Starting phenix.real_space_refine on Wed Jun 11 06:44:24 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dku_27491/06_2025/8dku_27491.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dku_27491/06_2025/8dku_27491.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8dku_27491/06_2025/8dku_27491.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dku_27491/06_2025/8dku_27491.map" model { file = "/net/cci-nas-00/data/ceres_data/8dku_27491/06_2025/8dku_27491.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dku_27491/06_2025/8dku_27491.cif" } resolution = 3.2 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= 0.000 sd= 0.095 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 2340 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 32 5.16 5 C 7089 2.51 5 N 1666 2.21 5 O 1857 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 79 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 10644 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 3175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 395, 3175 Classifications: {'peptide': 395} Link IDs: {'PTRANS': 12, 'TRANS': 382} Chain: "B" Number of atoms: 2131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 255, 2131 Classifications: {'peptide': 255} Link IDs: {'PTRANS': 11, 'TRANS': 243} Chain: "C" Number of atoms: 3175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 395, 3175 Classifications: {'peptide': 395} Link IDs: {'PTRANS': 12, 'TRANS': 382} Chain: "D" Number of atoms: 2131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 255, 2131 Classifications: {'peptide': 255} Link IDs: {'PTRANS': 11, 'TRANS': 243} Chain: "F" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {'UBH': 1, 'UBO': 1, 'XXR': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 6.77, per 1000 atoms: 0.64 Number of scatterers: 10644 At special positions: 0 Unit cell: (91.8, 100.44, 141.48, 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 32 16.00 O 1857 8.00 N 1666 7.00 C 7089 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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 Links applied ?1-2 " XXR F 1 " - " UBO F 2 " ?1-3 " UBO F 2 " - " UBH F 3 " Time building additional restraints: 2.97 Conformation dependent library (CDL) restraints added in 1.4 seconds 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2416 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 11 sheets defined 49.9% alpha, 15.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.17 Creating SS restraints... Processing helix chain 'A' and resid 17 through 27 removed outlier: 4.451A pdb=" N LEU A 21 " --> pdb=" O PRO A 17 " (cutoff:3.500A) Processing helix chain 'A' and resid 59 through 69 Processing helix chain 'A' and resid 101 through 112 Processing helix chain 'A' and resid 114 through 129 removed outlier: 5.060A pdb=" N GLU A 123 " --> pdb=" O ASP A 119 " (cutoff:3.500A) removed outlier: 5.177A pdb=" N SER A 124 " --> pdb=" O GLU A 120 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N SER A 129 " --> pdb=" O ILE A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 138 through 142 removed outlier: 3.666A pdb=" N THR A 141 " --> pdb=" O PRO A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 157 removed outlier: 3.859A pdb=" N HIS A 157 " --> pdb=" O SER A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 172 removed outlier: 3.953A pdb=" N VAL A 171 " --> pdb=" O ALA A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 190 removed outlier: 3.591A pdb=" N LYS A 179 " --> pdb=" O HIS A 175 " (cutoff:3.500A) Processing helix chain 'A' and resid 200 through 205 removed outlier: 3.727A pdb=" N VAL A 204 " --> pdb=" O ASP A 200 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LYS A 205 " --> pdb=" O MET A 201 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 200 through 205' Processing helix chain 'A' and resid 224 through 239 Processing helix chain 'A' and resid 314 through 318 Processing helix chain 'B' and resid 3 through 18 Processing helix chain 'B' and resid 20 through 26 Processing helix chain 'B' and resid 30 through 43 removed outlier: 3.605A pdb=" N LEU B 41 " --> pdb=" O LEU B 37 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ILE B 42 " --> pdb=" O ILE B 38 " (cutoff:3.500A) Processing helix chain 'B' and resid 57 through 83 removed outlier: 3.608A pdb=" N GLY B 67 " --> pdb=" O TYR B 63 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N PHE B 69 " --> pdb=" O SER B 65 " (cutoff:3.500A) Proline residue: B 70 - end of helix removed outlier: 3.792A pdb=" N ILE B 81 " --> pdb=" O SER B 77 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N GLY B 83 " --> pdb=" O SER B 79 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 88 Processing helix chain 'B' and resid 88 through 93 Processing helix chain 'B' and resid 98 through 100 No H-bonds generated for 'chain 'B' and resid 98 through 100' Processing helix chain 'B' and resid 101 through 129 removed outlier: 3.659A pdb=" N ASN B 113 " --> pdb=" O SER B 109 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ILE B 127 " --> pdb=" O LEU B 123 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N THR B 128 " --> pdb=" O ILE B 124 " (cutoff:3.500A) Processing helix chain 'B' and resid 132 through 137 removed outlier: 4.046A pdb=" N LYS B 135 " --> pdb=" O GLU B 132 " (cutoff:3.500A) Processing helix chain 'B' and resid 139 through 163 removed outlier: 3.712A pdb=" N LEU B 161 " --> pdb=" O VAL B 157 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N VAL B 163 " --> pdb=" O GLY B 159 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 179 removed outlier: 3.746A pdb=" N GLN B 177 " --> pdb=" O GLY B 173 " (cutoff:3.500A) Processing helix chain 'B' and resid 180 through 183 removed outlier: 3.639A pdb=" N THR B 183 " --> pdb=" O PHE B 180 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 180 through 183' Processing helix chain 'B' and resid 188 through 192 removed outlier: 3.860A pdb=" N ILE B 191 " --> pdb=" O THR B 188 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N LEU B 192 " --> pdb=" O LEU B 189 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 188 through 192' Processing helix chain 'B' and resid 195 through 202 removed outlier: 3.803A pdb=" N LEU B 199 " --> pdb=" O PHE B 195 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N TYR B 202 " --> pdb=" O LYS B 198 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 217 Processing helix chain 'B' and resid 223 through 254 Proline residue: B 235 - end of helix removed outlier: 4.633A pdb=" N LYS B 250 " --> pdb=" O LYS B 246 " (cutoff:3.500A) removed outlier: 5.174A pdb=" N ASP B 251 " --> pdb=" O LYS B 247 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 27 removed outlier: 4.173A pdb=" N ARG C 20 " --> pdb=" O LYS C 16 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N LEU C 21 " --> pdb=" O PRO C 17 " (cutoff:3.500A) Processing helix chain 'C' and resid 59 through 69 Processing helix chain 'C' and resid 100 through 102 No H-bonds generated for 'chain 'C' and resid 100 through 102' Processing helix chain 'C' and resid 103 through 112 Processing helix chain 'C' and resid 114 through 130 removed outlier: 5.092A pdb=" N GLU C 123 " --> pdb=" O ASP C 119 " (cutoff:3.500A) removed outlier: 5.253A pdb=" N SER C 124 " --> pdb=" O GLU C 120 " (cutoff:3.500A) Processing helix chain 'C' and resid 138 through 142 Processing helix chain 'C' and resid 143 through 157 Processing helix chain 'C' and resid 167 through 171 removed outlier: 4.141A pdb=" N ALA C 170 " --> pdb=" O GLU C 167 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N VAL C 171 " --> pdb=" O ALA C 168 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 167 through 171' Processing helix chain 'C' and resid 174 through 188 removed outlier: 4.076A pdb=" N LYS C 188 " --> pdb=" O LEU C 184 " (cutoff:3.500A) Processing helix chain 'C' and resid 224 through 240 Processing helix chain 'D' and resid 3 through 18 Processing helix chain 'D' and resid 23 through 43 removed outlier: 3.835A pdb=" N TRP D 27 " --> pdb=" O LEU D 23 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ALA D 28 " --> pdb=" O GLY D 24 " (cutoff:3.500A) removed outlier: 5.156A pdb=" N TRP D 31 " --> pdb=" O TRP D 27 " (cutoff:3.500A) Proline residue: D 32 - end of helix removed outlier: 3.522A pdb=" N LEU D 41 " --> pdb=" O LEU D 37 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ILE D 42 " --> pdb=" O ILE D 38 " (cutoff:3.500A) Processing helix chain 'D' and resid 47 through 51 removed outlier: 3.901A pdb=" N LEU D 51 " --> pdb=" O GLY D 48 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 88 removed outlier: 3.693A pdb=" N GLY D 67 " --> pdb=" O TYR D 63 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N PHE D 69 " --> pdb=" O SER D 65 " (cutoff:3.500A) Proline residue: D 70 - end of helix removed outlier: 3.840A pdb=" N ILE D 81 " --> pdb=" O SER D 77 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N THR D 82 " --> pdb=" O LEU D 78 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N GLY D 83 " --> pdb=" O SER D 79 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N PHE D 85 " --> pdb=" O ILE D 81 " (cutoff:3.500A) removed outlier: 5.300A pdb=" N THR D 86 " --> pdb=" O THR D 82 " (cutoff:3.500A) Processing helix chain 'D' and resid 88 through 93 removed outlier: 4.053A pdb=" N PHE D 92 " --> pdb=" O LYS D 88 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N THR D 93 " --> pdb=" O LYS D 89 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 88 through 93' Processing helix chain 'D' and resid 98 through 100 No H-bonds generated for 'chain 'D' and resid 98 through 100' Processing helix chain 'D' and resid 101 through 129 removed outlier: 3.754A pdb=" N ILE D 112 " --> pdb=" O ILE D 108 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N ASN D 113 " --> pdb=" O SER D 109 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N TYR D 114 " --> pdb=" O GLU D 110 " (cutoff:3.500A) Processing helix chain 'D' and resid 139 through 163 removed outlier: 4.166A pdb=" N ILE D 154 " --> pdb=" O TYR D 150 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLY D 155 " --> pdb=" O SER D 151 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N VAL D 163 " --> pdb=" O GLY D 159 " (cutoff:3.500A) Processing helix chain 'D' and resid 167 through 180 removed outlier: 4.314A pdb=" N GLY D 173 " --> pdb=" O LYS D 169 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N VAL D 174 " --> pdb=" O GLU D 170 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N GLN D 177 " --> pdb=" O GLY D 173 " (cutoff:3.500A) Processing helix chain 'D' and resid 193 through 201 removed outlier: 3.819A pdb=" N LYS D 198 " --> pdb=" O PRO D 194 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N LEU D 199 " --> pdb=" O PHE D 195 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N TYR D 201 " --> pdb=" O LYS D 197 " (cutoff:3.500A) Processing helix chain 'D' and resid 205 through 217 Processing helix chain 'D' and resid 225 through 248 removed outlier: 3.737A pdb=" N GLY D 229 " --> pdb=" O TYR D 225 " (cutoff:3.500A) Proline residue: D 235 - end of helix Processing helix chain 'D' and resid 249 through 256 removed outlier: 4.543A pdb=" N ALA D 256 " --> pdb=" O ILE D 252 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 32 through 40 removed outlier: 3.660A pdb=" N GLU A 32 " --> pdb=" O TYR A 13 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N TYR A 13 " --> pdb=" O GLU A 32 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N LYS A 9 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N LYS A 38 " --> pdb=" O VAL A 7 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N VAL A 7 " --> pdb=" O LYS A 38 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N ILE A 40 " --> pdb=" O PHE A 5 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N PHE A 5 " --> pdb=" O ILE A 40 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 32 through 40 removed outlier: 3.660A pdb=" N GLU A 32 " --> pdb=" O TYR A 13 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N TYR A 13 " --> pdb=" O GLU A 32 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N LYS A 9 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N LYS A 38 " --> pdb=" O VAL A 7 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N VAL A 7 " --> pdb=" O LYS A 38 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N ILE A 40 " --> pdb=" O PHE A 5 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N PHE A 5 " --> pdb=" O ILE A 40 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N VAL A 7 " --> pdb=" O LYS A 75 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N LYS A 75 " --> pdb=" O VAL A 7 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 162 through 165 removed outlier: 6.280A pdb=" N PHE A 163 " --> pdb=" O ILE A 195 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N VAL A 197 " --> pdb=" O PHE A 163 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N ILE A 165 " --> pdb=" O VAL A 197 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N LEU A 50 " --> pdb=" O PHE A 196 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N VAL A 49 " --> pdb=" O ARG A 210 " (cutoff:3.500A) removed outlier: 7.887A pdb=" N ILE A 212 " --> pdb=" O VAL A 49 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N GLY A 51 " --> pdb=" O ILE A 212 " (cutoff:3.500A) removed outlier: 7.522A pdb=" N LEU A 214 " --> pdb=" O GLY A 51 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N VAL A 53 " --> pdb=" O LEU A 214 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N GLU A 221 " --> pdb=" O LEU A 213 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 257 through 259 removed outlier: 4.339A pdb=" N VAL A 286 " --> pdb=" O TYR A 328 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ALA A 288 " --> pdb=" O GLY A 326 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE A 282 " --> pdb=" O PHE A 332 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 257 through 259 removed outlier: 4.339A pdb=" N VAL A 286 " --> pdb=" O TYR A 328 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ALA A 288 " --> pdb=" O GLY A 326 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N LYS A 327 " --> pdb=" O ILE C 394 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 273 through 276 removed outlier: 3.500A pdb=" N ASN A 372 " --> pdb=" O PHE A 274 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N SER A 276 " --> pdb=" O ASN A 372 " (cutoff:3.500A) removed outlier: 5.481A pdb=" N PHE A 374 " --> pdb=" O SER A 276 " (cutoff:3.500A) removed outlier: 8.151A pdb=" N ILE A 363 " --> pdb=" O LEU A 349 " (cutoff:3.500A) removed outlier: 8.243A pdb=" N LEU A 349 " --> pdb=" O ILE A 363 " (cutoff:3.500A) removed outlier: 7.265A pdb=" N ASN A 365 " --> pdb=" O VAL A 347 " (cutoff:3.500A) removed outlier: 8.140A pdb=" N VAL A 347 " --> pdb=" O ASN A 365 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N CYS A 367 " --> pdb=" O LEU A 345 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N ALA A 297 " --> pdb=" O ASN A 313 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N ASN A 313 " --> pdb=" O ALA A 297 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N ILE A 299 " --> pdb=" O GLY A 311 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N GLY A 311 " --> pdb=" O ILE A 299 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N ILE A 301 " --> pdb=" O ILE A 309 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 388 through 392 removed outlier: 3.697A pdb=" N LEU C 329 " --> pdb=" O ARG A 392 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N GLY C 326 " --> pdb=" O ALA C 288 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ALA C 288 " --> pdb=" O GLY C 326 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N THR C 279 " --> pdb=" O SER C 266 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N SER C 266 " --> pdb=" O THR C 279 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N PHE C 281 " --> pdb=" O LEU C 264 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N LEU C 264 " --> pdb=" O PHE C 281 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N GLU C 283 " --> pdb=" O VAL C 262 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N VAL C 262 " --> pdb=" O GLU C 283 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N ASP C 285 " --> pdb=" O LYS C 260 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N GLY C 269 " --> pdb=" O SER C 266 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 43 through 44 removed outlier: 3.528A pdb=" N ILE C 2 " --> pdb=" O ILE C 44 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 84 through 86 removed outlier: 7.313A pdb=" N VAL C 85 " --> pdb=" O ILE C 164 " (cutoff:3.500A) removed outlier: 5.598A pdb=" N PHE C 163 " --> pdb=" O ILE C 195 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N VAL C 197 " --> pdb=" O PHE C 163 " (cutoff:3.500A) removed outlier: 5.869A pdb=" N ILE C 165 " --> pdb=" O VAL C 197 " (cutoff:3.500A) removed outlier: 5.684A pdb=" N LEU C 50 " --> pdb=" O PHE C 196 " (cutoff:3.500A) removed outlier: 7.604A pdb=" N ILE C 212 " --> pdb=" O VAL C 49 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N GLY C 51 " --> pdb=" O ILE C 212 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N GLU C 221 " --> pdb=" O LEU C 213 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 308 through 313 removed outlier: 3.506A pdb=" N GLY C 298 " --> pdb=" O ALA C 348 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 341 through 342 469 hydrogen bonds defined for protein. 1350 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: 3.08 Time building geometry restraints manager: 3.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2806 1.33 - 1.45: 2038 1.45 - 1.57: 6026 1.57 - 1.69: 0 1.69 - 1.81: 52 Bond restraints: 10922 Sorted by residual: bond pdb=" C LYS A 137 " pdb=" N PRO A 138 " ideal model delta sigma weight residual 1.331 1.372 -0.041 1.21e-02 6.83e+03 1.15e+01 bond pdb=" C4 UBO F 2 " pdb=" O4 UBO F 2 " ideal model delta sigma weight residual 1.430 1.367 0.063 2.00e-02 2.50e+03 9.88e+00 bond pdb=" N GLU D 132 " pdb=" CA GLU D 132 " ideal model delta sigma weight residual 1.457 1.489 -0.032 1.16e-02 7.43e+03 7.52e+00 bond pdb=" N ILE B 127 " pdb=" CA ILE B 127 " ideal model delta sigma weight residual 1.462 1.494 -0.032 1.17e-02 7.31e+03 7.35e+00 bond pdb=" N MET C 353 " pdb=" CA MET C 353 " ideal model delta sigma weight residual 1.458 1.488 -0.031 1.19e-02 7.06e+03 6.61e+00 ... (remaining 10917 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.27: 14562 2.27 - 4.54: 177 4.54 - 6.80: 27 6.80 - 9.07: 4 9.07 - 11.34: 3 Bond angle restraints: 14773 Sorted by residual: angle pdb=" N VAL D 22 " pdb=" CA VAL D 22 " pdb=" C VAL D 22 " ideal model delta sigma weight residual 112.96 108.31 4.65 1.00e+00 1.00e+00 2.17e+01 angle pdb=" C LEU B 91 " pdb=" N PHE B 92 " pdb=" CA PHE B 92 " ideal model delta sigma weight residual 122.54 115.64 6.90 1.65e+00 3.67e-01 1.75e+01 angle pdb=" C5 UBO F 2 " pdb=" C4 UBO F 2 " pdb=" O4 UBO F 2 " ideal model delta sigma weight residual 111.37 100.03 11.34 3.00e+00 1.11e-01 1.43e+01 angle pdb=" N ASP A 354 " pdb=" CA ASP A 354 " pdb=" C ASP A 354 " ideal model delta sigma weight residual 109.94 115.80 -5.86 1.57e+00 4.06e-01 1.40e+01 angle pdb=" CA TYR C 360 " pdb=" C TYR C 360 " pdb=" O TYR C 360 " ideal model delta sigma weight residual 120.82 117.09 3.73 1.05e+00 9.07e-01 1.26e+01 ... (remaining 14768 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.78: 5694 16.78 - 33.57: 594 33.57 - 50.35: 108 50.35 - 67.13: 26 67.13 - 83.92: 8 Dihedral angle restraints: 6430 sinusoidal: 2650 harmonic: 3780 Sorted by residual: dihedral pdb=" CA TRP B 26 " pdb=" C TRP B 26 " pdb=" N TRP B 27 " pdb=" CA TRP B 27 " ideal model delta harmonic sigma weight residual 180.00 157.85 22.15 0 5.00e+00 4.00e-02 1.96e+01 dihedral pdb=" CA HIS C 361 " pdb=" C HIS C 361 " pdb=" N TRP C 362 " pdb=" CA TRP C 362 " ideal model delta harmonic sigma weight residual -180.00 -161.19 -18.81 0 5.00e+00 4.00e-02 1.42e+01 dihedral pdb=" CA ASN B 16 " pdb=" C ASN B 16 " pdb=" N ARG B 17 " pdb=" CA ARG B 17 " ideal model delta harmonic sigma weight residual 180.00 162.83 17.17 0 5.00e+00 4.00e-02 1.18e+01 ... (remaining 6427 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 1465 0.070 - 0.139: 189 0.139 - 0.209: 1 0.209 - 0.279: 2 0.279 - 0.349: 2 Chirality restraints: 1659 Sorted by residual: chirality pdb=" C3 UBO F 2 " pdb=" C2 UBO F 2 " pdb=" C4 UBO F 2 " pdb=" O3 UBO F 2 " both_signs ideal model delta sigma weight residual False 2.39 2.74 -0.35 2.00e-01 2.50e+01 3.04e+00 chirality pdb=" C5 UBH F 3 " pdb=" C4 UBH F 3 " pdb=" C6 UBH F 3 " pdb=" O5 UBH F 3 " both_signs ideal model delta sigma weight residual False -2.50 -2.22 -0.29 2.00e-01 2.50e+01 2.07e+00 chirality pdb=" C2 XXR F 1 " pdb=" C1 XXR F 1 " pdb=" C3 XXR F 1 " pdb=" O2 XXR F 1 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.47e+00 ... (remaining 1656 not shown) Planarity restraints: 1814 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS A 28 " -0.032 5.00e-02 4.00e+02 4.98e-02 3.97e+00 pdb=" N PRO A 29 " 0.086 5.00e-02 4.00e+02 pdb=" CA PRO A 29 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 29 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE C 274 " 0.027 5.00e-02 4.00e+02 4.07e-02 2.65e+00 pdb=" N PRO C 275 " -0.070 5.00e-02 4.00e+02 pdb=" CA PRO C 275 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO C 275 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE B 95 " 0.026 5.00e-02 4.00e+02 3.93e-02 2.47e+00 pdb=" N PRO B 96 " -0.068 5.00e-02 4.00e+02 pdb=" CA PRO B 96 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO B 96 " 0.022 5.00e-02 4.00e+02 ... (remaining 1811 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 888 2.74 - 3.28: 10341 3.28 - 3.82: 16866 3.82 - 4.36: 19536 4.36 - 4.90: 35545 Nonbonded interactions: 83176 Sorted by model distance: nonbonded pdb=" OG SER C 114 " pdb=" OE1 GLU C 117 " model vdw 2.201 3.040 nonbonded pdb=" OH TYR A 252 " pdb=" OD2 ASP A 364 " model vdw 2.259 3.040 nonbonded pdb=" O THR D 40 " pdb=" OG SER D 44 " model vdw 2.270 3.040 nonbonded pdb=" OE1 GLU C 186 " pdb=" NZ LYS C 190 " model vdw 2.272 3.120 nonbonded pdb=" O VAL B 36 " pdb=" OG1 THR B 40 " model vdw 2.282 3.040 ... (remaining 83171 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 'A' selection = chain 'C' } ncs_group { reference = chain 'B' selection = chain 'D' } 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: 1.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.070 Construct map_model_manager: 0.010 Extract box with map and model: 0.350 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 27.270 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.050 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:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7562 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 : 0.004 0.063 10924 Z= 0.200 Angle : 0.641 11.341 14779 Z= 0.353 Chirality : 0.045 0.349 1659 Planarity : 0.003 0.050 1814 Dihedral : 14.084 83.918 4014 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.96 % Favored : 94.04 % Rotamer: Outliers : 0.00 % Allowed : 0.69 % Favored : 99.31 % 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: -0.86 (0.24), residues: 1292 helix: 0.60 (0.22), residues: 603 sheet: -0.52 (0.42), residues: 177 loop : -2.02 (0.25), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 26 HIS 0.007 0.001 HIS A 355 PHE 0.020 0.001 PHE B 179 TYR 0.014 0.001 TYR D 63 ARG 0.012 0.001 ARG C 3 Details of bonding type rmsd hydrogen bonds : bond 0.14573 ( 462) hydrogen bonds : angle 5.96974 ( 1350) glycosidic custom : bond 0.04487 ( 2) glycosidic custom : angle 4.40534 ( 6) covalent geometry : bond 0.00392 (10922) covalent geometry : angle 0.63480 (14773) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 206 time to evaluate : 1.274 Fit side-chains revert: symmetry clash REVERT: A 119 ASP cc_start: 0.7826 (m-30) cc_final: 0.7459 (m-30) REVERT: B 11 ARG cc_start: 0.7711 (mtm110) cc_final: 0.6667 (mmt180) REVERT: B 13 GLU cc_start: 0.7440 (tp30) cc_final: 0.7165 (tp30) REVERT: C 263 ARG cc_start: 0.7399 (mtm110) cc_final: 0.7012 (mtm110) REVERT: D 110 GLU cc_start: 0.7595 (tp30) cc_final: 0.7225 (tp30) outliers start: 0 outliers final: 0 residues processed: 206 average time/residue: 0.2555 time to fit residues: 72.4601 Evaluate side-chains 162 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 162 time to evaluate : 1.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 108 optimal weight: 2.9990 chunk 97 optimal weight: 3.9990 chunk 53 optimal weight: 0.9990 chunk 33 optimal weight: 4.9990 chunk 65 optimal weight: 2.9990 chunk 51 optimal weight: 0.0030 chunk 100 optimal weight: 3.9990 chunk 38 optimal weight: 0.5980 chunk 61 optimal weight: 0.8980 chunk 74 optimal weight: 10.0000 chunk 116 optimal weight: 0.0770 overall best weight: 0.5150 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 372 ASN C 215 HIS D 16 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4204 r_free = 0.4204 target = 0.192540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.132395 restraints weight = 12611.835| |-----------------------------------------------------------------------------| r_work (start): 0.3589 rms_B_bonded: 2.58 r_work: 0.3421 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3421 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7676 moved from start: 0.1158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10924 Z= 0.117 Angle : 0.546 10.262 14779 Z= 0.282 Chirality : 0.042 0.161 1659 Planarity : 0.004 0.038 1814 Dihedral : 4.101 23.537 1456 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 0.69 % Allowed : 8.53 % Favored : 90.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.24), residues: 1292 helix: 0.91 (0.22), residues: 599 sheet: -0.36 (0.43), residues: 175 loop : -1.95 (0.25), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 26 HIS 0.004 0.001 HIS C 268 PHE 0.031 0.001 PHE B 92 TYR 0.019 0.001 TYR C 384 ARG 0.003 0.000 ARG C 27 Details of bonding type rmsd hydrogen bonds : bond 0.03953 ( 462) hydrogen bonds : angle 4.61290 ( 1350) glycosidic custom : bond 0.00006 ( 2) glycosidic custom : angle 1.65474 ( 6) covalent geometry : bond 0.00267 (10922) covalent geometry : angle 0.54518 (14773) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 184 time to evaluate : 1.150 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 119 ASP cc_start: 0.7829 (m-30) cc_final: 0.7437 (m-30) REVERT: A 122 LEU cc_start: 0.7264 (tt) cc_final: 0.6948 (tp) REVERT: A 273 ASN cc_start: 0.8434 (t0) cc_final: 0.8116 (t0) REVERT: A 372 ASN cc_start: 0.7705 (OUTLIER) cc_final: 0.7366 (p0) REVERT: B 11 ARG cc_start: 0.7800 (mtm110) cc_final: 0.6497 (mmt180) REVERT: C 117 GLU cc_start: 0.8627 (mp0) cc_final: 0.8297 (mp0) REVERT: C 128 PHE cc_start: 0.7247 (t80) cc_final: 0.7032 (t80) REVERT: C 190 LYS cc_start: 0.7785 (mtmm) cc_final: 0.7021 (pptt) REVERT: C 289 LYS cc_start: 0.7288 (mmtm) cc_final: 0.7004 (mmtm) REVERT: D 110 GLU cc_start: 0.8053 (tp30) cc_final: 0.7640 (tp30) outliers start: 8 outliers final: 4 residues processed: 189 average time/residue: 0.2319 time to fit residues: 62.1367 Evaluate side-chains 174 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 169 time to evaluate : 1.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 372 ASN Chi-restraints excluded: chain B residue 25 ILE Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain C residue 19 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 94 optimal weight: 2.9990 chunk 119 optimal weight: 0.8980 chunk 59 optimal weight: 1.9990 chunk 124 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 85 optimal weight: 2.9990 chunk 41 optimal weight: 4.9990 chunk 18 optimal weight: 0.7980 chunk 68 optimal weight: 7.9990 chunk 58 optimal weight: 0.0870 chunk 25 optimal weight: 0.4980 overall best weight: 0.8560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 16 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.190830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.130540 restraints weight = 12864.628| |-----------------------------------------------------------------------------| r_work (start): 0.3570 rms_B_bonded: 2.61 r_work: 0.3400 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3400 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7705 moved from start: 0.1409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10924 Z= 0.135 Angle : 0.529 10.347 14779 Z= 0.276 Chirality : 0.042 0.160 1659 Planarity : 0.003 0.038 1814 Dihedral : 4.037 21.841 1456 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 1.38 % Allowed : 11.55 % Favored : 87.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.24), residues: 1292 helix: 0.99 (0.22), residues: 600 sheet: -0.28 (0.43), residues: 175 loop : -1.90 (0.25), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 26 HIS 0.004 0.001 HIS C 268 PHE 0.027 0.001 PHE B 92 TYR 0.022 0.001 TYR D 243 ARG 0.004 0.000 ARG B 17 Details of bonding type rmsd hydrogen bonds : bond 0.03907 ( 462) hydrogen bonds : angle 4.39102 ( 1350) glycosidic custom : bond 0.00066 ( 2) glycosidic custom : angle 1.49773 ( 6) covalent geometry : bond 0.00324 (10922) covalent geometry : angle 0.52853 (14773) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 169 time to evaluate : 1.089 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 ASP cc_start: 0.7983 (m-30) cc_final: 0.7532 (m-30) REVERT: A 122 LEU cc_start: 0.7359 (tt) cc_final: 0.7148 (tp) REVERT: A 274 PHE cc_start: 0.8086 (m-10) cc_final: 0.7853 (m-10) REVERT: B 8 GLU cc_start: 0.8090 (mm-30) cc_final: 0.7699 (tp30) REVERT: B 11 ARG cc_start: 0.7793 (mtm110) cc_final: 0.6475 (mmt180) REVERT: B 224 LEU cc_start: 0.8029 (OUTLIER) cc_final: 0.7729 (mp) REVERT: C 16 LYS cc_start: 0.7009 (tttt) cc_final: 0.6800 (tttp) REVERT: C 117 GLU cc_start: 0.8446 (mp0) cc_final: 0.8180 (mp0) REVERT: C 182 ARG cc_start: 0.8465 (ptm-80) cc_final: 0.7962 (ptt-90) REVERT: C 190 LYS cc_start: 0.7757 (mtmm) cc_final: 0.7009 (pptt) REVERT: C 236 MET cc_start: 0.7730 (ttp) cc_final: 0.7339 (tpp) REVERT: C 289 LYS cc_start: 0.7275 (mmtm) cc_final: 0.6883 (mmtm) REVERT: D 110 GLU cc_start: 0.8131 (tp30) cc_final: 0.7693 (tp30) outliers start: 16 outliers final: 10 residues processed: 176 average time/residue: 0.2332 time to fit residues: 58.9747 Evaluate side-chains 174 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 163 time to evaluate : 1.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 353 MET Chi-restraints excluded: chain B residue 16 ASN Chi-restraints excluded: chain B residue 25 ILE Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 195 PHE Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain C residue 21 LEU Chi-restraints excluded: chain C residue 140 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 19 optimal weight: 3.9990 chunk 36 optimal weight: 4.9990 chunk 34 optimal weight: 0.7980 chunk 68 optimal weight: 7.9990 chunk 28 optimal weight: 6.9990 chunk 45 optimal weight: 0.9990 chunk 109 optimal weight: 0.9980 chunk 14 optimal weight: 10.0000 chunk 81 optimal weight: 10.0000 chunk 97 optimal weight: 4.9990 chunk 86 optimal weight: 10.0000 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 372 ASN B 53 HIS B 177 GLN C 215 HIS C 268 HIS D 16 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.184391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.123346 restraints weight = 12821.373| |-----------------------------------------------------------------------------| r_work (start): 0.3487 rms_B_bonded: 2.56 r_work: 0.3312 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3312 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.1835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.069 10924 Z= 0.281 Angle : 0.653 11.831 14779 Z= 0.336 Chirality : 0.046 0.153 1659 Planarity : 0.004 0.045 1814 Dihedral : 4.533 21.102 1456 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.58 % Favored : 93.42 % Rotamer: Outliers : 2.50 % Allowed : 13.10 % Favored : 84.40 % 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: -0.91 (0.23), residues: 1292 helix: 0.47 (0.22), residues: 600 sheet: -0.74 (0.40), residues: 188 loop : -1.84 (0.25), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP B 26 HIS 0.005 0.001 HIS C 268 PHE 0.029 0.002 PHE B 180 TYR 0.022 0.002 TYR D 243 ARG 0.003 0.000 ARG D 166 Details of bonding type rmsd hydrogen bonds : bond 0.05300 ( 462) hydrogen bonds : angle 4.57383 ( 1350) glycosidic custom : bond 0.00329 ( 2) glycosidic custom : angle 1.64027 ( 6) covalent geometry : bond 0.00698 (10922) covalent geometry : angle 0.65193 (14773) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2584 Ramachandran restraints generated. 1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 171 time to evaluate : 1.502 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 PHE cc_start: 0.7845 (m-80) cc_final: 0.7445 (m-80) REVERT: A 119 ASP cc_start: 0.8063 (m-30) cc_final: 0.7817 (m-30) REVERT: A 372 ASN cc_start: 0.7689 (OUTLIER) cc_final: 0.7470 (p0) REVERT: B 8 GLU cc_start: 0.7987 (mm-30) cc_final: 0.7641 (tp30) REVERT: B 13 GLU cc_start: 0.7977 (tp30) cc_final: 0.7677 (tp30) REVERT: C 117 GLU cc_start: 0.8501 (mp0) cc_final: 0.8120 (mp0) REVERT: C 190 LYS cc_start: 0.7810 (mtmm) cc_final: 0.7006 (pptt) REVERT: C 236 MET cc_start: 0.7705 (ttp) cc_final: 0.7288 (tpp) REVERT: C 255 PHE cc_start: 0.8784 (m-80) cc_final: 0.8503 (m-80) REVERT: C 289 LYS cc_start: 0.7401 (mmtm) cc_final: 0.6881 (mmtm) REVERT: D 110 GLU cc_start: 0.8304 (tp30) cc_final: 0.7839 (tp30) outliers start: 29 outliers final: 21 residues processed: 189 average time/residue: 0.2442 time to fit residues: 65.7362 Evaluate side-chains 180 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 158 time to evaluate : 1.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 353 MET Chi-restraints excluded: chain A residue 372 ASN Chi-restraints excluded: chain B residue 16 ASN Chi-restraints excluded: chain B residue 25 ILE Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 118 ILE Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 175 PHE Chi-restraints excluded: chain B residue 195 PHE Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain C residue 21 LEU Chi-restraints excluded: chain C residue 140 LYS Chi-restraints excluded: chain C residue 180 CYS Chi-restraints excluded: chain C residue 299 ILE Chi-restraints excluded: chain C residue 331 THR Chi-restraints excluded: chain D residue 68 ILE Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain D residue 174 VAL Chi-restraints excluded: chain D residue 186 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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-5710/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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-5710/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-5710/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-5710/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-5710/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-5710/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-5710/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-5710/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-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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-5710/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-5710/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-5710/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-5710/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: 51.6521 > 50: distance: 38 - 47: 3.010 distance: 68 - 88: 5.560 distance: 74 - 100: 12.075 distance: 77 - 82: 4.731 distance: 78 - 112: 5.283 distance: 82 - 83: 4.514 distance: 83 - 84: 7.243 distance: 83 - 86: 14.037 distance: 84 - 85: 10.331 distance: 84 - 88: 3.030 distance: 85 - 123: 20.820 distance: 86 - 87: 3.648 distance: 88 - 89: 6.196 distance: 89 - 90: 8.276 distance: 90 - 91: 11.056 distance: 90 - 100: 11.073 distance: 91 - 134: 19.080 distance: 92 - 93: 5.069 distance: 93 - 94: 5.329 distance: 93 - 95: 5.587 distance: 94 - 96: 3.705 distance: 95 - 97: 4.753 distance: 97 - 98: 4.856 distance: 98 - 99: 6.953 distance: 100 - 101: 6.070 distance: 101 - 102: 11.779 distance: 101 - 104: 3.567 distance: 102 - 103: 5.105 distance: 102 - 112: 4.290 distance: 103 - 143: 18.731 distance: 105 - 106: 7.729 distance: 105 - 107: 7.512 distance: 106 - 108: 5.617 distance: 108 - 110: 6.662 distance: 109 - 110: 3.508 distance: 110 - 111: 3.591 distance: 112 - 113: 4.232 distance: 113 - 114: 5.525 distance: 113 - 116: 11.292 distance: 114 - 115: 11.043 distance: 114 - 123: 3.825 distance: 115 - 152: 13.789 distance: 116 - 117: 16.908 distance: 117 - 118: 16.009 distance: 117 - 119: 14.044 distance: 118 - 120: 9.135 distance: 119 - 121: 8.854 distance: 120 - 122: 4.204 distance: 121 - 122: 17.174 distance: 123 - 124: 11.115 distance: 124 - 125: 8.452 distance: 124 - 127: 11.664 distance: 125 - 126: 3.283 distance: 125 - 134: 8.352 distance: 127 - 128: 8.349 distance: 128 - 129: 7.486 distance: 128 - 130: 5.898 distance: 129 - 131: 7.924 distance: 130 - 132: 9.192 distance: 131 - 133: 5.952 distance: 132 - 133: 7.237 distance: 134 - 135: 6.989 distance: 135 - 136: 3.148 distance: 135 - 138: 4.988 distance: 136 - 137: 5.578 distance: 138 - 139: 16.012 distance: 139 - 140: 5.638 distance: 140 - 141: 5.011 distance: 143 - 144: 13.208 distance: 144 - 145: 16.506 distance: 144 - 147: 15.734 distance: 145 - 146: 18.434 distance: 145 - 152: 14.080 distance: 147 - 148: 10.080 distance: 148 - 149: 18.865 distance: 149 - 150: 25.006 distance: 150 - 151: 4.990 distance: 152 - 153: 19.698 distance: 153 - 154: 27.852 distance: 153 - 156: 20.662 distance: 154 - 155: 37.640 distance: 154 - 160: 38.566 distance: 156 - 157: 8.061 distance: 157 - 158: 14.624 distance: 157 - 159: 28.103 distance: 160 - 161: 20.087 distance: 161 - 162: 11.717 distance: 161 - 164: 8.407 distance: 162 - 163: 5.761 distance: 162 - 169: 8.328 distance: 163 - 193: 10.757 distance: 164 - 165: 18.358 distance: 165 - 166: 17.903 distance: 166 - 167: 8.638 distance: 166 - 168: 6.580 distance: 169 - 170: 7.002 distance: 170 - 171: 5.708 distance: 170 - 173: 8.581 distance: 171 - 172: 8.293 distance: 171 - 178: 7.544 distance: 172 - 202: 7.613 distance: 173 - 174: 7.607 distance: 175 - 176: 8.125 distance: 176 - 177: 9.196