Starting phenix.real_space_refine on Fri Aug 22 23:01:01 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8i7w_35235/08_2025/8i7w_35235.cif Found real_map, /net/cci-nas-00/data/ceres_data/8i7w_35235/08_2025/8i7w_35235.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.39 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8i7w_35235/08_2025/8i7w_35235.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8i7w_35235/08_2025/8i7w_35235.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8i7w_35235/08_2025/8i7w_35235.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8i7w_35235/08_2025/8i7w_35235.map" } resolution = 3.39 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= -0.001 sd= 0.040 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 60 5.16 5 Cl 1 4.86 5 C 5396 2.51 5 N 1451 2.21 5 O 1553 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8461 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2328 Number of conformers: 1 Conformer: "" Number of residues, atoms: 291, 2328 Classifications: {'peptide': 291} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 10, 'TRANS': 280} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 62 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 58 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 2, 'PHE:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "B" Number of atoms: 1274 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1274 Classifications: {'peptide': 159} Modifications used: {'COO': 1} Link IDs: {'TRANS': 158} Chain breaks: 3 Chain: "C" Number of atoms: 2606 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2606 Classifications: {'peptide': 339} Link IDs: {'PTRANS': 5, 'TRANS': 333} Chain: "D" 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: "A" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 17 Unusual residues: {'OKL': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.69, per 1000 atoms: 0.20 Number of scatterers: 8461 At special positions: 0 Unit cell: (110.805, 85.905, 131.97, 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 60 16.00 O 1553 8.00 N 1451 7.00 C 5396 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 18 " - pdb=" SG CYS A 183 " distance=2.03 Simple disulfide: pdb=" SG CYS A 100 " - pdb=" SG CYS A 177 " distance=2.03 Simple disulfide: pdb=" SG CYS C 121 " - pdb=" SG CYS C 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=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.53 Conformation dependent library (CDL) restraints added in 360.0 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2016 Finding SS restraints... Secondary structure from input PDB file: 19 helices and 14 sheets defined 34.6% alpha, 19.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.26 Creating SS restraints... Processing helix chain 'A' and resid 29 through 54 removed outlier: 4.068A pdb=" N LEU A 43 " --> pdb=" O ILE A 39 " (cutoff:3.500A) Processing helix chain 'A' and resid 60 through 89 Proline residue: A 81 - end of helix Processing helix chain 'A' and resid 97 through 130 Processing helix chain 'A' and resid 134 through 138 Processing helix chain 'A' and resid 140 through 166 removed outlier: 5.124A pdb=" N HIS A 161 " --> pdb=" O GLY A 157 " (cutoff:3.500A) removed outlier: 5.210A pdb=" N LEU A 162 " --> pdb=" O LEU A 158 " (cutoff:3.500A) removed outlier: 4.881A pdb=" N LYS A 166 " --> pdb=" O LEU A 162 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 218 removed outlier: 3.817A pdb=" N ALA A 191 " --> pdb=" O GLN A 187 " (cutoff:3.500A) Proline residue: A 200 - end of helix Processing helix chain 'A' and resid 223 through 260 removed outlier: 3.718A pdb=" N LYS A 227 " --> pdb=" O HIS A 223 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ARG A 228 " --> pdb=" O ALA A 224 " (cutoff:3.500A) Proline residue: A 246 - end of helix Processing helix chain 'A' and resid 266 through 294 removed outlier: 3.597A pdb=" N ARG A 270 " --> pdb=" O CYS A 266 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N SER A 271 " --> pdb=" O GLU A 267 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N VAL A 272 " --> pdb=" O VAL A 268 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N ALA A 275 " --> pdb=" O SER A 271 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N PHE A 277 " --> pdb=" O ASP A 273 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ILE A 278 " --> pdb=" O LEU A 274 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N THR A 279 " --> pdb=" O ALA A 275 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N THR A 283 " --> pdb=" O THR A 279 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N TYR A 284 " --> pdb=" O LEU A 280 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N MET A 285 " --> pdb=" O SER A 281 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ASN A 286 " --> pdb=" O PHE A 282 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N SER A 287 " --> pdb=" O THR A 283 " (cutoff:3.500A) Proline residue: A 291 - end of helix Processing helix chain 'B' and resid 6 through 32 removed outlier: 4.251A pdb=" N ARG B 32 " --> pdb=" O GLU B 28 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 55 removed outlier: 3.598A pdb=" N ILE B 55 " --> pdb=" O LYS B 51 " (cutoff:3.500A) Processing helix chain 'B' and resid 209 through 217 removed outlier: 4.249A pdb=" N HIS B 213 " --> pdb=" O LYS B 210 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N GLU B 216 " --> pdb=" O HIS B 213 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N GLY B 217 " --> pdb=" O CYS B 214 " (cutoff:3.500A) Processing helix chain 'B' and resid 246 through 255 removed outlier: 3.660A pdb=" N ASN B 255 " --> pdb=" O ASP B 251 " (cutoff:3.500A) Processing helix chain 'B' and resid 327 through 351 removed outlier: 4.236A pdb=" N ASN B 331 " --> pdb=" O THR B 327 " (cutoff:3.500A) Processing helix chain 'C' and resid 3 through 25 removed outlier: 3.946A pdb=" N CYS C 25 " --> pdb=" O ALA C 21 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 35 Processing helix chain 'D' and resid 7 through 22 Processing helix chain 'D' and resid 29 through 44 Processing helix chain 'E' and resid 53 through 56 removed outlier: 4.059A pdb=" N GLY E 56 " --> pdb=" O SER E 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 53 through 56' Processing helix chain 'E' and resid 87 through 91 removed outlier: 3.659A pdb=" N ASP E 90 " --> pdb=" O ARG E 87 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N THR E 91 " --> pdb=" O SER E 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 87 through 91' Processing sheet with id=AA1, first strand: chain 'A' and resid 10 through 12 Processing sheet with id=AA2, first strand: chain 'A' and resid 169 through 171 Processing sheet with id=AA3, first strand: chain 'B' and resid 185 through 190 removed outlier: 10.256A pdb=" N ALA B 220 " --> pdb=" O GLU B 33 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N LYS B 35 " --> pdb=" O ALA B 220 " (cutoff:3.500A) removed outlier: 7.953A pdb=" N ILE B 222 " --> pdb=" O LYS B 35 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N LEU B 37 " --> pdb=" O ILE B 222 " (cutoff:3.500A) removed outlier: 7.836A pdb=" N CYS B 224 " --> pdb=" O LEU B 37 " (cutoff:3.500A) removed outlier: 7.405A pdb=" N LEU B 39 " --> pdb=" O CYS B 224 " (cutoff:3.500A) removed outlier: 5.841A pdb=" N ILE B 221 " --> pdb=" O ILE B 265 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N PHE B 267 " --> pdb=" O ILE B 221 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N PHE B 223 " --> pdb=" O PHE B 267 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 46 through 51 removed outlier: 5.599A pdb=" N THR C 47 " --> pdb=" O ASN C 340 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N ASN C 340 " --> pdb=" O THR C 47 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ARG C 49 " --> pdb=" O ILE C 338 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LYS C 337 " --> pdb=" O THR C 329 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 61 through 63 removed outlier: 3.564A pdb=" N LEU C 70 " --> pdb=" O TRP C 82 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N HIS C 91 " --> pdb=" O ILE C 81 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 100 through 103 removed outlier: 6.575A pdb=" N ILE C 123 " --> pdb=" O SER C 136 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ARG C 134 " --> pdb=" O ASN C 125 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 150 through 151 removed outlier: 3.743A pdb=" N ILE C 157 " --> pdb=" O TRP C 169 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N THR C 178 " --> pdb=" O LEU C 168 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N ASP C 170 " --> pdb=" O GLN C 176 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N GLN C 176 " --> pdb=" O ASP C 170 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 198 through 202 removed outlier: 3.894A pdb=" N PHE C 199 " --> pdb=" O TRP C 211 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LYS C 209 " --> pdb=" O SER C 201 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLN C 220 " --> pdb=" O LEU C 210 " (cutoff:3.500A) removed outlier: 7.267A pdb=" N ASP C 212 " --> pdb=" O CYS C 218 " (cutoff:3.500A) removed outlier: 7.179A pdb=" N CYS C 218 " --> pdb=" O ASP C 212 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 229 through 234 removed outlier: 6.098A pdb=" N GLY C 244 " --> pdb=" O ASN C 230 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N ILE C 232 " --> pdb=" O ALA C 242 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N ALA C 242 " --> pdb=" O ILE C 232 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N PHE C 234 " --> pdb=" O ALA C 240 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N ALA C 240 " --> pdb=" O PHE C 234 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N PHE C 241 " --> pdb=" O PHE C 253 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N SER C 245 " --> pdb=" O THR C 249 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N THR C 249 " --> pdb=" O SER C 245 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N CYS C 250 " --> pdb=" O THR C 263 " (cutoff:3.500A) removed outlier: 5.034A pdb=" N THR C 263 " --> pdb=" O CYS C 250 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N LEU C 252 " --> pdb=" O LEU C 261 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLN C 259 " --> pdb=" O ASP C 254 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 273 through 277 removed outlier: 6.716A pdb=" N GLY C 288 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N VAL C 276 " --> pdb=" O LEU C 286 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N LEU C 286 " --> pdb=" O VAL C 276 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ASN C 295 " --> pdb=" O ALA C 287 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 4 through 5 removed outlier: 3.631A pdb=" N LEU E 20 " --> pdb=" O LEU E 81 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 58 through 60 removed outlier: 6.416A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N TYR E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N MET E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N VAL E 97 " --> pdb=" O HIS E 35 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N VAL E 37 " --> pdb=" O TYR E 95 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 140 through 141 removed outlier: 3.933A pdb=" N VAL E 155 " --> pdb=" O ILE E 216 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ILE E 216 " --> pdb=" O VAL E 155 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N PHE E 212 " --> pdb=" O CYS E 159 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ALA E 211 " --> pdb=" O SER E 208 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 146 through 148 removed outlier: 3.799A pdb=" N GLY E 225 " --> pdb=" O LEU E 245 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ILE E 189 " --> pdb=" O TRP E 176 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N LEU E 178 " --> pdb=" O LEU E 187 " (cutoff:3.500A) removed outlier: 5.853A pdb=" N LEU E 187 " --> pdb=" O LEU E 178 " (cutoff:3.500A) 378 hydrogen bonds defined for protein. 1074 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: 1.04 Time building geometry restraints manager: 0.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2734 1.34 - 1.47: 2168 1.47 - 1.59: 3654 1.59 - 1.71: 0 1.71 - 1.83: 88 Bond restraints: 8644 Sorted by residual: bond pdb=" C07 OKL A 401 " pdb=" O08 OKL A 401 " ideal model delta sigma weight residual 1.214 1.398 -0.184 2.00e-02 2.50e+03 8.51e+01 bond pdb=" C10 OKL A 401 " pdb=" O11 OKL A 401 " ideal model delta sigma weight residual 1.215 1.397 -0.182 2.00e-02 2.50e+03 8.24e+01 bond pdb=" C15 OKL A 401 " pdb="CL17 OKL A 401 " ideal model delta sigma weight residual 1.692 1.784 -0.092 2.00e-02 2.50e+03 2.10e+01 bond pdb=" C10 OKL A 401 " pdb=" N09 OKL A 401 " ideal model delta sigma weight residual 1.390 1.324 0.066 2.00e-02 2.50e+03 1.08e+01 bond pdb=" C07 OKL A 401 " pdb=" N09 OKL A 401 " ideal model delta sigma weight residual 1.384 1.328 0.056 2.00e-02 2.50e+03 7.83e+00 ... (remaining 8639 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.90: 11490 1.90 - 3.79: 169 3.79 - 5.69: 35 5.69 - 7.59: 7 7.59 - 9.49: 4 Bond angle restraints: 11705 Sorted by residual: angle pdb=" N VAL A 27 " pdb=" CA VAL A 27 " pdb=" C VAL A 27 " ideal model delta sigma weight residual 111.91 108.66 3.25 8.90e-01 1.26e+00 1.34e+01 angle pdb=" N PRO A 31 " pdb=" CA PRO A 31 " pdb=" C PRO A 31 " ideal model delta sigma weight residual 110.70 114.65 -3.95 1.22e+00 6.72e-01 1.05e+01 angle pdb=" CA PRO A 31 " pdb=" C PRO A 31 " pdb=" N PRO A 32 " ideal model delta sigma weight residual 117.93 121.75 -3.82 1.20e+00 6.94e-01 1.01e+01 angle pdb=" C07 OKL A 401 " pdb=" N09 OKL A 401 " pdb=" C10 OKL A 401 " ideal model delta sigma weight residual 129.77 120.34 9.43 3.00e+00 1.11e-01 9.87e+00 angle pdb=" C12 OKL A 401 " pdb=" C10 OKL A 401 " pdb=" N09 OKL A 401 " ideal model delta sigma weight residual 109.84 119.22 -9.38 3.00e+00 1.11e-01 9.78e+00 ... (remaining 11700 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.18: 4682 27.18 - 54.37: 383 54.37 - 81.55: 27 81.55 - 108.74: 5 108.74 - 135.92: 1 Dihedral angle restraints: 5098 sinusoidal: 1981 harmonic: 3117 Sorted by residual: dihedral pdb=" CB CYS E 159 " pdb=" SG CYS E 159 " pdb=" SG CYS E 229 " pdb=" CB CYS E 229 " ideal model delta sinusoidal sigma weight residual 93.00 146.24 -53.24 1 1.00e+01 1.00e-02 3.85e+01 dihedral pdb=" C03 OKL A 401 " pdb=" C04 OKL A 401 " pdb=" C05 OKL A 401 " pdb=" N06 OKL A 401 " ideal model delta sinusoidal sigma weight residual 183.45 47.53 135.92 1 3.00e+01 1.11e-03 1.83e+01 dihedral pdb=" CA PHE E 32 " pdb=" C PHE E 32 " pdb=" N GLY E 33 " pdb=" CA GLY E 33 " ideal model delta harmonic sigma weight residual 180.00 162.13 17.87 0 5.00e+00 4.00e-02 1.28e+01 ... (remaining 5095 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 940 0.037 - 0.074: 265 0.074 - 0.112: 93 0.112 - 0.149: 21 0.149 - 0.186: 4 Chirality restraints: 1323 Sorted by residual: chirality pdb=" CA ASN A 110 " pdb=" N ASN A 110 " pdb=" C ASN A 110 " pdb=" CB ASN A 110 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.65e-01 chirality pdb=" CA PRO A 31 " pdb=" N PRO A 31 " pdb=" C PRO A 31 " pdb=" CB PRO A 31 " both_signs ideal model delta sigma weight residual False 2.72 2.54 0.18 2.00e-01 2.50e+01 8.06e-01 chirality pdb=" CB THR C 47 " pdb=" CA THR C 47 " pdb=" OG1 THR C 47 " pdb=" CG2 THR C 47 " both_signs ideal model delta sigma weight residual False 2.55 2.39 0.16 2.00e-01 2.50e+01 6.28e-01 ... (remaining 1320 not shown) Planarity restraints: 1476 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN D 24 " -0.010 2.00e-02 2.50e+03 1.94e-02 3.75e+00 pdb=" C ASN D 24 " 0.034 2.00e-02 2.50e+03 pdb=" O ASN D 24 " -0.013 2.00e-02 2.50e+03 pdb=" N ILE D 25 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C MET A 167 " 0.030 5.00e-02 4.00e+02 4.53e-02 3.29e+00 pdb=" N PRO A 168 " -0.078 5.00e-02 4.00e+02 pdb=" CA PRO A 168 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 168 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 31 " -0.029 5.00e-02 4.00e+02 4.31e-02 2.98e+00 pdb=" N PRO A 32 " 0.075 5.00e-02 4.00e+02 pdb=" CA PRO A 32 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 32 " -0.025 5.00e-02 4.00e+02 ... (remaining 1473 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 337 2.71 - 3.26: 8449 3.26 - 3.80: 13449 3.80 - 4.35: 16469 4.35 - 4.90: 28460 Nonbonded interactions: 67164 Sorted by model distance: nonbonded pdb=" OE2 GLU B 8 " pdb=" OH TYR E 175 " model vdw 2.159 3.040 nonbonded pdb=" OG1 THR C 274 " pdb=" O GLY C 288 " model vdw 2.189 3.040 nonbonded pdb=" O ILE E 138 " pdb=" OG1 THR E 238 " model vdw 2.198 3.040 nonbonded pdb=" O ILE A 278 " pdb=" OG SER A 281 " model vdw 2.202 3.040 nonbonded pdb=" OG1 THR C 184 " pdb=" OD2 ASP C 205 " model vdw 2.208 3.040 ... (remaining 67159 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: 0.480 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: 0.000 Extract box with map and model: 0.090 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 7.510 Find NCS groups from input model: 0.040 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: 0.010 Load rotamer database and sin/cos tables:0.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.184 8649 Z= 0.201 Angle : 0.612 9.487 11715 Z= 0.317 Chirality : 0.042 0.186 1323 Planarity : 0.004 0.045 1476 Dihedral : 18.046 135.922 3067 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 11.81 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.48 % Favored : 96.42 % Rotamer: Outliers : 0.55 % Allowed : 36.50 % Favored : 62.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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 aren not related in a simple way. whole: -0.49 (0.26), residues: 1062 helix: 1.73 (0.28), residues: 337 sheet: -1.07 (0.30), residues: 286 loop : -1.40 (0.28), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 27 TYR 0.007 0.001 TYR E 235 PHE 0.011 0.001 PHE A 197 TRP 0.010 0.001 TRP C 63 HIS 0.004 0.001 HIS C 311 Details of bonding type rmsd covalent geometry : bond 0.00415 ( 8644) covalent geometry : angle 0.61194 (11705) SS BOND : bond 0.00521 ( 5) SS BOND : angle 0.99318 ( 10) hydrogen bonds : bond 0.17031 ( 378) hydrogen bonds : angle 6.42909 ( 1074) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 219 time to evaluate : 0.198 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 16 LYS cc_start: 0.7345 (ttmt) cc_final: 0.7139 (mmtm) REVERT: A 63 ARG cc_start: 0.8063 (ttp-110) cc_final: 0.7731 (mmt-90) REVERT: A 288 MET cc_start: 0.7798 (ttm) cc_final: 0.7248 (ttp) REVERT: C 145 TYR cc_start: 0.9107 (p90) cc_final: 0.8734 (p90) REVERT: C 172 GLU cc_start: 0.7195 (pm20) cc_final: 0.6978 (pm20) outliers start: 5 outliers final: 2 residues processed: 221 average time/residue: 0.0767 time to fit residues: 23.5103 Evaluate side-chains 198 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 196 time to evaluate : 0.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 9 ASP Chi-restraints excluded: chain B residue 188 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 49 optimal weight: 6.9990 chunk 97 optimal weight: 3.9990 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 7.9990 chunk 65 optimal weight: 6.9990 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 0.6980 chunk 100 optimal weight: 5.9990 chunk 38 optimal weight: 6.9990 chunk 61 optimal weight: 4.9990 overall best weight: 2.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 110 ASN A 133 HIS A 134 HIS A 223 HIS ** C 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.188271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.136068 restraints weight = 10783.799| |-----------------------------------------------------------------------------| r_work (start): 0.3566 rms_B_bonded: 2.92 r_work: 0.3349 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.3349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.1715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 8649 Z= 0.241 Angle : 0.662 7.364 11715 Z= 0.349 Chirality : 0.045 0.165 1323 Planarity : 0.004 0.047 1476 Dihedral : 6.514 141.080 1169 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.27 % Favored : 94.63 % Rotamer: Outliers : 4.37 % Allowed : 31.91 % Favored : 63.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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 aren not related in a simple way. whole: -0.62 (0.25), residues: 1062 helix: 1.33 (0.27), residues: 351 sheet: -1.08 (0.31), residues: 265 loop : -1.36 (0.28), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 101 TYR 0.022 0.002 TYR A 284 PHE 0.016 0.002 PHE E 27 TRP 0.013 0.002 TRP E 47 HIS 0.009 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00568 ( 8644) covalent geometry : angle 0.66049 (11705) SS BOND : bond 0.00859 ( 5) SS BOND : angle 1.85351 ( 10) hydrogen bonds : bond 0.04642 ( 378) hydrogen bonds : angle 5.14480 ( 1074) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 212 time to evaluate : 0.335 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 16 LYS cc_start: 0.7472 (ttmt) cc_final: 0.6265 (mtpp) REVERT: A 37 GLU cc_start: 0.8180 (mm-30) cc_final: 0.7928 (mm-30) REVERT: A 63 ARG cc_start: 0.8309 (ttp-110) cc_final: 0.7691 (mmt-90) REVERT: A 66 LEU cc_start: 0.8880 (OUTLIER) cc_final: 0.8619 (mm) REVERT: A 82 PHE cc_start: 0.8504 (m-80) cc_final: 0.8025 (m-80) REVERT: A 93 TRP cc_start: 0.8406 (t-100) cc_final: 0.7895 (t-100) REVERT: A 97 ASP cc_start: 0.6156 (t0) cc_final: 0.5733 (t0) REVERT: A 137 ASN cc_start: 0.6628 (m-40) cc_final: 0.5960 (m-40) REVERT: A 236 VAL cc_start: 0.8812 (OUTLIER) cc_final: 0.8439 (t) REVERT: A 269 TYR cc_start: 0.8021 (m-10) cc_final: 0.7793 (m-10) REVERT: A 288 MET cc_start: 0.8381 (ttm) cc_final: 0.8119 (ttp) REVERT: C 246 ASP cc_start: 0.7969 (m-30) cc_final: 0.7663 (m-30) REVERT: E 140 MET cc_start: 0.8757 (OUTLIER) cc_final: 0.8412 (ttm) REVERT: E 166 LEU cc_start: 0.8474 (OUTLIER) cc_final: 0.8258 (tt) outliers start: 40 outliers final: 24 residues processed: 238 average time/residue: 0.0803 time to fit residues: 26.8290 Evaluate side-chains 221 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 193 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 53 CYS Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 230 ILE Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 281 SER Chi-restraints excluded: chain A residue 282 PHE Chi-restraints excluded: chain B residue 6 SER Chi-restraints excluded: chain B residue 9 ASP Chi-restraints excluded: chain B residue 222 ILE Chi-restraints excluded: chain B residue 263 SER Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain C residue 74 SER Chi-restraints excluded: chain C residue 136 SER Chi-restraints excluded: chain C residue 321 THR Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain E residue 22 CYS Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 140 MET Chi-restraints excluded: chain E residue 166 LEU Chi-restraints excluded: chain E residue 192 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 92 optimal weight: 0.6980 chunk 48 optimal weight: 0.0970 chunk 41 optimal weight: 6.9990 chunk 86 optimal weight: 4.9990 chunk 42 optimal weight: 0.9990 chunk 37 optimal weight: 0.4980 chunk 81 optimal weight: 3.9990 chunk 55 optimal weight: 0.9980 chunk 103 optimal weight: 0.7980 chunk 82 optimal weight: 6.9990 chunk 24 optimal weight: 0.8980 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 ASN A 68 ASN A 110 ASN B 188 HIS B 331 ASN B 347 ASN ** C 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4200 r_free = 0.4200 target = 0.193050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.141966 restraints weight = 10594.969| |-----------------------------------------------------------------------------| r_work (start): 0.3641 rms_B_bonded: 2.92 r_work: 0.3414 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.3414 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.1937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 8649 Z= 0.124 Angle : 0.571 7.165 11715 Z= 0.299 Chirality : 0.042 0.151 1323 Planarity : 0.004 0.044 1476 Dihedral : 6.030 137.477 1167 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.39 % Favored : 96.52 % Rotamer: Outliers : 4.04 % Allowed : 31.04 % Favored : 64.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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 aren not related in a simple way. whole: -0.40 (0.26), residues: 1062 helix: 1.56 (0.28), residues: 351 sheet: -0.96 (0.31), residues: 253 loop : -1.27 (0.28), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 128 TYR 0.012 0.001 TYR A 126 PHE 0.025 0.001 PHE A 38 TRP 0.010 0.001 TRP C 63 HIS 0.004 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00281 ( 8644) covalent geometry : angle 0.56803 (11705) SS BOND : bond 0.00613 ( 5) SS BOND : angle 1.98987 ( 10) hydrogen bonds : bond 0.03856 ( 378) hydrogen bonds : angle 4.67429 ( 1074) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 213 time to evaluate : 0.322 Fit side-chains revert: symmetry clash REVERT: A 13 ILE cc_start: 0.8330 (mp) cc_final: 0.8061 (mp) REVERT: A 14 ASP cc_start: 0.8620 (t70) cc_final: 0.8221 (t70) REVERT: A 16 LYS cc_start: 0.7687 (ttmt) cc_final: 0.6765 (mtpp) REVERT: A 21 PHE cc_start: 0.6637 (OUTLIER) cc_final: 0.5646 (m-10) REVERT: A 63 ARG cc_start: 0.8446 (ttp-110) cc_final: 0.7749 (mmt180) REVERT: A 137 ASN cc_start: 0.6864 (m-40) cc_final: 0.6302 (m-40) REVERT: A 167 MET cc_start: 0.5798 (OUTLIER) cc_final: 0.5584 (mmp) REVERT: A 196 GLU cc_start: 0.8248 (pt0) cc_final: 0.7949 (pt0) REVERT: A 236 VAL cc_start: 0.8708 (OUTLIER) cc_final: 0.8380 (t) REVERT: A 269 TYR cc_start: 0.7955 (m-10) cc_final: 0.7656 (m-10) REVERT: A 288 MET cc_start: 0.8291 (ttm) cc_final: 0.8052 (ttp) REVERT: C 246 ASP cc_start: 0.7979 (m-30) cc_final: 0.7763 (m-30) REVERT: C 332 TRP cc_start: 0.9015 (m-10) cc_final: 0.8705 (m-10) REVERT: D 48 ASP cc_start: 0.7941 (t0) cc_final: 0.7629 (t0) REVERT: E 140 MET cc_start: 0.8740 (ttm) cc_final: 0.8244 (ttm) REVERT: E 166 LEU cc_start: 0.8429 (OUTLIER) cc_final: 0.8187 (tt) outliers start: 37 outliers final: 15 residues processed: 234 average time/residue: 0.0718 time to fit residues: 23.9470 Evaluate side-chains 209 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 190 time to evaluate : 0.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 PHE Chi-restraints excluded: chain A residue 53 CYS Chi-restraints excluded: chain A residue 167 MET Chi-restraints excluded: chain A residue 182 ILE Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 281 SER Chi-restraints excluded: chain A residue 282 PHE Chi-restraints excluded: chain B residue 188 HIS Chi-restraints excluded: chain B residue 222 ILE Chi-restraints excluded: chain B residue 263 SER Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 74 SER Chi-restraints excluded: chain E residue 22 CYS Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain E residue 166 LEU Chi-restraints excluded: chain E residue 192 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 23 optimal weight: 3.9990 chunk 63 optimal weight: 0.0770 chunk 86 optimal weight: 6.9990 chunk 28 optimal weight: 0.9990 chunk 5 optimal weight: 3.9990 chunk 93 optimal weight: 1.9990 chunk 26 optimal weight: 0.7980 chunk 83 optimal weight: 0.9990 chunk 4 optimal weight: 0.9990 chunk 34 optimal weight: 10.0000 chunk 70 optimal weight: 6.9990 overall best weight: 0.7744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 ASN A 110 ASN A 171 ASN B 188 HIS ** C 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.190879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.141479 restraints weight = 10848.011| |-----------------------------------------------------------------------------| r_work (start): 0.3670 rms_B_bonded: 2.57 r_work: 0.3444 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.3444 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.2136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8649 Z= 0.133 Angle : 0.591 7.364 11715 Z= 0.307 Chirality : 0.042 0.154 1323 Planarity : 0.004 0.044 1476 Dihedral : 5.811 134.775 1165 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.05 % Favored : 95.86 % Rotamer: Outliers : 5.68 % Allowed : 30.27 % Favored : 64.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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 aren not related in a simple way. whole: -0.32 (0.26), residues: 1062 helix: 1.64 (0.28), residues: 352 sheet: -0.92 (0.30), residues: 266 loop : -1.23 (0.29), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 128 TYR 0.010 0.001 TYR A 126 PHE 0.018 0.001 PHE A 197 TRP 0.011 0.001 TRP C 297 HIS 0.004 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00308 ( 8644) covalent geometry : angle 0.58723 (11705) SS BOND : bond 0.00798 ( 5) SS BOND : angle 2.40527 ( 10) hydrogen bonds : bond 0.03771 ( 378) hydrogen bonds : angle 4.55031 ( 1074) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 202 time to evaluate : 0.340 Fit side-chains revert: symmetry clash REVERT: A 16 LYS cc_start: 0.7585 (ttmt) cc_final: 0.7094 (mtpp) REVERT: A 21 PHE cc_start: 0.6616 (OUTLIER) cc_final: 0.5668 (m-10) REVERT: A 45 ASN cc_start: 0.7405 (m-40) cc_final: 0.7012 (m110) REVERT: A 63 ARG cc_start: 0.8400 (ttp-110) cc_final: 0.7644 (mmt180) REVERT: A 137 ASN cc_start: 0.6919 (m-40) cc_final: 0.6466 (m-40) REVERT: A 167 MET cc_start: 0.5650 (OUTLIER) cc_final: 0.5300 (mmp) REVERT: A 192 MET cc_start: 0.7870 (ppp) cc_final: 0.7655 (ppp) REVERT: A 236 VAL cc_start: 0.8764 (OUTLIER) cc_final: 0.8440 (t) REVERT: C 332 TRP cc_start: 0.9031 (m-10) cc_final: 0.8721 (m-10) REVERT: D 48 ASP cc_start: 0.7993 (t0) cc_final: 0.7648 (t0) REVERT: E 140 MET cc_start: 0.8781 (OUTLIER) cc_final: 0.8298 (ttm) REVERT: E 166 LEU cc_start: 0.8406 (OUTLIER) cc_final: 0.8177 (tt) outliers start: 52 outliers final: 34 residues processed: 232 average time/residue: 0.0827 time to fit residues: 27.4575 Evaluate side-chains 230 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 191 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 CYS Chi-restraints excluded: chain A residue 21 PHE Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 53 CYS Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 167 MET Chi-restraints excluded: chain A residue 182 ILE Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 281 SER Chi-restraints excluded: chain A residue 282 PHE Chi-restraints excluded: chain B residue 6 SER Chi-restraints excluded: chain B residue 9 ASP Chi-restraints excluded: chain B residue 188 HIS Chi-restraints excluded: chain B residue 212 ILE Chi-restraints excluded: chain B residue 222 ILE Chi-restraints excluded: chain B residue 263 SER Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 74 SER Chi-restraints excluded: chain C residue 120 ILE Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 136 SER Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 266 HIS Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain C residue 301 LYS Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain D residue 31 SER Chi-restraints excluded: chain E residue 22 CYS Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain E residue 140 MET Chi-restraints excluded: chain E residue 166 LEU Chi-restraints excluded: chain E residue 192 MET Chi-restraints excluded: chain E residue 213 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 9 optimal weight: 0.8980 chunk 78 optimal weight: 10.0000 chunk 87 optimal weight: 3.9990 chunk 79 optimal weight: 5.9990 chunk 0 optimal weight: 20.0000 chunk 44 optimal weight: 10.0000 chunk 17 optimal weight: 7.9990 chunk 89 optimal weight: 0.7980 chunk 41 optimal weight: 6.9990 chunk 42 optimal weight: 3.9990 chunk 100 optimal weight: 6.9990 overall best weight: 3.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 110 ASN A 141 ASN A 171 ASN B 188 HIS B 347 ASN ** C 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 239 ASN D 18 GLN D 24 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.183221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.131296 restraints weight = 10851.476| |-----------------------------------------------------------------------------| r_work (start): 0.3547 rms_B_bonded: 2.87 r_work: 0.3335 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.3335 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.2536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.063 8649 Z= 0.331 Angle : 0.724 8.473 11715 Z= 0.379 Chirality : 0.046 0.174 1323 Planarity : 0.005 0.047 1476 Dihedral : 6.127 129.728 1165 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 10.98 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.74 % Favored : 94.16 % Rotamer: Outliers : 6.89 % Allowed : 30.16 % Favored : 62.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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 aren not related in a simple way. whole: -0.69 (0.25), residues: 1062 helix: 1.38 (0.27), residues: 345 sheet: -1.14 (0.30), residues: 267 loop : -1.45 (0.28), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 111 TYR 0.025 0.002 TYR A 284 PHE 0.020 0.002 PHE E 27 TRP 0.037 0.002 TRP A 93 HIS 0.011 0.002 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00786 ( 8644) covalent geometry : angle 0.72189 (11705) SS BOND : bond 0.01057 ( 5) SS BOND : angle 2.21676 ( 10) hydrogen bonds : bond 0.04545 ( 378) hydrogen bonds : angle 4.94795 ( 1074) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 191 time to evaluate : 0.346 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 LYS cc_start: 0.7616 (ttmt) cc_final: 0.6901 (mtpp) REVERT: A 45 ASN cc_start: 0.7606 (m-40) cc_final: 0.7187 (m110) REVERT: A 63 ARG cc_start: 0.8425 (ttp-110) cc_final: 0.7863 (mmt180) REVERT: A 73 ASP cc_start: 0.8692 (t70) cc_final: 0.8418 (t70) REVERT: A 137 ASN cc_start: 0.7264 (m-40) cc_final: 0.6930 (m-40) REVERT: A 167 MET cc_start: 0.5969 (OUTLIER) cc_final: 0.5691 (mmp) REVERT: A 192 MET cc_start: 0.8030 (ppp) cc_final: 0.7691 (ppp) REVERT: A 236 VAL cc_start: 0.8880 (OUTLIER) cc_final: 0.8539 (t) REVERT: A 255 PHE cc_start: 0.7826 (OUTLIER) cc_final: 0.7402 (m-10) REVERT: B 9 ASP cc_start: 0.8446 (OUTLIER) cc_final: 0.8112 (t0) REVERT: B 188 HIS cc_start: 0.7177 (OUTLIER) cc_final: 0.6967 (p-80) REVERT: C 332 TRP cc_start: 0.9048 (m-10) cc_final: 0.8832 (m-10) REVERT: E 166 LEU cc_start: 0.8650 (OUTLIER) cc_final: 0.8379 (tt) outliers start: 63 outliers final: 40 residues processed: 227 average time/residue: 0.0805 time to fit residues: 26.3105 Evaluate side-chains 229 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 183 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 CYS Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 62 SER Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 167 MET Chi-restraints excluded: chain A residue 182 ILE Chi-restraints excluded: chain A residue 183 CYS Chi-restraints excluded: chain A residue 222 ARG Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 255 PHE Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 281 SER Chi-restraints excluded: chain B residue 6 SER Chi-restraints excluded: chain B residue 9 ASP Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 188 HIS Chi-restraints excluded: chain B residue 212 ILE Chi-restraints excluded: chain B residue 222 ILE Chi-restraints excluded: chain B residue 263 SER Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 74 SER Chi-restraints excluded: chain C residue 136 SER Chi-restraints excluded: chain C residue 160 SER Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 266 HIS Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain C residue 301 LYS Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain D residue 24 ASN Chi-restraints excluded: chain D residue 27 ARG Chi-restraints excluded: chain D residue 31 SER Chi-restraints excluded: chain E residue 22 CYS Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain E residue 166 LEU Chi-restraints excluded: chain E residue 192 MET Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain E residue 208 SER Chi-restraints excluded: chain E residue 213 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 25 optimal weight: 5.9990 chunk 1 optimal weight: 6.9990 chunk 63 optimal weight: 0.7980 chunk 33 optimal weight: 9.9990 chunk 57 optimal weight: 0.6980 chunk 30 optimal weight: 0.9990 chunk 21 optimal weight: 0.6980 chunk 99 optimal weight: 0.9980 chunk 94 optimal weight: 5.9990 chunk 55 optimal weight: 0.8980 chunk 6 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 ASN A 134 HIS A 171 ASN B 188 HIS ** C 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.186867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.132567 restraints weight = 10713.830| |-----------------------------------------------------------------------------| r_work (start): 0.3539 rms_B_bonded: 2.93 r_work: 0.3370 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7655 moved from start: 0.2502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8649 Z= 0.141 Angle : 0.608 7.016 11715 Z= 0.318 Chirality : 0.043 0.240 1323 Planarity : 0.004 0.042 1476 Dihedral : 5.901 132.549 1165 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.95 % Favored : 95.95 % Rotamer: Outliers : 4.59 % Allowed : 33.77 % Favored : 61.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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 aren not related in a simple way. whole: -0.47 (0.26), residues: 1062 helix: 1.48 (0.28), residues: 352 sheet: -1.05 (0.30), residues: 265 loop : -1.25 (0.29), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 49 TYR 0.012 0.001 TYR E 60 PHE 0.020 0.001 PHE A 197 TRP 0.029 0.001 TRP A 93 HIS 0.008 0.001 HIS B 188 Details of bonding type rmsd covalent geometry : bond 0.00322 ( 8644) covalent geometry : angle 0.60642 (11705) SS BOND : bond 0.00656 ( 5) SS BOND : angle 1.41942 ( 10) hydrogen bonds : bond 0.03894 ( 378) hydrogen bonds : angle 4.64572 ( 1074) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 192 time to evaluate : 0.381 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 LYS cc_start: 0.7683 (ttmt) cc_final: 0.7224 (mtpp) REVERT: A 21 PHE cc_start: 0.6514 (OUTLIER) cc_final: 0.5542 (m-10) REVERT: A 63 ARG cc_start: 0.8333 (ttp-110) cc_final: 0.7564 (mmt180) REVERT: A 73 ASP cc_start: 0.8588 (OUTLIER) cc_final: 0.8284 (t70) REVERT: A 137 ASN cc_start: 0.7131 (m-40) cc_final: 0.6807 (m-40) REVERT: A 167 MET cc_start: 0.6012 (OUTLIER) cc_final: 0.5700 (mmp) REVERT: A 192 MET cc_start: 0.7946 (ppp) cc_final: 0.7665 (ppp) REVERT: A 236 VAL cc_start: 0.8503 (t) cc_final: 0.8185 (t) REVERT: B 9 ASP cc_start: 0.8312 (OUTLIER) cc_final: 0.8011 (t0) REVERT: D 48 ASP cc_start: 0.8111 (t70) cc_final: 0.7785 (t0) REVERT: E 166 LEU cc_start: 0.8654 (OUTLIER) cc_final: 0.8396 (tt) outliers start: 42 outliers final: 29 residues processed: 214 average time/residue: 0.0881 time to fit residues: 26.7926 Evaluate side-chains 214 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 180 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 PHE Chi-restraints excluded: chain A residue 26 ILE Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 73 ASP Chi-restraints excluded: chain A residue 167 MET Chi-restraints excluded: chain A residue 182 ILE Chi-restraints excluded: chain A residue 187 GLN Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 281 SER Chi-restraints excluded: chain B residue 6 SER Chi-restraints excluded: chain B residue 9 ASP Chi-restraints excluded: chain B residue 188 HIS Chi-restraints excluded: chain B residue 212 ILE Chi-restraints excluded: chain B residue 222 ILE Chi-restraints excluded: chain B residue 263 SER Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 74 SER Chi-restraints excluded: chain C residue 120 ILE Chi-restraints excluded: chain C residue 136 SER Chi-restraints excluded: chain C residue 266 HIS Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain D residue 27 ARG Chi-restraints excluded: chain E residue 22 CYS Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain E residue 98 ARG Chi-restraints excluded: chain E residue 166 LEU Chi-restraints excluded: chain E residue 192 MET Chi-restraints excluded: chain E residue 208 SER Chi-restraints excluded: chain E residue 213 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 75 optimal weight: 0.8980 chunk 15 optimal weight: 1.9990 chunk 45 optimal weight: 7.9990 chunk 9 optimal weight: 0.7980 chunk 54 optimal weight: 1.9990 chunk 78 optimal weight: 20.0000 chunk 68 optimal weight: 0.5980 chunk 84 optimal weight: 2.9990 chunk 31 optimal weight: 6.9990 chunk 79 optimal weight: 2.9990 chunk 5 optimal weight: 3.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 ASN A 110 ASN A 171 ASN ** B 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 347 ASN C 32 GLN ** C 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.190614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.135518 restraints weight = 10897.364| |-----------------------------------------------------------------------------| r_work (start): 0.3573 rms_B_bonded: 3.01 r_work: 0.3390 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3390 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.2616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 8649 Z= 0.171 Angle : 0.645 11.005 11715 Z= 0.335 Chirality : 0.043 0.190 1323 Planarity : 0.004 0.042 1476 Dihedral : 5.873 129.567 1165 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.71 % Favored : 95.20 % Rotamer: Outliers : 5.46 % Allowed : 33.33 % Favored : 61.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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 aren not related in a simple way. whole: -0.51 (0.25), residues: 1062 helix: 1.37 (0.27), residues: 355 sheet: -1.01 (0.30), residues: 260 loop : -1.27 (0.28), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 111 TYR 0.012 0.001 TYR A 269 PHE 0.031 0.002 PHE A 38 TRP 0.019 0.001 TRP C 332 HIS 0.006 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00404 ( 8644) covalent geometry : angle 0.63429 (11705) SS BOND : bond 0.01048 ( 5) SS BOND : angle 3.96517 ( 10) hydrogen bonds : bond 0.04004 ( 378) hydrogen bonds : angle 4.67371 ( 1074) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 188 time to evaluate : 0.343 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 LYS cc_start: 0.7628 (ttmt) cc_final: 0.6829 (mtpp) REVERT: A 63 ARG cc_start: 0.8416 (ttp-110) cc_final: 0.7733 (mmt180) REVERT: A 73 ASP cc_start: 0.8695 (OUTLIER) cc_final: 0.8374 (t70) REVERT: A 137 ASN cc_start: 0.7225 (m-40) cc_final: 0.6906 (m-40) REVERT: A 167 MET cc_start: 0.5827 (OUTLIER) cc_final: 0.5370 (mmp) REVERT: A 192 MET cc_start: 0.8138 (ppp) cc_final: 0.7866 (ppp) REVERT: A 236 VAL cc_start: 0.8637 (OUTLIER) cc_final: 0.8316 (t) REVERT: A 255 PHE cc_start: 0.7821 (OUTLIER) cc_final: 0.7376 (m-10) REVERT: C 262 MET cc_start: 0.7270 (ttt) cc_final: 0.7054 (ttt) REVERT: D 48 ASP cc_start: 0.8199 (t70) cc_final: 0.7876 (t0) REVERT: E 166 LEU cc_start: 0.8654 (OUTLIER) cc_final: 0.8405 (tt) outliers start: 50 outliers final: 35 residues processed: 217 average time/residue: 0.0796 time to fit residues: 24.6055 Evaluate side-chains 220 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 180 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 ILE Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 62 SER Chi-restraints excluded: chain A residue 73 ASP Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 167 MET Chi-restraints excluded: chain A residue 182 ILE Chi-restraints excluded: chain A residue 187 GLN Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 255 PHE Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain B residue 6 SER Chi-restraints excluded: chain B residue 9 ASP Chi-restraints excluded: chain B residue 188 HIS Chi-restraints excluded: chain B residue 212 ILE Chi-restraints excluded: chain B residue 222 ILE Chi-restraints excluded: chain B residue 263 SER Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 74 SER Chi-restraints excluded: chain C residue 120 ILE Chi-restraints excluded: chain C residue 136 SER Chi-restraints excluded: chain C residue 161 SER Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 266 HIS Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain C residue 301 LYS Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain D residue 31 SER Chi-restraints excluded: chain E residue 22 CYS Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain E residue 98 ARG Chi-restraints excluded: chain E residue 166 LEU Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain E residue 208 SER Chi-restraints excluded: chain E residue 213 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 98 optimal weight: 0.8980 chunk 61 optimal weight: 8.9990 chunk 71 optimal weight: 0.6980 chunk 43 optimal weight: 0.9980 chunk 18 optimal weight: 1.9990 chunk 4 optimal weight: 6.9990 chunk 75 optimal weight: 0.5980 chunk 90 optimal weight: 2.9990 chunk 95 optimal weight: 9.9990 chunk 27 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 ASN A 110 ASN A 171 ASN B 188 HIS ** C 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4183 r_free = 0.4183 target = 0.191995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.136279 restraints weight = 10699.511| |-----------------------------------------------------------------------------| r_work (start): 0.3590 rms_B_bonded: 3.01 r_work: 0.3406 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3406 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7775 moved from start: 0.2690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 8649 Z= 0.155 Angle : 0.663 11.563 11715 Z= 0.341 Chirality : 0.044 0.259 1323 Planarity : 0.004 0.041 1476 Dihedral : 5.854 130.463 1165 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.43 % Favored : 95.48 % Rotamer: Outliers : 5.46 % Allowed : 33.77 % Favored : 60.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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 aren not related in a simple way. whole: -0.45 (0.25), residues: 1062 helix: 1.41 (0.27), residues: 352 sheet: -1.02 (0.30), residues: 255 loop : -1.18 (0.28), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 49 TYR 0.011 0.001 TYR E 190 PHE 0.032 0.001 PHE A 38 TRP 0.020 0.001 TRP A 93 HIS 0.006 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00365 ( 8644) covalent geometry : angle 0.65420 (11705) SS BOND : bond 0.01000 ( 5) SS BOND : angle 3.73365 ( 10) hydrogen bonds : bond 0.03913 ( 378) hydrogen bonds : angle 4.63144 ( 1074) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 185 time to evaluate : 0.369 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 LYS cc_start: 0.7574 (ttmt) cc_final: 0.6659 (mtpp) REVERT: A 21 PHE cc_start: 0.6466 (OUTLIER) cc_final: 0.5515 (m-10) REVERT: A 63 ARG cc_start: 0.8363 (ttp-110) cc_final: 0.7712 (mmt180) REVERT: A 73 ASP cc_start: 0.8660 (OUTLIER) cc_final: 0.8344 (t70) REVERT: A 93 TRP cc_start: 0.7772 (t-100) cc_final: 0.7560 (t-100) REVERT: A 137 ASN cc_start: 0.7261 (m-40) cc_final: 0.6952 (m-40) REVERT: A 167 MET cc_start: 0.5882 (OUTLIER) cc_final: 0.5406 (mmp) REVERT: A 192 MET cc_start: 0.8123 (ppp) cc_final: 0.7838 (ppp) REVERT: A 236 VAL cc_start: 0.8602 (t) cc_final: 0.8278 (t) REVERT: A 255 PHE cc_start: 0.7828 (OUTLIER) cc_final: 0.7379 (m-10) REVERT: A 285 MET cc_start: 0.7615 (ttm) cc_final: 0.7399 (tpp) REVERT: D 27 ARG cc_start: 0.7220 (ttp-110) cc_final: 0.6830 (ttp-110) REVERT: D 44 HIS cc_start: 0.8559 (m90) cc_final: 0.7833 (m90) REVERT: D 48 ASP cc_start: 0.8181 (t70) cc_final: 0.7825 (t0) REVERT: E 166 LEU cc_start: 0.8642 (OUTLIER) cc_final: 0.8390 (tt) outliers start: 50 outliers final: 37 residues processed: 216 average time/residue: 0.0784 time to fit residues: 24.0169 Evaluate side-chains 222 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 180 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 PHE Chi-restraints excluded: chain A residue 26 ILE Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 62 SER Chi-restraints excluded: chain A residue 73 ASP Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain A residue 110 ASN Chi-restraints excluded: chain A residue 167 MET Chi-restraints excluded: chain A residue 182 ILE Chi-restraints excluded: chain A residue 187 GLN Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 255 PHE Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain B residue 6 SER Chi-restraints excluded: chain B residue 9 ASP Chi-restraints excluded: chain B residue 188 HIS Chi-restraints excluded: chain B residue 212 ILE Chi-restraints excluded: chain B residue 222 ILE Chi-restraints excluded: chain B residue 263 SER Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 74 SER Chi-restraints excluded: chain C residue 120 ILE Chi-restraints excluded: chain C residue 136 SER Chi-restraints excluded: chain C residue 161 SER Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 266 HIS Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain C residue 301 LYS Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain D residue 31 SER Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 22 CYS Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain E residue 98 ARG Chi-restraints excluded: chain E residue 166 LEU Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain E residue 208 SER Chi-restraints excluded: chain E residue 213 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 52 optimal weight: 0.5980 chunk 71 optimal weight: 0.9980 chunk 102 optimal weight: 7.9990 chunk 20 optimal weight: 3.9990 chunk 35 optimal weight: 3.9990 chunk 73 optimal weight: 3.9990 chunk 85 optimal weight: 2.9990 chunk 74 optimal weight: 5.9990 chunk 28 optimal weight: 0.0470 chunk 98 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 overall best weight: 1.3282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 110 ASN A 161 HIS A 171 ASN ** B 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4163 r_free = 0.4163 target = 0.189781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.137201 restraints weight = 10836.829| |-----------------------------------------------------------------------------| r_work (start): 0.3608 rms_B_bonded: 2.71 r_work: 0.3398 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.3398 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.2753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 8649 Z= 0.178 Angle : 0.692 10.352 11715 Z= 0.354 Chirality : 0.045 0.238 1323 Planarity : 0.004 0.042 1476 Dihedral : 5.867 128.791 1165 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.71 % Favored : 95.20 % Rotamer: Outliers : 5.36 % Allowed : 33.77 % Favored : 60.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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 aren not related in a simple way. whole: -0.49 (0.25), residues: 1062 helix: 1.37 (0.27), residues: 354 sheet: -1.03 (0.30), residues: 260 loop : -1.22 (0.28), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 125 TYR 0.016 0.001 TYR A 269 PHE 0.022 0.001 PHE A 197 TRP 0.020 0.001 TRP C 332 HIS 0.006 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00423 ( 8644) covalent geometry : angle 0.68361 (11705) SS BOND : bond 0.01031 ( 5) SS BOND : angle 3.68758 ( 10) hydrogen bonds : bond 0.03993 ( 378) hydrogen bonds : angle 4.67709 ( 1074) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 180 time to evaluate : 0.196 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 LYS cc_start: 0.7480 (ttmt) cc_final: 0.7063 (mtpp) REVERT: A 63 ARG cc_start: 0.8476 (ttp-110) cc_final: 0.7863 (mmt180) REVERT: A 137 ASN cc_start: 0.7334 (m-40) cc_final: 0.7022 (m-40) REVERT: A 167 MET cc_start: 0.5857 (OUTLIER) cc_final: 0.5276 (mmp) REVERT: A 192 MET cc_start: 0.8306 (ppp) cc_final: 0.8016 (ppp) REVERT: A 236 VAL cc_start: 0.8822 (t) cc_final: 0.8503 (t) REVERT: A 255 PHE cc_start: 0.7764 (OUTLIER) cc_final: 0.7334 (m-10) REVERT: E 166 LEU cc_start: 0.8583 (OUTLIER) cc_final: 0.8337 (tt) outliers start: 49 outliers final: 41 residues processed: 212 average time/residue: 0.0737 time to fit residues: 22.1698 Evaluate side-chains 221 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 177 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 ILE Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 62 SER Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 110 ASN Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 161 HIS Chi-restraints excluded: chain A residue 167 MET Chi-restraints excluded: chain A residue 182 ILE Chi-restraints excluded: chain A residue 187 GLN Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 255 PHE Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain B residue 6 SER Chi-restraints excluded: chain B residue 9 ASP Chi-restraints excluded: chain B residue 188 HIS Chi-restraints excluded: chain B residue 212 ILE Chi-restraints excluded: chain B residue 222 ILE Chi-restraints excluded: chain B residue 263 SER Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 74 SER Chi-restraints excluded: chain C residue 120 ILE Chi-restraints excluded: chain C residue 136 SER Chi-restraints excluded: chain C residue 161 SER Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 266 HIS Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain C residue 301 LYS Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain D residue 31 SER Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 22 CYS Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain E residue 98 ARG Chi-restraints excluded: chain E residue 166 LEU Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain E residue 208 SER Chi-restraints excluded: chain E residue 213 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 37 optimal weight: 1.9990 chunk 56 optimal weight: 0.0060 chunk 100 optimal weight: 2.9990 chunk 9 optimal weight: 4.9990 chunk 13 optimal weight: 0.7980 chunk 48 optimal weight: 3.9990 chunk 29 optimal weight: 5.9990 chunk 14 optimal weight: 3.9990 chunk 81 optimal weight: 0.0470 chunk 22 optimal weight: 1.9990 chunk 27 optimal weight: 0.8980 overall best weight: 0.7496 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 ASN A 110 ASN A 161 HIS ** A 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 188 HIS ** C 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4194 r_free = 0.4194 target = 0.193072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.137571 restraints weight = 10730.693| |-----------------------------------------------------------------------------| r_work (start): 0.3603 rms_B_bonded: 3.07 r_work: 0.3427 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3427 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7753 moved from start: 0.2778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 8649 Z= 0.145 Angle : 0.682 9.865 11715 Z= 0.349 Chirality : 0.044 0.229 1323 Planarity : 0.004 0.041 1476 Dihedral : 5.831 130.781 1165 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.24 % Favored : 95.67 % Rotamer: Outliers : 4.70 % Allowed : 34.75 % Favored : 60.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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 aren not related in a simple way. whole: -0.45 (0.25), residues: 1062 helix: 1.41 (0.27), residues: 354 sheet: -0.94 (0.31), residues: 254 loop : -1.25 (0.28), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 125 TYR 0.012 0.001 TYR E 60 PHE 0.038 0.001 PHE A 38 TRP 0.022 0.001 TRP C 332 HIS 0.009 0.001 HIS A 161 Details of bonding type rmsd covalent geometry : bond 0.00337 ( 8644) covalent geometry : angle 0.67437 (11705) SS BOND : bond 0.00937 ( 5) SS BOND : angle 3.55137 ( 10) hydrogen bonds : bond 0.03832 ( 378) hydrogen bonds : angle 4.62676 ( 1074) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 180 time to evaluate : 0.385 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 LYS cc_start: 0.7354 (OUTLIER) cc_final: 0.6663 (mtpp) REVERT: A 63 ARG cc_start: 0.8325 (ttp-110) cc_final: 0.7727 (mmt180) REVERT: A 73 ASP cc_start: 0.8346 (t70) cc_final: 0.7868 (t70) REVERT: A 137 ASN cc_start: 0.7269 (m-40) cc_final: 0.6994 (m-40) REVERT: A 167 MET cc_start: 0.5922 (OUTLIER) cc_final: 0.5363 (mmp) REVERT: A 192 MET cc_start: 0.8176 (ppp) cc_final: 0.7881 (ppp) REVERT: A 236 VAL cc_start: 0.8582 (t) cc_final: 0.8270 (t) REVERT: A 255 PHE cc_start: 0.7811 (OUTLIER) cc_final: 0.7374 (m-10) REVERT: C 262 MET cc_start: 0.7362 (ttt) cc_final: 0.7147 (ttt) REVERT: E 166 LEU cc_start: 0.8606 (OUTLIER) cc_final: 0.8362 (tt) outliers start: 43 outliers final: 38 residues processed: 208 average time/residue: 0.0766 time to fit residues: 23.0579 Evaluate side-chains 217 residues out of total 932 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 175 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LYS Chi-restraints excluded: chain A residue 26 ILE Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 62 SER Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 110 ASN Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 161 HIS Chi-restraints excluded: chain A residue 167 MET Chi-restraints excluded: chain A residue 182 ILE Chi-restraints excluded: chain A residue 187 GLN Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 255 PHE Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain B residue 6 SER Chi-restraints excluded: chain B residue 9 ASP Chi-restraints excluded: chain B residue 188 HIS Chi-restraints excluded: chain B residue 212 ILE Chi-restraints excluded: chain B residue 222 ILE Chi-restraints excluded: chain B residue 263 SER Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 74 SER Chi-restraints excluded: chain C residue 120 ILE Chi-restraints excluded: chain C residue 136 SER Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 266 HIS Chi-restraints excluded: chain C residue 301 LYS Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain D residue 31 SER Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 22 CYS Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 97 VAL Chi-restraints excluded: chain E residue 98 ARG Chi-restraints excluded: chain E residue 166 LEU Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain E residue 208 SER Chi-restraints excluded: chain E residue 213 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 83 optimal weight: 5.9990 chunk 34 optimal weight: 8.9990 chunk 72 optimal weight: 1.9990 chunk 97 optimal weight: 3.9990 chunk 16 optimal weight: 10.0000 chunk 60 optimal weight: 5.9990 chunk 2 optimal weight: 0.7980 chunk 17 optimal weight: 0.8980 chunk 0 optimal weight: 5.9990 chunk 24 optimal weight: 0.8980 chunk 102 optimal weight: 7.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 110 ASN A 161 HIS ** A 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4166 r_free = 0.4166 target = 0.190307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.138995 restraints weight = 10803.995| |-----------------------------------------------------------------------------| r_work (start): 0.3621 rms_B_bonded: 2.68 r_work: 0.3382 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.3382 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.2843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 8649 Z= 0.209 Angle : 0.727 12.002 11715 Z= 0.371 Chirality : 0.046 0.336 1323 Planarity : 0.004 0.043 1476 Dihedral : 5.865 126.755 1165 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 11.27 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.27 % Favored : 94.63 % Rotamer: Outliers : 5.36 % Allowed : 33.88 % Favored : 60.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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 aren not related in a simple way. whole: -0.52 (0.25), residues: 1062 helix: 1.32 (0.27), residues: 355 sheet: -0.99 (0.30), residues: 270 loop : -1.26 (0.29), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 68 TYR 0.021 0.002 TYR A 269 PHE 0.024 0.002 PHE A 40 TRP 0.028 0.002 TRP C 332 HIS 0.010 0.001 HIS A 161 Details of bonding type rmsd covalent geometry : bond 0.00497 ( 8644) covalent geometry : angle 0.71971 (11705) SS BOND : bond 0.01034 ( 5) SS BOND : angle 3.57658 ( 10) hydrogen bonds : bond 0.04101 ( 378) hydrogen bonds : angle 4.73838 ( 1074) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2135.66 seconds wall clock time: 37 minutes 24.27 seconds (2244.27 seconds total)