Starting phenix.real_space_refine on Thu Nov 14 03:18:45 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8byn_16329/11_2024/8byn_16329.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8byn_16329/11_2024/8byn_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 { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8byn_16329/11_2024/8byn_16329.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8byn_16329/11_2024/8byn_16329.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8byn_16329/11_2024/8byn_16329.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8byn_16329/11_2024/8byn_16329.cif" } resolution = 2.6 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= 0.001 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): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/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: 2.93, per 1000 atoms: 0.82 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: 0.91 Conformation dependent library (CDL) restraints added in 421.4 milliseconds 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 792 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 18 sheets defined 0.0% alpha, 49.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.53 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'C' and resid 306 through 310 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: 0.85 Time building geometry restraints manager: 1.00 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: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 305 through 379) selection = (chain 'B' and resid 305 through 379) selection = chain 'C' selection = chain 'D' selection = (chain 'E' and resid 305 through 379) selection = (chain 'F' and resid 305 through 379) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.310 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: 0.170 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 13.230 Find NCS groups from input model: 0.160 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:11.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.850 ------------------------------------------------------------------------------- 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= 0.613 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 : 6.44 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 (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: -1.93 (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 HIS 0.003 0.001 HIS A 374 PHE 0.006 0.002 PHE B 346 TYR 0.007 0.002 TYR C 310 ARG 0.010 0.003 ARG F 349 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 143 time to evaluate : 0.414 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: 1.8686 time to fit residues: 271.8964 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 : 0.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 2.9990 chunk 31 optimal weight: 20.0000 chunk 17 optimal weight: 10.0000 chunk 10 optimal weight: 9.9990 chunk 21 optimal weight: 6.9990 chunk 32 optimal weight: 3.9990 chunk 12 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 24 optimal weight: 9.9990 chunk 38 optimal weight: 5.9990 chunk 11 optimal weight: 4.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8894 moved from start: 0.1719 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= 0.243 Angle : 0.508 4.854 4878 Z= 0.262 Chirality : 0.051 0.148 528 Planarity : 0.004 0.033 606 Dihedral : 8.152 33.205 486 Min Nonbonded Distance : 2.641 Molprobity Statistics. All-atom Clashscore : 2.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 1.01 % Allowed : 16.92 % Favored : 82.07 % 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: -1.82 (0.33), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.38 (0.25), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 374 PHE 0.008 0.001 PHE F 346 TYR 0.011 0.002 TYR A 310 ARG 0.008 0.002 ARG D 349 *********************** 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 90 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 86 time to evaluate : 0.428 Fit side-chains REVERT: C 314 ASP cc_start: 0.8687 (t0) cc_final: 0.8485 (t0) outliers start: 4 outliers final: 0 residues processed: 87 average time/residue: 1.6179 time to fit residues: 143.9425 Evaluate side-chains 78 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 78 time to evaluate : 0.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 31 optimal weight: 10.0000 chunk 25 optimal weight: 1.9990 chunk 10 optimal weight: 9.9990 chunk 38 optimal weight: 1.9990 chunk 41 optimal weight: 0.0980 chunk 34 optimal weight: 0.0470 chunk 37 optimal weight: 0.8980 chunk 13 optimal weight: 0.9980 chunk 30 optimal weight: 5.9990 chunk 28 optimal weight: 0.8980 chunk 19 optimal weight: 7.9990 overall best weight: 0.5878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8817 moved from start: 0.2136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.016 3636 Z= 0.090 Angle : 0.430 4.336 4878 Z= 0.220 Chirality : 0.049 0.129 528 Planarity : 0.004 0.041 606 Dihedral : 6.562 27.457 486 Min Nonbonded Distance : 2.644 Molprobity Statistics. All-atom Clashscore : 2.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 0.76 % Allowed : 20.20 % Favored : 79.04 % 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: -1.76 (0.33), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.33 (0.25), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS C 374 PHE 0.003 0.001 PHE F 346 TYR 0.007 0.001 TYR A 310 ARG 0.009 0.002 ARG D 349 *********************** 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 92 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 89 time to evaluate : 0.517 Fit side-chains outliers start: 3 outliers final: 1 residues processed: 91 average time/residue: 1.4651 time to fit residues: 136.6112 Evaluate side-chains 79 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 78 time to evaluate : 0.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 331 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 4 optimal weight: 9.9990 chunk 18 optimal weight: 1.9990 chunk 25 optimal weight: 9.9990 chunk 38 optimal weight: 9.9990 chunk 40 optimal weight: 9.9990 chunk 20 optimal weight: 9.9990 chunk 36 optimal weight: 9.9990 chunk 10 optimal weight: 5.9990 chunk 33 optimal weight: 10.0000 chunk 23 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8942 moved from start: 0.1822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.045 3636 Z= 0.525 Angle : 0.608 6.326 4878 Z= 0.310 Chirality : 0.051 0.137 528 Planarity : 0.004 0.044 606 Dihedral : 9.179 39.414 486 Min Nonbonded Distance : 2.639 Molprobity Statistics. All-atom Clashscore : 3.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 1.52 % Allowed : 21.72 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.80 (0.33), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.36 (0.25), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS C 374 PHE 0.008 0.002 PHE F 346 TYR 0.013 0.003 TYR C 310 ARG 0.010 0.002 ARG A 349 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 80 time to evaluate : 0.403 Fit side-chains REVERT: C 375 LYS cc_start: 0.8630 (OUTLIER) cc_final: 0.8401 (tttp) REVERT: D 342 GLU cc_start: 0.7972 (tt0) cc_final: 0.7756 (tt0) outliers start: 6 outliers final: 2 residues processed: 85 average time/residue: 1.7446 time to fit residues: 151.4131 Evaluate side-chains 82 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 79 time to evaluate : 0.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 331 LYS Chi-restraints excluded: chain C residue 375 LYS Chi-restraints excluded: chain D residue 331 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 30 optimal weight: 5.9990 chunk 16 optimal weight: 0.8980 chunk 34 optimal weight: 3.9990 chunk 28 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 20 optimal weight: 0.7980 chunk 36 optimal weight: 9.9990 chunk 10 optimal weight: 4.9990 chunk 13 optimal weight: 6.9990 chunk 8 optimal weight: 6.9990 chunk 23 optimal weight: 2.9990 overall best weight: 2.7386 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8906 moved from start: 0.1971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 3636 Z= 0.216 Angle : 0.489 4.509 4878 Z= 0.250 Chirality : 0.049 0.127 528 Planarity : 0.004 0.052 606 Dihedral : 8.170 33.922 486 Min Nonbonded Distance : 2.641 Molprobity Statistics. All-atom Clashscore : 2.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 2.02 % Allowed : 21.46 % 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: -1.80 (0.33), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.37 (0.25), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 374 PHE 0.005 0.001 PHE F 346 TYR 0.010 0.002 TYR A 310 ARG 0.012 0.002 ARG D 349 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 79 time to evaluate : 0.461 Fit side-chains outliers start: 8 outliers final: 3 residues processed: 84 average time/residue: 1.6146 time to fit residues: 138.7901 Evaluate side-chains 90 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 87 time to evaluate : 0.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 331 LYS Chi-restraints excluded: chain D residue 331 LYS Chi-restraints excluded: chain F residue 331 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 10 optimal weight: 10.0000 chunk 40 optimal weight: 10.0000 chunk 33 optimal weight: 10.0000 chunk 18 optimal weight: 4.9990 chunk 3 optimal weight: 9.9990 chunk 13 optimal weight: 10.0000 chunk 21 optimal weight: 5.9990 chunk 39 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 23 optimal weight: 0.2980 chunk 29 optimal weight: 6.9990 overall best weight: 3.4588 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8917 moved from start: 0.1977 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= 0.266 Angle : 0.510 4.531 4878 Z= 0.261 Chirality : 0.049 0.129 528 Planarity : 0.004 0.051 606 Dihedral : 8.384 34.849 486 Min Nonbonded Distance : 2.640 Molprobity Statistics. All-atom Clashscore : 2.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 1.52 % Allowed : 21.46 % 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 (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: -1.83 (0.34), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.39 (0.26), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 374 PHE 0.006 0.001 PHE F 346 TYR 0.010 0.002 TYR A 310 ARG 0.012 0.002 ARG D 349 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 90 time to evaluate : 0.446 Fit side-chains REVERT: D 342 GLU cc_start: 0.7934 (tt0) cc_final: 0.7718 (tt0) REVERT: E 311 LYS cc_start: 0.8420 (mttt) cc_final: 0.7890 (mmtt) outliers start: 6 outliers final: 4 residues processed: 95 average time/residue: 1.6627 time to fit residues: 161.3240 Evaluate side-chains 92 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 88 time to evaluate : 0.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 331 LYS Chi-restraints excluded: chain D residue 331 LYS Chi-restraints excluded: chain D residue 348 ASP 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 22 optimal weight: 10.0000 chunk 34 optimal weight: 4.9990 chunk 40 optimal weight: 10.0000 chunk 25 optimal weight: 10.0000 chunk 24 optimal weight: 5.9990 chunk 18 optimal weight: 5.9990 chunk 16 optimal weight: 4.9990 chunk 12 optimal weight: 4.9990 chunk 7 optimal weight: 10.0000 chunk 27 optimal weight: 5.9990 chunk 20 optimal weight: 8.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8934 moved from start: 0.1951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.034 3636 Z= 0.398 Angle : 0.569 4.888 4878 Z= 0.291 Chirality : 0.050 0.135 528 Planarity : 0.005 0.069 606 Dihedral : 8.990 37.561 486 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 3.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 2.78 % Allowed : 21.21 % Favored : 76.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.88 (0.33), 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 HIS 0.003 0.001 HIS C 374 PHE 0.006 0.002 PHE F 346 TYR 0.012 0.003 TYR C 310 ARG 0.014 0.002 ARG D 349 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 90 time to evaluate : 0.461 Fit side-chains REVERT: D 342 GLU cc_start: 0.7950 (tt0) cc_final: 0.7731 (tt0) REVERT: E 311 LYS cc_start: 0.8448 (mttt) cc_final: 0.7931 (mmtt) outliers start: 11 outliers final: 5 residues processed: 98 average time/residue: 1.6650 time to fit residues: 166.5865 Evaluate side-chains 86 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 81 time to evaluate : 0.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 320 SER Chi-restraints excluded: chain A residue 331 LYS 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 3 optimal weight: 10.0000 chunk 31 optimal weight: 1.9990 chunk 36 optimal weight: 10.0000 chunk 38 optimal weight: 8.9990 chunk 35 optimal weight: 1.9990 chunk 37 optimal weight: 6.9990 chunk 22 optimal weight: 2.9990 chunk 16 optimal weight: 6.9990 chunk 29 optimal weight: 7.9990 chunk 11 optimal weight: 7.9990 chunk 34 optimal weight: 10.0000 overall best weight: 4.1990 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8925 moved from start: 0.1977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.027 3636 Z= 0.316 Angle : 0.538 4.578 4878 Z= 0.275 Chirality : 0.049 0.133 528 Planarity : 0.005 0.065 606 Dihedral : 8.656 35.867 486 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 2.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 1.77 % Allowed : 22.73 % Favored : 75.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.91 (0.33), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.44 (0.26), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 374 PHE 0.006 0.001 PHE F 346 TYR 0.011 0.002 TYR A 310 ARG 0.014 0.003 ARG D 349 *********************** 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 86 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 79 time to evaluate : 0.455 Fit side-chains REVERT: A 349 ARG cc_start: 0.8328 (mtt90) cc_final: 0.8027 (mtt90) REVERT: D 342 GLU cc_start: 0.7941 (tt0) cc_final: 0.7719 (tt0) outliers start: 7 outliers final: 5 residues processed: 85 average time/residue: 1.5763 time to fit residues: 137.0804 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 : 0.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 320 SER Chi-restraints excluded: chain A residue 331 LYS Chi-restraints excluded: chain B residue 331 LYS Chi-restraints excluded: chain D residue 331 LYS Chi-restraints excluded: chain F residue 331 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 0.0040 chunk 37 optimal weight: 10.0000 chunk 24 optimal weight: 10.0000 chunk 39 optimal weight: 9.9990 chunk 18 optimal weight: 0.0060 chunk 27 optimal weight: 8.9990 chunk 41 optimal weight: 8.9990 chunk 38 optimal weight: 10.0000 chunk 33 optimal weight: 0.5980 chunk 3 optimal weight: 10.0000 chunk 25 optimal weight: 0.4980 overall best weight: 2.0210 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8891 moved from start: 0.2140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 3636 Z= 0.167 Angle : 0.473 4.333 4878 Z= 0.241 Chirality : 0.049 0.127 528 Planarity : 0.004 0.046 606 Dihedral : 7.682 31.572 486 Min Nonbonded Distance : 2.631 Molprobity Statistics. All-atom Clashscore : 2.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 1.77 % Allowed : 22.73 % 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: -1.86 (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 HIS 0.002 0.000 HIS C 374 PHE 0.004 0.001 PHE F 346 TYR 0.009 0.002 TYR A 310 ARG 0.011 0.002 ARG B 349 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 79 time to evaluate : 0.416 Fit side-chains REVERT: A 349 ARG cc_start: 0.8342 (mtt90) cc_final: 0.8046 (mtt90) REVERT: B 331 LYS cc_start: 0.8584 (OUTLIER) cc_final: 0.8162 (tmtm) outliers start: 7 outliers final: 4 residues processed: 86 average time/residue: 1.6317 time to fit residues: 143.5173 Evaluate side-chains 83 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 78 time to evaluate : 0.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 320 SER Chi-restraints excluded: chain A residue 331 LYS Chi-restraints excluded: chain B residue 331 LYS Chi-restraints excluded: chain D residue 331 LYS Chi-restraints excluded: chain E residue 325 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 20 optimal weight: 10.0000 chunk 26 optimal weight: 7.9990 chunk 35 optimal weight: 0.0270 chunk 10 optimal weight: 10.0000 chunk 30 optimal weight: 10.0000 chunk 4 optimal weight: 8.9990 chunk 9 optimal weight: 1.9990 chunk 33 optimal weight: 5.9990 chunk 13 optimal weight: 9.9990 chunk 34 optimal weight: 10.0000 chunk 6 optimal weight: 5.9990 overall best weight: 4.4046 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8926 moved from start: 0.2003 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= 0.331 Angle : 0.548 4.740 4878 Z= 0.280 Chirality : 0.049 0.133 528 Planarity : 0.005 0.067 606 Dihedral : 8.659 36.103 486 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 2.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 2.02 % Allowed : 22.47 % 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: -1.90 (0.34), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.44 (0.26), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 374 PHE 0.006 0.001 PHE F 346 TYR 0.011 0.002 TYR C 310 ARG 0.015 0.003 ARG D 349 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 79 time to evaluate : 0.425 Fit side-chains REVERT: A 349 ARG cc_start: 0.8345 (mtt90) cc_final: 0.8051 (mtt90) REVERT: D 342 GLU cc_start: 0.7940 (tt0) cc_final: 0.7717 (tt0) outliers start: 8 outliers final: 3 residues processed: 85 average time/residue: 1.5929 time to fit residues: 138.4841 Evaluate side-chains 82 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 79 time to evaluate : 0.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 320 SER Chi-restraints excluded: chain A residue 331 LYS Chi-restraints excluded: chain D residue 331 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 29 optimal weight: 0.8980 chunk 1 optimal weight: 10.0000 chunk 24 optimal weight: 9.9990 chunk 38 optimal weight: 10.0000 chunk 22 optimal weight: 10.0000 chunk 28 optimal weight: 0.7980 chunk 26 optimal weight: 10.0000 chunk 25 optimal weight: 6.9990 chunk 16 optimal weight: 4.9990 chunk 15 optimal weight: 10.0000 chunk 41 optimal weight: 8.9990 overall best weight: 4.5386 ------------------------------------------------------------------------------- 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 = 0.3565 r_free = 0.3565 target = 0.118666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.098460 restraints weight = 3706.356| |-----------------------------------------------------------------------------| r_work (start): 0.3260 rms_B_bonded: 1.25 r_work: 0.3142 rms_B_bonded: 1.58 restraints_weight: 0.5000 r_work: 0.3049 rms_B_bonded: 2.63 restraints_weight: 0.2500 r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9124 moved from start: 0.2009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.029 3636 Z= 0.340 Angle : 0.553 5.025 4878 Z= 0.281 Chirality : 0.050 0.134 528 Planarity : 0.004 0.049 606 Dihedral : 8.736 36.439 486 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 3.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 0.76 % Allowed : 23.99 % 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: -1.91 (0.34), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.44 (0.26), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 374 PHE 0.006 0.002 PHE F 346 TYR 0.011 0.002 TYR C 310 ARG 0.011 0.002 ARG A 349 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2787.98 seconds wall clock time: 50 minutes 21.43 seconds (3021.43 seconds total)