Starting phenix.real_space_refine on Tue Mar 3 21:11:23 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7jvr_22511/03_2026/7jvr_22511.cif Found real_map, /net/cci-nas-00/data/ceres_data/7jvr_22511/03_2026/7jvr_22511.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 { model { file = "/net/cci-nas-00/data/ceres_data/7jvr_22511/03_2026/7jvr_22511.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7jvr_22511/03_2026/7jvr_22511.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7jvr_22511/03_2026/7jvr_22511.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7jvr_22511/03_2026/7jvr_22511.map" } 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= 0.029 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Br 1 7.06 5 S 64 5.16 5 C 5648 2.51 5 N 1496 2.21 5 O 1663 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8872 Number of models: 1 Model: "" Number of chains: 6 Chain: "R" Number of atoms: 2164 Number of conformers: 1 Conformer: "" Number of residues, atoms: 269, 2164 Classifications: {'peptide': 269} Link IDs: {'PTRANS': 9, 'TRANS': 259} Chain breaks: 1 Chain: "A" Number of atoms: 1807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1807 Classifications: {'peptide': 224} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 221} Chain breaks: 1 Chain: "B" Number of atoms: 2622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 342, 2622 Classifications: {'peptide': 342} Link IDs: {'PTRANS': 5, 'TRANS': 336} Chain: "C" Number of atoms: 445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 445 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 4, 'TRANS': 53} Chain: "E" Number of atoms: 1791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1791 Classifications: {'peptide': 233} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 222} Chain breaks: 1 Chain: "R" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'08Y': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.00, per 1000 atoms: 0.23 Number of scatterers: 8872 At special positions: 0 Unit cell: (103.455, 123.31, 118.085, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Br 1 34.99 S 64 16.00 O 1663 8.00 N 1496 7.00 C 5648 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS R 107 " - pdb=" SG CYS R 182 " distance=2.03 Simple disulfide: pdb=" SG CYS R 399 " - pdb=" SG CYS R 401 " distance=2.03 Simple disulfide: pdb=" SG CYS B 121 " - pdb=" SG CYS B 149 " distance=2.04 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.03 Simple disulfide: pdb=" SG CYS E 159 " - pdb=" SG CYS E 229 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.67 Conformation dependent library (CDL) restraints added in 321.5 milliseconds 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2120 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 13 sheets defined 38.6% alpha, 22.7% 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 34 through 62 removed outlier: 3.718A pdb=" N LEU R 40 " --> pdb=" O TYR R 36 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU R 41 " --> pdb=" O TYR R 37 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU R 44 " --> pdb=" O LEU R 40 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ILE R 45 " --> pdb=" O LEU R 41 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ALA R 46 " --> pdb=" O THR R 42 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU R 54 " --> pdb=" O PHE R 50 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N SER R 60 " --> pdb=" O CYS R 56 " (cutoff:3.500A) Processing helix chain 'R' and resid 67 through 87 removed outlier: 3.521A pdb=" N TYR R 71 " --> pdb=" O THR R 67 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N LEU R 72 " --> pdb=" O THR R 68 " (cutoff:3.500A) Processing helix chain 'R' and resid 87 through 98 Processing helix chain 'R' and resid 103 through 138 Processing helix chain 'R' and resid 138 through 144 removed outlier: 3.914A pdb=" N TYR R 142 " --> pdb=" O MET R 138 " (cutoff:3.500A) Processing helix chain 'R' and resid 144 through 173 Proline residue: R 169 - end of helix removed outlier: 3.705A pdb=" N PHE R 172 " --> pdb=" O CYS R 168 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLY R 173 " --> pdb=" O PRO R 169 " (cutoff:3.500A) Processing helix chain 'R' and resid 186 through 198 removed outlier: 3.747A pdb=" N VAL R 190 " --> pdb=" O ASN R 186 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N TYR R 192 " --> pdb=" O ALA R 188 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N VAL R 196 " --> pdb=" O TYR R 192 " (cutoff:3.500A) Processing helix chain 'R' and resid 198 through 225 Processing helix chain 'R' and resid 366 through 386 Processing helix chain 'R' and resid 386 through 400 removed outlier: 3.985A pdb=" N PHE R 390 " --> pdb=" O TRP R 386 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N HIS R 393 " --> pdb=" O PHE R 389 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ILE R 394 " --> pdb=" O PHE R 390 " (cutoff:3.500A) Processing helix chain 'R' and resid 404 through 427 removed outlier: 4.268A pdb=" N TYR R 408 " --> pdb=" O PRO R 404 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ASN R 418 " --> pdb=" O LEU R 414 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N SER R 419 " --> pdb=" O GLY R 415 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ALA R 420 " --> pdb=" O TYR R 416 " (cutoff:3.500A) Proline residue: R 423 - end of helix Processing helix chain 'R' and resid 430 through 441 removed outlier: 3.577A pdb=" N ARG R 434 " --> pdb=" O ASN R 430 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N LYS R 435 " --> pdb=" O ILE R 431 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N ALA R 436 " --> pdb=" O GLU R 432 " (cutoff:3.500A) Processing helix chain 'A' and resid 6 through 33 Processing helix chain 'A' and resid 45 through 55 removed outlier: 3.623A pdb=" N ILE A 49 " --> pdb=" O GLY A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 217 removed outlier: 3.677A pdb=" N LYS A 210 " --> pdb=" O GLU A 207 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N ILE A 212 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 5.830A pdb=" N HIS A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N CYS A 214 " --> pdb=" O TRP A 211 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLU A 216 " --> pdb=" O HIS A 213 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N GLY A 217 " --> pdb=" O CYS A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 230 removed outlier: 3.569A pdb=" N ASP A 229 " --> pdb=" O ALA A 226 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N TYR A 230 " --> pdb=" O LEU A 227 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 226 through 230' Processing helix chain 'A' and resid 241 through 255 Processing helix chain 'A' and resid 270 through 281 removed outlier: 3.785A pdb=" N GLU A 276 " --> pdb=" O ASP A 272 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N LYS A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LYS A 280 " --> pdb=" O GLU A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 286 removed outlier: 3.938A pdb=" N ILE A 285 " --> pdb=" O PRO A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 311 removed outlier: 3.840A pdb=" N ALA A 301 " --> pdb=" O GLU A 297 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ASN A 311 " --> pdb=" O PHE A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 352 removed outlier: 3.866A pdb=" N ASN A 331 " --> pdb=" O THR A 327 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL A 332 " --> pdb=" O ASP A 328 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 25 removed outlier: 3.749A pdb=" N ALA B 21 " --> pdb=" O GLN B 17 " (cutoff:3.500A) Processing helix chain 'C' and resid 7 through 24 Processing helix chain 'C' and resid 29 through 44 Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 190 removed outlier: 7.294A pdb=" N LYS A 35 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 7.932A pdb=" N ILE A 222 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 5.950A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.368A pdb=" N CYS A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N LEU A 39 " --> pdb=" O CYS A 224 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 45 through 52 removed outlier: 5.345A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N PHE B 335 " --> pdb=" O SER B 331 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N SER B 331 " --> pdb=" O PHE B 335 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N ALA B 328 " --> pdb=" O LEU B 318 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N LEU B 318 " --> pdb=" O ALA B 328 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N GLY B 330 " --> pdb=" O SER B 316 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.715A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 3.507A pdb=" N GLY B 115 " --> pdb=" O THR B 102 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 5.438A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.630A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.915A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 191 through 192 removed outlier: 3.590A pdb=" N VAL B 200 " --> pdb=" O SER B 191 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LYS B 209 " --> pdb=" O SER B 201 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 233 through 234 removed outlier: 3.693A pdb=" N ARG B 251 " --> pdb=" O THR B 243 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 5.729A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.615A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.677A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'E' and resid 58 through 60 removed outlier: 6.663A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N TYR E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N MET E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N PHE E 110 " --> pdb=" O ARG E 98 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 58 through 60 removed outlier: 6.663A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N TYR E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N MET E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 140 through 141 removed outlier: 3.608A pdb=" N VAL E 155 " --> pdb=" O ILE E 216 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 146 through 148 removed outlier: 3.769A pdb=" N GLU E 246 " --> pdb=" O VAL E 147 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ILE E 189 " --> pdb=" O TRP E 176 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N LEU E 178 " --> pdb=" O LEU E 187 " (cutoff:3.500A) removed outlier: 5.687A pdb=" N LEU E 187 " --> pdb=" O LEU E 178 " (cutoff:3.500A) 452 hydrogen bonds defined for protein. 1290 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: 1.37 Time building geometry restraints manager: 0.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.32: 1441 1.32 - 1.45: 2608 1.45 - 1.59: 4912 1.59 - 1.73: 0 1.73 - 1.87: 94 Bond restraints: 9055 Sorted by residual: bond pdb=" C15 08Y R 500 " pdb=" N3 08Y R 500 " ideal model delta sigma weight residual 1.359 1.493 -0.134 2.00e-02 2.50e+03 4.48e+01 bond pdb=" C25 08Y R 500 " pdb=" C26 08Y R 500 " ideal model delta sigma weight residual 1.420 1.318 0.102 2.00e-02 2.50e+03 2.60e+01 bond pdb=" C26 08Y R 500 " pdb=" C28 08Y R 500 " ideal model delta sigma weight residual 1.407 1.325 0.082 2.00e-02 2.50e+03 1.67e+01 bond pdb=" C6 08Y R 500 " pdb=" C7 08Y R 500 " ideal model delta sigma weight residual 1.533 1.472 0.061 2.00e-02 2.50e+03 9.17e+00 bond pdb=" C LEU R 387 " pdb=" N PRO R 388 " ideal model delta sigma weight residual 1.335 1.368 -0.033 1.38e-02 5.25e+03 5.84e+00 ... (remaining 9050 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.07: 11889 2.07 - 4.13: 336 4.13 - 6.20: 34 6.20 - 8.26: 18 8.26 - 10.33: 6 Bond angle restraints: 12283 Sorted by residual: angle pdb=" C ARG E 191 " pdb=" N MET E 192 " pdb=" CA MET E 192 " ideal model delta sigma weight residual 121.54 130.95 -9.41 1.91e+00 2.74e-01 2.43e+01 angle pdb=" C ASP B 118 " pdb=" N ASN B 119 " pdb=" CA ASN B 119 " ideal model delta sigma weight residual 123.47 130.29 -6.82 1.53e+00 4.27e-01 1.99e+01 angle pdb=" CA ASN B 119 " pdb=" CB ASN B 119 " pdb=" CG ASN B 119 " ideal model delta sigma weight residual 112.60 117.04 -4.44 1.00e+00 1.00e+00 1.97e+01 angle pdb=" C ASP A 237 " pdb=" N GLU A 238 " pdb=" CA GLU A 238 " ideal model delta sigma weight residual 121.54 130.01 -8.47 1.91e+00 2.74e-01 1.97e+01 angle pdb=" C ASP B 195 " pdb=" N THR B 196 " pdb=" CA THR B 196 " ideal model delta sigma weight residual 123.05 128.04 -4.99 1.57e+00 4.06e-01 1.01e+01 ... (remaining 12278 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.08: 5179 14.08 - 28.17: 205 28.17 - 42.25: 52 42.25 - 56.34: 13 56.34 - 70.42: 5 Dihedral angle restraints: 5454 sinusoidal: 2172 harmonic: 3282 Sorted by residual: dihedral pdb=" CB CYS B 121 " pdb=" SG CYS B 121 " pdb=" SG CYS B 149 " pdb=" CB CYS B 149 " ideal model delta sinusoidal sigma weight residual 93.00 161.30 -68.30 1 1.00e+01 1.00e-02 6.05e+01 dihedral pdb=" CA PHE B 234 " pdb=" C PHE B 234 " pdb=" N PHE B 235 " pdb=" CA PHE B 235 " ideal model delta harmonic sigma weight residual 180.00 156.61 23.39 0 5.00e+00 4.00e-02 2.19e+01 dihedral pdb=" CA LEU A 268 " pdb=" C LEU A 268 " pdb=" N ASN A 269 " pdb=" CA ASN A 269 " ideal model delta harmonic sigma weight residual -180.00 -156.96 -23.04 0 5.00e+00 4.00e-02 2.12e+01 ... (remaining 5451 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 1148 0.061 - 0.121: 211 0.121 - 0.182: 36 0.182 - 0.242: 10 0.242 - 0.303: 2 Chirality restraints: 1407 Sorted by residual: chirality pdb=" CB ILE E 70 " pdb=" CA ILE E 70 " pdb=" CG1 ILE E 70 " pdb=" CG2 ILE E 70 " both_signs ideal model delta sigma weight residual False 2.64 2.34 0.30 2.00e-01 2.50e+01 2.29e+00 chirality pdb=" CA ASN B 119 " pdb=" N ASN B 119 " pdb=" C ASN B 119 " pdb=" CB ASN B 119 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.27 2.00e-01 2.50e+01 1.76e+00 chirality pdb=" CB THR B 47 " pdb=" CA THR B 47 " pdb=" OG1 THR B 47 " pdb=" CG2 THR B 47 " both_signs ideal model delta sigma weight residual False 2.55 2.33 0.22 2.00e-01 2.50e+01 1.22e+00 ... (remaining 1404 not shown) Planarity restraints: 1543 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C15 08Y R 500 " -0.018 2.00e-02 2.50e+03 3.06e-02 1.17e+01 pdb=" C16 08Y R 500 " 0.030 2.00e-02 2.50e+03 pdb=" C5 08Y R 500 " 0.037 2.00e-02 2.50e+03 pdb=" N3 08Y R 500 " -0.045 2.00e-02 2.50e+03 pdb=" O5 08Y R 500 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C16 08Y R 500 " 0.027 2.00e-02 2.50e+03 3.02e-02 1.14e+01 pdb=" C17 08Y R 500 " -0.018 2.00e-02 2.50e+03 pdb=" C21 08Y R 500 " 0.031 2.00e-02 2.50e+03 pdb=" C22 08Y R 500 " -0.050 2.00e-02 2.50e+03 pdb=" C24 08Y R 500 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE R 403 " 0.040 5.00e-02 4.00e+02 6.02e-02 5.80e+00 pdb=" N PRO R 404 " -0.104 5.00e-02 4.00e+02 pdb=" CA PRO R 404 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO R 404 " 0.033 5.00e-02 4.00e+02 ... (remaining 1540 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 1137 2.77 - 3.30: 8461 3.30 - 3.83: 14656 3.83 - 4.37: 17086 4.37 - 4.90: 30161 Nonbonded interactions: 71501 Sorted by model distance: nonbonded pdb=" OG SER B 331 " pdb=" OD1 ASP B 333 " model vdw 2.235 3.040 nonbonded pdb=" OG SER A 263 " pdb=" O GLU A 318 " model vdw 2.332 3.040 nonbonded pdb=" OE2 GLU B 260 " pdb=" OG1 THR B 263 " model vdw 2.347 3.040 nonbonded pdb=" OG1 THR R 69 " pdb=" OH TYR R 142 " model vdw 2.356 3.040 nonbonded pdb=" O CYS B 218 " pdb=" NE2 GLN C 18 " model vdw 2.364 3.120 ... (remaining 71496 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: 0.460 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: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 8.440 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 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:6.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7136 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 0.134 9060 Z= 0.236 Angle : 0.854 10.326 12293 Z= 0.472 Chirality : 0.052 0.303 1407 Planarity : 0.006 0.060 1543 Dihedral : 8.952 70.421 3319 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: -0.85 (0.22), residues: 1110 helix: 1.15 (0.22), residues: 384 sheet: -0.83 (0.32), residues: 251 loop : -1.86 (0.23), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG B 68 TYR 0.026 0.002 TYR R 408 PHE 0.024 0.003 PHE B 151 TRP 0.033 0.003 TRP E 111 HIS 0.009 0.002 HIS B 62 Details of bonding type rmsd covalent geometry : bond 0.00464 ( 9055) covalent geometry : angle 0.85349 (12283) SS BOND : bond 0.00418 ( 5) SS BOND : angle 1.19412 ( 10) hydrogen bonds : bond 0.25429 ( 439) hydrogen bonds : angle 7.97003 ( 1290) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 286 time to evaluate : 0.323 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 57 MET cc_start: 0.5462 (mtp) cc_final: 0.5188 (mtp) REVERT: R 158 ILE cc_start: 0.8055 (mt) cc_final: 0.7781 (tt) REVERT: A 189 PHE cc_start: 0.7927 (p90) cc_final: 0.7616 (p90) REVERT: A 201 VAL cc_start: 0.7929 (m) cc_final: 0.7701 (p) REVERT: A 209 LYS cc_start: 0.7902 (ttpm) cc_final: 0.7700 (ttpm) REVERT: A 225 VAL cc_start: 0.8115 (t) cc_final: 0.7883 (m) REVERT: A 259 PHE cc_start: 0.8279 (m-80) cc_final: 0.7907 (m-80) REVERT: A 273 LEU cc_start: 0.8323 (tp) cc_final: 0.8111 (tt) REVERT: A 345 LYS cc_start: 0.7958 (mttm) cc_final: 0.7752 (mptp) REVERT: B 47 THR cc_start: 0.8039 (t) cc_final: 0.6898 (p) REVERT: B 50 THR cc_start: 0.7875 (m) cc_final: 0.7638 (t) REVERT: B 110 ASN cc_start: 0.7360 (m-40) cc_final: 0.7072 (m110) REVERT: B 125 ASN cc_start: 0.8274 (t0) cc_final: 0.8008 (t0) REVERT: B 186 ASP cc_start: 0.7662 (m-30) cc_final: 0.7254 (m-30) REVERT: B 290 ASP cc_start: 0.7651 (p0) cc_final: 0.7447 (p0) REVERT: B 298 ASP cc_start: 0.7505 (t0) cc_final: 0.7227 (t70) REVERT: E 52 SER cc_start: 0.8142 (m) cc_final: 0.7938 (p) REVERT: E 116 THR cc_start: 0.8494 (m) cc_final: 0.8277 (p) REVERT: E 220 GLU cc_start: 0.6946 (mt-10) cc_final: 0.6620 (mt-10) outliers start: 0 outliers final: 0 residues processed: 286 average time/residue: 0.3661 time to fit residues: 114.5951 Evaluate side-chains 244 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 244 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 108 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 0.9990 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 0.0970 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 0.7980 chunk 62 optimal weight: 0.1980 chunk 51 optimal weight: 0.8980 chunk 100 optimal weight: 0.0970 chunk 106 optimal weight: 0.8980 overall best weight: 0.4176 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 52 ASN R 106 HIS R 398 HIS A 188 HIS A 244 HIS A 322 HIS B 237 ASN B 239 ASN B 259 GLN B 340 ASN C 44 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.163290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.141067 restraints weight = 11981.608| |-----------------------------------------------------------------------------| r_work (start): 0.3833 rms_B_bonded: 2.14 r_work: 0.3706 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3546 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3546 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7275 moved from start: 0.2206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9060 Z= 0.151 Angle : 0.604 8.020 12293 Z= 0.318 Chirality : 0.043 0.199 1407 Planarity : 0.004 0.057 1543 Dihedral : 5.473 52.199 1300 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 4.01 % Allowed : 10.89 % Favored : 85.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 0.06 (0.24), residues: 1110 helix: 2.23 (0.24), residues: 391 sheet: -0.69 (0.31), residues: 262 loop : -1.50 (0.25), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 251 TYR 0.016 0.002 TYR B 289 PHE 0.018 0.002 PHE A 334 TRP 0.018 0.002 TRP B 339 HIS 0.003 0.001 HIS B 311 Details of bonding type rmsd covalent geometry : bond 0.00304 ( 9055) covalent geometry : angle 0.60327 (12283) SS BOND : bond 0.01126 ( 5) SS BOND : angle 1.42992 ( 10) hydrogen bonds : bond 0.05318 ( 439) hydrogen bonds : angle 5.22812 ( 1290) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 260 time to evaluate : 0.298 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 57 MET cc_start: 0.5633 (mtp) cc_final: 0.5349 (mtp) REVERT: R 158 ILE cc_start: 0.7955 (mt) cc_final: 0.7725 (tt) REVERT: A 209 LYS cc_start: 0.7942 (ttpm) cc_final: 0.7739 (ttpm) REVERT: A 272 ASP cc_start: 0.7884 (t0) cc_final: 0.7593 (t0) REVERT: A 308 GLU cc_start: 0.7385 (OUTLIER) cc_final: 0.7183 (mp0) REVERT: A 323 PHE cc_start: 0.7948 (m-10) cc_final: 0.7531 (m-10) REVERT: B 49 ARG cc_start: 0.8119 (mmt-90) cc_final: 0.7849 (mmt-90) REVERT: B 96 ARG cc_start: 0.7474 (mtt-85) cc_final: 0.7238 (mtt180) REVERT: B 137 ARG cc_start: 0.6883 (OUTLIER) cc_final: 0.6326 (ttp-110) REVERT: B 161 SER cc_start: 0.7317 (m) cc_final: 0.6965 (t) REVERT: B 290 ASP cc_start: 0.7653 (p0) cc_final: 0.7450 (p0) REVERT: B 291 ASP cc_start: 0.8084 (p0) cc_final: 0.7783 (p0) REVERT: B 314 ARG cc_start: 0.7656 (OUTLIER) cc_final: 0.7265 (ptt180) REVERT: E 116 THR cc_start: 0.8554 (m) cc_final: 0.8330 (p) REVERT: E 141 THR cc_start: 0.8226 (t) cc_final: 0.8018 (p) REVERT: E 189 ILE cc_start: 0.8263 (OUTLIER) cc_final: 0.8037 (mt) outliers start: 39 outliers final: 11 residues processed: 275 average time/residue: 0.3856 time to fit residues: 115.4100 Evaluate side-chains 250 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 235 time to evaluate : 0.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 78 VAL Chi-restraints excluded: chain R residue 83 VAL Chi-restraints excluded: chain R residue 130 ILE Chi-restraints excluded: chain R residue 424 ILE Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 137 ARG Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 314 ARG Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 189 ILE Chi-restraints excluded: chain E residue 204 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 42 optimal weight: 4.9990 chunk 90 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 47 optimal weight: 0.7980 chunk 18 optimal weight: 1.9990 chunk 40 optimal weight: 0.4980 chunk 43 optimal weight: 0.9980 chunk 10 optimal weight: 0.5980 chunk 32 optimal weight: 0.9990 chunk 102 optimal weight: 0.0050 chunk 106 optimal weight: 0.9980 overall best weight: 0.5794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 175 ASN ** R 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 62 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.157050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.135326 restraints weight = 11875.501| |-----------------------------------------------------------------------------| r_work (start): 0.3798 rms_B_bonded: 2.07 r_work: 0.3677 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3522 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3522 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7321 moved from start: 0.2906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9060 Z= 0.144 Angle : 0.595 9.193 12293 Z= 0.307 Chirality : 0.043 0.182 1407 Planarity : 0.004 0.058 1543 Dihedral : 5.349 48.150 1300 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 4.21 % Allowed : 15.21 % Favored : 80.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 0.29 (0.24), residues: 1110 helix: 2.34 (0.25), residues: 388 sheet: -0.60 (0.30), residues: 270 loop : -1.21 (0.26), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 49 TYR 0.016 0.002 TYR A 296 PHE 0.020 0.002 PHE R 110 TRP 0.016 0.002 TRP B 82 HIS 0.003 0.001 HIS B 54 Details of bonding type rmsd covalent geometry : bond 0.00322 ( 9055) covalent geometry : angle 0.59488 (12283) SS BOND : bond 0.00339 ( 5) SS BOND : angle 1.01598 ( 10) hydrogen bonds : bond 0.04569 ( 439) hydrogen bonds : angle 4.96690 ( 1290) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 247 time to evaluate : 0.312 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 57 MET cc_start: 0.5347 (mtp) cc_final: 0.5106 (mtp) REVERT: R 116 MET cc_start: 0.7419 (tmm) cc_final: 0.7215 (ttp) REVERT: R 155 MET cc_start: 0.7275 (OUTLIER) cc_final: 0.6502 (mpp) REVERT: R 158 ILE cc_start: 0.7985 (mt) cc_final: 0.7732 (tt) REVERT: A 10 LYS cc_start: 0.8361 (ttmm) cc_final: 0.8115 (mtpp) REVERT: A 272 ASP cc_start: 0.7845 (t0) cc_final: 0.7567 (t0) REVERT: A 308 GLU cc_start: 0.7501 (OUTLIER) cc_final: 0.7268 (mp0) REVERT: A 323 PHE cc_start: 0.7872 (m-10) cc_final: 0.7567 (m-10) REVERT: B 49 ARG cc_start: 0.8155 (mmt-90) cc_final: 0.7937 (tpp-160) REVERT: B 96 ARG cc_start: 0.7644 (mtt-85) cc_final: 0.7417 (mtt180) REVERT: B 217 MET cc_start: 0.7590 (OUTLIER) cc_final: 0.7229 (pmt) REVERT: B 314 ARG cc_start: 0.7699 (OUTLIER) cc_final: 0.7335 (ptt180) REVERT: E 67 ARG cc_start: 0.7810 (ttp80) cc_final: 0.7579 (ttp-170) outliers start: 41 outliers final: 17 residues processed: 264 average time/residue: 0.4005 time to fit residues: 115.0951 Evaluate side-chains 249 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 228 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 78 VAL Chi-restraints excluded: chain R residue 125 LEU Chi-restraints excluded: chain R residue 155 MET Chi-restraints excluded: chain R residue 162 LEU Chi-restraints excluded: chain R residue 379 LEU Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 149 CYS Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 314 ARG Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 38 MET Chi-restraints excluded: chain E residue 166 LEU Chi-restraints excluded: chain E residue 204 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 90 optimal weight: 0.0980 chunk 14 optimal weight: 9.9990 chunk 48 optimal weight: 0.9990 chunk 37 optimal weight: 0.8980 chunk 62 optimal weight: 0.4980 chunk 15 optimal weight: 2.9990 chunk 71 optimal weight: 0.5980 chunk 36 optimal weight: 0.9980 chunk 97 optimal weight: 0.8980 chunk 22 optimal weight: 0.3980 chunk 40 optimal weight: 0.8980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 88 ASN B 125 ASN B 239 ASN E 186 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.159082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.136226 restraints weight = 11785.349| |-----------------------------------------------------------------------------| r_work (start): 0.3802 rms_B_bonded: 2.14 r_work: 0.3676 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3513 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3513 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7350 moved from start: 0.3313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9060 Z= 0.134 Angle : 0.592 8.691 12293 Z= 0.302 Chirality : 0.043 0.257 1407 Planarity : 0.004 0.048 1543 Dihedral : 5.148 42.887 1300 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 4.42 % Allowed : 16.75 % Favored : 78.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.43 (0.24), residues: 1110 helix: 2.38 (0.25), residues: 388 sheet: -0.47 (0.30), residues: 270 loop : -1.10 (0.26), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 283 TYR 0.018 0.002 TYR E 190 PHE 0.023 0.002 PHE R 110 TRP 0.018 0.002 TRP B 82 HIS 0.003 0.001 HIS A 195 Details of bonding type rmsd covalent geometry : bond 0.00298 ( 9055) covalent geometry : angle 0.59100 (12283) SS BOND : bond 0.01323 ( 5) SS BOND : angle 1.18454 ( 10) hydrogen bonds : bond 0.04026 ( 439) hydrogen bonds : angle 4.74587 ( 1290) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 247 time to evaluate : 0.211 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 48 ILE cc_start: 0.7786 (mt) cc_final: 0.7562 (mp) REVERT: R 57 MET cc_start: 0.5338 (mtp) cc_final: 0.5097 (mtp) REVERT: R 81 LEU cc_start: 0.7597 (OUTLIER) cc_final: 0.7326 (mm) REVERT: R 116 MET cc_start: 0.7501 (tmm) cc_final: 0.7299 (ttp) REVERT: R 155 MET cc_start: 0.7276 (OUTLIER) cc_final: 0.6499 (mpp) REVERT: R 158 ILE cc_start: 0.7931 (mt) cc_final: 0.7690 (tt) REVERT: R 372 THR cc_start: 0.7314 (m) cc_final: 0.7076 (m) REVERT: A 272 ASP cc_start: 0.7844 (t0) cc_final: 0.7424 (t0) REVERT: A 316 THR cc_start: 0.8142 (p) cc_final: 0.7897 (p) REVERT: A 323 PHE cc_start: 0.7840 (m-10) cc_final: 0.7483 (m-10) REVERT: B 48 ARG cc_start: 0.8523 (mmt90) cc_final: 0.8172 (mpt-90) REVERT: B 49 ARG cc_start: 0.8175 (mmt-90) cc_final: 0.7966 (tpp-160) REVERT: B 95 LEU cc_start: 0.7366 (mt) cc_final: 0.7001 (mt) REVERT: B 96 ARG cc_start: 0.7677 (mtt-85) cc_final: 0.7403 (mtt180) REVERT: B 124 TYR cc_start: 0.8602 (m-80) cc_final: 0.8374 (m-80) REVERT: B 170 ASP cc_start: 0.8192 (OUTLIER) cc_final: 0.7878 (t0) REVERT: B 217 MET cc_start: 0.7663 (OUTLIER) cc_final: 0.7098 (pmt) REVERT: B 277 SER cc_start: 0.8315 (t) cc_final: 0.7887 (m) REVERT: B 314 ARG cc_start: 0.7736 (OUTLIER) cc_final: 0.7196 (ptt180) REVERT: E 46 GLU cc_start: 0.7861 (mt-10) cc_final: 0.7602 (mt-10) REVERT: E 192 MET cc_start: 0.7988 (OUTLIER) cc_final: 0.7734 (ptp) REVERT: E 230 MET cc_start: 0.7969 (ttp) cc_final: 0.7757 (ttm) outliers start: 43 outliers final: 17 residues processed: 263 average time/residue: 0.4160 time to fit residues: 118.2140 Evaluate side-chains 247 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 224 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 81 LEU Chi-restraints excluded: chain R residue 125 LEU Chi-restraints excluded: chain R residue 130 ILE Chi-restraints excluded: chain R residue 155 MET Chi-restraints excluded: chain R residue 203 ILE Chi-restraints excluded: chain R residue 379 LEU Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 314 ARG Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain C residue 21 MET Chi-restraints excluded: chain C residue 38 MET Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 166 LEU Chi-restraints excluded: chain E residue 192 MET Chi-restraints excluded: chain E residue 204 SER Chi-restraints excluded: chain E residue 224 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 80 optimal weight: 1.9990 chunk 73 optimal weight: 2.9990 chunk 16 optimal weight: 0.9980 chunk 104 optimal weight: 3.9990 chunk 95 optimal weight: 0.6980 chunk 83 optimal weight: 1.9990 chunk 96 optimal weight: 0.7980 chunk 23 optimal weight: 0.4980 chunk 6 optimal weight: 6.9990 chunk 107 optimal weight: 0.8980 chunk 20 optimal weight: 0.0870 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 88 ASN B 125 ASN B 239 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.157831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.134822 restraints weight = 11675.035| |-----------------------------------------------------------------------------| r_work (start): 0.3779 rms_B_bonded: 2.12 r_work: 0.3658 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3498 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3498 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7365 moved from start: 0.3675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9060 Z= 0.144 Angle : 0.586 8.304 12293 Z= 0.299 Chirality : 0.043 0.286 1407 Planarity : 0.003 0.046 1543 Dihedral : 4.964 40.365 1300 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 4.93 % Allowed : 17.57 % Favored : 77.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 0.48 (0.25), residues: 1110 helix: 2.31 (0.25), residues: 394 sheet: -0.44 (0.30), residues: 271 loop : -1.01 (0.27), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 251 TYR 0.020 0.002 TYR E 50 PHE 0.025 0.002 PHE R 110 TRP 0.012 0.001 TRP B 339 HIS 0.003 0.001 HIS B 54 Details of bonding type rmsd covalent geometry : bond 0.00331 ( 9055) covalent geometry : angle 0.58512 (12283) SS BOND : bond 0.00793 ( 5) SS BOND : angle 1.01615 ( 10) hydrogen bonds : bond 0.03819 ( 439) hydrogen bonds : angle 4.70724 ( 1290) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 236 time to evaluate : 0.315 Fit side-chains revert: symmetry clash REVERT: R 48 ILE cc_start: 0.7808 (mt) cc_final: 0.7579 (mp) REVERT: R 57 MET cc_start: 0.5332 (mtp) cc_final: 0.5127 (mtp) REVERT: R 81 LEU cc_start: 0.7648 (OUTLIER) cc_final: 0.7352 (mm) REVERT: R 155 MET cc_start: 0.7297 (OUTLIER) cc_final: 0.6531 (mpp) REVERT: R 158 ILE cc_start: 0.7947 (mt) cc_final: 0.7679 (tt) REVERT: R 372 THR cc_start: 0.7293 (m) cc_final: 0.7025 (m) REVERT: A 10 LYS cc_start: 0.8337 (ttmm) cc_final: 0.8097 (mtpp) REVERT: A 316 THR cc_start: 0.8226 (p) cc_final: 0.7969 (p) REVERT: A 323 PHE cc_start: 0.7888 (m-10) cc_final: 0.7540 (m-10) REVERT: B 19 ARG cc_start: 0.7624 (ttp80) cc_final: 0.7253 (ttp80) REVERT: B 48 ARG cc_start: 0.8530 (mmt90) cc_final: 0.8192 (mpt-90) REVERT: B 68 ARG cc_start: 0.8512 (ttt-90) cc_final: 0.8291 (ttt180) REVERT: B 96 ARG cc_start: 0.7778 (mtt-85) cc_final: 0.7511 (mtt180) REVERT: B 170 ASP cc_start: 0.8143 (t70) cc_final: 0.7815 (t0) REVERT: B 217 MET cc_start: 0.7595 (OUTLIER) cc_final: 0.7071 (pmt) REVERT: B 249 THR cc_start: 0.8347 (t) cc_final: 0.8091 (m) REVERT: B 277 SER cc_start: 0.8320 (t) cc_final: 0.7871 (m) REVERT: B 314 ARG cc_start: 0.7690 (OUTLIER) cc_final: 0.7285 (ptt180) REVERT: E 46 GLU cc_start: 0.7816 (mt-10) cc_final: 0.7564 (mt-10) REVERT: E 192 MET cc_start: 0.7986 (OUTLIER) cc_final: 0.7766 (ptp) outliers start: 48 outliers final: 21 residues processed: 251 average time/residue: 0.3902 time to fit residues: 106.3426 Evaluate side-chains 258 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 232 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 78 VAL Chi-restraints excluded: chain R residue 81 LEU Chi-restraints excluded: chain R residue 125 LEU Chi-restraints excluded: chain R residue 130 ILE Chi-restraints excluded: chain R residue 155 MET Chi-restraints excluded: chain R residue 162 LEU Chi-restraints excluded: chain R residue 203 ILE Chi-restraints excluded: chain R residue 427 THR Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 314 ARG Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 38 MET Chi-restraints excluded: chain E residue 30 SER Chi-restraints excluded: chain E residue 166 LEU Chi-restraints excluded: chain E residue 192 MET Chi-restraints excluded: chain E residue 204 SER Chi-restraints excluded: chain E residue 224 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 86 optimal weight: 0.1980 chunk 33 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 13 optimal weight: 4.9990 chunk 39 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 101 optimal weight: 6.9990 chunk 21 optimal weight: 0.7980 chunk 26 optimal weight: 0.0030 chunk 41 optimal weight: 0.4980 chunk 29 optimal weight: 2.9990 overall best weight: 0.6992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 331 ASN B 88 ASN B 125 ASN B 239 ASN B 259 GLN B 340 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.155076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.132934 restraints weight = 11620.797| |-----------------------------------------------------------------------------| r_work (start): 0.3769 rms_B_bonded: 2.04 r_work: 0.3647 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3487 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3487 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7382 moved from start: 0.3894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9060 Z= 0.153 Angle : 0.591 8.448 12293 Z= 0.302 Chirality : 0.043 0.305 1407 Planarity : 0.003 0.038 1543 Dihedral : 4.887 39.116 1300 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 5.04 % Allowed : 18.50 % Favored : 76.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 0.52 (0.25), residues: 1110 helix: 2.29 (0.25), residues: 393 sheet: -0.42 (0.31), residues: 272 loop : -0.92 (0.28), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 251 TYR 0.025 0.002 TYR E 50 PHE 0.024 0.002 PHE R 110 TRP 0.014 0.001 TRP B 82 HIS 0.003 0.001 HIS E 232 Details of bonding type rmsd covalent geometry : bond 0.00352 ( 9055) covalent geometry : angle 0.59064 (12283) SS BOND : bond 0.00768 ( 5) SS BOND : angle 0.95756 ( 10) hydrogen bonds : bond 0.03714 ( 439) hydrogen bonds : angle 4.71402 ( 1290) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 239 time to evaluate : 0.325 Fit side-chains revert: symmetry clash REVERT: R 48 ILE cc_start: 0.7872 (mt) cc_final: 0.7647 (mp) REVERT: R 57 MET cc_start: 0.5448 (mtp) cc_final: 0.5230 (mtp) REVERT: R 81 LEU cc_start: 0.7650 (OUTLIER) cc_final: 0.7350 (mm) REVERT: R 155 MET cc_start: 0.7380 (OUTLIER) cc_final: 0.6621 (mpp) REVERT: R 158 ILE cc_start: 0.7972 (mt) cc_final: 0.7689 (tt) REVERT: R 372 THR cc_start: 0.7269 (m) cc_final: 0.7003 (m) REVERT: A 10 LYS cc_start: 0.8357 (ttmm) cc_final: 0.8097 (mtpp) REVERT: A 272 ASP cc_start: 0.7637 (t0) cc_final: 0.7308 (t0) REVERT: A 316 THR cc_start: 0.8268 (p) cc_final: 0.7996 (p) REVERT: A 323 PHE cc_start: 0.7934 (m-10) cc_final: 0.7584 (m-10) REVERT: B 14 LEU cc_start: 0.8568 (mp) cc_final: 0.8328 (mt) REVERT: B 96 ARG cc_start: 0.7694 (mtt-85) cc_final: 0.7440 (mtt180) REVERT: B 170 ASP cc_start: 0.8182 (t70) cc_final: 0.7866 (t0) REVERT: B 172 GLU cc_start: 0.7955 (tt0) cc_final: 0.7592 (mt-10) REVERT: B 217 MET cc_start: 0.7608 (OUTLIER) cc_final: 0.7107 (pmt) REVERT: B 239 ASN cc_start: 0.8016 (m110) cc_final: 0.7395 (m-40) REVERT: B 249 THR cc_start: 0.8334 (t) cc_final: 0.8120 (m) REVERT: B 258 ASP cc_start: 0.7416 (t0) cc_final: 0.6616 (t0) REVERT: B 314 ARG cc_start: 0.7762 (OUTLIER) cc_final: 0.7317 (ptt180) REVERT: E 46 GLU cc_start: 0.7791 (mt-10) cc_final: 0.7564 (mt-10) REVERT: E 91 THR cc_start: 0.7933 (OUTLIER) cc_final: 0.7698 (p) REVERT: E 98 ARG cc_start: 0.8272 (ppt-90) cc_final: 0.8044 (ptt-90) REVERT: E 117 LEU cc_start: 0.8143 (OUTLIER) cc_final: 0.7913 (tt) REVERT: E 192 MET cc_start: 0.7997 (OUTLIER) cc_final: 0.7783 (ptp) REVERT: E 230 MET cc_start: 0.7982 (ttp) cc_final: 0.7731 (ttm) outliers start: 49 outliers final: 28 residues processed: 257 average time/residue: 0.4095 time to fit residues: 113.9370 Evaluate side-chains 260 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 225 time to evaluate : 0.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 45 ILE Chi-restraints excluded: chain R residue 78 VAL Chi-restraints excluded: chain R residue 81 LEU Chi-restraints excluded: chain R residue 125 LEU Chi-restraints excluded: chain R residue 155 MET Chi-restraints excluded: chain R residue 162 LEU Chi-restraints excluded: chain R residue 191 VAL Chi-restraints excluded: chain R residue 203 ILE Chi-restraints excluded: chain R residue 394 ILE Chi-restraints excluded: chain R residue 427 THR Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 314 ARG Chi-restraints excluded: chain C residue 21 MET Chi-restraints excluded: chain C residue 38 MET Chi-restraints excluded: chain E residue 30 SER Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain E residue 166 LEU Chi-restraints excluded: chain E residue 186 GLN Chi-restraints excluded: chain E residue 192 MET Chi-restraints excluded: chain E residue 204 SER Chi-restraints excluded: chain E residue 224 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 40 optimal weight: 0.9980 chunk 20 optimal weight: 0.8980 chunk 99 optimal weight: 0.3980 chunk 42 optimal weight: 0.0980 chunk 46 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 chunk 60 optimal weight: 0.6980 chunk 43 optimal weight: 0.9990 chunk 66 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 85 optimal weight: 1.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.154852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.132811 restraints weight = 11640.581| |-----------------------------------------------------------------------------| r_work (start): 0.3771 rms_B_bonded: 2.03 r_work: 0.3647 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3486 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3486 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7390 moved from start: 0.4036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9060 Z= 0.150 Angle : 0.604 8.716 12293 Z= 0.307 Chirality : 0.043 0.310 1407 Planarity : 0.003 0.038 1543 Dihedral : 4.820 38.390 1300 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 4.83 % Allowed : 19.63 % Favored : 75.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 0.53 (0.25), residues: 1110 helix: 2.29 (0.25), residues: 393 sheet: -0.45 (0.31), residues: 276 loop : -0.87 (0.28), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 251 TYR 0.020 0.002 TYR R 142 PHE 0.024 0.002 PHE R 110 TRP 0.015 0.001 TRP B 82 HIS 0.003 0.001 HIS B 54 Details of bonding type rmsd covalent geometry : bond 0.00346 ( 9055) covalent geometry : angle 0.60323 (12283) SS BOND : bond 0.00677 ( 5) SS BOND : angle 0.93024 ( 10) hydrogen bonds : bond 0.03695 ( 439) hydrogen bonds : angle 4.70902 ( 1290) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 236 time to evaluate : 0.320 Fit side-chains revert: symmetry clash REVERT: R 48 ILE cc_start: 0.7845 (mt) cc_final: 0.7638 (mp) REVERT: R 57 MET cc_start: 0.5516 (mtp) cc_final: 0.5296 (mtp) REVERT: R 155 MET cc_start: 0.7369 (OUTLIER) cc_final: 0.6571 (mpp) REVERT: R 158 ILE cc_start: 0.7966 (mt) cc_final: 0.7677 (tt) REVERT: R 372 THR cc_start: 0.7259 (m) cc_final: 0.6995 (m) REVERT: A 10 LYS cc_start: 0.8332 (ttmm) cc_final: 0.8087 (mtpm) REVERT: A 29 LYS cc_start: 0.8272 (mtpp) cc_final: 0.7973 (ttmm) REVERT: A 308 GLU cc_start: 0.7451 (OUTLIER) cc_final: 0.6411 (mp0) REVERT: A 316 THR cc_start: 0.8258 (p) cc_final: 0.8013 (p) REVERT: A 323 PHE cc_start: 0.7945 (m-10) cc_final: 0.7604 (m-10) REVERT: B 19 ARG cc_start: 0.7583 (ttp80) cc_final: 0.7103 (ttp80) REVERT: B 22 ARG cc_start: 0.7750 (mpt-90) cc_final: 0.7531 (mtt180) REVERT: B 96 ARG cc_start: 0.7705 (mtt-85) cc_final: 0.7446 (mtt180) REVERT: B 170 ASP cc_start: 0.8165 (t70) cc_final: 0.7861 (t0) REVERT: B 172 GLU cc_start: 0.7915 (tt0) cc_final: 0.7592 (mt-10) REVERT: B 197 ARG cc_start: 0.7843 (mtt180) cc_final: 0.7585 (tpp80) REVERT: B 217 MET cc_start: 0.7529 (OUTLIER) cc_final: 0.7033 (pmt) REVERT: B 239 ASN cc_start: 0.7796 (m110) cc_final: 0.7264 (m-40) REVERT: B 249 THR cc_start: 0.8378 (t) cc_final: 0.8177 (m) REVERT: B 258 ASP cc_start: 0.7477 (t0) cc_final: 0.6616 (t0) REVERT: B 312 ASP cc_start: 0.7519 (m-30) cc_final: 0.7302 (m-30) REVERT: B 314 ARG cc_start: 0.7726 (OUTLIER) cc_final: 0.7279 (ptt180) REVERT: E 46 GLU cc_start: 0.7808 (mt-10) cc_final: 0.7589 (mt-10) REVERT: E 91 THR cc_start: 0.7895 (OUTLIER) cc_final: 0.7672 (p) REVERT: E 117 LEU cc_start: 0.8163 (OUTLIER) cc_final: 0.7929 (tt) REVERT: E 155 VAL cc_start: 0.8009 (p) cc_final: 0.7526 (m) outliers start: 47 outliers final: 30 residues processed: 251 average time/residue: 0.3770 time to fit residues: 103.8560 Evaluate side-chains 264 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 228 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 45 ILE Chi-restraints excluded: chain R residue 78 VAL Chi-restraints excluded: chain R residue 81 LEU Chi-restraints excluded: chain R residue 125 LEU Chi-restraints excluded: chain R residue 130 ILE Chi-restraints excluded: chain R residue 155 MET Chi-restraints excluded: chain R residue 162 LEU Chi-restraints excluded: chain R residue 191 VAL Chi-restraints excluded: chain R residue 203 ILE Chi-restraints excluded: chain R residue 394 ILE Chi-restraints excluded: chain R residue 427 THR Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 275 GLU Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 314 ARG Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 21 MET Chi-restraints excluded: chain C residue 38 MET Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain E residue 166 LEU Chi-restraints excluded: chain E residue 186 GLN Chi-restraints excluded: chain E residue 204 SER Chi-restraints excluded: chain E residue 224 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 81 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 chunk 60 optimal weight: 0.7980 chunk 98 optimal weight: 0.7980 chunk 7 optimal weight: 0.9980 chunk 12 optimal weight: 0.3980 chunk 73 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 chunk 108 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 88 ASN B 259 GLN B 340 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.155316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.133754 restraints weight = 11743.208| |-----------------------------------------------------------------------------| r_work (start): 0.3773 rms_B_bonded: 2.01 r_work: 0.3654 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3497 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3497 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7405 moved from start: 0.4221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 9060 Z= 0.167 Angle : 0.630 9.332 12293 Z= 0.321 Chirality : 0.045 0.400 1407 Planarity : 0.004 0.041 1543 Dihedral : 4.807 37.648 1300 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 11.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 4.73 % Allowed : 19.94 % Favored : 75.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 0.57 (0.25), residues: 1110 helix: 2.31 (0.25), residues: 393 sheet: -0.44 (0.30), residues: 279 loop : -0.82 (0.29), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 134 TYR 0.022 0.002 TYR E 50 PHE 0.028 0.002 PHE R 198 TRP 0.014 0.001 TRP B 82 HIS 0.003 0.001 HIS B 54 Details of bonding type rmsd covalent geometry : bond 0.00388 ( 9055) covalent geometry : angle 0.62956 (12283) SS BOND : bond 0.00812 ( 5) SS BOND : angle 0.94279 ( 10) hydrogen bonds : bond 0.03716 ( 439) hydrogen bonds : angle 4.75660 ( 1290) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 228 time to evaluate : 0.230 Fit side-chains REVERT: R 44 LEU cc_start: 0.7975 (tt) cc_final: 0.7681 (tp) REVERT: R 48 ILE cc_start: 0.7887 (mt) cc_final: 0.7645 (mp) REVERT: R 155 MET cc_start: 0.7318 (OUTLIER) cc_final: 0.6524 (mpp) REVERT: R 158 ILE cc_start: 0.7983 (mt) cc_final: 0.7683 (tt) REVERT: R 372 THR cc_start: 0.7221 (m) cc_final: 0.6965 (m) REVERT: R 382 PHE cc_start: 0.7658 (t80) cc_final: 0.7439 (t80) REVERT: A 10 LYS cc_start: 0.8314 (ttmm) cc_final: 0.8059 (mtpm) REVERT: A 308 GLU cc_start: 0.7503 (OUTLIER) cc_final: 0.6505 (mp0) REVERT: A 316 THR cc_start: 0.8268 (p) cc_final: 0.8020 (p) REVERT: A 323 PHE cc_start: 0.7978 (m-10) cc_final: 0.7656 (m-10) REVERT: B 14 LEU cc_start: 0.8561 (mp) cc_final: 0.8330 (mt) REVERT: B 19 ARG cc_start: 0.7628 (ttp80) cc_final: 0.7129 (ttp80) REVERT: B 22 ARG cc_start: 0.7823 (mpt-90) cc_final: 0.7568 (mtt180) REVERT: B 32 GLN cc_start: 0.8143 (mt0) cc_final: 0.7845 (mt0) REVERT: B 170 ASP cc_start: 0.8165 (t70) cc_final: 0.7877 (t0) REVERT: B 171 ILE cc_start: 0.7750 (mm) cc_final: 0.7548 (mm) REVERT: B 172 GLU cc_start: 0.7917 (tt0) cc_final: 0.7595 (mt-10) REVERT: B 197 ARG cc_start: 0.7848 (mtt180) cc_final: 0.7628 (tpp80) REVERT: B 217 MET cc_start: 0.7540 (OUTLIER) cc_final: 0.7065 (pmt) REVERT: B 258 ASP cc_start: 0.7361 (t0) cc_final: 0.6740 (t0) REVERT: B 259 GLN cc_start: 0.8183 (OUTLIER) cc_final: 0.7947 (pt0) REVERT: B 314 ARG cc_start: 0.7782 (OUTLIER) cc_final: 0.7336 (ptt180) REVERT: E 46 GLU cc_start: 0.7763 (mt-10) cc_final: 0.7551 (mt-10) REVERT: E 91 THR cc_start: 0.7889 (OUTLIER) cc_final: 0.7680 (p) REVERT: E 98 ARG cc_start: 0.8313 (ppt-90) cc_final: 0.8104 (ptt-90) REVERT: E 117 LEU cc_start: 0.8170 (OUTLIER) cc_final: 0.7942 (tt) REVERT: E 155 VAL cc_start: 0.8028 (p) cc_final: 0.7555 (m) REVERT: E 192 MET cc_start: 0.8021 (ptp) cc_final: 0.7804 (ptp) REVERT: E 230 MET cc_start: 0.7907 (ttp) cc_final: 0.7652 (ttm) outliers start: 46 outliers final: 32 residues processed: 247 average time/residue: 0.3777 time to fit residues: 102.1362 Evaluate side-chains 266 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 227 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 45 ILE Chi-restraints excluded: chain R residue 78 VAL Chi-restraints excluded: chain R residue 125 LEU Chi-restraints excluded: chain R residue 130 ILE Chi-restraints excluded: chain R residue 155 MET Chi-restraints excluded: chain R residue 162 LEU Chi-restraints excluded: chain R residue 191 VAL Chi-restraints excluded: chain R residue 379 LEU Chi-restraints excluded: chain R residue 394 ILE Chi-restraints excluded: chain R residue 427 THR Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 259 GLN Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain B residue 314 ARG Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 21 MET Chi-restraints excluded: chain C residue 38 MET Chi-restraints excluded: chain E residue 30 SER Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain E residue 166 LEU Chi-restraints excluded: chain E residue 186 GLN Chi-restraints excluded: chain E residue 204 SER Chi-restraints excluded: chain E residue 224 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 59 optimal weight: 0.5980 chunk 99 optimal weight: 1.9990 chunk 11 optimal weight: 6.9990 chunk 10 optimal weight: 0.7980 chunk 49 optimal weight: 0.9980 chunk 0 optimal weight: 20.0000 chunk 62 optimal weight: 0.5980 chunk 13 optimal weight: 6.9990 chunk 100 optimal weight: 10.0000 chunk 96 optimal weight: 0.9980 chunk 3 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 88 ASN B 220 GLN B 239 ASN B 259 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.154943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.133277 restraints weight = 11752.089| |-----------------------------------------------------------------------------| r_work (start): 0.3770 rms_B_bonded: 2.01 r_work: 0.3650 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3491 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3491 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7415 moved from start: 0.4299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 9060 Z= 0.171 Angle : 0.638 10.880 12293 Z= 0.325 Chirality : 0.045 0.420 1407 Planarity : 0.004 0.041 1543 Dihedral : 4.833 37.584 1300 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 11.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 4.42 % Allowed : 21.17 % Favored : 74.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 0.56 (0.25), residues: 1110 helix: 2.32 (0.25), residues: 392 sheet: -0.46 (0.30), residues: 279 loop : -0.83 (0.29), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 67 TYR 0.022 0.002 TYR E 50 PHE 0.028 0.002 PHE R 110 TRP 0.014 0.001 TRP B 82 HIS 0.003 0.001 HIS B 54 Details of bonding type rmsd covalent geometry : bond 0.00399 ( 9055) covalent geometry : angle 0.63785 (12283) SS BOND : bond 0.00759 ( 5) SS BOND : angle 0.93298 ( 10) hydrogen bonds : bond 0.03701 ( 439) hydrogen bonds : angle 4.74637 ( 1290) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 230 time to evaluate : 0.254 Fit side-chains REVERT: R 48 ILE cc_start: 0.7873 (mt) cc_final: 0.7646 (mp) REVERT: R 155 MET cc_start: 0.7304 (OUTLIER) cc_final: 0.6528 (mpp) REVERT: R 158 ILE cc_start: 0.7981 (mt) cc_final: 0.7683 (tt) REVERT: R 372 THR cc_start: 0.7228 (m) cc_final: 0.6988 (m) REVERT: A 10 LYS cc_start: 0.8315 (ttmm) cc_final: 0.8054 (mtpm) REVERT: A 308 GLU cc_start: 0.7424 (OUTLIER) cc_final: 0.6445 (mp0) REVERT: A 316 THR cc_start: 0.8251 (p) cc_final: 0.7995 (p) REVERT: A 323 PHE cc_start: 0.8010 (m-10) cc_final: 0.7674 (m-10) REVERT: B 14 LEU cc_start: 0.8557 (mp) cc_final: 0.8320 (mt) REVERT: B 19 ARG cc_start: 0.7626 (ttp80) cc_final: 0.7265 (ttp80) REVERT: B 22 ARG cc_start: 0.7842 (mpt-90) cc_final: 0.7600 (mtm-85) REVERT: B 32 GLN cc_start: 0.8136 (mt0) cc_final: 0.7839 (mt0) REVERT: B 156 GLN cc_start: 0.8453 (mt0) cc_final: 0.8202 (mt0) REVERT: B 170 ASP cc_start: 0.8157 (t70) cc_final: 0.7872 (t0) REVERT: B 172 GLU cc_start: 0.7920 (tt0) cc_final: 0.7596 (mt-10) REVERT: B 197 ARG cc_start: 0.7839 (mtt180) cc_final: 0.7600 (tpp80) REVERT: B 217 MET cc_start: 0.7541 (OUTLIER) cc_final: 0.7066 (pmt) REVERT: B 258 ASP cc_start: 0.7346 (t0) cc_final: 0.6686 (t0) REVERT: B 259 GLN cc_start: 0.8091 (pt0) cc_final: 0.7781 (pt0) REVERT: B 314 ARG cc_start: 0.7811 (OUTLIER) cc_final: 0.7340 (ptt180) REVERT: E 46 GLU cc_start: 0.7774 (mt-10) cc_final: 0.7569 (mt-10) REVERT: E 98 ARG cc_start: 0.8311 (ppt-90) cc_final: 0.8103 (ptt-90) REVERT: E 117 LEU cc_start: 0.8205 (OUTLIER) cc_final: 0.7971 (tt) REVERT: E 155 VAL cc_start: 0.8048 (p) cc_final: 0.7575 (m) outliers start: 43 outliers final: 31 residues processed: 245 average time/residue: 0.3920 time to fit residues: 105.0807 Evaluate side-chains 263 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 227 time to evaluate : 0.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 45 ILE Chi-restraints excluded: chain R residue 78 VAL Chi-restraints excluded: chain R residue 125 LEU Chi-restraints excluded: chain R residue 130 ILE Chi-restraints excluded: chain R residue 155 MET Chi-restraints excluded: chain R residue 162 LEU Chi-restraints excluded: chain R residue 191 VAL Chi-restraints excluded: chain R residue 394 ILE Chi-restraints excluded: chain R residue 427 THR Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 275 GLU Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain B residue 314 ARG Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain C residue 21 MET Chi-restraints excluded: chain C residue 38 MET Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain E residue 166 LEU Chi-restraints excluded: chain E residue 186 GLN Chi-restraints excluded: chain E residue 204 SER Chi-restraints excluded: chain E residue 224 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 14 optimal weight: 5.9990 chunk 46 optimal weight: 1.9990 chunk 37 optimal weight: 0.9980 chunk 60 optimal weight: 1.9990 chunk 79 optimal weight: 0.6980 chunk 15 optimal weight: 0.8980 chunk 76 optimal weight: 0.5980 chunk 109 optimal weight: 0.0050 chunk 16 optimal weight: 0.9980 chunk 61 optimal weight: 1.9990 chunk 32 optimal weight: 0.7980 overall best weight: 0.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 88 ASN B 176 GLN B 220 GLN B 239 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.155735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.134219 restraints weight = 11753.136| |-----------------------------------------------------------------------------| r_work (start): 0.3784 rms_B_bonded: 2.00 r_work: 0.3665 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3507 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3507 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7402 moved from start: 0.4406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9060 Z= 0.151 Angle : 0.630 9.255 12293 Z= 0.323 Chirality : 0.045 0.423 1407 Planarity : 0.004 0.039 1543 Dihedral : 4.848 37.477 1300 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 11.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 4.11 % Allowed : 21.99 % Favored : 73.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 0.57 (0.25), residues: 1110 helix: 2.36 (0.25), residues: 392 sheet: -0.46 (0.30), residues: 284 loop : -0.86 (0.29), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 67 TYR 0.022 0.002 TYR E 50 PHE 0.034 0.002 PHE R 198 TRP 0.014 0.001 TRP B 82 HIS 0.003 0.001 HIS B 54 Details of bonding type rmsd covalent geometry : bond 0.00351 ( 9055) covalent geometry : angle 0.62952 (12283) SS BOND : bond 0.00697 ( 5) SS BOND : angle 0.97468 ( 10) hydrogen bonds : bond 0.03676 ( 439) hydrogen bonds : angle 4.71103 ( 1290) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 228 time to evaluate : 0.316 Fit side-chains REVERT: R 48 ILE cc_start: 0.7869 (mt) cc_final: 0.7639 (mp) REVERT: R 155 MET cc_start: 0.7326 (OUTLIER) cc_final: 0.6572 (mpp) REVERT: R 158 ILE cc_start: 0.7978 (mt) cc_final: 0.7678 (tt) REVERT: A 10 LYS cc_start: 0.8300 (ttmm) cc_final: 0.8053 (mtpm) REVERT: A 308 GLU cc_start: 0.7410 (OUTLIER) cc_final: 0.6418 (mp0) REVERT: A 316 THR cc_start: 0.8247 (p) cc_final: 0.7992 (p) REVERT: A 323 PHE cc_start: 0.7982 (m-10) cc_final: 0.7658 (m-10) REVERT: B 14 LEU cc_start: 0.8554 (mp) cc_final: 0.8317 (mt) REVERT: B 19 ARG cc_start: 0.7618 (ttp80) cc_final: 0.7281 (ttp80) REVERT: B 22 ARG cc_start: 0.7796 (mpt-90) cc_final: 0.7505 (mtm-85) REVERT: B 96 ARG cc_start: 0.7528 (mtt180) cc_final: 0.7250 (mtt180) REVERT: B 156 GLN cc_start: 0.8438 (mt0) cc_final: 0.8165 (mt0) REVERT: B 170 ASP cc_start: 0.8021 (t70) cc_final: 0.7741 (t0) REVERT: B 172 GLU cc_start: 0.7880 (tt0) cc_final: 0.7566 (mt-10) REVERT: B 197 ARG cc_start: 0.7837 (mtt180) cc_final: 0.7599 (tpp80) REVERT: B 217 MET cc_start: 0.7500 (OUTLIER) cc_final: 0.7016 (pmt) REVERT: B 258 ASP cc_start: 0.7358 (t0) cc_final: 0.6712 (t0) REVERT: B 314 ARG cc_start: 0.7808 (OUTLIER) cc_final: 0.7327 (ptt180) REVERT: E 60 TYR cc_start: 0.8260 (m-80) cc_final: 0.8059 (m-80) REVERT: E 117 LEU cc_start: 0.8156 (OUTLIER) cc_final: 0.7921 (tt) outliers start: 40 outliers final: 29 residues processed: 241 average time/residue: 0.4100 time to fit residues: 107.7678 Evaluate side-chains 260 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 226 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 78 VAL Chi-restraints excluded: chain R residue 125 LEU Chi-restraints excluded: chain R residue 130 ILE Chi-restraints excluded: chain R residue 155 MET Chi-restraints excluded: chain R residue 166 ILE Chi-restraints excluded: chain R residue 191 VAL Chi-restraints excluded: chain R residue 394 ILE Chi-restraints excluded: chain R residue 427 THR Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 275 GLU Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain B residue 314 ARG Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain C residue 21 MET Chi-restraints excluded: chain C residue 38 MET Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain E residue 166 LEU Chi-restraints excluded: chain E residue 204 SER Chi-restraints excluded: chain E residue 224 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 8 optimal weight: 0.9980 chunk 97 optimal weight: 0.9990 chunk 96 optimal weight: 3.9990 chunk 85 optimal weight: 0.6980 chunk 5 optimal weight: 0.0370 chunk 90 optimal weight: 0.7980 chunk 67 optimal weight: 0.9980 chunk 94 optimal weight: 0.4980 chunk 93 optimal weight: 0.6980 chunk 68 optimal weight: 0.9980 chunk 35 optimal weight: 2.9990 overall best weight: 0.5458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 88 ASN B 119 ASN B 176 GLN B 220 GLN B 239 ASN B 259 GLN B 340 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.155514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.132608 restraints weight = 11437.525| |-----------------------------------------------------------------------------| r_work (start): 0.3759 rms_B_bonded: 2.06 r_work: 0.3641 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3480 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3480 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7379 moved from start: 0.4454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9060 Z= 0.147 Angle : 0.632 8.986 12293 Z= 0.323 Chirality : 0.045 0.414 1407 Planarity : 0.004 0.065 1543 Dihedral : 4.850 36.913 1300 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 12.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 4.21 % Allowed : 22.10 % Favored : 73.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 0.57 (0.25), residues: 1110 helix: 2.32 (0.25), residues: 393 sheet: -0.42 (0.30), residues: 284 loop : -0.86 (0.29), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG B 134 TYR 0.021 0.002 TYR E 50 PHE 0.030 0.002 PHE R 198 TRP 0.014 0.001 TRP B 82 HIS 0.003 0.001 HIS B 183 Details of bonding type rmsd covalent geometry : bond 0.00341 ( 9055) covalent geometry : angle 0.63200 (12283) SS BOND : bond 0.00716 ( 5) SS BOND : angle 0.95750 ( 10) hydrogen bonds : bond 0.03658 ( 439) hydrogen bonds : angle 4.66767 ( 1290) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3733.59 seconds wall clock time: 64 minutes 18.35 seconds (3858.35 seconds total)