Starting phenix.real_space_refine on Fri Oct 10 15:20:04 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8q9m_18286/10_2025/8q9m_18286.cif Found real_map, /net/cci-nas-00/data/ceres_data/8q9m_18286/10_2025/8q9m_18286.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.65 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8q9m_18286/10_2025/8q9m_18286.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8q9m_18286/10_2025/8q9m_18286.map" model { file = "/net/cci-nas-00/data/ceres_data/8q9m_18286/10_2025/8q9m_18286.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8q9m_18286/10_2025/8q9m_18286.cif" } resolution = 2.65 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= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 6 5.16 5 C 2160 2.51 5 N 636 2.21 5 O 642 1.98 5 H 3588 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 36 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 7032 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1172 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "G" Number of atoms: 1172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1172 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "B" Number of atoms: 1172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1172 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "C" Number of atoms: 1172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1172 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "D" Number of atoms: 1172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1172 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "E" Number of atoms: 1172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1172 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Time building chain proxies: 1.52, per 1000 atoms: 0.22 Number of scatterers: 7032 At special positions: 0 Unit cell: (114.536, 118.656, 40.376, 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 O 642 8.00 N 636 7.00 C 2160 6.00 H 3588 1.00 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: 0.59 Conformation dependent library (CDL) restraints added in 244.6 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, 50.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.23 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'G' and resid 306 through 310 removed outlier: 6.446A pdb=" N VAL A 306 " --> pdb=" O GLN G 307 " (cutoff:3.500A) removed outlier: 7.887A pdb=" N VAL G 309 " --> pdb=" O VAL A 306 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N ILE A 308 " --> pdb=" O VAL G 309 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'G' and resid 313 through 314 removed outlier: 6.713A pdb=" N VAL A 313 " --> pdb=" O ASP B 314 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'G' and resid 317 through 322 removed outlier: 6.368A pdb=" N VAL A 318 " --> pdb=" O THR G 319 " (cutoff:3.500A) removed outlier: 8.177A pdb=" N LYS G 321 " --> pdb=" O VAL A 318 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N SER A 320 " --> pdb=" O LYS G 321 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N LYS A 317 " --> pdb=" O VAL B 318 " (cutoff:3.500A) removed outlier: 8.110A pdb=" N SER B 320 " --> pdb=" O LYS A 317 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N THR A 319 " --> pdb=" O SER B 320 " (cutoff:3.500A) removed outlier: 8.191A pdb=" N CYS B 322 " --> pdb=" O THR A 319 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N LYS A 321 " --> pdb=" O CYS B 322 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'G' and resid 325 through 330 removed outlier: 6.214A pdb=" N GLY A 326 " --> pdb=" O ASN G 327 " (cutoff:3.500A) removed outlier: 8.571A pdb=" N HIS G 329 " --> pdb=" O GLY A 326 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N ILE A 328 " --> pdb=" O HIS G 329 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N GLY B 326 " --> pdb=" O LEU A 325 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N ASN A 327 " --> pdb=" O GLY B 326 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'G' and resid 337 through 342 removed outlier: 6.519A pdb=" N GLU A 338 " --> pdb=" O VAL B 339 " (cutoff:3.500A) removed outlier: 7.874A pdb=" N SER B 341 " --> pdb=" O GLU A 338 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N LYS A 340 " --> pdb=" O SER B 341 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'G' and resid 345 through 346 removed outlier: 6.376A pdb=" N ASP A 345 " --> pdb=" O PHE B 346 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 350 through 357 removed outlier: 6.293A pdb=" N VAL A 350 " --> pdb=" O GLN G 351 " (cutoff:3.500A) removed outlier: 8.079A pdb=" N LYS G 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N SER A 352 " --> pdb=" O LYS G 353 " (cutoff:3.500A) removed outlier: 8.288A pdb=" N GLY G 355 " --> pdb=" O SER A 352 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N ILE A 354 " --> pdb=" O GLY G 355 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N LEU G 357 " --> pdb=" O ILE A 354 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N SER A 356 " --> pdb=" O LEU G 357 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'G' and resid 360 through 362 removed outlier: 6.429A pdb=" N THR A 361 " --> pdb=" O HIS G 362 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'G' and resid 369 through 377 removed outlier: 6.482A pdb=" N LYS A 369 " --> pdb=" O LYS B 370 " (cutoff:3.500A) removed outlier: 7.962A pdb=" N GLU B 372 " --> pdb=" O LYS A 369 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N ILE A 371 " --> pdb=" O GLU B 372 " (cutoff:3.500A) removed outlier: 7.984A pdb=" N HIS B 374 " --> pdb=" O ILE A 371 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N THR A 373 " --> pdb=" O HIS B 374 " (cutoff:3.500A) removed outlier: 7.787A pdb=" N LEU B 376 " --> pdb=" O THR A 373 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N LYS A 375 " --> pdb=" O LEU B 376 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 306 through 310 removed outlier: 6.550A pdb=" N GLN C 307 " --> pdb=" O ILE E 308 " (cutoff:3.500A) removed outlier: 7.752A pdb=" N TYR E 310 " --> pdb=" O GLN C 307 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N VAL C 309 " --> pdb=" O TYR E 310 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 313 through 314 removed outlier: 6.755A pdb=" N VAL C 313 " --> pdb=" O ASP E 314 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 317 through 322 removed outlier: 6.376A pdb=" N LYS C 317 " --> pdb=" O VAL E 318 " (cutoff:3.500A) removed outlier: 8.089A pdb=" N SER E 320 " --> pdb=" O LYS C 317 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N THR C 319 " --> pdb=" O SER E 320 " (cutoff:3.500A) removed outlier: 8.197A pdb=" N CYS E 322 " --> pdb=" O THR C 319 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N LYS C 321 " --> pdb=" O CYS E 322 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 325 through 330 removed outlier: 6.108A pdb=" N GLY C 326 " --> pdb=" O ASN D 327 " (cutoff:3.500A) removed outlier: 8.520A pdb=" N HIS D 329 " --> pdb=" O GLY C 326 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N ILE C 328 " --> pdb=" O HIS D 329 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N GLY E 326 " --> pdb=" O LEU C 325 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N ASN C 327 " --> pdb=" O GLY E 326 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 337 through 342 removed outlier: 6.501A pdb=" N GLU C 338 " --> pdb=" O VAL E 339 " (cutoff:3.500A) removed outlier: 7.900A pdb=" N SER E 341 " --> pdb=" O GLU C 338 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N LYS C 340 " --> pdb=" O SER E 341 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 345 through 346 removed outlier: 6.347A pdb=" N ASP C 345 " --> pdb=" O PHE E 346 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 350 through 357 removed outlier: 6.325A pdb=" N VAL C 350 " --> pdb=" O GLN D 351 " (cutoff:3.500A) removed outlier: 8.081A pdb=" N LYS D 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N SER C 352 " --> pdb=" O LYS D 353 " (cutoff:3.500A) removed outlier: 8.270A pdb=" N GLY D 355 " --> pdb=" O SER C 352 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N ILE C 354 " --> pdb=" O GLY D 355 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N LEU D 357 " --> pdb=" O ILE C 354 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N SER C 356 " --> pdb=" O LEU D 357 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 360 through 362 removed outlier: 6.460A pdb=" N THR C 361 " --> pdb=" O HIS D 362 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 369 through 377 removed outlier: 6.455A pdb=" N LYS C 369 " --> pdb=" O LYS E 370 " (cutoff:3.500A) removed outlier: 7.779A pdb=" N GLU E 372 " --> pdb=" O LYS C 369 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N ILE C 371 " --> pdb=" O GLU E 372 " (cutoff:3.500A) removed outlier: 8.054A pdb=" N HIS E 374 " --> pdb=" O ILE C 371 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N THR C 373 " --> pdb=" O HIS E 374 " (cutoff:3.500A) removed outlier: 7.844A pdb=" N LEU E 376 " --> pdb=" O THR C 373 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N LYS C 375 " --> pdb=" O LEU E 376 " (cutoff:3.500A) 67 hydrogen bonds defined for protein. 201 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.24 Time building geometry restraints manager: 0.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.94 - 1.11: 3582 1.11 - 1.29: 570 1.29 - 1.46: 925 1.46 - 1.63: 2003 1.63 - 1.81: 6 Bond restraints: 7086 Sorted by residual: bond pdb=" NE2 GLN D 336 " pdb="HE22 GLN D 336 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.69e+01 bond pdb=" N ASP G 314 " pdb=" H ASP G 314 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.69e+01 bond pdb=" N GLU D 372 " pdb=" H GLU D 372 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.69e+01 bond pdb=" N ILE A 354 " pdb=" H ILE A 354 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.68e+01 bond pdb=" N SER D 356 " pdb=" H SER D 356 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.68e+01 ... (remaining 7081 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.50: 10923 2.50 - 5.00: 1516 5.00 - 7.50: 457 7.50 - 10.00: 10 10.00 - 12.50: 6 Bond angle restraints: 12912 Sorted by residual: angle pdb=" N GLY C 326 " pdb=" CA GLY C 326 " pdb=" C GLY C 326 " ideal model delta sigma weight residual 110.69 118.13 -7.44 1.33e+00 5.65e-01 3.13e+01 angle pdb=" CA ASP A 345 " pdb=" CB ASP A 345 " pdb=" CG ASP A 345 " ideal model delta sigma weight residual 112.60 117.48 -4.88 1.00e+00 1.00e+00 2.38e+01 angle pdb=" N GLY A 326 " pdb=" CA GLY A 326 " pdb=" C GLY A 326 " ideal model delta sigma weight residual 110.69 116.99 -6.30 1.33e+00 5.65e-01 2.24e+01 angle pdb=" C GLY E 334 " pdb=" N GLY E 335 " pdb=" CA GLY E 335 " ideal model delta sigma weight residual 120.60 125.37 -4.77 1.01e+00 9.80e-01 2.23e+01 angle pdb=" N GLY D 326 " pdb=" CA GLY D 326 " pdb=" C GLY D 326 " ideal model delta sigma weight residual 110.69 116.71 -6.02 1.33e+00 5.65e-01 2.05e+01 ... (remaining 12907 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.01: 2839 13.01 - 26.01: 210 26.01 - 39.02: 78 39.02 - 52.02: 50 52.02 - 65.03: 87 Dihedral angle restraints: 3264 sinusoidal: 1866 harmonic: 1398 Sorted by residual: dihedral pdb=" CA ILE D 360 " pdb=" C ILE D 360 " pdb=" N THR D 361 " pdb=" CA THR D 361 " ideal model delta harmonic sigma weight residual 180.00 157.58 22.42 0 5.00e+00 4.00e-02 2.01e+01 dihedral pdb=" CA SER A 320 " pdb=" C SER A 320 " pdb=" N LYS A 321 " pdb=" CA LYS A 321 " ideal model delta harmonic sigma weight residual 180.00 158.39 21.61 0 5.00e+00 4.00e-02 1.87e+01 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 180.00 158.64 21.36 0 5.00e+00 4.00e-02 1.82e+01 ... (remaining 3261 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 288 0.056 - 0.112: 143 0.112 - 0.168: 65 0.168 - 0.223: 27 0.223 - 0.279: 5 Chirality restraints: 528 Sorted by residual: chirality pdb=" CA LYS D 347 " pdb=" N LYS D 347 " pdb=" C LYS D 347 " pdb=" CB LYS D 347 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.95e+00 chirality pdb=" CA LYS D 343 " pdb=" N LYS D 343 " pdb=" C LYS D 343 " pdb=" CB LYS D 343 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.89e+00 chirality pdb=" CA LYS G 347 " pdb=" N LYS G 347 " pdb=" C LYS G 347 " pdb=" CB LYS G 347 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.60e+00 ... (remaining 525 not shown) Planarity restraints: 1020 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR G 310 " -0.093 2.00e-02 2.50e+03 3.89e-02 4.54e+01 pdb=" CG TYR G 310 " 0.016 2.00e-02 2.50e+03 pdb=" CD1 TYR G 310 " 0.029 2.00e-02 2.50e+03 pdb=" CD2 TYR G 310 " 0.031 2.00e-02 2.50e+03 pdb=" CE1 TYR G 310 " 0.028 2.00e-02 2.50e+03 pdb=" CE2 TYR G 310 " 0.003 2.00e-02 2.50e+03 pdb=" CZ TYR G 310 " -0.010 2.00e-02 2.50e+03 pdb=" OH TYR G 310 " -0.066 2.00e-02 2.50e+03 pdb=" HD1 TYR G 310 " 0.003 2.00e-02 2.50e+03 pdb=" HD2 TYR G 310 " 0.042 2.00e-02 2.50e+03 pdb=" HE1 TYR G 310 " 0.020 2.00e-02 2.50e+03 pdb=" HE2 TYR G 310 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 327 " 0.035 2.00e-02 2.50e+03 5.23e-02 4.10e+01 pdb=" CG ASN C 327 " -0.029 2.00e-02 2.50e+03 pdb=" OD1 ASN C 327 " 0.005 2.00e-02 2.50e+03 pdb=" ND2 ASN C 327 " -0.097 2.00e-02 2.50e+03 pdb="HD21 ASN C 327 " 0.020 2.00e-02 2.50e+03 pdb="HD22 ASN C 327 " 0.067 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 379 " -0.156 9.50e-02 1.11e+02 6.58e-02 3.93e+01 pdb=" NE ARG A 379 " -0.027 2.00e-02 2.50e+03 pdb=" CZ ARG A 379 " -0.009 2.00e-02 2.50e+03 pdb=" NH1 ARG A 379 " -0.011 2.00e-02 2.50e+03 pdb=" NH2 ARG A 379 " 0.016 2.00e-02 2.50e+03 pdb="HH11 ARG A 379 " 0.080 2.00e-02 2.50e+03 pdb="HH12 ARG A 379 " -0.076 2.00e-02 2.50e+03 pdb="HH21 ARG A 379 " 0.001 2.00e-02 2.50e+03 pdb="HH22 ARG A 379 " 0.035 2.00e-02 2.50e+03 ... (remaining 1017 not shown) Histogram of nonbonded interaction distances: 1.71 - 2.28: 979 2.28 - 2.86: 14743 2.86 - 3.44: 17783 3.44 - 4.02: 24326 4.02 - 4.60: 33831 Nonbonded interactions: 91662 Sorted by model distance: nonbonded pdb=" O SER C 316 " pdb=" HG SER D 316 " model vdw 1.706 2.450 nonbonded pdb=" OD2 ASP B 314 " pdb=" HZ2 LYS B 370 " model vdw 1.726 2.450 nonbonded pdb=" OD2 ASP E 314 " pdb=" HZ2 LYS E 370 " model vdw 1.732 2.450 nonbonded pdb=" HG SER A 316 " pdb=" O SER B 316 " model vdw 1.740 2.450 nonbonded pdb=" O SER A 316 " pdb=" HG SER G 316 " model vdw 1.741 2.450 ... (remaining 91657 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' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'G' } 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: 3.840 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: 0.030 Extract box with map and model: 0.090 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.980 Find NCS groups from input model: 0.080 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:6.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7719 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 : 0.011 0.036 3498 Z= 0.664 Angle : 1.761 7.439 4680 Z= 1.164 Chirality : 0.086 0.279 528 Planarity : 0.009 0.055 594 Dihedral : 11.563 62.118 1344 Min Nonbonded Distance : 2.640 Molprobity Statistics. All-atom Clashscore : 0.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % 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: -1.02 (0.32), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.77 (0.25), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 379 TYR 0.081 0.019 TYR G 310 PHE 0.036 0.010 PHE E 346 HIS 0.018 0.005 HIS C 330 Details of bonding type rmsd covalent geometry : bond 0.01070 ( 3498) covalent geometry : angle 1.76057 ( 4680) hydrogen bonds : bond 0.08375 ( 67) hydrogen bonds : angle 8.00651 ( 201) *********************** 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 159 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 159 time to evaluate : 0.215 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 314 ASP cc_start: 0.4992 (t0) cc_final: 0.3955 (t0) REVERT: A 316 SER cc_start: 0.6151 (t) cc_final: 0.5616 (p) REVERT: A 317 LYS cc_start: 0.6109 (ptmt) cc_final: 0.5845 (ptpp) REVERT: A 321 LYS cc_start: 0.7254 (ttmt) cc_final: 0.6968 (mttt) REVERT: A 369 LYS cc_start: 0.7384 (tttt) cc_final: 0.6915 (ttmt) REVERT: G 311 LYS cc_start: 0.5741 (mtmt) cc_final: 0.5175 (tppt) REVERT: G 321 LYS cc_start: 0.7366 (ttmt) cc_final: 0.7002 (mttt) REVERT: G 340 LYS cc_start: 0.8317 (mtpt) cc_final: 0.7865 (mttt) REVERT: G 343 LYS cc_start: 0.8990 (mttt) cc_final: 0.8699 (mttp) REVERT: G 345 ASP cc_start: 0.8167 (m-30) cc_final: 0.7904 (m-30) REVERT: G 349 ARG cc_start: 0.8173 (mtt180) cc_final: 0.6322 (mmp-170) REVERT: G 369 LYS cc_start: 0.7396 (tttt) cc_final: 0.6814 (mtmt) REVERT: G 375 LYS cc_start: 0.5138 (tttt) cc_final: 0.4906 (tttp) REVERT: B 311 LYS cc_start: 0.6266 (mtmt) cc_final: 0.5744 (mttt) REVERT: B 314 ASP cc_start: 0.5184 (t0) cc_final: 0.4673 (t0) REVERT: B 320 SER cc_start: 0.8248 (t) cc_final: 0.7873 (p) REVERT: B 321 LYS cc_start: 0.7739 (ttmt) cc_final: 0.7517 (mtmt) REVERT: B 342 GLU cc_start: 0.8757 (mt-10) cc_final: 0.8276 (tt0) REVERT: B 347 LYS cc_start: 0.8617 (mttt) cc_final: 0.7736 (pptt) REVERT: B 369 LYS cc_start: 0.7960 (tttt) cc_final: 0.7623 (ttpt) REVERT: C 314 ASP cc_start: 0.4957 (t0) cc_final: 0.4309 (t0) REVERT: C 317 LYS cc_start: 0.6008 (ptmt) cc_final: 0.5743 (ptpp) REVERT: C 321 LYS cc_start: 0.7209 (ttmt) cc_final: 0.6935 (mtmt) REVERT: C 338 GLU cc_start: 0.8287 (tt0) cc_final: 0.8064 (tt0) REVERT: C 342 GLU cc_start: 0.8435 (mt-10) cc_final: 0.7902 (mt-10) REVERT: C 369 LYS cc_start: 0.7385 (tttt) cc_final: 0.6979 (ttmt) REVERT: D 311 LYS cc_start: 0.6166 (mtmt) cc_final: 0.5376 (tppt) REVERT: D 314 ASP cc_start: 0.5909 (t0) cc_final: 0.5648 (t0) REVERT: D 315 LEU cc_start: 0.7022 (mp) cc_final: 0.6788 (mp) REVERT: D 321 LYS cc_start: 0.7126 (ttmt) cc_final: 0.6916 (mtmt) REVERT: D 340 LYS cc_start: 0.8416 (mtpt) cc_final: 0.8050 (mttt) REVERT: D 345 ASP cc_start: 0.8201 (m-30) cc_final: 0.8000 (m-30) REVERT: D 348 ASP cc_start: 0.8984 (t0) cc_final: 0.8735 (t70) REVERT: D 349 ARG cc_start: 0.8284 (mtt180) cc_final: 0.6278 (mmp-170) REVERT: E 307 GLN cc_start: 0.6439 (mt0) cc_final: 0.6200 (tt0) REVERT: E 311 LYS cc_start: 0.6198 (mtmt) cc_final: 0.5668 (mtpt) REVERT: E 314 ASP cc_start: 0.5037 (t0) cc_final: 0.4516 (t0) REVERT: E 317 LYS cc_start: 0.7079 (ptmt) cc_final: 0.6736 (mttt) REVERT: E 321 LYS cc_start: 0.7839 (ttmt) cc_final: 0.7453 (mttt) REVERT: E 338 GLU cc_start: 0.8427 (tt0) cc_final: 0.8176 (tt0) REVERT: E 342 GLU cc_start: 0.8626 (mt-10) cc_final: 0.8232 (tt0) REVERT: E 347 LYS cc_start: 0.8539 (mttt) cc_final: 0.7768 (pptt) REVERT: E 369 LYS cc_start: 0.8182 (tttt) cc_final: 0.7907 (ttmt) REVERT: E 379 ARG cc_start: 0.5591 (mmt-90) cc_final: 0.3179 (mtm-85) outliers start: 0 outliers final: 0 residues processed: 159 average time/residue: 1.6843 time to fit residues: 272.8055 Evaluate side-chains 117 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 117 time to evaluate : 0.199 ------------------------------------------------------------------------------- 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: 5.9990 chunk 26 optimal weight: 0.9990 chunk 2 optimal weight: 3.9990 chunk 16 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 31 optimal weight: 0.9980 chunk 25 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 chunk 30 optimal weight: 0.8980 chunk 22 optimal weight: 5.9990 chunk 37 optimal weight: 0.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 307 GLN G 351 GLN B 307 GLN B 327 ASN D 307 GLN D 327 ASN E 351 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.135318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.119681 restraints weight = 11857.391| |-----------------------------------------------------------------------------| r_work (start): 0.3856 rms_B_bonded: 1.47 r_work: 0.3772 rms_B_bonded: 1.49 restraints_weight: 0.5000 r_work: 0.3698 rms_B_bonded: 2.60 restraints_weight: 0.2500 r_work (final): 0.3698 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8854 moved from start: 0.3236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3498 Z= 0.119 Angle : 0.544 4.282 4680 Z= 0.285 Chirality : 0.051 0.143 528 Planarity : 0.003 0.017 594 Dihedral : 6.212 18.236 462 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 0.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 0.00 % Allowed : 13.38 % Favored : 86.62 % 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: -1.08 (0.33), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.82 (0.25), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG E 349 TYR 0.007 0.001 TYR A 310 PHE 0.004 0.001 PHE A 346 HIS 0.003 0.001 HIS C 330 Details of bonding type rmsd covalent geometry : bond 0.00272 ( 3498) covalent geometry : angle 0.54415 ( 4680) hydrogen bonds : bond 0.02716 ( 67) hydrogen bonds : angle 5.23388 ( 201) *********************** 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 121 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 121 time to evaluate : 0.135 Fit side-chains REVERT: A 307 GLN cc_start: 0.7659 (mt0) cc_final: 0.7306 (tt0) REVERT: A 314 ASP cc_start: 0.8439 (t0) cc_final: 0.8202 (t0) REVERT: A 340 LYS cc_start: 0.8290 (mtpt) cc_final: 0.7984 (mttt) REVERT: A 342 GLU cc_start: 0.8116 (mt-10) cc_final: 0.7790 (mt-10) REVERT: A 369 LYS cc_start: 0.8491 (tttt) cc_final: 0.8263 (mttt) REVERT: G 311 LYS cc_start: 0.8381 (mtmt) cc_final: 0.7627 (tppt) REVERT: G 340 LYS cc_start: 0.8227 (mtpt) cc_final: 0.7886 (mttt) REVERT: G 342 GLU cc_start: 0.8127 (mt-10) cc_final: 0.7879 (mt-10) REVERT: G 343 LYS cc_start: 0.9046 (mttt) cc_final: 0.8778 (mttp) REVERT: G 349 ARG cc_start: 0.8375 (mtt180) cc_final: 0.6907 (mmp-170) REVERT: G 375 LYS cc_start: 0.8519 (tttt) cc_final: 0.8197 (tptt) REVERT: B 311 LYS cc_start: 0.8702 (mtmt) cc_final: 0.8322 (mttt) REVERT: B 342 GLU cc_start: 0.8294 (mt-10) cc_final: 0.7925 (tt0) REVERT: B 347 LYS cc_start: 0.8740 (mttt) cc_final: 0.8137 (pptt) REVERT: C 317 LYS cc_start: 0.8497 (ptmt) cc_final: 0.8241 (ptpp) REVERT: C 338 GLU cc_start: 0.8178 (tt0) cc_final: 0.7805 (tt0) REVERT: C 342 GLU cc_start: 0.7991 (mt-10) cc_final: 0.7660 (mt-10) REVERT: C 348 ASP cc_start: 0.8879 (t0) cc_final: 0.8607 (t70) REVERT: D 311 LYS cc_start: 0.8370 (mtmt) cc_final: 0.7618 (tppt) REVERT: D 340 LYS cc_start: 0.8350 (mtpt) cc_final: 0.8035 (mttt) REVERT: D 349 ARG cc_start: 0.8384 (mtt180) cc_final: 0.6799 (mmp-170) REVERT: E 311 LYS cc_start: 0.8809 (mtmt) cc_final: 0.8418 (mtpt) REVERT: E 338 GLU cc_start: 0.8253 (tt0) cc_final: 0.8005 (tt0) REVERT: E 342 GLU cc_start: 0.8101 (mt-10) cc_final: 0.7883 (tt0) REVERT: E 347 LYS cc_start: 0.8518 (mttt) cc_final: 0.8118 (pptt) REVERT: E 379 ARG cc_start: 0.7746 (mmt-90) cc_final: 0.4691 (mtm-85) outliers start: 0 outliers final: 0 residues processed: 121 average time/residue: 1.7737 time to fit residues: 218.5064 Evaluate side-chains 94 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 94 time to evaluate : 0.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 6 optimal weight: 6.9990 chunk 28 optimal weight: 4.9990 chunk 12 optimal weight: 0.0040 chunk 22 optimal weight: 8.9990 chunk 38 optimal weight: 6.9990 chunk 20 optimal weight: 4.9990 chunk 21 optimal weight: 0.9980 chunk 39 optimal weight: 5.9990 chunk 1 optimal weight: 0.9980 chunk 27 optimal weight: 1.9990 chunk 41 optimal weight: 0.9990 overall best weight: 0.9996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 307 GLN C 327 ASN C 351 GLN D 307 GLN E 351 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.136533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.121220 restraints weight = 12098.993| |-----------------------------------------------------------------------------| r_work (start): 0.3855 rms_B_bonded: 1.48 r_work: 0.3776 rms_B_bonded: 1.49 restraints_weight: 0.5000 r_work: 0.3702 rms_B_bonded: 2.59 restraints_weight: 0.2500 r_work (final): 0.3702 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8882 moved from start: 0.4242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 3498 Z= 0.093 Angle : 0.496 4.243 4680 Z= 0.257 Chirality : 0.052 0.139 528 Planarity : 0.002 0.029 594 Dihedral : 5.309 14.629 462 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 0.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Rotamer: Outliers : 1.77 % Allowed : 15.66 % 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: -1.25 (0.33), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.94 (0.25), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 349 TYR 0.008 0.002 TYR A 310 PHE 0.004 0.001 PHE G 378 HIS 0.002 0.001 HIS D 374 Details of bonding type rmsd covalent geometry : bond 0.00213 ( 3498) covalent geometry : angle 0.49626 ( 4680) hydrogen bonds : bond 0.01898 ( 67) hydrogen bonds : angle 4.38694 ( 201) *********************** 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 105 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 98 time to evaluate : 0.221 Fit side-chains revert: symmetry clash REVERT: A 307 GLN cc_start: 0.7643 (mt0) cc_final: 0.7315 (tt0) REVERT: A 340 LYS cc_start: 0.8286 (mtpt) cc_final: 0.7969 (mttt) REVERT: A 342 GLU cc_start: 0.8146 (mt-10) cc_final: 0.7817 (tt0) REVERT: A 369 LYS cc_start: 0.8461 (tttt) cc_final: 0.8238 (mttt) REVERT: G 311 LYS cc_start: 0.8345 (mtmt) cc_final: 0.7548 (tppt) REVERT: G 342 GLU cc_start: 0.8104 (mt-10) cc_final: 0.7884 (mt-10) REVERT: G 349 ARG cc_start: 0.8393 (mtt180) cc_final: 0.6963 (mmp-170) REVERT: B 311 LYS cc_start: 0.8674 (mtmt) cc_final: 0.8287 (mttt) REVERT: B 342 GLU cc_start: 0.8250 (mt-10) cc_final: 0.7914 (tt0) REVERT: B 347 LYS cc_start: 0.8722 (mttt) cc_final: 0.8096 (pptt) REVERT: C 317 LYS cc_start: 0.8469 (ptmt) cc_final: 0.8260 (ptpp) REVERT: C 338 GLU cc_start: 0.8168 (tt0) cc_final: 0.7797 (tt0) REVERT: C 342 GLU cc_start: 0.8009 (mt-10) cc_final: 0.7699 (mt-10) REVERT: C 348 ASP cc_start: 0.8809 (t0) cc_final: 0.8597 (t70) REVERT: C 349 ARG cc_start: 0.8264 (mtp85) cc_final: 0.7870 (mtp85) REVERT: C 351 GLN cc_start: 0.8665 (mt0) cc_final: 0.8397 (mt0) REVERT: D 307 GLN cc_start: 0.7838 (mt0) cc_final: 0.7531 (tt0) REVERT: D 311 LYS cc_start: 0.8281 (mtmt) cc_final: 0.7513 (tppt) REVERT: D 340 LYS cc_start: 0.8337 (mtpt) cc_final: 0.8017 (mttt) REVERT: D 349 ARG cc_start: 0.8407 (mtt180) cc_final: 0.6810 (mmp-170) REVERT: E 311 LYS cc_start: 0.8787 (mtmt) cc_final: 0.8436 (mtpt) REVERT: E 317 LYS cc_start: 0.8609 (mttt) cc_final: 0.8233 (mtmt) REVERT: E 338 GLU cc_start: 0.8307 (tt0) cc_final: 0.8055 (tt0) REVERT: E 342 GLU cc_start: 0.8112 (mt-10) cc_final: 0.7893 (tt0) REVERT: E 347 LYS cc_start: 0.8506 (mttt) cc_final: 0.8007 (pptt) REVERT: E 348 ASP cc_start: 0.8816 (OUTLIER) cc_final: 0.8299 (t70) REVERT: E 349 ARG cc_start: 0.8478 (mtp85) cc_final: 0.7704 (mtt90) REVERT: E 379 ARG cc_start: 0.7732 (mmt-90) cc_final: 0.4750 (mtm-85) outliers start: 7 outliers final: 1 residues processed: 99 average time/residue: 1.6668 time to fit residues: 168.1314 Evaluate side-chains 90 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 88 time to evaluate : 0.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 336 GLN Chi-restraints excluded: chain E residue 348 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 21 optimal weight: 5.9990 chunk 2 optimal weight: 5.9990 chunk 27 optimal weight: 3.9990 chunk 0 optimal weight: 6.9990 chunk 32 optimal weight: 6.9990 chunk 38 optimal weight: 6.9990 chunk 39 optimal weight: 5.9990 chunk 3 optimal weight: 10.0000 chunk 14 optimal weight: 0.9990 chunk 18 optimal weight: 4.9990 chunk 40 optimal weight: 0.6980 overall best weight: 3.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 351 GLN B 307 GLN E 351 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.124618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.108339 restraints weight = 12348.684| |-----------------------------------------------------------------------------| r_work (start): 0.3684 rms_B_bonded: 1.50 r_work: 0.3605 rms_B_bonded: 1.48 restraints_weight: 0.5000 r_work: 0.3529 rms_B_bonded: 2.56 restraints_weight: 0.2500 r_work (final): 0.3529 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8945 moved from start: 0.4435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.024 3498 Z= 0.205 Angle : 0.534 3.831 4680 Z= 0.283 Chirality : 0.051 0.145 528 Planarity : 0.004 0.050 594 Dihedral : 5.383 14.985 462 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 1.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Rotamer: Outliers : 2.02 % Allowed : 14.14 % Favored : 83.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -1.47 (0.32), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.11 (0.25), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 379 TYR 0.014 0.003 TYR A 310 PHE 0.008 0.002 PHE G 378 HIS 0.003 0.001 HIS G 329 Details of bonding type rmsd covalent geometry : bond 0.00461 ( 3498) covalent geometry : angle 0.53383 ( 4680) hydrogen bonds : bond 0.02260 ( 67) hydrogen bonds : angle 4.32450 ( 201) *********************** 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 93 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 85 time to evaluate : 0.132 Fit side-chains REVERT: A 307 GLN cc_start: 0.7681 (mt0) cc_final: 0.7369 (tt0) REVERT: A 340 LYS cc_start: 0.8324 (mtpt) cc_final: 0.7986 (mttt) REVERT: A 342 GLU cc_start: 0.8212 (mt-10) cc_final: 0.7860 (tt0) REVERT: A 369 LYS cc_start: 0.8433 (tttt) cc_final: 0.8190 (mttt) REVERT: G 311 LYS cc_start: 0.8461 (mtmt) cc_final: 0.7714 (mttm) REVERT: G 342 GLU cc_start: 0.8118 (mt-10) cc_final: 0.7884 (mt-10) REVERT: G 349 ARG cc_start: 0.8415 (mtt180) cc_final: 0.6944 (mmp-170) REVERT: B 311 LYS cc_start: 0.8746 (mtmt) cc_final: 0.8366 (mttt) REVERT: B 340 LYS cc_start: 0.8455 (mtpt) cc_final: 0.7994 (mttm) REVERT: B 342 GLU cc_start: 0.8349 (mt-10) cc_final: 0.7984 (tt0) REVERT: B 347 LYS cc_start: 0.8725 (mttt) cc_final: 0.8126 (pptt) REVERT: C 317 LYS cc_start: 0.8425 (ptmt) cc_final: 0.8199 (ptpp) REVERT: C 338 GLU cc_start: 0.8239 (tt0) cc_final: 0.7873 (tt0) REVERT: C 342 GLU cc_start: 0.8049 (mt-10) cc_final: 0.7715 (mt-10) REVERT: C 349 ARG cc_start: 0.8384 (mtp85) cc_final: 0.7992 (mtp85) REVERT: C 351 GLN cc_start: 0.8739 (mt0) cc_final: 0.8449 (mt0) REVERT: D 307 GLN cc_start: 0.7957 (mt0) cc_final: 0.7598 (tt0) REVERT: D 311 LYS cc_start: 0.8517 (mtmt) cc_final: 0.7725 (tppt) REVERT: D 349 ARG cc_start: 0.8457 (mtt180) cc_final: 0.6807 (mmp-170) REVERT: E 311 LYS cc_start: 0.8816 (mtmt) cc_final: 0.8465 (mtpt) REVERT: E 317 LYS cc_start: 0.8666 (mttt) cc_final: 0.8279 (mtmt) REVERT: E 338 GLU cc_start: 0.8394 (tt0) cc_final: 0.8166 (tt0) REVERT: E 342 GLU cc_start: 0.8154 (mt-10) cc_final: 0.7890 (tt0) REVERT: E 347 LYS cc_start: 0.8518 (mttt) cc_final: 0.8002 (pptt) REVERT: E 349 ARG cc_start: 0.8562 (mtp85) cc_final: 0.8338 (mtt180) outliers start: 8 outliers final: 2 residues processed: 89 average time/residue: 1.6127 time to fit residues: 146.2568 Evaluate side-chains 83 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 81 time to evaluate : 0.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 348 ASP Chi-restraints excluded: chain D residue 336 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 34 optimal weight: 5.9990 chunk 9 optimal weight: 3.9990 chunk 39 optimal weight: 5.9990 chunk 25 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 chunk 6 optimal weight: 4.9990 chunk 14 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 16 optimal weight: 4.9990 chunk 36 optimal weight: 6.9990 chunk 29 optimal weight: 0.6980 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 307 GLN C 307 GLN E 351 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.125141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.108468 restraints weight = 12217.385| |-----------------------------------------------------------------------------| r_work (start): 0.3678 rms_B_bonded: 1.52 r_work: 0.3587 rms_B_bonded: 1.52 restraints_weight: 0.5000 r_work: 0.3510 rms_B_bonded: 2.61 restraints_weight: 0.2500 r_work (final): 0.3510 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8954 moved from start: 0.4617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 3498 Z= 0.171 Angle : 0.510 4.119 4680 Z= 0.266 Chirality : 0.051 0.141 528 Planarity : 0.003 0.027 594 Dihedral : 5.173 14.888 462 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 0.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Rotamer: Outliers : 1.52 % Allowed : 15.15 % Favored : 83.33 % 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: -1.57 (0.32), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.19 (0.24), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG G 379 TYR 0.011 0.002 TYR A 310 PHE 0.006 0.001 PHE B 378 HIS 0.002 0.000 HIS G 329 Details of bonding type rmsd covalent geometry : bond 0.00379 ( 3498) covalent geometry : angle 0.50982 ( 4680) hydrogen bonds : bond 0.02012 ( 67) hydrogen bonds : angle 4.19195 ( 201) *********************** 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 86 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 80 time to evaluate : 0.171 Fit side-chains REVERT: A 340 LYS cc_start: 0.8320 (mtpt) cc_final: 0.8011 (mttt) REVERT: A 342 GLU cc_start: 0.8252 (mt-10) cc_final: 0.7903 (tt0) REVERT: G 311 LYS cc_start: 0.8421 (mtmt) cc_final: 0.7667 (tppt) REVERT: G 342 GLU cc_start: 0.8165 (mt-10) cc_final: 0.7927 (mt-10) REVERT: G 349 ARG cc_start: 0.8462 (mtt180) cc_final: 0.7044 (mmp-170) REVERT: B 311 LYS cc_start: 0.8770 (mtmt) cc_final: 0.8404 (mttt) REVERT: B 340 LYS cc_start: 0.8452 (mtpt) cc_final: 0.8016 (mttm) REVERT: B 342 GLU cc_start: 0.8314 (mt-10) cc_final: 0.7957 (tt0) REVERT: B 347 LYS cc_start: 0.8716 (mttt) cc_final: 0.8101 (pptt) REVERT: C 317 LYS cc_start: 0.8455 (ptmt) cc_final: 0.8235 (ptpp) REVERT: C 338 GLU cc_start: 0.8230 (tt0) cc_final: 0.7876 (tt0) REVERT: C 342 GLU cc_start: 0.8110 (mt-10) cc_final: 0.7756 (mt-10) REVERT: C 349 ARG cc_start: 0.8430 (mtp85) cc_final: 0.8140 (mtp85) REVERT: D 307 GLN cc_start: 0.7918 (mt0) cc_final: 0.7592 (tt0) REVERT: D 311 LYS cc_start: 0.8524 (mtmt) cc_final: 0.7735 (tppt) REVERT: D 349 ARG cc_start: 0.8475 (mtt180) cc_final: 0.6920 (mmp-170) REVERT: E 311 LYS cc_start: 0.8815 (mtmt) cc_final: 0.8478 (mtpt) REVERT: E 317 LYS cc_start: 0.8623 (mttt) cc_final: 0.8264 (mtmt) REVERT: E 338 GLU cc_start: 0.8306 (tt0) cc_final: 0.8077 (tt0) REVERT: E 342 GLU cc_start: 0.8178 (mt-10) cc_final: 0.7916 (tt0) REVERT: E 347 LYS cc_start: 0.8523 (mttt) cc_final: 0.8013 (pptt) outliers start: 6 outliers final: 4 residues processed: 82 average time/residue: 1.6871 time to fit residues: 141.1128 Evaluate side-chains 81 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 77 time to evaluate : 0.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 348 ASP Chi-restraints excluded: chain D residue 336 GLN Chi-restraints excluded: chain E residue 343 LYS Chi-restraints excluded: chain E residue 348 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 33 optimal weight: 5.9990 chunk 23 optimal weight: 6.9990 chunk 39 optimal weight: 4.9990 chunk 1 optimal weight: 5.9990 chunk 32 optimal weight: 0.6980 chunk 28 optimal weight: 4.9990 chunk 18 optimal weight: 4.9990 chunk 38 optimal weight: 5.9990 chunk 26 optimal weight: 1.9990 chunk 29 optimal weight: 5.9990 chunk 31 optimal weight: 5.9990 overall best weight: 3.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 307 GLN C 307 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.123586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.106761 restraints weight = 12324.456| |-----------------------------------------------------------------------------| r_work (start): 0.3645 rms_B_bonded: 1.54 r_work: 0.3553 rms_B_bonded: 1.54 restraints_weight: 0.5000 r_work: 0.3476 rms_B_bonded: 2.64 restraints_weight: 0.2500 r_work (final): 0.3476 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8971 moved from start: 0.4723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.027 3498 Z= 0.218 Angle : 0.527 4.181 4680 Z= 0.277 Chirality : 0.051 0.145 528 Planarity : 0.003 0.027 594 Dihedral : 5.242 15.446 462 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 1.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Rotamer: Outliers : 1.77 % Allowed : 15.40 % Favored : 82.83 % 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: -1.61 (0.32), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.22 (0.24), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 379 TYR 0.013 0.003 TYR A 310 PHE 0.007 0.001 PHE A 378 HIS 0.002 0.000 HIS G 329 Details of bonding type rmsd covalent geometry : bond 0.00491 ( 3498) covalent geometry : angle 0.52665 ( 4680) hydrogen bonds : bond 0.02249 ( 67) hydrogen bonds : angle 4.29548 ( 201) *********************** 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 81 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 74 time to evaluate : 0.216 Fit side-chains REVERT: A 342 GLU cc_start: 0.8272 (mt-10) cc_final: 0.7912 (tt0) REVERT: G 311 LYS cc_start: 0.8433 (mtmt) cc_final: 0.7654 (tppt) REVERT: G 342 GLU cc_start: 0.8212 (mt-10) cc_final: 0.7953 (mt-10) REVERT: G 349 ARG cc_start: 0.8489 (mtt180) cc_final: 0.6968 (mmp-170) REVERT: B 311 LYS cc_start: 0.8780 (mtmt) cc_final: 0.8403 (mttt) REVERT: B 340 LYS cc_start: 0.8492 (mtpt) cc_final: 0.8036 (mttm) REVERT: B 342 GLU cc_start: 0.8345 (mt-10) cc_final: 0.7988 (tt0) REVERT: B 347 LYS cc_start: 0.8707 (mttt) cc_final: 0.8065 (pptt) REVERT: B 349 ARG cc_start: 0.8512 (mtp85) cc_final: 0.8234 (mtt90) REVERT: C 317 LYS cc_start: 0.8471 (ptmt) cc_final: 0.8243 (ptpp) REVERT: C 338 GLU cc_start: 0.8268 (tt0) cc_final: 0.7910 (tt0) REVERT: C 342 GLU cc_start: 0.8110 (mt-10) cc_final: 0.7748 (mt-10) REVERT: C 349 ARG cc_start: 0.8492 (mtp85) cc_final: 0.8201 (mtp85) REVERT: D 307 GLN cc_start: 0.7943 (mt0) cc_final: 0.7591 (tt0) REVERT: D 349 ARG cc_start: 0.8484 (mtt180) cc_final: 0.6887 (mmp-170) REVERT: E 311 LYS cc_start: 0.8824 (mtmt) cc_final: 0.8479 (mtpt) REVERT: E 317 LYS cc_start: 0.8663 (mttt) cc_final: 0.8292 (mtmt) REVERT: E 338 GLU cc_start: 0.8324 (tt0) cc_final: 0.8095 (tt0) REVERT: E 342 GLU cc_start: 0.8222 (mt-10) cc_final: 0.7895 (tt0) REVERT: E 347 LYS cc_start: 0.8565 (mttt) cc_final: 0.8039 (pptt) outliers start: 7 outliers final: 3 residues processed: 77 average time/residue: 1.6722 time to fit residues: 131.4738 Evaluate side-chains 76 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 73 time to evaluate : 0.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 348 ASP Chi-restraints excluded: chain D residue 336 GLN Chi-restraints excluded: chain E residue 348 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 37 optimal weight: 3.9990 chunk 17 optimal weight: 5.9990 chunk 24 optimal weight: 8.9990 chunk 4 optimal weight: 4.9990 chunk 12 optimal weight: 3.9990 chunk 19 optimal weight: 1.9990 chunk 26 optimal weight: 5.9990 chunk 3 optimal weight: 1.9990 chunk 41 optimal weight: 4.9990 chunk 25 optimal weight: 4.9990 chunk 11 optimal weight: 2.9990 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 307 GLN C 307 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.123932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.107407 restraints weight = 12294.733| |-----------------------------------------------------------------------------| r_work (start): 0.3659 rms_B_bonded: 1.52 r_work: 0.3567 rms_B_bonded: 1.53 restraints_weight: 0.5000 r_work: 0.3490 rms_B_bonded: 2.63 restraints_weight: 0.2500 r_work (final): 0.3490 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8965 moved from start: 0.4801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 3498 Z= 0.187 Angle : 0.508 4.429 4680 Z= 0.267 Chirality : 0.050 0.142 528 Planarity : 0.003 0.028 594 Dihedral : 5.149 15.065 462 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 1.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Rotamer: Outliers : 1.26 % Allowed : 15.40 % Favored : 83.33 % 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: -1.64 (0.32), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.24 (0.24), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 379 TYR 0.011 0.002 TYR A 310 PHE 0.006 0.001 PHE A 378 HIS 0.002 0.000 HIS G 329 Details of bonding type rmsd covalent geometry : bond 0.00416 ( 3498) covalent geometry : angle 0.50844 ( 4680) hydrogen bonds : bond 0.02079 ( 67) hydrogen bonds : angle 4.18844 ( 201) *********************** 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 78 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 73 time to evaluate : 0.200 Fit side-chains REVERT: A 342 GLU cc_start: 0.8255 (mt-10) cc_final: 0.7909 (tt0) REVERT: A 349 ARG cc_start: 0.8418 (OUTLIER) cc_final: 0.8113 (mtp180) REVERT: G 311 LYS cc_start: 0.8415 (mtmt) cc_final: 0.7668 (mttm) REVERT: G 342 GLU cc_start: 0.8178 (mt-10) cc_final: 0.7942 (mt-10) REVERT: G 349 ARG cc_start: 0.8507 (mtt180) cc_final: 0.7026 (mmp-170) REVERT: B 311 LYS cc_start: 0.8761 (mtmt) cc_final: 0.8379 (mttt) REVERT: B 340 LYS cc_start: 0.8493 (mtpt) cc_final: 0.8029 (mttm) REVERT: B 342 GLU cc_start: 0.8347 (mt-10) cc_final: 0.7998 (tt0) REVERT: B 347 LYS cc_start: 0.8693 (mttt) cc_final: 0.8072 (pptt) REVERT: B 349 ARG cc_start: 0.8482 (mtp85) cc_final: 0.8193 (mtt90) REVERT: C 317 LYS cc_start: 0.8477 (ptmt) cc_final: 0.8242 (ptpp) REVERT: C 338 GLU cc_start: 0.8264 (tt0) cc_final: 0.7913 (tt0) REVERT: C 342 GLU cc_start: 0.8093 (mt-10) cc_final: 0.7747 (mt-10) REVERT: C 349 ARG cc_start: 0.8501 (mtp85) cc_final: 0.8204 (mtp85) REVERT: D 307 GLN cc_start: 0.7941 (mt0) cc_final: 0.7593 (tt0) REVERT: D 349 ARG cc_start: 0.8490 (mtt180) cc_final: 0.6917 (mmp-170) REVERT: E 311 LYS cc_start: 0.8818 (mtmt) cc_final: 0.8469 (mtpt) REVERT: E 317 LYS cc_start: 0.8645 (mttt) cc_final: 0.8279 (mtmt) REVERT: E 338 GLU cc_start: 0.8325 (tt0) cc_final: 0.8090 (tt0) REVERT: E 342 GLU cc_start: 0.8188 (mt-10) cc_final: 0.7880 (tt0) REVERT: E 347 LYS cc_start: 0.8569 (mttt) cc_final: 0.8043 (pptt) outliers start: 5 outliers final: 3 residues processed: 75 average time/residue: 1.5277 time to fit residues: 117.1451 Evaluate side-chains 74 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 70 time to evaluate : 0.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 348 ASP Chi-restraints excluded: chain A residue 349 ARG Chi-restraints excluded: chain D residue 336 GLN Chi-restraints excluded: chain E residue 348 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 21 optimal weight: 5.9990 chunk 26 optimal weight: 5.9990 chunk 30 optimal weight: 0.5980 chunk 20 optimal weight: 3.9990 chunk 18 optimal weight: 4.9990 chunk 13 optimal weight: 4.9990 chunk 33 optimal weight: 0.6980 chunk 36 optimal weight: 5.9990 chunk 14 optimal weight: 1.9990 chunk 6 optimal weight: 0.7980 chunk 23 optimal weight: 1.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 351 GLN B 307 GLN C 307 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.128068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.111772 restraints weight = 12214.634| |-----------------------------------------------------------------------------| r_work (start): 0.3721 rms_B_bonded: 1.52 r_work: 0.3631 rms_B_bonded: 1.53 restraints_weight: 0.5000 r_work: 0.3555 rms_B_bonded: 2.64 restraints_weight: 0.2500 r_work (final): 0.3555 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8938 moved from start: 0.4896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 3498 Z= 0.100 Angle : 0.466 4.913 4680 Z= 0.240 Chirality : 0.050 0.135 528 Planarity : 0.002 0.020 594 Dihedral : 4.775 13.608 462 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 0.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Rotamer: Outliers : 1.01 % Allowed : 15.91 % Favored : 83.08 % 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: -1.61 (0.32), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.22 (0.24), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 379 TYR 0.006 0.002 TYR A 310 PHE 0.002 0.000 PHE A 378 HIS 0.003 0.001 HIS G 362 Details of bonding type rmsd covalent geometry : bond 0.00221 ( 3498) covalent geometry : angle 0.46594 ( 4680) hydrogen bonds : bond 0.01583 ( 67) hydrogen bonds : angle 3.88368 ( 201) *********************** 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 80 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 76 time to evaluate : 0.157 Fit side-chains REVERT: A 342 GLU cc_start: 0.8206 (mt-10) cc_final: 0.7900 (tt0) REVERT: G 311 LYS cc_start: 0.8353 (mtmt) cc_final: 0.7565 (tppt) REVERT: G 342 GLU cc_start: 0.8153 (mt-10) cc_final: 0.7873 (tt0) REVERT: G 349 ARG cc_start: 0.8473 (mtt180) cc_final: 0.6958 (mmp-170) REVERT: B 311 LYS cc_start: 0.8733 (mtmt) cc_final: 0.8369 (mttt) REVERT: B 340 LYS cc_start: 0.8449 (mtpt) cc_final: 0.8006 (mttm) REVERT: B 342 GLU cc_start: 0.8300 (mt-10) cc_final: 0.7958 (tt0) REVERT: B 347 LYS cc_start: 0.8668 (mttt) cc_final: 0.8037 (pptt) REVERT: B 349 ARG cc_start: 0.8459 (mtp85) cc_final: 0.8160 (mtt90) REVERT: C 317 LYS cc_start: 0.8493 (ptmt) cc_final: 0.8258 (ptpp) REVERT: C 338 GLU cc_start: 0.8241 (tt0) cc_final: 0.7890 (tt0) REVERT: C 342 GLU cc_start: 0.8108 (mt-10) cc_final: 0.7783 (mt-10) REVERT: C 349 ARG cc_start: 0.8468 (mtp85) cc_final: 0.8250 (mtp85) REVERT: D 307 GLN cc_start: 0.7903 (mt0) cc_final: 0.7589 (tt0) REVERT: D 311 LYS cc_start: 0.8553 (mtmt) cc_final: 0.7747 (tppt) REVERT: D 342 GLU cc_start: 0.8212 (mt-10) cc_final: 0.7918 (mt-10) REVERT: D 349 ARG cc_start: 0.8489 (mtt180) cc_final: 0.6954 (mmp-170) REVERT: E 311 LYS cc_start: 0.8787 (mtmt) cc_final: 0.8454 (mtpt) REVERT: E 317 LYS cc_start: 0.8585 (mttt) cc_final: 0.8233 (mtmt) REVERT: E 338 GLU cc_start: 0.8246 (tt0) cc_final: 0.8006 (tt0) REVERT: E 342 GLU cc_start: 0.8157 (mt-10) cc_final: 0.7901 (tt0) REVERT: E 347 LYS cc_start: 0.8562 (mttt) cc_final: 0.8039 (pptt) outliers start: 4 outliers final: 3 residues processed: 78 average time/residue: 1.4243 time to fit residues: 113.5450 Evaluate side-chains 76 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 73 time to evaluate : 0.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 348 ASP Chi-restraints excluded: chain D residue 336 GLN Chi-restraints excluded: chain E residue 348 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 24 optimal weight: 8.9990 chunk 41 optimal weight: 5.9990 chunk 11 optimal weight: 3.9990 chunk 39 optimal weight: 0.9980 chunk 13 optimal weight: 4.9990 chunk 17 optimal weight: 0.3980 chunk 4 optimal weight: 0.9990 chunk 33 optimal weight: 4.9990 chunk 1 optimal weight: 5.9990 chunk 19 optimal weight: 4.9990 chunk 30 optimal weight: 3.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 351 GLN B 307 GLN C 307 GLN D 351 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.123896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.108418 restraints weight = 12483.913| |-----------------------------------------------------------------------------| r_work (start): 0.3694 rms_B_bonded: 1.47 r_work: 0.3601 rms_B_bonded: 1.52 restraints_weight: 0.5000 r_work: 0.3524 rms_B_bonded: 2.62 restraints_weight: 0.2500 r_work (final): 0.3524 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8951 moved from start: 0.4891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3498 Z= 0.140 Angle : 0.478 4.795 4680 Z= 0.249 Chirality : 0.050 0.139 528 Planarity : 0.003 0.024 594 Dihedral : 4.802 13.528 462 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 0.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Rotamer: Outliers : 1.26 % Allowed : 15.91 % Favored : 82.83 % 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: -1.61 (0.32), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.22 (0.24), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 379 TYR 0.010 0.002 TYR A 310 PHE 0.004 0.001 PHE A 378 HIS 0.002 0.000 HIS G 362 Details of bonding type rmsd covalent geometry : bond 0.00312 ( 3498) covalent geometry : angle 0.47807 ( 4680) hydrogen bonds : bond 0.01738 ( 67) hydrogen bonds : angle 3.89347 ( 201) *********************** 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 79 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 74 time to evaluate : 0.214 Fit side-chains REVERT: A 342 GLU cc_start: 0.8207 (mt-10) cc_final: 0.7902 (tt0) REVERT: A 349 ARG cc_start: 0.8437 (OUTLIER) cc_final: 0.8083 (mtp180) REVERT: G 311 LYS cc_start: 0.8396 (mtmt) cc_final: 0.7656 (mttm) REVERT: G 342 GLU cc_start: 0.8160 (mt-10) cc_final: 0.7875 (tt0) REVERT: G 349 ARG cc_start: 0.8463 (mtt180) cc_final: 0.7034 (mmp-170) REVERT: G 351 GLN cc_start: 0.8786 (mt0) cc_final: 0.8528 (mt0) REVERT: B 311 LYS cc_start: 0.8746 (mtmt) cc_final: 0.8382 (mttt) REVERT: B 340 LYS cc_start: 0.8487 (mtpt) cc_final: 0.8029 (mttm) REVERT: B 342 GLU cc_start: 0.8306 (mt-10) cc_final: 0.7974 (tt0) REVERT: B 347 LYS cc_start: 0.8687 (mttt) cc_final: 0.8072 (pptt) REVERT: B 349 ARG cc_start: 0.8479 (mtp85) cc_final: 0.8194 (mtt90) REVERT: C 317 LYS cc_start: 0.8511 (ptmt) cc_final: 0.8275 (ptpp) REVERT: C 338 GLU cc_start: 0.8266 (tt0) cc_final: 0.7911 (tt0) REVERT: C 342 GLU cc_start: 0.8118 (mt-10) cc_final: 0.7783 (mt-10) REVERT: C 349 ARG cc_start: 0.8507 (mtp85) cc_final: 0.8303 (mtp85) REVERT: D 307 GLN cc_start: 0.7910 (mt0) cc_final: 0.7594 (tt0) REVERT: D 342 GLU cc_start: 0.8221 (mt-10) cc_final: 0.7925 (mt-10) REVERT: D 349 ARG cc_start: 0.8498 (mtt180) cc_final: 0.6951 (mmp-170) REVERT: E 311 LYS cc_start: 0.8794 (mtmt) cc_final: 0.8462 (mtpt) REVERT: E 317 LYS cc_start: 0.8616 (mttt) cc_final: 0.8256 (mtmt) REVERT: E 338 GLU cc_start: 0.8275 (tt0) cc_final: 0.8024 (tt0) REVERT: E 342 GLU cc_start: 0.8159 (mt-10) cc_final: 0.7893 (tt0) REVERT: E 347 LYS cc_start: 0.8567 (mttt) cc_final: 0.8023 (pptt) outliers start: 5 outliers final: 3 residues processed: 76 average time/residue: 1.4909 time to fit residues: 115.8549 Evaluate side-chains 78 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 74 time to evaluate : 0.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 348 ASP Chi-restraints excluded: chain A residue 349 ARG Chi-restraints excluded: chain D residue 336 GLN Chi-restraints excluded: chain E residue 348 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 27 optimal weight: 5.9990 chunk 24 optimal weight: 8.9990 chunk 6 optimal weight: 5.9990 chunk 31 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 3 optimal weight: 10.0000 chunk 19 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 26 optimal weight: 3.9990 chunk 38 optimal weight: 0.9990 chunk 15 optimal weight: 6.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 307 GLN C 307 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.125255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.108718 restraints weight = 12277.377| |-----------------------------------------------------------------------------| r_work (start): 0.3676 rms_B_bonded: 1.52 r_work: 0.3585 rms_B_bonded: 1.53 restraints_weight: 0.5000 r_work: 0.3509 rms_B_bonded: 2.63 restraints_weight: 0.2500 r_work (final): 0.3509 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8956 moved from start: 0.4916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3498 Z= 0.154 Angle : 0.487 4.720 4680 Z= 0.254 Chirality : 0.050 0.140 528 Planarity : 0.002 0.021 594 Dihedral : 4.863 13.951 462 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 1.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Rotamer: Outliers : 1.26 % Allowed : 16.16 % 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: -1.64 (0.32), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.24 (0.24), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 379 TYR 0.010 0.002 TYR A 310 PHE 0.004 0.001 PHE A 378 HIS 0.001 0.000 HIS C 329 Details of bonding type rmsd covalent geometry : bond 0.00345 ( 3498) covalent geometry : angle 0.48716 ( 4680) hydrogen bonds : bond 0.01853 ( 67) hydrogen bonds : angle 3.92719 ( 201) ********************** 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 78 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 73 time to evaluate : 0.211 Fit side-chains REVERT: A 342 GLU cc_start: 0.8231 (mt-10) cc_final: 0.7919 (tt0) REVERT: A 349 ARG cc_start: 0.8434 (OUTLIER) cc_final: 0.8035 (mtp180) REVERT: G 311 LYS cc_start: 0.8425 (mtmt) cc_final: 0.7683 (mttm) REVERT: G 342 GLU cc_start: 0.8183 (mt-10) cc_final: 0.7945 (mt-10) REVERT: G 349 ARG cc_start: 0.8471 (mtt180) cc_final: 0.7035 (mmp-170) REVERT: B 311 LYS cc_start: 0.8757 (mtmt) cc_final: 0.8387 (mttt) REVERT: B 340 LYS cc_start: 0.8493 (mtpt) cc_final: 0.8032 (mttm) REVERT: B 342 GLU cc_start: 0.8338 (mt-10) cc_final: 0.8001 (tt0) REVERT: B 347 LYS cc_start: 0.8675 (mttt) cc_final: 0.8054 (pptt) REVERT: B 349 ARG cc_start: 0.8488 (mtp85) cc_final: 0.8134 (mtt90) REVERT: C 317 LYS cc_start: 0.8507 (ptmt) cc_final: 0.8271 (ptpp) REVERT: C 338 GLU cc_start: 0.8262 (tt0) cc_final: 0.7910 (tt0) REVERT: C 342 GLU cc_start: 0.8111 (mt-10) cc_final: 0.7749 (mt-10) REVERT: D 307 GLN cc_start: 0.7910 (mt0) cc_final: 0.7589 (tt0) REVERT: D 349 ARG cc_start: 0.8502 (mtt180) cc_final: 0.6959 (mmp-170) REVERT: E 311 LYS cc_start: 0.8803 (mtmt) cc_final: 0.8464 (mtpt) REVERT: E 317 LYS cc_start: 0.8626 (mttt) cc_final: 0.8266 (mtmt) REVERT: E 338 GLU cc_start: 0.8323 (tt0) cc_final: 0.8083 (tt0) REVERT: E 342 GLU cc_start: 0.8194 (mt-10) cc_final: 0.7910 (tt0) REVERT: E 347 LYS cc_start: 0.8548 (mttt) cc_final: 0.8019 (pptt) outliers start: 5 outliers final: 3 residues processed: 75 average time/residue: 1.5758 time to fit residues: 120.8231 Evaluate side-chains 73 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 69 time to evaluate : 0.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 348 ASP Chi-restraints excluded: chain A residue 349 ARG Chi-restraints excluded: chain D residue 336 GLN Chi-restraints excluded: chain E residue 348 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 39 optimal weight: 5.9990 chunk 7 optimal weight: 1.9990 chunk 34 optimal weight: 5.9990 chunk 21 optimal weight: 5.9990 chunk 28 optimal weight: 0.8980 chunk 35 optimal weight: 0.0670 chunk 3 optimal weight: 9.9990 chunk 8 optimal weight: 0.9980 chunk 9 optimal weight: 2.9990 chunk 4 optimal weight: 5.9990 chunk 11 optimal weight: 0.9990 overall best weight: 0.9922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 351 GLN G 351 GLN B 307 GLN C 307 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.128724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.112713 restraints weight = 12048.238| |-----------------------------------------------------------------------------| r_work (start): 0.3735 rms_B_bonded: 1.49 r_work: 0.3646 rms_B_bonded: 1.52 restraints_weight: 0.5000 r_work: 0.3571 rms_B_bonded: 2.61 restraints_weight: 0.2500 r_work (final): 0.3571 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8927 moved from start: 0.5014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 3498 Z= 0.089 Angle : 0.456 4.976 4680 Z= 0.234 Chirality : 0.050 0.134 528 Planarity : 0.002 0.019 594 Dihedral : 4.529 12.486 462 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 0.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Rotamer: Outliers : 1.26 % Allowed : 16.41 % Favored : 82.32 % 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: -1.60 (0.32), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.21 (0.25), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 379 TYR 0.006 0.002 TYR C 310 PHE 0.002 0.000 PHE A 378 HIS 0.003 0.001 HIS G 362 Details of bonding type rmsd covalent geometry : bond 0.00206 ( 3498) covalent geometry : angle 0.45556 ( 4680) hydrogen bonds : bond 0.01427 ( 67) hydrogen bonds : angle 3.68617 ( 201) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3916.26 seconds wall clock time: 66 minutes 57.04 seconds (4017.04 seconds total)