Starting phenix.real_space_refine on Tue Apr 29 07:49:06 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xvh_38704/04_2025/8xvh_38704.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xvh_38704/04_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_38704/04_2025/8xvh_38704.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xvh_38704/04_2025/8xvh_38704.map" model { file = "/net/cci-nas-00/data/ceres_data/8xvh_38704/04_2025/8xvh_38704.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xvh_38704/04_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-5669/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: 5.20, per 1000 atoms: 0.61 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: 2.38 Conformation dependent library (CDL) restraints added in 988.0 milliseconds 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: 0.90 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: 2.18 Time building geometry restraints manager: 2.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2791 1.34 - 1.46: 2019 1.46 - 1.58: 3823 1.58 - 1.70: 0 1.70 - 1.82: 84 Bond restraints: 8717 Sorted by residual: bond pdb=" CA TRP R 167 " pdb=" C TRP R 167 " ideal model delta sigma weight residual 1.523 1.497 0.026 1.24e-02 6.50e+03 4.42e+00 bond pdb=" CB LYS A 32 " pdb=" CG LYS A 32 " ideal model delta sigma weight residual 1.520 1.563 -0.043 3.00e-02 1.11e+03 2.01e+00 bond pdb=" CA PHE R 363 " pdb=" CB PHE R 363 " ideal model delta sigma weight residual 1.528 1.545 -0.016 1.56e-02 4.11e+03 1.07e+00 bond pdb=" CA ASN B 88 " pdb=" CB ASN B 88 " ideal model delta sigma weight residual 1.536 1.556 -0.021 2.08e-02 2.31e+03 9.78e-01 bond pdb=" C TRP R 167 " pdb=" O TRP R 167 " ideal model delta sigma weight residual 1.237 1.226 0.011 1.17e-02 7.31e+03 9.24e-01 ... (remaining 8712 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.83: 11624 1.83 - 3.66: 139 3.66 - 5.50: 24 5.50 - 7.33: 13 7.33 - 9.16: 3 Bond angle restraints: 11803 Sorted by residual: angle pdb=" CA LYS A 32 " pdb=" CB LYS A 32 " pdb=" CG LYS A 32 " ideal model delta sigma weight residual 114.10 121.04 -6.94 2.00e+00 2.50e-01 1.21e+01 angle pdb=" CA GLU A 317 " pdb=" CB GLU A 317 " pdb=" CG GLU A 317 " ideal model delta sigma weight residual 114.10 120.79 -6.69 2.00e+00 2.50e-01 1.12e+01 angle pdb=" CB LYS A 32 " pdb=" CG LYS A 32 " pdb=" CD LYS A 32 " ideal model delta sigma weight residual 111.30 118.72 -7.42 2.30e+00 1.89e-01 1.04e+01 angle pdb=" CA LYS R 346 " pdb=" CB LYS R 346 " pdb=" CG LYS R 346 " ideal model delta sigma weight residual 114.10 120.49 -6.39 2.00e+00 2.50e-01 1.02e+01 angle pdb=" CA GLU A 16 " pdb=" CB GLU A 16 " pdb=" CG GLU A 16 " ideal model delta sigma weight residual 114.10 119.99 -5.89 2.00e+00 2.50e-01 8.67e+00 ... (remaining 11798 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.52: 4503 16.52 - 33.04: 554 33.04 - 49.56: 144 49.56 - 66.08: 37 66.08 - 82.60: 2 Dihedral angle restraints: 5240 sinusoidal: 2093 harmonic: 3147 Sorted by residual: dihedral pdb=" CB CYS N 22 " pdb=" SG CYS N 22 " pdb=" SG CYS N 96 " pdb=" CB CYS N 96 " ideal model delta sinusoidal sigma weight residual -86.00 -6.52 -79.48 1 1.00e+01 1.00e-02 7.85e+01 dihedral pdb=" CB CYS N 99 " pdb=" SG CYS N 99 " pdb=" SG CYS N 107 " pdb=" CB CYS N 107 " ideal model delta sinusoidal sigma weight residual -86.00 -29.44 -56.56 1 1.00e+01 1.00e-02 4.31e+01 dihedral pdb=" CB CYS T 1 " pdb=" SG CYS T 1 " pdb=" SG CYS T 15 " pdb=" CB CYS T 15 " ideal model delta sinusoidal sigma weight residual 93.00 145.94 -52.94 1 1.00e+01 1.00e-02 3.81e+01 ... (remaining 5237 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 788 0.027 - 0.053: 334 0.053 - 0.080: 123 0.080 - 0.107: 59 0.107 - 0.134: 29 Chirality restraints: 1333 Sorted by residual: chirality pdb=" CA ILE A 278 " pdb=" N ILE A 278 " pdb=" C ILE A 278 " pdb=" CB ILE A 278 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.46e-01 chirality pdb=" CA ILE A 244 " pdb=" N ILE A 244 " pdb=" C ILE A 244 " pdb=" CB ILE A 244 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.08e-01 chirality pdb=" CA VAL G 54 " pdb=" N VAL G 54 " pdb=" C VAL G 54 " pdb=" CB VAL G 54 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 3.97e-01 ... (remaining 1330 not shown) Planarity restraints: 1501 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY R 135 " 0.039 5.00e-02 4.00e+02 5.86e-02 5.49e+00 pdb=" N PRO R 136 " -0.101 5.00e-02 4.00e+02 pdb=" CA PRO R 136 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO R 136 " 0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE T 14 " 0.010 2.00e-02 2.50e+03 1.31e-02 3.01e+00 pdb=" CG PHE T 14 " -0.030 2.00e-02 2.50e+03 pdb=" CD1 PHE T 14 " 0.009 2.00e-02 2.50e+03 pdb=" CD2 PHE T 14 " 0.009 2.00e-02 2.50e+03 pdb=" CE1 PHE T 14 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE T 14 " 0.001 2.00e-02 2.50e+03 pdb=" CZ PHE T 14 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C HIS R 258 " 0.027 5.00e-02 4.00e+02 4.03e-02 2.60e+00 pdb=" N PRO R 259 " -0.070 5.00e-02 4.00e+02 pdb=" CA PRO R 259 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO R 259 " 0.023 5.00e-02 4.00e+02 ... (remaining 1498 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 168 2.69 - 3.24: 8124 3.24 - 3.80: 12776 3.80 - 4.35: 16343 4.35 - 4.90: 27250 Nonbonded interactions: 64661 Sorted by model distance: nonbonded pdb=" O ARG A 363 " pdb=" ND2 ASN A 367 " model vdw 2.140 3.120 nonbonded pdb=" OG SER B 331 " pdb=" OD1 ASP B 333 " model vdw 2.251 3.040 nonbonded pdb=" NH2 ARG A 228 " pdb=" OE1 GLU A 230 " model vdw 2.306 3.120 nonbonded pdb=" OH TYR A 308 " pdb=" OD2 ASP A 333 " model vdw 2.309 3.040 nonbonded pdb=" O THR A 315 " pdb=" OG1 THR A 315 " model vdw 2.313 3.040 ... (remaining 64656 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.190 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: 0.320 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 21.630 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7112 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 8723 Z= 0.121 Angle : 0.575 9.159 11815 Z= 0.304 Chirality : 0.040 0.134 1333 Planarity : 0.004 0.059 1501 Dihedral : 15.342 82.596 3184 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 0.21 % Allowed : 26.82 % Favored : 72.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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 Details of bonding type rmsd hydrogen bonds : bond 0.27035 ( 366) hydrogen bonds : angle 7.72734 ( 1056) SS BOND : bond 0.00242 ( 6) SS BOND : angle 1.44316 ( 12) covalent geometry : bond 0.00242 ( 8717) covalent geometry : angle 0.57361 (11803) *********************** 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 : 1.011 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: 0.3051 time to fit residues: 74.6873 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 : 0.873 ------------------------------------------------------------------------------- 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: 0.7980 chunk 95 optimal weight: 0.5980 overall best weight: 0.4918 ------------------------------------------------------------------------------- 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 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 = 0.4118 r_free = 0.4118 target = 0.165636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.137479 restraints weight = 12126.892| |-----------------------------------------------------------------------------| r_work (start): 0.3744 rms_B_bonded: 2.63 r_work: 0.3593 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3593 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7022 moved from start: 0.1109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8723 Z= 0.142 Angle : 0.571 6.642 11815 Z= 0.300 Chirality : 0.041 0.163 1333 Planarity : 0.004 0.053 1501 Dihedral : 4.067 38.733 1175 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 2.88 % Allowed : 23.40 % 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: 0.02 (0.25), residues: 1064 helix: 1.47 (0.26), residues: 400 sheet: -0.23 (0.35), residues: 227 loop : -1.22 (0.26), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 234 HIS 0.004 0.001 HIS A 347 PHE 0.013 0.001 PHE A 366 TYR 0.010 0.001 TYR R 281 ARG 0.005 0.000 ARG A 273 Details of bonding type rmsd hydrogen bonds : bond 0.06603 ( 366) hydrogen bonds : angle 4.98231 ( 1056) SS BOND : bond 0.00369 ( 6) SS BOND : angle 1.48911 ( 12) covalent geometry : bond 0.00286 ( 8717) covalent geometry : angle 0.56916 (11803) *********************** 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 215 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 188 time to evaluate : 1.028 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 16 GLU cc_start: 0.7091 (pp20) cc_final: 0.6775 (pp20) REVERT: A 367 ASN cc_start: 0.7750 (m-40) cc_final: 0.7548 (m-40) REVERT: B 61 MET cc_start: 0.8057 (tmm) cc_final: 0.7828 (ppp) REVERT: B 205 ASP cc_start: 0.6858 (p0) cc_final: 0.6632 (p0) REVERT: N 118 ARG cc_start: 0.7881 (OUTLIER) cc_final: 0.6432 (mtm-85) REVERT: R 120 SER cc_start: 0.8087 (p) cc_final: 0.7618 (m) REVERT: R 125 ILE cc_start: 0.8151 (OUTLIER) cc_final: 0.7925 (mp) REVERT: R 175 LYS cc_start: 0.7491 (mmpt) cc_final: 0.7143 (mmtm) REVERT: R 192 LEU cc_start: 0.8072 (OUTLIER) cc_final: 0.7815 (tt) outliers start: 27 outliers final: 14 residues processed: 203 average time/residue: 0.2706 time to fit residues: 71.8729 Evaluate side-chains 196 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 179 time to evaluate : 0.851 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 24 optimal weight: 5.9990 chunk 29 optimal weight: 0.9990 chunk 79 optimal weight: 3.9990 chunk 93 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 85 optimal weight: 1.9990 chunk 88 optimal weight: 1.9990 chunk 102 optimal weight: 0.7980 chunk 70 optimal weight: 0.9980 chunk 14 optimal weight: 4.9990 chunk 100 optimal weight: 0.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- 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 = 0.4094 r_free = 0.4094 target = 0.163415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.134779 restraints weight = 12188.149| |-----------------------------------------------------------------------------| r_work (start): 0.3722 rms_B_bonded: 2.59 r_work: 0.3584 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3584 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7058 moved from start: 0.1509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 8723 Z= 0.176 Angle : 0.595 8.369 11815 Z= 0.309 Chirality : 0.042 0.173 1333 Planarity : 0.004 0.051 1501 Dihedral : 4.179 24.416 1175 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 4.70 % Allowed : 22.86 % Favored : 72.44 % 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: 0.05 (0.25), residues: 1064 helix: 1.55 (0.26), residues: 401 sheet: -0.21 (0.36), residues: 224 loop : -1.27 (0.26), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP N 47 HIS 0.005 0.001 HIS A 347 PHE 0.017 0.002 PHE T 14 TYR 0.013 0.002 TYR N 95 ARG 0.003 0.000 ARG A 273 Details of bonding type rmsd hydrogen bonds : bond 0.06386 ( 366) hydrogen bonds : angle 4.68357 ( 1056) SS BOND : bond 0.00907 ( 6) SS BOND : angle 2.20793 ( 12) covalent geometry : bond 0.00395 ( 8717) covalent geometry : angle 0.59111 (11803) *********************** 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 226 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 182 time to evaluate : 0.944 Fit side-chains revert: symmetry clash REVERT: A 317 GLU cc_start: 0.6402 (tm-30) cc_final: 0.6172 (tm-30) REVERT: A 367 ASN cc_start: 0.7838 (m-40) cc_final: 0.7578 (m-40) REVERT: B 66 ASP cc_start: 0.7372 (p0) cc_final: 0.7100 (p0) REVERT: G 27 ARG cc_start: 0.7919 (ptp-170) cc_final: 0.7649 (ptp90) REVERT: N 118 ARG cc_start: 0.8006 (OUTLIER) cc_final: 0.6534 (mtm-85) REVERT: R 120 SER cc_start: 0.8035 (p) cc_final: 0.7587 (m) REVERT: R 125 ILE cc_start: 0.8179 (OUTLIER) cc_final: 0.7952 (mp) REVERT: R 175 LYS cc_start: 0.7602 (mtpt) cc_final: 0.7316 (mttm) REVERT: R 192 LEU cc_start: 0.7968 (OUTLIER) cc_final: 0.7744 (tt) REVERT: R 327 CYS cc_start: 0.7174 (OUTLIER) cc_final: 0.6833 (p) outliers start: 44 outliers final: 29 residues processed: 207 average time/residue: 0.2507 time to fit residues: 67.7315 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 : 0.911 ------------------------------------------------------------------------------- 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 10 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 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 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 Chi-restraints excluded: chain R residue 334 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 75 optimal weight: 5.9990 chunk 71 optimal weight: 0.0870 chunk 42 optimal weight: 0.9990 chunk 28 optimal weight: 0.9980 chunk 98 optimal weight: 0.8980 chunk 24 optimal weight: 3.9990 chunk 99 optimal weight: 0.9990 chunk 32 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 59 optimal weight: 0.9990 overall best weight: 0.7962 ------------------------------------------------------------------------------- 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 = 0.4098 r_free = 0.4098 target = 0.163648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.134956 restraints weight = 12110.677| |-----------------------------------------------------------------------------| r_work (start): 0.3727 rms_B_bonded: 2.59 r_work: 0.3588 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3588 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7055 moved from start: 0.1799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 8723 Z= 0.156 Angle : 0.588 8.779 11815 Z= 0.302 Chirality : 0.042 0.163 1333 Planarity : 0.004 0.051 1501 Dihedral : 4.127 18.864 1174 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 4.38 % Allowed : 23.93 % Favored : 71.69 % 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: 0.12 (0.25), residues: 1064 helix: 1.68 (0.26), residues: 404 sheet: -0.09 (0.36), residues: 216 loop : -1.37 (0.26), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 234 HIS 0.004 0.001 HIS A 220 PHE 0.017 0.002 PHE T 14 TYR 0.027 0.001 TYR R 160 ARG 0.003 0.000 ARG A 323 Details of bonding type rmsd hydrogen bonds : bond 0.05746 ( 366) hydrogen bonds : angle 4.47141 ( 1056) SS BOND : bond 0.00509 ( 6) SS BOND : angle 2.33597 ( 12) covalent geometry : bond 0.00353 ( 8717) covalent geometry : angle 0.58314 (11803) *********************** 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 221 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 180 time to evaluate : 1.163 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 317 GLU cc_start: 0.6451 (tm-30) cc_final: 0.6155 (tm-30) REVERT: A 367 ASN cc_start: 0.7854 (m-40) cc_final: 0.7651 (m-40) REVERT: B 66 ASP cc_start: 0.7333 (p0) cc_final: 0.7057 (p0) REVERT: G 27 ARG cc_start: 0.7885 (ptp-170) cc_final: 0.7652 (ptp90) REVERT: N 118 ARG cc_start: 0.7983 (OUTLIER) cc_final: 0.6590 (mtm-85) REVERT: R 120 SER cc_start: 0.8017 (p) cc_final: 0.7614 (m) REVERT: R 125 ILE cc_start: 0.8172 (OUTLIER) cc_final: 0.7925 (mp) REVERT: R 175 LYS cc_start: 0.7682 (mtpt) cc_final: 0.7422 (mttm) REVERT: R 327 CYS cc_start: 0.7104 (OUTLIER) cc_final: 0.6792 (p) outliers start: 41 outliers final: 22 residues processed: 206 average time/residue: 0.2830 time to fit residues: 76.4941 Evaluate side-chains 203 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 178 time to evaluate : 0.907 ------------------------------------------------------------------------------- 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 74 SER Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 246 ASP 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 91 THR Chi-restraints excluded: chain N residue 118 ARG Chi-restraints excluded: chain R residue 90 CYS Chi-restraints excluded: chain R residue 125 ILE Chi-restraints excluded: chain R residue 173 MET Chi-restraints excluded: chain R residue 181 GLN Chi-restraints excluded: chain R residue 205 SER 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 344 ILE 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: 0.0030 chunk 27 optimal weight: 1.9990 chunk 21 optimal weight: 0.8980 chunk 90 optimal weight: 0.8980 chunk 33 optimal weight: 0.9990 chunk 5 optimal weight: 2.9990 chunk 29 optimal weight: 0.9980 chunk 46 optimal weight: 0.7980 chunk 24 optimal weight: 5.9990 overall best weight: 0.7190 ------------------------------------------------------------------------------- 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 = 0.4099 r_free = 0.4099 target = 0.164015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.135357 restraints weight = 12189.710| |-----------------------------------------------------------------------------| r_work (start): 0.3715 rms_B_bonded: 2.61 r_work: 0.3560 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3560 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7095 moved from start: 0.2040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8723 Z= 0.146 Angle : 0.590 11.115 11815 Z= 0.299 Chirality : 0.042 0.161 1333 Planarity : 0.004 0.052 1501 Dihedral : 4.054 19.539 1174 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 5.45 % Allowed : 23.40 % 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: 0.23 (0.25), residues: 1064 helix: 1.82 (0.26), residues: 407 sheet: -0.04 (0.36), residues: 217 loop : -1.36 (0.26), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 234 HIS 0.005 0.001 HIS A 347 PHE 0.014 0.001 PHE A 366 TYR 0.022 0.001 TYR R 160 ARG 0.010 0.000 ARG A 273 Details of bonding type rmsd hydrogen bonds : bond 0.05433 ( 366) hydrogen bonds : angle 4.31248 ( 1056) SS BOND : bond 0.00429 ( 6) SS BOND : angle 2.31247 ( 12) covalent geometry : bond 0.00329 ( 8717) covalent geometry : angle 0.58537 (11803) *********************** 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 239 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 188 time to evaluate : 0.884 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 317 GLU cc_start: 0.6406 (tm-30) cc_final: 0.6127 (tm-30) REVERT: A 367 ASN cc_start: 0.7870 (m-40) cc_final: 0.7627 (m-40) REVERT: A 374 LEU cc_start: 0.8084 (tt) cc_final: 0.7881 (tp) REVERT: B 66 ASP cc_start: 0.7323 (p0) cc_final: 0.7054 (p0) REVERT: B 171 ILE cc_start: 0.7362 (OUTLIER) cc_final: 0.6930 (mm) REVERT: B 289 TYR cc_start: 0.8087 (m-80) cc_final: 0.7677 (m-80) REVERT: G 27 ARG cc_start: 0.7972 (ptp-170) cc_final: 0.7750 (ptp90) REVERT: N 76 LYS cc_start: 0.7876 (OUTLIER) cc_final: 0.7600 (ttpp) REVERT: N 118 ARG cc_start: 0.7976 (OUTLIER) cc_final: 0.6560 (mtm-85) REVERT: R 120 SER cc_start: 0.8080 (p) cc_final: 0.7690 (m) REVERT: R 125 ILE cc_start: 0.8158 (OUTLIER) cc_final: 0.7932 (mp) REVERT: R 158 ASN cc_start: 0.7675 (OUTLIER) cc_final: 0.7402 (t0) REVERT: R 327 CYS cc_start: 0.7223 (OUTLIER) cc_final: 0.6913 (p) outliers start: 51 outliers final: 28 residues processed: 220 average time/residue: 0.2491 time to fit residues: 72.1753 Evaluate side-chains 215 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 181 time to evaluate : 0.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ASP Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 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 171 ILE Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 196 THR 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 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 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 323 LYS 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: 0.8980 chunk 60 optimal weight: 4.9990 chunk 72 optimal weight: 1.9990 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: 1.9990 chunk 40 optimal weight: 0.2980 chunk 82 optimal weight: 0.3980 chunk 32 optimal weight: 0.0980 overall best weight: 0.4380 ------------------------------------------------------------------------------- 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 = 0.4115 r_free = 0.4115 target = 0.165529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.136976 restraints weight = 11982.490| |-----------------------------------------------------------------------------| r_work (start): 0.3734 rms_B_bonded: 2.56 r_work: 0.3589 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3589 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7064 moved from start: 0.2219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8723 Z= 0.116 Angle : 0.565 9.926 11815 Z= 0.285 Chirality : 0.041 0.151 1333 Planarity : 0.004 0.052 1501 Dihedral : 3.912 20.074 1174 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 4.91 % Allowed : 23.72 % Favored : 71.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.42 (0.26), residues: 1064 helix: 2.01 (0.26), residues: 404 sheet: 0.10 (0.36), residues: 217 loop : -1.31 (0.26), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP R 275 HIS 0.003 0.001 HIS A 220 PHE 0.016 0.001 PHE T 14 TYR 0.020 0.001 TYR R 160 ARG 0.005 0.000 ARG A 273 Details of bonding type rmsd hydrogen bonds : bond 0.04730 ( 366) hydrogen bonds : angle 4.13652 ( 1056) SS BOND : bond 0.00292 ( 6) SS BOND : angle 2.41368 ( 12) covalent geometry : bond 0.00254 ( 8717) covalent geometry : angle 0.55991 (11803) *********************** 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 237 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 191 time to evaluate : 1.145 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 317 GLU cc_start: 0.6444 (tm-30) cc_final: 0.6226 (tm-30) REVERT: A 367 ASN cc_start: 0.7836 (m-40) cc_final: 0.7587 (m-40) REVERT: B 66 ASP cc_start: 0.7274 (p0) cc_final: 0.6995 (p0) REVERT: B 153 ASP cc_start: 0.6751 (OUTLIER) cc_final: 0.6473 (p0) REVERT: B 171 ILE cc_start: 0.7384 (OUTLIER) cc_final: 0.6889 (mm) REVERT: B 289 TYR cc_start: 0.8072 (m-80) cc_final: 0.7677 (m-80) REVERT: N 118 ARG cc_start: 0.7941 (OUTLIER) cc_final: 0.6508 (mtm-85) REVERT: R 120 SER cc_start: 0.8051 (p) cc_final: 0.7670 (m) REVERT: R 125 ILE cc_start: 0.8148 (OUTLIER) cc_final: 0.7933 (mp) REVERT: R 158 ASN cc_start: 0.7639 (OUTLIER) cc_final: 0.7356 (t0) REVERT: R 327 CYS cc_start: 0.7242 (OUTLIER) cc_final: 0.6983 (p) outliers start: 46 outliers final: 25 residues processed: 218 average time/residue: 0.2438 time to fit residues: 69.6448 Evaluate side-chains 220 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 189 time to evaluate : 0.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 91 THR Chi-restraints excluded: chain N residue 118 ARG Chi-restraints excluded: chain R residue 97 LYS Chi-restraints excluded: chain R residue 125 ILE Chi-restraints excluded: chain R residue 158 ASN Chi-restraints excluded: chain R residue 173 MET Chi-restraints excluded: chain R residue 181 GLN Chi-restraints excluded: chain R residue 254 ILE Chi-restraints excluded: chain R residue 260 VAL Chi-restraints excluded: chain R residue 300 MET 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 337 LEU 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: 0.9980 chunk 89 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 chunk 40 optimal weight: 0.0040 chunk 62 optimal weight: 0.9980 chunk 67 optimal weight: 0.2980 chunk 6 optimal weight: 0.5980 chunk 58 optimal weight: 6.9990 chunk 10 optimal weight: 0.3980 chunk 14 optimal weight: 4.9990 chunk 45 optimal weight: 0.7980 overall best weight: 0.4192 ------------------------------------------------------------------------------- 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 = 0.4115 r_free = 0.4115 target = 0.165664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.137294 restraints weight = 12118.718| |-----------------------------------------------------------------------------| r_work (start): 0.3735 rms_B_bonded: 2.58 r_work: 0.3588 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3588 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7059 moved from start: 0.2331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8723 Z= 0.117 Angle : 0.566 12.195 11815 Z= 0.285 Chirality : 0.040 0.150 1333 Planarity : 0.003 0.051 1501 Dihedral : 3.855 19.321 1174 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 4.91 % Allowed : 24.36 % Favored : 70.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.55 (0.26), residues: 1064 helix: 2.16 (0.26), residues: 407 sheet: 0.17 (0.36), residues: 217 loop : -1.30 (0.26), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP R 275 HIS 0.003 0.001 HIS A 347 PHE 0.016 0.001 PHE T 14 TYR 0.018 0.001 TYR R 160 ARG 0.003 0.000 ARG A 273 Details of bonding type rmsd hydrogen bonds : bond 0.04586 ( 366) hydrogen bonds : angle 4.06490 ( 1056) SS BOND : bond 0.00357 ( 6) SS BOND : angle 2.56052 ( 12) covalent geometry : bond 0.00254 ( 8717) covalent geometry : angle 0.56047 (11803) *********************** 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 232 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 186 time to evaluate : 1.118 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 367 ASN cc_start: 0.7836 (m-40) cc_final: 0.7587 (m-40) REVERT: B 66 ASP cc_start: 0.7244 (p0) cc_final: 0.6967 (p0) REVERT: B 153 ASP cc_start: 0.6767 (OUTLIER) cc_final: 0.6484 (p0) REVERT: B 171 ILE cc_start: 0.7379 (OUTLIER) cc_final: 0.6902 (mm) REVERT: B 289 TYR cc_start: 0.8069 (m-80) cc_final: 0.7681 (m-80) REVERT: N 35 ASN cc_start: 0.8332 (OUTLIER) cc_final: 0.8089 (p0) REVERT: N 68 PHE cc_start: 0.7287 (m-10) cc_final: 0.7037 (m-10) REVERT: N 76 LYS cc_start: 0.7817 (OUTLIER) cc_final: 0.7513 (ttpp) REVERT: N 118 ARG cc_start: 0.7950 (OUTLIER) cc_final: 0.6504 (mtm-85) REVERT: R 120 SER cc_start: 0.8050 (p) cc_final: 0.7662 (m) REVERT: R 125 ILE cc_start: 0.8149 (OUTLIER) cc_final: 0.7928 (mp) REVERT: R 158 ASN cc_start: 0.7621 (OUTLIER) cc_final: 0.7363 (t0) REVERT: R 327 CYS cc_start: 0.7225 (OUTLIER) cc_final: 0.7003 (p) REVERT: R 374 MET cc_start: 0.7018 (ptp) cc_final: 0.6769 (mtm) outliers start: 46 outliers final: 31 residues processed: 214 average time/residue: 0.2771 time to fit residues: 78.5154 Evaluate side-chains 221 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 182 time to evaluate : 0.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ASP 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 74 SER Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 220 GLN Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain N residue 22 CYS Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 76 LYS Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 118 ARG Chi-restraints excluded: chain R residue 97 LYS Chi-restraints excluded: chain R residue 125 ILE Chi-restraints excluded: chain R residue 158 ASN Chi-restraints excluded: chain R residue 173 MET Chi-restraints excluded: chain R residue 181 GLN Chi-restraints excluded: chain R residue 252 LEU 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 323 LYS Chi-restraints excluded: chain R residue 325 VAL Chi-restraints excluded: chain R residue 327 CYS Chi-restraints excluded: chain R residue 337 LEU Chi-restraints excluded: chain R residue 393 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 65 optimal weight: 0.8980 chunk 63 optimal weight: 1.9990 chunk 103 optimal weight: 0.9990 chunk 45 optimal weight: 0.7980 chunk 6 optimal weight: 1.9990 chunk 26 optimal weight: 0.0970 chunk 44 optimal weight: 0.4980 chunk 78 optimal weight: 0.9990 chunk 73 optimal weight: 7.9990 chunk 52 optimal weight: 0.9990 chunk 61 optimal weight: 2.9990 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 ** 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 = 0.4103 r_free = 0.4103 target = 0.164557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.135778 restraints weight = 12221.967| |-----------------------------------------------------------------------------| r_work (start): 0.3718 rms_B_bonded: 2.61 r_work: 0.3569 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3569 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7084 moved from start: 0.2407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8723 Z= 0.139 Angle : 0.600 12.360 11815 Z= 0.301 Chirality : 0.041 0.152 1333 Planarity : 0.004 0.052 1501 Dihedral : 3.936 19.460 1174 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 4.81 % Allowed : 24.25 % Favored : 70.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.57 (0.26), residues: 1064 helix: 2.22 (0.27), residues: 405 sheet: 0.27 (0.36), residues: 213 loop : -1.36 (0.26), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP R 275 HIS 0.003 0.001 HIS A 347 PHE 0.015 0.001 PHE T 14 TYR 0.019 0.001 TYR R 160 ARG 0.003 0.000 ARG A 273 Details of bonding type rmsd hydrogen bonds : bond 0.04952 ( 366) hydrogen bonds : angle 4.12204 ( 1056) SS BOND : bond 0.00391 ( 6) SS BOND : angle 2.65477 ( 12) covalent geometry : bond 0.00317 ( 8717) covalent geometry : angle 0.59437 (11803) *********************** 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 232 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 187 time to evaluate : 0.963 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 367 ASN cc_start: 0.7862 (m-40) cc_final: 0.7630 (m-40) REVERT: A 374 LEU cc_start: 0.8099 (tt) cc_final: 0.7889 (tp) REVERT: A 376 MET cc_start: 0.7586 (mtm) cc_final: 0.7272 (mtt) REVERT: B 66 ASP cc_start: 0.7221 (p0) cc_final: 0.6949 (p0) REVERT: B 153 ASP cc_start: 0.6788 (OUTLIER) cc_final: 0.6529 (p0) REVERT: B 171 ILE cc_start: 0.7384 (OUTLIER) cc_final: 0.6961 (mm) REVERT: B 289 TYR cc_start: 0.8071 (m-80) cc_final: 0.7663 (m-80) REVERT: N 76 LYS cc_start: 0.7829 (OUTLIER) cc_final: 0.7518 (ttpp) REVERT: N 118 ARG cc_start: 0.7981 (OUTLIER) cc_final: 0.6482 (mtm-85) REVERT: R 120 SER cc_start: 0.8082 (p) cc_final: 0.7672 (m) REVERT: R 125 ILE cc_start: 0.8167 (OUTLIER) cc_final: 0.7945 (mp) REVERT: R 158 ASN cc_start: 0.7627 (OUTLIER) cc_final: 0.7369 (t0) REVERT: R 327 CYS cc_start: 0.7204 (OUTLIER) cc_final: 0.6957 (p) outliers start: 45 outliers final: 32 residues processed: 216 average time/residue: 0.2788 time to fit residues: 78.3847 Evaluate side-chains 223 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 184 time to evaluate : 1.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 GLU 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 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 147 SER Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 220 GLN Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain N residue 22 CYS Chi-restraints excluded: chain N residue 76 LYS Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 118 ARG Chi-restraints excluded: chain R residue 97 LYS Chi-restraints excluded: chain R residue 125 ILE Chi-restraints excluded: chain R residue 158 ASN Chi-restraints excluded: chain R residue 173 MET Chi-restraints excluded: chain R residue 174 CYS Chi-restraints excluded: chain R residue 181 GLN Chi-restraints excluded: chain R residue 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 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: 0.6980 chunk 95 optimal weight: 0.9980 chunk 19 optimal weight: 0.9980 chunk 90 optimal weight: 0.9980 chunk 9 optimal weight: 1.9990 chunk 25 optimal weight: 6.9990 chunk 28 optimal weight: 0.0870 chunk 40 optimal weight: 0.0970 chunk 4 optimal weight: 1.9990 chunk 14 optimal weight: 0.0060 overall best weight: 0.3772 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.166171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.137482 restraints weight = 12132.457| |-----------------------------------------------------------------------------| r_work (start): 0.3738 rms_B_bonded: 2.61 r_work: 0.3590 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3590 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7058 moved from start: 0.2553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8723 Z= 0.115 Angle : 0.593 11.497 11815 Z= 0.295 Chirality : 0.040 0.147 1333 Planarity : 0.004 0.048 1501 Dihedral : 3.864 19.437 1174 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 3.74 % Allowed : 25.21 % Favored : 71.05 % 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: 0.65 (0.26), residues: 1064 helix: 2.25 (0.27), residues: 407 sheet: 0.16 (0.36), residues: 220 loop : -1.22 (0.26), residues: 437 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 0.016 0.001 PHE T 14 TYR 0.017 0.001 TYR R 160 ARG 0.006 0.000 ARG R 208 Details of bonding type rmsd hydrogen bonds : bond 0.04464 ( 366) hydrogen bonds : angle 4.03261 ( 1056) SS BOND : bond 0.00333 ( 6) SS BOND : angle 2.53218 ( 12) covalent geometry : bond 0.00254 ( 8717) covalent geometry : angle 0.58819 (11803) *********************** 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: 35 poor density : 189 time to evaluate : 0.838 Fit side-chains revert: symmetry clash REVERT: A 367 ASN cc_start: 0.7811 (m-40) cc_final: 0.7595 (m-40) REVERT: A 374 LEU cc_start: 0.8098 (tt) cc_final: 0.7895 (tp) REVERT: A 376 MET cc_start: 0.7561 (mtm) cc_final: 0.7252 (mtt) REVERT: B 66 ASP cc_start: 0.7234 (p0) cc_final: 0.6955 (p0) REVERT: B 171 ILE cc_start: 0.7354 (OUTLIER) cc_final: 0.6900 (mm) REVERT: B 289 TYR cc_start: 0.8034 (m-80) cc_final: 0.7647 (m-80) REVERT: N 68 PHE cc_start: 0.7271 (m-10) cc_final: 0.7030 (m-10) REVERT: N 76 LYS cc_start: 0.7796 (OUTLIER) cc_final: 0.7478 (ttpp) REVERT: N 118 ARG cc_start: 0.7958 (OUTLIER) cc_final: 0.6472 (mtm-85) REVERT: R 104 ASN cc_start: 0.7277 (m-40) cc_final: 0.7020 (m-40) REVERT: R 120 SER cc_start: 0.8072 (p) cc_final: 0.7656 (m) REVERT: R 125 ILE cc_start: 0.8159 (OUTLIER) cc_final: 0.7932 (mp) REVERT: R 158 ASN cc_start: 0.7627 (OUTLIER) cc_final: 0.7375 (t0) REVERT: R 347 LEU cc_start: 0.7881 (tp) cc_final: 0.7624 (mt) REVERT: R 374 MET cc_start: 0.7042 (ptp) cc_final: 0.6817 (mtm) outliers start: 35 outliers final: 24 residues processed: 211 average time/residue: 0.2512 time to fit residues: 68.8844 Evaluate side-chains 212 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 183 time to evaluate : 0.957 ------------------------------------------------------------------------------- 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 133 VAL Chi-restraints excluded: chain B residue 147 SER 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 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 Chi-restraints excluded: chain R residue 393 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 64 optimal weight: 0.8980 chunk 47 optimal weight: 0.9990 chunk 49 optimal weight: 0.9980 chunk 97 optimal weight: 0.9990 chunk 20 optimal weight: 0.6980 chunk 95 optimal weight: 0.0980 chunk 55 optimal weight: 7.9990 chunk 87 optimal weight: 0.8980 chunk 24 optimal weight: 6.9990 chunk 103 optimal weight: 0.7980 chunk 51 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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** B 239 ASN 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 = 0.164944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.136163 restraints weight = 11994.059| |-----------------------------------------------------------------------------| r_work (start): 0.3721 rms_B_bonded: 2.58 r_work: 0.3573 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3573 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7082 moved from start: 0.2626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8723 Z= 0.143 Angle : 0.639 16.405 11815 Z= 0.315 Chirality : 0.042 0.179 1333 Planarity : 0.004 0.050 1501 Dihedral : 3.897 16.890 1174 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 2.99 % Allowed : 26.60 % 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: 0.58 (0.26), residues: 1064 helix: 2.10 (0.27), residues: 411 sheet: 0.39 (0.38), residues: 202 loop : -1.29 (0.26), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP R 275 HIS 0.004 0.001 HIS A 347 PHE 0.015 0.001 PHE A 246 TYR 0.017 0.001 TYR R 160 ARG 0.002 0.000 ARG A 273 Details of bonding type rmsd hydrogen bonds : bond 0.04919 ( 366) hydrogen bonds : angle 4.14843 ( 1056) SS BOND : bond 0.00326 ( 6) SS BOND : angle 2.54765 ( 12) covalent geometry : bond 0.00327 ( 8717) covalent geometry : angle 0.63406 (11803) ********************** 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 208 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 180 time to evaluate : 0.875 Fit side-chains revert: symmetry clash REVERT: A 367 ASN cc_start: 0.7848 (m-40) cc_final: 0.7631 (m-40) REVERT: A 374 LEU cc_start: 0.8103 (tt) cc_final: 0.7889 (tp) REVERT: B 66 ASP cc_start: 0.7226 (p0) cc_final: 0.6952 (p0) REVERT: B 171 ILE cc_start: 0.7358 (OUTLIER) cc_final: 0.6956 (mm) REVERT: B 188 MET cc_start: 0.8173 (mmm) cc_final: 0.7903 (mmt) REVERT: B 289 TYR cc_start: 0.8038 (m-80) cc_final: 0.7653 (m-80) REVERT: N 68 PHE cc_start: 0.7238 (m-10) cc_final: 0.6973 (m-10) REVERT: N 76 LYS cc_start: 0.7823 (OUTLIER) cc_final: 0.7513 (ttpp) REVERT: N 118 ARG cc_start: 0.7986 (OUTLIER) cc_final: 0.6469 (mtm-85) REVERT: R 104 ASN cc_start: 0.7275 (m-40) cc_final: 0.7009 (m-40) REVERT: R 120 SER cc_start: 0.8093 (p) cc_final: 0.7667 (m) REVERT: R 125 ILE cc_start: 0.8164 (OUTLIER) cc_final: 0.7953 (mp) REVERT: R 158 ASN cc_start: 0.7622 (OUTLIER) cc_final: 0.7384 (t0) REVERT: R 296 MET cc_start: 0.7487 (tmm) cc_final: 0.7257 (ttp) REVERT: R 374 MET cc_start: 0.7136 (ptp) cc_final: 0.6902 (mtm) outliers start: 28 outliers final: 21 residues processed: 197 average time/residue: 0.2479 time to fit residues: 63.4574 Evaluate side-chains 205 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 179 time to evaluate : 0.962 ------------------------------------------------------------------------------- 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 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 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 76 LYS Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 118 ARG Chi-restraints excluded: chain R residue 125 ILE Chi-restraints excluded: chain R residue 158 ASN Chi-restraints excluded: chain R residue 173 MET Chi-restraints excluded: chain R residue 181 GLN Chi-restraints excluded: chain R residue 254 ILE Chi-restraints excluded: chain R residue 260 VAL Chi-restraints excluded: chain R residue 286 LEU Chi-restraints excluded: chain R residue 298 CYS Chi-restraints excluded: chain R residue 301 LEU Chi-restraints excluded: chain R residue 325 VAL Chi-restraints excluded: chain R residue 337 LEU Chi-restraints excluded: chain R residue 393 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 103 optimal weight: 0.9980 chunk 45 optimal weight: 0.7980 chunk 75 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 20 optimal weight: 0.4980 chunk 64 optimal weight: 1.9990 chunk 31 optimal weight: 0.8980 chunk 73 optimal weight: 8.9990 chunk 21 optimal weight: 0.5980 chunk 39 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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** R 91 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.164534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.135653 restraints weight = 12206.374| |-----------------------------------------------------------------------------| r_work (start): 0.3713 rms_B_bonded: 2.61 r_work: 0.3563 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3563 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7093 moved from start: 0.2691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8723 Z= 0.151 Angle : 0.641 17.167 11815 Z= 0.319 Chirality : 0.042 0.199 1333 Planarity : 0.004 0.050 1501 Dihedral : 3.969 17.296 1174 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 3.74 % Allowed : 26.18 % Favored : 70.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.00 (0.27), residues: 410 sheet: 0.49 (0.38), residues: 199 loop : -1.32 (0.26), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP R 275 HIS 0.003 0.001 HIS A 347 PHE 0.018 0.002 PHE T 14 TYR 0.018 0.001 TYR R 160 ARG 0.002 0.000 ARG A 273 Details of bonding type rmsd hydrogen bonds : bond 0.05117 ( 366) hydrogen bonds : angle 4.20432 ( 1056) SS BOND : bond 0.00443 ( 6) SS BOND : angle 2.54352 ( 12) covalent geometry : bond 0.00346 ( 8717) covalent geometry : angle 0.63645 (11803) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4801.54 seconds wall clock time: 85 minutes 22.84 seconds (5122.84 seconds total)