Starting phenix.real_space_refine on Wed Mar 12 02:05:15 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8q9m_18286/03_2025/8q9m_18286.cif Found real_map, /net/cci-nas-00/data/ceres_data/8q9m_18286/03_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_18286/03_2025/8q9m_18286.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8q9m_18286/03_2025/8q9m_18286.map" model { file = "/net/cci-nas-00/data/ceres_data/8q9m_18286/03_2025/8q9m_18286.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8q9m_18286/03_2025/8q9m_18286.cif" } resolution = 2.65 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: 4.04, per 1000 atoms: 0.57 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: 1.69 Conformation dependent library (CDL) restraints added in 720.0 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, 50.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.75 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: 2.20 Time building geometry restraints manager: 2.12 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: 0.01 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: 2.340 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: 0.120 Extract box with map and model: 0.240 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 19.170 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:14.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.140 ------------------------------------------------------------------------------- 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= 0.727 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 (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: -1.02 (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 HIS 0.018 0.005 HIS C 330 PHE 0.036 0.010 PHE E 346 TYR 0.081 0.019 TYR G 310 ARG 0.005 0.001 ARG B 379 *********************** 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 : 0.608 Fit side-chains revert: symmetry clash 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: 0.3958 (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: 0.4670 (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: 0.7518 (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: 0.7010 (ttmt) REVERT: D 311 LYS cc_start: 0.6166 (mtmt) cc_final: 0.5365 (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: 0.8762 (t70) REVERT: D 349 ARG cc_start: 0.8284 (mtt180) cc_final: 0.6267 (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: 0.5677 (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: 0.7908 (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: 3.2520 time to fit residues: 527.6173 Evaluate side-chains 115 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 115 time to evaluate : 0.605 ------------------------------------------------------------------------------- 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: 0.7980 chunk 31 optimal weight: 1.9990 chunk 17 optimal weight: 3.9990 chunk 10 optimal weight: 5.9990 chunk 21 optimal weight: 0.9990 chunk 32 optimal weight: 0.9990 chunk 12 optimal weight: 0.9990 chunk 20 optimal weight: 0.9990 chunk 24 optimal weight: 5.9990 chunk 38 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 overall best weight: 0.9588 ------------------------------------------------------------------------------- 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 = 0.4047 r_free = 0.4047 target = 0.135643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.119966 restraints weight = 11767.910| |-----------------------------------------------------------------------------| r_work (start): 0.3860 rms_B_bonded: 1.46 r_work: 0.3778 rms_B_bonded: 1.48 restraints_weight: 0.5000 r_work: 0.3703 rms_B_bonded: 2.58 restraints_weight: 0.2500 r_work (final): 0.3703 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8851 moved from start: 0.3211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 3498 Z= 0.186 Angle : 0.543 4.238 4680 Z= 0.284 Chirality : 0.051 0.143 528 Planarity : 0.002 0.016 594 Dihedral : 6.220 18.175 462 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 0.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 0.00 % Allowed : 13.13 % Favored : 86.87 % 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: -1.08 (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 HIS 0.003 0.001 HIS C 330 PHE 0.004 0.001 PHE A 346 TYR 0.008 0.001 TYR A 310 ARG 0.003 0.001 ARG C 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 118 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 118 time to evaluate : 0.594 Fit side-chains REVERT: A 307 GLN cc_start: 0.7668 (mt0) cc_final: 0.7308 (tt0) REVERT: A 314 ASP cc_start: 0.8431 (t0) cc_final: 0.8187 (t0) REVERT: A 340 LYS cc_start: 0.8287 (mtpt) cc_final: 0.7981 (mttt) REVERT: A 342 GLU cc_start: 0.8111 (mt-10) cc_final: 0.7808 (mt-10) REVERT: A 369 LYS cc_start: 0.8492 (tttt) cc_final: 0.8257 (mttt) REVERT: G 311 LYS cc_start: 0.8380 (mtmt) cc_final: 0.7623 (tppt) REVERT: G 340 LYS cc_start: 0.8228 (mtpt) cc_final: 0.7884 (mttt) REVERT: G 342 GLU cc_start: 0.8128 (mt-10) cc_final: 0.7865 (mt-10) REVERT: G 343 LYS cc_start: 0.9047 (mttt) cc_final: 0.8776 (mttp) REVERT: G 349 ARG cc_start: 0.8366 (mtt180) cc_final: 0.6905 (mmp-170) REVERT: G 375 LYS cc_start: 0.8498 (tttt) cc_final: 0.8173 (tptt) REVERT: B 311 LYS cc_start: 0.8703 (mtmt) cc_final: 0.8323 (mttt) REVERT: B 342 GLU cc_start: 0.8283 (mt-10) cc_final: 0.7917 (tt0) REVERT: B 347 LYS cc_start: 0.8744 (mttt) cc_final: 0.8153 (pptt) REVERT: C 317 LYS cc_start: 0.8489 (ptmt) cc_final: 0.8232 (ptpp) REVERT: C 338 GLU cc_start: 0.8171 (tt0) cc_final: 0.7801 (tt0) REVERT: C 342 GLU cc_start: 0.7985 (mt-10) cc_final: 0.7653 (mt-10) REVERT: C 348 ASP cc_start: 0.8927 (t0) cc_final: 0.8637 (t70) REVERT: C 349 ARG cc_start: 0.8185 (mtt180) cc_final: 0.7837 (mtp85) REVERT: D 311 LYS cc_start: 0.8418 (mtmt) cc_final: 0.7647 (tppt) REVERT: D 340 LYS cc_start: 0.8353 (mtpt) cc_final: 0.8035 (mttt) REVERT: D 349 ARG cc_start: 0.8398 (mtt180) cc_final: 0.6819 (mmp-170) REVERT: E 311 LYS cc_start: 0.8805 (mtmt) cc_final: 0.8417 (mtpt) REVERT: E 338 GLU cc_start: 0.8240 (tt0) cc_final: 0.7991 (tt0) REVERT: E 342 GLU cc_start: 0.8097 (mt-10) cc_final: 0.7879 (tt0) REVERT: E 347 LYS cc_start: 0.8534 (mttt) cc_final: 0.8098 (pptt) REVERT: E 379 ARG cc_start: 0.7746 (mmt-90) cc_final: 0.4683 (mtm-85) outliers start: 0 outliers final: 0 residues processed: 118 average time/residue: 3.4516 time to fit residues: 415.4558 Evaluate side-chains 91 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 91 time to evaluate : 0.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 20 optimal weight: 0.0000 chunk 21 optimal weight: 5.9990 chunk 1 optimal weight: 5.9990 chunk 15 optimal weight: 2.9990 chunk 34 optimal weight: 3.9990 chunk 12 optimal weight: 2.9990 chunk 36 optimal weight: 6.9990 chunk 18 optimal weight: 5.9990 chunk 11 optimal weight: 0.8980 chunk 5 optimal weight: 0.9980 chunk 10 optimal weight: 2.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- 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 = 0.3970 r_free = 0.3970 target = 0.130201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.114152 restraints weight = 11946.177| |-----------------------------------------------------------------------------| r_work (start): 0.3779 rms_B_bonded: 1.47 r_work: 0.3700 rms_B_bonded: 1.48 restraints_weight: 0.5000 r_work: 0.3626 rms_B_bonded: 2.57 restraints_weight: 0.2500 r_work (final): 0.3626 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8902 moved from start: 0.4244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 3498 Z= 0.185 Angle : 0.509 4.162 4680 Z= 0.264 Chirality : 0.052 0.143 528 Planarity : 0.003 0.045 594 Dihedral : 5.294 14.476 462 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 1.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Rotamer: Outliers : 2.02 % Allowed : 15.15 % 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 (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: -1.30 (0.33), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.98 (0.25), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS G 330 PHE 0.006 0.001 PHE G 378 TYR 0.010 0.002 TYR A 310 ARG 0.004 0.001 ARG G 379 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 95 time to evaluate : 0.551 Fit side-chains REVERT: A 307 GLN cc_start: 0.7688 (mt0) cc_final: 0.7352 (tt0) REVERT: A 340 LYS cc_start: 0.8291 (mtpt) cc_final: 0.7996 (mttt) REVERT: A 342 GLU cc_start: 0.8139 (mt-10) cc_final: 0.7816 (tt0) REVERT: A 369 LYS cc_start: 0.8454 (tttt) cc_final: 0.8234 (mttt) REVERT: G 311 LYS cc_start: 0.8346 (mtmt) cc_final: 0.7553 (tppt) REVERT: G 342 GLU cc_start: 0.8105 (mt-10) cc_final: 0.7898 (mt-10) REVERT: G 349 ARG cc_start: 0.8405 (mtt180) cc_final: 0.6969 (mmp-170) REVERT: B 311 LYS cc_start: 0.8693 (mtmt) cc_final: 0.8302 (mttt) REVERT: B 342 GLU cc_start: 0.8260 (mt-10) cc_final: 0.7920 (tt0) REVERT: B 347 LYS cc_start: 0.8718 (mttt) cc_final: 0.8132 (pptt) REVERT: C 317 LYS cc_start: 0.8446 (ptmt) cc_final: 0.8224 (ptpp) REVERT: C 338 GLU cc_start: 0.8203 (tt0) cc_final: 0.7845 (tt0) REVERT: C 342 GLU cc_start: 0.8032 (mt-10) cc_final: 0.7711 (mt-10) REVERT: C 351 GLN cc_start: 0.8699 (mt0) cc_final: 0.8418 (mt0) REVERT: D 307 GLN cc_start: 0.7867 (mt0) cc_final: 0.7534 (tt0) REVERT: D 311 LYS cc_start: 0.8455 (mtmt) cc_final: 0.7689 (tppt) REVERT: D 349 ARG cc_start: 0.8425 (mtt180) cc_final: 0.6886 (mmp-170) REVERT: E 311 LYS cc_start: 0.8802 (mtmt) cc_final: 0.8458 (mtpt) REVERT: E 317 LYS cc_start: 0.8594 (mttt) cc_final: 0.8228 (mtmt) REVERT: E 338 GLU cc_start: 0.8329 (tt0) cc_final: 0.8078 (tt0) REVERT: E 342 GLU cc_start: 0.8100 (mt-10) cc_final: 0.7870 (tt0) REVERT: E 347 LYS cc_start: 0.8490 (mttt) cc_final: 0.8121 (pptt) REVERT: E 379 ARG cc_start: 0.7735 (mmt-90) cc_final: 0.4781 (mtm-85) outliers start: 8 outliers final: 1 residues processed: 97 average time/residue: 3.3571 time to fit residues: 332.4259 Evaluate side-chains 85 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 84 time to evaluate : 0.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 336 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 20 optimal weight: 2.9990 chunk 37 optimal weight: 3.9990 chunk 10 optimal weight: 8.9990 chunk 12 optimal weight: 3.9990 chunk 40 optimal weight: 4.9990 chunk 35 optimal weight: 0.4980 chunk 2 optimal weight: 6.9990 chunk 14 optimal weight: 0.0020 chunk 21 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 chunk 16 optimal weight: 0.8980 overall best weight: 1.4792 ------------------------------------------------------------------------------- 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 E 351 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.132603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.116427 restraints weight = 11815.211| |-----------------------------------------------------------------------------| r_work (start): 0.3794 rms_B_bonded: 1.45 r_work: 0.3701 rms_B_bonded: 1.52 restraints_weight: 0.5000 r_work: 0.3626 rms_B_bonded: 2.62 restraints_weight: 0.2500 r_work (final): 0.3626 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8916 moved from start: 0.4500 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= 0.173 Angle : 0.480 4.293 4680 Z= 0.248 Chirality : 0.051 0.137 528 Planarity : 0.003 0.038 594 Dihedral : 4.918 13.549 462 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 0.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Rotamer: Outliers : 1.52 % Allowed : 14.39 % Favored : 84.09 % 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: -1.43 (0.32), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.08 (0.25), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS G 329 PHE 0.004 0.001 PHE G 378 TYR 0.009 0.002 TYR A 310 ARG 0.004 0.001 ARG G 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 94 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 88 time to evaluate : 0.551 Fit side-chains revert: symmetry clash REVERT: A 340 LYS cc_start: 0.8296 (mtpt) cc_final: 0.8001 (mttt) REVERT: A 342 GLU cc_start: 0.8190 (mt-10) cc_final: 0.7874 (tt0) REVERT: G 311 LYS cc_start: 0.8339 (mtmt) cc_final: 0.7546 (tppt) REVERT: G 342 GLU cc_start: 0.8173 (mt-10) cc_final: 0.7962 (mt-10) REVERT: G 348 ASP cc_start: 0.8861 (t70) cc_final: 0.8645 (t70) REVERT: G 349 ARG cc_start: 0.8433 (mtt180) cc_final: 0.6859 (mmp-170) REVERT: B 311 LYS cc_start: 0.8711 (mtmt) cc_final: 0.8319 (mttt) REVERT: B 342 GLU cc_start: 0.8250 (mt-10) cc_final: 0.7898 (tt0) REVERT: B 347 LYS cc_start: 0.8681 (mttt) cc_final: 0.8145 (pptt) REVERT: C 317 LYS cc_start: 0.8491 (ptmt) cc_final: 0.8266 (ptpp) REVERT: C 338 GLU cc_start: 0.8221 (tt0) cc_final: 0.7862 (tt0) REVERT: C 342 GLU cc_start: 0.8071 (mt-10) cc_final: 0.7810 (mt-10) REVERT: C 351 GLN cc_start: 0.8718 (mt0) cc_final: 0.8439 (mt0) REVERT: D 307 GLN cc_start: 0.7884 (mt0) cc_final: 0.7595 (tt0) REVERT: D 311 LYS cc_start: 0.8486 (mtmt) cc_final: 0.7743 (mttm) REVERT: D 342 GLU cc_start: 0.8173 (mt-10) cc_final: 0.7883 (mt-10) REVERT: D 349 ARG cc_start: 0.8415 (mtt180) cc_final: 0.6881 (mmp-170) REVERT: E 311 LYS cc_start: 0.8790 (mtmt) cc_final: 0.8456 (mtpt) REVERT: E 317 LYS cc_start: 0.8598 (mttt) cc_final: 0.8233 (mtmt) REVERT: E 338 GLU cc_start: 0.8322 (tt0) cc_final: 0.8080 (tt0) REVERT: E 347 LYS cc_start: 0.8561 (mttt) cc_final: 0.8076 (pptt) REVERT: E 379 ARG cc_start: 0.7710 (mmt-90) cc_final: 0.4837 (mtm-85) outliers start: 6 outliers final: 2 residues processed: 91 average time/residue: 3.3498 time to fit residues: 311.3007 Evaluate side-chains 81 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 79 time to evaluate : 0.532 ------------------------------------------------------------------------------- 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 33 optimal weight: 5.9990 chunk 29 optimal weight: 6.9990 chunk 21 optimal weight: 5.9990 chunk 38 optimal weight: 5.9990 chunk 30 optimal weight: 0.9990 chunk 13 optimal weight: 4.9990 chunk 12 optimal weight: 1.9990 chunk 4 optimal weight: 5.9990 chunk 40 optimal weight: 4.9990 chunk 14 optimal weight: 2.9990 chunk 37 optimal weight: 3.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 351 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.124470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.107756 restraints weight = 12160.111| |-----------------------------------------------------------------------------| r_work (start): 0.3667 rms_B_bonded: 1.53 r_work: 0.3576 rms_B_bonded: 1.52 restraints_weight: 0.5000 r_work: 0.3499 rms_B_bonded: 2.61 restraints_weight: 0.2500 r_work (final): 0.3499 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8958 moved from start: 0.4611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 3498 Z= 0.298 Angle : 0.515 4.081 4680 Z= 0.270 Chirality : 0.051 0.142 528 Planarity : 0.003 0.037 594 Dihedral : 5.072 14.389 462 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 : 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 (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: -1.50 (0.32), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.13 (0.25), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS G 329 PHE 0.006 0.001 PHE A 378 TYR 0.012 0.003 TYR A 310 ARG 0.003 0.001 ARG E 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 : 0.580 Fit side-chains REVERT: A 342 GLU cc_start: 0.8248 (mt-10) cc_final: 0.7925 (tt0) REVERT: G 311 LYS cc_start: 0.8439 (mtmt) cc_final: 0.7663 (tppt) REVERT: G 342 GLU cc_start: 0.8189 (mt-10) cc_final: 0.7943 (mt-10) REVERT: G 349 ARG cc_start: 0.8470 (mtt180) cc_final: 0.7007 (mmp-170) REVERT: B 311 LYS cc_start: 0.8731 (mtmt) cc_final: 0.8365 (mttt) REVERT: B 340 LYS cc_start: 0.8506 (mtpt) cc_final: 0.8040 (mttm) REVERT: B 342 GLU cc_start: 0.8282 (mt-10) cc_final: 0.7934 (tt0) REVERT: B 347 LYS cc_start: 0.8688 (mttt) cc_final: 0.8137 (pptt) REVERT: B 349 ARG cc_start: 0.8413 (mtp85) cc_final: 0.8122 (mtt90) REVERT: C 317 LYS cc_start: 0.8496 (ptmt) cc_final: 0.8276 (ptpp) REVERT: C 338 GLU cc_start: 0.8251 (tt0) cc_final: 0.7903 (tt0) REVERT: C 342 GLU cc_start: 0.8094 (mt-10) cc_final: 0.7736 (mt-10) REVERT: D 307 GLN cc_start: 0.7914 (mt0) cc_final: 0.7606 (tt0) REVERT: D 311 LYS cc_start: 0.8508 (mtmt) cc_final: 0.7709 (tppt) REVERT: D 349 ARG cc_start: 0.8427 (mtt180) cc_final: 0.6883 (mmp-170) REVERT: E 311 LYS cc_start: 0.8806 (mtmt) cc_final: 0.8477 (mtpt) REVERT: E 317 LYS cc_start: 0.8617 (mttt) cc_final: 0.8255 (mtmt) REVERT: E 338 GLU cc_start: 0.8327 (tt0) cc_final: 0.8091 (tt0) REVERT: E 347 LYS cc_start: 0.8519 (mttt) cc_final: 0.8017 (pptt) outliers start: 8 outliers final: 2 residues processed: 83 average time/residue: 3.3542 time to fit residues: 284.4374 Evaluate side-chains 81 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 79 time to evaluate : 0.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 348 ASP Chi-restraints excluded: chain D residue 336 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 7 optimal weight: 3.9990 chunk 25 optimal weight: 6.9990 chunk 6 optimal weight: 5.9990 chunk 21 optimal weight: 5.9990 chunk 29 optimal weight: 7.9990 chunk 4 optimal weight: 5.9990 chunk 23 optimal weight: 6.9990 chunk 15 optimal weight: 6.9990 chunk 8 optimal weight: 3.9990 chunk 37 optimal weight: 0.9990 chunk 16 optimal weight: 2.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3872 r_free = 0.3872 target = 0.123148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.106596 restraints weight = 12265.045| |-----------------------------------------------------------------------------| r_work (start): 0.3642 rms_B_bonded: 1.52 r_work: 0.3552 rms_B_bonded: 1.53 restraints_weight: 0.5000 r_work: 0.3474 rms_B_bonded: 2.61 restraints_weight: 0.2500 r_work (final): 0.3474 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8971 moved from start: 0.4731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.028 3498 Z= 0.345 Angle : 0.531 3.965 4680 Z= 0.279 Chirality : 0.051 0.146 528 Planarity : 0.004 0.049 594 Dihedral : 5.194 15.132 462 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 0.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Rotamer: Outliers : 1.52 % Allowed : 14.65 % 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 (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: -1.59 (0.32), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.21 (0.24), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS G 329 PHE 0.007 0.001 PHE A 378 TYR 0.014 0.003 TYR A 310 ARG 0.004 0.001 ARG A 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 81 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 75 time to evaluate : 0.557 Fit side-chains REVERT: A 342 GLU cc_start: 0.8281 (mt-10) cc_final: 0.7936 (tt0) REVERT: A 349 ARG cc_start: 0.8443 (OUTLIER) cc_final: 0.8182 (mtp180) REVERT: G 311 LYS cc_start: 0.8465 (mtmt) cc_final: 0.7713 (mttm) REVERT: G 342 GLU cc_start: 0.8210 (mt-10) cc_final: 0.7954 (mt-10) REVERT: G 349 ARG cc_start: 0.8481 (mtt180) cc_final: 0.7011 (mmp-170) REVERT: B 311 LYS cc_start: 0.8780 (mtmt) cc_final: 0.8408 (mttt) REVERT: B 340 LYS cc_start: 0.8513 (mtpt) cc_final: 0.8039 (mttm) REVERT: B 342 GLU cc_start: 0.8359 (mt-10) cc_final: 0.8004 (tt0) REVERT: B 347 LYS cc_start: 0.8697 (mttt) cc_final: 0.8100 (pptt) REVERT: C 317 LYS cc_start: 0.8494 (ptmt) cc_final: 0.8276 (ptpp) REVERT: C 338 GLU cc_start: 0.8268 (tt0) cc_final: 0.7920 (tt0) REVERT: C 342 GLU cc_start: 0.8095 (mt-10) cc_final: 0.7732 (mt-10) REVERT: D 307 GLN cc_start: 0.7934 (mt0) cc_final: 0.7600 (tt0) REVERT: D 349 ARG cc_start: 0.8456 (mtt180) cc_final: 0.6879 (mmp-170) REVERT: E 311 LYS cc_start: 0.8819 (mtmt) cc_final: 0.8479 (mtpt) REVERT: E 317 LYS cc_start: 0.8648 (mttt) cc_final: 0.8286 (mtmt) REVERT: E 338 GLU cc_start: 0.8340 (tt0) cc_final: 0.8105 (tt0) REVERT: E 347 LYS cc_start: 0.8546 (mttt) cc_final: 0.8019 (pptt) outliers start: 6 outliers final: 3 residues processed: 78 average time/residue: 2.9824 time to fit residues: 238.1639 Evaluate side-chains 75 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 71 time to evaluate : 0.617 ------------------------------------------------------------------------------- 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 32 optimal weight: 6.9990 chunk 15 optimal weight: 6.9990 chunk 6 optimal weight: 5.9990 chunk 14 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 38 optimal weight: 4.9990 chunk 12 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 29 optimal weight: 7.9990 chunk 24 optimal weight: 0.9980 overall best weight: 1.7988 ------------------------------------------------------------------------------- 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 = 0.3889 r_free = 0.3889 target = 0.124084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.108409 restraints weight = 12278.701| |-----------------------------------------------------------------------------| r_work (start): 0.3702 rms_B_bonded: 1.48 r_work: 0.3610 rms_B_bonded: 1.52 restraints_weight: 0.5000 r_work: 0.3534 rms_B_bonded: 2.61 restraints_weight: 0.2500 r_work (final): 0.3534 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8948 moved from start: 0.4802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 3498 Z= 0.199 Angle : 0.484 4.322 4680 Z= 0.250 Chirality : 0.050 0.136 528 Planarity : 0.003 0.038 594 Dihedral : 4.891 13.984 462 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 1.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Rotamer: Outliers : 1.26 % Allowed : 14.90 % 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 (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: -1.61 (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 HIS 0.002 0.000 HIS G 362 PHE 0.004 0.001 PHE A 378 TYR 0.008 0.002 TYR A 310 ARG 0.003 0.001 ARG E 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 79 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 74 time to evaluate : 0.600 Fit side-chains REVERT: A 342 GLU cc_start: 0.8226 (mt-10) cc_final: 0.7921 (tt0) REVERT: G 311 LYS cc_start: 0.8393 (mtmt) cc_final: 0.7628 (tppt) REVERT: G 342 GLU cc_start: 0.8161 (mt-10) cc_final: 0.7936 (mt-10) REVERT: G 349 ARG cc_start: 0.8444 (mtt180) cc_final: 0.7009 (mmp-170) REVERT: B 311 LYS cc_start: 0.8750 (mtmt) cc_final: 0.8382 (mttt) REVERT: B 340 LYS cc_start: 0.8488 (mtpt) cc_final: 0.8027 (mttm) REVERT: B 342 GLU cc_start: 0.8314 (mt-10) cc_final: 0.7972 (tt0) REVERT: B 347 LYS cc_start: 0.8672 (mttt) cc_final: 0.8060 (pptt) REVERT: B 349 ARG cc_start: 0.8488 (mtp85) cc_final: 0.8249 (mtt90) REVERT: C 317 LYS cc_start: 0.8485 (ptmt) cc_final: 0.8260 (ptpp) REVERT: C 338 GLU cc_start: 0.8252 (tt0) cc_final: 0.7905 (tt0) REVERT: C 342 GLU cc_start: 0.8096 (mt-10) cc_final: 0.7748 (mt-10) REVERT: D 307 GLN cc_start: 0.7904 (mt0) cc_final: 0.7591 (tt0) REVERT: D 311 LYS cc_start: 0.8561 (mtmt) cc_final: 0.7751 (tppt) REVERT: D 342 GLU cc_start: 0.8207 (mt-10) cc_final: 0.7924 (mt-10) REVERT: D 349 ARG cc_start: 0.8428 (mtt180) cc_final: 0.6912 (mmp-170) REVERT: E 311 LYS cc_start: 0.8775 (mtmt) cc_final: 0.8472 (mtpt) REVERT: E 317 LYS cc_start: 0.8588 (mttt) cc_final: 0.8242 (mtmt) REVERT: E 338 GLU cc_start: 0.8296 (tt0) cc_final: 0.8063 (tt0) REVERT: E 347 LYS cc_start: 0.8559 (mttt) cc_final: 0.8041 (pptt) outliers start: 5 outliers final: 3 residues processed: 76 average time/residue: 3.1127 time to fit residues: 242.0148 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 : 0.640 ------------------------------------------------------------------------------- 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 39 optimal weight: 4.9990 chunk 38 optimal weight: 3.9990 chunk 15 optimal weight: 6.9990 chunk 29 optimal weight: 7.9990 chunk 20 optimal weight: 0.9980 chunk 33 optimal weight: 0.0980 chunk 24 optimal weight: 2.9990 chunk 16 optimal weight: 3.9990 chunk 2 optimal weight: 2.9990 chunk 17 optimal weight: 5.9990 chunk 3 optimal weight: 4.9990 overall best weight: 2.2186 ------------------------------------------------------------------------------- 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 D 351 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.125730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.109134 restraints weight = 12242.220| |-----------------------------------------------------------------------------| r_work (start): 0.3686 rms_B_bonded: 1.52 r_work: 0.3594 rms_B_bonded: 1.54 restraints_weight: 0.5000 r_work: 0.3517 rms_B_bonded: 2.64 restraints_weight: 0.2500 r_work (final): 0.3517 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8957 moved from start: 0.4845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 3498 Z= 0.232 Angle : 0.487 4.423 4680 Z= 0.254 Chirality : 0.050 0.140 528 Planarity : 0.003 0.034 594 Dihedral : 4.862 13.848 462 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 1.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Rotamer: Outliers : 1.01 % Allowed : 15.40 % Favored : 83.59 % 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: -1.63 (0.32), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.23 (0.24), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS G 362 PHE 0.005 0.001 PHE A 378 TYR 0.010 0.002 TYR A 310 ARG 0.002 0.000 ARG G 379 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 876 Ramachandran restraints generated. 438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 73 time to evaluate : 0.593 Fit side-chains REVERT: A 342 GLU cc_start: 0.8240 (mt-10) cc_final: 0.7927 (tt0) REVERT: G 311 LYS cc_start: 0.8418 (mtmt) cc_final: 0.7678 (mttm) REVERT: G 342 GLU cc_start: 0.8171 (mt-10) cc_final: 0.7938 (mt-10) REVERT: G 349 ARG cc_start: 0.8442 (mtt180) cc_final: 0.6864 (mmp-170) REVERT: B 311 LYS cc_start: 0.8759 (mtmt) cc_final: 0.8389 (mttt) REVERT: B 340 LYS cc_start: 0.8499 (mtpt) cc_final: 0.8039 (mttm) REVERT: B 342 GLU cc_start: 0.8330 (mt-10) cc_final: 0.7983 (tt0) REVERT: B 347 LYS cc_start: 0.8679 (mttt) cc_final: 0.8043 (pptt) REVERT: B 349 ARG cc_start: 0.8484 (mtp85) cc_final: 0.8171 (mtt90) REVERT: C 317 LYS cc_start: 0.8509 (ptmt) cc_final: 0.8276 (ptpp) REVERT: C 338 GLU cc_start: 0.8270 (tt0) cc_final: 0.7922 (tt0) REVERT: C 342 GLU cc_start: 0.8106 (mt-10) cc_final: 0.7748 (mt-10) REVERT: D 307 GLN cc_start: 0.7921 (mt0) cc_final: 0.7594 (tt0) REVERT: D 342 GLU cc_start: 0.8224 (mt-10) cc_final: 0.7931 (mt-10) REVERT: D 349 ARG cc_start: 0.8437 (mtt180) cc_final: 0.6888 (mmp-170) REVERT: E 311 LYS cc_start: 0.8795 (mtmt) cc_final: 0.8487 (mtpt) REVERT: E 317 LYS cc_start: 0.8607 (mttt) cc_final: 0.8253 (mtmt) REVERT: E 338 GLU cc_start: 0.8316 (tt0) cc_final: 0.8082 (tt0) REVERT: E 347 LYS cc_start: 0.8559 (mttt) cc_final: 0.8011 (pptt) outliers start: 4 outliers final: 3 residues processed: 74 average time/residue: 3.2213 time to fit residues: 243.8447 Evaluate side-chains 75 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 72 time to evaluate : 0.605 ------------------------------------------------------------------------------- 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 10 optimal weight: 7.9990 chunk 25 optimal weight: 6.9990 chunk 12 optimal weight: 2.9990 chunk 40 optimal weight: 3.9990 chunk 29 optimal weight: 6.9990 chunk 41 optimal weight: 4.9990 chunk 15 optimal weight: 5.9990 chunk 38 optimal weight: 4.9990 chunk 19 optimal weight: 1.9990 chunk 39 optimal weight: 0.9990 chunk 9 optimal weight: 0.8980 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 351 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 = 0.3909 r_free = 0.3909 target = 0.125837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.109441 restraints weight = 12203.249| |-----------------------------------------------------------------------------| r_work (start): 0.3689 rms_B_bonded: 1.52 r_work: 0.3599 rms_B_bonded: 1.52 restraints_weight: 0.5000 r_work: 0.3521 rms_B_bonded: 2.62 restraints_weight: 0.2500 r_work (final): 0.3521 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8954 moved from start: 0.4875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 3498 Z= 0.222 Angle : 0.483 4.388 4680 Z= 0.251 Chirality : 0.050 0.139 528 Planarity : 0.003 0.030 594 Dihedral : 4.813 13.860 462 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 1.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Rotamer: Outliers : 1.01 % Allowed : 15.66 % 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 (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: -1.65 (0.32), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.25 (0.24), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS G 362 PHE 0.004 0.001 PHE A 378 TYR 0.009 0.002 TYR A 310 ARG 0.003 0.000 ARG A 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 79 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 75 time to evaluate : 0.561 Fit side-chains REVERT: A 342 GLU cc_start: 0.8238 (mt-10) cc_final: 0.7930 (tt0) REVERT: G 311 LYS cc_start: 0.8412 (mtmt) cc_final: 0.7681 (mttm) REVERT: G 342 GLU cc_start: 0.8167 (mt-10) cc_final: 0.7936 (mt-10) REVERT: G 349 ARG cc_start: 0.8461 (mtt180) cc_final: 0.6999 (mmp-170) REVERT: B 307 GLN cc_start: 0.8172 (mt0) cc_final: 0.7931 (tt0) REVERT: B 311 LYS cc_start: 0.8759 (mtmt) cc_final: 0.8389 (mttt) REVERT: B 340 LYS cc_start: 0.8502 (mtpt) cc_final: 0.8042 (mttm) REVERT: B 342 GLU cc_start: 0.8337 (mt-10) cc_final: 0.7983 (tt0) REVERT: B 347 LYS cc_start: 0.8661 (mttt) cc_final: 0.8046 (pptt) REVERT: B 349 ARG cc_start: 0.8499 (mtp85) cc_final: 0.8104 (mtt90) REVERT: C 317 LYS cc_start: 0.8511 (ptmt) cc_final: 0.8284 (ptpp) REVERT: C 338 GLU cc_start: 0.8267 (tt0) cc_final: 0.7915 (tt0) REVERT: C 342 GLU cc_start: 0.8086 (mt-10) cc_final: 0.7740 (mt-10) REVERT: D 307 GLN cc_start: 0.7897 (mt0) cc_final: 0.7588 (tt0) REVERT: D 342 GLU cc_start: 0.8216 (mt-10) cc_final: 0.7929 (mt-10) REVERT: D 349 ARG cc_start: 0.8437 (mtt180) cc_final: 0.6917 (mmp-170) REVERT: E 311 LYS cc_start: 0.8788 (mtmt) cc_final: 0.8481 (mtpt) REVERT: E 317 LYS cc_start: 0.8601 (mttt) cc_final: 0.8254 (mtmt) REVERT: E 338 GLU cc_start: 0.8309 (tt0) cc_final: 0.8075 (tt0) REVERT: E 347 LYS cc_start: 0.8525 (mttt) cc_final: 0.8005 (pptt) outliers start: 4 outliers final: 3 residues processed: 77 average time/residue: 3.1533 time to fit residues: 248.5159 Evaluate side-chains 75 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 72 time to evaluate : 0.564 ------------------------------------------------------------------------------- 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 5 optimal weight: 5.9990 chunk 41 optimal weight: 3.9990 chunk 25 optimal weight: 5.9990 chunk 21 optimal weight: 5.9990 chunk 4 optimal weight: 0.8980 chunk 32 optimal weight: 0.7980 chunk 18 optimal weight: 0.6980 chunk 17 optimal weight: 3.9990 chunk 8 optimal weight: 5.9990 chunk 6 optimal weight: 1.9990 chunk 31 optimal weight: 7.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 307 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.126891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.110675 restraints weight = 12343.315| |-----------------------------------------------------------------------------| r_work (start): 0.3706 rms_B_bonded: 1.52 r_work: 0.3614 rms_B_bonded: 1.53 restraints_weight: 0.5000 r_work: 0.3538 rms_B_bonded: 2.63 restraints_weight: 0.2500 r_work (final): 0.3538 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8943 moved from start: 0.4941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3498 Z= 0.187 Angle : 0.471 4.720 4680 Z= 0.243 Chirality : 0.050 0.138 528 Planarity : 0.002 0.026 594 Dihedral : 4.669 13.177 462 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 1.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Rotamer: Outliers : 1.01 % Allowed : 15.66 % 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 (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: -1.62 (0.32), residues: 438 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.23 (0.25), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS G 362 PHE 0.004 0.001 PHE A 378 TYR 0.008 0.002 TYR A 310 ARG 0.002 0.000 ARG A 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 79 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 75 time to evaluate : 0.614 Fit side-chains REVERT: A 342 GLU cc_start: 0.8211 (mt-10) cc_final: 0.7905 (tt0) REVERT: G 311 LYS cc_start: 0.8394 (mtmt) cc_final: 0.7658 (tppt) REVERT: G 342 GLU cc_start: 0.8169 (mt-10) cc_final: 0.7866 (tt0) REVERT: G 349 ARG cc_start: 0.8442 (mtt180) cc_final: 0.6906 (mmp-170) REVERT: B 307 GLN cc_start: 0.8155 (mt0) cc_final: 0.7924 (tt0) REVERT: B 311 LYS cc_start: 0.8743 (mtmt) cc_final: 0.8386 (mttt) REVERT: B 340 LYS cc_start: 0.8496 (mtpt) cc_final: 0.8022 (mttm) REVERT: B 342 GLU cc_start: 0.8309 (mt-10) cc_final: 0.7978 (tt0) REVERT: B 347 LYS cc_start: 0.8657 (mttt) cc_final: 0.8046 (pptt) REVERT: B 349 ARG cc_start: 0.8496 (mtp85) cc_final: 0.8112 (mtt90) REVERT: C 317 LYS cc_start: 0.8518 (ptmt) cc_final: 0.8281 (ptpp) REVERT: C 338 GLU cc_start: 0.8260 (tt0) cc_final: 0.7910 (tt0) REVERT: C 342 GLU cc_start: 0.8084 (mt-10) cc_final: 0.7750 (mt-10) REVERT: D 307 GLN cc_start: 0.7894 (mt0) cc_final: 0.7574 (tt0) REVERT: D 311 LYS cc_start: 0.8520 (mtmt) cc_final: 0.7710 (tppt) REVERT: D 342 GLU cc_start: 0.8229 (mt-10) cc_final: 0.7937 (mt-10) REVERT: D 349 ARG cc_start: 0.8427 (mtt180) cc_final: 0.6856 (mmp-170) REVERT: E 311 LYS cc_start: 0.8770 (mtmt) cc_final: 0.8445 (mtpt) REVERT: E 317 LYS cc_start: 0.8577 (mttt) cc_final: 0.8243 (mtmt) REVERT: E 338 GLU cc_start: 0.8304 (tt0) cc_final: 0.8063 (tt0) REVERT: E 347 LYS cc_start: 0.8534 (mttt) cc_final: 0.7997 (pptt) outliers start: 4 outliers final: 3 residues processed: 77 average time/residue: 3.0811 time to fit residues: 243.5761 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 : 0.647 ------------------------------------------------------------------------------- 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 30 optimal weight: 5.9990 chunk 41 optimal weight: 4.9990 chunk 34 optimal weight: 5.9990 chunk 36 optimal weight: 0.9990 chunk 6 optimal weight: 3.9990 chunk 0 optimal weight: 6.9990 chunk 5 optimal weight: 4.9990 chunk 4 optimal weight: 2.9990 chunk 8 optimal weight: 4.9990 chunk 9 optimal weight: 0.6980 chunk 22 optimal weight: 2.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 351 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 = 0.3901 r_free = 0.3901 target = 0.125346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.108812 restraints weight = 12332.368| |-----------------------------------------------------------------------------| r_work (start): 0.3681 rms_B_bonded: 1.54 r_work: 0.3589 rms_B_bonded: 1.53 restraints_weight: 0.5000 r_work: 0.3511 rms_B_bonded: 2.64 restraints_weight: 0.2500 r_work (final): 0.3511 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8956 moved from start: 0.4926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3498 Z= 0.236 Angle : 0.486 4.586 4680 Z= 0.253 Chirality : 0.050 0.139 528 Planarity : 0.003 0.027 594 Dihedral : 4.767 13.512 462 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 1.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Rotamer: Outliers : 0.76 % Allowed : 16.16 % 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 (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: -1.64 (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 HIS 0.002 0.000 HIS D 374 PHE 0.005 0.001 PHE A 378 TYR 0.010 0.002 TYR A 310 ARG 0.002 0.000 ARG A 349 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7378.78 seconds wall clock time: 125 minutes 37.58 seconds (7537.58 seconds total)