Starting phenix.real_space_refine on Sat Aug 23 21:38:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7w0l_32243/08_2025/7w0l_32243.cif Found real_map, /net/cci-nas-00/data/ceres_data/7w0l_32243/08_2025/7w0l_32243.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.57 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7w0l_32243/08_2025/7w0l_32243.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7w0l_32243/08_2025/7w0l_32243.map" model { file = "/net/cci-nas-00/data/ceres_data/7w0l_32243/08_2025/7w0l_32243.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7w0l_32243/08_2025/7w0l_32243.cif" } resolution = 3.57 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.027 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 4236 atoms to isotropic. 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 90 5.16 5 C 7396 2.51 5 N 1932 2.21 5 O 2108 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 11526 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 1819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1819 Classifications: {'peptide': 226} Link IDs: {'PTRANS': 2, 'TRANS': 223} Chain breaks: 1 Chain: "B" Number of atoms: 2607 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2607 Classifications: {'peptide': 339} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 333} Chain: "C" Number of atoms: 457 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 457 Classifications: {'peptide': 61} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 56} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "Q" Number of atoms: 2376 Number of conformers: 1 Conformer: "" Number of residues, atoms: 297, 2376 Classifications: {'peptide': 297} Link IDs: {'PTRANS': 11, 'TRANS': 285} Chain: "R" Number of atoms: 2393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 298, 2393 Classifications: {'peptide': 298} Link IDs: {'PTRANS': 11, 'TRANS': 286} Chain: "S" Number of atoms: 1800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1800 Classifications: {'peptide': 234} Link IDs: {'PTRANS': 10, 'TRANS': 223} Chain breaks: 1 Chain: "Q" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 37 Unusual residues: {'8EH': 1} Classifications: {'undetermined': 1} Chain: "R" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 37 Unusual residues: {'8EH': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.38, per 1000 atoms: 0.21 Number of scatterers: 11526 At special positions: 0 Unit cell: (125.8, 106.25, 136.85, 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 90 16.00 O 2108 8.00 N 1932 7.00 C 7396 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS Q 102 " - pdb=" SG CYS Q 181 " distance=2.04 Simple disulfide: pdb=" SG CYS R 102 " - pdb=" SG CYS R 181 " distance=2.05 Simple disulfide: pdb=" SG CYS S 159 " - pdb=" SG CYS S 229 " distance=2.05 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.74 Conformation dependent library (CDL) restraints added in 500.5 milliseconds Enol-peptide restraints added in 1.2 microseconds 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2732 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 14 sheets defined 47.2% alpha, 13.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.32 Creating SS restraints... Processing helix chain 'A' and resid 6 through 32 removed outlier: 3.657A pdb=" N ARG A 32 " --> pdb=" O GLU A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 55 removed outlier: 4.040A pdb=" N VAL A 50 " --> pdb=" O LYS A 46 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ILE A 55 " --> pdb=" O LYS A 51 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 212 removed outlier: 4.355A pdb=" N TRP A 211 " --> pdb=" O GLU A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 215 No H-bonds generated for 'chain 'A' and resid 213 through 215' Processing helix chain 'A' and resid 241 through 255 removed outlier: 3.739A pdb=" N GLU A 245 " --> pdb=" O ASN A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 278 removed outlier: 3.564A pdb=" N PHE A 274 " --> pdb=" O LYS A 270 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N GLU A 276 " --> pdb=" O ASP A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 309 removed outlier: 3.562A pdb=" N PHE A 307 " --> pdb=" O ILE A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 351 removed outlier: 3.730A pdb=" N VAL A 335 " --> pdb=" O ASN A 331 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 26 removed outlier: 3.758A pdb=" N ALA B 21 " --> pdb=" O GLN B 17 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ALA B 26 " --> pdb=" O ARG B 22 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'B' and resid 280 through 282 No H-bonds generated for 'chain 'B' and resid 280 through 282' Processing helix chain 'C' and resid 35 through 55 removed outlier: 3.966A pdb=" N ALA C 41 " --> pdb=" O THR C 37 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLN C 49 " --> pdb=" O LYS C 45 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N LEU C 50 " --> pdb=" O LEU C 46 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N LYS C 51 " --> pdb=" O VAL C 47 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N MET C 52 " --> pdb=" O GLU C 48 " (cutoff:3.500A) Processing helix chain 'C' and resid 60 through 75 removed outlier: 3.686A pdb=" N ALA C 64 " --> pdb=" O LYS C 60 " (cutoff:3.500A) Processing helix chain 'Q' and resid 27 through 56 Proline residue: Q 32 - end of helix removed outlier: 3.542A pdb=" N SER Q 56 " --> pdb=" O THR Q 52 " (cutoff:3.500A) Processing helix chain 'Q' and resid 57 through 61 Processing helix chain 'Q' and resid 62 through 81 removed outlier: 4.033A pdb=" N SER Q 70 " --> pdb=" O ILE Q 66 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N THR Q 81 " --> pdb=" O THR Q 77 " (cutoff:3.500A) Processing helix chain 'Q' and resid 82 through 91 removed outlier: 3.711A pdb=" N TYR Q 88 " --> pdb=" O LEU Q 84 " (cutoff:3.500A) Processing helix chain 'Q' and resid 98 through 137 removed outlier: 4.042A pdb=" N CYS Q 102 " --> pdb=" O GLY Q 98 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N LYS Q 103 " --> pdb=" O THR Q 99 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ILE Q 131 " --> pdb=" O ARG Q 127 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N VAL Q 132 " --> pdb=" O TYR Q 128 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ARG Q 133 " --> pdb=" O LEU Q 129 " (cutoff:3.500A) Proline residue: Q 134 - end of helix Processing helix chain 'Q' and resid 145 through 161 removed outlier: 3.518A pdb=" N ALA Q 161 " --> pdb=" O ALA Q 157 " (cutoff:3.500A) Processing helix chain 'Q' and resid 162 through 167 Processing helix chain 'Q' and resid 190 through 192 No H-bonds generated for 'chain 'Q' and resid 190 through 192' Processing helix chain 'Q' and resid 193 through 232 removed outlier: 3.957A pdb=" N TRP Q 197 " --> pdb=" O SER Q 193 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N GLU Q 198 " --> pdb=" O GLU Q 194 " (cutoff:3.500A) removed outlier: 5.521A pdb=" N VAL Q 212 " --> pdb=" O VAL Q 208 " (cutoff:3.500A) Proline residue: Q 213 - end of helix removed outlier: 3.670A pdb=" N ILE Q 224 " --> pdb=" O CYS Q 220 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N PHE Q 232 " --> pdb=" O ILE Q 228 " (cutoff:3.500A) Processing helix chain 'Q' and resid 238 through 278 removed outlier: 3.820A pdb=" N LYS Q 242 " --> pdb=" O GLU Q 238 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ILE Q 249 " --> pdb=" O ARG Q 245 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ILE Q 250 " --> pdb=" O LEU Q 246 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N VAL Q 251 " --> pdb=" O LEU Q 247 " (cutoff:3.500A) Proline residue: Q 263 - end of helix removed outlier: 4.135A pdb=" N SER Q 275 " --> pdb=" O TYR Q 271 " (cutoff:3.500A) removed outlier: 5.020A pdb=" N LEU Q 276 " --> pdb=" O MET Q 272 " (cutoff:3.500A) Processing helix chain 'Q' and resid 280 through 299 Proline residue: Q 292 - end of helix removed outlier: 4.119A pdb=" N TYR Q 299 " --> pdb=" O THR Q 295 " (cutoff:3.500A) Processing helix chain 'Q' and resid 299 through 311 Proline residue: Q 306 - end of helix Processing helix chain 'Q' and resid 312 through 322 Processing helix chain 'R' and resid 30 through 61 removed outlier: 3.790A pdb=" N ILE R 34 " --> pdb=" O LEU R 30 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N VAL R 49 " --> pdb=" O GLY R 45 " (cutoff:3.500A) removed outlier: 5.698A pdb=" N ARG R 58 " --> pdb=" O PHE R 54 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N GLU R 59 " --> pdb=" O ARG R 55 " (cutoff:3.500A) Processing helix chain 'R' and resid 64 through 81 removed outlier: 4.005A pdb=" N ILE R 68 " --> pdb=" O ALA R 64 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N THR R 81 " --> pdb=" O THR R 77 " (cutoff:3.500A) Processing helix chain 'R' and resid 81 through 91 removed outlier: 4.560A pdb=" N TRP R 85 " --> pdb=" O THR R 81 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N ARG R 91 " --> pdb=" O THR R 87 " (cutoff:3.500A) Processing helix chain 'R' and resid 99 through 132 removed outlier: 3.728A pdb=" N LYS R 103 " --> pdb=" O THR R 99 " (cutoff:3.500A) Processing helix chain 'R' and resid 137 through 139 No H-bonds generated for 'chain 'R' and resid 137 through 139' Processing helix chain 'R' and resid 140 through 145 removed outlier: 3.922A pdb=" N VAL R 144 " --> pdb=" O LEU R 140 " (cutoff:3.500A) Processing helix chain 'R' and resid 146 through 167 removed outlier: 3.841A pdb=" N THR R 150 " --> pdb=" O GLY R 146 " (cutoff:3.500A) Proline residue: R 163 - end of helix Processing helix chain 'R' and resid 184 through 188 removed outlier: 4.105A pdb=" N MET R 187 " --> pdb=" O ASP R 184 " (cutoff:3.500A) Processing helix chain 'R' and resid 193 through 232 removed outlier: 3.905A pdb=" N VAL R 208 " --> pdb=" O SER R 204 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N VAL R 212 " --> pdb=" O VAL R 208 " (cutoff:3.500A) Proline residue: R 213 - end of helix removed outlier: 3.946A pdb=" N PHE R 232 " --> pdb=" O ILE R 228 " (cutoff:3.500A) Processing helix chain 'R' and resid 238 through 275 removed outlier: 3.558A pdb=" N LYS R 242 " --> pdb=" O GLU R 238 " (cutoff:3.500A) Proline residue: R 263 - end of helix Processing helix chain 'R' and resid 281 through 298 Proline residue: R 292 - end of helix Processing helix chain 'R' and resid 299 through 311 Proline residue: R 306 - end of helix Processing helix chain 'R' and resid 313 through 321 Processing helix chain 'S' and resid 220 through 224 Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 190 removed outlier: 7.096A pdb=" N LYS A 35 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 7.849A pdb=" N ILE A 222 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.843A pdb=" N CYS A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 7.435A pdb=" N LEU A 39 " --> pdb=" O CYS A 224 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N VAL A 225 " --> pdb=" O PHE A 267 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51 removed outlier: 6.941A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.853A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N ALA B 328 " --> pdb=" O LEU B 318 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N LEU B 318 " --> pdb=" O ALA B 328 " (cutoff:3.500A) removed outlier: 6.842A 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: 6.743A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.178A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.317A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LEU B 70 " --> pdb=" O TRP B 82 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.859A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ASP B 83 " --> pdb=" O ASN B 88 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ASN B 88 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 3.701A pdb=" N ARG B 137 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 5.925A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 148 through 151 removed outlier: 3.599A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.817A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.834A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 232 through 234 removed outlier: 3.623A pdb=" N LEU B 252 " --> pdb=" O MET B 262 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 5.981A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.199A 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: 4.069A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU B 285 " --> pdb=" O TRP B 297 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ASN B 293 " --> pdb=" O TYR B 289 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'R' and resid 171 through 172 Processing sheet with id=AB1, first strand: chain 'S' and resid 4 through 7 removed outlier: 3.527A pdb=" N ARG S 18 " --> pdb=" O MET S 83 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N THR S 78 " --> pdb=" O ASP S 73 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'S' and resid 45 through 51 removed outlier: 3.614A pdb=" N GLU S 46 " --> pdb=" O ARG S 38 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N TRP S 36 " --> pdb=" O VAL S 48 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N TYR S 50 " --> pdb=" O MET S 34 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N MET S 34 " --> pdb=" O TYR S 50 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N VAL S 97 " --> pdb=" O HIS S 35 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'S' and resid 146 through 147 removed outlier: 3.909A pdb=" N GLY S 225 " --> pdb=" O LEU S 245 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'S' and resid 155 through 160 removed outlier: 3.758A pdb=" N VAL S 155 " --> pdb=" O ILE S 216 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N SER S 208 " --> pdb=" O ALA S 211 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'S' and resid 186 through 189 removed outlier: 6.878A pdb=" N TRP S 176 " --> pdb=" O LEU S 188 " (cutoff:3.500A) 550 hydrogen bonds defined for protein. 1602 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.47 Time building geometry restraints manager: 1.02 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: 3635 1.34 - 1.47: 3155 1.47 - 1.60: 4872 1.60 - 1.72: 2 1.72 - 1.85: 131 Bond restraints: 11795 Sorted by residual: bond pdb=" C30 8EH R 401 " pdb=" C31 8EH R 401 " ideal model delta sigma weight residual 1.472 1.567 -0.095 2.00e-02 2.50e+03 2.25e+01 bond pdb=" C30 8EH Q 401 " pdb=" C31 8EH Q 401 " ideal model delta sigma weight residual 1.472 1.564 -0.092 2.00e-02 2.50e+03 2.12e+01 bond pdb=" C30 8EH R 401 " pdb=" N29 8EH R 401 " ideal model delta sigma weight residual 1.313 1.404 -0.091 2.00e-02 2.50e+03 2.08e+01 bond pdb=" C30 8EH Q 401 " pdb=" N29 8EH Q 401 " ideal model delta sigma weight residual 1.313 1.403 -0.090 2.00e-02 2.50e+03 2.04e+01 bond pdb=" C12 8EH R 401 " pdb=" N28 8EH R 401 " ideal model delta sigma weight residual 1.307 1.393 -0.086 2.00e-02 2.50e+03 1.83e+01 ... (remaining 11790 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.45: 15578 2.45 - 4.91: 369 4.91 - 7.36: 56 7.36 - 9.81: 7 9.81 - 12.27: 2 Bond angle restraints: 16012 Sorted by residual: angle pdb=" C ALA B 257 " pdb=" N ASP B 258 " pdb=" CA ASP B 258 " ideal model delta sigma weight residual 122.40 130.46 -8.06 1.45e+00 4.76e-01 3.09e+01 angle pdb=" CA TYR S 235 " pdb=" CB TYR S 235 " pdb=" CG TYR S 235 " ideal model delta sigma weight residual 113.90 105.20 8.70 1.80e+00 3.09e-01 2.34e+01 angle pdb=" C GLY B 162 " pdb=" N ASP B 163 " pdb=" CA ASP B 163 " ideal model delta sigma weight residual 121.71 115.94 5.77 1.39e+00 5.18e-01 1.72e+01 angle pdb=" O15 8EH Q 401 " pdb=" S14 8EH Q 401 " pdb=" O16 8EH Q 401 " ideal model delta sigma weight residual 119.97 107.70 12.27 3.00e+00 1.11e-01 1.67e+01 angle pdb=" O15 8EH R 401 " pdb=" S14 8EH R 401 " pdb=" O16 8EH R 401 " ideal model delta sigma weight residual 119.97 107.73 12.24 3.00e+00 1.11e-01 1.66e+01 ... (remaining 16007 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.86: 6721 30.86 - 61.71: 219 61.71 - 92.57: 12 92.57 - 123.43: 0 123.43 - 154.28: 2 Dihedral angle restraints: 6954 sinusoidal: 2716 harmonic: 4238 Sorted by residual: dihedral pdb=" CA GLU Q 174 " pdb=" C GLU Q 174 " pdb=" N ASN Q 175 " pdb=" CA ASN Q 175 " ideal model delta harmonic sigma weight residual -180.00 -150.69 -29.31 0 5.00e+00 4.00e-02 3.44e+01 dihedral pdb=" CA GLY A 352 " pdb=" C GLY A 352 " pdb=" N LEU A 353 " pdb=" CA LEU A 353 " ideal model delta harmonic sigma weight residual -180.00 -151.58 -28.42 0 5.00e+00 4.00e-02 3.23e+01 dihedral pdb=" CA LEU A 268 " pdb=" C LEU A 268 " pdb=" N ASN A 269 " pdb=" CA ASN A 269 " ideal model delta harmonic sigma weight residual 180.00 -152.40 -27.60 0 5.00e+00 4.00e-02 3.05e+01 ... (remaining 6951 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 1560 0.069 - 0.139: 232 0.139 - 0.208: 18 0.208 - 0.278: 2 0.278 - 0.347: 2 Chirality restraints: 1814 Sorted by residual: chirality pdb=" C19 8EH Q 401 " pdb=" C17 8EH Q 401 " pdb=" C21 8EH Q 401 " pdb=" O20 8EH Q 401 " both_signs ideal model delta sigma weight residual False -2.43 -2.78 0.35 2.00e-01 2.50e+01 3.01e+00 chirality pdb=" C19 8EH R 401 " pdb=" C17 8EH R 401 " pdb=" C21 8EH R 401 " pdb=" O20 8EH R 401 " both_signs ideal model delta sigma weight residual False -2.43 -2.77 0.34 2.00e-01 2.50e+01 2.92e+00 chirality pdb=" CA TYR S 235 " pdb=" N TYR S 235 " pdb=" C TYR S 235 " pdb=" CB TYR S 235 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.90e+00 ... (remaining 1811 not shown) Planarity restraints: 1995 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE R 291 " 0.032 2.00e-02 2.50e+03 2.56e-02 1.15e+01 pdb=" CG PHE R 291 " -0.057 2.00e-02 2.50e+03 pdb=" CD1 PHE R 291 " 0.002 2.00e-02 2.50e+03 pdb=" CD2 PHE R 291 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 PHE R 291 " 0.010 2.00e-02 2.50e+03 pdb=" CE2 PHE R 291 " 0.012 2.00e-02 2.50e+03 pdb=" CZ PHE R 291 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN R 289 " 0.016 2.00e-02 2.50e+03 3.22e-02 1.04e+01 pdb=" C ASN R 289 " -0.056 2.00e-02 2.50e+03 pdb=" O ASN R 289 " 0.021 2.00e-02 2.50e+03 pdb=" N ILE R 290 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR S 190 " 0.028 2.00e-02 2.50e+03 1.87e-02 7.02e+00 pdb=" CG TYR S 190 " -0.044 2.00e-02 2.50e+03 pdb=" CD1 TYR S 190 " 0.000 2.00e-02 2.50e+03 pdb=" CD2 TYR S 190 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR S 190 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR S 190 " 0.002 2.00e-02 2.50e+03 pdb=" CZ TYR S 190 " 0.005 2.00e-02 2.50e+03 pdb=" OH TYR S 190 " 0.004 2.00e-02 2.50e+03 ... (remaining 1992 not shown) Histogram of nonbonded interaction distances: 1.89 - 2.49: 72 2.49 - 3.09: 8734 3.09 - 3.70: 17063 3.70 - 4.30: 23276 4.30 - 4.90: 38672 Nonbonded interactions: 87817 Sorted by model distance: nonbonded pdb=" O ALA B 257 " pdb=" OD1 ASP B 258 " model vdw 1.891 3.040 nonbonded pdb=" O ILE B 37 " pdb=" NZ LYS B 301 " model vdw 2.207 3.120 nonbonded pdb=" O LYS B 280 " pdb=" OG SER B 281 " model vdw 2.207 3.040 nonbonded pdb=" OE1 GLN S 142 " pdb=" OG1 THR S 243 " model vdw 2.209 3.040 nonbonded pdb=" OG1 THR B 102 " pdb=" O SER B 147 " model vdw 2.214 3.040 ... (remaining 87812 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 Found NCS groups: ncs_group { reference = (chain 'Q' and (resid 26 through 321 or resid 401)) selection = (chain 'R' and resid 26 through 401) } 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 group one per residue 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: 1.890 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.010 Extract box with map and model: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 9.600 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7590 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 : 0.010 0.095 11798 Z= 0.457 Angle : 0.942 12.266 16018 Z= 0.527 Chirality : 0.051 0.347 1814 Planarity : 0.005 0.056 1995 Dihedral : 15.214 154.284 4213 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 14.69 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.62 % Favored : 91.31 % Rotamer: Outliers : 0.08 % Allowed : 9.37 % Favored : 90.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.27 (0.19), residues: 1439 helix: -1.17 (0.18), residues: 622 sheet: -2.12 (0.29), residues: 278 loop : -3.30 (0.21), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 205 TYR 0.044 0.003 TYR S 190 PHE 0.057 0.003 PHE R 291 TRP 0.019 0.002 TRP A 211 HIS 0.008 0.002 HIS B 183 Details of bonding type rmsd covalent geometry : bond 0.00974 (11795) covalent geometry : angle 0.93912 (16012) SS BOND : bond 0.01496 ( 3) SS BOND : angle 3.67820 ( 6) hydrogen bonds : bond 0.18111 ( 550) hydrogen bonds : angle 6.41359 ( 1602) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 1251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 374 time to evaluate : 0.284 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 192 LYS cc_start: 0.8259 (mttp) cc_final: 0.8039 (mttp) REVERT: A 197 LYS cc_start: 0.8250 (mtpp) cc_final: 0.7851 (mttp) REVERT: A 209 LYS cc_start: 0.8482 (mtpt) cc_final: 0.8217 (mtpt) REVERT: A 231 ASP cc_start: 0.7473 (t70) cc_final: 0.7239 (t70) REVERT: A 242 ARG cc_start: 0.7781 (mtt90) cc_final: 0.7536 (mtt90) REVERT: A 247 MET cc_start: 0.7829 (mtm) cc_final: 0.7557 (mtm) REVERT: A 289 GLU cc_start: 0.7175 (pm20) cc_final: 0.6616 (pm20) REVERT: A 308 GLU cc_start: 0.7565 (tt0) cc_final: 0.7187 (tt0) REVERT: A 341 ASP cc_start: 0.8326 (t70) cc_final: 0.8056 (t70) REVERT: A 345 LYS cc_start: 0.8253 (mtpt) cc_final: 0.7880 (mtpp) REVERT: B 14 LEU cc_start: 0.9095 (mp) cc_final: 0.8622 (mp) REVERT: B 34 THR cc_start: 0.7617 (p) cc_final: 0.7381 (t) REVERT: B 59 TYR cc_start: 0.8437 (m-10) cc_final: 0.8209 (m-80) REVERT: B 61 MET cc_start: 0.7405 (tmm) cc_final: 0.6946 (tmm) REVERT: B 79 LEU cc_start: 0.7931 (tp) cc_final: 0.7485 (tt) REVERT: B 98 SER cc_start: 0.8326 (m) cc_final: 0.7828 (t) REVERT: B 179 THR cc_start: 0.8609 (t) cc_final: 0.8348 (p) REVERT: B 195 ASP cc_start: 0.7773 (t70) cc_final: 0.7525 (t0) REVERT: B 291 ASP cc_start: 0.7635 (t70) cc_final: 0.7325 (t70) REVERT: B 300 LEU cc_start: 0.8370 (mt) cc_final: 0.8161 (mt) REVERT: B 308 LEU cc_start: 0.8160 (mt) cc_final: 0.7955 (mp) REVERT: B 338 ILE cc_start: 0.8370 (mt) cc_final: 0.8110 (mm) REVERT: C 42 GLN cc_start: 0.8148 (tp40) cc_final: 0.7904 (tp40) REVERT: Q 36 MET cc_start: 0.8180 (mmm) cc_final: 0.7468 (mpp) REVERT: Q 71 LEU cc_start: 0.8823 (tt) cc_final: 0.8606 (tt) REVERT: Q 88 TYR cc_start: 0.8528 (t80) cc_final: 0.8316 (t80) REVERT: Q 107 TYR cc_start: 0.8173 (t80) cc_final: 0.7897 (t80) REVERT: Q 201 LEU cc_start: 0.7888 (tp) cc_final: 0.7630 (tp) REVERT: Q 262 MET cc_start: 0.6484 (tmm) cc_final: 0.6230 (tmm) REVERT: Q 295 THR cc_start: 0.8152 (t) cc_final: 0.7828 (p) REVERT: Q 301 ASN cc_start: 0.8480 (t0) cc_final: 0.8218 (t0) REVERT: Q 308 LEU cc_start: 0.7691 (mm) cc_final: 0.7487 (mm) REVERT: R 46 ASN cc_start: 0.8696 (m-40) cc_final: 0.8361 (m-40) REVERT: R 165 MET cc_start: 0.8275 (tpt) cc_final: 0.7811 (tpp) REVERT: R 216 ILE cc_start: 0.8335 (mt) cc_final: 0.8135 (mt) REVERT: R 222 PHE cc_start: 0.7931 (t80) cc_final: 0.7700 (t80) REVERT: R 228 ILE cc_start: 0.8542 (tp) cc_final: 0.8166 (tt) REVERT: R 245 ARG cc_start: 0.7743 (ttt90) cc_final: 0.7479 (ttt90) REVERT: R 288 MET cc_start: 0.7108 (mmm) cc_final: 0.6832 (mmm) REVERT: S 3 GLN cc_start: 0.7457 (tm-30) cc_final: 0.6869 (tm-30) REVERT: S 140 MET cc_start: 0.7912 (mtp) cc_final: 0.7693 (mtp) outliers start: 1 outliers final: 0 residues processed: 375 average time/residue: 0.0947 time to fit residues: 49.3568 Evaluate side-chains 348 residues out of total 1251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 348 time to evaluate : 0.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 98 optimal weight: 0.5980 chunk 107 optimal weight: 0.2980 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 0.7980 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 0.2980 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 0.8980 chunk 55 optimal weight: 0.6980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 331 ASN B 259 GLN Q 318 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.126979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.103381 restraints weight = 19291.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.106895 restraints weight = 9246.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.109183 restraints weight = 5820.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.110659 restraints weight = 4302.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.111423 restraints weight = 3516.221| |-----------------------------------------------------------------------------| r_work (final): 0.3358 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7463 moved from start: 0.1634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 11798 Z= 0.146 Angle : 0.680 8.793 16018 Z= 0.351 Chirality : 0.043 0.196 1814 Planarity : 0.004 0.060 1995 Dihedral : 7.747 99.611 1646 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.07 % Favored : 94.86 % Rotamer: Outliers : 1.84 % Allowed : 16.17 % Favored : 81.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.80 (0.21), residues: 1439 helix: 0.37 (0.20), residues: 619 sheet: -1.59 (0.31), residues: 280 loop : -2.83 (0.22), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 219 TYR 0.027 0.001 TYR S 235 PHE 0.019 0.002 PHE A 196 TRP 0.013 0.001 TRP S 47 HIS 0.005 0.001 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00308 (11795) covalent geometry : angle 0.67908 (16012) SS BOND : bond 0.01317 ( 3) SS BOND : angle 1.89542 ( 6) hydrogen bonds : bond 0.05086 ( 550) hydrogen bonds : angle 4.75918 ( 1602) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 1251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 341 time to evaluate : 0.449 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 32 ARG cc_start: 0.7853 (ptt-90) cc_final: 0.7617 (ptt-90) REVERT: A 46 LYS cc_start: 0.8671 (ptmt) cc_final: 0.8427 (ptpp) REVERT: A 209 LYS cc_start: 0.8411 (mtpt) cc_final: 0.8149 (mtpt) REVERT: A 231 ASP cc_start: 0.7351 (t70) cc_final: 0.7060 (t70) REVERT: A 242 ARG cc_start: 0.7689 (mtt90) cc_final: 0.7095 (mtt90) REVERT: A 247 MET cc_start: 0.7757 (mtm) cc_final: 0.7464 (mtm) REVERT: A 289 GLU cc_start: 0.7008 (pm20) cc_final: 0.6614 (pm20) REVERT: A 308 GLU cc_start: 0.7573 (tt0) cc_final: 0.7265 (tt0) REVERT: A 345 LYS cc_start: 0.8213 (mtpt) cc_final: 0.7859 (mtpp) REVERT: B 19 ARG cc_start: 0.7714 (ttp-110) cc_final: 0.7398 (ttp-110) REVERT: B 61 MET cc_start: 0.7503 (tmm) cc_final: 0.6904 (tmm) REVERT: B 98 SER cc_start: 0.8298 (m) cc_final: 0.7725 (t) REVERT: B 111 TYR cc_start: 0.8563 (m-80) cc_final: 0.8111 (m-80) REVERT: B 120 ILE cc_start: 0.8336 (pt) cc_final: 0.7782 (mt) REVERT: B 173 THR cc_start: 0.8435 (t) cc_final: 0.8134 (p) REVERT: B 195 ASP cc_start: 0.7679 (t70) cc_final: 0.7356 (t0) REVERT: B 291 ASP cc_start: 0.7559 (t70) cc_final: 0.7188 (t70) REVERT: B 300 LEU cc_start: 0.8227 (mt) cc_final: 0.7820 (mt) REVERT: B 308 LEU cc_start: 0.8124 (mt) cc_final: 0.7923 (mp) REVERT: B 325 MET cc_start: 0.7852 (mtt) cc_final: 0.7631 (mtm) REVERT: B 338 ILE cc_start: 0.8186 (mt) cc_final: 0.7909 (mm) REVERT: C 55 ASN cc_start: 0.7720 (m-40) cc_final: 0.7354 (m-40) REVERT: Q 71 LEU cc_start: 0.8805 (tt) cc_final: 0.8556 (tp) REVERT: Q 107 TYR cc_start: 0.7994 (t80) cc_final: 0.7504 (t80) REVERT: Q 162 MET cc_start: 0.7712 (tpp) cc_final: 0.7203 (mpp) REVERT: Q 179 VAL cc_start: 0.7012 (OUTLIER) cc_final: 0.6583 (t) REVERT: Q 201 LEU cc_start: 0.7911 (tp) cc_final: 0.7676 (tp) REVERT: Q 262 MET cc_start: 0.6271 (tmm) cc_final: 0.6000 (tmm) REVERT: Q 283 PHE cc_start: 0.7135 (t80) cc_final: 0.6651 (t80) REVERT: Q 295 THR cc_start: 0.8392 (t) cc_final: 0.8145 (p) REVERT: Q 304 LEU cc_start: 0.8432 (pp) cc_final: 0.8181 (pp) REVERT: R 46 ASN cc_start: 0.8473 (m-40) cc_final: 0.8254 (m-40) REVERT: R 228 ILE cc_start: 0.8467 (tp) cc_final: 0.8101 (tt) REVERT: R 245 ARG cc_start: 0.7708 (ttt90) cc_final: 0.7462 (ttt90) REVERT: S 3 GLN cc_start: 0.7507 (tm-30) cc_final: 0.6907 (tm-30) REVERT: S 5 VAL cc_start: 0.8301 (OUTLIER) cc_final: 0.8097 (t) REVERT: S 42 GLU cc_start: 0.7096 (mp0) cc_final: 0.6857 (mp0) REVERT: S 213 THR cc_start: 0.8361 (t) cc_final: 0.8042 (p) REVERT: S 230 MET cc_start: 0.7840 (ttp) cc_final: 0.7632 (ttm) outliers start: 23 outliers final: 13 residues processed: 349 average time/residue: 0.0953 time to fit residues: 46.9436 Evaluate side-chains 339 residues out of total 1251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 324 time to evaluate : 0.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 312 LYS Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain Q residue 67 PHE Chi-restraints excluded: chain Q residue 153 LEU Chi-restraints excluded: chain Q residue 179 VAL Chi-restraints excluded: chain R residue 124 SER Chi-restraints excluded: chain R residue 153 LEU Chi-restraints excluded: chain R residue 284 ASP Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 53 SER Chi-restraints excluded: chain S residue 169 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 82 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 chunk 40 optimal weight: 1.9990 chunk 84 optimal weight: 0.9980 chunk 76 optimal weight: 2.9990 chunk 135 optimal weight: 0.7980 chunk 28 optimal weight: 1.9990 chunk 139 optimal weight: 1.9990 chunk 34 optimal weight: 0.0980 chunk 87 optimal weight: 0.7980 chunk 105 optimal weight: 0.8980 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 176 GLN B 259 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.126800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.103022 restraints weight = 19379.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.106554 restraints weight = 9325.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.108853 restraints weight = 5865.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.110290 restraints weight = 4329.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.111113 restraints weight = 3565.643| |-----------------------------------------------------------------------------| r_work (final): 0.3358 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7475 moved from start: 0.1976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 11798 Z= 0.154 Angle : 0.654 7.345 16018 Z= 0.337 Chirality : 0.042 0.197 1814 Planarity : 0.004 0.064 1995 Dihedral : 6.848 65.900 1646 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.25 % Favored : 93.68 % Rotamer: Outliers : 2.96 % Allowed : 19.62 % Favored : 77.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.32 (0.22), residues: 1439 helix: 0.73 (0.20), residues: 622 sheet: -1.34 (0.31), residues: 288 loop : -2.57 (0.23), residues: 529 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 219 TYR 0.025 0.001 TYR S 235 PHE 0.019 0.001 PHE R 78 TRP 0.013 0.001 TRP S 47 HIS 0.005 0.001 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00346 (11795) covalent geometry : angle 0.65278 (16012) SS BOND : bond 0.00815 ( 3) SS BOND : angle 2.09403 ( 6) hydrogen bonds : bond 0.04888 ( 550) hydrogen bonds : angle 4.54871 ( 1602) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 377 residues out of total 1251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 340 time to evaluate : 0.290 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 32 ARG cc_start: 0.7815 (ptt-90) cc_final: 0.7589 (ptt-90) REVERT: A 209 LYS cc_start: 0.8441 (mtpt) cc_final: 0.8202 (mtpt) REVERT: A 231 ASP cc_start: 0.7367 (t70) cc_final: 0.7053 (t0) REVERT: A 242 ARG cc_start: 0.7888 (mtt90) cc_final: 0.7260 (mtt90) REVERT: A 247 MET cc_start: 0.7696 (mtm) cc_final: 0.7440 (mtm) REVERT: A 289 GLU cc_start: 0.7012 (pm20) cc_final: 0.6674 (pm20) REVERT: A 303 ILE cc_start: 0.8017 (tp) cc_final: 0.7769 (tp) REVERT: A 308 GLU cc_start: 0.7618 (tt0) cc_final: 0.7299 (tt0) REVERT: A 345 LYS cc_start: 0.8224 (mtpt) cc_final: 0.7851 (mtpp) REVERT: B 61 MET cc_start: 0.7301 (tmm) cc_final: 0.6816 (tmm) REVERT: B 98 SER cc_start: 0.8303 (m) cc_final: 0.7688 (t) REVERT: B 111 TYR cc_start: 0.8579 (m-80) cc_final: 0.8071 (m-80) REVERT: B 120 ILE cc_start: 0.8336 (pt) cc_final: 0.7749 (mt) REVERT: B 188 MET cc_start: 0.7871 (mmm) cc_final: 0.7408 (mmm) REVERT: B 195 ASP cc_start: 0.7611 (t70) cc_final: 0.7324 (t0) REVERT: B 237 ASN cc_start: 0.7665 (t0) cc_final: 0.7254 (t0) REVERT: B 239 ASN cc_start: 0.8367 (m-40) cc_final: 0.7801 (m-40) REVERT: B 291 ASP cc_start: 0.7684 (t70) cc_final: 0.7258 (t70) REVERT: B 300 LEU cc_start: 0.8201 (mt) cc_final: 0.7727 (mt) REVERT: B 338 ILE cc_start: 0.8129 (mt) cc_final: 0.7877 (mm) REVERT: C 55 ASN cc_start: 0.7686 (m-40) cc_final: 0.7352 (m-40) REVERT: Q 107 TYR cc_start: 0.8004 (t80) cc_final: 0.7540 (t80) REVERT: Q 179 VAL cc_start: 0.7001 (OUTLIER) cc_final: 0.6702 (m) REVERT: Q 201 LEU cc_start: 0.7934 (tp) cc_final: 0.7694 (tp) REVERT: Q 253 LEU cc_start: 0.8519 (mm) cc_final: 0.8300 (mm) REVERT: Q 262 MET cc_start: 0.6328 (tmm) cc_final: 0.5996 (tmm) REVERT: Q 283 PHE cc_start: 0.7171 (t80) cc_final: 0.6658 (t80) REVERT: R 46 ASN cc_start: 0.8471 (m-40) cc_final: 0.8269 (m-40) REVERT: R 55 ARG cc_start: 0.7806 (ttm110) cc_final: 0.6998 (ttm110) REVERT: R 228 ILE cc_start: 0.8492 (tp) cc_final: 0.8179 (tt) REVERT: R 245 ARG cc_start: 0.7698 (ttt90) cc_final: 0.7484 (ttt90) REVERT: S 3 GLN cc_start: 0.7482 (tm-30) cc_final: 0.6821 (tm-30) REVERT: S 42 GLU cc_start: 0.7119 (mp0) cc_final: 0.6876 (mp0) REVERT: S 77 ASN cc_start: 0.8897 (m-40) cc_final: 0.8653 (m-40) REVERT: S 230 MET cc_start: 0.7814 (ttp) cc_final: 0.7590 (ttm) outliers start: 37 outliers final: 22 residues processed: 359 average time/residue: 0.0885 time to fit residues: 45.2698 Evaluate side-chains 354 residues out of total 1251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 331 time to evaluate : 0.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 312 LYS Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain Q residue 67 PHE Chi-restraints excluded: chain Q residue 109 ILE Chi-restraints excluded: chain Q residue 153 LEU Chi-restraints excluded: chain Q residue 179 VAL Chi-restraints excluded: chain R residue 81 THR Chi-restraints excluded: chain R residue 102 CYS Chi-restraints excluded: chain R residue 124 SER Chi-restraints excluded: chain R residue 176 THR Chi-restraints excluded: chain R residue 253 LEU Chi-restraints excluded: chain R residue 284 ASP Chi-restraints excluded: chain S residue 57 THR Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 97 VAL Chi-restraints excluded: chain S residue 168 SER Chi-restraints excluded: chain S residue 169 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 60.4452 > 50: distance: 44 - 61: 16.733 distance: 48 - 72: 11.992 distance: 54 - 83: 11.210 distance: 57 - 61: 17.293 distance: 58 - 94: 16.131 distance: 61 - 62: 4.568 distance: 62 - 63: 7.488 distance: 62 - 65: 28.194 distance: 63 - 64: 7.986 distance: 63 - 72: 16.785 distance: 64 - 102: 38.585 distance: 65 - 66: 25.749 distance: 66 - 67: 33.575 distance: 67 - 68: 6.413 distance: 69 - 71: 10.306 distance: 72 - 73: 15.861 distance: 73 - 74: 19.194 distance: 73 - 76: 20.002 distance: 74 - 75: 13.410 distance: 74 - 83: 24.123 distance: 75 - 110: 22.378 distance: 76 - 77: 26.016 distance: 77 - 78: 16.543 distance: 78 - 79: 24.707 distance: 79 - 80: 16.615 distance: 80 - 81: 24.905 distance: 80 - 82: 32.194 distance: 83 - 84: 13.878 distance: 84 - 85: 9.129 distance: 84 - 87: 26.453 distance: 85 - 86: 4.173 distance: 85 - 94: 15.462 distance: 86 - 116: 31.612 distance: 87 - 88: 29.242 distance: 88 - 89: 8.652 distance: 89 - 90: 24.200 distance: 90 - 91: 26.281 distance: 91 - 92: 25.548 distance: 91 - 93: 38.446 distance: 95 - 96: 4.682 distance: 95 - 98: 25.724 distance: 96 - 97: 43.442 distance: 96 - 102: 19.598 distance: 97 - 124: 21.230 distance: 98 - 99: 14.467 distance: 99 - 100: 34.678 distance: 99 - 101: 12.596 distance: 102 - 103: 30.312 distance: 103 - 104: 6.814 distance: 103 - 106: 19.859 distance: 104 - 105: 11.452 distance: 104 - 110: 27.721 distance: 105 - 132: 23.844 distance: 106 - 107: 40.890 distance: 107 - 108: 28.812 distance: 107 - 109: 15.468 distance: 110 - 111: 11.587 distance: 111 - 112: 9.328 distance: 111 - 114: 13.716 distance: 112 - 113: 20.073 distance: 112 - 116: 9.130 distance: 113 - 139: 22.710 distance: 114 - 115: 11.482 distance: 116 - 117: 12.897 distance: 117 - 118: 9.773 distance: 117 - 120: 22.182 distance: 118 - 119: 16.784 distance: 118 - 124: 10.410 distance: 119 - 146: 17.982 distance: 120 - 121: 7.953 distance: 120 - 122: 23.083 distance: 121 - 123: 33.507 distance: 124 - 125: 18.328 distance: 125 - 126: 9.798 distance: 125 - 128: 3.593 distance: 126 - 127: 14.620 distance: 126 - 132: 19.057 distance: 127 - 153: 17.055 distance: 128 - 129: 8.908 distance: 128 - 130: 27.124 distance: 129 - 131: 19.678 distance: 132 - 133: 12.665 distance: 133 - 134: 13.946 distance: 133 - 136: 10.890 distance: 134 - 135: 7.772 distance: 134 - 139: 30.146 distance: 135 - 159: 17.465 distance: 136 - 137: 36.226 distance: 136 - 138: 12.734 distance: 139 - 140: 10.708 distance: 140 - 141: 29.505 distance: 140 - 143: 13.025 distance: 141 - 142: 13.477 distance: 141 - 146: 18.739 distance: 142 - 164: 29.373 distance: 143 - 144: 33.627 distance: 143 - 145: 26.002 distance: 149 - 170: 3.052