Starting phenix.real_space_refine on Mon Sep 23 13:06:21 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8caq_16532/09_2024/8caq_16532.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8caq_16532/09_2024/8caq_16532.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8caq_16532/09_2024/8caq_16532.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8caq_16532/09_2024/8caq_16532.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8caq_16532/09_2024/8caq_16532.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8caq_16532/09_2024/8caq_16532.cif" } resolution = 2.3 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= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 5 5.16 5 C 1800 2.51 5 N 530 2.21 5 O 535 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 35 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 2870 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 574 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 574 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Restraints were copied for chains: C, B, E, D Time building chain proxies: 2.68, per 1000 atoms: 0.93 Number of scatterers: 2870 At special positions: 0 Unit cell: (139.256, 119.48, 32.136, 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 5 16.00 O 535 8.00 N 530 7.00 C 1800 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: 0.61 Conformation dependent library (CDL) restraints added in 351.8 milliseconds 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 660 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 16 sheets defined 0.0% alpha, 56.0% 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 'B' and resid 306 through 310 removed outlier: 6.367A pdb=" N GLN A 307 " --> pdb=" O ILE B 308 " (cutoff:3.500A) removed outlier: 7.578A pdb=" N TYR B 310 " --> pdb=" O GLN A 307 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N VAL A 309 " --> pdb=" O TYR B 310 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 313 through 314 removed outlier: 6.822A pdb=" N VAL A 313 " --> pdb=" O ASP B 314 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 317 through 322 removed outlier: 6.403A pdb=" N LYS A 317 " --> pdb=" O VAL B 318 " (cutoff:3.500A) removed outlier: 7.835A pdb=" N SER B 320 " --> pdb=" O LYS A 317 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N THR A 319 " --> pdb=" O SER B 320 " (cutoff:3.500A) removed outlier: 8.473A pdb=" N CYS B 322 " --> pdb=" O THR A 319 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N LYS A 321 " --> pdb=" O CYS B 322 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 325 through 330 removed outlier: 8.567A pdb=" N LEU A 325 " --> pdb=" O GLY B 326 " (cutoff:3.500A) removed outlier: 9.308A pdb=" N ILE B 328 " --> pdb=" O LEU A 325 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N ASN A 327 " --> pdb=" O ILE B 328 " (cutoff:3.500A) removed outlier: 7.785A pdb=" N HIS B 330 " --> pdb=" O ASN A 327 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N HIS A 329 " --> pdb=" O HIS B 330 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N GLY A 326 " --> pdb=" O LEU E 325 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N ASN E 327 " --> pdb=" O GLY A 326 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 337 through 346 removed outlier: 6.861A pdb=" N LEU A 344 " --> pdb=" O LYS B 343 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N ASP B 345 " --> pdb=" O LEU A 344 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N PHE A 346 " --> pdb=" O ASP B 345 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N VAL A 337 " --> pdb=" O GLU E 338 " (cutoff:3.500A) removed outlier: 7.736A pdb=" N LYS E 340 " --> pdb=" O VAL A 337 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N VAL A 339 " --> pdb=" O LYS E 340 " (cutoff:3.500A) removed outlier: 8.145A pdb=" N GLU E 342 " --> pdb=" O VAL A 339 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N SER A 341 " --> pdb=" O GLU E 342 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N LEU E 344 " --> pdb=" O SER A 341 " (cutoff:3.500A) removed outlier: 7.642A pdb=" N LYS A 343 " --> pdb=" O LEU E 344 " (cutoff:3.500A) removed outlier: 10.141A pdb=" N PHE E 346 " --> pdb=" O LYS A 343 " (cutoff:3.500A) removed outlier: 9.199A pdb=" N ASP A 345 " --> pdb=" O PHE E 346 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 350 through 357 removed outlier: 6.411A pdb=" N GLN A 351 " --> pdb=" O SER B 352 " (cutoff:3.500A) removed outlier: 8.124A pdb=" N ILE B 354 " --> pdb=" O GLN A 351 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N LYS A 353 " --> pdb=" O ILE B 354 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N SER B 356 " --> pdb=" O LYS A 353 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N GLY A 355 " --> pdb=" O SER B 356 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 360 through 362 removed outlier: 6.229A pdb=" N THR A 361 " --> pdb=" O HIS E 362 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 369 through 378 removed outlier: 6.825A pdb=" N LYS A 369 " --> pdb=" O LYS B 370 " (cutoff:3.500A) removed outlier: 8.232A pdb=" N GLU B 372 " --> pdb=" O LYS A 369 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N ILE A 371 " --> pdb=" O GLU B 372 " (cutoff:3.500A) removed outlier: 8.005A pdb=" N HIS B 374 " --> pdb=" O ILE A 371 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N THR A 373 " --> pdb=" O HIS B 374 " (cutoff:3.500A) removed outlier: 8.019A pdb=" N LEU B 376 " --> pdb=" O THR A 373 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N LYS A 375 " --> pdb=" O LEU B 376 " (cutoff:3.500A) removed outlier: 7.893A pdb=" N PHE B 378 " --> pdb=" O LYS A 375 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N THR A 377 " --> pdb=" O PHE B 378 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 306 through 310 Processing sheet with id=AB1, first strand: chain 'C' and resid 313 through 314 Processing sheet with id=AB2, first strand: chain 'C' and resid 317 through 322 Processing sheet with id=AB3, first strand: chain 'C' and resid 325 through 330 removed outlier: 6.806A pdb=" N GLY C 326 " --> pdb=" O LEU D 325 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N ASN D 327 " --> pdb=" O GLY C 326 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 337 through 346 removed outlier: 6.316A pdb=" N VAL C 337 " --> pdb=" O GLU D 338 " (cutoff:3.500A) removed outlier: 7.736A pdb=" N LYS D 340 " --> pdb=" O VAL C 337 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N VAL C 339 " --> pdb=" O LYS D 340 " (cutoff:3.500A) removed outlier: 8.144A pdb=" N GLU D 342 " --> pdb=" O VAL C 339 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N SER C 341 " --> pdb=" O GLU D 342 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N LEU D 344 " --> pdb=" O SER C 341 " (cutoff:3.500A) removed outlier: 7.642A pdb=" N LYS C 343 " --> pdb=" O LEU D 344 " (cutoff:3.500A) removed outlier: 10.141A pdb=" N PHE D 346 " --> pdb=" O LYS C 343 " (cutoff:3.500A) removed outlier: 9.199A pdb=" N ASP C 345 " --> pdb=" O PHE D 346 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'C' and resid 350 through 357 Processing sheet with id=AB6, first strand: chain 'C' and resid 360 through 362 removed outlier: 6.229A pdb=" N THR C 361 " --> pdb=" O HIS D 362 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'C' and resid 369 through 378 66 hydrogen bonds defined for protein. 198 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: 0.66 Time building geometry restraints manager: 0.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 681 1.34 - 1.46: 697 1.46 - 1.57: 1532 1.57 - 1.69: 0 1.69 - 1.81: 5 Bond restraints: 2915 Sorted by residual: bond pdb=" CG HIS C 362 " pdb=" CD2 HIS C 362 " ideal model delta sigma weight residual 1.354 1.328 0.026 1.10e-02 8.26e+03 5.44e+00 bond pdb=" CG HIS A 362 " pdb=" CD2 HIS A 362 " ideal model delta sigma weight residual 1.354 1.328 0.026 1.10e-02 8.26e+03 5.44e+00 bond pdb=" CG HIS B 362 " pdb=" CD2 HIS B 362 " ideal model delta sigma weight residual 1.354 1.328 0.026 1.10e-02 8.26e+03 5.43e+00 bond pdb=" CG HIS D 362 " pdb=" CD2 HIS D 362 " ideal model delta sigma weight residual 1.354 1.328 0.026 1.10e-02 8.26e+03 5.42e+00 bond pdb=" CG HIS E 362 " pdb=" CD2 HIS E 362 " ideal model delta sigma weight residual 1.354 1.328 0.026 1.10e-02 8.26e+03 5.39e+00 ... (remaining 2910 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.22: 2935 1.22 - 2.44: 780 2.44 - 3.66: 140 3.66 - 4.89: 40 4.89 - 6.11: 5 Bond angle restraints: 3900 Sorted by residual: angle pdb=" N GLY D 326 " pdb=" CA GLY D 326 " pdb=" C GLY D 326 " ideal model delta sigma weight residual 110.42 116.53 -6.11 1.49e+00 4.50e-01 1.68e+01 angle pdb=" N GLY B 326 " pdb=" CA GLY B 326 " pdb=" C GLY B 326 " ideal model delta sigma weight residual 110.42 116.52 -6.10 1.49e+00 4.50e-01 1.68e+01 angle pdb=" N GLY A 326 " pdb=" CA GLY A 326 " pdb=" C GLY A 326 " ideal model delta sigma weight residual 110.42 116.52 -6.10 1.49e+00 4.50e-01 1.67e+01 angle pdb=" N GLY E 326 " pdb=" CA GLY E 326 " pdb=" C GLY E 326 " ideal model delta sigma weight residual 110.42 116.51 -6.09 1.49e+00 4.50e-01 1.67e+01 angle pdb=" N GLY C 326 " pdb=" CA GLY C 326 " pdb=" C GLY C 326 " ideal model delta sigma weight residual 110.42 116.51 -6.09 1.49e+00 4.50e-01 1.67e+01 ... (remaining 3895 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.14: 1645 15.14 - 30.28: 95 30.28 - 45.42: 25 45.42 - 60.55: 10 60.55 - 75.69: 5 Dihedral angle restraints: 1780 sinusoidal: 745 harmonic: 1035 Sorted by residual: dihedral pdb=" CA GLY B 335 " pdb=" C GLY B 335 " pdb=" N GLN B 336 " pdb=" CA GLN B 336 " ideal model delta harmonic sigma weight residual -180.00 -161.01 -18.99 0 5.00e+00 4.00e-02 1.44e+01 dihedral pdb=" CA GLY E 335 " pdb=" C GLY E 335 " pdb=" N GLN E 336 " pdb=" CA GLN E 336 " ideal model delta harmonic sigma weight residual 180.00 -161.02 -18.98 0 5.00e+00 4.00e-02 1.44e+01 dihedral pdb=" CA GLY A 335 " pdb=" C GLY A 335 " pdb=" N GLN A 336 " pdb=" CA GLN A 336 " ideal model delta harmonic sigma weight residual -180.00 -161.02 -18.98 0 5.00e+00 4.00e-02 1.44e+01 ... (remaining 1777 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 163 0.043 - 0.085: 173 0.085 - 0.127: 79 0.127 - 0.169: 20 0.169 - 0.212: 5 Chirality restraints: 440 Sorted by residual: chirality pdb=" CA LYS B 369 " pdb=" N LYS B 369 " pdb=" C LYS B 369 " pdb=" CB LYS B 369 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.12e+00 chirality pdb=" CA LYS E 369 " pdb=" N LYS E 369 " pdb=" C LYS E 369 " pdb=" CB LYS E 369 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.12e+00 chirality pdb=" CA LYS D 369 " pdb=" N LYS D 369 " pdb=" C LYS D 369 " pdb=" CB LYS D 369 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.11e+00 ... (remaining 437 not shown) Planarity restraints: 495 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR D 310 " 0.017 2.00e-02 2.50e+03 1.13e-02 2.56e+00 pdb=" CG TYR D 310 " -0.026 2.00e-02 2.50e+03 pdb=" CD1 TYR D 310 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 TYR D 310 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR D 310 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR D 310 " 0.004 2.00e-02 2.50e+03 pdb=" CZ TYR D 310 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR D 310 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 310 " -0.017 2.00e-02 2.50e+03 1.13e-02 2.55e+00 pdb=" CG TYR A 310 " 0.026 2.00e-02 2.50e+03 pdb=" CD1 TYR A 310 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 TYR A 310 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR A 310 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR A 310 " -0.004 2.00e-02 2.50e+03 pdb=" CZ TYR A 310 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR A 310 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 310 " 0.017 2.00e-02 2.50e+03 1.13e-02 2.54e+00 pdb=" CG TYR C 310 " -0.026 2.00e-02 2.50e+03 pdb=" CD1 TYR C 310 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 TYR C 310 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR C 310 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR C 310 " 0.004 2.00e-02 2.50e+03 pdb=" CZ TYR C 310 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR C 310 " 0.004 2.00e-02 2.50e+03 ... (remaining 492 not shown) Histogram of nonbonded interaction distances: 2.61 - 3.06: 1590 3.06 - 3.52: 2604 3.52 - 3.98: 4241 3.98 - 4.44: 4342 4.44 - 4.90: 8817 Nonbonded interactions: 21594 Sorted by model distance: nonbonded pdb=" N ASP B 348 " pdb=" O ASP B 348 " model vdw 2.606 2.496 nonbonded pdb=" N ASP A 348 " pdb=" O ASP A 348 " model vdw 2.606 2.496 nonbonded pdb=" N ASP C 348 " pdb=" O ASP C 348 " model vdw 2.607 2.496 nonbonded pdb=" N ASP D 348 " pdb=" O ASP D 348 " model vdw 2.607 2.496 nonbonded pdb=" N ASP E 348 " pdb=" O ASP E 348 " model vdw 2.607 2.496 ... (remaining 21589 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } 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: 2.670 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: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 12.330 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8922 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 : 0.007 0.042 2915 Z= 0.497 Angle : 1.178 6.107 3900 Z= 0.758 Chirality : 0.071 0.212 440 Planarity : 0.007 0.031 495 Dihedral : 12.141 75.692 1120 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 1.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 1.52 % Allowed : 3.03 % Favored : 95.45 % 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: -3.61 (0.31), residues: 365 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.74 (0.24), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.003 HIS E 362 PHE 0.008 0.003 PHE B 378 TYR 0.026 0.007 TYR D 310 ARG 0.002 0.001 ARG A 349 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 105 time to evaluate : 0.398 Fit side-chains REVERT: B 349 ARG cc_start: 0.9009 (mtt180) cc_final: 0.6996 (pmt-80) REVERT: B 379 ARG cc_start: 0.8324 (mtt180) cc_final: 0.7517 (pmt170) REVERT: C 349 ARG cc_start: 0.9022 (mtt180) cc_final: 0.7029 (pmt170) REVERT: C 379 ARG cc_start: 0.8316 (mtt180) cc_final: 0.7436 (pmt170) REVERT: D 311 LYS cc_start: 0.8725 (mtmt) cc_final: 0.8389 (mmtt) REVERT: D 349 ARG cc_start: 0.8992 (mtt180) cc_final: 0.7199 (mmm160) REVERT: E 307 GLN cc_start: 0.8274 (tt0) cc_final: 0.7991 (mt0) REVERT: E 311 LYS cc_start: 0.8817 (mtmt) cc_final: 0.8461 (mmtt) REVERT: E 349 ARG cc_start: 0.8975 (mtt180) cc_final: 0.7581 (mmp-170) outliers start: 5 outliers final: 0 residues processed: 110 average time/residue: 1.3959 time to fit residues: 156.4396 Evaluate side-chains 71 residues out of total 330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 71 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 29 optimal weight: 1.9990 chunk 26 optimal weight: 4.9990 chunk 14 optimal weight: 6.9990 chunk 9 optimal weight: 0.0970 chunk 17 optimal weight: 4.9990 chunk 27 optimal weight: 2.9990 chunk 10 optimal weight: 7.9990 chunk 16 optimal weight: 3.9990 chunk 20 optimal weight: 0.9990 chunk 31 optimal weight: 9.9990 chunk 21 optimal weight: 20.0000 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 307 GLN B 351 GLN C 351 GLN C 368 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8947 moved from start: 0.2183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 2915 Z= 0.222 Angle : 0.585 6.314 3900 Z= 0.289 Chirality : 0.048 0.127 440 Planarity : 0.004 0.025 495 Dihedral : 5.100 15.670 385 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 1.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 3.94 % Allowed : 12.42 % Favored : 83.64 % 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: -2.69 (0.35), residues: 365 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.04 (0.26), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 362 PHE 0.004 0.001 PHE A 346 TYR 0.012 0.003 TYR C 310 ARG 0.003 0.001 ARG A 379 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 74 time to evaluate : 0.327 Fit side-chains REVERT: A 338 GLU cc_start: 0.8642 (OUTLIER) cc_final: 0.8365 (tt0) REVERT: B 348 ASP cc_start: 0.9092 (t0) cc_final: 0.7936 (p0) REVERT: B 349 ARG cc_start: 0.8989 (mtt180) cc_final: 0.6974 (pmt-80) REVERT: B 379 ARG cc_start: 0.8349 (mtt180) cc_final: 0.7630 (pmt170) REVERT: C 349 ARG cc_start: 0.9027 (mtt180) cc_final: 0.7014 (pmt-80) REVERT: C 379 ARG cc_start: 0.8317 (mtt180) cc_final: 0.7458 (pmt170) REVERT: D 349 ARG cc_start: 0.9048 (mtt180) cc_final: 0.7245 (mmm160) REVERT: D 379 ARG cc_start: 0.4573 (OUTLIER) cc_final: 0.3527 (mmt180) REVERT: E 349 ARG cc_start: 0.9029 (mtt180) cc_final: 0.7394 (mmm160) outliers start: 13 outliers final: 1 residues processed: 79 average time/residue: 1.3773 time to fit residues: 111.0764 Evaluate side-chains 71 residues out of total 330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 68 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 338 GLU Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain D residue 379 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 8 optimal weight: 0.4980 chunk 31 optimal weight: 10.0000 chunk 34 optimal weight: 8.9990 chunk 28 optimal weight: 0.9990 chunk 10 optimal weight: 9.9990 chunk 25 optimal weight: 10.0000 chunk 23 optimal weight: 9.9990 chunk 16 optimal weight: 3.9990 chunk 3 optimal weight: 3.9990 chunk 15 optimal weight: 9.9990 chunk 21 optimal weight: 10.0000 overall best weight: 3.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 307 GLN C 307 GLN C 351 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8990 moved from start: 0.2482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 2915 Z= 0.361 Angle : 0.619 5.808 3900 Z= 0.315 Chirality : 0.051 0.135 440 Planarity : 0.004 0.021 495 Dihedral : 5.025 15.950 385 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 1.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 2.12 % Allowed : 14.55 % 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: -2.32 (0.36), residues: 365 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.76 (0.27), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS C 362 PHE 0.005 0.001 PHE E 346 TYR 0.017 0.004 TYR C 310 ARG 0.003 0.001 ARG E 379 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 70 time to evaluate : 0.367 Fit side-chains REVERT: A 338 GLU cc_start: 0.8692 (OUTLIER) cc_final: 0.8450 (tt0) REVERT: B 348 ASP cc_start: 0.9087 (t0) cc_final: 0.7971 (p0) REVERT: B 349 ARG cc_start: 0.9009 (mtt180) cc_final: 0.6994 (pmt-80) REVERT: B 379 ARG cc_start: 0.8455 (mtt180) cc_final: 0.7679 (pmt170) REVERT: C 349 ARG cc_start: 0.9039 (mtt180) cc_final: 0.7021 (pmt170) REVERT: C 379 ARG cc_start: 0.8362 (mtt180) cc_final: 0.7463 (pmt170) REVERT: D 349 ARG cc_start: 0.9056 (mtt180) cc_final: 0.7228 (mmm160) REVERT: D 379 ARG cc_start: 0.4721 (OUTLIER) cc_final: 0.3547 (mmt180) REVERT: E 349 ARG cc_start: 0.9042 (mtt180) cc_final: 0.7398 (mmm160) outliers start: 7 outliers final: 0 residues processed: 75 average time/residue: 1.4411 time to fit residues: 110.3394 Evaluate side-chains 70 residues out of total 330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 68 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 338 GLU Chi-restraints excluded: chain D residue 379 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 31 optimal weight: 4.9990 chunk 33 optimal weight: 0.0470 chunk 16 optimal weight: 9.9990 chunk 30 optimal weight: 0.9980 chunk 9 optimal weight: 0.0060 chunk 28 optimal weight: 10.0000 chunk 19 optimal weight: 5.9990 chunk 0 optimal weight: 0.8980 chunk 25 optimal weight: 8.9990 chunk 13 optimal weight: 6.9990 chunk 23 optimal weight: 0.9990 overall best weight: 0.5896 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 307 GLN C 307 GLN C 351 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8928 moved from start: 0.2773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 2915 Z= 0.124 Angle : 0.517 5.256 3900 Z= 0.250 Chirality : 0.048 0.122 440 Planarity : 0.003 0.018 495 Dihedral : 4.600 15.537 385 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 1.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % Rotamer: Outliers : 1.21 % Allowed : 16.97 % 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: -2.16 (0.37), residues: 365 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.64 (0.28), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS E 374 PHE 0.003 0.001 PHE A 346 TYR 0.006 0.001 TYR A 310 ARG 0.002 0.000 ARG A 349 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 72 time to evaluate : 0.363 Fit side-chains REVERT: A 338 GLU cc_start: 0.8698 (OUTLIER) cc_final: 0.8442 (tt0) REVERT: B 348 ASP cc_start: 0.9031 (t0) cc_final: 0.7873 (p0) REVERT: B 349 ARG cc_start: 0.8984 (mtt180) cc_final: 0.6795 (pmt-80) REVERT: B 379 ARG cc_start: 0.8386 (mtt180) cc_final: 0.7700 (pmt170) REVERT: C 349 ARG cc_start: 0.9005 (mtt180) cc_final: 0.7071 (pmt-80) REVERT: C 379 ARG cc_start: 0.8314 (mtt180) cc_final: 0.7537 (pmt170) REVERT: D 307 GLN cc_start: 0.8368 (tt0) cc_final: 0.8105 (mt0) REVERT: D 349 ARG cc_start: 0.9034 (mtt180) cc_final: 0.7266 (mmm160) REVERT: E 349 ARG cc_start: 0.9017 (mtt180) cc_final: 0.7357 (mmm160) outliers start: 4 outliers final: 0 residues processed: 74 average time/residue: 1.5770 time to fit residues: 119.0225 Evaluate side-chains 70 residues out of total 330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 69 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 338 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 0 optimal weight: 10.0000 chunk 17 optimal weight: 10.0000 chunk 30 optimal weight: 10.0000 chunk 8 optimal weight: 10.0000 chunk 11 optimal weight: 4.9990 chunk 6 optimal weight: 5.9990 chunk 19 optimal weight: 7.9990 chunk 33 optimal weight: 0.7980 chunk 28 optimal weight: 3.9990 chunk 15 optimal weight: 3.9990 chunk 2 optimal weight: 1.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 307 GLN B 327 ASN C 307 GLN C 351 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8985 moved from start: 0.2759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.026 2915 Z= 0.326 Angle : 0.595 5.803 3900 Z= 0.300 Chirality : 0.050 0.133 440 Planarity : 0.003 0.016 495 Dihedral : 4.775 15.259 385 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 2.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 1.82 % Allowed : 17.58 % Favored : 80.61 % 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: -2.09 (0.36), residues: 365 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.59 (0.28), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 362 PHE 0.005 0.001 PHE E 346 TYR 0.016 0.004 TYR C 310 ARG 0.003 0.000 ARG E 379 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 71 time to evaluate : 0.374 Fit side-chains REVERT: A 338 GLU cc_start: 0.8726 (OUTLIER) cc_final: 0.8487 (tt0) REVERT: B 348 ASP cc_start: 0.9042 (t0) cc_final: 0.7899 (p0) REVERT: B 349 ARG cc_start: 0.9008 (mtt180) cc_final: 0.7001 (pmt-80) REVERT: B 379 ARG cc_start: 0.8442 (mtt180) cc_final: 0.7715 (pmt170) REVERT: C 349 ARG cc_start: 0.9040 (mtt180) cc_final: 0.7062 (pmt-80) REVERT: C 379 ARG cc_start: 0.8375 (mtt180) cc_final: 0.7548 (pmt170) REVERT: D 349 ARG cc_start: 0.9033 (mtt180) cc_final: 0.7198 (mmm160) REVERT: D 379 ARG cc_start: 0.4813 (OUTLIER) cc_final: 0.3676 (mmt180) REVERT: E 349 ARG cc_start: 0.9025 (mtt180) cc_final: 0.7356 (mmm160) outliers start: 6 outliers final: 0 residues processed: 75 average time/residue: 1.5558 time to fit residues: 118.9714 Evaluate side-chains 72 residues out of total 330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 70 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 338 GLU Chi-restraints excluded: chain D residue 379 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 11 optimal weight: 5.9990 chunk 17 optimal weight: 9.9990 chunk 32 optimal weight: 5.9990 chunk 3 optimal weight: 9.9990 chunk 19 optimal weight: 4.9990 chunk 24 optimal weight: 7.9990 chunk 28 optimal weight: 9.9990 chunk 18 optimal weight: 1.9990 chunk 33 optimal weight: 4.9990 chunk 21 optimal weight: 8.9990 chunk 20 optimal weight: 0.8980 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 307 GLN C 307 GLN C 351 GLN E 307 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8992 moved from start: 0.2872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.030 2915 Z= 0.377 Angle : 0.616 6.486 3900 Z= 0.309 Chirality : 0.050 0.135 440 Planarity : 0.003 0.014 495 Dihedral : 4.935 16.061 385 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 2.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 1.82 % Allowed : 16.97 % Favored : 81.21 % 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: -2.08 (0.36), residues: 365 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.57 (0.27), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS E 330 PHE 0.005 0.001 PHE D 378 TYR 0.016 0.004 TYR E 310 ARG 0.004 0.001 ARG D 379 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 71 time to evaluate : 0.363 Fit side-chains REVERT: A 338 GLU cc_start: 0.8736 (OUTLIER) cc_final: 0.8474 (tt0) REVERT: B 348 ASP cc_start: 0.9095 (t0) cc_final: 0.8000 (p0) REVERT: B 349 ARG cc_start: 0.9011 (mtt180) cc_final: 0.7019 (pmt-80) REVERT: B 379 ARG cc_start: 0.8439 (mtt180) cc_final: 0.7690 (pmt170) REVERT: C 349 ARG cc_start: 0.9047 (mtt180) cc_final: 0.7090 (pmt-80) REVERT: C 379 ARG cc_start: 0.8451 (mtt180) cc_final: 0.7569 (pmt170) REVERT: D 349 ARG cc_start: 0.9038 (mtt180) cc_final: 0.7177 (mmm160) REVERT: D 379 ARG cc_start: 0.4813 (OUTLIER) cc_final: 0.3621 (mmt180) REVERT: E 349 ARG cc_start: 0.9032 (mtt180) cc_final: 0.7384 (mmm160) outliers start: 6 outliers final: 0 residues processed: 74 average time/residue: 1.4889 time to fit residues: 112.4115 Evaluate side-chains 73 residues out of total 330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 71 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 338 GLU Chi-restraints excluded: chain D residue 379 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 15 optimal weight: 3.9990 chunk 20 optimal weight: 0.1980 chunk 13 optimal weight: 7.9990 chunk 10 optimal weight: 0.9990 chunk 6 optimal weight: 2.9990 chunk 21 optimal weight: 10.0000 chunk 22 optimal weight: 4.9990 chunk 16 optimal weight: 5.9990 chunk 3 optimal weight: 9.9990 chunk 26 optimal weight: 7.9990 chunk 30 optimal weight: 0.0980 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 307 GLN B 362 HIS C 307 GLN C 351 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8958 moved from start: 0.2976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 2915 Z= 0.203 Angle : 0.571 5.875 3900 Z= 0.281 Chirality : 0.049 0.128 440 Planarity : 0.002 0.016 495 Dihedral : 4.692 15.825 385 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 2.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 0.91 % Allowed : 18.79 % 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: -2.00 (0.36), residues: 365 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.52 (0.28), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS C 374 PHE 0.004 0.001 PHE E 346 TYR 0.009 0.002 TYR E 310 ARG 0.002 0.000 ARG D 379 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 72 time to evaluate : 0.314 Fit side-chains REVERT: A 338 GLU cc_start: 0.8722 (OUTLIER) cc_final: 0.8495 (tt0) REVERT: B 348 ASP cc_start: 0.9039 (t0) cc_final: 0.7901 (p0) REVERT: B 349 ARG cc_start: 0.8999 (mtt180) cc_final: 0.6962 (pmt-80) REVERT: B 379 ARG cc_start: 0.8445 (mtt180) cc_final: 0.7772 (pmt170) REVERT: C 348 ASP cc_start: 0.8951 (t0) cc_final: 0.7640 (p0) REVERT: C 349 ARG cc_start: 0.9029 (mtt180) cc_final: 0.7044 (pmt-80) REVERT: C 379 ARG cc_start: 0.8372 (mtt180) cc_final: 0.7536 (pmt170) REVERT: D 349 ARG cc_start: 0.9015 (mtt180) cc_final: 0.7206 (mmm160) REVERT: E 349 ARG cc_start: 0.9019 (mtt180) cc_final: 0.7356 (mmm160) outliers start: 3 outliers final: 1 residues processed: 73 average time/residue: 1.4377 time to fit residues: 107.0473 Evaluate side-chains 74 residues out of total 330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 72 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 338 GLU Chi-restraints excluded: chain C residue 314 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 32 optimal weight: 6.9990 chunk 29 optimal weight: 9.9990 chunk 31 optimal weight: 0.7980 chunk 18 optimal weight: 4.9990 chunk 13 optimal weight: 5.9990 chunk 24 optimal weight: 8.9990 chunk 9 optimal weight: 0.0170 chunk 28 optimal weight: 5.9990 chunk 20 optimal weight: 5.9990 chunk 33 optimal weight: 0.8980 chunk 15 optimal weight: 2.9990 overall best weight: 1.9422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 307 GLN C 307 GLN C 351 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8961 moved from start: 0.3040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 2915 Z= 0.218 Angle : 0.559 6.224 3900 Z= 0.275 Chirality : 0.049 0.128 440 Planarity : 0.002 0.017 495 Dihedral : 4.649 15.522 385 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 2.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 0.61 % Allowed : 18.79 % Favored : 80.61 % 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: -1.97 (0.36), residues: 365 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.50 (0.28), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS B 362 PHE 0.004 0.001 PHE A 346 TYR 0.011 0.003 TYR E 310 ARG 0.002 0.000 ARG D 379 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 71 time to evaluate : 0.358 Fit side-chains REVERT: A 338 GLU cc_start: 0.8750 (OUTLIER) cc_final: 0.8476 (tt0) REVERT: B 348 ASP cc_start: 0.9037 (t0) cc_final: 0.7895 (p0) REVERT: B 349 ARG cc_start: 0.8995 (mtt180) cc_final: 0.6970 (pmt-80) REVERT: B 379 ARG cc_start: 0.8443 (mtt180) cc_final: 0.7779 (pmt170) REVERT: C 348 ASP cc_start: 0.8950 (t0) cc_final: 0.7648 (p0) REVERT: C 349 ARG cc_start: 0.9032 (mtt180) cc_final: 0.7038 (pmt-80) REVERT: C 379 ARG cc_start: 0.8434 (mtt180) cc_final: 0.7560 (pmt170) REVERT: D 307 GLN cc_start: 0.8405 (tt0) cc_final: 0.8121 (mt0) REVERT: D 349 ARG cc_start: 0.9018 (mtt180) cc_final: 0.7176 (mmm160) REVERT: D 379 ARG cc_start: 0.4643 (OUTLIER) cc_final: 0.3488 (mmt180) REVERT: E 349 ARG cc_start: 0.9023 (mtt180) cc_final: 0.7341 (mmm160) outliers start: 2 outliers final: 0 residues processed: 71 average time/residue: 1.5327 time to fit residues: 110.9197 Evaluate side-chains 73 residues out of total 330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 71 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 338 GLU Chi-restraints excluded: chain D residue 379 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 23 optimal weight: 9.9990 chunk 34 optimal weight: 6.9990 chunk 32 optimal weight: 0.1980 chunk 27 optimal weight: 1.9990 chunk 2 optimal weight: 6.9990 chunk 21 optimal weight: 6.9990 chunk 17 optimal weight: 5.9990 chunk 22 optimal weight: 5.9990 chunk 29 optimal weight: 5.9990 chunk 8 optimal weight: 2.9990 chunk 25 optimal weight: 3.9990 overall best weight: 3.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 307 GLN C 307 GLN C 351 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8981 moved from start: 0.2979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.027 2915 Z= 0.318 Angle : 0.618 6.118 3900 Z= 0.310 Chirality : 0.050 0.132 440 Planarity : 0.002 0.014 495 Dihedral : 4.804 15.450 385 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 2.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 1.52 % Allowed : 17.88 % Favored : 80.61 % 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: -1.97 (0.36), residues: 365 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.49 (0.28), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS B 362 PHE 0.006 0.001 PHE D 378 TYR 0.015 0.004 TYR E 310 ARG 0.003 0.001 ARG D 379 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 72 time to evaluate : 0.375 Fit side-chains REVERT: A 338 GLU cc_start: 0.8725 (OUTLIER) cc_final: 0.8495 (tt0) REVERT: B 348 ASP cc_start: 0.9029 (t0) cc_final: 0.7856 (p0) REVERT: B 349 ARG cc_start: 0.9003 (mtt180) cc_final: 0.6959 (pmt-80) REVERT: B 379 ARG cc_start: 0.8420 (mtt180) cc_final: 0.7711 (pmt170) REVERT: C 349 ARG cc_start: 0.9039 (mtt180) cc_final: 0.7060 (pmt-80) REVERT: C 379 ARG cc_start: 0.8471 (mtt180) cc_final: 0.7566 (pmt170) REVERT: D 349 ARG cc_start: 0.9016 (mtt180) cc_final: 0.7179 (mmm160) REVERT: E 349 ARG cc_start: 0.9019 (mtt180) cc_final: 0.7363 (mmm160) outliers start: 5 outliers final: 1 residues processed: 75 average time/residue: 1.4938 time to fit residues: 114.2712 Evaluate side-chains 74 residues out of total 330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 72 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 338 GLU Chi-restraints excluded: chain C residue 314 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 4 optimal weight: 6.9990 chunk 7 optimal weight: 7.9990 chunk 27 optimal weight: 7.9990 chunk 11 optimal weight: 4.9990 chunk 28 optimal weight: 1.9990 chunk 3 optimal weight: 7.9990 chunk 5 optimal weight: 9.9990 chunk 24 optimal weight: 5.9990 chunk 1 optimal weight: 0.6980 chunk 20 optimal weight: 0.6980 chunk 31 optimal weight: 1.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 307 GLN C 307 GLN C 351 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8967 moved from start: 0.3040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 2915 Z= 0.233 Angle : 0.587 6.235 3900 Z= 0.288 Chirality : 0.049 0.128 440 Planarity : 0.002 0.016 495 Dihedral : 4.754 15.869 385 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 2.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 0.30 % Allowed : 19.70 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.96 (0.36), residues: 365 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.49 (0.28), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS B 362 PHE 0.004 0.001 PHE D 378 TYR 0.012 0.003 TYR C 310 ARG 0.002 0.000 ARG D 379 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 730 Ramachandran restraints generated. 365 Oldfield, 0 Emsley, 365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 72 time to evaluate : 0.373 Fit side-chains REVERT: A 338 GLU cc_start: 0.8752 (OUTLIER) cc_final: 0.8472 (tt0) REVERT: B 348 ASP cc_start: 0.9022 (t0) cc_final: 0.7858 (p0) REVERT: B 349 ARG cc_start: 0.8996 (mtt180) cc_final: 0.6969 (pmt-80) REVERT: B 379 ARG cc_start: 0.8422 (mtt180) cc_final: 0.7734 (pmt170) REVERT: C 349 ARG cc_start: 0.9035 (mtt180) cc_final: 0.7064 (pmt-80) REVERT: C 379 ARG cc_start: 0.8467 (mtt180) cc_final: 0.7571 (pmt170) REVERT: D 349 ARG cc_start: 0.9023 (mtt180) cc_final: 0.7177 (mmm160) REVERT: E 349 ARG cc_start: 0.9024 (mtt180) cc_final: 0.7366 (mmm160) outliers start: 1 outliers final: 0 residues processed: 72 average time/residue: 1.4741 time to fit residues: 108.2649 Evaluate side-chains 73 residues out of total 330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 72 time to evaluate : 0.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 338 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 18 optimal weight: 5.9990 chunk 23 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 22 optimal weight: 3.9990 chunk 21 optimal weight: 5.9990 chunk 20 optimal weight: 5.9990 chunk 13 optimal weight: 5.9990 chunk 12 optimal weight: 7.9990 chunk 34 optimal weight: 3.9990 chunk 1 optimal weight: 9.9990 chunk 33 optimal weight: 8.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 307 GLN C 307 GLN C 351 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.100705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.091228 restraints weight = 4599.939| |-----------------------------------------------------------------------------| r_work (start): 0.3709 rms_B_bonded: 1.94 r_work: 0.3620 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.3542 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.3542 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9057 moved from start: 0.2961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.040 2915 Z= 0.520 Angle : 0.693 6.383 3900 Z= 0.354 Chirality : 0.052 0.138 440 Planarity : 0.003 0.017 495 Dihedral : 5.083 16.280 385 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 2.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 0.30 % Allowed : 19.70 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.02 (0.36), residues: 365 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.53 (0.27), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 362 PHE 0.008 0.002 PHE D 378 TYR 0.021 0.005 TYR E 310 ARG 0.005 0.001 ARG D 379 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2348.50 seconds wall clock time: 41 minutes 19.81 seconds (2479.81 seconds total)