Starting phenix.real_space_refine on Wed Feb 4 14:07:32 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ns5_49743/02_2026/9ns5_49743.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ns5_49743/02_2026/9ns5_49743.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.19 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9ns5_49743/02_2026/9ns5_49743.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ns5_49743/02_2026/9ns5_49743.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ns5_49743/02_2026/9ns5_49743.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ns5_49743/02_2026/9ns5_49743.map" } resolution = 3.19 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= 0.019 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 1 6.06 5 P 6 5.49 5 Mg 2 5.21 5 S 52 5.16 5 C 6986 2.51 5 N 1766 2.21 5 O 2088 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10901 Number of models: 1 Model: "" Number of chains: 8 Chain: "C" Number of atoms: 386 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 386 Classifications: {'peptide': 48} Link IDs: {'PTRANS': 6, 'TRANS': 41} Chain: "F" Number of atoms: 386 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 386 Classifications: {'peptide': 48} Link IDs: {'PTRANS': 6, 'TRANS': 41} Chain: "A" Number of atoms: 2560 Number of conformers: 1 Conformer: "" Number of residues, atoms: 326, 2560 Classifications: {'peptide': 326} Link IDs: {'PTRANS': 11, 'TRANS': 314} Chain breaks: 1 Chain: "B" Number of atoms: 2472 Number of conformers: 1 Conformer: "" Number of residues, atoms: 298, 2472 Classifications: {'peptide': 298} Link IDs: {'PTRANS': 5, 'TRANS': 292} Chain: "D" Number of atoms: 2560 Number of conformers: 1 Conformer: "" Number of residues, atoms: 326, 2560 Classifications: {'peptide': 326} Link IDs: {'PTRANS': 11, 'TRANS': 314} Chain breaks: 1 Chain: "E" Number of atoms: 2472 Number of conformers: 1 Conformer: "" Number of residues, atoms: 298, 2472 Classifications: {'peptide': 298} Link IDs: {'PTRANS': 5, 'TRANS': 292} Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, ' ZN': 1, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2775 SG CYS A 285 38.114 72.520 92.246 1.00 77.71 S ATOM 2801 SG CYS A 288 37.317 73.088 88.575 1.00 66.76 S ATOM 7807 SG CYS D 285 39.730 75.752 91.320 1.00 78.47 S Time building chain proxies: 2.48, per 1000 atoms: 0.23 Number of scatterers: 10901 At special positions: 0 Unit cell: (75.9375, 148.838, 105.3, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 1 29.99 S 52 16.00 P 6 15.00 Mg 2 11.99 O 2088 8.00 N 1766 7.00 C 6986 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 Time building additional restraints: 0.69 Conformation dependent library (CDL) restraints added in 451.2 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 401 " pdb="ZN ZN A 401 " - pdb=" SG CYS A 288 " pdb="ZN ZN A 401 " - pdb=" SG CYS A 285 " pdb="ZN ZN A 401 " - pdb=" SG CYS D 285 " 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2544 Finding SS restraints... Secondary structure from input PDB file: 56 helices and 4 sheets defined 64.5% alpha, 7.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.35 Creating SS restraints... Processing helix chain 'C' and resid 7 through 21 removed outlier: 4.013A pdb=" N GLU C 11 " --> pdb=" O GLY C 7 " (cutoff:3.500A) Processing helix chain 'C' and resid 34 through 38 Processing helix chain 'F' and resid 8 through 21 Processing helix chain 'F' and resid 34 through 38 Processing helix chain 'A' and resid 9 through 14 Processing helix chain 'A' and resid 30 through 46 Processing helix chain 'A' and resid 61 through 67 Processing helix chain 'A' and resid 128 through 132 removed outlier: 3.562A pdb=" N SER A 132 " --> pdb=" O ASP A 128 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 128 through 132' Processing helix chain 'A' and resid 135 through 155 Processing helix chain 'A' and resid 169 through 205 Proline residue: A 180 - end of helix Proline residue: A 199 - end of helix Processing helix chain 'A' and resid 211 through 231 Processing helix chain 'A' and resid 245 through 263 Processing helix chain 'A' and resid 285 through 306 removed outlier: 4.245A pdb=" N TRP A 292 " --> pdb=" O CYS A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 336 removed outlier: 4.666A pdb=" N PHE A 333 " --> pdb=" O LYS A 329 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N LEU A 334 " --> pdb=" O PHE A 330 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ASN A 335 " --> pdb=" O SER A 331 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LYS A 336 " --> pdb=" O GLN A 332 " (cutoff:3.500A) Processing helix chain 'B' and resid 13 through 27 Processing helix chain 'B' and resid 28 through 46 Processing helix chain 'B' and resid 48 through 66 removed outlier: 3.513A pdb=" N ALA B 52 " --> pdb=" O SER B 48 " (cutoff:3.500A) Processing helix chain 'B' and resid 68 through 87 Processing helix chain 'B' and resid 91 through 105 removed outlier: 3.599A pdb=" N LEU B 98 " --> pdb=" O SER B 94 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LEU B 101 " --> pdb=" O ARG B 97 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 126 Processing helix chain 'B' and resid 133 through 147 removed outlier: 3.691A pdb=" N THR B 139 " --> pdb=" O TYR B 135 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N SER B 142 " --> pdb=" O ASN B 138 " (cutoff:3.500A) Processing helix chain 'B' and resid 149 through 158 removed outlier: 3.796A pdb=" N ARG B 155 " --> pdb=" O TYR B 151 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N TYR B 156 " --> pdb=" O GLU B 152 " (cutoff:3.500A) Processing helix chain 'B' and resid 161 through 179 removed outlier: 3.654A pdb=" N VAL B 179 " --> pdb=" O TRP B 175 " (cutoff:3.500A) Processing helix chain 'B' and resid 185 through 201 removed outlier: 3.792A pdb=" N ARG B 193 " --> pdb=" O GLU B 189 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU B 194 " --> pdb=" O PHE B 190 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N TYR B 198 " --> pdb=" O LEU B 194 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ILE B 201 " --> pdb=" O ASN B 197 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 222 Processing helix chain 'B' and resid 242 through 258 removed outlier: 3.923A pdb=" N ASN B 246 " --> pdb=" O TYR B 242 " (cutoff:3.500A) Processing helix chain 'B' and resid 259 through 270 removed outlier: 3.534A pdb=" N PHE B 263 " --> pdb=" O ASP B 259 " (cutoff:3.500A) Processing helix chain 'B' and resid 270 through 277 Processing helix chain 'B' and resid 277 through 289 Processing helix chain 'B' and resid 298 through 307 Processing helix chain 'D' and resid 9 through 14 Processing helix chain 'D' and resid 30 through 46 Processing helix chain 'D' and resid 61 through 67 Processing helix chain 'D' and resid 128 through 132 removed outlier: 3.561A pdb=" N SER D 132 " --> pdb=" O ASP D 128 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 128 through 132' Processing helix chain 'D' and resid 135 through 155 Processing helix chain 'D' and resid 169 through 205 Proline residue: D 180 - end of helix Proline residue: D 199 - end of helix Processing helix chain 'D' and resid 211 through 231 Processing helix chain 'D' and resid 245 through 263 Processing helix chain 'D' and resid 285 through 306 removed outlier: 3.884A pdb=" N TRP D 292 " --> pdb=" O CYS D 288 " (cutoff:3.500A) Processing helix chain 'D' and resid 323 through 336 removed outlier: 4.666A pdb=" N PHE D 333 " --> pdb=" O LYS D 329 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N LEU D 334 " --> pdb=" O PHE D 330 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ASN D 335 " --> pdb=" O SER D 331 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LYS D 336 " --> pdb=" O GLN D 332 " (cutoff:3.500A) Processing helix chain 'E' and resid 13 through 27 Processing helix chain 'E' and resid 28 through 46 Processing helix chain 'E' and resid 48 through 66 removed outlier: 3.514A pdb=" N ALA E 52 " --> pdb=" O SER E 48 " (cutoff:3.500A) Processing helix chain 'E' and resid 68 through 87 Processing helix chain 'E' and resid 91 through 105 removed outlier: 3.599A pdb=" N LEU E 98 " --> pdb=" O SER E 94 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LEU E 101 " --> pdb=" O ARG E 97 " (cutoff:3.500A) Processing helix chain 'E' and resid 111 through 126 Processing helix chain 'E' and resid 133 through 147 removed outlier: 3.689A pdb=" N THR E 139 " --> pdb=" O TYR E 135 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N SER E 142 " --> pdb=" O ASN E 138 " (cutoff:3.500A) Processing helix chain 'E' and resid 149 through 158 removed outlier: 3.796A pdb=" N ARG E 155 " --> pdb=" O TYR E 151 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N TYR E 156 " --> pdb=" O GLU E 152 " (cutoff:3.500A) Processing helix chain 'E' and resid 161 through 179 removed outlier: 3.654A pdb=" N VAL E 179 " --> pdb=" O TRP E 175 " (cutoff:3.500A) Processing helix chain 'E' and resid 185 through 201 removed outlier: 3.792A pdb=" N ARG E 193 " --> pdb=" O GLU E 189 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU E 194 " --> pdb=" O PHE E 190 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N TYR E 198 " --> pdb=" O LEU E 194 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ILE E 201 " --> pdb=" O ASN E 197 " (cutoff:3.500A) Processing helix chain 'E' and resid 203 through 222 Processing helix chain 'E' and resid 242 through 258 removed outlier: 3.922A pdb=" N ASN E 246 " --> pdb=" O TYR E 242 " (cutoff:3.500A) Processing helix chain 'E' and resid 259 through 270 removed outlier: 3.534A pdb=" N PHE E 263 " --> pdb=" O ASP E 259 " (cutoff:3.500A) Processing helix chain 'E' and resid 270 through 277 Processing helix chain 'E' and resid 277 through 289 Processing helix chain 'E' and resid 298 through 307 Processing sheet with id=AA1, first strand: chain 'A' and resid 75 through 76 removed outlier: 6.489A pdb=" N PHE A 51 " --> pdb=" O SER A 84 " (cutoff:3.500A) removed outlier: 7.960A pdb=" N MET A 86 " --> pdb=" O PHE A 51 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N LEU A 53 " --> pdb=" O MET A 86 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N LEU A 52 " --> pdb=" O ILE A 164 " (cutoff:3.500A) removed outlier: 7.715A pdb=" N ASP A 166 " --> pdb=" O LEU A 52 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N ILE A 54 " --> pdb=" O ASP A 166 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N ILE A 21 " --> pdb=" O PHE A 165 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N TRP A 20 " --> pdb=" O THR A 237 " (cutoff:3.500A) removed outlier: 8.024A pdb=" N VAL A 239 " --> pdb=" O TRP A 20 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N PHE A 22 " --> pdb=" O VAL A 239 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N VAL A 241 " --> pdb=" O PHE A 22 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N GLY A 24 " --> pdb=" O VAL A 241 " (cutoff:3.500A) removed outlier: 8.685A pdb=" N ILE A 243 " --> pdb=" O GLY A 24 " (cutoff:3.500A) removed outlier: 11.478A pdb=" N THR A 236 " --> pdb=" O VAL A 266 " (cutoff:3.500A) removed outlier: 9.569A pdb=" N SER A 268 " --> pdb=" O THR A 236 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N PHE A 238 " --> pdb=" O SER A 268 " (cutoff:3.500A) removed outlier: 8.077A pdb=" N ILE A 270 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N CYS A 240 " --> pdb=" O ILE A 270 " (cutoff:3.500A) removed outlier: 7.288A pdb=" N ASN A 272 " --> pdb=" O CYS A 240 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N CYS A 242 " --> pdb=" O ASN A 272 " (cutoff:3.500A) removed outlier: 7.255A pdb=" N LEU A 274 " --> pdb=" O CYS A 242 " (cutoff:3.500A) removed outlier: 7.493A pdb=" N ASN A 267 " --> pdb=" O HIS A 310 " (cutoff:3.500A) removed outlier: 7.956A pdb=" N VAL A 312 " --> pdb=" O ASN A 267 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N ILE A 269 " --> pdb=" O VAL A 312 " (cutoff:3.500A) removed outlier: 7.588A pdb=" N MET A 314 " --> pdb=" O ILE A 269 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N VAL A 271 " --> pdb=" O MET A 314 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 226 through 231 Processing sheet with id=AA3, first strand: chain 'D' and resid 75 through 76 removed outlier: 6.487A pdb=" N PHE D 51 " --> pdb=" O SER D 84 " (cutoff:3.500A) removed outlier: 7.960A pdb=" N MET D 86 " --> pdb=" O PHE D 51 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N LEU D 53 " --> pdb=" O MET D 86 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N LEU D 52 " --> pdb=" O ILE D 164 " (cutoff:3.500A) removed outlier: 7.714A pdb=" N ASP D 166 " --> pdb=" O LEU D 52 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N ILE D 54 " --> pdb=" O ASP D 166 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N ILE D 21 " --> pdb=" O PHE D 165 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N TRP D 20 " --> pdb=" O THR D 237 " (cutoff:3.500A) removed outlier: 8.024A pdb=" N VAL D 239 " --> pdb=" O TRP D 20 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N PHE D 22 " --> pdb=" O VAL D 239 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N VAL D 241 " --> pdb=" O PHE D 22 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N GLY D 24 " --> pdb=" O VAL D 241 " (cutoff:3.500A) removed outlier: 8.683A pdb=" N ILE D 243 " --> pdb=" O GLY D 24 " (cutoff:3.500A) removed outlier: 11.478A pdb=" N THR D 236 " --> pdb=" O VAL D 266 " (cutoff:3.500A) removed outlier: 9.570A pdb=" N SER D 268 " --> pdb=" O THR D 236 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N PHE D 238 " --> pdb=" O SER D 268 " (cutoff:3.500A) removed outlier: 8.078A pdb=" N ILE D 270 " --> pdb=" O PHE D 238 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N CYS D 240 " --> pdb=" O ILE D 270 " (cutoff:3.500A) removed outlier: 7.293A pdb=" N ASN D 272 " --> pdb=" O CYS D 240 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N CYS D 242 " --> pdb=" O ASN D 272 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N LEU D 274 " --> pdb=" O CYS D 242 " (cutoff:3.500A) removed outlier: 7.495A pdb=" N ASN D 267 " --> pdb=" O HIS D 310 " (cutoff:3.500A) removed outlier: 7.955A pdb=" N VAL D 312 " --> pdb=" O ASN D 267 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N ILE D 269 " --> pdb=" O VAL D 312 " (cutoff:3.500A) removed outlier: 7.587A pdb=" N MET D 314 " --> pdb=" O ILE D 269 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N VAL D 271 " --> pdb=" O MET D 314 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 226 through 231 608 hydrogen bonds defined for protein. 1800 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: 1.59 Time building geometry restraints manager: 0.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 3478 1.35 - 1.47: 2625 1.47 - 1.59: 4941 1.59 - 1.72: 0 1.72 - 1.84: 86 Bond restraints: 11130 Sorted by residual: bond pdb=" N ASN A 284 " pdb=" CA ASN A 284 " ideal model delta sigma weight residual 1.457 1.491 -0.034 1.29e-02 6.01e+03 6.75e+00 bond pdb=" N TYR F 50 " pdb=" CA TYR F 50 " ideal model delta sigma weight residual 1.454 1.483 -0.029 1.17e-02 7.31e+03 6.27e+00 bond pdb=" N LYS C 49 " pdb=" CA LYS C 49 " ideal model delta sigma weight residual 1.458 1.484 -0.027 1.12e-02 7.97e+03 5.69e+00 bond pdb=" N LYS F 51 " pdb=" CA LYS F 51 " ideal model delta sigma weight residual 1.458 1.485 -0.027 1.16e-02 7.43e+03 5.56e+00 bond pdb=" N LYS F 53 " pdb=" CA LYS F 53 " ideal model delta sigma weight residual 1.461 1.483 -0.022 9.70e-03 1.06e+04 5.20e+00 ... (remaining 11125 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.74: 14755 1.74 - 3.48: 239 3.48 - 5.22: 33 5.22 - 6.96: 4 6.96 - 8.69: 7 Bond angle restraints: 15038 Sorted by residual: angle pdb=" CB GLU A 282 " pdb=" CG GLU A 282 " pdb=" CD GLU A 282 " ideal model delta sigma weight residual 112.60 120.65 -8.05 1.70e+00 3.46e-01 2.24e+01 angle pdb=" CB GLU D 282 " pdb=" CG GLU D 282 " pdb=" CD GLU D 282 " ideal model delta sigma weight residual 112.60 120.63 -8.03 1.70e+00 3.46e-01 2.23e+01 angle pdb=" CA LYS A 286 " pdb=" C LYS A 286 " pdb=" O LYS A 286 " ideal model delta sigma weight residual 120.92 116.60 4.32 1.12e+00 7.97e-01 1.49e+01 angle pdb=" CA CYS A 285 " pdb=" CB CYS A 285 " pdb=" SG CYS A 285 " ideal model delta sigma weight residual 114.40 105.71 8.69 2.30e+00 1.89e-01 1.43e+01 angle pdb=" N LYS C 49 " pdb=" CA LYS C 49 " pdb=" C LYS C 49 " ideal model delta sigma weight residual 112.97 109.60 3.37 1.06e+00 8.90e-01 1.01e+01 ... (remaining 15033 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.91: 5580 17.91 - 35.82: 825 35.82 - 53.73: 225 53.73 - 71.64: 65 71.64 - 89.55: 25 Dihedral angle restraints: 6720 sinusoidal: 2784 harmonic: 3936 Sorted by residual: dihedral pdb=" CA LYS D 26 " pdb=" C LYS D 26 " pdb=" N GLY D 27 " pdb=" CA GLY D 27 " ideal model delta harmonic sigma weight residual 180.00 157.12 22.88 0 5.00e+00 4.00e-02 2.09e+01 dihedral pdb=" CA LYS A 26 " pdb=" C LYS A 26 " pdb=" N GLY A 27 " pdb=" CA GLY A 27 " ideal model delta harmonic sigma weight residual 180.00 157.12 22.88 0 5.00e+00 4.00e-02 2.09e+01 dihedral pdb=" N CYS A 285 " pdb=" C CYS A 285 " pdb=" CA CYS A 285 " pdb=" CB CYS A 285 " ideal model delta harmonic sigma weight residual 122.80 113.57 9.23 0 2.50e+00 1.60e-01 1.36e+01 ... (remaining 6717 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 1464 0.062 - 0.123: 192 0.123 - 0.185: 9 0.185 - 0.247: 0 0.247 - 0.308: 1 Chirality restraints: 1666 Sorted by residual: chirality pdb=" CA CYS A 285 " pdb=" N CYS A 285 " pdb=" C CYS A 285 " pdb=" CB CYS A 285 " both_signs ideal model delta sigma weight residual False 2.51 2.82 -0.31 2.00e-01 2.50e+01 2.37e+00 chirality pdb=" CA CYS D 285 " pdb=" N CYS D 285 " pdb=" C CYS D 285 " pdb=" CB CYS D 285 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.18 2.00e-01 2.50e+01 8.01e-01 chirality pdb=" CA LYS C 49 " pdb=" N LYS C 49 " pdb=" C LYS C 49 " pdb=" CB LYS C 49 " both_signs ideal model delta sigma weight residual False 2.51 2.67 -0.16 2.00e-01 2.50e+01 6.14e-01 ... (remaining 1663 not shown) Planarity restraints: 1910 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU D 282 " -0.014 2.00e-02 2.50e+03 2.76e-02 7.62e+00 pdb=" C GLU D 282 " 0.048 2.00e-02 2.50e+03 pdb=" O GLU D 282 " -0.018 2.00e-02 2.50e+03 pdb=" N HIS D 283 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 282 " 0.014 2.00e-02 2.50e+03 2.76e-02 7.61e+00 pdb=" C GLU A 282 " -0.048 2.00e-02 2.50e+03 pdb=" O GLU A 282 " 0.018 2.00e-02 2.50e+03 pdb=" N HIS A 283 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP B 106 " 0.041 5.00e-02 4.00e+02 6.22e-02 6.19e+00 pdb=" N PRO B 107 " -0.108 5.00e-02 4.00e+02 pdb=" CA PRO B 107 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO B 107 " 0.034 5.00e-02 4.00e+02 ... (remaining 1907 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 97 2.60 - 3.18: 9193 3.18 - 3.75: 17354 3.75 - 4.33: 23346 4.33 - 4.90: 40172 Nonbonded interactions: 90162 Sorted by model distance: nonbonded pdb=" OG1 THR A 32 " pdb="MG MG A 403 " model vdw 2.028 2.170 nonbonded pdb=" OG1 THR D 32 " pdb="MG MG D 402 " model vdw 2.028 2.170 nonbonded pdb=" O VAL A 23 " pdb=" OG1 THR A 167 " model vdw 2.203 3.040 nonbonded pdb=" O VAL D 23 " pdb=" OG1 THR D 167 " model vdw 2.205 3.040 nonbonded pdb=" O LYS B 130 " pdb=" ND2 ASN D 98 " model vdw 2.215 3.120 ... (remaining 90157 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' and resid 4 through 351) selection = (chain 'D' and resid 4 through 351) } ncs_group { reference = chain 'B' selection = chain 'E' } ncs_group { reference = chain 'C' selection = chain 'F' } 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: 1.900 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.170 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 11.760 Find NCS groups from input model: 0.160 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:1.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 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 : 0.009 0.665 11133 Z= 0.330 Angle : 0.552 8.694 15038 Z= 0.304 Chirality : 0.040 0.308 1666 Planarity : 0.005 0.092 1910 Dihedral : 19.006 89.553 4176 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.22 % Favored : 95.63 % Rotamer: Outliers : 0.66 % Allowed : 22.06 % Favored : 77.28 % 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 are not related in a simple way. whole: 1.26 (0.24), residues: 1328 helix: 1.82 (0.18), residues: 842 sheet: -1.25 (0.52), residues: 64 loop : -0.83 (0.31), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 322 TYR 0.021 0.001 TYR E 226 PHE 0.008 0.001 PHE B 299 TRP 0.010 0.001 TRP B 122 HIS 0.006 0.001 HIS A 172 Details of bonding type rmsd covalent geometry : bond 0.00331 (11130) covalent geometry : angle 0.55190 (15038) hydrogen bonds : bond 0.10997 ( 608) hydrogen bonds : angle 4.64421 ( 1800) metal coordination : bond 0.52307 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 190 time to evaluate : 0.436 Fit side-chains REVERT: C 12 PHE cc_start: 0.9290 (t80) cc_final: 0.8703 (t80) REVERT: C 14 SER cc_start: 0.9411 (t) cc_final: 0.9210 (m) REVERT: C 19 LEU cc_start: 0.9689 (mt) cc_final: 0.9450 (tp) REVERT: F 12 PHE cc_start: 0.9271 (t80) cc_final: 0.8681 (t80) REVERT: F 19 LEU cc_start: 0.9691 (mt) cc_final: 0.9439 (tp) REVERT: F 30 SER cc_start: 0.9262 (p) cc_final: 0.9051 (t) REVERT: A 166 ASP cc_start: 0.8688 (t0) cc_final: 0.8391 (t0) REVERT: B 164 SER cc_start: 0.8940 (m) cc_final: 0.8725 (t) REVERT: B 286 GLN cc_start: 0.9169 (tm-30) cc_final: 0.8483 (tm-30) REVERT: D 166 ASP cc_start: 0.8697 (t0) cc_final: 0.8401 (t0) REVERT: D 220 LYS cc_start: 0.8055 (mttt) cc_final: 0.7836 (mtmt) REVERT: E 164 SER cc_start: 0.8930 (m) cc_final: 0.8707 (t) REVERT: E 286 GLN cc_start: 0.9181 (tm-30) cc_final: 0.8495 (tm-30) outliers start: 8 outliers final: 3 residues processed: 194 average time/residue: 0.1274 time to fit residues: 33.4300 Evaluate side-chains 162 residues out of total 1206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 159 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 53 LYS Chi-restraints excluded: chain A residue 285 CYS Chi-restraints excluded: chain A residue 286 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 98 optimal weight: 0.9980 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 0.4980 chunk 66 optimal weight: 0.9980 chunk 124 optimal weight: 0.0770 chunk 103 optimal weight: 0.9980 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 0.5980 chunk 55 optimal weight: 2.9990 chunk 129 optimal weight: 0.0000 overall best weight: 0.4142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.143469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.092750 restraints weight = 15128.933| |-----------------------------------------------------------------------------| r_work (start): 0.3136 rms_B_bonded: 2.11 r_work: 0.2979 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2820 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.1283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 11133 Z= 0.119 Angle : 0.504 7.504 15038 Z= 0.260 Chirality : 0.039 0.133 1666 Planarity : 0.004 0.054 1910 Dihedral : 7.867 68.937 1505 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.52 % Favored : 95.33 % Rotamer: Outliers : 2.40 % Allowed : 22.22 % Favored : 75.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.50 (0.24), residues: 1328 helix: 1.94 (0.18), residues: 852 sheet: -1.21 (0.52), residues: 64 loop : -0.64 (0.31), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 104 TYR 0.013 0.001 TYR D 250 PHE 0.009 0.001 PHE E 283 TRP 0.008 0.001 TRP E 122 HIS 0.005 0.001 HIS A 172 Details of bonding type rmsd covalent geometry : bond 0.00269 (11130) covalent geometry : angle 0.50412 (15038) hydrogen bonds : bond 0.03422 ( 608) hydrogen bonds : angle 3.90846 ( 1800) metal coordination : bond 0.00552 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 170 time to evaluate : 0.360 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 30 SER cc_start: 0.9289 (p) cc_final: 0.9066 (t) REVERT: A 138 GLU cc_start: 0.7599 (OUTLIER) cc_final: 0.6093 (mp0) REVERT: A 166 ASP cc_start: 0.8544 (t0) cc_final: 0.8236 (t0) REVERT: A 286 LYS cc_start: 0.8336 (OUTLIER) cc_final: 0.7994 (mtmt) REVERT: A 306 TYR cc_start: 0.9257 (m-80) cc_final: 0.8959 (m-80) REVERT: A 348 TYR cc_start: 0.8551 (m-80) cc_final: 0.8338 (m-80) REVERT: B 164 SER cc_start: 0.8827 (m) cc_final: 0.8611 (t) REVERT: B 286 GLN cc_start: 0.9299 (tm-30) cc_final: 0.8695 (tm-30) REVERT: D 138 GLU cc_start: 0.7585 (OUTLIER) cc_final: 0.6081 (mp0) REVERT: D 166 ASP cc_start: 0.8568 (t0) cc_final: 0.8267 (t0) REVERT: D 306 TYR cc_start: 0.9262 (m-80) cc_final: 0.8964 (m-80) REVERT: E 164 SER cc_start: 0.8822 (m) cc_final: 0.8596 (t) REVERT: E 286 GLN cc_start: 0.9288 (tm-30) cc_final: 0.8674 (tm-30) outliers start: 29 outliers final: 10 residues processed: 189 average time/residue: 0.0995 time to fit residues: 26.9041 Evaluate side-chains 167 residues out of total 1206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 154 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 32 THR Chi-restraints excluded: chain C residue 50 TYR Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 138 GLU Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 286 LYS Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 257 THR Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 138 GLU Chi-restraints excluded: chain D residue 226 ILE Chi-restraints excluded: chain E residue 250 LEU Chi-restraints excluded: chain E residue 257 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 45 optimal weight: 1.9990 chunk 122 optimal weight: 7.9990 chunk 85 optimal weight: 0.9990 chunk 1 optimal weight: 0.9980 chunk 0 optimal weight: 0.7980 chunk 68 optimal weight: 0.0050 chunk 53 optimal weight: 1.9990 chunk 100 optimal weight: 2.9990 chunk 121 optimal weight: 0.6980 chunk 125 optimal weight: 0.9980 chunk 51 optimal weight: 0.7980 overall best weight: 0.6594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 275 GLN ** E 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 275 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.140304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.096412 restraints weight = 15503.476| |-----------------------------------------------------------------------------| r_work (start): 0.3198 rms_B_bonded: 2.33 r_work: 0.2937 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2781 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.1576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 11133 Z= 0.140 Angle : 0.504 6.949 15038 Z= 0.260 Chirality : 0.040 0.148 1666 Planarity : 0.004 0.052 1910 Dihedral : 7.298 70.971 1500 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.99 % Favored : 95.86 % Rotamer: Outliers : 2.24 % Allowed : 22.97 % Favored : 74.79 % 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 are not related in a simple way. whole: 1.61 (0.24), residues: 1328 helix: 2.02 (0.18), residues: 852 sheet: -1.28 (0.51), residues: 64 loop : -0.55 (0.31), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 104 TYR 0.019 0.001 TYR F 31 PHE 0.012 0.001 PHE C 12 TRP 0.007 0.001 TRP E 122 HIS 0.005 0.001 HIS D 172 Details of bonding type rmsd covalent geometry : bond 0.00328 (11130) covalent geometry : angle 0.50398 (15038) hydrogen bonds : bond 0.03333 ( 608) hydrogen bonds : angle 3.75169 ( 1800) metal coordination : bond 0.00219 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2656 Ramachandran restraints generated. 1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 167 time to evaluate : 0.360 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 9 GLU cc_start: 0.8906 (tt0) cc_final: 0.8610 (tp30) REVERT: F 9 GLU cc_start: 0.8854 (tt0) cc_final: 0.8579 (tp30) REVERT: A 166 ASP cc_start: 0.8566 (t0) cc_final: 0.8245 (t0) REVERT: A 222 ASN cc_start: 0.7648 (OUTLIER) cc_final: 0.7149 (t0) REVERT: A 306 TYR cc_start: 0.9298 (m-80) cc_final: 0.9096 (m-80) REVERT: A 348 TYR cc_start: 0.8597 (m-80) cc_final: 0.8370 (m-80) REVERT: B 286 GLN cc_start: 0.9302 (tm-30) cc_final: 0.8682 (tm-30) REVERT: D 185 LYS cc_start: 0.7840 (mptt) cc_final: 0.7618 (mptt) REVERT: D 306 TYR cc_start: 0.9306 (m-80) cc_final: 0.9099 (m-80) REVERT: E 286 GLN cc_start: 0.9306 (tm-30) cc_final: 0.8691 (tm-30) outliers start: 27 outliers final: 12 residues processed: 181 average time/residue: 0.0925 time to fit residues: 23.7577 Evaluate side-chains 172 residues out of total 1206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 159 time to evaluate : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 32 THR Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 50 TYR Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 222 ASN Chi-restraints excluded: chain A residue 347 ILE Chi-restraints excluded: chain B residue 255 CYS Chi-restraints excluded: chain B residue 257 THR Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain D residue 347 ILE Chi-restraints excluded: chain E residue 176 LEU Chi-restraints excluded: chain E residue 257 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/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-2.0-5952/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-2.0-5952/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-2.0-5952/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-2.0-5952/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-2.0-5952/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-2.0-5952/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-2.0-5952/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-2.0-5952/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-2.0-5952/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-2.0-5952/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-2.0-5952/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-2.0-5952/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-2.0-5952/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-2.0-5952/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-2.0-5952/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-2.0-5952/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-2.0-5952/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-2.0-5952/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-2.0-5952/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: 66.2419 > 50: distance: 4 - 9: 25.842 distance: 9 - 10: 19.634 distance: 10 - 11: 29.604 distance: 10 - 13: 16.938 distance: 11 - 18: 27.212 distance: 13 - 14: 27.692 distance: 14 - 15: 45.300 distance: 15 - 16: 47.204 distance: 16 - 17: 43.400 distance: 18 - 19: 21.854 distance: 19 - 20: 37.800 distance: 19 - 22: 18.195 distance: 20 - 21: 37.333 distance: 20 - 26: 3.254 distance: 22 - 23: 15.623 distance: 23 - 24: 41.696 distance: 23 - 25: 49.401 distance: 33 - 34: 19.632 distance: 34 - 35: 26.747 distance: 34 - 37: 35.461 distance: 35 - 36: 17.336 distance: 35 - 42: 9.248 distance: 37 - 38: 22.214 distance: 38 - 39: 40.382 distance: 39 - 40: 15.549 distance: 40 - 41: 19.676 distance: 42 - 43: 8.602 distance: 43 - 44: 7.387 distance: 43 - 46: 6.905 distance: 44 - 48: 11.066 distance: 48 - 49: 36.709 distance: 49 - 50: 4.105 distance: 49 - 52: 36.894 distance: 50 - 51: 8.169 distance: 50 - 60: 29.597 distance: 52 - 53: 25.737 distance: 53 - 54: 14.221 distance: 53 - 55: 26.518 distance: 54 - 56: 14.523 distance: 55 - 57: 5.833 distance: 56 - 58: 16.519 distance: 57 - 58: 5.433 distance: 58 - 59: 12.094 distance: 60 - 61: 32.617 distance: 61 - 62: 35.762 distance: 61 - 64: 18.459 distance: 62 - 63: 20.806 distance: 62 - 67: 12.852 distance: 64 - 65: 28.936 distance: 64 - 66: 4.117 distance: 67 - 68: 19.701 distance: 68 - 69: 38.607 distance: 69 - 70: 25.645 distance: 69 - 76: 14.199 distance: 71 - 72: 31.485 distance: 72 - 73: 29.543 distance: 73 - 74: 41.714 distance: 74 - 75: 43.920 distance: 76 - 77: 10.723 distance: 76 - 82: 24.129 distance: 77 - 78: 29.327 distance: 77 - 80: 17.081 distance: 78 - 79: 3.838 distance: 78 - 83: 10.613 distance: 79 - 97: 31.683 distance: 80 - 81: 43.193 distance: 81 - 82: 18.781 distance: 83 - 84: 21.699 distance: 84 - 85: 10.558 distance: 84 - 87: 24.261 distance: 85 - 86: 19.311 distance: 85 - 91: 25.923 distance: 86 - 105: 26.764 distance: 87 - 88: 6.625 distance: 88 - 89: 16.350 distance: 88 - 90: 31.293