Starting phenix.real_space_refine on Tue Mar 3 21:41:12 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wic_32528/03_2026/7wic_32528.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wic_32528/03_2026/7wic_32528.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7wic_32528/03_2026/7wic_32528.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wic_32528/03_2026/7wic_32528.map" model { file = "/net/cci-nas-00/data/ceres_data/7wic_32528/03_2026/7wic_32528.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wic_32528/03_2026/7wic_32528.cif" } resolution = 2.8 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= 0.002 sd= 0.034 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 70 5.16 5 C 5769 2.51 5 N 1527 2.21 5 O 1682 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9048 Number of models: 1 Model: "" Number of chains: 6 Chain: "L" Number of atoms: 114 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 114 Classifications: {'peptide': 14} Link IDs: {'TRANS': 13} Chain: "R" Number of atoms: 2277 Number of conformers: 1 Conformer: "" Number of residues, atoms: 288, 2277 Classifications: {'peptide': 288} Link IDs: {'PTRANS': 11, 'TRANS': 276} Chain: "A" Number of atoms: 1811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1811 Classifications: {'peptide': 225} Link IDs: {'PTRANS': 2, 'TRANS': 222} Chain breaks: 1 Chain: "B" Number of atoms: 2607 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2607 Classifications: {'peptide': 339} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 333} Chain: "G" Number of atoms: 444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 444 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 4, 'TRANS': 53} Chain: "S" Number of atoms: 1795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1795 Classifications: {'peptide': 234} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 223} Chain breaks: 1 Time building chain proxies: 2.03, per 1000 atoms: 0.22 Number of scatterers: 9048 At special positions: 0 Unit cell: (107.484, 127.764, 115.596, 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 70 16.00 O 1682 8.00 N 1527 7.00 C 5769 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS L 3 " - pdb=" SG CYS L 14 " distance=2.03 Simple disulfide: pdb=" SG CYS R 115 " - pdb=" SG CYS R 193 " distance=2.03 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 96 " distance=2.04 Simple disulfide: pdb=" SG CYS S 159 " - pdb=" SG CYS S 229 " distance=2.04 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: 0.72 Conformation dependent library (CDL) restraints added in 338.7 milliseconds 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2162 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 14 sheets defined 37.5% alpha, 22.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.29 Creating SS restraints... Processing helix chain 'R' and resid 41 through 69 removed outlier: 3.799A pdb=" N PHE R 48 " --> pdb=" O ALA R 44 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N ILE R 49 " --> pdb=" O VAL R 45 " (cutoff:3.500A) Processing helix chain 'R' and resid 76 through 96 Processing helix chain 'R' and resid 97 through 105 removed outlier: 4.014A pdb=" N MET R 101 " --> pdb=" O PRO R 97 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N GLN R 102 " --> pdb=" O PHE R 98 " (cutoff:3.500A) Processing helix chain 'R' and resid 112 through 146 removed outlier: 3.845A pdb=" N THR R 128 " --> pdb=" O ILE R 124 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N HIS R 146 " --> pdb=" O LEU R 142 " (cutoff:3.500A) Processing helix chain 'R' and resid 149 through 154 removed outlier: 4.340A pdb=" N TRP R 153 " --> pdb=" O LYS R 149 " (cutoff:3.500A) Processing helix chain 'R' and resid 155 through 174 removed outlier: 3.638A pdb=" N ILE R 174 " --> pdb=" O SER R 170 " (cutoff:3.500A) Processing helix chain 'R' and resid 174 through 180 Processing helix chain 'R' and resid 202 through 243 removed outlier: 5.470A pdb=" N VAL R 219 " --> pdb=" O LEU R 215 " (cutoff:3.500A) Proline residue: R 220 - end of helix removed outlier: 3.592A pdb=" N VAL R 242 " --> pdb=" O SER R 238 " (cutoff:3.500A) Processing helix chain 'R' and resid 246 through 282 Proline residue: R 271 - end of helix Processing helix chain 'R' and resid 287 through 313 removed outlier: 4.140A pdb=" N THR R 301 " --> pdb=" O VAL R 297 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N TYR R 302 " --> pdb=" O VAL R 298 " (cutoff:3.500A) Proline residue: R 309 - end of helix Processing helix chain 'R' and resid 318 through 327 removed outlier: 4.267A pdb=" N SER R 322 " --> pdb=" O ASN R 318 " (cutoff:3.500A) Processing helix chain 'A' and resid 6 through 32 removed outlier: 3.925A pdb=" N ARG A 32 " --> pdb=" O GLU A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 53 Processing helix chain 'A' and resid 207 through 216 removed outlier: 5.081A pdb=" N ILE A 212 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 5.773A pdb=" N HIS A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N PHE A 215 " --> pdb=" O ILE A 212 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 255 Processing helix chain 'A' and resid 270 through 279 removed outlier: 4.166A pdb=" N LYS A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 286 removed outlier: 3.722A pdb=" N ILE A 285 " --> pdb=" O PRO A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 309 Processing helix chain 'A' and resid 330 through 352 Processing helix chain 'B' and resid 3 through 25 Processing helix chain 'B' and resid 33 through 37 removed outlier: 4.174A pdb=" N ASN B 36 " --> pdb=" O ILE B 33 " (cutoff:3.500A) Processing helix chain 'G' and resid 6 through 24 removed outlier: 3.558A pdb=" N ALA G 10 " --> pdb=" O THR G 6 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ASN G 24 " --> pdb=" O LYS G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'S' and resid 53 through 56 removed outlier: 4.080A pdb=" N GLY S 56 " --> pdb=" O SER S 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 53 through 56' Processing helix chain 'S' and resid 87 through 91 removed outlier: 3.731A pdb=" N THR S 91 " --> pdb=" O SER S 88 " (cutoff:3.500A) Processing helix chain 'S' and resid 220 through 224 removed outlier: 3.915A pdb=" N VAL S 224 " --> pdb=" O ALA S 221 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'R' and resid 181 through 182 Processing sheet with id=AA2, first strand: chain 'A' and resid 185 through 190 removed outlier: 6.173A pdb=" N VAL A 34 " --> pdb=" O LYS A 197 " (cutoff:3.500A) removed outlier: 7.586A pdb=" N PHE A 199 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N LEU A 36 " --> pdb=" O PHE A 199 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ALA A 220 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N CYS A 224 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 7.290A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N ASN A 269 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N VAL A 225 " --> pdb=" O ASN A 269 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 46 through 51 removed outlier: 6.545A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.852A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.909A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.872A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.923A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ARG B 137 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.546A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.797A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.460A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.215A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.649A pdb=" N THR B 243 " --> pdb=" O ARG B 251 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.552A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'S' and resid 3 through 7 Processing sheet with id=AB2, first strand: chain 'S' and resid 10 through 12 removed outlier: 6.889A pdb=" N MET S 34 " --> pdb=" O TYR S 50 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N TYR S 50 " --> pdb=" O MET S 34 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N TRP S 36 " --> pdb=" O VAL S 48 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ALA S 40 " --> pdb=" O GLY S 44 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N GLY S 44 " --> pdb=" O ALA S 40 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'S' and resid 10 through 12 removed outlier: 4.156A pdb=" N PHE S 110 " --> pdb=" O ARG S 98 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'S' and resid 140 through 141 Processing sheet with id=AB5, first strand: chain 'S' and resid 146 through 148 455 hydrogen bonds defined for protein. 1275 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: 1.29 Time building geometry restraints manager: 0.95 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 1461 1.30 - 1.43: 2445 1.43 - 1.56: 5229 1.56 - 1.69: 0 1.69 - 1.82: 102 Bond restraints: 9237 Sorted by residual: bond pdb=" CA VAL R 299 " pdb=" CB VAL R 299 " ideal model delta sigma weight residual 1.540 1.458 0.083 1.45e-02 4.76e+03 3.25e+01 bond pdb=" C ALA R 307 " pdb=" O ALA R 307 " ideal model delta sigma weight residual 1.236 1.169 0.067 1.29e-02 6.01e+03 2.70e+01 bond pdb=" C CYS R 306 " pdb=" O CYS R 306 " ideal model delta sigma weight residual 1.237 1.181 0.055 1.19e-02 7.06e+03 2.14e+01 bond pdb=" CB ASP R 122 " pdb=" CG ASP R 122 " ideal model delta sigma weight residual 1.516 1.404 0.112 2.50e-02 1.60e+03 2.01e+01 bond pdb=" N THR R 301 " pdb=" CA THR R 301 " ideal model delta sigma weight residual 1.459 1.407 0.052 1.21e-02 6.83e+03 1.84e+01 ... (remaining 9232 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.95: 12265 1.95 - 3.89: 198 3.89 - 5.84: 29 5.84 - 7.79: 7 7.79 - 9.74: 4 Bond angle restraints: 12503 Sorted by residual: angle pdb=" C ASP R 122 " pdb=" CA ASP R 122 " pdb=" CB ASP R 122 " ideal model delta sigma weight residual 110.88 102.64 8.24 1.57e+00 4.06e-01 2.76e+01 angle pdb=" N ASP R 122 " pdb=" CA ASP R 122 " pdb=" C ASP R 122 " ideal model delta sigma weight residual 111.07 115.70 -4.63 1.07e+00 8.73e-01 1.87e+01 angle pdb=" N THR R 120 " pdb=" CA THR R 120 " pdb=" C THR R 120 " ideal model delta sigma weight residual 111.28 115.54 -4.26 1.09e+00 8.42e-01 1.53e+01 angle pdb=" N CYS R 306 " pdb=" CA CYS R 306 " pdb=" C CYS R 306 " ideal model delta sigma weight residual 111.36 115.28 -3.92 1.09e+00 8.42e-01 1.29e+01 angle pdb=" CB MET A 240 " pdb=" CG MET A 240 " pdb=" SD MET A 240 " ideal model delta sigma weight residual 112.70 122.41 -9.71 3.00e+00 1.11e-01 1.05e+01 ... (remaining 12498 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.59: 4943 16.59 - 33.18: 440 33.18 - 49.77: 88 49.77 - 66.36: 9 66.36 - 82.95: 7 Dihedral angle restraints: 5487 sinusoidal: 2134 harmonic: 3353 Sorted by residual: dihedral pdb=" CB CYS L 3 " pdb=" SG CYS L 3 " pdb=" SG CYS L 14 " pdb=" CB CYS L 14 " ideal model delta sinusoidal sigma weight residual -86.00 -127.89 41.89 1 1.00e+01 1.00e-02 2.45e+01 dihedral pdb=" CB CYS R 115 " pdb=" SG CYS R 115 " pdb=" SG CYS R 193 " pdb=" CB CYS R 193 " ideal model delta sinusoidal sigma weight residual 93.00 130.96 -37.96 1 1.00e+01 1.00e-02 2.03e+01 dihedral pdb=" CA PHE A 323 " pdb=" C PHE A 323 " pdb=" N THR A 324 " pdb=" CA THR A 324 " ideal model delta harmonic sigma weight residual -180.00 -157.54 -22.46 0 5.00e+00 4.00e-02 2.02e+01 ... (remaining 5484 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.085: 1310 0.085 - 0.170: 104 0.170 - 0.255: 6 0.255 - 0.340: 0 0.340 - 0.425: 1 Chirality restraints: 1421 Sorted by residual: chirality pdb=" CA THR R 120 " pdb=" N THR R 120 " pdb=" C THR R 120 " pdb=" CB THR R 120 " both_signs ideal model delta sigma weight residual False 2.53 2.10 0.43 2.00e-01 2.50e+01 4.52e+00 chirality pdb=" CB VAL R 299 " pdb=" CA VAL R 299 " pdb=" CG1 VAL R 299 " pdb=" CG2 VAL R 299 " both_signs ideal model delta sigma weight residual False -2.63 -2.38 -0.25 2.00e-01 2.50e+01 1.58e+00 chirality pdb=" CA THR R 301 " pdb=" N THR R 301 " pdb=" C THR R 301 " pdb=" CB THR R 301 " both_signs ideal model delta sigma weight residual False 2.53 2.30 0.22 2.00e-01 2.50e+01 1.26e+00 ... (remaining 1418 not shown) Planarity restraints: 1571 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR R 302 " 0.037 2.00e-02 2.50e+03 2.28e-02 1.04e+01 pdb=" CG TYR R 302 " -0.052 2.00e-02 2.50e+03 pdb=" CD1 TYR R 302 " -0.003 2.00e-02 2.50e+03 pdb=" CD2 TYR R 302 " -0.003 2.00e-02 2.50e+03 pdb=" CE1 TYR R 302 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR R 302 " 0.006 2.00e-02 2.50e+03 pdb=" CZ TYR R 302 " 0.004 2.00e-02 2.50e+03 pdb=" OH TYR R 302 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS R 306 " -0.014 2.00e-02 2.50e+03 2.89e-02 8.34e+00 pdb=" C CYS R 306 " 0.050 2.00e-02 2.50e+03 pdb=" O CYS R 306 " -0.019 2.00e-02 2.50e+03 pdb=" N ALA R 307 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE R 92 " -0.023 2.00e-02 2.50e+03 2.05e-02 7.36e+00 pdb=" CG PHE R 92 " 0.047 2.00e-02 2.50e+03 pdb=" CD1 PHE R 92 " -0.010 2.00e-02 2.50e+03 pdb=" CD2 PHE R 92 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE R 92 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE R 92 " -0.010 2.00e-02 2.50e+03 pdb=" CZ PHE R 92 " -0.001 2.00e-02 2.50e+03 ... (remaining 1568 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 337 2.72 - 3.27: 8706 3.27 - 3.81: 14534 3.81 - 4.36: 17379 4.36 - 4.90: 30871 Nonbonded interactions: 71827 Sorted by model distance: nonbonded pdb=" OG SER B 245 " pdb=" OD1 ASP B 247 " model vdw 2.176 3.040 nonbonded pdb=" OG SER B 161 " pdb=" OD1 ASP B 163 " model vdw 2.192 3.040 nonbonded pdb=" CB SER R 244 " pdb=" OE2 GLU A 318 " model vdw 2.194 3.440 nonbonded pdb=" O HIS R 146 " pdb=" OG SER R 150 " model vdw 2.232 3.040 nonbonded pdb=" OG1 THR A 182 " pdb=" N GLY A 183 " model vdw 2.273 3.120 ... (remaining 71822 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=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: 0.510 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: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 9.210 Find NCS groups from input model: 0.040 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:9.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7258 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 : 0.005 0.112 9241 Z= 0.271 Angle : 0.620 9.737 12511 Z= 0.343 Chirality : 0.047 0.425 1421 Planarity : 0.004 0.038 1571 Dihedral : 12.934 82.950 3313 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 0.00 % Allowed : 0.30 % Favored : 99.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.61 (0.25), residues: 1142 helix: 1.85 (0.27), residues: 393 sheet: 0.47 (0.31), residues: 300 loop : -0.94 (0.28), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 52 TYR 0.052 0.002 TYR R 302 PHE 0.047 0.002 PHE R 92 TRP 0.020 0.002 TRP R 269 HIS 0.002 0.001 HIS G 44 Details of bonding type rmsd covalent geometry : bond 0.00497 ( 9237) covalent geometry : angle 0.61984 (12503) SS BOND : bond 0.00398 ( 4) SS BOND : angle 1.06052 ( 8) hydrogen bonds : bond 0.17117 ( 448) hydrogen bonds : angle 6.57897 ( 1275) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 237 time to evaluate : 0.352 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 244 SER cc_start: 0.7953 (p) cc_final: 0.7625 (p) REVERT: A 29 LYS cc_start: 0.8167 (tmtt) cc_final: 0.7782 (tmtt) REVERT: A 231 ASP cc_start: 0.7026 (m-30) cc_final: 0.6711 (m-30) REVERT: A 237 ASP cc_start: 0.7227 (t0) cc_final: 0.6997 (t0) REVERT: A 262 THR cc_start: 0.8600 (m) cc_final: 0.8353 (t) REVERT: B 254 ASP cc_start: 0.7076 (t70) cc_final: 0.6787 (t70) REVERT: B 267 ASP cc_start: 0.7614 (m-30) cc_final: 0.7358 (m-30) REVERT: B 271 CYS cc_start: 0.7347 (p) cc_final: 0.7080 (p) REVERT: S 38 ARG cc_start: 0.7988 (ptt180) cc_final: 0.7742 (ptt180) outliers start: 0 outliers final: 0 residues processed: 237 average time/residue: 0.4559 time to fit residues: 116.0195 Evaluate side-chains 216 residues out of total 993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 216 time to evaluate : 0.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 108 optimal weight: 0.9980 chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 5.9990 chunk 53 optimal weight: 7.9990 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 0.8980 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 7.9990 chunk 100 optimal weight: 1.9990 chunk 106 optimal weight: 3.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN A 331 ASN B 132 ASN B 220 GLN B 230 ASN S 142 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.137641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.117509 restraints weight = 12306.399| |-----------------------------------------------------------------------------| r_work (start): 0.3559 rms_B_bonded: 2.09 r_work: 0.3433 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3277 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7669 moved from start: 0.1116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 9241 Z= 0.197 Angle : 0.589 11.887 12511 Z= 0.310 Chirality : 0.044 0.238 1421 Planarity : 0.004 0.034 1571 Dihedral : 4.316 24.399 1247 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 2.32 % Allowed : 10.27 % Favored : 87.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.75 (0.25), residues: 1142 helix: 2.04 (0.27), residues: 397 sheet: 0.54 (0.30), residues: 301 loop : -0.96 (0.28), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG R 247 TYR 0.028 0.002 TYR S 190 PHE 0.048 0.002 PHE R 92 TRP 0.020 0.002 TRP R 108 HIS 0.003 0.001 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00469 ( 9237) covalent geometry : angle 0.58840 (12503) SS BOND : bond 0.00735 ( 4) SS BOND : angle 1.09853 ( 8) hydrogen bonds : bond 0.05080 ( 448) hydrogen bonds : angle 4.74819 ( 1275) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 228 time to evaluate : 0.332 Fit side-chains REVERT: R 116 ARG cc_start: 0.7692 (mtp180) cc_final: 0.7353 (mtp180) REVERT: R 174 ILE cc_start: 0.7857 (tp) cc_final: 0.7528 (pp) REVERT: R 244 SER cc_start: 0.8005 (p) cc_final: 0.7562 (t) REVERT: A 29 LYS cc_start: 0.8452 (tmtt) cc_final: 0.7986 (tmtt) REVERT: A 33 GLU cc_start: 0.7795 (mt-10) cc_final: 0.7566 (mt-10) REVERT: A 231 ASP cc_start: 0.7343 (m-30) cc_final: 0.6998 (m-30) REVERT: A 237 ASP cc_start: 0.7473 (t0) cc_final: 0.7158 (t0) REVERT: B 45 MET cc_start: 0.8384 (OUTLIER) cc_final: 0.7957 (mtm) REVERT: B 267 ASP cc_start: 0.8128 (m-30) cc_final: 0.7862 (m-30) REVERT: B 271 CYS cc_start: 0.8000 (p) cc_final: 0.7713 (p) REVERT: S 30 SER cc_start: 0.8336 (m) cc_final: 0.7998 (t) REVERT: S 57 THR cc_start: 0.8156 (m) cc_final: 0.7944 (t) REVERT: S 87 ARG cc_start: 0.7628 (mtp85) cc_final: 0.7348 (mtp85) outliers start: 23 outliers final: 9 residues processed: 232 average time/residue: 0.5025 time to fit residues: 124.6866 Evaluate side-chains 238 residues out of total 993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 228 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 101 MET Chi-restraints excluded: chain R residue 185 SER Chi-restraints excluded: chain R residue 306 CYS Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain S residue 238 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 88 optimal weight: 3.9990 chunk 42 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 21 optimal weight: 0.7980 chunk 12 optimal weight: 0.9990 chunk 46 optimal weight: 3.9990 chunk 58 optimal weight: 1.9990 chunk 91 optimal weight: 4.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 304 ASN B 36 ASN B 132 ASN B 230 ASN B 340 ASN S 142 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.137056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.117091 restraints weight = 12192.957| |-----------------------------------------------------------------------------| r_work (start): 0.3540 rms_B_bonded: 2.05 r_work: 0.3417 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3261 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7677 moved from start: 0.1382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 9241 Z= 0.211 Angle : 0.590 14.369 12511 Z= 0.307 Chirality : 0.045 0.243 1421 Planarity : 0.004 0.038 1571 Dihedral : 4.349 24.189 1247 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 3.22 % Allowed : 12.99 % Favored : 83.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.75 (0.25), residues: 1142 helix: 2.09 (0.27), residues: 395 sheet: 0.45 (0.29), residues: 303 loop : -0.93 (0.28), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 52 TYR 0.032 0.002 TYR S 190 PHE 0.038 0.002 PHE R 92 TRP 0.021 0.002 TRP R 108 HIS 0.003 0.001 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00502 ( 9237) covalent geometry : angle 0.58932 (12503) SS BOND : bond 0.00724 ( 4) SS BOND : angle 1.23839 ( 8) hydrogen bonds : bond 0.04942 ( 448) hydrogen bonds : angle 4.52616 ( 1275) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 222 time to evaluate : 0.359 Fit side-chains REVERT: R 90 GLU cc_start: 0.8078 (tt0) cc_final: 0.7821 (tt0) REVERT: R 99 LEU cc_start: 0.6927 (OUTLIER) cc_final: 0.6677 (pt) REVERT: R 116 ARG cc_start: 0.7673 (mtp180) cc_final: 0.7372 (mtp180) REVERT: R 174 ILE cc_start: 0.8068 (tp) cc_final: 0.7719 (pp) REVERT: R 230 PHE cc_start: 0.8507 (m-10) cc_final: 0.8304 (m-10) REVERT: R 244 SER cc_start: 0.8077 (p) cc_final: 0.7606 (t) REVERT: A 29 LYS cc_start: 0.8434 (tmtt) cc_final: 0.7939 (tmtt) REVERT: A 33 GLU cc_start: 0.7750 (mt-10) cc_final: 0.7527 (mt-10) REVERT: A 237 ASP cc_start: 0.7454 (t0) cc_final: 0.7155 (t0) REVERT: B 45 MET cc_start: 0.8392 (OUTLIER) cc_final: 0.7975 (mtm) REVERT: B 130 GLU cc_start: 0.7954 (OUTLIER) cc_final: 0.7236 (pm20) REVERT: B 254 ASP cc_start: 0.7922 (t70) cc_final: 0.7712 (p0) REVERT: B 267 ASP cc_start: 0.8118 (m-30) cc_final: 0.7849 (m-30) REVERT: B 271 CYS cc_start: 0.7968 (p) cc_final: 0.7679 (p) REVERT: S 87 ARG cc_start: 0.7627 (mtp85) cc_final: 0.7312 (mtp85) outliers start: 32 outliers final: 17 residues processed: 231 average time/residue: 0.4993 time to fit residues: 123.3607 Evaluate side-chains 246 residues out of total 993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 226 time to evaluate : 0.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 99 LEU Chi-restraints excluded: chain R residue 101 MET Chi-restraints excluded: chain R residue 128 THR Chi-restraints excluded: chain R residue 158 THR Chi-restraints excluded: chain R residue 238 SER Chi-restraints excluded: chain R residue 274 ILE Chi-restraints excluded: chain R residue 297 VAL Chi-restraints excluded: chain R residue 306 CYS Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 201 SER Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain S residue 30 SER Chi-restraints excluded: chain S residue 158 SER Chi-restraints excluded: chain S residue 160 ARG Chi-restraints excluded: chain S residue 238 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 28 optimal weight: 0.1980 chunk 15 optimal weight: 0.9980 chunk 104 optimal weight: 3.9990 chunk 76 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 100 optimal weight: 0.6980 chunk 19 optimal weight: 0.9980 chunk 37 optimal weight: 1.9990 chunk 79 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 304 ASN B 36 ASN B 176 GLN B 230 ASN S 142 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.139731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.119303 restraints weight = 12146.866| |-----------------------------------------------------------------------------| r_work (start): 0.3592 rms_B_bonded: 2.09 r_work: 0.3469 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3311 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7651 moved from start: 0.1469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9241 Z= 0.129 Angle : 0.523 14.455 12511 Z= 0.273 Chirality : 0.042 0.206 1421 Planarity : 0.003 0.034 1571 Dihedral : 4.151 23.018 1247 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 3.63 % Allowed : 14.10 % Favored : 82.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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 (0.25), residues: 1142 helix: 2.27 (0.27), residues: 397 sheet: 0.53 (0.29), residues: 300 loop : -0.83 (0.29), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 256 TYR 0.026 0.001 TYR S 190 PHE 0.022 0.001 PHE R 92 TRP 0.014 0.001 TRP R 108 HIS 0.003 0.001 HIS R 107 Details of bonding type rmsd covalent geometry : bond 0.00295 ( 9237) covalent geometry : angle 0.52261 (12503) SS BOND : bond 0.00578 ( 4) SS BOND : angle 1.09769 ( 8) hydrogen bonds : bond 0.04130 ( 448) hydrogen bonds : angle 4.30373 ( 1275) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 221 time to evaluate : 0.375 Fit side-chains REVERT: R 90 GLU cc_start: 0.8041 (tt0) cc_final: 0.7784 (tt0) REVERT: R 116 ARG cc_start: 0.7635 (mtp180) cc_final: 0.7305 (mtp180) REVERT: R 163 THR cc_start: 0.8063 (m) cc_final: 0.7711 (m) REVERT: A 29 LYS cc_start: 0.8496 (tmtt) cc_final: 0.8106 (tttt) REVERT: A 33 GLU cc_start: 0.7745 (mt-10) cc_final: 0.7407 (mt-10) REVERT: A 231 ASP cc_start: 0.7443 (m-30) cc_final: 0.7112 (m-30) REVERT: A 237 ASP cc_start: 0.7465 (t0) cc_final: 0.7162 (t0) REVERT: A 243 MET cc_start: 0.8315 (tpp) cc_final: 0.7432 (tpp) REVERT: B 45 MET cc_start: 0.8334 (OUTLIER) cc_final: 0.7888 (mtm) REVERT: B 130 GLU cc_start: 0.7900 (OUTLIER) cc_final: 0.7249 (pm20) REVERT: B 254 ASP cc_start: 0.7878 (t70) cc_final: 0.7485 (p0) REVERT: B 267 ASP cc_start: 0.8109 (m-30) cc_final: 0.7862 (m-30) REVERT: B 271 CYS cc_start: 0.7987 (p) cc_final: 0.7699 (p) REVERT: S 30 SER cc_start: 0.8369 (m) cc_final: 0.8025 (t) REVERT: S 87 ARG cc_start: 0.7643 (mtp85) cc_final: 0.7365 (mtp85) outliers start: 36 outliers final: 20 residues processed: 231 average time/residue: 0.5180 time to fit residues: 127.8055 Evaluate side-chains 240 residues out of total 993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 218 time to evaluate : 0.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 74 MET Chi-restraints excluded: chain R residue 101 MET Chi-restraints excluded: chain R residue 128 THR Chi-restraints excluded: chain R residue 137 SER Chi-restraints excluded: chain R residue 287 THR Chi-restraints excluded: chain R residue 297 VAL Chi-restraints excluded: chain R residue 306 CYS Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 201 SER Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain S residue 21 SER Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 158 SER Chi-restraints excluded: chain S residue 238 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 65 optimal weight: 0.6980 chunk 71 optimal weight: 4.9990 chunk 50 optimal weight: 0.9990 chunk 41 optimal weight: 2.9990 chunk 63 optimal weight: 0.7980 chunk 79 optimal weight: 0.8980 chunk 18 optimal weight: 2.9990 chunk 100 optimal weight: 0.9980 chunk 61 optimal weight: 2.9990 chunk 103 optimal weight: 0.8980 chunk 29 optimal weight: 4.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 304 ASN B 36 ASN B 230 ASN B 295 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.139591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.119205 restraints weight = 12067.749| |-----------------------------------------------------------------------------| r_work (start): 0.3573 rms_B_bonded: 2.09 r_work: 0.3448 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3290 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7654 moved from start: 0.1569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9241 Z= 0.136 Angle : 0.532 14.343 12511 Z= 0.274 Chirality : 0.042 0.212 1421 Planarity : 0.003 0.034 1571 Dihedral : 4.081 22.549 1247 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 3.32 % Allowed : 15.51 % Favored : 81.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 1.00 (0.25), residues: 1142 helix: 2.34 (0.26), residues: 397 sheet: 0.51 (0.29), residues: 300 loop : -0.79 (0.29), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 256 TYR 0.026 0.001 TYR S 190 PHE 0.019 0.001 PHE R 92 TRP 0.022 0.002 TRP R 269 HIS 0.003 0.001 HIS R 107 Details of bonding type rmsd covalent geometry : bond 0.00313 ( 9237) covalent geometry : angle 0.53130 (12503) SS BOND : bond 0.00595 ( 4) SS BOND : angle 1.13491 ( 8) hydrogen bonds : bond 0.04049 ( 448) hydrogen bonds : angle 4.22395 ( 1275) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 226 time to evaluate : 0.344 Fit side-chains REVERT: R 90 GLU cc_start: 0.8075 (tt0) cc_final: 0.7807 (tt0) REVERT: R 99 LEU cc_start: 0.6842 (OUTLIER) cc_final: 0.6638 (pt) REVERT: R 116 ARG cc_start: 0.7661 (mtp180) cc_final: 0.7336 (mtp180) REVERT: R 163 THR cc_start: 0.8102 (m) cc_final: 0.7747 (m) REVERT: R 174 ILE cc_start: 0.7987 (tp) cc_final: 0.7658 (tp) REVERT: R 178 MET cc_start: 0.8190 (ttm) cc_final: 0.7328 (ttm) REVERT: A 29 LYS cc_start: 0.8467 (tmtt) cc_final: 0.8091 (tttt) REVERT: A 197 LYS cc_start: 0.8403 (ttmm) cc_final: 0.8122 (mtpp) REVERT: A 231 ASP cc_start: 0.7454 (m-30) cc_final: 0.7122 (m-30) REVERT: A 237 ASP cc_start: 0.7474 (t0) cc_final: 0.7154 (t0) REVERT: A 243 MET cc_start: 0.8312 (tpp) cc_final: 0.7006 (tpp) REVERT: B 45 MET cc_start: 0.8341 (OUTLIER) cc_final: 0.7905 (mtm) REVERT: B 130 GLU cc_start: 0.7862 (OUTLIER) cc_final: 0.7209 (pm20) REVERT: B 135 VAL cc_start: 0.8616 (OUTLIER) cc_final: 0.8272 (p) REVERT: B 254 ASP cc_start: 0.7848 (t70) cc_final: 0.7635 (t0) REVERT: B 267 ASP cc_start: 0.8095 (m-30) cc_final: 0.7836 (m-30) REVERT: B 271 CYS cc_start: 0.8042 (p) cc_final: 0.7747 (p) REVERT: S 30 SER cc_start: 0.8373 (m) cc_final: 0.8026 (t) REVERT: S 87 ARG cc_start: 0.7624 (mtp85) cc_final: 0.7330 (mtp85) outliers start: 33 outliers final: 21 residues processed: 237 average time/residue: 0.4832 time to fit residues: 122.7241 Evaluate side-chains 247 residues out of total 993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 222 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 74 MET Chi-restraints excluded: chain R residue 99 LEU Chi-restraints excluded: chain R residue 101 MET Chi-restraints excluded: chain R residue 128 THR Chi-restraints excluded: chain R residue 137 SER Chi-restraints excluded: chain R residue 185 SER Chi-restraints excluded: chain R residue 287 THR Chi-restraints excluded: chain R residue 297 VAL Chi-restraints excluded: chain R residue 306 CYS Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 201 SER Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain S residue 21 SER Chi-restraints excluded: chain S residue 160 ARG Chi-restraints excluded: chain S residue 238 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 83 optimal weight: 0.6980 chunk 12 optimal weight: 0.9980 chunk 43 optimal weight: 5.9990 chunk 93 optimal weight: 2.9990 chunk 49 optimal weight: 0.7980 chunk 45 optimal weight: 0.0070 chunk 90 optimal weight: 0.4980 chunk 34 optimal weight: 7.9990 chunk 15 optimal weight: 4.9990 chunk 65 optimal weight: 5.9990 chunk 79 optimal weight: 0.8980 overall best weight: 0.5798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 304 ASN B 36 ASN B 230 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.139994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.119728 restraints weight = 12100.643| |-----------------------------------------------------------------------------| r_work (start): 0.3587 rms_B_bonded: 2.09 r_work: 0.3464 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3305 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7632 moved from start: 0.1633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9241 Z= 0.112 Angle : 0.508 13.987 12511 Z= 0.263 Chirality : 0.042 0.205 1421 Planarity : 0.003 0.034 1571 Dihedral : 3.986 21.476 1247 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 3.83 % Allowed : 15.71 % Favored : 80.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 1.07 (0.25), residues: 1142 helix: 2.48 (0.27), residues: 397 sheet: 0.55 (0.29), residues: 291 loop : -0.80 (0.28), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 256 TYR 0.023 0.001 TYR S 190 PHE 0.014 0.001 PHE R 92 TRP 0.021 0.001 TRP R 269 HIS 0.011 0.001 HIS R 107 Details of bonding type rmsd covalent geometry : bond 0.00252 ( 9237) covalent geometry : angle 0.50724 (12503) SS BOND : bond 0.00522 ( 4) SS BOND : angle 1.07280 ( 8) hydrogen bonds : bond 0.03724 ( 448) hydrogen bonds : angle 4.13076 ( 1275) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 216 time to evaluate : 0.296 Fit side-chains REVERT: R 90 GLU cc_start: 0.8054 (tt0) cc_final: 0.7787 (tt0) REVERT: R 163 THR cc_start: 0.8026 (m) cc_final: 0.7715 (m) REVERT: R 284 ILE cc_start: 0.7361 (OUTLIER) cc_final: 0.6813 (pt) REVERT: A 29 LYS cc_start: 0.8461 (tmtt) cc_final: 0.8072 (tttt) REVERT: A 197 LYS cc_start: 0.8309 (ttmm) cc_final: 0.8104 (mtpp) REVERT: A 231 ASP cc_start: 0.7467 (m-30) cc_final: 0.7131 (m-30) REVERT: A 237 ASP cc_start: 0.7477 (t0) cc_final: 0.7183 (t0) REVERT: A 240 MET cc_start: 0.7828 (tpp) cc_final: 0.7420 (tpp) REVERT: A 243 MET cc_start: 0.8279 (tpp) cc_final: 0.6969 (tpp) REVERT: B 130 GLU cc_start: 0.7843 (OUTLIER) cc_final: 0.7199 (pm20) REVERT: B 135 VAL cc_start: 0.8603 (OUTLIER) cc_final: 0.8262 (p) REVERT: B 201 SER cc_start: 0.8220 (OUTLIER) cc_final: 0.7988 (t) REVERT: B 254 ASP cc_start: 0.7857 (t70) cc_final: 0.7625 (t0) REVERT: B 267 ASP cc_start: 0.8095 (m-30) cc_final: 0.7852 (m-30) REVERT: B 271 CYS cc_start: 0.8032 (p) cc_final: 0.7726 (p) REVERT: S 30 SER cc_start: 0.8371 (m) cc_final: 0.8034 (t) outliers start: 38 outliers final: 21 residues processed: 227 average time/residue: 0.4605 time to fit residues: 112.5034 Evaluate side-chains 238 residues out of total 993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 213 time to evaluate : 0.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 74 MET Chi-restraints excluded: chain R residue 101 MET Chi-restraints excluded: chain R residue 128 THR Chi-restraints excluded: chain R residue 137 SER Chi-restraints excluded: chain R residue 238 SER Chi-restraints excluded: chain R residue 284 ILE Chi-restraints excluded: chain R residue 287 THR Chi-restraints excluded: chain R residue 297 VAL Chi-restraints excluded: chain R residue 306 CYS Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 201 SER Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 251 ARG Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain S residue 21 SER Chi-restraints excluded: chain S residue 158 SER Chi-restraints excluded: chain S residue 160 ARG Chi-restraints excluded: chain S residue 238 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 24 optimal weight: 0.6980 chunk 68 optimal weight: 0.9980 chunk 34 optimal weight: 8.9990 chunk 2 optimal weight: 3.9990 chunk 37 optimal weight: 0.9980 chunk 56 optimal weight: 3.9990 chunk 35 optimal weight: 0.9980 chunk 33 optimal weight: 4.9990 chunk 45 optimal weight: 8.9990 chunk 1 optimal weight: 0.9990 chunk 41 optimal weight: 2.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 84 ASN R 102 GLN R 304 ASN B 36 ASN B 132 ASN B 230 ASN B 295 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.139249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.118923 restraints weight = 12137.649| |-----------------------------------------------------------------------------| r_work (start): 0.3564 rms_B_bonded: 2.09 r_work: 0.3440 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3282 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3282 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7648 moved from start: 0.1729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9241 Z= 0.142 Angle : 0.537 14.209 12511 Z= 0.275 Chirality : 0.043 0.215 1421 Planarity : 0.003 0.034 1571 Dihedral : 4.029 21.735 1247 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 3.52 % Allowed : 16.62 % Favored : 79.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 1.03 (0.25), residues: 1142 helix: 2.44 (0.26), residues: 397 sheet: 0.50 (0.29), residues: 295 loop : -0.81 (0.28), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG R 116 TYR 0.025 0.001 TYR S 190 PHE 0.020 0.001 PHE R 92 TRP 0.028 0.002 TRP R 269 HIS 0.010 0.001 HIS R 107 Details of bonding type rmsd covalent geometry : bond 0.00331 ( 9237) covalent geometry : angle 0.53613 (12503) SS BOND : bond 0.00608 ( 4) SS BOND : angle 1.29328 ( 8) hydrogen bonds : bond 0.03969 ( 448) hydrogen bonds : angle 4.15803 ( 1275) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 216 time to evaluate : 0.333 Fit side-chains REVERT: R 90 GLU cc_start: 0.8072 (tt0) cc_final: 0.7790 (tt0) REVERT: R 163 THR cc_start: 0.8054 (m) cc_final: 0.7792 (m) REVERT: R 284 ILE cc_start: 0.7367 (OUTLIER) cc_final: 0.6802 (pt) REVERT: A 29 LYS cc_start: 0.8463 (tmtt) cc_final: 0.8079 (tttt) REVERT: A 237 ASP cc_start: 0.7480 (t0) cc_final: 0.7156 (t0) REVERT: A 240 MET cc_start: 0.7821 (tpp) cc_final: 0.7410 (tpp) REVERT: A 243 MET cc_start: 0.8284 (tpp) cc_final: 0.7109 (tpp) REVERT: A 317 LYS cc_start: 0.8365 (ptpp) cc_final: 0.7930 (ptpt) REVERT: B 45 MET cc_start: 0.8358 (OUTLIER) cc_final: 0.8030 (mtm) REVERT: B 70 LEU cc_start: 0.8068 (tp) cc_final: 0.7829 (tt) REVERT: B 130 GLU cc_start: 0.7830 (OUTLIER) cc_final: 0.7220 (pm20) REVERT: B 135 VAL cc_start: 0.8614 (OUTLIER) cc_final: 0.8291 (p) REVERT: B 201 SER cc_start: 0.8279 (OUTLIER) cc_final: 0.8058 (t) REVERT: B 254 ASP cc_start: 0.7857 (t70) cc_final: 0.7630 (t0) REVERT: B 267 ASP cc_start: 0.8100 (m-30) cc_final: 0.7848 (m-30) REVERT: B 271 CYS cc_start: 0.8026 (p) cc_final: 0.7743 (p) REVERT: S 30 SER cc_start: 0.8376 (m) cc_final: 0.8044 (t) outliers start: 35 outliers final: 22 residues processed: 226 average time/residue: 0.4688 time to fit residues: 113.8913 Evaluate side-chains 242 residues out of total 993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 215 time to evaluate : 0.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 74 MET Chi-restraints excluded: chain R residue 101 MET Chi-restraints excluded: chain R residue 128 THR Chi-restraints excluded: chain R residue 137 SER Chi-restraints excluded: chain R residue 185 SER Chi-restraints excluded: chain R residue 238 SER Chi-restraints excluded: chain R residue 284 ILE Chi-restraints excluded: chain R residue 287 THR Chi-restraints excluded: chain R residue 297 VAL Chi-restraints excluded: chain R residue 306 CYS Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 201 SER Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain S residue 21 SER Chi-restraints excluded: chain S residue 158 SER Chi-restraints excluded: chain S residue 160 ARG Chi-restraints excluded: chain S residue 199 VAL Chi-restraints excluded: chain S residue 238 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 4 optimal weight: 5.9990 chunk 27 optimal weight: 0.4980 chunk 61 optimal weight: 0.5980 chunk 50 optimal weight: 0.7980 chunk 53 optimal weight: 5.9990 chunk 83 optimal weight: 0.9990 chunk 73 optimal weight: 2.9990 chunk 63 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 62 optimal weight: 0.6980 chunk 17 optimal weight: 3.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 36 ASN S 142 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.140470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.120011 restraints weight = 12172.614| |-----------------------------------------------------------------------------| r_work (start): 0.3558 rms_B_bonded: 2.12 r_work: 0.3434 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3277 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7646 moved from start: 0.1775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9241 Z= 0.122 Angle : 0.524 14.100 12511 Z= 0.268 Chirality : 0.042 0.205 1421 Planarity : 0.003 0.034 1571 Dihedral : 3.968 21.437 1247 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 3.52 % Allowed : 17.62 % Favored : 78.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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 (0.25), residues: 1142 helix: 2.52 (0.26), residues: 397 sheet: 0.53 (0.29), residues: 292 loop : -0.77 (0.28), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG R 116 TYR 0.023 0.001 TYR S 190 PHE 0.016 0.001 PHE R 92 TRP 0.033 0.002 TRP R 269 HIS 0.010 0.001 HIS R 107 Details of bonding type rmsd covalent geometry : bond 0.00279 ( 9237) covalent geometry : angle 0.52299 (12503) SS BOND : bond 0.00565 ( 4) SS BOND : angle 1.27253 ( 8) hydrogen bonds : bond 0.03749 ( 448) hydrogen bonds : angle 4.11778 ( 1275) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 214 time to evaluate : 0.347 Fit side-chains REVERT: R 90 GLU cc_start: 0.8063 (tt0) cc_final: 0.7793 (tt0) REVERT: R 284 ILE cc_start: 0.7289 (OUTLIER) cc_final: 0.6701 (pt) REVERT: A 29 LYS cc_start: 0.8474 (tmtt) cc_final: 0.8086 (tttt) REVERT: A 237 ASP cc_start: 0.7474 (t0) cc_final: 0.7142 (t0) REVERT: A 240 MET cc_start: 0.7797 (tpp) cc_final: 0.7389 (tpp) REVERT: A 243 MET cc_start: 0.8295 (tpp) cc_final: 0.7119 (tpp) REVERT: A 317 LYS cc_start: 0.8332 (ptpp) cc_final: 0.7869 (ptpt) REVERT: B 45 MET cc_start: 0.8360 (OUTLIER) cc_final: 0.8041 (mtm) REVERT: B 70 LEU cc_start: 0.8054 (tp) cc_final: 0.7808 (tt) REVERT: B 130 GLU cc_start: 0.7828 (OUTLIER) cc_final: 0.7231 (pm20) REVERT: B 135 VAL cc_start: 0.8590 (OUTLIER) cc_final: 0.8267 (p) REVERT: B 201 SER cc_start: 0.8251 (OUTLIER) cc_final: 0.8048 (t) REVERT: B 214 ARG cc_start: 0.7655 (mtm-85) cc_final: 0.7336 (mtm-85) REVERT: B 254 ASP cc_start: 0.7823 (t70) cc_final: 0.7612 (t0) REVERT: B 267 ASP cc_start: 0.8088 (m-30) cc_final: 0.7829 (m-30) REVERT: B 271 CYS cc_start: 0.8055 (p) cc_final: 0.7777 (p) REVERT: S 30 SER cc_start: 0.8380 (m) cc_final: 0.8057 (t) outliers start: 35 outliers final: 25 residues processed: 223 average time/residue: 0.4716 time to fit residues: 113.1193 Evaluate side-chains 240 residues out of total 993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 210 time to evaluate : 0.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 74 MET Chi-restraints excluded: chain R residue 101 MET Chi-restraints excluded: chain R residue 128 THR Chi-restraints excluded: chain R residue 137 SER Chi-restraints excluded: chain R residue 185 SER Chi-restraints excluded: chain R residue 238 SER Chi-restraints excluded: chain R residue 284 ILE Chi-restraints excluded: chain R residue 287 THR Chi-restraints excluded: chain R residue 297 VAL Chi-restraints excluded: chain R residue 306 CYS Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 127 LYS Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 201 SER Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 251 ARG Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain S residue 21 SER Chi-restraints excluded: chain S residue 158 SER Chi-restraints excluded: chain S residue 160 ARG Chi-restraints excluded: chain S residue 199 VAL Chi-restraints excluded: chain S residue 238 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 81 optimal weight: 5.9990 chunk 29 optimal weight: 3.9990 chunk 88 optimal weight: 0.1980 chunk 71 optimal weight: 4.9990 chunk 70 optimal weight: 0.9980 chunk 36 optimal weight: 2.9990 chunk 44 optimal weight: 0.0270 chunk 91 optimal weight: 5.9990 chunk 90 optimal weight: 0.0170 chunk 78 optimal weight: 2.9990 chunk 15 optimal weight: 5.9990 overall best weight: 0.8478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 36 ASN B 230 ASN S 142 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.140195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.119600 restraints weight = 12043.667| |-----------------------------------------------------------------------------| r_work (start): 0.3566 rms_B_bonded: 2.12 r_work: 0.3444 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3286 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7641 moved from start: 0.1825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9241 Z= 0.136 Angle : 0.545 14.125 12511 Z= 0.277 Chirality : 0.043 0.214 1421 Planarity : 0.003 0.034 1571 Dihedral : 3.987 21.374 1247 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 3.22 % Allowed : 17.93 % Favored : 78.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 1.09 (0.25), residues: 1142 helix: 2.50 (0.26), residues: 397 sheet: 0.55 (0.29), residues: 291 loop : -0.80 (0.28), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG R 116 TYR 0.023 0.001 TYR S 190 PHE 0.017 0.001 PHE R 92 TRP 0.027 0.002 TRP R 269 HIS 0.010 0.001 HIS R 107 Details of bonding type rmsd covalent geometry : bond 0.00314 ( 9237) covalent geometry : angle 0.54466 (12503) SS BOND : bond 0.00594 ( 4) SS BOND : angle 1.28612 ( 8) hydrogen bonds : bond 0.03841 ( 448) hydrogen bonds : angle 4.12839 ( 1275) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 216 time to evaluate : 0.312 Fit side-chains REVERT: R 90 GLU cc_start: 0.8072 (tt0) cc_final: 0.7795 (tt0) REVERT: R 238 SER cc_start: 0.7830 (OUTLIER) cc_final: 0.7554 (m) REVERT: R 284 ILE cc_start: 0.7266 (OUTLIER) cc_final: 0.6685 (pt) REVERT: A 29 LYS cc_start: 0.8466 (tmtt) cc_final: 0.8062 (tttt) REVERT: A 237 ASP cc_start: 0.7465 (t0) cc_final: 0.7131 (t0) REVERT: A 240 MET cc_start: 0.7819 (tpp) cc_final: 0.7424 (tpp) REVERT: A 243 MET cc_start: 0.8271 (tpp) cc_final: 0.7113 (tpp) REVERT: A 317 LYS cc_start: 0.8358 (ptpp) cc_final: 0.8064 (ptmt) REVERT: B 45 MET cc_start: 0.8370 (OUTLIER) cc_final: 0.7905 (mtm) REVERT: B 70 LEU cc_start: 0.8060 (tp) cc_final: 0.7828 (tt) REVERT: B 130 GLU cc_start: 0.7829 (OUTLIER) cc_final: 0.7208 (pm20) REVERT: B 135 VAL cc_start: 0.8601 (OUTLIER) cc_final: 0.8271 (p) REVERT: B 201 SER cc_start: 0.8283 (OUTLIER) cc_final: 0.8083 (t) REVERT: B 254 ASP cc_start: 0.7812 (t70) cc_final: 0.7598 (t0) REVERT: B 267 ASP cc_start: 0.8092 (m-30) cc_final: 0.7834 (m-30) REVERT: B 271 CYS cc_start: 0.8040 (p) cc_final: 0.7763 (p) REVERT: S 30 SER cc_start: 0.8387 (m) cc_final: 0.8057 (t) REVERT: S 199 VAL cc_start: 0.8599 (OUTLIER) cc_final: 0.8256 (m) REVERT: S 215 THR cc_start: 0.8237 (m) cc_final: 0.7672 (p) outliers start: 32 outliers final: 21 residues processed: 224 average time/residue: 0.4644 time to fit residues: 111.9567 Evaluate side-chains 243 residues out of total 993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 215 time to evaluate : 0.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 74 MET Chi-restraints excluded: chain R residue 101 MET Chi-restraints excluded: chain R residue 128 THR Chi-restraints excluded: chain R residue 137 SER Chi-restraints excluded: chain R residue 185 SER Chi-restraints excluded: chain R residue 238 SER Chi-restraints excluded: chain R residue 284 ILE Chi-restraints excluded: chain R residue 287 THR Chi-restraints excluded: chain R residue 297 VAL Chi-restraints excluded: chain R residue 306 CYS Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 127 LYS Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 201 SER Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain S residue 21 SER Chi-restraints excluded: chain S residue 158 SER Chi-restraints excluded: chain S residue 199 VAL Chi-restraints excluded: chain S residue 238 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 85 optimal weight: 3.9990 chunk 67 optimal weight: 0.8980 chunk 0 optimal weight: 2.9990 chunk 37 optimal weight: 0.5980 chunk 58 optimal weight: 0.7980 chunk 64 optimal weight: 0.9990 chunk 60 optimal weight: 2.9990 chunk 99 optimal weight: 0.2980 chunk 45 optimal weight: 0.8980 chunk 52 optimal weight: 2.9990 chunk 78 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 36 ASN B 230 ASN S 142 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.140728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.120162 restraints weight = 12097.290| |-----------------------------------------------------------------------------| r_work (start): 0.3577 rms_B_bonded: 2.12 r_work: 0.3453 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3295 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3295 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7635 moved from start: 0.1850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9241 Z= 0.121 Angle : 0.544 14.049 12511 Z= 0.274 Chirality : 0.042 0.204 1421 Planarity : 0.003 0.034 1571 Dihedral : 3.946 20.862 1247 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 3.02 % Allowed : 18.73 % Favored : 78.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 1.15 (0.25), residues: 1142 helix: 2.54 (0.26), residues: 397 sheet: 0.59 (0.29), residues: 291 loop : -0.75 (0.28), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG R 116 TYR 0.022 0.001 TYR S 190 PHE 0.016 0.001 PHE R 92 TRP 0.028 0.001 TRP R 269 HIS 0.010 0.001 HIS R 107 Details of bonding type rmsd covalent geometry : bond 0.00278 ( 9237) covalent geometry : angle 0.54369 (12503) SS BOND : bond 0.00598 ( 4) SS BOND : angle 1.02157 ( 8) hydrogen bonds : bond 0.03664 ( 448) hydrogen bonds : angle 4.10794 ( 1275) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 218 time to evaluate : 0.307 Fit side-chains REVERT: R 90 GLU cc_start: 0.8071 (tt0) cc_final: 0.7788 (tt0) REVERT: R 238 SER cc_start: 0.7815 (OUTLIER) cc_final: 0.7543 (m) REVERT: R 284 ILE cc_start: 0.7222 (OUTLIER) cc_final: 0.6654 (pt) REVERT: A 29 LYS cc_start: 0.8468 (tmtt) cc_final: 0.8067 (tttt) REVERT: A 237 ASP cc_start: 0.7453 (t0) cc_final: 0.7108 (t0) REVERT: A 240 MET cc_start: 0.7821 (tpp) cc_final: 0.7422 (tpp) REVERT: A 243 MET cc_start: 0.8279 (tpp) cc_final: 0.7110 (tpp) REVERT: A 317 LYS cc_start: 0.8331 (ptpp) cc_final: 0.8056 (ptmt) REVERT: B 45 MET cc_start: 0.8363 (OUTLIER) cc_final: 0.7908 (mtm) REVERT: B 70 LEU cc_start: 0.8055 (tp) cc_final: 0.7807 (tt) REVERT: B 130 GLU cc_start: 0.7838 (OUTLIER) cc_final: 0.7218 (pm20) REVERT: B 135 VAL cc_start: 0.8607 (OUTLIER) cc_final: 0.8258 (p) REVERT: B 254 ASP cc_start: 0.7796 (t70) cc_final: 0.7582 (t0) REVERT: B 267 ASP cc_start: 0.8097 (m-30) cc_final: 0.7846 (m-30) REVERT: B 271 CYS cc_start: 0.8031 (p) cc_final: 0.7769 (p) REVERT: S 30 SER cc_start: 0.8382 (m) cc_final: 0.8054 (t) REVERT: S 215 THR cc_start: 0.8232 (m) cc_final: 0.7821 (p) outliers start: 30 outliers final: 22 residues processed: 226 average time/residue: 0.4582 time to fit residues: 111.3967 Evaluate side-chains 242 residues out of total 993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 215 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 74 MET Chi-restraints excluded: chain R residue 101 MET Chi-restraints excluded: chain R residue 128 THR Chi-restraints excluded: chain R residue 137 SER Chi-restraints excluded: chain R residue 238 SER Chi-restraints excluded: chain R residue 284 ILE Chi-restraints excluded: chain R residue 287 THR Chi-restraints excluded: chain R residue 297 VAL Chi-restraints excluded: chain R residue 306 CYS Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 127 LYS Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 21 SER Chi-restraints excluded: chain S residue 158 SER Chi-restraints excluded: chain S residue 199 VAL Chi-restraints excluded: chain S residue 238 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 111 optimal weight: 0.9990 chunk 23 optimal weight: 0.7980 chunk 13 optimal weight: 0.6980 chunk 14 optimal weight: 4.9990 chunk 65 optimal weight: 4.9990 chunk 31 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 58 optimal weight: 0.9990 chunk 81 optimal weight: 4.9990 chunk 105 optimal weight: 1.9990 chunk 78 optimal weight: 2.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 36 ASN B 230 ASN S 142 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.139484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.119019 restraints weight = 11952.262| |-----------------------------------------------------------------------------| r_work (start): 0.3569 rms_B_bonded: 2.09 r_work: 0.3446 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3288 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7651 moved from start: 0.1841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9241 Z= 0.159 Angle : 0.577 14.380 12511 Z= 0.291 Chirality : 0.043 0.224 1421 Planarity : 0.004 0.035 1571 Dihedral : 4.040 21.664 1247 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 3.22 % Allowed : 19.13 % Favored : 77.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 1.04 (0.25), residues: 1142 helix: 2.42 (0.26), residues: 398 sheet: 0.54 (0.29), residues: 292 loop : -0.81 (0.28), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG R 116 TYR 0.025 0.001 TYR S 190 PHE 0.020 0.001 PHE R 92 TRP 0.028 0.002 TRP R 269 HIS 0.010 0.001 HIS R 107 Details of bonding type rmsd covalent geometry : bond 0.00376 ( 9237) covalent geometry : angle 0.57695 (12503) SS BOND : bond 0.00689 ( 4) SS BOND : angle 1.11629 ( 8) hydrogen bonds : bond 0.04053 ( 448) hydrogen bonds : angle 4.15787 ( 1275) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3701.64 seconds wall clock time: 63 minutes 41.31 seconds (3821.31 seconds total)