Starting phenix.real_space_refine on Wed Aug 5 18:39:57 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ns5_49743/08_2026/9ns5_49743.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ns5_49743/08_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9ns5_49743/08_2026/9ns5_49743.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ns5_49743/08_2026/9ns5_49743.map" model { file = "/net/cci-nas-00/data/ceres_data/9ns5_49743/08_2026/9ns5_49743.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ns5_49743/08_2026/9ns5_49743.cif" } 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-2.2rc3-6140/lib/python3.11/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: 2.00, per 1000 atoms: 0.18 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: 0.84 Conformation dependent library (CDL) restraints added in 286.8 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: 0.24 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: 1.21 Time building geometry restraints manager: 1.04 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: 1.840 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: 0.040 Set scattering table: 0.050 Process input model: 9.620 Find NCS groups from input model: 0.120 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:0.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8659 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/Z covalent geometry : bond 0.00331 / 0.16 (11130) covalent geometry : angle 0.55190 / 0.30 (15038) hydrogen bonds : bond 0.10997 / 7.43 ( 608) hydrogen bonds : angle 4.64421 / 3.23 ( 1800) metal coordination : bond 0.52307 / 28.11 ( 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 : 0.375 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: 0.1026 time to fit residues: 27.5642 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 : 0.384 ------------------------------------------------------------------------------- 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... ** 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: 0.8657 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/Z covalent geometry : bond 0.00269 / 0.12 (11130) covalent geometry : angle 0.50412 / 0.26 (15038) hydrogen bonds : bond 0.03422 / 2.23 ( 608) hydrogen bonds : angle 3.90846 / 2.70 ( 1800) metal coordination : bond 0.00552 / 0.30 ( 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 : 0.282 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: 0.0938 time to fit residues: 25.4852 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 : 0.300 ------------------------------------------------------------------------------- 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... ** 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: 0.8590 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/Z covalent geometry : bond 0.00328 / 0.14 (11130) covalent geometry : angle 0.50398 / 0.26 (15038) hydrogen bonds : bond 0.03333 / 2.17 ( 608) hydrogen bonds : angle 3.75169 / 2.60 ( 1800) metal coordination : bond 0.00219 / 0.12 ( 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 : 0.291 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: 0.0889 time to fit residues: 22.9711 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 : 0.438 ------------------------------------------------------------------------------- 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 ************** Weight determination summary: number of chunks: 130 random chunks: chunk 127 optimal weight: 4.9990 chunk 43 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 2 optimal weight: 0.1980 chunk 3 optimal weight: 0.9990 chunk 6 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 66.2419 > 50:) chunk 63 optimal weight: 3.9990 chunk 15 optimal weight: 1.9990 chunk 116 optimal weight: 0.6980 chunk 72 optimal weight: 0.7980 chunk 48 optimal weight: 0.9990 overall best weight: 0.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3834 r_free = 0.3834 target = 0.142201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.090338 restraints weight = 15610.285| |-----------------------------------------------------------------------------| r_work (start): 0.3109 rms_B_bonded: 2.33 r_work: 0.2951 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2792 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2792 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8610 moved from start: 0.1743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 11133 Z= 0.149 Angle : 0.501 6.753 15038 Z= 0.258 Chirality : 0.040 0.147 1666 Planarity : 0.004 0.052 1910 Dihedral : 7.092 71.630 1496 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.37 % Favored : 95.48 % Rotamer: Outliers : 2.65 % Allowed : 23.22 % Favored : 74.13 % 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: 1.65 (0.24), residues: 1328 helix: 2.06 (0.18), residues: 852 sheet: -1.35 (0.50), residues: 64 loop : -0.53 (0.31), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 155 TYR 0.016 0.001 TYR B 226 PHE 0.022 0.001 PHE F 12 TRP 0.007 0.001 TRP E 122 HIS 0.005 0.001 HIS D 172 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.15 (11130) covalent geometry : angle 0.50094 / 0.26 (15038) hydrogen bonds : bond 0.03248 / 2.11 ( 608) hydrogen bonds : angle 3.67980 / 2.55 ( 1800) metal coordination : bond 0.00195 / 0.10 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 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 192 residues out of total 1206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 160 time to evaluate : 0.287 Fit side-chains revert: symmetry clash REVERT: C 9 GLU cc_start: 0.8998 (tt0) cc_final: 0.8700 (tp30) REVERT: F 9 GLU cc_start: 0.8936 (tt0) cc_final: 0.8682 (tp30) REVERT: A 220 LYS cc_start: 0.7887 (mtmt) cc_final: 0.7670 (mtmm) REVERT: A 249 LEU cc_start: 0.8976 (OUTLIER) cc_final: 0.8593 (tp) REVERT: A 306 TYR cc_start: 0.9333 (m-80) cc_final: 0.9116 (m-80) REVERT: B 165 MET cc_start: 0.9216 (tmm) cc_final: 0.8931 (tmm) REVERT: B 286 GLN cc_start: 0.9311 (tm-30) cc_final: 0.8702 (tm-30) REVERT: D 222 ASN cc_start: 0.7632 (OUTLIER) cc_final: 0.7132 (t0) REVERT: D 249 LEU cc_start: 0.9024 (OUTLIER) cc_final: 0.8678 (tp) REVERT: D 306 TYR cc_start: 0.9332 (m-80) cc_final: 0.9118 (m-80) REVERT: E 165 MET cc_start: 0.9219 (tmm) cc_final: 0.8935 (tmm) REVERT: E 286 GLN cc_start: 0.9317 (tm-30) cc_final: 0.8710 (tm-30) outliers start: 32 outliers final: 23 residues processed: 179 average time/residue: 0.0867 time to fit residues: 22.5693 Evaluate side-chains 174 residues out of total 1206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 148 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 32 THR Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain F residue 23 THR Chi-restraints excluded: chain F residue 32 THR Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 11 SER Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 269 ILE Chi-restraints excluded: chain A residue 347 ILE Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 176 LEU 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 11 SER Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain D residue 222 ASN Chi-restraints excluded: chain D residue 249 LEU Chi-restraints excluded: chain D residue 269 ILE Chi-restraints excluded: chain D residue 347 ILE Chi-restraints excluded: chain E residue 159 LEU Chi-restraints excluded: chain E residue 176 LEU Chi-restraints excluded: chain E residue 257 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 53 optimal weight: 0.9990 chunk 6 optimal weight: 3.9990 chunk 94 optimal weight: 0.7980 chunk 74 optimal weight: 0.0070 chunk 117 optimal weight: 0.0980 chunk 37 optimal weight: 0.8980 chunk 89 optimal weight: 2.9990 chunk 107 optimal weight: 0.8980 chunk 55 optimal weight: 0.9980 chunk 33 optimal weight: 0.0770 chunk 104 optimal weight: 0.8980 overall best weight: 0.3756 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3839 r_free = 0.3839 target = 0.142062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.091130 restraints weight = 15395.118| |-----------------------------------------------------------------------------| r_work (start): 0.3131 rms_B_bonded: 2.30 r_work: 0.2974 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2814 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8578 moved from start: 0.1960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 11133 Z= 0.107 Angle : 0.483 9.235 15038 Z= 0.247 Chirality : 0.039 0.151 1666 Planarity : 0.004 0.053 1910 Dihedral : 6.844 68.603 1496 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.92 % Favored : 95.93 % Rotamer: Outliers : 1.91 % Allowed : 24.54 % Favored : 73.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.77 (0.24), residues: 1328 helix: 2.12 (0.18), residues: 854 sheet: -1.35 (0.50), residues: 64 loop : -0.41 (0.32), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 155 TYR 0.017 0.001 TYR F 31 PHE 0.016 0.001 PHE F 12 TRP 0.007 0.001 TRP E 122 HIS 0.004 0.001 HIS E 33 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.11 (11130) covalent geometry : angle 0.48328 / 0.25 (15038) hydrogen bonds : bond 0.02971 / 1.93 ( 608) hydrogen bonds : angle 3.61567 / 2.51 ( 1800) metal coordination : bond 0.00148 / 0.08 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 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 190 residues out of total 1206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 167 time to evaluate : 0.294 Fit side-chains revert: symmetry clash REVERT: C 9 GLU cc_start: 0.9006 (tt0) cc_final: 0.8630 (tp30) REVERT: F 9 GLU cc_start: 0.8936 (tt0) cc_final: 0.8615 (tp30) REVERT: F 31 TYR cc_start: 0.7622 (t80) cc_final: 0.7382 (t80) REVERT: A 185 LYS cc_start: 0.8020 (mptt) cc_final: 0.7692 (mptt) REVERT: A 249 LEU cc_start: 0.8932 (OUTLIER) cc_final: 0.8543 (tp) REVERT: B 28 ASP cc_start: 0.8331 (t0) cc_final: 0.7820 (m-30) REVERT: B 158 MET cc_start: 0.8581 (tpp) cc_final: 0.8246 (tpp) REVERT: B 286 GLN cc_start: 0.9295 (tm-30) cc_final: 0.8686 (tm-30) REVERT: D 185 LYS cc_start: 0.7968 (mptt) cc_final: 0.7603 (mptt) REVERT: D 222 ASN cc_start: 0.7651 (OUTLIER) cc_final: 0.7162 (t0) REVERT: D 249 LEU cc_start: 0.8958 (OUTLIER) cc_final: 0.8621 (tp) REVERT: E 28 ASP cc_start: 0.8342 (t0) cc_final: 0.7827 (m-30) REVERT: E 158 MET cc_start: 0.8551 (tpp) cc_final: 0.8226 (tpp) REVERT: E 286 GLN cc_start: 0.9308 (tm-30) cc_final: 0.8692 (tm-30) outliers start: 23 outliers final: 16 residues processed: 177 average time/residue: 0.0892 time to fit residues: 22.4269 Evaluate side-chains 173 residues out of total 1206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 154 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 32 THR Chi-restraints excluded: chain F residue 23 THR Chi-restraints excluded: chain F residue 32 THR Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 176 LEU 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 212 ILE Chi-restraints excluded: chain D residue 222 ASN Chi-restraints excluded: chain D residue 249 LEU Chi-restraints excluded: chain E residue 115 VAL Chi-restraints excluded: chain E residue 159 LEU Chi-restraints excluded: chain E residue 176 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 24 optimal weight: 0.9980 chunk 59 optimal weight: 0.9980 chunk 84 optimal weight: 2.9990 chunk 90 optimal weight: 0.7980 chunk 111 optimal weight: 1.9990 chunk 64 optimal weight: 3.9990 chunk 74 optimal weight: 0.0980 chunk 60 optimal weight: 2.9990 chunk 67 optimal weight: 2.9990 chunk 120 optimal weight: 0.7980 chunk 72 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 275 GLN ** E 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 256 GLN E 275 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.140568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.094632 restraints weight = 15489.923| |-----------------------------------------------------------------------------| r_work (start): 0.3200 rms_B_bonded: 2.50 r_work: 0.2956 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2801 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2801 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8604 moved from start: 0.2051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11133 Z= 0.137 Angle : 0.488 6.586 15038 Z= 0.251 Chirality : 0.040 0.151 1666 Planarity : 0.004 0.056 1910 Dihedral : 6.826 70.464 1496 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.44 % Favored : 95.41 % Rotamer: Outliers : 2.49 % Allowed : 23.80 % Favored : 73.71 % 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: 1.75 (0.24), residues: 1328 helix: 2.10 (0.18), residues: 854 sheet: -1.35 (0.52), residues: 64 loop : -0.41 (0.31), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 104 TYR 0.018 0.001 TYR E 226 PHE 0.020 0.001 PHE C 12 TRP 0.006 0.001 TRP B 122 HIS 0.005 0.001 HIS A 172 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.14 (11130) covalent geometry : angle 0.48804 / 0.25 (15038) hydrogen bonds : bond 0.03089 / 2.00 ( 608) hydrogen bonds : angle 3.60761 / 2.49 ( 1800) metal coordination : bond 0.00186 / 0.09 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 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 189 residues out of total 1206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 159 time to evaluate : 0.395 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 9 GLU cc_start: 0.9033 (tt0) cc_final: 0.8724 (tp30) REVERT: F 9 GLU cc_start: 0.8924 (tt0) cc_final: 0.8607 (tp30) REVERT: F 27 LEU cc_start: 0.8775 (tp) cc_final: 0.8447 (tp) REVERT: F 53 LYS cc_start: 0.8449 (mtmm) cc_final: 0.8227 (ptpp) REVERT: A 222 ASN cc_start: 0.7687 (OUTLIER) cc_final: 0.7137 (t0) REVERT: A 249 LEU cc_start: 0.8976 (OUTLIER) cc_final: 0.8578 (tp) REVERT: B 28 ASP cc_start: 0.8399 (t0) cc_final: 0.7921 (m-30) REVERT: B 165 MET cc_start: 0.9181 (tmm) cc_final: 0.8933 (tmm) REVERT: B 286 GLN cc_start: 0.9322 (tm-30) cc_final: 0.8702 (tm-30) REVERT: D 185 LYS cc_start: 0.8013 (mptt) cc_final: 0.7640 (mptt) REVERT: D 249 LEU cc_start: 0.8996 (OUTLIER) cc_final: 0.8654 (tp) REVERT: E 28 ASP cc_start: 0.8389 (t0) cc_final: 0.7916 (m-30) REVERT: E 165 MET cc_start: 0.9213 (tmm) cc_final: 0.8969 (tmm) REVERT: E 286 GLN cc_start: 0.9314 (tm-30) cc_final: 0.8689 (tm-30) outliers start: 30 outliers final: 22 residues processed: 176 average time/residue: 0.0852 time to fit residues: 21.8008 Evaluate side-chains 179 residues out of total 1206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 154 time to evaluate : 0.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 32 THR Chi-restraints excluded: chain F residue 23 THR Chi-restraints excluded: chain F residue 32 THR Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 11 SER Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 222 ASN Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 269 ILE Chi-restraints excluded: chain A residue 347 ILE Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 204 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 11 SER Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain D residue 212 ILE Chi-restraints excluded: chain D residue 249 LEU Chi-restraints excluded: chain D residue 269 ILE Chi-restraints excluded: chain E residue 115 VAL Chi-restraints excluded: chain E residue 159 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 74 optimal weight: 0.0270 chunk 121 optimal weight: 3.9990 chunk 82 optimal weight: 0.9990 chunk 83 optimal weight: 0.6980 chunk 85 optimal weight: 2.9990 chunk 109 optimal weight: 0.9980 chunk 65 optimal weight: 0.9990 chunk 112 optimal weight: 0.9990 chunk 5 optimal weight: 1.9990 chunk 124 optimal weight: 1.9990 chunk 104 optimal weight: 1.9990 overall best weight: 0.7442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3819 r_free = 0.3819 target = 0.140058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.089230 restraints weight = 15339.981| |-----------------------------------------------------------------------------| r_work (start): 0.3099 rms_B_bonded: 2.30 r_work: 0.2937 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2777 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8651 moved from start: 0.2101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 11133 Z= 0.149 Angle : 0.501 6.523 15038 Z= 0.256 Chirality : 0.040 0.157 1666 Planarity : 0.004 0.058 1910 Dihedral : 6.884 71.048 1496 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.07 % Favored : 95.78 % Rotamer: Outliers : 2.90 % Allowed : 22.89 % Favored : 74.21 % 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: 1.74 (0.24), residues: 1328 helix: 2.10 (0.18), residues: 852 sheet: -1.35 (0.54), residues: 64 loop : -0.40 (0.31), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 104 TYR 0.022 0.001 TYR B 226 PHE 0.016 0.001 PHE C 12 TRP 0.006 0.001 TRP E 122 HIS 0.005 0.001 HIS A 172 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.15 (11130) covalent geometry : angle 0.50078 / 0.26 (15038) hydrogen bonds : bond 0.03149 / 2.04 ( 608) hydrogen bonds : angle 3.59395 / 2.49 ( 1800) metal coordination : bond 0.00145 / 0.07 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 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 189 residues out of total 1206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 154 time to evaluate : 0.367 Fit side-chains revert: symmetry clash REVERT: C 9 GLU cc_start: 0.9017 (tt0) cc_final: 0.8583 (tp30) REVERT: F 9 GLU cc_start: 0.8959 (tt0) cc_final: 0.8565 (tp30) REVERT: A 185 LYS cc_start: 0.8091 (mptt) cc_final: 0.7788 (mptt) REVERT: A 220 LYS cc_start: 0.7775 (mtmt) cc_final: 0.7552 (mtmm) REVERT: A 222 ASN cc_start: 0.7706 (OUTLIER) cc_final: 0.7156 (t0) REVERT: A 249 LEU cc_start: 0.9019 (OUTLIER) cc_final: 0.8611 (tp) REVERT: B 28 ASP cc_start: 0.8397 (t0) cc_final: 0.7950 (m-30) REVERT: B 165 MET cc_start: 0.9207 (tmm) cc_final: 0.8930 (tmm) REVERT: B 286 GLN cc_start: 0.9323 (tm-30) cc_final: 0.8711 (tm-30) REVERT: D 138 GLU cc_start: 0.7543 (OUTLIER) cc_final: 0.6055 (mp0) REVERT: D 185 LYS cc_start: 0.8019 (mptt) cc_final: 0.7637 (mptt) REVERT: D 222 ASN cc_start: 0.7669 (OUTLIER) cc_final: 0.7178 (t0) REVERT: D 249 LEU cc_start: 0.9011 (OUTLIER) cc_final: 0.8592 (tp) REVERT: E 28 ASP cc_start: 0.8388 (t0) cc_final: 0.7942 (m-30) REVERT: E 165 MET cc_start: 0.9219 (tmm) cc_final: 0.8944 (tmm) REVERT: E 286 GLN cc_start: 0.9314 (tm-30) cc_final: 0.8694 (tm-30) outliers start: 35 outliers final: 26 residues processed: 174 average time/residue: 0.0824 time to fit residues: 20.7022 Evaluate side-chains 183 residues out of total 1206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 152 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 32 THR Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain F residue 23 THR Chi-restraints excluded: chain F residue 32 THR Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 11 SER Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 222 ASN Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 269 ILE Chi-restraints excluded: chain A residue 347 ILE Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 176 LEU 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 11 SER Chi-restraints excluded: chain D residue 138 GLU Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain D residue 212 ILE Chi-restraints excluded: chain D residue 222 ASN Chi-restraints excluded: chain D residue 249 LEU Chi-restraints excluded: chain D residue 269 ILE Chi-restraints excluded: chain D residue 347 ILE Chi-restraints excluded: chain E residue 115 VAL Chi-restraints excluded: chain E residue 159 LEU Chi-restraints excluded: chain E residue 176 LEU Chi-restraints excluded: chain E residue 204 ILE Chi-restraints excluded: chain E residue 257 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 41 optimal weight: 1.9990 chunk 42 optimal weight: 0.9990 chunk 79 optimal weight: 9.9990 chunk 6 optimal weight: 0.2980 chunk 36 optimal weight: 0.8980 chunk 119 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 chunk 123 optimal weight: 1.9990 chunk 96 optimal weight: 0.9980 chunk 50 optimal weight: 0.8980 chunk 2 optimal weight: 2.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 54 GLN ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.139526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.088382 restraints weight = 15452.437| |-----------------------------------------------------------------------------| r_work (start): 0.3106 rms_B_bonded: 2.32 r_work: 0.2947 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2788 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.2788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8658 moved from start: 0.2162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 11133 Z= 0.161 Angle : 0.511 8.720 15038 Z= 0.262 Chirality : 0.040 0.160 1666 Planarity : 0.004 0.060 1910 Dihedral : 6.946 71.370 1496 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.14 % Favored : 95.71 % Rotamer: Outliers : 2.90 % Allowed : 24.05 % Favored : 73.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.75 (0.24), residues: 1328 helix: 2.11 (0.18), residues: 852 sheet: -1.37 (0.55), residues: 64 loop : -0.40 (0.31), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 104 TYR 0.022 0.001 TYR E 226 PHE 0.013 0.001 PHE C 12 TRP 0.006 0.001 TRP E 122 HIS 0.005 0.001 HIS D 172 Details of bonding type rmsd/Z covalent geometry : bond 0.00385 / 0.16 (11130) covalent geometry : angle 0.51074 / 0.26 (15038) hydrogen bonds : bond 0.03189 / 2.06 ( 608) hydrogen bonds : angle 3.59093 / 2.48 ( 1800) metal coordination : bond 0.00157 / 0.08 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 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 184 residues out of total 1206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 149 time to evaluate : 0.268 Fit side-chains revert: symmetry clash REVERT: C 9 GLU cc_start: 0.9061 (tt0) cc_final: 0.8611 (tp30) REVERT: F 9 GLU cc_start: 0.8982 (tt0) cc_final: 0.8584 (tp30) REVERT: A 138 GLU cc_start: 0.7553 (OUTLIER) cc_final: 0.6061 (mp0) REVERT: A 185 LYS cc_start: 0.8102 (mptt) cc_final: 0.7783 (mptt) REVERT: A 222 ASN cc_start: 0.7686 (OUTLIER) cc_final: 0.7126 (t0) REVERT: A 249 LEU cc_start: 0.9034 (OUTLIER) cc_final: 0.8621 (tp) REVERT: B 28 ASP cc_start: 0.8409 (t0) cc_final: 0.7960 (m-30) REVERT: B 165 MET cc_start: 0.9191 (tmm) cc_final: 0.8900 (tmm) REVERT: B 286 GLN cc_start: 0.9329 (tm-30) cc_final: 0.8705 (tm-30) REVERT: D 138 GLU cc_start: 0.7556 (OUTLIER) cc_final: 0.6074 (mp0) REVERT: D 185 LYS cc_start: 0.8024 (mptt) cc_final: 0.7638 (mptt) REVERT: D 222 ASN cc_start: 0.7659 (OUTLIER) cc_final: 0.7149 (t0) REVERT: D 249 LEU cc_start: 0.9026 (OUTLIER) cc_final: 0.8614 (tp) REVERT: E 28 ASP cc_start: 0.8386 (t0) cc_final: 0.7944 (m-30) REVERT: E 165 MET cc_start: 0.9205 (tmm) cc_final: 0.8920 (tmm) REVERT: E 286 GLN cc_start: 0.9322 (tm-30) cc_final: 0.8694 (tm-30) outliers start: 35 outliers final: 25 residues processed: 173 average time/residue: 0.0819 time to fit residues: 20.6495 Evaluate side-chains 182 residues out of total 1206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 151 time to evaluate : 0.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 32 THR Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain F residue 23 THR Chi-restraints excluded: chain F residue 32 THR Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 11 SER Chi-restraints excluded: chain A residue 138 GLU Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 222 ASN Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 269 ILE Chi-restraints excluded: chain A residue 337 GLU Chi-restraints excluded: chain A residue 347 ILE Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 257 THR Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 11 SER Chi-restraints excluded: chain D residue 138 GLU Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain D residue 212 ILE Chi-restraints excluded: chain D residue 222 ASN Chi-restraints excluded: chain D residue 249 LEU Chi-restraints excluded: chain D residue 269 ILE Chi-restraints excluded: chain D residue 347 ILE Chi-restraints excluded: chain E residue 115 VAL Chi-restraints excluded: chain E residue 159 LEU Chi-restraints excluded: chain E residue 176 LEU Chi-restraints excluded: chain E residue 204 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 30 optimal weight: 0.5980 chunk 109 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 15 optimal weight: 0.9990 chunk 12 optimal weight: 0.6980 chunk 21 optimal weight: 0.6980 chunk 8 optimal weight: 0.4980 chunk 93 optimal weight: 0.9980 chunk 2 optimal weight: 3.9990 chunk 49 optimal weight: 0.6980 chunk 77 optimal weight: 0.7980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 178 GLN ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.140334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.092365 restraints weight = 15359.523| |-----------------------------------------------------------------------------| r_work (start): 0.3155 rms_B_bonded: 2.24 r_work: 0.2960 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2804 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.2804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8630 moved from start: 0.2241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11133 Z= 0.136 Angle : 0.499 7.736 15038 Z= 0.255 Chirality : 0.039 0.162 1666 Planarity : 0.004 0.062 1910 Dihedral : 6.855 69.070 1496 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.84 % Favored : 96.01 % Rotamer: Outliers : 2.74 % Allowed : 23.96 % Favored : 73.30 % 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: 1.81 (0.24), residues: 1328 helix: 2.14 (0.18), residues: 852 sheet: -1.38 (0.55), residues: 64 loop : -0.35 (0.31), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 104 TYR 0.032 0.001 TYR F 31 PHE 0.013 0.001 PHE C 12 TRP 0.007 0.001 TRP B 122 HIS 0.005 0.001 HIS D 172 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.14 (11130) covalent geometry : angle 0.49916 / 0.26 (15038) hydrogen bonds : bond 0.03042 / 1.96 ( 608) hydrogen bonds : angle 3.56076 / 2.47 ( 1800) metal coordination : bond 0.00118 / 0.06 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 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 191 residues out of total 1206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 158 time to evaluate : 0.423 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 9 GLU cc_start: 0.9025 (tt0) cc_final: 0.8538 (tp30) REVERT: F 9 GLU cc_start: 0.8965 (tt0) cc_final: 0.8561 (tp30) REVERT: A 138 GLU cc_start: 0.7571 (OUTLIER) cc_final: 0.6117 (mp0) REVERT: A 185 LYS cc_start: 0.8068 (mptt) cc_final: 0.7753 (mptt) REVERT: A 220 LYS cc_start: 0.7816 (mtmt) cc_final: 0.7597 (mtmm) REVERT: A 222 ASN cc_start: 0.7697 (OUTLIER) cc_final: 0.7141 (t0) REVERT: A 249 LEU cc_start: 0.8985 (OUTLIER) cc_final: 0.8558 (tp) REVERT: B 28 ASP cc_start: 0.8377 (t0) cc_final: 0.7928 (m-30) REVERT: B 165 MET cc_start: 0.9180 (tmm) cc_final: 0.8877 (tmm) REVERT: B 286 GLN cc_start: 0.9323 (tm-30) cc_final: 0.8700 (tm-30) REVERT: D 138 GLU cc_start: 0.7571 (OUTLIER) cc_final: 0.6127 (mp0) REVERT: D 185 LYS cc_start: 0.8067 (mptt) cc_final: 0.7725 (mptt) REVERT: D 222 ASN cc_start: 0.7660 (OUTLIER) cc_final: 0.7201 (t0) REVERT: D 249 LEU cc_start: 0.8982 (OUTLIER) cc_final: 0.8572 (tp) REVERT: E 28 ASP cc_start: 0.8346 (t0) cc_final: 0.7907 (m-30) REVERT: E 165 MET cc_start: 0.9200 (tmm) cc_final: 0.8905 (tmm) REVERT: E 286 GLN cc_start: 0.9299 (tm-30) cc_final: 0.8675 (tm-30) outliers start: 33 outliers final: 24 residues processed: 178 average time/residue: 0.0802 time to fit residues: 20.7185 Evaluate side-chains 180 residues out of total 1206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 150 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 32 THR Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 50 TYR Chi-restraints excluded: chain F residue 23 THR Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 11 SER Chi-restraints excluded: chain A residue 138 GLU Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 222 ASN Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 269 ILE Chi-restraints excluded: chain A residue 337 GLU Chi-restraints excluded: chain A residue 347 ILE Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 257 THR Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 11 SER Chi-restraints excluded: chain D residue 138 GLU Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain D residue 212 ILE Chi-restraints excluded: chain D residue 222 ASN Chi-restraints excluded: chain D residue 249 LEU Chi-restraints excluded: chain D residue 269 ILE Chi-restraints excluded: chain D residue 347 ILE Chi-restraints excluded: chain E residue 115 VAL Chi-restraints excluded: chain E residue 159 LEU Chi-restraints excluded: chain E residue 257 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 45 optimal weight: 1.9990 chunk 31 optimal weight: 0.0770 chunk 8 optimal weight: 0.9980 chunk 100 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 33 optimal weight: 0.0370 chunk 21 optimal weight: 0.7980 chunk 77 optimal weight: 0.2980 chunk 90 optimal weight: 0.2980 chunk 75 optimal weight: 0.6980 chunk 36 optimal weight: 0.9980 overall best weight: 0.2816 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 54 GLN ** B 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 256 GLN ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.143758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.099524 restraints weight = 15269.074| |-----------------------------------------------------------------------------| r_work (start): 0.3260 rms_B_bonded: 2.22 r_work: 0.3020 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2864 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8583 moved from start: 0.2405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 11133 Z= 0.101 Angle : 0.490 7.667 15038 Z= 0.249 Chirality : 0.040 0.212 1666 Planarity : 0.004 0.063 1910 Dihedral : 6.601 67.471 1496 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.69 % Favored : 96.16 % Rotamer: Outliers : 1.24 % Allowed : 25.79 % Favored : 72.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.89 (0.24), residues: 1328 helix: 2.19 (0.18), residues: 852 sheet: -1.32 (0.56), residues: 64 loop : -0.29 (0.31), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 104 TYR 0.019 0.001 TYR B 226 PHE 0.010 0.001 PHE C 12 TRP 0.008 0.001 TRP B 122 HIS 0.004 0.001 HIS B 33 Details of bonding type rmsd/Z covalent geometry : bond 0.00226 / 0.10 (11130) covalent geometry : angle 0.48995 / 0.25 (15038) hydrogen bonds : bond 0.02786 / 1.81 ( 608) hydrogen bonds : angle 3.53181 / 2.45 ( 1800) metal coordination : bond 0.00113 / 0.06 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 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 173 residues out of total 1206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 158 time to evaluate : 0.290 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 9 GLU cc_start: 0.9060 (tt0) cc_final: 0.8601 (tp30) REVERT: F 9 GLU cc_start: 0.8934 (tt0) cc_final: 0.8545 (tp30) REVERT: A 185 LYS cc_start: 0.8055 (mptt) cc_final: 0.7753 (mptt) REVERT: A 220 LYS cc_start: 0.7760 (mtmt) cc_final: 0.7547 (mtmm) REVERT: A 222 ASN cc_start: 0.7676 (OUTLIER) cc_final: 0.7136 (t0) REVERT: B 28 ASP cc_start: 0.8152 (t0) cc_final: 0.7768 (m-30) REVERT: B 165 MET cc_start: 0.9185 (tmm) cc_final: 0.8893 (tmm) REVERT: B 232 ASN cc_start: 0.8452 (t0) cc_final: 0.7994 (t0) REVERT: B 286 GLN cc_start: 0.9309 (tm-30) cc_final: 0.8684 (tm-30) REVERT: D 185 LYS cc_start: 0.8040 (mptt) cc_final: 0.7713 (mptt) REVERT: D 222 ASN cc_start: 0.7718 (OUTLIER) cc_final: 0.7241 (t0) REVERT: E 28 ASP cc_start: 0.8140 (t0) cc_final: 0.7758 (m-30) REVERT: E 165 MET cc_start: 0.9193 (tmm) cc_final: 0.8900 (tmm) REVERT: E 286 GLN cc_start: 0.9284 (tm-30) cc_final: 0.8652 (tm-30) outliers start: 15 outliers final: 11 residues processed: 167 average time/residue: 0.0817 time to fit residues: 19.7216 Evaluate side-chains 159 residues out of total 1206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 146 time to evaluate : 0.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 32 THR Chi-restraints excluded: chain F residue 23 THR Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 222 ASN Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain D residue 5 VAL Chi-restraints excluded: chain D residue 11 SER Chi-restraints excluded: chain D residue 212 ILE Chi-restraints excluded: chain D residue 222 ASN Chi-restraints excluded: chain E residue 115 VAL Chi-restraints excluded: chain E residue 159 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 29 optimal weight: 0.6980 chunk 81 optimal weight: 1.9990 chunk 37 optimal weight: 0.0050 chunk 103 optimal weight: 0.9990 chunk 71 optimal weight: 0.9980 chunk 121 optimal weight: 3.9990 chunk 72 optimal weight: 0.5980 chunk 14 optimal weight: 0.8980 chunk 58 optimal weight: 2.9990 chunk 101 optimal weight: 2.9990 chunk 118 optimal weight: 0.9990 overall best weight: 0.6394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 54 GLN B 208 HIS ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.141906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.096902 restraints weight = 15272.850| |-----------------------------------------------------------------------------| r_work (start): 0.3220 rms_B_bonded: 2.24 r_work: 0.2976 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2822 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8691 moved from start: 0.2393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 11133 Z= 0.139 Angle : 0.526 7.331 15038 Z= 0.265 Chirality : 0.041 0.205 1666 Planarity : 0.004 0.062 1910 Dihedral : 6.673 68.931 1496 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.37 % Favored : 95.48 % Rotamer: Outliers : 1.74 % Allowed : 25.54 % Favored : 72.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.88 (0.24), residues: 1328 helix: 2.18 (0.18), residues: 852 sheet: -1.37 (0.56), residues: 64 loop : -0.27 (0.31), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 104 TYR 0.057 0.001 TYR F 31 PHE 0.015 0.001 PHE F 12 TRP 0.006 0.001 TRP B 122 HIS 0.005 0.001 HIS D 172 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.14 (11130) covalent geometry : angle 0.52584 / 0.27 (15038) hydrogen bonds : bond 0.03056 / 1.98 ( 608) hydrogen bonds : angle 3.53393 / 2.46 ( 1800) metal coordination : bond 0.00159 / 0.08 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2563.51 seconds wall clock time: 44 minutes 31.48 seconds (2671.48 seconds total)