Starting phenix.real_space_refine on Thu Jul 2 13:38:14 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7ljd_23391/07_2026/7ljd_23391.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ljd_23391/07_2026/7ljd_23391.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7ljd_23391/07_2026/7ljd_23391.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ljd_23391/07_2026/7ljd_23391.map" model { file = "/net/cci-nas-00/data/ceres_data/7ljd_23391/07_2026/7ljd_23391.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ljd_23391/07_2026/7ljd_23391.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7ljd_23391/07_2026/7ljd_23391.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7ljd_23391/07_2026/7ljd_23391.cif" } resolution = 3.2 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= 0.013 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 56 5.16 5 Cl 2 4.86 5 C 5468 2.51 5 N 1447 2.21 5 O 1545 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8518 Number of models: 1 Model: "" Number of chains: 6 Chain: "R" Number of atoms: 2269 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2269 Classifications: {'peptide': 285} Link IDs: {'PTRANS': 10, 'TRANS': 274} Chain breaks: 3 Chain: "A" Number of atoms: 1987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1987 Classifications: {'peptide': 238} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 231} Chain: "B" Number of atoms: 2600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2600 Classifications: {'peptide': 338} Link IDs: {'PTRANS': 5, 'TRANS': 332} Chain: "G" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 436 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Chain: "N" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 973 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 5, 'TRANS': 122} Chain: "R" Number of atoms: 253 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 253 Unusual residues: {'CLR': 5, 'G4C': 1, 'LDP': 1, 'PLM': 4} Classifications: {'undetermined': 11} Link IDs: {None: 10} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" C1 LDP R 501 " occ=0.50 ... (9 atoms not shown) pdb=" O2 LDP R 501 " occ=0.50 Time building chain proxies: 1.51, per 1000 atoms: 0.18 Number of scatterers: 8518 At special positions: 0 Unit cell: (95.316, 99.372, 121.68, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Cl 2 17.00 S 56 16.00 O 1545 8.00 N 1447 7.00 C 5468 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS R 96 " - pdb=" SG CYS R 186 " distance=2.03 Simple disulfide: pdb=" SG CYS R 298 " - pdb=" SG CYS R 307 " distance=2.03 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.03 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: 0.42 Conformation dependent library (CDL) restraints added in 310.2 milliseconds 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1984 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 10 sheets defined 43.4% alpha, 19.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.22 Creating SS restraints... Processing helix chain 'R' and resid 21 through 50 removed outlier: 4.292A pdb=" N LEU R 25 " --> pdb=" O SER R 21 " (cutoff:3.500A) Processing helix chain 'R' and resid 52 through 57 removed outlier: 4.131A pdb=" N LYS R 57 " --> pdb=" O HIS R 53 " (cutoff:3.500A) Processing helix chain 'R' and resid 59 through 77 removed outlier: 3.886A pdb=" N VAL R 63 " --> pdb=" O THR R 59 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N VAL R 73 " --> pdb=" O SER R 69 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ALA R 74 " --> pdb=" O ASP R 70 " (cutoff:3.500A) Processing helix chain 'R' and resid 77 through 88 removed outlier: 3.845A pdb=" N LYS R 81 " --> pdb=" O VAL R 77 " (cutoff:3.500A) Processing helix chain 'R' and resid 94 through 127 removed outlier: 4.162A pdb=" N ILE R 98 " --> pdb=" O SER R 94 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ALA R 101 " --> pdb=" O ASN R 97 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N SER R 118 " --> pdb=" O LEU R 114 " (cutoff:3.500A) Processing helix chain 'R' and resid 127 through 135 removed outlier: 3.676A pdb=" N GLU R 132 " --> pdb=" O PRO R 128 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ARG R 133 " --> pdb=" O PHE R 129 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N MET R 135 " --> pdb=" O TYR R 131 " (cutoff:3.500A) Processing helix chain 'R' and resid 136 through 162 removed outlier: 4.784A pdb=" N ILE R 157 " --> pdb=" O LEU R 153 " (cutoff:3.500A) Proline residue: R 158 - end of helix Processing helix chain 'R' and resid 191 through 203 removed outlier: 3.599A pdb=" N ILE R 196 " --> pdb=" O ARG R 192 " (cutoff:3.500A) Processing helix chain 'R' and resid 203 through 242 Processing helix chain 'R' and resid 265 through 298 removed outlier: 3.576A pdb=" N LEU R 274 " --> pdb=" O VAL R 270 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N PHE R 281 " --> pdb=" O ILE R 277 " (cutoff:3.500A) Proline residue: R 287 - end of helix removed outlier: 4.145A pdb=" N LEU R 291 " --> pdb=" O PRO R 287 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N CYS R 293 " --> pdb=" O PHE R 289 " (cutoff:3.500A) Proline residue: R 296 - end of helix Processing helix chain 'R' and resid 309 through 332 removed outlier: 3.648A pdb=" N TRP R 318 " --> pdb=" O ASP R 314 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N PHE R 319 " --> pdb=" O VAL R 315 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ASN R 323 " --> pdb=" O PHE R 319 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N SER R 324 " --> pdb=" O GLY R 320 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N SER R 325 " --> pdb=" O TRP R 321 " (cutoff:3.500A) Proline residue: R 328 - end of helix Processing helix chain 'R' and resid 334 through 346 Processing helix chain 'A' and resid 10 through 40 Processing helix chain 'A' and resid 95 through 103 removed outlier: 3.580A pdb=" N GLN A 98 " --> pdb=" O LYS A 95 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N CYS A 99 " --> pdb=" O TRP A 96 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ASN A 101 " --> pdb=" O GLN A 98 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N ASP A 102 " --> pdb=" O CYS A 99 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N VAL A 103 " --> pdb=" O PHE A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 131 Processing helix chain 'A' and resid 145 through 154 removed outlier: 3.668A pdb=" N LEU A 149 " --> pdb=" O LYS A 145 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LEU A 154 " --> pdb=" O ALA A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 164 removed outlier: 4.155A pdb=" N ASP A 162 " --> pdb=" O SER A 158 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 169 Processing helix chain 'A' and resid 183 through 205 removed outlier: 3.559A pdb=" N PHE A 197 " --> pdb=" O ILE A 193 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N SER A 204 " --> pdb=" O ILE A 200 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N GLY A 205 " --> pdb=" O SER A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 243 Processing helix chain 'B' and resid 4 through 26 Processing helix chain 'B' and resid 29 through 34 removed outlier: 3.673A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 37 No H-bonds generated for 'chain 'B' and resid 35 through 37' Processing helix chain 'G' and resid 7 through 24 removed outlier: 3.919A pdb=" N LYS G 14 " --> pdb=" O ALA G 10 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'N' and resid 61 through 65 removed outlier: 3.527A pdb=" N VAL N 64 " --> pdb=" O THR N 61 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 64 through 65 removed outlier: 6.180A pdb=" N HIS A 41 " --> pdb=" O HIS A 82 " (cutoff:3.500A) removed outlier: 7.603A pdb=" N PHE A 84 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N LEU A 43 " --> pdb=" O PHE A 84 " (cutoff:3.500A) removed outlier: 7.678A pdb=" N VAL A 86 " --> pdb=" O LEU A 43 " (cutoff:3.500A) removed outlier: 7.767A pdb=" N LEU A 45 " --> pdb=" O VAL A 86 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ALA A 105 " --> pdb=" O ARG A 42 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51 removed outlier: 5.977A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 62 removed outlier: 3.785A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.940A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 4.071A pdb=" N THR B 102 " --> pdb=" O GLY B 115 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.680A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.474A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.765A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 3.612A pdb=" N SER B 189 " --> pdb=" O GLY B 202 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N ALA B 208 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N THR B 221 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N LEU B 210 " --> pdb=" O ARG B 219 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.617A pdb=" N ALA B 231 " --> pdb=" O GLY B 244 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.602A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 5.092A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 7.393A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 7 removed outlier: 3.576A pdb=" N THR N 78 " --> pdb=" O ASP N 73 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'N' and resid 10 through 12 removed outlier: 6.698A pdb=" N ARG N 38 " --> pdb=" O TRP N 47 " (cutoff:3.500A) removed outlier: 5.534A pdb=" N TRP N 47 " --> pdb=" O ARG N 38 " (cutoff:3.500A) 427 hydrogen bonds defined for protein. 1236 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: 0.95 Time building geometry restraints manager: 0.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2114 1.33 - 1.45: 1750 1.45 - 1.58: 4760 1.58 - 1.70: 0 1.70 - 1.82: 78 Bond restraints: 8702 Sorted by residual: bond pdb=" C05 G4C R 502 " pdb=" N04 G4C R 502 " ideal model delta sigma weight residual 1.355 1.497 -0.142 2.00e-02 2.50e+03 5.03e+01 bond pdb=" C03 G4C R 502 " pdb=" N04 G4C R 502 " ideal model delta sigma weight residual 1.460 1.497 -0.037 2.00e-02 2.50e+03 3.36e+00 bond pdb=" C ILE R 205 " pdb=" N PRO R 206 " ideal model delta sigma weight residual 1.335 1.358 -0.023 1.28e-02 6.10e+03 3.31e+00 bond pdb=" C MET R 78 " pdb=" N PRO R 79 " ideal model delta sigma weight residual 1.335 1.358 -0.023 1.30e-02 5.92e+03 3.19e+00 bond pdb=" C5 CLR R 505 " pdb=" C6 CLR R 505 " ideal model delta sigma weight residual 1.332 1.300 0.032 2.00e-02 2.50e+03 2.53e+00 ... (remaining 8697 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.02: 11335 2.02 - 4.05: 409 4.05 - 6.07: 34 6.07 - 8.10: 13 8.10 - 10.12: 4 Bond angle restraints: 11795 Sorted by residual: angle pdb=" C ASP B 118 " pdb=" N ASN B 119 " pdb=" CA ASN B 119 " ideal model delta sigma weight residual 121.54 130.97 -9.43 1.91e+00 2.74e-01 2.44e+01 angle pdb=" C ILE R 294 " pdb=" N LEU R 295 " pdb=" CA LEU R 295 " ideal model delta sigma weight residual 121.62 127.01 -5.39 1.57e+00 4.06e-01 1.18e+01 angle pdb=" CA ASN B 119 " pdb=" CB ASN B 119 " pdb=" CG ASN B 119 " ideal model delta sigma weight residual 112.60 115.60 -3.00 1.00e+00 1.00e+00 8.97e+00 angle pdb=" C ASP B 163 " pdb=" N THR B 164 " pdb=" CA THR B 164 " ideal model delta sigma weight residual 122.40 126.70 -4.30 1.45e+00 4.76e-01 8.78e+00 angle pdb=" N MET R 78 " pdb=" CA MET R 78 " pdb=" C MET R 78 " ideal model delta sigma weight residual 112.75 116.65 -3.90 1.36e+00 5.41e-01 8.23e+00 ... (remaining 11790 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.89: 5033 17.89 - 35.77: 90 35.77 - 53.65: 23 53.65 - 71.54: 1 71.54 - 89.42: 5 Dihedral angle restraints: 5152 sinusoidal: 2097 harmonic: 3055 Sorted by residual: dihedral pdb=" CB CYS R 298 " pdb=" SG CYS R 298 " pdb=" SG CYS R 307 " pdb=" CB CYS R 307 " ideal model delta sinusoidal sigma weight residual 93.00 -179.67 -87.33 1 1.00e+01 1.00e-02 9.15e+01 dihedral pdb=" CB CYS N 22 " pdb=" SG CYS N 22 " pdb=" SG CYS N 96 " pdb=" CB CYS N 96 " ideal model delta sinusoidal sigma weight residual 93.00 166.82 -73.82 1 1.00e+01 1.00e-02 6.93e+01 dihedral pdb=" CA LEU B 198 " pdb=" C LEU B 198 " pdb=" N PHE B 199 " pdb=" CA PHE B 199 " ideal model delta harmonic sigma weight residual 180.00 159.61 20.39 0 5.00e+00 4.00e-02 1.66e+01 ... (remaining 5149 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.082: 1173 0.082 - 0.163: 126 0.163 - 0.245: 19 0.245 - 0.327: 6 0.327 - 0.408: 5 Chirality restraints: 1329 Sorted by residual: chirality pdb=" C14 CLR R 507 " pdb=" C13 CLR R 507 " pdb=" C15 CLR R 507 " pdb=" C8 CLR R 507 " both_signs ideal model delta sigma weight residual False -2.32 -2.73 0.41 2.00e-01 2.50e+01 4.17e+00 chirality pdb=" C14 CLR R 504 " pdb=" C13 CLR R 504 " pdb=" C15 CLR R 504 " pdb=" C8 CLR R 504 " both_signs ideal model delta sigma weight residual False -2.32 -2.70 0.39 2.00e-01 2.50e+01 3.75e+00 chirality pdb=" C14 CLR R 503 " pdb=" C13 CLR R 503 " pdb=" C15 CLR R 503 " pdb=" C8 CLR R 503 " both_signs ideal model delta sigma weight residual False -2.32 -2.70 0.39 2.00e-01 2.50e+01 3.73e+00 ... (remaining 1326 not shown) Planarity restraints: 1463 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C03 G4C R 502 " -0.215 2.00e-02 2.50e+03 1.50e-01 3.37e+02 pdb=" C05 G4C R 502 " 0.047 2.00e-02 2.50e+03 pdb=" C06 G4C R 502 " -0.169 2.00e-02 2.50e+03 pdb=" C16 G4C R 502 " 0.029 2.00e-02 2.50e+03 pdb=" N04 G4C R 502 " 0.222 2.00e-02 2.50e+03 pdb=" O15 G4C R 502 " 0.086 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL R 207 " 0.014 2.00e-02 2.50e+03 2.69e-02 7.25e+00 pdb=" C VAL R 207 " -0.047 2.00e-02 2.50e+03 pdb=" O VAL R 207 " 0.017 2.00e-02 2.50e+03 pdb=" N ALA R 208 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE B 93 " -0.035 5.00e-02 4.00e+02 5.38e-02 4.64e+00 pdb=" N PRO B 94 " 0.093 5.00e-02 4.00e+02 pdb=" CA PRO B 94 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO B 94 " -0.030 5.00e-02 4.00e+02 ... (remaining 1460 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.82: 2234 2.82 - 3.34: 7304 3.34 - 3.86: 13145 3.86 - 4.38: 15218 4.38 - 4.90: 27054 Nonbonded interactions: 64955 Sorted by model distance: nonbonded pdb=" OG SER B 147 " pdb=" O MET B 188 " model vdw 2.294 3.040 nonbonded pdb=" OG SER B 331 " pdb=" OD1 ASP B 333 " model vdw 2.309 3.040 nonbonded pdb=" OH TYR A 170 " pdb=" OD2 ASP A 195 " model vdw 2.322 3.040 nonbonded pdb=" OG1 THR N 104 " pdb=" OD1 ASP N 106 " model vdw 2.337 3.040 nonbonded pdb=" OG SER R 198 " pdb=" O2 LDP R 501 " model vdw 2.349 3.040 ... (remaining 64950 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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=0.50 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: 0.590 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: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 6.750 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7194 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 : 0.004 0.142 8706 Z= 0.221 Angle : 0.853 10.120 11803 Z= 0.464 Chirality : 0.062 0.408 1329 Planarity : 0.007 0.150 1463 Dihedral : 8.494 89.425 3156 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.10 (0.23), residues: 1030 helix: -1.11 (0.24), residues: 402 sheet: -0.32 (0.34), residues: 218 loop : -2.18 (0.25), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 150 TYR 0.014 0.002 TYR A 243 PHE 0.032 0.002 PHE A 108 TRP 0.028 0.002 TRP A 133 HIS 0.013 0.003 HIS A 209 Details of bonding type rmsd/Z covalent geometry : bond 0.00410 / 0.22 ( 8702) covalent geometry : angle 0.85274 / 0.46 (11795) SS BOND : bond 0.00181 / 0.09 ( 4) SS BOND : angle 1.47153 / 0.79 ( 8) hydrogen bonds : bond 0.28320 / 19.66 ( 427) hydrogen bonds : angle 8.41991 / 6.12 ( 1236) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 210 time to evaluate : 0.254 Fit side-chains REVERT: R 35 LEU cc_start: 0.7128 (mt) cc_final: 0.6898 (mt) REVERT: R 57 LYS cc_start: 0.8101 (mmtp) cc_final: 0.7800 (mtmt) REVERT: R 193 THR cc_start: 0.8282 (t) cc_final: 0.8063 (m) REVERT: R 197 SER cc_start: 0.8489 (t) cc_final: 0.7878 (m) REVERT: A 124 ASP cc_start: 0.7062 (m-30) cc_final: 0.6733 (m-30) REVERT: A 237 ARG cc_start: 0.7324 (mtt-85) cc_final: 0.7053 (mtt90) REVERT: B 13 GLN cc_start: 0.8091 (mm-40) cc_final: 0.7839 (pp30) REVERT: B 66 ASP cc_start: 0.7119 (p0) cc_final: 0.6493 (t0) REVERT: B 170 ASP cc_start: 0.8247 (t0) cc_final: 0.7930 (t0) REVERT: B 178 THR cc_start: 0.7687 (m) cc_final: 0.7237 (p) REVERT: G 21 MET cc_start: 0.7768 (mtt) cc_final: 0.7549 (ttp) outliers start: 0 outliers final: 0 residues processed: 210 average time/residue: 0.1065 time to fit residues: 28.7576 Evaluate side-chains 138 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 138 time to evaluate : 0.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 10.0000 chunk 53 optimal weight: 5.9990 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 8.9990 chunk 65 optimal weight: 7.9990 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 6.9990 chunk 100 optimal weight: 7.9990 chunk 38 optimal weight: 3.9990 chunk 61 optimal weight: 5.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 60 ASN R 113 ASN R 242 GLN A 14 ASN A 82 HIS B 62 HIS B 91 HIS B 239 ASN B 268 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.171694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.126920 restraints weight = 9065.883| |-----------------------------------------------------------------------------| r_work (start): 0.3426 rms_B_bonded: 1.91 r_work: 0.3217 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3068 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3058 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3058 r_free = 0.3058 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3057 r_free = 0.3057 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.82 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.3057 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.3556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.077 8706 Z= 0.333 Angle : 0.764 8.377 11803 Z= 0.406 Chirality : 0.050 0.206 1329 Planarity : 0.006 0.052 1463 Dihedral : 7.101 83.725 1249 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 1.78 % Allowed : 6.44 % Favored : 91.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.64 (0.25), residues: 1030 helix: 0.65 (0.25), residues: 413 sheet: -0.26 (0.35), residues: 210 loop : -1.60 (0.27), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 304 TYR 0.024 0.003 TYR N 94 PHE 0.036 0.003 PHE R 129 TRP 0.026 0.003 TRP A 133 HIS 0.012 0.003 HIS B 142 Details of bonding type rmsd/Z covalent geometry : bond 0.00753 / 0.33 ( 8702) covalent geometry : angle 0.76345 / 0.41 (11795) SS BOND : bond 0.00419 / 0.21 ( 4) SS BOND : angle 1.70254 / 1.03 ( 8) hydrogen bonds : bond 0.07145 / 4.93 ( 427) hydrogen bonds : angle 5.54612 / 4.09 ( 1236) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 149 time to evaluate : 0.262 Fit side-chains REVERT: R 76 LEU cc_start: 0.8505 (tp) cc_final: 0.8299 (tt) REVERT: R 283 CYS cc_start: 0.8155 (t) cc_final: 0.7773 (m) REVERT: R 333 PHE cc_start: 0.7179 (OUTLIER) cc_final: 0.6493 (m-10) REVERT: A 163 TYR cc_start: 0.7646 (m-80) cc_final: 0.7443 (m-80) REVERT: A 192 PHE cc_start: 0.8666 (t80) cc_final: 0.8397 (t80) REVERT: B 19 ARG cc_start: 0.6705 (mtp180) cc_final: 0.6387 (mmt90) REVERT: B 66 ASP cc_start: 0.7227 (p0) cc_final: 0.6884 (t0) REVERT: B 197 ARG cc_start: 0.8583 (mmm160) cc_final: 0.8016 (mtp85) REVERT: G 21 MET cc_start: 0.8366 (mtt) cc_final: 0.7595 (tmm) REVERT: N 25 SER cc_start: 0.8410 (t) cc_final: 0.8025 (p) outliers start: 16 outliers final: 6 residues processed: 160 average time/residue: 0.0829 time to fit residues: 17.9989 Evaluate side-chains 125 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 118 time to evaluate : 0.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 277 ILE Chi-restraints excluded: chain R residue 333 PHE Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 263 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 53 optimal weight: 1.9990 chunk 76 optimal weight: 0.0060 chunk 64 optimal weight: 0.9980 chunk 97 optimal weight: 9.9990 chunk 22 optimal weight: 2.9990 chunk 18 optimal weight: 0.6980 chunk 85 optimal weight: 10.0000 chunk 6 optimal weight: 0.8980 chunk 94 optimal weight: 9.9990 chunk 30 optimal weight: 0.9980 chunk 12 optimal weight: 0.9980 overall best weight: 0.7196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 41 ASN R 242 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.178046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.135048 restraints weight = 8878.105| |-----------------------------------------------------------------------------| r_work (start): 0.3521 rms_B_bonded: 1.96 r_work: 0.3291 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.3138 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3118 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3118 r_free = 0.3118 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.82 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3118 r_free = 0.3118 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.84 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3118 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.3747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8706 Z= 0.127 Angle : 0.531 8.664 11803 Z= 0.282 Chirality : 0.041 0.147 1329 Planarity : 0.004 0.049 1463 Dihedral : 6.406 78.784 1249 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 1.89 % Allowed : 8.77 % Favored : 89.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.22 (0.26), residues: 1030 helix: 1.71 (0.25), residues: 414 sheet: -0.18 (0.35), residues: 218 loop : -1.36 (0.28), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG R 226 TYR 0.012 0.001 TYR B 105 PHE 0.012 0.001 PHE R 141 TRP 0.019 0.002 TRP B 169 HIS 0.005 0.001 HIS A 209 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.13 ( 8702) covalent geometry : angle 0.53016 / 0.28 (11795) SS BOND : bond 0.00109 / 0.05 ( 4) SS BOND : angle 0.90512 / 0.52 ( 8) hydrogen bonds : bond 0.05459 / 3.74 ( 427) hydrogen bonds : angle 4.81458 / 3.54 ( 1236) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 122 time to evaluate : 0.251 Fit side-chains REVERT: R 226 ARG cc_start: 0.7711 (mtt-85) cc_final: 0.7422 (mtt90) REVERT: R 233 ARG cc_start: 0.7213 (ttm110) cc_final: 0.6454 (mtp85) REVERT: R 283 CYS cc_start: 0.7907 (t) cc_final: 0.7663 (m) REVERT: R 333 PHE cc_start: 0.7113 (OUTLIER) cc_final: 0.6205 (m-10) REVERT: A 163 TYR cc_start: 0.7605 (m-80) cc_final: 0.7403 (m-80) REVERT: A 233 ASP cc_start: 0.8363 (m-30) cc_final: 0.8161 (m-30) REVERT: B 66 ASP cc_start: 0.7187 (p0) cc_final: 0.6769 (t0) REVERT: B 195 ASP cc_start: 0.8415 (t0) cc_final: 0.8107 (t0) REVERT: B 197 ARG cc_start: 0.8471 (mmm160) cc_final: 0.8053 (mtp85) REVERT: G 21 MET cc_start: 0.8338 (mtt) cc_final: 0.7572 (tmm) REVERT: G 38 MET cc_start: 0.7541 (mtm) cc_final: 0.7341 (mtm) outliers start: 17 outliers final: 11 residues processed: 133 average time/residue: 0.0796 time to fit residues: 14.6732 Evaluate side-chains 115 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 103 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 76 LEU Chi-restraints excluded: chain R residue 193 THR Chi-restraints excluded: chain R residue 236 VAL Chi-restraints excluded: chain R residue 325 SER Chi-restraints excluded: chain R residue 333 PHE Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 132 LYS Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 85 SER Chi-restraints excluded: chain N residue 91 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 12 optimal weight: 2.9990 chunk 90 optimal weight: 10.0000 chunk 25 optimal weight: 1.9990 chunk 15 optimal weight: 5.9990 chunk 7 optimal weight: 3.9990 chunk 52 optimal weight: 3.9990 chunk 33 optimal weight: 0.2980 chunk 76 optimal weight: 4.9990 chunk 98 optimal weight: 5.9990 chunk 17 optimal weight: 0.2980 chunk 97 optimal weight: 5.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 239 ASN B 266 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.173582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.128116 restraints weight = 9109.606| |-----------------------------------------------------------------------------| r_work (start): 0.3426 rms_B_bonded: 2.00 r_work: 0.3216 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3062 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3045 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3045 r_free = 0.3045 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.84 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3045 r_free = 0.3045 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.85 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3045 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.4109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 8706 Z= 0.195 Angle : 0.585 7.972 11803 Z= 0.307 Chirality : 0.043 0.164 1329 Planarity : 0.004 0.052 1463 Dihedral : 6.570 74.842 1249 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 3.33 % Allowed : 8.10 % Favored : 88.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.35 (0.26), residues: 1030 helix: 1.94 (0.25), residues: 407 sheet: -0.30 (0.34), residues: 215 loop : -1.23 (0.29), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 237 TYR 0.012 0.001 TYR N 94 PHE 0.017 0.002 PHE R 333 TRP 0.021 0.002 TRP B 82 HIS 0.007 0.002 HIS A 209 Details of bonding type rmsd/Z covalent geometry : bond 0.00449 / 0.19 ( 8702) covalent geometry : angle 0.58212 / 0.31 (11795) SS BOND : bond 0.00367 / 0.18 ( 4) SS BOND : angle 2.24299 / 1.19 ( 8) hydrogen bonds : bond 0.05669 / 3.87 ( 427) hydrogen bonds : angle 4.82181 / 3.55 ( 1236) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 113 time to evaluate : 0.334 Fit side-chains REVERT: R 163 TRP cc_start: 0.5234 (m100) cc_final: 0.4444 (t60) REVERT: R 233 ARG cc_start: 0.7263 (ttm110) cc_final: 0.6532 (mtp85) REVERT: R 283 CYS cc_start: 0.8108 (t) cc_final: 0.7833 (m) REVERT: R 333 PHE cc_start: 0.7328 (OUTLIER) cc_final: 0.6438 (m-10) REVERT: A 40 THR cc_start: 0.8116 (OUTLIER) cc_final: 0.7858 (m) REVERT: A 163 TYR cc_start: 0.7622 (m-80) cc_final: 0.7395 (m-80) REVERT: B 66 ASP cc_start: 0.7185 (p0) cc_final: 0.6752 (t0) REVERT: G 21 MET cc_start: 0.8298 (mtt) cc_final: 0.7607 (tmm) outliers start: 30 outliers final: 23 residues processed: 135 average time/residue: 0.0905 time to fit residues: 16.6692 Evaluate side-chains 131 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 106 time to evaluate : 0.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 75 VAL Chi-restraints excluded: chain R residue 76 LEU Chi-restraints excluded: chain R residue 132 GLU Chi-restraints excluded: chain R residue 136 THR Chi-restraints excluded: chain R residue 193 THR Chi-restraints excluded: chain R residue 197 SER Chi-restraints excluded: chain R residue 236 VAL Chi-restraints excluded: chain R residue 269 LYS Chi-restraints excluded: chain R residue 277 ILE Chi-restraints excluded: chain R residue 325 SER Chi-restraints excluded: chain R residue 333 PHE Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 132 LYS Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 89 LYS Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 110 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 37 optimal weight: 1.9990 chunk 27 optimal weight: 0.6980 chunk 17 optimal weight: 0.9980 chunk 52 optimal weight: 4.9990 chunk 44 optimal weight: 9.9990 chunk 6 optimal weight: 4.9990 chunk 46 optimal weight: 0.7980 chunk 59 optimal weight: 0.8980 chunk 82 optimal weight: 0.9990 chunk 13 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.176576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.131536 restraints weight = 8947.877| |-----------------------------------------------------------------------------| r_work (start): 0.3474 rms_B_bonded: 1.94 r_work: 0.3270 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3117 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3092 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3092 r_free = 0.3092 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.85 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3092 r_free = 0.3092 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.85 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (11 function evaluations) r_final: 0.3092 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.4292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8706 Z= 0.124 Angle : 0.519 8.157 11803 Z= 0.272 Chirality : 0.041 0.147 1329 Planarity : 0.003 0.051 1463 Dihedral : 6.108 71.180 1249 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 2.66 % Allowed : 9.43 % Favored : 87.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.78 (0.27), residues: 1030 helix: 2.44 (0.25), residues: 396 sheet: -0.30 (0.34), residues: 229 loop : -0.94 (0.30), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG R 226 TYR 0.018 0.001 TYR B 105 PHE 0.017 0.001 PHE A 192 TRP 0.018 0.001 TRP B 82 HIS 0.005 0.001 HIS A 209 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.12 ( 8702) covalent geometry : angle 0.51706 / 0.27 (11795) SS BOND : bond 0.00119 / 0.06 ( 4) SS BOND : angle 1.68318 / 0.87 ( 8) hydrogen bonds : bond 0.04806 / 3.29 ( 427) hydrogen bonds : angle 4.53682 / 3.33 ( 1236) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 111 time to evaluate : 0.295 Fit side-chains REVERT: R 85 GLU cc_start: 0.6539 (tp30) cc_final: 0.5895 (mm-30) REVERT: R 163 TRP cc_start: 0.5258 (m100) cc_final: 0.4359 (t60) REVERT: R 283 CYS cc_start: 0.7852 (t) cc_final: 0.7630 (m) REVERT: A 40 THR cc_start: 0.7963 (OUTLIER) cc_final: 0.7710 (m) REVERT: B 66 ASP cc_start: 0.6981 (p0) cc_final: 0.6687 (t0) REVERT: G 21 MET cc_start: 0.8269 (mtt) cc_final: 0.7653 (tmm) outliers start: 24 outliers final: 17 residues processed: 129 average time/residue: 0.0773 time to fit residues: 14.2527 Evaluate side-chains 119 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 101 time to evaluate : 0.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 76 LEU Chi-restraints excluded: chain R residue 136 THR Chi-restraints excluded: chain R residue 193 THR Chi-restraints excluded: chain R residue 197 SER Chi-restraints excluded: chain R residue 236 VAL Chi-restraints excluded: chain R residue 325 SER Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 85 SER Chi-restraints excluded: chain N residue 91 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 92 optimal weight: 3.9990 chunk 4 optimal weight: 0.9980 chunk 30 optimal weight: 0.9980 chunk 51 optimal weight: 7.9990 chunk 37 optimal weight: 2.9990 chunk 40 optimal weight: 4.9990 chunk 94 optimal weight: 0.9980 chunk 86 optimal weight: 20.0000 chunk 27 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 43 optimal weight: 3.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.173108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.127889 restraints weight = 8851.127| |-----------------------------------------------------------------------------| r_work (start): 0.3437 rms_B_bonded: 1.91 r_work: 0.3237 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3087 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3060 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3060 r_free = 0.3060 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.85 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3060 r_free = 0.3060 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.85 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.3060 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.4486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 8706 Z= 0.167 Angle : 0.557 7.803 11803 Z= 0.292 Chirality : 0.042 0.168 1329 Planarity : 0.004 0.053 1463 Dihedral : 5.979 67.966 1249 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 3.00 % Allowed : 10.32 % Favored : 86.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.63 (0.26), residues: 1030 helix: 2.24 (0.25), residues: 408 sheet: -0.30 (0.34), residues: 219 loop : -1.09 (0.30), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG R 226 TYR 0.018 0.001 TYR A 163 PHE 0.015 0.001 PHE N 108 TRP 0.019 0.002 TRP B 82 HIS 0.005 0.001 HIS A 209 Details of bonding type rmsd/Z covalent geometry : bond 0.00384 / 0.17 ( 8702) covalent geometry : angle 0.55514 / 0.29 (11795) SS BOND : bond 0.00230 / 0.12 ( 4) SS BOND : angle 1.80107 / 0.94 ( 8) hydrogen bonds : bond 0.05138 / 3.50 ( 427) hydrogen bonds : angle 4.63051 / 3.41 ( 1236) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 103 time to evaluate : 0.319 Fit side-chains revert: symmetry clash REVERT: R 50 ARG cc_start: 0.7469 (mtt-85) cc_final: 0.7150 (ttm-80) REVERT: R 163 TRP cc_start: 0.5449 (m100) cc_final: 0.4458 (t60) REVERT: R 283 CYS cc_start: 0.8015 (t) cc_final: 0.7799 (m) REVERT: A 40 THR cc_start: 0.8206 (OUTLIER) cc_final: 0.7950 (m) REVERT: A 163 TYR cc_start: 0.7839 (m-80) cc_final: 0.7588 (m-80) REVERT: B 66 ASP cc_start: 0.6980 (p0) cc_final: 0.6668 (t0) REVERT: B 195 ASP cc_start: 0.8456 (t0) cc_final: 0.8215 (t0) REVERT: B 197 ARG cc_start: 0.8811 (ttm110) cc_final: 0.8463 (mtp85) REVERT: G 21 MET cc_start: 0.8219 (mtt) cc_final: 0.7640 (tmm) outliers start: 27 outliers final: 22 residues processed: 122 average time/residue: 0.0738 time to fit residues: 12.7443 Evaluate side-chains 123 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 100 time to evaluate : 0.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 75 VAL Chi-restraints excluded: chain R residue 76 LEU Chi-restraints excluded: chain R residue 132 GLU Chi-restraints excluded: chain R residue 136 THR Chi-restraints excluded: chain R residue 193 THR Chi-restraints excluded: chain R residue 197 SER Chi-restraints excluded: chain R residue 236 VAL Chi-restraints excluded: chain R residue 277 ILE Chi-restraints excluded: chain R residue 325 SER Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain B residue 89 LYS Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 85 SER Chi-restraints excluded: chain N residue 91 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 92 optimal weight: 8.9990 chunk 32 optimal weight: 9.9990 chunk 80 optimal weight: 5.9990 chunk 56 optimal weight: 2.9990 chunk 23 optimal weight: 0.9980 chunk 19 optimal weight: 0.9980 chunk 14 optimal weight: 10.0000 chunk 50 optimal weight: 0.9990 chunk 7 optimal weight: 0.3980 chunk 61 optimal weight: 0.0050 chunk 74 optimal weight: 0.8980 overall best weight: 0.6594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.176979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.131967 restraints weight = 8980.691| |-----------------------------------------------------------------------------| r_work (start): 0.3478 rms_B_bonded: 1.95 r_work: 0.3277 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3121 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3101 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3101 r_free = 0.3101 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.85 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3101 r_free = 0.3101 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.85 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.3101 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.4580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 8706 Z= 0.112 Angle : 0.501 8.039 11803 Z= 0.262 Chirality : 0.040 0.154 1329 Planarity : 0.003 0.053 1463 Dihedral : 5.592 64.913 1249 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 2.66 % Allowed : 10.65 % Favored : 86.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.95 (0.27), residues: 1030 helix: 2.67 (0.26), residues: 396 sheet: -0.32 (0.33), residues: 228 loop : -0.89 (0.31), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG R 226 TYR 0.015 0.001 TYR A 163 PHE 0.011 0.001 PHE A 74 TRP 0.017 0.001 TRP B 82 HIS 0.004 0.001 HIS A 209 Details of bonding type rmsd/Z covalent geometry : bond 0.00232 / 0.11 ( 8702) covalent geometry : angle 0.50006 / 0.26 (11795) SS BOND : bond 0.00057 / 0.03 ( 4) SS BOND : angle 1.51444 / 0.80 ( 8) hydrogen bonds : bond 0.04419 / 3.00 ( 427) hydrogen bonds : angle 4.42788 / 3.27 ( 1236) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 105 time to evaluate : 0.324 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 163 TRP cc_start: 0.5293 (m100) cc_final: 0.4425 (t60) REVERT: R 283 CYS cc_start: 0.8039 (t) cc_final: 0.7801 (m) REVERT: A 60 MET cc_start: 0.5104 (ttt) cc_final: 0.4872 (ttm) REVERT: A 163 TYR cc_start: 0.7715 (m-80) cc_final: 0.7478 (m-80) REVERT: B 66 ASP cc_start: 0.6841 (p0) cc_final: 0.6539 (t0) REVERT: B 195 ASP cc_start: 0.8471 (t0) cc_final: 0.8226 (t0) REVERT: B 197 ARG cc_start: 0.8779 (ttm110) cc_final: 0.8460 (mtp85) REVERT: G 21 MET cc_start: 0.8176 (mtt) cc_final: 0.7588 (tmm) outliers start: 24 outliers final: 18 residues processed: 124 average time/residue: 0.0902 time to fit residues: 15.7164 Evaluate side-chains 114 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 96 time to evaluate : 0.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 136 THR Chi-restraints excluded: chain R residue 193 THR Chi-restraints excluded: chain R residue 236 VAL Chi-restraints excluded: chain R residue 275 SER Chi-restraints excluded: chain R residue 325 SER Chi-restraints excluded: chain R residue 329 ILE Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 85 SER Chi-restraints excluded: chain N residue 91 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 57 optimal weight: 1.9990 chunk 42 optimal weight: 8.9990 chunk 16 optimal weight: 1.9990 chunk 24 optimal weight: 0.0170 chunk 12 optimal weight: 0.8980 chunk 13 optimal weight: 0.6980 chunk 38 optimal weight: 0.9980 chunk 85 optimal weight: 0.9990 chunk 35 optimal weight: 4.9990 chunk 87 optimal weight: 0.0770 chunk 5 optimal weight: 0.0570 overall best weight: 0.3494 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.180648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.135582 restraints weight = 8860.629| |-----------------------------------------------------------------------------| r_work (start): 0.3513 rms_B_bonded: 1.94 r_work: 0.3333 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3179 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3161 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3161 r_free = 0.3161 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.85 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3161 r_free = 0.3161 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.83 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3161 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7839 moved from start: 0.4670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 8706 Z= 0.100 Angle : 0.486 8.385 11803 Z= 0.254 Chirality : 0.040 0.153 1329 Planarity : 0.003 0.054 1463 Dihedral : 5.262 62.561 1249 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 1.78 % Allowed : 12.10 % Favored : 86.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.08 (0.27), residues: 1030 helix: 2.84 (0.26), residues: 397 sheet: -0.30 (0.33), residues: 228 loop : -0.86 (0.31), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG R 226 TYR 0.011 0.001 TYR A 163 PHE 0.010 0.001 PHE A 192 TRP 0.017 0.001 TRP B 82 HIS 0.003 0.001 HIS A 209 Details of bonding type rmsd/Z covalent geometry : bond 0.00196 / 0.10 ( 8702) covalent geometry : angle 0.48510 / 0.25 (11795) SS BOND : bond 0.00038 / 0.02 ( 4) SS BOND : angle 1.38377 / 0.74 ( 8) hydrogen bonds : bond 0.04023 / 2.74 ( 427) hydrogen bonds : angle 4.26837 / 3.15 ( 1236) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 107 time to evaluate : 0.186 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 163 TRP cc_start: 0.5262 (m100) cc_final: 0.4372 (t60) REVERT: R 283 CYS cc_start: 0.8041 (t) cc_final: 0.7831 (m) REVERT: A 163 TYR cc_start: 0.7684 (m-80) cc_final: 0.7438 (m-80) REVERT: B 66 ASP cc_start: 0.6797 (p0) cc_final: 0.6526 (t0) REVERT: B 195 ASP cc_start: 0.8489 (t0) cc_final: 0.8243 (t0) REVERT: B 197 ARG cc_start: 0.8776 (ttm110) cc_final: 0.8476 (mtp85) REVERT: G 21 MET cc_start: 0.8184 (mtt) cc_final: 0.7623 (tmm) REVERT: N 110 VAL cc_start: 0.7491 (t) cc_final: 0.7176 (p) outliers start: 16 outliers final: 12 residues processed: 119 average time/residue: 0.0713 time to fit residues: 11.9180 Evaluate side-chains 110 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 98 time to evaluate : 0.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 136 THR Chi-restraints excluded: chain R residue 193 THR Chi-restraints excluded: chain R residue 197 SER Chi-restraints excluded: chain R residue 325 SER Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain N residue 91 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 40 optimal weight: 0.2980 chunk 69 optimal weight: 4.9990 chunk 27 optimal weight: 0.0670 chunk 1 optimal weight: 0.9980 chunk 44 optimal weight: 3.9990 chunk 20 optimal weight: 8.9990 chunk 78 optimal weight: 5.9990 chunk 18 optimal weight: 2.9990 chunk 41 optimal weight: 4.9990 chunk 8 optimal weight: 0.9990 chunk 43 optimal weight: 0.5980 overall best weight: 0.5920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.179551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.134279 restraints weight = 8926.373| |-----------------------------------------------------------------------------| r_work (start): 0.3495 rms_B_bonded: 1.96 r_work: 0.3312 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3158 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3141 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3141 r_free = 0.3141 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.83 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3141 r_free = 0.3141 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.83 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (12 function evaluations) r_final: 0.3141 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.4710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 8706 Z= 0.106 Angle : 0.496 8.405 11803 Z= 0.258 Chirality : 0.040 0.160 1329 Planarity : 0.003 0.053 1463 Dihedral : 5.150 60.072 1249 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 1.89 % Allowed : 11.99 % Favored : 86.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.10 (0.27), residues: 1030 helix: 2.84 (0.26), residues: 397 sheet: -0.26 (0.33), residues: 228 loop : -0.83 (0.31), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG R 226 TYR 0.011 0.001 TYR A 163 PHE 0.024 0.001 PHE A 192 TRP 0.017 0.001 TRP B 82 HIS 0.004 0.001 HIS A 209 Details of bonding type rmsd/Z covalent geometry : bond 0.00221 / 0.11 ( 8702) covalent geometry : angle 0.49477 / 0.26 (11795) SS BOND : bond 0.00043 / 0.02 ( 4) SS BOND : angle 1.40302 / 0.73 ( 8) hydrogen bonds : bond 0.04122 / 2.81 ( 427) hydrogen bonds : angle 4.25817 / 3.14 ( 1236) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 103 time to evaluate : 0.274 Fit side-chains revert: symmetry clash REVERT: R 163 TRP cc_start: 0.5381 (m100) cc_final: 0.4444 (t60) REVERT: R 283 CYS cc_start: 0.7996 (t) cc_final: 0.7767 (m) REVERT: A 163 TYR cc_start: 0.7676 (m-80) cc_final: 0.7430 (m-80) REVERT: B 66 ASP cc_start: 0.6825 (p0) cc_final: 0.6533 (t0) REVERT: G 21 MET cc_start: 0.8147 (mtt) cc_final: 0.7572 (tmm) REVERT: N 110 VAL cc_start: 0.7533 (t) cc_final: 0.7212 (p) outliers start: 17 outliers final: 16 residues processed: 117 average time/residue: 0.0747 time to fit residues: 12.1553 Evaluate side-chains 118 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 102 time to evaluate : 0.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 136 THR Chi-restraints excluded: chain R residue 193 THR Chi-restraints excluded: chain R residue 197 SER Chi-restraints excluded: chain R residue 275 SER Chi-restraints excluded: chain R residue 325 SER Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 21 SER Chi-restraints excluded: chain N residue 91 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 77 optimal weight: 0.2980 chunk 20 optimal weight: 8.9990 chunk 76 optimal weight: 1.9990 chunk 70 optimal weight: 2.9990 chunk 1 optimal weight: 0.7980 chunk 54 optimal weight: 1.9990 chunk 10 optimal weight: 0.7980 chunk 16 optimal weight: 2.9990 chunk 52 optimal weight: 7.9990 chunk 15 optimal weight: 7.9990 chunk 48 optimal weight: 0.9980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.176714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.131777 restraints weight = 8926.152| |-----------------------------------------------------------------------------| r_work (start): 0.3488 rms_B_bonded: 1.95 r_work: 0.3283 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3129 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3094 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3094 r_free = 0.3094 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.83 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3094 r_free = 0.3094 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.82 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3094 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.4768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8706 Z= 0.127 Angle : 0.529 9.502 11803 Z= 0.274 Chirality : 0.041 0.165 1329 Planarity : 0.004 0.053 1463 Dihedral : 5.175 57.122 1249 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 1.89 % Allowed : 12.76 % Favored : 85.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.02 (0.27), residues: 1030 helix: 2.73 (0.25), residues: 397 sheet: -0.27 (0.33), residues: 228 loop : -0.86 (0.30), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG R 226 TYR 0.010 0.001 TYR A 163 PHE 0.025 0.001 PHE A 192 TRP 0.017 0.001 TRP B 82 HIS 0.004 0.001 HIS A 209 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.13 ( 8702) covalent geometry : angle 0.52774 / 0.27 (11795) SS BOND : bond 0.00093 / 0.05 ( 4) SS BOND : angle 1.46962 / 0.77 ( 8) hydrogen bonds : bond 0.04384 / 2.98 ( 427) hydrogen bonds : angle 4.32448 / 3.19 ( 1236) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2060 Ramachandran restraints generated. 1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 106 time to evaluate : 0.198 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 160 GLN cc_start: 0.6408 (mm-40) cc_final: 0.6162 (mm-40) REVERT: A 163 TYR cc_start: 0.7759 (m-80) cc_final: 0.7513 (m-80) REVERT: B 66 ASP cc_start: 0.6877 (p0) cc_final: 0.6590 (t0) REVERT: G 21 MET cc_start: 0.8151 (mtt) cc_final: 0.7594 (tmm) REVERT: N 110 VAL cc_start: 0.7626 (t) cc_final: 0.7274 (p) outliers start: 17 outliers final: 14 residues processed: 121 average time/residue: 0.0785 time to fit residues: 13.0160 Evaluate side-chains 117 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 103 time to evaluate : 0.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 136 THR Chi-restraints excluded: chain R residue 193 THR Chi-restraints excluded: chain R residue 197 SER Chi-restraints excluded: chain R residue 275 SER Chi-restraints excluded: chain R residue 325 SER Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain N residue 91 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 98 optimal weight: 6.9990 chunk 100 optimal weight: 6.9990 chunk 1 optimal weight: 0.9980 chunk 17 optimal weight: 0.5980 chunk 27 optimal weight: 4.9990 chunk 54 optimal weight: 5.9990 chunk 75 optimal weight: 1.9990 chunk 96 optimal weight: 3.9990 chunk 12 optimal weight: 0.6980 chunk 89 optimal weight: 3.9990 chunk 63 optimal weight: 5.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.172706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.128379 restraints weight = 8891.019| |-----------------------------------------------------------------------------| r_work (start): 0.3431 rms_B_bonded: 1.90 r_work: 0.3219 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3066 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3050 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3050 r_free = 0.3050 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.82 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3050 r_free = 0.3050 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.83 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3050 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.4894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8706 Z= 0.173 Angle : 0.573 8.214 11803 Z= 0.299 Chirality : 0.042 0.171 1329 Planarity : 0.004 0.051 1463 Dihedral : 5.463 54.362 1249 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 2.00 % Allowed : 13.21 % Favored : 84.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.80 (0.26), residues: 1030 helix: 2.44 (0.25), residues: 404 sheet: -0.35 (0.33), residues: 227 loop : -0.93 (0.31), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 237 TYR 0.010 0.001 TYR R 194 PHE 0.025 0.002 PHE A 192 TRP 0.019 0.002 TRP B 82 HIS 0.005 0.001 HIS A 209 Details of bonding type rmsd/Z covalent geometry : bond 0.00402 / 0.17 ( 8702) covalent geometry : angle 0.57162 / 0.30 (11795) SS BOND : bond 0.00186 / 0.09 ( 4) SS BOND : angle 1.64059 / 0.86 ( 8) hydrogen bonds : bond 0.04994 / 3.39 ( 427) hydrogen bonds : angle 4.53829 / 3.34 ( 1236) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2301.82 seconds wall clock time: 39 minutes 56.81 seconds (2396.81 seconds total)