Starting phenix.real_space_refine on Thu Mar 13 01:29:55 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xvh_38704/03_2025/8xvh_38704.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xvh_38704/03_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_38704/03_2025/8xvh_38704.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xvh_38704/03_2025/8xvh_38704.map" model { file = "/net/cci-nas-00/data/ceres_data/8xvh_38704/03_2025/8xvh_38704.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xvh_38704/03_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-5624/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: 5.32, per 1000 atoms: 0.62 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: 1.96 Conformation dependent library (CDL) restraints added in 921.5 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: 0.87 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: 2.25 Time building geometry restraints manager: 2.28 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: 1.370 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.340 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 21.610 Find NCS groups from input model: 0.090 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: 0.000 Load rotamer database and sin/cos tables:2.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7112 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 8717 Z= 0.160 Angle : 0.574 9.159 11803 Z= 0.303 Chirality : 0.040 0.134 1333 Planarity : 0.004 0.059 1501 Dihedral : 15.342 82.596 3184 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 0.21 % Allowed : 26.82 % Favored : 72.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.25), residues: 1064 helix: 0.66 (0.26), residues: 403 sheet: -0.41 (0.35), residues: 221 loop : -1.27 (0.26), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 234 HIS 0.003 0.001 HIS A 347 PHE 0.030 0.001 PHE T 14 TYR 0.006 0.001 TYR N 95 ARG 0.007 0.000 ARG A 273 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 185 time to evaluate : 0.892 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: 0.2620 time to fit residues: 64.2262 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 : 1.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 349 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 88 optimal weight: 0.9980 chunk 79 optimal weight: 0.0670 chunk 44 optimal weight: 0.8980 chunk 27 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 82 optimal weight: 0.9980 chunk 31 optimal weight: 0.0980 chunk 50 optimal weight: 1.9990 chunk 61 optimal weight: 3.9990 chunk 95 optimal weight: 0.5980 overall best weight: 0.5318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.165476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.137590 restraints weight = 12121.649| |-----------------------------------------------------------------------------| r_work (start): 0.3744 rms_B_bonded: 2.59 r_work: 0.3595 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3595 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7049 moved from start: 0.1130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8717 Z= 0.196 Angle : 0.575 6.988 11803 Z= 0.301 Chirality : 0.042 0.168 1333 Planarity : 0.004 0.051 1501 Dihedral : 4.097 38.582 1175 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 3.10 % Allowed : 23.18 % Favored : 73.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.25), residues: 1064 helix: 1.44 (0.26), residues: 399 sheet: -0.24 (0.35), residues: 227 loop : -1.22 (0.26), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 234 HIS 0.005 0.001 HIS A 347 PHE 0.014 0.001 PHE A 366 TYR 0.010 0.001 TYR R 281 ARG 0.005 0.000 ARG A 273 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 187 time to evaluate : 0.752 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 16 GLU cc_start: 0.7092 (pp20) cc_final: 0.6807 (pp20) REVERT: B 61 MET cc_start: 0.8011 (tmm) cc_final: 0.7791 (ppp) REVERT: B 205 ASP cc_start: 0.6893 (p0) cc_final: 0.6666 (p0) REVERT: N 118 ARG cc_start: 0.7905 (OUTLIER) cc_final: 0.6472 (mtm-85) REVERT: R 120 SER cc_start: 0.8140 (p) cc_final: 0.7671 (m) REVERT: R 125 ILE cc_start: 0.8183 (OUTLIER) cc_final: 0.7954 (mp) REVERT: R 175 LYS cc_start: 0.7436 (mmpt) cc_final: 0.7022 (mttm) REVERT: R 192 LEU cc_start: 0.8079 (OUTLIER) cc_final: 0.7830 (tt) REVERT: R 327 CYS cc_start: 0.7241 (OUTLIER) cc_final: 0.6922 (p) outliers start: 29 outliers final: 14 residues processed: 203 average time/residue: 0.2886 time to fit residues: 76.9338 Evaluate side-chains 197 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 179 time to evaluate : 0.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 349 CYS Chi-restraints excluded: chain B residue 42 ARG Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 220 GLN Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain N residue 22 CYS Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 118 ARG Chi-restraints excluded: chain R residue 125 ILE Chi-restraints excluded: chain R residue 153 ILE Chi-restraints excluded: chain R residue 181 GLN Chi-restraints excluded: chain R residue 192 LEU Chi-restraints excluded: chain R residue 205 SER Chi-restraints excluded: chain R residue 325 VAL Chi-restraints excluded: chain R residue 327 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 24 optimal weight: 7.9990 chunk 29 optimal weight: 0.7980 chunk 79 optimal weight: 1.9990 chunk 93 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 85 optimal weight: 1.9990 chunk 88 optimal weight: 0.7980 chunk 102 optimal weight: 0.9980 chunk 70 optimal weight: 3.9990 chunk 14 optimal weight: 3.9990 chunk 100 optimal weight: 3.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 367 ASN ** B 220 GLN ** 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 = 0.4082 r_free = 0.4082 target = 0.162457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.133772 restraints weight = 12196.793| |-----------------------------------------------------------------------------| r_work (start): 0.3707 rms_B_bonded: 2.59 r_work: 0.3568 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3568 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7074 moved from start: 0.1611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 8717 Z= 0.303 Angle : 0.612 8.880 11803 Z= 0.319 Chirality : 0.043 0.174 1333 Planarity : 0.004 0.053 1501 Dihedral : 4.287 23.495 1175 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 4.70 % Allowed : 22.76 % Favored : 72.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.25), residues: 1064 helix: 1.43 (0.26), residues: 401 sheet: -0.24 (0.35), residues: 224 loop : -1.31 (0.26), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP R 206 HIS 0.006 0.001 HIS A 347 PHE 0.016 0.002 PHE A 366 TYR 0.014 0.002 TYR N 95 ARG 0.004 0.000 ARG N 72 *********************** 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 229 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 185 time to evaluate : 0.957 Fit side-chains revert: symmetry clash REVERT: A 317 GLU cc_start: 0.6433 (tm-30) cc_final: 0.6188 (tm-30) REVERT: A 346 ARG cc_start: 0.7267 (mtp85) cc_final: 0.7022 (mtp85) REVERT: B 66 ASP cc_start: 0.7337 (p0) cc_final: 0.7078 (p0) REVERT: B 289 TYR cc_start: 0.8101 (m-80) cc_final: 0.7706 (m-80) REVERT: G 27 ARG cc_start: 0.7895 (ptp-170) cc_final: 0.7665 (ptp90) REVERT: N 118 ARG cc_start: 0.8037 (OUTLIER) cc_final: 0.6589 (mtm-85) REVERT: R 120 SER cc_start: 0.8018 (p) cc_final: 0.7596 (m) REVERT: R 125 ILE cc_start: 0.8191 (OUTLIER) cc_final: 0.7963 (mp) REVERT: R 175 LYS cc_start: 0.7650 (mtpt) cc_final: 0.7377 (mttm) REVERT: R 192 LEU cc_start: 0.7943 (OUTLIER) cc_final: 0.7726 (tt) outliers start: 44 outliers final: 28 residues processed: 212 average time/residue: 0.2584 time to fit residues: 72.6452 Evaluate side-chains 209 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 178 time to evaluate : 1.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 337 ARG Chi-restraints excluded: chain A residue 380 GLU Chi-restraints excluded: chain B residue 42 ARG Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 96 ARG Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 220 GLN Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain N residue 3 GLN Chi-restraints excluded: chain N residue 22 CYS Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 118 ARG Chi-restraints excluded: chain R residue 90 CYS Chi-restraints excluded: chain R residue 125 ILE Chi-restraints excluded: chain R residue 153 ILE Chi-restraints excluded: chain R residue 173 MET Chi-restraints excluded: chain R residue 181 GLN Chi-restraints excluded: chain R residue 189 VAL Chi-restraints excluded: chain R residue 192 LEU Chi-restraints excluded: chain R residue 301 LEU Chi-restraints excluded: chain R residue 323 LYS Chi-restraints excluded: chain R residue 325 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 75 optimal weight: 0.4980 chunk 71 optimal weight: 0.5980 chunk 42 optimal weight: 0.8980 chunk 28 optimal weight: 0.9980 chunk 98 optimal weight: 0.7980 chunk 24 optimal weight: 7.9990 chunk 99 optimal weight: 0.7980 chunk 32 optimal weight: 0.8980 chunk 45 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 59 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.4100 r_free = 0.4100 target = 0.163828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.135255 restraints weight = 12110.568| |-----------------------------------------------------------------------------| r_work (start): 0.3728 rms_B_bonded: 2.57 r_work: 0.3590 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3590 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7052 moved from start: 0.1865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8717 Z= 0.219 Angle : 0.583 10.606 11803 Z= 0.299 Chirality : 0.042 0.164 1333 Planarity : 0.004 0.052 1501 Dihedral : 4.128 19.085 1174 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 4.81 % Allowed : 23.61 % Favored : 71.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.25), residues: 1064 helix: 1.69 (0.26), residues: 399 sheet: -0.09 (0.36), residues: 216 loop : -1.34 (0.26), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 234 HIS 0.005 0.001 HIS A 220 PHE 0.017 0.001 PHE T 14 TYR 0.025 0.001 TYR R 160 ARG 0.003 0.000 ARG A 323 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 180 time to evaluate : 1.017 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 317 GLU cc_start: 0.6463 (tm-30) cc_final: 0.6165 (tm-30) REVERT: B 66 ASP cc_start: 0.7280 (p0) cc_final: 0.7013 (p0) REVERT: B 171 ILE cc_start: 0.7305 (OUTLIER) cc_final: 0.6857 (mm) REVERT: B 289 TYR cc_start: 0.8097 (m-80) cc_final: 0.7678 (m-80) REVERT: G 27 ARG cc_start: 0.7907 (ptp-170) cc_final: 0.7656 (ptp90) REVERT: N 118 ARG cc_start: 0.7991 (OUTLIER) cc_final: 0.6610 (mtm-85) REVERT: T 14 PHE cc_start: 0.8525 (t80) cc_final: 0.8315 (t80) REVERT: R 120 SER cc_start: 0.8019 (p) cc_final: 0.7615 (m) REVERT: R 125 ILE cc_start: 0.8172 (OUTLIER) cc_final: 0.7923 (mp) REVERT: R 158 ASN cc_start: 0.7588 (OUTLIER) cc_final: 0.7275 (t0) REVERT: R 175 LYS cc_start: 0.7684 (mtpt) cc_final: 0.7421 (mttm) REVERT: R 327 CYS cc_start: 0.7099 (OUTLIER) cc_final: 0.6791 (p) outliers start: 45 outliers final: 26 residues processed: 207 average time/residue: 0.2550 time to fit residues: 68.9796 Evaluate side-chains 204 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 173 time to evaluate : 1.005 ------------------------------------------------------------------------------- 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 133 VAL Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 220 GLN Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain N residue 22 CYS Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 118 ARG Chi-restraints excluded: chain R residue 90 CYS Chi-restraints excluded: chain R residue 125 ILE Chi-restraints excluded: chain R residue 158 ASN Chi-restraints excluded: chain R residue 173 MET Chi-restraints excluded: chain R residue 181 GLN Chi-restraints excluded: chain R residue 205 SER Chi-restraints excluded: chain R residue 254 ILE Chi-restraints excluded: chain R residue 301 LEU Chi-restraints excluded: chain R residue 323 LYS Chi-restraints excluded: chain R residue 325 VAL Chi-restraints excluded: chain R residue 327 CYS Chi-restraints excluded: chain R residue 344 ILE 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: 0.0970 chunk 27 optimal weight: 0.8980 chunk 21 optimal weight: 0.9980 chunk 90 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 5 optimal weight: 2.9990 chunk 29 optimal weight: 0.9990 chunk 46 optimal weight: 0.5980 chunk 24 optimal weight: 5.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 220 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.163924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.135393 restraints weight = 12172.220| |-----------------------------------------------------------------------------| r_work (start): 0.3712 rms_B_bonded: 2.61 r_work: 0.3562 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3562 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7092 moved from start: 0.2061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8717 Z= 0.221 Angle : 0.589 10.996 11803 Z= 0.300 Chirality : 0.042 0.162 1333 Planarity : 0.004 0.052 1501 Dihedral : 4.095 19.750 1174 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 5.02 % Allowed : 23.93 % 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: 0.19 (0.25), residues: 1064 helix: 1.74 (0.26), residues: 404 sheet: 0.02 (0.36), residues: 216 loop : -1.36 (0.26), residues: 444 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 0.013 0.001 PHE T 14 TYR 0.021 0.001 TYR R 160 ARG 0.008 0.000 ARG A 273 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 182 time to evaluate : 0.865 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 317 GLU cc_start: 0.6412 (tm-30) cc_final: 0.6133 (tm-30) REVERT: B 66 ASP cc_start: 0.7312 (p0) cc_final: 0.7049 (p0) REVERT: B 171 ILE cc_start: 0.7366 (OUTLIER) cc_final: 0.6935 (mm) REVERT: B 289 TYR cc_start: 0.8086 (m-80) cc_final: 0.7670 (m-80) REVERT: N 118 ARG cc_start: 0.7971 (OUTLIER) cc_final: 0.6576 (mtm-85) REVERT: R 120 SER cc_start: 0.8068 (p) cc_final: 0.7671 (m) REVERT: R 125 ILE cc_start: 0.8165 (OUTLIER) cc_final: 0.7935 (mp) REVERT: R 158 ASN cc_start: 0.7679 (OUTLIER) cc_final: 0.7397 (t0) REVERT: R 327 CYS cc_start: 0.7213 (OUTLIER) cc_final: 0.6905 (p) outliers start: 47 outliers final: 29 residues processed: 212 average time/residue: 0.2501 time to fit residues: 69.3700 Evaluate side-chains 213 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 179 time to evaluate : 0.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 249 ASP Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 380 GLU Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 220 GLN Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain N residue 22 CYS Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 118 ARG Chi-restraints excluded: chain R residue 90 CYS Chi-restraints excluded: chain R residue 97 LYS Chi-restraints excluded: chain R residue 125 ILE Chi-restraints excluded: chain R residue 158 ASN Chi-restraints excluded: chain R residue 173 MET Chi-restraints excluded: chain R residue 181 GLN Chi-restraints excluded: chain R residue 254 ILE Chi-restraints excluded: chain R residue 260 VAL Chi-restraints excluded: chain R residue 301 LEU Chi-restraints excluded: chain R residue 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: 0.6980 chunk 60 optimal weight: 0.4980 chunk 72 optimal weight: 0.8980 chunk 103 optimal weight: 0.5980 chunk 18 optimal weight: 0.9980 chunk 21 optimal weight: 0.9990 chunk 83 optimal weight: 5.9990 chunk 37 optimal weight: 1.9990 chunk 40 optimal weight: 0.0050 chunk 82 optimal weight: 0.3980 chunk 32 optimal weight: 1.9990 overall best weight: 0.4394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 367 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.165097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.136620 restraints weight = 11982.115| |-----------------------------------------------------------------------------| r_work (start): 0.3730 rms_B_bonded: 2.57 r_work: 0.3583 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3583 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7070 moved from start: 0.2201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8717 Z= 0.176 Angle : 0.582 10.028 11803 Z= 0.294 Chirality : 0.041 0.171 1333 Planarity : 0.004 0.050 1501 Dihedral : 3.972 20.155 1174 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 4.59 % Allowed : 24.47 % 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: 0.32 (0.26), residues: 1064 helix: 1.90 (0.27), residues: 402 sheet: 0.07 (0.36), residues: 217 loop : -1.33 (0.26), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 234 HIS 0.004 0.001 HIS A 220 PHE 0.014 0.001 PHE T 14 TYR 0.018 0.001 TYR R 160 ARG 0.005 0.000 ARG A 273 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 185 time to evaluate : 0.929 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 317 GLU cc_start: 0.6447 (tm-30) cc_final: 0.6224 (tm-30) REVERT: B 66 ASP cc_start: 0.7279 (p0) cc_final: 0.7004 (p0) REVERT: B 153 ASP cc_start: 0.6756 (OUTLIER) cc_final: 0.6480 (p0) REVERT: B 171 ILE cc_start: 0.7361 (OUTLIER) cc_final: 0.6873 (mm) REVERT: B 289 TYR cc_start: 0.8072 (m-80) cc_final: 0.7656 (m-80) REVERT: G 27 ARG cc_start: 0.7870 (ptp90) cc_final: 0.7602 (ptp90) REVERT: N 76 LYS cc_start: 0.7816 (OUTLIER) cc_final: 0.7528 (ttpp) REVERT: N 118 ARG cc_start: 0.7951 (OUTLIER) cc_final: 0.6515 (mtm-85) REVERT: R 120 SER cc_start: 0.8041 (p) cc_final: 0.7665 (m) REVERT: R 125 ILE cc_start: 0.8155 (OUTLIER) cc_final: 0.7929 (mp) REVERT: R 158 ASN cc_start: 0.7626 (OUTLIER) cc_final: 0.7357 (t0) REVERT: R 296 MET cc_start: 0.7410 (tmm) cc_final: 0.7198 (ttp) REVERT: R 327 CYS cc_start: 0.7215 (OUTLIER) cc_final: 0.6933 (p) outliers start: 43 outliers final: 25 residues processed: 213 average time/residue: 0.2609 time to fit residues: 71.7935 Evaluate side-chains 218 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 186 time to evaluate : 0.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 249 ASP Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 349 CYS Chi-restraints excluded: chain A residue 380 GLU Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 220 GLN Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain N residue 22 CYS Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 76 LYS Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 118 ARG Chi-restraints excluded: chain R residue 90 CYS Chi-restraints excluded: chain R residue 97 LYS Chi-restraints excluded: chain R residue 125 ILE Chi-restraints excluded: chain R residue 158 ASN Chi-restraints excluded: chain R residue 173 MET Chi-restraints excluded: chain R residue 181 GLN Chi-restraints excluded: chain R residue 254 ILE Chi-restraints excluded: chain R residue 260 VAL Chi-restraints excluded: chain R residue 298 CYS 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 393 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 100 optimal weight: 4.9990 chunk 89 optimal weight: 0.9980 chunk 12 optimal weight: 1.9990 chunk 40 optimal weight: 0.0970 chunk 62 optimal weight: 1.9990 chunk 67 optimal weight: 0.0270 chunk 6 optimal weight: 0.7980 chunk 58 optimal weight: 8.9990 chunk 10 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 overall best weight: 0.7838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 367 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.163746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.135003 restraints weight = 12112.575| |-----------------------------------------------------------------------------| r_work (start): 0.3705 rms_B_bonded: 2.60 r_work: 0.3556 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3556 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7099 moved from start: 0.2317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 8717 Z= 0.235 Angle : 0.605 10.836 11803 Z= 0.307 Chirality : 0.042 0.175 1333 Planarity : 0.004 0.050 1501 Dihedral : 4.045 20.183 1174 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 5.02 % Allowed : 23.93 % 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: 0.31 (0.26), residues: 1064 helix: 1.87 (0.27), residues: 407 sheet: 0.04 (0.36), residues: 219 loop : -1.34 (0.26), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP N 47 HIS 0.004 0.001 HIS A 220 PHE 0.015 0.002 PHE T 14 TYR 0.019 0.001 TYR R 160 ARG 0.003 0.000 ARG A 273 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2128 Ramachandran restraints generated. 1064 Oldfield, 0 Emsley, 1064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 185 time to evaluate : 0.922 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 66 ASP cc_start: 0.7238 (p0) cc_final: 0.6970 (p0) REVERT: B 153 ASP cc_start: 0.6824 (OUTLIER) cc_final: 0.6552 (p0) REVERT: B 171 ILE cc_start: 0.7380 (OUTLIER) cc_final: 0.6956 (mm) REVERT: N 76 LYS cc_start: 0.7838 (OUTLIER) cc_final: 0.7540 (ttpp) REVERT: N 118 ARG cc_start: 0.7992 (OUTLIER) cc_final: 0.6555 (mtm-85) REVERT: R 120 SER cc_start: 0.8058 (p) cc_final: 0.7653 (m) REVERT: R 125 ILE cc_start: 0.8167 (OUTLIER) cc_final: 0.7940 (mp) REVERT: R 158 ASN cc_start: 0.7638 (OUTLIER) cc_final: 0.7383 (t0) REVERT: R 327 CYS cc_start: 0.7182 (OUTLIER) cc_final: 0.6901 (p) outliers start: 47 outliers final: 32 residues processed: 216 average time/residue: 0.2446 time to fit residues: 69.1432 Evaluate side-chains 220 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 181 time to evaluate : 0.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 249 ASP Chi-restraints excluded: chain A residue 337 ARG Chi-restraints excluded: chain A residue 349 CYS Chi-restraints excluded: chain A residue 380 GLU Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 220 GLN Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain N residue 22 CYS Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 76 LYS Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 118 ARG Chi-restraints excluded: chain R residue 90 CYS Chi-restraints excluded: chain R residue 97 LYS Chi-restraints excluded: chain R residue 125 ILE Chi-restraints excluded: chain R residue 158 ASN Chi-restraints excluded: chain R residue 173 MET Chi-restraints excluded: chain R residue 181 GLN Chi-restraints excluded: chain R residue 254 ILE Chi-restraints excluded: chain R residue 260 VAL Chi-restraints excluded: chain R residue 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 65 optimal weight: 0.7980 chunk 63 optimal weight: 0.7980 chunk 103 optimal weight: 0.4980 chunk 45 optimal weight: 0.5980 chunk 6 optimal weight: 0.4980 chunk 26 optimal weight: 0.7980 chunk 44 optimal weight: 0.4980 chunk 78 optimal weight: 0.6980 chunk 73 optimal weight: 7.9990 chunk 52 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 367 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.164716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.136001 restraints weight = 12233.362| |-----------------------------------------------------------------------------| r_work (start): 0.3719 rms_B_bonded: 2.60 r_work: 0.3573 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3573 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7083 moved from start: 0.2412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8717 Z= 0.195 Angle : 0.604 12.814 11803 Z= 0.304 Chirality : 0.041 0.171 1333 Planarity : 0.004 0.047 1501 Dihedral : 3.990 20.027 1174 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 4.59 % Allowed : 25.32 % 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: 0.40 (0.26), residues: 1064 helix: 1.97 (0.27), residues: 407 sheet: 0.11 (0.36), residues: 218 loop : -1.32 (0.26), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 234 HIS 0.004 0.001 HIS A 220 PHE 0.014 0.001 PHE T 14 TYR 0.018 0.001 TYR R 160 ARG 0.002 0.000 ARG A 273 *********************** 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 226 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 183 time to evaluate : 0.902 Fit side-chains revert: symmetry clash REVERT: A 374 LEU cc_start: 0.8113 (tt) cc_final: 0.7895 (tp) REVERT: B 66 ASP cc_start: 0.7220 (p0) cc_final: 0.6946 (p0) REVERT: B 153 ASP cc_start: 0.6763 (OUTLIER) cc_final: 0.6482 (p0) REVERT: B 171 ILE cc_start: 0.7383 (OUTLIER) cc_final: 0.6929 (mm) REVERT: G 27 ARG cc_start: 0.7874 (ptp90) cc_final: 0.7507 (ptp90) REVERT: N 76 LYS cc_start: 0.7816 (OUTLIER) cc_final: 0.7512 (ttpp) REVERT: N 118 ARG cc_start: 0.7974 (OUTLIER) cc_final: 0.6515 (mtm-85) REVERT: R 120 SER cc_start: 0.8068 (p) cc_final: 0.7669 (m) REVERT: R 125 ILE cc_start: 0.8157 (OUTLIER) cc_final: 0.7932 (mp) REVERT: R 158 ASN cc_start: 0.7612 (OUTLIER) cc_final: 0.7359 (t0) REVERT: R 327 CYS cc_start: 0.7193 (OUTLIER) cc_final: 0.6944 (p) REVERT: R 347 LEU cc_start: 0.7846 (tp) cc_final: 0.7617 (mt) outliers start: 43 outliers final: 27 residues processed: 210 average time/residue: 0.2534 time to fit residues: 69.2698 Evaluate side-chains 213 residues out of total 936 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 179 time to evaluate : 0.829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 249 ASP Chi-restraints excluded: chain A residue 349 CYS Chi-restraints excluded: chain A residue 380 GLU Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 220 GLN Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain N residue 22 CYS Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 76 LYS Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 118 ARG Chi-restraints excluded: chain R residue 90 CYS Chi-restraints excluded: chain R residue 97 LYS Chi-restraints excluded: chain R residue 125 ILE Chi-restraints excluded: chain R residue 158 ASN Chi-restraints excluded: chain R residue 173 MET Chi-restraints excluded: chain R residue 174 CYS Chi-restraints excluded: chain R residue 181 GLN Chi-restraints excluded: chain R residue 254 ILE Chi-restraints excluded: chain R residue 260 VAL Chi-restraints excluded: chain R residue 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 ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/iotbx/cli_parser.py", line 980, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 62.2146 > 50: distance: 22 - 131: 28.942 distance: 25 - 128: 31.192 distance: 33 - 117: 30.689 distance: 64 - 69: 14.781 distance: 69 - 70: 6.862 distance: 70 - 71: 14.532 distance: 70 - 73: 23.557 distance: 71 - 72: 28.641 distance: 71 - 78: 32.985 distance: 74 - 75: 10.623 distance: 75 - 76: 14.278 distance: 75 - 77: 4.935 distance: 78 - 79: 29.732 distance: 79 - 80: 15.081 distance: 79 - 82: 25.993 distance: 80 - 81: 17.172 distance: 80 - 85: 18.319 distance: 82 - 83: 24.008 distance: 82 - 84: 46.718 distance: 85 - 86: 20.619 distance: 86 - 87: 13.251 distance: 87 - 88: 23.133 distance: 87 - 89: 35.127 distance: 89 - 90: 27.331 distance: 90 - 91: 6.151 distance: 90 - 93: 9.665 distance: 91 - 92: 20.149 distance: 91 - 98: 7.727 distance: 93 - 94: 22.222 distance: 94 - 95: 17.377 distance: 95 - 97: 6.310 distance: 98 - 99: 16.275 distance: 99 - 100: 25.283 distance: 99 - 102: 9.251 distance: 100 - 101: 39.495 distance: 100 - 107: 22.310 distance: 102 - 103: 16.238 distance: 103 - 104: 16.754 distance: 104 - 105: 8.821 distance: 104 - 106: 30.194 distance: 107 - 108: 16.304 distance: 108 - 109: 23.188 distance: 108 - 111: 35.752 distance: 109 - 110: 18.794 distance: 111 - 112: 9.868 distance: 114 - 115: 16.316 distance: 115 - 116: 7.156 distance: 115 - 118: 21.792 distance: 116 - 121: 38.533 distance: 118 - 119: 18.125 distance: 118 - 120: 33.655 distance: 121 - 122: 25.463 distance: 122 - 123: 19.199 distance: 122 - 125: 14.315 distance: 123 - 124: 5.765 distance: 123 - 128: 45.704 distance: 125 - 126: 3.142 distance: 125 - 127: 23.324 distance: 128 - 129: 23.716 distance: 129 - 130: 16.777 distance: 129 - 132: 18.450 distance: 130 - 131: 15.691 distance: 130 - 139: 26.465 distance: 132 - 133: 8.860 distance: 133 - 134: 40.069 distance: 133 - 135: 37.238 distance: 134 - 136: 10.166 distance: 135 - 137: 13.197 distance: 136 - 138: 34.309 distance: 137 - 138: 50.470 distance: 139 - 140: 17.160 distance: 140 - 141: 11.934 distance: 140 - 143: 18.908 distance: 141 - 142: 9.921 distance: 141 - 146: 5.537 distance: 143 - 144: 9.161 distance: 143 - 145: 18.362