue 317 LYS Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain B residue 341 SER Chi-restraints excluded: chain B residue 342 GLU Chi-restraints excluded: chain F residue 305 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 11 optimal weight: 6.9990 chunk 15 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 20 optimal weight: 10.0000 chunk 12 optimal weight: 10.0000 chunk 31 optimal weight: 7.9990 chunk 34 optimal weight: 0.3980 chunk 36 optimal weight: 4.9990 chunk 32 optimal weight: 8.9990 chunk 18 optimal weight: 0.9990 chunk 38 optimal weight: 4.9990 overall best weight: 3.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 351 GLN C 351 GLN E 351 GLN F 351 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.136736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.121930 restraints weight = 4091.390| |-----------------------------------------------------------------------------| r_work (start): 0.3992 rms_B_bonded: 2.24 r_work: 0.3862 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3745 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.4227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 3522 Z= 0.239 Angle : 0.695 6.589 4710 Z= 0.354 Chirality : 0.051 0.152 528 Planarity : 0.004 0.037 600 Dihedral : 5.678 16.383 468 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 2.53 % Allowed : 17.42 % Favored : 80.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.24 (0.34), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.70 (0.26), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 379 TYR 0.019 0.003 TYR B 310 PHE 0.017 0.003 PHE F 378 HIS 0.007 0.002 HIS A 330 Details of bonding type rmsd covalent geometry : bond 0.00547 ( 3522) covalent geometry : angle 0.69480 ( 4710) hydrogen bonds : bond 0.01586 ( 71) hydrogen bonds : angle 4.60886 ( 213) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 40 time to evaluate : 0.155 Fit side-chains REVERT: B 340 LYS cc_start: 0.8327 (ttmt) cc_final: 0.8068 (ttmm) REVERT: B 342 GLU cc_start: 0.8343 (OUTLIER) cc_final: 0.6270 (mp0) REVERT: C 320 SER cc_start: 0.8655 (m) cc_final: 0.8390 (t) REVERT: C 369 LYS cc_start: 0.8758 (mtpt) cc_final: 0.8415 (mttt) REVERT: D 340 LYS cc_start: 0.7745 (ttmt) cc_final: 0.7539 (ttmt) REVERT: E 317 LYS cc_start: 0.8301 (pttt) cc_final: 0.7730 (ptpt) outliers start: 10 outliers final: 8 residues processed: 48 average time/residue: 0.7702 time to fit residues: 37.8381 Evaluate side-chains 45 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 36 time to evaluate : 0.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 356 SER Chi-restraints excluded: chain B residue 317 LYS Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain B residue 342 GLU Chi-restraints excluded: chain B residue 356 SER Chi-restraints excluded: chain D residue 317 LYS Chi-restraints excluded: chain D residue 356 SER Chi-restraints excluded: chain F residue 311 LYS Chi-restraints excluded: chain F residue 317 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 25 optimal weight: 4.9990 chunk 29 optimal weight: 5.9990 chunk 11 optimal weight: 0.8980 chunk 20 optimal weight: 3.9990 chunk 32 optimal weight: 8.9990 chunk 36 optimal weight: 9.9990 chunk 13 optimal weight: 6.9990 chunk 40 optimal weight: 0.1980 chunk 28 optimal weight: 0.8980 chunk 33 optimal weight: 0.3980 chunk 0 optimal weight: 10.0000 overall best weight: 1.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 368 ASN C 351 GLN E 351 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.140257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.125581 restraints weight = 4023.129| |-----------------------------------------------------------------------------| r_work (start): 0.4040 rms_B_bonded: 2.22 r_work: 0.3919 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3797 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.4350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 3522 Z= 0.110 Angle : 0.597 5.856 4710 Z= 0.298 Chirality : 0.049 0.134 528 Planarity : 0.004 0.039 600 Dihedral : 5.226 15.049 468 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 1.52 % Allowed : 18.43 % Favored : 80.05 % 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: -2.22 (0.35), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.68 (0.27), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 379 TYR 0.018 0.003 TYR B 310 PHE 0.013 0.002 PHE F 378 HIS 0.008 0.001 HIS C 330 Details of bonding type rmsd covalent geometry : bond 0.00244 ( 3522) covalent geometry : angle 0.59688 ( 4710) hydrogen bonds : bond 0.01133 ( 71) hydrogen bonds : angle 4.32558 ( 213) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 48 time to evaluate : 0.143 Fit side-chains REVERT: B 342 GLU cc_start: 0.8226 (OUTLIER) cc_final: 0.6309 (mp0) REVERT: C 320 SER cc_start: 0.8653 (m) cc_final: 0.8394 (t) REVERT: C 331 LYS cc_start: 0.7837 (OUTLIER) cc_final: 0.7574 (mptt) REVERT: C 369 LYS cc_start: 0.8644 (mtpt) cc_final: 0.8386 (mttt) REVERT: D 340 LYS cc_start: 0.7836 (ttmt) cc_final: 0.7588 (ttmt) REVERT: E 317 LYS cc_start: 0.8262 (pttt) cc_final: 0.7709 (ptpt) REVERT: E 331 LYS cc_start: 0.8033 (pttt) cc_final: 0.6786 (tppt) REVERT: E 340 LYS cc_start: 0.8132 (ttmt) cc_final: 0.7633 (mtpm) REVERT: F 331 LYS cc_start: 0.8131 (mptt) cc_final: 0.7776 (mptt) outliers start: 6 outliers final: 4 residues processed: 52 average time/residue: 0.7469 time to fit residues: 39.7379 Evaluate side-chains 48 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 42 time to evaluate : 0.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 356 SER Chi-restraints excluded: chain B residue 317 LYS Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain B residue 341 SER Chi-restraints excluded: chain B residue 342 GLU Chi-restraints excluded: chain C residue 331 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 39 optimal weight: 8.9990 chunk 12 optimal weight: 5.9990 chunk 33 optimal weight: 9.9990 chunk 10 optimal weight: 4.9990 chunk 34 optimal weight: 0.0870 chunk 19 optimal weight: 6.9990 chunk 40 optimal weight: 6.9990 chunk 29 optimal weight: 9.9990 chunk 15 optimal weight: 7.9990 chunk 41 optimal weight: 3.9990 chunk 5 optimal weight: 5.9990 overall best weight: 4.2166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 351 GLN E 351 GLN F 351 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.135364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.120633 restraints weight = 4179.149| |-----------------------------------------------------------------------------| r_work (start): 0.3955 rms_B_bonded: 2.25 r_work: 0.3829 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3714 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8411 moved from start: 0.4441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.034 3522 Z= 0.264 Angle : 0.702 6.657 4710 Z= 0.359 Chirality : 0.051 0.157 528 Planarity : 0.005 0.041 600 Dihedral : 5.603 16.468 468 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 2.02 % Allowed : 17.68 % Favored : 80.30 % 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 (0.35), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.79 (0.26), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 379 TYR 0.028 0.004 TYR F 310 PHE 0.017 0.003 PHE F 378 HIS 0.006 0.002 HIS A 330 Details of bonding type rmsd covalent geometry : bond 0.00609 ( 3522) covalent geometry : angle 0.70247 ( 4710) hydrogen bonds : bond 0.01614 ( 71) hydrogen bonds : angle 4.53707 ( 213) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 35 time to evaluate : 0.161 Fit side-chains REVERT: B 342 GLU cc_start: 0.8335 (OUTLIER) cc_final: 0.6261 (mp0) REVERT: C 320 SER cc_start: 0.8682 (m) cc_final: 0.8431 (t) REVERT: C 331 LYS cc_start: 0.7897 (OUTLIER) cc_final: 0.7594 (mptt) REVERT: C 369 LYS cc_start: 0.8701 (mtpt) cc_final: 0.8377 (mttt) REVERT: E 317 LYS cc_start: 0.8297 (pttt) cc_final: 0.7702 (ptpt) REVERT: F 331 LYS cc_start: 0.8131 (mptt) cc_final: 0.7749 (mptt) outliers start: 8 outliers final: 5 residues processed: 41 average time/residue: 0.8272 time to fit residues: 34.6873 Evaluate side-chains 40 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 33 time to evaluate : 0.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 317 LYS Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain B residue 341 SER Chi-restraints excluded: chain B residue 342 GLU Chi-restraints excluded: chain C residue 331 LYS Chi-restraints excluded: chain D residue 317 LYS Chi-restraints excluded: chain F residue 317 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 41 optimal weight: 5.9990 chunk 16 optimal weight: 4.9990 chunk 3 optimal weight: 1.9990 chunk 8 optimal weight: 5.9990 chunk 37 optimal weight: 7.9990 chunk 40 optimal weight: 4.9990 chunk 39 optimal weight: 7.9990 chunk 23 optimal weight: 5.9990 chunk 10 optimal weight: 5.9990 chunk 4 optimal weight: 6.9990 chunk 25 optimal weight: 5.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 351 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 = 0.4119 r_free = 0.4119 target = 0.133762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.119335 restraints weight = 4147.014| |-----------------------------------------------------------------------------| r_work (start): 0.3938 rms_B_bonded: 2.21 r_work: 0.3816 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3702 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3702 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8431 moved from start: 0.4546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.039 3522 Z= 0.298 Angle : 0.740 6.471 4710 Z= 0.381 Chirality : 0.052 0.167 528 Planarity : 0.005 0.042 600 Dihedral : 5.821 17.022 468 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 2.02 % Allowed : 18.69 % Favored : 79.29 % 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: -2.53 (0.33), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.92 (0.26), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 379 TYR 0.026 0.004 TYR F 310 PHE 0.018 0.003 PHE F 378 HIS 0.006 0.002 HIS A 330 Details of bonding type rmsd covalent geometry : bond 0.00689 ( 3522) covalent geometry : angle 0.74016 ( 4710) hydrogen bonds : bond 0.01661 ( 71) hydrogen bonds : angle 4.64224 ( 213) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 36 time to evaluate : 0.149 Fit side-chains REVERT: B 342 GLU cc_start: 0.8330 (OUTLIER) cc_final: 0.6220 (mp0) REVERT: C 320 SER cc_start: 0.8696 (m) cc_final: 0.8479 (t) REVERT: C 369 LYS cc_start: 0.8796 (mtpt) cc_final: 0.8432 (mttt) REVERT: E 317 LYS cc_start: 0.8328 (pttt) cc_final: 0.7746 (ptpt) REVERT: E 331 LYS cc_start: 0.8061 (pttt) cc_final: 0.6642 (tppt) REVERT: F 331 LYS cc_start: 0.8183 (mptt) cc_final: 0.7818 (mptt) outliers start: 8 outliers final: 6 residues processed: 43 average time/residue: 0.7508 time to fit residues: 33.0395 Evaluate side-chains 40 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 33 time to evaluate : 0.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 317 LYS Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain B residue 341 SER Chi-restraints excluded: chain B residue 342 GLU Chi-restraints excluded: chain D residue 317 LYS Chi-restraints excluded: chain D residue 356 SER Chi-restraints excluded: chain F residue 317 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 19 optimal weight: 8.9990 chunk 11 optimal weight: 4.9990 chunk 34 optimal weight: 1.9990 chunk 6 optimal weight: 5.9990 chunk 36 optimal weight: 0.9980 chunk 35 optimal weight: 4.9990 chunk 7 optimal weight: 10.0000 chunk 27 optimal weight: 0.8980 chunk 20 optimal weight: 0.8980 chunk 17 optimal weight: 3.9990 chunk 38 optimal weight: 5.9990 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 351 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 = 0.4190 r_free = 0.4190 target = 0.139044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.125003 restraints weight = 3993.619| |-----------------------------------------------------------------------------| r_work (start): 0.4004 rms_B_bonded: 2.10 r_work: 0.3887 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3772 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.4541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 3522 Z= 0.133 Angle : 0.625 6.920 4710 Z= 0.312 Chirality : 0.049 0.136 528 Planarity : 0.005 0.043 600 Dihedral : 5.350 15.534 468 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 2.02 % Allowed : 18.43 % Favored : 79.55 % 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: -2.39 (0.35), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.82 (0.27), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 379 TYR 0.023 0.003 TYR F 310 PHE 0.016 0.002 PHE F 378 HIS 0.007 0.001 HIS A 330 Details of bonding type rmsd covalent geometry : bond 0.00301 ( 3522) covalent geometry : angle 0.62506 ( 4710) hydrogen bonds : bond 0.01166 ( 71) hydrogen bonds : angle 4.37366 ( 213) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 44 time to evaluate : 0.091 Fit side-chains REVERT: B 342 GLU cc_start: 0.8281 (OUTLIER) cc_final: 0.6312 (mp0) REVERT: C 320 SER cc_start: 0.8677 (m) cc_final: 0.8464 (t) REVERT: C 369 LYS cc_start: 0.8688 (mtpt) cc_final: 0.8427 (mttt) REVERT: E 317 LYS cc_start: 0.8317 (pttt) cc_final: 0.7775 (ptpt) REVERT: E 331 LYS cc_start: 0.8017 (pttt) cc_final: 0.6750 (tppt) REVERT: F 331 LYS cc_start: 0.8139 (mptt) cc_final: 0.7806 (mptt) outliers start: 8 outliers final: 3 residues processed: 49 average time/residue: 0.8121 time to fit residues: 40.6585 Evaluate side-chains 45 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 41 time to evaluate : 0.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 317 LYS Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain B residue 341 SER Chi-restraints excluded: chain B residue 342 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 1 optimal weight: 7.9990 chunk 33 optimal weight: 0.5980 chunk 34 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 3 optimal weight: 0.6980 chunk 29 optimal weight: 10.0000 chunk 16 optimal weight: 5.9990 chunk 7 optimal weight: 10.0000 chunk 6 optimal weight: 4.9990 chunk 35 optimal weight: 6.9990 chunk 5 optimal weight: 0.9980 overall best weight: 1.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 351 GLN E 351 GLN F 351 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.137408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.122891 restraints weight = 4012.007| |-----------------------------------------------------------------------------| r_work (start): 0.4007 rms_B_bonded: 2.18 r_work: 0.3888 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3769 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.4603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 3522 Z= 0.136 Angle : 0.624 6.871 4710 Z= 0.312 Chirality : 0.049 0.136 528 Planarity : 0.005 0.043 600 Dihedral : 5.202 15.277 468 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 1.26 % Allowed : 19.44 % Favored : 79.29 % 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: -2.39 (0.35), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.82 (0.27), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 379 TYR 0.020 0.003 TYR B 310 PHE 0.015 0.002 PHE F 378 HIS 0.007 0.001 HIS A 330 Details of bonding type rmsd covalent geometry : bond 0.00311 ( 3522) covalent geometry : angle 0.62394 ( 4710) hydrogen bonds : bond 0.01192 ( 71) hydrogen bonds : angle 4.28491 ( 213) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1487.25 seconds wall clock time: 26 minutes 18.84 seconds (1578.84 seconds total)