Starting phenix.real_space_refine on Wed Feb 4 05:31:30 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9kfj_62298/02_2026/9kfj_62298.cif Found real_map, /net/cci-nas-00/data/ceres_data/9kfj_62298/02_2026/9kfj_62298.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9kfj_62298/02_2026/9kfj_62298.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9kfj_62298/02_2026/9kfj_62298.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9kfj_62298/02_2026/9kfj_62298.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9kfj_62298/02_2026/9kfj_62298.map" } resolution = 3.1 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= 0.031 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 64 5.16 5 Cl 1 4.86 5 C 5704 2.51 5 N 1525 2.21 5 O 1654 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8948 Number of models: 1 Model: "" Number of chains: 6 Chain: "C" Number of atoms: 2336 Number of conformers: 1 Conformer: "" Number of residues, atoms: 295, 2336 Classifications: {'peptide': 295} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 10, 'TRANS': 284} Chain breaks: 2 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "G" Number of atoms: 424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 424 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 4, 'TRANS': 50} Chain: "I" Number of atoms: 1789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1789 Classifications: {'peptide': 224} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 221} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "S" Number of atoms: 1771 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1771 Classifications: {'peptide': 230} Link IDs: {'PTRANS': 10, 'TRANS': 219} Chain breaks: 1 Chain: "T" Number of atoms: 2601 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2601 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 332} Chain: "C" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'IYF': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.94, per 1000 atoms: 0.22 Number of scatterers: 8948 At special positions: 0 Unit cell: (86.52, 121.952, 127.72, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Cl 1 17.00 S 64 16.00 O 1654 8.00 N 1525 7.00 C 5704 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS C 155 " - pdb=" SG CYS C 247 " distance=2.04 Simple disulfide: pdb=" SG CYS S 159 " - pdb=" SG CYS S 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: 0.59 Conformation dependent library (CDL) restraints added in 285.6 milliseconds 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2144 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 14 sheets defined 38.4% alpha, 21.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.31 Creating SS restraints... Processing helix chain 'C' and resid 79 through 109 removed outlier: 4.249A pdb=" N LEU C 83 " --> pdb=" O ARG C 79 " (cutoff:3.500A) Processing helix chain 'C' and resid 111 through 114 removed outlier: 3.555A pdb=" N LYS C 114 " --> pdb=" O GLY C 111 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 111 through 114' Processing helix chain 'C' and resid 115 through 134 removed outlier: 3.739A pdb=" N LEU C 119 " --> pdb=" O SER C 115 " (cutoff:3.500A) Processing helix chain 'C' and resid 134 through 144 removed outlier: 4.286A pdb=" N TRP C 138 " --> pdb=" O THR C 134 " (cutoff:3.500A) Processing helix chain 'C' and resid 152 through 186 removed outlier: 4.017A pdb=" N LYS C 156 " --> pdb=" O LYS C 152 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N VAL C 158 " --> pdb=" O MET C 154 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N TYR C 167 " --> pdb=" O SER C 163 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N VAL C 170 " --> pdb=" O MET C 166 " (cutoff:3.500A) Processing helix chain 'C' and resid 214 through 235 Proline residue: C 231 - end of helix Processing helix chain 'C' and resid 269 through 276 removed outlier: 3.557A pdb=" N PHE C 276 " --> pdb=" O VAL C 272 " (cutoff:3.500A) Processing helix chain 'C' and resid 276 through 299 removed outlier: 3.633A pdb=" N ASP C 296 " --> pdb=" O ARG C 292 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N ARG C 297 " --> pdb=" O PHE C 293 " (cutoff:3.500A) Processing helix chain 'C' and resid 317 through 355 removed outlier: 4.041A pdb=" N VAL C 332 " --> pdb=" O VAL C 328 " (cutoff:3.500A) Proline residue: C 341 - end of helix Processing helix chain 'C' and resid 362 through 380 removed outlier: 4.045A pdb=" N PHE C 371 " --> pdb=" O GLN C 367 " (cutoff:3.500A) Proline residue: C 372 - end of helix Processing helix chain 'C' and resid 380 through 391 Proline residue: C 386 - end of helix Processing helix chain 'C' and resid 393 through 404 removed outlier: 3.542A pdb=" N ALA C 399 " --> pdb=" O GLU C 395 " (cutoff:3.500A) Processing helix chain 'G' and resid 9 through 24 Processing helix chain 'G' and resid 29 through 42 Processing helix chain 'G' and resid 43 through 48 removed outlier: 5.703A pdb=" N LYS G 46 " --> pdb=" O ALA G 43 " (cutoff:3.500A) Processing helix chain 'G' and resid 55 through 59 Processing helix chain 'I' and resid 6 through 32 Processing helix chain 'I' and resid 45 through 54 removed outlier: 3.830A pdb=" N LYS I 54 " --> pdb=" O VAL I 50 " (cutoff:3.500A) Processing helix chain 'I' and resid 208 through 217 removed outlier: 4.366A pdb=" N ILE I 213 " --> pdb=" O LYS I 210 " (cutoff:3.500A) removed outlier: 5.961A pdb=" N HIS I 214 " --> pdb=" O LYS I 211 " (cutoff:3.500A) Processing helix chain 'I' and resid 242 through 256 Processing helix chain 'I' and resid 257 through 261 removed outlier: 4.065A pdb=" N THR I 261 " --> pdb=" O LYS I 258 " (cutoff:3.500A) Processing helix chain 'I' and resid 271 through 280 removed outlier: 4.345A pdb=" N THR I 280 " --> pdb=" O GLU I 276 " (cutoff:3.500A) Processing helix chain 'I' and resid 283 through 287 removed outlier: 3.970A pdb=" N ILE I 286 " --> pdb=" O PRO I 283 " (cutoff:3.500A) Processing helix chain 'I' and resid 296 through 310 removed outlier: 5.168A pdb=" N SER I 302 " --> pdb=" O ASP I 298 " (cutoff:3.500A) Processing helix chain 'I' and resid 331 through 353 Processing helix chain 'S' and resid 28 through 32 Processing helix chain 'S' and resid 74 through 76 No H-bonds generated for 'chain 'S' and resid 74 through 76' Processing helix chain 'S' and resid 87 through 91 Processing helix chain 'T' and resid 5 through 26 removed outlier: 3.710A pdb=" N ALA T 26 " --> pdb=" O ARG T 22 " (cutoff:3.500A) Processing helix chain 'T' and resid 29 through 34 removed outlier: 3.762A pdb=" N ILE T 33 " --> pdb=" O THR T 29 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 239 through 240 removed outlier: 4.091A pdb=" N VAL C 239 " --> pdb=" O LEU C 246 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N LEU C 246 " --> pdb=" O VAL C 239 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'I' and resid 186 through 192 removed outlier: 6.605A pdb=" N VAL I 34 " --> pdb=" O LYS I 198 " (cutoff:3.500A) removed outlier: 7.791A pdb=" N PHE I 200 " --> pdb=" O VAL I 34 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N LEU I 36 " --> pdb=" O PHE I 200 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N LYS I 35 " --> pdb=" O ALA I 221 " (cutoff:3.500A) removed outlier: 7.585A pdb=" N ILE I 223 " --> pdb=" O LYS I 35 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N LEU I 37 " --> pdb=" O ILE I 223 " (cutoff:3.500A) removed outlier: 7.497A pdb=" N CYS I 225 " --> pdb=" O LEU I 37 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N LEU I 39 " --> pdb=" O CYS I 225 " (cutoff:3.500A) removed outlier: 8.731A pdb=" N ALA I 227 " --> pdb=" O LEU I 39 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N ILE I 222 " --> pdb=" O ILE I 266 " (cutoff:3.500A) removed outlier: 7.263A pdb=" N PHE I 268 " --> pdb=" O ILE I 222 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N PHE I 224 " --> pdb=" O PHE I 268 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N ASN I 270 " --> pdb=" O PHE I 224 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N VAL I 226 " --> pdb=" O ASN I 270 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N ILE I 265 " --> pdb=" O TYR I 321 " (cutoff:3.500A) removed outlier: 8.260A pdb=" N HIS I 323 " --> pdb=" O ILE I 265 " (cutoff:3.500A) removed outlier: 7.808A pdb=" N LEU I 267 " --> pdb=" O HIS I 323 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'S' and resid 4 through 7 Processing sheet with id=AA4, first strand: chain 'S' and resid 11 through 12 Processing sheet with id=AA5, first strand: chain 'S' and resid 59 through 60 removed outlier: 5.280A pdb=" N TRP S 47 " --> pdb=" O ARG S 38 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N ARG S 38 " --> pdb=" O TRP S 47 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'S' and resid 146 through 148 removed outlier: 5.886A pdb=" N VAL S 147 " --> pdb=" O GLU S 246 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N GLY S 225 " --> pdb=" O LEU S 245 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N TRP S 176 " --> pdb=" O LEU S 188 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'S' and resid 155 through 160 Processing sheet with id=AA8, first strand: chain 'T' and resid 47 through 51 Processing sheet with id=AA9, first strand: chain 'T' and resid 58 through 63 removed outlier: 3.716A pdb=" N LEU T 70 " --> pdb=" O TRP T 82 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N SER T 74 " --> pdb=" O LYS T 78 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N LYS T 78 " --> pdb=" O SER T 74 " (cutoff:3.500A) removed outlier: 5.882A pdb=" N LEU T 79 " --> pdb=" O ALA T 92 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N ALA T 92 " --> pdb=" O LEU T 79 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N ILE T 81 " --> pdb=" O VAL T 90 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'T' and resid 100 through 105 removed outlier: 3.552A pdb=" N GLY T 115 " --> pdb=" O THR T 102 " (cutoff:3.500A) removed outlier: 5.893A pdb=" N CYS T 121 " --> pdb=" O GLU T 138 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N GLU T 138 " --> pdb=" O CYS T 121 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N ILE T 123 " --> pdb=" O SER T 136 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'T' and resid 146 through 151 removed outlier: 6.691A pdb=" N SER T 160 " --> pdb=" O SER T 147 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N CYS T 149 " --> pdb=" O VAL T 158 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N VAL T 158 " --> pdb=" O CYS T 149 " (cutoff:3.500A) removed outlier: 5.082A pdb=" N PHE T 151 " --> pdb=" O GLN T 156 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N GLN T 156 " --> pdb=" O PHE T 151 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N THR T 165 " --> pdb=" O SER T 161 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N ASP T 170 " --> pdb=" O GLN T 176 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N GLN T 176 " --> pdb=" O ASP T 170 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'T' and resid 187 through 192 removed outlier: 6.868A pdb=" N GLY T 202 " --> pdb=" O MET T 188 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N LEU T 190 " --> pdb=" O VAL T 200 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N VAL T 200 " --> pdb=" O LEU T 190 " (cutoff:3.500A) removed outlier: 4.904A pdb=" N LEU T 192 " --> pdb=" O LEU T 198 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N LEU T 198 " --> pdb=" O LEU T 192 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N ALA T 208 " --> pdb=" O THR T 221 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N THR T 221 " --> pdb=" O ALA T 208 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N LEU T 210 " --> pdb=" O ARG T 219 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'T' and resid 229 through 234 removed outlier: 6.617A pdb=" N GLY T 244 " --> pdb=" O ASN T 230 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N ILE T 232 " --> pdb=" O ALA T 242 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N ALA T 242 " --> pdb=" O ILE T 232 " (cutoff:3.500A) removed outlier: 4.931A pdb=" N PHE T 234 " --> pdb=" O ALA T 240 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N ALA T 240 " --> pdb=" O PHE T 234 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N CYS T 250 " --> pdb=" O THR T 263 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N THR T 263 " --> pdb=" O CYS T 250 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N LEU T 252 " --> pdb=" O LEU T 261 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLN T 259 " --> pdb=" O ASP T 254 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'T' and resid 273 through 277 removed outlier: 6.607A pdb=" N GLY T 288 " --> pdb=" O THR T 274 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N VAL T 276 " --> pdb=" O LEU T 286 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N LEU T 286 " --> pdb=" O VAL T 276 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N ASP T 298 " --> pdb=" O ARG T 304 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N ARG T 304 " --> pdb=" O ASP T 298 " (cutoff:3.500A) 419 hydrogen bonds defined for protein. 1167 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: 1.20 Time building geometry restraints manager: 0.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 2253 1.33 - 1.46: 2438 1.46 - 1.58: 4351 1.58 - 1.71: 0 1.71 - 1.84: 94 Bond restraints: 9136 Sorted by residual: bond pdb=" C10 IYF C 701 " pdb=" N11 IYF C 701 " ideal model delta sigma weight residual 1.274 1.481 -0.207 2.00e-02 2.50e+03 1.07e+02 bond pdb=" C27 IYF C 701 " pdb=" N26 IYF C 701 " ideal model delta sigma weight residual 1.374 1.499 -0.125 2.00e-02 2.50e+03 3.88e+01 bond pdb=" C10 IYF C 701 " pdb=" C9 IYF C 701 " ideal model delta sigma weight residual 1.444 1.554 -0.110 2.00e-02 2.50e+03 3.01e+01 bond pdb=" C25 IYF C 701 " pdb=" C9 IYF C 701 " ideal model delta sigma weight residual 1.376 1.270 0.106 2.00e-02 2.50e+03 2.82e+01 bond pdb=" C13 IYF C 701 " pdb=" N12 IYF C 701 " ideal model delta sigma weight residual 1.380 1.482 -0.102 2.00e-02 2.50e+03 2.58e+01 ... (remaining 9131 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.64: 12284 3.64 - 7.28: 69 7.28 - 10.93: 14 10.93 - 14.57: 1 14.57 - 18.21: 2 Bond angle restraints: 12370 Sorted by residual: angle pdb=" C25 IYF C 701 " pdb=" C9 IYF C 701 " pdb=" C8 IYF C 701 " ideal model delta sigma weight residual 106.34 124.55 -18.21 3.00e+00 1.11e-01 3.68e+01 angle pdb=" C13 IYF C 701 " pdb=" N15 IYF C 701 " pdb=" C16 IYF C 701 " ideal model delta sigma weight residual 126.12 108.29 17.83 3.00e+00 1.11e-01 3.53e+01 angle pdb=" N TYR S 235 " pdb=" CA TYR S 235 " pdb=" C TYR S 235 " ideal model delta sigma weight residual 109.81 122.01 -12.20 2.21e+00 2.05e-01 3.05e+01 angle pdb=" N LEU S 188 " pdb=" CA LEU S 188 " pdb=" C LEU S 188 " ideal model delta sigma weight residual 112.93 106.48 6.45 1.33e+00 5.65e-01 2.35e+01 angle pdb=" C TYR S 235 " pdb=" N PRO S 236 " pdb=" CA PRO S 236 " ideal model delta sigma weight residual 119.84 115.11 4.73 1.25e+00 6.40e-01 1.43e+01 ... (remaining 12365 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.27: 4878 17.27 - 34.53: 433 34.53 - 51.80: 80 51.80 - 69.07: 18 69.07 - 86.33: 8 Dihedral angle restraints: 5417 sinusoidal: 2103 harmonic: 3314 Sorted by residual: dihedral pdb=" CA MET C 154 " pdb=" C MET C 154 " pdb=" N CYS C 155 " pdb=" CA CYS C 155 " ideal model delta harmonic sigma weight residual 180.00 156.46 23.54 0 5.00e+00 4.00e-02 2.22e+01 dihedral pdb=" CA LEU C 264 " pdb=" C LEU C 264 " pdb=" N GLY C 265 " pdb=" CA GLY C 265 " ideal model delta harmonic sigma weight residual 180.00 157.31 22.69 0 5.00e+00 4.00e-02 2.06e+01 dihedral pdb=" CA PHE T 234 " pdb=" C PHE T 234 " pdb=" N PHE T 235 " pdb=" CA PHE T 235 " ideal model delta harmonic sigma weight residual 180.00 159.05 20.95 0 5.00e+00 4.00e-02 1.75e+01 ... (remaining 5414 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.089: 1306 0.089 - 0.177: 93 0.177 - 0.266: 3 0.266 - 0.354: 1 0.354 - 0.443: 1 Chirality restraints: 1404 Sorted by residual: chirality pdb=" CA TYR S 235 " pdb=" N TYR S 235 " pdb=" C TYR S 235 " pdb=" CB TYR S 235 " both_signs ideal model delta sigma weight residual False 2.51 2.07 0.44 2.00e-01 2.50e+01 4.91e+00 chirality pdb=" CA TYR S 190 " pdb=" N TYR S 190 " pdb=" C TYR S 190 " pdb=" CB TYR S 190 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.68e+00 chirality pdb=" CA VAL T 276 " pdb=" N VAL T 276 " pdb=" C VAL T 276 " pdb=" CB VAL T 276 " both_signs ideal model delta sigma weight residual False 2.44 2.64 -0.20 2.00e-01 2.50e+01 9.90e-01 ... (remaining 1401 not shown) Planarity restraints: 1555 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C13 IYF C 701 " 0.249 2.00e-02 2.50e+03 2.61e-01 1.02e+03 pdb=" C16 IYF C 701 " -0.253 2.00e-02 2.50e+03 pdb=" N11 IYF C 701 " -0.282 2.00e-02 2.50e+03 pdb=" N12 IYF C 701 " 0.408 2.00e-02 2.50e+03 pdb=" N14 IYF C 701 " -0.182 2.00e-02 2.50e+03 pdb=" N15 IYF C 701 " 0.060 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 IYF C 701 " 0.164 2.00e-02 2.50e+03 1.67e-01 2.77e+02 pdb=" C9 IYF C 701 " -0.160 2.00e-02 2.50e+03 pdb=" N11 IYF C 701 " 0.169 2.00e-02 2.50e+03 pdb=" N12 IYF C 701 " -0.173 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL G 54 " 0.030 5.00e-02 4.00e+02 4.55e-02 3.32e+00 pdb=" N PRO G 55 " -0.079 5.00e-02 4.00e+02 pdb=" CA PRO G 55 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO G 55 " 0.025 5.00e-02 4.00e+02 ... (remaining 1552 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 799 2.74 - 3.28: 8956 3.28 - 3.82: 15306 3.82 - 4.36: 18298 4.36 - 4.90: 31237 Nonbonded interactions: 74596 Sorted by model distance: nonbonded pdb=" O LEU C 377 " pdb=" OG SER C 380 " model vdw 2.198 3.040 nonbonded pdb=" O ILE T 58 " pdb=" OG SER T 316 " model vdw 2.211 3.040 nonbonded pdb=" NE1 TRP S 47 " pdb=" O ALA S 49 " model vdw 2.251 3.120 nonbonded pdb=" O ARG S 67 " pdb=" OG1 THR S 84 " model vdw 2.283 3.040 nonbonded pdb=" OG SER I 6 " pdb=" OH TYR S 173 " model vdw 2.314 3.040 ... (remaining 74591 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: 1.160 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 8.630 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:0.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6753 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 : 0.006 0.207 9138 Z= 0.282 Angle : 0.807 18.211 12374 Z= 0.431 Chirality : 0.048 0.443 1404 Planarity : 0.009 0.261 1555 Dihedral : 14.095 86.333 3267 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.12 % Favored : 92.88 % Rotamer: Outliers : 0.62 % Allowed : 1.95 % Favored : 97.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.45 (0.25), residues: 1124 helix: 1.38 (0.27), residues: 382 sheet: -0.35 (0.33), residues: 259 loop : -1.67 (0.27), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG T 49 TYR 0.022 0.002 TYR S 190 PHE 0.023 0.002 PHE I 200 TRP 0.014 0.002 TRP T 99 HIS 0.008 0.001 HIS T 142 Details of bonding type rmsd covalent geometry : bond 0.00580 ( 9136) covalent geometry : angle 0.80666 (12370) SS BOND : bond 0.00291 ( 2) SS BOND : angle 2.19563 ( 4) hydrogen bonds : bond 0.18907 ( 419) hydrogen bonds : angle 6.89643 ( 1167) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 155 time to evaluate : 0.339 Fit side-chains REVERT: C 371 PHE cc_start: 0.6573 (t80) cc_final: 0.6357 (t80) REVERT: I 198 LYS cc_start: 0.7126 (mttm) cc_final: 0.6768 (mttm) REVERT: I 273 ASP cc_start: 0.6453 (p0) cc_final: 0.5771 (p0) REVERT: I 277 GLU cc_start: 0.6230 (mp0) cc_final: 0.5780 (mp0) REVERT: S 228 TYR cc_start: 0.7505 (m-80) cc_final: 0.7278 (m-80) REVERT: T 155 ASN cc_start: 0.7683 (t0) cc_final: 0.7311 (t0) REVERT: T 323 ASP cc_start: 0.7183 (p0) cc_final: 0.6808 (p0) outliers start: 6 outliers final: 1 residues processed: 160 average time/residue: 0.0872 time to fit residues: 19.6457 Evaluate side-chains 149 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 148 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain T residue 274 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 108 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 2.9990 chunk 53 optimal weight: 0.4980 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 0.8980 chunk 100 optimal weight: 4.9990 chunk 106 optimal weight: 2.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 194 ASN S 232 HIS T 88 ASN T 176 GLN T 220 GLN T 340 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.167342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.139098 restraints weight = 12040.769| |-----------------------------------------------------------------------------| r_work (start): 0.3736 rms_B_bonded: 2.08 r_work: 0.3603 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3430 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3430 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7244 moved from start: 0.0989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 9138 Z= 0.223 Angle : 0.675 11.266 12374 Z= 0.348 Chirality : 0.045 0.162 1404 Planarity : 0.005 0.047 1555 Dihedral : 5.734 68.991 1240 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.85 % Favored : 93.15 % Rotamer: Outliers : 1.23 % Allowed : 11.11 % Favored : 87.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.29 (0.26), residues: 1124 helix: 1.35 (0.27), residues: 384 sheet: -0.28 (0.32), residues: 272 loop : -1.43 (0.29), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG T 49 TYR 0.017 0.002 TYR S 190 PHE 0.020 0.002 PHE T 199 TRP 0.019 0.002 TRP T 169 HIS 0.005 0.001 HIS T 142 Details of bonding type rmsd covalent geometry : bond 0.00525 ( 9136) covalent geometry : angle 0.67371 (12370) SS BOND : bond 0.00828 ( 2) SS BOND : angle 2.54211 ( 4) hydrogen bonds : bond 0.04647 ( 419) hydrogen bonds : angle 5.30167 ( 1167) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 159 time to evaluate : 0.204 Fit side-chains REVERT: C 109 MET cc_start: 0.6512 (mmm) cc_final: 0.6278 (mmm) REVERT: C 173 LEU cc_start: 0.7355 (OUTLIER) cc_final: 0.6935 (tp) REVERT: C 371 PHE cc_start: 0.7096 (t80) cc_final: 0.6766 (t80) REVERT: I 198 LYS cc_start: 0.7791 (mttm) cc_final: 0.7513 (mttm) REVERT: I 277 GLU cc_start: 0.6784 (mp0) cc_final: 0.6046 (mp0) REVERT: S 82 GLN cc_start: 0.7908 (tp-100) cc_final: 0.7645 (tp-100) REVERT: S 192 MET cc_start: 0.6664 (tpt) cc_final: 0.6323 (tpt) REVERT: T 155 ASN cc_start: 0.8172 (t0) cc_final: 0.7699 (t0) REVERT: T 258 ASP cc_start: 0.7342 (t0) cc_final: 0.7010 (t0) REVERT: T 273 ILE cc_start: 0.8031 (mp) cc_final: 0.7769 (mp) REVERT: T 323 ASP cc_start: 0.7495 (p0) cc_final: 0.7147 (p0) outliers start: 12 outliers final: 6 residues processed: 162 average time/residue: 0.0803 time to fit residues: 18.4920 Evaluate side-chains 162 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 155 time to evaluate : 0.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 173 LEU Chi-restraints excluded: chain C residue 269 SER Chi-restraints excluded: chain C residue 325 THR Chi-restraints excluded: chain I residue 25 GLU Chi-restraints excluded: chain S residue 30 SER Chi-restraints excluded: chain T residue 101 MET Chi-restraints excluded: chain T residue 274 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 47 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 34 optimal weight: 0.8980 chunk 107 optimal weight: 0.6980 chunk 106 optimal weight: 2.9990 chunk 96 optimal weight: 0.9980 chunk 42 optimal weight: 0.6980 chunk 22 optimal weight: 0.6980 chunk 33 optimal weight: 0.8980 chunk 27 optimal weight: 0.5980 chunk 12 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 220 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.168620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.141413 restraints weight = 11882.131| |-----------------------------------------------------------------------------| r_work (start): 0.3764 rms_B_bonded: 1.96 r_work: 0.3636 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3468 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3468 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7204 moved from start: 0.1313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9138 Z= 0.147 Angle : 0.591 8.517 12374 Z= 0.306 Chirality : 0.042 0.268 1404 Planarity : 0.004 0.060 1555 Dihedral : 5.484 64.875 1240 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.96 % Favored : 94.04 % Rotamer: Outliers : 2.16 % Allowed : 12.96 % Favored : 84.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.14 (0.26), residues: 1124 helix: 1.46 (0.27), residues: 385 sheet: -0.26 (0.32), residues: 286 loop : -1.31 (0.29), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG T 49 TYR 0.017 0.001 TYR S 190 PHE 0.016 0.001 PHE T 199 TRP 0.015 0.001 TRP T 169 HIS 0.004 0.001 HIS I 323 Details of bonding type rmsd covalent geometry : bond 0.00339 ( 9136) covalent geometry : angle 0.58959 (12370) SS BOND : bond 0.00558 ( 2) SS BOND : angle 2.01625 ( 4) hydrogen bonds : bond 0.03905 ( 419) hydrogen bonds : angle 4.93885 ( 1167) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 162 time to evaluate : 0.243 Fit side-chains REVERT: C 109 MET cc_start: 0.6436 (mmm) cc_final: 0.6184 (mmm) REVERT: C 274 LEU cc_start: 0.8468 (OUTLIER) cc_final: 0.8169 (tp) REVERT: G 42 GLU cc_start: 0.7088 (OUTLIER) cc_final: 0.6632 (pm20) REVERT: I 248 MET cc_start: 0.8259 (mtp) cc_final: 0.8017 (mtp) REVERT: I 277 GLU cc_start: 0.6709 (mp0) cc_final: 0.6093 (mp0) REVERT: S 82 GLN cc_start: 0.7950 (tp-100) cc_final: 0.7679 (tp-100) REVERT: S 192 MET cc_start: 0.6550 (tpt) cc_final: 0.6167 (tpt) REVERT: S 228 TYR cc_start: 0.8012 (m-80) cc_final: 0.7699 (m-80) REVERT: T 133 VAL cc_start: 0.7704 (t) cc_final: 0.7378 (p) REVERT: T 155 ASN cc_start: 0.8195 (t0) cc_final: 0.7693 (t0) REVERT: T 258 ASP cc_start: 0.7361 (t0) cc_final: 0.6963 (t0) REVERT: T 273 ILE cc_start: 0.7986 (mp) cc_final: 0.7702 (mp) REVERT: T 323 ASP cc_start: 0.7564 (p0) cc_final: 0.7210 (p0) outliers start: 21 outliers final: 11 residues processed: 170 average time/residue: 0.0749 time to fit residues: 18.0945 Evaluate side-chains 171 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 158 time to evaluate : 0.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 162 THR Chi-restraints excluded: chain C residue 269 SER Chi-restraints excluded: chain C residue 274 LEU Chi-restraints excluded: chain C residue 325 THR Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain G residue 42 GLU Chi-restraints excluded: chain I residue 25 GLU Chi-restraints excluded: chain S residue 48 VAL Chi-restraints excluded: chain S residue 97 VAL Chi-restraints excluded: chain T residue 101 MET Chi-restraints excluded: chain T residue 226 GLU Chi-restraints excluded: chain T residue 269 ILE Chi-restraints excluded: chain T residue 274 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 109 optimal weight: 2.9990 chunk 29 optimal weight: 7.9990 chunk 73 optimal weight: 0.9980 chunk 5 optimal weight: 0.6980 chunk 1 optimal weight: 0.6980 chunk 70 optimal weight: 0.9990 chunk 100 optimal weight: 4.9990 chunk 64 optimal weight: 0.8980 chunk 71 optimal weight: 0.7980 chunk 45 optimal weight: 2.9990 chunk 69 optimal weight: 3.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 220 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.168327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.140884 restraints weight = 12092.721| |-----------------------------------------------------------------------------| r_work (start): 0.3757 rms_B_bonded: 1.98 r_work: 0.3631 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3463 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3463 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7214 moved from start: 0.1445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 9138 Z= 0.158 Angle : 0.586 8.804 12374 Z= 0.304 Chirality : 0.042 0.136 1404 Planarity : 0.004 0.059 1555 Dihedral : 5.444 61.762 1240 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.58 % Favored : 93.42 % Rotamer: Outliers : 3.09 % Allowed : 13.17 % Favored : 83.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.08 (0.26), residues: 1124 helix: 1.55 (0.27), residues: 385 sheet: -0.24 (0.31), residues: 286 loop : -1.32 (0.29), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG T 49 TYR 0.016 0.001 TYR S 190 PHE 0.016 0.001 PHE T 199 TRP 0.013 0.001 TRP T 169 HIS 0.003 0.001 HIS I 214 Details of bonding type rmsd covalent geometry : bond 0.00368 ( 9136) covalent geometry : angle 0.58489 (12370) SS BOND : bond 0.00624 ( 2) SS BOND : angle 2.18951 ( 4) hydrogen bonds : bond 0.03821 ( 419) hydrogen bonds : angle 4.82854 ( 1167) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 162 time to evaluate : 0.199 Fit side-chains REVERT: C 173 LEU cc_start: 0.7315 (OUTLIER) cc_final: 0.6607 (tp) REVERT: C 274 LEU cc_start: 0.8388 (OUTLIER) cc_final: 0.8082 (tp) REVERT: G 42 GLU cc_start: 0.7068 (OUTLIER) cc_final: 0.6652 (pm20) REVERT: I 248 MET cc_start: 0.8259 (mtp) cc_final: 0.7975 (mtp) REVERT: I 277 GLU cc_start: 0.6713 (mp0) cc_final: 0.6141 (mp0) REVERT: S 22 CYS cc_start: 0.7110 (OUTLIER) cc_final: 0.6860 (t) REVERT: S 82 GLN cc_start: 0.7923 (tp-100) cc_final: 0.7646 (tp-100) REVERT: S 192 MET cc_start: 0.6607 (tpt) cc_final: 0.6164 (tpt) REVERT: S 228 TYR cc_start: 0.8010 (m-80) cc_final: 0.7730 (m-80) REVERT: T 133 VAL cc_start: 0.7758 (t) cc_final: 0.7493 (p) REVERT: T 155 ASN cc_start: 0.8174 (t0) cc_final: 0.7657 (t0) REVERT: T 258 ASP cc_start: 0.7318 (t0) cc_final: 0.6918 (t0) REVERT: T 273 ILE cc_start: 0.7908 (mp) cc_final: 0.7624 (mp) REVERT: T 323 ASP cc_start: 0.7565 (p0) cc_final: 0.7219 (p0) outliers start: 30 outliers final: 17 residues processed: 176 average time/residue: 0.0797 time to fit residues: 19.9646 Evaluate side-chains 182 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 161 time to evaluate : 0.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 162 THR Chi-restraints excluded: chain C residue 173 LEU Chi-restraints excluded: chain C residue 249 VAL Chi-restraints excluded: chain C residue 269 SER Chi-restraints excluded: chain C residue 274 LEU Chi-restraints excluded: chain C residue 325 THR Chi-restraints excluded: chain C residue 357 VAL Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 42 GLU Chi-restraints excluded: chain I residue 25 GLU Chi-restraints excluded: chain I residue 185 ILE Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 22 CYS Chi-restraints excluded: chain S residue 30 SER Chi-restraints excluded: chain S residue 48 VAL Chi-restraints excluded: chain S residue 172 THR Chi-restraints excluded: chain T residue 101 MET Chi-restraints excluded: chain T residue 226 GLU Chi-restraints excluded: chain T residue 228 ASP Chi-restraints excluded: chain T residue 269 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 38 optimal weight: 3.9990 chunk 99 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 64 optimal weight: 0.0060 chunk 70 optimal weight: 2.9990 chunk 50 optimal weight: 0.6980 chunk 6 optimal weight: 0.9980 chunk 73 optimal weight: 0.7980 chunk 16 optimal weight: 20.0000 chunk 80 optimal weight: 1.9990 chunk 40 optimal weight: 0.0980 overall best weight: 0.5196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 220 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.169474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.142102 restraints weight = 11911.281| |-----------------------------------------------------------------------------| r_work (start): 0.3777 rms_B_bonded: 1.97 r_work: 0.3648 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3482 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3482 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7193 moved from start: 0.1625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9138 Z= 0.124 Angle : 0.555 7.777 12374 Z= 0.289 Chirality : 0.041 0.140 1404 Planarity : 0.004 0.057 1555 Dihedral : 5.076 58.448 1239 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 2.67 % Allowed : 14.92 % Favored : 82.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.02 (0.26), residues: 1124 helix: 1.68 (0.27), residues: 385 sheet: -0.16 (0.31), residues: 287 loop : -1.32 (0.29), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG T 49 TYR 0.016 0.001 TYR S 190 PHE 0.014 0.001 PHE I 197 TRP 0.014 0.001 TRP T 169 HIS 0.003 0.001 HIS I 323 Details of bonding type rmsd covalent geometry : bond 0.00281 ( 9136) covalent geometry : angle 0.55351 (12370) SS BOND : bond 0.00641 ( 2) SS BOND : angle 2.04695 ( 4) hydrogen bonds : bond 0.03513 ( 419) hydrogen bonds : angle 4.71209 ( 1167) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 166 time to evaluate : 0.217 Fit side-chains REVERT: C 163 SER cc_start: 0.8228 (m) cc_final: 0.7718 (t) REVERT: C 173 LEU cc_start: 0.7298 (OUTLIER) cc_final: 0.6672 (tp) REVERT: I 248 MET cc_start: 0.8260 (mtp) cc_final: 0.7945 (mtp) REVERT: I 277 GLU cc_start: 0.6654 (mp0) cc_final: 0.6110 (mp0) REVERT: S 22 CYS cc_start: 0.7025 (OUTLIER) cc_final: 0.6816 (t) REVERT: S 82 GLN cc_start: 0.7910 (tp-100) cc_final: 0.7650 (tp-100) REVERT: S 192 MET cc_start: 0.6470 (tpt) cc_final: 0.6079 (tpt) REVERT: S 228 TYR cc_start: 0.7978 (m-80) cc_final: 0.7745 (m-80) REVERT: T 133 VAL cc_start: 0.7755 (t) cc_final: 0.7495 (p) REVERT: T 155 ASN cc_start: 0.8174 (t0) cc_final: 0.7643 (t0) REVERT: T 258 ASP cc_start: 0.7319 (t0) cc_final: 0.6896 (t0) REVERT: T 273 ILE cc_start: 0.7885 (mp) cc_final: 0.7577 (mp) REVERT: T 323 ASP cc_start: 0.7568 (p0) cc_final: 0.7216 (p0) outliers start: 26 outliers final: 19 residues processed: 177 average time/residue: 0.0887 time to fit residues: 21.9613 Evaluate side-chains 184 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 163 time to evaluate : 0.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 162 THR Chi-restraints excluded: chain C residue 173 LEU Chi-restraints excluded: chain C residue 249 VAL Chi-restraints excluded: chain C residue 269 SER Chi-restraints excluded: chain C residue 325 THR Chi-restraints excluded: chain C residue 357 VAL Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 42 GLU Chi-restraints excluded: chain I residue 25 GLU Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 22 CYS Chi-restraints excluded: chain S residue 30 SER Chi-restraints excluded: chain S residue 48 VAL Chi-restraints excluded: chain S residue 97 VAL Chi-restraints excluded: chain T residue 81 ILE Chi-restraints excluded: chain T residue 101 MET Chi-restraints excluded: chain T residue 226 GLU Chi-restraints excluded: chain T residue 228 ASP Chi-restraints excluded: chain T residue 234 PHE Chi-restraints excluded: chain T residue 269 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 13 optimal weight: 2.9990 chunk 29 optimal weight: 4.9990 chunk 80 optimal weight: 0.9990 chunk 50 optimal weight: 0.6980 chunk 0 optimal weight: 10.0000 chunk 73 optimal weight: 0.3980 chunk 59 optimal weight: 0.7980 chunk 75 optimal weight: 1.9990 chunk 72 optimal weight: 0.5980 chunk 14 optimal weight: 5.9990 chunk 28 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: T 220 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.168694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.141125 restraints weight = 11960.001| |-----------------------------------------------------------------------------| r_work (start): 0.3763 rms_B_bonded: 1.99 r_work: 0.3635 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3468 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3468 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7204 moved from start: 0.1688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9138 Z= 0.143 Angle : 0.582 10.645 12374 Z= 0.299 Chirality : 0.042 0.310 1404 Planarity : 0.004 0.058 1555 Dihedral : 5.095 58.053 1239 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.41 % Favored : 93.59 % Rotamer: Outliers : 3.29 % Allowed : 15.84 % Favored : 80.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.01 (0.26), residues: 1124 helix: 1.60 (0.27), residues: 388 sheet: -0.15 (0.31), residues: 286 loop : -1.32 (0.29), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG T 49 TYR 0.015 0.001 TYR S 190 PHE 0.014 0.001 PHE T 199 TRP 0.013 0.001 TRP T 169 HIS 0.003 0.001 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00332 ( 9136) covalent geometry : angle 0.58134 (12370) SS BOND : bond 0.00538 ( 2) SS BOND : angle 1.94359 ( 4) hydrogen bonds : bond 0.03594 ( 419) hydrogen bonds : angle 4.72022 ( 1167) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 159 time to evaluate : 0.344 Fit side-chains REVERT: C 163 SER cc_start: 0.8173 (m) cc_final: 0.7701 (t) REVERT: C 173 LEU cc_start: 0.7302 (OUTLIER) cc_final: 0.6611 (tp) REVERT: I 248 MET cc_start: 0.8255 (mtp) cc_final: 0.7937 (mtp) REVERT: I 277 GLU cc_start: 0.6696 (mp0) cc_final: 0.6168 (mp0) REVERT: S 22 CYS cc_start: 0.7059 (OUTLIER) cc_final: 0.6822 (t) REVERT: S 82 GLN cc_start: 0.7926 (tp-100) cc_final: 0.7662 (tp-100) REVERT: S 192 MET cc_start: 0.6523 (tpt) cc_final: 0.6196 (tpt) REVERT: S 228 TYR cc_start: 0.7974 (m-80) cc_final: 0.7736 (m-80) REVERT: T 133 VAL cc_start: 0.7765 (t) cc_final: 0.7527 (p) REVERT: T 155 ASN cc_start: 0.8152 (t0) cc_final: 0.7634 (t0) REVERT: T 258 ASP cc_start: 0.7351 (t0) cc_final: 0.6932 (t0) REVERT: T 273 ILE cc_start: 0.7899 (mp) cc_final: 0.7618 (mp) REVERT: T 323 ASP cc_start: 0.7582 (p0) cc_final: 0.7245 (p0) outliers start: 32 outliers final: 25 residues processed: 178 average time/residue: 0.0877 time to fit residues: 22.1084 Evaluate side-chains 181 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 154 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 162 THR Chi-restraints excluded: chain C residue 173 LEU Chi-restraints excluded: chain C residue 249 VAL Chi-restraints excluded: chain C residue 269 SER Chi-restraints excluded: chain C residue 325 THR Chi-restraints excluded: chain C residue 357 VAL Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 42 GLU Chi-restraints excluded: chain I residue 25 GLU Chi-restraints excluded: chain I residue 185 ILE Chi-restraints excluded: chain I residue 330 THR Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 22 CYS Chi-restraints excluded: chain S residue 30 SER Chi-restraints excluded: chain S residue 48 VAL Chi-restraints excluded: chain S residue 97 VAL Chi-restraints excluded: chain S residue 172 THR Chi-restraints excluded: chain T residue 51 LEU Chi-restraints excluded: chain T residue 81 ILE Chi-restraints excluded: chain T residue 101 MET Chi-restraints excluded: chain T residue 146 LEU Chi-restraints excluded: chain T residue 226 GLU Chi-restraints excluded: chain T residue 228 ASP Chi-restraints excluded: chain T residue 234 PHE Chi-restraints excluded: chain T residue 269 ILE Chi-restraints excluded: chain T residue 316 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 57 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 18 optimal weight: 0.9980 chunk 32 optimal weight: 0.9980 chunk 93 optimal weight: 0.5980 chunk 89 optimal weight: 0.9980 chunk 56 optimal weight: 3.9990 chunk 103 optimal weight: 3.9990 chunk 52 optimal weight: 0.8980 chunk 51 optimal weight: 0.7980 chunk 80 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: T 220 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.168181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.140667 restraints weight = 12002.659| |-----------------------------------------------------------------------------| r_work (start): 0.3756 rms_B_bonded: 1.98 r_work: 0.3626 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3459 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3459 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7217 moved from start: 0.1717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 9138 Z= 0.163 Angle : 0.604 14.139 12374 Z= 0.309 Chirality : 0.042 0.139 1404 Planarity : 0.004 0.057 1555 Dihedral : 5.176 59.289 1239 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.49 % Favored : 93.51 % Rotamer: Outliers : 3.50 % Allowed : 15.84 % Favored : 80.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.23 % 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 (0.26), residues: 1124 helix: 1.57 (0.27), residues: 387 sheet: -0.22 (0.31), residues: 289 loop : -1.34 (0.29), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG T 49 TYR 0.014 0.001 TYR S 190 PHE 0.017 0.002 PHE I 200 TRP 0.013 0.001 TRP T 99 HIS 0.003 0.001 HIS I 214 Details of bonding type rmsd covalent geometry : bond 0.00382 ( 9136) covalent geometry : angle 0.60313 (12370) SS BOND : bond 0.00572 ( 2) SS BOND : angle 2.08035 ( 4) hydrogen bonds : bond 0.03711 ( 419) hydrogen bonds : angle 4.76415 ( 1167) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 161 time to evaluate : 0.258 Fit side-chains REVERT: C 163 SER cc_start: 0.8198 (m) cc_final: 0.7736 (t) REVERT: C 173 LEU cc_start: 0.7310 (OUTLIER) cc_final: 0.6603 (tp) REVERT: I 248 MET cc_start: 0.8258 (mtp) cc_final: 0.7912 (mtp) REVERT: I 277 GLU cc_start: 0.6738 (OUTLIER) cc_final: 0.6233 (mp0) REVERT: S 22 CYS cc_start: 0.7091 (OUTLIER) cc_final: 0.6862 (t) REVERT: S 82 GLN cc_start: 0.7933 (tp-100) cc_final: 0.7666 (tp-100) REVERT: S 192 MET cc_start: 0.6618 (tpt) cc_final: 0.6314 (tpt) REVERT: T 133 VAL cc_start: 0.7762 (t) cc_final: 0.7535 (p) REVERT: T 155 ASN cc_start: 0.8145 (t0) cc_final: 0.7621 (t0) REVERT: T 220 GLN cc_start: 0.8028 (mt0) cc_final: 0.7811 (mt0) REVERT: T 273 ILE cc_start: 0.7877 (mp) cc_final: 0.7584 (mp) REVERT: T 323 ASP cc_start: 0.7610 (p0) cc_final: 0.7260 (p0) outliers start: 34 outliers final: 27 residues processed: 181 average time/residue: 0.0853 time to fit residues: 21.8979 Evaluate side-chains 185 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 155 time to evaluate : 0.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 162 THR Chi-restraints excluded: chain C residue 173 LEU Chi-restraints excluded: chain C residue 238 THR Chi-restraints excluded: chain C residue 249 VAL Chi-restraints excluded: chain C residue 269 SER Chi-restraints excluded: chain C residue 325 THR Chi-restraints excluded: chain C residue 357 VAL Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 42 GLU Chi-restraints excluded: chain I residue 25 GLU Chi-restraints excluded: chain I residue 185 ILE Chi-restraints excluded: chain I residue 277 GLU Chi-restraints excluded: chain I residue 330 THR Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 22 CYS Chi-restraints excluded: chain S residue 30 SER Chi-restraints excluded: chain S residue 48 VAL Chi-restraints excluded: chain S residue 97 VAL Chi-restraints excluded: chain S residue 172 THR Chi-restraints excluded: chain T residue 43 ILE Chi-restraints excluded: chain T residue 51 LEU Chi-restraints excluded: chain T residue 101 MET Chi-restraints excluded: chain T residue 146 LEU Chi-restraints excluded: chain T residue 178 THR Chi-restraints excluded: chain T residue 226 GLU Chi-restraints excluded: chain T residue 228 ASP Chi-restraints excluded: chain T residue 234 PHE Chi-restraints excluded: chain T residue 269 ILE Chi-restraints excluded: chain T residue 316 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 7 optimal weight: 0.9990 chunk 107 optimal weight: 0.6980 chunk 39 optimal weight: 2.9990 chunk 38 optimal weight: 0.9980 chunk 71 optimal weight: 1.9990 chunk 3 optimal weight: 10.0000 chunk 77 optimal weight: 1.9990 chunk 4 optimal weight: 0.6980 chunk 34 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 24 optimal weight: 0.0470 overall best weight: 0.6880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 186 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.168811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.141572 restraints weight = 11912.226| |-----------------------------------------------------------------------------| r_work (start): 0.3766 rms_B_bonded: 1.97 r_work: 0.3641 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3471 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3471 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7198 moved from start: 0.1808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9138 Z= 0.143 Angle : 0.609 16.888 12374 Z= 0.307 Chirality : 0.041 0.156 1404 Planarity : 0.004 0.057 1555 Dihedral : 5.108 57.565 1239 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.96 % Favored : 94.04 % Rotamer: Outliers : 3.50 % Allowed : 16.56 % Favored : 79.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.04 (0.26), residues: 1124 helix: 1.58 (0.27), residues: 388 sheet: -0.19 (0.31), residues: 283 loop : -1.34 (0.29), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG T 49 TYR 0.016 0.001 TYR T 289 PHE 0.021 0.001 PHE I 200 TRP 0.015 0.001 TRP T 99 HIS 0.003 0.001 HIS I 323 Details of bonding type rmsd covalent geometry : bond 0.00332 ( 9136) covalent geometry : angle 0.60837 (12370) SS BOND : bond 0.00536 ( 2) SS BOND : angle 1.91026 ( 4) hydrogen bonds : bond 0.03584 ( 419) hydrogen bonds : angle 4.72243 ( 1167) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 158 time to evaluate : 0.247 Fit side-chains REVERT: C 163 SER cc_start: 0.8195 (m) cc_final: 0.7748 (t) REVERT: C 173 LEU cc_start: 0.7275 (OUTLIER) cc_final: 0.6623 (tp) REVERT: I 248 MET cc_start: 0.8227 (mtp) cc_final: 0.7863 (mtp) REVERT: I 277 GLU cc_start: 0.6737 (OUTLIER) cc_final: 0.6240 (mp0) REVERT: S 22 CYS cc_start: 0.7049 (OUTLIER) cc_final: 0.6816 (t) REVERT: S 82 GLN cc_start: 0.7896 (tp-100) cc_final: 0.7616 (tp-100) REVERT: S 192 MET cc_start: 0.6552 (tpt) cc_final: 0.6318 (tpt) REVERT: T 133 VAL cc_start: 0.7753 (t) cc_final: 0.7529 (p) REVERT: T 155 ASN cc_start: 0.8123 (t0) cc_final: 0.7593 (t0) REVERT: T 323 ASP cc_start: 0.7611 (p0) cc_final: 0.7273 (p0) outliers start: 34 outliers final: 30 residues processed: 177 average time/residue: 0.0766 time to fit residues: 19.1250 Evaluate side-chains 190 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 157 time to evaluate : 0.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 155 CYS Chi-restraints excluded: chain C residue 162 THR Chi-restraints excluded: chain C residue 173 LEU Chi-restraints excluded: chain C residue 238 THR Chi-restraints excluded: chain C residue 249 VAL Chi-restraints excluded: chain C residue 269 SER Chi-restraints excluded: chain C residue 325 THR Chi-restraints excluded: chain C residue 357 VAL Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 42 GLU Chi-restraints excluded: chain I residue 25 GLU Chi-restraints excluded: chain I residue 185 ILE Chi-restraints excluded: chain I residue 258 LYS Chi-restraints excluded: chain I residue 277 GLU Chi-restraints excluded: chain I residue 330 THR Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 22 CYS Chi-restraints excluded: chain S residue 30 SER Chi-restraints excluded: chain S residue 48 VAL Chi-restraints excluded: chain S residue 97 VAL Chi-restraints excluded: chain S residue 172 THR Chi-restraints excluded: chain T residue 43 ILE Chi-restraints excluded: chain T residue 65 THR Chi-restraints excluded: chain T residue 101 MET Chi-restraints excluded: chain T residue 146 LEU Chi-restraints excluded: chain T residue 178 THR Chi-restraints excluded: chain T residue 226 GLU Chi-restraints excluded: chain T residue 228 ASP Chi-restraints excluded: chain T residue 234 PHE Chi-restraints excluded: chain T residue 269 ILE Chi-restraints excluded: chain T residue 316 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 55 optimal weight: 0.5980 chunk 95 optimal weight: 0.5980 chunk 61 optimal weight: 0.0970 chunk 20 optimal weight: 5.9990 chunk 57 optimal weight: 0.3980 chunk 80 optimal weight: 1.9990 chunk 83 optimal weight: 3.9990 chunk 43 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 52 optimal weight: 0.0770 chunk 41 optimal weight: 4.9990 overall best weight: 0.3536 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 220 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.170283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.143104 restraints weight = 12060.846| |-----------------------------------------------------------------------------| r_work (start): 0.3787 rms_B_bonded: 1.99 r_work: 0.3659 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3492 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3492 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7173 moved from start: 0.1984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 9138 Z= 0.110 Angle : 0.552 10.115 12374 Z= 0.285 Chirality : 0.041 0.213 1404 Planarity : 0.004 0.055 1555 Dihedral : 4.933 51.536 1239 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % Rotamer: Outliers : 3.19 % Allowed : 17.59 % Favored : 79.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.07 (0.26), residues: 1124 helix: 1.72 (0.27), residues: 386 sheet: -0.10 (0.31), residues: 281 loop : -1.32 (0.29), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG T 49 TYR 0.016 0.001 TYR S 190 PHE 0.016 0.001 PHE I 200 TRP 0.015 0.001 TRP T 169 HIS 0.002 0.001 HIS I 323 Details of bonding type rmsd covalent geometry : bond 0.00245 ( 9136) covalent geometry : angle 0.55108 (12370) SS BOND : bond 0.00421 ( 2) SS BOND : angle 1.46020 ( 4) hydrogen bonds : bond 0.03318 ( 419) hydrogen bonds : angle 4.63831 ( 1167) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 162 time to evaluate : 0.342 Fit side-chains REVERT: C 163 SER cc_start: 0.8180 (m) cc_final: 0.7709 (t) REVERT: C 173 LEU cc_start: 0.7271 (OUTLIER) cc_final: 0.6657 (tp) REVERT: I 248 MET cc_start: 0.8230 (mtp) cc_final: 0.7869 (mtp) REVERT: I 277 GLU cc_start: 0.6709 (OUTLIER) cc_final: 0.6245 (mp0) REVERT: S 82 GLN cc_start: 0.7900 (tp-100) cc_final: 0.7630 (tp-100) REVERT: T 133 VAL cc_start: 0.7758 (t) cc_final: 0.7525 (p) REVERT: T 155 ASN cc_start: 0.8142 (t0) cc_final: 0.7761 (t0) REVERT: T 323 ASP cc_start: 0.7594 (p0) cc_final: 0.7227 (p0) outliers start: 31 outliers final: 24 residues processed: 180 average time/residue: 0.0799 time to fit residues: 20.5044 Evaluate side-chains 183 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 157 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 173 LEU Chi-restraints excluded: chain C residue 238 THR Chi-restraints excluded: chain C residue 249 VAL Chi-restraints excluded: chain C residue 269 SER Chi-restraints excluded: chain C residue 325 THR Chi-restraints excluded: chain C residue 357 VAL Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 42 GLU Chi-restraints excluded: chain I residue 25 GLU Chi-restraints excluded: chain I residue 277 GLU Chi-restraints excluded: chain I residue 330 THR Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 30 SER Chi-restraints excluded: chain S residue 48 VAL Chi-restraints excluded: chain S residue 97 VAL Chi-restraints excluded: chain S residue 172 THR Chi-restraints excluded: chain T residue 43 ILE Chi-restraints excluded: chain T residue 65 THR Chi-restraints excluded: chain T residue 101 MET Chi-restraints excluded: chain T residue 146 LEU Chi-restraints excluded: chain T residue 178 THR Chi-restraints excluded: chain T residue 228 ASP Chi-restraints excluded: chain T residue 234 PHE Chi-restraints excluded: chain T residue 316 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 57 optimal weight: 1.9990 chunk 51 optimal weight: 0.8980 chunk 22 optimal weight: 0.6980 chunk 79 optimal weight: 6.9990 chunk 87 optimal weight: 2.9990 chunk 32 optimal weight: 0.4980 chunk 24 optimal weight: 10.0000 chunk 48 optimal weight: 0.8980 chunk 11 optimal weight: 7.9990 chunk 40 optimal weight: 0.7980 chunk 53 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 220 GLN T 340 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.169225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.142076 restraints weight = 11956.271| |-----------------------------------------------------------------------------| r_work (start): 0.3771 rms_B_bonded: 1.96 r_work: 0.3645 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3476 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3476 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7198 moved from start: 0.1954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9138 Z= 0.148 Angle : 0.612 19.349 12374 Z= 0.309 Chirality : 0.042 0.249 1404 Planarity : 0.004 0.057 1555 Dihedral : 5.028 55.052 1239 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.23 % Favored : 93.77 % Rotamer: Outliers : 3.09 % Allowed : 17.39 % Favored : 79.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.07 (0.26), residues: 1124 helix: 1.70 (0.28), residues: 386 sheet: -0.10 (0.31), residues: 281 loop : -1.30 (0.29), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG T 49 TYR 0.013 0.001 TYR S 190 PHE 0.026 0.002 PHE I 200 TRP 0.016 0.001 TRP T 99 HIS 0.003 0.001 HIS I 323 Details of bonding type rmsd covalent geometry : bond 0.00348 ( 9136) covalent geometry : angle 0.61101 (12370) SS BOND : bond 0.00502 ( 2) SS BOND : angle 1.76240 ( 4) hydrogen bonds : bond 0.03545 ( 419) hydrogen bonds : angle 4.75361 ( 1167) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 160 time to evaluate : 0.340 Fit side-chains REVERT: C 163 SER cc_start: 0.8140 (m) cc_final: 0.7754 (t) REVERT: C 173 LEU cc_start: 0.7296 (OUTLIER) cc_final: 0.6575 (tp) REVERT: I 248 MET cc_start: 0.8224 (mtp) cc_final: 0.7883 (mtp) REVERT: I 277 GLU cc_start: 0.6713 (OUTLIER) cc_final: 0.6275 (mp0) REVERT: S 82 GLN cc_start: 0.7914 (tp-100) cc_final: 0.7643 (tp-100) REVERT: T 133 VAL cc_start: 0.7758 (t) cc_final: 0.7537 (p) REVERT: T 155 ASN cc_start: 0.8114 (t0) cc_final: 0.7591 (t0) REVERT: T 323 ASP cc_start: 0.7593 (p0) cc_final: 0.7236 (p0) outliers start: 30 outliers final: 28 residues processed: 178 average time/residue: 0.0835 time to fit residues: 21.1223 Evaluate side-chains 189 residues out of total 977 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 159 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 155 CYS Chi-restraints excluded: chain C residue 162 THR Chi-restraints excluded: chain C residue 173 LEU Chi-restraints excluded: chain C residue 238 THR Chi-restraints excluded: chain C residue 249 VAL Chi-restraints excluded: chain C residue 269 SER Chi-restraints excluded: chain C residue 325 THR Chi-restraints excluded: chain C residue 357 VAL Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 42 GLU Chi-restraints excluded: chain I residue 25 GLU Chi-restraints excluded: chain I residue 185 ILE Chi-restraints excluded: chain I residue 277 GLU Chi-restraints excluded: chain I residue 330 THR Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 30 SER Chi-restraints excluded: chain S residue 97 VAL Chi-restraints excluded: chain S residue 172 THR Chi-restraints excluded: chain T residue 43 ILE Chi-restraints excluded: chain T residue 65 THR Chi-restraints excluded: chain T residue 100 VAL Chi-restraints excluded: chain T residue 101 MET Chi-restraints excluded: chain T residue 146 LEU Chi-restraints excluded: chain T residue 178 THR Chi-restraints excluded: chain T residue 226 GLU Chi-restraints excluded: chain T residue 228 ASP Chi-restraints excluded: chain T residue 234 PHE Chi-restraints excluded: chain T residue 316 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 80 optimal weight: 3.9990 chunk 5 optimal weight: 0.0030 chunk 58 optimal weight: 1.9990 chunk 39 optimal weight: 0.9990 chunk 94 optimal weight: 3.9990 chunk 10 optimal weight: 0.8980 chunk 110 optimal weight: 0.6980 chunk 23 optimal weight: 1.9990 chunk 27 optimal weight: 0.7980 chunk 62 optimal weight: 5.9990 chunk 18 optimal weight: 0.7980 overall best weight: 0.6390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: T 220 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.169607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.142340 restraints weight = 11863.136| |-----------------------------------------------------------------------------| r_work (start): 0.3777 rms_B_bonded: 1.97 r_work: 0.3653 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3487 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3487 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7183 moved from start: 0.2021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9138 Z= 0.138 Angle : 0.584 10.128 12374 Z= 0.300 Chirality : 0.042 0.245 1404 Planarity : 0.004 0.056 1555 Dihedral : 5.044 53.713 1239 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.14 % Favored : 93.86 % Rotamer: Outliers : 3.40 % Allowed : 17.59 % Favored : 79.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.08 (0.26), residues: 1124 helix: 1.72 (0.28), residues: 386 sheet: -0.13 (0.31), residues: 281 loop : -1.29 (0.29), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG T 49 TYR 0.014 0.001 TYR S 190 PHE 0.023 0.001 PHE I 200 TRP 0.016 0.001 TRP T 99 HIS 0.003 0.001 HIS I 323 Details of bonding type rmsd covalent geometry : bond 0.00323 ( 9136) covalent geometry : angle 0.58351 (12370) SS BOND : bond 0.00487 ( 2) SS BOND : angle 1.87985 ( 4) hydrogen bonds : bond 0.03496 ( 419) hydrogen bonds : angle 4.74352 ( 1167) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2421.46 seconds wall clock time: 42 minutes 17.02 seconds (2537.02 seconds total)