Starting phenix.real_space_refine on Sat Jun 7 16:17:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wic_32528/06_2025/7wic_32528.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wic_32528/06_2025/7wic_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_32528/06_2025/7wic_32528.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wic_32528/06_2025/7wic_32528.map" model { file = "/net/cci-nas-00/data/ceres_data/7wic_32528/06_2025/7wic_32528.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wic_32528/06_2025/7wic_32528.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 5.48, per 1000 atoms: 0.61 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: 2.07 Conformation dependent library (CDL) restraints added in 1.0 seconds 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: 0.99 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: 2.91 Time building geometry restraints manager: 2.49 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: 0.520 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: 0.320 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 22.850 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.030 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:14.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.080 ------------------------------------------------------------------------------- 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 : 7.87 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.020 0.002 TRP R 269 HIS 0.002 0.001 HIS G 44 PHE 0.047 0.002 PHE R 92 TYR 0.052 0.002 TYR R 302 ARG 0.003 0.000 ARG B 52 Details of bonding type rmsd hydrogen bonds : bond 0.17117 ( 448) hydrogen bonds : angle 6.57897 ( 1275) SS BOND : bond 0.00398 ( 4) SS BOND : angle 1.06052 ( 8) covalent geometry : bond 0.00497 ( 9237) covalent geometry : angle 0.61984 (12503) *********************** 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 : 1.003 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: 1.0671 time to fit residues: 272.4917 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 : 1.029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 0.5980 chunk 84 optimal weight: 3.9990 chunk 47 optimal weight: 1.9990 chunk 28 optimal weight: 0.0770 chunk 57 optimal weight: 2.9990 chunk 45 optimal weight: 4.9990 chunk 87 optimal weight: 0.9980 chunk 33 optimal weight: 4.9990 chunk 53 optimal weight: 5.9990 chunk 65 optimal weight: 0.8980 chunk 101 optimal weight: 0.6980 overall best weight: 0.6538 ------------------------------------------------------------------------------- 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 91 HIS B 132 ASN B 220 GLN B 230 ASN S 142 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.139141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.119221 restraints weight = 12233.707| |-----------------------------------------------------------------------------| r_work (start): 0.3588 rms_B_bonded: 2.07 r_work: 0.3463 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3309 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3309 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7632 moved from start: 0.1075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 9241 Z= 0.133 Angle : 0.547 10.842 12511 Z= 0.288 Chirality : 0.042 0.202 1421 Planarity : 0.004 0.035 1571 Dihedral : 4.138 23.038 1247 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 2.11 % Allowed : 10.17 % Favored : 87.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.25), residues: 1142 helix: 2.20 (0.27), residues: 398 sheet: 0.59 (0.30), residues: 298 loop : -0.89 (0.28), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP S 47 HIS 0.002 0.001 HIS S 35 PHE 0.043 0.001 PHE R 92 TYR 0.025 0.001 TYR S 190 ARG 0.005 0.000 ARG R 247 Details of bonding type rmsd hydrogen bonds : bond 0.04567 ( 448) hydrogen bonds : angle 4.66754 ( 1275) SS BOND : bond 0.00539 ( 4) SS BOND : angle 0.91869 ( 8) covalent geometry : bond 0.00302 ( 9237) covalent geometry : angle 0.54680 (12503) *********************** 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 240 residues out of total 993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 219 time to evaluate : 1.064 Fit side-chains REVERT: R 116 ARG cc_start: 0.7611 (mtp180) cc_final: 0.7240 (mtp180) REVERT: R 119 MET cc_start: 0.7444 (mmp) cc_final: 0.7108 (mpp) REVERT: R 174 ILE cc_start: 0.7788 (tp) cc_final: 0.7570 (tp) REVERT: A 29 LYS cc_start: 0.8430 (tmtt) cc_final: 0.7989 (tmtt) REVERT: A 231 ASP cc_start: 0.7355 (m-30) cc_final: 0.7009 (m-30) REVERT: A 237 ASP cc_start: 0.7452 (t0) cc_final: 0.7141 (t0) REVERT: B 45 MET cc_start: 0.8366 (OUTLIER) cc_final: 0.7953 (mtm) REVERT: B 267 ASP cc_start: 0.8097 (m-30) cc_final: 0.7848 (m-30) REVERT: B 271 CYS cc_start: 0.8003 (p) cc_final: 0.7696 (p) REVERT: S 30 SER cc_start: 0.8305 (m) cc_final: 0.7966 (t) REVERT: S 57 THR cc_start: 0.8073 (m) cc_final: 0.7872 (t) REVERT: S 87 ARG cc_start: 0.7644 (mtp85) cc_final: 0.7415 (mtp85) outliers start: 21 outliers final: 10 residues processed: 223 average time/residue: 1.1591 time to fit residues: 276.5349 Evaluate side-chains 220 residues out of total 993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 209 time to evaluate : 1.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 101 MET Chi-restraints excluded: chain R residue 128 THR 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 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 262 MET 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 89 optimal weight: 0.0980 chunk 7 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 chunk 40 optimal weight: 0.9990 chunk 11 optimal weight: 3.9990 chunk 68 optimal weight: 2.9990 chunk 57 optimal weight: 1.9990 chunk 37 optimal weight: 0.7980 chunk 36 optimal weight: 0.8980 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 304 ASN B 132 ASN B 220 GLN 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 = 0.3824 r_free = 0.3824 target = 0.138629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.118624 restraints weight = 12336.881| |-----------------------------------------------------------------------------| r_work (start): 0.3567 rms_B_bonded: 2.08 r_work: 0.3444 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3288 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7638 moved from start: 0.1309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9241 Z= 0.130 Angle : 0.531 12.860 12511 Z= 0.274 Chirality : 0.042 0.206 1421 Planarity : 0.003 0.034 1571 Dihedral : 4.059 22.442 1247 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.52 % Allowed : 13.19 % Favored : 84.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.05 (0.25), residues: 1142 helix: 2.37 (0.27), residues: 398 sheet: 0.60 (0.30), residues: 299 loop : -0.79 (0.29), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP R 108 HIS 0.002 0.001 HIS A 213 PHE 0.031 0.001 PHE R 92 TYR 0.025 0.001 TYR S 190 ARG 0.008 0.000 ARG B 256 Details of bonding type rmsd hydrogen bonds : bond 0.04150 ( 448) hydrogen bonds : angle 4.32838 ( 1275) SS BOND : bond 0.00542 ( 4) SS BOND : angle 0.82479 ( 8) covalent geometry : bond 0.00295 ( 9237) covalent geometry : angle 0.53055 (12503) *********************** 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 243 residues out of total 993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 218 time to evaluate : 1.044 Fit side-chains REVERT: R 116 ARG cc_start: 0.7570 (mtp180) cc_final: 0.7216 (mtp180) REVERT: R 119 MET cc_start: 0.7416 (mmp) cc_final: 0.7119 (mpp) REVERT: R 163 THR cc_start: 0.8007 (m) cc_final: 0.7749 (m) REVERT: R 174 ILE cc_start: 0.7991 (tp) cc_final: 0.7708 (tp) REVERT: R 304 ASN cc_start: 0.7750 (OUTLIER) cc_final: 0.7546 (t0) REVERT: A 29 LYS cc_start: 0.8478 (tmtt) cc_final: 0.7996 (tmtt) REVERT: A 33 GLU cc_start: 0.7728 (mt-10) cc_final: 0.7478 (mt-10) REVERT: A 237 ASP cc_start: 0.7484 (t0) cc_final: 0.7177 (t0) REVERT: A 262 THR cc_start: 0.8736 (OUTLIER) cc_final: 0.8502 (m) REVERT: B 45 MET cc_start: 0.8375 (OUTLIER) cc_final: 0.7952 (mtm) REVERT: B 130 GLU cc_start: 0.7893 (OUTLIER) cc_final: 0.7253 (pm20) REVERT: B 267 ASP cc_start: 0.8107 (m-30) cc_final: 0.7856 (m-30) REVERT: B 271 CYS cc_start: 0.7985 (p) cc_final: 0.7689 (p) REVERT: S 30 SER cc_start: 0.8348 (m) cc_final: 0.8024 (t) REVERT: S 87 ARG cc_start: 0.7619 (mtp85) cc_final: 0.7342 (mtp85) REVERT: S 215 THR cc_start: 0.8240 (m) cc_final: 0.7784 (p) outliers start: 25 outliers final: 8 residues processed: 223 average time/residue: 1.1092 time to fit residues: 264.8333 Evaluate side-chains 229 residues out of total 993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 217 time to evaluate : 0.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 101 MET Chi-restraints excluded: chain R residue 128 THR Chi-restraints excluded: chain R residue 304 ASN 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 54 optimal weight: 0.2980 chunk 16 optimal weight: 0.8980 chunk 94 optimal weight: 0.7980 chunk 111 optimal weight: 0.9990 chunk 28 optimal weight: 0.9990 chunk 15 optimal weight: 3.9990 chunk 107 optimal weight: 0.3980 chunk 63 optimal weight: 3.9990 chunk 88 optimal weight: 3.9990 chunk 36 optimal weight: 4.9990 chunk 109 optimal weight: 5.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 132 ASN B 156 GLN 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 = 0.3846 r_free = 0.3846 target = 0.140629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.120244 restraints weight = 12080.690| |-----------------------------------------------------------------------------| r_work (start): 0.3607 rms_B_bonded: 2.09 r_work: 0.3484 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3328 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7634 moved from start: 0.1504 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= 0.121 Angle : 0.515 12.926 12511 Z= 0.266 Chirality : 0.042 0.201 1421 Planarity : 0.003 0.035 1571 Dihedral : 4.007 21.946 1247 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 2.82 % Allowed : 14.00 % Favored : 83.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.10 (0.25), residues: 1142 helix: 2.44 (0.27), residues: 399 sheet: 0.61 (0.29), residues: 297 loop : -0.78 (0.29), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP R 269 HIS 0.002 0.001 HIS A 213 PHE 0.022 0.001 PHE R 92 TYR 0.025 0.001 TYR S 190 ARG 0.004 0.000 ARG B 256 Details of bonding type rmsd hydrogen bonds : bond 0.03890 ( 448) hydrogen bonds : angle 4.19704 ( 1275) SS BOND : bond 0.00548 ( 4) SS BOND : angle 0.84024 ( 8) covalent geometry : bond 0.00275 ( 9237) covalent geometry : angle 0.51441 (12503) *********************** 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 242 residues out of total 993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 214 time to evaluate : 0.890 Fit side-chains REVERT: R 116 ARG cc_start: 0.7568 (mtp180) cc_final: 0.7211 (mtp180) REVERT: R 119 MET cc_start: 0.7404 (mmp) cc_final: 0.7083 (mpp) REVERT: R 174 ILE cc_start: 0.7874 (tp) cc_final: 0.7547 (tp) REVERT: A 29 LYS cc_start: 0.8504 (tmtt) cc_final: 0.8010 (tmtt) REVERT: A 33 GLU cc_start: 0.7709 (mt-10) cc_final: 0.7420 (tt0) REVERT: A 237 ASP cc_start: 0.7502 (t0) cc_final: 0.7180 (t0) REVERT: B 45 MET cc_start: 0.8316 (OUTLIER) cc_final: 0.7844 (mtm) REVERT: B 130 GLU cc_start: 0.7878 (OUTLIER) cc_final: 0.7251 (pm20) REVERT: B 267 ASP cc_start: 0.8102 (m-30) cc_final: 0.7872 (m-30) REVERT: B 271 CYS cc_start: 0.8000 (p) cc_final: 0.7687 (p) REVERT: S 30 SER cc_start: 0.8390 (m) cc_final: 0.8056 (t) REVERT: S 87 ARG cc_start: 0.7634 (mtp85) cc_final: 0.7377 (mtp85) outliers start: 28 outliers final: 18 residues processed: 219 average time/residue: 1.1341 time to fit residues: 265.3890 Evaluate side-chains 232 residues out of total 993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 212 time to evaluate : 0.927 ------------------------------------------------------------------------------- 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 238 SER 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 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 217 MET Chi-restraints excluded: chain B residue 294 CYS 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 160 ARG 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 106 optimal weight: 3.9990 chunk 72 optimal weight: 2.9990 chunk 104 optimal weight: 3.9990 chunk 59 optimal weight: 0.5980 chunk 16 optimal weight: 0.9980 chunk 66 optimal weight: 0.4980 chunk 51 optimal weight: 0.0470 chunk 13 optimal weight: 0.6980 chunk 65 optimal weight: 3.9990 chunk 22 optimal weight: 3.9990 chunk 20 optimal weight: 0.9980 overall best weight: 0.5678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 156 GLN 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 = 0.3853 r_free = 0.3853 target = 0.141199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.120915 restraints weight = 12024.499| |-----------------------------------------------------------------------------| r_work (start): 0.3615 rms_B_bonded: 2.09 r_work: 0.3493 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3336 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3336 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7624 moved from start: 0.1629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 9241 Z= 0.109 Angle : 0.507 13.006 12511 Z= 0.260 Chirality : 0.042 0.194 1421 Planarity : 0.003 0.036 1571 Dihedral : 3.923 21.006 1247 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 2.42 % Allowed : 15.21 % Favored : 82.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.18 (0.25), residues: 1142 helix: 2.56 (0.27), residues: 399 sheet: 0.62 (0.29), residues: 295 loop : -0.76 (0.29), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP R 269 HIS 0.002 0.001 HIS R 107 PHE 0.019 0.001 PHE R 92 TYR 0.024 0.001 TYR S 190 ARG 0.004 0.000 ARG B 256 Details of bonding type rmsd hydrogen bonds : bond 0.03654 ( 448) hydrogen bonds : angle 4.08273 ( 1275) SS BOND : bond 0.00498 ( 4) SS BOND : angle 0.79477 ( 8) covalent geometry : bond 0.00241 ( 9237) covalent geometry : angle 0.50634 (12503) *********************** 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 235 residues out of total 993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 211 time to evaluate : 0.909 Fit side-chains REVERT: R 116 ARG cc_start: 0.7535 (mtp180) cc_final: 0.7188 (mtp180) REVERT: R 119 MET cc_start: 0.7419 (mmp) cc_final: 0.7092 (mpp) REVERT: R 174 ILE cc_start: 0.7952 (tp) cc_final: 0.7749 (tp) REVERT: A 29 LYS cc_start: 0.8511 (tmtt) cc_final: 0.8115 (tttt) REVERT: A 197 LYS cc_start: 0.8401 (ttmm) cc_final: 0.8082 (mtpp) REVERT: A 237 ASP cc_start: 0.7500 (t0) cc_final: 0.7182 (t0) REVERT: B 45 MET cc_start: 0.8329 (OUTLIER) cc_final: 0.7874 (mtm) REVERT: B 130 GLU cc_start: 0.7864 (OUTLIER) cc_final: 0.7234 (pm20) REVERT: B 267 ASP cc_start: 0.8101 (m-30) cc_final: 0.7870 (m-30) REVERT: B 271 CYS cc_start: 0.8041 (p) cc_final: 0.7724 (p) REVERT: G 21 MET cc_start: 0.7762 (mtp) cc_final: 0.7561 (ttp) REVERT: S 30 SER cc_start: 0.8395 (m) cc_final: 0.8063 (t) REVERT: S 199 VAL cc_start: 0.8564 (m) cc_final: 0.8359 (p) REVERT: S 215 THR cc_start: 0.8220 (m) cc_final: 0.7750 (p) outliers start: 24 outliers final: 16 residues processed: 216 average time/residue: 1.0388 time to fit residues: 241.0413 Evaluate side-chains 228 residues out of total 993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 210 time to evaluate : 0.989 ------------------------------------------------------------------------------- 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 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 146 LEU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain S residue 21 SER Chi-restraints excluded: chain S residue 158 SER 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 43 optimal weight: 6.9990 chunk 104 optimal weight: 3.9990 chunk 53 optimal weight: 6.9990 chunk 94 optimal weight: 0.9990 chunk 51 optimal weight: 0.9980 chunk 4 optimal weight: 0.3980 chunk 42 optimal weight: 0.0570 chunk 97 optimal weight: 5.9990 chunk 106 optimal weight: 3.9990 chunk 66 optimal weight: 0.7980 chunk 18 optimal weight: 0.7980 overall best weight: 0.6098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 102 GLN B 36 ASN B 156 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 = 0.3847 r_free = 0.3847 target = 0.140739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.120589 restraints weight = 12121.631| |-----------------------------------------------------------------------------| r_work (start): 0.3589 rms_B_bonded: 2.09 r_work: 0.3465 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3307 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7626 moved from start: 0.1705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 9241 Z= 0.111 Angle : 0.496 12.940 12511 Z= 0.256 Chirality : 0.041 0.196 1421 Planarity : 0.003 0.036 1571 Dihedral : 3.871 20.404 1247 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 2.82 % Allowed : 15.61 % Favored : 81.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.21 (0.25), residues: 1142 helix: 2.66 (0.26), residues: 397 sheet: 0.60 (0.29), residues: 295 loop : -0.78 (0.29), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP R 269 HIS 0.002 0.001 HIS R 107 PHE 0.017 0.001 PHE R 92 TYR 0.024 0.001 TYR S 190 ARG 0.004 0.000 ARG B 256 Details of bonding type rmsd hydrogen bonds : bond 0.03584 ( 448) hydrogen bonds : angle 4.02228 ( 1275) SS BOND : bond 0.00520 ( 4) SS BOND : angle 0.76931 ( 8) covalent geometry : bond 0.00250 ( 9237) covalent geometry : angle 0.49599 (12503) *********************** 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 238 residues out of total 993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 210 time to evaluate : 0.928 Fit side-chains REVERT: R 116 ARG cc_start: 0.7532 (mtp180) cc_final: 0.7191 (mtp180) REVERT: R 119 MET cc_start: 0.7402 (mmp) cc_final: 0.7090 (mpp) REVERT: R 275 PHE cc_start: 0.7354 (t80) cc_final: 0.7133 (t80) REVERT: A 29 LYS cc_start: 0.8497 (tmtt) cc_final: 0.8104 (tttt) REVERT: A 237 ASP cc_start: 0.7504 (t0) cc_final: 0.7176 (t0) REVERT: B 45 MET cc_start: 0.8322 (OUTLIER) cc_final: 0.7899 (mtm) REVERT: B 70 LEU cc_start: 0.8066 (tp) cc_final: 0.7816 (tt) REVERT: B 130 GLU cc_start: 0.7852 (OUTLIER) cc_final: 0.7222 (pm20) REVERT: B 201 SER cc_start: 0.8219 (OUTLIER) cc_final: 0.8009 (t) REVERT: B 254 ASP cc_start: 0.8102 (OUTLIER) cc_final: 0.7780 (p0) REVERT: B 267 ASP cc_start: 0.8094 (m-30) cc_final: 0.7862 (m-30) REVERT: B 271 CYS cc_start: 0.8017 (p) cc_final: 0.7698 (p) REVERT: S 30 SER cc_start: 0.8396 (m) cc_final: 0.8063 (t) outliers start: 28 outliers final: 17 residues processed: 217 average time/residue: 1.0926 time to fit residues: 256.5869 Evaluate side-chains 226 residues out of total 993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 205 time to evaluate : 0.912 ------------------------------------------------------------------------------- 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 238 SER 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 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 B residue 254 ASP Chi-restraints excluded: chain B residue 294 CYS 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 108 optimal weight: 2.9990 chunk 62 optimal weight: 0.8980 chunk 0 optimal weight: 2.9990 chunk 14 optimal weight: 0.4980 chunk 67 optimal weight: 2.9990 chunk 65 optimal weight: 0.9990 chunk 6 optimal weight: 0.9980 chunk 47 optimal weight: 0.0770 chunk 91 optimal weight: 4.9990 chunk 35 optimal weight: 3.9990 chunk 38 optimal weight: 3.9990 overall best weight: 0.6940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 36 ASN B 156 GLN S 142 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.140544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.120306 restraints weight = 12201.404| |-----------------------------------------------------------------------------| r_work (start): 0.3587 rms_B_bonded: 2.10 r_work: 0.3464 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3308 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7626 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 0.029 9241 Z= 0.118 Angle : 0.521 13.100 12511 Z= 0.264 Chirality : 0.042 0.203 1421 Planarity : 0.003 0.036 1571 Dihedral : 3.866 20.284 1247 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 2.92 % Allowed : 16.11 % Favored : 80.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.23 (0.25), residues: 1142 helix: 2.69 (0.26), residues: 397 sheet: 0.56 (0.29), residues: 296 loop : -0.75 (0.29), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP R 269 HIS 0.002 0.001 HIS S 35 PHE 0.017 0.001 PHE R 92 TYR 0.024 0.001 TYR S 190 ARG 0.005 0.000 ARG B 52 Details of bonding type rmsd hydrogen bonds : bond 0.03636 ( 448) hydrogen bonds : angle 3.99492 ( 1275) SS BOND : bond 0.00526 ( 4) SS BOND : angle 0.83903 ( 8) covalent geometry : bond 0.00269 ( 9237) covalent geometry : angle 0.52123 (12503) *********************** 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 245 residues out of total 993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 216 time to evaluate : 0.904 Fit side-chains REVERT: R 90 GLU cc_start: 0.8010 (tt0) cc_final: 0.7754 (tt0) REVERT: R 116 ARG cc_start: 0.7516 (mtp180) cc_final: 0.7180 (mtp180) REVERT: R 119 MET cc_start: 0.7396 (mmp) cc_final: 0.7078 (mpp) REVERT: R 163 THR cc_start: 0.7989 (m) cc_final: 0.7775 (m) REVERT: R 174 ILE cc_start: 0.7951 (tp) cc_final: 0.7723 (tp) REVERT: R 275 PHE cc_start: 0.7351 (t80) cc_final: 0.7146 (t80) REVERT: A 29 LYS cc_start: 0.8455 (tmtt) cc_final: 0.8065 (tttt) REVERT: A 237 ASP cc_start: 0.7496 (t0) cc_final: 0.7171 (t0) REVERT: A 240 MET cc_start: 0.7772 (tpp) cc_final: 0.7354 (tpp) REVERT: A 317 LYS cc_start: 0.8338 (ptpp) cc_final: 0.8009 (ptmt) REVERT: B 45 MET cc_start: 0.8324 (OUTLIER) cc_final: 0.7904 (mtm) REVERT: B 70 LEU cc_start: 0.8057 (tp) cc_final: 0.7824 (tt) REVERT: B 130 GLU cc_start: 0.7857 (OUTLIER) cc_final: 0.7239 (pm20) REVERT: B 201 SER cc_start: 0.8253 (OUTLIER) cc_final: 0.8047 (t) REVERT: B 254 ASP cc_start: 0.8092 (OUTLIER) cc_final: 0.7764 (p0) REVERT: B 267 ASP cc_start: 0.8094 (m-30) cc_final: 0.7853 (m-30) REVERT: B 271 CYS cc_start: 0.8027 (p) cc_final: 0.7734 (p) REVERT: S 30 SER cc_start: 0.8403 (m) cc_final: 0.8080 (t) outliers start: 29 outliers final: 18 residues processed: 226 average time/residue: 1.0246 time to fit residues: 249.2092 Evaluate side-chains 235 residues out of total 993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 213 time to evaluate : 0.919 ------------------------------------------------------------------------------- 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 238 SER 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 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 B residue 254 ASP Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 294 CYS 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 49 optimal weight: 0.9990 chunk 108 optimal weight: 1.9990 chunk 22 optimal weight: 6.9990 chunk 85 optimal weight: 1.9990 chunk 65 optimal weight: 3.9990 chunk 39 optimal weight: 6.9990 chunk 90 optimal weight: 0.0170 chunk 64 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 76 optimal weight: 2.9990 chunk 61 optimal weight: 0.8980 overall best weight: 1.1824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 36 ASN B 156 GLN B 220 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 = 0.3828 r_free = 0.3828 target = 0.139097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.118660 restraints weight = 12259.419| |-----------------------------------------------------------------------------| r_work (start): 0.3567 rms_B_bonded: 2.11 r_work: 0.3443 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3283 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3283 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7655 moved from start: 0.1755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9241 Z= 0.167 Angle : 0.554 13.827 12511 Z= 0.282 Chirality : 0.043 0.226 1421 Planarity : 0.003 0.037 1571 Dihedral : 3.992 21.504 1247 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 3.02 % Allowed : 16.82 % Favored : 80.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.12 (0.25), residues: 1142 helix: 2.59 (0.26), residues: 396 sheet: 0.48 (0.29), residues: 301 loop : -0.79 (0.28), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP R 269 HIS 0.010 0.001 HIS R 107 PHE 0.021 0.002 PHE R 92 TYR 0.026 0.001 TYR S 190 ARG 0.004 0.000 ARG B 52 Details of bonding type rmsd hydrogen bonds : bond 0.04095 ( 448) hydrogen bonds : angle 4.08923 ( 1275) SS BOND : bond 0.00669 ( 4) SS BOND : angle 0.99093 ( 8) covalent geometry : bond 0.00396 ( 9237) covalent geometry : angle 0.55368 (12503) *********************** 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 245 residues out of total 993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 215 time to evaluate : 1.009 Fit side-chains REVERT: R 90 GLU cc_start: 0.8025 (tt0) cc_final: 0.7780 (tt0) REVERT: R 116 ARG cc_start: 0.7569 (mtp180) cc_final: 0.7231 (mtp180) REVERT: R 119 MET cc_start: 0.7430 (mmp) cc_final: 0.7110 (mpp) REVERT: R 163 THR cc_start: 0.8042 (m) cc_final: 0.7839 (m) REVERT: R 178 MET cc_start: 0.8179 (ttm) cc_final: 0.7680 (ttm) REVERT: A 29 LYS cc_start: 0.8482 (tmtt) cc_final: 0.8084 (tttt) REVERT: A 237 ASP cc_start: 0.7503 (t0) cc_final: 0.7161 (t0) REVERT: A 317 LYS cc_start: 0.8377 (ptpp) cc_final: 0.8038 (ptmt) REVERT: B 45 MET cc_start: 0.8345 (OUTLIER) cc_final: 0.7924 (mtm) REVERT: B 70 LEU cc_start: 0.8075 (tp) cc_final: 0.7846 (tt) REVERT: B 130 GLU cc_start: 0.7858 (OUTLIER) cc_final: 0.7235 (pm20) REVERT: B 267 ASP cc_start: 0.8114 (m-30) cc_final: 0.7871 (m-30) REVERT: B 271 CYS cc_start: 0.8033 (p) cc_final: 0.7741 (p) REVERT: S 30 SER cc_start: 0.8424 (m) cc_final: 0.8099 (t) outliers start: 30 outliers final: 22 residues processed: 224 average time/residue: 1.0696 time to fit residues: 257.7037 Evaluate side-chains 231 residues out of total 993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 207 time to evaluate : 0.934 ------------------------------------------------------------------------------- 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 238 SER 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 316 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 135 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 254 ASP Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 294 CYS 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 90 optimal weight: 0.0050 chunk 40 optimal weight: 0.3980 chunk 43 optimal weight: 6.9990 chunk 3 optimal weight: 0.9980 chunk 8 optimal weight: 3.9990 chunk 79 optimal weight: 0.5980 chunk 26 optimal weight: 0.4980 chunk 103 optimal weight: 6.9990 chunk 10 optimal weight: 0.6980 chunk 91 optimal weight: 0.5980 chunk 23 optimal weight: 0.8980 overall best weight: 0.4194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 36 ASN B 156 GLN B 230 ASN S 142 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.142081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.121572 restraints weight = 12106.106| |-----------------------------------------------------------------------------| r_work (start): 0.3623 rms_B_bonded: 2.12 r_work: 0.3500 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3342 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3342 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7621 moved from start: 0.1867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 9241 Z= 0.100 Angle : 0.524 13.294 12511 Z= 0.263 Chirality : 0.042 0.216 1421 Planarity : 0.003 0.035 1571 Dihedral : 3.825 19.964 1247 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.42 % Allowed : 17.93 % Favored : 79.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.25 (0.25), residues: 1142 helix: 2.72 (0.26), residues: 397 sheet: 0.62 (0.29), residues: 290 loop : -0.76 (0.28), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP R 269 HIS 0.010 0.001 HIS R 107 PHE 0.013 0.001 PHE A 336 TYR 0.020 0.001 TYR S 190 ARG 0.004 0.000 ARG B 52 Details of bonding type rmsd hydrogen bonds : bond 0.03390 ( 448) hydrogen bonds : angle 3.97120 ( 1275) SS BOND : bond 0.00468 ( 4) SS BOND : angle 0.74252 ( 8) covalent geometry : bond 0.00215 ( 9237) covalent geometry : angle 0.52382 (12503) *********************** 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 233 residues out of total 993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 209 time to evaluate : 0.977 Fit side-chains REVERT: L 7 PHE cc_start: 0.8786 (t80) cc_final: 0.8466 (t80) REVERT: R 90 GLU cc_start: 0.8013 (tt0) cc_final: 0.7746 (tt0) REVERT: R 116 ARG cc_start: 0.7508 (mtp180) cc_final: 0.7173 (mtp180) REVERT: R 119 MET cc_start: 0.7366 (mmp) cc_final: 0.7036 (mpp) REVERT: R 174 ILE cc_start: 0.7927 (tp) cc_final: 0.7694 (tp) REVERT: A 29 LYS cc_start: 0.8466 (tmtt) cc_final: 0.8072 (tttt) REVERT: A 237 ASP cc_start: 0.7455 (t0) cc_final: 0.7131 (t0) REVERT: A 240 MET cc_start: 0.7814 (tpp) cc_final: 0.7411 (tpp) REVERT: A 317 LYS cc_start: 0.8309 (ptpp) cc_final: 0.8028 (ptmt) REVERT: B 45 MET cc_start: 0.8309 (OUTLIER) cc_final: 0.7893 (mtm) REVERT: B 70 LEU cc_start: 0.8051 (tp) cc_final: 0.7795 (tt) REVERT: B 130 GLU cc_start: 0.7866 (OUTLIER) cc_final: 0.7215 (pm20) REVERT: B 135 VAL cc_start: 0.8594 (t) cc_final: 0.8199 (p) REVERT: B 146 LEU cc_start: 0.8497 (OUTLIER) cc_final: 0.8190 (tp) REVERT: B 254 ASP cc_start: 0.8065 (OUTLIER) cc_final: 0.7767 (p0) REVERT: B 267 ASP cc_start: 0.8096 (m-30) cc_final: 0.7853 (m-30) REVERT: B 271 CYS cc_start: 0.8027 (p) cc_final: 0.7734 (p) REVERT: S 30 SER cc_start: 0.8393 (m) cc_final: 0.8067 (t) outliers start: 24 outliers final: 17 residues processed: 215 average time/residue: 1.1006 time to fit residues: 254.1718 Evaluate side-chains 229 residues out of total 993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 208 time to evaluate : 1.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 74 MET Chi-restraints excluded: chain R residue 92 PHE Chi-restraints excluded: chain R residue 101 MET Chi-restraints excluded: chain R residue 128 THR Chi-restraints excluded: chain R residue 238 SER 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 130 GLU Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 254 ASP Chi-restraints excluded: chain B residue 275 SER 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 29 optimal weight: 3.9990 chunk 77 optimal weight: 0.7980 chunk 49 optimal weight: 1.9990 chunk 109 optimal weight: 1.9990 chunk 91 optimal weight: 4.9990 chunk 74 optimal weight: 0.0060 chunk 46 optimal weight: 1.9990 chunk 44 optimal weight: 0.9980 chunk 47 optimal weight: 0.9990 chunk 45 optimal weight: 5.9990 chunk 89 optimal weight: 4.9990 overall best weight: 0.9600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 36 ASN B 132 ASN B 156 GLN B 220 GLN S 142 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.140400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.119708 restraints weight = 12181.851| |-----------------------------------------------------------------------------| r_work (start): 0.3575 rms_B_bonded: 2.13 r_work: 0.3451 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3292 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7646 moved from start: 0.1829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9241 Z= 0.146 Angle : 0.546 13.732 12511 Z= 0.278 Chirality : 0.043 0.224 1421 Planarity : 0.003 0.037 1571 Dihedral : 3.925 20.847 1247 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 2.62 % Allowed : 17.93 % Favored : 79.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.15 (0.25), residues: 1142 helix: 2.63 (0.26), residues: 396 sheet: 0.55 (0.29), residues: 292 loop : -0.80 (0.28), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP R 269 HIS 0.010 0.001 HIS R 107 PHE 0.019 0.001 PHE R 92 TYR 0.025 0.001 TYR S 190 ARG 0.004 0.000 ARG B 52 Details of bonding type rmsd hydrogen bonds : bond 0.03865 ( 448) hydrogen bonds : angle 4.03877 ( 1275) SS BOND : bond 0.00617 ( 4) SS BOND : angle 0.93441 ( 8) covalent geometry : bond 0.00343 ( 9237) covalent geometry : angle 0.54575 (12503) ********************** 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 237 residues out of total 993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 211 time to evaluate : 0.926 Fit side-chains REVERT: R 90 GLU cc_start: 0.8051 (tt0) cc_final: 0.7793 (tt0) REVERT: R 116 ARG cc_start: 0.7574 (mtp180) cc_final: 0.7229 (mtp180) REVERT: R 119 MET cc_start: 0.7378 (mmp) cc_final: 0.7062 (mpp) REVERT: R 178 MET cc_start: 0.8162 (ttm) cc_final: 0.7628 (ttm) REVERT: R 275 PHE cc_start: 0.7407 (t80) cc_final: 0.7201 (t80) REVERT: A 29 LYS cc_start: 0.8491 (tmtt) cc_final: 0.8092 (tttt) REVERT: A 237 ASP cc_start: 0.7450 (t0) cc_final: 0.7124 (t0) REVERT: A 240 MET cc_start: 0.7750 (tpp) cc_final: 0.7377 (tpp) REVERT: A 317 LYS cc_start: 0.8359 (ptpp) cc_final: 0.7840 (ptpt) REVERT: B 45 MET cc_start: 0.8347 (OUTLIER) cc_final: 0.7923 (mtm) REVERT: B 70 LEU cc_start: 0.8066 (tp) cc_final: 0.7829 (tt) REVERT: B 130 GLU cc_start: 0.7861 (OUTLIER) cc_final: 0.7244 (pm20) REVERT: B 135 VAL cc_start: 0.8626 (t) cc_final: 0.8270 (p) REVERT: B 254 ASP cc_start: 0.8107 (OUTLIER) cc_final: 0.7781 (p0) REVERT: B 267 ASP cc_start: 0.8102 (m-30) cc_final: 0.7856 (m-30) REVERT: B 271 CYS cc_start: 0.8044 (p) cc_final: 0.7774 (p) REVERT: S 30 SER cc_start: 0.8424 (m) cc_final: 0.8097 (t) outliers start: 26 outliers final: 18 residues processed: 218 average time/residue: 1.1290 time to fit residues: 265.2571 Evaluate side-chains 231 residues out of total 993 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 210 time to evaluate : 1.243 ------------------------------------------------------------------------------- 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 136 MET Chi-restraints excluded: chain R residue 238 SER 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 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 B residue 254 ASP Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain S residue 21 SER Chi-restraints excluded: chain S residue 158 SER Chi-restraints excluded: chain S residue 199 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 8 optimal weight: 0.8980 chunk 45 optimal weight: 0.9990 chunk 36 optimal weight: 2.9990 chunk 86 optimal weight: 0.8980 chunk 17 optimal weight: 0.7980 chunk 49 optimal weight: 0.8980 chunk 7 optimal weight: 0.4980 chunk 72 optimal weight: 0.0970 chunk 91 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 chunk 12 optimal weight: 2.9990 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3853 r_free = 0.3853 target = 0.141282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.120723 restraints weight = 12073.294| |-----------------------------------------------------------------------------| r_work (start): 0.3592 rms_B_bonded: 2.11 r_work: 0.3470 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3311 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7627 moved from start: 0.1875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9241 Z= 0.116 Angle : 0.544 13.548 12511 Z= 0.272 Chirality : 0.042 0.213 1421 Planarity : 0.003 0.035 1571 Dihedral : 3.879 20.220 1247 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 2.52 % Allowed : 18.23 % Favored : 79.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.19 (0.25), residues: 1142 helix: 2.66 (0.26), residues: 397 sheet: 0.56 (0.29), residues: 291 loop : -0.76 (0.28), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP R 269 HIS 0.010 0.001 HIS R 107 PHE 0.014 0.001 PHE R 92 TYR 0.022 0.001 TYR S 190 ARG 0.004 0.000 ARG B 52 Details of bonding type rmsd hydrogen bonds : bond 0.03579 ( 448) hydrogen bonds : angle 4.00560 ( 1275) SS BOND : bond 0.00563 ( 4) SS BOND : angle 0.90309 ( 8) covalent geometry : bond 0.00263 ( 9237) covalent geometry : angle 0.54399 (12503) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7970.00 seconds wall clock time: 137 minutes 21.81 seconds (8241.81 seconds total)