Starting phenix.real_space_refine on Wed Jan 15 14:35:02 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xvh_38704/01_2025/8xvh_38704.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xvh_38704/01_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_38704/01_2025/8xvh_38704.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xvh_38704/01_2025/8xvh_38704.map" model { file = "/net/cci-nas-00/data/ceres_data/8xvh_38704/01_2025/8xvh_38704.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xvh_38704/01_2025/8xvh_38704.cif" } resolution = 3.26 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/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: 4.75, per 1000 atoms: 0.56 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: 2.16 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 0.92 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: 2.12 Time building geometry restraints manager: 2.49 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 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: 0.850 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.300 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 20.870 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.020 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:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.190 ------------------------------------------------------------------------------- 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 8717 Z= 0.160 Angle : 0.574 9.159 11803 Z= 0.303 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (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 TRP 0.012 0.001 TRP A 234 HIS 0.003 0.001 HIS A 347 PHE 0.030 0.001 PHE T 14 TYR 0.006 0.001 TYR N 95 ARG 0.007 0.000 ARG A 273 *********************** 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 : 0.969 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: 0.2612 time to fit residues: 63.7445 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 : 0.980 ------------------------------------------------------------------------------- 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 88 optimal weight: 0.9980 chunk 79 optimal weight: 0.0670 chunk 44 optimal weight: 0.8980 chunk 27 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 82 optimal weight: 0.9980 chunk 31 optimal weight: 0.0980 chunk 50 optimal weight: 1.9990 chunk 61 optimal weight: 3.9990 chunk 95 optimal weight: 0.5980 overall best weight: 0.5318 ------------------------------------------------------------------------------- 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** ** B 239 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 = 0.4116 r_free = 0.4116 target = 0.165440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.137101 restraints weight = 12127.136| |-----------------------------------------------------------------------------| r_work (start): 0.3735 rms_B_bonded: 2.68 r_work: 0.3581 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3581 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7016 moved from start: 0.1130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8717 Z= 0.196 Angle : 0.575 6.988 11803 Z= 0.301 Chirality : 0.042 0.168 1333 Planarity : 0.004 0.051 1501 Dihedral : 4.097 38.582 1175 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 3.10 % Allowed : 23.18 % Favored : 73.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.25), residues: 1064 helix: 1.44 (0.26), residues: 399 sheet: -0.24 (0.35), residues: 227 loop : -1.22 (0.26), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 234 HIS 0.005 0.001 HIS A 347 PHE 0.014 0.001 PHE A 366 TYR 0.010 0.001 TYR R 281 ARG 0.005 0.000 ARG A 273 *********************** 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 216 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 187 time to evaluate : 0.920 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 16 GLU cc_start: 0.7090 (pp20) cc_final: 0.6807 (pp20) REVERT: A 367 ASN cc_start: 0.7741 (m-40) cc_final: 0.7527 (m-40) REVERT: B 61 MET cc_start: 0.8075 (tmm) cc_final: 0.7846 (ppp) REVERT: B 205 ASP cc_start: 0.6853 (p0) cc_final: 0.6631 (p0) REVERT: N 118 ARG cc_start: 0.7874 (OUTLIER) cc_final: 0.6410 (mtm-85) REVERT: R 120 SER cc_start: 0.8059 (p) cc_final: 0.7593 (m) REVERT: R 125 ILE cc_start: 0.8135 (OUTLIER) cc_final: 0.7908 (mp) REVERT: R 175 LYS cc_start: 0.7525 (mmpt) cc_final: 0.7100 (mttm) REVERT: R 192 LEU cc_start: 0.8069 (OUTLIER) cc_final: 0.7803 (tt) REVERT: R 327 CYS cc_start: 0.7136 (OUTLIER) cc_final: 0.6781 (p) outliers start: 29 outliers final: 14 residues processed: 203 average time/residue: 0.2670 time to fit residues: 70.5369 Evaluate side-chains 197 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 179 time to evaluate : 1.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 325 THR 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 147 SER Chi-restraints excluded: chain B residue 220 GLN 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 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 205 SER Chi-restraints excluded: chain R residue 325 VAL Chi-restraints excluded: chain R residue 327 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 24 optimal weight: 7.9990 chunk 29 optimal weight: 0.7980 chunk 79 optimal weight: 1.9990 chunk 93 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 85 optimal weight: 1.9990 chunk 88 optimal weight: 0.8980 chunk 102 optimal weight: 0.9980 chunk 70 optimal weight: 3.9990 chunk 14 optimal weight: 3.9990 chunk 100 optimal weight: 3.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- 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 = 0.4083 r_free = 0.4083 target = 0.162500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.133868 restraints weight = 12194.261| |-----------------------------------------------------------------------------| r_work (start): 0.3709 rms_B_bonded: 2.59 r_work: 0.3570 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3570 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7075 moved from start: 0.1615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 8717 Z= 0.304 Angle : 0.616 8.876 11803 Z= 0.321 Chirality : 0.043 0.175 1333 Planarity : 0.004 0.053 1501 Dihedral : 4.299 23.995 1175 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 4.91 % Allowed : 22.44 % Favored : 72.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.25), residues: 1064 helix: 1.43 (0.26), residues: 401 sheet: -0.24 (0.35), residues: 224 loop : -1.31 (0.26), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP R 206 HIS 0.006 0.001 HIS A 347 PHE 0.016 0.002 PHE T 14 TYR 0.014 0.002 TYR N 95 ARG 0.003 0.000 ARG A 228 *********************** 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 232 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 186 time to evaluate : 1.096 Fit side-chains revert: symmetry clash REVERT: A 317 GLU cc_start: 0.6410 (tm-30) cc_final: 0.6170 (tm-30) REVERT: A 346 ARG cc_start: 0.7261 (mtp85) cc_final: 0.7026 (mtp85) REVERT: A 367 ASN cc_start: 0.7891 (m-40) cc_final: 0.7633 (m-40) REVERT: B 66 ASP cc_start: 0.7337 (p0) cc_final: 0.7080 (p0) REVERT: B 289 TYR cc_start: 0.8102 (m-80) cc_final: 0.7706 (m-80) REVERT: G 27 ARG cc_start: 0.7900 (ptp-170) cc_final: 0.7670 (ptp90) REVERT: N 118 ARG cc_start: 0.8035 (OUTLIER) cc_final: 0.6580 (mtm-85) REVERT: R 120 SER cc_start: 0.8026 (p) cc_final: 0.7606 (m) REVERT: R 125 ILE cc_start: 0.8190 (OUTLIER) cc_final: 0.7963 (mp) REVERT: R 175 LYS cc_start: 0.7641 (mtpt) cc_final: 0.7372 (mttm) REVERT: R 192 LEU cc_start: 0.7940 (OUTLIER) cc_final: 0.7721 (tt) REVERT: R 327 CYS cc_start: 0.7129 (OUTLIER) cc_final: 0.6775 (p) outliers start: 46 outliers final: 29 residues processed: 215 average time/residue: 0.2558 time to fit residues: 71.6488 Evaluate side-chains 213 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 180 time to evaluate : 0.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 337 ARG Chi-restraints excluded: chain A residue 380 GLU Chi-restraints excluded: chain B residue 42 ARG 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 133 VAL Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 220 GLN Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 263 THR 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 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 153 ILE 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 192 LEU 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 327 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 75 optimal weight: 0.1980 chunk 71 optimal weight: 0.8980 chunk 42 optimal weight: 0.7980 chunk 28 optimal weight: 0.8980 chunk 98 optimal weight: 0.9980 chunk 24 optimal weight: 4.9990 chunk 99 optimal weight: 0.9990 chunk 32 optimal weight: 0.9990 chunk 45 optimal weight: 0.5980 chunk 14 optimal weight: 0.8980 chunk 59 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.4101 r_free = 0.4101 target = 0.164060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.135511 restraints weight = 12114.649| |-----------------------------------------------------------------------------| r_work (start): 0.3718 rms_B_bonded: 2.58 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: 0.7081 moved from start: 0.1858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8717 Z= 0.211 Angle : 0.579 10.368 11803 Z= 0.297 Chirality : 0.042 0.163 1333 Planarity : 0.004 0.051 1501 Dihedral : 4.108 18.955 1174 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 4.59 % Allowed : 23.82 % Favored : 71.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.25), residues: 1064 helix: 1.71 (0.26), residues: 399 sheet: -0.10 (0.36), residues: 216 loop : -1.34 (0.26), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 234 HIS 0.004 0.001 HIS A 347 PHE 0.017 0.001 PHE T 14 TYR 0.026 0.001 TYR R 160 ARG 0.003 0.000 ARG A 323 *********************** 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 222 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 179 time to evaluate : 0.966 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 317 GLU cc_start: 0.6452 (tm-30) cc_final: 0.6156 (tm-30) REVERT: A 367 ASN cc_start: 0.7877 (m-40) cc_final: 0.7625 (m-40) REVERT: B 66 ASP cc_start: 0.7267 (p0) cc_final: 0.7008 (p0) REVERT: B 171 ILE cc_start: 0.7372 (OUTLIER) cc_final: 0.6917 (mm) REVERT: B 289 TYR cc_start: 0.8086 (m-80) cc_final: 0.7678 (m-80) REVERT: G 27 ARG cc_start: 0.7932 (ptp-170) cc_final: 0.7687 (ptp90) REVERT: N 118 ARG cc_start: 0.7990 (OUTLIER) cc_final: 0.6635 (mtm-85) REVERT: R 120 SER cc_start: 0.8071 (p) cc_final: 0.7662 (m) REVERT: R 125 ILE cc_start: 0.8185 (OUTLIER) cc_final: 0.7936 (mp) REVERT: R 158 ASN cc_start: 0.7593 (OUTLIER) cc_final: 0.7282 (t0) REVERT: R 175 LYS cc_start: 0.7651 (mtpt) cc_final: 0.7383 (mttm) REVERT: R 327 CYS cc_start: 0.7153 (OUTLIER) cc_final: 0.6856 (p) outliers start: 43 outliers final: 25 residues processed: 205 average time/residue: 0.2582 time to fit residues: 69.1661 Evaluate side-chains 202 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 172 time to evaluate : 0.941 ------------------------------------------------------------------------------- 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 325 THR Chi-restraints excluded: chain A residue 337 ARG Chi-restraints excluded: chain A residue 380 GLU Chi-restraints excluded: chain B residue 10 GLU 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 246 ASP 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 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 158 ASN 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 301 LEU 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 344 ILE 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 23 optimal weight: 50.0000 chunk 48 optimal weight: 2.9990 chunk 89 optimal weight: 0.8980 chunk 27 optimal weight: 0.9980 chunk 21 optimal weight: 0.9980 chunk 90 optimal weight: 1.9990 chunk 33 optimal weight: 0.6980 chunk 5 optimal weight: 0.9980 chunk 29 optimal weight: 0.8980 chunk 46 optimal weight: 0.9990 chunk 24 optimal weight: 5.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- 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 = 0.4087 r_free = 0.4087 target = 0.163370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.134532 restraints weight = 12178.644| |-----------------------------------------------------------------------------| r_work (start): 0.3702 rms_B_bonded: 2.65 r_work: 0.3552 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3552 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7064 moved from start: 0.2039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 8717 Z= 0.256 Angle : 0.614 11.564 11803 Z= 0.313 Chirality : 0.042 0.163 1333 Planarity : 0.004 0.050 1501 Dihedral : 4.164 19.689 1174 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.25), residues: 1064 helix: 1.69 (0.26), residues: 407 sheet: -0.14 (0.36), residues: 216 loop : -1.36 (0.26), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP N 47 HIS 0.005 0.001 HIS A 220 PHE 0.014 0.002 PHE T 14 TYR 0.023 0.002 TYR R 160 ARG 0.010 0.000 ARG A 273 *********************** 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 234 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 182 time to evaluate : 0.990 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 317 GLU cc_start: 0.6529 (tm-30) cc_final: 0.6216 (tm-30) REVERT: A 367 ASN cc_start: 0.7850 (m-40) cc_final: 0.7600 (m-40) REVERT: B 66 ASP cc_start: 0.7360 (p0) cc_final: 0.7067 (p0) REVERT: B 171 ILE cc_start: 0.7233 (OUTLIER) cc_final: 0.6836 (mm) REVERT: B 289 TYR cc_start: 0.8116 (m-80) cc_final: 0.7667 (m-80) REVERT: G 27 ARG cc_start: 0.8000 (ptp-170) cc_final: 0.7749 (ptp90) REVERT: N 118 ARG cc_start: 0.7942 (OUTLIER) cc_final: 0.6486 (mtm-85) REVERT: R 120 SER cc_start: 0.8002 (p) cc_final: 0.7598 (m) REVERT: R 125 ILE cc_start: 0.8096 (OUTLIER) cc_final: 0.7868 (mp) REVERT: R 158 ASN cc_start: 0.7660 (OUTLIER) cc_final: 0.7385 (t0) REVERT: R 327 CYS cc_start: 0.7100 (OUTLIER) cc_final: 0.6759 (p) outliers start: 52 outliers final: 35 residues processed: 217 average time/residue: 0.2502 time to fit residues: 71.2287 Evaluate side-chains 217 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 177 time to evaluate : 0.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LEU 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 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 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 171 ILE Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 192 LEU 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 91 THR Chi-restraints excluded: chain N residue 118 ARG Chi-restraints excluded: chain R residue 90 CYS 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 205 SER 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 389 VAL 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 98 optimal weight: 0.7980 chunk 60 optimal weight: 3.9990 chunk 72 optimal weight: 0.6980 chunk 103 optimal weight: 0.5980 chunk 18 optimal weight: 0.7980 chunk 21 optimal weight: 1.9990 chunk 83 optimal weight: 5.9990 chunk 37 optimal weight: 0.3980 chunk 40 optimal weight: 0.9980 chunk 82 optimal weight: 0.1980 chunk 32 optimal weight: 2.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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 = 0.4105 r_free = 0.4105 target = 0.164588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.136165 restraints weight = 11957.335| |-----------------------------------------------------------------------------| r_work (start): 0.3725 rms_B_bonded: 2.56 r_work: 0.3577 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3577 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7077 moved from start: 0.2197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8717 Z= 0.188 Angle : 0.580 9.854 11803 Z= 0.294 Chirality : 0.041 0.171 1333 Planarity : 0.004 0.051 1501 Dihedral : 4.018 19.799 1174 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 4.49 % Allowed : 25.00 % Favored : 70.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.26), residues: 1064 helix: 1.85 (0.26), residues: 407 sheet: 0.03 (0.36), residues: 217 loop : -1.37 (0.26), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP R 275 HIS 0.003 0.001 HIS A 347 PHE 0.014 0.001 PHE T 14 TYR 0.020 0.001 TYR R 160 ARG 0.004 0.000 ARG A 273 *********************** 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 227 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 185 time to evaluate : 1.001 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 317 GLU cc_start: 0.6429 (tm-30) cc_final: 0.6207 (tm-30) REVERT: A 367 ASN cc_start: 0.7847 (m-40) cc_final: 0.7644 (m-40) REVERT: B 66 ASP cc_start: 0.7284 (p0) cc_final: 0.7009 (p0) REVERT: B 153 ASP cc_start: 0.6766 (OUTLIER) cc_final: 0.6484 (p0) REVERT: B 171 ILE cc_start: 0.7373 (OUTLIER) cc_final: 0.6935 (mm) REVERT: B 289 TYR cc_start: 0.8070 (m-80) cc_final: 0.7666 (m-80) REVERT: N 76 LYS cc_start: 0.7825 (OUTLIER) cc_final: 0.7538 (ttpp) REVERT: N 118 ARG cc_start: 0.7949 (OUTLIER) cc_final: 0.6606 (mtm-85) REVERT: R 120 SER cc_start: 0.8059 (p) cc_final: 0.7663 (m) REVERT: R 125 ILE cc_start: 0.8157 (OUTLIER) cc_final: 0.7940 (mp) REVERT: R 158 ASN cc_start: 0.7651 (OUTLIER) cc_final: 0.7402 (t0) outliers start: 42 outliers final: 24 residues processed: 212 average time/residue: 0.2599 time to fit residues: 71.6950 Evaluate side-chains 212 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 182 time to evaluate : 0.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 133 VAL Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 171 ILE 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 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 90 CYS 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 254 ILE Chi-restraints excluded: chain R residue 260 VAL Chi-restraints excluded: chain R residue 301 LEU Chi-restraints excluded: chain R residue 325 VAL Chi-restraints excluded: chain R residue 389 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 100 optimal weight: 5.9990 chunk 89 optimal weight: 0.3980 chunk 12 optimal weight: 1.9990 chunk 40 optimal weight: 0.9990 chunk 62 optimal weight: 0.9990 chunk 67 optimal weight: 0.9980 chunk 6 optimal weight: 0.5980 chunk 58 optimal weight: 0.0870 chunk 10 optimal weight: 0.8980 chunk 14 optimal weight: 2.9990 chunk 45 optimal weight: 0.8980 overall best weight: 0.5758 ------------------------------------------------------------------------------- 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 = 0.4104 r_free = 0.4104 target = 0.164775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.136085 restraints weight = 12114.162| |-----------------------------------------------------------------------------| r_work (start): 0.3722 rms_B_bonded: 2.59 r_work: 0.3574 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3574 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7080 moved from start: 0.2312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8717 Z= 0.195 Angle : 0.596 10.577 11803 Z= 0.300 Chirality : 0.042 0.184 1333 Planarity : 0.004 0.051 1501 Dihedral : 3.982 19.834 1174 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 4.27 % Allowed : 25.53 % Favored : 70.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.26), residues: 1064 helix: 1.91 (0.26), residues: 407 sheet: 0.07 (0.36), residues: 217 loop : -1.32 (0.26), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 234 HIS 0.004 0.001 HIS A 220 PHE 0.015 0.001 PHE T 14 TYR 0.019 0.001 TYR R 160 ARG 0.003 0.000 ARG A 273 *********************** 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 221 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 181 time to evaluate : 0.931 Fit side-chains revert: symmetry clash REVERT: A 367 ASN cc_start: 0.7859 (m-40) cc_final: 0.7633 (m-40) REVERT: A 374 LEU cc_start: 0.8083 (tt) cc_final: 0.7866 (tp) REVERT: A 376 MET cc_start: 0.7583 (mtm) cc_final: 0.7325 (mtt) REVERT: B 66 ASP cc_start: 0.7235 (p0) cc_final: 0.6968 (p0) REVERT: B 153 ASP cc_start: 0.6796 (OUTLIER) cc_final: 0.6519 (p0) REVERT: B 171 ILE cc_start: 0.7382 (OUTLIER) cc_final: 0.6933 (mm) REVERT: B 289 TYR cc_start: 0.8077 (m-80) cc_final: 0.7683 (m-80) REVERT: N 35 ASN cc_start: 0.8355 (OUTLIER) cc_final: 0.8118 (p0) REVERT: N 76 LYS cc_start: 0.7821 (OUTLIER) cc_final: 0.7504 (ttpp) REVERT: N 118 ARG cc_start: 0.7973 (OUTLIER) cc_final: 0.6797 (mtm180) REVERT: R 120 SER cc_start: 0.8067 (p) cc_final: 0.7673 (m) REVERT: R 125 ILE cc_start: 0.8158 (OUTLIER) cc_final: 0.7939 (mp) REVERT: R 158 ASN cc_start: 0.7626 (OUTLIER) cc_final: 0.7356 (t0) REVERT: R 327 CYS cc_start: 0.7195 (OUTLIER) cc_final: 0.6937 (p) outliers start: 40 outliers final: 26 residues processed: 207 average time/residue: 0.2622 time to fit residues: 70.2650 Evaluate side-chains 214 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 180 time to evaluate : 0.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 249 ASP 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 133 VAL Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 171 ILE 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 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 90 CYS 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 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 337 LEU Chi-restraints excluded: chain R residue 389 VAL 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 65 optimal weight: 0.5980 chunk 63 optimal weight: 0.8980 chunk 103 optimal weight: 0.7980 chunk 45 optimal weight: 0.7980 chunk 6 optimal weight: 0.8980 chunk 26 optimal weight: 0.0970 chunk 44 optimal weight: 0.8980 chunk 78 optimal weight: 0.6980 chunk 73 optimal weight: 7.9990 chunk 52 optimal weight: 1.9990 chunk 61 optimal weight: 0.0570 overall best weight: 0.4496 ------------------------------------------------------------------------------- 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 = 0.4111 r_free = 0.4111 target = 0.165377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.136554 restraints weight = 12214.913| |-----------------------------------------------------------------------------| r_work (start): 0.3728 rms_B_bonded: 2.62 r_work: 0.3580 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3580 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7070 moved from start: 0.2395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8717 Z= 0.181 Angle : 0.598 11.444 11803 Z= 0.301 Chirality : 0.041 0.156 1333 Planarity : 0.004 0.047 1501 Dihedral : 3.948 20.084 1174 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 4.91 % Allowed : 24.57 % Favored : 70.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.26), residues: 1064 helix: 2.06 (0.26), residues: 405 sheet: 0.13 (0.36), residues: 217 loop : -1.32 (0.27), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 234 HIS 0.004 0.001 HIS A 220 PHE 0.014 0.001 PHE T 14 TYR 0.019 0.001 TYR R 160 ARG 0.003 0.000 ARG B 219 *********************** 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 229 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 183 time to evaluate : 1.053 Fit side-chains revert: symmetry clash REVERT: A 367 ASN cc_start: 0.7833 (m-40) cc_final: 0.7617 (m-40) REVERT: A 374 LEU cc_start: 0.8104 (tt) cc_final: 0.7894 (tp) REVERT: B 66 ASP cc_start: 0.7251 (p0) cc_final: 0.6979 (p0) REVERT: B 153 ASP cc_start: 0.6772 (OUTLIER) cc_final: 0.6493 (p0) REVERT: B 171 ILE cc_start: 0.7366 (OUTLIER) cc_final: 0.6893 (mm) REVERT: B 289 TYR cc_start: 0.8070 (m-80) cc_final: 0.7649 (m-80) REVERT: N 35 ASN cc_start: 0.8327 (OUTLIER) cc_final: 0.8073 (p0) REVERT: N 68 PHE cc_start: 0.7270 (m-10) cc_final: 0.7020 (m-10) REVERT: N 76 LYS cc_start: 0.7821 (OUTLIER) cc_final: 0.7515 (ttpp) REVERT: N 118 ARG cc_start: 0.7953 (OUTLIER) cc_final: 0.6488 (mtm-85) REVERT: R 120 SER cc_start: 0.8060 (p) cc_final: 0.7665 (m) REVERT: R 125 ILE cc_start: 0.8152 (OUTLIER) cc_final: 0.7932 (mp) REVERT: R 158 ASN cc_start: 0.7606 (OUTLIER) cc_final: 0.7339 (t0) REVERT: R 327 CYS cc_start: 0.7191 (OUTLIER) cc_final: 0.6966 (p) REVERT: R 347 LEU cc_start: 0.7799 (tp) cc_final: 0.7562 (mt) outliers start: 46 outliers final: 33 residues processed: 214 average time/residue: 0.2462 time to fit residues: 68.0982 Evaluate side-chains 222 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 181 time to evaluate : 0.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 249 ASP 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 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 90 CYS 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 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 300 MET 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 389 VAL 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 23 optimal weight: 50.0000 chunk 85 optimal weight: 0.9980 chunk 95 optimal weight: 0.7980 chunk 19 optimal weight: 4.9990 chunk 90 optimal weight: 0.7980 chunk 9 optimal weight: 0.5980 chunk 25 optimal weight: 5.9990 chunk 28 optimal weight: 0.2980 chunk 40 optimal weight: 0.4980 chunk 4 optimal weight: 0.9990 chunk 14 optimal weight: 0.0030 overall best weight: 0.4390 ------------------------------------------------------------------------------- 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 = 0.4114 r_free = 0.4114 target = 0.165397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.136639 restraints weight = 12131.573| |-----------------------------------------------------------------------------| r_work (start): 0.3733 rms_B_bonded: 2.61 r_work: 0.3585 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3585 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7065 moved from start: 0.2502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 8717 Z= 0.187 Angle : 0.637 13.665 11803 Z= 0.321 Chirality : 0.042 0.181 1333 Planarity : 0.004 0.048 1501 Dihedral : 3.986 19.901 1174 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 4.06 % Allowed : 25.75 % Favored : 70.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.26), residues: 1064 helix: 2.07 (0.27), residues: 405 sheet: 0.14 (0.36), residues: 220 loop : -1.23 (0.27), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 234 HIS 0.003 0.001 HIS A 220 PHE 0.017 0.001 PHE N 29 TYR 0.018 0.001 TYR R 160 ARG 0.003 0.000 ARG R 357 *********************** 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: 38 poor density : 186 time to evaluate : 0.890 Fit side-chains revert: symmetry clash REVERT: A 367 ASN cc_start: 0.7832 (m-40) cc_final: 0.7613 (m-40) REVERT: A 374 LEU cc_start: 0.8102 (tt) cc_final: 0.7893 (tp) REVERT: B 66 ASP cc_start: 0.7234 (p0) cc_final: 0.6957 (p0) REVERT: B 153 ASP cc_start: 0.6765 (OUTLIER) cc_final: 0.6480 (p0) REVERT: B 171 ILE cc_start: 0.7365 (OUTLIER) cc_final: 0.6912 (mm) REVERT: B 289 TYR cc_start: 0.8042 (m-80) cc_final: 0.7648 (m-80) REVERT: N 68 PHE cc_start: 0.7252 (m-10) cc_final: 0.7007 (m-10) REVERT: N 76 LYS cc_start: 0.7807 (OUTLIER) cc_final: 0.7486 (ttpp) REVERT: N 118 ARG cc_start: 0.7955 (OUTLIER) cc_final: 0.6766 (mtm180) REVERT: R 120 SER cc_start: 0.8059 (p) cc_final: 0.7659 (m) REVERT: R 125 ILE cc_start: 0.8164 (OUTLIER) cc_final: 0.7943 (mp) REVERT: R 158 ASN cc_start: 0.7591 (OUTLIER) cc_final: 0.7342 (t0) REVERT: R 347 LEU cc_start: 0.7779 (tp) cc_final: 0.7540 (mt) REVERT: R 374 MET cc_start: 0.7057 (ptp) cc_final: 0.6811 (mtm) outliers start: 38 outliers final: 28 residues processed: 210 average time/residue: 0.2689 time to fit residues: 73.0733 Evaluate side-chains 218 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 184 time to evaluate : 0.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ASP Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 249 ASP 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 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 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 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 300 MET Chi-restraints excluded: chain R residue 301 LEU Chi-restraints excluded: chain R residue 325 VAL Chi-restraints excluded: chain R residue 337 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 64 optimal weight: 1.9990 chunk 47 optimal weight: 0.6980 chunk 49 optimal weight: 0.3980 chunk 97 optimal weight: 2.9990 chunk 20 optimal weight: 0.0770 chunk 95 optimal weight: 0.5980 chunk 55 optimal weight: 3.9990 chunk 87 optimal weight: 0.6980 chunk 24 optimal weight: 7.9990 chunk 103 optimal weight: 0.9990 chunk 51 optimal weight: 0.0670 overall best weight: 0.3676 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 220 GLN ** B 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.165995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.136503 restraints weight = 12225.013| |-----------------------------------------------------------------------------| r_work (start): 0.3756 rms_B_bonded: 2.65 r_work: 0.3624 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3624 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7013 moved from start: 0.2669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 8717 Z= 0.171 Angle : 0.614 12.088 11803 Z= 0.307 Chirality : 0.041 0.175 1333 Planarity : 0.004 0.049 1501 Dihedral : 3.937 19.225 1174 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 3.42 % Allowed : 26.18 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.26), residues: 1064 helix: 2.14 (0.27), residues: 404 sheet: 0.28 (0.37), residues: 215 loop : -1.22 (0.27), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 234 HIS 0.003 0.001 HIS A 220 PHE 0.015 0.001 PHE T 14 TYR 0.018 0.001 TYR R 160 ARG 0.002 0.000 ARG A 273 ********************** 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 215 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 183 time to evaluate : 0.836 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 367 ASN cc_start: 0.7763 (m-40) cc_final: 0.7534 (m-40) REVERT: A 374 LEU cc_start: 0.8036 (tt) cc_final: 0.7834 (tp) REVERT: B 66 ASP cc_start: 0.7221 (p0) cc_final: 0.6929 (p0) REVERT: B 171 ILE cc_start: 0.7277 (OUTLIER) cc_final: 0.6813 (mm) REVERT: B 289 TYR cc_start: 0.8047 (m-80) cc_final: 0.7651 (m-80) REVERT: N 68 PHE cc_start: 0.7248 (m-10) cc_final: 0.7007 (m-10) REVERT: N 76 LYS cc_start: 0.7769 (OUTLIER) cc_final: 0.7440 (ttpp) REVERT: N 118 ARG cc_start: 0.7930 (OUTLIER) cc_final: 0.6428 (mtm-85) REVERT: R 120 SER cc_start: 0.8005 (p) cc_final: 0.7603 (m) REVERT: R 125 ILE cc_start: 0.8144 (OUTLIER) cc_final: 0.7937 (mp) REVERT: R 158 ASN cc_start: 0.7594 (OUTLIER) cc_final: 0.7363 (t0) outliers start: 32 outliers final: 25 residues processed: 204 average time/residue: 0.2610 time to fit residues: 68.9015 Evaluate side-chains 208 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 178 time to evaluate : 0.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 249 ASP Chi-restraints excluded: chain A residue 349 CYS Chi-restraints excluded: chain A residue 380 GLU 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 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 254 ILE Chi-restraints excluded: chain R residue 260 VAL Chi-restraints excluded: chain R residue 298 CYS Chi-restraints excluded: chain R residue 300 MET Chi-restraints excluded: chain R residue 301 LEU Chi-restraints excluded: chain R residue 325 VAL Chi-restraints excluded: chain R residue 337 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 103 optimal weight: 1.9990 chunk 45 optimal weight: 0.8980 chunk 75 optimal weight: 0.4980 chunk 32 optimal weight: 0.6980 chunk 20 optimal weight: 0.0370 chunk 64 optimal weight: 1.9990 chunk 31 optimal weight: 0.0770 chunk 73 optimal weight: 7.9990 chunk 21 optimal weight: 0.6980 chunk 39 optimal weight: 0.6980 chunk 19 optimal weight: 1.9990 overall best weight: 0.4016 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 220 GLN ** B 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.165929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.136489 restraints weight = 12420.015| |-----------------------------------------------------------------------------| r_work (start): 0.3739 rms_B_bonded: 2.67 r_work: 0.3595 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3595 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7045 moved from start: 0.2708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.114 8717 Z= 0.229 Angle : 0.943 59.195 11803 Z= 0.533 Chirality : 0.042 0.306 1333 Planarity : 0.004 0.048 1501 Dihedral : 3.929 20.995 1174 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 3.53 % Allowed : 26.28 % Favored : 70.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.26), residues: 1064 helix: 2.13 (0.27), residues: 404 sheet: 0.30 (0.36), residues: 215 loop : -1.22 (0.27), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 234 HIS 0.003 0.001 HIS A 220 PHE 0.014 0.001 PHE T 14 TYR 0.014 0.001 TYR R 160 ARG 0.002 0.000 ARG B 304 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4239.53 seconds wall clock time: 76 minutes 26.80 seconds (4586.80 seconds total)