Starting phenix.real_space_refine on Fri Aug 22 23:10:01 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xvh_38704/08_2025/8xvh_38704.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xvh_38704/08_2025/8xvh_38704.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.26 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8xvh_38704/08_2025/8xvh_38704.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xvh_38704/08_2025/8xvh_38704.map" model { file = "/net/cci-nas-00/data/ceres_data/8xvh_38704/08_2025/8xvh_38704.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xvh_38704/08_2025/8xvh_38704.cif" } resolution = 3.26 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= 0.028 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 62 5.16 5 C 5427 2.51 5 N 1480 2.21 5 O 1575 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s 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: 8544 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1935 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1935 Classifications: {'peptide': 233} Link IDs: {'PTRANS': 6, 'TRANS': 226} Chain breaks: 1 Chain: "B" Number of atoms: 2600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2600 Classifications: {'peptide': 338} Link IDs: {'PTRANS': 5, 'TRANS': 332} Chain: "G" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 436 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Chain: "N" Number of atoms: 961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 961 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 5, 'TRANS': 120} Chain: "T" Number of atoms: 171 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 171 Classifications: {'peptide': 21} Modifications used: {'COO': 1} Link IDs: {'TRANS': 20} Chain: "R" Number of atoms: 2441 Number of conformers: 1 Conformer: "" Number of residues, atoms: 305, 2441 Classifications: {'peptide': 305} Link IDs: {'PTRANS': 14, 'TRANS': 290} Chain breaks: 1 Time building chain proxies: 1.62, per 1000 atoms: 0.19 Number of scatterers: 8544 At special positions: 0 Unit cell: (82.56, 104.64, 144.96, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 62 16.00 O 1575 8.00 N 1480 7.00 C 5427 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.04 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.03 Simple disulfide: pdb=" SG CYS T 1 " - pdb=" SG CYS T 15 " distance=2.03 Simple disulfide: pdb=" SG CYS T 3 " - pdb=" SG CYS T 11 " distance=2.03 Simple disulfide: pdb=" SG CYS R 90 " - pdb=" SG CYS R 358 " distance=2.03 Simple disulfide: pdb=" SG CYS R 174 " - pdb=" SG CYS R 255 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.40 Conformation dependent library (CDL) restraints added in 278.2 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2038 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 12 sheets defined 42.4% alpha, 18.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.20 Creating SS restraints... Processing helix chain 'A' and resid 9 through 38 removed outlier: 3.521A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ARG A 38 " --> pdb=" O LYS A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 62 Processing helix chain 'A' and resid 233 through 239 removed outlier: 3.534A pdb=" N GLN A 236 " --> pdb=" O LYS A 233 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N CYS A 237 " --> pdb=" O TRP A 234 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N PHE A 238 " --> pdb=" O ILE A 235 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ASN A 239 " --> pdb=" O GLN A 236 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 233 through 239' Processing helix chain 'A' and resid 255 through 268 Processing helix chain 'A' and resid 283 through 294 Processing helix chain 'A' and resid 297 through 302 removed outlier: 4.236A pdb=" N TYR A 301 " --> pdb=" O LYS A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 304 through 308 Processing helix chain 'A' and resid 321 through 342 removed outlier: 3.727A pdb=" N THR A 325 " --> pdb=" O ASP A 321 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N PHE A 335 " --> pdb=" O ILE A 331 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ALA A 341 " --> pdb=" O ARG A 337 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N SER A 342 " --> pdb=" O ILE A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 360 through 381 removed outlier: 3.713A pdb=" N ARG A 364 " --> pdb=" O GLU A 360 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N TYR A 381 " --> pdb=" O ASN A 377 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 25 Processing helix chain 'B' and resid 29 through 35 removed outlier: 3.839A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 7 through 24 Processing helix chain 'G' and resid 29 through 44 removed outlier: 3.624A pdb=" N ALA G 33 " --> pdb=" O LYS G 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 45 through 48 removed outlier: 3.504A pdb=" N ASP G 48 " --> pdb=" O ALA G 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 45 through 48' Processing helix chain 'N' and resid 28 through 32 removed outlier: 3.774A pdb=" N ASN N 31 " --> pdb=" O THR N 28 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N TYR N 32 " --> pdb=" O PHE N 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 28 through 32' Processing helix chain 'T' and resid 8 through 17 Processing helix chain 'R' and resid 97 through 129 removed outlier: 3.996A pdb=" N LYS R 101 " --> pdb=" O LYS R 97 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N TYR R 102 " --> pdb=" O GLU R 98 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LEU R 110 " --> pdb=" O VAL R 106 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ILE R 116 " --> pdb=" O PHE R 112 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ILE R 117 " --> pdb=" O VAL R 113 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LEU R 122 " --> pdb=" O GLY R 118 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ILE R 126 " --> pdb=" O LEU R 122 " (cutoff:3.500A) Processing helix chain 'R' and resid 134 through 165 removed outlier: 3.893A pdb=" N ILE R 140 " --> pdb=" O PRO R 136 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LEU R 143 " --> pdb=" O LEU R 139 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LEU R 149 " --> pdb=" O LEU R 145 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ILE R 155 " --> pdb=" O ILE R 151 " (cutoff:3.500A) Proline residue: R 156 - end of helix removed outlier: 3.590A pdb=" N LEU R 162 " --> pdb=" O ASN R 158 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LEU R 163 " --> pdb=" O VAL R 159 " (cutoff:3.500A) Processing helix chain 'R' and resid 172 through 175 Processing helix chain 'R' and resid 176 through 205 removed outlier: 3.775A pdb=" N LYS R 182 " --> pdb=" O PRO R 178 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLY R 186 " --> pdb=" O LYS R 182 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N SER R 196 " --> pdb=" O LEU R 192 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ILE R 197 " --> pdb=" O CYS R 193 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N TYR R 200 " --> pdb=" O SER R 196 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N VAL R 203 " --> pdb=" O ARG R 199 " (cutoff:3.500A) Processing helix chain 'R' and resid 215 through 232 removed outlier: 3.569A pdb=" N ALA R 219 " --> pdb=" O PRO R 215 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VAL R 220 " --> pdb=" O LYS R 216 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N VAL R 230 " --> pdb=" O TRP R 226 " (cutoff:3.500A) Processing helix chain 'R' and resid 233 through 239 removed outlier: 3.685A pdb=" N ALA R 237 " --> pdb=" O ALA R 233 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ILE R 238 " --> pdb=" O VAL R 234 " (cutoff:3.500A) Processing helix chain 'R' and resid 264 through 282 removed outlier: 3.701A pdb=" N THR R 271 " --> pdb=" O GLN R 267 " (cutoff:3.500A) removed outlier: 5.195A pdb=" N ASP R 274 " --> pdb=" O LYS R 270 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N TRP R 275 " --> pdb=" O THR R 271 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N PHE R 278 " --> pdb=" O ASP R 274 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N SER R 279 " --> pdb=" O TRP R 275 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N PHE R 280 " --> pdb=" O TRP R 276 " (cutoff:3.500A) Processing helix chain 'R' and resid 282 through 302 removed outlier: 3.533A pdb=" N ILE R 288 " --> pdb=" O LEU R 284 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LEU R 295 " --> pdb=" O PHE R 291 " (cutoff:3.500A) Processing helix chain 'R' and resid 312 through 336 removed outlier: 3.748A pdb=" N VAL R 329 " --> pdb=" O VAL R 325 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N TRP R 336 " --> pdb=" O PHE R 332 " (cutoff:3.500A) Processing helix chain 'R' and resid 336 through 350 removed outlier: 3.551A pdb=" N HIS R 340 " --> pdb=" O TRP R 336 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ARG R 343 " --> pdb=" O LEU R 339 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ILE R 344 " --> pdb=" O HIS R 340 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N TYR R 350 " --> pdb=" O LYS R 346 " (cutoff:3.500A) Processing helix chain 'R' and resid 356 through 376 removed outlier: 3.591A pdb=" N LEU R 360 " --> pdb=" O ASN R 356 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N VAL R 366 " --> pdb=" O SER R 362 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N LEU R 367 " --> pdb=" O PHE R 363 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ASP R 368 " --> pdb=" O LEU R 364 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N TYR R 369 " --> pdb=" O LEU R 365 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ILE R 370 " --> pdb=" O VAL R 366 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N ASN R 373 " --> pdb=" O TYR R 369 " (cutoff:3.500A) Processing helix chain 'R' and resid 377 through 388 removed outlier: 4.430A pdb=" N ASN R 382 " --> pdb=" O ASN R 378 " (cutoff:3.500A) Proline residue: R 383 - end of helix Processing helix chain 'R' and resid 390 through 399 Processing sheet with id=AA1, first strand: chain 'A' and resid 208 through 214 removed outlier: 3.687A pdb=" N THR A 210 " --> pdb=" O MET A 221 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N MET A 221 " --> pdb=" O THR A 210 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N PHE A 212 " --> pdb=" O PHE A 219 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N HIS A 41 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 7.892A pdb=" N PHE A 222 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N LEU A 43 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 9.846A pdb=" N ALA A 243 " --> pdb=" O THR A 40 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 7.970A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 7.174A pdb=" N VAL A 277 " --> pdb=" O TYR A 350 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51 removed outlier: 3.919A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N ALA B 328 " --> pdb=" O LEU B 318 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N LEU B 318 " --> pdb=" O ALA B 328 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N GLY B 330 " --> pdb=" O SER B 316 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 4.029A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N LEU B 70 " --> pdb=" O TRP B 82 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ILE B 81 " --> pdb=" O HIS B 91 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.031A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 3.601A pdb=" N THR B 102 " --> pdb=" O GLY B 115 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N VAL B 112 " --> pdb=" O TYR B 124 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.885A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.684A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 189 through 192 removed outlier: 3.900A pdb=" N SER B 189 " --> pdb=" O GLY B 202 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N GLY B 202 " --> pdb=" O SER B 189 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N SER B 191 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N VAL B 200 " --> pdb=" O SER B 191 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N PHE B 199 " --> pdb=" O TRP B 211 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 7.264A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 232 removed outlier: 6.688A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ARG B 251 " --> pdb=" O THR B 243 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.921A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.427A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 5.381A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 7.559A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 7 removed outlier: 3.930A pdb=" N GLN N 3 " --> pdb=" O SER N 25 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N SER N 25 " --> pdb=" O GLN N 3 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N SER N 21 " --> pdb=" O SER N 7 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N THR N 78 " --> pdb=" O ASP N 73 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'N' and resid 58 through 60 removed outlier: 3.819A pdb=" N SER N 59 " --> pdb=" O ASP N 50 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ALA N 92 " --> pdb=" O VAL N 124 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'R' and resid 240 through 243 Processing sheet with id=AB3, first strand: chain 'R' and resid 246 through 247 366 hydrogen bonds defined for protein. 1056 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: 0.86 Time building geometry restraints manager: 0.58 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: 2791 1.34 - 1.46: 2019 1.46 - 1.58: 3823 1.58 - 1.70: 0 1.70 - 1.82: 84 Bond restraints: 8717 Sorted by residual: bond pdb=" CA TRP R 167 " pdb=" C TRP R 167 " ideal model delta sigma weight residual 1.523 1.497 0.026 1.24e-02 6.50e+03 4.42e+00 bond pdb=" CB LYS A 32 " pdb=" CG LYS A 32 " ideal model delta sigma weight residual 1.520 1.563 -0.043 3.00e-02 1.11e+03 2.01e+00 bond pdb=" CA PHE R 363 " pdb=" CB PHE R 363 " ideal model delta sigma weight residual 1.528 1.545 -0.016 1.56e-02 4.11e+03 1.07e+00 bond pdb=" CA ASN B 88 " pdb=" CB ASN B 88 " ideal model delta sigma weight residual 1.536 1.556 -0.021 2.08e-02 2.31e+03 9.78e-01 bond pdb=" C TRP R 167 " pdb=" O TRP R 167 " ideal model delta sigma weight residual 1.237 1.226 0.011 1.17e-02 7.31e+03 9.24e-01 ... (remaining 8712 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.83: 11624 1.83 - 3.66: 139 3.66 - 5.50: 24 5.50 - 7.33: 13 7.33 - 9.16: 3 Bond angle restraints: 11803 Sorted by residual: angle pdb=" CA LYS A 32 " pdb=" CB LYS A 32 " pdb=" CG LYS A 32 " ideal model delta sigma weight residual 114.10 121.04 -6.94 2.00e+00 2.50e-01 1.21e+01 angle pdb=" CA GLU A 317 " pdb=" CB GLU A 317 " pdb=" CG GLU A 317 " ideal model delta sigma weight residual 114.10 120.79 -6.69 2.00e+00 2.50e-01 1.12e+01 angle pdb=" CB LYS A 32 " pdb=" CG LYS A 32 " pdb=" CD LYS A 32 " ideal model delta sigma weight residual 111.30 118.72 -7.42 2.30e+00 1.89e-01 1.04e+01 angle pdb=" CA LYS R 346 " pdb=" CB LYS R 346 " pdb=" CG LYS R 346 " ideal model delta sigma weight residual 114.10 120.49 -6.39 2.00e+00 2.50e-01 1.02e+01 angle pdb=" CA GLU A 16 " pdb=" CB GLU A 16 " pdb=" CG GLU A 16 " ideal model delta sigma weight residual 114.10 119.99 -5.89 2.00e+00 2.50e-01 8.67e+00 ... (remaining 11798 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.52: 4503 16.52 - 33.04: 554 33.04 - 49.56: 144 49.56 - 66.08: 37 66.08 - 82.60: 2 Dihedral angle restraints: 5240 sinusoidal: 2093 harmonic: 3147 Sorted by residual: dihedral pdb=" CB CYS N 22 " pdb=" SG CYS N 22 " pdb=" SG CYS N 96 " pdb=" CB CYS N 96 " ideal model delta sinusoidal sigma weight residual -86.00 -6.52 -79.48 1 1.00e+01 1.00e-02 7.85e+01 dihedral pdb=" CB CYS N 99 " pdb=" SG CYS N 99 " pdb=" SG CYS N 107 " pdb=" CB CYS N 107 " ideal model delta sinusoidal sigma weight residual -86.00 -29.44 -56.56 1 1.00e+01 1.00e-02 4.31e+01 dihedral pdb=" CB CYS T 1 " pdb=" SG CYS T 1 " pdb=" SG CYS T 15 " pdb=" CB CYS T 15 " ideal model delta sinusoidal sigma weight residual 93.00 145.94 -52.94 1 1.00e+01 1.00e-02 3.81e+01 ... (remaining 5237 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 788 0.027 - 0.053: 334 0.053 - 0.080: 123 0.080 - 0.107: 59 0.107 - 0.134: 29 Chirality restraints: 1333 Sorted by residual: chirality pdb=" CA ILE A 278 " pdb=" N ILE A 278 " pdb=" C ILE A 278 " pdb=" CB ILE A 278 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.46e-01 chirality pdb=" CA ILE A 244 " pdb=" N ILE A 244 " pdb=" C ILE A 244 " pdb=" CB ILE A 244 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.08e-01 chirality pdb=" CA VAL G 54 " pdb=" N VAL G 54 " pdb=" C VAL G 54 " pdb=" CB VAL G 54 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 3.97e-01 ... (remaining 1330 not shown) Planarity restraints: 1501 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY R 135 " 0.039 5.00e-02 4.00e+02 5.86e-02 5.49e+00 pdb=" N PRO R 136 " -0.101 5.00e-02 4.00e+02 pdb=" CA PRO R 136 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO R 136 " 0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE T 14 " 0.010 2.00e-02 2.50e+03 1.31e-02 3.01e+00 pdb=" CG PHE T 14 " -0.030 2.00e-02 2.50e+03 pdb=" CD1 PHE T 14 " 0.009 2.00e-02 2.50e+03 pdb=" CD2 PHE T 14 " 0.009 2.00e-02 2.50e+03 pdb=" CE1 PHE T 14 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE T 14 " 0.001 2.00e-02 2.50e+03 pdb=" CZ PHE T 14 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C HIS R 258 " 0.027 5.00e-02 4.00e+02 4.03e-02 2.60e+00 pdb=" N PRO R 259 " -0.070 5.00e-02 4.00e+02 pdb=" CA PRO R 259 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO R 259 " 0.023 5.00e-02 4.00e+02 ... (remaining 1498 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 168 2.69 - 3.24: 8124 3.24 - 3.80: 12776 3.80 - 4.35: 16343 4.35 - 4.90: 27250 Nonbonded interactions: 64661 Sorted by model distance: nonbonded pdb=" O ARG A 363 " pdb=" ND2 ASN A 367 " model vdw 2.140 3.120 nonbonded pdb=" OG SER B 331 " pdb=" OD1 ASP B 333 " model vdw 2.251 3.040 nonbonded pdb=" NH2 ARG A 228 " pdb=" OE1 GLU A 230 " model vdw 2.306 3.120 nonbonded pdb=" OH TYR A 308 " pdb=" OD2 ASP A 333 " model vdw 2.309 3.040 nonbonded pdb=" O THR A 315 " pdb=" OG1 THR A 315 " model vdw 2.313 3.040 ... (remaining 64656 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.020 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: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.020 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7112 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 : 0.002 0.043 8723 Z= 0.121 Angle : 0.575 9.159 11815 Z= 0.304 Chirality : 0.040 0.134 1333 Planarity : 0.004 0.059 1501 Dihedral : 15.342 82.596 3184 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 0.21 % Allowed : 26.82 % Favored : 72.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.56 (0.25), residues: 1064 helix: 0.66 (0.26), residues: 403 sheet: -0.41 (0.35), residues: 221 loop : -1.27 (0.26), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 273 TYR 0.006 0.001 TYR N 95 PHE 0.030 0.001 PHE T 14 TRP 0.012 0.001 TRP A 234 HIS 0.003 0.001 HIS A 347 Details of bonding type rmsd covalent geometry : bond 0.00242 ( 8717) covalent geometry : angle 0.57361 (11803) SS BOND : bond 0.00242 ( 6) SS BOND : angle 1.44316 ( 12) hydrogen bonds : bond 0.27035 ( 366) hydrogen bonds : angle 7.72734 ( 1056) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 185 time to evaluate : 0.342 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 205 ASP cc_start: 0.6955 (p0) cc_final: 0.6640 (p0) outliers start: 2 outliers final: 1 residues processed: 187 average time/residue: 0.1049 time to fit residues: 25.5707 Evaluate side-chains 182 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 181 time to evaluate : 0.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 349 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 49 optimal weight: 5.9990 chunk 97 optimal weight: 0.8980 chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 0.6980 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 100 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 0.7980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.162285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.133712 restraints weight = 12082.892| |-----------------------------------------------------------------------------| r_work (start): 0.3711 rms_B_bonded: 2.58 r_work: 0.3573 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3573 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7071 moved from start: 0.1270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 8723 Z= 0.222 Angle : 0.640 8.457 11815 Z= 0.336 Chirality : 0.044 0.176 1333 Planarity : 0.004 0.053 1501 Dihedral : 4.360 36.888 1175 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 3.31 % Allowed : 23.18 % Favored : 73.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.25 (0.25), residues: 1064 helix: 1.16 (0.26), residues: 401 sheet: -0.42 (0.35), residues: 226 loop : -1.25 (0.27), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 273 TYR 0.012 0.002 TYR B 111 PHE 0.016 0.002 PHE A 366 TRP 0.014 0.002 TRP A 234 HIS 0.007 0.002 HIS A 347 Details of bonding type rmsd covalent geometry : bond 0.00501 ( 8717) covalent geometry : angle 0.63794 (11803) SS BOND : bond 0.00521 ( 6) SS BOND : angle 1.84331 ( 12) hydrogen bonds : bond 0.07794 ( 366) hydrogen bonds : angle 5.20893 ( 1056) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 182 time to evaluate : 0.232 Fit side-chains revert: symmetry clash REVERT: A 16 GLU cc_start: 0.7161 (pp20) cc_final: 0.6934 (pp20) REVERT: A 317 GLU cc_start: 0.6251 (tm-30) cc_final: 0.5922 (tm-30) REVERT: A 367 ASN cc_start: 0.7831 (m-40) cc_final: 0.7598 (m-40) REVERT: N 29 PHE cc_start: 0.7728 (t80) cc_final: 0.7421 (t80) REVERT: N 118 ARG cc_start: 0.8013 (OUTLIER) cc_final: 0.6857 (mtm180) REVERT: R 120 SER cc_start: 0.8145 (p) cc_final: 0.7659 (m) REVERT: R 125 ILE cc_start: 0.8194 (OUTLIER) cc_final: 0.7963 (mp) REVERT: R 175 LYS cc_start: 0.7646 (mmpt) cc_final: 0.7227 (mttm) REVERT: R 192 LEU cc_start: 0.8051 (OUTLIER) cc_final: 0.7779 (tt) outliers start: 31 outliers final: 19 residues processed: 200 average time/residue: 0.1021 time to fit residues: 26.6960 Evaluate side-chains 200 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 178 time to evaluate : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 298 ILE Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 337 ARG Chi-restraints excluded: chain A residue 349 CYS Chi-restraints excluded: chain B residue 42 ARG Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 96 ARG Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 220 GLN Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain N residue 3 GLN Chi-restraints excluded: chain N residue 22 CYS Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 118 ARG Chi-restraints excluded: chain R residue 125 ILE Chi-restraints excluded: chain R residue 153 ILE Chi-restraints excluded: chain R residue 181 GLN Chi-restraints excluded: chain R residue 192 LEU Chi-restraints excluded: chain R residue 301 LEU Chi-restraints excluded: chain R residue 325 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 10 optimal weight: 0.9990 chunk 47 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 chunk 11 optimal weight: 0.7980 chunk 40 optimal weight: 2.9990 chunk 82 optimal weight: 0.8980 chunk 101 optimal weight: 0.6980 chunk 49 optimal weight: 2.9990 chunk 15 optimal weight: 0.6980 chunk 65 optimal weight: 1.9990 chunk 41 optimal weight: 0.0770 overall best weight: 0.6338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 220 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.164186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.135822 restraints weight = 12036.803| |-----------------------------------------------------------------------------| r_work (start): 0.3734 rms_B_bonded: 2.58 r_work: 0.3597 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3597 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7040 moved from start: 0.1594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8723 Z= 0.140 Angle : 0.574 10.248 11815 Z= 0.296 Chirality : 0.042 0.229 1333 Planarity : 0.004 0.050 1501 Dihedral : 4.192 25.445 1175 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 4.17 % Allowed : 22.97 % Favored : 72.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.00 (0.25), residues: 1064 helix: 1.53 (0.26), residues: 400 sheet: -0.14 (0.36), residues: 214 loop : -1.34 (0.26), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 323 TYR 0.011 0.001 TYR A 381 PHE 0.014 0.001 PHE R 282 TRP 0.013 0.001 TRP A 234 HIS 0.004 0.001 HIS A 347 Details of bonding type rmsd covalent geometry : bond 0.00302 ( 8717) covalent geometry : angle 0.57185 (11803) SS BOND : bond 0.00584 ( 6) SS BOND : angle 1.75752 ( 12) hydrogen bonds : bond 0.05954 ( 366) hydrogen bonds : angle 4.64526 ( 1056) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 179 time to evaluate : 0.200 Fit side-chains revert: symmetry clash REVERT: A 317 GLU cc_start: 0.6323 (tm-30) cc_final: 0.5941 (tm-30) REVERT: A 367 ASN cc_start: 0.7809 (m-40) cc_final: 0.7540 (m-40) REVERT: A 380 GLU cc_start: 0.6878 (OUTLIER) cc_final: 0.6500 (pp20) REVERT: B 66 ASP cc_start: 0.7363 (p0) cc_final: 0.7098 (p0) REVERT: G 27 ARG cc_start: 0.7883 (ptp-170) cc_final: 0.7653 (ptp90) REVERT: N 4 LEU cc_start: 0.8459 (mt) cc_final: 0.8145 (mp) REVERT: N 118 ARG cc_start: 0.7947 (OUTLIER) cc_final: 0.6607 (mtm-85) REVERT: R 120 SER cc_start: 0.8008 (p) cc_final: 0.7599 (m) REVERT: R 125 ILE cc_start: 0.8166 (OUTLIER) cc_final: 0.7928 (mp) REVERT: R 175 LYS cc_start: 0.7622 (mtpt) cc_final: 0.7355 (mttm) REVERT: R 192 LEU cc_start: 0.7938 (OUTLIER) cc_final: 0.7724 (tt) outliers start: 39 outliers final: 21 residues processed: 205 average time/residue: 0.0902 time to fit residues: 24.4156 Evaluate side-chains 202 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 177 time to evaluate : 0.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ASP Chi-restraints excluded: chain A residue 266 ILE Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 298 ILE Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 380 GLU Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 220 GLN Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain N residue 22 CYS Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 118 ARG Chi-restraints excluded: chain R residue 90 CYS Chi-restraints excluded: chain R residue 125 ILE Chi-restraints excluded: chain R residue 173 MET Chi-restraints excluded: chain R residue 181 GLN Chi-restraints excluded: chain R residue 192 LEU Chi-restraints excluded: chain R residue 323 LYS Chi-restraints excluded: chain R residue 325 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 21 optimal weight: 0.6980 chunk 70 optimal weight: 0.9990 chunk 63 optimal weight: 0.0670 chunk 34 optimal weight: 0.1980 chunk 26 optimal weight: 0.1980 chunk 83 optimal weight: 4.9990 chunk 47 optimal weight: 0.7980 chunk 78 optimal weight: 0.9990 chunk 94 optimal weight: 0.5980 chunk 15 optimal weight: 0.9990 chunk 72 optimal weight: 1.9990 overall best weight: 0.3518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.165685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.137089 restraints weight = 12317.996| |-----------------------------------------------------------------------------| r_work (start): 0.3738 rms_B_bonded: 2.61 r_work: 0.3591 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3591 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7057 moved from start: 0.1817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 8723 Z= 0.115 Angle : 0.549 8.310 11815 Z= 0.281 Chirality : 0.041 0.164 1333 Planarity : 0.004 0.050 1501 Dihedral : 3.971 19.104 1174 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 3.63 % Allowed : 23.82 % Favored : 72.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.19 (0.25), residues: 1064 helix: 1.76 (0.26), residues: 399 sheet: -0.03 (0.36), residues: 217 loop : -1.32 (0.25), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 273 TYR 0.011 0.001 TYR A 381 PHE 0.017 0.001 PHE T 14 TRP 0.012 0.001 TRP A 234 HIS 0.004 0.001 HIS A 347 Details of bonding type rmsd covalent geometry : bond 0.00242 ( 8717) covalent geometry : angle 0.54492 (11803) SS BOND : bond 0.00392 ( 6) SS BOND : angle 2.16780 ( 12) hydrogen bonds : bond 0.05044 ( 366) hydrogen bonds : angle 4.35928 ( 1056) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 186 time to evaluate : 0.258 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 317 GLU cc_start: 0.6265 (tm-30) cc_final: 0.5951 (tm-30) REVERT: A 367 ASN cc_start: 0.7809 (m-40) cc_final: 0.7558 (m-40) REVERT: A 380 GLU cc_start: 0.6926 (OUTLIER) cc_final: 0.6486 (pp20) REVERT: B 66 ASP cc_start: 0.7314 (p0) cc_final: 0.7028 (p0) REVERT: B 178 THR cc_start: 0.8518 (OUTLIER) cc_final: 0.8248 (m) REVERT: N 4 LEU cc_start: 0.8412 (mt) cc_final: 0.8044 (mp) REVERT: N 118 ARG cc_start: 0.7922 (OUTLIER) cc_final: 0.6557 (mtm-85) REVERT: T 14 PHE cc_start: 0.8522 (t80) cc_final: 0.8294 (t80) REVERT: R 120 SER cc_start: 0.8023 (p) cc_final: 0.7653 (m) REVERT: R 125 ILE cc_start: 0.8201 (OUTLIER) cc_final: 0.7954 (mp) REVERT: R 175 LYS cc_start: 0.7541 (mtpt) cc_final: 0.7295 (mttm) REVERT: R 327 CYS cc_start: 0.7232 (OUTLIER) cc_final: 0.6960 (p) outliers start: 34 outliers final: 15 residues processed: 208 average time/residue: 0.1037 time to fit residues: 28.0673 Evaluate side-chains 198 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 178 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 249 ASP Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 380 GLU Chi-restraints excluded: chain B residue 10 GLU Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain N residue 22 CYS Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 118 ARG Chi-restraints excluded: chain R residue 125 ILE Chi-restraints excluded: chain R residue 173 MET Chi-restraints excluded: chain R residue 181 GLN Chi-restraints excluded: chain R residue 205 SER Chi-restraints excluded: chain R residue 254 ILE Chi-restraints excluded: chain R residue 323 LYS Chi-restraints excluded: chain R residue 325 VAL Chi-restraints excluded: chain R residue 327 CYS Chi-restraints excluded: chain R residue 393 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 29 optimal weight: 1.9990 chunk 35 optimal weight: 0.9980 chunk 85 optimal weight: 0.8980 chunk 5 optimal weight: 2.9990 chunk 80 optimal weight: 0.4980 chunk 30 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 40 optimal weight: 0.7980 chunk 47 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.162582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.134091 restraints weight = 12279.395| |-----------------------------------------------------------------------------| r_work (start): 0.3696 rms_B_bonded: 2.61 r_work: 0.3544 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3544 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7114 moved from start: 0.2059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 8723 Z= 0.187 Angle : 0.647 11.014 11815 Z= 0.332 Chirality : 0.043 0.163 1333 Planarity : 0.004 0.051 1501 Dihedral : 4.232 19.462 1174 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 5.24 % Allowed : 23.40 % Favored : 71.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.12 (0.26), residues: 1064 helix: 1.62 (0.26), residues: 408 sheet: -0.07 (0.36), residues: 218 loop : -1.33 (0.27), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 273 TYR 0.025 0.002 TYR R 160 PHE 0.014 0.002 PHE B 241 TRP 0.014 0.002 TRP N 47 HIS 0.005 0.001 HIS A 220 Details of bonding type rmsd covalent geometry : bond 0.00429 ( 8717) covalent geometry : angle 0.63316 (11803) SS BOND : bond 0.00828 ( 6) SS BOND : angle 4.29505 ( 12) hydrogen bonds : bond 0.06082 ( 366) hydrogen bonds : angle 4.44167 ( 1056) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 187 time to evaluate : 0.302 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 317 GLU cc_start: 0.6204 (tm-30) cc_final: 0.5921 (tm-30) REVERT: B 66 ASP cc_start: 0.7399 (p0) cc_final: 0.7146 (p0) REVERT: B 171 ILE cc_start: 0.7365 (OUTLIER) cc_final: 0.6954 (mm) REVERT: B 289 TYR cc_start: 0.8101 (m-80) cc_final: 0.7726 (m-80) REVERT: G 27 ARG cc_start: 0.7912 (ptp90) cc_final: 0.7672 (ptp90) REVERT: N 29 PHE cc_start: 0.7772 (t80) cc_final: 0.7500 (t80) REVERT: N 35 ASN cc_start: 0.8345 (OUTLIER) cc_final: 0.8110 (p0) REVERT: N 76 LYS cc_start: 0.7909 (OUTLIER) cc_final: 0.7625 (ttpp) REVERT: N 118 ARG cc_start: 0.7994 (OUTLIER) cc_final: 0.6514 (mtm-85) REVERT: T 14 PHE cc_start: 0.8534 (t80) cc_final: 0.8330 (t80) REVERT: R 120 SER cc_start: 0.8064 (p) cc_final: 0.7665 (m) REVERT: R 125 ILE cc_start: 0.8127 (OUTLIER) cc_final: 0.7898 (mp) REVERT: R 158 ASN cc_start: 0.7667 (OUTLIER) cc_final: 0.7411 (t0) outliers start: 49 outliers final: 30 residues processed: 217 average time/residue: 0.0983 time to fit residues: 28.1993 Evaluate side-chains 220 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 184 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 249 ASP Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 298 ILE Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 337 ARG Chi-restraints excluded: chain A residue 349 CYS Chi-restraints excluded: chain A residue 380 GLU Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 96 ARG Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 220 GLN Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain N residue 3 GLN Chi-restraints excluded: chain N residue 22 CYS Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 76 LYS Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 118 ARG Chi-restraints excluded: chain R residue 125 ILE Chi-restraints excluded: chain R residue 158 ASN Chi-restraints excluded: chain R residue 173 MET Chi-restraints excluded: chain R residue 181 GLN Chi-restraints excluded: chain R residue 189 VAL Chi-restraints excluded: chain R residue 301 LEU Chi-restraints excluded: chain R residue 323 LYS Chi-restraints excluded: chain R residue 325 VAL Chi-restraints excluded: chain R residue 344 ILE Chi-restraints excluded: chain R residue 393 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 88 optimal weight: 0.7980 chunk 24 optimal weight: 3.9990 chunk 43 optimal weight: 2.9990 chunk 34 optimal weight: 0.7980 chunk 66 optimal weight: 3.9990 chunk 46 optimal weight: 0.8980 chunk 95 optimal weight: 0.7980 chunk 25 optimal weight: 5.9990 chunk 103 optimal weight: 1.9990 chunk 96 optimal weight: 0.9980 chunk 12 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.163078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.133709 restraints weight = 12302.109| |-----------------------------------------------------------------------------| r_work (start): 0.3700 rms_B_bonded: 2.64 r_work: 0.3554 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3554 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7105 moved from start: 0.2220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 8723 Z= 0.160 Angle : 0.607 12.313 11815 Z= 0.309 Chirality : 0.042 0.158 1333 Planarity : 0.004 0.049 1501 Dihedral : 4.178 19.939 1174 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 5.56 % Allowed : 23.29 % Favored : 71.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.16 (0.26), residues: 1064 helix: 1.66 (0.26), residues: 407 sheet: -0.03 (0.36), residues: 216 loop : -1.32 (0.27), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG N 118 TYR 0.022 0.002 TYR R 160 PHE 0.013 0.001 PHE A 366 TRP 0.030 0.002 TRP R 275 HIS 0.004 0.001 HIS A 347 Details of bonding type rmsd covalent geometry : bond 0.00365 ( 8717) covalent geometry : angle 0.60187 (11803) SS BOND : bond 0.00705 ( 6) SS BOND : angle 2.64741 ( 12) hydrogen bonds : bond 0.05606 ( 366) hydrogen bonds : angle 4.33812 ( 1056) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 184 time to evaluate : 0.248 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 317 GLU cc_start: 0.6263 (tm-30) cc_final: 0.6003 (tm-30) REVERT: A 328 LYS cc_start: 0.8061 (OUTLIER) cc_final: 0.7348 (ptmm) REVERT: A 367 ASN cc_start: 0.7913 (m-40) cc_final: 0.7661 (m-40) REVERT: B 66 ASP cc_start: 0.7258 (p0) cc_final: 0.6993 (p0) REVERT: B 153 ASP cc_start: 0.6774 (OUTLIER) cc_final: 0.6504 (p0) REVERT: B 171 ILE cc_start: 0.7352 (OUTLIER) cc_final: 0.6919 (mm) REVERT: N 29 PHE cc_start: 0.7796 (t80) cc_final: 0.7542 (t80) REVERT: N 35 ASN cc_start: 0.8378 (OUTLIER) cc_final: 0.8138 (p0) REVERT: N 76 LYS cc_start: 0.7875 (OUTLIER) cc_final: 0.7587 (ttpp) REVERT: N 118 ARG cc_start: 0.8000 (OUTLIER) cc_final: 0.6605 (mtm-85) REVERT: R 120 SER cc_start: 0.8066 (p) cc_final: 0.7655 (m) REVERT: R 125 ILE cc_start: 0.8163 (OUTLIER) cc_final: 0.7942 (mp) REVERT: R 158 ASN cc_start: 0.7634 (OUTLIER) cc_final: 0.7385 (t0) REVERT: R 296 MET cc_start: 0.7466 (tmm) cc_final: 0.7255 (ttp) outliers start: 52 outliers final: 36 residues processed: 219 average time/residue: 0.0985 time to fit residues: 28.5503 Evaluate side-chains 224 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 180 time to evaluate : 0.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ASP Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 249 ASP Chi-restraints excluded: chain A residue 298 ILE Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 328 LYS Chi-restraints excluded: chain A residue 349 CYS Chi-restraints excluded: chain A residue 380 GLU Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 96 ARG Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 220 GLN Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain N residue 22 CYS Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 76 LYS Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 118 ARG Chi-restraints excluded: chain R residue 97 LYS Chi-restraints excluded: chain R residue 125 ILE Chi-restraints excluded: chain R residue 158 ASN Chi-restraints excluded: chain R residue 173 MET Chi-restraints excluded: chain R residue 181 GLN Chi-restraints excluded: chain R residue 182 LYS Chi-restraints excluded: chain R residue 205 SER Chi-restraints excluded: chain R residue 254 ILE Chi-restraints excluded: chain R residue 260 VAL Chi-restraints excluded: chain R residue 286 LEU Chi-restraints excluded: chain R residue 298 CYS Chi-restraints excluded: chain R residue 301 LEU Chi-restraints excluded: chain R residue 325 VAL Chi-restraints excluded: chain R residue 329 VAL Chi-restraints excluded: chain R residue 393 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 101 optimal weight: 1.9990 chunk 60 optimal weight: 4.9990 chunk 82 optimal weight: 0.0980 chunk 76 optimal weight: 1.9990 chunk 56 optimal weight: 30.0000 chunk 89 optimal weight: 0.6980 chunk 51 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 chunk 46 optimal weight: 0.9980 chunk 97 optimal weight: 0.7980 chunk 6 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.163403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.134543 restraints weight = 12277.102| |-----------------------------------------------------------------------------| r_work (start): 0.3713 rms_B_bonded: 2.61 r_work: 0.3565 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3565 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7091 moved from start: 0.2359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8723 Z= 0.141 Angle : 0.612 12.832 11815 Z= 0.305 Chirality : 0.042 0.157 1333 Planarity : 0.004 0.051 1501 Dihedral : 4.094 19.986 1174 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 5.24 % Allowed : 24.68 % Favored : 70.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.28 (0.26), residues: 1064 helix: 1.79 (0.26), residues: 407 sheet: 0.05 (0.37), residues: 216 loop : -1.29 (0.27), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG N 118 TYR 0.021 0.001 TYR R 160 PHE 0.015 0.001 PHE T 14 TRP 0.021 0.002 TRP R 275 HIS 0.004 0.001 HIS A 347 Details of bonding type rmsd covalent geometry : bond 0.00317 ( 8717) covalent geometry : angle 0.60712 (11803) SS BOND : bond 0.00583 ( 6) SS BOND : angle 2.48776 ( 12) hydrogen bonds : bond 0.05242 ( 366) hydrogen bonds : angle 4.25677 ( 1056) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 187 time to evaluate : 0.274 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 317 GLU cc_start: 0.6261 (tm-30) cc_final: 0.5955 (tm-30) REVERT: A 320 GLU cc_start: 0.6411 (tt0) cc_final: 0.6195 (tt0) REVERT: A 367 ASN cc_start: 0.7867 (m-40) cc_final: 0.7625 (m-40) REVERT: A 374 LEU cc_start: 0.8080 (tt) cc_final: 0.7872 (tp) REVERT: B 66 ASP cc_start: 0.7225 (p0) cc_final: 0.6959 (p0) REVERT: B 153 ASP cc_start: 0.6759 (OUTLIER) cc_final: 0.6482 (p0) REVERT: B 171 ILE cc_start: 0.7363 (OUTLIER) cc_final: 0.6924 (mm) REVERT: N 29 PHE cc_start: 0.7797 (t80) cc_final: 0.7540 (t80) REVERT: N 76 LYS cc_start: 0.7871 (OUTLIER) cc_final: 0.7576 (ttpp) REVERT: N 118 ARG cc_start: 0.7985 (OUTLIER) cc_final: 0.6569 (mtm-85) REVERT: R 120 SER cc_start: 0.8050 (p) cc_final: 0.7653 (m) REVERT: R 125 ILE cc_start: 0.8156 (OUTLIER) cc_final: 0.7944 (mp) REVERT: R 158 ASN cc_start: 0.7634 (OUTLIER) cc_final: 0.7384 (t0) REVERT: R 327 CYS cc_start: 0.7169 (OUTLIER) cc_final: 0.6897 (p) outliers start: 49 outliers final: 33 residues processed: 219 average time/residue: 0.1037 time to fit residues: 30.1295 Evaluate side-chains 227 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 187 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ASP Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 249 ASP Chi-restraints excluded: chain A residue 298 ILE Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 349 CYS Chi-restraints excluded: chain A residue 380 GLU Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 220 GLN Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain N residue 22 CYS Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 76 LYS Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 118 ARG Chi-restraints excluded: chain R residue 97 LYS Chi-restraints excluded: chain R residue 125 ILE Chi-restraints excluded: chain R residue 158 ASN Chi-restraints excluded: chain R residue 173 MET Chi-restraints excluded: chain R residue 181 GLN Chi-restraints excluded: chain R residue 182 LYS Chi-restraints excluded: chain R residue 254 ILE Chi-restraints excluded: chain R residue 260 VAL Chi-restraints excluded: chain R residue 286 LEU Chi-restraints excluded: chain R residue 295 LEU Chi-restraints excluded: chain R residue 301 LEU Chi-restraints excluded: chain R residue 325 VAL Chi-restraints excluded: chain R residue 327 CYS Chi-restraints excluded: chain R residue 337 LEU Chi-restraints excluded: chain R residue 393 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 69 optimal weight: 0.3980 chunk 39 optimal weight: 0.6980 chunk 7 optimal weight: 0.0670 chunk 97 optimal weight: 0.8980 chunk 17 optimal weight: 0.7980 chunk 22 optimal weight: 0.6980 chunk 18 optimal weight: 0.8980 chunk 54 optimal weight: 0.9990 chunk 99 optimal weight: 0.9990 chunk 96 optimal weight: 0.8980 chunk 83 optimal weight: 2.9990 overall best weight: 0.5318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.164429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.135043 restraints weight = 12309.983| |-----------------------------------------------------------------------------| r_work (start): 0.3718 rms_B_bonded: 2.64 r_work: 0.3573 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3573 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7083 moved from start: 0.2448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 8723 Z= 0.130 Angle : 0.626 12.347 11815 Z= 0.310 Chirality : 0.041 0.154 1333 Planarity : 0.004 0.050 1501 Dihedral : 4.079 20.322 1174 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 4.49 % Allowed : 25.21 % Favored : 70.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.38 (0.26), residues: 1064 helix: 1.90 (0.27), residues: 406 sheet: 0.09 (0.36), residues: 218 loop : -1.28 (0.27), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG N 118 TYR 0.019 0.001 TYR R 160 PHE 0.017 0.001 PHE T 14 TRP 0.016 0.002 TRP R 275 HIS 0.004 0.001 HIS A 347 Details of bonding type rmsd covalent geometry : bond 0.00292 ( 8717) covalent geometry : angle 0.61853 (11803) SS BOND : bond 0.00688 ( 6) SS BOND : angle 3.01110 ( 12) hydrogen bonds : bond 0.04991 ( 366) hydrogen bonds : angle 4.17768 ( 1056) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 181 time to evaluate : 0.326 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 298 ILE cc_start: 0.7022 (OUTLIER) cc_final: 0.6671 (mp) REVERT: A 317 GLU cc_start: 0.6275 (tm-30) cc_final: 0.5979 (tm-30) REVERT: A 320 GLU cc_start: 0.6428 (tt0) cc_final: 0.6212 (tt0) REVERT: A 367 ASN cc_start: 0.7861 (m-40) cc_final: 0.7608 (m-40) REVERT: A 374 LEU cc_start: 0.8110 (tt) cc_final: 0.7902 (tp) REVERT: B 66 ASP cc_start: 0.7202 (p0) cc_final: 0.6932 (p0) REVERT: B 153 ASP cc_start: 0.6722 (OUTLIER) cc_final: 0.6446 (p0) REVERT: B 171 ILE cc_start: 0.7381 (OUTLIER) cc_final: 0.6955 (mm) REVERT: G 27 ARG cc_start: 0.7852 (ptp90) cc_final: 0.7447 (ptp90) REVERT: N 29 PHE cc_start: 0.7788 (t80) cc_final: 0.7522 (t80) REVERT: N 76 LYS cc_start: 0.7833 (OUTLIER) cc_final: 0.7545 (ttpp) REVERT: N 118 ARG cc_start: 0.7967 (OUTLIER) cc_final: 0.6500 (mtm-85) REVERT: R 120 SER cc_start: 0.8061 (p) cc_final: 0.7659 (m) REVERT: R 125 ILE cc_start: 0.8169 (OUTLIER) cc_final: 0.7950 (mp) REVERT: R 158 ASN cc_start: 0.7626 (OUTLIER) cc_final: 0.7379 (t0) REVERT: R 327 CYS cc_start: 0.7176 (OUTLIER) cc_final: 0.6919 (p) outliers start: 42 outliers final: 28 residues processed: 208 average time/residue: 0.1043 time to fit residues: 28.4871 Evaluate side-chains 214 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 178 time to evaluate : 0.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 249 ASP Chi-restraints excluded: chain A residue 298 ILE Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 349 CYS Chi-restraints excluded: chain A residue 380 GLU Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain N residue 22 CYS Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 76 LYS Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 118 ARG Chi-restraints excluded: chain R residue 97 LYS Chi-restraints excluded: chain R residue 125 ILE Chi-restraints excluded: chain R residue 158 ASN Chi-restraints excluded: chain R residue 173 MET Chi-restraints excluded: chain R residue 174 CYS Chi-restraints excluded: chain R residue 181 GLN Chi-restraints excluded: chain R residue 182 LYS Chi-restraints excluded: chain R residue 254 ILE Chi-restraints excluded: chain R residue 260 VAL Chi-restraints excluded: chain R residue 298 CYS Chi-restraints excluded: chain R residue 301 LEU Chi-restraints excluded: chain R residue 325 VAL Chi-restraints excluded: chain R residue 327 CYS Chi-restraints excluded: chain R residue 393 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 70 optimal weight: 3.9990 chunk 22 optimal weight: 0.4980 chunk 63 optimal weight: 0.9990 chunk 94 optimal weight: 0.9980 chunk 25 optimal weight: 10.0000 chunk 90 optimal weight: 0.1980 chunk 32 optimal weight: 0.6980 chunk 35 optimal weight: 0.7980 chunk 13 optimal weight: 0.6980 chunk 46 optimal weight: 0.9990 chunk 50 optimal weight: 0.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.163995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.134584 restraints weight = 12255.701| |-----------------------------------------------------------------------------| r_work (start): 0.3714 rms_B_bonded: 2.64 r_work: 0.3570 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3570 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7085 moved from start: 0.2534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8723 Z= 0.133 Angle : 0.635 15.429 11815 Z= 0.313 Chirality : 0.042 0.152 1333 Planarity : 0.004 0.047 1501 Dihedral : 4.045 20.141 1174 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 4.49 % Allowed : 24.79 % Favored : 70.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.41 (0.26), residues: 1064 helix: 1.89 (0.27), residues: 406 sheet: 0.24 (0.37), residues: 213 loop : -1.28 (0.27), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG N 118 TYR 0.019 0.001 TYR R 160 PHE 0.018 0.001 PHE T 14 TRP 0.015 0.002 TRP R 275 HIS 0.004 0.001 HIS A 347 Details of bonding type rmsd covalent geometry : bond 0.00300 ( 8717) covalent geometry : angle 0.62780 (11803) SS BOND : bond 0.00572 ( 6) SS BOND : angle 3.01663 ( 12) hydrogen bonds : bond 0.04954 ( 366) hydrogen bonds : angle 4.19042 ( 1056) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 182 time to evaluate : 0.209 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 298 ILE cc_start: 0.7023 (OUTLIER) cc_final: 0.6671 (mp) REVERT: A 317 GLU cc_start: 0.6300 (tm-30) cc_final: 0.6017 (tm-30) REVERT: A 320 GLU cc_start: 0.6407 (tt0) cc_final: 0.6196 (tt0) REVERT: A 367 ASN cc_start: 0.7871 (m-40) cc_final: 0.7623 (m-40) REVERT: A 374 LEU cc_start: 0.8115 (tt) cc_final: 0.7897 (tp) REVERT: B 66 ASP cc_start: 0.7186 (p0) cc_final: 0.6918 (p0) REVERT: B 153 ASP cc_start: 0.6723 (OUTLIER) cc_final: 0.6447 (p0) REVERT: B 171 ILE cc_start: 0.7372 (OUTLIER) cc_final: 0.6942 (mm) REVERT: N 29 PHE cc_start: 0.7796 (t80) cc_final: 0.7534 (t80) REVERT: N 68 PHE cc_start: 0.7271 (m-10) cc_final: 0.7011 (m-10) REVERT: N 76 LYS cc_start: 0.7834 (OUTLIER) cc_final: 0.7540 (ttpp) REVERT: N 118 ARG cc_start: 0.7980 (OUTLIER) cc_final: 0.6788 (mtm180) REVERT: R 120 SER cc_start: 0.8073 (p) cc_final: 0.7668 (m) REVERT: R 125 ILE cc_start: 0.8164 (OUTLIER) cc_final: 0.7942 (mp) REVERT: R 158 ASN cc_start: 0.7605 (OUTLIER) cc_final: 0.7376 (t0) REVERT: R 327 CYS cc_start: 0.7175 (OUTLIER) cc_final: 0.6924 (p) outliers start: 42 outliers final: 30 residues processed: 211 average time/residue: 0.1089 time to fit residues: 30.0486 Evaluate side-chains 219 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 181 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 249 ASP Chi-restraints excluded: chain A residue 298 ILE Chi-restraints excluded: chain A residue 349 CYS Chi-restraints excluded: chain A residue 380 GLU Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 220 GLN Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain N residue 22 CYS Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 76 LYS Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 118 ARG Chi-restraints excluded: chain R residue 97 LYS Chi-restraints excluded: chain R residue 125 ILE Chi-restraints excluded: chain R residue 158 ASN Chi-restraints excluded: chain R residue 173 MET Chi-restraints excluded: chain R residue 174 CYS Chi-restraints excluded: chain R residue 181 GLN Chi-restraints excluded: chain R residue 182 LYS Chi-restraints excluded: chain R residue 254 ILE Chi-restraints excluded: chain R residue 260 VAL Chi-restraints excluded: chain R residue 286 LEU Chi-restraints excluded: chain R residue 301 LEU Chi-restraints excluded: chain R residue 325 VAL Chi-restraints excluded: chain R residue 327 CYS Chi-restraints excluded: chain R residue 337 LEU Chi-restraints excluded: chain R residue 393 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 43 optimal weight: 0.5980 chunk 54 optimal weight: 0.0010 chunk 6 optimal weight: 0.8980 chunk 44 optimal weight: 1.9990 chunk 60 optimal weight: 4.9990 chunk 48 optimal weight: 0.9980 chunk 23 optimal weight: 50.0000 chunk 12 optimal weight: 0.5980 chunk 45 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 chunk 72 optimal weight: 0.0570 overall best weight: 0.4304 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.165538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.136262 restraints weight = 12267.795| |-----------------------------------------------------------------------------| r_work (start): 0.3731 rms_B_bonded: 2.64 r_work: 0.3588 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3588 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7060 moved from start: 0.2656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8723 Z= 0.124 Angle : 0.654 18.387 11815 Z= 0.318 Chirality : 0.041 0.192 1333 Planarity : 0.004 0.048 1501 Dihedral : 3.974 20.072 1174 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 3.95 % Allowed : 25.32 % Favored : 70.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.48 (0.26), residues: 1064 helix: 2.00 (0.27), residues: 402 sheet: 0.14 (0.36), residues: 220 loop : -1.20 (0.27), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 61 TYR 0.018 0.001 TYR R 160 PHE 0.018 0.001 PHE T 14 TRP 0.014 0.001 TRP A 234 HIS 0.003 0.001 HIS A 347 Details of bonding type rmsd covalent geometry : bond 0.00276 ( 8717) covalent geometry : angle 0.64777 (11803) SS BOND : bond 0.00536 ( 6) SS BOND : angle 2.93189 ( 12) hydrogen bonds : bond 0.04739 ( 366) hydrogen bonds : angle 4.16898 ( 1056) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 179 time to evaluate : 0.239 Fit side-chains revert: symmetry clash REVERT: A 298 ILE cc_start: 0.7012 (OUTLIER) cc_final: 0.6652 (mp) REVERT: A 317 GLU cc_start: 0.6261 (tm-30) cc_final: 0.5958 (tm-30) REVERT: A 320 GLU cc_start: 0.6395 (tt0) cc_final: 0.6187 (tt0) REVERT: A 367 ASN cc_start: 0.7831 (m-40) cc_final: 0.7586 (m-40) REVERT: B 66 ASP cc_start: 0.7183 (p0) cc_final: 0.6893 (p0) REVERT: B 153 ASP cc_start: 0.6721 (OUTLIER) cc_final: 0.6441 (p0) REVERT: B 171 ILE cc_start: 0.7350 (OUTLIER) cc_final: 0.6896 (mm) REVERT: B 217 MET cc_start: 0.7796 (ptt) cc_final: 0.7474 (ptp) REVERT: B 289 TYR cc_start: 0.8044 (m-80) cc_final: 0.7647 (m-80) REVERT: N 29 PHE cc_start: 0.7778 (t80) cc_final: 0.7500 (t80) REVERT: N 68 PHE cc_start: 0.7248 (m-10) cc_final: 0.6993 (m-10) REVERT: N 76 LYS cc_start: 0.7812 (OUTLIER) cc_final: 0.7527 (ttpp) REVERT: N 118 ARG cc_start: 0.7954 (OUTLIER) cc_final: 0.6452 (mtm-85) REVERT: R 120 SER cc_start: 0.8056 (p) cc_final: 0.7652 (m) REVERT: R 125 ILE cc_start: 0.8148 (OUTLIER) cc_final: 0.7925 (mp) REVERT: R 158 ASN cc_start: 0.7592 (OUTLIER) cc_final: 0.7352 (t0) REVERT: R 281 TYR cc_start: 0.6749 (m-80) cc_final: 0.6277 (m-80) REVERT: R 327 CYS cc_start: 0.7151 (OUTLIER) cc_final: 0.6931 (p) REVERT: R 374 MET cc_start: 0.7116 (ptp) cc_final: 0.6887 (mtm) outliers start: 37 outliers final: 25 residues processed: 203 average time/residue: 0.1082 time to fit residues: 28.7568 Evaluate side-chains 209 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 176 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 249 ASP Chi-restraints excluded: chain A residue 298 ILE Chi-restraints excluded: chain A residue 349 CYS Chi-restraints excluded: chain A residue 380 GLU Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain N residue 22 CYS Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 76 LYS Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 118 ARG Chi-restraints excluded: chain R residue 125 ILE Chi-restraints excluded: chain R residue 158 ASN Chi-restraints excluded: chain R residue 173 MET Chi-restraints excluded: chain R residue 174 CYS Chi-restraints excluded: chain R residue 181 GLN Chi-restraints excluded: chain R residue 182 LYS Chi-restraints excluded: chain R residue 254 ILE Chi-restraints excluded: chain R residue 260 VAL Chi-restraints excluded: chain R residue 286 LEU Chi-restraints excluded: chain R residue 325 VAL Chi-restraints excluded: chain R residue 327 CYS Chi-restraints excluded: chain R residue 337 LEU Chi-restraints excluded: chain R residue 393 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 32 optimal weight: 2.9990 chunk 80 optimal weight: 0.0270 chunk 63 optimal weight: 0.9980 chunk 23 optimal weight: 50.0000 chunk 93 optimal weight: 0.5980 chunk 35 optimal weight: 0.9980 chunk 101 optimal weight: 0.8980 chunk 52 optimal weight: 3.9990 chunk 77 optimal weight: 0.8980 chunk 65 optimal weight: 0.6980 chunk 75 optimal weight: 0.7980 overall best weight: 0.6038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.164537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.135307 restraints weight = 12218.889| |-----------------------------------------------------------------------------| r_work (start): 0.3720 rms_B_bonded: 2.63 r_work: 0.3573 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3573 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7085 moved from start: 0.2725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8723 Z= 0.137 Angle : 0.637 12.943 11815 Z= 0.317 Chirality : 0.042 0.177 1333 Planarity : 0.004 0.048 1501 Dihedral : 3.994 20.003 1174 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 4.38 % Allowed : 25.21 % Favored : 70.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.46 (0.26), residues: 1064 helix: 1.95 (0.27), residues: 406 sheet: 0.20 (0.37), residues: 213 loop : -1.22 (0.27), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG R 357 TYR 0.018 0.001 TYR R 160 PHE 0.017 0.001 PHE T 14 TRP 0.012 0.002 TRP R 275 HIS 0.003 0.001 HIS A 347 Details of bonding type rmsd covalent geometry : bond 0.00310 ( 8717) covalent geometry : angle 0.63005 (11803) SS BOND : bond 0.00520 ( 6) SS BOND : angle 2.94734 ( 12) hydrogen bonds : bond 0.04989 ( 366) hydrogen bonds : angle 4.24131 ( 1056) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1912.46 seconds wall clock time: 33 minutes 23.18 seconds (2003.18 seconds total)