Starting phenix.real_space_refine on Mon Jan 13 16:54:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9h5j_51886/01_2025/9h5j_51886.cif Found real_map, /net/cci-nas-00/data/ceres_data/9h5j_51886/01_2025/9h5j_51886.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.72 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9h5j_51886/01_2025/9h5j_51886.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9h5j_51886/01_2025/9h5j_51886.map" model { file = "/net/cci-nas-00/data/ceres_data/9h5j_51886/01_2025/9h5j_51886.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9h5j_51886/01_2025/9h5j_51886.cif" } resolution = 2.72 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= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 6 5.16 5 C 2076 2.51 5 N 600 2.21 5 O 618 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 3300 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 550 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 550 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 3, 'TRANS': 68} Chain: "B" Number of atoms: 550 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 550 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 3, 'TRANS': 68} Chain: "C" Number of atoms: 550 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 550 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 3, 'TRANS': 68} Chain: "D" Number of atoms: 550 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 550 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 3, 'TRANS': 68} Chain: "E" Number of atoms: 550 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 550 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 3, 'TRANS': 68} Chain: "F" Number of atoms: 550 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 550 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 3, 'TRANS': 68} Time building chain proxies: 3.26, per 1000 atoms: 0.99 Number of scatterers: 3300 At special positions: 0 Unit cell: (146.568, 75.144, 34.968, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 6 16.00 O 618 8.00 N 600 7.00 C 2076 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: 0.84 Conformation dependent library (CDL) restraints added in 381.0 milliseconds 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 756 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 20 sheets defined 0.0% alpha, 48.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.60 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 308 through 310 removed outlier: 6.889A pdb=" N ILE B 308 " --> pdb=" O VAL D 309 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 313 through 314 removed outlier: 6.892A pdb=" N VAL A 313 " --> pdb=" O ASP D 314 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 317 through 322 removed outlier: 6.625A pdb=" N VAL B 318 " --> pdb=" O THR D 319 " (cutoff:3.500A) removed outlier: 8.513A pdb=" N LYS D 321 " --> pdb=" O VAL B 318 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N SER B 320 " --> pdb=" O LYS D 321 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 325 through 330 removed outlier: 7.024A pdb=" N GLY D 326 " --> pdb=" O LEU A 325 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N ASN A 327 " --> pdb=" O GLY D 326 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N GLY B 326 " --> pdb=" O LEU D 325 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N ASN D 327 " --> pdb=" O GLY B 326 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 336 through 340 removed outlier: 6.658A pdb=" N GLN A 336 " --> pdb=" O VAL D 337 " (cutoff:3.500A) removed outlier: 8.446A pdb=" N VAL D 339 " --> pdb=" O GLN A 336 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N GLU A 338 " --> pdb=" O VAL D 339 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 343 through 347 removed outlier: 6.670A pdb=" N LEU B 344 " --> pdb=" O ASP D 345 " (cutoff:3.500A) removed outlier: 8.035A pdb=" N LYS D 347 " --> pdb=" O LEU B 344 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N PHE B 346 " --> pdb=" O LYS D 347 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 350 through 356 removed outlier: 6.778A pdb=" N SER D 356 " --> pdb=" O GLY A 355 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N VAL B 350 " --> pdb=" O GLN D 351 " (cutoff:3.500A) removed outlier: 8.018A pdb=" N LYS D 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N SER B 352 " --> pdb=" O LYS D 353 " (cutoff:3.500A) removed outlier: 8.390A pdb=" N GLY D 355 " --> pdb=" O SER B 352 " (cutoff:3.500A) removed outlier: 8.283A pdb=" N ILE B 354 " --> pdb=" O GLY D 355 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 359 through 362 removed outlier: 6.662A pdb=" N ASN B 359 " --> pdb=" O ILE D 360 " (cutoff:3.500A) removed outlier: 7.941A pdb=" N HIS D 362 " --> pdb=" O ASN B 359 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N THR B 361 " --> pdb=" O HIS D 362 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 369 through 371 removed outlier: 6.607A pdb=" N LYS B 370 " --> pdb=" O ILE D 371 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 374 through 377 removed outlier: 6.578A pdb=" N HIS B 374 " --> pdb=" O LYS D 375 " (cutoff:3.500A) removed outlier: 8.283A pdb=" N THR D 377 " --> pdb=" O HIS B 374 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N LEU B 376 " --> pdb=" O THR D 377 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 308 through 310 removed outlier: 6.949A pdb=" N ILE C 308 " --> pdb=" O VAL E 309 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N ILE E 308 " --> pdb=" O VAL F 309 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'C' and resid 313 through 314 Processing sheet with id=AB4, first strand: chain 'C' and resid 317 through 322 Processing sheet with id=AB5, first strand: chain 'C' and resid 325 through 330 removed outlier: 6.969A pdb=" N GLY C 326 " --> pdb=" O LEU E 325 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N ASN E 327 " --> pdb=" O GLY C 326 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N GLY E 326 " --> pdb=" O LEU F 325 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N ASN F 327 " --> pdb=" O GLY E 326 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 336 through 340 Processing sheet with id=AB7, first strand: chain 'C' and resid 343 through 347 removed outlier: 6.658A pdb=" N LEU C 344 " --> pdb=" O ASP E 345 " (cutoff:3.500A) removed outlier: 7.994A pdb=" N LYS E 347 " --> pdb=" O LEU C 344 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N PHE C 346 " --> pdb=" O LYS E 347 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N LEU E 344 " --> pdb=" O ASP F 345 " (cutoff:3.500A) removed outlier: 8.083A pdb=" N LYS F 347 " --> pdb=" O LEU E 344 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N PHE E 346 " --> pdb=" O LYS F 347 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'C' and resid 350 through 356 removed outlier: 6.295A pdb=" N VAL C 350 " --> pdb=" O GLN E 351 " (cutoff:3.500A) removed outlier: 8.046A pdb=" N LYS E 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N SER C 352 " --> pdb=" O LYS E 353 " (cutoff:3.500A) removed outlier: 8.423A pdb=" N GLY E 355 " --> pdb=" O SER C 352 " (cutoff:3.500A) removed outlier: 8.289A pdb=" N ILE C 354 " --> pdb=" O GLY E 355 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N VAL E 350 " --> pdb=" O GLN F 351 " (cutoff:3.500A) removed outlier: 8.029A pdb=" N LYS F 353 " --> pdb=" O VAL E 350 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N SER E 352 " --> pdb=" O LYS F 353 " (cutoff:3.500A) removed outlier: 8.387A pdb=" N GLY F 355 " --> pdb=" O SER E 352 " (cutoff:3.500A) removed outlier: 8.231A pdb=" N ILE E 354 " --> pdb=" O GLY F 355 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'C' and resid 359 through 362 removed outlier: 6.624A pdb=" N ASN C 359 " --> pdb=" O ILE E 360 " (cutoff:3.500A) removed outlier: 7.923A pdb=" N HIS E 362 " --> pdb=" O ASN C 359 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N THR C 361 " --> pdb=" O HIS E 362 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N ASN E 359 " --> pdb=" O ILE F 360 " (cutoff:3.500A) removed outlier: 7.987A pdb=" N HIS F 362 " --> pdb=" O ASN E 359 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N THR E 361 " --> pdb=" O HIS F 362 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'C' and resid 369 through 371 removed outlier: 6.592A pdb=" N LYS C 370 " --> pdb=" O ILE E 371 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N LYS E 370 " --> pdb=" O ILE F 371 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'C' and resid 374 through 377 removed outlier: 6.532A pdb=" N HIS C 374 " --> pdb=" O LYS E 375 " (cutoff:3.500A) removed outlier: 8.274A pdb=" N THR E 377 " --> pdb=" O HIS C 374 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N LEU C 376 " --> pdb=" O THR E 377 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N HIS E 374 " --> pdb=" O LYS F 375 " (cutoff:3.500A) removed outlier: 8.290A pdb=" N THR F 377 " --> pdb=" O HIS E 374 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N LEU E 376 " --> pdb=" O THR F 377 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 61 hydrogen bonds defined for protein. 183 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: 0.93 Time building geometry restraints manager: 0.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 690 1.33 - 1.45: 638 1.45 - 1.57: 2020 1.57 - 1.69: 0 1.69 - 1.81: 6 Bond restraints: 3354 Sorted by residual: bond pdb=" CZ ARG D 349 " pdb=" NH2 ARG D 349 " ideal model delta sigma weight residual 1.330 1.290 0.040 1.30e-02 5.92e+03 9.34e+00 bond pdb=" CZ ARG E 349 " pdb=" NH2 ARG E 349 " ideal model delta sigma weight residual 1.330 1.291 0.039 1.30e-02 5.92e+03 9.09e+00 bond pdb=" CZ ARG A 349 " pdb=" NH2 ARG A 349 " ideal model delta sigma weight residual 1.330 1.292 0.038 1.30e-02 5.92e+03 8.71e+00 bond pdb=" CZ ARG F 349 " pdb=" NH2 ARG F 349 " ideal model delta sigma weight residual 1.330 1.295 0.035 1.30e-02 5.92e+03 7.30e+00 bond pdb=" CZ ARG B 349 " pdb=" NH2 ARG B 349 " ideal model delta sigma weight residual 1.330 1.297 0.033 1.30e-02 5.92e+03 6.26e+00 ... (remaining 3349 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.26: 2212 1.26 - 2.53: 1398 2.53 - 3.79: 618 3.79 - 5.05: 210 5.05 - 6.32: 50 Bond angle restraints: 4488 Sorted by residual: angle pdb=" CA PHE B 346 " pdb=" CB PHE B 346 " pdb=" CG PHE B 346 " ideal model delta sigma weight residual 113.80 119.06 -5.26 1.00e+00 1.00e+00 2.76e+01 angle pdb=" CA PHE E 346 " pdb=" CB PHE E 346 " pdb=" CG PHE E 346 " ideal model delta sigma weight residual 113.80 118.84 -5.04 1.00e+00 1.00e+00 2.54e+01 angle pdb=" CB HIS F 362 " pdb=" CG HIS F 362 " pdb=" CD2 HIS F 362 " ideal model delta sigma weight residual 131.20 124.99 6.21 1.30e+00 5.92e-01 2.28e+01 angle pdb=" N GLY E 326 " pdb=" CA GLY E 326 " pdb=" C GLY E 326 " ideal model delta sigma weight residual 110.69 117.00 -6.31 1.33e+00 5.65e-01 2.25e+01 angle pdb=" CB HIS D 329 " pdb=" CG HIS D 329 " pdb=" CD2 HIS D 329 " ideal model delta sigma weight residual 131.20 125.21 5.99 1.30e+00 5.92e-01 2.12e+01 ... (remaining 4483 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.56: 1906 16.56 - 33.13: 115 33.13 - 49.69: 12 49.69 - 66.25: 2 66.25 - 82.81: 5 Dihedral angle restraints: 2040 sinusoidal: 852 harmonic: 1188 Sorted by residual: dihedral pdb=" CA SER D 341 " pdb=" C SER D 341 " pdb=" N GLU D 342 " pdb=" CA GLU D 342 " ideal model delta harmonic sigma weight residual 180.00 160.50 19.50 0 5.00e+00 4.00e-02 1.52e+01 dihedral pdb=" CA LYS C 347 " pdb=" C LYS C 347 " pdb=" N ASP C 348 " pdb=" CA ASP C 348 " ideal model delta harmonic sigma weight residual 180.00 160.67 19.33 0 5.00e+00 4.00e-02 1.49e+01 dihedral pdb=" CA SER E 341 " pdb=" C SER E 341 " pdb=" N GLU E 342 " pdb=" CA GLU E 342 " ideal model delta harmonic sigma weight residual 180.00 160.93 19.07 0 5.00e+00 4.00e-02 1.45e+01 ... (remaining 2037 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 223 0.050 - 0.100: 158 0.100 - 0.150: 86 0.150 - 0.200: 29 0.200 - 0.250: 8 Chirality restraints: 504 Sorted by residual: chirality pdb=" CA PRO D 332 " pdb=" N PRO D 332 " pdb=" C PRO D 332 " pdb=" CB PRO D 332 " both_signs ideal model delta sigma weight residual False 2.72 2.47 0.25 2.00e-01 2.50e+01 1.56e+00 chirality pdb=" CA PRO E 332 " pdb=" N PRO E 332 " pdb=" C PRO E 332 " pdb=" CB PRO E 332 " both_signs ideal model delta sigma weight residual False 2.72 2.47 0.25 2.00e-01 2.50e+01 1.56e+00 chirality pdb=" CA LYS C 317 " pdb=" N LYS C 317 " pdb=" C LYS C 317 " pdb=" CB LYS C 317 " both_signs ideal model delta sigma weight residual False 2.51 2.73 -0.22 2.00e-01 2.50e+01 1.23e+00 ... (remaining 501 not shown) Planarity restraints: 570 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR F 310 " 0.123 2.00e-02 2.50e+03 6.81e-02 9.28e+01 pdb=" CG TYR F 310 " -0.036 2.00e-02 2.50e+03 pdb=" CD1 TYR F 310 " -0.048 2.00e-02 2.50e+03 pdb=" CD2 TYR F 310 " -0.062 2.00e-02 2.50e+03 pdb=" CE1 TYR F 310 " -0.044 2.00e-02 2.50e+03 pdb=" CE2 TYR F 310 " -0.036 2.00e-02 2.50e+03 pdb=" CZ TYR F 310 " -0.004 2.00e-02 2.50e+03 pdb=" OH TYR F 310 " 0.106 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 310 " -0.113 2.00e-02 2.50e+03 6.62e-02 8.77e+01 pdb=" CG TYR A 310 " 0.022 2.00e-02 2.50e+03 pdb=" CD1 TYR A 310 " 0.045 2.00e-02 2.50e+03 pdb=" CD2 TYR A 310 " 0.055 2.00e-02 2.50e+03 pdb=" CE1 TYR A 310 " 0.049 2.00e-02 2.50e+03 pdb=" CE2 TYR A 310 " 0.044 2.00e-02 2.50e+03 pdb=" CZ TYR A 310 " 0.009 2.00e-02 2.50e+03 pdb=" OH TYR A 310 " -0.112 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR E 310 " 0.092 2.00e-02 2.50e+03 5.10e-02 5.21e+01 pdb=" CG TYR E 310 " -0.030 2.00e-02 2.50e+03 pdb=" CD1 TYR E 310 " -0.032 2.00e-02 2.50e+03 pdb=" CD2 TYR E 310 " -0.046 2.00e-02 2.50e+03 pdb=" CE1 TYR E 310 " -0.036 2.00e-02 2.50e+03 pdb=" CE2 TYR E 310 " -0.024 2.00e-02 2.50e+03 pdb=" CZ TYR E 310 " -0.003 2.00e-02 2.50e+03 pdb=" OH TYR E 310 " 0.079 2.00e-02 2.50e+03 ... (remaining 567 not shown) Histogram of nonbonded interaction distances: 2.56 - 3.02: 1613 3.02 - 3.49: 2756 3.49 - 3.96: 5062 3.96 - 4.43: 5166 4.43 - 4.90: 10090 Nonbonded interactions: 24687 Sorted by model distance: nonbonded pdb=" OD1 ASP A 314 " pdb=" OG SER A 316 " model vdw 2.556 3.040 nonbonded pdb=" OD1 ASP F 314 " pdb=" OG SER F 316 " model vdw 2.557 3.040 nonbonded pdb=" OD1 ASP B 314 " pdb=" OG SER B 316 " model vdw 2.562 3.040 nonbonded pdb=" OD1 ASP D 314 " pdb=" OG SER D 316 " model vdw 2.564 3.040 nonbonded pdb=" OD1 ASP E 314 " pdb=" OG SER E 316 " model vdw 2.575 3.040 ... (remaining 24682 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.410 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: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 13.410 Find NCS groups from input model: 0.130 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:13.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 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 3354 Z= 0.780 Angle : 1.959 6.317 4488 Z= 1.294 Chirality : 0.083 0.250 504 Planarity : 0.016 0.141 570 Dihedral : 11.324 82.812 1284 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 0.00 Ramachandran Plot: Outliers : 1.67 % Allowed : 6.19 % Favored : 92.14 % Rotamer: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.25 (0.33), residues: 420 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.70 (0.25), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.014 0.005 HIS D 374 PHE 0.044 0.016 PHE D 378 TYR 0.123 0.038 TYR F 310 ARG 0.007 0.002 ARG E 349 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 127 time to evaluate : 0.424 Fit side-chains revert: symmetry clash REVERT: C 343 LYS cc_start: 0.8412 (mttt) cc_final: 0.8208 (mtpp) REVERT: E 343 LYS cc_start: 0.8233 (mttt) cc_final: 0.7997 (mtpp) REVERT: F 338 GLU cc_start: 0.7477 (tt0) cc_final: 0.7183 (tt0) outliers start: 0 outliers final: 0 residues processed: 127 average time/residue: 1.4643 time to fit residues: 189.9894 Evaluate side-chains 111 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 111 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 32 optimal weight: 3.9990 chunk 12 optimal weight: 0.4980 chunk 20 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 38 optimal weight: 5.9990 chunk 11 optimal weight: 0.9990 overall best weight: 1.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 351 GLN C 368 ASN D 368 ASN E 336 GLN F 351 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4199 r_free = 0.4199 target = 0.159445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.129773 restraints weight = 3383.922| |-----------------------------------------------------------------------------| r_work (start): 0.3817 rms_B_bonded: 1.70 r_work: 0.3704 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3597 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.3597 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8704 moved from start: 0.3394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3354 Z= 0.192 Angle : 0.693 7.496 4488 Z= 0.348 Chirality : 0.048 0.122 504 Planarity : 0.003 0.028 570 Dihedral : 5.887 19.302 438 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 2.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.19 % Favored : 93.81 % Rotamer: Outliers : 5.29 % Allowed : 14.29 % Favored : 80.42 % 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: -2.48 (0.32), residues: 420 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.88 (0.24), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS E 362 PHE 0.004 0.001 PHE D 346 TYR 0.010 0.002 TYR D 310 ARG 0.001 0.000 ARG E 349 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 121 time to evaluate : 0.410 Fit side-chains REVERT: A 321 LYS cc_start: 0.8653 (mttp) cc_final: 0.8419 (mppt) REVERT: A 338 GLU cc_start: 0.8529 (OUTLIER) cc_final: 0.8003 (tm-30) REVERT: A 343 LYS cc_start: 0.8631 (mttt) cc_final: 0.8273 (mtpp) REVERT: B 338 GLU cc_start: 0.8596 (tt0) cc_final: 0.8336 (tm-30) REVERT: B 370 LYS cc_start: 0.8717 (tttm) cc_final: 0.8470 (tmtt) REVERT: B 375 LYS cc_start: 0.8270 (ttmt) cc_final: 0.7891 (tttm) REVERT: C 338 GLU cc_start: 0.8387 (tm-30) cc_final: 0.7895 (tm-30) REVERT: C 343 LYS cc_start: 0.8543 (mttt) cc_final: 0.8201 (mtpp) REVERT: C 345 ASP cc_start: 0.8503 (t0) cc_final: 0.8082 (m-30) REVERT: C 349 ARG cc_start: 0.8362 (mtp180) cc_final: 0.8099 (mtp180) REVERT: D 311 LYS cc_start: 0.8260 (tmtt) cc_final: 0.8020 (tmtt) REVERT: D 338 GLU cc_start: 0.8502 (tt0) cc_final: 0.8116 (tm-30) REVERT: D 370 LYS cc_start: 0.8422 (tttm) cc_final: 0.8177 (tmtt) REVERT: D 375 LYS cc_start: 0.8172 (ttmt) cc_final: 0.7783 (tttm) REVERT: E 338 GLU cc_start: 0.8462 (OUTLIER) cc_final: 0.7858 (tm-30) REVERT: E 340 LYS cc_start: 0.8508 (mttt) cc_final: 0.8172 (mttt) REVERT: F 338 GLU cc_start: 0.8451 (tt0) cc_final: 0.8157 (tm-30) REVERT: F 343 LYS cc_start: 0.8737 (mttt) cc_final: 0.8402 (mtpp) REVERT: F 345 ASP cc_start: 0.8442 (t0) cc_final: 0.7943 (m-30) REVERT: F 370 LYS cc_start: 0.8767 (tttm) cc_final: 0.8502 (tmtt) outliers start: 20 outliers final: 5 residues processed: 129 average time/residue: 1.4960 time to fit residues: 197.0417 Evaluate side-chains 118 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 111 time to evaluate : 0.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 338 GLU Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain C residue 320 SER Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain E residue 320 SER Chi-restraints excluded: chain E residue 338 GLU Chi-restraints excluded: chain F residue 320 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 26 optimal weight: 10.0000 chunk 35 optimal weight: 10.0000 chunk 30 optimal weight: 10.0000 chunk 41 optimal weight: 0.7980 chunk 14 optimal weight: 10.0000 chunk 31 optimal weight: 10.0000 chunk 29 optimal weight: 10.0000 chunk 33 optimal weight: 1.9990 chunk 34 optimal weight: 6.9990 chunk 11 optimal weight: 7.9990 chunk 16 optimal weight: 9.9990 overall best weight: 5.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 336 GLN E 374 HIS ** F 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.150687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.120523 restraints weight = 3353.823| |-----------------------------------------------------------------------------| r_work (start): 0.3674 rms_B_bonded: 1.76 r_work: 0.3558 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.3446 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.3446 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8840 moved from start: 0.3766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.041 3354 Z= 0.454 Angle : 0.807 7.140 4488 Z= 0.408 Chirality : 0.051 0.129 504 Planarity : 0.006 0.054 570 Dihedral : 6.515 22.119 438 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 2.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.86 % Favored : 92.14 % Rotamer: Outliers : 5.29 % Allowed : 19.05 % Favored : 75.66 % 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: -2.94 (0.30), residues: 420 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.23 (0.23), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS A 362 PHE 0.008 0.002 PHE D 346 TYR 0.014 0.004 TYR D 310 ARG 0.002 0.001 ARG A 349 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 130 time to evaluate : 0.527 Fit side-chains REVERT: A 321 LYS cc_start: 0.8612 (mttp) cc_final: 0.8401 (mppt) REVERT: A 331 LYS cc_start: 0.9175 (OUTLIER) cc_final: 0.8689 (mtpp) REVERT: A 338 GLU cc_start: 0.8675 (OUTLIER) cc_final: 0.8055 (tm-30) REVERT: A 343 LYS cc_start: 0.8493 (mttt) cc_final: 0.8131 (mtpp) REVERT: B 338 GLU cc_start: 0.8676 (tt0) cc_final: 0.8423 (tm-30) REVERT: B 375 LYS cc_start: 0.8320 (ttmt) cc_final: 0.7917 (tttm) REVERT: C 311 LYS cc_start: 0.8637 (tptm) cc_final: 0.8423 (tptp) REVERT: C 338 GLU cc_start: 0.8481 (OUTLIER) cc_final: 0.8025 (tm-30) REVERT: C 343 LYS cc_start: 0.8631 (mttt) cc_final: 0.8253 (mtpp) REVERT: C 345 ASP cc_start: 0.8613 (t0) cc_final: 0.8165 (m-30) REVERT: C 375 LYS cc_start: 0.8366 (ttmt) cc_final: 0.8000 (tttm) REVERT: D 338 GLU cc_start: 0.8596 (tt0) cc_final: 0.8111 (tm-30) REVERT: D 347 LYS cc_start: 0.8820 (mtpp) cc_final: 0.8536 (mtpt) REVERT: D 375 LYS cc_start: 0.8319 (ttmt) cc_final: 0.7922 (tttm) REVERT: E 338 GLU cc_start: 0.8597 (OUTLIER) cc_final: 0.8087 (tm-30) REVERT: E 340 LYS cc_start: 0.8549 (mttt) cc_final: 0.8195 (mttt) REVERT: E 343 LYS cc_start: 0.8639 (mttt) cc_final: 0.8099 (mtpp) REVERT: E 347 LYS cc_start: 0.8662 (mtpp) cc_final: 0.8284 (mtpt) REVERT: F 321 LYS cc_start: 0.8549 (mttp) cc_final: 0.8221 (mppt) REVERT: F 336 GLN cc_start: 0.9134 (tt0) cc_final: 0.8865 (tt0) REVERT: F 338 GLU cc_start: 0.8517 (tt0) cc_final: 0.8244 (tm-30) REVERT: F 340 LYS cc_start: 0.8759 (mttt) cc_final: 0.8508 (mptt) REVERT: F 343 LYS cc_start: 0.8705 (mttt) cc_final: 0.8313 (mtpp) outliers start: 20 outliers final: 7 residues processed: 138 average time/residue: 1.6992 time to fit residues: 238.8139 Evaluate side-chains 132 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 121 time to evaluate : 0.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 331 LYS Chi-restraints excluded: chain A residue 338 GLU Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 320 SER Chi-restraints excluded: chain C residue 338 GLU Chi-restraints excluded: chain D residue 320 SER Chi-restraints excluded: chain E residue 315 LEU Chi-restraints excluded: chain E residue 320 SER Chi-restraints excluded: chain E residue 338 GLU Chi-restraints excluded: chain F residue 320 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 26 optimal weight: 7.9990 chunk 16 optimal weight: 5.9990 chunk 4 optimal weight: 0.7980 chunk 40 optimal weight: 2.9990 chunk 20 optimal weight: 8.9990 chunk 18 optimal weight: 4.9990 chunk 32 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 29 optimal weight: 9.9990 chunk 41 optimal weight: 7.9990 chunk 34 optimal weight: 5.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.153941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.123940 restraints weight = 3409.728| |-----------------------------------------------------------------------------| r_work (start): 0.3673 rms_B_bonded: 1.77 r_work: 0.3570 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.3461 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.3461 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8800 moved from start: 0.4158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 3354 Z= 0.237 Angle : 0.643 5.690 4488 Z= 0.323 Chirality : 0.048 0.127 504 Planarity : 0.006 0.058 570 Dihedral : 5.788 19.490 438 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 2.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer: Outliers : 5.29 % Allowed : 21.96 % Favored : 72.75 % 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: -2.88 (0.31), residues: 420 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.19 (0.23), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 362 PHE 0.004 0.001 PHE A 346 TYR 0.010 0.002 TYR F 310 ARG 0.001 0.000 ARG D 349 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 125 time to evaluate : 0.436 Fit side-chains REVERT: A 321 LYS cc_start: 0.8587 (mttp) cc_final: 0.8371 (mppt) REVERT: A 338 GLU cc_start: 0.8664 (OUTLIER) cc_final: 0.8036 (tm-30) REVERT: A 343 LYS cc_start: 0.8537 (mttt) cc_final: 0.8140 (mtpp) REVERT: B 311 LYS cc_start: 0.8519 (tptm) cc_final: 0.8288 (tptp) REVERT: B 375 LYS cc_start: 0.8316 (ttmt) cc_final: 0.7923 (tttm) REVERT: C 343 LYS cc_start: 0.8436 (mttt) cc_final: 0.8118 (mtpp) REVERT: C 345 ASP cc_start: 0.8559 (t0) cc_final: 0.8189 (OUTLIER) REVERT: C 375 LYS cc_start: 0.8334 (ttmt) cc_final: 0.7973 (tttm) REVERT: D 315 LEU cc_start: 0.8100 (OUTLIER) cc_final: 0.7756 (tt) REVERT: D 321 LYS cc_start: 0.8657 (mttp) cc_final: 0.8300 (mppt) REVERT: D 338 GLU cc_start: 0.8535 (tt0) cc_final: 0.8200 (tm-30) REVERT: D 375 LYS cc_start: 0.8296 (ttmt) cc_final: 0.7923 (tttm) REVERT: E 338 GLU cc_start: 0.8564 (OUTLIER) cc_final: 0.7970 (tm-30) REVERT: E 343 LYS cc_start: 0.8672 (mttt) cc_final: 0.8181 (mtpp) REVERT: E 347 LYS cc_start: 0.8577 (mtpp) cc_final: 0.8364 (mtpt) REVERT: E 375 LYS cc_start: 0.8206 (ttmt) cc_final: 0.7769 (tttm) REVERT: F 321 LYS cc_start: 0.8492 (mttp) cc_final: 0.8160 (mppt) REVERT: F 338 GLU cc_start: 0.8497 (tt0) cc_final: 0.8231 (tm-30) REVERT: F 340 LYS cc_start: 0.8688 (mttt) cc_final: 0.8474 (mptt) REVERT: F 343 LYS cc_start: 0.8724 (mttt) cc_final: 0.8364 (mtpp) REVERT: F 344 LEU cc_start: 0.9237 (mt) cc_final: 0.8972 (mt) REVERT: F 345 ASP cc_start: 0.8521 (t0) cc_final: 0.7918 (OUTLIER) outliers start: 20 outliers final: 10 residues processed: 133 average time/residue: 1.6075 time to fit residues: 217.8960 Evaluate side-chains 131 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 120 time to evaluate : 0.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 320 SER Chi-restraints excluded: chain A residue 338 GLU Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 320 SER Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 320 SER Chi-restraints excluded: chain E residue 315 LEU Chi-restraints excluded: chain E residue 320 SER Chi-restraints excluded: chain E residue 338 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 39 optimal weight: 0.8980 chunk 24 optimal weight: 10.0000 chunk 16 optimal weight: 8.9990 chunk 35 optimal weight: 0.0570 chunk 21 optimal weight: 9.9990 chunk 31 optimal weight: 4.9990 chunk 23 optimal weight: 9.9990 chunk 10 optimal weight: 1.9990 chunk 29 optimal weight: 7.9990 chunk 8 optimal weight: 10.0000 chunk 4 optimal weight: 4.9990 overall best weight: 2.5904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.152844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.122805 restraints weight = 3405.386| |-----------------------------------------------------------------------------| r_work (start): 0.3704 rms_B_bonded: 1.79 r_work: 0.3591 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.3481 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.3481 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8805 moved from start: 0.4274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.022 3354 Z= 0.239 Angle : 0.638 6.621 4488 Z= 0.316 Chirality : 0.048 0.127 504 Planarity : 0.006 0.057 570 Dihedral : 5.659 18.662 438 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 2.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.38 % Favored : 92.62 % Rotamer: Outliers : 4.50 % Allowed : 24.34 % Favored : 71.16 % 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: -2.93 (0.31), residues: 420 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.23 (0.23), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS C 362 PHE 0.004 0.001 PHE A 346 TYR 0.010 0.002 TYR F 310 ARG 0.001 0.000 ARG A 349 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 126 time to evaluate : 0.402 Fit side-chains REVERT: A 338 GLU cc_start: 0.8663 (OUTLIER) cc_final: 0.7957 (tm-30) REVERT: A 343 LYS cc_start: 0.8567 (mttt) cc_final: 0.8135 (mtpp) REVERT: B 345 ASP cc_start: 0.8551 (t0) cc_final: 0.8165 (m-30) REVERT: B 370 LYS cc_start: 0.8727 (tttp) cc_final: 0.8486 (tmtt) REVERT: B 375 LYS cc_start: 0.8331 (ttmt) cc_final: 0.7923 (tttm) REVERT: C 311 LYS cc_start: 0.8549 (tptm) cc_final: 0.8281 (tptp) REVERT: C 343 LYS cc_start: 0.8546 (mttt) cc_final: 0.8188 (mtpp) REVERT: C 345 ASP cc_start: 0.8543 (t0) cc_final: 0.8202 (OUTLIER) REVERT: C 375 LYS cc_start: 0.8304 (ttmt) cc_final: 0.7931 (tttm) REVERT: D 315 LEU cc_start: 0.8097 (OUTLIER) cc_final: 0.7802 (tt) REVERT: D 321 LYS cc_start: 0.8656 (mttp) cc_final: 0.8297 (mppt) REVERT: D 338 GLU cc_start: 0.8493 (tt0) cc_final: 0.8072 (tm-30) REVERT: D 345 ASP cc_start: 0.8631 (t0) cc_final: 0.7987 (m-30) REVERT: D 347 LYS cc_start: 0.8690 (mtpp) cc_final: 0.8456 (mtpt) REVERT: D 375 LYS cc_start: 0.8327 (ttmt) cc_final: 0.7939 (tttm) REVERT: E 338 GLU cc_start: 0.8605 (OUTLIER) cc_final: 0.8009 (tm-30) REVERT: E 343 LYS cc_start: 0.8706 (mttt) cc_final: 0.8220 (mtpp) REVERT: E 375 LYS cc_start: 0.8231 (ttmt) cc_final: 0.7799 (tttm) REVERT: F 321 LYS cc_start: 0.8466 (mttp) cc_final: 0.8131 (mppt) REVERT: F 338 GLU cc_start: 0.8493 (tt0) cc_final: 0.8219 (tm-30) REVERT: F 340 LYS cc_start: 0.8686 (mttt) cc_final: 0.8468 (mttt) REVERT: F 343 LYS cc_start: 0.8720 (mttt) cc_final: 0.8330 (mtpp) REVERT: F 345 ASP cc_start: 0.8561 (t0) cc_final: 0.7942 (OUTLIER) outliers start: 17 outliers final: 11 residues processed: 133 average time/residue: 1.6563 time to fit residues: 224.5087 Evaluate side-chains 128 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 116 time to evaluate : 0.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 320 SER Chi-restraints excluded: chain A residue 338 GLU Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 320 SER Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 320 SER Chi-restraints excluded: chain E residue 315 LEU Chi-restraints excluded: chain E residue 320 SER Chi-restraints excluded: chain E residue 338 GLU Chi-restraints excluded: chain F residue 320 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 10.0000 chunk 18 optimal weight: 0.0870 chunk 33 optimal weight: 8.9990 chunk 23 optimal weight: 6.9990 chunk 14 optimal weight: 10.0000 chunk 6 optimal weight: 3.9990 chunk 3 optimal weight: 0.7980 chunk 21 optimal weight: 10.0000 chunk 31 optimal weight: 10.0000 chunk 36 optimal weight: 0.0050 chunk 20 optimal weight: 7.9990 overall best weight: 2.3776 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.155047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.124668 restraints weight = 3449.047| |-----------------------------------------------------------------------------| r_work (start): 0.3719 rms_B_bonded: 1.81 r_work: 0.3609 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.3497 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.3497 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8805 moved from start: 0.4392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 3354 Z= 0.222 Angle : 0.637 7.945 4488 Z= 0.311 Chirality : 0.048 0.126 504 Planarity : 0.006 0.049 570 Dihedral : 5.531 17.890 438 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 4.23 % Allowed : 25.93 % Favored : 69.84 % 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: -2.93 (0.31), residues: 420 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.22 (0.24), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 362 PHE 0.004 0.001 PHE A 346 TYR 0.010 0.002 TYR F 310 ARG 0.001 0.000 ARG A 349 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 116 time to evaluate : 0.497 Fit side-chains REVERT: A 343 LYS cc_start: 0.8589 (mttt) cc_final: 0.8162 (mtpp) REVERT: B 345 ASP cc_start: 0.8506 (t0) cc_final: 0.8206 (m-30) REVERT: B 370 LYS cc_start: 0.8735 (tttp) cc_final: 0.8494 (tmtt) REVERT: C 311 LYS cc_start: 0.8491 (tptm) cc_final: 0.8246 (tptp) REVERT: C 343 LYS cc_start: 0.8345 (mttt) cc_final: 0.8014 (mtpp) REVERT: C 345 ASP cc_start: 0.8506 (t0) cc_final: 0.8202 (m-30) REVERT: C 375 LYS cc_start: 0.8314 (ttmt) cc_final: 0.7940 (tttm) REVERT: D 315 LEU cc_start: 0.8135 (OUTLIER) cc_final: 0.7859 (tt) REVERT: D 321 LYS cc_start: 0.8600 (mttp) cc_final: 0.8285 (mppt) REVERT: D 345 ASP cc_start: 0.8620 (t0) cc_final: 0.8011 (m-30) REVERT: D 347 LYS cc_start: 0.8701 (mtpp) cc_final: 0.8488 (mtpt) REVERT: D 370 LYS cc_start: 0.8285 (tttm) cc_final: 0.8024 (tmtt) REVERT: D 375 LYS cc_start: 0.8359 (ttmt) cc_final: 0.7959 (tttm) REVERT: E 338 GLU cc_start: 0.8592 (OUTLIER) cc_final: 0.7999 (tm-30) REVERT: E 343 LYS cc_start: 0.8766 (mttt) cc_final: 0.8243 (mtpp) REVERT: E 345 ASP cc_start: 0.8454 (t70) cc_final: 0.7983 (m-30) REVERT: E 375 LYS cc_start: 0.8236 (ttmt) cc_final: 0.7806 (tttm) REVERT: F 321 LYS cc_start: 0.8464 (mttp) cc_final: 0.8132 (mppt) REVERT: F 338 GLU cc_start: 0.8468 (tt0) cc_final: 0.8225 (tm-30) REVERT: F 340 LYS cc_start: 0.8671 (mttt) cc_final: 0.8454 (mttt) REVERT: F 343 LYS cc_start: 0.8766 (mttt) cc_final: 0.8360 (mtpp) REVERT: F 345 ASP cc_start: 0.8554 (t0) cc_final: 0.7942 (m-30) outliers start: 16 outliers final: 10 residues processed: 124 average time/residue: 1.6981 time to fit residues: 214.7035 Evaluate side-chains 126 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 114 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 320 SER Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 320 SER Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 320 SER Chi-restraints excluded: chain E residue 315 LEU Chi-restraints excluded: chain E residue 320 SER Chi-restraints excluded: chain E residue 338 GLU Chi-restraints excluded: chain F residue 320 SER Chi-restraints excluded: chain F residue 373 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 33 optimal weight: 3.9990 chunk 19 optimal weight: 0.9990 chunk 16 optimal weight: 10.0000 chunk 29 optimal weight: 8.9990 chunk 1 optimal weight: 9.9990 chunk 9 optimal weight: 8.9990 chunk 6 optimal weight: 0.5980 chunk 30 optimal weight: 0.4980 chunk 22 optimal weight: 0.9990 chunk 7 optimal weight: 10.0000 chunk 23 optimal weight: 2.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.156758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.126807 restraints weight = 3391.056| |-----------------------------------------------------------------------------| r_work (start): 0.3755 rms_B_bonded: 1.79 r_work: 0.3650 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.3546 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.3546 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8763 moved from start: 0.4570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 3354 Z= 0.154 Angle : 0.587 9.299 4488 Z= 0.282 Chirality : 0.047 0.126 504 Planarity : 0.005 0.046 570 Dihedral : 5.153 16.126 438 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 2.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 3.97 % Allowed : 25.66 % Favored : 70.37 % 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: -2.82 (0.32), residues: 420 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.14 (0.24), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS E 362 PHE 0.003 0.001 PHE A 346 TYR 0.006 0.001 TYR D 310 ARG 0.001 0.000 ARG A 349 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 115 time to evaluate : 0.406 Fit side-chains REVERT: A 343 LYS cc_start: 0.8565 (mttt) cc_final: 0.8158 (mtpp) REVERT: B 345 ASP cc_start: 0.8420 (t0) cc_final: 0.8203 (m-30) REVERT: B 370 LYS cc_start: 0.8724 (tttp) cc_final: 0.8489 (tmtt) REVERT: C 321 LYS cc_start: 0.8466 (mttp) cc_final: 0.8234 (mppt) REVERT: C 343 LYS cc_start: 0.8268 (mttt) cc_final: 0.7971 (mtpp) REVERT: C 345 ASP cc_start: 0.8390 (t0) cc_final: 0.8137 (m-30) REVERT: C 375 LYS cc_start: 0.8303 (ttmt) cc_final: 0.7934 (tttm) REVERT: D 315 LEU cc_start: 0.8043 (OUTLIER) cc_final: 0.7799 (tt) REVERT: D 321 LYS cc_start: 0.8513 (mttp) cc_final: 0.8173 (mppt) REVERT: D 331 LYS cc_start: 0.9112 (mtpm) cc_final: 0.8891 (mtmm) REVERT: D 338 GLU cc_start: 0.8450 (OUTLIER) cc_final: 0.7942 (tm-30) REVERT: D 345 ASP cc_start: 0.8590 (t0) cc_final: 0.8027 (m-30) REVERT: D 370 LYS cc_start: 0.8228 (tttm) cc_final: 0.7975 (tmtt) REVERT: D 375 LYS cc_start: 0.8328 (ttmt) cc_final: 0.7938 (tttm) REVERT: E 343 LYS cc_start: 0.8777 (mttt) cc_final: 0.8297 (mtpp) REVERT: E 345 ASP cc_start: 0.8358 (t70) cc_final: 0.7982 (m-30) REVERT: E 375 LYS cc_start: 0.8248 (ttmt) cc_final: 0.7822 (tttm) REVERT: F 321 LYS cc_start: 0.8458 (mttp) cc_final: 0.8126 (mppt) REVERT: F 338 GLU cc_start: 0.8439 (tt0) cc_final: 0.8193 (tm-30) REVERT: F 343 LYS cc_start: 0.8788 (mttt) cc_final: 0.8412 (mtpp) REVERT: F 345 ASP cc_start: 0.8504 (t0) cc_final: 0.7932 (m-30) REVERT: F 375 LYS cc_start: 0.8252 (ttmt) cc_final: 0.7884 (tttm) outliers start: 15 outliers final: 7 residues processed: 122 average time/residue: 1.7034 time to fit residues: 211.8226 Evaluate side-chains 121 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 112 time to evaluate : 0.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 320 SER Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 320 SER Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 320 SER Chi-restraints excluded: chain D residue 338 GLU Chi-restraints excluded: chain F residue 320 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 2 optimal weight: 10.0000 chunk 24 optimal weight: 9.9990 chunk 40 optimal weight: 10.0000 chunk 29 optimal weight: 10.0000 chunk 12 optimal weight: 0.5980 chunk 6 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 chunk 5 optimal weight: 5.9990 chunk 25 optimal weight: 5.9990 chunk 4 optimal weight: 5.9990 chunk 28 optimal weight: 10.0000 overall best weight: 3.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 336 GLN E 368 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.151956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.121899 restraints weight = 3376.660| |-----------------------------------------------------------------------------| r_work (start): 0.3672 rms_B_bonded: 1.78 r_work: 0.3562 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.3455 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.3455 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8827 moved from start: 0.4449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 3354 Z= 0.327 Angle : 0.732 10.482 4488 Z= 0.350 Chirality : 0.049 0.126 504 Planarity : 0.006 0.054 570 Dihedral : 5.827 19.618 438 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 2.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.10 % Favored : 91.90 % Rotamer: Outliers : 4.76 % Allowed : 25.13 % Favored : 70.11 % 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: -2.96 (0.31), residues: 420 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.25 (0.24), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS C 362 PHE 0.006 0.002 PHE D 346 TYR 0.011 0.003 TYR D 310 ARG 0.002 0.001 ARG D 349 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 116 time to evaluate : 0.381 Fit side-chains REVERT: A 343 LYS cc_start: 0.8606 (mttt) cc_final: 0.8182 (mtpp) REVERT: B 345 ASP cc_start: 0.8511 (t0) cc_final: 0.8199 (m-30) REVERT: B 370 LYS cc_start: 0.8712 (tttp) cc_final: 0.8476 (tmtt) REVERT: C 343 LYS cc_start: 0.8545 (mttt) cc_final: 0.8209 (mtpp) REVERT: C 345 ASP cc_start: 0.8467 (t0) cc_final: 0.8159 (m-30) REVERT: C 375 LYS cc_start: 0.8298 (ttmt) cc_final: 0.7950 (tttm) REVERT: D 315 LEU cc_start: 0.8125 (OUTLIER) cc_final: 0.7832 (tt) REVERT: D 321 LYS cc_start: 0.8595 (mttp) cc_final: 0.8261 (mppt) REVERT: D 338 GLU cc_start: 0.8494 (OUTLIER) cc_final: 0.7964 (tm-30) REVERT: D 345 ASP cc_start: 0.8620 (t0) cc_final: 0.7997 (m-30) REVERT: D 347 LYS cc_start: 0.8754 (mtpp) cc_final: 0.8473 (mtpt) REVERT: D 375 LYS cc_start: 0.8368 (ttmt) cc_final: 0.7976 (tttm) REVERT: E 343 LYS cc_start: 0.8769 (mttt) cc_final: 0.8279 (mtpp) REVERT: E 345 ASP cc_start: 0.8454 (t70) cc_final: 0.7997 (m-30) REVERT: E 370 LYS cc_start: 0.8550 (tttm) cc_final: 0.8350 (tttm) REVERT: E 375 LYS cc_start: 0.8278 (ttmt) cc_final: 0.7847 (tttm) REVERT: F 311 LYS cc_start: 0.8502 (tmtt) cc_final: 0.8291 (tmtt) REVERT: F 321 LYS cc_start: 0.8485 (mttp) cc_final: 0.8183 (mppt) REVERT: F 340 LYS cc_start: 0.8789 (mttt) cc_final: 0.8550 (mptt) REVERT: F 343 LYS cc_start: 0.8743 (mttt) cc_final: 0.8368 (mtpp) REVERT: F 345 ASP cc_start: 0.8532 (t0) cc_final: 0.7950 (OUTLIER) REVERT: F 347 LYS cc_start: 0.8741 (mtpp) cc_final: 0.8443 (mtpt) outliers start: 18 outliers final: 11 residues processed: 127 average time/residue: 1.5405 time to fit residues: 199.6273 Evaluate side-chains 128 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 116 time to evaluate : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 320 SER Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 320 SER Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 320 SER Chi-restraints excluded: chain D residue 338 GLU Chi-restraints excluded: chain E residue 320 SER Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain F residue 320 SER Chi-restraints excluded: chain F residue 373 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 37 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 31 optimal weight: 7.9990 chunk 41 optimal weight: 0.7980 chunk 2 optimal weight: 2.9990 chunk 28 optimal weight: 10.0000 chunk 32 optimal weight: 0.9980 chunk 40 optimal weight: 3.9990 chunk 23 optimal weight: 2.9990 chunk 35 optimal weight: 9.9990 chunk 11 optimal weight: 7.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 336 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.154354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.124159 restraints weight = 3398.553| |-----------------------------------------------------------------------------| r_work (start): 0.3690 rms_B_bonded: 1.80 r_work: 0.3585 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.3477 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.3477 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8798 moved from start: 0.4578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 3354 Z= 0.229 Angle : 0.688 11.850 4488 Z= 0.324 Chirality : 0.048 0.125 504 Planarity : 0.006 0.052 570 Dihedral : 5.577 18.470 438 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 3.70 % Allowed : 25.93 % Favored : 70.37 % 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: -2.93 (0.31), residues: 420 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.22 (0.24), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 362 PHE 0.004 0.001 PHE F 346 TYR 0.008 0.002 TYR F 310 ARG 0.001 0.000 ARG E 349 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 117 time to evaluate : 0.431 Fit side-chains REVERT: A 343 LYS cc_start: 0.8582 (mttt) cc_final: 0.8146 (mtpp) REVERT: B 345 ASP cc_start: 0.8486 (t0) cc_final: 0.8206 (m-30) REVERT: B 370 LYS cc_start: 0.8712 (tttp) cc_final: 0.8450 (tmtt) REVERT: C 343 LYS cc_start: 0.8426 (mttt) cc_final: 0.8086 (mtpp) REVERT: C 345 ASP cc_start: 0.8473 (t0) cc_final: 0.8161 (m-30) REVERT: C 375 LYS cc_start: 0.8303 (ttmt) cc_final: 0.7933 (tttm) REVERT: D 315 LEU cc_start: 0.8131 (OUTLIER) cc_final: 0.7876 (tt) REVERT: D 321 LYS cc_start: 0.8543 (mttp) cc_final: 0.8202 (mppt) REVERT: D 338 GLU cc_start: 0.8548 (OUTLIER) cc_final: 0.8074 (tm-30) REVERT: D 345 ASP cc_start: 0.8617 (t0) cc_final: 0.8013 (m-30) REVERT: D 347 LYS cc_start: 0.8688 (mtpp) cc_final: 0.8326 (mtpt) REVERT: D 370 LYS cc_start: 0.8292 (tttm) cc_final: 0.8007 (tmtt) REVERT: D 375 LYS cc_start: 0.8360 (ttmt) cc_final: 0.7962 (tttm) REVERT: E 343 LYS cc_start: 0.8768 (mttt) cc_final: 0.8266 (mtpp) REVERT: E 345 ASP cc_start: 0.8423 (t70) cc_final: 0.7986 (m-30) REVERT: E 375 LYS cc_start: 0.8268 (ttmt) cc_final: 0.7830 (tttm) REVERT: F 321 LYS cc_start: 0.8476 (mttp) cc_final: 0.8160 (mppt) REVERT: F 343 LYS cc_start: 0.8784 (mttt) cc_final: 0.8386 (mtpp) REVERT: F 345 ASP cc_start: 0.8545 (t0) cc_final: 0.7958 (OUTLIER) REVERT: F 347 LYS cc_start: 0.8672 (mtpp) cc_final: 0.8371 (mtpt) outliers start: 14 outliers final: 10 residues processed: 125 average time/residue: 1.6015 time to fit residues: 204.1586 Evaluate side-chains 125 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 114 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 320 SER Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 320 SER Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 320 SER Chi-restraints excluded: chain D residue 338 GLU Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain F residue 320 SER Chi-restraints excluded: chain F residue 373 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 18 optimal weight: 6.9990 chunk 29 optimal weight: 10.0000 chunk 13 optimal weight: 9.9990 chunk 33 optimal weight: 6.9990 chunk 21 optimal weight: 7.9990 chunk 4 optimal weight: 6.9990 chunk 26 optimal weight: 10.0000 chunk 24 optimal weight: 9.9990 chunk 15 optimal weight: 3.9990 chunk 3 optimal weight: 3.9990 chunk 22 optimal weight: 6.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 374 HIS E 336 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.149670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.119765 restraints weight = 3372.200| |-----------------------------------------------------------------------------| r_work (start): 0.3632 rms_B_bonded: 1.77 r_work: 0.3521 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.3412 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.3412 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8856 moved from start: 0.4547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.049 3354 Z= 0.489 Angle : 0.852 12.635 4488 Z= 0.407 Chirality : 0.051 0.135 504 Planarity : 0.007 0.060 570 Dihedral : 6.347 21.542 438 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.29 % Favored : 90.71 % Rotamer: Outliers : 4.50 % Allowed : 25.40 % Favored : 70.11 % 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: -3.21 (0.30), residues: 420 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.44 (0.23), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS A 362 PHE 0.009 0.003 PHE D 346 TYR 0.014 0.003 TYR D 310 ARG 0.002 0.001 ARG E 349 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 120 time to evaluate : 0.372 Fit side-chains REVERT: A 343 LYS cc_start: 0.8604 (mttt) cc_final: 0.8159 (mtpp) REVERT: B 345 ASP cc_start: 0.8603 (t0) cc_final: 0.8182 (m-30) REVERT: B 370 LYS cc_start: 0.8710 (tttp) cc_final: 0.8446 (tmtt) REVERT: C 343 LYS cc_start: 0.8634 (mttt) cc_final: 0.8273 (mtpp) REVERT: C 345 ASP cc_start: 0.8553 (t0) cc_final: 0.8199 (OUTLIER) REVERT: C 375 LYS cc_start: 0.8327 (ttmt) cc_final: 0.7956 (tttm) REVERT: D 315 LEU cc_start: 0.8200 (OUTLIER) cc_final: 0.7875 (tt) REVERT: D 321 LYS cc_start: 0.8626 (mttp) cc_final: 0.8280 (mppt) REVERT: D 338 GLU cc_start: 0.8583 (OUTLIER) cc_final: 0.8051 (tm-30) REVERT: D 345 ASP cc_start: 0.8632 (t0) cc_final: 0.7971 (m-30) REVERT: D 347 LYS cc_start: 0.8783 (mtpp) cc_final: 0.8436 (mtpt) REVERT: D 375 LYS cc_start: 0.8390 (ttmt) cc_final: 0.7987 (tttm) REVERT: E 343 LYS cc_start: 0.8795 (mttt) cc_final: 0.8259 (mtpp) REVERT: E 345 ASP cc_start: 0.8507 (t70) cc_final: 0.7999 (m-30) REVERT: E 375 LYS cc_start: 0.8280 (ttmt) cc_final: 0.7843 (tttm) REVERT: F 343 LYS cc_start: 0.8792 (mttt) cc_final: 0.8400 (mtpp) REVERT: F 347 LYS cc_start: 0.8774 (mtpp) cc_final: 0.8501 (mtpt) outliers start: 17 outliers final: 10 residues processed: 129 average time/residue: 1.5403 time to fit residues: 202.7236 Evaluate side-chains 129 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 118 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 320 SER Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 320 SER Chi-restraints excluded: chain D residue 338 GLU Chi-restraints excluded: chain E residue 320 SER Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain F residue 320 SER Chi-restraints excluded: chain F residue 373 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 24 optimal weight: 10.0000 chunk 10 optimal weight: 5.9990 chunk 22 optimal weight: 8.9990 chunk 11 optimal weight: 4.9990 chunk 33 optimal weight: 7.9990 chunk 23 optimal weight: 2.9990 chunk 12 optimal weight: 0.9980 chunk 20 optimal weight: 8.9990 chunk 5 optimal weight: 0.9980 chunk 2 optimal weight: 0.5980 chunk 18 optimal weight: 4.9990 overall best weight: 2.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 336 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.153565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.123749 restraints weight = 3363.667| |-----------------------------------------------------------------------------| r_work (start): 0.3709 rms_B_bonded: 1.77 r_work: 0.3602 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3497 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.3497 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8798 moved from start: 0.4692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 3354 Z= 0.219 Angle : 0.698 12.707 4488 Z= 0.328 Chirality : 0.048 0.124 504 Planarity : 0.006 0.052 570 Dihedral : 5.628 18.561 438 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 2.91 % Allowed : 26.98 % Favored : 70.11 % 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: -3.06 (0.31), residues: 420 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.32 (0.24), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 362 PHE 0.003 0.001 PHE A 346 TYR 0.008 0.002 TYR D 310 ARG 0.001 0.000 ARG D 349 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4194.60 seconds wall clock time: 76 minutes 11.89 seconds (4571.89 seconds total)