Starting phenix.real_space_refine on Fri Aug 22 13:52:06 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8byn_16329/08_2025/8byn_16329.cif Found real_map, /net/cci-nas-00/data/ceres_data/8byn_16329/08_2025/8byn_16329.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8byn_16329/08_2025/8byn_16329.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8byn_16329/08_2025/8byn_16329.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8byn_16329/08_2025/8byn_16329.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8byn_16329/08_2025/8byn_16329.map" } resolution = 2.6 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.001 sd= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 6 5.16 5 C 2256 2.51 5 N 654 2.21 5 O 642 1.98 5 F 6 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 3564 Number of models: 1 Model: "" Number of chains: 10 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} Chain: "A" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 20 Unusual residues: {'S9C': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 20 Unusual residues: {'S9C': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 40 Unusual residues: {'S9C': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 40 Unusual residues: {'S9C': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 1.10, per 1000 atoms: 0.31 Number of scatterers: 3564 At special positions: 0 Unit cell: (122.776, 142.552, 43.672, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 6 16.00 F 6 9.00 O 642 8.00 N 654 7.00 C 2256 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: 0.28 Conformation dependent library (CDL) restraints added in 134.3 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 792 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 18 sheets defined 0.0% alpha, 49.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.17 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'C' and resid 306 through 310 Processing sheet with id=AA2, first strand: chain 'C' and resid 313 through 314 removed outlier: 6.712A pdb=" N VAL A 313 " --> pdb=" O ASP C 314 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 317 through 322 removed outlier: 6.362A pdb=" N LYS A 317 " --> pdb=" O VAL C 318 " (cutoff:3.500A) removed outlier: 7.978A pdb=" N SER C 320 " --> pdb=" O LYS A 317 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N THR A 319 " --> pdb=" O SER C 320 " (cutoff:3.500A) removed outlier: 8.554A pdb=" N CYS C 322 " --> pdb=" O THR A 319 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N LYS A 321 " --> pdb=" O CYS C 322 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 325 through 330 removed outlier: 8.504A pdb=" N LEU A 325 " --> pdb=" O GLY C 326 " (cutoff:3.500A) removed outlier: 9.402A pdb=" N ILE C 328 " --> pdb=" O LEU A 325 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N ASN A 327 " --> pdb=" O ILE C 328 " (cutoff:3.500A) removed outlier: 7.906A pdb=" N HIS C 330 " --> pdb=" O ASN A 327 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N HIS A 329 " --> pdb=" O HIS C 330 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N GLY A 326 " --> pdb=" O ASN E 327 " (cutoff:3.500A) removed outlier: 8.499A pdb=" N HIS E 329 " --> pdb=" O GLY A 326 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N ILE A 328 " --> pdb=" O HIS E 329 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 337 through 340 removed outlier: 6.435A pdb=" N VAL A 337 " --> pdb=" O GLU E 338 " (cutoff:3.500A) removed outlier: 7.903A pdb=" N LYS E 340 " --> pdb=" O VAL A 337 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N VAL A 339 " --> pdb=" O LYS E 340 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 345 through 346 removed outlier: 6.184A pdb=" N ASP A 345 " --> pdb=" O PHE C 346 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 350 through 357 removed outlier: 6.419A pdb=" N GLN A 351 " --> pdb=" O SER C 352 " (cutoff:3.500A) removed outlier: 8.036A pdb=" N ILE C 354 " --> pdb=" O GLN A 351 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N LYS A 353 " --> pdb=" O ILE C 354 " (cutoff:3.500A) removed outlier: 7.393A pdb=" N SER C 356 " --> pdb=" O LYS A 353 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N GLY A 355 " --> pdb=" O SER C 356 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 360 through 362 removed outlier: 6.390A pdb=" N THR A 361 " --> pdb=" O HIS E 362 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 369 through 378 removed outlier: 6.241A pdb=" N LYS A 370 " --> pdb=" O ILE E 371 " (cutoff:3.500A) removed outlier: 8.053A pdb=" N THR E 373 " --> pdb=" O LYS A 370 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N GLU A 372 " --> pdb=" O THR E 373 " (cutoff:3.500A) removed outlier: 8.391A pdb=" N LYS E 375 " --> pdb=" O GLU A 372 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N HIS A 374 " --> pdb=" O LYS E 375 " (cutoff:3.500A) removed outlier: 7.902A pdb=" N THR E 377 " --> pdb=" O HIS A 374 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N LEU A 376 " --> pdb=" O THR E 377 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 306 through 310 removed outlier: 6.264A pdb=" N VAL B 306 " --> pdb=" O GLN F 307 " (cutoff:3.500A) removed outlier: 7.913A pdb=" N VAL F 309 " --> pdb=" O VAL B 306 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N ILE B 308 " --> pdb=" O VAL F 309 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 313 through 314 removed outlier: 6.715A 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 322 removed outlier: 6.364A pdb=" N LYS B 317 " --> pdb=" O VAL D 318 " (cutoff:3.500A) removed outlier: 7.978A pdb=" N SER D 320 " --> pdb=" O LYS B 317 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N THR B 319 " --> pdb=" O SER D 320 " (cutoff:3.500A) removed outlier: 8.553A pdb=" N CYS D 322 " --> pdb=" O THR B 319 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N LYS B 321 " --> pdb=" O CYS D 322 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 325 through 330 removed outlier: 6.756A pdb=" N GLY D 326 " --> pdb=" O LEU B 325 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N ASN B 327 " --> pdb=" O GLY D 326 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N GLY B 326 " --> pdb=" O ASN F 327 " (cutoff:3.500A) removed outlier: 8.525A pdb=" N HIS F 329 " --> pdb=" O GLY B 326 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N ILE B 328 " --> pdb=" O HIS F 329 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 337 through 340 removed outlier: 6.466A pdb=" N VAL B 337 " --> pdb=" O GLU F 338 " (cutoff:3.500A) removed outlier: 7.935A pdb=" N LYS F 340 " --> pdb=" O VAL B 337 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N VAL B 339 " --> pdb=" O LYS F 340 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 345 through 346 removed outlier: 6.201A pdb=" N ASP B 345 " --> pdb=" O PHE D 346 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 350 through 357 removed outlier: 6.397A pdb=" N GLN B 351 " --> pdb=" O SER D 352 " (cutoff:3.500A) removed outlier: 8.012A pdb=" N ILE D 354 " --> pdb=" O GLN B 351 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N LYS B 353 " --> pdb=" O ILE D 354 " (cutoff:3.500A) removed outlier: 7.373A pdb=" N SER D 356 " --> pdb=" O LYS B 353 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N GLY B 355 " --> pdb=" O SER D 356 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 360 through 362 removed outlier: 6.387A pdb=" N THR B 361 " --> pdb=" O HIS F 362 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 369 through 378 removed outlier: 6.270A pdb=" N LYS B 370 " --> pdb=" O ILE F 371 " (cutoff:3.500A) removed outlier: 8.083A pdb=" N THR F 373 " --> pdb=" O LYS B 370 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N GLU B 372 " --> pdb=" O THR F 373 " (cutoff:3.500A) removed outlier: 8.417A pdb=" N LYS F 375 " --> pdb=" O GLU B 372 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N HIS B 374 " --> pdb=" O LYS F 375 " (cutoff:3.500A) removed outlier: 7.929A pdb=" N THR F 377 " --> pdb=" O HIS B 374 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N LEU B 376 " --> pdb=" O THR F 377 " (cutoff:3.500A) 71 hydrogen bonds defined for protein. 213 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: 0.49 Time building geometry restraints manager: 0.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1164 1.34 - 1.45: 448 1.45 - 1.57: 2018 1.57 - 1.68: 0 1.68 - 1.80: 6 Bond restraints: 3636 Sorted by residual: bond pdb=" C15 S9C F 501 " pdb=" C16 S9C F 501 " ideal model delta sigma weight residual 1.386 1.317 0.069 2.00e-02 2.50e+03 1.18e+01 bond pdb=" C15 S9C E 501 " pdb=" C16 S9C E 501 " ideal model delta sigma weight residual 1.386 1.317 0.069 2.00e-02 2.50e+03 1.18e+01 bond pdb=" C15 S9C B 501 " pdb=" C16 S9C B 501 " ideal model delta sigma weight residual 1.386 1.318 0.068 2.00e-02 2.50e+03 1.17e+01 bond pdb=" C15 S9C A 501 " pdb=" C16 S9C A 501 " ideal model delta sigma weight residual 1.386 1.318 0.068 2.00e-02 2.50e+03 1.16e+01 bond pdb=" C15 S9C F 502 " pdb=" C16 S9C F 502 " ideal model delta sigma weight residual 1.386 1.318 0.068 2.00e-02 2.50e+03 1.16e+01 ... (remaining 3631 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.28: 4470 1.28 - 2.56: 293 2.56 - 3.84: 97 3.84 - 5.12: 12 5.12 - 6.40: 6 Bond angle restraints: 4878 Sorted by residual: angle pdb=" C TYR F 310 " pdb=" N LYS F 311 " pdb=" CA LYS F 311 " ideal model delta sigma weight residual 122.89 118.48 4.41 1.12e+00 7.97e-01 1.55e+01 angle pdb=" C TYR E 310 " pdb=" N LYS E 311 " pdb=" CA LYS E 311 " ideal model delta sigma weight residual 122.89 118.57 4.32 1.12e+00 7.97e-01 1.49e+01 angle pdb=" C TYR A 310 " pdb=" N LYS A 311 " pdb=" CA LYS A 311 " ideal model delta sigma weight residual 122.89 118.61 4.28 1.12e+00 7.97e-01 1.46e+01 angle pdb=" C TYR C 310 " pdb=" N LYS C 311 " pdb=" CA LYS C 311 " ideal model delta sigma weight residual 122.89 118.66 4.23 1.12e+00 7.97e-01 1.43e+01 angle pdb=" C TYR D 310 " pdb=" N LYS D 311 " pdb=" CA LYS D 311 " ideal model delta sigma weight residual 122.89 118.73 4.16 1.12e+00 7.97e-01 1.38e+01 ... (remaining 4873 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.91: 1858 15.91 - 31.83: 194 31.83 - 47.74: 102 47.74 - 63.65: 0 63.65 - 79.56: 6 Dihedral angle restraints: 2160 sinusoidal: 918 harmonic: 1242 Sorted by residual: dihedral pdb=" CA ILE E 360 " pdb=" C ILE E 360 " pdb=" N THR E 361 " pdb=" CA THR E 361 " ideal model delta harmonic sigma weight residual 180.00 161.99 18.01 0 5.00e+00 4.00e-02 1.30e+01 dihedral pdb=" CA ILE F 360 " pdb=" C ILE F 360 " pdb=" N THR F 361 " pdb=" CA THR F 361 " ideal model delta harmonic sigma weight residual 180.00 162.00 18.00 0 5.00e+00 4.00e-02 1.30e+01 dihedral pdb=" CA ILE B 360 " pdb=" C ILE B 360 " pdb=" N THR B 361 " pdb=" CA THR B 361 " ideal model delta harmonic sigma weight residual 180.00 162.00 18.00 0 5.00e+00 4.00e-02 1.30e+01 ... (remaining 2157 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 261 0.026 - 0.051: 140 0.051 - 0.077: 37 0.077 - 0.102: 55 0.102 - 0.128: 35 Chirality restraints: 528 Sorted by residual: chirality pdb=" CA ILE E 328 " pdb=" N ILE E 328 " pdb=" C ILE E 328 " pdb=" CB ILE E 328 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.10e-01 chirality pdb=" CA ILE C 328 " pdb=" N ILE C 328 " pdb=" C ILE C 328 " pdb=" CB ILE C 328 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.06e-01 chirality pdb=" CA ILE B 328 " pdb=" N ILE B 328 " pdb=" C ILE B 328 " pdb=" CB ILE B 328 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.03e-01 ... (remaining 525 not shown) Planarity restraints: 606 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1 S9C E 502 " 0.001 2.00e-02 2.50e+03 5.96e-03 1.24e+00 pdb=" C10 S9C E 502 " -0.000 2.00e-02 2.50e+03 pdb=" C11 S9C E 502 " -0.016 2.00e-02 2.50e+03 pdb=" C12 S9C E 502 " -0.001 2.00e-02 2.50e+03 pdb=" C2 S9C E 502 " 0.001 2.00e-02 2.50e+03 pdb=" C3 S9C E 502 " 0.001 2.00e-02 2.50e+03 pdb=" C4 S9C E 502 " -0.000 2.00e-02 2.50e+03 pdb=" C5 S9C E 502 " 0.004 2.00e-02 2.50e+03 pdb=" C6 S9C E 502 " 0.014 2.00e-02 2.50e+03 pdb=" C7 S9C E 502 " 0.002 2.00e-02 2.50e+03 pdb=" C8 S9C E 502 " 0.001 2.00e-02 2.50e+03 pdb=" C9 S9C E 502 " -0.004 2.00e-02 2.50e+03 pdb=" N1 S9C E 502 " -0.001 2.00e-02 2.50e+03 pdb=" N2 S9C E 502 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1 S9C F 501 " -0.001 2.00e-02 2.50e+03 5.95e-03 1.24e+00 pdb=" C10 S9C F 501 " 0.001 2.00e-02 2.50e+03 pdb=" C11 S9C F 501 " 0.017 2.00e-02 2.50e+03 pdb=" C12 S9C F 501 " 0.001 2.00e-02 2.50e+03 pdb=" C2 S9C F 501 " -0.001 2.00e-02 2.50e+03 pdb=" C3 S9C F 501 " -0.001 2.00e-02 2.50e+03 pdb=" C4 S9C F 501 " 0.000 2.00e-02 2.50e+03 pdb=" C5 S9C F 501 " -0.005 2.00e-02 2.50e+03 pdb=" C6 S9C F 501 " -0.013 2.00e-02 2.50e+03 pdb=" C7 S9C F 501 " -0.001 2.00e-02 2.50e+03 pdb=" C8 S9C F 501 " -0.002 2.00e-02 2.50e+03 pdb=" C9 S9C F 501 " 0.004 2.00e-02 2.50e+03 pdb=" N1 S9C F 501 " 0.000 2.00e-02 2.50e+03 pdb=" N2 S9C F 501 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1 S9C E 501 " 0.002 2.00e-02 2.50e+03 5.94e-03 1.24e+00 pdb=" C10 S9C E 501 " -0.001 2.00e-02 2.50e+03 pdb=" C11 S9C E 501 " -0.016 2.00e-02 2.50e+03 pdb=" C12 S9C E 501 " -0.001 2.00e-02 2.50e+03 pdb=" C2 S9C E 501 " 0.001 2.00e-02 2.50e+03 pdb=" C3 S9C E 501 " 0.001 2.00e-02 2.50e+03 pdb=" C4 S9C E 501 " -0.000 2.00e-02 2.50e+03 pdb=" C5 S9C E 501 " 0.004 2.00e-02 2.50e+03 pdb=" C6 S9C E 501 " 0.013 2.00e-02 2.50e+03 pdb=" C7 S9C E 501 " 0.001 2.00e-02 2.50e+03 pdb=" C8 S9C E 501 " 0.002 2.00e-02 2.50e+03 pdb=" C9 S9C E 501 " -0.004 2.00e-02 2.50e+03 pdb=" N1 S9C E 501 " -0.000 2.00e-02 2.50e+03 pdb=" N2 S9C E 501 " -0.001 2.00e-02 2.50e+03 ... (remaining 603 not shown) Histogram of nonbonded interaction distances: 2.42 - 2.91: 1348 2.91 - 3.41: 2690 3.41 - 3.91: 6468 3.91 - 4.40: 6153 4.40 - 4.90: 12280 Nonbonded interactions: 28939 Sorted by model distance: nonbonded pdb=" OD2 ASP F 314 " pdb=" NZ LYS F 370 " model vdw 2.417 3.120 nonbonded pdb=" OD2 ASP E 314 " pdb=" NZ LYS E 370 " model vdw 2.418 3.120 nonbonded pdb=" OD2 ASP C 314 " pdb=" NZ LYS C 370 " model vdw 2.418 3.120 nonbonded pdb=" OD2 ASP D 314 " pdb=" NZ LYS D 370 " model vdw 2.418 3.120 nonbonded pdb=" OD2 ASP B 314 " pdb=" NZ LYS B 370 " model vdw 2.418 3.120 ... (remaining 28934 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' } ncs_group { reference = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.000 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: 0.100 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 5.480 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8867 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 : 0.009 0.069 3636 Z= 0.450 Angle : 0.793 6.403 4878 Z= 0.421 Chirality : 0.051 0.128 528 Planarity : 0.004 0.022 606 Dihedral : 15.402 79.561 1368 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.93 (0.33), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.46 (0.25), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.003 ARG F 349 TYR 0.007 0.002 TYR C 310 PHE 0.006 0.002 PHE B 346 HIS 0.003 0.001 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00949 ( 3636) covalent geometry : angle 0.79301 ( 4878) hydrogen bonds : bond 0.10717 ( 71) hydrogen bonds : angle 7.81384 ( 213) *********************** 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 143 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 143 time to evaluate : 0.155 Fit side-chains REVERT: D 342 GLU cc_start: 0.7990 (tt0) cc_final: 0.7771 (tt0) REVERT: E 311 LYS cc_start: 0.8492 (mttt) cc_final: 0.8250 (mmtm) REVERT: F 311 LYS cc_start: 0.8401 (mttt) cc_final: 0.8110 (mmtm) outliers start: 0 outliers final: 0 residues processed: 143 average time/residue: 0.9278 time to fit residues: 134.8884 Evaluate side-chains 83 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 83 time to evaluate : 0.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 24 optimal weight: 0.0170 chunk 26 optimal weight: 0.7980 chunk 2 optimal weight: 0.9990 chunk 16 optimal weight: 6.9990 chunk 32 optimal weight: 9.9990 chunk 31 optimal weight: 1.9990 chunk 25 optimal weight: 6.9990 chunk 19 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 22 optimal weight: 10.0000 chunk 37 optimal weight: 5.9990 overall best weight: 1.1624 ------------------------------------------------------------------------------- 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 = 0.3666 r_free = 0.3666 target = 0.126201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.106844 restraints weight = 3778.687| |-----------------------------------------------------------------------------| r_work (start): 0.3355 rms_B_bonded: 1.28 r_work: 0.3245 rms_B_bonded: 1.59 restraints_weight: 0.5000 r_work: 0.3155 rms_B_bonded: 2.67 restraints_weight: 0.2500 r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9042 moved from start: 0.1802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 3636 Z= 0.092 Angle : 0.462 4.713 4878 Z= 0.236 Chirality : 0.050 0.127 528 Planarity : 0.004 0.030 606 Dihedral : 7.511 30.997 486 Min Nonbonded Distance : 2.640 Molprobity Statistics. All-atom Clashscore : 2.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 0.51 % Allowed : 16.92 % Favored : 82.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.84 (0.33), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.39 (0.25), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.002 ARG D 349 TYR 0.009 0.002 TYR A 310 PHE 0.006 0.001 PHE F 346 HIS 0.002 0.000 HIS C 374 Details of bonding type rmsd covalent geometry : bond 0.00205 ( 3636) covalent geometry : angle 0.46220 ( 4878) hydrogen bonds : bond 0.01964 ( 71) hydrogen bonds : angle 5.72248 ( 213) *********************** 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 93 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 91 time to evaluate : 0.142 Fit side-chains REVERT: C 314 ASP cc_start: 0.9168 (t0) cc_final: 0.8929 (t0) REVERT: D 340 LYS cc_start: 0.8555 (tttm) cc_final: 0.8326 (mtpt) outliers start: 2 outliers final: 0 residues processed: 91 average time/residue: 0.7806 time to fit residues: 72.4956 Evaluate side-chains 79 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 79 time to evaluate : 0.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 0.0170 chunk 36 optimal weight: 10.0000 chunk 33 optimal weight: 10.0000 chunk 40 optimal weight: 5.9990 chunk 39 optimal weight: 1.9990 chunk 27 optimal weight: 3.9990 chunk 38 optimal weight: 9.9990 chunk 25 optimal weight: 8.9990 chunk 41 optimal weight: 9.9990 chunk 16 optimal weight: 10.0000 chunk 30 optimal weight: 3.9990 overall best weight: 3.2026 ------------------------------------------------------------------------------- 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 = 0.3588 r_free = 0.3588 target = 0.120373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.100325 restraints weight = 3715.053| |-----------------------------------------------------------------------------| r_work (start): 0.3285 rms_B_bonded: 1.26 r_work: 0.3164 rms_B_bonded: 1.61 restraints_weight: 0.5000 r_work: 0.3071 rms_B_bonded: 2.68 restraints_weight: 0.2500 r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9112 moved from start: 0.1763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 3636 Z= 0.161 Angle : 0.501 4.607 4878 Z= 0.257 Chirality : 0.050 0.135 528 Planarity : 0.004 0.043 606 Dihedral : 8.307 35.018 486 Min Nonbonded Distance : 2.643 Molprobity Statistics. All-atom Clashscore : 2.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 1.77 % Allowed : 19.70 % Favored : 78.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.77 (0.33), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.34 (0.25), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.002 ARG D 349 TYR 0.010 0.002 TYR A 310 PHE 0.007 0.001 PHE F 346 HIS 0.002 0.001 HIS C 374 Details of bonding type rmsd covalent geometry : bond 0.00363 ( 3636) covalent geometry : angle 0.50065 ( 4878) hydrogen bonds : bond 0.01996 ( 71) hydrogen bonds : angle 5.39053 ( 213) *********************** 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 87 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 80 time to evaluate : 0.172 Fit side-chains REVERT: B 338 GLU cc_start: 0.8547 (OUTLIER) cc_final: 0.8157 (tm-30) REVERT: D 338 GLU cc_start: 0.8670 (tt0) cc_final: 0.8248 (tm-30) outliers start: 7 outliers final: 0 residues processed: 82 average time/residue: 0.8195 time to fit residues: 68.6802 Evaluate side-chains 86 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 85 time to evaluate : 0.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 338 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 0 optimal weight: 10.0000 chunk 19 optimal weight: 10.0000 chunk 17 optimal weight: 9.9990 chunk 21 optimal weight: 8.9990 chunk 39 optimal weight: 0.0980 chunk 3 optimal weight: 4.9990 chunk 22 optimal weight: 0.5980 chunk 10 optimal weight: 10.0000 chunk 26 optimal weight: 10.0000 chunk 5 optimal weight: 6.9990 chunk 27 optimal weight: 2.9990 overall best weight: 3.1386 ------------------------------------------------------------------------------- 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 = 0.3592 r_free = 0.3592 target = 0.120514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.100503 restraints weight = 3706.599| |-----------------------------------------------------------------------------| r_work (start): 0.3290 rms_B_bonded: 1.27 r_work: 0.3171 rms_B_bonded: 1.60 restraints_weight: 0.5000 r_work: 0.3078 rms_B_bonded: 2.68 restraints_weight: 0.2500 r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9111 moved from start: 0.1849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.022 3636 Z= 0.156 Angle : 0.500 4.576 4878 Z= 0.256 Chirality : 0.049 0.128 528 Planarity : 0.004 0.046 606 Dihedral : 8.181 33.986 486 Min Nonbonded Distance : 2.640 Molprobity Statistics. All-atom Clashscore : 2.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 2.02 % Allowed : 19.95 % Favored : 78.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.77 (0.33), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.34 (0.26), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.002 ARG D 349 TYR 0.010 0.002 TYR A 310 PHE 0.006 0.001 PHE F 346 HIS 0.002 0.001 HIS C 374 Details of bonding type rmsd covalent geometry : bond 0.00352 ( 3636) covalent geometry : angle 0.50049 ( 4878) hydrogen bonds : bond 0.01775 ( 71) hydrogen bonds : angle 5.20228 ( 213) *********************** 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 95 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 87 time to evaluate : 0.168 Fit side-chains REVERT: B 338 GLU cc_start: 0.8597 (OUTLIER) cc_final: 0.8226 (tm-30) REVERT: D 338 GLU cc_start: 0.8688 (tt0) cc_final: 0.8247 (tm-30) REVERT: E 311 LYS cc_start: 0.8831 (mttt) cc_final: 0.8066 (mmtm) outliers start: 8 outliers final: 4 residues processed: 92 average time/residue: 0.8155 time to fit residues: 76.5204 Evaluate side-chains 84 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 79 time to evaluate : 0.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 331 LYS Chi-restraints excluded: chain B residue 338 GLU Chi-restraints excluded: chain D residue 331 LYS Chi-restraints excluded: chain F residue 331 LYS Chi-restraints excluded: chain F residue 351 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 34 optimal weight: 0.0980 chunk 1 optimal weight: 20.0000 chunk 0 optimal weight: 10.0000 chunk 20 optimal weight: 9.9990 chunk 4 optimal weight: 9.9990 chunk 23 optimal weight: 4.9990 chunk 2 optimal weight: 10.0000 chunk 13 optimal weight: 9.9990 chunk 30 optimal weight: 0.9990 chunk 35 optimal weight: 4.9990 chunk 37 optimal weight: 9.9990 overall best weight: 4.2188 ------------------------------------------------------------------------------- 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 = 0.3566 r_free = 0.3566 target = 0.118779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.098695 restraints weight = 3707.068| |-----------------------------------------------------------------------------| r_work (start): 0.3263 rms_B_bonded: 1.26 r_work: 0.3143 rms_B_bonded: 1.60 restraints_weight: 0.5000 r_work: 0.3049 rms_B_bonded: 2.67 restraints_weight: 0.2500 r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9124 moved from start: 0.1855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.028 3636 Z= 0.199 Angle : 0.530 4.607 4878 Z= 0.272 Chirality : 0.049 0.130 528 Planarity : 0.005 0.051 606 Dihedral : 8.654 36.180 486 Min Nonbonded Distance : 2.637 Molprobity Statistics. All-atom Clashscore : 2.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 1.77 % Allowed : 20.71 % Favored : 77.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.78 (0.34), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.35 (0.26), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.002 ARG D 349 TYR 0.011 0.002 TYR A 310 PHE 0.007 0.001 PHE F 346 HIS 0.002 0.001 HIS C 374 Details of bonding type rmsd covalent geometry : bond 0.00454 ( 3636) covalent geometry : angle 0.53011 ( 4878) hydrogen bonds : bond 0.01915 ( 71) hydrogen bonds : angle 5.22496 ( 213) *********************** 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 89 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 82 time to evaluate : 0.159 Fit side-chains REVERT: B 338 GLU cc_start: 0.8632 (OUTLIER) cc_final: 0.8240 (tm-30) REVERT: D 338 GLU cc_start: 0.8702 (tt0) cc_final: 0.8239 (tm-30) REVERT: D 342 GLU cc_start: 0.8635 (tt0) cc_final: 0.8412 (tt0) outliers start: 7 outliers final: 4 residues processed: 86 average time/residue: 0.7569 time to fit residues: 66.4639 Evaluate side-chains 92 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 87 time to evaluate : 0.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 331 LYS Chi-restraints excluded: chain B residue 338 GLU Chi-restraints excluded: chain D residue 331 LYS Chi-restraints excluded: chain F residue 331 LYS Chi-restraints excluded: chain F residue 351 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 34 optimal weight: 2.9990 chunk 32 optimal weight: 9.9990 chunk 16 optimal weight: 5.9990 chunk 28 optimal weight: 0.0670 chunk 33 optimal weight: 7.9990 chunk 27 optimal weight: 8.9990 chunk 39 optimal weight: 9.9990 chunk 19 optimal weight: 0.9990 chunk 8 optimal weight: 10.0000 chunk 18 optimal weight: 8.9990 chunk 25 optimal weight: 7.9990 overall best weight: 3.6126 ------------------------------------------------------------------------------- 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 = 0.3581 r_free = 0.3581 target = 0.119826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.099725 restraints weight = 3704.808| |-----------------------------------------------------------------------------| r_work (start): 0.3275 rms_B_bonded: 1.27 r_work: 0.3156 rms_B_bonded: 1.60 restraints_weight: 0.5000 r_work: 0.3062 rms_B_bonded: 2.67 restraints_weight: 0.2500 r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9118 moved from start: 0.1938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 3636 Z= 0.173 Angle : 0.512 4.556 4878 Z= 0.262 Chirality : 0.049 0.129 528 Planarity : 0.004 0.050 606 Dihedral : 8.372 34.703 486 Min Nonbonded Distance : 2.638 Molprobity Statistics. All-atom Clashscore : 2.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 2.53 % Allowed : 19.70 % Favored : 77.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.81 (0.34), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.37 (0.26), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.002 ARG D 349 TYR 0.010 0.002 TYR A 310 PHE 0.006 0.001 PHE F 346 HIS 0.002 0.001 HIS C 374 Details of bonding type rmsd covalent geometry : bond 0.00391 ( 3636) covalent geometry : angle 0.51223 ( 4878) hydrogen bonds : bond 0.01769 ( 71) hydrogen bonds : angle 5.12507 ( 213) *********************** 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 96 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 86 time to evaluate : 0.097 Fit side-chains REVERT: B 331 LYS cc_start: 0.9031 (OUTLIER) cc_final: 0.8315 (tmtm) REVERT: B 338 GLU cc_start: 0.8642 (OUTLIER) cc_final: 0.8273 (tm-30) REVERT: C 314 ASP cc_start: 0.9172 (t0) cc_final: 0.8932 (t0) REVERT: D 338 GLU cc_start: 0.8699 (tt0) cc_final: 0.8237 (tm-30) REVERT: E 311 LYS cc_start: 0.8831 (mttt) cc_final: 0.8008 (mmtt) outliers start: 10 outliers final: 3 residues processed: 93 average time/residue: 0.8208 time to fit residues: 77.8100 Evaluate side-chains 101 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 96 time to evaluate : 0.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 331 LYS Chi-restraints excluded: chain B residue 331 LYS Chi-restraints excluded: chain B residue 338 GLU Chi-restraints excluded: chain D residue 331 LYS Chi-restraints excluded: chain F residue 331 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 40 optimal weight: 10.0000 chunk 32 optimal weight: 10.0000 chunk 7 optimal weight: 10.0000 chunk 26 optimal weight: 7.9990 chunk 1 optimal weight: 20.0000 chunk 37 optimal weight: 7.9990 chunk 34 optimal weight: 2.9990 chunk 23 optimal weight: 10.0000 chunk 19 optimal weight: 10.0000 chunk 21 optimal weight: 4.9990 chunk 3 optimal weight: 9.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- 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 = 0.3537 r_free = 0.3537 target = 0.116484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.096279 restraints weight = 3815.205| |-----------------------------------------------------------------------------| r_work (start): 0.3205 rms_B_bonded: 1.27 r_work: 0.3085 rms_B_bonded: 1.59 restraints_weight: 0.5000 r_work: 0.2990 rms_B_bonded: 2.64 restraints_weight: 0.2500 r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9141 moved from start: 0.1881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.040 3636 Z= 0.301 Angle : 0.606 5.204 4878 Z= 0.311 Chirality : 0.051 0.137 528 Planarity : 0.005 0.067 606 Dihedral : 9.250 38.854 486 Min Nonbonded Distance : 2.631 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 2.53 % Allowed : 20.45 % Favored : 77.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.84 (0.33), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.40 (0.26), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.002 ARG A 349 TYR 0.013 0.003 TYR C 310 PHE 0.007 0.002 PHE C 378 HIS 0.002 0.001 HIS D 374 Details of bonding type rmsd covalent geometry : bond 0.00697 ( 3636) covalent geometry : angle 0.60561 ( 4878) hydrogen bonds : bond 0.02257 ( 71) hydrogen bonds : angle 5.41000 ( 213) *********************** 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 109 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 99 time to evaluate : 0.213 Fit side-chains REVERT: B 338 GLU cc_start: 0.8701 (OUTLIER) cc_final: 0.8238 (tm-30) REVERT: C 340 LYS cc_start: 0.8660 (tttm) cc_final: 0.8374 (tttp) REVERT: D 338 GLU cc_start: 0.8725 (tt0) cc_final: 0.8229 (tm-30) REVERT: D 342 GLU cc_start: 0.8652 (tt0) cc_final: 0.8425 (tt0) REVERT: E 311 LYS cc_start: 0.8847 (mttt) cc_final: 0.8016 (mmtt) outliers start: 10 outliers final: 3 residues processed: 106 average time/residue: 0.8693 time to fit residues: 93.8690 Evaluate side-chains 85 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 81 time to evaluate : 0.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 331 LYS Chi-restraints excluded: chain B residue 338 GLU Chi-restraints excluded: chain D residue 331 LYS Chi-restraints excluded: chain F residue 331 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 20 optimal weight: 10.0000 chunk 1 optimal weight: 10.0000 chunk 38 optimal weight: 10.0000 chunk 6 optimal weight: 6.9990 chunk 15 optimal weight: 5.9990 chunk 5 optimal weight: 0.9980 chunk 21 optimal weight: 2.9990 chunk 25 optimal weight: 6.9990 chunk 8 optimal weight: 10.0000 chunk 33 optimal weight: 2.9990 chunk 22 optimal weight: 5.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- 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 = 0.3569 r_free = 0.3569 target = 0.118964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.098883 restraints weight = 3765.017| |-----------------------------------------------------------------------------| r_work (start): 0.3250 rms_B_bonded: 1.26 r_work: 0.3132 rms_B_bonded: 1.59 restraints_weight: 0.5000 r_work: 0.3037 rms_B_bonded: 2.65 restraints_weight: 0.2500 r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9122 moved from start: 0.1947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 3636 Z= 0.183 Angle : 0.530 4.525 4878 Z= 0.271 Chirality : 0.049 0.131 528 Planarity : 0.005 0.062 606 Dihedral : 8.557 35.200 486 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 2.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 1.77 % Allowed : 21.46 % Favored : 76.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.84 (0.34), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.40 (0.26), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.002 ARG D 349 TYR 0.011 0.002 TYR C 310 PHE 0.005 0.001 PHE F 346 HIS 0.002 0.001 HIS C 374 Details of bonding type rmsd covalent geometry : bond 0.00414 ( 3636) covalent geometry : angle 0.52968 ( 4878) hydrogen bonds : bond 0.01861 ( 71) hydrogen bonds : angle 5.18511 ( 213) *********************** 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 88 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 81 time to evaluate : 0.133 Fit side-chains REVERT: B 338 GLU cc_start: 0.8678 (OUTLIER) cc_final: 0.8243 (tm-30) REVERT: C 314 ASP cc_start: 0.9177 (t0) cc_final: 0.8974 (t0) REVERT: D 338 GLU cc_start: 0.8713 (tt0) cc_final: 0.8224 (tm-30) REVERT: D 342 GLU cc_start: 0.8627 (tt0) cc_final: 0.8397 (tt0) REVERT: E 331 LYS cc_start: 0.9080 (OUTLIER) cc_final: 0.8540 (tmtm) outliers start: 7 outliers final: 3 residues processed: 87 average time/residue: 0.6894 time to fit residues: 61.2203 Evaluate side-chains 85 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 80 time to evaluate : 0.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 331 LYS Chi-restraints excluded: chain B residue 338 GLU Chi-restraints excluded: chain D residue 331 LYS Chi-restraints excluded: chain E residue 325 LEU Chi-restraints excluded: chain E residue 331 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 33 optimal weight: 7.9990 chunk 9 optimal weight: 2.9990 chunk 24 optimal weight: 10.0000 chunk 26 optimal weight: 7.9990 chunk 32 optimal weight: 7.9990 chunk 20 optimal weight: 10.0000 chunk 28 optimal weight: 0.9990 chunk 18 optimal weight: 2.9990 chunk 41 optimal weight: 6.9990 chunk 14 optimal weight: 8.9990 chunk 31 optimal weight: 2.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- 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 = 0.3580 r_free = 0.3580 target = 0.119609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.099468 restraints weight = 3736.287| |-----------------------------------------------------------------------------| r_work (start): 0.3278 rms_B_bonded: 1.27 r_work: 0.3159 rms_B_bonded: 1.60 restraints_weight: 0.5000 r_work: 0.3066 rms_B_bonded: 2.67 restraints_weight: 0.2500 r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9117 moved from start: 0.1985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.022 3636 Z= 0.167 Angle : 0.522 4.521 4878 Z= 0.267 Chirality : 0.049 0.131 528 Planarity : 0.005 0.063 606 Dihedral : 8.380 34.501 486 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 2.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 1.26 % Allowed : 21.72 % Favored : 77.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.85 (0.34), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.40 (0.26), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.002 ARG D 349 TYR 0.010 0.002 TYR C 310 PHE 0.005 0.001 PHE F 346 HIS 0.002 0.001 HIS C 374 Details of bonding type rmsd covalent geometry : bond 0.00378 ( 3636) covalent geometry : angle 0.52156 ( 4878) hydrogen bonds : bond 0.01763 ( 71) hydrogen bonds : angle 5.10405 ( 213) *********************** 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 85 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 80 time to evaluate : 0.157 Fit side-chains REVERT: B 338 GLU cc_start: 0.8668 (OUTLIER) cc_final: 0.8234 (tm-30) REVERT: C 314 ASP cc_start: 0.9176 (t0) cc_final: 0.8909 (t0) REVERT: D 338 GLU cc_start: 0.8710 (tt0) cc_final: 0.8223 (tm-30) REVERT: D 342 GLU cc_start: 0.8630 (tt0) cc_final: 0.8401 (tt0) REVERT: E 331 LYS cc_start: 0.9074 (OUTLIER) cc_final: 0.8542 (tmtm) outliers start: 5 outliers final: 2 residues processed: 84 average time/residue: 0.6905 time to fit residues: 59.2763 Evaluate side-chains 83 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 79 time to evaluate : 0.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 331 LYS Chi-restraints excluded: chain B residue 338 GLU Chi-restraints excluded: chain E residue 325 LEU Chi-restraints excluded: chain E residue 331 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 15 optimal weight: 9.9990 chunk 10 optimal weight: 10.0000 chunk 27 optimal weight: 9.9990 chunk 28 optimal weight: 1.9990 chunk 40 optimal weight: 10.0000 chunk 5 optimal weight: 10.0000 chunk 3 optimal weight: 10.0000 chunk 23 optimal weight: 2.9990 chunk 20 optimal weight: 7.9990 chunk 13 optimal weight: 2.9990 chunk 38 optimal weight: 0.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- 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 = 0.3581 r_free = 0.3581 target = 0.119719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.099555 restraints weight = 3791.398| |-----------------------------------------------------------------------------| r_work (start): 0.3275 rms_B_bonded: 1.28 r_work: 0.3156 rms_B_bonded: 1.61 restraints_weight: 0.5000 r_work: 0.3062 rms_B_bonded: 2.67 restraints_weight: 0.2500 r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9117 moved from start: 0.2025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.022 3636 Z= 0.166 Angle : 0.514 4.455 4878 Z= 0.263 Chirality : 0.049 0.131 528 Planarity : 0.004 0.051 606 Dihedral : 8.362 34.530 486 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 2.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 1.26 % Allowed : 22.22 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.86 (0.34), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.41 (0.26), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.002 ARG B 349 TYR 0.010 0.002 TYR C 310 PHE 0.005 0.001 PHE F 346 HIS 0.002 0.001 HIS C 374 Details of bonding type rmsd covalent geometry : bond 0.00375 ( 3636) covalent geometry : angle 0.51429 ( 4878) hydrogen bonds : bond 0.01756 ( 71) hydrogen bonds : angle 5.06726 ( 213) ********************** 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 84 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 79 time to evaluate : 0.124 Fit side-chains REVERT: B 338 GLU cc_start: 0.8675 (OUTLIER) cc_final: 0.8242 (tm-30) REVERT: D 338 GLU cc_start: 0.8711 (tt0) cc_final: 0.8223 (tm-30) REVERT: D 342 GLU cc_start: 0.8625 (tt0) cc_final: 0.8397 (tt0) REVERT: D 349 ARG cc_start: 0.8821 (mtt-85) cc_final: 0.8580 (mtt90) REVERT: E 331 LYS cc_start: 0.9077 (OUTLIER) cc_final: 0.8545 (tmtm) outliers start: 5 outliers final: 2 residues processed: 83 average time/residue: 0.6486 time to fit residues: 54.9808 Evaluate side-chains 83 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 79 time to evaluate : 0.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 331 LYS Chi-restraints excluded: chain B residue 338 GLU Chi-restraints excluded: chain E residue 325 LEU Chi-restraints excluded: chain E residue 331 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 7 optimal weight: 10.0000 chunk 23 optimal weight: 9.9990 chunk 8 optimal weight: 9.9990 chunk 2 optimal weight: 4.9990 chunk 36 optimal weight: 5.9990 chunk 14 optimal weight: 10.0000 chunk 27 optimal weight: 7.9990 chunk 38 optimal weight: 8.9990 chunk 37 optimal weight: 5.9990 chunk 18 optimal weight: 0.0470 chunk 28 optimal weight: 10.0000 overall best weight: 5.0086 ------------------------------------------------------------------------------- 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 = 0.3555 r_free = 0.3555 target = 0.117742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.097529 restraints weight = 3743.821| |-----------------------------------------------------------------------------| r_work (start): 0.3231 rms_B_bonded: 1.26 r_work: 0.3112 rms_B_bonded: 1.58 restraints_weight: 0.5000 r_work: 0.3017 rms_B_bonded: 2.64 restraints_weight: 0.2500 r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9130 moved from start: 0.1963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 3636 Z= 0.232 Angle : 0.567 4.569 4878 Z= 0.289 Chirality : 0.050 0.133 528 Planarity : 0.004 0.037 606 Dihedral : 8.904 37.357 486 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 2.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 1.26 % Allowed : 22.22 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.89 (0.34), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.43 (0.26), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.002 ARG C 349 TYR 0.012 0.003 TYR C 310 PHE 0.006 0.002 PHE F 346 HIS 0.002 0.001 HIS C 374 Details of bonding type rmsd covalent geometry : bond 0.00532 ( 3636) covalent geometry : angle 0.56651 ( 4878) hydrogen bonds : bond 0.02011 ( 71) hydrogen bonds : angle 5.20668 ( 213) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2025.49 seconds wall clock time: 35 minutes 18.91 seconds (2118.91 seconds total)