Starting phenix.real_space_refine on Wed Mar 4 04:27:29 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7w0o_32246/03_2026/7w0o_32246.cif Found real_map, /net/cci-nas-00/data/ceres_data/7w0o_32246/03_2026/7w0o_32246.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.78 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7w0o_32246/03_2026/7w0o_32246.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7w0o_32246/03_2026/7w0o_32246.map" model { file = "/net/cci-nas-00/data/ceres_data/7w0o_32246/03_2026/7w0o_32246.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7w0o_32246/03_2026/7w0o_32246.cif" } resolution = 3.78 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= 0.026 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 2064 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 68 5.16 5 C 5799 2.51 5 N 1543 2.21 5 O 1696 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9106 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1813 Classifications: {'peptide': 225} Link IDs: {'PTRANS': 2, 'TRANS': 222} Chain breaks: 1 Chain: "B" Number of atoms: 2601 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2601 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 332} Chain: "C" Number of atoms: 418 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 418 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 4, 'TRANS': 50} Chain: "D" Number of atoms: 128 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 128 Classifications: {'peptide': 15} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 11} Chain: "R" Number of atoms: 2352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2352 Classifications: {'peptide': 293} Link IDs: {'PTRANS': 11, 'TRANS': 281} Chain: "S" Number of atoms: 1794 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1794 Classifications: {'peptide': 233} Link IDs: {'PTRANS': 10, 'TRANS': 222} Chain breaks: 1 Time building chain proxies: 2.11, per 1000 atoms: 0.23 Number of scatterers: 9106 At special positions: 0 Unit cell: (92.4, 123.2, 136.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 68 16.00 O 1696 8.00 N 1543 7.00 C 5799 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS R 102 " - pdb=" SG CYS R 181 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.69 Conformation dependent library (CDL) restraints added in 293.3 milliseconds 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2168 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 13 sheets defined 35.3% alpha, 17.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.47 Creating SS restraints... Processing helix chain 'A' and resid 6 through 31 removed outlier: 3.582A pdb=" N LYS A 10 " --> pdb=" O SER A 6 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 55 Processing helix chain 'A' and resid 212 through 216 removed outlier: 3.910A pdb=" N GLU A 216 " --> pdb=" O HIS A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 255 removed outlier: 3.875A pdb=" N GLU A 245 " --> pdb=" O ASN A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 256 through 260 removed outlier: 3.637A pdb=" N PHE A 259 " --> pdb=" O ASN A 256 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N THR A 260 " --> pdb=" O LYS A 257 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 256 through 260' Processing helix chain 'A' and resid 271 through 279 removed outlier: 3.910A pdb=" N LYS A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 286 Processing helix chain 'A' and resid 295 through 310 removed outlier: 3.651A pdb=" N ALA A 299 " --> pdb=" O THR A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 351 Processing helix chain 'B' and resid 4 through 26 removed outlier: 3.541A pdb=" N ALA B 26 " --> pdb=" O ARG B 22 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 removed outlier: 3.742A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 282 No H-bonds generated for 'chain 'B' and resid 280 through 282' Processing helix chain 'C' and resid 39 through 55 removed outlier: 3.688A pdb=" N ASN C 55 " --> pdb=" O LYS C 51 " (cutoff:3.500A) Processing helix chain 'C' and resid 60 through 76 removed outlier: 3.582A pdb=" N ALA C 64 " --> pdb=" O LYS C 60 " (cutoff:3.500A) Processing helix chain 'R' and resid 32 through 56 removed outlier: 3.790A pdb=" N LEU R 37 " --> pdb=" O ALA R 33 " (cutoff:3.500A) Processing helix chain 'R' and resid 64 through 80 Processing helix chain 'R' and resid 82 through 89 removed outlier: 4.197A pdb=" N THR R 89 " --> pdb=" O TRP R 85 " (cutoff:3.500A) Processing helix chain 'R' and resid 97 through 131 removed outlier: 4.037A pdb=" N PHE R 101 " --> pdb=" O PHE R 97 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N CYS R 102 " --> pdb=" O GLY R 98 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ASN R 112 " --> pdb=" O LEU R 108 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N MET R 113 " --> pdb=" O ILE R 109 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N TYR R 114 " --> pdb=" O PHE R 110 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N VAL R 117 " --> pdb=" O MET R 113 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N THR R 121 " --> pdb=" O VAL R 117 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N LEU R 123 " --> pdb=" O CYS R 119 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ASP R 126 " --> pdb=" O GLY R 122 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N ARG R 127 " --> pdb=" O LEU R 123 " (cutoff:3.500A) Processing helix chain 'R' and resid 148 through 162 removed outlier: 3.551A pdb=" N VAL R 152 " --> pdb=" O VAL R 148 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N ALA R 157 " --> pdb=" O LEU R 153 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N ALA R 158 " --> pdb=" O TRP R 154 " (cutoff:3.500A) Processing helix chain 'R' and resid 163 through 165 No H-bonds generated for 'chain 'R' and resid 163 through 165' Processing helix chain 'R' and resid 190 through 209 removed outlier: 3.808A pdb=" N GLU R 194 " --> pdb=" O THR R 190 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N TRP R 195 " --> pdb=" O VAL R 191 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N SER R 205 " --> pdb=" O LEU R 201 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N GLY R 209 " --> pdb=" O SER R 205 " (cutoff:3.500A) Processing helix chain 'R' and resid 210 through 232 removed outlier: 3.538A pdb=" N PHE R 214 " --> pdb=" O PHE R 210 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N THR R 215 " --> pdb=" O VAL R 211 " (cutoff:3.500A) Processing helix chain 'R' and resid 236 through 261 removed outlier: 4.104A pdb=" N ARG R 241 " --> pdb=" O ILE R 237 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N LYS R 242 " --> pdb=" O GLU R 238 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N PHE R 257 " --> pdb=" O LEU R 253 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N TRP R 261 " --> pdb=" O PHE R 257 " (cutoff:3.500A) Processing helix chain 'R' and resid 262 through 277 Processing helix chain 'R' and resid 280 through 310 Proline residue: R 292 - end of helix removed outlier: 3.891A pdb=" N THR R 295 " --> pdb=" O PHE R 291 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N CYS R 296 " --> pdb=" O PRO R 292 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N ASN R 301 " --> pdb=" O ILE R 297 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N SER R 302 " --> pdb=" O SER R 298 " (cutoff:3.500A) Proline residue: R 306 - end of helix Processing helix chain 'S' and resid 52 through 56 removed outlier: 3.931A pdb=" N GLY S 56 " --> pdb=" O SER S 53 " (cutoff:3.500A) Processing helix chain 'S' and resid 87 through 91 removed outlier: 4.066A pdb=" N THR S 91 " --> pdb=" O SER S 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 187 through 190 removed outlier: 3.503A pdb=" N PHE A 189 " --> pdb=" O PHE A 196 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N VAL A 34 " --> pdb=" O HIS A 195 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N LYS A 35 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 8.140A pdb=" N ILE A 222 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.642A pdb=" N CYS A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N LEU A 39 " --> pdb=" O CYS A 224 " (cutoff:3.500A) removed outlier: 5.979A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 7.264A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 8.684A pdb=" N HIS A 322 " --> pdb=" O ILE A 264 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N LEU A 266 " --> pdb=" O HIS A 322 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51 removed outlier: 7.244A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.968A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 7.219A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LYS B 337 " --> pdb=" O THR B 329 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N TRP B 339 " --> pdb=" O VAL B 327 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 4.866A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N VAL B 71 " --> pdb=" O HIS B 62 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N LEU B 70 " --> pdb=" O TRP B 82 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ILE B 80 " --> pdb=" O SER B 72 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 102 through 105 removed outlier: 3.529A pdb=" N THR B 102 " --> pdb=" O GLY B 115 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLY B 115 " --> pdb=" O THR B 102 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N SER B 122 " --> pdb=" O CYS B 114 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ILE B 123 " --> pdb=" O ARG B 137 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ARG B 137 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 148 through 151 removed outlier: 3.903A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N CYS B 166 " --> pdb=" O THR B 179 " (cutoff:3.500A) removed outlier: 5.398A pdb=" N THR B 179 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 7.397A pdb=" N LEU B 168 " --> pdb=" O THR B 177 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N ASP B 170 " --> pdb=" O GLN B 175 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N GLN B 175 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 191 through 192 removed outlier: 3.710A pdb=" N SER B 191 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N VAL B 200 " --> pdb=" O SER B 191 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N PHE B 199 " --> pdb=" O TRP B 211 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N LEU B 210 " --> pdb=" O GLN B 220 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.874A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.945A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 7.259A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 5.369A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.696A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N PHE B 241 " --> pdb=" O PHE B 253 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N CYS B 250 " --> pdb=" O TYR B 264 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LEU B 252 " --> pdb=" O MET B 262 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.925A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N SER B 277 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.999A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'S' and resid 5 through 7 removed outlier: 3.532A pdb=" N CYS S 22 " --> pdb=" O LEU S 79 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LEU S 79 " --> pdb=" O CYS S 22 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N THR S 78 " --> pdb=" O ASP S 73 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ASP S 73 " --> pdb=" O THR S 78 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N SER S 71 " --> pdb=" O PHE S 80 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N THR S 69 " --> pdb=" O GLN S 82 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'S' and resid 10 through 11 removed outlier: 6.587A pdb=" N GLY S 10 " --> pdb=" O THR S 118 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LEU S 117 " --> pdb=" O ALA S 92 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ALA S 92 " --> pdb=" O LEU S 117 " (cutoff:3.500A) removed outlier: 7.732A pdb=" N MET S 34 " --> pdb=" O TYR S 50 " (cutoff:3.500A) removed outlier: 5.408A pdb=" N TYR S 50 " --> pdb=" O MET S 34 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N TRP S 36 " --> pdb=" O VAL S 48 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N VAL S 48 " --> pdb=" O TRP S 36 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'S' and resid 10 through 11 removed outlier: 6.587A pdb=" N GLY S 10 " --> pdb=" O THR S 118 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LEU S 117 " --> pdb=" O ALA S 92 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ALA S 92 " --> pdb=" O LEU S 117 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N VAL S 97 " --> pdb=" O HIS S 35 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'S' and resid 146 through 147 removed outlier: 3.649A pdb=" N TYR S 228 " --> pdb=" O PHE S 177 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N PHE S 177 " --> pdb=" O TYR S 228 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N ILE S 189 " --> pdb=" O TRP S 176 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N LEU S 178 " --> pdb=" O LEU S 187 " (cutoff:3.500A) removed outlier: 6.120A pdb=" N LEU S 187 " --> pdb=" O LEU S 178 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N ARG S 191 " --> pdb=" O ASN S 194 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'S' and resid 156 through 159 removed outlier: 3.559A pdb=" N SER S 206 " --> pdb=" O THR S 213 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N THR S 215 " --> pdb=" O SER S 204 " (cutoff:3.500A) 343 hydrogen bonds defined for protein. 969 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: 1.27 Time building geometry restraints manager: 0.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2875 1.34 - 1.46: 1518 1.46 - 1.57: 4811 1.57 - 1.69: 0 1.69 - 1.81: 100 Bond restraints: 9304 Sorted by residual: bond pdb=" CB PRO C 91 " pdb=" CG PRO C 91 " ideal model delta sigma weight residual 1.492 1.569 -0.077 5.00e-02 4.00e+02 2.36e+00 bond pdb=" C ILE R 31 " pdb=" N PRO R 32 " ideal model delta sigma weight residual 1.334 1.369 -0.035 2.34e-02 1.83e+03 2.23e+00 bond pdb=" CG1 ILE R 216 " pdb=" CD1 ILE R 216 " ideal model delta sigma weight residual 1.513 1.459 0.054 3.90e-02 6.57e+02 1.94e+00 bond pdb=" CG GLU A 14 " pdb=" CD GLU A 14 " ideal model delta sigma weight residual 1.516 1.486 0.030 2.50e-02 1.60e+03 1.43e+00 bond pdb=" CG PRO D 24 " pdb=" CD PRO D 24 " ideal model delta sigma weight residual 1.503 1.468 0.035 3.40e-02 8.65e+02 1.09e+00 ... (remaining 9299 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.70: 12183 1.70 - 3.40: 325 3.40 - 5.10: 73 5.10 - 6.80: 18 6.80 - 8.50: 6 Bond angle restraints: 12605 Sorted by residual: angle pdb=" N GLU B 10 " pdb=" CA GLU B 10 " pdb=" CB GLU B 10 " ideal model delta sigma weight residual 110.16 116.12 -5.96 1.48e+00 4.57e-01 1.62e+01 angle pdb=" N GLU A 14 " pdb=" CA GLU A 14 " pdb=" CB GLU A 14 " ideal model delta sigma weight residual 110.12 115.10 -4.98 1.47e+00 4.63e-01 1.15e+01 angle pdb=" CA MET D 23 " pdb=" CB MET D 23 " pdb=" CG MET D 23 " ideal model delta sigma weight residual 114.10 120.82 -6.72 2.00e+00 2.50e-01 1.13e+01 angle pdb=" N GLN A 304 " pdb=" CA GLN A 304 " pdb=" CB GLN A 304 " ideal model delta sigma weight residual 110.39 116.14 -5.75 1.75e+00 3.27e-01 1.08e+01 angle pdb=" N PHE R 78 " pdb=" CA PHE R 78 " pdb=" C PHE R 78 " ideal model delta sigma weight residual 114.04 110.16 3.88 1.24e+00 6.50e-01 9.81e+00 ... (remaining 12600 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.46: 4998 17.46 - 34.91: 418 34.91 - 52.37: 79 52.37 - 69.82: 8 69.82 - 87.28: 5 Dihedral angle restraints: 5508 sinusoidal: 2145 harmonic: 3363 Sorted by residual: dihedral pdb=" CB CYS R 102 " pdb=" SG CYS R 102 " pdb=" SG CYS R 181 " pdb=" CB CYS R 181 " ideal model delta sinusoidal sigma weight residual 93.00 172.97 -79.97 1 1.00e+01 1.00e-02 7.93e+01 dihedral pdb=" CA CYS R 119 " pdb=" C CYS R 119 " pdb=" N LEU R 120 " pdb=" CA LEU R 120 " ideal model delta harmonic sigma weight residual 180.00 151.11 28.89 0 5.00e+00 4.00e-02 3.34e+01 dihedral pdb=" CA THR R 77 " pdb=" C THR R 77 " pdb=" N PHE R 78 " pdb=" CA PHE R 78 " ideal model delta harmonic sigma weight residual 180.00 155.92 24.08 0 5.00e+00 4.00e-02 2.32e+01 ... (remaining 5505 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 1012 0.042 - 0.085: 297 0.085 - 0.127: 100 0.127 - 0.170: 11 0.170 - 0.212: 2 Chirality restraints: 1422 Sorted by residual: chirality pdb=" CA GLN A 304 " pdb=" N GLN A 304 " pdb=" C GLN A 304 " pdb=" CB GLN A 304 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.13e+00 chirality pdb=" CB THR B 47 " pdb=" CA THR B 47 " pdb=" OG1 THR B 47 " pdb=" CG2 THR B 47 " both_signs ideal model delta sigma weight residual False 2.55 2.37 0.18 2.00e-01 2.50e+01 8.08e-01 chirality pdb=" CA GLN A 306 " pdb=" N GLN A 306 " pdb=" C GLN A 306 " pdb=" CB GLN A 306 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.49e-01 ... (remaining 1419 not shown) Planarity restraints: 1593 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN C 90 " 0.069 5.00e-02 4.00e+02 1.03e-01 1.71e+01 pdb=" N PRO C 91 " -0.179 5.00e-02 4.00e+02 pdb=" CA PRO C 91 " 0.053 5.00e-02 4.00e+02 pdb=" CD PRO C 91 " 0.056 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE R 286 " 0.015 2.00e-02 2.50e+03 1.89e-02 6.28e+00 pdb=" CG PHE R 286 " -0.044 2.00e-02 2.50e+03 pdb=" CD1 PHE R 286 " 0.015 2.00e-02 2.50e+03 pdb=" CD2 PHE R 286 " 0.013 2.00e-02 2.50e+03 pdb=" CE1 PHE R 286 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE R 286 " 0.002 2.00e-02 2.50e+03 pdb=" CZ PHE R 286 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " 0.040 5.00e-02 4.00e+02 6.04e-02 5.84e+00 pdb=" N PRO B 236 " -0.104 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " 0.034 5.00e-02 4.00e+02 ... (remaining 1590 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 772 2.74 - 3.28: 9355 3.28 - 3.82: 14185 3.82 - 4.36: 15742 4.36 - 4.90: 27125 Nonbonded interactions: 67179 Sorted by model distance: nonbonded pdb=" O PRO R 292 " pdb=" OG1 THR R 295 " model vdw 2.199 3.040 nonbonded pdb=" O VAL R 212 " pdb=" OG1 THR R 215 " model vdw 2.209 3.040 nonbonded pdb=" NE1 TRP S 47 " pdb=" O ALA S 49 " model vdw 2.252 3.120 nonbonded pdb=" O MET R 272 " pdb=" OG SER R 275 " model vdw 2.278 3.040 nonbonded pdb=" NE1 TRP R 95 " pdb=" O GLY R 98 " model vdw 2.291 3.120 ... (remaining 67174 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.480 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.000 Extract box with map and model: 0.120 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 9.440 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7037 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 : 0.003 0.077 9305 Z= 0.135 Angle : 0.716 8.501 12607 Z= 0.377 Chirality : 0.045 0.212 1422 Planarity : 0.005 0.103 1593 Dihedral : 13.045 87.278 3337 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 13.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.19 % Favored : 90.81 % Rotamer: Outliers : 0.00 % Allowed : 0.20 % Favored : 99.80 % 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 (0.25), residues: 1143 helix: 0.85 (0.27), residues: 366 sheet: -0.92 (0.33), residues: 262 loop : -2.48 (0.25), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 21 TYR 0.028 0.001 TYR A 302 PHE 0.044 0.002 PHE R 286 TRP 0.027 0.002 TRP R 279 HIS 0.006 0.001 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00296 ( 9304) covalent geometry : angle 0.71570 (12605) SS BOND : bond 0.00408 ( 1) SS BOND : angle 0.84619 ( 2) hydrogen bonds : bond 0.18468 ( 339) hydrogen bonds : angle 6.60182 ( 969) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 374 time to evaluate : 0.346 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 LYS cc_start: 0.8601 (mtmm) cc_final: 0.8378 (mtmm) REVERT: A 191 PHE cc_start: 0.8011 (t80) cc_final: 0.7803 (t80) REVERT: A 204 GLN cc_start: 0.8645 (mm-40) cc_final: 0.8405 (mm-40) REVERT: A 212 ILE cc_start: 0.8915 (tp) cc_final: 0.8681 (tp) REVERT: A 240 MET cc_start: 0.4663 (mtp) cc_final: 0.4397 (mtp) REVERT: A 245 GLU cc_start: 0.6973 (mm-30) cc_final: 0.6247 (mm-30) REVERT: A 248 LYS cc_start: 0.8406 (mtmm) cc_final: 0.7981 (mtmm) REVERT: A 251 ASP cc_start: 0.8678 (t0) cc_final: 0.8368 (t0) REVERT: A 264 ILE cc_start: 0.8523 (mm) cc_final: 0.8233 (mm) REVERT: A 266 LEU cc_start: 0.7761 (tp) cc_final: 0.7532 (tp) REVERT: A 274 PHE cc_start: 0.8572 (t80) cc_final: 0.8239 (t80) REVERT: A 276 GLU cc_start: 0.7988 (pp20) cc_final: 0.7611 (pp20) REVERT: A 277 LYS cc_start: 0.8512 (mtmm) cc_final: 0.7224 (mtmm) REVERT: A 302 TYR cc_start: 0.7145 (t80) cc_final: 0.6896 (t80) REVERT: A 303 ILE cc_start: 0.8137 (mm) cc_final: 0.7931 (tp) REVERT: A 306 GLN cc_start: 0.7773 (mp10) cc_final: 0.7339 (mp10) REVERT: A 316 THR cc_start: 0.7699 (p) cc_final: 0.7391 (p) REVERT: A 317 LYS cc_start: 0.7671 (mttp) cc_final: 0.7284 (mttm) REVERT: A 341 ASP cc_start: 0.8155 (t0) cc_final: 0.7913 (t0) REVERT: A 343 ILE cc_start: 0.8394 (tp) cc_final: 0.7767 (tp) REVERT: A 345 LYS cc_start: 0.7682 (tppp) cc_final: 0.7383 (tppp) REVERT: A 347 ASN cc_start: 0.8128 (m110) cc_final: 0.7574 (m-40) REVERT: A 350 ASP cc_start: 0.7704 (m-30) cc_final: 0.7377 (m-30) REVERT: B 22 ARG cc_start: 0.8512 (mtt-85) cc_final: 0.8243 (mtt-85) REVERT: B 45 MET cc_start: 0.7589 (mmm) cc_final: 0.7003 (mmp) REVERT: B 125 ASN cc_start: 0.8356 (t0) cc_final: 0.7755 (t0) REVERT: B 127 LYS cc_start: 0.8178 (mmtp) cc_final: 0.7875 (mmtp) REVERT: B 148 CYS cc_start: 0.7472 (t) cc_final: 0.7115 (t) REVERT: B 170 ASP cc_start: 0.7309 (p0) cc_final: 0.6878 (p0) REVERT: B 217 MET cc_start: 0.7813 (ppp) cc_final: 0.7460 (ppp) REVERT: B 219 ARG cc_start: 0.7758 (tpp-160) cc_final: 0.7327 (tpp80) REVERT: B 225 HIS cc_start: 0.8483 (m170) cc_final: 0.8183 (m170) REVERT: B 233 CYS cc_start: 0.7872 (t) cc_final: 0.7657 (t) REVERT: B 247 ASP cc_start: 0.7659 (t0) cc_final: 0.7218 (t0) REVERT: B 253 PHE cc_start: 0.8216 (m-80) cc_final: 0.7686 (m-80) REVERT: B 290 ASP cc_start: 0.7249 (t0) cc_final: 0.7036 (t0) REVERT: B 298 ASP cc_start: 0.8210 (t0) cc_final: 0.7695 (t0) REVERT: B 322 ASP cc_start: 0.7682 (m-30) cc_final: 0.7346 (m-30) REVERT: C 44 ARG cc_start: 0.8883 (mpp80) cc_final: 0.8639 (ptt-90) REVERT: C 48 GLU cc_start: 0.9016 (mp0) cc_final: 0.8497 (mp0) REVERT: C 51 LYS cc_start: 0.9241 (ptpp) cc_final: 0.8765 (pttm) REVERT: C 52 MET cc_start: 0.8470 (mmp) cc_final: 0.7945 (mmp) REVERT: C 69 MET cc_start: 0.8565 (mtm) cc_final: 0.8138 (mtm) REVERT: C 73 GLU cc_start: 0.8123 (pp20) cc_final: 0.7774 (pp20) REVERT: R 108 LEU cc_start: 0.7847 (tp) cc_final: 0.7543 (tp) REVERT: R 114 TYR cc_start: 0.7835 (m-80) cc_final: 0.7400 (m-80) REVERT: R 117 VAL cc_start: 0.8863 (p) cc_final: 0.8656 (m) REVERT: R 120 LEU cc_start: 0.9004 (tp) cc_final: 0.8788 (tp) REVERT: R 182 TYR cc_start: 0.8489 (p90) cc_final: 0.8161 (p90) REVERT: R 183 MET cc_start: 0.6444 (tmm) cc_final: 0.5938 (tmm) REVERT: R 252 VAL cc_start: 0.7834 (p) cc_final: 0.7575 (m) REVERT: R 257 PHE cc_start: 0.8113 (t80) cc_final: 0.7837 (t80) REVERT: R 268 LYS cc_start: 0.9082 (pttt) cc_final: 0.8859 (pttt) REVERT: R 295 THR cc_start: 0.8591 (p) cc_final: 0.7503 (p) REVERT: R 299 TYR cc_start: 0.7688 (m-80) cc_final: 0.7397 (m-80) REVERT: S 34 MET cc_start: 0.7646 (pmm) cc_final: 0.7220 (ptm) REVERT: S 79 LEU cc_start: 0.7486 (tp) cc_final: 0.7118 (tp) REVERT: S 160 ARG cc_start: 0.7173 (mtm110) cc_final: 0.6724 (mtm110) REVERT: S 166 LEU cc_start: 0.8654 (tp) cc_final: 0.8434 (tp) REVERT: S 174 LEU cc_start: 0.8064 (tt) cc_final: 0.7819 (tt) outliers start: 0 outliers final: 0 residues processed: 374 average time/residue: 0.1144 time to fit residues: 55.6049 Evaluate side-chains 352 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 352 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 108 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 5.9990 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 0.6980 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 0.9980 chunk 100 optimal weight: 0.9980 chunk 106 optimal weight: 0.6980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 16 ASN C 75 HIS R 137 ASN S 194 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.152480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.120920 restraints weight = 17078.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.125411 restraints weight = 9062.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.128344 restraints weight = 5839.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.130359 restraints weight = 4278.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.131602 restraints weight = 3428.893| |-----------------------------------------------------------------------------| r_work (final): 0.3737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7028 moved from start: 0.1610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 9305 Z= 0.163 Angle : 0.737 11.456 12607 Z= 0.380 Chirality : 0.046 0.183 1422 Planarity : 0.005 0.069 1593 Dihedral : 5.177 27.923 1262 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 11.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.54 % Favored : 90.46 % Rotamer: Outliers : 2.21 % Allowed : 13.48 % Favored : 84.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -1.43 (0.24), residues: 1143 helix: 1.02 (0.27), residues: 371 sheet: -0.84 (0.33), residues: 251 loop : -2.55 (0.25), residues: 521 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 20 TYR 0.025 0.002 TYR R 88 PHE 0.032 0.002 PHE R 286 TRP 0.025 0.002 TRP R 85 HIS 0.007 0.001 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00358 ( 9304) covalent geometry : angle 0.73680 (12605) SS BOND : bond 0.00374 ( 1) SS BOND : angle 1.16121 ( 2) hydrogen bonds : bond 0.04977 ( 339) hydrogen bonds : angle 5.40995 ( 969) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 388 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 366 time to evaluate : 0.410 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 ARG cc_start: 0.7460 (ptp90) cc_final: 0.7162 (ptp90) REVERT: A 35 LYS cc_start: 0.8376 (mtmm) cc_final: 0.8108 (mtmm) REVERT: A 204 GLN cc_start: 0.8673 (mm-40) cc_final: 0.8447 (mm-40) REVERT: A 212 ILE cc_start: 0.8876 (tp) cc_final: 0.8647 (tp) REVERT: A 240 MET cc_start: 0.4669 (mtp) cc_final: 0.4454 (mtp) REVERT: A 245 GLU cc_start: 0.6926 (mm-30) cc_final: 0.6182 (mm-30) REVERT: A 248 LYS cc_start: 0.8375 (mtmm) cc_final: 0.7960 (mtmm) REVERT: A 251 ASP cc_start: 0.8706 (t0) cc_final: 0.8408 (t0) REVERT: A 264 ILE cc_start: 0.8437 (mm) cc_final: 0.8130 (mm) REVERT: A 266 LEU cc_start: 0.8032 (tp) cc_final: 0.7713 (tp) REVERT: A 267 PHE cc_start: 0.6958 (m-10) cc_final: 0.6746 (m-10) REVERT: A 276 GLU cc_start: 0.7976 (pp20) cc_final: 0.7731 (pp20) REVERT: A 302 TYR cc_start: 0.7232 (t80) cc_final: 0.6521 (t80) REVERT: A 303 ILE cc_start: 0.8195 (mm) cc_final: 0.7887 (tp) REVERT: A 304 GLN cc_start: 0.8185 (pm20) cc_final: 0.7855 (pm20) REVERT: A 313 ARG cc_start: 0.8312 (mmm160) cc_final: 0.7247 (tpt90) REVERT: A 314 LYS cc_start: 0.8079 (mmmt) cc_final: 0.7819 (mmmt) REVERT: A 333 GLN cc_start: 0.7917 (tp40) cc_final: 0.7128 (tp40) REVERT: A 341 ASP cc_start: 0.8085 (t0) cc_final: 0.7874 (t0) REVERT: A 343 ILE cc_start: 0.8419 (tp) cc_final: 0.7747 (tp) REVERT: A 345 LYS cc_start: 0.7726 (tppp) cc_final: 0.7402 (tppp) REVERT: A 347 ASN cc_start: 0.8207 (m110) cc_final: 0.7623 (m110) REVERT: A 350 ASP cc_start: 0.7710 (m-30) cc_final: 0.7367 (m-30) REVERT: B 15 LYS cc_start: 0.9105 (ptpp) cc_final: 0.8614 (pttm) REVERT: B 45 MET cc_start: 0.7615 (mmm) cc_final: 0.7088 (mmp) REVERT: B 46 ARG cc_start: 0.6948 (mpp-170) cc_final: 0.6441 (mpp-170) REVERT: B 125 ASN cc_start: 0.8218 (t0) cc_final: 0.7904 (t0) REVERT: B 127 LYS cc_start: 0.8286 (mmtp) cc_final: 0.7943 (mmtp) REVERT: B 148 CYS cc_start: 0.7193 (t) cc_final: 0.6686 (t) REVERT: B 170 ASP cc_start: 0.7284 (p0) cc_final: 0.6868 (p0) REVERT: B 205 ASP cc_start: 0.7618 (t0) cc_final: 0.7369 (t0) REVERT: B 219 ARG cc_start: 0.7848 (tpp-160) cc_final: 0.7587 (tpp80) REVERT: B 233 CYS cc_start: 0.7990 (t) cc_final: 0.7594 (t) REVERT: B 235 PHE cc_start: 0.7511 (t80) cc_final: 0.7270 (t80) REVERT: B 247 ASP cc_start: 0.7695 (t0) cc_final: 0.7157 (t0) REVERT: B 284 LEU cc_start: 0.8850 (mp) cc_final: 0.8563 (mm) REVERT: B 298 ASP cc_start: 0.8286 (t0) cc_final: 0.7660 (t0) REVERT: B 322 ASP cc_start: 0.7659 (m-30) cc_final: 0.7234 (m-30) REVERT: C 51 LYS cc_start: 0.9288 (ptpp) cc_final: 0.8688 (pttm) REVERT: C 52 MET cc_start: 0.8456 (mmp) cc_final: 0.7984 (mmp) REVERT: C 69 MET cc_start: 0.8457 (mtm) cc_final: 0.8044 (mtm) REVERT: C 73 GLU cc_start: 0.8097 (pp20) cc_final: 0.7710 (pp20) REVERT: D 23 MET cc_start: 0.7506 (ppp) cc_final: 0.6698 (ppp) REVERT: R 114 TYR cc_start: 0.7915 (m-80) cc_final: 0.7287 (m-80) REVERT: R 120 LEU cc_start: 0.8978 (tp) cc_final: 0.8742 (tp) REVERT: R 182 TYR cc_start: 0.8459 (p90) cc_final: 0.8146 (p90) REVERT: R 183 MET cc_start: 0.6617 (tmm) cc_final: 0.5904 (tmm) REVERT: R 257 PHE cc_start: 0.7999 (t80) cc_final: 0.7756 (t80) REVERT: R 261 TRP cc_start: 0.6409 (t-100) cc_final: 0.5931 (t-100) REVERT: R 265 HIS cc_start: 0.8008 (m-70) cc_final: 0.7207 (m-70) REVERT: R 295 THR cc_start: 0.8573 (p) cc_final: 0.7520 (p) REVERT: R 299 TYR cc_start: 0.7798 (m-80) cc_final: 0.7572 (m-80) REVERT: S 34 MET cc_start: 0.7581 (pmm) cc_final: 0.7265 (ptm) REVERT: S 79 LEU cc_start: 0.7306 (tp) cc_final: 0.6915 (tp) REVERT: S 93 MET cc_start: 0.7020 (mmm) cc_final: 0.6737 (mmm) REVERT: S 160 ARG cc_start: 0.7315 (mtm110) cc_final: 0.7032 (mtm110) REVERT: S 239 PHE cc_start: 0.8078 (m-80) cc_final: 0.7799 (m-10) outliers start: 22 outliers final: 17 residues processed: 371 average time/residue: 0.1119 time to fit residues: 54.1254 Evaluate side-chains 373 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 356 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 216 GLU Chi-restraints excluded: chain A residue 247 MET Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain R residue 30 LEU Chi-restraints excluded: chain R residue 249 ILE Chi-restraints excluded: chain R residue 285 LEU Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 178 LEU Chi-restraints excluded: chain S residue 224 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 13 optimal weight: 0.5980 chunk 104 optimal weight: 4.9990 chunk 101 optimal weight: 0.1980 chunk 12 optimal weight: 0.7980 chunk 108 optimal weight: 0.9980 chunk 39 optimal weight: 1.9990 chunk 59 optimal weight: 0.0060 chunk 105 optimal weight: 2.9990 chunk 94 optimal weight: 0.5980 chunk 17 optimal weight: 0.7980 chunk 54 optimal weight: 2.9990 overall best weight: 0.4396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 HIS C 75 HIS S 194 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.153701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.121971 restraints weight = 17077.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.126481 restraints weight = 9027.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.129398 restraints weight = 5801.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.131388 restraints weight = 4248.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.132762 restraints weight = 3406.241| |-----------------------------------------------------------------------------| r_work (final): 0.3759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6997 moved from start: 0.2123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9305 Z= 0.129 Angle : 0.707 12.698 12607 Z= 0.358 Chirality : 0.045 0.178 1422 Planarity : 0.005 0.058 1593 Dihedral : 5.024 28.774 1262 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.40 % Favored : 91.60 % Rotamer: Outliers : 3.22 % Allowed : 17.30 % Favored : 79.48 % 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: -1.35 (0.24), residues: 1143 helix: 0.89 (0.27), residues: 379 sheet: -0.68 (0.32), residues: 262 loop : -2.49 (0.25), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 52 TYR 0.025 0.001 TYR R 88 PHE 0.023 0.002 PHE R 312 TRP 0.017 0.002 TRP R 85 HIS 0.005 0.001 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00281 ( 9304) covalent geometry : angle 0.70675 (12605) SS BOND : bond 0.00419 ( 1) SS BOND : angle 1.17408 ( 2) hydrogen bonds : bond 0.04280 ( 339) hydrogen bonds : angle 4.93518 ( 969) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 395 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 363 time to evaluate : 0.349 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 ARG cc_start: 0.7458 (ptp90) cc_final: 0.7128 (ptp90) REVERT: A 212 ILE cc_start: 0.8851 (tp) cc_final: 0.8641 (tp) REVERT: A 240 MET cc_start: 0.4448 (mtp) cc_final: 0.4247 (mtp) REVERT: A 245 GLU cc_start: 0.6913 (mm-30) cc_final: 0.6157 (mm-30) REVERT: A 248 LYS cc_start: 0.8348 (mtmm) cc_final: 0.7936 (mtmm) REVERT: A 251 ASP cc_start: 0.8672 (t0) cc_final: 0.8353 (t0) REVERT: A 264 ILE cc_start: 0.8382 (mm) cc_final: 0.8131 (mm) REVERT: A 266 LEU cc_start: 0.8146 (tp) cc_final: 0.7926 (tp) REVERT: A 276 GLU cc_start: 0.7963 (pp20) cc_final: 0.7701 (pp20) REVERT: A 304 GLN cc_start: 0.8090 (OUTLIER) cc_final: 0.7880 (pm20) REVERT: A 306 GLN cc_start: 0.7729 (mp10) cc_final: 0.7401 (mp10) REVERT: A 313 ARG cc_start: 0.8278 (mmm160) cc_final: 0.7245 (tpt90) REVERT: A 318 GLU cc_start: 0.7486 (pm20) cc_final: 0.7276 (pm20) REVERT: A 333 GLN cc_start: 0.7893 (tp40) cc_final: 0.7119 (tp40) REVERT: A 343 ILE cc_start: 0.8416 (tp) cc_final: 0.7717 (tp) REVERT: A 345 LYS cc_start: 0.7671 (tppp) cc_final: 0.7239 (tppp) REVERT: A 347 ASN cc_start: 0.8223 (m110) cc_final: 0.7807 (m110) REVERT: A 350 ASP cc_start: 0.7679 (m-30) cc_final: 0.7339 (m-30) REVERT: B 15 LYS cc_start: 0.9097 (ptpp) cc_final: 0.8571 (pttm) REVERT: B 22 ARG cc_start: 0.7333 (tpm170) cc_final: 0.7089 (tpm170) REVERT: B 45 MET cc_start: 0.7634 (mmm) cc_final: 0.7236 (mmp) REVERT: B 46 ARG cc_start: 0.6820 (mpp-170) cc_final: 0.6235 (mpp-170) REVERT: B 76 ASP cc_start: 0.7305 (m-30) cc_final: 0.6747 (m-30) REVERT: B 125 ASN cc_start: 0.8243 (t0) cc_final: 0.7940 (t0) REVERT: B 127 LYS cc_start: 0.8268 (mmtp) cc_final: 0.7826 (mmtp) REVERT: B 128 THR cc_start: 0.8862 (t) cc_final: 0.8214 (p) REVERT: B 132 ASN cc_start: 0.7226 (m110) cc_final: 0.7019 (m110) REVERT: B 153 ASP cc_start: 0.7932 (t0) cc_final: 0.7153 (p0) REVERT: B 170 ASP cc_start: 0.7251 (p0) cc_final: 0.6863 (p0) REVERT: B 205 ASP cc_start: 0.7661 (t0) cc_final: 0.7417 (t0) REVERT: B 219 ARG cc_start: 0.7829 (tpp-160) cc_final: 0.7590 (tpp80) REVERT: B 233 CYS cc_start: 0.7848 (t) cc_final: 0.7414 (t) REVERT: B 235 PHE cc_start: 0.7545 (t80) cc_final: 0.7189 (t80) REVERT: B 247 ASP cc_start: 0.7669 (t0) cc_final: 0.7051 (t0) REVERT: B 284 LEU cc_start: 0.8802 (mp) cc_final: 0.8561 (mm) REVERT: B 298 ASP cc_start: 0.8280 (t0) cc_final: 0.7683 (t0) REVERT: B 322 ASP cc_start: 0.7544 (m-30) cc_final: 0.7186 (m-30) REVERT: C 48 GLU cc_start: 0.8728 (mp0) cc_final: 0.8132 (mm-30) REVERT: C 51 LYS cc_start: 0.9257 (ptpp) cc_final: 0.7985 (pttm) REVERT: C 52 MET cc_start: 0.8396 (mmp) cc_final: 0.7925 (mmp) REVERT: C 69 MET cc_start: 0.8474 (mtm) cc_final: 0.8020 (mtm) REVERT: C 73 GLU cc_start: 0.8059 (pp20) cc_final: 0.7707 (pp20) REVERT: R 82 LEU cc_start: 0.8303 (OUTLIER) cc_final: 0.7974 (tt) REVERT: R 114 TYR cc_start: 0.7890 (m-80) cc_final: 0.7189 (m-80) REVERT: R 120 LEU cc_start: 0.9025 (tp) cc_final: 0.8780 (tp) REVERT: R 182 TYR cc_start: 0.8384 (p90) cc_final: 0.8124 (p90) REVERT: R 183 MET cc_start: 0.6653 (tmm) cc_final: 0.5744 (tmm) REVERT: R 261 TRP cc_start: 0.6456 (t-100) cc_final: 0.6194 (t-100) REVERT: R 265 HIS cc_start: 0.8046 (m-70) cc_final: 0.7414 (m-70) REVERT: R 286 PHE cc_start: 0.8230 (m-80) cc_final: 0.7548 (m-80) REVERT: R 295 THR cc_start: 0.8427 (p) cc_final: 0.7284 (p) REVERT: R 299 TYR cc_start: 0.7782 (m-80) cc_final: 0.7530 (m-80) REVERT: S 79 LEU cc_start: 0.7493 (tp) cc_final: 0.7068 (tp) REVERT: S 93 MET cc_start: 0.6983 (mmm) cc_final: 0.6783 (mmm) REVERT: S 160 ARG cc_start: 0.7276 (mtm110) cc_final: 0.6972 (mtm110) outliers start: 32 outliers final: 24 residues processed: 375 average time/residue: 0.1154 time to fit residues: 56.1634 Evaluate side-chains 384 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 358 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 270 LYS Chi-restraints excluded: chain A residue 274 PHE Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 304 GLN Chi-restraints excluded: chain A residue 312 LYS Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain R residue 82 LEU Chi-restraints excluded: chain R residue 212 VAL Chi-restraints excluded: chain R residue 249 ILE Chi-restraints excluded: chain R residue 285 LEU Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 140 MET Chi-restraints excluded: chain S residue 178 LEU Chi-restraints excluded: chain S residue 210 THR Chi-restraints excluded: chain S residue 224 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 64 optimal weight: 5.9990 chunk 69 optimal weight: 2.9990 chunk 60 optimal weight: 0.5980 chunk 58 optimal weight: 4.9990 chunk 73 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 9 optimal weight: 0.7980 chunk 61 optimal weight: 10.0000 chunk 15 optimal weight: 5.9990 chunk 84 optimal weight: 0.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.149731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.117983 restraints weight = 17288.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.122401 restraints weight = 9166.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.125292 restraints weight = 5906.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.127280 restraints weight = 4350.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.128622 restraints weight = 3491.635| |-----------------------------------------------------------------------------| r_work (final): 0.3698 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7075 moved from start: 0.2477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9305 Z= 0.199 Angle : 0.754 12.953 12607 Z= 0.385 Chirality : 0.047 0.167 1422 Planarity : 0.005 0.060 1593 Dihedral : 5.197 27.726 1262 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 13.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.97 % Favored : 90.03 % Rotamer: Outliers : 5.33 % Allowed : 19.72 % Favored : 74.95 % 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: -1.37 (0.24), residues: 1143 helix: 1.05 (0.27), residues: 371 sheet: -0.65 (0.32), residues: 253 loop : -2.61 (0.24), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 52 TYR 0.019 0.002 TYR R 309 PHE 0.023 0.002 PHE R 39 TRP 0.023 0.002 TRP B 332 HIS 0.010 0.001 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00437 ( 9304) covalent geometry : angle 0.75405 (12605) SS BOND : bond 0.00250 ( 1) SS BOND : angle 1.00397 ( 2) hydrogen bonds : bond 0.05006 ( 339) hydrogen bonds : angle 4.94562 ( 969) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 410 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 357 time to evaluate : 0.329 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 208 ARG cc_start: 0.8297 (ttp80) cc_final: 0.8028 (ttp-170) REVERT: A 212 ILE cc_start: 0.8861 (tp) cc_final: 0.8646 (tp) REVERT: A 245 GLU cc_start: 0.6999 (mm-30) cc_final: 0.6222 (mm-30) REVERT: A 248 LYS cc_start: 0.8454 (mtmm) cc_final: 0.8000 (mtmm) REVERT: A 251 ASP cc_start: 0.8774 (t0) cc_final: 0.8447 (t0) REVERT: A 264 ILE cc_start: 0.8360 (mm) cc_final: 0.8112 (mm) REVERT: A 266 LEU cc_start: 0.8253 (tp) cc_final: 0.8035 (tp) REVERT: A 276 GLU cc_start: 0.8041 (pp20) cc_final: 0.7815 (pp20) REVERT: A 287 TYR cc_start: 0.8407 (m-80) cc_final: 0.7727 (m-80) REVERT: A 302 TYR cc_start: 0.7045 (t80) cc_final: 0.6474 (t80) REVERT: A 313 ARG cc_start: 0.8184 (mmm160) cc_final: 0.7174 (tpt90) REVERT: A 318 GLU cc_start: 0.7493 (pm20) cc_final: 0.7173 (pm20) REVERT: A 333 GLN cc_start: 0.7947 (tp40) cc_final: 0.7224 (tp40) REVERT: A 343 ILE cc_start: 0.8458 (tp) cc_final: 0.7779 (tp) REVERT: A 347 ASN cc_start: 0.8278 (m110) cc_final: 0.7805 (m-40) REVERT: A 350 ASP cc_start: 0.7759 (m-30) cc_final: 0.7411 (m-30) REVERT: B 15 LYS cc_start: 0.9122 (ptpp) cc_final: 0.8623 (pttm) REVERT: B 22 ARG cc_start: 0.7525 (tpm170) cc_final: 0.7203 (tpm170) REVERT: B 45 MET cc_start: 0.7618 (mmm) cc_final: 0.7249 (mmp) REVERT: B 46 ARG cc_start: 0.6852 (mpp-170) cc_final: 0.6259 (mpp-170) REVERT: B 125 ASN cc_start: 0.8270 (t0) cc_final: 0.7997 (t0) REVERT: B 127 LYS cc_start: 0.8260 (mmtp) cc_final: 0.7784 (mmtp) REVERT: B 128 THR cc_start: 0.8812 (t) cc_final: 0.8136 (p) REVERT: B 132 ASN cc_start: 0.7632 (m110) cc_final: 0.7230 (m110) REVERT: B 153 ASP cc_start: 0.7914 (t0) cc_final: 0.7284 (p0) REVERT: B 164 THR cc_start: 0.7831 (OUTLIER) cc_final: 0.7555 (m) REVERT: B 170 ASP cc_start: 0.7132 (p0) cc_final: 0.6774 (p0) REVERT: B 188 MET cc_start: 0.8241 (OUTLIER) cc_final: 0.7663 (mmm) REVERT: B 219 ARG cc_start: 0.7917 (tpp-160) cc_final: 0.7611 (tpp80) REVERT: B 233 CYS cc_start: 0.7900 (t) cc_final: 0.7577 (t) REVERT: B 235 PHE cc_start: 0.7628 (t80) cc_final: 0.7256 (t80) REVERT: B 247 ASP cc_start: 0.7783 (t0) cc_final: 0.7189 (t0) REVERT: B 298 ASP cc_start: 0.8281 (t0) cc_final: 0.7756 (t0) REVERT: B 322 ASP cc_start: 0.7575 (m-30) cc_final: 0.7182 (m-30) REVERT: C 48 GLU cc_start: 0.8718 (OUTLIER) cc_final: 0.8218 (mm-30) REVERT: C 51 LYS cc_start: 0.9279 (ptpp) cc_final: 0.8094 (pttm) REVERT: C 52 MET cc_start: 0.8436 (mmp) cc_final: 0.7976 (mmp) REVERT: C 69 MET cc_start: 0.8494 (mtm) cc_final: 0.8050 (mtm) REVERT: C 73 GLU cc_start: 0.8106 (pp20) cc_final: 0.7746 (pp20) REVERT: R 113 MET cc_start: 0.8030 (ppp) cc_final: 0.7657 (ppp) REVERT: R 114 TYR cc_start: 0.7874 (m-80) cc_final: 0.6935 (m-80) REVERT: R 253 LEU cc_start: 0.8547 (mp) cc_final: 0.8238 (mp) REVERT: R 261 TRP cc_start: 0.6788 (t-100) cc_final: 0.6171 (t-100) REVERT: R 265 HIS cc_start: 0.8201 (m-70) cc_final: 0.7419 (m-70) REVERT: R 286 PHE cc_start: 0.8251 (m-80) cc_final: 0.7513 (m-80) REVERT: R 295 THR cc_start: 0.8419 (p) cc_final: 0.7152 (p) REVERT: R 299 TYR cc_start: 0.7862 (m-80) cc_final: 0.7597 (m-80) REVERT: S 6 GLU cc_start: 0.6953 (mp0) cc_final: 0.6467 (mp0) REVERT: S 160 ARG cc_start: 0.7253 (mtm110) cc_final: 0.6959 (mtm110) outliers start: 53 outliers final: 41 residues processed: 377 average time/residue: 0.1172 time to fit residues: 57.2637 Evaluate side-chains 391 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 347 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 247 MET Chi-restraints excluded: chain A residue 267 PHE Chi-restraints excluded: chain A residue 270 LYS Chi-restraints excluded: chain A residue 274 PHE Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 304 GLN Chi-restraints excluded: chain A residue 312 LYS Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 188 MET Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain C residue 48 GLU Chi-restraints excluded: chain D residue 29 VAL Chi-restraints excluded: chain R residue 108 LEU Chi-restraints excluded: chain R residue 112 ASN Chi-restraints excluded: chain R residue 116 SER Chi-restraints excluded: chain R residue 117 VAL Chi-restraints excluded: chain R residue 166 VAL Chi-restraints excluded: chain R residue 198 GLU Chi-restraints excluded: chain R residue 212 VAL Chi-restraints excluded: chain R residue 249 ILE Chi-restraints excluded: chain R residue 285 LEU Chi-restraints excluded: chain R residue 287 LEU Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 70 ILE Chi-restraints excluded: chain S residue 140 MET Chi-restraints excluded: chain S residue 172 THR Chi-restraints excluded: chain S residue 174 LEU Chi-restraints excluded: chain S residue 210 THR Chi-restraints excluded: chain S residue 224 VAL Chi-restraints excluded: chain S residue 244 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 40 optimal weight: 0.0970 chunk 92 optimal weight: 0.7980 chunk 32 optimal weight: 0.9990 chunk 60 optimal weight: 1.9990 chunk 54 optimal weight: 0.9980 chunk 98 optimal weight: 0.5980 chunk 103 optimal weight: 0.0020 chunk 89 optimal weight: 0.4980 chunk 96 optimal weight: 0.8980 chunk 46 optimal weight: 2.9990 chunk 34 optimal weight: 0.5980 overall best weight: 0.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 44 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.154646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.122920 restraints weight = 17128.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.127318 restraints weight = 8975.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.130229 restraints weight = 5747.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.132230 restraints weight = 4200.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.133561 restraints weight = 3351.613| |-----------------------------------------------------------------------------| r_work (final): 0.3745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6997 moved from start: 0.2692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 9305 Z= 0.129 Angle : 0.747 12.409 12607 Z= 0.374 Chirality : 0.045 0.184 1422 Planarity : 0.004 0.057 1593 Dihedral : 5.038 29.534 1262 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 11.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.52 % Favored : 92.48 % Rotamer: Outliers : 5.13 % Allowed : 22.13 % Favored : 72.74 % 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: -1.35 (0.24), residues: 1143 helix: 0.93 (0.27), residues: 373 sheet: -0.65 (0.31), residues: 266 loop : -2.52 (0.25), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 52 TYR 0.013 0.001 TYR R 309 PHE 0.025 0.002 PHE R 312 TRP 0.020 0.002 TRP R 279 HIS 0.004 0.001 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00284 ( 9304) covalent geometry : angle 0.74645 (12605) SS BOND : bond 0.00531 ( 1) SS BOND : angle 1.11536 ( 2) hydrogen bonds : bond 0.04179 ( 339) hydrogen bonds : angle 4.83495 ( 969) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 402 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 351 time to evaluate : 0.300 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 208 ARG cc_start: 0.8283 (ttp80) cc_final: 0.7998 (ttp-170) REVERT: A 212 ILE cc_start: 0.8821 (tp) cc_final: 0.8611 (tp) REVERT: A 216 GLU cc_start: 0.7544 (tm-30) cc_final: 0.7240 (tm-30) REVERT: A 245 GLU cc_start: 0.6917 (mm-30) cc_final: 0.6142 (mm-30) REVERT: A 248 LYS cc_start: 0.8356 (mtmm) cc_final: 0.7918 (mtmm) REVERT: A 251 ASP cc_start: 0.8652 (t0) cc_final: 0.8424 (t0) REVERT: A 266 LEU cc_start: 0.8149 (tp) cc_final: 0.7896 (tp) REVERT: A 287 TYR cc_start: 0.8268 (m-80) cc_final: 0.7621 (m-80) REVERT: A 302 TYR cc_start: 0.6992 (t80) cc_final: 0.6747 (t80) REVERT: A 306 GLN cc_start: 0.7802 (mp10) cc_final: 0.7583 (mp10) REVERT: A 313 ARG cc_start: 0.8045 (mmm160) cc_final: 0.6979 (tpt90) REVERT: A 314 LYS cc_start: 0.7942 (mmmt) cc_final: 0.7691 (mmmt) REVERT: A 316 THR cc_start: 0.7751 (p) cc_final: 0.7099 (p) REVERT: A 318 GLU cc_start: 0.7444 (pm20) cc_final: 0.6781 (pm20) REVERT: A 333 GLN cc_start: 0.7876 (tp40) cc_final: 0.7108 (tp40) REVERT: A 343 ILE cc_start: 0.8431 (tp) cc_final: 0.7735 (tp) REVERT: A 347 ASN cc_start: 0.8216 (m110) cc_final: 0.7755 (m-40) REVERT: A 350 ASP cc_start: 0.7682 (m-30) cc_final: 0.7354 (m-30) REVERT: B 15 LYS cc_start: 0.9099 (ptpp) cc_final: 0.8653 (pttm) REVERT: B 22 ARG cc_start: 0.7518 (tpm170) cc_final: 0.7280 (tpm170) REVERT: B 45 MET cc_start: 0.7594 (mmm) cc_final: 0.7343 (mmp) REVERT: B 46 ARG cc_start: 0.6887 (mpp-170) cc_final: 0.6281 (mpp-170) REVERT: B 76 ASP cc_start: 0.7194 (m-30) cc_final: 0.6598 (m-30) REVERT: B 125 ASN cc_start: 0.8123 (t0) cc_final: 0.7908 (t0) REVERT: B 127 LYS cc_start: 0.8161 (mmtp) cc_final: 0.7749 (mmtp) REVERT: B 132 ASN cc_start: 0.7598 (m110) cc_final: 0.7216 (m110) REVERT: B 153 ASP cc_start: 0.7904 (t0) cc_final: 0.7159 (p0) REVERT: B 164 THR cc_start: 0.7668 (OUTLIER) cc_final: 0.7386 (m) REVERT: B 170 ASP cc_start: 0.7121 (p0) cc_final: 0.6874 (p0) REVERT: B 205 ASP cc_start: 0.7626 (t0) cc_final: 0.7411 (t0) REVERT: B 212 ASP cc_start: 0.7900 (t70) cc_final: 0.7616 (t0) REVERT: B 219 ARG cc_start: 0.7850 (tpp-160) cc_final: 0.7434 (tpp80) REVERT: B 233 CYS cc_start: 0.7891 (t) cc_final: 0.7597 (t) REVERT: B 235 PHE cc_start: 0.7515 (t80) cc_final: 0.7042 (t80) REVERT: B 247 ASP cc_start: 0.7728 (t0) cc_final: 0.7109 (t0) REVERT: B 298 ASP cc_start: 0.8237 (t0) cc_final: 0.7744 (t0) REVERT: B 322 ASP cc_start: 0.7537 (m-30) cc_final: 0.7147 (m-30) REVERT: C 48 GLU cc_start: 0.8693 (OUTLIER) cc_final: 0.8149 (mm-30) REVERT: C 51 LYS cc_start: 0.9249 (ptpp) cc_final: 0.8027 (pttm) REVERT: C 52 MET cc_start: 0.8420 (mmp) cc_final: 0.7834 (mmp) REVERT: C 69 MET cc_start: 0.8465 (mtm) cc_final: 0.8055 (mtm) REVERT: C 73 GLU cc_start: 0.8090 (pp20) cc_final: 0.7819 (pp20) REVERT: R 82 LEU cc_start: 0.8227 (OUTLIER) cc_final: 0.7849 (tt) REVERT: R 114 TYR cc_start: 0.7795 (m-80) cc_final: 0.7336 (m-80) REVERT: R 183 MET cc_start: 0.6789 (tmm) cc_final: 0.6234 (tmm) REVERT: R 187 MET cc_start: 0.3753 (mpp) cc_final: 0.2968 (ptp) REVERT: R 253 LEU cc_start: 0.8502 (mp) cc_final: 0.8185 (mp) REVERT: R 261 TRP cc_start: 0.6737 (t-100) cc_final: 0.5988 (t-100) REVERT: R 265 HIS cc_start: 0.8203 (m-70) cc_final: 0.7338 (m-70) REVERT: R 286 PHE cc_start: 0.8193 (m-80) cc_final: 0.7443 (m-80) REVERT: R 295 THR cc_start: 0.8271 (p) cc_final: 0.6998 (p) REVERT: R 299 TYR cc_start: 0.7793 (m-80) cc_final: 0.7490 (m-80) REVERT: S 6 GLU cc_start: 0.6885 (mp0) cc_final: 0.6284 (mp0) REVERT: S 32 PHE cc_start: 0.7779 (m-10) cc_final: 0.7475 (m-10) REVERT: S 38 ARG cc_start: 0.7617 (ttm-80) cc_final: 0.6995 (ptm160) REVERT: S 160 ARG cc_start: 0.7219 (mtm110) cc_final: 0.6802 (mtm110) outliers start: 51 outliers final: 38 residues processed: 371 average time/residue: 0.1140 time to fit residues: 55.2972 Evaluate side-chains 381 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 340 time to evaluate : 0.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 247 MET Chi-restraints excluded: chain A residue 267 PHE Chi-restraints excluded: chain A residue 274 PHE Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 304 GLN Chi-restraints excluded: chain A residue 307 PHE Chi-restraints excluded: chain A residue 312 LYS Chi-restraints excluded: chain B residue 42 ARG Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain C residue 48 GLU Chi-restraints excluded: chain R residue 82 LEU Chi-restraints excluded: chain R residue 108 LEU Chi-restraints excluded: chain R residue 116 SER Chi-restraints excluded: chain R residue 117 VAL Chi-restraints excluded: chain R residue 166 VAL Chi-restraints excluded: chain R residue 206 THR Chi-restraints excluded: chain R residue 212 VAL Chi-restraints excluded: chain R residue 249 ILE Chi-restraints excluded: chain R residue 285 LEU Chi-restraints excluded: chain R residue 287 LEU Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 70 ILE Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 174 LEU Chi-restraints excluded: chain S residue 195 LEU Chi-restraints excluded: chain S residue 210 THR Chi-restraints excluded: chain S residue 224 VAL Chi-restraints excluded: chain S residue 244 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 87 optimal weight: 0.6980 chunk 104 optimal weight: 5.9990 chunk 27 optimal weight: 3.9990 chunk 25 optimal weight: 3.9990 chunk 45 optimal weight: 1.9990 chunk 30 optimal weight: 0.6980 chunk 102 optimal weight: 2.9990 chunk 112 optimal weight: 0.6980 chunk 54 optimal weight: 0.9990 chunk 103 optimal weight: 2.9990 chunk 93 optimal weight: 1.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 175 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.150978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.119446 restraints weight = 17034.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.123781 restraints weight = 8906.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.126666 restraints weight = 5698.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.128575 restraints weight = 4155.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.129927 restraints weight = 3333.323| |-----------------------------------------------------------------------------| r_work (final): 0.3702 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7048 moved from start: 0.2882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 9305 Z= 0.171 Angle : 0.756 10.045 12607 Z= 0.383 Chirality : 0.046 0.176 1422 Planarity : 0.005 0.058 1593 Dihedral : 5.088 26.272 1262 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 13.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.36 % Favored : 90.64 % Rotamer: Outliers : 5.53 % Allowed : 23.44 % Favored : 71.03 % 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: -1.42 (0.24), residues: 1143 helix: 1.03 (0.27), residues: 365 sheet: -0.80 (0.31), residues: 270 loop : -2.58 (0.24), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 52 TYR 0.016 0.001 TYR S 102 PHE 0.026 0.002 PHE A 191 TRP 0.024 0.002 TRP R 279 HIS 0.008 0.001 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00377 ( 9304) covalent geometry : angle 0.75571 (12605) SS BOND : bond 0.00182 ( 1) SS BOND : angle 1.11009 ( 2) hydrogen bonds : bond 0.04678 ( 339) hydrogen bonds : angle 4.89830 ( 969) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 405 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 350 time to evaluate : 0.300 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 208 ARG cc_start: 0.8300 (ttp80) cc_final: 0.8001 (ttp-170) REVERT: A 216 GLU cc_start: 0.7540 (tm-30) cc_final: 0.7263 (tm-30) REVERT: A 245 GLU cc_start: 0.6966 (mm-30) cc_final: 0.6196 (mm-30) REVERT: A 248 LYS cc_start: 0.8456 (mtmm) cc_final: 0.7883 (mtmm) REVERT: A 251 ASP cc_start: 0.8737 (t0) cc_final: 0.8501 (t0) REVERT: A 266 LEU cc_start: 0.8199 (tp) cc_final: 0.7980 (tp) REVERT: A 287 TYR cc_start: 0.8384 (m-80) cc_final: 0.7717 (m-80) REVERT: A 290 TYR cc_start: 0.6751 (t80) cc_final: 0.5926 (t80) REVERT: A 302 TYR cc_start: 0.6987 (t80) cc_final: 0.6637 (t80) REVERT: A 313 ARG cc_start: 0.8114 (mmm160) cc_final: 0.7189 (tpt90) REVERT: A 316 THR cc_start: 0.7813 (p) cc_final: 0.7466 (p) REVERT: A 317 LYS cc_start: 0.8064 (mttt) cc_final: 0.7590 (mttm) REVERT: A 333 GLN cc_start: 0.7914 (tp40) cc_final: 0.7183 (tp40) REVERT: A 343 ILE cc_start: 0.8460 (tp) cc_final: 0.7765 (tp) REVERT: A 347 ASN cc_start: 0.8218 (m110) cc_final: 0.7764 (m-40) REVERT: A 350 ASP cc_start: 0.7748 (m-30) cc_final: 0.7409 (m-30) REVERT: B 22 ARG cc_start: 0.7597 (tpm170) cc_final: 0.7355 (tpm170) REVERT: B 45 MET cc_start: 0.7599 (mmm) cc_final: 0.7266 (mmp) REVERT: B 46 ARG cc_start: 0.6913 (mpp-170) cc_final: 0.6356 (mpp-170) REVERT: B 76 ASP cc_start: 0.7191 (m-30) cc_final: 0.6633 (m-30) REVERT: B 125 ASN cc_start: 0.8177 (t0) cc_final: 0.7944 (t0) REVERT: B 127 LYS cc_start: 0.8278 (mmtp) cc_final: 0.7840 (mmtp) REVERT: B 132 ASN cc_start: 0.7666 (m110) cc_final: 0.7297 (m110) REVERT: B 153 ASP cc_start: 0.7906 (t0) cc_final: 0.7251 (p0) REVERT: B 164 THR cc_start: 0.7765 (OUTLIER) cc_final: 0.7485 (m) REVERT: B 170 ASP cc_start: 0.6986 (p0) cc_final: 0.6630 (p0) REVERT: B 188 MET cc_start: 0.8235 (OUTLIER) cc_final: 0.7725 (mmm) REVERT: B 205 ASP cc_start: 0.7562 (t0) cc_final: 0.7315 (t0) REVERT: B 212 ASP cc_start: 0.8068 (t70) cc_final: 0.7685 (t0) REVERT: B 219 ARG cc_start: 0.7901 (tpp-160) cc_final: 0.7556 (tpp80) REVERT: B 233 CYS cc_start: 0.7908 (t) cc_final: 0.7700 (t) REVERT: B 247 ASP cc_start: 0.7804 (t0) cc_final: 0.7181 (t0) REVERT: B 262 MET cc_start: 0.7266 (mpp) cc_final: 0.7052 (mmm) REVERT: B 284 LEU cc_start: 0.8786 (mp) cc_final: 0.8577 (mm) REVERT: B 298 ASP cc_start: 0.8319 (t0) cc_final: 0.7791 (t0) REVERT: B 322 ASP cc_start: 0.7604 (m-30) cc_final: 0.7187 (m-30) REVERT: C 48 GLU cc_start: 0.8794 (OUTLIER) cc_final: 0.8093 (mm-30) REVERT: C 51 LYS cc_start: 0.9267 (ptpp) cc_final: 0.8014 (pttm) REVERT: C 52 MET cc_start: 0.8468 (mmp) cc_final: 0.7870 (mmp) REVERT: C 69 MET cc_start: 0.8515 (mtm) cc_final: 0.8055 (mtm) REVERT: C 71 TYR cc_start: 0.8374 (t80) cc_final: 0.8162 (t80) REVERT: C 73 GLU cc_start: 0.8128 (pp20) cc_final: 0.7785 (pp20) REVERT: R 82 LEU cc_start: 0.8243 (OUTLIER) cc_final: 0.7857 (tt) REVERT: R 113 MET cc_start: 0.8072 (ppp) cc_final: 0.7602 (ppp) REVERT: R 114 TYR cc_start: 0.7870 (m-80) cc_final: 0.6977 (m-80) REVERT: R 183 MET cc_start: 0.6866 (tmm) cc_final: 0.6085 (tmm) REVERT: R 253 LEU cc_start: 0.8590 (mp) cc_final: 0.8386 (mp) REVERT: R 261 TRP cc_start: 0.6800 (t-100) cc_final: 0.6078 (t-100) REVERT: R 265 HIS cc_start: 0.8187 (m-70) cc_final: 0.7358 (m-70) REVERT: R 286 PHE cc_start: 0.8304 (m-80) cc_final: 0.7544 (m-80) REVERT: R 295 THR cc_start: 0.8288 (p) cc_final: 0.6969 (p) REVERT: R 299 TYR cc_start: 0.7939 (m-80) cc_final: 0.7646 (m-80) REVERT: S 6 GLU cc_start: 0.6907 (mp0) cc_final: 0.6325 (mp0) REVERT: S 83 MET cc_start: 0.7784 (mpp) cc_final: 0.7277 (mpp) REVERT: S 160 ARG cc_start: 0.7291 (mtm110) cc_final: 0.7046 (mtm110) REVERT: S 234 GLU cc_start: 0.6625 (OUTLIER) cc_final: 0.6401 (tm-30) outliers start: 55 outliers final: 43 residues processed: 372 average time/residue: 0.1131 time to fit residues: 54.7853 Evaluate side-chains 393 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 345 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 247 MET Chi-restraints excluded: chain A residue 267 PHE Chi-restraints excluded: chain A residue 270 LYS Chi-restraints excluded: chain A residue 274 PHE Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 304 GLN Chi-restraints excluded: chain A residue 307 PHE Chi-restraints excluded: chain A residue 312 LYS Chi-restraints excluded: chain B residue 42 ARG Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 188 MET Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain C residue 48 GLU Chi-restraints excluded: chain R residue 82 LEU Chi-restraints excluded: chain R residue 117 VAL Chi-restraints excluded: chain R residue 166 VAL Chi-restraints excluded: chain R residue 212 VAL Chi-restraints excluded: chain R residue 249 ILE Chi-restraints excluded: chain R residue 262 MET Chi-restraints excluded: chain R residue 285 LEU Chi-restraints excluded: chain R residue 287 LEU Chi-restraints excluded: chain R residue 302 SER Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 70 ILE Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 174 LEU Chi-restraints excluded: chain S residue 195 LEU Chi-restraints excluded: chain S residue 210 THR Chi-restraints excluded: chain S residue 224 VAL Chi-restraints excluded: chain S residue 234 GLU Chi-restraints excluded: chain S residue 244 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 18 optimal weight: 2.9990 chunk 72 optimal weight: 5.9990 chunk 21 optimal weight: 0.7980 chunk 5 optimal weight: 4.9990 chunk 53 optimal weight: 2.9990 chunk 99 optimal weight: 0.7980 chunk 83 optimal weight: 0.0570 chunk 89 optimal weight: 0.4980 chunk 1 optimal weight: 0.7980 chunk 0 optimal weight: 3.9990 chunk 104 optimal weight: 2.9990 overall best weight: 0.5898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.153098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.121384 restraints weight = 17216.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.125809 restraints weight = 9066.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.128694 restraints weight = 5798.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.130673 restraints weight = 4231.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.131997 restraints weight = 3384.412| |-----------------------------------------------------------------------------| r_work (final): 0.3726 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7023 moved from start: 0.2985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 9305 Z= 0.142 Angle : 0.760 10.459 12607 Z= 0.384 Chirality : 0.046 0.226 1422 Planarity : 0.005 0.059 1593 Dihedral : 5.002 21.758 1262 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 13.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.70 % Favored : 92.30 % Rotamer: Outliers : 4.83 % Allowed : 25.25 % Favored : 69.92 % 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: -1.33 (0.24), residues: 1143 helix: 1.02 (0.28), residues: 367 sheet: -0.64 (0.31), residues: 267 loop : -2.55 (0.24), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 52 TYR 0.020 0.001 TYR R 35 PHE 0.028 0.002 PHE R 223 TRP 0.011 0.001 TRP R 85 HIS 0.006 0.001 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00319 ( 9304) covalent geometry : angle 0.75968 (12605) SS BOND : bond 0.00547 ( 1) SS BOND : angle 0.74824 ( 2) hydrogen bonds : bond 0.04484 ( 339) hydrogen bonds : angle 4.81850 ( 969) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 397 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 349 time to evaluate : 0.289 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 208 ARG cc_start: 0.8269 (ttp80) cc_final: 0.7969 (ttp-170) REVERT: A 216 GLU cc_start: 0.7511 (tm-30) cc_final: 0.7272 (tm-30) REVERT: A 245 GLU cc_start: 0.6936 (mm-30) cc_final: 0.6158 (mm-30) REVERT: A 248 LYS cc_start: 0.8441 (mtmm) cc_final: 0.7846 (mtmm) REVERT: A 251 ASP cc_start: 0.8713 (t0) cc_final: 0.8504 (t0) REVERT: A 266 LEU cc_start: 0.8208 (tp) cc_final: 0.7978 (tp) REVERT: A 287 TYR cc_start: 0.8319 (m-80) cc_final: 0.7670 (m-80) REVERT: A 290 TYR cc_start: 0.6733 (t80) cc_final: 0.5915 (t80) REVERT: A 313 ARG cc_start: 0.8020 (mmm160) cc_final: 0.7270 (tpt90) REVERT: A 316 THR cc_start: 0.7808 (p) cc_final: 0.7517 (p) REVERT: A 317 LYS cc_start: 0.7992 (mttt) cc_final: 0.7493 (mttm) REVERT: A 333 GLN cc_start: 0.7865 (tp40) cc_final: 0.7143 (tp40) REVERT: A 343 ILE cc_start: 0.8488 (tp) cc_final: 0.7784 (tp) REVERT: A 347 ASN cc_start: 0.8246 (m110) cc_final: 0.7766 (m-40) REVERT: A 350 ASP cc_start: 0.7693 (m-30) cc_final: 0.7356 (m-30) REVERT: B 15 LYS cc_start: 0.9108 (ptpp) cc_final: 0.8624 (ptpp) REVERT: B 22 ARG cc_start: 0.7565 (tpm170) cc_final: 0.7307 (tpm170) REVERT: B 45 MET cc_start: 0.7521 (mmm) cc_final: 0.7289 (mmp) REVERT: B 46 ARG cc_start: 0.6883 (mpp-170) cc_final: 0.6322 (mpp-170) REVERT: B 76 ASP cc_start: 0.7154 (m-30) cc_final: 0.6630 (m-30) REVERT: B 125 ASN cc_start: 0.8162 (t0) cc_final: 0.7939 (t0) REVERT: B 127 LYS cc_start: 0.8229 (mmtp) cc_final: 0.7774 (mmtp) REVERT: B 132 ASN cc_start: 0.7642 (m110) cc_final: 0.7295 (m110) REVERT: B 153 ASP cc_start: 0.7886 (t0) cc_final: 0.7252 (p0) REVERT: B 164 THR cc_start: 0.7709 (OUTLIER) cc_final: 0.7438 (m) REVERT: B 170 ASP cc_start: 0.7048 (p0) cc_final: 0.6686 (p0) REVERT: B 188 MET cc_start: 0.8194 (OUTLIER) cc_final: 0.7700 (mmm) REVERT: B 205 ASP cc_start: 0.7544 (t0) cc_final: 0.7296 (t0) REVERT: B 212 ASP cc_start: 0.8067 (t70) cc_final: 0.7711 (t0) REVERT: B 219 ARG cc_start: 0.7855 (tpp-160) cc_final: 0.7362 (tpp80) REVERT: B 233 CYS cc_start: 0.7859 (t) cc_final: 0.7637 (t) REVERT: B 247 ASP cc_start: 0.7760 (t0) cc_final: 0.7131 (t0) REVERT: B 298 ASP cc_start: 0.8313 (t0) cc_final: 0.7791 (t0) REVERT: B 322 ASP cc_start: 0.7566 (m-30) cc_final: 0.7166 (m-30) REVERT: C 48 GLU cc_start: 0.8768 (OUTLIER) cc_final: 0.8112 (mm-30) REVERT: C 51 LYS cc_start: 0.9253 (ptpp) cc_final: 0.8024 (pttm) REVERT: C 52 MET cc_start: 0.8431 (mmp) cc_final: 0.7827 (mmp) REVERT: C 69 MET cc_start: 0.8471 (mtm) cc_final: 0.8065 (mtm) REVERT: D 20 ARG cc_start: 0.7794 (tmm-80) cc_final: 0.7072 (tmm-80) REVERT: R 82 LEU cc_start: 0.8156 (OUTLIER) cc_final: 0.7775 (tt) REVERT: R 113 MET cc_start: 0.8033 (ppp) cc_final: 0.7574 (ppp) REVERT: R 114 TYR cc_start: 0.7737 (m-80) cc_final: 0.6778 (m-80) REVERT: R 182 TYR cc_start: 0.8109 (p90) cc_final: 0.7543 (p90) REVERT: R 183 MET cc_start: 0.6599 (tmm) cc_final: 0.5876 (tmm) REVERT: R 187 MET cc_start: 0.3472 (mtt) cc_final: 0.3005 (mtt) REVERT: R 253 LEU cc_start: 0.8564 (mp) cc_final: 0.8347 (mp) REVERT: R 261 TRP cc_start: 0.6699 (t-100) cc_final: 0.6202 (t-100) REVERT: R 265 HIS cc_start: 0.8159 (m-70) cc_final: 0.7306 (m-70) REVERT: R 286 PHE cc_start: 0.8264 (m-80) cc_final: 0.7503 (m-80) REVERT: R 295 THR cc_start: 0.8295 (p) cc_final: 0.6837 (p) REVERT: R 299 TYR cc_start: 0.7873 (m-80) cc_final: 0.7572 (m-80) REVERT: S 6 GLU cc_start: 0.6909 (mp0) cc_final: 0.6332 (mp0) REVERT: S 32 PHE cc_start: 0.7805 (m-10) cc_final: 0.7478 (m-10) REVERT: S 38 ARG cc_start: 0.7600 (ttm-80) cc_final: 0.7231 (ptm160) REVERT: S 83 MET cc_start: 0.7728 (mpp) cc_final: 0.7245 (mpp) REVERT: S 160 ARG cc_start: 0.7309 (mtm110) cc_final: 0.7016 (mtm110) outliers start: 48 outliers final: 38 residues processed: 367 average time/residue: 0.1169 time to fit residues: 55.7223 Evaluate side-chains 383 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 341 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 247 MET Chi-restraints excluded: chain A residue 267 PHE Chi-restraints excluded: chain A residue 274 PHE Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 304 GLN Chi-restraints excluded: chain A residue 307 PHE Chi-restraints excluded: chain A residue 312 LYS Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 188 MET Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain C residue 48 GLU Chi-restraints excluded: chain R residue 82 LEU Chi-restraints excluded: chain R residue 117 VAL Chi-restraints excluded: chain R residue 166 VAL Chi-restraints excluded: chain R residue 212 VAL Chi-restraints excluded: chain R residue 262 MET Chi-restraints excluded: chain R residue 285 LEU Chi-restraints excluded: chain R residue 287 LEU Chi-restraints excluded: chain R residue 302 SER Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 42 GLU Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 70 ILE Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 174 LEU Chi-restraints excluded: chain S residue 195 LEU Chi-restraints excluded: chain S residue 210 THR Chi-restraints excluded: chain S residue 224 VAL Chi-restraints excluded: chain S residue 244 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 21 optimal weight: 0.8980 chunk 44 optimal weight: 4.9990 chunk 104 optimal weight: 5.9990 chunk 91 optimal weight: 7.9990 chunk 53 optimal weight: 0.8980 chunk 90 optimal weight: 5.9990 chunk 101 optimal weight: 1.9990 chunk 35 optimal weight: 4.9990 chunk 108 optimal weight: 1.9990 chunk 54 optimal weight: 3.9990 chunk 22 optimal weight: 4.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 311 ASN S 169 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.146981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.115988 restraints weight = 17085.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.120263 restraints weight = 9065.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.123068 restraints weight = 5854.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.125030 restraints weight = 4299.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.126321 restraints weight = 3436.246| |-----------------------------------------------------------------------------| r_work (final): 0.3661 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7114 moved from start: 0.3275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 9305 Z= 0.284 Angle : 0.868 15.728 12607 Z= 0.448 Chirality : 0.050 0.198 1422 Planarity : 0.006 0.061 1593 Dihedral : 5.495 26.278 1262 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 17.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.24 % Favored : 89.76 % Rotamer: Outliers : 5.33 % Allowed : 25.45 % Favored : 69.22 % 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: -1.55 (0.24), residues: 1143 helix: 0.80 (0.27), residues: 371 sheet: -0.82 (0.32), residues: 256 loop : -2.59 (0.25), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG B 52 TYR 0.026 0.002 TYR R 221 PHE 0.030 0.003 PHE R 78 TRP 0.032 0.003 TRP B 332 HIS 0.015 0.002 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00617 ( 9304) covalent geometry : angle 0.86793 (12605) SS BOND : bond 0.00371 ( 1) SS BOND : angle 0.81399 ( 2) hydrogen bonds : bond 0.05942 ( 339) hydrogen bonds : angle 5.20368 ( 969) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 406 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 353 time to evaluate : 0.352 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 MET cc_start: 0.6644 (mpp) cc_final: 0.5698 (mpp) REVERT: A 208 ARG cc_start: 0.8343 (ttp80) cc_final: 0.8035 (ttp-170) REVERT: A 243 MET cc_start: 0.7373 (tpp) cc_final: 0.7146 (tpp) REVERT: A 245 GLU cc_start: 0.7116 (mm-30) cc_final: 0.6290 (mm-30) REVERT: A 248 LYS cc_start: 0.8495 (mtmm) cc_final: 0.7904 (mtmm) REVERT: A 251 ASP cc_start: 0.8926 (t0) cc_final: 0.8685 (t0) REVERT: A 266 LEU cc_start: 0.8202 (tp) cc_final: 0.7999 (tp) REVERT: A 287 TYR cc_start: 0.8486 (m-80) cc_final: 0.7797 (m-80) REVERT: A 290 TYR cc_start: 0.7022 (t80) cc_final: 0.5904 (t80) REVERT: A 317 LYS cc_start: 0.8212 (mttt) cc_final: 0.7785 (mttm) REVERT: A 331 ASN cc_start: 0.7858 (p0) cc_final: 0.6828 (p0) REVERT: A 343 ILE cc_start: 0.8495 (tp) cc_final: 0.7795 (tp) REVERT: A 347 ASN cc_start: 0.8324 (m110) cc_final: 0.7873 (m110) REVERT: A 350 ASP cc_start: 0.7803 (m-30) cc_final: 0.7449 (m-30) REVERT: B 15 LYS cc_start: 0.9133 (ptpp) cc_final: 0.8670 (ptpp) REVERT: B 22 ARG cc_start: 0.7651 (tpm170) cc_final: 0.7424 (tpm170) REVERT: B 45 MET cc_start: 0.7307 (mmm) cc_final: 0.7046 (mmp) REVERT: B 46 ARG cc_start: 0.7038 (mpp-170) cc_final: 0.6366 (mpp-170) REVERT: B 48 ARG cc_start: 0.7914 (mmt180) cc_final: 0.7295 (mmt180) REVERT: B 75 GLN cc_start: 0.8750 (tp40) cc_final: 0.8494 (tp40) REVERT: B 76 ASP cc_start: 0.7242 (m-30) cc_final: 0.7033 (t0) REVERT: B 125 ASN cc_start: 0.8263 (t0) cc_final: 0.8042 (t0) REVERT: B 126 LEU cc_start: 0.7920 (mp) cc_final: 0.7492 (mt) REVERT: B 127 LYS cc_start: 0.8272 (mmtp) cc_final: 0.7878 (mmtp) REVERT: B 132 ASN cc_start: 0.7699 (m110) cc_final: 0.7354 (m110) REVERT: B 153 ASP cc_start: 0.7838 (t0) cc_final: 0.7268 (p0) REVERT: B 164 THR cc_start: 0.7842 (OUTLIER) cc_final: 0.7582 (m) REVERT: B 188 MET cc_start: 0.8296 (OUTLIER) cc_final: 0.7846 (mmm) REVERT: B 205 ASP cc_start: 0.7561 (t0) cc_final: 0.7325 (t0) REVERT: B 212 ASP cc_start: 0.8091 (t70) cc_final: 0.7767 (t0) REVERT: B 219 ARG cc_start: 0.7881 (tpp-160) cc_final: 0.7513 (tpp80) REVERT: B 233 CYS cc_start: 0.8031 (t) cc_final: 0.7780 (t) REVERT: B 247 ASP cc_start: 0.7956 (t0) cc_final: 0.7345 (t0) REVERT: B 253 PHE cc_start: 0.8186 (m-80) cc_final: 0.7727 (m-80) REVERT: B 254 ASP cc_start: 0.7879 (t0) cc_final: 0.7524 (t0) REVERT: B 284 LEU cc_start: 0.8728 (mp) cc_final: 0.8502 (mm) REVERT: B 292 PHE cc_start: 0.7179 (m-80) cc_final: 0.6943 (m-80) REVERT: B 298 ASP cc_start: 0.8442 (t0) cc_final: 0.8040 (t0) REVERT: B 339 TRP cc_start: 0.8140 (m-10) cc_final: 0.7821 (m-10) REVERT: C 48 GLU cc_start: 0.8869 (OUTLIER) cc_final: 0.8092 (mm-30) REVERT: C 51 LYS cc_start: 0.9307 (ptpp) cc_final: 0.8067 (pttm) REVERT: C 52 MET cc_start: 0.8520 (mmp) cc_final: 0.7907 (mmp) REVERT: C 69 MET cc_start: 0.8469 (mtm) cc_final: 0.8190 (mtm) REVERT: D 20 ARG cc_start: 0.7845 (tmm-80) cc_final: 0.7316 (tmm-80) REVERT: R 82 LEU cc_start: 0.8158 (OUTLIER) cc_final: 0.7699 (tt) REVERT: R 112 ASN cc_start: 0.6329 (OUTLIER) cc_final: 0.5947 (t0) REVERT: R 113 MET cc_start: 0.8038 (ppp) cc_final: 0.7568 (ppp) REVERT: R 114 TYR cc_start: 0.7856 (m-80) cc_final: 0.6711 (m-80) REVERT: R 182 TYR cc_start: 0.8146 (p90) cc_final: 0.7691 (p90) REVERT: R 183 MET cc_start: 0.6674 (tmm) cc_final: 0.5966 (tmm) REVERT: R 187 MET cc_start: 0.3286 (mtt) cc_final: 0.2843 (mtt) REVERT: R 261 TRP cc_start: 0.6797 (t-100) cc_final: 0.6046 (t-100) REVERT: R 265 HIS cc_start: 0.8201 (m-70) cc_final: 0.7402 (m-70) REVERT: R 286 PHE cc_start: 0.8327 (m-80) cc_final: 0.7521 (m-80) REVERT: R 295 THR cc_start: 0.8372 (p) cc_final: 0.6842 (p) REVERT: R 299 TYR cc_start: 0.7963 (m-80) cc_final: 0.7616 (m-80) REVERT: S 6 GLU cc_start: 0.6883 (mp0) cc_final: 0.6434 (mp0) REVERT: S 39 GLN cc_start: 0.7270 (tm-30) cc_final: 0.6987 (tm-30) REVERT: S 160 ARG cc_start: 0.7249 (mtm110) cc_final: 0.6894 (mtm110) outliers start: 53 outliers final: 43 residues processed: 372 average time/residue: 0.1178 time to fit residues: 56.9220 Evaluate side-chains 399 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 351 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 247 MET Chi-restraints excluded: chain A residue 267 PHE Chi-restraints excluded: chain A residue 270 LYS Chi-restraints excluded: chain A residue 274 PHE Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 304 GLN Chi-restraints excluded: chain A residue 307 PHE Chi-restraints excluded: chain A residue 312 LYS Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain B residue 42 ARG Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 188 MET Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain C residue 48 GLU Chi-restraints excluded: chain R residue 82 LEU Chi-restraints excluded: chain R residue 112 ASN Chi-restraints excluded: chain R residue 117 VAL Chi-restraints excluded: chain R residue 166 VAL Chi-restraints excluded: chain R residue 212 VAL Chi-restraints excluded: chain R residue 249 ILE Chi-restraints excluded: chain R residue 271 TYR Chi-restraints excluded: chain R residue 285 LEU Chi-restraints excluded: chain R residue 287 LEU Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 35 HIS Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 70 ILE Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 172 THR Chi-restraints excluded: chain S residue 174 LEU Chi-restraints excluded: chain S residue 195 LEU Chi-restraints excluded: chain S residue 210 THR Chi-restraints excluded: chain S residue 215 THR Chi-restraints excluded: chain S residue 224 VAL Chi-restraints excluded: chain S residue 231 GLN Chi-restraints excluded: chain S residue 244 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 3 optimal weight: 2.9990 chunk 11 optimal weight: 7.9990 chunk 41 optimal weight: 0.1980 chunk 76 optimal weight: 2.9990 chunk 65 optimal weight: 0.7980 chunk 61 optimal weight: 7.9990 chunk 84 optimal weight: 0.8980 chunk 57 optimal weight: 4.9990 chunk 50 optimal weight: 0.9990 chunk 36 optimal weight: 0.0670 chunk 100 optimal weight: 0.0030 overall best weight: 0.3928 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 169 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.152897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.121274 restraints weight = 16974.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.125657 restraints weight = 8976.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.128582 restraints weight = 5778.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.130492 restraints weight = 4246.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.131825 restraints weight = 3415.847| |-----------------------------------------------------------------------------| r_work (final): 0.3723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7019 moved from start: 0.3324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 9305 Z= 0.152 Angle : 0.868 16.914 12607 Z= 0.434 Chirality : 0.047 0.207 1422 Planarity : 0.005 0.063 1593 Dihedral : 5.199 26.184 1262 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 12.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.70 % Favored : 92.30 % Rotamer: Outliers : 5.03 % Allowed : 27.36 % Favored : 67.61 % 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: -1.41 (0.24), residues: 1143 helix: 0.84 (0.28), residues: 368 sheet: -0.63 (0.31), residues: 266 loop : -2.52 (0.24), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG B 52 TYR 0.035 0.001 TYR R 221 PHE 0.033 0.002 PHE R 223 TRP 0.023 0.002 TRP R 261 HIS 0.004 0.001 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00342 ( 9304) covalent geometry : angle 0.86849 (12605) SS BOND : bond 0.00579 ( 1) SS BOND : angle 0.80785 ( 2) hydrogen bonds : bond 0.04631 ( 339) hydrogen bonds : angle 4.82515 ( 969) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 400 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 350 time to evaluate : 0.285 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 LYS cc_start: 0.7456 (ttmm) cc_final: 0.7178 (ttmm) REVERT: A 208 ARG cc_start: 0.8196 (ttp80) cc_final: 0.7972 (ttp-170) REVERT: A 245 GLU cc_start: 0.6907 (mm-30) cc_final: 0.6120 (mm-30) REVERT: A 248 LYS cc_start: 0.8440 (mtmm) cc_final: 0.7850 (mtmm) REVERT: A 251 ASP cc_start: 0.8860 (t0) cc_final: 0.8609 (t0) REVERT: A 266 LEU cc_start: 0.8161 (tp) cc_final: 0.7873 (tp) REVERT: A 287 TYR cc_start: 0.8335 (m-80) cc_final: 0.7690 (m-80) REVERT: A 313 ARG cc_start: 0.8114 (mmm160) cc_final: 0.7011 (tpt90) REVERT: A 317 LYS cc_start: 0.7990 (mttt) cc_final: 0.7569 (mttm) REVERT: A 343 ILE cc_start: 0.8453 (tp) cc_final: 0.7743 (tp) REVERT: A 347 ASN cc_start: 0.8216 (m110) cc_final: 0.7713 (m-40) REVERT: A 348 LEU cc_start: 0.7885 (OUTLIER) cc_final: 0.7582 (mm) REVERT: A 350 ASP cc_start: 0.7649 (m-30) cc_final: 0.7299 (m-30) REVERT: B 22 ARG cc_start: 0.7571 (tpm170) cc_final: 0.7320 (tpm170) REVERT: B 46 ARG cc_start: 0.6941 (mpp-170) cc_final: 0.6276 (mpp-170) REVERT: B 48 ARG cc_start: 0.7889 (mmt180) cc_final: 0.7429 (mmt180) REVERT: B 75 GLN cc_start: 0.8690 (tp40) cc_final: 0.8428 (tp40) REVERT: B 76 ASP cc_start: 0.7225 (m-30) cc_final: 0.7016 (t0) REVERT: B 125 ASN cc_start: 0.8145 (t0) cc_final: 0.7939 (t0) REVERT: B 127 LYS cc_start: 0.8238 (mmtp) cc_final: 0.7783 (mmtp) REVERT: B 132 ASN cc_start: 0.7607 (m110) cc_final: 0.7229 (m110) REVERT: B 153 ASP cc_start: 0.7811 (t0) cc_final: 0.7310 (p0) REVERT: B 164 THR cc_start: 0.7735 (OUTLIER) cc_final: 0.7459 (m) REVERT: B 188 MET cc_start: 0.8226 (OUTLIER) cc_final: 0.7744 (mmm) REVERT: B 205 ASP cc_start: 0.7552 (t0) cc_final: 0.7326 (t0) REVERT: B 212 ASP cc_start: 0.8026 (t70) cc_final: 0.7821 (t0) REVERT: B 233 CYS cc_start: 0.7991 (t) cc_final: 0.7775 (t) REVERT: B 247 ASP cc_start: 0.7778 (t0) cc_final: 0.7147 (t0) REVERT: B 298 ASP cc_start: 0.8228 (t0) cc_final: 0.7781 (t0) REVERT: B 301 LYS cc_start: 0.7943 (mmmm) cc_final: 0.7322 (mmtm) REVERT: B 304 ARG cc_start: 0.8444 (mtp-110) cc_final: 0.8099 (mtp-110) REVERT: C 48 GLU cc_start: 0.8838 (OUTLIER) cc_final: 0.8025 (mm-30) REVERT: C 51 LYS cc_start: 0.9265 (ptpp) cc_final: 0.7965 (pttm) REVERT: C 52 MET cc_start: 0.8467 (mmp) cc_final: 0.7868 (mmp) REVERT: C 69 MET cc_start: 0.8434 (mtm) cc_final: 0.8172 (mtm) REVERT: D 20 ARG cc_start: 0.7779 (tmm-80) cc_final: 0.7102 (tmm-80) REVERT: R 82 LEU cc_start: 0.8146 (OUTLIER) cc_final: 0.7682 (tt) REVERT: R 113 MET cc_start: 0.7926 (ppp) cc_final: 0.7496 (ppp) REVERT: R 114 TYR cc_start: 0.7736 (m-80) cc_final: 0.6591 (m-80) REVERT: R 182 TYR cc_start: 0.8318 (p90) cc_final: 0.7862 (p90) REVERT: R 183 MET cc_start: 0.6714 (tmm) cc_final: 0.5855 (tmm) REVERT: R 187 MET cc_start: 0.3615 (mtt) cc_final: 0.3121 (mtt) REVERT: R 286 PHE cc_start: 0.8186 (m-80) cc_final: 0.7409 (m-80) REVERT: R 295 THR cc_start: 0.8207 (p) cc_final: 0.6777 (p) REVERT: R 299 TYR cc_start: 0.7835 (m-80) cc_final: 0.7517 (m-80) REVERT: S 6 GLU cc_start: 0.6879 (mp0) cc_final: 0.6431 (mp0) REVERT: S 32 PHE cc_start: 0.7781 (m-10) cc_final: 0.7457 (m-10) REVERT: S 38 ARG cc_start: 0.7532 (ttm-80) cc_final: 0.7141 (ptm160) REVERT: S 83 MET cc_start: 0.7714 (mpp) cc_final: 0.7179 (mpp) REVERT: S 160 ARG cc_start: 0.7308 (mtm110) cc_final: 0.7010 (mtm110) outliers start: 50 outliers final: 40 residues processed: 369 average time/residue: 0.1103 time to fit residues: 53.3686 Evaluate side-chains 392 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 347 time to evaluate : 0.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 247 MET Chi-restraints excluded: chain A residue 267 PHE Chi-restraints excluded: chain A residue 274 PHE Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 304 GLN Chi-restraints excluded: chain A residue 307 PHE Chi-restraints excluded: chain A residue 312 LYS Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 188 MET Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain C residue 48 GLU Chi-restraints excluded: chain R residue 82 LEU Chi-restraints excluded: chain R residue 112 ASN Chi-restraints excluded: chain R residue 117 VAL Chi-restraints excluded: chain R residue 166 VAL Chi-restraints excluded: chain R residue 212 VAL Chi-restraints excluded: chain R residue 249 ILE Chi-restraints excluded: chain R residue 285 LEU Chi-restraints excluded: chain R residue 287 LEU Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 35 HIS Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 70 ILE Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 174 LEU Chi-restraints excluded: chain S residue 195 LEU Chi-restraints excluded: chain S residue 210 THR Chi-restraints excluded: chain S residue 215 THR Chi-restraints excluded: chain S residue 224 VAL Chi-restraints excluded: chain S residue 231 GLN Chi-restraints excluded: chain S residue 244 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 20 optimal weight: 1.9990 chunk 84 optimal weight: 0.5980 chunk 19 optimal weight: 0.6980 chunk 27 optimal weight: 0.9990 chunk 26 optimal weight: 0.7980 chunk 2 optimal weight: 0.0000 chunk 102 optimal weight: 10.0000 chunk 43 optimal weight: 3.9990 chunk 15 optimal weight: 1.9990 chunk 41 optimal weight: 0.9980 chunk 60 optimal weight: 2.9990 overall best weight: 0.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 169 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.151596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.120066 restraints weight = 16987.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.124480 restraints weight = 8932.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.127374 restraints weight = 5732.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.129335 restraints weight = 4190.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.130660 restraints weight = 3353.629| |-----------------------------------------------------------------------------| r_work (final): 0.3713 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7025 moved from start: 0.3471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 9305 Z= 0.164 Angle : 0.905 18.752 12607 Z= 0.455 Chirality : 0.048 0.234 1422 Planarity : 0.005 0.065 1593 Dihedral : 5.205 24.028 1262 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 14.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.10 % Favored : 90.90 % Rotamer: Outliers : 4.63 % Allowed : 28.77 % Favored : 66.60 % 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: -1.47 (0.24), residues: 1143 helix: 0.81 (0.27), residues: 365 sheet: -0.74 (0.32), residues: 255 loop : -2.48 (0.24), residues: 523 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG B 52 TYR 0.036 0.001 TYR R 221 PHE 0.039 0.002 PHE R 223 TRP 0.047 0.002 TRP R 261 HIS 0.008 0.001 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00372 ( 9304) covalent geometry : angle 0.90536 (12605) SS BOND : bond 0.00399 ( 1) SS BOND : angle 0.80810 ( 2) hydrogen bonds : bond 0.04919 ( 339) hydrogen bonds : angle 4.96793 ( 969) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 395 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 349 time to evaluate : 0.347 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 LYS cc_start: 0.7428 (ttmm) cc_final: 0.7196 (ttmm) REVERT: A 208 ARG cc_start: 0.8235 (ttp80) cc_final: 0.7978 (ttp-170) REVERT: A 245 GLU cc_start: 0.6907 (mm-30) cc_final: 0.6136 (mm-30) REVERT: A 248 LYS cc_start: 0.8455 (mtmm) cc_final: 0.7868 (mtmm) REVERT: A 251 ASP cc_start: 0.8837 (t0) cc_final: 0.8577 (t0) REVERT: A 266 LEU cc_start: 0.8168 (tp) cc_final: 0.7920 (tp) REVERT: A 287 TYR cc_start: 0.8395 (m-80) cc_final: 0.7738 (m-80) REVERT: A 290 TYR cc_start: 0.6825 (t80) cc_final: 0.5763 (t80) REVERT: A 317 LYS cc_start: 0.8009 (mttt) cc_final: 0.7638 (mttm) REVERT: A 343 ILE cc_start: 0.8432 (tp) cc_final: 0.7742 (tp) REVERT: A 347 ASN cc_start: 0.8256 (m110) cc_final: 0.7765 (m110) REVERT: A 348 LEU cc_start: 0.7889 (OUTLIER) cc_final: 0.7580 (mm) REVERT: A 350 ASP cc_start: 0.7663 (m-30) cc_final: 0.7309 (m-30) REVERT: B 22 ARG cc_start: 0.7576 (tpm170) cc_final: 0.7331 (tpm170) REVERT: B 46 ARG cc_start: 0.6866 (mpp-170) cc_final: 0.6174 (mpp-170) REVERT: B 48 ARG cc_start: 0.7893 (mmt180) cc_final: 0.7405 (mmt180) REVERT: B 75 GLN cc_start: 0.8708 (tp40) cc_final: 0.8418 (tp40) REVERT: B 76 ASP cc_start: 0.7144 (m-30) cc_final: 0.6904 (t0) REVERT: B 125 ASN cc_start: 0.8157 (t0) cc_final: 0.7947 (t0) REVERT: B 127 LYS cc_start: 0.8266 (mmtp) cc_final: 0.7813 (mmtp) REVERT: B 132 ASN cc_start: 0.7618 (m110) cc_final: 0.7234 (m110) REVERT: B 153 ASP cc_start: 0.7817 (t0) cc_final: 0.7192 (p0) REVERT: B 164 THR cc_start: 0.7778 (OUTLIER) cc_final: 0.7501 (m) REVERT: B 188 MET cc_start: 0.8247 (OUTLIER) cc_final: 0.7761 (mmm) REVERT: B 205 ASP cc_start: 0.7515 (t0) cc_final: 0.7264 (t0) REVERT: B 212 ASP cc_start: 0.8112 (t70) cc_final: 0.7855 (t0) REVERT: B 233 CYS cc_start: 0.7980 (t) cc_final: 0.7761 (t) REVERT: B 247 ASP cc_start: 0.7806 (t0) cc_final: 0.7168 (t0) REVERT: B 253 PHE cc_start: 0.8176 (m-80) cc_final: 0.7783 (m-80) REVERT: B 298 ASP cc_start: 0.8509 (t0) cc_final: 0.7885 (t0) REVERT: B 300 LEU cc_start: 0.9142 (mm) cc_final: 0.8898 (mm) REVERT: B 301 LYS cc_start: 0.7936 (mmmm) cc_final: 0.7284 (mmtm) REVERT: B 304 ARG cc_start: 0.8549 (mtp-110) cc_final: 0.8212 (mtp-110) REVERT: C 48 GLU cc_start: 0.8853 (OUTLIER) cc_final: 0.8026 (mm-30) REVERT: C 51 LYS cc_start: 0.9271 (ptpp) cc_final: 0.7961 (pttm) REVERT: C 52 MET cc_start: 0.8471 (mmp) cc_final: 0.7872 (mmp) REVERT: C 69 MET cc_start: 0.8494 (mtm) cc_final: 0.8206 (mtm) REVERT: D 20 ARG cc_start: 0.7794 (tmm-80) cc_final: 0.7254 (tmm-80) REVERT: R 82 LEU cc_start: 0.8196 (OUTLIER) cc_final: 0.7737 (tt) REVERT: R 113 MET cc_start: 0.8001 (ppp) cc_final: 0.7554 (ppp) REVERT: R 114 TYR cc_start: 0.7777 (m-80) cc_final: 0.6654 (m-80) REVERT: R 182 TYR cc_start: 0.8299 (p90) cc_final: 0.7794 (p90) REVERT: R 183 MET cc_start: 0.6718 (tmm) cc_final: 0.5856 (tmm) REVERT: R 187 MET cc_start: 0.3107 (mtt) cc_final: 0.2622 (mtt) REVERT: R 286 PHE cc_start: 0.8237 (m-80) cc_final: 0.7437 (m-80) REVERT: R 295 THR cc_start: 0.8220 (p) cc_final: 0.6814 (p) REVERT: R 299 TYR cc_start: 0.7903 (m-80) cc_final: 0.7524 (m-80) REVERT: S 6 GLU cc_start: 0.6840 (mp0) cc_final: 0.6389 (mp0) REVERT: S 38 ARG cc_start: 0.7644 (ttm-80) cc_final: 0.7341 (ptm160) REVERT: S 39 GLN cc_start: 0.7388 (tm-30) cc_final: 0.7142 (tm-30) REVERT: S 160 ARG cc_start: 0.7318 (mtm110) cc_final: 0.7016 (mtm110) outliers start: 46 outliers final: 39 residues processed: 368 average time/residue: 0.1152 time to fit residues: 55.6434 Evaluate side-chains 387 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 343 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 247 MET Chi-restraints excluded: chain A residue 267 PHE Chi-restraints excluded: chain A residue 270 LYS Chi-restraints excluded: chain A residue 274 PHE Chi-restraints excluded: chain A residue 304 GLN Chi-restraints excluded: chain A residue 307 PHE Chi-restraints excluded: chain A residue 312 LYS Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 188 MET Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain C residue 48 GLU Chi-restraints excluded: chain R residue 82 LEU Chi-restraints excluded: chain R residue 112 ASN Chi-restraints excluded: chain R residue 117 VAL Chi-restraints excluded: chain R residue 166 VAL Chi-restraints excluded: chain R residue 212 VAL Chi-restraints excluded: chain R residue 249 ILE Chi-restraints excluded: chain R residue 285 LEU Chi-restraints excluded: chain R residue 287 LEU Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 35 HIS Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 70 ILE Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 172 THR Chi-restraints excluded: chain S residue 174 LEU Chi-restraints excluded: chain S residue 195 LEU Chi-restraints excluded: chain S residue 210 THR Chi-restraints excluded: chain S residue 224 VAL Chi-restraints excluded: chain S residue 231 GLN Chi-restraints excluded: chain S residue 244 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 40 optimal weight: 0.1980 chunk 44 optimal weight: 2.9990 chunk 15 optimal weight: 0.7980 chunk 55 optimal weight: 0.0270 chunk 3 optimal weight: 0.0000 chunk 54 optimal weight: 3.9990 chunk 67 optimal weight: 0.6980 chunk 7 optimal weight: 0.9980 chunk 107 optimal weight: 0.8980 chunk 39 optimal weight: 1.9990 chunk 38 optimal weight: 0.8980 overall best weight: 0.3442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.154345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.122829 restraints weight = 16874.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.127242 restraints weight = 8982.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.130137 restraints weight = 5802.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.132122 restraints weight = 4256.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.133471 restraints weight = 3402.558| |-----------------------------------------------------------------------------| r_work (final): 0.3738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6996 moved from start: 0.3506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9305 Z= 0.150 Angle : 0.888 16.370 12607 Z= 0.444 Chirality : 0.048 0.235 1422 Planarity : 0.005 0.067 1593 Dihedral : 5.093 25.374 1262 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 12.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.26 % Favored : 92.74 % Rotamer: Outliers : 4.73 % Allowed : 28.57 % Favored : 66.70 % 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: -1.43 (0.24), residues: 1143 helix: 0.72 (0.28), residues: 368 sheet: -0.57 (0.32), residues: 251 loop : -2.45 (0.24), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG B 52 TYR 0.034 0.001 TYR R 221 PHE 0.035 0.002 PHE R 223 TRP 0.042 0.002 TRP R 261 HIS 0.004 0.001 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00342 ( 9304) covalent geometry : angle 0.88795 (12605) SS BOND : bond 0.00366 ( 1) SS BOND : angle 0.74861 ( 2) hydrogen bonds : bond 0.04498 ( 339) hydrogen bonds : angle 4.84811 ( 969) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1850.38 seconds wall clock time: 32 minutes 31.90 seconds (1951.90 seconds total)