Starting phenix.real_space_refine on Sat Sep 12 07:37:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6ubt_20715/09_2026/6ubt_20715.cif Found real_map, /net/cci-nas-00/data/ceres_data/6ubt_20715/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/6ubt_20715/09_2026/6ubt_20715.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6ubt_20715/09_2026/6ubt_20715.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6ubt_20715/09_2026/6ubt_20715.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6ubt_20715/09_2026/6ubt_20715.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6ubt_20715/09_2026/6ubt_20715.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6ubt_20715/09_2026/6ubt_20715.map" } 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/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 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: 3.05, per 1000 atoms: 0.21 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: 1.27 Conformation dependent library (CDL) restraints added in 810.6 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: 0.49 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: 2.68 Time building geometry restraints manager: 1.77 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: 7915 17.18 - 34.36: 778 34.36 - 51.54: 77 51.54 - 68.73: 20 68.73 - 85.91: 15 Dihedral angle restraints: 8805 sinusoidal: 3585 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 8802 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: 0.05 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: 2.420 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.240 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 15.150 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.040 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:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 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 : 12.868 85.906 5415 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/Z covalent geometry : bond 0.00750 / 0.36 (14855) covalent geometry : angle 1.51744 / 0.83 (20130) hydrogen bonds : bond 0.19930 / 12.73 ( 665) hydrogen bonds : angle 7.18209 / 4.87 ( 2055) link_BETA1-4 : bond 0.00126 / 0.07 ( 5) link_BETA1-4 : angle 2.58546 / 1.46 ( 15) link_NAG-ASN : bond 0.01528 / 0.89 ( 5) link_NAG-ASN : angle 7.26095 / 4.29 ( 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 : 0.566 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: 0.1149 time to fit residues: 44.2608 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 : 0.601 ------------------------------------------------------------------------------- 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... A 55 ASN A 139 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 168 ASN E 55 ASN E 139 ASN E 168 ASN E 174 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.072209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.059942 restraints weight = 55567.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.061964 restraints weight = 26892.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.063260 restraints weight = 16836.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.064136 restraints weight = 12330.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.064633 restraints weight = 9979.930| |-----------------------------------------------------------------------------| r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.2107 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= 0.143 Angle : 0.727 8.876 20160 Z= 0.373 Chirality : 0.046 0.258 2280 Planarity : 0.005 0.058 2510 Dihedral : 3.816 13.900 1925 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 2.26 % Allowed : 15.97 % Favored : 81.76 % 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: 1.72 (0.21), residues: 625 sheet: -1.45 (0.29), residues: 310 loop : -2.76 (0.17), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG C 400 TYR 0.011 0.001 TYR C 429 PHE 0.015 0.001 PHE B 169 TRP 0.015 0.001 TRP C 263 HIS 0.003 0.001 HIS C 335 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.14 (14855) covalent geometry : angle 0.71999 / 0.37 (20130) hydrogen bonds : bond 0.05213 / 3.44 ( 665) hydrogen bonds : angle 5.05080 / 3.42 ( 2055) link_BETA1-4 : bond 0.00265 / 0.14 ( 5) link_BETA1-4 : angle 1.61705 / 0.97 ( 15) link_NAG-ASN : bond 0.00664 / 0.39 ( 5) link_NAG-ASN : angle 3.36020 / 1.94 ( 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 202 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 166 time to evaluate : 0.620 Fit side-chains revert: symmetry clash REVERT: A 127 GLU cc_start: 0.7796 (tp30) cc_final: 0.7576 (mm-30) REVERT: A 210 GLN cc_start: 0.8819 (mm110) cc_final: 0.8495 (tp40) REVERT: C 270 MET cc_start: 0.8796 (ptp) cc_final: 0.8473 (tmm) REVERT: D 263 TRP cc_start: 0.8494 (m-10) cc_final: 0.8140 (m-10) REVERT: E 282 THR cc_start: 0.9069 (t) cc_final: 0.8785 (p) outliers start: 36 outliers final: 13 residues processed: 187 average time/residue: 0.0918 time to fit residues: 28.3910 Evaluate side-chains 155 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 142 time to evaluate : 0.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 264 VAL 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 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: 0.9980 chunk 109 optimal weight: 4.9990 chunk 28 optimal weight: 4.9990 chunk 58 optimal weight: 0.9990 chunk 40 optimal weight: 5.9990 chunk 89 optimal weight: 0.9990 chunk 21 optimal weight: 3.9990 chunk 36 optimal weight: 9.9990 chunk 60 optimal weight: 0.9990 chunk 126 optimal weight: 1.9990 chunk 85 optimal weight: 0.9980 overall best weight: 0.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 139 ASN C 139 ASN C 168 ASN D 139 ASN D 329 ASN E 139 ASN E 168 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.068008 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.056107 restraints weight = 57953.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.057968 restraints weight = 28340.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.059171 restraints weight = 17781.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.059970 restraints weight = 13060.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.060458 restraints weight = 10586.344| |-----------------------------------------------------------------------------| r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.2513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 14865 Z= 0.135 Angle : 0.670 8.764 20160 Z= 0.338 Chirality : 0.044 0.216 2280 Planarity : 0.004 0.047 2510 Dihedral : 3.861 16.628 1925 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 2.20 % Allowed : 17.48 % Favored : 80.31 % 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: -0.63 (0.20), residues: 1745 helix: 2.28 (0.20), residues: 620 sheet: -0.89 (0.31), residues: 310 loop : -2.53 (0.18), residues: 815 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 415 TYR 0.010 0.001 TYR C 429 PHE 0.023 0.001 PHE A 169 TRP 0.026 0.002 TRP C 263 HIS 0.003 0.001 HIS E 335 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.14 (14855) covalent geometry : angle 0.66581 / 0.34 (20130) hydrogen bonds : bond 0.04465 / 2.91 ( 665) hydrogen bonds : angle 4.54958 / 3.07 ( 2055) link_BETA1-4 : bond 0.00131 / 0.07 ( 5) link_BETA1-4 : angle 1.77956 / 1.05 ( 15) link_NAG-ASN : bond 0.00390 / 0.22 ( 5) link_NAG-ASN : angle 2.36064 / 1.32 ( 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 186 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 151 time to evaluate : 0.542 Fit side-chains REVERT: A 127 GLU cc_start: 0.7761 (tp30) cc_final: 0.7533 (mm-30) REVERT: A 210 GLN cc_start: 0.8818 (mm110) cc_final: 0.8252 (tp40) REVERT: C 187 MET cc_start: 0.9255 (mmm) cc_final: 0.9027 (tpp) REVERT: D 263 TRP cc_start: 0.8503 (m-10) cc_final: 0.8225 (m-10) REVERT: D 282 THR cc_start: 0.9184 (t) cc_final: 0.8735 (p) REVERT: E 263 TRP cc_start: 0.8179 (m-10) cc_final: 0.7523 (m-10) outliers start: 35 outliers final: 23 residues processed: 172 average time/residue: 0.0932 time to fit residues: 26.5598 Evaluate side-chains 165 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 142 time to evaluate : 0.571 ------------------------------------------------------------------------------- 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 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 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 234 ILE Chi-restraints excluded: chain D residue 257 LEU Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain E residue 138 ASP 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: 0.1980 chunk 85 optimal weight: 5.9990 chunk 148 optimal weight: 0.0040 chunk 126 optimal weight: 3.9990 chunk 32 optimal weight: 3.9990 chunk 70 optimal weight: 5.9990 chunk 158 optimal weight: 7.9990 chunk 95 optimal weight: 0.6980 chunk 146 optimal weight: 5.9990 chunk 43 optimal weight: 0.0970 chunk 12 optimal weight: 0.1980 overall best weight: 0.2390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3506 r_free = 0.3506 target = 0.072024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.059506 restraints weight = 55387.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.061512 restraints weight = 26774.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.062817 restraints weight = 16827.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.063671 restraints weight = 12386.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.064192 restraints weight = 10056.480| |-----------------------------------------------------------------------------| r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.2750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 14865 Z= 0.118 Angle : 0.655 9.717 20160 Z= 0.325 Chirality : 0.043 0.208 2280 Planarity : 0.004 0.041 2510 Dihedral : 3.884 18.894 1925 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 1.70 % Allowed : 18.74 % Favored : 79.56 % 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: -0.40 (0.20), residues: 1745 helix: 2.33 (0.20), residues: 625 sheet: -0.56 (0.31), residues: 310 loop : -2.39 (0.18), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 415 TYR 0.011 0.001 TYR B 325 PHE 0.015 0.001 PHE C 266 TRP 0.045 0.002 TRP A 263 HIS 0.002 0.000 HIS C 335 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.12 (14855) covalent geometry : angle 0.65109 / 0.32 (20130) hydrogen bonds : bond 0.04051 / 2.68 ( 665) hydrogen bonds : angle 4.36667 / 2.96 ( 2055) link_BETA1-4 : bond 0.00310 / 0.18 ( 5) link_BETA1-4 : angle 1.61418 / 0.96 ( 15) link_NAG-ASN : bond 0.00513 / 0.30 ( 5) link_NAG-ASN : angle 2.22208 / 1.23 ( 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 182 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 155 time to evaluate : 0.596 Fit side-chains REVERT: A 32 MET cc_start: 0.8536 (tmm) cc_final: 0.8238 (tmm) REVERT: B 32 MET cc_start: 0.8558 (tmm) cc_final: 0.8073 (tmm) REVERT: D 263 TRP cc_start: 0.8480 (m-10) cc_final: 0.7834 (m-10) REVERT: E 32 MET cc_start: 0.8504 (tmm) cc_final: 0.8232 (tmm) REVERT: E 263 TRP cc_start: 0.8160 (m-10) cc_final: 0.7471 (m-10) outliers start: 27 outliers final: 19 residues processed: 171 average time/residue: 0.0928 time to fit residues: 26.4091 Evaluate side-chains 163 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 144 time to evaluate : 0.570 ------------------------------------------------------------------------------- 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 B residue 137 THR 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 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 144 ILE Chi-restraints excluded: chain D residue 168 ASN Chi-restraints excluded: chain D residue 234 ILE 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: 0.0570 chunk 85 optimal weight: 8.9990 chunk 131 optimal weight: 10.0000 chunk 107 optimal weight: 3.9990 chunk 124 optimal weight: 0.7980 chunk 40 optimal weight: 4.9990 chunk 145 optimal weight: 0.7980 chunk 1 optimal weight: 8.9990 chunk 160 optimal weight: 4.9990 chunk 134 optimal weight: 10.0000 chunk 118 optimal weight: 4.9990 overall best weight: 2.1302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 149 ASN A 168 ASN A 239 HIS B 149 ASN B 239 HIS C 139 ASN C 149 ASN C 168 ASN C 239 HIS D 149 ASN D 239 HIS E 139 ASN E 149 ASN E 239 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.064429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.052188 restraints weight = 58216.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.053971 restraints weight = 28855.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.055176 restraints weight = 18357.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.055955 restraints weight = 13516.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.056395 restraints weight = 11040.424| |-----------------------------------------------------------------------------| r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.3344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 14865 Z= 0.195 Angle : 0.681 8.754 20160 Z= 0.344 Chirality : 0.044 0.203 2280 Planarity : 0.004 0.037 2510 Dihedral : 4.123 23.577 1925 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 2.20 % Allowed : 19.69 % Favored : 78.11 % 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: -0.43 (0.20), residues: 1745 helix: 2.14 (0.20), residues: 655 sheet: -0.93 (0.28), residues: 380 loop : -2.36 (0.19), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG E 415 TYR 0.015 0.002 TYR E 325 PHE 0.031 0.002 PHE E 266 TRP 0.060 0.002 TRP B 263 HIS 0.004 0.001 HIS A 133 Details of bonding type rmsd/Z covalent geometry : bond 0.00448 / 0.20 (14855) covalent geometry : angle 0.67746 / 0.34 (20130) hydrogen bonds : bond 0.04379 / 2.89 ( 665) hydrogen bonds : angle 4.35056 / 2.96 ( 2055) link_BETA1-4 : bond 0.00106 / 0.06 ( 5) link_BETA1-4 : angle 2.19315 / 1.32 ( 15) link_NAG-ASN : bond 0.00206 / 0.12 ( 5) link_NAG-ASN : angle 1.33093 / 0.74 ( 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 182 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 147 time to evaluate : 0.612 Fit side-chains REVERT: A 32 MET cc_start: 0.8507 (tmm) cc_final: 0.8276 (tmm) REVERT: A 80 MET cc_start: 0.8717 (mmm) cc_final: 0.8508 (mmm) REVERT: B 32 MET cc_start: 0.8514 (tmm) cc_final: 0.8177 (tmm) REVERT: C 270 MET cc_start: 0.8973 (OUTLIER) cc_final: 0.8555 (ppp) REVERT: D 263 TRP cc_start: 0.8477 (m-10) cc_final: 0.8220 (m-10) REVERT: E 32 MET cc_start: 0.8576 (tmm) cc_final: 0.8311 (tmm) REVERT: E 80 MET cc_start: 0.8521 (mmm) cc_final: 0.8305 (tpt) outliers start: 35 outliers final: 25 residues processed: 166 average time/residue: 0.0928 time to fit residues: 25.6505 Evaluate side-chains 163 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 137 time to evaluate : 0.673 ------------------------------------------------------------------------------- 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 B residue 61 VAL 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 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 270 MET 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 61 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: 6.9990 chunk 27 optimal weight: 4.9990 chunk 147 optimal weight: 0.3980 chunk 44 optimal weight: 0.6980 chunk 137 optimal weight: 1.9990 chunk 102 optimal weight: 3.9990 chunk 11 optimal weight: 4.9990 chunk 74 optimal weight: 4.9990 chunk 165 optimal weight: 2.9990 chunk 19 optimal weight: 4.9990 chunk 169 optimal weight: 8.9990 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 329 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.063954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.051583 restraints weight = 57551.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.053368 restraints weight = 28392.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.054536 restraints weight = 18162.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.055307 restraints weight = 13509.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.055790 restraints weight = 11060.683| |-----------------------------------------------------------------------------| r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8472 moved from start: 0.3549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 14865 Z= 0.180 Angle : 0.668 9.558 20160 Z= 0.335 Chirality : 0.043 0.193 2280 Planarity : 0.004 0.033 2510 Dihedral : 4.146 24.911 1925 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 1.95 % Allowed : 21.26 % 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: -0.18 (0.20), residues: 1745 helix: 2.65 (0.20), residues: 620 sheet: -0.61 (0.30), residues: 345 loop : -2.35 (0.19), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 415 TYR 0.014 0.002 TYR A 325 PHE 0.019 0.001 PHE A 266 TRP 0.030 0.002 TRP B 263 HIS 0.001 0.000 HIS C 335 Details of bonding type rmsd/Z covalent geometry : bond 0.00412 / 0.18 (14855) covalent geometry : angle 0.66463 / 0.33 (20130) hydrogen bonds : bond 0.04190 / 2.77 ( 665) hydrogen bonds : angle 4.28543 / 2.92 ( 2055) link_BETA1-4 : bond 0.00178 / 0.10 ( 5) link_BETA1-4 : angle 2.17608 / 1.29 ( 15) link_NAG-ASN : bond 0.00094 / 0.05 ( 5) link_NAG-ASN : angle 1.50463 / 0.82 ( 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 169 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 138 time to evaluate : 0.525 Fit side-chains REVERT: B 32 MET cc_start: 0.8557 (tmm) cc_final: 0.8253 (tmm) REVERT: C 80 MET cc_start: 0.8555 (mmm) cc_final: 0.8326 (tpt) REVERT: C 187 MET cc_start: 0.9248 (mmm) cc_final: 0.8914 (tpp) REVERT: C 270 MET cc_start: 0.8950 (OUTLIER) cc_final: 0.8518 (ppp) REVERT: D 80 MET cc_start: 0.8466 (mmm) cc_final: 0.8154 (tpt) REVERT: D 263 TRP cc_start: 0.8481 (m-10) cc_final: 0.8263 (m-10) REVERT: E 32 MET cc_start: 0.8535 (tmm) cc_final: 0.8249 (tmm) outliers start: 31 outliers final: 19 residues processed: 156 average time/residue: 0.0960 time to fit residues: 24.7679 Evaluate side-chains 153 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 133 time to evaluate : 0.605 ------------------------------------------------------------------------------- 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 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 234 ILE 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 168 ASN Chi-restraints excluded: chain D residue 234 ILE Chi-restraints excluded: chain D residue 264 VAL 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 105 optimal weight: 0.0980 chunk 69 optimal weight: 0.9980 chunk 126 optimal weight: 6.9990 chunk 97 optimal weight: 0.0970 chunk 165 optimal weight: 0.9990 chunk 112 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 118 optimal weight: 0.1980 chunk 68 optimal weight: 2.9990 chunk 131 optimal weight: 10.0000 chunk 168 optimal weight: 0.7980 overall best weight: 0.4378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 168 ASN C 139 ASN C 168 ASN E 168 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.065965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.053626 restraints weight = 57211.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.055473 restraints weight = 28106.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.056701 restraints weight = 17761.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.057477 restraints weight = 13048.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.057973 restraints weight = 10638.979| |-----------------------------------------------------------------------------| r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.3651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 14865 Z= 0.115 Angle : 0.646 9.868 20160 Z= 0.319 Chirality : 0.043 0.242 2280 Planarity : 0.003 0.032 2510 Dihedral : 4.067 24.480 1925 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 1.70 % Allowed : 21.70 % Favored : 76.60 % 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: 2.57 (0.19), residues: 620 sheet: -0.26 (0.33), residues: 300 loop : -2.26 (0.19), residues: 825 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 415 TYR 0.014 0.001 TYR E 325 PHE 0.021 0.001 PHE C 266 TRP 0.026 0.001 TRP B 263 HIS 0.002 0.000 HIS C 335 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.12 (14855) covalent geometry : angle 0.64213 / 0.32 (20130) hydrogen bonds : bond 0.03799 / 2.51 ( 665) hydrogen bonds : angle 4.10961 / 2.80 ( 2055) link_BETA1-4 : bond 0.00396 / 0.22 ( 5) link_BETA1-4 : angle 1.82084 / 1.07 ( 15) link_NAG-ASN : bond 0.00482 / 0.28 ( 5) link_NAG-ASN : angle 1.93994 / 1.06 ( 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 173 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 146 time to evaluate : 0.594 Fit side-chains revert: symmetry clash REVERT: B 32 MET cc_start: 0.8573 (tmm) cc_final: 0.8373 (tmm) REVERT: B 176 CYS cc_start: 0.8611 (m) cc_final: 0.8410 (m) REVERT: C 187 MET cc_start: 0.9272 (mmm) cc_final: 0.8998 (tpp) REVERT: C 270 MET cc_start: 0.8985 (OUTLIER) cc_final: 0.8550 (ppp) REVERT: E 32 MET cc_start: 0.8537 (tmm) cc_final: 0.8303 (tmm) REVERT: E 79 THR cc_start: 0.9233 (p) cc_final: 0.8980 (p) REVERT: E 80 MET cc_start: 0.8440 (mmm) cc_final: 0.8214 (tpt) outliers start: 27 outliers final: 18 residues processed: 167 average time/residue: 0.0944 time to fit residues: 26.0547 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 : 0.502 ------------------------------------------------------------------------------- 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 C residue 61 VAL Chi-restraints excluded: chain C residue 168 ASN Chi-restraints excluded: chain C residue 234 ILE Chi-restraints excluded: chain C residue 270 MET 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 E residue 61 VAL 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 136 optimal weight: 4.9990 chunk 149 optimal weight: 4.9990 chunk 141 optimal weight: 0.9980 chunk 156 optimal weight: 2.9990 chunk 86 optimal weight: 6.9990 chunk 0 optimal weight: 7.9990 chunk 96 optimal weight: 0.8980 chunk 10 optimal weight: 5.9990 chunk 44 optimal weight: 1.9990 chunk 148 optimal weight: 0.9980 chunk 53 optimal weight: 5.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 139 ASN C 168 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.064662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.052369 restraints weight = 57356.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.054162 restraints weight = 28087.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.055344 restraints weight = 17903.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.056078 restraints weight = 13269.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.056572 restraints weight = 10909.865| |-----------------------------------------------------------------------------| r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.3787 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= 0.159 Angle : 0.669 11.064 20160 Z= 0.331 Chirality : 0.043 0.192 2280 Planarity : 0.004 0.031 2510 Dihedral : 4.068 21.360 1925 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 2.01 % Allowed : 21.57 % 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: -0.13 (0.20), residues: 1745 helix: 2.59 (0.19), residues: 620 sheet: -0.49 (0.30), residues: 345 loop : -2.27 (0.19), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 415 TYR 0.014 0.001 TYR C 325 PHE 0.017 0.001 PHE C 266 TRP 0.037 0.002 TRP B 263 HIS 0.001 0.000 HIS C 335 Details of bonding type rmsd/Z covalent geometry : bond 0.00364 / 0.16 (14855) covalent geometry : angle 0.66610 / 0.33 (20130) hydrogen bonds : bond 0.03906 / 2.57 ( 665) hydrogen bonds : angle 4.14105 / 2.83 ( 2055) link_BETA1-4 : bond 0.00250 / 0.13 ( 5) link_BETA1-4 : angle 2.01466 / 1.19 ( 15) link_NAG-ASN : bond 0.00164 / 0.10 ( 5) link_NAG-ASN : angle 1.60214 / 0.86 ( 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 169 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 137 time to evaluate : 0.585 Fit side-chains revert: symmetry clash REVERT: B 176 CYS cc_start: 0.8478 (m) cc_final: 0.8135 (m) REVERT: C 187 MET cc_start: 0.9272 (mmm) cc_final: 0.9016 (tpp) REVERT: C 270 MET cc_start: 0.8956 (OUTLIER) cc_final: 0.8552 (ppp) outliers start: 32 outliers final: 21 residues processed: 162 average time/residue: 0.0925 time to fit residues: 24.9375 Evaluate side-chains 152 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 130 time to evaluate : 0.575 ------------------------------------------------------------------------------- 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 C residue 61 VAL 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 270 MET 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 61 VAL Chi-restraints excluded: chain E residue 232 THR Chi-restraints excluded: chain E residue 264 VAL 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: 5.9990 chunk 100 optimal weight: 2.9990 chunk 90 optimal weight: 4.9990 chunk 15 optimal weight: 3.9990 chunk 128 optimal weight: 0.9990 chunk 61 optimal weight: 5.9990 chunk 27 optimal weight: 5.9990 chunk 24 optimal weight: 5.9990 chunk 4 optimal weight: 4.9990 chunk 149 optimal weight: 2.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 139 ASN A 168 ASN B 329 ASN E 329 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.061361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.2881 r_free = 0.2881 target = 0.048842 restraints weight = 58451.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.050580 restraints weight = 29007.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.051709 restraints weight = 18711.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.052474 restraints weight = 13951.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.052959 restraints weight = 11507.280| |-----------------------------------------------------------------------------| r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8542 moved from start: 0.4198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 14865 Z= 0.255 Angle : 0.780 11.743 20160 Z= 0.388 Chirality : 0.045 0.213 2280 Planarity : 0.004 0.029 2510 Dihedral : 4.480 25.263 1925 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 10.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 2.08 % Allowed : 21.89 % Favored : 76.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.27 (0.20), residues: 1745 helix: 2.28 (0.20), residues: 655 sheet: -0.58 (0.30), residues: 345 loop : -2.36 (0.20), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 220 TYR 0.016 0.002 TYR A 325 PHE 0.028 0.002 PHE A 266 TRP 0.050 0.003 TRP B 263 HIS 0.004 0.001 HIS E 133 Details of bonding type rmsd/Z covalent geometry : bond 0.00590 / 0.26 (14855) covalent geometry : angle 0.77625 / 0.39 (20130) hydrogen bonds : bond 0.04698 / 3.09 ( 665) hydrogen bonds : angle 4.40512 / 3.02 ( 2055) link_BETA1-4 : bond 0.00135 / 0.08 ( 5) link_BETA1-4 : angle 2.72695 / 1.62 ( 15) link_NAG-ASN : bond 0.00287 / 0.16 ( 5) link_NAG-ASN : angle 0.92167 / 0.50 ( 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: 33 poor density : 131 time to evaluate : 0.662 Fit side-chains revert: symmetry clash REVERT: A 270 MET cc_start: 0.8979 (pmm) cc_final: 0.8764 (pmm) REVERT: B 80 MET cc_start: 0.8754 (mmm) cc_final: 0.8544 (tpt) REVERT: B 176 CYS cc_start: 0.8584 (m) cc_final: 0.8361 (m) REVERT: C 187 MET cc_start: 0.9240 (mmm) cc_final: 0.8959 (tpp) REVERT: C 270 MET cc_start: 0.9013 (OUTLIER) cc_final: 0.8558 (ppp) REVERT: D 270 MET cc_start: 0.9122 (pmm) cc_final: 0.8857 (pmm) outliers start: 33 outliers final: 23 residues processed: 156 average time/residue: 0.0980 time to fit residues: 25.1254 Evaluate side-chains 151 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 127 time to evaluate : 0.577 ------------------------------------------------------------------------------- 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 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 264 VAL Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain C residue 61 VAL 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 270 MET Chi-restraints excluded: chain D residue 89 ARG Chi-restraints excluded: chain D residue 168 ASN Chi-restraints excluded: chain D residue 232 THR 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 232 THR 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: 3.9990 chunk 80 optimal weight: 0.7980 chunk 115 optimal weight: 4.9990 chunk 158 optimal weight: 2.9990 chunk 65 optimal weight: 0.0770 chunk 76 optimal weight: 0.8980 chunk 57 optimal weight: 0.9990 chunk 110 optimal weight: 0.8980 chunk 172 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 14 optimal weight: 6.9990 overall best weight: 0.7340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 329 ASN C 168 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.063628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.051095 restraints weight = 57527.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.052912 restraints weight = 28503.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.054077 restraints weight = 18193.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.054858 restraints weight = 13544.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.055357 restraints weight = 11091.291| |-----------------------------------------------------------------------------| r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8472 moved from start: 0.4185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 14865 Z= 0.135 Angle : 0.712 11.540 20160 Z= 0.347 Chirality : 0.044 0.189 2280 Planarity : 0.004 0.028 2510 Dihedral : 4.309 22.773 1925 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 1.45 % Allowed : 23.21 % Favored : 75.35 % 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: -0.02 (0.20), residues: 1745 helix: 2.63 (0.19), residues: 620 sheet: -0.17 (0.33), residues: 300 loop : -2.19 (0.19), residues: 825 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 415 TYR 0.014 0.001 TYR E 325 PHE 0.016 0.001 PHE C 266 TRP 0.036 0.002 TRP B 263 HIS 0.002 0.000 HIS C 239 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.13 (14855) covalent geometry : angle 0.70831 / 0.35 (20130) hydrogen bonds : bond 0.04084 / 2.71 ( 665) hydrogen bonds : angle 4.20584 / 2.88 ( 2055) link_BETA1-4 : bond 0.00498 / 0.29 ( 5) link_BETA1-4 : angle 2.23073 / 1.32 ( 15) link_NAG-ASN : bond 0.00363 / 0.21 ( 5) link_NAG-ASN : angle 1.60556 / 0.87 ( 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 158 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 135 time to evaluate : 0.665 Fit side-chains revert: symmetry clash REVERT: A 270 MET cc_start: 0.8969 (pmm) cc_final: 0.8754 (pmm) REVERT: B 176 CYS cc_start: 0.8528 (m) cc_final: 0.8276 (m) REVERT: C 187 MET cc_start: 0.9237 (mmm) cc_final: 0.8993 (tpp) REVERT: C 270 MET cc_start: 0.8973 (OUTLIER) cc_final: 0.8545 (ppp) REVERT: D 270 MET cc_start: 0.9089 (pmm) cc_final: 0.8832 (pmm) outliers start: 23 outliers final: 19 residues processed: 153 average time/residue: 0.0954 time to fit residues: 24.0369 Evaluate side-chains 148 residues out of total 1590 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 128 time to evaluate : 0.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 168 ASN 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 C residue 61 VAL 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 270 MET Chi-restraints excluded: chain D residue 89 ARG Chi-restraints excluded: chain D residue 168 ASN Chi-restraints excluded: chain D residue 232 THR 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 232 THR 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 49 optimal weight: 2.9990 chunk 147 optimal weight: 2.9990 chunk 171 optimal weight: 6.9990 chunk 29 optimal weight: 4.9990 chunk 71 optimal weight: 4.9990 chunk 66 optimal weight: 6.9990 chunk 138 optimal weight: 0.8980 chunk 9 optimal weight: 0.9980 chunk 132 optimal weight: 4.9990 chunk 63 optimal weight: 2.9990 chunk 7 optimal weight: 7.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 168 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.062442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.049883 restraints weight = 57810.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.051662 restraints weight = 28521.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.052818 restraints weight = 18249.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.053543 restraints weight = 13620.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.054055 restraints weight = 11258.676| |-----------------------------------------------------------------------------| r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 moved from start: 0.4281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 14865 Z= 0.197 Angle : 0.742 12.395 20160 Z= 0.363 Chirality : 0.045 0.207 2280 Planarity : 0.004 0.028 2510 Dihedral : 4.330 24.901 1925 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 10.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 1.76 % Allowed : 22.89 % Favored : 75.35 % 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: -0.12 (0.20), residues: 1745 helix: 2.36 (0.19), residues: 650 sheet: -0.42 (0.31), residues: 345 loop : -2.25 (0.20), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 89 TYR 0.015 0.002 TYR B 325 PHE 0.025 0.001 PHE D 266 TRP 0.038 0.002 TRP B 263 HIS 0.002 0.001 HIS E 133 Details of bonding type rmsd/Z covalent geometry : bond 0.00457 / 0.20 (14855) covalent geometry : angle 0.73903 / 0.36 (20130) hydrogen bonds : bond 0.04172 / 2.76 ( 665) hydrogen bonds : angle 4.25868 / 2.92 ( 2055) link_BETA1-4 : bond 0.00288 / 0.16 ( 5) link_BETA1-4 : angle 2.39512 / 1.42 ( 15) link_NAG-ASN : bond 0.00044 / 0.03 ( 5) link_NAG-ASN : angle 1.31863 / 0.70 ( 15) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2091.65 seconds wall clock time: 37 minutes 19.87 seconds (2239.87 seconds total)