Starting phenix.real_space_refine (version: 1.21rc1) on Mon Oct 2 21:08:40 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q88_18249/10_2023/8q88_18249.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q88_18249/10_2023/8q88_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q88_18249/10_2023/8q88_18249.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q88_18249/10_2023/8q88_18249.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q88_18249/10_2023/8q88_18249.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q88_18249/10_2023/8q88_18249.pdb" } 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 Residue "A GLU 342": "OE1" <-> "OE2" Residue "B GLU 338": "OE1" <-> "OE2" Residue "B GLU 342": "OE1" <-> "OE2" Residue "C GLU 342": "OE1" <-> "OE2" Residue "D GLU 342": "OE1" <-> "OE2" Residue "E GLU 342": "OE1" <-> "OE2" Residue "F GLU 342": "OE1" <-> "OE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/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: 2.30, per 1000 atoms: 0.66 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 - 3.50 Amino acid : False - 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: 1.18 Conformation dependent library (CDL) restraints added in 472.9 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: 0.43 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: 0.75 Time building geometry restraints manager: 1.31 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: 101.96 - 107.26: 197 107.26 - 112.57: 1620 112.57 - 117.88: 872 117.88 - 123.18: 1599 123.18 - 128.49: 422 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 2.440 nonbonded pdb=" OD1 ASP A 314 " pdb=" OG SER A 316 " model vdw 2.510 2.440 nonbonded pdb=" OD1 ASP C 314 " pdb=" OG SER C 316 " model vdw 2.513 2.440 nonbonded pdb=" OD1 ASP D 314 " pdb=" OG SER D 316 " model vdw 2.528 2.440 nonbonded pdb=" OD1 ASP B 314 " pdb=" OG SER B 316 " model vdw 2.550 2.440 ... (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 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: 2.540 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: 11.240 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 13.750 Find NCS groups from input model: 0.220 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: 0.010 Load rotamer database and sin/cos tables:12.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.060 ------------------------------------------------------------------------------- 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 *********************** 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 fitting. rotamer outliers: 1 poor density : 79 time to evaluate : 0.411 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 79 average time/residue: 1.1087 time to fit residues: 90.4158 Evaluate side-chains 38 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 38 time to evaluate : 0.423 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6069 ------------------------------------------------------------------------------- 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: 1.9990 chunk 31 optimal weight: 10.0000 chunk 17 optimal weight: 5.9990 chunk 10 optimal weight: 1.9990 chunk 21 optimal weight: 6.9990 chunk 32 optimal weight: 3.9990 chunk 12 optimal weight: 3.9990 chunk 20 optimal weight: 4.9990 chunk 24 optimal weight: 2.9990 chunk 38 optimal weight: 5.9990 chunk 11 optimal weight: 0.9980 overall best weight: 2.3988 ------------------------------------------------------------------------------- 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** 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: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.2809 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= 0.286 Angle : 0.717 6.680 4710 Z= 0.366 Chirality : 0.052 0.136 528 Planarity : 0.003 0.019 600 Dihedral : 6.264 18.631 468 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 2.02 % Allowed : 9.34 % Favored : 88.64 % 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: -1.33 (0.31), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.01 (0.24), residues: 444 *********************** 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 55 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 47 time to evaluate : 0.445 Fit side-chains outliers start: 8 outliers final: 2 residues processed: 53 average time/residue: 1.0452 time to fit residues: 57.4316 Evaluate side-chains 40 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 38 time to evaluate : 0.430 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 2 residues processed: 0 time to fit residues: 0.6185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 31 optimal weight: 8.9990 chunk 25 optimal weight: 8.9990 chunk 10 optimal weight: 9.9990 chunk 38 optimal weight: 7.9990 chunk 41 optimal weight: 3.9990 chunk 34 optimal weight: 0.0870 chunk 37 optimal weight: 10.0000 chunk 13 optimal weight: 8.9990 chunk 30 optimal weight: 4.9990 chunk 28 optimal weight: 10.0000 chunk 19 optimal weight: 9.9990 overall best weight: 5.2166 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 351 GLN F 351 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.3614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.045 3522 Z= 0.518 Angle : 0.816 6.516 4710 Z= 0.424 Chirality : 0.054 0.147 528 Planarity : 0.004 0.023 600 Dihedral : 6.221 17.103 468 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 2.53 % Allowed : 12.63 % Favored : 84.85 % 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: -1.85 (0.30), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.40 (0.23), residues: 444 *********************** 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 51 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 41 time to evaluate : 0.444 Fit side-chains outliers start: 10 outliers final: 4 residues processed: 49 average time/residue: 1.3093 time to fit residues: 66.2170 Evaluate side-chains 35 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 31 time to evaluate : 0.407 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 4 residues processed: 0 time to fit residues: 0.5753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 4 optimal weight: 0.9980 chunk 18 optimal weight: 0.9980 chunk 25 optimal weight: 4.9990 chunk 38 optimal weight: 4.9990 chunk 40 optimal weight: 5.9990 chunk 20 optimal weight: 0.8980 chunk 36 optimal weight: 10.0000 chunk 10 optimal weight: 2.9990 chunk 33 optimal weight: 5.9990 chunk 23 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 overall best weight: 2.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 368 ASN ** E 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 351 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.3879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 3522 Z= 0.246 Angle : 0.660 6.951 4710 Z= 0.334 Chirality : 0.049 0.134 528 Planarity : 0.003 0.024 600 Dihedral : 5.681 16.068 468 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 2.27 % Allowed : 14.39 % Favored : 83.33 % 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: -1.97 (0.32), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.50 (0.25), residues: 444 *********************** 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 47 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 38 time to evaluate : 0.414 Fit side-chains outliers start: 9 outliers final: 6 residues processed: 44 average time/residue: 1.3145 time to fit residues: 59.6995 Evaluate side-chains 38 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 32 time to evaluate : 0.406 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 5 residues processed: 1 average time/residue: 0.0326 time to fit residues: 0.6335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 30 optimal weight: 10.0000 chunk 16 optimal weight: 5.9990 chunk 34 optimal weight: 4.9990 chunk 28 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 20 optimal weight: 0.6980 chunk 36 optimal weight: 9.9990 chunk 10 optimal weight: 0.9990 chunk 13 optimal weight: 6.9990 chunk 8 optimal weight: 0.0980 chunk 23 optimal weight: 7.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** D 368 ASN ** E 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 351 GLN F 351 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.4054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 3522 Z= 0.191 Angle : 0.615 6.736 4710 Z= 0.304 Chirality : 0.049 0.143 528 Planarity : 0.004 0.029 600 Dihedral : 5.275 15.492 468 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 2.27 % Allowed : 14.90 % Favored : 82.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.07 (0.34), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.57 (0.26), residues: 444 *********************** 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 49 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 40 time to evaluate : 0.416 Fit side-chains outliers start: 9 outliers final: 5 residues processed: 47 average time/residue: 1.3651 time to fit residues: 66.1187 Evaluate side-chains 41 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 36 time to evaluate : 0.519 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 5 residues processed: 0 time to fit residues: 0.7023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 10 optimal weight: 9.9990 chunk 40 optimal weight: 0.4980 chunk 33 optimal weight: 0.9980 chunk 18 optimal weight: 1.9990 chunk 3 optimal weight: 3.9990 chunk 13 optimal weight: 7.9990 chunk 21 optimal weight: 0.0980 chunk 39 optimal weight: 1.9990 chunk 4 optimal weight: 7.9990 chunk 23 optimal weight: 6.9990 chunk 29 optimal weight: 9.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 351 GLN F 351 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.4198 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= 0.149 Angle : 0.574 6.339 4710 Z= 0.284 Chirality : 0.049 0.144 528 Planarity : 0.004 0.033 600 Dihedral : 5.001 15.212 468 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 1.77 % Allowed : 16.41 % Favored : 81.82 % 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: -2.11 (0.34), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.60 (0.26), residues: 444 *********************** 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 45 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 38 time to evaluate : 0.418 Fit side-chains outliers start: 7 outliers final: 5 residues processed: 44 average time/residue: 1.3172 time to fit residues: 59.8027 Evaluate side-chains 39 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 34 time to evaluate : 0.407 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 5 residues processed: 0 time to fit residues: 0.5782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 22 optimal weight: 10.0000 chunk 34 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 25 optimal weight: 8.9990 chunk 24 optimal weight: 10.0000 chunk 18 optimal weight: 4.9990 chunk 16 optimal weight: 7.9990 chunk 12 optimal weight: 9.9990 chunk 7 optimal weight: 9.9990 chunk 27 optimal weight: 9.9990 chunk 20 optimal weight: 0.8980 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 351 GLN F 351 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.4362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 3522 Z= 0.362 Angle : 0.676 6.674 4710 Z= 0.343 Chirality : 0.051 0.157 528 Planarity : 0.004 0.035 600 Dihedral : 5.467 16.618 468 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 2.53 % Allowed : 16.16 % Favored : 81.31 % 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: -2.25 (0.34), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.71 (0.26), residues: 444 *********************** 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 44 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 34 time to evaluate : 0.401 Fit side-chains outliers start: 10 outliers final: 8 residues processed: 42 average time/residue: 1.3849 time to fit residues: 59.9694 Evaluate side-chains 39 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 31 time to evaluate : 0.423 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 7 residues processed: 1 average time/residue: 0.0334 time to fit residues: 0.6561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 3 optimal weight: 1.9990 chunk 31 optimal weight: 9.9990 chunk 36 optimal weight: 9.9990 chunk 38 optimal weight: 2.9990 chunk 35 optimal weight: 6.9990 chunk 37 optimal weight: 8.9990 chunk 22 optimal weight: 8.9990 chunk 16 optimal weight: 0.9980 chunk 29 optimal weight: 3.9990 chunk 11 optimal weight: 0.7980 chunk 34 optimal weight: 3.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 351 GLN ** E 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.4418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3522 Z= 0.237 Angle : 0.621 6.667 4710 Z= 0.310 Chirality : 0.049 0.150 528 Planarity : 0.004 0.041 600 Dihedral : 5.278 15.964 468 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 2.53 % Allowed : 16.67 % Favored : 80.81 % 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: -2.31 (0.34), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.75 (0.26), residues: 444 *********************** 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 48 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 38 time to evaluate : 0.442 Fit side-chains outliers start: 10 outliers final: 7 residues processed: 45 average time/residue: 1.4281 time to fit residues: 66.1732 Evaluate side-chains 40 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 33 time to evaluate : 0.391 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 6 residues processed: 1 average time/residue: 0.0367 time to fit residues: 0.6068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 10.0000 chunk 37 optimal weight: 10.0000 chunk 24 optimal weight: 0.0980 chunk 39 optimal weight: 3.9990 chunk 18 optimal weight: 0.9990 chunk 27 optimal weight: 9.9990 chunk 41 optimal weight: 4.9990 chunk 38 optimal weight: 1.9990 chunk 33 optimal weight: 8.9990 chunk 3 optimal weight: 0.5980 chunk 25 optimal weight: 7.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** C 351 GLN ** E 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 351 GLN F 351 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.4507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 3522 Z= 0.183 Angle : 0.595 6.896 4710 Z= 0.295 Chirality : 0.049 0.144 528 Planarity : 0.004 0.044 600 Dihedral : 5.074 15.338 468 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 2.02 % Allowed : 18.18 % Favored : 79.80 % 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: -2.28 (0.34), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.73 (0.26), residues: 444 *********************** 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 47 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 39 time to evaluate : 0.410 Fit side-chains outliers start: 8 outliers final: 6 residues processed: 45 average time/residue: 1.3970 time to fit residues: 64.7379 Evaluate side-chains 40 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 34 time to evaluate : 0.403 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 6 residues processed: 0 time to fit residues: 0.5690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 20 optimal weight: 10.0000 chunk 26 optimal weight: 10.0000 chunk 35 optimal weight: 7.9990 chunk 10 optimal weight: 8.9990 chunk 30 optimal weight: 1.9990 chunk 4 optimal weight: 5.9990 chunk 9 optimal weight: 5.9990 chunk 33 optimal weight: 6.9990 chunk 13 optimal weight: 5.9990 chunk 34 optimal weight: 0.0470 chunk 6 optimal weight: 3.9990 overall best weight: 3.6086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 351 GLN ** E 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 351 GLN F 351 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.4527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 3522 Z= 0.365 Angle : 0.693 7.955 4710 Z= 0.349 Chirality : 0.051 0.170 528 Planarity : 0.005 0.043 600 Dihedral : 5.439 16.515 468 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 1.52 % Allowed : 18.94 % 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 (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: -2.41 (0.34), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.83 (0.26), residues: 444 ********************** 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 41 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 35 time to evaluate : 0.375 Fit side-chains outliers start: 6 outliers final: 5 residues processed: 41 average time/residue: 1.5054 time to fit residues: 63.4880 Evaluate side-chains 39 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 34 time to evaluate : 0.460 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 5 residues processed: 0 time to fit residues: 0.5742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 29 optimal weight: 0.5980 chunk 1 optimal weight: 2.9990 chunk 24 optimal weight: 10.0000 chunk 38 optimal weight: 3.9990 chunk 22 optimal weight: 10.0000 chunk 28 optimal weight: 8.9990 chunk 26 optimal weight: 0.9980 chunk 25 optimal weight: 5.9990 chunk 16 optimal weight: 1.9990 chunk 15 optimal weight: 7.9990 chunk 41 optimal weight: 0.8980 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 351 GLN ** E 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 351 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4253 r_free = 0.4253 target = 0.143249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.128062 restraints weight = 3897.946| |-----------------------------------------------------------------------------| r_work (start): 0.4067 rms_B_bonded: 2.17 r_work: 0.3952 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3835 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.4610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 3522 Z= 0.182 Angle : 0.620 7.615 4710 Z= 0.302 Chirality : 0.049 0.145 528 Planarity : 0.005 0.042 600 Dihedral : 5.105 15.384 468 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 1.26 % Allowed : 19.95 % Favored : 78.79 % 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: -2.38 (0.35), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.80 (0.26), residues: 444 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1779.41 seconds wall clock time: 32 minutes 20.21 seconds (1940.21 seconds total)