Starting phenix.real_space_refine on Wed Mar 4 15:23:32 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6ubt_20715/03_2026/6ubt_20715.cif Found real_map, /net/cci-nas-00/data/ceres_data/6ubt_20715/03_2026/6ubt_20715.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.55 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6ubt_20715/03_2026/6ubt_20715.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6ubt_20715/03_2026/6ubt_20715.map" model { file = "/net/cci-nas-00/data/ceres_data/6ubt_20715/03_2026/6ubt_20715.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6ubt_20715/03_2026/6ubt_20715.cif" } resolution = 3.55 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: 4 Type Number sf(0) Gaussians S 100 5.16 5 C 9425 2.51 5 N 2355 2.21 5 O 2625 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 50 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14505 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 2868 Number of conformers: 1 Conformer: "" Number of residues, atoms: 353, 2868 Classifications: {'peptide': 353} Link IDs: {'PTRANS': 16, 'TRANS': 336} Chain breaks: 1 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Restraints were copied for chains: B, C, D, E, G, H, I, J Time building chain proxies: 2.08, per 1000 atoms: 0.14 Number of scatterers: 14505 At special positions: 0 Unit cell: (97.2, 97.2, 135, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 100 16.00 O 2625 8.00 N 2355 7.00 C 9425 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " NAG-ASN " NAG F 1 " - " ASN A 62 " " NAG G 1 " - " ASN B 62 " " NAG H 1 " - " ASN C 62 " " NAG I 1 " - " ASN D 62 " " NAG J 1 " - " ASN E 62 " Time building additional restraints: 0.99 Conformation dependent library (CDL) restraints added in 470.7 milliseconds 3490 Ramachandran restraints generated. 1745 Oldfield, 0 Emsley, 1745 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3390 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 30 sheets defined 37.6% alpha, 25.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.48 Creating SS restraints... Processing helix chain 'A' and resid 33 through 41 Processing helix chain 'A' and resid 246 through 251 Processing helix chain 'A' and resid 251 through 267 removed outlier: 3.845A pdb=" N LEU A 261 " --> pdb=" O LEU A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 295 removed outlier: 3.747A pdb=" N ARG A 295 " --> pdb=" O SER A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 339 Processing helix chain 'A' and resid 398 through 440 Proline residue: A 419 - end of helix Processing helix chain 'B' and resid 33 through 41 Processing helix chain 'B' and resid 246 through 251 Processing helix chain 'B' and resid 251 through 267 removed outlier: 3.845A pdb=" N LEU B 261 " --> pdb=" O LEU B 257 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 295 removed outlier: 3.747A pdb=" N ARG B 295 " --> pdb=" O SER B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 305 through 339 Processing helix chain 'B' and resid 398 through 440 Proline residue: B 419 - end of helix Processing helix chain 'C' and resid 33 through 41 Processing helix chain 'C' and resid 246 through 251 Processing helix chain 'C' and resid 251 through 267 removed outlier: 3.845A pdb=" N LEU C 261 " --> pdb=" O LEU C 257 " (cutoff:3.500A) Processing helix chain 'C' and resid 273 through 295 removed outlier: 3.748A pdb=" N ARG C 295 " --> pdb=" O SER C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 305 through 339 Processing helix chain 'C' and resid 398 through 440 Proline residue: C 419 - end of helix Processing helix chain 'D' and resid 33 through 41 Processing helix chain 'D' and resid 246 through 251 Processing helix chain 'D' and resid 251 through 267 removed outlier: 3.845A pdb=" N LEU D 261 " --> pdb=" O LEU D 257 " (cutoff:3.500A) Processing helix chain 'D' and resid 273 through 295 removed outlier: 3.748A pdb=" N ARG D 295 " --> pdb=" O SER D 291 " (cutoff:3.500A) Processing helix chain 'D' and resid 305 through 339 Processing helix chain 'D' and resid 398 through 440 Proline residue: D 419 - end of helix Processing helix chain 'E' and resid 33 through 41 Processing helix chain 'E' and resid 246 through 251 Processing helix chain 'E' and resid 251 through 267 removed outlier: 3.845A pdb=" N LEU E 261 " --> pdb=" O LEU E 257 " (cutoff:3.500A) Processing helix chain 'E' and resid 273 through 295 removed outlier: 3.747A pdb=" N ARG E 295 " --> pdb=" O SER E 291 " (cutoff:3.500A) Processing helix chain 'E' and resid 305 through 339 Processing helix chain 'E' and resid 398 through 440 Proline residue: E 419 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 89 through 91 removed outlier: 5.721A pdb=" N VAL A 61 " --> pdb=" O ILE A 191 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N GLU A 193 " --> pdb=" O VAL A 61 " (cutoff:3.500A) removed outlier: 5.671A pdb=" N VAL A 63 " --> pdb=" O GLU A 193 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 89 through 91 removed outlier: 8.604A pdb=" N GLN A 201 " --> pdb=" O CYS A 65 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N ILE A 67 " --> pdb=" O GLN A 201 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 73 through 76 removed outlier: 4.987A pdb=" N SER A 74 " --> pdb=" O ARG A 83 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ARG A 83 " --> pdb=" O SER A 74 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 106 through 108 Processing sheet with id=AA5, first strand: chain 'A' and resid 123 through 124 removed outlier: 3.665A pdb=" N MET A 178 " --> pdb=" O ALA A 236 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N GLU A 241 " --> pdb=" O ILE A 212 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 123 through 124 removed outlier: 3.665A pdb=" N MET A 178 " --> pdb=" O ALA A 236 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N CYS A 233 " --> pdb=" O CYS A 222 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 89 through 91 removed outlier: 5.721A pdb=" N VAL B 61 " --> pdb=" O ILE B 191 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N GLU B 193 " --> pdb=" O VAL B 61 " (cutoff:3.500A) removed outlier: 5.670A pdb=" N VAL B 63 " --> pdb=" O GLU B 193 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 89 through 91 removed outlier: 8.604A pdb=" N GLN B 201 " --> pdb=" O CYS B 65 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N ILE B 67 " --> pdb=" O GLN B 201 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 73 through 76 removed outlier: 4.986A pdb=" N SER B 74 " --> pdb=" O ARG B 83 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ARG B 83 " --> pdb=" O SER B 74 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 106 through 108 Processing sheet with id=AB2, first strand: chain 'B' and resid 123 through 124 removed outlier: 3.665A pdb=" N MET B 178 " --> pdb=" O ALA B 236 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLU B 241 " --> pdb=" O ILE B 212 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 123 through 124 removed outlier: 3.665A pdb=" N MET B 178 " --> pdb=" O ALA B 236 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N CYS B 233 " --> pdb=" O CYS B 222 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 89 through 91 removed outlier: 5.722A pdb=" N VAL C 61 " --> pdb=" O ILE C 191 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N GLU C 193 " --> pdb=" O VAL C 61 " (cutoff:3.500A) removed outlier: 5.670A pdb=" N VAL C 63 " --> pdb=" O GLU C 193 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 89 through 91 removed outlier: 8.606A pdb=" N GLN C 201 " --> pdb=" O CYS C 65 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N ILE C 67 " --> pdb=" O GLN C 201 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 73 through 76 removed outlier: 4.985A pdb=" N SER C 74 " --> pdb=" O ARG C 83 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ARG C 83 " --> pdb=" O SER C 74 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 106 through 108 Processing sheet with id=AB8, first strand: chain 'C' and resid 123 through 124 removed outlier: 3.665A pdb=" N MET C 178 " --> pdb=" O ALA C 236 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLU C 241 " --> pdb=" O ILE C 212 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 123 through 124 removed outlier: 3.665A pdb=" N MET C 178 " --> pdb=" O ALA C 236 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N CYS C 233 " --> pdb=" O CYS C 222 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 89 through 91 removed outlier: 5.720A pdb=" N VAL D 61 " --> pdb=" O ILE D 191 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N GLU D 193 " --> pdb=" O VAL D 61 " (cutoff:3.500A) removed outlier: 5.670A pdb=" N VAL D 63 " --> pdb=" O GLU D 193 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 89 through 91 removed outlier: 8.605A pdb=" N GLN D 201 " --> pdb=" O CYS D 65 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N ILE D 67 " --> pdb=" O GLN D 201 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 73 through 76 removed outlier: 4.985A pdb=" N SER D 74 " --> pdb=" O ARG D 83 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ARG D 83 " --> pdb=" O SER D 74 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 106 through 108 Processing sheet with id=AC5, first strand: chain 'D' and resid 123 through 124 removed outlier: 3.666A pdb=" N MET D 178 " --> pdb=" O ALA D 236 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLU D 241 " --> pdb=" O ILE D 212 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 123 through 124 removed outlier: 3.666A pdb=" N MET D 178 " --> pdb=" O ALA D 236 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N CYS D 233 " --> pdb=" O CYS D 222 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 89 through 91 removed outlier: 5.721A pdb=" N VAL E 61 " --> pdb=" O ILE E 191 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N GLU E 193 " --> pdb=" O VAL E 61 " (cutoff:3.500A) removed outlier: 5.670A pdb=" N VAL E 63 " --> pdb=" O GLU E 193 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 89 through 91 removed outlier: 8.605A pdb=" N GLN E 201 " --> pdb=" O CYS E 65 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N ILE E 67 " --> pdb=" O GLN E 201 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 73 through 76 removed outlier: 4.986A pdb=" N SER E 74 " --> pdb=" O ARG E 83 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ARG E 83 " --> pdb=" O SER E 74 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 106 through 108 Processing sheet with id=AD2, first strand: chain 'E' and resid 123 through 124 removed outlier: 3.665A pdb=" N MET E 178 " --> pdb=" O ALA E 236 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLU E 241 " --> pdb=" O ILE E 212 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 123 through 124 removed outlier: 3.665A pdb=" N MET E 178 " --> pdb=" O ALA E 236 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N CYS E 233 " --> pdb=" O CYS E 222 " (cutoff:3.500A) 730 hydrogen bonds defined for protein. 2055 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: 2.27 Time building geometry restraints manager: 1.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3782 1.34 - 1.46: 3065 1.46 - 1.58: 7833 1.58 - 1.70: 5 1.70 - 1.81: 170 Bond restraints: 14855 Sorted by residual: bond pdb=" C ALA D 273 " pdb=" N PRO D 274 " ideal model delta sigma weight residual 1.334 1.421 -0.087 2.34e-02 1.83e+03 1.37e+01 bond pdb=" CB ILE D 268 " pdb=" CG2 ILE D 268 " ideal model delta sigma weight residual 1.521 1.399 0.122 3.30e-02 9.18e+02 1.37e+01 bond pdb=" C ALA C 273 " pdb=" N PRO C 274 " ideal model delta sigma weight residual 1.334 1.420 -0.087 2.34e-02 1.83e+03 1.37e+01 bond pdb=" C ALA A 273 " pdb=" N PRO A 274 " ideal model delta sigma weight residual 1.334 1.420 -0.086 2.34e-02 1.83e+03 1.36e+01 bond pdb=" CB ILE A 268 " pdb=" CG2 ILE A 268 " ideal model delta sigma weight residual 1.521 1.399 0.122 3.30e-02 9.18e+02 1.36e+01 ... (remaining 14850 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.67: 19496 3.67 - 7.34: 529 7.34 - 11.01: 60 11.01 - 14.67: 40 14.67 - 18.34: 5 Bond angle restraints: 20130 Sorted by residual: angle pdb=" CG ARG B 276 " pdb=" CD ARG B 276 " pdb=" NE ARG B 276 " ideal model delta sigma weight residual 112.00 123.93 -11.93 2.20e+00 2.07e-01 2.94e+01 angle pdb=" CG ARG D 276 " pdb=" CD ARG D 276 " pdb=" NE ARG D 276 " ideal model delta sigma weight residual 112.00 123.93 -11.93 2.20e+00 2.07e-01 2.94e+01 angle pdb=" CG ARG E 276 " pdb=" CD ARG E 276 " pdb=" NE ARG E 276 " ideal model delta sigma weight residual 112.00 123.93 -11.93 2.20e+00 2.07e-01 2.94e+01 angle pdb=" CG ARG C 276 " pdb=" CD ARG C 276 " pdb=" NE ARG C 276 " ideal model delta sigma weight residual 112.00 123.89 -11.89 2.20e+00 2.07e-01 2.92e+01 angle pdb=" CG ARG A 276 " pdb=" CD ARG A 276 " pdb=" NE ARG A 276 " ideal model delta sigma weight residual 112.00 123.87 -11.87 2.20e+00 2.07e-01 2.91e+01 ... (remaining 20125 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.18: 8100 17.18 - 34.36: 803 34.36 - 51.54: 77 51.54 - 68.73: 20 68.73 - 85.91: 15 Dihedral angle restraints: 9015 sinusoidal: 3795 harmonic: 5220 Sorted by residual: dihedral pdb=" C ASN E 168 " pdb=" N ASN E 168 " pdb=" CA ASN E 168 " pdb=" CB ASN E 168 " ideal model delta harmonic sigma weight residual -122.60 -130.90 8.30 0 2.50e+00 1.60e-01 1.10e+01 dihedral pdb=" C ASN D 168 " pdb=" N ASN D 168 " pdb=" CA ASN D 168 " pdb=" CB ASN D 168 " ideal model delta harmonic sigma weight residual -122.60 -130.88 8.28 0 2.50e+00 1.60e-01 1.10e+01 dihedral pdb=" C ASN C 168 " pdb=" N ASN C 168 " pdb=" CA ASN C 168 " pdb=" CB ASN C 168 " ideal model delta harmonic sigma weight residual -122.60 -130.85 8.25 0 2.50e+00 1.60e-01 1.09e+01 ... (remaining 9012 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.096: 1859 0.096 - 0.192: 356 0.192 - 0.288: 50 0.288 - 0.383: 5 0.383 - 0.479: 10 Chirality restraints: 2280 Sorted by residual: chirality pdb=" C1 NAG F 1 " pdb=" ND2 ASN A 62 " pdb=" C2 NAG F 1 " pdb=" O5 NAG F 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.92 -0.48 2.00e-01 2.50e+01 5.74e+00 chirality pdb=" C1 NAG H 1 " pdb=" ND2 ASN C 62 " pdb=" C2 NAG H 1 " pdb=" O5 NAG H 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.92 -0.48 2.00e-01 2.50e+01 5.72e+00 chirality pdb=" C1 NAG G 1 " pdb=" ND2 ASN B 62 " pdb=" C2 NAG G 1 " pdb=" O5 NAG G 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.92 -0.48 2.00e-01 2.50e+01 5.71e+00 ... (remaining 2277 not shown) Planarity restraints: 2515 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TRP E 118 " -0.026 2.00e-02 2.50e+03 5.09e-02 2.59e+01 pdb=" C TRP E 118 " 0.088 2.00e-02 2.50e+03 pdb=" O TRP E 118 " -0.033 2.00e-02 2.50e+03 pdb=" N LYS E 119 " -0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TRP B 118 " -0.026 2.00e-02 2.50e+03 5.08e-02 2.58e+01 pdb=" C TRP B 118 " 0.088 2.00e-02 2.50e+03 pdb=" O TRP B 118 " -0.033 2.00e-02 2.50e+03 pdb=" N LYS B 119 " -0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TRP D 118 " 0.026 2.00e-02 2.50e+03 5.07e-02 2.57e+01 pdb=" C TRP D 118 " -0.088 2.00e-02 2.50e+03 pdb=" O TRP D 118 " 0.033 2.00e-02 2.50e+03 pdb=" N LYS D 119 " 0.029 2.00e-02 2.50e+03 ... (remaining 2512 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 3349 2.80 - 3.32: 13070 3.32 - 3.85: 24126 3.85 - 4.37: 25449 4.37 - 4.90: 45931 Nonbonded interactions: 111925 Sorted by model distance: nonbonded pdb=" O ILE B 268 " pdb=" NH2 ARG B 276 " model vdw 2.274 3.120 nonbonded pdb=" O ILE A 268 " pdb=" NH2 ARG A 276 " model vdw 2.274 3.120 nonbonded pdb=" O ILE E 268 " pdb=" NH2 ARG E 276 " model vdw 2.274 3.120 nonbonded pdb=" O ILE D 268 " pdb=" NH2 ARG D 276 " model vdw 2.274 3.120 nonbonded pdb=" O ILE C 268 " pdb=" NH2 ARG C 276 " model vdw 2.275 3.120 ... (remaining 111920 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.700 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.160 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 11.680 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 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 : 0.008 0.122 14865 Z= 0.355 Angle : 1.531 18.344 20160 Z= 0.835 Chirality : 0.083 0.479 2280 Planarity : 0.009 0.074 2510 Dihedral : 12.821 85.906 5625 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.11 % Favored : 92.89 % Rotamer: Outliers : 0.31 % Allowed : 13.40 % Favored : 86.29 % 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 are not related in a simple way. whole: -1.97 (0.20), residues: 1745 helix: 0.86 (0.22), residues: 650 sheet: -2.38 (0.26), residues: 335 loop : -2.79 (0.18), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 400 TYR 0.046 0.004 TYR E 325 PHE 0.032 0.003 PHE C 169 TRP 0.028 0.003 TRP B 430 HIS 0.005 0.001 HIS C 335 Details of bonding type rmsd covalent geometry : bond 0.00750 (14855) covalent geometry : angle 1.51744 (20130) hydrogen bonds : bond 0.19930 ( 665) hydrogen bonds : angle 7.18209 ( 2055) link_BETA1-4 : bond 0.00126 ( 5) link_BETA1-4 : angle 2.58546 ( 15) link_NAG-ASN : bond 0.01528 ( 5) link_NAG-ASN : angle 7.26095 ( 15) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3490 Ramachandran restraints generated. 1745 Oldfield, 0 Emsley, 1745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3490 Ramachandran restraints generated. 1745 Oldfield, 0 Emsley, 1745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 252 time to evaluate : 0.527 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 263 TRP cc_start: 0.8287 (m-10) cc_final: 0.7961 (m-10) REVERT: E 263 TRP cc_start: 0.7949 (m-10) cc_final: 0.7578 (m-90) outliers start: 5 outliers final: 0 residues processed: 252 average time/residue: 0.1059 time to fit residues: 40.7298 Evaluate side-chains 153 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 153 time to evaluate : 0.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 98 optimal weight: 0.9990 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 0.5980 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 0.6980 chunk 103 optimal weight: 0.9980 chunk 77 optimal weight: 9.9990 chunk 122 optimal weight: 0.0020 chunk 91 optimal weight: 0.8980 chunk 149 optimal weight: 0.8980 overall best weight: 0.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 ASN A 168 ASN A 174 GLN B 55 ASN B 139 ASN B 168 ASN C 55 ASN C 139 ASN C 168 ASN C 174 GLN D 55 ASN D 139 ASN D 168 ASN E 55 ASN E 168 ASN E 174 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.069487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.057764 restraints weight = 57023.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.059640 restraints weight = 27731.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.060860 restraints weight = 17386.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.061693 restraints weight = 12704.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.062199 restraints weight = 10215.689| |-----------------------------------------------------------------------------| r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.2030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 14865 Z= 0.149 Angle : 0.741 9.241 20160 Z= 0.381 Chirality : 0.046 0.275 2280 Planarity : 0.005 0.059 2510 Dihedral : 4.804 36.524 2135 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 1.76 % Allowed : 16.42 % Favored : 81.82 % 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 are not related in a simple way. whole: -1.24 (0.19), residues: 1745 helix: 1.77 (0.21), residues: 625 sheet: -1.52 (0.29), residues: 310 loop : -2.77 (0.17), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 242 TYR 0.012 0.001 TYR C 429 PHE 0.016 0.001 PHE B 169 TRP 0.014 0.001 TRP A 263 HIS 0.003 0.001 HIS C 335 Details of bonding type rmsd covalent geometry : bond 0.00313 (14855) covalent geometry : angle 0.73288 (20130) hydrogen bonds : bond 0.05413 ( 665) hydrogen bonds : angle 5.11217 ( 2055) link_BETA1-4 : bond 0.00384 ( 5) link_BETA1-4 : angle 1.81034 ( 15) link_NAG-ASN : bond 0.00791 ( 5) link_NAG-ASN : angle 3.71423 ( 15) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3490 Ramachandran restraints generated. 1745 Oldfield, 0 Emsley, 1745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3490 Ramachandran restraints generated. 1745 Oldfield, 0 Emsley, 1745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 166 time to evaluate : 0.596 Fit side-chains revert: symmetry clash REVERT: A 127 GLU cc_start: 0.7815 (tp30) cc_final: 0.7552 (mm-30) REVERT: A 187 MET cc_start: 0.9095 (tpp) cc_final: 0.8449 (mpp) REVERT: C 270 MET cc_start: 0.8849 (ptp) cc_final: 0.8487 (tmm) REVERT: D 263 TRP cc_start: 0.8518 (m-10) cc_final: 0.8170 (m-10) outliers start: 28 outliers final: 11 residues processed: 183 average time/residue: 0.0862 time to fit residues: 26.0812 Evaluate side-chains 152 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 141 time to evaluate : 0.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain C residue 257 LEU Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain D residue 201 GLN Chi-restraints excluded: chain D residue 257 LEU Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain E residue 257 LEU Chi-restraints excluded: chain E residue 264 VAL Chi-restraints excluded: chain E residue 285 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 103 optimal weight: 0.8980 chunk 109 optimal weight: 0.3980 chunk 28 optimal weight: 0.9990 chunk 58 optimal weight: 4.9990 chunk 40 optimal weight: 0.6980 chunk 89 optimal weight: 0.9980 chunk 21 optimal weight: 0.6980 chunk 36 optimal weight: 9.9990 chunk 60 optimal weight: 0.8980 chunk 126 optimal weight: 7.9990 chunk 85 optimal weight: 0.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 139 ASN B 329 ASN C 139 ASN C 168 ASN C 329 ASN D 329 ASN E 139 ASN E 168 ASN E 329 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.068716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.056705 restraints weight = 57829.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.058604 restraints weight = 27835.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.059854 restraints weight = 17286.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.060660 restraints weight = 12636.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.061190 restraints weight = 10212.024| |-----------------------------------------------------------------------------| r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.2503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14865 Z= 0.125 Angle : 0.658 9.062 20160 Z= 0.331 Chirality : 0.044 0.240 2280 Planarity : 0.004 0.047 2510 Dihedral : 4.684 33.994 2135 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 2.39 % Allowed : 17.23 % Favored : 80.38 % 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 are not related in a simple way. whole: -0.65 (0.20), residues: 1745 helix: 2.29 (0.20), residues: 620 sheet: -0.88 (0.30), residues: 310 loop : -2.58 (0.18), residues: 815 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 415 TYR 0.010 0.001 TYR A 429 PHE 0.023 0.001 PHE A 169 TRP 0.028 0.001 TRP C 263 HIS 0.002 0.000 HIS E 335 Details of bonding type rmsd covalent geometry : bond 0.00268 (14855) covalent geometry : angle 0.65274 (20130) hydrogen bonds : bond 0.04404 ( 665) hydrogen bonds : angle 4.53942 ( 2055) link_BETA1-4 : bond 0.00204 ( 5) link_BETA1-4 : angle 1.78730 ( 15) link_NAG-ASN : bond 0.00422 ( 5) link_NAG-ASN : angle 2.64404 ( 15) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3490 Ramachandran restraints generated. 1745 Oldfield, 0 Emsley, 1745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3490 Ramachandran restraints generated. 1745 Oldfield, 0 Emsley, 1745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 152 time to evaluate : 0.544 Fit side-chains REVERT: A 32 MET cc_start: 0.8554 (tmm) cc_final: 0.8303 (tmm) REVERT: A 113 MET cc_start: 0.7735 (tpp) cc_final: 0.7406 (tpt) REVERT: A 127 GLU cc_start: 0.7769 (tp30) cc_final: 0.7520 (mm-30) REVERT: A 210 GLN cc_start: 0.8833 (mm110) cc_final: 0.8264 (tp40) REVERT: D 263 TRP cc_start: 0.8482 (m-10) cc_final: 0.8200 (m-10) REVERT: D 282 THR cc_start: 0.9127 (t) cc_final: 0.8705 (p) REVERT: E 263 TRP cc_start: 0.8138 (m-10) cc_final: 0.7447 (m-10) outliers start: 38 outliers final: 22 residues processed: 177 average time/residue: 0.0860 time to fit residues: 25.3044 Evaluate side-chains 165 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 143 time to evaluate : 0.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 168 ASN Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 168 ASN Chi-restraints excluded: chain B residue 234 ILE Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 319 PHE Chi-restraints excluded: chain C residue 137 THR Chi-restraints excluded: chain C residue 168 ASN Chi-restraints excluded: chain C residue 234 ILE Chi-restraints excluded: chain C residue 257 LEU Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain D residue 168 ASN Chi-restraints excluded: chain D residue 234 ILE Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain E residue 264 VAL Chi-restraints excluded: chain E residue 285 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 92 optimal weight: 5.9990 chunk 85 optimal weight: 8.9990 chunk 148 optimal weight: 1.9990 chunk 126 optimal weight: 4.9990 chunk 32 optimal weight: 0.9990 chunk 70 optimal weight: 3.9990 chunk 158 optimal weight: 7.9990 chunk 95 optimal weight: 0.9990 chunk 146 optimal weight: 2.9990 chunk 43 optimal weight: 0.9980 chunk 12 optimal weight: 2.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 139 ASN A 149 ASN A 168 ASN B 149 ASN C 139 ASN C 149 ASN D 149 ASN E 139 ASN E 149 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.066656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.054526 restraints weight = 57829.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.056350 restraints weight = 28464.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.057538 restraints weight = 18042.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.058330 restraints weight = 13326.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.058835 restraints weight = 10824.535| |-----------------------------------------------------------------------------| r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.2889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 14865 Z= 0.158 Angle : 0.663 9.504 20160 Z= 0.333 Chirality : 0.044 0.226 2280 Planarity : 0.004 0.041 2510 Dihedral : 4.705 33.515 2135 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 2.20 % Allowed : 19.12 % Favored : 78.68 % 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 are not related in a simple way. whole: -0.37 (0.20), residues: 1745 helix: 2.35 (0.20), residues: 625 sheet: -0.54 (0.32), residues: 310 loop : -2.37 (0.18), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 415 TYR 0.012 0.001 TYR E 325 PHE 0.021 0.001 PHE C 266 TRP 0.045 0.002 TRP A 263 HIS 0.002 0.001 HIS A 133 Details of bonding type rmsd covalent geometry : bond 0.00361 (14855) covalent geometry : angle 0.65890 (20130) hydrogen bonds : bond 0.04323 ( 665) hydrogen bonds : angle 4.40240 ( 2055) link_BETA1-4 : bond 0.00155 ( 5) link_BETA1-4 : angle 2.01283 ( 15) link_NAG-ASN : bond 0.00166 ( 5) link_NAG-ASN : angle 2.05650 ( 15) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3490 Ramachandran restraints generated. 1745 Oldfield, 0 Emsley, 1745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3490 Ramachandran restraints generated. 1745 Oldfield, 0 Emsley, 1745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 145 time to evaluate : 0.556 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 32 MET cc_start: 0.8516 (tmm) cc_final: 0.8099 (tmm) REVERT: D 263 TRP cc_start: 0.8532 (m-10) cc_final: 0.7885 (m-10) REVERT: E 32 MET cc_start: 0.8541 (tmm) cc_final: 0.8132 (tmm) REVERT: E 263 TRP cc_start: 0.8265 (m-10) cc_final: 0.7606 (m-10) outliers start: 35 outliers final: 28 residues processed: 165 average time/residue: 0.0867 time to fit residues: 23.9172 Evaluate side-chains 165 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 137 time to evaluate : 0.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 168 ASN Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 320 SER Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 168 ASN Chi-restraints excluded: chain B residue 234 ILE Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 319 PHE Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain C residue 138 ASP Chi-restraints excluded: chain C residue 168 ASN Chi-restraints excluded: chain C residue 234 ILE Chi-restraints excluded: chain C residue 257 LEU Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain D residue 164 MET Chi-restraints excluded: chain D residue 168 ASN Chi-restraints excluded: chain D residue 201 GLN Chi-restraints excluded: chain D residue 234 ILE Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain E residue 138 ASP Chi-restraints excluded: chain E residue 168 ASN Chi-restraints excluded: chain E residue 264 VAL Chi-restraints excluded: chain E residue 285 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 166 optimal weight: 0.8980 chunk 85 optimal weight: 8.9990 chunk 131 optimal weight: 0.4980 chunk 107 optimal weight: 2.9990 chunk 124 optimal weight: 0.8980 chunk 40 optimal weight: 4.9990 chunk 145 optimal weight: 0.9990 chunk 1 optimal weight: 10.0000 chunk 160 optimal weight: 5.9990 chunk 134 optimal weight: 3.9990 chunk 118 optimal weight: 0.9980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 139 ASN C 168 ASN E 139 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.066871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.054685 restraints weight = 57653.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.056550 restraints weight = 28022.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.057769 restraints weight = 17571.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.058532 restraints weight = 12881.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.059077 restraints weight = 10521.903| |-----------------------------------------------------------------------------| r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.3083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 14865 Z= 0.123 Angle : 0.632 8.862 20160 Z= 0.315 Chirality : 0.043 0.224 2280 Planarity : 0.003 0.038 2510 Dihedral : 4.580 31.323 2135 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 2.01 % Allowed : 19.75 % Favored : 78.24 % 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 are not related in a simple way. whole: -0.22 (0.20), residues: 1745 helix: 2.45 (0.20), residues: 625 sheet: -0.38 (0.32), residues: 310 loop : -2.30 (0.18), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 415 TYR 0.013 0.001 TYR E 325 PHE 0.019 0.001 PHE B 266 TRP 0.046 0.002 TRP B 263 HIS 0.002 0.000 HIS C 335 Details of bonding type rmsd covalent geometry : bond 0.00266 (14855) covalent geometry : angle 0.62710 (20130) hydrogen bonds : bond 0.04030 ( 665) hydrogen bonds : angle 4.27166 ( 2055) link_BETA1-4 : bond 0.00277 ( 5) link_BETA1-4 : angle 1.94458 ( 15) link_NAG-ASN : bond 0.00363 ( 5) link_NAG-ASN : angle 2.13832 ( 15) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3490 Ramachandran restraints generated. 1745 Oldfield, 0 Emsley, 1745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3490 Ramachandran restraints generated. 1745 Oldfield, 0 Emsley, 1745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 147 time to evaluate : 0.457 Fit side-chains revert: symmetry clash REVERT: A 32 MET cc_start: 0.8528 (tmm) cc_final: 0.8176 (tmm) REVERT: A 80 MET cc_start: 0.8754 (mmm) cc_final: 0.8543 (mmm) REVERT: B 32 MET cc_start: 0.8521 (tmm) cc_final: 0.8147 (tmm) REVERT: D 263 TRP cc_start: 0.8525 (m-10) cc_final: 0.7933 (m-10) REVERT: E 32 MET cc_start: 0.8532 (tmm) cc_final: 0.8250 (tmm) REVERT: E 263 TRP cc_start: 0.8157 (m-10) cc_final: 0.7513 (m-10) outliers start: 32 outliers final: 25 residues processed: 162 average time/residue: 0.0857 time to fit residues: 23.3313 Evaluate side-chains 163 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 138 time to evaluate : 0.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 VAL Chi-restraints excluded: chain A residue 168 ASN Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 168 ASN Chi-restraints excluded: chain B residue 234 ILE Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 319 PHE Chi-restraints excluded: chain C residue 138 ASP Chi-restraints excluded: chain C residue 168 ASN Chi-restraints excluded: chain C residue 234 ILE Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain D residue 80 MET Chi-restraints excluded: chain D residue 168 ASN Chi-restraints excluded: chain D residue 201 GLN Chi-restraints excluded: chain D residue 234 ILE Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain E residue 138 ASP Chi-restraints excluded: chain E residue 168 ASN Chi-restraints excluded: chain E residue 264 VAL Chi-restraints excluded: chain E residue 285 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 85 optimal weight: 5.9990 chunk 27 optimal weight: 3.9990 chunk 147 optimal weight: 8.9990 chunk 44 optimal weight: 0.6980 chunk 137 optimal weight: 2.9990 chunk 102 optimal weight: 3.9990 chunk 11 optimal weight: 6.9990 chunk 74 optimal weight: 1.9990 chunk 165 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 169 optimal weight: 5.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 139 ASN C 139 ASN E 139 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.064796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.052533 restraints weight = 57427.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.054316 restraints weight = 28265.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.055484 restraints weight = 17998.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.056259 restraints weight = 13359.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.056727 restraints weight = 10909.108| |-----------------------------------------------------------------------------| r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.3378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 14865 Z= 0.174 Angle : 0.651 9.542 20160 Z= 0.328 Chirality : 0.044 0.217 2280 Planarity : 0.004 0.035 2510 Dihedral : 4.722 32.197 2135 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 2.45 % Allowed : 20.44 % Favored : 77.11 % 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 are not related in a simple way. whole: -0.23 (0.20), residues: 1745 helix: 2.54 (0.20), residues: 625 sheet: -0.65 (0.30), residues: 345 loop : -2.33 (0.19), residues: 775 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 415 TYR 0.014 0.001 TYR E 325 PHE 0.023 0.001 PHE B 266 TRP 0.057 0.002 TRP A 263 HIS 0.002 0.001 HIS A 133 Details of bonding type rmsd covalent geometry : bond 0.00395 (14855) covalent geometry : angle 0.64699 (20130) hydrogen bonds : bond 0.04117 ( 665) hydrogen bonds : angle 4.27091 ( 2055) link_BETA1-4 : bond 0.00203 ( 5) link_BETA1-4 : angle 2.18536 ( 15) link_NAG-ASN : bond 0.00064 ( 5) link_NAG-ASN : angle 1.75503 ( 15) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3490 Ramachandran restraints generated. 1745 Oldfield, 0 Emsley, 1745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3490 Ramachandran restraints generated. 1745 Oldfield, 0 Emsley, 1745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 136 time to evaluate : 0.345 Fit side-chains revert: symmetry clash REVERT: A 32 MET cc_start: 0.8518 (tmm) cc_final: 0.8163 (tmm) REVERT: B 32 MET cc_start: 0.8557 (tmm) cc_final: 0.8262 (tmm) REVERT: C 270 MET cc_start: 0.8999 (OUTLIER) cc_final: 0.8566 (ppp) REVERT: D 263 TRP cc_start: 0.8464 (m-10) cc_final: 0.8246 (m-10) REVERT: E 32 MET cc_start: 0.8493 (tmm) cc_final: 0.8256 (tmm) outliers start: 39 outliers final: 26 residues processed: 159 average time/residue: 0.0888 time to fit residues: 23.4642 Evaluate side-chains 159 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 132 time to evaluate : 0.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 168 ASN Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 168 ASN Chi-restraints excluded: chain B residue 234 ILE Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 319 PHE Chi-restraints excluded: chain C residue 61 VAL Chi-restraints excluded: chain C residue 138 ASP Chi-restraints excluded: chain C residue 234 ILE Chi-restraints excluded: chain C residue 257 LEU Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 270 MET Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain D residue 80 MET Chi-restraints excluded: chain D residue 168 ASN Chi-restraints excluded: chain D residue 234 ILE Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain E residue 61 VAL Chi-restraints excluded: chain E residue 138 ASP Chi-restraints excluded: chain E residue 168 ASN Chi-restraints excluded: chain E residue 180 LEU Chi-restraints excluded: chain E residue 264 VAL Chi-restraints excluded: chain E residue 285 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 105 optimal weight: 0.7980 chunk 69 optimal weight: 3.9990 chunk 126 optimal weight: 0.9990 chunk 97 optimal weight: 1.9990 chunk 165 optimal weight: 0.9990 chunk 112 optimal weight: 0.0980 chunk 65 optimal weight: 0.9980 chunk 118 optimal weight: 0.9990 chunk 68 optimal weight: 3.9990 chunk 131 optimal weight: 1.9990 chunk 168 optimal weight: 0.7980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 139 ASN C 139 ASN E 139 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.066080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.053885 restraints weight = 57247.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.055711 restraints weight = 28008.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.056910 restraints weight = 17765.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.057682 restraints weight = 13130.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.058170 restraints weight = 10706.783| |-----------------------------------------------------------------------------| r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.3508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14865 Z= 0.117 Angle : 0.631 9.777 20160 Z= 0.314 Chirality : 0.043 0.221 2280 Planarity : 0.003 0.033 2510 Dihedral : 4.521 29.259 2135 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 1.76 % Allowed : 21.45 % Favored : 76.79 % 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 are not related in a simple way. whole: -0.09 (0.20), residues: 1745 helix: 2.62 (0.20), residues: 620 sheet: -0.31 (0.33), residues: 300 loop : -2.24 (0.19), residues: 825 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 415 TYR 0.013 0.001 TYR E 325 PHE 0.023 0.001 PHE A 266 TRP 0.037 0.002 TRP A 263 HIS 0.001 0.000 HIS C 335 Details of bonding type rmsd covalent geometry : bond 0.00254 (14855) covalent geometry : angle 0.62648 (20130) hydrogen bonds : bond 0.03779 ( 665) hydrogen bonds : angle 4.10872 ( 2055) link_BETA1-4 : bond 0.00298 ( 5) link_BETA1-4 : angle 2.00228 ( 15) link_NAG-ASN : bond 0.00447 ( 5) link_NAG-ASN : angle 2.15731 ( 15) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3490 Ramachandran restraints generated. 1745 Oldfield, 0 Emsley, 1745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3490 Ramachandran restraints generated. 1745 Oldfield, 0 Emsley, 1745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 143 time to evaluate : 0.409 Fit side-chains REVERT: A 32 MET cc_start: 0.8531 (tmm) cc_final: 0.8212 (tmm) REVERT: B 176 CYS cc_start: 0.8616 (m) cc_final: 0.8360 (m) REVERT: C 80 MET cc_start: 0.8467 (tpt) cc_final: 0.8261 (mmm) REVERT: C 270 MET cc_start: 0.9002 (OUTLIER) cc_final: 0.8560 (ppp) REVERT: E 32 MET cc_start: 0.8540 (tmm) cc_final: 0.8335 (tmm) REVERT: E 80 MET cc_start: 0.8289 (mmm) cc_final: 0.8043 (tpt) outliers start: 28 outliers final: 18 residues processed: 162 average time/residue: 0.0860 time to fit residues: 23.2130 Evaluate side-chains 153 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 134 time to evaluate : 0.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 168 ASN Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 168 ASN Chi-restraints excluded: chain B residue 234 ILE Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 319 PHE Chi-restraints excluded: chain C residue 234 ILE Chi-restraints excluded: chain C residue 257 LEU Chi-restraints excluded: chain C residue 270 MET Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 168 ASN Chi-restraints excluded: chain D residue 234 ILE Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain E residue 61 VAL Chi-restraints excluded: chain E residue 168 ASN Chi-restraints excluded: chain E residue 180 LEU Chi-restraints excluded: chain E residue 285 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 136 optimal weight: 6.9990 chunk 149 optimal weight: 0.9990 chunk 141 optimal weight: 0.2980 chunk 156 optimal weight: 3.9990 chunk 86 optimal weight: 6.9990 chunk 0 optimal weight: 7.9990 chunk 96 optimal weight: 2.9990 chunk 10 optimal weight: 0.2980 chunk 44 optimal weight: 1.9990 chunk 148 optimal weight: 0.0980 chunk 53 optimal weight: 2.9990 overall best weight: 0.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 139 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.066415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.054126 restraints weight = 56955.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.055955 restraints weight = 27996.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.057155 restraints weight = 17788.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.057904 restraints weight = 13146.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.058454 restraints weight = 10756.887| |-----------------------------------------------------------------------------| r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.3655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14865 Z= 0.123 Angle : 0.642 10.479 20160 Z= 0.318 Chirality : 0.043 0.259 2280 Planarity : 0.003 0.032 2510 Dihedral : 4.472 28.176 2135 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 1.32 % Allowed : 22.26 % Favored : 76.42 % 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 are not related in a simple way. whole: -0.12 (0.20), residues: 1745 helix: 2.53 (0.19), residues: 620 sheet: -0.26 (0.33), residues: 300 loop : -2.21 (0.19), residues: 825 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 415 TYR 0.013 0.001 TYR E 325 PHE 0.020 0.001 PHE A 266 TRP 0.045 0.002 TRP B 263 HIS 0.001 0.000 HIS C 335 Details of bonding type rmsd covalent geometry : bond 0.00272 (14855) covalent geometry : angle 0.63803 (20130) hydrogen bonds : bond 0.03798 ( 665) hydrogen bonds : angle 4.09552 ( 2055) link_BETA1-4 : bond 0.00286 ( 5) link_BETA1-4 : angle 1.97091 ( 15) link_NAG-ASN : bond 0.00346 ( 5) link_NAG-ASN : angle 2.07251 ( 15) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3490 Ramachandran restraints generated. 1745 Oldfield, 0 Emsley, 1745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3490 Ramachandran restraints generated. 1745 Oldfield, 0 Emsley, 1745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 145 time to evaluate : 0.537 Fit side-chains REVERT: A 32 MET cc_start: 0.8519 (tmm) cc_final: 0.8262 (tmm) REVERT: A 261 LEU cc_start: 0.9429 (tp) cc_final: 0.9212 (tp) REVERT: B 80 MET cc_start: 0.8571 (mmm) cc_final: 0.8370 (tpt) REVERT: B 176 CYS cc_start: 0.8608 (m) cc_final: 0.8359 (m) REVERT: C 270 MET cc_start: 0.8995 (OUTLIER) cc_final: 0.8580 (ppp) REVERT: D 80 MET cc_start: 0.8605 (mmm) cc_final: 0.8216 (tpt) REVERT: E 80 MET cc_start: 0.8288 (mmm) cc_final: 0.7976 (tpt) outliers start: 21 outliers final: 17 residues processed: 161 average time/residue: 0.0815 time to fit residues: 22.1297 Evaluate side-chains 153 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 135 time to evaluate : 0.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 168 ASN Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 168 ASN Chi-restraints excluded: chain B residue 234 ILE Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 319 PHE Chi-restraints excluded: chain C residue 234 ILE Chi-restraints excluded: chain C residue 257 LEU Chi-restraints excluded: chain C residue 270 MET Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 168 ASN Chi-restraints excluded: chain D residue 234 ILE Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain E residue 61 VAL Chi-restraints excluded: chain E residue 168 ASN Chi-restraints excluded: chain E residue 285 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 110 optimal weight: 3.9990 chunk 20 optimal weight: 3.9990 chunk 100 optimal weight: 0.3980 chunk 90 optimal weight: 1.9990 chunk 15 optimal weight: 0.9980 chunk 128 optimal weight: 0.9980 chunk 61 optimal weight: 6.9990 chunk 27 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 chunk 4 optimal weight: 5.9990 chunk 149 optimal weight: 4.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 139 ASN C 139 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.065146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.052732 restraints weight = 57534.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.054559 restraints weight = 28514.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.055722 restraints weight = 18128.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.056531 restraints weight = 13417.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.057048 restraints weight = 10936.429| |-----------------------------------------------------------------------------| r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.3812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 14865 Z= 0.154 Angle : 0.675 11.386 20160 Z= 0.332 Chirality : 0.044 0.219 2280 Planarity : 0.003 0.029 2510 Dihedral : 4.556 28.421 2135 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 1.57 % Allowed : 22.14 % Favored : 76.29 % 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 are not related in a simple way. whole: -0.12 (0.20), residues: 1745 helix: 2.53 (0.20), residues: 620 sheet: -0.27 (0.33), residues: 300 loop : -2.21 (0.19), residues: 825 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 220 TYR 0.013 0.001 TYR E 325 PHE 0.020 0.001 PHE D 266 TRP 0.066 0.002 TRP D 263 HIS 0.001 0.001 HIS A 133 Details of bonding type rmsd covalent geometry : bond 0.00356 (14855) covalent geometry : angle 0.67159 (20130) hydrogen bonds : bond 0.03941 ( 665) hydrogen bonds : angle 4.12492 ( 2055) link_BETA1-4 : bond 0.00238 ( 5) link_BETA1-4 : angle 2.10761 ( 15) link_NAG-ASN : bond 0.00163 ( 5) link_NAG-ASN : angle 1.80910 ( 15) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3490 Ramachandran restraints generated. 1745 Oldfield, 0 Emsley, 1745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3490 Ramachandran restraints generated. 1745 Oldfield, 0 Emsley, 1745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 139 time to evaluate : 0.627 Fit side-chains REVERT: A 32 MET cc_start: 0.8499 (tmm) cc_final: 0.8294 (tmm) REVERT: A 170 PRO cc_start: 0.8664 (Cg_exo) cc_final: 0.8312 (Cg_endo) REVERT: A 261 LEU cc_start: 0.9429 (tp) cc_final: 0.9220 (tp) REVERT: B 176 CYS cc_start: 0.8557 (m) cc_final: 0.8294 (m) REVERT: B 270 MET cc_start: 0.8966 (ptp) cc_final: 0.8620 (ppp) REVERT: B 419 PRO cc_start: 0.8479 (Cg_exo) cc_final: 0.8218 (Cg_endo) REVERT: C 176 CYS cc_start: 0.8345 (m) cc_final: 0.8050 (m) REVERT: C 270 MET cc_start: 0.8983 (OUTLIER) cc_final: 0.8558 (ppp) REVERT: D 270 MET cc_start: 0.9078 (pmm) cc_final: 0.8835 (pmm) outliers start: 25 outliers final: 22 residues processed: 157 average time/residue: 0.0866 time to fit residues: 22.8318 Evaluate side-chains 159 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 136 time to evaluate : 0.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 168 ASN Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 168 ASN Chi-restraints excluded: chain B residue 232 THR Chi-restraints excluded: chain B residue 234 ILE Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 319 PHE Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain C residue 234 ILE Chi-restraints excluded: chain C residue 257 LEU Chi-restraints excluded: chain C residue 270 MET Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 168 ASN Chi-restraints excluded: chain D residue 234 ILE Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain E residue 61 VAL Chi-restraints excluded: chain E residue 138 ASP Chi-restraints excluded: chain E residue 168 ASN Chi-restraints excluded: chain E residue 180 LEU Chi-restraints excluded: chain E residue 264 VAL Chi-restraints excluded: chain E residue 285 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 11 optimal weight: 5.9990 chunk 80 optimal weight: 7.9990 chunk 115 optimal weight: 0.9990 chunk 158 optimal weight: 0.9990 chunk 65 optimal weight: 0.9980 chunk 76 optimal weight: 3.9990 chunk 57 optimal weight: 0.9990 chunk 110 optimal weight: 0.9990 chunk 172 optimal weight: 5.9990 chunk 40 optimal weight: 4.9990 chunk 14 optimal weight: 7.9990 overall best weight: 0.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 139 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.065677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.053273 restraints weight = 57259.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.055098 restraints weight = 28201.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.056277 restraints weight = 17985.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.057028 restraints weight = 13328.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.057568 restraints weight = 10931.318| |-----------------------------------------------------------------------------| r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.3939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 14865 Z= 0.132 Angle : 0.668 11.501 20160 Z= 0.327 Chirality : 0.044 0.219 2280 Planarity : 0.003 0.028 2510 Dihedral : 4.432 26.592 2135 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 1.45 % Allowed : 22.20 % Favored : 76.35 % 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 are not related in a simple way. whole: -0.15 (0.20), residues: 1745 helix: 2.41 (0.19), residues: 625 sheet: -0.22 (0.33), residues: 300 loop : -2.20 (0.19), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 415 TYR 0.013 0.001 TYR E 325 PHE 0.017 0.001 PHE C 266 TRP 0.039 0.002 TRP D 263 HIS 0.001 0.000 HIS C 335 Details of bonding type rmsd covalent geometry : bond 0.00299 (14855) covalent geometry : angle 0.66347 (20130) hydrogen bonds : bond 0.03840 ( 665) hydrogen bonds : angle 4.09344 ( 2055) link_BETA1-4 : bond 0.00290 ( 5) link_BETA1-4 : angle 2.06557 ( 15) link_NAG-ASN : bond 0.00389 ( 5) link_NAG-ASN : angle 2.00188 ( 15) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3490 Ramachandran restraints generated. 1745 Oldfield, 0 Emsley, 1745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3490 Ramachandran restraints generated. 1745 Oldfield, 0 Emsley, 1745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 141 time to evaluate : 0.581 Fit side-chains REVERT: B 176 CYS cc_start: 0.8591 (m) cc_final: 0.8335 (m) REVERT: B 270 MET cc_start: 0.8914 (ptp) cc_final: 0.8590 (ppp) REVERT: C 176 CYS cc_start: 0.8275 (m) cc_final: 0.8000 (m) REVERT: C 178 MET cc_start: 0.8822 (OUTLIER) cc_final: 0.8306 (ptp) REVERT: C 270 MET cc_start: 0.8992 (OUTLIER) cc_final: 0.8538 (ppp) REVERT: D 270 MET cc_start: 0.9102 (pmm) cc_final: 0.8818 (pmm) outliers start: 23 outliers final: 19 residues processed: 154 average time/residue: 0.0874 time to fit residues: 22.6209 Evaluate side-chains 154 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 133 time to evaluate : 0.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 168 ASN Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 168 ASN Chi-restraints excluded: chain B residue 232 THR Chi-restraints excluded: chain B residue 234 ILE Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 319 PHE Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain C residue 178 MET Chi-restraints excluded: chain C residue 234 ILE Chi-restraints excluded: chain C residue 257 LEU Chi-restraints excluded: chain C residue 270 MET Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 168 ASN Chi-restraints excluded: chain D residue 234 ILE Chi-restraints excluded: chain E residue 61 VAL Chi-restraints excluded: chain E residue 168 ASN Chi-restraints excluded: chain E residue 180 LEU Chi-restraints excluded: chain E residue 285 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 49 optimal weight: 0.4980 chunk 147 optimal weight: 0.9990 chunk 171 optimal weight: 0.9990 chunk 29 optimal weight: 2.9990 chunk 71 optimal weight: 6.9990 chunk 66 optimal weight: 2.9990 chunk 138 optimal weight: 0.7980 chunk 9 optimal weight: 0.7980 chunk 132 optimal weight: 3.9990 chunk 63 optimal weight: 0.6980 chunk 7 optimal weight: 20.0000 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 139 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.066071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.053691 restraints weight = 56979.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.055526 restraints weight = 28259.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.056697 restraints weight = 18019.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.057496 restraints weight = 13327.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.057993 restraints weight = 10869.092| |-----------------------------------------------------------------------------| r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.4029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 14865 Z= 0.127 Angle : 0.688 12.567 20160 Z= 0.332 Chirality : 0.044 0.221 2280 Planarity : 0.003 0.027 2510 Dihedral : 4.396 25.470 2135 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 1.32 % Allowed : 22.96 % Favored : 75.72 % 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 are not related in a simple way. whole: -0.10 (0.20), residues: 1745 helix: 2.46 (0.19), residues: 620 sheet: -0.16 (0.33), residues: 300 loop : -2.16 (0.19), residues: 825 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 415 TYR 0.014 0.001 TYR D 325 PHE 0.016 0.001 PHE A 266 TRP 0.027 0.002 TRP A 263 HIS 0.001 0.000 HIS C 335 Details of bonding type rmsd covalent geometry : bond 0.00283 (14855) covalent geometry : angle 0.68374 (20130) hydrogen bonds : bond 0.03730 ( 665) hydrogen bonds : angle 4.08120 ( 2055) link_BETA1-4 : bond 0.00312 ( 5) link_BETA1-4 : angle 2.01361 ( 15) link_NAG-ASN : bond 0.00370 ( 5) link_NAG-ASN : angle 1.99725 ( 15) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1845.33 seconds wall clock time: 32 minutes 58.13 seconds (1978.13 seconds total)