Starting phenix.real_space_refine on Wed Aug 5 09:55:20 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9xnp_67055/08_2026/9xnp_67055.cif Found real_map, /net/cci-nas-00/data/ceres_data/9xnp_67055/08_2026/9xnp_67055.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.82 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9xnp_67055/08_2026/9xnp_67055.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9xnp_67055/08_2026/9xnp_67055.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9xnp_67055/08_2026/9xnp_67055.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9xnp_67055/08_2026/9xnp_67055.map" } resolution = 2.82 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= 0.053 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 6 5.49 5 Mg 2 5.21 5 S 29 5.16 5 C 5779 2.51 5 N 1592 2.21 5 O 1639 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 38 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9047 Number of models: 1 Model: "" Number of chains: 4 Chain: "D" Number of atoms: 4550 Number of conformers: 1 Conformer: "" Number of residues, atoms: 583, 4550 Classifications: {'peptide': 583} Link IDs: {'PTRANS': 27, 'TRANS': 555} Chain: "C" Number of atoms: 4433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 573, 4433 Classifications: {'peptide': 573} Link IDs: {'PTRANS': 18, 'TRANS': 554} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 1.53, per 1000 atoms: 0.17 Number of scatterers: 9047 At special positions: 0 Unit cell: (74.8, 99, 146.3, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 29 16.00 P 6 15.00 Mg 2 11.99 O 1639 8.00 N 1592 7.00 C 5779 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.78 Conformation dependent library (CDL) restraints added in 241.1 milliseconds 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2138 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 8 sheets defined 60.0% alpha, 5.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.23 Creating SS restraints... Processing helix chain 'D' and resid 4 through 16 removed outlier: 4.035A pdb=" N THR D 10 " --> pdb=" O GLN D 6 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ARG D 11 " --> pdb=" O LYS D 7 " (cutoff:3.500A) Processing helix chain 'D' and resid 17 through 21 removed outlier: 3.934A pdb=" N GLN D 21 " --> pdb=" O VAL D 18 " (cutoff:3.500A) Processing helix chain 'D' and resid 22 through 30 removed outlier: 3.598A pdb=" N ILE D 26 " --> pdb=" O ARG D 22 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N SER D 27 " --> pdb=" O TRP D 23 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ARG D 28 " --> pdb=" O LEU D 24 " (cutoff:3.500A) Processing helix chain 'D' and resid 33 through 56 removed outlier: 3.908A pdb=" N ILE D 38 " --> pdb=" O SER D 34 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ILE D 39 " --> pdb=" O GLY D 35 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ARG D 47 " --> pdb=" O TRP D 43 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLU D 55 " --> pdb=" O HIS D 51 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ASN D 56 " --> pdb=" O MET D 52 " (cutoff:3.500A) Processing helix chain 'D' and resid 58 through 61 Processing helix chain 'D' and resid 62 through 110 removed outlier: 3.587A pdb=" N PHE D 66 " --> pdb=" O LEU D 62 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N VAL D 70 " --> pdb=" O PHE D 66 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LEU D 71 " --> pdb=" O THR D 67 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N THR D 72 " --> pdb=" O LEU D 68 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N PHE D 73 " --> pdb=" O LEU D 69 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N GLU D 84 " --> pdb=" O VAL D 80 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ARG D 85 " --> pdb=" O TRP D 81 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N VAL D 86 " --> pdb=" O LEU D 82 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N GLY D 87 " --> pdb=" O ARG D 83 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N TYR D 88 " --> pdb=" O GLU D 84 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N HIS D 89 " --> pdb=" O ARG D 85 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N ALA D 90 " --> pdb=" O VAL D 86 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLY D 91 " --> pdb=" O GLY D 87 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ILE D 94 " --> pdb=" O ALA D 90 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ARG D 95 " --> pdb=" O GLY D 91 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ALA D 97 " --> pdb=" O HIS D 93 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ARG D 100 " --> pdb=" O PHE D 96 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLN D 101 " --> pdb=" O ALA D 97 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLY D 110 " --> pdb=" O LEU D 106 " (cutoff:3.500A) Processing helix chain 'D' and resid 110 through 115 Processing helix chain 'D' and resid 122 through 127 Processing helix chain 'D' and resid 130 through 132 No H-bonds generated for 'chain 'D' and resid 130 through 132' Processing helix chain 'D' and resid 133 through 139 removed outlier: 3.904A pdb=" N TYR D 137 " --> pdb=" O MET D 133 " (cutoff:3.500A) Processing helix chain 'D' and resid 139 through 147 removed outlier: 3.748A pdb=" N ALA D 145 " --> pdb=" O LEU D 141 " (cutoff:3.500A) Processing helix chain 'D' and resid 149 through 159 removed outlier: 3.687A pdb=" N VAL D 155 " --> pdb=" O PRO D 151 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N VAL D 156 " --> pdb=" O LEU D 152 " (cutoff:3.500A) Processing helix chain 'D' and resid 162 through 171 removed outlier: 3.757A pdb=" N ALA D 166 " --> pdb=" O ASN D 162 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N LEU D 167 " --> pdb=" O TRP D 163 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ILE D 168 " --> pdb=" O ALA D 164 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N LEU D 169 " --> pdb=" O ALA D 165 " (cutoff:3.500A) Processing helix chain 'D' and resid 175 through 194 removed outlier: 4.754A pdb=" N ALA D 181 " --> pdb=" O PRO D 177 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N LEU D 182 " --> pdb=" O LEU D 178 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N VAL D 183 " --> pdb=" O PHE D 179 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N GLY D 184 " --> pdb=" O MET D 180 " (cutoff:3.500A) removed outlier: 5.804A pdb=" N MET D 185 " --> pdb=" O ALA D 181 " (cutoff:3.500A) removed outlier: 5.463A pdb=" N GLY D 186 " --> pdb=" O LEU D 182 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N ASP D 189 " --> pdb=" O MET D 185 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ARG D 192 " --> pdb=" O ALA D 188 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ARG D 193 " --> pdb=" O ASP D 189 " (cutoff:3.500A) Processing helix chain 'D' and resid 203 through 211 Processing helix chain 'D' and resid 211 through 219 Processing helix chain 'D' and resid 223 through 240 removed outlier: 3.937A pdb=" N SER D 227 " --> pdb=" O ALA D 223 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ILE D 228 " --> pdb=" O GLU D 224 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLU D 233 " --> pdb=" O ARG D 229 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ASP D 234 " --> pdb=" O SER D 230 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N PHE D 235 " --> pdb=" O ALA D 231 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ARG D 236 " --> pdb=" O SER D 232 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N GLN D 237 " --> pdb=" O GLU D 233 " (cutoff:3.500A) Processing helix chain 'D' and resid 242 through 247 Processing helix chain 'D' and resid 249 through 267 removed outlier: 4.541A pdb=" N LEU D 253 " --> pdb=" O SER D 249 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N GLU D 254 " --> pdb=" O SER D 250 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ILE D 261 " --> pdb=" O THR D 257 " (cutoff:3.500A) Processing helix chain 'D' and resid 269 through 274 removed outlier: 3.898A pdb=" N LEU D 273 " --> pdb=" O GLY D 269 " (cutoff:3.500A) Processing helix chain 'D' and resid 286 through 297 removed outlier: 3.849A pdb=" N GLY D 290 " --> pdb=" O THR D 286 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ALA D 293 " --> pdb=" O ALA D 289 " (cutoff:3.500A) Processing helix chain 'D' and resid 298 through 300 No H-bonds generated for 'chain 'D' and resid 298 through 300' Processing helix chain 'D' and resid 301 through 310 removed outlier: 3.525A pdb=" N GLY D 308 " --> pdb=" O LEU D 304 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N THR D 309 " --> pdb=" O ARG D 305 " (cutoff:3.500A) Processing helix chain 'D' and resid 311 through 320 removed outlier: 3.813A pdb=" N ALA D 315 " --> pdb=" O TYR D 311 " (cutoff:3.500A) Processing helix chain 'D' and resid 321 through 328 Processing helix chain 'D' and resid 389 through 398 removed outlier: 3.985A pdb=" N LEU D 393 " --> pdb=" O LYS D 389 " (cutoff:3.500A) Processing helix chain 'D' and resid 417 through 422 Processing helix chain 'D' and resid 438 through 444 removed outlier: 3.819A pdb=" N VAL D 443 " --> pdb=" O LEU D 439 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU D 444 " --> pdb=" O ARG D 440 " (cutoff:3.500A) Processing helix chain 'D' and resid 451 through 462 removed outlier: 3.930A pdb=" N LEU D 455 " --> pdb=" O SER D 451 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLN D 456 " --> pdb=" O GLU D 452 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N ALA D 457 " --> pdb=" O GLN D 453 " (cutoff:3.500A) Processing helix chain 'D' and resid 473 through 477 removed outlier: 4.052A pdb=" N ASP D 476 " --> pdb=" O GLN D 473 " (cutoff:3.500A) Processing helix chain 'D' and resid 487 through 499 removed outlier: 3.886A pdb=" N ARG D 493 " --> pdb=" O GLY D 489 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N VAL D 494 " --> pdb=" O GLN D 490 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ALA D 495 " --> pdb=" O ALA D 491 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ALA D 497 " --> pdb=" O ARG D 493 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ALA D 499 " --> pdb=" O ALA D 495 " (cutoff:3.500A) Processing helix chain 'D' and resid 517 through 532 removed outlier: 3.784A pdb=" N GLN D 522 " --> pdb=" O ALA D 518 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLU D 526 " --> pdb=" O GLN D 522 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ALA D 527 " --> pdb=" O ARG D 523 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ASN D 529 " --> pdb=" O MET D 525 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ALA D 530 " --> pdb=" O GLU D 526 " (cutoff:3.500A) Processing helix chain 'D' and resid 566 through 571 Processing helix chain 'D' and resid 578 through 583 Processing helix chain 'C' and resid 4 through 12 removed outlier: 3.617A pdb=" N ALA C 9 " --> pdb=" O LEU C 5 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N LEU C 10 " --> pdb=" O PRO C 6 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N TYR C 11 " --> pdb=" O TYR C 7 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LYS C 12 " --> pdb=" O LEU C 8 " (cutoff:3.500A) Processing helix chain 'C' and resid 14 through 19 Processing helix chain 'C' and resid 22 through 44 removed outlier: 3.741A pdb=" N THR C 28 " --> pdb=" O LEU C 24 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU C 29 " --> pdb=" O ALA C 25 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N LEU C 36 " --> pdb=" O SER C 32 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N TRP C 41 " --> pdb=" O THR C 37 " (cutoff:3.500A) Processing helix chain 'C' and resid 64 through 87 removed outlier: 3.619A pdb=" N THR C 74 " --> pdb=" O ALA C 70 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N ARG C 77 " --> pdb=" O ARG C 73 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N TYR C 78 " --> pdb=" O THR C 74 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N PHE C 79 " --> pdb=" O ALA C 75 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N HIS C 85 " --> pdb=" O ARG C 81 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA C 87 " --> pdb=" O VAL C 83 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 104 removed outlier: 3.947A pdb=" N HIS C 94 " --> pdb=" O ARG C 90 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LYS C 102 " --> pdb=" O TYR C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 105 through 107 No H-bonds generated for 'chain 'C' and resid 105 through 107' Processing helix chain 'C' and resid 119 through 128 removed outlier: 3.808A pdb=" N ASP C 128 " --> pdb=" O VAL C 124 " (cutoff:3.500A) Processing helix chain 'C' and resid 129 through 131 No H-bonds generated for 'chain 'C' and resid 129 through 131' Processing helix chain 'C' and resid 132 through 156 removed outlier: 5.166A pdb=" N SER C 139 " --> pdb=" O LEU C 135 " (cutoff:3.500A) Proline residue: C 140 - end of helix removed outlier: 3.650A pdb=" N SER C 156 " --> pdb=" O THR C 152 " (cutoff:3.500A) Processing helix chain 'C' and resid 159 through 174 removed outlier: 3.570A pdb=" N LEU C 166 " --> pdb=" O LEU C 162 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLY C 167 " --> pdb=" O ALA C 163 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ILE C 169 " --> pdb=" O THR C 165 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LEU C 172 " --> pdb=" O GLY C 168 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N THR C 173 " --> pdb=" O ILE C 169 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N LEU C 174 " --> pdb=" O MET C 170 " (cutoff:3.500A) Processing helix chain 'C' and resid 176 through 183 Processing helix chain 'C' and resid 186 through 209 removed outlier: 3.558A pdb=" N ASN C 191 " --> pdb=" O SER C 187 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N LEU C 192 " --> pdb=" O THR C 188 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N THR C 193 " --> pdb=" O GLY C 189 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N HIS C 194 " --> pdb=" O GLN C 190 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ARG C 200 " --> pdb=" O ARG C 196 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N GLN C 201 " --> pdb=" O GLY C 197 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N GLN C 202 " --> pdb=" O GLN C 198 " (cutoff:3.500A) removed outlier: 5.316A pdb=" N LEU C 203 " --> pdb=" O TYR C 199 " (cutoff:3.500A) Processing helix chain 'C' and resid 209 through 216 Processing helix chain 'C' and resid 223 through 240 removed outlier: 3.598A pdb=" N THR C 229 " --> pdb=" O GLN C 225 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ARG C 238 " --> pdb=" O LEU C 234 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ARG C 239 " --> pdb=" O GLU C 235 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N GLN C 240 " --> pdb=" O ALA C 236 " (cutoff:3.500A) Processing helix chain 'C' and resid 245 through 254 removed outlier: 3.864A pdb=" N ALA C 249 " --> pdb=" O ALA C 245 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N MET C 251 " --> pdb=" O SER C 247 " (cutoff:3.500A) Processing helix chain 'C' and resid 255 through 267 removed outlier: 3.618A pdb=" N VAL C 259 " --> pdb=" O GLY C 255 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N SER C 267 " --> pdb=" O LEU C 263 " (cutoff:3.500A) Processing helix chain 'C' and resid 278 through 290 removed outlier: 3.660A pdb=" N CYS C 286 " --> pdb=" O LEU C 282 " (cutoff:3.500A) Processing helix chain 'C' and resid 291 through 293 No H-bonds generated for 'chain 'C' and resid 291 through 293' Processing helix chain 'C' and resid 298 through 302 removed outlier: 4.133A pdb=" N PHE C 301 " --> pdb=" O THR C 298 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLN C 302 " --> pdb=" O GLY C 299 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 298 through 302' Processing helix chain 'C' and resid 304 through 318 removed outlier: 3.771A pdb=" N ILE C 308 " --> pdb=" O LEU C 304 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ALA C 309 " --> pdb=" O GLY C 305 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N SER C 310 " --> pdb=" O GLN C 306 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N LEU C 317 " --> pdb=" O ARG C 313 " (cutoff:3.500A) Processing helix chain 'C' and resid 378 through 383 Processing helix chain 'C' and resid 403 through 407 removed outlier: 3.702A pdb=" N SER C 406 " --> pdb=" O PRO C 403 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N LEU C 407 " --> pdb=" O ILE C 404 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 403 through 407' Processing helix chain 'C' and resid 408 through 413 Processing helix chain 'C' and resid 431 through 436 removed outlier: 4.017A pdb=" N LEU C 436 " --> pdb=" O ASP C 432 " (cutoff:3.500A) Processing helix chain 'C' and resid 444 through 453 removed outlier: 4.148A pdb=" N GLU C 448 " --> pdb=" O GLU C 444 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ILE C 449 " --> pdb=" O ALA C 445 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N LEU C 450 " --> pdb=" O LEU C 446 " (cutoff:3.500A) Processing helix chain 'C' and resid 462 through 466 removed outlier: 3.995A pdb=" N SER C 466 " --> pdb=" O GLY C 463 " (cutoff:3.500A) Processing helix chain 'C' and resid 479 through 492 removed outlier: 3.733A pdb=" N ALA C 484 " --> pdb=" O LEU C 480 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N ILE C 485 " --> pdb=" O ARG C 481 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ASP C 492 " --> pdb=" O ALA C 488 " (cutoff:3.500A) Processing helix chain 'C' and resid 506 through 520 removed outlier: 3.766A pdb=" N SER C 511 " --> pdb=" O ALA C 507 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N GLN C 512 " --> pdb=" O THR C 508 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ILE C 513 " --> pdb=" O THR C 509 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N LEU C 514 " --> pdb=" O GLU C 510 " (cutoff:3.500A) Processing helix chain 'C' and resid 564 through 572 removed outlier: 3.630A pdb=" N GLY C 572 " --> pdb=" O GLN C 568 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'D' and resid 350 through 351 Processing sheet with id=AA2, first strand: chain 'D' and resid 357 through 358 removed outlier: 6.608A pdb=" N ILE D 357 " --> pdb=" O LEU D 365 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 378 through 381 removed outlier: 6.461A pdb=" N ALA D 379 " --> pdb=" O MET D 539 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N SER D 426 " --> pdb=" O LEU D 508 " (cutoff:3.500A) removed outlier: 8.312A pdb=" N ASP D 510 " --> pdb=" O SER D 426 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N VAL D 428 " --> pdb=" O ASP D 510 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 407 through 408 Processing sheet with id=AA5, first strand: chain 'D' and resid 555 through 556 removed outlier: 7.124A pdb=" N VAL D 555 " --> pdb=" O ILE D 562 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 356 through 357 removed outlier: 3.535A pdb=" N LEU C 356 " --> pdb=" O PHE C 346 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 356 through 357 removed outlier: 3.535A pdb=" N LEU C 356 " --> pdb=" O PHE C 346 " (cutoff:3.500A) removed outlier: 5.558A pdb=" N LEU C 341 " --> pdb=" O LEU C 398 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N LEU C 398 " --> pdb=" O LEU C 341 " (cutoff:3.500A) removed outlier: 5.709A pdb=" N ASP C 343 " --> pdb=" O GLU C 396 " (cutoff:3.500A) removed outlier: 5.209A pdb=" N GLU C 396 " --> pdb=" O ASP C 343 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N GLN C 394 " --> pdb=" O GLN C 345 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 417 through 419 removed outlier: 6.284A pdb=" N ILE C 369 " --> pdb=" O MET C 528 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N GLN C 541 " --> pdb=" O HIS C 368 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N ILE C 542 " --> pdb=" O GLN C 553 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N GLN C 553 " --> pdb=" O ILE C 542 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N VAL C 544 " --> pdb=" O ILE C 551 " (cutoff:3.500A) 331 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: 1.29 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: 3000 1.34 - 1.46: 1253 1.46 - 1.57: 4904 1.57 - 1.69: 15 1.69 - 1.80: 55 Bond restraints: 9227 Sorted by residual: bond pdb=" C2' ATP C 602 " pdb=" C3' ATP C 602 " ideal model delta sigma weight residual 1.531 1.229 0.302 1.20e-02 6.94e+03 6.33e+02 bond pdb=" C2' ATP D 602 " pdb=" C3' ATP D 602 " ideal model delta sigma weight residual 1.531 1.229 0.302 1.20e-02 6.94e+03 6.32e+02 bond pdb=" C4' ATP C 602 " pdb=" O4' ATP C 602 " ideal model delta sigma weight residual 1.444 1.277 0.167 1.10e-02 8.26e+03 2.30e+02 bond pdb=" C4' ATP D 602 " pdb=" O4' ATP D 602 " ideal model delta sigma weight residual 1.444 1.279 0.165 1.10e-02 8.26e+03 2.26e+02 bond pdb=" C3' ATP C 602 " pdb=" C4' ATP C 602 " ideal model delta sigma weight residual 1.526 1.668 -0.142 1.10e-02 8.26e+03 1.66e+02 ... (remaining 9222 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.60: 12452 3.60 - 7.20: 80 7.20 - 10.80: 12 10.80 - 14.40: 2 14.40 - 18.00: 2 Bond angle restraints: 12548 Sorted by residual: angle pdb=" PB ATP D 602 " pdb=" O3B ATP D 602 " pdb=" PG ATP D 602 " ideal model delta sigma weight residual 139.87 121.87 18.00 1.00e+00 1.00e+00 3.24e+02 angle pdb=" PB ATP C 602 " pdb=" O3B ATP C 602 " pdb=" PG ATP C 602 " ideal model delta sigma weight residual 139.87 121.87 18.00 1.00e+00 1.00e+00 3.24e+02 angle pdb=" PA ATP D 602 " pdb=" O3A ATP D 602 " pdb=" PB ATP D 602 " ideal model delta sigma weight residual 136.83 124.61 12.22 1.00e+00 1.00e+00 1.49e+02 angle pdb=" PA ATP C 602 " pdb=" O3A ATP C 602 " pdb=" PB ATP C 602 " ideal model delta sigma weight residual 136.83 124.63 12.20 1.00e+00 1.00e+00 1.49e+02 angle pdb=" C5 ATP D 602 " pdb=" C4 ATP D 602 " pdb=" N3 ATP D 602 " ideal model delta sigma weight residual 126.80 119.05 7.75 1.00e+00 1.00e+00 6.01e+01 ... (remaining 12543 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.49: 4975 17.49 - 34.98: 469 34.98 - 52.47: 61 52.47 - 69.95: 26 69.95 - 87.44: 9 Dihedral angle restraints: 5540 sinusoidal: 2224 harmonic: 3316 Sorted by residual: dihedral pdb=" CA GLY C 504 " pdb=" C GLY C 504 " pdb=" N LEU C 505 " pdb=" CA LEU C 505 " ideal model delta harmonic sigma weight residual 180.00 153.50 26.50 0 5.00e+00 4.00e-02 2.81e+01 dihedral pdb=" CA LEU C 106 " pdb=" C LEU C 106 " pdb=" N SER C 107 " pdb=" CA SER C 107 " ideal model delta harmonic sigma weight residual -180.00 -156.83 -23.17 0 5.00e+00 4.00e-02 2.15e+01 dihedral pdb=" CA PHE C 301 " pdb=" C PHE C 301 " pdb=" N GLN C 302 " pdb=" CA GLN C 302 " ideal model delta harmonic sigma weight residual 180.00 158.98 21.02 0 5.00e+00 4.00e-02 1.77e+01 ... (remaining 5537 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 1240 0.062 - 0.125: 198 0.125 - 0.187: 12 0.187 - 0.250: 3 0.250 - 0.312: 2 Chirality restraints: 1455 Sorted by residual: chirality pdb=" C2' ATP C 602 " pdb=" C1' ATP C 602 " pdb=" C3' ATP C 602 " pdb=" O2' ATP C 602 " both_signs ideal model delta sigma weight residual False -2.68 -2.37 -0.31 2.00e-01 2.50e+01 2.43e+00 chirality pdb=" C2' ATP D 602 " pdb=" C1' ATP D 602 " pdb=" C3' ATP D 602 " pdb=" O2' ATP D 602 " both_signs ideal model delta sigma weight residual False -2.68 -2.37 -0.31 2.00e-01 2.50e+01 2.41e+00 chirality pdb=" C3' ATP D 602 " pdb=" C2' ATP D 602 " pdb=" C4' ATP D 602 " pdb=" O3' ATP D 602 " both_signs ideal model delta sigma weight residual False -2.63 -2.41 -0.22 2.00e-01 2.50e+01 1.24e+00 ... (remaining 1452 not shown) Planarity restraints: 1596 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER D 359 " -0.038 5.00e-02 4.00e+02 5.74e-02 5.28e+00 pdb=" N PRO D 360 " 0.099 5.00e-02 4.00e+02 pdb=" CA PRO D 360 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO D 360 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU D 141 " -0.033 5.00e-02 4.00e+02 4.93e-02 3.90e+00 pdb=" N PRO D 142 " 0.085 5.00e-02 4.00e+02 pdb=" CA PRO D 142 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO D 142 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA TYR C 134 " -0.008 2.00e-02 2.50e+03 1.53e-02 2.34e+00 pdb=" C TYR C 134 " 0.026 2.00e-02 2.50e+03 pdb=" O TYR C 134 " -0.010 2.00e-02 2.50e+03 pdb=" N LEU C 135 " -0.009 2.00e-02 2.50e+03 ... (remaining 1593 not shown) Histogram of nonbonded interaction distances: 1.93 - 2.53: 40 2.53 - 3.12: 6217 3.12 - 3.71: 12248 3.71 - 4.31: 17952 4.31 - 4.90: 30924 Nonbonded interactions: 67381 Sorted by model distance: nonbonded pdb=" OG SER C 380 " pdb="MG MG C 601 " model vdw 1.932 2.170 nonbonded pdb=" NE2 GLN C 421 " pdb="MG MG C 601 " model vdw 2.122 2.250 nonbonded pdb="MG MG C 601 " pdb=" O2G ATP C 602 " model vdw 2.165 2.170 nonbonded pdb=" OG SER D 417 " pdb=" OG SER D 420 " model vdw 2.206 3.040 nonbonded pdb="MG MG D 601 " pdb=" O1G ATP D 602 " model vdw 2.252 2.170 ... (remaining 67376 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.120 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 7.640 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:6.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.302 9227 Z= 0.622 Angle : 0.822 17.998 12548 Z= 0.529 Chirality : 0.047 0.312 1455 Planarity : 0.005 0.057 1596 Dihedral : 14.345 87.443 3402 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.16 % Favored : 91.84 % Rotamer: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.59 (0.20), residues: 1152 helix: -2.56 (0.17), residues: 637 sheet: -2.77 (0.57), residues: 70 loop : -3.69 (0.22), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 238 TYR 0.009 0.002 TYR C 78 PHE 0.015 0.001 PHE C 216 TRP 0.020 0.002 TRP D 122 HIS 0.004 0.001 HIS C 531 Details of bonding type rmsd/Z covalent geometry : bond 0.00856 / 0.62 ( 9227) covalent geometry : angle 0.82178 / 0.53 (12548) hydrogen bonds : bond 0.13424 / 8.82 ( 330) hydrogen bonds : angle 4.87467 / 3.50 ( 969) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 123 time to evaluate : 0.213 Fit side-chains REVERT: D 6 GLN cc_start: 0.7906 (tm-30) cc_final: 0.7649 (tm-30) REVERT: D 14 LYS cc_start: 0.8602 (mttm) cc_final: 0.8337 (mttm) REVERT: D 22 ARG cc_start: 0.7977 (ptm-80) cc_final: 0.7763 (ptm160) REVERT: D 45 MET cc_start: 0.8227 (mtm) cc_final: 0.7979 (mtm) REVERT: D 178 LEU cc_start: 0.7631 (tt) cc_final: 0.7420 (tm) REVERT: D 182 LEU cc_start: 0.8278 (tt) cc_final: 0.8067 (tt) REVERT: D 423 LYS cc_start: 0.8609 (mttt) cc_final: 0.7907 (mmtt) REVERT: D 539 MET cc_start: 0.9108 (ttt) cc_final: 0.8897 (ttt) REVERT: C 394 GLN cc_start: 0.7941 (tp40) cc_final: 0.7484 (tt0) REVERT: C 545 MET cc_start: 0.8189 (ttt) cc_final: 0.7884 (ttt) outliers start: 0 outliers final: 0 residues processed: 123 average time/residue: 0.6705 time to fit residues: 86.6387 Evaluate side-chains 90 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 90 time to evaluate : 0.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 108 optimal weight: 4.9990 chunk 49 optimal weight: 0.9980 chunk 97 optimal weight: 3.9990 chunk 113 optimal weight: 1.9990 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 0.0050 chunk 33 optimal weight: 10.0000 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 3.9990 chunk 100 optimal weight: 0.9980 overall best weight: 1.1998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 50 GLN D 101 GLN D 129 GLN D 336 GLN D 377 GLN D 430 GLN D 543 GLN C 93 GLN C 198 GLN C 210 GLN C 275 GLN C 320 GLN C 345 GLN C 362 GLN C 556 HIS C 563 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.128637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.102045 restraints weight = 11226.865| |-----------------------------------------------------------------------------| r_work (start): 0.3209 rms_B_bonded: 2.22 r_work: 0.3065 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2927 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.2927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.1209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 9227 Z= 0.145 Angle : 0.621 6.740 12548 Z= 0.312 Chirality : 0.041 0.156 1455 Planarity : 0.005 0.051 1596 Dihedral : 7.733 68.171 1328 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 2.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.81 % Favored : 92.19 % Rotamer: Outliers : 1.39 % Allowed : 9.06 % Favored : 89.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.52 (0.22), residues: 1152 helix: -1.70 (0.19), residues: 632 sheet: -1.90 (0.61), residues: 69 loop : -3.25 (0.22), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 562 TYR 0.009 0.001 TYR C 78 PHE 0.013 0.001 PHE C 216 TRP 0.014 0.001 TRP D 421 HIS 0.005 0.001 HIS C 424 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.14 ( 9227) covalent geometry : angle 0.62068 / 0.31 (12548) hydrogen bonds : bond 0.04636 / 3.06 ( 330) hydrogen bonds : angle 4.02786 / 2.86 ( 969) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 103 time to evaluate : 0.248 Fit side-chains REVERT: D 6 GLN cc_start: 0.7892 (tm-30) cc_final: 0.6844 (mp10) REVERT: D 14 LYS cc_start: 0.8586 (mttm) cc_final: 0.8375 (mttp) REVERT: D 115 GLN cc_start: 0.7676 (pt0) cc_final: 0.7317 (mt0) REVERT: D 178 LEU cc_start: 0.7485 (tt) cc_final: 0.7280 (tm) REVERT: D 423 LYS cc_start: 0.8755 (mttt) cc_final: 0.7924 (mmtt) REVERT: C 115 ARG cc_start: 0.8296 (mtm-85) cc_final: 0.8087 (mtm-85) REVERT: C 292 GLU cc_start: 0.7945 (OUTLIER) cc_final: 0.6988 (mp0) REVERT: C 522 ARG cc_start: 0.8497 (ttm-80) cc_final: 0.8239 (ttm170) REVERT: C 534 ARG cc_start: 0.8311 (tpt-90) cc_final: 0.8002 (tpt-90) outliers start: 13 outliers final: 3 residues processed: 106 average time/residue: 0.7086 time to fit residues: 78.6905 Evaluate side-chains 94 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 90 time to evaluate : 0.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 222 GLU Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 153 ILE Chi-restraints excluded: chain C residue 292 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 21 optimal weight: 3.9990 chunk 88 optimal weight: 0.6980 chunk 42 optimal weight: 1.9990 chunk 20 optimal weight: 0.5980 chunk 31 optimal weight: 6.9990 chunk 61 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 58 optimal weight: 0.5980 chunk 91 optimal weight: 7.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 543 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.135786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.110535 restraints weight = 11812.313| |-----------------------------------------------------------------------------| r_work (start): 0.3451 rms_B_bonded: 2.13 r_work: 0.3351 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3244 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.1460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9227 Z= 0.140 Angle : 0.599 7.360 12548 Z= 0.300 Chirality : 0.041 0.145 1455 Planarity : 0.004 0.048 1596 Dihedral : 7.494 74.538 1328 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 2.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.38 % Favored : 92.62 % Rotamer: Outliers : 2.03 % Allowed : 10.55 % Favored : 87.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.01 (0.23), residues: 1152 helix: -1.34 (0.20), residues: 646 sheet: -1.58 (0.58), residues: 79 loop : -3.00 (0.24), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 562 TYR 0.009 0.001 TYR C 59 PHE 0.013 0.001 PHE D 467 TRP 0.012 0.001 TRP D 421 HIS 0.008 0.001 HIS C 556 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.14 ( 9227) covalent geometry : angle 0.59896 / 0.30 (12548) hydrogen bonds : bond 0.04523 / 2.99 ( 330) hydrogen bonds : angle 3.92222 / 2.78 ( 969) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 103 time to evaluate : 0.263 Fit side-chains REVERT: D 6 GLN cc_start: 0.7750 (tm-30) cc_final: 0.6662 (mp10) REVERT: D 14 LYS cc_start: 0.8347 (mttm) cc_final: 0.8090 (mttp) REVERT: D 423 LYS cc_start: 0.8436 (mttt) cc_final: 0.7498 (mmtt) REVERT: C 59 TYR cc_start: 0.8337 (p90) cc_final: 0.8112 (p90) REVERT: C 235 GLU cc_start: 0.8081 (tp30) cc_final: 0.7431 (tt0) REVERT: C 292 GLU cc_start: 0.7799 (OUTLIER) cc_final: 0.6972 (mp0) REVERT: C 361 LEU cc_start: 0.8196 (OUTLIER) cc_final: 0.7905 (mt) REVERT: C 534 ARG cc_start: 0.8327 (tpt-90) cc_final: 0.7963 (tpt-90) outliers start: 19 outliers final: 9 residues processed: 106 average time/residue: 0.6570 time to fit residues: 72.7933 Evaluate side-chains 102 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 91 time to evaluate : 0.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 22 ARG Chi-restraints excluded: chain D residue 222 GLU Chi-restraints excluded: chain D residue 545 GLU Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 153 ILE Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 292 GLU Chi-restraints excluded: chain C residue 315 SER Chi-restraints excluded: chain C residue 319 ASP Chi-restraints excluded: chain C residue 361 LEU Chi-restraints excluded: chain C residue 442 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 28 optimal weight: 0.1980 chunk 15 optimal weight: 0.9980 chunk 104 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 75 optimal weight: 4.9990 chunk 78 optimal weight: 3.9990 chunk 71 optimal weight: 3.9990 chunk 100 optimal weight: 1.9990 chunk 19 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 chunk 79 optimal weight: 0.4980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 334 HIS D 543 GLN C 306 GLN C 491 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.136267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.110691 restraints weight = 11981.498| |-----------------------------------------------------------------------------| r_work (start): 0.3451 rms_B_bonded: 2.16 r_work: 0.3349 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3242 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.1630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9227 Z= 0.135 Angle : 0.586 7.506 12548 Z= 0.292 Chirality : 0.040 0.145 1455 Planarity : 0.004 0.047 1596 Dihedral : 7.378 74.582 1328 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 2.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.64 % Favored : 92.36 % Rotamer: Outliers : 2.24 % Allowed : 12.37 % Favored : 85.39 % 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: -2.64 (0.23), residues: 1152 helix: -1.07 (0.20), residues: 644 sheet: -1.40 (0.57), residues: 82 loop : -2.78 (0.25), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 562 TYR 0.009 0.001 TYR C 78 PHE 0.012 0.001 PHE D 467 TRP 0.012 0.001 TRP D 421 HIS 0.006 0.001 HIS C 556 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.14 ( 9227) covalent geometry : angle 0.58581 / 0.29 (12548) hydrogen bonds : bond 0.04373 / 2.89 ( 330) hydrogen bonds : angle 3.88747 / 2.76 ( 969) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 100 time to evaluate : 0.324 Fit side-chains REVERT: D 6 GLN cc_start: 0.7679 (tm-30) cc_final: 0.6703 (mp10) REVERT: D 14 LYS cc_start: 0.8336 (mttm) cc_final: 0.8099 (mttp) REVERT: D 115 GLN cc_start: 0.7697 (pt0) cc_final: 0.6938 (mm-40) REVERT: D 384 ARG cc_start: 0.7651 (OUTLIER) cc_final: 0.7254 (mtt-85) REVERT: D 423 LYS cc_start: 0.8434 (mttt) cc_final: 0.7521 (mmtt) REVERT: C 59 TYR cc_start: 0.8369 (p90) cc_final: 0.8095 (p90) REVERT: C 235 GLU cc_start: 0.8122 (tp30) cc_final: 0.7781 (tp30) REVERT: C 361 LEU cc_start: 0.8136 (OUTLIER) cc_final: 0.7896 (mt) REVERT: C 534 ARG cc_start: 0.8344 (tpt-90) cc_final: 0.7981 (tpt-90) outliers start: 21 outliers final: 8 residues processed: 105 average time/residue: 0.7006 time to fit residues: 77.0331 Evaluate side-chains 109 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 99 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 222 GLU Chi-restraints excluded: chain D residue 384 ARG Chi-restraints excluded: chain D residue 509 LEU Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 149 MET Chi-restraints excluded: chain C residue 153 ILE Chi-restraints excluded: chain C residue 315 SER Chi-restraints excluded: chain C residue 319 ASP Chi-restraints excluded: chain C residue 361 LEU Chi-restraints excluded: chain C residue 442 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 10 optimal weight: 0.8980 chunk 65 optimal weight: 0.9990 chunk 71 optimal weight: 3.9990 chunk 50 optimal weight: 0.5980 chunk 41 optimal weight: 0.6980 chunk 63 optimal weight: 0.9990 chunk 79 optimal weight: 3.9990 chunk 18 optimal weight: 1.9990 chunk 100 optimal weight: 0.6980 chunk 61 optimal weight: 4.9990 chunk 103 optimal weight: 5.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 334 HIS D 542 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.137955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.112491 restraints weight = 11829.902| |-----------------------------------------------------------------------------| r_work (start): 0.3467 rms_B_bonded: 2.14 r_work: 0.3368 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3261 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.1798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9227 Z= 0.108 Angle : 0.544 7.682 12548 Z= 0.272 Chirality : 0.039 0.137 1455 Planarity : 0.004 0.046 1596 Dihedral : 7.112 75.614 1328 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 2.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.86 % Favored : 93.14 % Rotamer: Outliers : 2.35 % Allowed : 13.01 % Favored : 84.65 % 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: -2.27 (0.24), residues: 1152 helix: -0.76 (0.21), residues: 640 sheet: -1.15 (0.59), residues: 75 loop : -2.64 (0.25), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 562 TYR 0.009 0.001 TYR C 199 PHE 0.011 0.001 PHE D 467 TRP 0.012 0.001 TRP D 421 HIS 0.005 0.001 HIS C 556 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.11 ( 9227) covalent geometry : angle 0.54365 / 0.27 (12548) hydrogen bonds : bond 0.03565 / 2.36 ( 330) hydrogen bonds : angle 3.74936 / 2.66 ( 969) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 104 time to evaluate : 0.341 Fit side-chains REVERT: D 6 GLN cc_start: 0.7577 (tm-30) cc_final: 0.6500 (mp10) REVERT: D 14 LYS cc_start: 0.8327 (mttm) cc_final: 0.8014 (mttp) REVERT: D 182 LEU cc_start: 0.7437 (OUTLIER) cc_final: 0.7066 (mp) REVERT: D 353 GLU cc_start: 0.6257 (pt0) cc_final: 0.6010 (pm20) REVERT: D 423 LYS cc_start: 0.8416 (mttt) cc_final: 0.7516 (mmtt) REVERT: C 59 TYR cc_start: 0.8314 (p90) cc_final: 0.8080 (p90) REVERT: C 235 GLU cc_start: 0.8132 (tp30) cc_final: 0.7772 (tp30) REVERT: C 292 GLU cc_start: 0.7728 (OUTLIER) cc_final: 0.6888 (mp0) REVERT: C 361 LEU cc_start: 0.7987 (OUTLIER) cc_final: 0.7706 (mt) REVERT: C 394 GLN cc_start: 0.8047 (tp40) cc_final: 0.7188 (tt0) REVERT: C 534 ARG cc_start: 0.8253 (tpt-90) cc_final: 0.7883 (tpt-90) outliers start: 22 outliers final: 8 residues processed: 111 average time/residue: 0.6595 time to fit residues: 76.8005 Evaluate side-chains 110 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 99 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 22 ARG Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain D residue 222 GLU Chi-restraints excluded: chain D residue 380 VAL Chi-restraints excluded: chain D residue 509 LEU Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 292 GLU Chi-restraints excluded: chain C residue 315 SER Chi-restraints excluded: chain C residue 361 LEU Chi-restraints excluded: chain C residue 442 SER Chi-restraints excluded: chain C residue 449 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 54 optimal weight: 8.9990 chunk 71 optimal weight: 3.9990 chunk 83 optimal weight: 3.9990 chunk 12 optimal weight: 2.9990 chunk 43 optimal weight: 4.9990 chunk 93 optimal weight: 0.7980 chunk 49 optimal weight: 0.6980 chunk 45 optimal weight: 0.9990 chunk 90 optimal weight: 0.5980 chunk 34 optimal weight: 3.9990 chunk 15 optimal weight: 0.0070 overall best weight: 0.6200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 334 HIS D 543 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.139431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.113874 restraints weight = 11773.564| |-----------------------------------------------------------------------------| r_work (start): 0.3492 rms_B_bonded: 2.14 r_work: 0.3391 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3286 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.1956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 9227 Z= 0.099 Angle : 0.529 7.939 12548 Z= 0.264 Chirality : 0.039 0.132 1455 Planarity : 0.004 0.046 1596 Dihedral : 6.949 76.469 1328 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 2.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.68 % Favored : 93.32 % Rotamer: Outliers : 2.03 % Allowed : 14.29 % Favored : 83.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.89 (0.24), residues: 1152 helix: -0.46 (0.21), residues: 637 sheet: -0.93 (0.60), residues: 72 loop : -2.45 (0.26), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 562 TYR 0.010 0.001 TYR C 199 PHE 0.014 0.001 PHE C 301 TRP 0.012 0.001 TRP D 421 HIS 0.004 0.001 HIS C 556 Details of bonding type rmsd/Z covalent geometry : bond 0.00223 / 0.10 ( 9227) covalent geometry : angle 0.52869 / 0.26 (12548) hydrogen bonds : bond 0.03252 / 2.16 ( 330) hydrogen bonds : angle 3.64336 / 2.59 ( 969) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 104 time to evaluate : 0.251 Fit side-chains REVERT: D 6 GLN cc_start: 0.7535 (tm-30) cc_final: 0.6493 (mp10) REVERT: D 14 LYS cc_start: 0.8285 (mttm) cc_final: 0.7980 (mttp) REVERT: D 115 GLN cc_start: 0.7564 (pt0) cc_final: 0.6781 (mm-40) REVERT: D 182 LEU cc_start: 0.7552 (OUTLIER) cc_final: 0.7220 (mp) REVERT: D 353 GLU cc_start: 0.6299 (pt0) cc_final: 0.6075 (pm20) REVERT: D 423 LYS cc_start: 0.8366 (mttt) cc_final: 0.7475 (mmtt) REVERT: C 59 TYR cc_start: 0.8266 (p90) cc_final: 0.7990 (p90) REVERT: C 235 GLU cc_start: 0.8118 (tp30) cc_final: 0.7768 (tp30) REVERT: C 292 GLU cc_start: 0.7675 (OUTLIER) cc_final: 0.6811 (mp0) REVERT: C 361 LEU cc_start: 0.7969 (OUTLIER) cc_final: 0.7686 (mt) REVERT: C 394 GLN cc_start: 0.8063 (tp40) cc_final: 0.7202 (tt0) REVERT: C 534 ARG cc_start: 0.8186 (tpt-90) cc_final: 0.7785 (tpt-90) REVERT: C 555 THR cc_start: 0.8419 (OUTLIER) cc_final: 0.8215 (p) outliers start: 19 outliers final: 7 residues processed: 112 average time/residue: 0.6312 time to fit residues: 74.2745 Evaluate side-chains 112 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 101 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 22 ARG Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain D residue 222 GLU Chi-restraints excluded: chain D residue 380 VAL Chi-restraints excluded: chain D residue 509 LEU Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 292 GLU Chi-restraints excluded: chain C residue 315 SER Chi-restraints excluded: chain C residue 361 LEU Chi-restraints excluded: chain C residue 442 SER Chi-restraints excluded: chain C residue 555 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 110 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 chunk 47 optimal weight: 0.0870 chunk 79 optimal weight: 3.9990 chunk 24 optimal weight: 4.9990 chunk 112 optimal weight: 5.9990 chunk 68 optimal weight: 2.9990 chunk 34 optimal weight: 0.7980 chunk 2 optimal weight: 2.9990 chunk 37 optimal weight: 5.9990 chunk 56 optimal weight: 10.0000 overall best weight: 1.9764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 334 HIS D 542 HIS D 543 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.134071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.108571 restraints weight = 12019.449| |-----------------------------------------------------------------------------| r_work (start): 0.3430 rms_B_bonded: 2.16 r_work: 0.3324 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3219 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.1825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 9227 Z= 0.204 Angle : 0.671 8.221 12548 Z= 0.331 Chirality : 0.044 0.152 1455 Planarity : 0.005 0.045 1596 Dihedral : 7.541 73.758 1328 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 2.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.16 % Favored : 91.84 % Rotamer: Outliers : 2.67 % Allowed : 14.18 % Favored : 83.16 % 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: -2.24 (0.24), residues: 1152 helix: -0.78 (0.21), residues: 641 sheet: -1.44 (0.58), residues: 78 loop : -2.49 (0.26), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 562 TYR 0.010 0.002 TYR D 88 PHE 0.022 0.002 PHE C 301 TRP 0.009 0.001 TRP C 390 HIS 0.006 0.001 HIS C 424 Details of bonding type rmsd/Z covalent geometry : bond 0.00508 / 0.20 ( 9227) covalent geometry : angle 0.67140 / 0.33 (12548) hydrogen bonds : bond 0.05712 / 3.77 ( 330) hydrogen bonds : angle 3.98723 / 2.81 ( 969) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 96 time to evaluate : 0.246 Fit side-chains REVERT: D 6 GLN cc_start: 0.7499 (tm-30) cc_final: 0.6502 (mp10) REVERT: D 14 LYS cc_start: 0.8368 (mttm) cc_final: 0.8047 (mttp) REVERT: D 115 GLN cc_start: 0.7603 (pt0) cc_final: 0.6848 (mm-40) REVERT: D 384 ARG cc_start: 0.7523 (OUTLIER) cc_final: 0.7093 (mtt-85) REVERT: D 423 LYS cc_start: 0.8416 (mttt) cc_final: 0.7535 (mmtt) REVERT: C 59 TYR cc_start: 0.8384 (p90) cc_final: 0.8108 (p90) REVERT: C 235 GLU cc_start: 0.8138 (tp30) cc_final: 0.7711 (tp30) REVERT: C 361 LEU cc_start: 0.8453 (OUTLIER) cc_final: 0.8208 (mt) REVERT: C 470 GLU cc_start: 0.6587 (mm-30) cc_final: 0.6338 (pt0) REVERT: C 555 THR cc_start: 0.8427 (OUTLIER) cc_final: 0.8103 (p) outliers start: 25 outliers final: 12 residues processed: 109 average time/residue: 0.6173 time to fit residues: 70.6763 Evaluate side-chains 109 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 94 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 152 LEU Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain D residue 222 GLU Chi-restraints excluded: chain D residue 380 VAL Chi-restraints excluded: chain D residue 384 ARG Chi-restraints excluded: chain D residue 509 LEU Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 149 MET Chi-restraints excluded: chain C residue 153 ILE Chi-restraints excluded: chain C residue 297 VAL Chi-restraints excluded: chain C residue 315 SER Chi-restraints excluded: chain C residue 361 LEU Chi-restraints excluded: chain C residue 449 ILE Chi-restraints excluded: chain C residue 555 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 53 optimal weight: 0.5980 chunk 20 optimal weight: 0.9980 chunk 63 optimal weight: 1.9990 chunk 104 optimal weight: 2.9990 chunk 41 optimal weight: 3.9990 chunk 55 optimal weight: 4.9990 chunk 101 optimal weight: 0.9990 chunk 51 optimal weight: 0.6980 chunk 4 optimal weight: 0.8980 chunk 27 optimal weight: 5.9990 chunk 61 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 334 HIS D 543 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.137409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.111791 restraints weight = 11917.515| |-----------------------------------------------------------------------------| r_work (start): 0.3475 rms_B_bonded: 2.16 r_work: 0.3371 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3267 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.1943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9227 Z= 0.114 Angle : 0.561 8.256 12548 Z= 0.280 Chirality : 0.039 0.135 1455 Planarity : 0.004 0.047 1596 Dihedral : 7.177 75.816 1328 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 2.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.68 % Favored : 93.32 % Rotamer: Outliers : 2.13 % Allowed : 15.03 % Favored : 82.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.88 (0.24), residues: 1152 helix: -0.47 (0.21), residues: 637 sheet: -1.05 (0.58), residues: 75 loop : -2.39 (0.26), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 562 TYR 0.009 0.001 TYR C 199 PHE 0.017 0.001 PHE C 301 TRP 0.011 0.001 TRP D 421 HIS 0.005 0.001 HIS C 556 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.11 ( 9227) covalent geometry : angle 0.56132 / 0.28 (12548) hydrogen bonds : bond 0.03776 / 2.51 ( 330) hydrogen bonds : angle 3.76871 / 2.66 ( 969) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 96 time to evaluate : 0.362 Fit side-chains REVERT: D 6 GLN cc_start: 0.7409 (tm-30) cc_final: 0.6446 (mp10) REVERT: D 14 LYS cc_start: 0.8284 (mttm) cc_final: 0.7966 (mttp) REVERT: D 115 GLN cc_start: 0.7644 (pt0) cc_final: 0.6849 (mm-40) REVERT: D 182 LEU cc_start: 0.7535 (OUTLIER) cc_final: 0.7187 (mp) REVERT: D 353 GLU cc_start: 0.6350 (pt0) cc_final: 0.6053 (pm20) REVERT: D 423 LYS cc_start: 0.8322 (mttt) cc_final: 0.7441 (mmtt) REVERT: C 59 TYR cc_start: 0.8237 (p90) cc_final: 0.7997 (p90) REVERT: C 235 GLU cc_start: 0.8116 (tp30) cc_final: 0.7730 (tp30) REVERT: C 361 LEU cc_start: 0.8028 (OUTLIER) cc_final: 0.7748 (mt) REVERT: C 394 GLN cc_start: 0.8047 (tp40) cc_final: 0.7229 (tt0) REVERT: C 470 GLU cc_start: 0.6521 (mm-30) cc_final: 0.6292 (pt0) REVERT: C 555 THR cc_start: 0.8384 (OUTLIER) cc_final: 0.8139 (p) outliers start: 20 outliers final: 12 residues processed: 106 average time/residue: 0.6175 time to fit residues: 68.8409 Evaluate side-chains 110 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 95 time to evaluate : 0.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 152 LEU Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain D residue 222 GLU Chi-restraints excluded: chain D residue 380 VAL Chi-restraints excluded: chain D residue 509 LEU Chi-restraints excluded: chain D residue 544 LEU Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 149 MET Chi-restraints excluded: chain C residue 153 ILE Chi-restraints excluded: chain C residue 361 LEU Chi-restraints excluded: chain C residue 442 SER Chi-restraints excluded: chain C residue 449 ILE Chi-restraints excluded: chain C residue 520 MET Chi-restraints excluded: chain C residue 555 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 111 optimal weight: 3.9990 chunk 5 optimal weight: 0.5980 chunk 41 optimal weight: 0.9990 chunk 23 optimal weight: 0.4980 chunk 56 optimal weight: 2.9990 chunk 22 optimal weight: 0.9980 chunk 42 optimal weight: 4.9990 chunk 50 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 81 optimal weight: 2.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 334 HIS D 543 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.136918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.111342 restraints weight = 11812.339| |-----------------------------------------------------------------------------| r_work (start): 0.3468 rms_B_bonded: 2.15 r_work: 0.3363 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3257 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.1946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9227 Z= 0.126 Angle : 0.575 8.313 12548 Z= 0.286 Chirality : 0.040 0.136 1455 Planarity : 0.004 0.046 1596 Dihedral : 7.154 76.036 1328 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 2.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.47 % Favored : 92.53 % Rotamer: Outliers : 2.45 % Allowed : 14.61 % Favored : 82.94 % 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: -1.82 (0.24), residues: 1152 helix: -0.43 (0.21), residues: 641 sheet: -0.93 (0.59), residues: 74 loop : -2.38 (0.26), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 562 TYR 0.008 0.001 TYR C 199 PHE 0.018 0.001 PHE C 301 TRP 0.011 0.001 TRP D 421 HIS 0.005 0.001 HIS C 556 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.13 ( 9227) covalent geometry : angle 0.57519 / 0.29 (12548) hydrogen bonds : bond 0.04140 / 2.74 ( 330) hydrogen bonds : angle 3.77151 / 2.66 ( 969) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 97 time to evaluate : 0.231 Fit side-chains REVERT: D 6 GLN cc_start: 0.7441 (tm-30) cc_final: 0.6489 (mp10) REVERT: D 14 LYS cc_start: 0.8303 (mttm) cc_final: 0.7983 (mttp) REVERT: D 115 GLN cc_start: 0.7645 (pt0) cc_final: 0.6873 (mm-40) REVERT: D 182 LEU cc_start: 0.7554 (OUTLIER) cc_final: 0.7241 (mp) REVERT: D 353 GLU cc_start: 0.6366 (pt0) cc_final: 0.6085 (pm20) REVERT: D 423 LYS cc_start: 0.8337 (mttt) cc_final: 0.7463 (mmtt) REVERT: C 59 TYR cc_start: 0.8257 (p90) cc_final: 0.7986 (p90) REVERT: C 235 GLU cc_start: 0.8124 (tp30) cc_final: 0.7748 (tp30) REVERT: C 361 LEU cc_start: 0.8158 (OUTLIER) cc_final: 0.7905 (mt) REVERT: C 394 GLN cc_start: 0.8068 (tp40) cc_final: 0.7265 (tt0) REVERT: C 470 GLU cc_start: 0.6579 (mm-30) cc_final: 0.6311 (pt0) REVERT: C 555 THR cc_start: 0.8375 (OUTLIER) cc_final: 0.8142 (p) outliers start: 23 outliers final: 14 residues processed: 109 average time/residue: 0.6143 time to fit residues: 70.3120 Evaluate side-chains 115 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 98 time to evaluate : 0.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 22 ARG Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain D residue 212 MET Chi-restraints excluded: chain D residue 222 GLU Chi-restraints excluded: chain D residue 380 VAL Chi-restraints excluded: chain D residue 509 LEU Chi-restraints excluded: chain D residue 544 LEU Chi-restraints excluded: chain D residue 552 VAL Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 149 MET Chi-restraints excluded: chain C residue 153 ILE Chi-restraints excluded: chain C residue 361 LEU Chi-restraints excluded: chain C residue 442 SER Chi-restraints excluded: chain C residue 449 ILE Chi-restraints excluded: chain C residue 513 ILE Chi-restraints excluded: chain C residue 555 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 104 optimal weight: 2.9990 chunk 81 optimal weight: 2.9990 chunk 103 optimal weight: 0.0010 chunk 58 optimal weight: 0.8980 chunk 112 optimal weight: 0.6980 chunk 84 optimal weight: 3.9990 chunk 4 optimal weight: 0.5980 chunk 37 optimal weight: 6.9990 chunk 24 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 chunk 91 optimal weight: 7.9990 overall best weight: 1.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 334 HIS D 543 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.137080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.111470 restraints weight = 11875.146| |-----------------------------------------------------------------------------| r_work (start): 0.3448 rms_B_bonded: 2.15 r_work: 0.3344 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3239 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3239 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 moved from start: 0.1977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9227 Z= 0.127 Angle : 0.575 8.565 12548 Z= 0.286 Chirality : 0.040 0.136 1455 Planarity : 0.004 0.046 1596 Dihedral : 7.146 76.152 1328 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 2.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.03 % Favored : 92.97 % Rotamer: Outliers : 2.13 % Allowed : 15.03 % Favored : 82.84 % 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: -1.78 (0.24), residues: 1152 helix: -0.41 (0.21), residues: 641 sheet: -0.93 (0.58), residues: 75 loop : -2.35 (0.27), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 11 TYR 0.008 0.001 TYR C 199 PHE 0.018 0.001 PHE C 301 TRP 0.011 0.001 TRP D 421 HIS 0.005 0.001 HIS C 556 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.13 ( 9227) covalent geometry : angle 0.57536 / 0.29 (12548) hydrogen bonds : bond 0.04097 / 2.72 ( 330) hydrogen bonds : angle 3.76884 / 2.66 ( 969) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 98 time to evaluate : 0.248 Fit side-chains REVERT: D 6 GLN cc_start: 0.7357 (tm-30) cc_final: 0.6392 (mp10) REVERT: D 14 LYS cc_start: 0.8255 (mttm) cc_final: 0.7935 (mttp) REVERT: D 28 ARG cc_start: 0.7896 (mtm110) cc_final: 0.7128 (ttp80) REVERT: D 115 GLN cc_start: 0.7686 (pt0) cc_final: 0.6885 (mm-40) REVERT: D 182 LEU cc_start: 0.7436 (OUTLIER) cc_final: 0.7109 (mp) REVERT: D 353 GLU cc_start: 0.6333 (pt0) cc_final: 0.6028 (pm20) REVERT: D 423 LYS cc_start: 0.8272 (mttt) cc_final: 0.7386 (mmtt) REVERT: C 59 TYR cc_start: 0.8177 (p90) cc_final: 0.7957 (p90) REVERT: C 235 GLU cc_start: 0.8047 (tp30) cc_final: 0.7660 (tp30) REVERT: C 361 LEU cc_start: 0.8021 (OUTLIER) cc_final: 0.7766 (mt) REVERT: C 394 GLN cc_start: 0.8002 (tp40) cc_final: 0.7193 (tt0) REVERT: C 470 GLU cc_start: 0.6534 (mm-30) cc_final: 0.6254 (pt0) REVERT: C 555 THR cc_start: 0.8329 (OUTLIER) cc_final: 0.8093 (p) outliers start: 20 outliers final: 15 residues processed: 109 average time/residue: 0.6186 time to fit residues: 70.9044 Evaluate side-chains 114 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 96 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 22 ARG Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain D residue 212 MET Chi-restraints excluded: chain D residue 222 GLU Chi-restraints excluded: chain D residue 380 VAL Chi-restraints excluded: chain D residue 509 LEU Chi-restraints excluded: chain D residue 544 LEU Chi-restraints excluded: chain D residue 552 VAL Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 149 MET Chi-restraints excluded: chain C residue 153 ILE Chi-restraints excluded: chain C residue 297 VAL Chi-restraints excluded: chain C residue 361 LEU Chi-restraints excluded: chain C residue 442 SER Chi-restraints excluded: chain C residue 449 ILE Chi-restraints excluded: chain C residue 513 ILE Chi-restraints excluded: chain C residue 555 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 5 optimal weight: 0.5980 chunk 54 optimal weight: 6.9990 chunk 27 optimal weight: 0.7980 chunk 48 optimal weight: 2.9990 chunk 37 optimal weight: 3.9990 chunk 8 optimal weight: 0.9990 chunk 105 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 103 optimal weight: 0.1980 chunk 70 optimal weight: 2.9990 chunk 83 optimal weight: 1.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 334 HIS D 543 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.137626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.112013 restraints weight = 11727.677| |-----------------------------------------------------------------------------| r_work (start): 0.3452 rms_B_bonded: 2.14 r_work: 0.3350 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3245 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.2006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9227 Z= 0.118 Angle : 0.561 8.393 12548 Z= 0.279 Chirality : 0.040 0.134 1455 Planarity : 0.004 0.046 1596 Dihedral : 7.074 76.591 1328 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 2.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.29 % Favored : 92.71 % Rotamer: Outliers : 2.35 % Allowed : 14.61 % Favored : 83.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.77 (0.24), residues: 1152 helix: -0.39 (0.21), residues: 647 sheet: -0.89 (0.58), residues: 75 loop : -2.38 (0.27), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 11 TYR 0.009 0.001 TYR C 199 PHE 0.017 0.001 PHE C 301 TRP 0.011 0.001 TRP D 421 HIS 0.005 0.001 HIS C 556 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.12 ( 9227) covalent geometry : angle 0.56095 / 0.28 (12548) hydrogen bonds : bond 0.03864 / 2.56 ( 330) hydrogen bonds : angle 3.72300 / 2.63 ( 969) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2579.03 seconds wall clock time: 44 minutes 23.60 seconds (2663.60 seconds total)