Starting phenix.real_space_refine on Sat Aug 3 05:34:29 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q8v_18262/08_2024/8q8v_18262.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q8v_18262/08_2024/8q8v_18262.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q8v_18262/08_2024/8q8v_18262.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q8v_18262/08_2024/8q8v_18262.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q8v_18262/08_2024/8q8v_18262.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q8v_18262/08_2024/8q8v_18262.cif" } resolution = 3.8 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: 5 Type Number sf(0) Gaussians S 6 5.16 5 C 2160 2.51 5 N 636 2.21 5 O 642 1.98 5 H 3588 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ARG 349": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ARG 349": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 7032 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1172 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "C" Number of atoms: 1172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1172 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "E" Number of atoms: 1172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1172 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "B" Number of atoms: 1172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1172 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "D" Number of atoms: 1172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1172 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "F" Number of atoms: 1172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1172 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Time building chain proxies: 4.61, per 1000 atoms: 0.66 Number of scatterers: 7032 At special positions: 0 Unit cell: (146.672, 119.48, 50.264, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 6 16.00 O 642 8.00 N 636 7.00 C 2160 6.00 H 3588 1.00 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: 5.03 Conformation dependent library (CDL) restraints added in 878.2 milliseconds 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 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, 39.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.79 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'C' and resid 306 through 310 removed outlier: 6.410A pdb=" N GLN A 307 " --> pdb=" O ILE C 308 " (cutoff:3.500A) removed outlier: 8.107A pdb=" N TYR C 310 " --> pdb=" O GLN A 307 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N VAL A 309 " --> pdb=" O TYR C 310 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 313 through 314 removed outlier: 6.983A pdb=" N VAL A 313 " --> pdb=" O ASP C 314 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 317 through 325 removed outlier: 6.199A pdb=" N LYS A 317 " --> pdb=" O VAL C 318 " (cutoff:3.500A) removed outlier: 8.057A pdb=" N SER C 320 " --> pdb=" O LYS A 317 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N THR A 319 " --> pdb=" O SER C 320 " (cutoff:3.500A) removed outlier: 8.226A pdb=" N CYS C 322 " --> pdb=" O THR A 319 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N LYS A 321 " --> pdb=" O CYS C 322 " (cutoff:3.500A) removed outlier: 7.597A pdb=" N SER C 324 " --> pdb=" O LYS A 321 " (cutoff:3.500A) removed outlier: 6.012A pdb=" N GLY A 323 " --> pdb=" O SER C 324 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 328 through 330 removed outlier: 6.258A pdb=" N ILE A 328 " --> pdb=" O HIS C 329 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 337 through 339 removed outlier: 6.531A pdb=" N VAL A 337 " --> pdb=" O GLU E 338 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 345 through 346 removed outlier: 6.961A pdb=" N ASP A 345 " --> pdb=" O PHE C 346 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 350 through 353 removed outlier: 6.278A pdb=" N VAL A 350 " --> pdb=" O GLN E 351 " (cutoff:3.500A) removed outlier: 8.129A pdb=" N LYS E 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N SER A 352 " --> pdb=" O LYS E 353 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 357 through 362 removed outlier: 6.340A pdb=" N ASP A 358 " --> pdb=" O ASN C 359 " (cutoff:3.500A) removed outlier: 8.018A pdb=" N THR C 361 " --> pdb=" O ASP A 358 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N ILE A 360 " --> pdb=" O THR C 361 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 369 through 373 removed outlier: 6.436A pdb=" N LYS A 370 " --> pdb=" O ILE E 371 " (cutoff:3.500A) removed outlier: 8.067A pdb=" N THR E 373 " --> pdb=" O LYS A 370 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N GLU A 372 " --> pdb=" O THR E 373 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 306 through 310 removed outlier: 6.409A pdb=" N GLN B 307 " --> pdb=" O ILE D 308 " (cutoff:3.500A) removed outlier: 8.107A pdb=" N TYR D 310 " --> pdb=" O GLN B 307 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N VAL B 309 " --> pdb=" O TYR D 310 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 313 through 314 removed outlier: 6.983A pdb=" N VAL B 313 " --> pdb=" O ASP D 314 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 317 through 325 removed outlier: 6.199A pdb=" N LYS B 317 " --> pdb=" O VAL D 318 " (cutoff:3.500A) removed outlier: 8.057A pdb=" N SER D 320 " --> pdb=" O LYS B 317 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N THR B 319 " --> pdb=" O SER D 320 " (cutoff:3.500A) removed outlier: 8.226A pdb=" N CYS D 322 " --> pdb=" O THR B 319 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N LYS B 321 " --> pdb=" O CYS D 322 " (cutoff:3.500A) removed outlier: 7.596A pdb=" N SER D 324 " --> pdb=" O LYS B 321 " (cutoff:3.500A) removed outlier: 6.012A pdb=" N GLY B 323 " --> pdb=" O SER D 324 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 328 through 330 removed outlier: 6.257A pdb=" N ILE B 328 " --> pdb=" O HIS D 329 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 337 through 339 removed outlier: 6.532A pdb=" N VAL B 337 " --> pdb=" O GLU F 338 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 345 through 346 removed outlier: 6.961A pdb=" N ASP B 345 " --> pdb=" O PHE D 346 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 350 through 353 removed outlier: 6.278A pdb=" N VAL B 350 " --> pdb=" O GLN F 351 " (cutoff:3.500A) removed outlier: 8.130A pdb=" N LYS F 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N SER B 352 " --> pdb=" O LYS F 353 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 357 through 362 removed outlier: 6.340A pdb=" N ASP B 358 " --> pdb=" O ASN D 359 " (cutoff:3.500A) removed outlier: 8.018A pdb=" N THR D 361 " --> pdb=" O ASP B 358 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N ILE B 360 " --> pdb=" O THR D 361 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 369 through 373 removed outlier: 6.437A pdb=" N LYS B 370 " --> pdb=" O ILE F 371 " (cutoff:3.500A) removed outlier: 8.067A pdb=" N THR F 373 " --> pdb=" O LYS B 370 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N GLU B 372 " --> pdb=" O THR F 373 " (cutoff:3.500A) 60 hydrogen bonds defined for protein. 180 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: 2.31 Time building geometry restraints manager: 5.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.94 - 1.12: 3582 1.12 - 1.29: 573 1.29 - 1.47: 1092 1.47 - 1.64: 1833 1.64 - 1.82: 6 Bond restraints: 7086 Sorted by residual: bond pdb=" CE2 PHE B 346 " pdb=" HE2 PHE B 346 " ideal model delta sigma weight residual 0.930 1.082 -0.152 2.00e-02 2.50e+03 5.76e+01 bond pdb=" NH1 ARG B 349 " pdb="HH11 ARG B 349 " ideal model delta sigma weight residual 0.860 1.012 -0.152 2.00e-02 2.50e+03 5.74e+01 bond pdb=" CE1 HIS B 330 " pdb=" HE1 HIS B 330 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.74e+01 bond pdb=" N GLU B 338 " pdb=" H GLU B 338 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.74e+01 bond pdb=" NE2 HIS D 374 " pdb=" HE2 HIS D 374 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.72e+01 ... (remaining 7081 not shown) Histogram of bond angle deviations from ideal: 96.65 - 103.26: 36 103.26 - 109.87: 6174 109.87 - 116.48: 3150 116.48 - 123.08: 2957 123.08 - 129.69: 595 Bond angle restraints: 12912 Sorted by residual: angle pdb=" CA LYS A 331 " pdb=" C LYS A 331 " pdb=" N PRO A 332 " ideal model delta sigma weight residual 118.16 123.34 -5.18 7.00e-01 2.04e+00 5.47e+01 angle pdb=" C ASP E 348 " pdb=" N ARG E 349 " pdb=" CA ARG E 349 " ideal model delta sigma weight residual 121.31 129.69 -8.38 1.49e+00 4.50e-01 3.16e+01 angle pdb=" C ASP F 348 " pdb=" N ARG F 349 " pdb=" CA ARG F 349 " ideal model delta sigma weight residual 121.31 129.65 -8.34 1.49e+00 4.50e-01 3.13e+01 angle pdb=" C LYS E 343 " pdb=" N LEU E 344 " pdb=" CA LEU E 344 " ideal model delta sigma weight residual 120.71 128.24 -7.53 1.42e+00 4.96e-01 2.81e+01 angle pdb=" C LYS F 343 " pdb=" N LEU F 344 " pdb=" CA LEU F 344 " ideal model delta sigma weight residual 120.71 128.22 -7.51 1.42e+00 4.96e-01 2.80e+01 ... (remaining 12907 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.61: 2836 15.61 - 31.21: 200 31.21 - 46.82: 98 46.82 - 62.43: 82 62.43 - 78.03: 48 Dihedral angle restraints: 3264 sinusoidal: 1866 harmonic: 1398 Sorted by residual: dihedral pdb=" CA ASN D 359 " pdb=" C ASN D 359 " pdb=" N ILE D 360 " pdb=" CA ILE D 360 " ideal model delta harmonic sigma weight residual -180.00 -152.74 -27.26 0 5.00e+00 4.00e-02 2.97e+01 dihedral pdb=" CA ASN C 359 " pdb=" C ASN C 359 " pdb=" N ILE C 360 " pdb=" CA ILE C 360 " ideal model delta harmonic sigma weight residual -180.00 -152.77 -27.23 0 5.00e+00 4.00e-02 2.97e+01 dihedral pdb=" CA SER C 341 " pdb=" C SER C 341 " pdb=" N GLU C 342 " pdb=" CA GLU C 342 " ideal model delta harmonic sigma weight residual -180.00 -154.37 -25.63 0 5.00e+00 4.00e-02 2.63e+01 ... (remaining 3261 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 309 0.070 - 0.139: 170 0.139 - 0.209: 41 0.209 - 0.279: 6 0.279 - 0.348: 2 Chirality restraints: 528 Sorted by residual: chirality pdb=" CA LYS E 343 " pdb=" N LYS E 343 " pdb=" C LYS E 343 " pdb=" CB LYS E 343 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.03e+00 chirality pdb=" CA LYS F 343 " pdb=" N LYS F 343 " pdb=" C LYS F 343 " pdb=" CB LYS F 343 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 2.98e+00 chirality pdb=" CA LYS F 331 " pdb=" N LYS F 331 " pdb=" C LYS F 331 " pdb=" CB LYS F 331 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.85e+00 ... (remaining 525 not shown) Planarity restraints: 1020 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR E 310 " -0.161 2.00e-02 2.50e+03 7.45e-02 1.66e+02 pdb=" CG TYR E 310 " 0.013 2.00e-02 2.50e+03 pdb=" CD1 TYR E 310 " 0.048 2.00e-02 2.50e+03 pdb=" CD2 TYR E 310 " 0.056 2.00e-02 2.50e+03 pdb=" CE1 TYR E 310 " 0.063 2.00e-02 2.50e+03 pdb=" CE2 TYR E 310 " 0.032 2.00e-02 2.50e+03 pdb=" CZ TYR E 310 " 0.007 2.00e-02 2.50e+03 pdb=" OH TYR E 310 " -0.161 2.00e-02 2.50e+03 pdb=" HD1 TYR E 310 " 0.004 2.00e-02 2.50e+03 pdb=" HD2 TYR E 310 " 0.052 2.00e-02 2.50e+03 pdb=" HE1 TYR E 310 " 0.039 2.00e-02 2.50e+03 pdb=" HE2 TYR E 310 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR F 310 " -0.160 2.00e-02 2.50e+03 7.43e-02 1.66e+02 pdb=" CG TYR F 310 " 0.013 2.00e-02 2.50e+03 pdb=" CD1 TYR F 310 " 0.048 2.00e-02 2.50e+03 pdb=" CD2 TYR F 310 " 0.056 2.00e-02 2.50e+03 pdb=" CE1 TYR F 310 " 0.063 2.00e-02 2.50e+03 pdb=" CE2 TYR F 310 " 0.031 2.00e-02 2.50e+03 pdb=" CZ TYR F 310 " 0.007 2.00e-02 2.50e+03 pdb=" OH TYR F 310 " -0.160 2.00e-02 2.50e+03 pdb=" HD1 TYR F 310 " 0.004 2.00e-02 2.50e+03 pdb=" HD2 TYR F 310 " 0.051 2.00e-02 2.50e+03 pdb=" HE1 TYR F 310 " 0.039 2.00e-02 2.50e+03 pdb=" HE2 TYR F 310 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 346 " -0.144 2.00e-02 2.50e+03 5.79e-02 1.01e+02 pdb=" CG PHE B 346 " 0.031 2.00e-02 2.50e+03 pdb=" CD1 PHE B 346 " 0.066 2.00e-02 2.50e+03 pdb=" CD2 PHE B 346 " 0.049 2.00e-02 2.50e+03 pdb=" CE1 PHE B 346 " 0.030 2.00e-02 2.50e+03 pdb=" CE2 PHE B 346 " 0.028 2.00e-02 2.50e+03 pdb=" CZ PHE B 346 " -0.006 2.00e-02 2.50e+03 pdb=" HD1 PHE B 346 " 0.039 2.00e-02 2.50e+03 pdb=" HD2 PHE B 346 " 0.024 2.00e-02 2.50e+03 pdb=" HE1 PHE B 346 " -0.028 2.00e-02 2.50e+03 pdb=" HE2 PHE B 346 " -0.002 2.00e-02 2.50e+03 pdb=" HZ PHE B 346 " -0.085 2.00e-02 2.50e+03 ... (remaining 1017 not shown) Histogram of nonbonded interaction distances: 1.55 - 2.16: 435 2.16 - 2.77: 11926 2.77 - 3.38: 19125 3.38 - 3.99: 23717 3.99 - 4.60: 34447 Nonbonded interactions: 89650 Sorted by model distance: nonbonded pdb=" OD1 ASP E 314 " pdb=" HG SER E 316 " model vdw 1.551 2.450 nonbonded pdb=" OD1 ASP F 314 " pdb=" HG SER F 316 " model vdw 1.551 2.450 nonbonded pdb=" OD1 ASP B 314 " pdb=" HG SER B 316 " model vdw 1.561 2.450 nonbonded pdb=" OD1 ASP A 314 " pdb=" HG SER A 316 " model vdw 1.561 2.450 nonbonded pdb=" OD1 ASP D 314 " pdb=" HG SER D 316 " model vdw 1.619 2.450 ... (remaining 89645 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.980 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: 0.100 Extract box with map and model: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 27.200 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6737 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 : 0.012 0.040 3498 Z= 0.810 Angle : 1.996 8.922 4680 Z= 1.302 Chirality : 0.087 0.348 528 Planarity : 0.013 0.087 594 Dihedral : 12.459 78.032 1344 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 1.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.39 % Favored : 93.61 % Rotamer: Outliers : 0.00 % Allowed : 1.01 % Favored : 98.99 % Cbeta Deviations : 0.51 % 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: -2.75 (0.32), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.08 (0.25), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.003 HIS A 362 PHE 0.089 0.028 PHE E 346 TYR 0.149 0.029 TYR E 310 ARG 0.005 0.001 ARG A 349 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 101 time to evaluate : 0.528 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 314 ASP cc_start: 0.7689 (t0) cc_final: 0.7426 (t0) REVERT: C 338 GLU cc_start: 0.7117 (tt0) cc_final: 0.6669 (tm-30) REVERT: E 375 LYS cc_start: 0.7172 (tttt) cc_final: 0.6914 (tttm) outliers start: 0 outliers final: 0 residues processed: 101 average time/residue: 0.5875 time to fit residues: 66.4767 Evaluate side-chains 64 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 64 time to evaluate : 0.582 ------------------------------------------------------------------------------- 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: 5.9990 chunk 31 optimal weight: 5.9990 chunk 17 optimal weight: 6.9990 chunk 10 optimal weight: 5.9990 chunk 21 optimal weight: 5.9990 chunk 32 optimal weight: 7.9990 chunk 12 optimal weight: 5.9990 chunk 20 optimal weight: 5.9990 chunk 24 optimal weight: 5.9990 chunk 38 optimal weight: 5.9990 chunk 11 optimal weight: 5.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 327 ASN D 327 ASN ** D 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 327 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7160 moved from start: 0.4361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.061 3498 Z= 0.514 Angle : 0.858 6.603 4680 Z= 0.469 Chirality : 0.052 0.145 528 Planarity : 0.006 0.037 594 Dihedral : 8.311 24.966 462 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 12.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % Rotamer: Outliers : 0.76 % Allowed : 6.31 % Favored : 92.93 % 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: -2.92 (0.32), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.22 (0.24), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.002 HIS F 374 PHE 0.014 0.003 PHE A 378 TYR 0.022 0.004 TYR F 310 ARG 0.006 0.001 ARG C 379 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 74 time to evaluate : 0.599 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 317 LYS cc_start: 0.7638 (mttt) cc_final: 0.7346 (mptt) REVERT: C 338 GLU cc_start: 0.7449 (tt0) cc_final: 0.6961 (tm-30) REVERT: E 349 ARG cc_start: 0.6981 (mtm180) cc_final: 0.5956 (mmm160) REVERT: B 375 LYS cc_start: 0.8102 (tttt) cc_final: 0.7708 (tttm) REVERT: D 368 ASN cc_start: 0.8087 (m-40) cc_final: 0.7865 (m-40) REVERT: D 375 LYS cc_start: 0.8336 (tttt) cc_final: 0.8132 (tttm) REVERT: F 368 ASN cc_start: 0.7492 (m-40) cc_final: 0.7217 (m-40) REVERT: F 375 LYS cc_start: 0.8393 (tttt) cc_final: 0.7969 (tttm) outliers start: 3 outliers final: 1 residues processed: 76 average time/residue: 0.5803 time to fit residues: 50.2053 Evaluate side-chains 62 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 61 time to evaluate : 0.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 306 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 31 optimal weight: 0.9990 chunk 25 optimal weight: 7.9990 chunk 10 optimal weight: 5.9990 chunk 38 optimal weight: 4.9990 chunk 41 optimal weight: 0.8980 chunk 34 optimal weight: 0.0040 chunk 37 optimal weight: 4.9990 chunk 13 optimal weight: 6.9990 chunk 30 optimal weight: 4.9990 chunk 28 optimal weight: 0.5980 chunk 19 optimal weight: 0.6980 overall best weight: 0.6394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 327 ASN C 327 ASN C 368 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7077 moved from start: 0.5134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3498 Z= 0.194 Angle : 0.618 4.528 4680 Z= 0.323 Chirality : 0.053 0.132 528 Planarity : 0.004 0.032 594 Dihedral : 6.860 21.165 462 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 0.76 % Allowed : 7.32 % Favored : 91.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.39 (0.31), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.81 (0.24), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS E 330 PHE 0.017 0.003 PHE C 378 TYR 0.013 0.002 TYR C 310 ARG 0.006 0.001 ARG C 379 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 63 time to evaluate : 0.594 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 317 LYS cc_start: 0.7697 (mttt) cc_final: 0.7408 (mptt) REVERT: E 349 ARG cc_start: 0.6752 (mtm180) cc_final: 0.6039 (mmm160) REVERT: B 375 LYS cc_start: 0.7919 (tttt) cc_final: 0.7544 (tttm) REVERT: D 368 ASN cc_start: 0.7850 (m-40) cc_final: 0.7548 (m-40) REVERT: D 375 LYS cc_start: 0.8225 (tttt) cc_final: 0.7914 (tttm) REVERT: F 368 ASN cc_start: 0.7458 (m-40) cc_final: 0.7195 (m-40) REVERT: F 375 LYS cc_start: 0.8323 (tttt) cc_final: 0.7985 (tttm) outliers start: 3 outliers final: 2 residues processed: 64 average time/residue: 0.5855 time to fit residues: 42.4260 Evaluate side-chains 59 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 57 time to evaluate : 0.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 327 ASN Chi-restraints excluded: chain F residue 306 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 4 optimal weight: 9.9990 chunk 18 optimal weight: 2.9990 chunk 25 optimal weight: 0.7980 chunk 38 optimal weight: 9.9990 chunk 40 optimal weight: 3.9990 chunk 20 optimal weight: 5.9990 chunk 36 optimal weight: 8.9990 chunk 10 optimal weight: 9.9990 chunk 33 optimal weight: 6.9990 chunk 23 optimal weight: 5.9990 chunk 0 optimal weight: 7.9990 overall best weight: 3.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7204 moved from start: 0.5759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 3498 Z= 0.332 Angle : 0.641 5.149 4680 Z= 0.341 Chirality : 0.051 0.133 528 Planarity : 0.005 0.037 594 Dihedral : 6.710 21.354 462 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 0.51 % Allowed : 8.33 % Favored : 91.16 % 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 (0.30), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.04 (0.23), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS E 374 PHE 0.012 0.002 PHE C 378 TYR 0.016 0.003 TYR F 310 ARG 0.002 0.000 ARG B 379 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 63 time to evaluate : 0.560 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 317 LYS cc_start: 0.7695 (mttt) cc_final: 0.7455 (mttp) REVERT: C 317 LYS cc_start: 0.8134 (mttt) cc_final: 0.7872 (mptt) REVERT: E 349 ARG cc_start: 0.6992 (mtm180) cc_final: 0.6011 (mmm160) REVERT: D 368 ASN cc_start: 0.8131 (m-40) cc_final: 0.7927 (m-40) REVERT: F 368 ASN cc_start: 0.7685 (m-40) cc_final: 0.7353 (m-40) REVERT: F 375 LYS cc_start: 0.8469 (tttt) cc_final: 0.8146 (tttm) outliers start: 2 outliers final: 1 residues processed: 64 average time/residue: 0.6191 time to fit residues: 44.8370 Evaluate side-chains 64 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 63 time to evaluate : 0.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 306 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 30 optimal weight: 4.9990 chunk 16 optimal weight: 3.9990 chunk 34 optimal weight: 0.0570 chunk 28 optimal weight: 6.9990 chunk 0 optimal weight: 7.9990 chunk 20 optimal weight: 10.0000 chunk 36 optimal weight: 6.9990 chunk 10 optimal weight: 6.9990 chunk 13 optimal weight: 5.9990 chunk 8 optimal weight: 0.5980 chunk 23 optimal weight: 3.9990 overall best weight: 2.7304 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 327 ASN C 329 HIS E 327 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7221 moved from start: 0.6215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3498 Z= 0.231 Angle : 0.587 4.874 4680 Z= 0.308 Chirality : 0.051 0.129 528 Planarity : 0.004 0.035 594 Dihedral : 6.085 20.182 462 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 0.51 % Allowed : 11.62 % Favored : 87.88 % 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: -2.83 (0.30), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.15 (0.23), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS F 362 PHE 0.022 0.002 PHE C 378 TYR 0.010 0.002 TYR F 310 ARG 0.003 0.000 ARG C 379 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 69 time to evaluate : 0.578 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 317 LYS cc_start: 0.7706 (mttt) cc_final: 0.7443 (mttp) REVERT: C 317 LYS cc_start: 0.8122 (mttt) cc_final: 0.7822 (mptt) REVERT: E 349 ARG cc_start: 0.7028 (mtm180) cc_final: 0.6018 (mmm160) REVERT: B 375 LYS cc_start: 0.8105 (tttt) cc_final: 0.7772 (tttm) REVERT: D 368 ASN cc_start: 0.8108 (m-40) cc_final: 0.7878 (m-40) REVERT: F 314 ASP cc_start: 0.6588 (t0) cc_final: 0.6306 (t0) REVERT: F 375 LYS cc_start: 0.8411 (tttt) cc_final: 0.8018 (tttm) outliers start: 2 outliers final: 1 residues processed: 70 average time/residue: 0.5971 time to fit residues: 47.0704 Evaluate side-chains 65 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 64 time to evaluate : 0.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 306 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 10 optimal weight: 6.9990 chunk 40 optimal weight: 5.9990 chunk 33 optimal weight: 6.9990 chunk 18 optimal weight: 2.9990 chunk 3 optimal weight: 5.9990 chunk 13 optimal weight: 5.9990 chunk 21 optimal weight: 8.9990 chunk 39 optimal weight: 5.9990 chunk 4 optimal weight: 1.9990 chunk 23 optimal weight: 6.9990 chunk 29 optimal weight: 3.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 329 HIS D 368 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7303 moved from start: 0.6702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 3498 Z= 0.341 Angle : 0.647 6.144 4680 Z= 0.340 Chirality : 0.052 0.132 528 Planarity : 0.005 0.032 594 Dihedral : 6.154 20.760 462 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 11.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.45 % Favored : 91.55 % Rotamer: Outliers : 0.51 % Allowed : 13.13 % Favored : 86.36 % 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: -3.33 (0.30), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.53 (0.23), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS C 374 PHE 0.008 0.002 PHE A 346 TYR 0.017 0.003 TYR F 310 ARG 0.001 0.000 ARG E 349 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 67 time to evaluate : 0.575 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 317 LYS cc_start: 0.7739 (mttt) cc_final: 0.7493 (mttp) REVERT: C 317 LYS cc_start: 0.8208 (mttt) cc_final: 0.7911 (mttp) REVERT: E 349 ARG cc_start: 0.7388 (mtm180) cc_final: 0.6337 (mmp80) REVERT: B 336 GLN cc_start: 0.7432 (tt0) cc_final: 0.7063 (mp10) REVERT: D 336 GLN cc_start: 0.7377 (tt0) cc_final: 0.7011 (mp10) REVERT: F 336 GLN cc_start: 0.7673 (tt0) cc_final: 0.7390 (mp10) REVERT: F 375 LYS cc_start: 0.8383 (tttt) cc_final: 0.8066 (tttm) outliers start: 2 outliers final: 2 residues processed: 68 average time/residue: 0.5641 time to fit residues: 43.4960 Evaluate side-chains 68 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 66 time to evaluate : 0.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 306 VAL Chi-restraints excluded: chain F residue 315 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 22 optimal weight: 6.9990 chunk 34 optimal weight: 0.8980 chunk 40 optimal weight: 5.9990 chunk 25 optimal weight: 7.9990 chunk 24 optimal weight: 5.9990 chunk 18 optimal weight: 4.9990 chunk 16 optimal weight: 9.9990 chunk 12 optimal weight: 10.0000 chunk 7 optimal weight: 5.9990 chunk 27 optimal weight: 2.9990 chunk 20 optimal weight: 4.9990 overall best weight: 3.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7328 moved from start: 0.7118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 3498 Z= 0.296 Angle : 0.633 5.240 4680 Z= 0.334 Chirality : 0.052 0.135 528 Planarity : 0.004 0.036 594 Dihedral : 5.994 20.410 462 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 12.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.45 % Favored : 91.55 % Rotamer: Outliers : 0.76 % Allowed : 13.13 % Favored : 86.11 % 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: -3.53 (0.30), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.68 (0.23), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS E 329 PHE 0.008 0.002 PHE E 346 TYR 0.015 0.003 TYR B 310 ARG 0.002 0.000 ARG E 349 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 68 time to evaluate : 0.625 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 317 LYS cc_start: 0.7705 (mttt) cc_final: 0.7453 (mttp) REVERT: C 317 LYS cc_start: 0.8280 (mttt) cc_final: 0.7996 (mttp) REVERT: E 340 LYS cc_start: 0.7671 (tptm) cc_final: 0.6565 (mttt) REVERT: E 349 ARG cc_start: 0.7438 (mtm180) cc_final: 0.6223 (mmp80) REVERT: B 336 GLN cc_start: 0.7658 (tt0) cc_final: 0.7237 (mp10) REVERT: B 375 LYS cc_start: 0.8161 (tttt) cc_final: 0.7834 (tttm) REVERT: D 336 GLN cc_start: 0.7471 (tt0) cc_final: 0.6973 (mp10) REVERT: F 336 GLN cc_start: 0.7656 (tt0) cc_final: 0.7318 (mp10) REVERT: F 370 LYS cc_start: 0.8484 (tttt) cc_final: 0.7917 (tttp) REVERT: F 375 LYS cc_start: 0.8350 (tttt) cc_final: 0.8018 (tttm) outliers start: 3 outliers final: 3 residues processed: 70 average time/residue: 0.5495 time to fit residues: 43.7502 Evaluate side-chains 69 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 66 time to evaluate : 0.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 358 ASP Chi-restraints excluded: chain F residue 306 VAL Chi-restraints excluded: chain F residue 315 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 3 optimal weight: 10.0000 chunk 31 optimal weight: 5.9990 chunk 36 optimal weight: 6.9990 chunk 38 optimal weight: 0.2980 chunk 35 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 chunk 22 optimal weight: 0.9990 chunk 16 optimal weight: 6.9990 chunk 29 optimal weight: 0.9980 chunk 11 optimal weight: 8.9990 chunk 34 optimal weight: 1.9990 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7268 moved from start: 0.7212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3498 Z= 0.179 Angle : 0.560 4.744 4680 Z= 0.287 Chirality : 0.053 0.131 528 Planarity : 0.005 0.052 594 Dihedral : 5.398 18.990 462 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 0.76 % Allowed : 13.89 % Favored : 85.35 % 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: -3.18 (0.31), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.41 (0.24), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS D 362 PHE 0.009 0.002 PHE B 346 TYR 0.009 0.001 TYR D 310 ARG 0.009 0.001 ARG C 379 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 67 time to evaluate : 0.579 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 317 LYS cc_start: 0.7707 (mttt) cc_final: 0.7463 (mttp) REVERT: C 317 LYS cc_start: 0.8183 (mttt) cc_final: 0.7900 (mttp) REVERT: E 340 LYS cc_start: 0.7493 (tptm) cc_final: 0.6367 (mttt) REVERT: E 349 ARG cc_start: 0.7287 (mtm180) cc_final: 0.6171 (mmp80) REVERT: B 375 LYS cc_start: 0.7944 (tttt) cc_final: 0.7612 (tttp) REVERT: F 370 LYS cc_start: 0.8474 (tttt) cc_final: 0.7934 (tttm) REVERT: F 375 LYS cc_start: 0.8172 (tttt) cc_final: 0.7841 (tttm) outliers start: 3 outliers final: 2 residues processed: 68 average time/residue: 0.5725 time to fit residues: 44.1440 Evaluate side-chains 64 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 62 time to evaluate : 0.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 306 VAL Chi-restraints excluded: chain F residue 315 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 0.4980 chunk 37 optimal weight: 7.9990 chunk 24 optimal weight: 7.9990 chunk 39 optimal weight: 5.9990 chunk 18 optimal weight: 6.9990 chunk 27 optimal weight: 5.9990 chunk 41 optimal weight: 0.9980 chunk 38 optimal weight: 3.9990 chunk 33 optimal weight: 0.8980 chunk 3 optimal weight: 8.9990 chunk 25 optimal weight: 0.5980 overall best weight: 1.3982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7268 moved from start: 0.7403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 3498 Z= 0.179 Angle : 0.537 4.507 4680 Z= 0.273 Chirality : 0.052 0.143 528 Planarity : 0.004 0.037 594 Dihedral : 5.091 17.965 462 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 0.51 % Allowed : 14.65 % 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: -3.08 (0.32), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.34 (0.25), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS D 362 PHE 0.007 0.001 PHE A 378 TYR 0.009 0.001 TYR B 310 ARG 0.001 0.000 ARG A 349 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 61 time to evaluate : 0.571 Fit side-chains revert: symmetry clash REVERT: A 317 LYS cc_start: 0.7702 (mttt) cc_final: 0.7437 (mttp) REVERT: C 317 LYS cc_start: 0.8166 (mttt) cc_final: 0.7877 (mttp) REVERT: C 375 LYS cc_start: 0.8078 (tttt) cc_final: 0.7869 (tttm) REVERT: E 340 LYS cc_start: 0.7557 (tptm) cc_final: 0.6543 (mttt) REVERT: E 349 ARG cc_start: 0.7189 (mtm180) cc_final: 0.6170 (mmp80) REVERT: B 375 LYS cc_start: 0.8012 (tttt) cc_final: 0.7678 (tttp) REVERT: F 370 LYS cc_start: 0.8488 (tttt) cc_final: 0.7931 (tttm) REVERT: F 375 LYS cc_start: 0.8165 (tttt) cc_final: 0.7834 (tttm) outliers start: 2 outliers final: 2 residues processed: 62 average time/residue: 0.5497 time to fit residues: 38.8570 Evaluate side-chains 62 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 60 time to evaluate : 0.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 306 VAL Chi-restraints excluded: chain F residue 315 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 20 optimal weight: 6.9990 chunk 26 optimal weight: 8.9990 chunk 35 optimal weight: 4.9990 chunk 10 optimal weight: 3.9990 chunk 30 optimal weight: 5.9990 chunk 4 optimal weight: 9.9990 chunk 9 optimal weight: 0.8980 chunk 33 optimal weight: 0.9980 chunk 13 optimal weight: 6.9990 chunk 34 optimal weight: 5.9990 chunk 6 optimal weight: 4.9990 overall best weight: 3.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7313 moved from start: 0.7545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 3498 Z= 0.251 Angle : 0.584 4.979 4680 Z= 0.300 Chirality : 0.051 0.137 528 Planarity : 0.004 0.038 594 Dihedral : 5.276 18.268 462 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.82 % Favored : 90.18 % Rotamer: Outliers : 0.76 % Allowed : 14.39 % 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: -3.28 (0.32), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.49 (0.24), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS C 374 PHE 0.006 0.002 PHE E 346 TYR 0.012 0.002 TYR B 310 ARG 0.004 0.000 ARG C 379 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 64 time to evaluate : 0.588 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 317 LYS cc_start: 0.7726 (mttt) cc_final: 0.7467 (mttp) REVERT: C 317 LYS cc_start: 0.8251 (mttt) cc_final: 0.7938 (mttp) REVERT: E 340 LYS cc_start: 0.7591 (tptm) cc_final: 0.6590 (mttt) REVERT: E 349 ARG cc_start: 0.7298 (mtm180) cc_final: 0.6199 (mmp80) REVERT: B 375 LYS cc_start: 0.8059 (tttt) cc_final: 0.7718 (tttp) REVERT: F 336 GLN cc_start: 0.7599 (tt0) cc_final: 0.7190 (mp10) REVERT: F 375 LYS cc_start: 0.8243 (tttt) cc_final: 0.7914 (tttm) outliers start: 3 outliers final: 3 residues processed: 66 average time/residue: 0.5786 time to fit residues: 43.2373 Evaluate side-chains 65 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 62 time to evaluate : 0.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 358 ASP Chi-restraints excluded: chain F residue 306 VAL Chi-restraints excluded: chain F residue 315 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 29 optimal weight: 8.9990 chunk 1 optimal weight: 8.9990 chunk 24 optimal weight: 7.9990 chunk 38 optimal weight: 2.9990 chunk 22 optimal weight: 3.9990 chunk 28 optimal weight: 0.0870 chunk 26 optimal weight: 0.9980 chunk 25 optimal weight: 5.9990 chunk 16 optimal weight: 8.9990 chunk 15 optimal weight: 2.9990 chunk 41 optimal weight: 0.6980 overall best weight: 1.5562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 351 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4326 r_free = 0.4326 target = 0.129651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.107299 restraints weight = 15607.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.110564 restraints weight = 5370.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.112441 restraints weight = 2773.515| |-----------------------------------------------------------------------------| r_work (final): 0.4123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7668 moved from start: 0.7598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 3498 Z= 0.181 Angle : 0.554 5.002 4680 Z= 0.280 Chirality : 0.052 0.137 528 Planarity : 0.005 0.051 594 Dihedral : 5.031 17.510 462 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 0.51 % Allowed : 14.65 % 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: -3.14 (0.32), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.39 (0.25), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS D 362 PHE 0.007 0.001 PHE E 346 TYR 0.008 0.001 TYR B 310 ARG 0.008 0.000 ARG C 379 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2619.99 seconds wall clock time: 46 minutes 13.57 seconds (2773.57 seconds total)