Starting phenix.real_space_refine on Wed Mar 5 19:49:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8oti_17180/03_2025/8oti_17180.cif Found real_map, /net/cci-nas-00/data/ceres_data/8oti_17180/03_2025/8oti_17180.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8oti_17180/03_2025/8oti_17180.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8oti_17180/03_2025/8oti_17180.map" model { file = "/net/cci-nas-00/data/ceres_data/8oti_17180/03_2025/8oti_17180.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8oti_17180/03_2025/8oti_17180.cif" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 6 5.16 5 C 2160 2.51 5 N 636 2.21 5 O 642 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 30 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 3444 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 574 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 574 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "B" Number of atoms: 574 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 574 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "C" Number of atoms: 574 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 574 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "D" Number of atoms: 574 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 574 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "E" Number of atoms: 574 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 574 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "F" Number of atoms: 574 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 574 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Time building chain proxies: 2.93, per 1000 atoms: 0.85 Number of scatterers: 3444 At special positions: 0 Unit cell: (98.056, 126.072, 37.08, 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 642 8.00 N 636 7.00 C 2160 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: 0.79 Conformation dependent library (CDL) restraints added in 518.4 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 17 sheets defined 0.0% alpha, 54.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.53 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'C' and resid 306 through 310 removed outlier: 6.400A pdb=" N GLN A 307 " --> pdb=" O ILE E 308 " (cutoff:3.500A) removed outlier: 8.123A pdb=" N TYR E 310 " --> pdb=" O GLN A 307 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N VAL A 309 " --> pdb=" O TYR E 310 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 313 through 314 removed outlier: 6.766A pdb=" N VAL A 313 " --> pdb=" O ASP E 314 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 317 through 319 removed outlier: 6.523A pdb=" N VAL A 318 " --> pdb=" O THR C 319 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 322 through 330 removed outlier: 6.737A pdb=" N SER A 324 " --> pdb=" O GLY C 323 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N LEU C 325 " --> pdb=" O SER A 324 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N GLY A 326 " --> pdb=" O LEU C 325 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N ASN C 327 " --> pdb=" O GLY A 326 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N GLY A 323 " --> pdb=" O SER E 324 " (cutoff:3.500A) removed outlier: 9.808A pdb=" N GLY E 326 " --> pdb=" O GLY A 323 " (cutoff:3.500A) removed outlier: 8.610A pdb=" N LEU A 325 " --> pdb=" O GLY E 326 " (cutoff:3.500A) removed outlier: 9.229A pdb=" N ILE E 328 " --> pdb=" O LEU A 325 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N ASN A 327 " --> pdb=" O ILE E 328 " (cutoff:3.500A) removed outlier: 8.011A pdb=" N HIS E 330 " --> pdb=" O ASN A 327 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N HIS A 329 " --> pdb=" O HIS E 330 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 337 through 346 removed outlier: 6.414A pdb=" N VAL A 337 " --> pdb=" O GLU C 338 " (cutoff:3.500A) removed outlier: 7.954A pdb=" N LYS C 340 " --> pdb=" O VAL A 337 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N VAL A 339 " --> pdb=" O LYS C 340 " (cutoff:3.500A) removed outlier: 7.835A pdb=" N GLU C 342 " --> pdb=" O VAL A 339 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N SER A 341 " --> pdb=" O GLU C 342 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N LEU C 344 " --> pdb=" O SER A 341 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N LYS A 343 " --> pdb=" O LEU C 344 " (cutoff:3.500A) removed outlier: 10.197A pdb=" N PHE C 346 " --> pdb=" O LYS A 343 " (cutoff:3.500A) removed outlier: 9.135A pdb=" N ASP A 345 " --> pdb=" O PHE C 346 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N LEU A 344 " --> pdb=" O LYS E 343 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N ASP E 345 " --> pdb=" O LEU A 344 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N PHE A 346 " --> pdb=" O ASP E 345 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 350 through 357 removed outlier: 6.211A pdb=" N VAL A 350 " --> pdb=" O GLN C 351 " (cutoff:3.500A) removed outlier: 8.024A pdb=" N LYS C 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N SER A 352 " --> pdb=" O LYS C 353 " (cutoff:3.500A) removed outlier: 8.404A pdb=" N GLY C 355 " --> pdb=" O SER A 352 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N ILE A 354 " --> pdb=" O GLY C 355 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N LEU C 357 " --> pdb=" O ILE A 354 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N SER A 356 " --> pdb=" O LEU C 357 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 360 through 362 removed outlier: 6.310A pdb=" N THR A 361 " --> pdb=" O HIS C 362 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 369 through 373 removed outlier: 6.329A pdb=" N LYS A 370 " --> pdb=" O ILE C 371 " (cutoff:3.500A) removed outlier: 8.008A pdb=" N THR C 373 " --> pdb=" O LYS A 370 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N GLU A 372 " --> pdb=" O THR C 373 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 376 through 378 removed outlier: 6.438A pdb=" N LEU A 376 " --> pdb=" O THR C 377 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 307 through 310 removed outlier: 6.504A pdb=" N GLN B 307 " --> pdb=" O ILE D 308 " (cutoff:3.500A) removed outlier: 8.222A pdb=" N TYR D 310 " --> pdb=" O GLN B 307 " (cutoff:3.500A) removed outlier: 6.807A 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: 6.804A 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 319 removed outlier: 6.504A pdb=" N VAL B 318 " --> pdb=" O THR F 319 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 322 through 330 removed outlier: 6.042A pdb=" N CYS B 322 " --> pdb=" O GLY D 323 " (cutoff:3.500A) removed outlier: 7.712A pdb=" N LEU D 325 " --> pdb=" O CYS B 322 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N SER B 324 " --> pdb=" O LEU D 325 " (cutoff:3.500A) removed outlier: 8.043A pdb=" N ASN D 327 " --> pdb=" O SER B 324 " (cutoff:3.500A) removed outlier: 8.575A pdb=" N GLY B 326 " --> pdb=" O ASN D 327 " (cutoff:3.500A) removed outlier: 7.946A pdb=" N HIS D 329 " --> pdb=" O GLY B 326 " (cutoff:3.500A) removed outlier: 9.191A pdb=" N ILE B 328 " --> pdb=" O HIS D 329 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N GLY B 323 " --> pdb=" O CYS F 322 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N ILE F 328 " --> pdb=" O ASN B 327 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N HIS B 329 " --> pdb=" O ILE F 328 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N HIS F 330 " --> pdb=" O HIS B 329 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 336 through 346 removed outlier: 6.805A pdb=" N LEU B 344 " --> pdb=" O LYS D 343 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N ASP D 345 " --> pdb=" O LEU B 344 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N PHE B 346 " --> pdb=" O ASP D 345 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N VAL B 337 " --> pdb=" O GLU F 338 " (cutoff:3.500A) removed outlier: 7.977A pdb=" N LYS F 340 " --> pdb=" O VAL B 337 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N VAL B 339 " --> pdb=" O LYS F 340 " (cutoff:3.500A) removed outlier: 7.810A pdb=" N GLU F 342 " --> pdb=" O VAL B 339 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N SER B 341 " --> pdb=" O GLU F 342 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N LEU F 344 " --> pdb=" O SER B 341 " (cutoff:3.500A) removed outlier: 7.351A pdb=" N LYS B 343 " --> pdb=" O LEU F 344 " (cutoff:3.500A) removed outlier: 10.200A pdb=" N PHE F 346 " --> pdb=" O LYS B 343 " (cutoff:3.500A) removed outlier: 9.141A pdb=" N ASP B 345 " --> pdb=" O PHE F 346 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 350 through 357 removed outlier: 6.256A pdb=" N VAL B 350 " --> pdb=" O GLN F 351 " (cutoff:3.500A) removed outlier: 8.089A pdb=" N LYS F 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N SER B 352 " --> pdb=" O LYS F 353 " (cutoff:3.500A) removed outlier: 8.385A pdb=" N GLY F 355 " --> pdb=" O SER B 352 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N ILE B 354 " --> pdb=" O GLY F 355 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N LEU F 357 " --> pdb=" O ILE B 354 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N SER B 356 " --> pdb=" O LEU F 357 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 360 through 362 removed outlier: 6.322A pdb=" N THR B 361 " --> pdb=" O HIS F 362 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 369 through 378 removed outlier: 6.327A pdb=" N LYS B 370 " --> pdb=" O ILE F 371 " (cutoff:3.500A) removed outlier: 8.017A pdb=" N THR F 373 " --> pdb=" O LYS B 370 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N GLU B 372 " --> pdb=" O THR F 373 " (cutoff:3.500A) removed outlier: 8.225A pdb=" N LYS F 375 " --> pdb=" O GLU B 372 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N HIS B 374 " --> pdb=" O LYS F 375 " (cutoff:3.500A) removed outlier: 8.272A pdb=" N THR F 377 " --> pdb=" O HIS B 374 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N LEU B 376 " --> pdb=" O THR F 377 " (cutoff:3.500A) 67 hydrogen bonds defined for protein. 201 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: 0.81 Time building geometry restraints manager: 0.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 692 1.32 - 1.44: 744 1.44 - 1.56: 2056 1.56 - 1.69: 0 1.69 - 1.81: 6 Bond restraints: 3498 Sorted by residual: bond pdb=" CG HIS D 329 " pdb=" CD2 HIS D 329 " ideal model delta sigma weight residual 1.354 1.300 0.054 1.10e-02 8.26e+03 2.39e+01 bond pdb=" CG HIS F 329 " pdb=" CD2 HIS F 329 " ideal model delta sigma weight residual 1.354 1.300 0.054 1.10e-02 8.26e+03 2.39e+01 bond pdb=" CG HIS B 329 " pdb=" CD2 HIS B 329 " ideal model delta sigma weight residual 1.354 1.300 0.054 1.10e-02 8.26e+03 2.38e+01 bond pdb=" CA SER D 356 " pdb=" CB SER D 356 " ideal model delta sigma weight residual 1.527 1.467 0.060 1.30e-02 5.92e+03 2.13e+01 bond pdb=" CA SER F 356 " pdb=" CB SER F 356 " ideal model delta sigma weight residual 1.527 1.467 0.060 1.30e-02 5.92e+03 2.12e+01 ... (remaining 3493 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.37: 3107 1.37 - 2.75: 1114 2.75 - 4.12: 356 4.12 - 5.49: 79 5.49 - 6.87: 24 Bond angle restraints: 4680 Sorted by residual: angle pdb=" N GLY B 326 " pdb=" CA GLY B 326 " pdb=" C GLY B 326 " ideal model delta sigma weight residual 110.42 117.29 -6.87 1.49e+00 4.50e-01 2.12e+01 angle pdb=" N GLY F 326 " pdb=" CA GLY F 326 " pdb=" C GLY F 326 " ideal model delta sigma weight residual 110.42 117.28 -6.86 1.49e+00 4.50e-01 2.12e+01 angle pdb=" N GLY D 326 " pdb=" CA GLY D 326 " pdb=" C GLY D 326 " ideal model delta sigma weight residual 110.42 117.28 -6.86 1.49e+00 4.50e-01 2.12e+01 angle pdb=" N GLY C 326 " pdb=" CA GLY C 326 " pdb=" C GLY C 326 " ideal model delta sigma weight residual 110.75 116.85 -6.10 1.46e+00 4.69e-01 1.75e+01 angle pdb=" N GLY A 326 " pdb=" CA GLY A 326 " pdb=" C GLY A 326 " ideal model delta sigma weight residual 110.75 116.85 -6.10 1.46e+00 4.69e-01 1.74e+01 ... (remaining 4675 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.04: 1803 13.04 - 26.07: 252 26.07 - 39.10: 54 39.10 - 52.13: 18 52.13 - 65.16: 9 Dihedral angle restraints: 2136 sinusoidal: 894 harmonic: 1242 Sorted by residual: dihedral pdb=" CA GLY B 335 " pdb=" C GLY B 335 " pdb=" N GLN B 336 " pdb=" CA GLN B 336 " ideal model delta harmonic sigma weight residual 180.00 158.81 21.19 0 5.00e+00 4.00e-02 1.80e+01 dihedral pdb=" CA GLY F 335 " pdb=" C GLY F 335 " pdb=" N GLN F 336 " pdb=" CA GLN F 336 " ideal model delta harmonic sigma weight residual 180.00 158.81 21.19 0 5.00e+00 4.00e-02 1.80e+01 dihedral pdb=" CA GLY D 335 " pdb=" C GLY D 335 " pdb=" N GLN D 336 " pdb=" CA GLN D 336 " ideal model delta harmonic sigma weight residual 180.00 158.83 21.17 0 5.00e+00 4.00e-02 1.79e+01 ... (remaining 2133 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 250 0.069 - 0.137: 230 0.137 - 0.206: 30 0.206 - 0.274: 9 0.274 - 0.343: 9 Chirality restraints: 528 Sorted by residual: chirality pdb=" CB ILE D 328 " pdb=" CA ILE D 328 " pdb=" CG1 ILE D 328 " pdb=" CG2 ILE D 328 " both_signs ideal model delta sigma weight residual False 2.64 2.30 0.34 2.00e-01 2.50e+01 2.93e+00 chirality pdb=" CB ILE F 328 " pdb=" CA ILE F 328 " pdb=" CG1 ILE F 328 " pdb=" CG2 ILE F 328 " both_signs ideal model delta sigma weight residual False 2.64 2.30 0.34 2.00e-01 2.50e+01 2.92e+00 chirality pdb=" CB ILE B 328 " pdb=" CA ILE B 328 " pdb=" CG1 ILE B 328 " pdb=" CG2 ILE B 328 " both_signs ideal model delta sigma weight residual False 2.64 2.30 0.34 2.00e-01 2.50e+01 2.92e+00 ... (remaining 525 not shown) Planarity restraints: 594 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE E 328 " 0.015 2.00e-02 2.50e+03 2.93e-02 8.60e+00 pdb=" C ILE E 328 " -0.051 2.00e-02 2.50e+03 pdb=" O ILE E 328 " 0.019 2.00e-02 2.50e+03 pdb=" N HIS E 329 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 328 " 0.015 2.00e-02 2.50e+03 2.93e-02 8.56e+00 pdb=" C ILE A 328 " -0.051 2.00e-02 2.50e+03 pdb=" O ILE A 328 " 0.019 2.00e-02 2.50e+03 pdb=" N HIS A 329 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE C 328 " 0.015 2.00e-02 2.50e+03 2.92e-02 8.53e+00 pdb=" C ILE C 328 " -0.051 2.00e-02 2.50e+03 pdb=" O ILE C 328 " 0.019 2.00e-02 2.50e+03 pdb=" N HIS C 329 " 0.017 2.00e-02 2.50e+03 ... (remaining 591 not shown) Histogram of nonbonded interaction distances: 2.39 - 2.89: 1162 2.89 - 3.39: 2904 3.39 - 3.89: 5573 3.89 - 4.40: 5962 4.40 - 4.90: 11553 Nonbonded interactions: 27154 Sorted by model distance: nonbonded pdb=" OG SER A 305 " pdb=" N SER C 305 " model vdw 2.388 3.120 nonbonded pdb=" N SER A 305 " pdb=" OG SER E 305 " model vdw 2.388 3.120 nonbonded pdb=" N SER B 305 " pdb=" OG SER D 305 " model vdw 2.399 3.120 nonbonded pdb=" OG SER B 305 " pdb=" N SER F 305 " model vdw 2.399 3.120 nonbonded pdb=" OD1 ASP A 314 " pdb=" OG SER A 316 " model vdw 2.409 3.040 ... (remaining 27149 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: 1.010 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: 0.000 Extract box with map and model: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 13.700 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:14.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8876 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 0.101 3498 Z= 0.744 Angle : 1.631 6.866 4680 Z= 1.069 Chirality : 0.097 0.343 528 Planarity : 0.012 0.075 594 Dihedral : 13.672 65.161 1344 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 5.30 % Allowed : 3.03 % Favored : 91.67 % 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: -3.63 (0.27), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.76 (0.21), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.017 0.007 HIS F 329 PHE 0.036 0.006 PHE B 346 TYR 0.016 0.007 TYR F 310 ARG 0.017 0.003 ARG F 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 133 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 112 time to evaluate : 0.396 Fit side-chains REVERT: A 343 LYS cc_start: 0.8366 (mttm) cc_final: 0.8048 (mtmt) REVERT: A 347 LYS cc_start: 0.8412 (mttt) cc_final: 0.8050 (mptp) REVERT: B 353 LYS cc_start: 0.8991 (mttt) cc_final: 0.8750 (mttp) REVERT: B 369 LYS cc_start: 0.8702 (mttp) cc_final: 0.8486 (mttm) REVERT: C 343 LYS cc_start: 0.8502 (mttm) cc_final: 0.8137 (mtmt) REVERT: D 311 LYS cc_start: 0.8738 (mtmt) cc_final: 0.8339 (ttmt) REVERT: E 343 LYS cc_start: 0.8487 (mttm) cc_final: 0.8209 (mtmt) REVERT: E 347 LYS cc_start: 0.8472 (mttt) cc_final: 0.8137 (mptp) REVERT: F 311 LYS cc_start: 0.8613 (mtmt) cc_final: 0.8183 (ttmt) REVERT: F 349 ARG cc_start: 0.8369 (OUTLIER) cc_final: 0.8133 (ptp-170) REVERT: F 353 LYS cc_start: 0.9011 (mttt) cc_final: 0.8769 (mttp) outliers start: 21 outliers final: 4 residues processed: 122 average time/residue: 1.5995 time to fit residues: 199.1104 Evaluate side-chains 95 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 90 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain C residue 331 LYS Chi-restraints excluded: chain D residue 350 VAL Chi-restraints excluded: chain F residue 349 ARG Chi-restraints excluded: chain F residue 350 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 0.0470 chunk 31 optimal weight: 4.9990 chunk 17 optimal weight: 5.9990 chunk 10 optimal weight: 5.9990 chunk 21 optimal weight: 7.9990 chunk 32 optimal weight: 4.9990 chunk 12 optimal weight: 5.9990 chunk 20 optimal weight: 5.9990 chunk 24 optimal weight: 10.0000 chunk 38 optimal weight: 4.9990 chunk 11 optimal weight: 2.9990 overall best weight: 3.6086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 351 GLN E 362 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.129587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.100294 restraints weight = 3571.185| |-----------------------------------------------------------------------------| r_work (start): 0.3385 rms_B_bonded: 1.94 r_work: 0.3264 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3154 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8687 moved from start: 0.2120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 3498 Z= 0.265 Angle : 0.655 6.976 4680 Z= 0.333 Chirality : 0.050 0.135 528 Planarity : 0.004 0.032 594 Dihedral : 7.721 57.232 473 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 1.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Rotamer: Outliers : 5.05 % Allowed : 14.90 % Favored : 80.05 % 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: -2.51 (0.31), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.91 (0.23), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 329 PHE 0.007 0.002 PHE A 346 TYR 0.007 0.001 TYR C 310 ARG 0.003 0.000 ARG D 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 130 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 110 time to evaluate : 0.432 Fit side-chains REVERT: A 343 LYS cc_start: 0.8289 (mttm) cc_final: 0.7772 (mtmt) REVERT: A 347 LYS cc_start: 0.8092 (mttt) cc_final: 0.7642 (mptp) REVERT: B 311 LYS cc_start: 0.8208 (mtmt) cc_final: 0.7365 (tttt) REVERT: B 372 GLU cc_start: 0.7902 (tt0) cc_final: 0.7613 (tt0) REVERT: C 311 LYS cc_start: 0.8444 (OUTLIER) cc_final: 0.7805 (mttt) REVERT: C 343 LYS cc_start: 0.8462 (mttm) cc_final: 0.7970 (mtmt) REVERT: C 347 LYS cc_start: 0.8448 (mttp) cc_final: 0.7960 (mptp) REVERT: D 311 LYS cc_start: 0.8450 (mtmt) cc_final: 0.7779 (tttt) REVERT: D 347 LYS cc_start: 0.8539 (mptp) cc_final: 0.8275 (mptm) REVERT: E 329 HIS cc_start: 0.8558 (t70) cc_final: 0.7768 (m-70) REVERT: E 343 LYS cc_start: 0.8492 (mttm) cc_final: 0.8103 (mtmm) REVERT: E 347 LYS cc_start: 0.8114 (mttt) cc_final: 0.7813 (mptp) REVERT: F 311 LYS cc_start: 0.8356 (mtmt) cc_final: 0.7623 (tttt) REVERT: F 349 ARG cc_start: 0.8118 (OUTLIER) cc_final: 0.7801 (ptp-170) REVERT: F 353 LYS cc_start: 0.8856 (mttt) cc_final: 0.8518 (mttp) REVERT: F 369 LYS cc_start: 0.8535 (mttp) cc_final: 0.8164 (mttm) outliers start: 20 outliers final: 9 residues processed: 122 average time/residue: 1.3725 time to fit residues: 171.2561 Evaluate side-chains 108 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 97 time to evaluate : 0.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 341 SER Chi-restraints excluded: chain B residue 321 LYS Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain C residue 311 LYS Chi-restraints excluded: chain C residue 341 SER Chi-restraints excluded: chain D residue 350 VAL Chi-restraints excluded: chain E residue 341 SER Chi-restraints excluded: chain F residue 316 SER Chi-restraints excluded: chain F residue 320 SER Chi-restraints excluded: chain F residue 349 ARG Chi-restraints excluded: chain F residue 350 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 19 optimal weight: 0.6980 chunk 34 optimal weight: 8.9990 chunk 7 optimal weight: 10.0000 chunk 24 optimal weight: 9.9990 chunk 22 optimal weight: 9.9990 chunk 27 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 1 optimal weight: 9.9990 chunk 3 optimal weight: 9.9990 chunk 16 optimal weight: 9.9990 chunk 25 optimal weight: 7.9990 overall best weight: 7.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 329 HIS B 330 HIS C 329 HIS D 351 GLN F 330 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.122162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.093611 restraints weight = 3824.137| |-----------------------------------------------------------------------------| r_work (start): 0.3337 rms_B_bonded: 1.91 r_work: 0.3220 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3115 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8690 moved from start: 0.2524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.054 3498 Z= 0.490 Angle : 0.736 7.953 4680 Z= 0.376 Chirality : 0.052 0.131 528 Planarity : 0.004 0.026 594 Dihedral : 7.552 56.876 469 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 2.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 4.80 % Allowed : 18.69 % Favored : 76.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.28 (0.32), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.73 (0.24), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS E 329 PHE 0.010 0.002 PHE A 346 TYR 0.011 0.003 TYR A 310 ARG 0.002 0.000 ARG B 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 113 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 94 time to evaluate : 0.390 Fit side-chains REVERT: A 329 HIS cc_start: 0.8365 (t70) cc_final: 0.7420 (m90) REVERT: A 343 LYS cc_start: 0.8208 (mttm) cc_final: 0.7707 (mtmt) REVERT: A 347 LYS cc_start: 0.8155 (mttt) cc_final: 0.7639 (mptp) REVERT: A 370 LYS cc_start: 0.8860 (OUTLIER) cc_final: 0.8266 (ttmp) REVERT: B 317 LYS cc_start: 0.8070 (pttt) cc_final: 0.7522 (ptpp) REVERT: B 372 GLU cc_start: 0.8021 (tt0) cc_final: 0.7691 (tt0) REVERT: C 311 LYS cc_start: 0.8440 (OUTLIER) cc_final: 0.7773 (mttt) REVERT: C 329 HIS cc_start: 0.8434 (t-90) cc_final: 0.7592 (m90) REVERT: C 343 LYS cc_start: 0.8405 (mttm) cc_final: 0.7868 (mtmt) REVERT: C 347 LYS cc_start: 0.8433 (mttp) cc_final: 0.7853 (mptp) REVERT: E 329 HIS cc_start: 0.8599 (t70) cc_final: 0.7758 (m-70) REVERT: E 343 LYS cc_start: 0.8424 (mttm) cc_final: 0.8031 (mtmm) REVERT: E 347 LYS cc_start: 0.8231 (mttt) cc_final: 0.7830 (mptp) REVERT: F 311 LYS cc_start: 0.8303 (mtmt) cc_final: 0.7555 (tttt) REVERT: F 316 SER cc_start: 0.9204 (OUTLIER) cc_final: 0.8905 (p) REVERT: F 349 ARG cc_start: 0.8141 (OUTLIER) cc_final: 0.7908 (ptp-170) outliers start: 19 outliers final: 11 residues processed: 106 average time/residue: 1.5856 time to fit residues: 171.7390 Evaluate side-chains 108 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 93 time to evaluate : 0.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 341 SER Chi-restraints excluded: chain A residue 370 LYS Chi-restraints excluded: chain B residue 321 LYS Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain C residue 311 LYS Chi-restraints excluded: chain C residue 319 THR Chi-restraints excluded: chain C residue 341 SER Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain D residue 350 VAL Chi-restraints excluded: chain D residue 370 LYS Chi-restraints excluded: chain E residue 341 SER Chi-restraints excluded: chain F residue 316 SER Chi-restraints excluded: chain F residue 320 SER Chi-restraints excluded: chain F residue 349 ARG Chi-restraints excluded: chain F residue 350 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 26 optimal weight: 5.9990 chunk 13 optimal weight: 6.9990 chunk 7 optimal weight: 10.0000 chunk 33 optimal weight: 5.9990 chunk 29 optimal weight: 7.9990 chunk 22 optimal weight: 4.9990 chunk 25 optimal weight: 2.9990 chunk 18 optimal weight: 9.9990 chunk 21 optimal weight: 1.9990 chunk 14 optimal weight: 10.0000 chunk 11 optimal weight: 1.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 362 HIS D 351 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.126340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.097888 restraints weight = 3844.306| |-----------------------------------------------------------------------------| r_work (start): 0.3387 rms_B_bonded: 1.93 r_work: 0.3273 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3169 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8666 moved from start: 0.2787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 3498 Z= 0.246 Angle : 0.587 6.625 4680 Z= 0.296 Chirality : 0.048 0.132 528 Planarity : 0.003 0.022 594 Dihedral : 6.839 57.152 469 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 2.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.68 % Favored : 99.32 % Rotamer: Outliers : 5.05 % Allowed : 19.19 % Favored : 75.76 % 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: -2.06 (0.33), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.56 (0.25), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS E 329 PHE 0.006 0.001 PHE E 346 TYR 0.008 0.002 TYR A 310 ARG 0.001 0.000 ARG D 349 *********************** 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 116 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 96 time to evaluate : 0.403 Fit side-chains REVERT: A 329 HIS cc_start: 0.8357 (t70) cc_final: 0.7477 (m-70) REVERT: A 343 LYS cc_start: 0.8258 (mttm) cc_final: 0.7753 (mtmt) REVERT: A 347 LYS cc_start: 0.8159 (mttt) cc_final: 0.7628 (mptp) REVERT: A 370 LYS cc_start: 0.8864 (OUTLIER) cc_final: 0.8253 (ttmp) REVERT: B 311 LYS cc_start: 0.8158 (mtmt) cc_final: 0.7300 (tttt) REVERT: B 317 LYS cc_start: 0.8113 (pttt) cc_final: 0.7604 (ptpp) REVERT: B 372 GLU cc_start: 0.7999 (tt0) cc_final: 0.7647 (tt0) REVERT: C 311 LYS cc_start: 0.8411 (OUTLIER) cc_final: 0.7735 (mttt) REVERT: C 329 HIS cc_start: 0.8392 (t-90) cc_final: 0.7567 (m90) REVERT: C 343 LYS cc_start: 0.8423 (mttm) cc_final: 0.7903 (mtmt) REVERT: C 347 LYS cc_start: 0.8427 (mttp) cc_final: 0.7884 (mptp) REVERT: D 311 LYS cc_start: 0.8451 (mtmt) cc_final: 0.7681 (tttt) REVERT: E 329 HIS cc_start: 0.8531 (t70) cc_final: 0.7770 (m-70) REVERT: E 343 LYS cc_start: 0.8432 (mttm) cc_final: 0.8015 (mtmm) REVERT: E 347 LYS cc_start: 0.8238 (mttt) cc_final: 0.7839 (mptp) REVERT: F 311 LYS cc_start: 0.8260 (mtmt) cc_final: 0.7521 (tttt) REVERT: F 349 ARG cc_start: 0.8126 (OUTLIER) cc_final: 0.7831 (ptp-170) outliers start: 20 outliers final: 10 residues processed: 105 average time/residue: 1.4874 time to fit residues: 159.6658 Evaluate side-chains 109 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 96 time to evaluate : 0.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 341 SER Chi-restraints excluded: chain A residue 370 LYS Chi-restraints excluded: chain B residue 321 LYS Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain C residue 311 LYS Chi-restraints excluded: chain C residue 341 SER Chi-restraints excluded: chain D residue 350 VAL Chi-restraints excluded: chain D residue 370 LYS Chi-restraints excluded: chain E residue 341 SER Chi-restraints excluded: chain F residue 316 SER Chi-restraints excluded: chain F residue 320 SER Chi-restraints excluded: chain F residue 349 ARG Chi-restraints excluded: chain F residue 350 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 41 optimal weight: 0.9980 chunk 24 optimal weight: 10.0000 chunk 7 optimal weight: 20.0000 chunk 15 optimal weight: 10.0000 chunk 30 optimal weight: 8.9990 chunk 25 optimal weight: 2.9990 chunk 6 optimal weight: 0.0170 chunk 22 optimal weight: 3.9990 chunk 3 optimal weight: 9.9990 chunk 32 optimal weight: 9.9990 chunk 1 optimal weight: 6.9990 overall best weight: 3.0024 ------------------------------------------------------------------------------- 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 = 0.3783 r_free = 0.3783 target = 0.125908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.097980 restraints weight = 3847.972| |-----------------------------------------------------------------------------| r_work (start): 0.3407 rms_B_bonded: 1.91 r_work: 0.3291 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3186 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8658 moved from start: 0.2918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3498 Z= 0.209 Angle : 0.550 6.142 4680 Z= 0.276 Chirality : 0.047 0.128 528 Planarity : 0.003 0.019 594 Dihedral : 6.387 54.293 469 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 2.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 4.55 % Allowed : 19.19 % Favored : 76.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.96 (0.33), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.49 (0.25), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS E 329 PHE 0.005 0.001 PHE A 346 TYR 0.008 0.002 TYR E 310 ARG 0.001 0.000 ARG F 349 *********************** 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 119 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 101 time to evaluate : 0.383 Fit side-chains REVERT: A 329 HIS cc_start: 0.8355 (t70) cc_final: 0.7513 (m-70) REVERT: A 343 LYS cc_start: 0.8263 (mttm) cc_final: 0.7782 (mtmt) REVERT: A 347 LYS cc_start: 0.8174 (mttt) cc_final: 0.7652 (mptp) REVERT: A 370 LYS cc_start: 0.8859 (OUTLIER) cc_final: 0.8235 (ttmp) REVERT: B 311 LYS cc_start: 0.8075 (mtmt) cc_final: 0.7247 (tttt) REVERT: B 317 LYS cc_start: 0.8093 (pttt) cc_final: 0.7593 (ptpp) REVERT: B 347 LYS cc_start: 0.8202 (mptm) cc_final: 0.7999 (mptm) REVERT: B 372 GLU cc_start: 0.7982 (tt0) cc_final: 0.7612 (tt0) REVERT: C 311 LYS cc_start: 0.8406 (OUTLIER) cc_final: 0.7682 (mttt) REVERT: C 329 HIS cc_start: 0.8381 (t-90) cc_final: 0.7574 (m90) REVERT: C 343 LYS cc_start: 0.8458 (mttm) cc_final: 0.7931 (mtmt) REVERT: D 311 LYS cc_start: 0.8363 (mtmt) cc_final: 0.7653 (tttt) REVERT: D 328 ILE cc_start: 0.9281 (OUTLIER) cc_final: 0.8982 (mp) REVERT: E 329 HIS cc_start: 0.8518 (t70) cc_final: 0.7753 (m-70) REVERT: E 343 LYS cc_start: 0.8418 (mttm) cc_final: 0.8053 (mtmm) REVERT: E 347 LYS cc_start: 0.8237 (mttt) cc_final: 0.7832 (mptp) REVERT: F 311 LYS cc_start: 0.8228 (mtmt) cc_final: 0.7498 (tttt) REVERT: F 316 SER cc_start: 0.9227 (OUTLIER) cc_final: 0.8945 (p) REVERT: F 349 ARG cc_start: 0.8139 (OUTLIER) cc_final: 0.7812 (ptp-170) REVERT: F 379 ARG cc_start: 0.7141 (mpt180) cc_final: 0.6635 (mmt-90) outliers start: 18 outliers final: 9 residues processed: 112 average time/residue: 1.4277 time to fit residues: 163.5921 Evaluate side-chains 112 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 98 time to evaluate : 0.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 341 SER Chi-restraints excluded: chain A residue 370 LYS Chi-restraints excluded: chain B residue 321 LYS Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain C residue 311 LYS Chi-restraints excluded: chain C residue 341 SER Chi-restraints excluded: chain D residue 328 ILE Chi-restraints excluded: chain D residue 350 VAL Chi-restraints excluded: chain D residue 370 LYS Chi-restraints excluded: chain E residue 341 SER Chi-restraints excluded: chain F residue 316 SER Chi-restraints excluded: chain F residue 320 SER Chi-restraints excluded: chain F residue 349 ARG Chi-restraints excluded: chain F residue 350 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 25 optimal weight: 7.9990 chunk 24 optimal weight: 6.9990 chunk 6 optimal weight: 4.9990 chunk 21 optimal weight: 10.0000 chunk 7 optimal weight: 9.9990 chunk 27 optimal weight: 9.9990 chunk 2 optimal weight: 9.9990 chunk 15 optimal weight: 10.0000 chunk 40 optimal weight: 0.0970 chunk 4 optimal weight: 10.0000 chunk 16 optimal weight: 4.9990 overall best weight: 5.0186 ------------------------------------------------------------------------------- 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 = 0.3740 r_free = 0.3740 target = 0.121478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.092791 restraints weight = 3900.545| |-----------------------------------------------------------------------------| r_work (start): 0.3370 rms_B_bonded: 1.96 r_work: 0.3250 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3144 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8666 moved from start: 0.2927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 3498 Z= 0.325 Angle : 0.616 6.818 4680 Z= 0.312 Chirality : 0.048 0.127 528 Planarity : 0.003 0.022 594 Dihedral : 6.789 55.384 469 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 3.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 4.80 % Allowed : 20.20 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.03 (0.33), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.54 (0.25), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS E 329 PHE 0.007 0.002 PHE A 346 TYR 0.010 0.002 TYR A 310 ARG 0.001 0.000 ARG B 379 *********************** 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 116 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 97 time to evaluate : 0.542 Fit side-chains REVERT: A 329 HIS cc_start: 0.8390 (t70) cc_final: 0.7471 (m-70) REVERT: A 343 LYS cc_start: 0.8256 (mttm) cc_final: 0.7778 (mtmt) REVERT: A 347 LYS cc_start: 0.8177 (mttt) cc_final: 0.7605 (mptp) REVERT: A 370 LYS cc_start: 0.8882 (OUTLIER) cc_final: 0.8262 (ttmp) REVERT: B 311 LYS cc_start: 0.8183 (mtmt) cc_final: 0.7287 (tttt) REVERT: B 317 LYS cc_start: 0.8084 (pttt) cc_final: 0.7572 (ptpp) REVERT: B 372 GLU cc_start: 0.8051 (tt0) cc_final: 0.7668 (tt0) REVERT: C 311 LYS cc_start: 0.8413 (OUTLIER) cc_final: 0.7689 (mttt) REVERT: C 329 HIS cc_start: 0.8403 (t-90) cc_final: 0.7560 (m90) REVERT: C 343 LYS cc_start: 0.8399 (mttm) cc_final: 0.7874 (mtmt) REVERT: C 347 LYS cc_start: 0.8440 (mttp) cc_final: 0.7993 (mptt) REVERT: D 311 LYS cc_start: 0.8414 (mtmt) cc_final: 0.7637 (tttt) REVERT: D 328 ILE cc_start: 0.9262 (OUTLIER) cc_final: 0.8949 (mp) REVERT: E 329 HIS cc_start: 0.8630 (t70) cc_final: 0.7800 (m-70) REVERT: E 331 LYS cc_start: 0.9163 (OUTLIER) cc_final: 0.8930 (mtpt) REVERT: E 343 LYS cc_start: 0.8394 (mttm) cc_final: 0.8037 (mtmm) REVERT: E 347 LYS cc_start: 0.8261 (mttt) cc_final: 0.7798 (mptp) REVERT: F 311 LYS cc_start: 0.8286 (mtmt) cc_final: 0.7489 (tttt) REVERT: F 349 ARG cc_start: 0.8143 (OUTLIER) cc_final: 0.7822 (ptp-170) outliers start: 19 outliers final: 11 residues processed: 106 average time/residue: 1.4901 time to fit residues: 161.4247 Evaluate side-chains 112 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 96 time to evaluate : 0.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 341 SER Chi-restraints excluded: chain A residue 370 LYS Chi-restraints excluded: chain B residue 321 LYS Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain C residue 311 LYS Chi-restraints excluded: chain C residue 341 SER Chi-restraints excluded: chain D residue 328 ILE Chi-restraints excluded: chain D residue 350 VAL Chi-restraints excluded: chain D residue 370 LYS Chi-restraints excluded: chain E residue 314 ASP Chi-restraints excluded: chain E residue 331 LYS Chi-restraints excluded: chain E residue 341 SER Chi-restraints excluded: chain F residue 316 SER Chi-restraints excluded: chain F residue 320 SER Chi-restraints excluded: chain F residue 349 ARG Chi-restraints excluded: chain F residue 350 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 36 optimal weight: 0.2980 chunk 15 optimal weight: 8.9990 chunk 26 optimal weight: 3.9990 chunk 16 optimal weight: 9.9990 chunk 2 optimal weight: 1.9990 chunk 9 optimal weight: 10.0000 chunk 20 optimal weight: 7.9990 chunk 3 optimal weight: 20.0000 chunk 37 optimal weight: 0.0370 chunk 24 optimal weight: 8.9990 chunk 39 optimal weight: 9.9990 overall best weight: 2.8664 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 351 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.125281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.097165 restraints weight = 3842.515| |-----------------------------------------------------------------------------| r_work (start): 0.3405 rms_B_bonded: 1.93 r_work: 0.3288 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3183 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8660 moved from start: 0.3036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3498 Z= 0.200 Angle : 0.544 5.969 4680 Z= 0.275 Chirality : 0.047 0.126 528 Planarity : 0.002 0.019 594 Dihedral : 6.311 51.400 469 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 2.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.68 % Favored : 99.32 % Rotamer: Outliers : 4.80 % Allowed : 19.44 % Favored : 75.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.94 (0.33), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.47 (0.25), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS E 329 PHE 0.005 0.001 PHE E 346 TYR 0.008 0.002 TYR E 310 ARG 0.001 0.000 ARG F 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 116 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 97 time to evaluate : 0.396 Fit side-chains REVERT: A 329 HIS cc_start: 0.8377 (t70) cc_final: 0.7510 (m-70) REVERT: A 343 LYS cc_start: 0.8277 (mttm) cc_final: 0.7801 (mtmt) REVERT: A 347 LYS cc_start: 0.8179 (mttt) cc_final: 0.7626 (mptp) REVERT: A 370 LYS cc_start: 0.8856 (OUTLIER) cc_final: 0.8233 (ttmp) REVERT: B 311 LYS cc_start: 0.8076 (mtmt) cc_final: 0.7293 (tttt) REVERT: B 317 LYS cc_start: 0.8149 (pttt) cc_final: 0.7665 (ptpp) REVERT: B 372 GLU cc_start: 0.8035 (tt0) cc_final: 0.7668 (tt0) REVERT: C 311 LYS cc_start: 0.8381 (OUTLIER) cc_final: 0.7699 (mttt) REVERT: C 329 HIS cc_start: 0.8354 (t-90) cc_final: 0.7559 (m90) REVERT: C 343 LYS cc_start: 0.8422 (mttm) cc_final: 0.7889 (mtmt) REVERT: C 347 LYS cc_start: 0.8443 (mttp) cc_final: 0.8002 (mptt) REVERT: D 311 LYS cc_start: 0.8357 (mtmt) cc_final: 0.7656 (tttt) REVERT: D 328 ILE cc_start: 0.9272 (OUTLIER) cc_final: 0.8973 (mp) REVERT: E 329 HIS cc_start: 0.8572 (t70) cc_final: 0.7787 (m-70) REVERT: E 343 LYS cc_start: 0.8419 (mttm) cc_final: 0.8064 (mtmm) REVERT: E 347 LYS cc_start: 0.8276 (mttt) cc_final: 0.7842 (mptp) REVERT: F 311 LYS cc_start: 0.8249 (mtmt) cc_final: 0.7506 (tttt) REVERT: F 316 SER cc_start: 0.9186 (OUTLIER) cc_final: 0.8899 (p) REVERT: F 349 ARG cc_start: 0.8139 (OUTLIER) cc_final: 0.7796 (ptp-170) outliers start: 19 outliers final: 10 residues processed: 107 average time/residue: 1.4501 time to fit residues: 158.7430 Evaluate side-chains 111 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 96 time to evaluate : 0.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 341 SER Chi-restraints excluded: chain A residue 370 LYS Chi-restraints excluded: chain B residue 321 LYS Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain C residue 311 LYS Chi-restraints excluded: chain C residue 341 SER Chi-restraints excluded: chain D residue 328 ILE Chi-restraints excluded: chain D residue 350 VAL Chi-restraints excluded: chain D residue 370 LYS Chi-restraints excluded: chain E residue 341 SER Chi-restraints excluded: chain E residue 342 GLU Chi-restraints excluded: chain F residue 316 SER Chi-restraints excluded: chain F residue 320 SER Chi-restraints excluded: chain F residue 349 ARG Chi-restraints excluded: chain F residue 350 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 16 optimal weight: 10.0000 chunk 10 optimal weight: 20.0000 chunk 3 optimal weight: 20.0000 chunk 31 optimal weight: 8.9990 chunk 23 optimal weight: 5.9990 chunk 39 optimal weight: 8.9990 chunk 24 optimal weight: 5.9990 chunk 18 optimal weight: 8.9990 chunk 25 optimal weight: 7.9990 chunk 6 optimal weight: 0.5980 chunk 41 optimal weight: 0.7980 overall best weight: 4.2786 ------------------------------------------------------------------------------- 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 = 0.3769 r_free = 0.3769 target = 0.124728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.096365 restraints weight = 3873.850| |-----------------------------------------------------------------------------| r_work (start): 0.3384 rms_B_bonded: 1.93 r_work: 0.3266 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3161 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8695 moved from start: 0.3017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 3498 Z= 0.281 Angle : 0.584 6.296 4680 Z= 0.297 Chirality : 0.048 0.127 528 Planarity : 0.003 0.019 594 Dihedral : 6.542 51.354 469 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 3.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 5.30 % Allowed : 18.69 % Favored : 76.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.99 (0.33), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.51 (0.25), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS E 329 PHE 0.006 0.001 PHE A 346 TYR 0.010 0.002 TYR A 310 ARG 0.001 0.000 ARG F 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 118 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 97 time to evaluate : 0.385 Fit side-chains REVERT: A 329 HIS cc_start: 0.8364 (t70) cc_final: 0.7556 (m-70) REVERT: A 343 LYS cc_start: 0.8324 (mttm) cc_final: 0.7860 (mtmt) REVERT: A 347 LYS cc_start: 0.8215 (mttt) cc_final: 0.7692 (mptp) REVERT: A 370 LYS cc_start: 0.8891 (OUTLIER) cc_final: 0.8277 (ttmp) REVERT: B 311 LYS cc_start: 0.8206 (mtmt) cc_final: 0.7412 (tttt) REVERT: B 317 LYS cc_start: 0.8198 (pttt) cc_final: 0.7720 (ptpp) REVERT: B 372 GLU cc_start: 0.8054 (tt0) cc_final: 0.7694 (tt0) REVERT: C 311 LYS cc_start: 0.8440 (OUTLIER) cc_final: 0.7768 (mttt) REVERT: C 329 HIS cc_start: 0.8360 (t-90) cc_final: 0.7626 (m90) REVERT: C 343 LYS cc_start: 0.8405 (mttm) cc_final: 0.7910 (mtmt) REVERT: C 347 LYS cc_start: 0.8483 (mttp) cc_final: 0.8061 (mptt) REVERT: D 311 LYS cc_start: 0.8428 (mtmt) cc_final: 0.7705 (tttt) REVERT: D 317 LYS cc_start: 0.8558 (pttp) cc_final: 0.8017 (ptpp) REVERT: D 328 ILE cc_start: 0.9278 (OUTLIER) cc_final: 0.8995 (mp) REVERT: E 329 HIS cc_start: 0.8568 (t70) cc_final: 0.7845 (m-70) REVERT: E 331 LYS cc_start: 0.9144 (OUTLIER) cc_final: 0.8909 (mtpt) REVERT: E 343 LYS cc_start: 0.8432 (mttm) cc_final: 0.8078 (mtmm) REVERT: E 347 LYS cc_start: 0.8268 (mttt) cc_final: 0.7871 (mptp) REVERT: F 311 LYS cc_start: 0.8271 (mtmt) cc_final: 0.7541 (tttt) REVERT: F 349 ARG cc_start: 0.8190 (OUTLIER) cc_final: 0.7864 (ptp-170) outliers start: 21 outliers final: 13 residues processed: 105 average time/residue: 1.4764 time to fit residues: 158.4223 Evaluate side-chains 115 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 97 time to evaluate : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 341 SER Chi-restraints excluded: chain A residue 370 LYS Chi-restraints excluded: chain B residue 321 LYS Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain C residue 311 LYS Chi-restraints excluded: chain C residue 319 THR Chi-restraints excluded: chain C residue 341 SER Chi-restraints excluded: chain D residue 328 ILE Chi-restraints excluded: chain D residue 350 VAL Chi-restraints excluded: chain D residue 370 LYS Chi-restraints excluded: chain E residue 314 ASP Chi-restraints excluded: chain E residue 331 LYS Chi-restraints excluded: chain E residue 341 SER Chi-restraints excluded: chain E residue 342 GLU Chi-restraints excluded: chain F residue 316 SER Chi-restraints excluded: chain F residue 320 SER Chi-restraints excluded: chain F residue 349 ARG Chi-restraints excluded: chain F residue 350 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 22 optimal weight: 10.0000 chunk 8 optimal weight: 7.9990 chunk 27 optimal weight: 1.9990 chunk 37 optimal weight: 9.9990 chunk 39 optimal weight: 6.9990 chunk 17 optimal weight: 5.9990 chunk 14 optimal weight: 9.9990 chunk 13 optimal weight: 0.9980 chunk 3 optimal weight: 9.9990 chunk 40 optimal weight: 8.9990 chunk 21 optimal weight: 9.9990 overall best weight: 4.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 351 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.124394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.096098 restraints weight = 3806.889| |-----------------------------------------------------------------------------| r_work (start): 0.3378 rms_B_bonded: 1.92 r_work: 0.3260 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3155 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8699 moved from start: 0.3020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 3498 Z= 0.312 Angle : 0.601 6.429 4680 Z= 0.305 Chirality : 0.048 0.126 528 Planarity : 0.003 0.019 594 Dihedral : 6.603 51.366 469 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 2.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 4.55 % Allowed : 20.20 % Favored : 75.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.00 (0.33), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.51 (0.25), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS E 329 PHE 0.007 0.001 PHE A 346 TYR 0.010 0.002 TYR A 310 ARG 0.001 0.000 ARG F 379 *********************** 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 115 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 97 time to evaluate : 0.400 Fit side-chains REVERT: A 329 HIS cc_start: 0.8363 (t70) cc_final: 0.7552 (m-70) REVERT: A 343 LYS cc_start: 0.8327 (mttm) cc_final: 0.7860 (mtmt) REVERT: A 347 LYS cc_start: 0.8208 (mttt) cc_final: 0.7687 (mptp) REVERT: A 370 LYS cc_start: 0.8887 (OUTLIER) cc_final: 0.8275 (ttmp) REVERT: B 311 LYS cc_start: 0.8217 (mtmt) cc_final: 0.7403 (tttt) REVERT: B 317 LYS cc_start: 0.8195 (pttt) cc_final: 0.7719 (ptpp) REVERT: B 372 GLU cc_start: 0.8043 (tt0) cc_final: 0.7692 (tt0) REVERT: C 311 LYS cc_start: 0.8410 (OUTLIER) cc_final: 0.7760 (mttt) REVERT: C 329 HIS cc_start: 0.8361 (t-90) cc_final: 0.7628 (m90) REVERT: C 343 LYS cc_start: 0.8414 (mttm) cc_final: 0.7921 (mtmt) REVERT: C 347 LYS cc_start: 0.8492 (mttp) cc_final: 0.8071 (mptt) REVERT: D 311 LYS cc_start: 0.8458 (mtmt) cc_final: 0.7763 (tttt) REVERT: D 328 ILE cc_start: 0.9275 (OUTLIER) cc_final: 0.8989 (mp) REVERT: E 329 HIS cc_start: 0.8581 (t70) cc_final: 0.7856 (m-70) REVERT: E 331 LYS cc_start: 0.9158 (OUTLIER) cc_final: 0.8928 (mtpt) REVERT: E 343 LYS cc_start: 0.8441 (mttm) cc_final: 0.8081 (mtmm) REVERT: E 347 LYS cc_start: 0.8268 (mttt) cc_final: 0.7885 (mptp) REVERT: F 311 LYS cc_start: 0.8282 (mtmt) cc_final: 0.7538 (tttt) REVERT: F 349 ARG cc_start: 0.8174 (OUTLIER) cc_final: 0.7857 (ptp-170) outliers start: 18 outliers final: 12 residues processed: 105 average time/residue: 1.5359 time to fit residues: 164.7923 Evaluate side-chains 114 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 97 time to evaluate : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 341 SER Chi-restraints excluded: chain A residue 370 LYS Chi-restraints excluded: chain B residue 321 LYS Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain C residue 311 LYS Chi-restraints excluded: chain C residue 319 THR Chi-restraints excluded: chain C residue 341 SER Chi-restraints excluded: chain D residue 328 ILE Chi-restraints excluded: chain D residue 350 VAL Chi-restraints excluded: chain D residue 370 LYS Chi-restraints excluded: chain E residue 331 LYS Chi-restraints excluded: chain E residue 341 SER Chi-restraints excluded: chain E residue 342 GLU Chi-restraints excluded: chain F residue 316 SER Chi-restraints excluded: chain F residue 320 SER Chi-restraints excluded: chain F residue 349 ARG Chi-restraints excluded: chain F residue 350 VAL 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 8 optimal weight: 10.0000 chunk 32 optimal weight: 10.0000 chunk 23 optimal weight: 0.6980 chunk 16 optimal weight: 10.0000 chunk 27 optimal weight: 3.9990 chunk 18 optimal weight: 10.0000 chunk 38 optimal weight: 2.9990 chunk 15 optimal weight: 9.9990 chunk 1 optimal weight: 5.9990 chunk 19 optimal weight: 0.5980 overall best weight: 2.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 351 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.125129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.096945 restraints weight = 3865.387| |-----------------------------------------------------------------------------| r_work (start): 0.3416 rms_B_bonded: 1.94 r_work: 0.3299 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3194 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8656 moved from start: 0.3114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3498 Z= 0.198 Angle : 0.533 5.957 4680 Z= 0.270 Chirality : 0.047 0.126 528 Planarity : 0.002 0.019 594 Dihedral : 6.076 46.472 469 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 4.29 % Allowed : 20.20 % Favored : 75.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.91 (0.34), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.44 (0.26), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS E 329 PHE 0.005 0.001 PHE E 346 TYR 0.008 0.002 TYR A 310 ARG 0.001 0.000 ARG F 349 ********************** 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 116 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 99 time to evaluate : 0.550 Fit side-chains REVERT: A 329 HIS cc_start: 0.8392 (t70) cc_final: 0.7480 (m90) REVERT: A 343 LYS cc_start: 0.8293 (mttm) cc_final: 0.7816 (mtmt) REVERT: A 347 LYS cc_start: 0.8149 (mttt) cc_final: 0.7598 (mptp) REVERT: A 370 LYS cc_start: 0.8916 (OUTLIER) cc_final: 0.8291 (ttmp) REVERT: B 311 LYS cc_start: 0.8085 (mtmt) cc_final: 0.7271 (tttt) REVERT: B 317 LYS cc_start: 0.8133 (pttt) cc_final: 0.7645 (ptpp) REVERT: B 372 GLU cc_start: 0.8031 (tt0) cc_final: 0.7647 (tt0) REVERT: C 311 LYS cc_start: 0.8374 (OUTLIER) cc_final: 0.7695 (mttt) REVERT: C 329 HIS cc_start: 0.8363 (t-90) cc_final: 0.7557 (m90) REVERT: C 343 LYS cc_start: 0.8379 (mttm) cc_final: 0.7867 (mtmt) REVERT: C 347 LYS cc_start: 0.8457 (mttp) cc_final: 0.8000 (mptt) REVERT: D 311 LYS cc_start: 0.8384 (mtmt) cc_final: 0.7676 (tttt) REVERT: D 317 LYS cc_start: 0.8525 (pttp) cc_final: 0.7982 (ptpp) REVERT: D 328 ILE cc_start: 0.9272 (OUTLIER) cc_final: 0.8971 (mp) REVERT: E 329 HIS cc_start: 0.8579 (t70) cc_final: 0.7800 (m-70) REVERT: E 331 LYS cc_start: 0.9134 (OUTLIER) cc_final: 0.8897 (mtpt) REVERT: E 343 LYS cc_start: 0.8400 (mttm) cc_final: 0.8048 (mtmm) REVERT: E 347 LYS cc_start: 0.8261 (mttt) cc_final: 0.7806 (mptp) REVERT: F 311 LYS cc_start: 0.8244 (mtmt) cc_final: 0.7516 (tttt) REVERT: F 349 ARG cc_start: 0.8118 (OUTLIER) cc_final: 0.7769 (ptp-170) outliers start: 17 outliers final: 12 residues processed: 108 average time/residue: 1.4721 time to fit residues: 162.6571 Evaluate side-chains 115 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 98 time to evaluate : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 341 SER Chi-restraints excluded: chain A residue 370 LYS Chi-restraints excluded: chain B residue 321 LYS Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain C residue 311 LYS Chi-restraints excluded: chain C residue 319 THR Chi-restraints excluded: chain C residue 341 SER Chi-restraints excluded: chain D residue 328 ILE Chi-restraints excluded: chain D residue 350 VAL Chi-restraints excluded: chain D residue 370 LYS Chi-restraints excluded: chain E residue 331 LYS Chi-restraints excluded: chain E residue 341 SER Chi-restraints excluded: chain E residue 342 GLU Chi-restraints excluded: chain F residue 316 SER Chi-restraints excluded: chain F residue 320 SER Chi-restraints excluded: chain F residue 349 ARG Chi-restraints excluded: chain F residue 350 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 30 optimal weight: 9.9990 chunk 35 optimal weight: 9.9990 chunk 21 optimal weight: 0.1980 chunk 7 optimal weight: 0.9990 chunk 29 optimal weight: 8.9990 chunk 16 optimal weight: 10.0000 chunk 22 optimal weight: 6.9990 chunk 40 optimal weight: 0.0970 chunk 23 optimal weight: 0.9990 chunk 15 optimal weight: 3.9990 chunk 10 optimal weight: 20.0000 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 362 HIS C 362 HIS F 362 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.128879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.101282 restraints weight = 3831.857| |-----------------------------------------------------------------------------| r_work (start): 0.3488 rms_B_bonded: 1.96 r_work: 0.3372 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3267 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8607 moved from start: 0.3370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 3498 Z= 0.110 Angle : 0.472 4.886 4680 Z= 0.238 Chirality : 0.046 0.125 528 Planarity : 0.002 0.020 594 Dihedral : 4.955 35.094 469 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 2.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.68 % Favored : 99.32 % Rotamer: Outliers : 3.03 % Allowed : 21.21 % Favored : 75.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.80 (0.34), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.36 (0.26), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS E 329 PHE 0.003 0.001 PHE E 346 TYR 0.007 0.001 TYR A 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: 3899.65 seconds wall clock time: 67 minutes 20.46 seconds (4040.46 seconds total)