Starting phenix.real_space_refine on Wed Mar 5 20:17:57 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8q88_18249/03_2025/8q88_18249.cif Found real_map, /net/cci-nas-00/data/ceres_data/8q88_18249/03_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_18249/03_2025/8q88_18249.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8q88_18249/03_2025/8q88_18249.map" model { file = "/net/cci-nas-00/data/ceres_data/8q88_18249/03_2025/8q88_18249.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8q88_18249/03_2025/8q88_18249.cif" } resolution = 2.95 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: 3.64, per 1000 atoms: 1.05 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: 0.78 Conformation dependent library (CDL) restraints added in 429.5 milliseconds 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: 0.55 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: 0.83 Time building geometry restraints manager: 0.94 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: 0.01 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: 2.270 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: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 14.230 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.020 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:12.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.260 ------------------------------------------------------------------------------- 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= 0.731 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.51 (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 HIS 0.024 0.005 HIS F 330 PHE 0.060 0.012 PHE B 378 TYR 0.106 0.028 TYR E 310 ARG 0.006 0.001 ARG E 349 *********************** 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 : 0.369 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: 1.1194 time to fit residues: 91.1796 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 : 0.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 2.9990 chunk 31 optimal weight: 8.9990 chunk 17 optimal weight: 6.9990 chunk 10 optimal weight: 2.9990 chunk 21 optimal weight: 0.9980 chunk 32 optimal weight: 4.9990 chunk 12 optimal weight: 4.9990 chunk 20 optimal weight: 4.9990 chunk 24 optimal weight: 5.9990 chunk 38 optimal weight: 6.9990 chunk 11 optimal weight: 0.7980 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 330 HIS B 368 ASN ** C 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 351 GLN E 368 ASN ** F 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4310 r_free = 0.4310 target = 0.147918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.132599 restraints weight = 3929.885| |-----------------------------------------------------------------------------| r_work (start): 0.4121 rms_B_bonded: 2.19 r_work: 0.4000 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3882 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3882 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.2756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 3522 Z= 0.301 Angle : 0.732 6.233 4710 Z= 0.375 Chirality : 0.052 0.142 528 Planarity : 0.003 0.018 600 Dihedral : 6.302 17.497 468 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 2.02 % Allowed : 8.84 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.38 (0.32), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.04 (0.24), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.012 0.002 HIS D 330 PHE 0.017 0.002 PHE E 378 TYR 0.020 0.004 TYR B 310 ARG 0.003 0.001 ARG F 349 *********************** 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 57 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 49 time to evaluate : 0.385 Fit side-chains REVERT: A 340 LYS cc_start: 0.7794 (ttmt) cc_final: 0.7172 (mtmt) REVERT: E 317 LYS cc_start: 0.8070 (pttt) cc_final: 0.7505 (ptpt) REVERT: E 369 LYS cc_start: 0.8268 (mtmt) cc_final: 0.8055 (mttp) REVERT: F 331 LYS cc_start: 0.8199 (mttp) cc_final: 0.7947 (mptt) outliers start: 8 outliers final: 2 residues processed: 56 average time/residue: 1.1379 time to fit residues: 65.8789 Evaluate side-chains 37 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 35 time to evaluate : 0.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 317 LYS Chi-restraints excluded: chain B residue 341 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 25 optimal weight: 7.9990 chunk 28 optimal weight: 0.8980 chunk 17 optimal weight: 5.9990 chunk 21 optimal weight: 9.9990 chunk 26 optimal weight: 10.0000 chunk 35 optimal weight: 9.9990 chunk 8 optimal weight: 8.9990 chunk 19 optimal weight: 8.9990 chunk 7 optimal weight: 0.8980 chunk 1 optimal weight: 7.9990 chunk 5 optimal weight: 1.9990 overall best weight: 3.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 351 GLN C 330 HIS E 330 HIS E 351 GLN F 330 HIS F 351 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4223 r_free = 0.4223 target = 0.141411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.126009 restraints weight = 3991.423| |-----------------------------------------------------------------------------| r_work (start): 0.4042 rms_B_bonded: 2.23 r_work: 0.3918 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3800 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.3501 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= 0.365 Angle : 0.737 6.311 4710 Z= 0.376 Chirality : 0.052 0.138 528 Planarity : 0.003 0.021 600 Dihedral : 5.928 16.217 468 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 2.78 % Allowed : 11.62 % Favored : 85.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.75 (0.31), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.32 (0.24), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.010 0.002 HIS A 330 PHE 0.017 0.003 PHE F 378 TYR 0.023 0.005 TYR F 310 ARG 0.003 0.000 ARG F 379 *********************** 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 58 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 47 time to evaluate : 0.410 Fit side-chains REVERT: B 342 GLU cc_start: 0.8246 (mm-30) cc_final: 0.6223 (mp0) REVERT: C 320 SER cc_start: 0.8564 (m) cc_final: 0.8283 (t) REVERT: C 369 LYS cc_start: 0.8637 (mtpt) cc_final: 0.8276 (mttt) REVERT: D 340 LYS cc_start: 0.7693 (ttmt) cc_final: 0.6925 (mttt) REVERT: E 317 LYS cc_start: 0.8172 (pttt) cc_final: 0.7595 (ptpt) outliers start: 11 outliers final: 7 residues processed: 56 average time/residue: 1.1883 time to fit residues: 68.9415 Evaluate side-chains 47 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 40 time to evaluate : 0.546 ------------------------------------------------------------------------------- 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 320 SER Chi-restraints excluded: chain B residue 341 SER Chi-restraints excluded: chain D residue 305 SER Chi-restraints excluded: chain D residue 356 SER Chi-restraints excluded: chain F residue 305 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 25 optimal weight: 7.9990 chunk 14 optimal weight: 10.0000 chunk 33 optimal weight: 8.9990 chunk 10 optimal weight: 7.9990 chunk 24 optimal weight: 0.9990 chunk 39 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 32 optimal weight: 0.9980 chunk 22 optimal weight: 7.9990 chunk 36 optimal weight: 8.9990 chunk 17 optimal weight: 6.9990 overall best weight: 4.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 351 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.135813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.120775 restraints weight = 4122.515| |-----------------------------------------------------------------------------| r_work (start): 0.3971 rms_B_bonded: 2.25 r_work: 0.3833 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3712 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3712 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.3998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.040 3522 Z= 0.473 Angle : 0.777 6.707 4710 Z= 0.399 Chirality : 0.053 0.147 528 Planarity : 0.004 0.020 600 Dihedral : 6.051 17.025 468 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 3.28 % Allowed : 14.65 % Favored : 82.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.15 (0.32), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.63 (0.24), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.002 HIS A 330 PHE 0.019 0.003 PHE F 378 TYR 0.025 0.005 TYR A 310 ARG 0.007 0.001 ARG E 379 *********************** 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 56 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 43 time to evaluate : 0.509 Fit side-chains REVERT: B 342 GLU cc_start: 0.8292 (OUTLIER) cc_final: 0.6169 (mp0) REVERT: C 320 SER cc_start: 0.8651 (m) cc_final: 0.8377 (t) REVERT: C 369 LYS cc_start: 0.8728 (mtpt) cc_final: 0.8341 (mttt) REVERT: D 340 LYS cc_start: 0.7711 (ttmt) cc_final: 0.7447 (ttmm) REVERT: D 349 ARG cc_start: 0.7937 (mtm180) cc_final: 0.7584 (mtm180) REVERT: E 317 LYS cc_start: 0.8213 (pttt) cc_final: 0.7627 (ptpt) REVERT: F 331 LYS cc_start: 0.8169 (mttp) cc_final: 0.7949 (mttt) outliers start: 13 outliers final: 9 residues processed: 53 average time/residue: 1.4923 time to fit residues: 81.1586 Evaluate side-chains 49 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 39 time to evaluate : 0.367 ------------------------------------------------------------------------------- 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 341 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 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 21 optimal weight: 7.9990 chunk 23 optimal weight: 7.9990 chunk 30 optimal weight: 7.9990 chunk 41 optimal weight: 2.9990 chunk 35 optimal weight: 7.9990 chunk 19 optimal weight: 8.9990 chunk 15 optimal weight: 9.9990 chunk 13 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 chunk 3 optimal weight: 5.9990 chunk 12 optimal weight: 0.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 351 GLN D 368 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4195 r_free = 0.4195 target = 0.139226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.124090 restraints weight = 4115.584| |-----------------------------------------------------------------------------| r_work (start): 0.4023 rms_B_bonded: 2.27 r_work: 0.3898 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3782 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.4131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 3522 Z= 0.276 Angle : 0.674 6.434 4710 Z= 0.338 Chirality : 0.050 0.138 528 Planarity : 0.004 0.033 600 Dihedral : 5.630 15.983 468 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 3.03 % Allowed : 16.67 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.22 (0.33), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.68 (0.26), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.001 HIS A 330 PHE 0.017 0.002 PHE F 378 TYR 0.019 0.003 TYR D 310 ARG 0.008 0.001 ARG E 379 *********************** 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 60 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 48 time to evaluate : 0.392 Fit side-chains REVERT: B 342 GLU cc_start: 0.8320 (OUTLIER) cc_final: 0.6266 (mp0) REVERT: C 320 SER cc_start: 0.8662 (m) cc_final: 0.8375 (t) REVERT: C 369 LYS cc_start: 0.8718 (mtpt) cc_final: 0.8322 (mttt) REVERT: D 340 LYS cc_start: 0.7711 (ttmt) cc_final: 0.7438 (ttmm) REVERT: E 317 LYS cc_start: 0.8241 (pttt) cc_final: 0.7669 (ptpt) REVERT: F 311 LYS cc_start: 0.8411 (ttmt) cc_final: 0.8152 (tttt) outliers start: 12 outliers final: 9 residues processed: 55 average time/residue: 1.3986 time to fit residues: 79.0082 Evaluate side-chains 54 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 44 time to evaluate : 0.396 ------------------------------------------------------------------------------- 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 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 305 SER Chi-restraints excluded: chain F residue 317 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 16 optimal weight: 8.9990 chunk 3 optimal weight: 4.9990 chunk 27 optimal weight: 6.9990 chunk 30 optimal weight: 0.3980 chunk 39 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 38 optimal weight: 6.9990 chunk 34 optimal weight: 0.0010 chunk 2 optimal weight: 0.7980 chunk 24 optimal weight: 7.9990 chunk 41 optimal weight: 4.9990 overall best weight: 1.2390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 351 GLN A 368 ASN C 351 GLN E 351 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4261 r_free = 0.4261 target = 0.144262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.129144 restraints weight = 4034.510| |-----------------------------------------------------------------------------| r_work (start): 0.4092 rms_B_bonded: 2.20 r_work: 0.3972 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3860 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.4294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 3522 Z= 0.161 Angle : 0.602 7.208 4710 Z= 0.300 Chirality : 0.049 0.127 528 Planarity : 0.004 0.040 600 Dihedral : 5.205 14.985 468 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 1.77 % Allowed : 17.17 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.21 (0.35), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.68 (0.26), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.001 HIS A 330 PHE 0.013 0.002 PHE F 378 TYR 0.018 0.003 TYR B 310 ARG 0.006 0.001 ARG C 379 *********************** 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 57 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 50 time to evaluate : 0.412 Fit side-chains REVERT: A 311 LYS cc_start: 0.8525 (ttpt) cc_final: 0.8316 (tmmt) REVERT: B 340 LYS cc_start: 0.8282 (ttmt) cc_final: 0.8015 (ttmm) REVERT: B 342 GLU cc_start: 0.8092 (OUTLIER) cc_final: 0.6270 (mp0) REVERT: C 320 SER cc_start: 0.8641 (m) cc_final: 0.8396 (t) REVERT: C 369 LYS cc_start: 0.8631 (mtpt) cc_final: 0.8372 (mttt) REVERT: D 340 LYS cc_start: 0.7839 (ttmt) cc_final: 0.7504 (ttmt) REVERT: E 317 LYS cc_start: 0.8238 (pttt) cc_final: 0.7702 (ptpt) REVERT: F 331 LYS cc_start: 0.8066 (mttt) cc_final: 0.7844 (mptt) outliers start: 7 outliers final: 3 residues processed: 54 average time/residue: 1.4570 time to fit residues: 80.7911 Evaluate side-chains 48 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 44 time to evaluate : 0.391 ------------------------------------------------------------------------------- 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 342 GLU Chi-restraints excluded: chain D residue 317 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 19 optimal weight: 9.9990 chunk 25 optimal weight: 7.9990 chunk 10 optimal weight: 8.9990 chunk 37 optimal weight: 9.9990 chunk 23 optimal weight: 10.0000 chunk 5 optimal weight: 8.9990 chunk 32 optimal weight: 10.0000 chunk 13 optimal weight: 6.9990 chunk 1 optimal weight: 9.9990 chunk 17 optimal weight: 2.9990 chunk 31 optimal weight: 10.0000 overall best weight: 7.1990 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.129259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.115927 restraints weight = 4175.245| |-----------------------------------------------------------------------------| r_work (start): 0.3873 rms_B_bonded: 2.05 r_work: 0.3755 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3643 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3643 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8483 moved from start: 0.4532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.047 3522 Z= 0.690 Angle : 0.850 7.296 4710 Z= 0.443 Chirality : 0.055 0.167 528 Planarity : 0.005 0.044 600 Dihedral : 6.120 17.352 468 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.31 % Favored : 93.69 % Rotamer: Outliers : 2.27 % Allowed : 18.43 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.60 (0.33), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.97 (0.25), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS A 330 PHE 0.020 0.004 PHE F 378 TYR 0.029 0.005 TYR A 310 ARG 0.011 0.002 ARG E 379 *********************** 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 50 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 41 time to evaluate : 0.366 Fit side-chains REVERT: B 342 GLU cc_start: 0.8490 (OUTLIER) cc_final: 0.6307 (mp0) REVERT: C 369 LYS cc_start: 0.8798 (mtpt) cc_final: 0.8521 (mttt) REVERT: E 317 LYS cc_start: 0.8368 (pttt) cc_final: 0.7829 (ptpt) REVERT: E 331 LYS cc_start: 0.8106 (mptt) cc_final: 0.7802 (mptt) REVERT: F 331 LYS cc_start: 0.8222 (mttt) cc_final: 0.7841 (mptt) outliers start: 9 outliers final: 4 residues processed: 49 average time/residue: 1.5833 time to fit residues: 79.7207 Evaluate side-chains 39 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 34 time to evaluate : 0.604 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 30 optimal weight: 0.7980 chunk 13 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 0 optimal weight: 7.9990 chunk 38 optimal weight: 2.9990 chunk 16 optimal weight: 0.9980 chunk 32 optimal weight: 0.9980 chunk 2 optimal weight: 0.8980 chunk 21 optimal weight: 4.9990 chunk 1 optimal weight: 6.9990 chunk 4 optimal weight: 0.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 351 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4211 r_free = 0.4211 target = 0.141068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.126659 restraints weight = 3908.403| |-----------------------------------------------------------------------------| r_work (start): 0.4018 rms_B_bonded: 2.07 r_work: 0.3898 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3786 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.4571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 3522 Z= 0.165 Angle : 0.643 7.355 4710 Z= 0.318 Chirality : 0.049 0.125 528 Planarity : 0.005 0.043 600 Dihedral : 5.367 15.402 468 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 2.78 % Allowed : 18.69 % Favored : 78.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.44 (0.35), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.85 (0.27), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.001 HIS A 330 PHE 0.013 0.002 PHE F 378 TYR 0.017 0.002 TYR A 310 ARG 0.009 0.001 ARG B 349 *********************** 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 57 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 46 time to evaluate : 0.432 Fit side-chains REVERT: B 342 GLU cc_start: 0.8307 (OUTLIER) cc_final: 0.6306 (mp0) REVERT: B 349 ARG cc_start: 0.8064 (mtm-85) cc_final: 0.7559 (mtp180) REVERT: C 331 LYS cc_start: 0.7733 (OUTLIER) cc_final: 0.7530 (mptt) REVERT: C 369 LYS cc_start: 0.8695 (mtpt) cc_final: 0.8424 (mttt) REVERT: E 317 LYS cc_start: 0.8313 (pttt) cc_final: 0.7769 (ptpt) REVERT: E 331 LYS cc_start: 0.7989 (mptt) cc_final: 0.6723 (tppt) REVERT: F 331 LYS cc_start: 0.8105 (mttt) cc_final: 0.7769 (mptt) REVERT: F 341 SER cc_start: 0.8376 (m) cc_final: 0.8171 (t) outliers start: 11 outliers final: 6 residues processed: 54 average time/residue: 1.4378 time to fit residues: 79.7655 Evaluate side-chains 48 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 40 time to evaluate : 0.400 ------------------------------------------------------------------------------- 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 B residue 356 SER Chi-restraints excluded: chain C residue 331 LYS Chi-restraints excluded: chain D residue 356 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 3 optimal weight: 2.9990 chunk 36 optimal weight: 9.9990 chunk 10 optimal weight: 6.9990 chunk 32 optimal weight: 6.9990 chunk 17 optimal weight: 2.9990 chunk 22 optimal weight: 9.9990 chunk 33 optimal weight: 8.9990 chunk 9 optimal weight: 3.9990 chunk 25 optimal weight: 9.9990 chunk 26 optimal weight: 6.9990 chunk 37 optimal weight: 3.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 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 = 0.4136 r_free = 0.4136 target = 0.134852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.120417 restraints weight = 4104.092| |-----------------------------------------------------------------------------| r_work (start): 0.3949 rms_B_bonded: 2.11 r_work: 0.3833 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3716 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8431 moved from start: 0.4616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.033 3522 Z= 0.424 Angle : 0.727 7.068 4710 Z= 0.371 Chirality : 0.051 0.150 528 Planarity : 0.006 0.053 600 Dihedral : 5.663 16.440 468 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % Rotamer: Outliers : 2.02 % Allowed : 20.45 % Favored : 77.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.55 (0.34), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.94 (0.26), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS A 330 PHE 0.018 0.003 PHE F 378 TYR 0.018 0.003 TYR B 310 ARG 0.012 0.002 ARG E 379 *********************** 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 49 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 41 time to evaluate : 0.409 Fit side-chains REVERT: B 342 GLU cc_start: 0.8366 (OUTLIER) cc_final: 0.6278 (mp0) REVERT: C 331 LYS cc_start: 0.7849 (OUTLIER) cc_final: 0.7627 (mptt) REVERT: C 369 LYS cc_start: 0.8774 (mtpt) cc_final: 0.8452 (mttt) REVERT: E 317 LYS cc_start: 0.8323 (pttt) cc_final: 0.7744 (ptpt) REVERT: E 331 LYS cc_start: 0.7984 (mptt) cc_final: 0.7610 (mptt) REVERT: F 331 LYS cc_start: 0.8153 (mttt) cc_final: 0.7758 (mptt) outliers start: 8 outliers final: 5 residues processed: 47 average time/residue: 1.3279 time to fit residues: 64.3246 Evaluate side-chains 44 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 37 time to evaluate : 0.393 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain D residue 356 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 38 optimal weight: 20.0000 chunk 13 optimal weight: 4.9990 chunk 29 optimal weight: 7.9990 chunk 24 optimal weight: 6.9990 chunk 11 optimal weight: 5.9990 chunk 19 optimal weight: 9.9990 chunk 4 optimal weight: 5.9990 chunk 39 optimal weight: 5.9990 chunk 22 optimal weight: 6.9990 chunk 16 optimal weight: 0.9990 chunk 40 optimal weight: 4.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- 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 = 0.4131 r_free = 0.4131 target = 0.134098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.119812 restraints weight = 4167.583| |-----------------------------------------------------------------------------| r_work (start): 0.3946 rms_B_bonded: 2.11 r_work: 0.3831 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3714 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 moved from start: 0.4706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.038 3522 Z= 0.455 Angle : 0.762 7.334 4710 Z= 0.387 Chirality : 0.051 0.153 528 Planarity : 0.006 0.057 600 Dihedral : 5.786 16.707 468 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 2.27 % Allowed : 19.19 % Favored : 78.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.66 (0.34), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.02 (0.26), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS C 330 PHE 0.018 0.003 PHE F 378 TYR 0.023 0.004 TYR A 310 ARG 0.008 0.002 ARG B 349 ********************** 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 47 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 38 time to evaluate : 0.369 Fit side-chains REVERT: B 342 GLU cc_start: 0.8354 (OUTLIER) cc_final: 0.6236 (mp0) REVERT: C 331 LYS cc_start: 0.7879 (OUTLIER) cc_final: 0.7643 (mptt) REVERT: C 369 LYS cc_start: 0.8815 (mtpt) cc_final: 0.8479 (mttt) REVERT: E 317 LYS cc_start: 0.8344 (pttt) cc_final: 0.7765 (ptpt) REVERT: E 331 LYS cc_start: 0.8009 (mptt) cc_final: 0.7622 (mptt) REVERT: F 331 LYS cc_start: 0.8200 (mttt) cc_final: 0.7799 (mptt) outliers start: 9 outliers final: 5 residues processed: 45 average time/residue: 1.3867 time to fit residues: 64.1853 Evaluate side-chains 42 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 35 time to evaluate : 0.365 ------------------------------------------------------------------------------- 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 D residue 356 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 41 optimal weight: 0.9980 chunk 22 optimal weight: 9.9990 chunk 37 optimal weight: 0.8980 chunk 35 optimal weight: 5.9990 chunk 15 optimal weight: 1.9990 chunk 23 optimal weight: 0.9990 chunk 2 optimal weight: 0.7980 chunk 26 optimal weight: 0.9980 chunk 11 optimal weight: 4.9990 chunk 10 optimal weight: 4.9990 chunk 27 optimal weight: 3.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 351 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4227 r_free = 0.4227 target = 0.141870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.127345 restraints weight = 3940.934| |-----------------------------------------------------------------------------| r_work (start): 0.4035 rms_B_bonded: 2.09 r_work: 0.3916 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3801 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3801 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.4709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 3522 Z= 0.142 Angle : 0.629 7.350 4710 Z= 0.307 Chirality : 0.049 0.128 528 Planarity : 0.006 0.060 600 Dihedral : 5.164 14.943 468 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 1.01 % Allowed : 20.96 % Favored : 78.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.47 (0.36), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.87 (0.27), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS A 330 PHE 0.015 0.002 PHE F 378 TYR 0.022 0.003 TYR B 310 ARG 0.008 0.001 ARG B 349 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2811.93 seconds wall clock time: 49 minutes 2.89 seconds (2942.89 seconds total)