Starting phenix.real_space_refine on Sat Oct 24 02:32:31 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9uej_64083/10_2026/9uej_64083.cif Found real_map, /net/cci-nas-00/data/ceres_data/9uej_64083/10_2026/9uej_64083.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.94 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9uej_64083/10_2026/9uej_64083.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9uej_64083/10_2026/9uej_64083.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9uej_64083/10_2026/9uej_64083.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9uej_64083/10_2026/9uej_64083.map" } resolution = 2.94 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= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 36 5.16 5 C 7500 2.51 5 N 2088 2.21 5 O 2236 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 11860 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2965 Number of conformers: 1 Conformer: "" Number of residues, atoms: 384, 2965 Classifications: {'peptide': 384} Link IDs: {'PCIS': 2, 'PTRANS': 15, 'TRANS': 366} Chain: "B" Number of atoms: 2965 Number of conformers: 1 Conformer: "" Number of residues, atoms: 384, 2965 Classifications: {'peptide': 384} Link IDs: {'PCIS': 2, 'PTRANS': 15, 'TRANS': 366} Chain: "C" Number of atoms: 2965 Number of conformers: 1 Conformer: "" Number of residues, atoms: 384, 2965 Classifications: {'peptide': 384} Link IDs: {'PCIS': 2, 'PTRANS': 15, 'TRANS': 366} Chain: "D" Number of atoms: 2965 Number of conformers: 1 Conformer: "" Number of residues, atoms: 384, 2965 Classifications: {'peptide': 384} Link IDs: {'PCIS': 2, 'PTRANS': 15, 'TRANS': 366} Time building chain proxies: 2.79, per 1000 atoms: 0.24 Number of scatterers: 11860 At special positions: 0 Unit cell: (118.5, 113.562, 95.7875, 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 36 16.00 O 2236 8.00 N 2088 7.00 C 7500 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.86 Conformation dependent library (CDL) restraints added in 592.6 milliseconds 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2816 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 16 sheets defined 42.6% alpha, 24.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.29 Creating SS restraints... Processing helix chain 'A' and resid 9 through 21 Processing helix chain 'A' and resid 34 through 46 Processing helix chain 'A' and resid 59 through 68 removed outlier: 3.569A pdb=" N LEU A 63 " --> pdb=" O ASP A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 78 through 80 No H-bonds generated for 'chain 'A' and resid 78 through 80' Processing helix chain 'A' and resid 81 through 93 Processing helix chain 'A' and resid 102 through 104 No H-bonds generated for 'chain 'A' and resid 102 through 104' Processing helix chain 'A' and resid 105 through 112 removed outlier: 3.576A pdb=" N ARG A 109 " --> pdb=" O HIS A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 120 Processing helix chain 'A' and resid 133 through 144 Processing helix chain 'A' and resid 174 through 184 Processing helix chain 'A' and resid 225 through 230 Processing helix chain 'A' and resid 245 through 256 removed outlier: 3.606A pdb=" N LEU A 252 " --> pdb=" O GLU A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 286 Proline residue: A 284 - end of helix Processing helix chain 'A' and resid 327 through 347 Processing helix chain 'A' and resid 356 through 361 removed outlier: 3.682A pdb=" N ILE A 360 " --> pdb=" O PRO A 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 374 Processing helix chain 'B' and resid 9 through 22 Processing helix chain 'B' and resid 34 through 46 Processing helix chain 'B' and resid 59 through 67 Processing helix chain 'B' and resid 78 through 80 No H-bonds generated for 'chain 'B' and resid 78 through 80' Processing helix chain 'B' and resid 81 through 93 Processing helix chain 'B' and resid 105 through 112 Processing helix chain 'B' and resid 113 through 121 Processing helix chain 'B' and resid 133 through 145 Processing helix chain 'B' and resid 174 through 184 Processing helix chain 'B' and resid 225 through 230 Processing helix chain 'B' and resid 245 through 256 removed outlier: 3.642A pdb=" N LEU B 253 " --> pdb=" O LYS B 249 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 286 Proline residue: B 284 - end of helix Processing helix chain 'B' and resid 327 through 347 Processing helix chain 'B' and resid 356 through 361 removed outlier: 3.690A pdb=" N ILE B 360 " --> pdb=" O PRO B 356 " (cutoff:3.500A) Processing helix chain 'B' and resid 362 through 373 Processing helix chain 'C' and resid 9 through 22 removed outlier: 3.520A pdb=" N ASP C 18 " --> pdb=" O GLU C 14 " (cutoff:3.500A) Processing helix chain 'C' and resid 34 through 45 Processing helix chain 'C' and resid 59 through 68 removed outlier: 3.615A pdb=" N LEU C 63 " --> pdb=" O ASP C 59 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 93 removed outlier: 4.439A pdb=" N GLU C 83 " --> pdb=" O TYR C 79 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N THR C 84 " --> pdb=" O GLN C 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 105 through 113 removed outlier: 3.544A pdb=" N LEU C 113 " --> pdb=" O ARG C 109 " (cutoff:3.500A) Processing helix chain 'C' and resid 113 through 120 Processing helix chain 'C' and resid 133 through 145 Processing helix chain 'C' and resid 174 through 184 Processing helix chain 'C' and resid 225 through 230 Processing helix chain 'C' and resid 245 through 256 Processing helix chain 'C' and resid 273 through 283 removed outlier: 3.507A pdb=" N VAL C 277 " --> pdb=" O LYS C 273 " (cutoff:3.500A) Processing helix chain 'C' and resid 327 through 346 Processing helix chain 'C' and resid 356 through 361 removed outlier: 3.667A pdb=" N ILE C 360 " --> pdb=" O PRO C 356 " (cutoff:3.500A) Processing helix chain 'C' and resid 362 through 373 Processing helix chain 'D' and resid 9 through 22 Processing helix chain 'D' and resid 34 through 46 removed outlier: 3.969A pdb=" N THR D 41 " --> pdb=" O LYS D 37 " (cutoff:3.500A) Processing helix chain 'D' and resid 59 through 68 Processing helix chain 'D' and resid 78 through 80 No H-bonds generated for 'chain 'D' and resid 78 through 80' Processing helix chain 'D' and resid 81 through 93 Processing helix chain 'D' and resid 104 through 112 Processing helix chain 'D' and resid 113 through 121 Processing helix chain 'D' and resid 133 through 145 Processing helix chain 'D' and resid 174 through 184 Processing helix chain 'D' and resid 225 through 230 Processing helix chain 'D' and resid 245 through 256 Processing helix chain 'D' and resid 273 through 286 removed outlier: 3.558A pdb=" N VAL D 277 " --> pdb=" O LYS D 273 " (cutoff:3.500A) Proline residue: D 284 - end of helix Processing helix chain 'D' and resid 327 through 347 Processing helix chain 'D' and resid 356 through 361 removed outlier: 3.674A pdb=" N ILE D 360 " --> pdb=" O PRO D 356 " (cutoff:3.500A) Processing helix chain 'D' and resid 362 through 373 Processing sheet with id=AA1, first strand: chain 'A' and resid 50 through 51 removed outlier: 6.753A pdb=" N VAL A 3 " --> pdb=" O THR A 29 " (cutoff:3.500A) removed outlier: 7.657A pdb=" N ALA A 31 " --> pdb=" O VAL A 3 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N VAL A 5 " --> pdb=" O ALA A 31 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N SER A 96 " --> pdb=" O ILE A 125 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 204 through 206 removed outlier: 10.073A pdb=" N ARG A 235 " --> pdb=" O GLU A 148 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N GLU A 150 " --> pdb=" O ARG A 235 " (cutoff:3.500A) removed outlier: 8.656A pdb=" N GLU A 237 " --> pdb=" O GLU A 150 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N ILE A 152 " --> pdb=" O GLU A 237 " (cutoff:3.500A) removed outlier: 7.900A pdb=" N LYS A 239 " --> pdb=" O ILE A 152 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N LEU A 154 " --> pdb=" O LYS A 239 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N ILE A 241 " --> pdb=" O LEU A 154 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N VAL A 156 " --> pdb=" O ILE A 241 " (cutoff:3.500A) removed outlier: 5.423A pdb=" N VAL A 149 " --> pdb=" O ARG A 304 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N ARG A 304 " --> pdb=" O VAL A 149 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 186 through 190 Processing sheet with id=AA4, first strand: chain 'A' and resid 265 through 267 Processing sheet with id=AA5, first strand: chain 'B' and resid 50 through 54 removed outlier: 6.552A pdb=" N LYS B 2 " --> pdb=" O VAL B 72 " (cutoff:3.500A) removed outlier: 7.777A pdb=" N VAL B 74 " --> pdb=" O LYS B 2 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N LEU B 4 " --> pdb=" O VAL B 74 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N SER B 96 " --> pdb=" O ILE B 125 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 193 through 197 removed outlier: 7.716A pdb=" N LEU B 187 " --> pdb=" O TYR B 238 " (cutoff:3.500A) removed outlier: 5.729A pdb=" N TYR B 238 " --> pdb=" O LEU B 187 " (cutoff:3.500A) removed outlier: 4.969A pdb=" N GLY B 212 " --> pdb=" O PHE B 208 " (cutoff:3.500A) removed outlier: 4.843A pdb=" N PHE B 208 " --> pdb=" O GLY B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 193 through 197 removed outlier: 7.716A pdb=" N LEU B 187 " --> pdb=" O TYR B 238 " (cutoff:3.500A) removed outlier: 5.729A pdb=" N TYR B 238 " --> pdb=" O LEU B 187 " (cutoff:3.500A) removed outlier: 10.119A pdb=" N ARG B 235 " --> pdb=" O GLU B 148 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N GLU B 150 " --> pdb=" O ARG B 235 " (cutoff:3.500A) removed outlier: 8.540A pdb=" N GLU B 237 " --> pdb=" O GLU B 150 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N ILE B 152 " --> pdb=" O GLU B 237 " (cutoff:3.500A) removed outlier: 7.924A pdb=" N LYS B 239 " --> pdb=" O ILE B 152 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N LEU B 154 " --> pdb=" O LYS B 239 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N ILE B 241 " --> pdb=" O LEU B 154 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N VAL B 156 " --> pdb=" O ILE B 241 " (cutoff:3.500A) removed outlier: 5.635A pdb=" N VAL B 149 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N ARG B 304 " --> pdb=" O VAL B 149 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 265 through 267 Processing sheet with id=AA9, first strand: chain 'C' and resid 27 through 31 removed outlier: 6.649A pdb=" N LYS C 2 " --> pdb=" O VAL C 72 " (cutoff:3.500A) removed outlier: 7.919A pdb=" N VAL C 74 " --> pdb=" O LYS C 2 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N LEU C 4 " --> pdb=" O VAL C 74 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N LEU C 99 " --> pdb=" O ASN C 75 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ASP C 127 " --> pdb=" O ASP C 98 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ILE C 124 " --> pdb=" O GLY C 353 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 204 through 206 removed outlier: 10.540A pdb=" N ARG C 235 " --> pdb=" O GLU C 148 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N GLU C 150 " --> pdb=" O ARG C 235 " (cutoff:3.500A) removed outlier: 8.602A pdb=" N GLU C 237 " --> pdb=" O GLU C 150 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N ILE C 152 " --> pdb=" O GLU C 237 " (cutoff:3.500A) removed outlier: 7.920A pdb=" N LYS C 239 " --> pdb=" O ILE C 152 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N LEU C 154 " --> pdb=" O LYS C 239 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N ILE C 241 " --> pdb=" O LEU C 154 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N VAL C 156 " --> pdb=" O ILE C 241 " (cutoff:3.500A) removed outlier: 9.376A pdb=" N TYR C 243 " --> pdb=" O VAL C 156 " (cutoff:3.500A) removed outlier: 11.132A pdb=" N GLY C 158 " --> pdb=" O TYR C 243 " (cutoff:3.500A) removed outlier: 5.209A pdb=" N VAL C 149 " --> pdb=" O ARG C 304 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N ARG C 304 " --> pdb=" O VAL C 149 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 186 through 190 Processing sheet with id=AB3, first strand: chain 'C' and resid 265 through 267 Processing sheet with id=AB4, first strand: chain 'D' and resid 50 through 52 removed outlier: 6.125A pdb=" N VAL D 28 " --> pdb=" O ALA D 51 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N VAL D 3 " --> pdb=" O THR D 29 " (cutoff:3.500A) removed outlier: 7.823A pdb=" N ALA D 31 " --> pdb=" O VAL D 3 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N VAL D 5 " --> pdb=" O ALA D 31 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N SER D 96 " --> pdb=" O ILE D 125 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ILE D 124 " --> pdb=" O GLY D 353 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 193 through 197 removed outlier: 7.660A pdb=" N LEU D 187 " --> pdb=" O TYR D 238 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N TYR D 238 " --> pdb=" O LEU D 187 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 193 through 197 removed outlier: 7.660A pdb=" N LEU D 187 " --> pdb=" O TYR D 238 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N TYR D 238 " --> pdb=" O LEU D 187 " (cutoff:3.500A) removed outlier: 9.773A pdb=" N ARG D 235 " --> pdb=" O GLU D 148 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N GLU D 150 " --> pdb=" O ARG D 235 " (cutoff:3.500A) removed outlier: 8.606A pdb=" N GLU D 237 " --> pdb=" O GLU D 150 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N ILE D 152 " --> pdb=" O GLU D 237 " (cutoff:3.500A) removed outlier: 7.884A pdb=" N LYS D 239 " --> pdb=" O ILE D 152 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N LEU D 154 " --> pdb=" O LYS D 239 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N ILE D 241 " --> pdb=" O LEU D 154 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N VAL D 156 " --> pdb=" O ILE D 241 " (cutoff:3.500A) removed outlier: 9.455A pdb=" N TYR D 243 " --> pdb=" O VAL D 156 " (cutoff:3.500A) removed outlier: 11.181A pdb=" N GLY D 158 " --> pdb=" O TYR D 243 " (cutoff:3.500A) removed outlier: 5.177A pdb=" N VAL D 149 " --> pdb=" O ARG D 304 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N ARG D 304 " --> pdb=" O VAL D 149 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N GLU D 309 " --> pdb=" O HIS D 384 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 265 through 267 638 hydrogen bonds defined for protein. 1812 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.89 Time building geometry restraints manager: 1.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.31: 2035 1.31 - 1.44: 2820 1.44 - 1.57: 7133 1.57 - 1.70: 0 1.70 - 1.84: 64 Bond restraints: 12052 Sorted by residual: bond pdb=" C PRO C 160 " pdb=" O PRO C 160 " ideal model delta sigma weight residual 1.233 1.174 0.059 1.10e-02 8.26e+03 2.89e+01 bond pdb=" C PRO B 160 " pdb=" O PRO B 160 " ideal model delta sigma weight residual 1.233 1.176 0.057 1.10e-02 8.26e+03 2.68e+01 bond pdb=" C PHE A 211 " pdb=" O PHE A 211 " ideal model delta sigma weight residual 1.235 1.177 0.059 1.23e-02 6.61e+03 2.28e+01 bond pdb=" C VAL C 295 " pdb=" O VAL C 295 " ideal model delta sigma weight residual 1.237 1.185 0.052 1.10e-02 8.26e+03 2.21e+01 bond pdb=" N ILE B 360 " pdb=" CA ILE B 360 " ideal model delta sigma weight residual 1.456 1.500 -0.043 9.50e-03 1.11e+04 2.07e+01 ... (remaining 12047 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.20: 13240 2.20 - 4.39: 2988 4.39 - 6.59: 92 6.59 - 8.79: 10 8.79 - 10.98: 2 Bond angle restraints: 16332 Sorted by residual: angle pdb=" CA GLY C 353 " pdb=" C GLY C 353 " pdb=" O GLY C 353 " ideal model delta sigma weight residual 122.22 117.85 4.37 6.50e-01 2.37e+00 4.53e+01 angle pdb=" CA GLY D 353 " pdb=" C GLY D 353 " pdb=" O GLY D 353 " ideal model delta sigma weight residual 122.22 117.94 4.28 6.50e-01 2.37e+00 4.35e+01 angle pdb=" CA GLY B 353 " pdb=" C GLY B 353 " pdb=" O GLY B 353 " ideal model delta sigma weight residual 122.37 118.54 3.83 7.30e-01 1.88e+00 2.76e+01 angle pdb=" CG ARG B 304 " pdb=" CD ARG B 304 " pdb=" NE ARG B 304 " ideal model delta sigma weight residual 112.00 101.02 10.98 2.20e+00 2.07e-01 2.49e+01 angle pdb=" CA HIS C 46 " pdb=" C HIS C 46 " pdb=" O HIS C 46 " ideal model delta sigma weight residual 122.13 116.73 5.40 1.13e+00 7.83e-01 2.28e+01 ... (remaining 16327 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.25: 6512 14.25 - 28.51: 561 28.51 - 42.76: 169 42.76 - 57.02: 69 57.02 - 71.27: 45 Dihedral angle restraints: 7356 sinusoidal: 2960 harmonic: 4396 Sorted by residual: dihedral pdb=" CA ASN C 320 " pdb=" C ASN C 320 " pdb=" N ASP C 321 " pdb=" CA ASP C 321 " ideal model delta harmonic sigma weight residual 180.00 160.09 19.91 0 5.00e+00 4.00e-02 1.59e+01 dihedral pdb=" C ASP C 180 " pdb=" N ASP C 180 " pdb=" CA ASP C 180 " pdb=" CB ASP C 180 " ideal model delta harmonic sigma weight residual -122.60 -132.13 9.53 0 2.50e+00 1.60e-01 1.45e+01 dihedral pdb=" C ILE A 360 " pdb=" N ILE A 360 " pdb=" CA ILE A 360 " pdb=" CB ILE A 360 " ideal model delta harmonic sigma weight residual -122.00 -130.26 8.26 0 2.50e+00 1.60e-01 1.09e+01 ... (remaining 7353 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 907 0.061 - 0.122: 643 0.122 - 0.183: 325 0.183 - 0.244: 48 0.244 - 0.305: 5 Chirality restraints: 1928 Sorted by residual: chirality pdb=" CA ASP C 180 " pdb=" N ASP C 180 " pdb=" C ASP C 180 " pdb=" CB ASP C 180 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.32e+00 chirality pdb=" CB ILE C 135 " pdb=" CA ILE C 135 " pdb=" CG1 ILE C 135 " pdb=" CG2 ILE C 135 " both_signs ideal model delta sigma weight residual False 2.64 2.37 0.27 2.00e-01 2.50e+01 1.83e+00 chirality pdb=" CA VAL D 53 " pdb=" N VAL D 53 " pdb=" C VAL D 53 " pdb=" CB VAL D 53 " both_signs ideal model delta sigma weight residual False 2.44 2.69 -0.25 2.00e-01 2.50e+01 1.60e+00 ... (remaining 1925 not shown) Planarity restraints: 2112 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 211 " 0.051 2.00e-02 2.50e+03 3.16e-02 1.75e+01 pdb=" CG PHE A 211 " -0.035 2.00e-02 2.50e+03 pdb=" CD1 PHE A 211 " -0.032 2.00e-02 2.50e+03 pdb=" CD2 PHE A 211 " -0.032 2.00e-02 2.50e+03 pdb=" CE1 PHE A 211 " 0.009 2.00e-02 2.50e+03 pdb=" CE2 PHE A 211 " 0.009 2.00e-02 2.50e+03 pdb=" CZ PHE A 211 " 0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 211 " 0.048 2.00e-02 2.50e+03 3.09e-02 1.67e+01 pdb=" CG PHE B 211 " -0.029 2.00e-02 2.50e+03 pdb=" CD1 PHE B 211 " -0.033 2.00e-02 2.50e+03 pdb=" CD2 PHE B 211 " -0.025 2.00e-02 2.50e+03 pdb=" CE1 PHE B 211 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE B 211 " -0.006 2.00e-02 2.50e+03 pdb=" CZ PHE B 211 " 0.042 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 355 " -0.015 2.00e-02 2.50e+03 2.54e-02 1.29e+01 pdb=" CG TYR A 355 " -0.024 2.00e-02 2.50e+03 pdb=" CD1 TYR A 355 " 0.029 2.00e-02 2.50e+03 pdb=" CD2 TYR A 355 " 0.005 2.00e-02 2.50e+03 pdb=" CE1 TYR A 355 " 0.016 2.00e-02 2.50e+03 pdb=" CE2 TYR A 355 " 0.041 2.00e-02 2.50e+03 pdb=" CZ TYR A 355 " -0.034 2.00e-02 2.50e+03 pdb=" OH TYR A 355 " -0.017 2.00e-02 2.50e+03 ... (remaining 2109 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 2143 2.81 - 3.34: 12236 3.34 - 3.86: 21049 3.86 - 4.38: 25412 4.38 - 4.90: 41703 Nonbonded interactions: 102543 Sorted by model distance: nonbonded pdb=" O VAL C 42 " pdb=" O LEU C 45 " model vdw 2.293 3.040 nonbonded pdb=" CB PHE A 319 " pdb=" NH1 ARG D 210 " model vdw 2.410 3.520 nonbonded pdb=" O PRO B 198 " pdb=" OG SER B 201 " model vdw 2.412 3.040 nonbonded pdb=" OG1 THR A 225 " pdb=" OE2 GLU A 358 " model vdw 2.425 3.040 nonbonded pdb=" O GLU D 176 " pdb=" NH2 ARG D 275 " model vdw 2.433 3.120 ... (remaining 102538 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.830 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: 0.190 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 11.220 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 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 : 0.013 0.104 12052 Z= 0.988 Angle : 1.643 10.984 16332 Z= 1.220 Chirality : 0.091 0.305 1928 Planarity : 0.012 0.122 2112 Dihedral : 14.162 71.270 4540 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 13.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 0.00 % Allowed : 7.74 % Favored : 92.26 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 11.76 % 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: -1.79 (0.19), residues: 1528 helix: -0.83 (0.18), residues: 596 sheet: -1.03 (0.25), residues: 384 loop : -1.46 (0.25), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.046 0.004 ARG B 298 TYR 0.041 0.010 TYR A 355 PHE 0.051 0.009 PHE A 211 HIS 0.033 0.005 HIS C 171 Details of bonding type rmsd/Z covalent geometry : bond 0.01344 / 0.99 (12052) covalent geometry : angle 1.64270 / 1.22 (16332) hydrogen bonds : bond 0.17048 / 11.67 ( 622) hydrogen bonds : angle 7.05464 / 5.03 ( 1812) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 407 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 407 time to evaluate : 0.475 Fit side-chains REVERT: A 26 GLU cc_start: 0.7141 (mt-10) cc_final: 0.6635 (mm-30) REVERT: A 40 GLN cc_start: 0.6617 (mt0) cc_final: 0.6187 (tp-100) REVERT: A 62 GLN cc_start: 0.5918 (pt0) cc_final: 0.5699 (pt0) REVERT: A 67 MET cc_start: 0.7900 (mtt) cc_final: 0.7565 (mtt) REVERT: A 80 GLN cc_start: 0.7765 (pt0) cc_final: 0.7301 (mm-40) REVERT: A 87 LYS cc_start: 0.7536 (ttmt) cc_final: 0.6996 (mtmt) REVERT: A 150 GLU cc_start: 0.8100 (mt-10) cc_final: 0.7584 (mm-30) REVERT: A 193 GLN cc_start: 0.7953 (mt0) cc_final: 0.7744 (mp10) REVERT: A 234 LYS cc_start: 0.7923 (ptpt) cc_final: 0.7349 (mmtm) REVERT: A 237 GLU cc_start: 0.8768 (mt-10) cc_final: 0.8542 (mt-10) REVERT: A 248 GLU cc_start: 0.7732 (pt0) cc_final: 0.7428 (mt-10) REVERT: A 283 LYS cc_start: 0.7245 (mtmp) cc_final: 0.7021 (ttpt) REVERT: A 321 ASP cc_start: 0.6950 (t70) cc_final: 0.6724 (t0) REVERT: A 324 ASN cc_start: 0.7268 (m-40) cc_final: 0.6997 (m110) REVERT: A 368 ASP cc_start: 0.7618 (t70) cc_final: 0.7370 (m-30) REVERT: A 376 LEU cc_start: 0.8358 (mm) cc_final: 0.8033 (tt) REVERT: A 378 SER cc_start: 0.8434 (t) cc_final: 0.8160 (p) REVERT: B 2 LYS cc_start: 0.7450 (mttt) cc_final: 0.7047 (mttp) REVERT: B 146 LEU cc_start: 0.8126 (mt) cc_final: 0.7904 (mp) REVERT: B 176 GLU cc_start: 0.7534 (mt-10) cc_final: 0.7058 (tt0) REVERT: B 184 ASP cc_start: 0.8326 (m-30) cc_final: 0.7983 (m-30) REVERT: B 234 LYS cc_start: 0.7845 (mtmt) cc_final: 0.7213 (mmtm) REVERT: B 251 LYS cc_start: 0.7111 (tttt) cc_final: 0.6798 (tttt) REVERT: B 257 THR cc_start: 0.8569 (m) cc_final: 0.8252 (p) REVERT: B 266 GLU cc_start: 0.7099 (mt-10) cc_final: 0.6789 (mt-10) REVERT: B 287 ASP cc_start: 0.7861 (t70) cc_final: 0.7586 (t70) REVERT: B 376 LEU cc_start: 0.8082 (tt) cc_final: 0.7716 (mt) REVERT: B 381 ARG cc_start: 0.7815 (ttm-80) cc_final: 0.7353 (mtp-110) REVERT: C 41 THR cc_start: 0.6742 (m) cc_final: 0.6395 (t) REVERT: C 71 ASP cc_start: 0.7099 (t0) cc_final: 0.6558 (m-30) REVERT: C 106 ILE cc_start: 0.7367 (mp) cc_final: 0.7152 (mp) REVERT: C 182 TYR cc_start: 0.8706 (m-10) cc_final: 0.8488 (m-10) REVERT: C 191 ASN cc_start: 0.7960 (m-40) cc_final: 0.7460 (m110) REVERT: C 193 GLN cc_start: 0.7107 (mt0) cc_final: 0.6806 (mm110) REVERT: C 195 GLN cc_start: 0.7388 (pt0) cc_final: 0.7164 (pt0) REVERT: C 234 LYS cc_start: 0.7751 (ttmt) cc_final: 0.7309 (tppt) REVERT: C 248 GLU cc_start: 0.7908 (tt0) cc_final: 0.7632 (mt-10) REVERT: C 313 GLU cc_start: 0.8414 (tt0) cc_final: 0.8163 (tt0) REVERT: C 359 GLN cc_start: 0.8116 (mt0) cc_final: 0.7735 (mt0) REVERT: D 1 MET cc_start: 0.5808 (ptp) cc_final: 0.5288 (ptm) REVERT: D 14 GLU cc_start: 0.6795 (tp30) cc_final: 0.6481 (mm-30) REVERT: D 26 GLU cc_start: 0.6819 (tt0) cc_final: 0.6070 (mm-30) REVERT: D 32 ASP cc_start: 0.5618 (t70) cc_final: 0.5312 (t70) REVERT: D 84 THR cc_start: 0.7512 (t) cc_final: 0.7300 (p) REVERT: D 148 GLU cc_start: 0.6469 (tt0) cc_final: 0.5539 (tp30) REVERT: D 176 GLU cc_start: 0.7420 (tt0) cc_final: 0.7019 (mp0) REVERT: D 183 THR cc_start: 0.8386 (t) cc_final: 0.8110 (m) REVERT: D 227 SER cc_start: 0.8094 (t) cc_final: 0.7835 (p) REVERT: D 248 GLU cc_start: 0.7803 (mt-10) cc_final: 0.7599 (mt-10) REVERT: D 267 ILE cc_start: 0.7345 (pt) cc_final: 0.6950 (tp) REVERT: D 283 LYS cc_start: 0.7622 (ttmm) cc_final: 0.7263 (tttt) REVERT: D 304 ARG cc_start: 0.6750 (mtp-110) cc_final: 0.6246 (mtp-110) REVERT: D 309 GLU cc_start: 0.6125 (tt0) cc_final: 0.5869 (mm-30) REVERT: D 329 MET cc_start: 0.8210 (mmt) cc_final: 0.8000 (mmt) REVERT: D 359 GLN cc_start: 0.8046 (mt0) cc_final: 0.7705 (mt0) REVERT: D 370 MET cc_start: 0.8185 (mmp) cc_final: 0.7950 (mmm) outliers start: 0 outliers final: 0 residues processed: 407 average time/residue: 0.6447 time to fit residues: 280.6581 Evaluate side-chains 229 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 229 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: [98, 107, 10, 66, 130, 124, 103, 77, 122, 91, 149] chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 9.9990 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 0.0570 chunk 91 optimal weight: 0.9990 chunk 149 optimal weight: 2.9990 overall best weight: 1.6106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 62 GLN A 136 ASN A 170 ASN A 246 HIS A 268 ASN A 342 GLN B 44 GLN B 82 ASN B 170 ASN B 246 HIS B 342 GLN B 384 HIS C 21 GLN C 61 GLN C 95 HIS ** C 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 114 HIS C 136 ASN C 170 ASN C 191 ASN C 195 GLN C 218 HIS C 246 HIS ** C 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 44 GLN D 95 HIS D 102 HIS D 114 HIS D 136 ASN D 170 ASN D 246 HIS D 261 HIS Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.139634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.101252 restraints weight = 13498.214| |-----------------------------------------------------------------------------| r_work (start): 0.3048 rms_B_bonded: 1.91 r_work: 0.2885 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2735 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2735 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.2678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 12052 Z= 0.157 Angle : 0.567 6.552 16332 Z= 0.302 Chirality : 0.046 0.158 1928 Planarity : 0.004 0.034 2112 Dihedral : 3.909 15.840 1672 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 3.17 % Allowed : 13.93 % Favored : 82.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % 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: -0.17 (0.21), residues: 1528 helix: 1.08 (0.21), residues: 620 sheet: -0.52 (0.25), residues: 428 loop : -1.16 (0.27), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 116 TYR 0.014 0.002 TYR B 355 PHE 0.020 0.002 PHE B 211 HIS 0.007 0.001 HIS C 171 Details of bonding type rmsd/Z covalent geometry : bond 0.00359 / 0.16 (12052) covalent geometry : angle 0.56671 / 0.30 (16332) hydrogen bonds : bond 0.04619 / 3.08 ( 622) hydrogen bonds : angle 5.14539 / 3.65 ( 1812) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 245 time to evaluate : 0.505 Fit side-chains REVERT: A 26 GLU cc_start: 0.7112 (mt-10) cc_final: 0.6699 (mm-30) REVERT: A 39 GLU cc_start: 0.7015 (mt-10) cc_final: 0.6669 (mp0) REVERT: A 40 GLN cc_start: 0.6913 (mt0) cc_final: 0.6525 (tp-100) REVERT: A 71 ASP cc_start: 0.7523 (t70) cc_final: 0.7048 (t0) REVERT: A 80 GLN cc_start: 0.7428 (pt0) cc_final: 0.7160 (mm-40) REVERT: A 150 GLU cc_start: 0.7809 (mt-10) cc_final: 0.7599 (mm-30) REVERT: A 234 LYS cc_start: 0.8177 (ptpt) cc_final: 0.7825 (mmtm) REVERT: A 237 GLU cc_start: 0.8654 (mt-10) cc_final: 0.8431 (mt-10) REVERT: A 271 ARG cc_start: 0.6906 (mtp85) cc_final: 0.6538 (mtp85) REVERT: A 304 ARG cc_start: 0.7869 (mmt180) cc_final: 0.7346 (mmt180) REVERT: A 309 GLU cc_start: 0.6134 (OUTLIER) cc_final: 0.5739 (mt-10) REVERT: A 364 ASP cc_start: 0.7845 (OUTLIER) cc_final: 0.7496 (p0) REVERT: B 34 ASP cc_start: 0.5551 (t0) cc_final: 0.5281 (t0) REVERT: B 48 LYS cc_start: 0.6836 (ptmm) cc_final: 0.6418 (mmmt) REVERT: B 59 ASP cc_start: 0.6001 (t0) cc_final: 0.5767 (t0) REVERT: B 176 GLU cc_start: 0.7720 (mt-10) cc_final: 0.7412 (tt0) REVERT: B 234 LYS cc_start: 0.8139 (mtmt) cc_final: 0.7647 (mmtm) REVERT: B 251 LYS cc_start: 0.7869 (tttt) cc_final: 0.7642 (ttpt) REVERT: B 266 GLU cc_start: 0.6624 (mt-10) cc_final: 0.6394 (mt-10) REVERT: B 285 LEU cc_start: 0.8349 (OUTLIER) cc_final: 0.8102 (mp) REVERT: B 321 ASP cc_start: 0.7579 (OUTLIER) cc_final: 0.7134 (m-30) REVERT: B 381 ARG cc_start: 0.7612 (ttm-80) cc_final: 0.7185 (mtp-110) REVERT: C 2 LYS cc_start: 0.6536 (mtmm) cc_final: 0.5996 (mppt) REVERT: C 28 VAL cc_start: 0.7993 (t) cc_final: 0.7789 (m) REVERT: C 43 ARG cc_start: 0.6564 (mtm-85) cc_final: 0.6214 (ttm110) REVERT: C 48 LYS cc_start: 0.6082 (mtmt) cc_final: 0.5857 (mptm) REVERT: C 63 LEU cc_start: 0.6378 (mt) cc_final: 0.5698 (tp) REVERT: C 80 GLN cc_start: 0.6887 (mm110) cc_final: 0.6340 (mm-40) REVERT: C 105 HIS cc_start: 0.4443 (OUTLIER) cc_final: 0.3674 (t-90) REVERT: C 191 ASN cc_start: 0.7940 (m110) cc_final: 0.7421 (m110) REVERT: C 194 LYS cc_start: 0.8412 (ttmm) cc_final: 0.8008 (mttm) REVERT: C 225 THR cc_start: 0.8532 (OUTLIER) cc_final: 0.8222 (p) REVERT: C 231 PRO cc_start: 0.8151 (Cg_endo) cc_final: 0.7830 (Cg_exo) REVERT: C 234 LYS cc_start: 0.8153 (ttmt) cc_final: 0.7736 (mmpt) REVERT: C 322 ARG cc_start: 0.6669 (mmm160) cc_final: 0.6205 (mtp180) REVERT: D 1 MET cc_start: 0.6652 (ptp) cc_final: 0.6235 (ptm) REVERT: D 26 GLU cc_start: 0.7165 (tt0) cc_final: 0.6240 (mp0) REVERT: D 46 HIS cc_start: 0.6149 (t-90) cc_final: 0.5910 (t70) REVERT: D 107 THR cc_start: 0.8034 (t) cc_final: 0.7800 (t) REVERT: D 148 GLU cc_start: 0.6953 (tt0) cc_final: 0.5841 (tp30) REVERT: D 183 THR cc_start: 0.8654 (t) cc_final: 0.8345 (m) REVERT: D 227 SER cc_start: 0.8452 (t) cc_final: 0.8141 (p) REVERT: D 263 VAL cc_start: 0.7210 (t) cc_final: 0.6934 (m) REVERT: D 304 ARG cc_start: 0.6648 (mtp-110) cc_final: 0.6393 (mtt-85) REVERT: D 323 GLU cc_start: 0.7315 (mp0) cc_final: 0.6735 (mp0) REVERT: D 348 VAL cc_start: 0.8036 (t) cc_final: 0.7704 (m) outliers start: 41 outliers final: 11 residues processed: 269 average time/residue: 0.5931 time to fit residues: 172.3764 Evaluate side-chains 230 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 213 time to evaluate : 0.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 227 SER Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 364 ASP Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 106 ILE Chi-restraints excluded: chain B residue 194 LYS Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 321 ASP Chi-restraints excluded: chain C residue 105 HIS Chi-restraints excluded: chain C residue 225 THR Chi-restraints excluded: chain C residue 263 VAL Chi-restraints excluded: chain C residue 272 VAL Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 368 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: [11, 17, 29, 49, 16, 106, 148, 147, 9, 103, 81] chunk 11 optimal weight: 10.0000 chunk 17 optimal weight: 5.9990 chunk 29 optimal weight: 0.9980 chunk 49 optimal weight: 7.9990 chunk 16 optimal weight: 0.5980 chunk 106 optimal weight: 10.0000 chunk 148 optimal weight: 1.9990 chunk 147 optimal weight: 0.8980 chunk 9 optimal weight: 10.0000 chunk 103 optimal weight: 7.9990 chunk 81 optimal weight: 7.9990 overall best weight: 2.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 118 GLN A 170 ASN A 171 HIS A 218 HIS B 170 ASN ** B 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 342 GLN C 21 GLN ** C 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 193 GLN ** C 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 102 HIS D 261 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.137427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.100212 restraints weight = 13501.768| |-----------------------------------------------------------------------------| r_work (start): 0.3052 rms_B_bonded: 1.80 r_work: 0.2885 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2743 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.2743 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.3224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 12052 Z= 0.159 Angle : 0.554 6.506 16332 Z= 0.287 Chirality : 0.045 0.217 1928 Planarity : 0.004 0.041 2112 Dihedral : 3.965 15.617 1672 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 2.94 % Allowed : 15.87 % Favored : 81.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % 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: 0.20 (0.22), residues: 1528 helix: 1.31 (0.21), residues: 620 sheet: -0.20 (0.25), residues: 428 loop : -0.98 (0.28), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 381 TYR 0.014 0.001 TYR D 79 PHE 0.020 0.002 PHE B 173 HIS 0.033 0.002 HIS C 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00372 / 0.16 (12052) covalent geometry : angle 0.55403 / 0.29 (16332) hydrogen bonds : bond 0.04119 / 2.75 ( 622) hydrogen bonds : angle 4.77486 / 3.38 ( 1812) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 222 time to evaluate : 0.434 Fit side-chains REVERT: A 24 ASP cc_start: 0.7335 (m-30) cc_final: 0.7089 (t0) REVERT: A 39 GLU cc_start: 0.7063 (mt-10) cc_final: 0.6482 (mm-30) REVERT: A 40 GLN cc_start: 0.6967 (mt0) cc_final: 0.6599 (tp-100) REVERT: A 54 ARG cc_start: 0.6969 (ptm-80) cc_final: 0.6531 (ttt-90) REVERT: A 71 ASP cc_start: 0.7525 (t70) cc_final: 0.7047 (t0) REVERT: A 80 GLN cc_start: 0.7429 (pt0) cc_final: 0.7207 (mm-40) REVERT: A 150 GLU cc_start: 0.7907 (mt-10) cc_final: 0.7540 (mm-30) REVERT: A 234 LYS cc_start: 0.8289 (ptpt) cc_final: 0.7822 (mmtm) REVERT: A 237 GLU cc_start: 0.8721 (mt-10) cc_final: 0.8519 (mt-10) REVERT: A 309 GLU cc_start: 0.6232 (OUTLIER) cc_final: 0.5934 (mt-10) REVERT: A 364 ASP cc_start: 0.7887 (OUTLIER) cc_final: 0.7449 (p0) REVERT: A 380 LYS cc_start: 0.8887 (OUTLIER) cc_final: 0.8604 (ttpm) REVERT: B 34 ASP cc_start: 0.5748 (t0) cc_final: 0.5436 (t0) REVERT: B 48 LYS cc_start: 0.6804 (ptmm) cc_final: 0.6495 (mmmt) REVERT: B 176 GLU cc_start: 0.7681 (mt-10) cc_final: 0.7374 (tt0) REVERT: B 234 LYS cc_start: 0.8122 (mtmt) cc_final: 0.7664 (mmtm) REVERT: B 251 LYS cc_start: 0.7844 (tttt) cc_final: 0.7598 (ttpt) REVERT: B 285 LEU cc_start: 0.8390 (OUTLIER) cc_final: 0.8126 (mp) REVERT: B 321 ASP cc_start: 0.7616 (OUTLIER) cc_final: 0.7169 (m-30) REVERT: C 21 GLN cc_start: 0.6890 (mt0) cc_final: 0.6640 (mt0) REVERT: C 62 GLN cc_start: 0.5639 (mm-40) cc_final: 0.4825 (mm-40) REVERT: C 63 LEU cc_start: 0.6588 (mt) cc_final: 0.5717 (mm) REVERT: C 67 MET cc_start: 0.6761 (OUTLIER) cc_final: 0.5644 (mtp) REVERT: C 80 GLN cc_start: 0.6990 (mm110) cc_final: 0.6363 (mm-40) REVERT: C 109 ARG cc_start: 0.6781 (mpp-170) cc_final: 0.6238 (mmm160) REVERT: C 191 ASN cc_start: 0.7863 (m110) cc_final: 0.7382 (m110) REVERT: C 225 THR cc_start: 0.8575 (OUTLIER) cc_final: 0.8298 (p) REVERT: C 231 PRO cc_start: 0.8310 (Cg_endo) cc_final: 0.7996 (Cg_exo) REVERT: C 234 LYS cc_start: 0.8188 (OUTLIER) cc_final: 0.7762 (mmtm) REVERT: C 321 ASP cc_start: 0.7703 (t70) cc_final: 0.7358 (t70) REVERT: C 322 ARG cc_start: 0.6652 (OUTLIER) cc_final: 0.6340 (mmt90) REVERT: C 324 ASN cc_start: 0.7864 (m-40) cc_final: 0.7603 (m-40) REVERT: D 32 ASP cc_start: 0.6328 (t70) cc_final: 0.5995 (t70) REVERT: D 39 GLU cc_start: 0.5296 (mm-30) cc_final: 0.5027 (mt-10) REVERT: D 180 ASP cc_start: 0.8460 (m-30) cc_final: 0.8147 (m-30) REVERT: D 183 THR cc_start: 0.8535 (t) cc_final: 0.8204 (m) REVERT: D 227 SER cc_start: 0.8482 (t) cc_final: 0.8173 (p) REVERT: D 263 VAL cc_start: 0.7335 (t) cc_final: 0.6996 (m) REVERT: D 283 LYS cc_start: 0.8321 (tttm) cc_final: 0.7998 (tttt) REVERT: D 285 LEU cc_start: 0.8428 (mp) cc_final: 0.8148 (mt) REVERT: D 315 GLU cc_start: 0.7892 (tt0) cc_final: 0.7542 (tt0) REVERT: D 348 VAL cc_start: 0.8073 (t) cc_final: 0.7774 (m) outliers start: 38 outliers final: 11 residues processed: 239 average time/residue: 0.6363 time to fit residues: 163.4189 Evaluate side-chains 216 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 196 time to evaluate : 0.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 227 SER Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 364 ASP Chi-restraints excluded: chain A residue 380 LYS Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 194 LYS Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 321 ASP Chi-restraints excluded: chain C residue 67 MET Chi-restraints excluded: chain C residue 225 THR Chi-restraints excluded: chain C residue 234 LYS Chi-restraints excluded: chain C residue 263 VAL Chi-restraints excluded: chain C residue 272 VAL Chi-restraints excluded: chain C residue 322 ARG Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 272 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: [67, 109, 93, 131, 138, 43, 51, 41, 65, 146, 145] chunk 67 optimal weight: 5.9990 chunk 109 optimal weight: 5.9990 chunk 93 optimal weight: 5.9990 chunk 131 optimal weight: 7.9990 chunk 138 optimal weight: 0.9980 chunk 43 optimal weight: 9.9990 chunk 51 optimal weight: 0.9990 chunk 41 optimal weight: 10.0000 chunk 65 optimal weight: 9.9990 chunk 146 optimal weight: 2.9990 chunk 145 optimal weight: 7.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 44 GLN A 118 GLN A 170 ASN A 171 HIS B 62 GLN ** B 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 114 HIS B 171 HIS C 105 HIS C 193 GLN C 342 GLN ** D 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 102 HIS D 261 HIS D 342 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.134990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.097440 restraints weight = 13604.144| |-----------------------------------------------------------------------------| r_work (start): 0.2980 rms_B_bonded: 1.77 r_work: 0.2804 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2658 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.2658 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.3566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 12052 Z= 0.215 Angle : 0.597 9.229 16332 Z= 0.306 Chirality : 0.047 0.240 1928 Planarity : 0.004 0.045 2112 Dihedral : 4.190 16.801 1672 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 3.72 % Allowed : 16.80 % Favored : 79.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % 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: -0.00 (0.21), residues: 1528 helix: 1.09 (0.20), residues: 636 sheet: -0.14 (0.25), residues: 428 loop : -1.27 (0.27), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 381 TYR 0.023 0.002 TYR D 79 PHE 0.024 0.002 PHE A 211 HIS 0.025 0.002 HIS C 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00516 / 0.21 (12052) covalent geometry : angle 0.59722 / 0.31 (16332) hydrogen bonds : bond 0.04285 / 2.87 ( 622) hydrogen bonds : angle 4.80882 / 3.40 ( 1812) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 205 time to evaluate : 0.436 Fit side-chains revert: symmetry clash REVERT: A 24 ASP cc_start: 0.7453 (m-30) cc_final: 0.7187 (t0) REVERT: A 40 GLN cc_start: 0.6825 (mt0) cc_final: 0.6564 (tp-100) REVERT: A 54 ARG cc_start: 0.6855 (ptm-80) cc_final: 0.6215 (ttt-90) REVERT: A 71 ASP cc_start: 0.7619 (t70) cc_final: 0.7108 (t0) REVERT: A 80 GLN cc_start: 0.7646 (pt0) cc_final: 0.7342 (mm-40) REVERT: A 150 GLU cc_start: 0.7927 (mt-10) cc_final: 0.7457 (mm-30) REVERT: A 304 ARG cc_start: 0.8014 (mmt180) cc_final: 0.7790 (mmt180) REVERT: A 309 GLU cc_start: 0.6217 (OUTLIER) cc_final: 0.6002 (mt-10) REVERT: A 364 ASP cc_start: 0.7987 (OUTLIER) cc_final: 0.7611 (p0) REVERT: A 380 LYS cc_start: 0.8877 (OUTLIER) cc_final: 0.8561 (ttpm) REVERT: B 34 ASP cc_start: 0.5722 (t0) cc_final: 0.5345 (t0) REVERT: B 193 GLN cc_start: 0.7950 (mm110) cc_final: 0.7599 (mm-40) REVERT: B 234 LYS cc_start: 0.8199 (mtmt) cc_final: 0.7660 (mmtm) REVERT: B 251 LYS cc_start: 0.7986 (tttt) cc_final: 0.7652 (ttpt) REVERT: B 285 LEU cc_start: 0.8391 (OUTLIER) cc_final: 0.8098 (mp) REVERT: C 30 LEU cc_start: 0.8133 (OUTLIER) cc_final: 0.7656 (tt) REVERT: C 62 GLN cc_start: 0.5564 (OUTLIER) cc_final: 0.4714 (mm-40) REVERT: C 63 LEU cc_start: 0.6678 (mt) cc_final: 0.5734 (mm) REVERT: C 67 MET cc_start: 0.6626 (OUTLIER) cc_final: 0.5830 (mtp) REVERT: C 80 GLN cc_start: 0.7082 (mm110) cc_final: 0.6461 (mm-40) REVERT: C 109 ARG cc_start: 0.6745 (OUTLIER) cc_final: 0.6176 (mmt-90) REVERT: C 191 ASN cc_start: 0.7867 (m110) cc_final: 0.7437 (m110) REVERT: C 231 PRO cc_start: 0.8239 (Cg_endo) cc_final: 0.7985 (Cg_exo) REVERT: C 234 LYS cc_start: 0.8218 (OUTLIER) cc_final: 0.7572 (tppt) REVERT: C 322 ARG cc_start: 0.6720 (OUTLIER) cc_final: 0.6411 (mmt90) REVERT: D 32 ASP cc_start: 0.6490 (t70) cc_final: 0.6013 (t70) REVERT: D 107 THR cc_start: 0.8075 (OUTLIER) cc_final: 0.7669 (m) REVERT: D 180 ASP cc_start: 0.8544 (m-30) cc_final: 0.8168 (m-30) REVERT: D 183 THR cc_start: 0.8547 (t) cc_final: 0.8182 (m) REVERT: D 227 SER cc_start: 0.8505 (t) cc_final: 0.8212 (p) REVERT: D 263 VAL cc_start: 0.7225 (t) cc_final: 0.6869 (m) REVERT: D 283 LYS cc_start: 0.8351 (tttm) cc_final: 0.8004 (tttt) REVERT: D 309 GLU cc_start: 0.6260 (tt0) cc_final: 0.5992 (tm-30) REVERT: D 348 VAL cc_start: 0.8009 (t) cc_final: 0.7733 (m) REVERT: D 358 GLU cc_start: 0.8328 (pm20) cc_final: 0.8108 (pm20) outliers start: 48 outliers final: 19 residues processed: 234 average time/residue: 0.6194 time to fit residues: 156.3517 Evaluate side-chains 225 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 195 time to evaluate : 0.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 227 SER Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 364 ASP Chi-restraints excluded: chain A residue 380 LYS Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 194 LYS Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 287 ASP Chi-restraints excluded: chain B residue 321 ASP Chi-restraints excluded: chain C residue 25 VAL Chi-restraints excluded: chain C residue 30 LEU Chi-restraints excluded: chain C residue 41 THR Chi-restraints excluded: chain C residue 62 GLN Chi-restraints excluded: chain C residue 67 MET Chi-restraints excluded: chain C residue 109 ARG Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 225 THR Chi-restraints excluded: chain C residue 234 LYS Chi-restraints excluded: chain C residue 263 VAL Chi-restraints excluded: chain C residue 272 VAL Chi-restraints excluded: chain C residue 322 ARG Chi-restraints excluded: chain C residue 378 SER Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain D residue 272 VAL Chi-restraints excluded: chain D residue 294 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: [111, 99, 139, 9, 4, 35, 127, 40, 114, 34, 91] chunk 111 optimal weight: 0.9990 chunk 99 optimal weight: 6.9990 chunk 139 optimal weight: 2.9990 chunk 9 optimal weight: 7.9990 chunk 4 optimal weight: 8.9990 chunk 35 optimal weight: 1.9990 chunk 127 optimal weight: 4.9990 chunk 40 optimal weight: 0.6980 chunk 114 optimal weight: 20.0000 chunk 34 optimal weight: 5.9990 chunk 91 optimal weight: 0.9980 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 44 GLN A 118 GLN ** B 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 40 GLN C 193 GLN D 261 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.136323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.098448 restraints weight = 13506.326| |-----------------------------------------------------------------------------| r_work (start): 0.3039 rms_B_bonded: 1.84 r_work: 0.2876 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2733 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.3757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12052 Z= 0.134 Angle : 0.531 9.532 16332 Z= 0.270 Chirality : 0.044 0.209 1928 Planarity : 0.003 0.041 2112 Dihedral : 3.975 15.731 1672 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 2.55 % Allowed : 18.58 % Favored : 78.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % 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: 0.14 (0.22), residues: 1528 helix: 1.25 (0.21), residues: 636 sheet: -0.09 (0.26), residues: 428 loop : -1.24 (0.27), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 271 TYR 0.017 0.001 TYR B 79 PHE 0.014 0.001 PHE A 211 HIS 0.005 0.001 HIS A 171 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.13 (12052) covalent geometry : angle 0.53113 / 0.27 (16332) hydrogen bonds : bond 0.03660 / 2.45 ( 622) hydrogen bonds : angle 4.56892 / 3.23 ( 1812) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 209 time to evaluate : 0.478 Fit side-chains revert: symmetry clash REVERT: A 24 ASP cc_start: 0.7478 (m-30) cc_final: 0.7263 (t0) REVERT: A 39 GLU cc_start: 0.6569 (mt-10) cc_final: 0.6237 (mm-30) REVERT: A 54 ARG cc_start: 0.7034 (ptm-80) cc_final: 0.6587 (ttt-90) REVERT: A 71 ASP cc_start: 0.7614 (t70) cc_final: 0.7147 (t0) REVERT: A 80 GLN cc_start: 0.7620 (pt0) cc_final: 0.7379 (mm-40) REVERT: A 87 LYS cc_start: 0.7938 (ttmm) cc_final: 0.7680 (ttpt) REVERT: A 150 GLU cc_start: 0.7880 (mt-10) cc_final: 0.7502 (mm-30) REVERT: A 273 LYS cc_start: 0.7524 (OUTLIER) cc_final: 0.7220 (mttt) REVERT: A 309 GLU cc_start: 0.6164 (OUTLIER) cc_final: 0.5882 (mt-10) REVERT: A 364 ASP cc_start: 0.7953 (OUTLIER) cc_final: 0.7597 (p0) REVERT: A 380 LYS cc_start: 0.8875 (OUTLIER) cc_final: 0.8595 (ttpm) REVERT: B 26 GLU cc_start: 0.8215 (tt0) cc_final: 0.7083 (mm-30) REVERT: B 34 ASP cc_start: 0.5591 (t0) cc_final: 0.5286 (t0) REVERT: B 234 LYS cc_start: 0.8140 (mtmt) cc_final: 0.7627 (mmtm) REVERT: B 251 LYS cc_start: 0.8006 (tttt) cc_final: 0.7652 (ttpt) REVERT: B 285 LEU cc_start: 0.8355 (OUTLIER) cc_final: 0.8088 (mp) REVERT: C 21 GLN cc_start: 0.6970 (mt0) cc_final: 0.6733 (mt0) REVERT: C 30 LEU cc_start: 0.8197 (OUTLIER) cc_final: 0.7711 (tt) REVERT: C 62 GLN cc_start: 0.5617 (OUTLIER) cc_final: 0.4823 (mm-40) REVERT: C 63 LEU cc_start: 0.6686 (mt) cc_final: 0.5754 (mm) REVERT: C 67 MET cc_start: 0.6615 (OUTLIER) cc_final: 0.5938 (mtp) REVERT: C 80 GLN cc_start: 0.7081 (mm110) cc_final: 0.6495 (mm-40) REVERT: C 191 ASN cc_start: 0.7928 (m110) cc_final: 0.7482 (m110) REVERT: C 225 THR cc_start: 0.8579 (OUTLIER) cc_final: 0.8258 (p) REVERT: C 231 PRO cc_start: 0.8241 (Cg_endo) cc_final: 0.7973 (Cg_exo) REVERT: C 234 LYS cc_start: 0.8225 (OUTLIER) cc_final: 0.7612 (tppt) REVERT: C 321 ASP cc_start: 0.7615 (t70) cc_final: 0.7263 (t70) REVERT: C 322 ARG cc_start: 0.6641 (OUTLIER) cc_final: 0.5852 (mmt180) REVERT: C 324 ASN cc_start: 0.7993 (m-40) cc_final: 0.7620 (m-40) REVERT: D 32 ASP cc_start: 0.6507 (t70) cc_final: 0.6022 (t70) REVERT: D 99 LEU cc_start: 0.8695 (mt) cc_final: 0.8330 (tp) REVERT: D 107 THR cc_start: 0.8012 (OUTLIER) cc_final: 0.7646 (m) REVERT: D 180 ASP cc_start: 0.8479 (m-30) cc_final: 0.8168 (m-30) REVERT: D 183 THR cc_start: 0.8463 (t) cc_final: 0.8089 (m) REVERT: D 227 SER cc_start: 0.8477 (t) cc_final: 0.8176 (p) REVERT: D 263 VAL cc_start: 0.7269 (t) cc_final: 0.7025 (m) REVERT: D 267 ILE cc_start: 0.6827 (OUTLIER) cc_final: 0.6419 (tp) REVERT: D 283 LYS cc_start: 0.8335 (tttm) cc_final: 0.7979 (tttt) REVERT: D 315 GLU cc_start: 0.7858 (tt0) cc_final: 0.7507 (tt0) REVERT: D 325 LYS cc_start: 0.8196 (mmtt) cc_final: 0.7545 (mppt) REVERT: D 348 VAL cc_start: 0.8017 (t) cc_final: 0.7747 (m) REVERT: D 358 GLU cc_start: 0.8337 (pm20) cc_final: 0.8100 (pm20) outliers start: 33 outliers final: 15 residues processed: 229 average time/residue: 0.6061 time to fit residues: 149.7477 Evaluate side-chains 231 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 203 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 ASP Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 227 SER Chi-restraints excluded: chain A residue 273 LYS Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 325 LYS Chi-restraints excluded: chain A residue 364 ASP Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain A residue 380 LYS Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 194 LYS Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 287 ASP Chi-restraints excluded: chain B residue 321 ASP Chi-restraints excluded: chain C residue 25 VAL Chi-restraints excluded: chain C residue 30 LEU Chi-restraints excluded: chain C residue 62 GLN Chi-restraints excluded: chain C residue 67 MET Chi-restraints excluded: chain C residue 109 ARG Chi-restraints excluded: chain C residue 225 THR Chi-restraints excluded: chain C residue 234 LYS Chi-restraints excluded: chain C residue 281 VAL Chi-restraints excluded: chain C residue 322 ARG Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain D residue 267 ILE Chi-restraints excluded: chain D residue 294 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: [22, 62, 108, 63, 126, 39, 40, 148, 58, 30, 27] chunk 22 optimal weight: 2.9990 chunk 62 optimal weight: 5.9990 chunk 108 optimal weight: 4.9990 chunk 63 optimal weight: 1.9990 chunk 126 optimal weight: 7.9990 chunk 39 optimal weight: 8.9990 chunk 40 optimal weight: 3.9990 chunk 148 optimal weight: 4.9990 chunk 58 optimal weight: 0.7980 chunk 30 optimal weight: 5.9990 chunk 27 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 68.8428 > 50:) overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 118 GLN ** B 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 21 GLN C 193 GLN D 105 HIS D 261 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.135597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.094351 restraints weight = 13260.344| |-----------------------------------------------------------------------------| r_work (start): 0.2934 rms_B_bonded: 1.95 r_work: 0.2769 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2616 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2616 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.3885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 12052 Z= 0.194 Angle : 0.570 8.211 16332 Z= 0.293 Chirality : 0.046 0.191 1928 Planarity : 0.004 0.045 2112 Dihedral : 4.114 15.996 1672 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 3.64 % Allowed : 18.58 % Favored : 77.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % 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: 0.19 (0.22), residues: 1528 helix: 1.34 (0.21), residues: 612 sheet: -0.11 (0.26), residues: 428 loop : -1.13 (0.27), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 54 TYR 0.018 0.002 TYR B 79 PHE 0.021 0.002 PHE B 211 HIS 0.005 0.001 HIS A 261 Details of bonding type rmsd/Z covalent geometry : bond 0.00466 / 0.19 (12052) covalent geometry : angle 0.57000 / 0.29 (16332) hydrogen bonds : bond 0.04001 / 2.68 ( 622) hydrogen bonds : angle 4.65157 / 3.29 ( 1812) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 199 time to evaluate : 0.456 Fit side-chains revert: symmetry clash REVERT: A 24 ASP cc_start: 0.7435 (m-30) cc_final: 0.7171 (t0) REVERT: A 54 ARG cc_start: 0.7072 (ptm-80) cc_final: 0.6626 (ttt-90) REVERT: A 71 ASP cc_start: 0.7659 (t70) cc_final: 0.7120 (t0) REVERT: A 80 GLN cc_start: 0.7717 (pt0) cc_final: 0.7416 (mm-40) REVERT: A 150 GLU cc_start: 0.7943 (mt-10) cc_final: 0.7446 (mm-30) REVERT: A 179 LEU cc_start: 0.8652 (OUTLIER) cc_final: 0.8254 (mp) REVERT: A 273 LYS cc_start: 0.7696 (OUTLIER) cc_final: 0.7348 (mttt) REVERT: A 364 ASP cc_start: 0.7947 (OUTLIER) cc_final: 0.7610 (p0) REVERT: A 380 LYS cc_start: 0.8858 (OUTLIER) cc_final: 0.8522 (ttpm) REVERT: B 26 GLU cc_start: 0.8289 (tt0) cc_final: 0.7078 (mm-30) REVERT: B 173 PHE cc_start: 0.7160 (m-10) cc_final: 0.6842 (m-10) REVERT: B 234 LYS cc_start: 0.8203 (mtmt) cc_final: 0.7625 (mmtm) REVERT: B 251 LYS cc_start: 0.8052 (tttt) cc_final: 0.7628 (ttpt) REVERT: B 285 LEU cc_start: 0.8384 (OUTLIER) cc_final: 0.8102 (mp) REVERT: B 351 LYS cc_start: 0.8083 (OUTLIER) cc_final: 0.7768 (mtmt) REVERT: C 21 GLN cc_start: 0.6813 (mt0) cc_final: 0.6555 (mm-40) REVERT: C 30 LEU cc_start: 0.8197 (OUTLIER) cc_final: 0.7729 (tt) REVERT: C 62 GLN cc_start: 0.5566 (OUTLIER) cc_final: 0.4739 (mm-40) REVERT: C 63 LEU cc_start: 0.6397 (mt) cc_final: 0.5629 (mm) REVERT: C 67 MET cc_start: 0.6624 (OUTLIER) cc_final: 0.5839 (mtp) REVERT: C 80 GLN cc_start: 0.7157 (mm110) cc_final: 0.6546 (mm-40) REVERT: C 109 ARG cc_start: 0.6709 (OUTLIER) cc_final: 0.6036 (mmt-90) REVERT: C 191 ASN cc_start: 0.7910 (m110) cc_final: 0.7458 (m110) REVERT: C 231 PRO cc_start: 0.8210 (Cg_endo) cc_final: 0.7933 (Cg_exo) REVERT: C 234 LYS cc_start: 0.8253 (OUTLIER) cc_final: 0.7549 (tppt) REVERT: C 322 ARG cc_start: 0.6639 (OUTLIER) cc_final: 0.5782 (mmt180) REVERT: C 352 ARG cc_start: 0.7856 (mmp-170) cc_final: 0.7575 (mmt180) REVERT: D 32 ASP cc_start: 0.6541 (t70) cc_final: 0.5979 (t70) REVERT: D 99 LEU cc_start: 0.8764 (mt) cc_final: 0.8395 (tp) REVERT: D 180 ASP cc_start: 0.8556 (m-30) cc_final: 0.8307 (m-30) REVERT: D 183 THR cc_start: 0.8470 (t) cc_final: 0.8103 (m) REVERT: D 187 LEU cc_start: 0.8338 (tp) cc_final: 0.8054 (tm) REVERT: D 227 SER cc_start: 0.8421 (t) cc_final: 0.8105 (p) REVERT: D 263 VAL cc_start: 0.7347 (t) cc_final: 0.6968 (m) REVERT: D 267 ILE cc_start: 0.6843 (OUTLIER) cc_final: 0.6304 (tp) REVERT: D 283 LYS cc_start: 0.8319 (tttm) cc_final: 0.7948 (tttt) REVERT: D 325 LYS cc_start: 0.8114 (mmtt) cc_final: 0.7440 (mppt) REVERT: D 348 VAL cc_start: 0.8020 (t) cc_final: 0.7752 (m) REVERT: D 358 GLU cc_start: 0.8406 (pm20) cc_final: 0.8185 (pm20) outliers start: 47 outliers final: 23 residues processed: 231 average time/residue: 0.6020 time to fit residues: 150.0302 Evaluate side-chains 230 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 194 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 227 SER Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain A residue 273 LYS Chi-restraints excluded: chain A residue 325 LYS Chi-restraints excluded: chain A residue 364 ASP Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain A residue 380 LYS Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 194 LYS Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 287 ASP Chi-restraints excluded: chain B residue 321 ASP Chi-restraints excluded: chain B residue 351 LYS Chi-restraints excluded: chain C residue 25 VAL Chi-restraints excluded: chain C residue 30 LEU Chi-restraints excluded: chain C residue 48 LYS Chi-restraints excluded: chain C residue 62 GLN Chi-restraints excluded: chain C residue 67 MET Chi-restraints excluded: chain C residue 109 ARG Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 225 THR Chi-restraints excluded: chain C residue 234 LYS Chi-restraints excluded: chain C residue 263 VAL Chi-restraints excluded: chain C residue 281 VAL Chi-restraints excluded: chain C residue 322 ARG Chi-restraints excluded: chain D residue 35 LEU Chi-restraints excluded: chain D residue 267 ILE Chi-restraints excluded: chain D residue 272 VAL Chi-restraints excluded: chain D residue 294 VAL Chi-restraints excluded: chain D residue 312 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: [133, 60, 52, 136, 41, 62, 137, 81, 147, 150, 79] chunk 133 optimal weight: 2.9990 chunk 60 optimal weight: 5.9990 chunk 52 optimal weight: 10.0000 chunk 136 optimal weight: 0.0020 chunk 41 optimal weight: 6.9990 chunk 62 optimal weight: 0.9980 chunk 137 optimal weight: 0.9980 chunk 81 optimal weight: 0.3980 chunk 147 optimal weight: 1.9990 chunk 150 optimal weight: 0.9990 chunk 79 optimal weight: 5.9990 overall best weight: 0.6790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 102 HIS B 268 ASN C 193 GLN D 261 HIS D 342 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.138362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.097693 restraints weight = 13250.168| |-----------------------------------------------------------------------------| r_work (start): 0.2988 rms_B_bonded: 1.96 r_work: 0.2831 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2679 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2679 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.4060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 12052 Z= 0.107 Angle : 0.494 7.391 16332 Z= 0.256 Chirality : 0.043 0.175 1928 Planarity : 0.003 0.038 2112 Dihedral : 3.809 14.686 1672 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 2.86 % Allowed : 19.58 % Favored : 77.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % 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 (0.22), residues: 1528 helix: 1.40 (0.21), residues: 636 sheet: -0.06 (0.26), residues: 428 loop : -1.21 (0.27), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 271 TYR 0.015 0.001 TYR B 79 PHE 0.010 0.001 PHE A 211 HIS 0.004 0.001 HIS B 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.11 (12052) covalent geometry : angle 0.49383 / 0.26 (16332) hydrogen bonds : bond 0.03234 / 2.15 ( 622) hydrogen bonds : angle 4.34911 / 3.08 ( 1812) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 211 time to evaluate : 0.416 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 24 ASP cc_start: 0.7448 (m-30) cc_final: 0.7199 (t0) REVERT: A 54 ARG cc_start: 0.7019 (ptm-80) cc_final: 0.6511 (tmt-80) REVERT: A 71 ASP cc_start: 0.7515 (t70) cc_final: 0.7020 (t0) REVERT: A 80 GLN cc_start: 0.7642 (pt0) cc_final: 0.7314 (mm-40) REVERT: A 150 GLU cc_start: 0.7861 (mt-10) cc_final: 0.7309 (mm-30) REVERT: A 179 LEU cc_start: 0.8595 (OUTLIER) cc_final: 0.8171 (mp) REVERT: A 264 GLU cc_start: 0.7313 (OUTLIER) cc_final: 0.6749 (tt0) REVERT: A 273 LYS cc_start: 0.7383 (OUTLIER) cc_final: 0.7078 (mttt) REVERT: A 364 ASP cc_start: 0.7892 (OUTLIER) cc_final: 0.7495 (p0) REVERT: A 368 ASP cc_start: 0.7762 (m-30) cc_final: 0.7458 (m-30) REVERT: A 380 LYS cc_start: 0.8810 (OUTLIER) cc_final: 0.8447 (ttpm) REVERT: B 26 GLU cc_start: 0.8270 (tt0) cc_final: 0.7052 (mm-30) REVERT: B 68 LYS cc_start: 0.7430 (mmmt) cc_final: 0.6660 (mttm) REVERT: B 118 GLN cc_start: 0.7626 (tt0) cc_final: 0.7038 (tp40) REVERT: B 234 LYS cc_start: 0.8105 (mtmt) cc_final: 0.7490 (mmtm) REVERT: B 251 LYS cc_start: 0.8038 (tttt) cc_final: 0.7569 (ttpt) REVERT: B 371 LYS cc_start: 0.8100 (tttt) cc_final: 0.7829 (ttmt) REVERT: C 21 GLN cc_start: 0.6756 (mt0) cc_final: 0.6554 (mm-40) REVERT: C 30 LEU cc_start: 0.8192 (OUTLIER) cc_final: 0.7703 (tt) REVERT: C 62 GLN cc_start: 0.5500 (OUTLIER) cc_final: 0.4266 (tp40) REVERT: C 63 LEU cc_start: 0.6409 (mt) cc_final: 0.5553 (mm) REVERT: C 67 MET cc_start: 0.6608 (OUTLIER) cc_final: 0.6186 (mtp) REVERT: C 80 GLN cc_start: 0.7021 (mm110) cc_final: 0.6437 (mm-40) REVERT: C 191 ASN cc_start: 0.7920 (m110) cc_final: 0.7417 (m110) REVERT: C 225 THR cc_start: 0.8508 (OUTLIER) cc_final: 0.8189 (p) REVERT: C 231 PRO cc_start: 0.8141 (Cg_endo) cc_final: 0.7767 (Cg_exo) REVERT: C 234 LYS cc_start: 0.8187 (OUTLIER) cc_final: 0.7491 (tppt) REVERT: C 322 ARG cc_start: 0.6608 (OUTLIER) cc_final: 0.5798 (mmt180) REVERT: C 352 ARG cc_start: 0.7775 (mmp-170) cc_final: 0.7521 (mmt180) REVERT: D 32 ASP cc_start: 0.6408 (t70) cc_final: 0.5880 (t70) REVERT: D 99 LEU cc_start: 0.8703 (mt) cc_final: 0.8406 (tp) REVERT: D 180 ASP cc_start: 0.8476 (m-30) cc_final: 0.8114 (m-30) REVERT: D 183 THR cc_start: 0.8381 (t) cc_final: 0.8023 (m) REVERT: D 187 LEU cc_start: 0.8313 (tp) cc_final: 0.8057 (tm) REVERT: D 227 SER cc_start: 0.8336 (t) cc_final: 0.7992 (p) REVERT: D 263 VAL cc_start: 0.7238 (t) cc_final: 0.7026 (m) REVERT: D 267 ILE cc_start: 0.6832 (OUTLIER) cc_final: 0.6318 (tp) REVERT: D 283 LYS cc_start: 0.8236 (tttm) cc_final: 0.7842 (tttt) REVERT: D 315 GLU cc_start: 0.7738 (tt0) cc_final: 0.7417 (mm-30) REVERT: D 325 LYS cc_start: 0.8064 (mmtt) cc_final: 0.7362 (mppt) REVERT: D 348 VAL cc_start: 0.7997 (t) cc_final: 0.7738 (m) REVERT: D 360 ILE cc_start: 0.8578 (tt) cc_final: 0.8226 (tp) outliers start: 37 outliers final: 17 residues processed: 236 average time/residue: 0.5804 time to fit residues: 147.9314 Evaluate side-chains 226 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 197 time to evaluate : 0.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 227 SER Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain A residue 264 GLU Chi-restraints excluded: chain A residue 273 LYS Chi-restraints excluded: chain A residue 364 ASP Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain A residue 380 LYS Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 194 LYS Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 287 ASP Chi-restraints excluded: chain B residue 321 ASP Chi-restraints excluded: chain C residue 30 LEU Chi-restraints excluded: chain C residue 62 GLN Chi-restraints excluded: chain C residue 67 MET Chi-restraints excluded: chain C residue 106 ILE Chi-restraints excluded: chain C residue 109 ARG Chi-restraints excluded: chain C residue 225 THR Chi-restraints excluded: chain C residue 234 LYS Chi-restraints excluded: chain C residue 263 VAL Chi-restraints excluded: chain C residue 281 VAL Chi-restraints excluded: chain C residue 322 ARG Chi-restraints excluded: chain D residue 35 LEU Chi-restraints excluded: chain D residue 267 ILE Chi-restraints excluded: chain D residue 272 VAL Chi-restraints excluded: chain D residue 294 VAL Chi-restraints excluded: chain D residue 312 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: [93, 78, 18, 101, 24, 15, 64, 128, 107, 133, 150] chunk 93 optimal weight: 5.9990 chunk 78 optimal weight: 0.9980 chunk 18 optimal weight: 0.9990 chunk 101 optimal weight: 0.9980 chunk 24 optimal weight: 1.9990 chunk 15 optimal weight: 6.9990 chunk 64 optimal weight: 0.8980 chunk 128 optimal weight: 4.9990 chunk 107 optimal weight: 8.9990 chunk 133 optimal weight: 2.9990 chunk 150 optimal weight: 0.7980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 44 GLN C 193 GLN C 195 GLN D 261 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.138497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.098484 restraints weight = 13267.553| |-----------------------------------------------------------------------------| r_work (start): 0.3009 rms_B_bonded: 1.90 r_work: 0.2851 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2702 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2702 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.4150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12052 Z= 0.113 Angle : 0.499 7.368 16332 Z= 0.257 Chirality : 0.044 0.177 1928 Planarity : 0.003 0.037 2112 Dihedral : 3.728 14.643 1672 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 2.86 % Allowed : 19.74 % Favored : 77.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.37 (0.22), residues: 1528 helix: 1.46 (0.21), residues: 636 sheet: 0.01 (0.26), residues: 428 loop : -1.15 (0.27), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 116 TYR 0.015 0.001 TYR B 79 PHE 0.013 0.001 PHE B 211 HIS 0.003 0.001 HIS D 261 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.11 (12052) covalent geometry : angle 0.49931 / 0.26 (16332) hydrogen bonds : bond 0.03219 / 2.14 ( 622) hydrogen bonds : angle 4.27465 / 3.04 ( 1812) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 200 time to evaluate : 0.503 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 24 ASP cc_start: 0.7465 (m-30) cc_final: 0.7263 (t0) REVERT: A 54 ARG cc_start: 0.7044 (ptm-80) cc_final: 0.6524 (tmt-80) REVERT: A 71 ASP cc_start: 0.7494 (t70) cc_final: 0.7052 (t0) REVERT: A 80 GLN cc_start: 0.7594 (pt0) cc_final: 0.7319 (mm-40) REVERT: A 150 GLU cc_start: 0.7799 (mt-10) cc_final: 0.7329 (mm-30) REVERT: A 179 LEU cc_start: 0.8641 (OUTLIER) cc_final: 0.8223 (mp) REVERT: A 304 ARG cc_start: 0.7921 (mmt180) cc_final: 0.7563 (mmt180) REVERT: A 364 ASP cc_start: 0.7933 (OUTLIER) cc_final: 0.7543 (p0) REVERT: A 368 ASP cc_start: 0.7771 (m-30) cc_final: 0.7454 (m-30) REVERT: B 26 GLU cc_start: 0.8317 (tt0) cc_final: 0.7153 (mt-10) REVERT: B 68 LYS cc_start: 0.7463 (mmmt) cc_final: 0.7053 (tmtt) REVERT: B 118 GLN cc_start: 0.7647 (tt0) cc_final: 0.7121 (tp40) REVERT: B 173 PHE cc_start: 0.7147 (m-10) cc_final: 0.6794 (m-10) REVERT: B 234 LYS cc_start: 0.8135 (mtmt) cc_final: 0.7546 (mmtm) REVERT: B 251 LYS cc_start: 0.8093 (tttt) cc_final: 0.7701 (ttpt) REVERT: B 285 LEU cc_start: 0.8366 (OUTLIER) cc_final: 0.8093 (mp) REVERT: B 351 LYS cc_start: 0.8093 (OUTLIER) cc_final: 0.7780 (mtmt) REVERT: B 371 LYS cc_start: 0.8114 (tttt) cc_final: 0.7849 (ttmt) REVERT: C 30 LEU cc_start: 0.8190 (OUTLIER) cc_final: 0.7709 (tt) REVERT: C 62 GLN cc_start: 0.5558 (OUTLIER) cc_final: 0.4394 (tp40) REVERT: C 63 LEU cc_start: 0.6480 (mt) cc_final: 0.5598 (mm) REVERT: C 67 MET cc_start: 0.6676 (OUTLIER) cc_final: 0.6258 (mtp) REVERT: C 80 GLN cc_start: 0.7046 (mm110) cc_final: 0.6407 (mm-40) REVERT: C 176 GLU cc_start: 0.8022 (tt0) cc_final: 0.7617 (mp0) REVERT: C 191 ASN cc_start: 0.7931 (m110) cc_final: 0.7477 (m110) REVERT: C 225 THR cc_start: 0.8528 (OUTLIER) cc_final: 0.8281 (p) REVERT: C 231 PRO cc_start: 0.8149 (Cg_endo) cc_final: 0.7772 (Cg_exo) REVERT: C 234 LYS cc_start: 0.8225 (OUTLIER) cc_final: 0.7545 (tppt) REVERT: C 322 ARG cc_start: 0.6549 (OUTLIER) cc_final: 0.6219 (mmt90) REVERT: C 352 ARG cc_start: 0.7816 (mmp-170) cc_final: 0.7464 (mmt180) REVERT: D 32 ASP cc_start: 0.6450 (t70) cc_final: 0.5893 (t70) REVERT: D 99 LEU cc_start: 0.8616 (mt) cc_final: 0.8363 (tp) REVERT: D 180 ASP cc_start: 0.8511 (m-30) cc_final: 0.8186 (m-30) REVERT: D 183 THR cc_start: 0.8415 (t) cc_final: 0.8038 (m) REVERT: D 227 SER cc_start: 0.8366 (t) cc_final: 0.8014 (p) REVERT: D 263 VAL cc_start: 0.7288 (t) cc_final: 0.7071 (m) REVERT: D 267 ILE cc_start: 0.6867 (OUTLIER) cc_final: 0.6362 (tp) REVERT: D 283 LYS cc_start: 0.8263 (tttm) cc_final: 0.7877 (tttt) REVERT: D 315 GLU cc_start: 0.7858 (tt0) cc_final: 0.7496 (mm-30) REVERT: D 325 LYS cc_start: 0.8028 (mmtt) cc_final: 0.7394 (mppt) REVERT: D 348 VAL cc_start: 0.8026 (t) cc_final: 0.7766 (m) outliers start: 37 outliers final: 17 residues processed: 226 average time/residue: 0.5896 time to fit residues: 143.9627 Evaluate side-chains 218 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 190 time to evaluate : 0.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain A residue 364 ASP Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 194 LYS Chi-restraints excluded: chain B residue 263 VAL Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 287 ASP Chi-restraints excluded: chain B residue 321 ASP Chi-restraints excluded: chain B residue 351 LYS Chi-restraints excluded: chain C residue 30 LEU Chi-restraints excluded: chain C residue 48 LYS Chi-restraints excluded: chain C residue 62 GLN Chi-restraints excluded: chain C residue 67 MET Chi-restraints excluded: chain C residue 106 ILE Chi-restraints excluded: chain C residue 109 ARG Chi-restraints excluded: chain C residue 225 THR Chi-restraints excluded: chain C residue 234 LYS Chi-restraints excluded: chain C residue 263 VAL Chi-restraints excluded: chain C residue 281 VAL Chi-restraints excluded: chain C residue 322 ARG Chi-restraints excluded: chain D residue 35 LEU Chi-restraints excluded: chain D residue 262 ASP Chi-restraints excluded: chain D residue 267 ILE Chi-restraints excluded: chain D residue 294 VAL Chi-restraints excluded: chain D residue 312 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: [61, 115, 146, 119, 143, 3, 77, 62, 98, 124, 110] chunk 61 optimal weight: 7.9990 chunk 115 optimal weight: 2.9990 chunk 146 optimal weight: 0.1980 chunk 119 optimal weight: 20.0000 chunk 143 optimal weight: 5.9990 chunk 3 optimal weight: 4.9990 chunk 77 optimal weight: 2.9990 chunk 62 optimal weight: 4.9990 chunk 98 optimal weight: 2.9990 chunk 124 optimal weight: 5.9990 chunk 110 optimal weight: 5.9990 overall best weight: 2.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 261 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.135539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.094508 restraints weight = 13118.666| |-----------------------------------------------------------------------------| r_work (start): 0.2928 rms_B_bonded: 1.95 r_work: 0.2771 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2621 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2621 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.4143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 12052 Z= 0.191 Angle : 0.576 9.611 16332 Z= 0.294 Chirality : 0.046 0.177 1928 Planarity : 0.004 0.044 2112 Dihedral : 4.007 15.509 1672 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 3.17 % Allowed : 19.74 % Favored : 77.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % 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: 0.34 (0.22), residues: 1528 helix: 1.43 (0.21), residues: 612 sheet: 0.17 (0.27), residues: 400 loop : -1.13 (0.26), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 116 TYR 0.018 0.002 TYR B 79 PHE 0.020 0.002 PHE A 211 HIS 0.005 0.001 HIS A 171 Details of bonding type rmsd/Z covalent geometry : bond 0.00460 / 0.19 (12052) covalent geometry : angle 0.57566 / 0.29 (16332) hydrogen bonds : bond 0.03874 / 2.58 ( 622) hydrogen bonds : angle 4.52594 / 3.21 ( 1812) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 192 time to evaluate : 0.515 Fit side-chains revert: symmetry clash REVERT: A 71 ASP cc_start: 0.7615 (t70) cc_final: 0.7088 (t0) REVERT: A 80 GLN cc_start: 0.7679 (pt0) cc_final: 0.7447 (mm-40) REVERT: A 150 GLU cc_start: 0.7852 (mt-10) cc_final: 0.7273 (mm-30) REVERT: A 273 LYS cc_start: 0.7625 (OUTLIER) cc_final: 0.7226 (mttt) REVERT: A 325 LYS cc_start: 0.7618 (OUTLIER) cc_final: 0.7246 (mppt) REVERT: A 364 ASP cc_start: 0.7977 (OUTLIER) cc_final: 0.7660 (p0) REVERT: B 26 GLU cc_start: 0.8286 (tt0) cc_final: 0.7109 (mt-10) REVERT: B 113 LEU cc_start: 0.8208 (mt) cc_final: 0.7913 (mp) REVERT: B 118 GLN cc_start: 0.7553 (tt0) cc_final: 0.6990 (tp40) REVERT: B 173 PHE cc_start: 0.7354 (m-10) cc_final: 0.7084 (m-10) REVERT: B 234 LYS cc_start: 0.8115 (mtmt) cc_final: 0.7523 (mmtm) REVERT: B 251 LYS cc_start: 0.7953 (tttt) cc_final: 0.7547 (ttpt) REVERT: B 285 LEU cc_start: 0.8416 (OUTLIER) cc_final: 0.8177 (mp) REVERT: B 351 LYS cc_start: 0.8056 (OUTLIER) cc_final: 0.7732 (mtmt) REVERT: B 371 LYS cc_start: 0.8112 (tttt) cc_final: 0.7835 (ttmt) REVERT: C 30 LEU cc_start: 0.8148 (OUTLIER) cc_final: 0.7701 (tt) REVERT: C 42 VAL cc_start: 0.6971 (t) cc_final: 0.6571 (m) REVERT: C 62 GLN cc_start: 0.5707 (OUTLIER) cc_final: 0.4357 (tp40) REVERT: C 63 LEU cc_start: 0.6403 (mt) cc_final: 0.5609 (mm) REVERT: C 67 MET cc_start: 0.6685 (OUTLIER) cc_final: 0.6107 (mtp) REVERT: C 80 GLN cc_start: 0.7094 (mm110) cc_final: 0.6456 (mm-40) REVERT: C 109 ARG cc_start: 0.6547 (OUTLIER) cc_final: 0.5880 (mmt-90) REVERT: C 191 ASN cc_start: 0.7839 (m110) cc_final: 0.7412 (m110) REVERT: C 231 PRO cc_start: 0.8143 (Cg_endo) cc_final: 0.7780 (Cg_exo) REVERT: C 234 LYS cc_start: 0.8231 (OUTLIER) cc_final: 0.7506 (tppt) REVERT: C 322 ARG cc_start: 0.6610 (OUTLIER) cc_final: 0.5765 (mmt180) REVERT: C 352 ARG cc_start: 0.7835 (mmp-170) cc_final: 0.7565 (mmt180) REVERT: D 32 ASP cc_start: 0.6387 (t70) cc_final: 0.5788 (t70) REVERT: D 46 HIS cc_start: 0.5900 (t-90) cc_final: 0.5668 (t70) REVERT: D 67 MET cc_start: 0.6902 (ptp) cc_final: 0.6692 (ptp) REVERT: D 99 LEU cc_start: 0.8551 (mt) cc_final: 0.8304 (tp) REVERT: D 180 ASP cc_start: 0.8462 (m-30) cc_final: 0.8210 (m-30) REVERT: D 183 THR cc_start: 0.8400 (t) cc_final: 0.8014 (m) REVERT: D 187 LEU cc_start: 0.8332 (tp) cc_final: 0.8056 (tm) REVERT: D 227 SER cc_start: 0.8357 (t) cc_final: 0.8026 (p) REVERT: D 263 VAL cc_start: 0.7342 (t) cc_final: 0.6974 (m) REVERT: D 267 ILE cc_start: 0.6816 (OUTLIER) cc_final: 0.6306 (tp) REVERT: D 283 LYS cc_start: 0.8254 (tttm) cc_final: 0.7847 (tttt) REVERT: D 315 GLU cc_start: 0.7918 (tt0) cc_final: 0.7444 (mt-10) REVERT: D 325 LYS cc_start: 0.8067 (mmtt) cc_final: 0.7372 (mppt) REVERT: D 348 VAL cc_start: 0.7995 (t) cc_final: 0.7718 (m) REVERT: D 360 ILE cc_start: 0.8570 (tt) cc_final: 0.8152 (tp) outliers start: 41 outliers final: 19 residues processed: 221 average time/residue: 0.6021 time to fit residues: 143.5572 Evaluate side-chains 222 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 191 time to evaluate : 0.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain A residue 273 LYS Chi-restraints excluded: chain A residue 325 LYS Chi-restraints excluded: chain A residue 364 ASP Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 194 LYS Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 287 ASP Chi-restraints excluded: chain B residue 321 ASP Chi-restraints excluded: chain B residue 351 LYS Chi-restraints excluded: chain C residue 30 LEU Chi-restraints excluded: chain C residue 48 LYS Chi-restraints excluded: chain C residue 62 GLN Chi-restraints excluded: chain C residue 67 MET Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 109 ARG Chi-restraints excluded: chain C residue 174 SER Chi-restraints excluded: chain C residue 225 THR Chi-restraints excluded: chain C residue 234 LYS Chi-restraints excluded: chain C residue 263 VAL Chi-restraints excluded: chain C residue 281 VAL Chi-restraints excluded: chain C residue 322 ARG Chi-restraints excluded: chain D residue 35 LEU Chi-restraints excluded: chain D residue 262 ASP Chi-restraints excluded: chain D residue 267 ILE Chi-restraints excluded: chain D residue 272 VAL Chi-restraints excluded: chain D residue 294 VAL Chi-restraints excluded: chain D residue 312 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: [111, 51, 8, 63, 29, 55, 16, 4, 89, 28, 102] chunk 111 optimal weight: 2.9990 chunk 51 optimal weight: 0.8980 chunk 8 optimal weight: 1.9990 chunk 63 optimal weight: 0.0270 chunk 29 optimal weight: 0.9990 chunk 55 optimal weight: 6.9990 chunk 16 optimal weight: 0.8980 chunk 4 optimal weight: 2.9990 chunk 89 optimal weight: 0.9990 chunk 28 optimal weight: 0.0770 chunk 102 optimal weight: 0.6980 overall best weight: 0.5196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 193 GLN D 261 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.138287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.101307 restraints weight = 13483.332| |-----------------------------------------------------------------------------| r_work (start): 0.3162 rms_B_bonded: 1.79 r_work: 0.2989 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2850 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2850 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.4290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 12052 Z= 0.108 Angle : 0.512 9.168 16332 Z= 0.264 Chirality : 0.044 0.171 1928 Planarity : 0.003 0.044 2112 Dihedral : 3.772 14.739 1672 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 2.09 % Allowed : 21.05 % Favored : 76.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % 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: 0.49 (0.22), residues: 1528 helix: 1.60 (0.21), residues: 612 sheet: 0.19 (0.27), residues: 400 loop : -1.08 (0.26), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 116 TYR 0.015 0.001 TYR B 79 PHE 0.009 0.001 PHE A 211 HIS 0.003 0.001 HIS B 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.11 (12052) covalent geometry : angle 0.51151 / 0.26 (16332) hydrogen bonds : bond 0.03153 / 2.09 ( 622) hydrogen bonds : angle 4.26762 / 3.03 ( 1812) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3056 Ramachandran restraints generated. 1528 Oldfield, 0 Emsley, 1528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 197 time to evaluate : 0.480 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 71 ASP cc_start: 0.7436 (t70) cc_final: 0.7088 (t0) REVERT: A 150 GLU cc_start: 0.7750 (mt-10) cc_final: 0.7439 (mm-30) REVERT: A 179 LEU cc_start: 0.8718 (OUTLIER) cc_final: 0.8327 (mp) REVERT: A 364 ASP cc_start: 0.8053 (OUTLIER) cc_final: 0.7693 (p0) REVERT: A 368 ASP cc_start: 0.7786 (m-30) cc_final: 0.7505 (m-30) REVERT: B 26 GLU cc_start: 0.8340 (tt0) cc_final: 0.7202 (mt-10) REVERT: B 68 LYS cc_start: 0.7467 (mmmt) cc_final: 0.6839 (mttm) REVERT: B 118 GLN cc_start: 0.7691 (tt0) cc_final: 0.7166 (tp40) REVERT: B 234 LYS cc_start: 0.8177 (mtmt) cc_final: 0.7640 (mmtm) REVERT: B 251 LYS cc_start: 0.8105 (tttt) cc_final: 0.7839 (ttpt) REVERT: B 371 LYS cc_start: 0.8158 (tttt) cc_final: 0.7905 (ttmt) REVERT: C 30 LEU cc_start: 0.8233 (OUTLIER) cc_final: 0.7802 (tt) REVERT: C 62 GLN cc_start: 0.5627 (OUTLIER) cc_final: 0.4473 (tp40) REVERT: C 63 LEU cc_start: 0.6584 (mt) cc_final: 0.5748 (mm) REVERT: C 67 MET cc_start: 0.6753 (OUTLIER) cc_final: 0.6432 (mtp) REVERT: C 80 GLN cc_start: 0.7101 (mm110) cc_final: 0.6485 (mm-40) REVERT: C 91 GLU cc_start: 0.7563 (mm-30) cc_final: 0.6916 (mt-10) REVERT: C 176 GLU cc_start: 0.8049 (tt0) cc_final: 0.7780 (mp0) REVERT: C 191 ASN cc_start: 0.7934 (m110) cc_final: 0.7498 (m110) REVERT: C 225 THR cc_start: 0.8578 (OUTLIER) cc_final: 0.8376 (p) REVERT: C 231 PRO cc_start: 0.8218 (Cg_endo) cc_final: 0.7828 (Cg_exo) REVERT: C 234 LYS cc_start: 0.8256 (ttmt) cc_final: 0.7660 (tppt) REVERT: C 322 ARG cc_start: 0.6688 (OUTLIER) cc_final: 0.5908 (mmt180) REVERT: C 352 ARG cc_start: 0.7878 (mmp-170) cc_final: 0.7562 (mmt180) REVERT: D 32 ASP cc_start: 0.6287 (t70) cc_final: 0.5773 (t70) REVERT: D 46 HIS cc_start: 0.6084 (t-90) cc_final: 0.5867 (t70) REVERT: D 61 GLN cc_start: 0.6942 (mp10) cc_final: 0.6509 (mt0) REVERT: D 68 LYS cc_start: 0.6663 (tptm) cc_final: 0.6407 (tptp) REVERT: D 107 THR cc_start: 0.8217 (t) cc_final: 0.8009 (t) REVERT: D 180 ASP cc_start: 0.8562 (m-30) cc_final: 0.8301 (m-30) REVERT: D 183 THR cc_start: 0.8417 (t) cc_final: 0.8035 (m) REVERT: D 187 LEU cc_start: 0.8411 (tp) cc_final: 0.8199 (tm) REVERT: D 227 SER cc_start: 0.8434 (t) cc_final: 0.8099 (p) REVERT: D 267 ILE cc_start: 0.6774 (OUTLIER) cc_final: 0.6361 (tp) REVERT: D 283 LYS cc_start: 0.8325 (tttm) cc_final: 0.7986 (tttt) REVERT: D 315 GLU cc_start: 0.7760 (tt0) cc_final: 0.7537 (mm-30) REVERT: D 325 LYS cc_start: 0.8205 (mmtt) cc_final: 0.7572 (mppt) REVERT: D 348 VAL cc_start: 0.8023 (t) cc_final: 0.7791 (m) REVERT: D 360 ILE cc_start: 0.8626 (tt) cc_final: 0.8265 (tp) outliers start: 27 outliers final: 18 residues processed: 218 average time/residue: 0.5997 time to fit residues: 141.1235 Evaluate side-chains 208 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 182 time to evaluate : 0.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 364 ASP Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 194 LYS Chi-restraints excluded: chain B residue 287 ASP Chi-restraints excluded: chain B residue 321 ASP Chi-restraints excluded: chain C residue 30 LEU Chi-restraints excluded: chain C residue 48 LYS Chi-restraints excluded: chain C residue 62 GLN Chi-restraints excluded: chain C residue 67 MET Chi-restraints excluded: chain C residue 106 ILE Chi-restraints excluded: chain C residue 109 ARG Chi-restraints excluded: chain C residue 225 THR Chi-restraints excluded: chain C residue 263 VAL Chi-restraints excluded: chain C residue 281 VAL Chi-restraints excluded: chain C residue 316 THR Chi-restraints excluded: chain C residue 322 ARG Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 35 LEU Chi-restraints excluded: chain D residue 262 ASP Chi-restraints excluded: chain D residue 267 ILE Chi-restraints excluded: chain D residue 294 VAL Chi-restraints excluded: chain D residue 312 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: [63, 80, 123, 34, 77, 135, 27, 44, 66, 108, 46] chunk 63 optimal weight: 0.8980 chunk 80 optimal weight: 5.9990 chunk 123 optimal weight: 6.9990 chunk 34 optimal weight: 5.9990 chunk 77 optimal weight: 5.9990 chunk 135 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 66 optimal weight: 0.5980 chunk 108 optimal weight: 1.9990 chunk 46 optimal weight: 6.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 193 GLN D 261 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.136414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.099102 restraints weight = 13388.260| |-----------------------------------------------------------------------------| r_work (start): 0.3134 rms_B_bonded: 1.79 r_work: 0.2962 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2823 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.4308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 12052 Z= 0.148 Angle : 0.544 10.062 16332 Z= 0.277 Chirality : 0.045 0.173 1928 Planarity : 0.004 0.044 2112 Dihedral : 3.863 15.566 1672 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 2.48 % Allowed : 21.28 % Favored : 76.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % 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: 0.46 (0.22), residues: 1528 helix: 1.56 (0.21), residues: 612 sheet: 0.21 (0.27), residues: 400 loop : -1.10 (0.26), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 116 TYR 0.015 0.001 TYR B 79 PHE 0.016 0.001 PHE B 211 HIS 0.004 0.001 HIS B 261 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.15 (12052) covalent geometry : angle 0.54450 / 0.28 (16332) hydrogen bonds : bond 0.03471 / 2.32 ( 622) hydrogen bonds : angle 4.35692 / 3.09 ( 1812) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4601.84 seconds wall clock time: 79 minutes 2.60 seconds (4742.60 seconds total)