Starting phenix.real_space_refine on Fri May 9 18:39:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8oti_17180/05_2025/8oti_17180.cif Found real_map, /net/cci-nas-00/data/ceres_data/8oti_17180/05_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_17180/05_2025/8oti_17180.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8oti_17180/05_2025/8oti_17180.map" model { file = "/net/cci-nas-00/data/ceres_data/8oti_17180/05_2025/8oti_17180.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8oti_17180/05_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-5687/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: 3.09, per 1000 atoms: 0.90 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: 0.75 Conformation dependent library (CDL) restraints added in 703.6 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: 0.43 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: 0.75 Time building geometry restraints manager: 0.91 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: 0.700 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: 0.130 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 13.480 Find NCS groups from input model: 0.120 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:11.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.090 ------------------------------------------------------------------------------- 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= 0.786 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 Details of bonding type rmsd hydrogen bonds : bond 0.13718 ( 67) hydrogen bonds : angle 6.72720 ( 201) covalent geometry : bond 0.01198 ( 3498) covalent geometry : angle 1.63061 ( 4680) *********************** 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 : 0.382 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: 1.4655 time to fit residues: 182.7139 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 : 0.383 ------------------------------------------------------------------------------- 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 = 0.100293 restraints weight = 3571.184| |-----------------------------------------------------------------------------| 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= 0.177 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 Details of bonding type rmsd hydrogen bonds : bond 0.02464 ( 67) hydrogen bonds : angle 5.30123 ( 201) covalent geometry : bond 0.00404 ( 3498) covalent geometry : angle 0.65512 ( 4680) *********************** 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 : 0.439 Fit side-chains REVERT: A 343 LYS cc_start: 0.8290 (mttm) cc_final: 0.7773 (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: 0.7901 (tt0) cc_final: 0.7613 (tt0) REVERT: C 311 LYS cc_start: 0.8443 (OUTLIER) cc_final: 0.7805 (mttt) REVERT: C 343 LYS cc_start: 0.8463 (mttm) cc_final: 0.7971 (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: 0.7780 (tttt) REVERT: D 347 LYS cc_start: 0.8539 (mptp) cc_final: 0.8276 (mptm) REVERT: E 329 HIS cc_start: 0.8559 (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: 0.8116 (mttt) cc_final: 0.7814 (mptp) REVERT: F 311 LYS cc_start: 0.8355 (mtmt) cc_final: 0.7624 (tttt) REVERT: F 349 ARG cc_start: 0.8118 (OUTLIER) cc_final: 0.7801 (ptp-170) REVERT: F 353 LYS cc_start: 0.8855 (mttt) cc_final: 0.8517 (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: 1.3634 time to fit residues: 170.2433 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 : 0.408 ------------------------------------------------------------------------------- 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: 0.3980 chunk 34 optimal weight: 8.9990 chunk 7 optimal weight: 10.0000 chunk 24 optimal weight: 9.9990 chunk 22 optimal weight: 6.9990 chunk 27 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 1 optimal weight: 9.9990 chunk 3 optimal weight: 10.0000 chunk 16 optimal weight: 10.0000 chunk 25 optimal weight: 4.9990 overall best weight: 6.0788 ------------------------------------------------------------------------------- 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 = 0.3736 r_free = 0.3736 target = 0.121165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.092265 restraints weight = 3794.415| |-----------------------------------------------------------------------------| r_work (start): 0.3366 rms_B_bonded: 1.93 r_work: 0.3247 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3142 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8680 moved from start: 0.2534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 3498 Z= 0.265 Angle : 0.690 7.768 4680 Z= 0.350 Chirality : 0.050 0.130 528 Planarity : 0.003 0.024 594 Dihedral : 7.380 58.631 469 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 2.42 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: -2.23 (0.32), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.69 (0.25), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS E 329 PHE 0.009 0.002 PHE A 346 TYR 0.010 0.002 TYR A 310 ARG 0.002 0.000 ARG B 379 Details of bonding type rmsd hydrogen bonds : bond 0.02624 ( 67) hydrogen bonds : angle 5.49477 ( 201) covalent geometry : bond 0.00617 ( 3498) covalent geometry : angle 0.69031 ( 4680) *********************** 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 111 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 92 time to evaluate : 0.407 Fit side-chains REVERT: A 329 HIS cc_start: 0.8372 (t70) cc_final: 0.7436 (m90) REVERT: A 343 LYS cc_start: 0.8208 (mttm) cc_final: 0.7715 (mtmt) REVERT: A 347 LYS cc_start: 0.8106 (mttt) cc_final: 0.7609 (mptp) REVERT: A 370 LYS cc_start: 0.8853 (OUTLIER) cc_final: 0.8244 (ttmp) REVERT: B 311 LYS cc_start: 0.8231 (mtmt) cc_final: 0.7278 (tttt) REVERT: B 317 LYS cc_start: 0.8059 (pttt) cc_final: 0.7521 (ptpp) REVERT: B 372 GLU cc_start: 0.7992 (tt0) cc_final: 0.7651 (tt0) REVERT: C 311 LYS cc_start: 0.8463 (OUTLIER) cc_final: 0.7785 (mttt) REVERT: C 329 HIS cc_start: 0.8431 (t-90) cc_final: 0.7606 (m90) REVERT: C 343 LYS cc_start: 0.8404 (mttm) cc_final: 0.7872 (mtmt) REVERT: C 347 LYS cc_start: 0.8424 (mttp) cc_final: 0.7849 (mptp) REVERT: D 311 LYS cc_start: 0.8500 (mtmt) cc_final: 0.7706 (tttt) REVERT: E 329 HIS cc_start: 0.8583 (t70) cc_final: 0.7764 (m-70) REVERT: E 343 LYS cc_start: 0.8413 (mttm) cc_final: 0.8002 (mtmm) REVERT: E 347 LYS cc_start: 0.8212 (mttt) cc_final: 0.7785 (mptp) REVERT: F 311 LYS cc_start: 0.8296 (mtmt) cc_final: 0.7524 (tttt) REVERT: F 316 SER cc_start: 0.9218 (OUTLIER) cc_final: 0.8913 (p) REVERT: F 349 ARG cc_start: 0.8128 (OUTLIER) cc_final: 0.7819 (ptp-170) outliers start: 19 outliers final: 11 residues processed: 103 average time/residue: 1.3876 time to fit residues: 146.2374 Evaluate side-chains 106 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 91 time to evaluate : 0.395 ------------------------------------------------------------------------------- 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: 6.9990 chunk 13 optimal weight: 0.9990 chunk 7 optimal weight: 10.0000 chunk 33 optimal weight: 10.0000 chunk 29 optimal weight: 8.9990 chunk 22 optimal weight: 3.9990 chunk 25 optimal weight: 4.9990 chunk 18 optimal weight: 10.0000 chunk 21 optimal weight: 10.0000 chunk 14 optimal weight: 9.9990 chunk 11 optimal weight: 5.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 351 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.124382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.096048 restraints weight = 3847.955| |-----------------------------------------------------------------------------| r_work (start): 0.3374 rms_B_bonded: 1.93 r_work: 0.3258 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3153 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8669 moved from start: 0.2781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 3498 Z= 0.203 Angle : 0.614 6.705 4680 Z= 0.311 Chirality : 0.048 0.132 528 Planarity : 0.003 0.023 594 Dihedral : 6.953 57.813 469 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 2.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 5.30 % Allowed : 18.94 % 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: -2.08 (0.33), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.57 (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 0.009 0.002 TYR A 310 ARG 0.001 0.000 ARG B 379 Details of bonding type rmsd hydrogen bonds : bond 0.02262 ( 67) hydrogen bonds : angle 5.36774 ( 201) covalent geometry : bond 0.00471 ( 3498) covalent geometry : angle 0.61414 ( 4680) *********************** 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: 21 poor density : 95 time to evaluate : 0.421 Fit side-chains REVERT: A 329 HIS cc_start: 0.8360 (t70) cc_final: 0.7472 (m-70) REVERT: A 343 LYS cc_start: 0.8238 (mttm) cc_final: 0.7739 (mtmt) REVERT: A 347 LYS cc_start: 0.8178 (mttt) cc_final: 0.7638 (mptp) REVERT: A 370 LYS cc_start: 0.8870 (OUTLIER) cc_final: 0.8252 (ttmp) REVERT: B 311 LYS cc_start: 0.8183 (mtmt) cc_final: 0.7301 (tttt) REVERT: B 317 LYS cc_start: 0.8084 (pttt) cc_final: 0.7567 (ptpp) REVERT: B 372 GLU cc_start: 0.8000 (tt0) cc_final: 0.7635 (tt0) REVERT: C 311 LYS cc_start: 0.8441 (OUTLIER) cc_final: 0.7768 (mttt) REVERT: C 329 HIS cc_start: 0.8397 (t-90) cc_final: 0.7554 (m90) REVERT: C 343 LYS cc_start: 0.8419 (mttm) cc_final: 0.7897 (mtmt) REVERT: C 347 LYS cc_start: 0.8438 (mttp) cc_final: 0.7873 (mptp) REVERT: D 311 LYS cc_start: 0.8454 (mtmt) cc_final: 0.7688 (tttt) REVERT: E 329 HIS cc_start: 0.8546 (t70) cc_final: 0.7774 (m-70) REVERT: E 343 LYS cc_start: 0.8420 (mttm) cc_final: 0.8003 (mtmm) REVERT: E 347 LYS cc_start: 0.8233 (mttt) cc_final: 0.7818 (mptp) REVERT: F 311 LYS cc_start: 0.8295 (mtmt) cc_final: 0.7545 (tttt) REVERT: F 349 ARG cc_start: 0.8111 (OUTLIER) cc_final: 0.7820 (ptp-170) outliers start: 21 outliers final: 11 residues processed: 103 average time/residue: 1.4196 time to fit residues: 149.6178 Evaluate side-chains 108 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 94 time to evaluate : 0.417 ------------------------------------------------------------------------------- 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 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: 2.9990 chunk 24 optimal weight: 8.9990 chunk 7 optimal weight: 10.0000 chunk 15 optimal weight: 5.9990 chunk 30 optimal weight: 4.9990 chunk 25 optimal weight: 10.0000 chunk 6 optimal weight: 0.7980 chunk 22 optimal weight: 3.9990 chunk 3 optimal weight: 20.0000 chunk 32 optimal weight: 10.0000 chunk 1 optimal weight: 8.9990 overall best weight: 3.7588 ------------------------------------------------------------------------------- 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 = 0.3767 r_free = 0.3767 target = 0.124457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.096198 restraints weight = 3856.172| |-----------------------------------------------------------------------------| r_work (start): 0.3390 rms_B_bonded: 1.93 r_work: 0.3271 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3166 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8663 moved from start: 0.2894 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= 0.170 Angle : 0.578 6.384 4680 Z= 0.291 Chirality : 0.048 0.127 528 Planarity : 0.003 0.018 594 Dihedral : 6.646 55.443 469 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 2.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 4.80 % Allowed : 19.70 % 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: -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 0.003 0.001 HIS E 329 PHE 0.006 0.001 PHE A 346 TYR 0.009 0.002 TYR E 310 ARG 0.001 0.000 ARG F 379 Details of bonding type rmsd hydrogen bonds : bond 0.02084 ( 67) hydrogen bonds : angle 5.32149 ( 201) covalent geometry : bond 0.00391 ( 3498) covalent geometry : angle 0.57832 ( 4680) *********************** 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 120 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 101 time to evaluate : 0.428 Fit side-chains REVERT: A 329 HIS cc_start: 0.8389 (t70) cc_final: 0.7506 (m-70) REVERT: A 343 LYS cc_start: 0.8265 (mttm) cc_final: 0.7778 (mtmt) REVERT: A 347 LYS cc_start: 0.8173 (mttt) cc_final: 0.7627 (mptp) REVERT: A 370 LYS cc_start: 0.8864 (OUTLIER) cc_final: 0.8237 (ttmp) REVERT: B 311 LYS cc_start: 0.8107 (mtmt) cc_final: 0.7247 (tttt) REVERT: B 317 LYS cc_start: 0.8104 (pttt) cc_final: 0.7599 (ptpp) REVERT: B 347 LYS cc_start: 0.8222 (mptm) cc_final: 0.8010 (mptm) REVERT: B 372 GLU cc_start: 0.8016 (tt0) cc_final: 0.7637 (tt0) REVERT: C 311 LYS cc_start: 0.8422 (OUTLIER) cc_final: 0.7688 (mttt) REVERT: C 329 HIS cc_start: 0.8377 (t-90) cc_final: 0.7559 (m90) REVERT: C 343 LYS cc_start: 0.8440 (mttm) cc_final: 0.7912 (mtmt) REVERT: D 311 LYS cc_start: 0.8399 (mtmt) cc_final: 0.7645 (tttt) REVERT: D 328 ILE cc_start: 0.9278 (OUTLIER) cc_final: 0.8971 (mp) REVERT: E 329 HIS cc_start: 0.8543 (t70) cc_final: 0.7770 (m-70) REVERT: E 343 LYS cc_start: 0.8418 (mttm) cc_final: 0.8051 (mtmm) REVERT: E 347 LYS cc_start: 0.8259 (mttt) cc_final: 0.7826 (mptp) REVERT: F 311 LYS cc_start: 0.8244 (mtmt) cc_final: 0.7489 (tttt) REVERT: F 316 SER cc_start: 0.9209 (OUTLIER) cc_final: 0.8901 (p) REVERT: F 349 ARG cc_start: 0.8124 (OUTLIER) cc_final: 0.7817 (ptp-170) REVERT: F 379 ARG cc_start: 0.7133 (mpt180) cc_final: 0.6660 (mmt-90) outliers start: 19 outliers final: 9 residues processed: 112 average time/residue: 1.3309 time to fit residues: 152.6095 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 : 0.377 ------------------------------------------------------------------------------- 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: 1.9990 chunk 24 optimal weight: 3.9990 chunk 6 optimal weight: 0.8980 chunk 21 optimal weight: 10.0000 chunk 7 optimal weight: 9.9990 chunk 27 optimal weight: 6.9990 chunk 2 optimal weight: 10.0000 chunk 15 optimal weight: 10.0000 chunk 40 optimal weight: 7.9990 chunk 4 optimal weight: 9.9990 chunk 16 optimal weight: 4.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- 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 = 0.3768 r_free = 0.3768 target = 0.124335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.096089 restraints weight = 3907.824| |-----------------------------------------------------------------------------| r_work (start): 0.3391 rms_B_bonded: 1.94 r_work: 0.3272 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3168 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8665 moved from start: 0.2962 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= 0.169 Angle : 0.574 6.232 4680 Z= 0.290 Chirality : 0.047 0.126 528 Planarity : 0.003 0.019 594 Dihedral : 6.538 53.606 469 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 2.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 4.80 % Allowed : 19.95 % 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: -2.01 (0.33), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.52 (0.25), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS E 329 PHE 0.006 0.001 PHE E 346 TYR 0.009 0.002 TYR E 310 ARG 0.001 0.000 ARG F 349 Details of bonding type rmsd hydrogen bonds : bond 0.02051 ( 67) hydrogen bonds : angle 5.24834 ( 201) covalent geometry : bond 0.00390 ( 3498) covalent geometry : angle 0.57365 ( 4680) *********************** 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 115 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 96 time to evaluate : 0.435 Fit side-chains REVERT: A 329 HIS cc_start: 0.8392 (t70) cc_final: 0.7498 (m-70) REVERT: A 343 LYS cc_start: 0.8289 (mttm) cc_final: 0.7804 (mtmt) REVERT: A 347 LYS cc_start: 0.8180 (mttt) cc_final: 0.7623 (mptp) REVERT: A 370 LYS cc_start: 0.8899 (OUTLIER) cc_final: 0.8275 (ttmp) REVERT: B 311 LYS cc_start: 0.8118 (mtmt) cc_final: 0.7287 (tttt) REVERT: B 317 LYS cc_start: 0.8116 (pttt) cc_final: 0.7617 (ptpp) REVERT: B 347 LYS cc_start: 0.8175 (mptm) cc_final: 0.7915 (mptm) REVERT: B 372 GLU cc_start: 0.8040 (tt0) cc_final: 0.7667 (tt0) REVERT: C 311 LYS cc_start: 0.8407 (OUTLIER) cc_final: 0.7678 (mttt) REVERT: C 329 HIS cc_start: 0.8383 (t-90) cc_final: 0.7560 (m90) REVERT: C 343 LYS cc_start: 0.8442 (mttm) cc_final: 0.7913 (mtmt) REVERT: C 347 LYS cc_start: 0.8435 (mttp) cc_final: 0.8012 (mptt) REVERT: D 311 LYS cc_start: 0.8389 (mtmt) cc_final: 0.7642 (tttt) REVERT: D 328 ILE cc_start: 0.9275 (OUTLIER) cc_final: 0.8999 (mp) REVERT: E 329 HIS cc_start: 0.8544 (t70) cc_final: 0.7772 (m-70) REVERT: E 343 LYS cc_start: 0.8422 (mttm) cc_final: 0.8061 (mtmm) REVERT: E 347 LYS cc_start: 0.8265 (mttt) cc_final: 0.7830 (mptp) REVERT: F 311 LYS cc_start: 0.8278 (mtmt) cc_final: 0.7512 (tttt) REVERT: F 349 ARG cc_start: 0.8122 (OUTLIER) cc_final: 0.7799 (ptp-170) REVERT: F 379 ARG cc_start: 0.7110 (mpt180) cc_final: 0.6573 (mmt-90) outliers start: 19 outliers final: 12 residues processed: 106 average time/residue: 1.4402 time to fit residues: 156.0945 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 : 0.423 ------------------------------------------------------------------------------- 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 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: 20.0000 chunk 15 optimal weight: 8.9990 chunk 26 optimal weight: 10.0000 chunk 16 optimal weight: 3.9990 chunk 2 optimal weight: 5.9990 chunk 9 optimal weight: 5.9990 chunk 20 optimal weight: 9.9990 chunk 3 optimal weight: 20.0000 chunk 37 optimal weight: 8.9990 chunk 24 optimal weight: 20.0000 chunk 39 optimal weight: 0.5980 overall best weight: 5.1188 ------------------------------------------------------------------------------- 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 = 0.3747 r_free = 0.3747 target = 0.122144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.093609 restraints weight = 3860.403| |-----------------------------------------------------------------------------| r_work (start): 0.3371 rms_B_bonded: 1.94 r_work: 0.3252 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3146 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8673 moved from start: 0.2955 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= 0.218 Angle : 0.612 6.646 4680 Z= 0.311 Chirality : 0.048 0.127 528 Planarity : 0.003 0.020 594 Dihedral : 6.743 54.763 469 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 2.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 4.29 % Allowed : 20.71 % 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: -2.05 (0.33), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.55 (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 0.003 TYR A 310 ARG 0.001 0.000 ARG F 379 Details of bonding type rmsd hydrogen bonds : bond 0.02251 ( 67) hydrogen bonds : angle 5.30439 ( 201) covalent geometry : bond 0.00506 ( 3498) covalent geometry : angle 0.61211 ( 4680) *********************** 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 112 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 95 time to evaluate : 0.392 Fit side-chains REVERT: A 329 HIS cc_start: 0.8386 (t70) cc_final: 0.7461 (m-70) REVERT: A 343 LYS cc_start: 0.8261 (mttm) cc_final: 0.7782 (mtmt) REVERT: A 347 LYS cc_start: 0.8203 (mttt) cc_final: 0.7619 (mptp) REVERT: A 370 LYS cc_start: 0.8891 (OUTLIER) cc_final: 0.8266 (ttmp) REVERT: B 311 LYS cc_start: 0.8156 (mtmt) cc_final: 0.7308 (tttt) REVERT: B 317 LYS cc_start: 0.8112 (pttt) cc_final: 0.7604 (ptpp) REVERT: B 372 GLU cc_start: 0.8035 (tt0) cc_final: 0.7659 (tt0) REVERT: C 311 LYS cc_start: 0.8412 (OUTLIER) cc_final: 0.7728 (mttt) REVERT: C 329 HIS cc_start: 0.8386 (t-90) cc_final: 0.7564 (m90) REVERT: C 343 LYS cc_start: 0.8429 (mttm) cc_final: 0.7911 (mtmt) REVERT: C 347 LYS cc_start: 0.8464 (mttp) cc_final: 0.8021 (mptt) REVERT: D 328 ILE cc_start: 0.9264 (OUTLIER) cc_final: 0.8979 (mp) REVERT: E 329 HIS cc_start: 0.8585 (t70) cc_final: 0.7776 (m-70) REVERT: E 343 LYS cc_start: 0.8404 (mttm) cc_final: 0.8042 (mtmm) REVERT: E 347 LYS cc_start: 0.8243 (mttt) cc_final: 0.7799 (mptp) REVERT: F 311 LYS cc_start: 0.8302 (mtmt) cc_final: 0.7514 (tttt) REVERT: F 316 SER cc_start: 0.9199 (OUTLIER) cc_final: 0.8884 (p) REVERT: F 349 ARG cc_start: 0.8131 (OUTLIER) cc_final: 0.7829 (ptp-170) outliers start: 17 outliers final: 11 residues processed: 103 average time/residue: 1.4383 time to fit residues: 151.4772 Evaluate side-chains 109 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 93 time to evaluate : 0.397 ------------------------------------------------------------------------------- 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 16 optimal weight: 9.9990 chunk 10 optimal weight: 20.0000 chunk 3 optimal weight: 9.9990 chunk 31 optimal weight: 7.9990 chunk 23 optimal weight: 8.9990 chunk 39 optimal weight: 1.9990 chunk 24 optimal weight: 5.9990 chunk 18 optimal weight: 7.9990 chunk 25 optimal weight: 0.0470 chunk 6 optimal weight: 0.0770 chunk 41 optimal weight: 9.9990 overall best weight: 3.2242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 362 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.126100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.097928 restraints weight = 3845.154| |-----------------------------------------------------------------------------| r_work (start): 0.3402 rms_B_bonded: 1.92 r_work: 0.3285 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3180 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8685 moved from start: 0.3071 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= 0.147 Angle : 0.552 6.040 4680 Z= 0.280 Chirality : 0.047 0.125 528 Planarity : 0.003 0.021 594 Dihedral : 6.383 51.412 469 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Rotamer: Outliers : 5.30 % Allowed : 19.19 % 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: -1.96 (0.33), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.48 (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 A 310 ARG 0.001 0.000 ARG F 349 Details of bonding type rmsd hydrogen bonds : bond 0.01947 ( 67) hydrogen bonds : angle 5.16064 ( 201) covalent geometry : bond 0.00337 ( 3498) covalent geometry : angle 0.55218 ( 4680) *********************** 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 : 0.391 Fit side-chains REVERT: A 329 HIS cc_start: 0.8378 (t70) cc_final: 0.7561 (m-70) REVERT: A 343 LYS cc_start: 0.8321 (mttm) cc_final: 0.7857 (mtmt) REVERT: A 347 LYS cc_start: 0.8196 (mttt) cc_final: 0.7689 (mptp) REVERT: A 370 LYS cc_start: 0.8911 (OUTLIER) cc_final: 0.8296 (ttmp) REVERT: B 311 LYS cc_start: 0.8142 (mtmt) cc_final: 0.7372 (tttt) REVERT: B 317 LYS cc_start: 0.8201 (pttt) cc_final: 0.7740 (ptpp) REVERT: B 372 GLU cc_start: 0.8046 (tt0) cc_final: 0.7688 (tt0) REVERT: C 311 LYS cc_start: 0.8405 (OUTLIER) cc_final: 0.7735 (mttt) REVERT: C 329 HIS cc_start: 0.8363 (t-90) cc_final: 0.7618 (m90) REVERT: C 343 LYS cc_start: 0.8470 (mttm) cc_final: 0.7961 (mtmt) REVERT: C 347 LYS cc_start: 0.8485 (mttp) cc_final: 0.8073 (mptt) REVERT: D 311 LYS cc_start: 0.8417 (mtmt) cc_final: 0.7720 (tttt) REVERT: D 328 ILE cc_start: 0.9277 (OUTLIER) cc_final: 0.9008 (mp) REVERT: E 329 HIS cc_start: 0.8533 (t70) cc_final: 0.7810 (m-70) REVERT: E 343 LYS cc_start: 0.8457 (mttm) cc_final: 0.8105 (mtmm) REVERT: E 347 LYS cc_start: 0.8267 (mttt) cc_final: 0.7868 (mptp) REVERT: F 311 LYS cc_start: 0.8286 (mtmt) cc_final: 0.7570 (tttt) REVERT: F 349 ARG cc_start: 0.8143 (OUTLIER) cc_final: 0.7812 (ptp-170) outliers start: 21 outliers final: 12 residues processed: 107 average time/residue: 1.4451 time to fit residues: 158.1323 Evaluate side-chains 113 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 97 time to evaluate : 0.416 ------------------------------------------------------------------------------- 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 22 optimal weight: 7.9990 chunk 8 optimal weight: 10.0000 chunk 27 optimal weight: 2.9990 chunk 37 optimal weight: 7.9990 chunk 39 optimal weight: 6.9990 chunk 17 optimal weight: 10.0000 chunk 14 optimal weight: 10.0000 chunk 13 optimal weight: 3.9990 chunk 3 optimal weight: 20.0000 chunk 40 optimal weight: 8.9990 chunk 21 optimal weight: 20.0000 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 330 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.123588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.095062 restraints weight = 3813.257| |-----------------------------------------------------------------------------| r_work (start): 0.3358 rms_B_bonded: 1.91 r_work: 0.3238 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3132 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8705 moved from start: 0.3032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 3498 Z= 0.253 Angle : 0.632 6.700 4680 Z= 0.323 Chirality : 0.049 0.127 528 Planarity : 0.003 0.019 594 Dihedral : 6.816 54.480 469 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 3.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 4.80 % Allowed : 19.19 % 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: -2.05 (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 0.005 0.001 HIS E 329 PHE 0.008 0.002 PHE A 346 TYR 0.012 0.003 TYR A 310 ARG 0.002 0.000 ARG F 379 Details of bonding type rmsd hydrogen bonds : bond 0.02356 ( 67) hydrogen bonds : angle 5.31918 ( 201) covalent geometry : bond 0.00589 ( 3498) covalent geometry : angle 0.63156 ( 4680) *********************** 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 114 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 95 time to evaluate : 0.417 Fit side-chains REVERT: A 329 HIS cc_start: 0.8371 (t70) cc_final: 0.7521 (m-70) REVERT: A 343 LYS cc_start: 0.8302 (mttm) cc_final: 0.7840 (mtmt) REVERT: A 347 LYS cc_start: 0.8227 (mttt) cc_final: 0.7716 (mptp) REVERT: A 370 LYS cc_start: 0.8904 (OUTLIER) cc_final: 0.8284 (ttmp) REVERT: B 311 LYS cc_start: 0.8223 (mtmt) cc_final: 0.7400 (tttt) REVERT: B 317 LYS cc_start: 0.8148 (pttt) cc_final: 0.7694 (ptpp) REVERT: B 372 GLU cc_start: 0.8060 (tt0) cc_final: 0.7694 (tt0) REVERT: C 311 LYS cc_start: 0.8410 (OUTLIER) cc_final: 0.7754 (mttt) REVERT: C 329 HIS cc_start: 0.8377 (t-90) cc_final: 0.7625 (m90) REVERT: C 343 LYS cc_start: 0.8412 (mttm) cc_final: 0.7910 (mtmt) REVERT: C 347 LYS cc_start: 0.8490 (mttp) cc_final: 0.8060 (mptt) REVERT: D 328 ILE cc_start: 0.9270 (OUTLIER) cc_final: 0.8977 (mp) REVERT: E 329 HIS cc_start: 0.8567 (t70) cc_final: 0.7831 (m-70) REVERT: E 343 LYS cc_start: 0.8452 (mttm) cc_final: 0.8094 (mtmm) REVERT: E 347 LYS cc_start: 0.8274 (mttt) cc_final: 0.7864 (mptp) REVERT: F 311 LYS cc_start: 0.8347 (mtmt) cc_final: 0.7584 (tttt) REVERT: F 349 ARG cc_start: 0.8178 (OUTLIER) cc_final: 0.7881 (ptp-170) outliers start: 19 outliers final: 13 residues processed: 104 average time/residue: 1.4248 time to fit residues: 151.4872 Evaluate side-chains 112 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 95 time to evaluate : 0.417 ------------------------------------------------------------------------------- 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 342 GLU 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 24 optimal weight: 9.9990 chunk 8 optimal weight: 10.0000 chunk 32 optimal weight: 6.9990 chunk 23 optimal weight: 0.2980 chunk 16 optimal weight: 10.0000 chunk 27 optimal weight: 6.9990 chunk 18 optimal weight: 0.9990 chunk 38 optimal weight: 3.9990 chunk 15 optimal weight: 10.0000 chunk 1 optimal weight: 5.9990 chunk 19 optimal weight: 6.9990 overall best weight: 3.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 351 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.125270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.097079 restraints weight = 3874.609| |-----------------------------------------------------------------------------| r_work (start): 0.3393 rms_B_bonded: 1.92 r_work: 0.3275 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3170 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8668 moved from start: 0.3093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 3498 Z= 0.165 Angle : 0.565 6.083 4680 Z= 0.287 Chirality : 0.047 0.126 528 Planarity : 0.002 0.020 594 Dihedral : 6.509 51.590 469 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Rotamer: Outliers : 4.04 % Allowed : 20.45 % 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: -1.99 (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 E 346 TYR 0.009 0.002 TYR A 310 ARG 0.001 0.000 ARG F 349 Details of bonding type rmsd hydrogen bonds : bond 0.02036 ( 67) hydrogen bonds : angle 5.19871 ( 201) covalent geometry : bond 0.00378 ( 3498) covalent geometry : angle 0.56456 ( 4680) ********************** 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 114 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 98 time to evaluate : 0.419 Fit side-chains REVERT: A 329 HIS cc_start: 0.8396 (t70) cc_final: 0.7507 (m-70) REVERT: A 343 LYS cc_start: 0.8266 (mttm) cc_final: 0.7799 (mtmt) REVERT: A 347 LYS cc_start: 0.8188 (mttt) cc_final: 0.7631 (mptp) REVERT: A 370 LYS cc_start: 0.8872 (OUTLIER) cc_final: 0.8247 (ttmp) REVERT: B 311 LYS cc_start: 0.8164 (mtmt) cc_final: 0.7319 (tttt) REVERT: B 317 LYS cc_start: 0.8145 (pttt) cc_final: 0.7651 (ptpp) REVERT: B 372 GLU cc_start: 0.8057 (tt0) cc_final: 0.7677 (tt0) REVERT: C 311 LYS cc_start: 0.8341 (OUTLIER) cc_final: 0.7658 (mttt) REVERT: C 329 HIS cc_start: 0.8363 (t-90) cc_final: 0.7568 (m90) REVERT: C 343 LYS cc_start: 0.8380 (mttm) cc_final: 0.7873 (mtmt) REVERT: C 347 LYS cc_start: 0.8473 (mttp) cc_final: 0.8016 (mptt) REVERT: D 311 LYS cc_start: 0.8409 (mtmt) cc_final: 0.7653 (tttt) REVERT: D 328 ILE cc_start: 0.9268 (OUTLIER) cc_final: 0.8996 (mp) REVERT: E 329 HIS cc_start: 0.8541 (t70) cc_final: 0.7766 (m-70) REVERT: E 343 LYS cc_start: 0.8442 (mttm) cc_final: 0.8082 (mtmm) REVERT: E 347 LYS cc_start: 0.8270 (mttt) cc_final: 0.7827 (mptp) REVERT: F 311 LYS cc_start: 0.8271 (mtmt) cc_final: 0.7516 (tttt) REVERT: F 349 ARG cc_start: 0.8139 (OUTLIER) cc_final: 0.7820 (ptp-170) outliers start: 16 outliers final: 12 residues processed: 106 average time/residue: 1.4492 time to fit residues: 157.0949 Evaluate side-chains 113 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 97 time to evaluate : 0.391 ------------------------------------------------------------------------------- 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 30 optimal weight: 9.9990 chunk 35 optimal weight: 6.9990 chunk 21 optimal weight: 8.9990 chunk 7 optimal weight: 0.9990 chunk 29 optimal weight: 3.9990 chunk 16 optimal weight: 10.0000 chunk 22 optimal weight: 2.9990 chunk 40 optimal weight: 9.9990 chunk 23 optimal weight: 0.7980 chunk 15 optimal weight: 10.0000 chunk 10 optimal weight: 20.0000 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 351 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.123616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.095341 restraints weight = 3850.343| |-----------------------------------------------------------------------------| r_work (start): 0.3401 rms_B_bonded: 1.94 r_work: 0.3284 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3179 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8657 moved from start: 0.3128 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= 0.146 Angle : 0.548 6.001 4680 Z= 0.278 Chirality : 0.047 0.126 528 Planarity : 0.002 0.020 594 Dihedral : 6.285 48.860 469 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 4.80 % Allowed : 19.70 % 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: -1.94 (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 0.009 0.002 TYR A 310 ARG 0.001 0.000 ARG F 349 Details of bonding type rmsd hydrogen bonds : bond 0.01933 ( 67) hydrogen bonds : angle 5.10609 ( 201) covalent geometry : bond 0.00333 ( 3498) covalent geometry : angle 0.54750 ( 4680) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3776.58 seconds wall clock time: 65 minutes 48.71 seconds (3948.71 seconds total)