Starting phenix.real_space_refine on Sun Aug 24 01:49:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9l7m_62874/08_2025/9l7m_62874_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9l7m_62874/08_2025/9l7m_62874.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.48 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9l7m_62874/08_2025/9l7m_62874.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9l7m_62874/08_2025/9l7m_62874.map" model { file = "/net/cci-nas-00/data/ceres_data/9l7m_62874/08_2025/9l7m_62874_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9l7m_62874/08_2025/9l7m_62874_neut.cif" } resolution = 3.48 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= 0.011 sd= 0.134 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 12 5.49 5 Mg 4 5.21 5 S 111 5.16 5 C 10140 2.51 5 N 2764 2.21 5 O 3150 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 74 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 16181 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 3430 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 3430 Classifications: {'peptide': 439} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 418} Chain: "B" Number of atoms: 3351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3351 Classifications: {'peptide': 426} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 405} Chain: "K" Number of atoms: 2487 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2487 Classifications: {'peptide': 317} Link IDs: {'PTRANS': 8, 'TRANS': 308} Chain breaks: 1 Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Restraints were copied for chains: C, D Time building chain proxies: 4.14, per 1000 atoms: 0.26 Number of scatterers: 16181 At special positions: 0 Unit cell: (76.56, 110.88, 198, 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 111 16.00 P 12 15.00 Mg 4 11.99 O 3150 8.00 N 2764 7.00 C 10140 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.10 Conformation dependent library (CDL) restraints added in 636.8 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 4070 Ramachandran restraints generated. 2035 Oldfield, 0 Emsley, 2035 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3790 Finding SS restraints... Secondary structure from input PDB file: 95 helices and 22 sheets defined 43.0% alpha, 17.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.41 Creating SS restraints... Processing helix chain 'A' and resid 10 through 28 removed outlier: 3.790A pdb=" N ALA A 19 " --> pdb=" O GLN A 15 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LEU A 26 " --> pdb=" O GLU A 22 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N HIS A 28 " --> pdb=" O TYR A 24 " (cutoff:3.500A) Processing helix chain 'A' and resid 49 through 53 Processing helix chain 'A' and resid 74 through 81 removed outlier: 4.051A pdb=" N VAL A 78 " --> pdb=" O VAL A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 108 removed outlier: 3.907A pdb=" N TYR A 108 " --> pdb=" O ALA A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 124 removed outlier: 4.116A pdb=" N ASP A 120 " --> pdb=" O ASP A 116 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ARG A 121 " --> pdb=" O LEU A 117 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 160 removed outlier: 5.310A pdb=" N THR A 150 " --> pdb=" O GLY A 146 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N SER A 151 " --> pdb=" O SER A 147 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N GLU A 155 " --> pdb=" O SER A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 190 removed outlier: 3.722A pdb=" N ASN A 186 " --> pdb=" O VAL A 182 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N ILE A 188 " --> pdb=" O PRO A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 197 removed outlier: 3.998A pdb=" N GLU A 196 " --> pdb=" O HIS A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 215 Processing helix chain 'A' and resid 223 through 234 removed outlier: 5.011A pdb=" N ARG A 229 " --> pdb=" O THR A 225 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N LEU A 230 " --> pdb=" O ASN A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 239 removed outlier: 3.503A pdb=" N THR A 239 " --> pdb=" O VAL A 235 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 260 removed outlier: 3.833A pdb=" N THR A 257 " --> pdb=" O THR A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 292 removed outlier: 3.686A pdb=" N ILE A 291 " --> pdb=" O SER A 287 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 297 removed outlier: 3.517A pdb=" N GLU A 297 " --> pdb=" O ALA A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 326 through 338 removed outlier: 3.612A pdb=" N THR A 337 " --> pdb=" O ALA A 333 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N LYS A 338 " --> pdb=" O THR A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 382 through 386 Processing helix chain 'A' and resid 387 through 393 Processing helix chain 'A' and resid 404 through 410 removed outlier: 4.164A pdb=" N TYR A 408 " --> pdb=" O PHE A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 435 removed outlier: 4.103A pdb=" N SER A 419 " --> pdb=" O GLU A 415 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ALA A 421 " --> pdb=" O GLU A 417 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N LEU A 428 " --> pdb=" O ASP A 424 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N GLU A 429 " --> pdb=" O MET A 425 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 28 removed outlier: 3.873A pdb=" N LYS B 19 " --> pdb=" O GLN B 15 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N GLU B 22 " --> pdb=" O ALA B 18 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N SER B 25 " --> pdb=" O TRP B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 51 removed outlier: 3.697A pdb=" N GLU B 47 " --> pdb=" O LEU B 42 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N ARG B 48 " --> pdb=" O GLN B 43 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N ILE B 49 " --> pdb=" O LEU B 44 " (cutoff:3.500A) removed outlier: 5.550A pdb=" N ASN B 50 " --> pdb=" O GLU B 47 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 81 removed outlier: 4.099A pdb=" N ARG B 79 " --> pdb=" O MET B 75 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 108 Processing helix chain 'B' and resid 115 through 123 removed outlier: 4.333A pdb=" N VAL B 121 " --> pdb=" O SER B 117 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ARG B 123 " --> pdb=" O LEU B 119 " (cutoff:3.500A) Processing helix chain 'B' and resid 144 through 158 removed outlier: 3.533A pdb=" N GLY B 148 " --> pdb=" O GLY B 144 " (cutoff:3.500A) Processing helix chain 'B' and resid 174 through 178 removed outlier: 3.536A pdb=" N VAL B 177 " --> pdb=" O SER B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 182 through 195 removed outlier: 4.448A pdb=" N THR B 188 " --> pdb=" O PRO B 184 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N HIS B 192 " --> pdb=" O THR B 188 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N GLN B 193 " --> pdb=" O LEU B 189 " (cutoff:3.500A) Processing helix chain 'B' and resid 206 through 215 removed outlier: 3.778A pdb=" N CYS B 213 " --> pdb=" O LEU B 209 " (cutoff:3.500A) Processing helix chain 'B' and resid 223 through 226 Processing helix chain 'B' and resid 227 through 239 removed outlier: 4.308A pdb=" N ALA B 233 " --> pdb=" O HIS B 229 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N THR B 239 " --> pdb=" O MET B 235 " (cutoff:3.500A) Processing helix chain 'B' and resid 251 through 259 Processing helix chain 'B' and resid 280 through 284 Processing helix chain 'B' and resid 287 through 295 removed outlier: 3.555A pdb=" N LEU B 291 " --> pdb=" O THR B 287 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 301 removed outlier: 4.107A pdb=" N MET B 301 " --> pdb=" O ALA B 298 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 310 removed outlier: 3.523A pdb=" N HIS B 309 " --> pdb=" O ASP B 306 " (cutoff:3.500A) Processing helix chain 'B' and resid 324 through 338 removed outlier: 3.799A pdb=" N VAL B 328 " --> pdb=" O SER B 324 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 385 No H-bonds generated for 'chain 'B' and resid 383 through 385' Processing helix chain 'B' and resid 386 through 397 removed outlier: 3.666A pdb=" N ILE B 391 " --> pdb=" O LEU B 387 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N SER B 392 " --> pdb=" O PHE B 388 " (cutoff:3.500A) Processing helix chain 'B' and resid 398 through 402 Processing helix chain 'B' and resid 405 through 410 Processing helix chain 'B' and resid 415 through 424 removed outlier: 3.979A pdb=" N THR B 419 " --> pdb=" O GLU B 415 " (cutoff:3.500A) Processing helix chain 'B' and resid 426 through 434 Processing helix chain 'C' and resid 10 through 28 removed outlier: 3.790A pdb=" N ALA C 19 " --> pdb=" O GLN C 15 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU C 26 " --> pdb=" O GLU C 22 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N HIS C 28 " --> pdb=" O TYR C 24 " (cutoff:3.500A) Processing helix chain 'C' and resid 49 through 53 Processing helix chain 'C' and resid 74 through 81 removed outlier: 4.050A pdb=" N VAL C 78 " --> pdb=" O VAL C 74 " (cutoff:3.500A) Processing helix chain 'C' and resid 103 through 108 removed outlier: 3.908A pdb=" N TYR C 108 " --> pdb=" O ALA C 104 " (cutoff:3.500A) Processing helix chain 'C' and resid 114 through 124 removed outlier: 4.117A pdb=" N ASP C 120 " --> pdb=" O ASP C 116 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ARG C 121 " --> pdb=" O LEU C 117 " (cutoff:3.500A) Processing helix chain 'C' and resid 144 through 160 removed outlier: 5.309A pdb=" N THR C 150 " --> pdb=" O GLY C 146 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N SER C 151 " --> pdb=" O SER C 147 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N GLU C 155 " --> pdb=" O SER C 151 " (cutoff:3.500A) Processing helix chain 'C' and resid 182 through 190 removed outlier: 3.722A pdb=" N ASN C 186 " --> pdb=" O VAL C 182 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N ILE C 188 " --> pdb=" O PRO C 184 " (cutoff:3.500A) Processing helix chain 'C' and resid 192 through 197 removed outlier: 3.999A pdb=" N GLU C 196 " --> pdb=" O HIS C 192 " (cutoff:3.500A) Processing helix chain 'C' and resid 206 through 215 Processing helix chain 'C' and resid 223 through 234 removed outlier: 5.010A pdb=" N ARG C 229 " --> pdb=" O THR C 225 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N LEU C 230 " --> pdb=" O ASN C 226 " (cutoff:3.500A) Processing helix chain 'C' and resid 234 through 239 removed outlier: 3.502A pdb=" N THR C 239 " --> pdb=" O VAL C 235 " (cutoff:3.500A) Processing helix chain 'C' and resid 253 through 260 removed outlier: 3.833A pdb=" N THR C 257 " --> pdb=" O THR C 253 " (cutoff:3.500A) Processing helix chain 'C' and resid 287 through 292 removed outlier: 3.685A pdb=" N ILE C 291 " --> pdb=" O SER C 287 " (cutoff:3.500A) Processing helix chain 'C' and resid 293 through 297 removed outlier: 3.518A pdb=" N GLU C 297 " --> pdb=" O ALA C 294 " (cutoff:3.500A) Processing helix chain 'C' and resid 326 through 338 removed outlier: 3.612A pdb=" N THR C 337 " --> pdb=" O ALA C 333 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N LYS C 338 " --> pdb=" O THR C 334 " (cutoff:3.500A) Processing helix chain 'C' and resid 382 through 386 Processing helix chain 'C' and resid 387 through 393 Processing helix chain 'C' and resid 404 through 410 removed outlier: 4.165A pdb=" N TYR C 408 " --> pdb=" O PHE C 404 " (cutoff:3.500A) Processing helix chain 'C' and resid 415 through 435 removed outlier: 4.103A pdb=" N SER C 419 " --> pdb=" O GLU C 415 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ALA C 421 " --> pdb=" O GLU C 417 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N LEU C 428 " --> pdb=" O ASP C 424 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N GLU C 429 " --> pdb=" O MET C 425 " (cutoff:3.500A) Processing helix chain 'D' and resid 10 through 28 removed outlier: 3.872A pdb=" N LYS D 19 " --> pdb=" O GLN D 15 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N GLU D 22 " --> pdb=" O ALA D 18 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N SER D 25 " --> pdb=" O TRP D 21 " (cutoff:3.500A) Processing helix chain 'D' and resid 42 through 51 removed outlier: 3.697A pdb=" N GLU D 47 " --> pdb=" O LEU D 42 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N ARG D 48 " --> pdb=" O GLN D 43 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N ILE D 49 " --> pdb=" O LEU D 44 " (cutoff:3.500A) removed outlier: 5.551A pdb=" N ASN D 50 " --> pdb=" O GLU D 47 " (cutoff:3.500A) Processing helix chain 'D' and resid 73 through 81 removed outlier: 4.099A pdb=" N ARG D 79 " --> pdb=" O MET D 75 " (cutoff:3.500A) Processing helix chain 'D' and resid 103 through 108 Processing helix chain 'D' and resid 115 through 123 removed outlier: 4.333A pdb=" N VAL D 121 " --> pdb=" O SER D 117 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ARG D 123 " --> pdb=" O LEU D 119 " (cutoff:3.500A) Processing helix chain 'D' and resid 144 through 158 removed outlier: 3.534A pdb=" N GLY D 148 " --> pdb=" O GLY D 144 " (cutoff:3.500A) Processing helix chain 'D' and resid 174 through 178 removed outlier: 3.536A pdb=" N VAL D 177 " --> pdb=" O SER D 174 " (cutoff:3.500A) Processing helix chain 'D' and resid 182 through 195 removed outlier: 4.448A pdb=" N THR D 188 " --> pdb=" O PRO D 184 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N HIS D 192 " --> pdb=" O THR D 188 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N GLN D 193 " --> pdb=" O LEU D 189 " (cutoff:3.500A) Processing helix chain 'D' and resid 206 through 215 removed outlier: 3.777A pdb=" N CYS D 213 " --> pdb=" O LEU D 209 " (cutoff:3.500A) Processing helix chain 'D' and resid 223 through 226 Processing helix chain 'D' and resid 227 through 239 removed outlier: 4.308A pdb=" N ALA D 233 " --> pdb=" O HIS D 229 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N THR D 239 " --> pdb=" O MET D 235 " (cutoff:3.500A) Processing helix chain 'D' and resid 251 through 259 Processing helix chain 'D' and resid 280 through 284 Processing helix chain 'D' and resid 287 through 295 removed outlier: 3.555A pdb=" N LEU D 291 " --> pdb=" O THR D 287 " (cutoff:3.500A) Processing helix chain 'D' and resid 297 through 301 removed outlier: 4.106A pdb=" N MET D 301 " --> pdb=" O ALA D 298 " (cutoff:3.500A) Processing helix chain 'D' and resid 306 through 310 removed outlier: 3.524A pdb=" N HIS D 309 " --> pdb=" O ASP D 306 " (cutoff:3.500A) Processing helix chain 'D' and resid 324 through 338 removed outlier: 3.798A pdb=" N VAL D 328 " --> pdb=" O SER D 324 " (cutoff:3.500A) Processing helix chain 'D' and resid 383 through 385 No H-bonds generated for 'chain 'D' and resid 383 through 385' Processing helix chain 'D' and resid 386 through 397 removed outlier: 3.667A pdb=" N ILE D 391 " --> pdb=" O LEU D 387 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N SER D 392 " --> pdb=" O PHE D 388 " (cutoff:3.500A) Processing helix chain 'D' and resid 398 through 402 Processing helix chain 'D' and resid 405 through 410 Processing helix chain 'D' and resid 415 through 424 removed outlier: 3.979A pdb=" N THR D 419 " --> pdb=" O GLU D 415 " (cutoff:3.500A) Processing helix chain 'D' and resid 426 through 434 Processing helix chain 'K' and resid 20 through 26 Processing helix chain 'K' and resid 57 through 66 removed outlier: 3.741A pdb=" N VAL K 61 " --> pdb=" O SER K 57 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N TYR K 62 " --> pdb=" O GLN K 58 " (cutoff:3.500A) Processing helix chain 'K' and resid 67 through 68 No H-bonds generated for 'chain 'K' and resid 67 through 68' Processing helix chain 'K' and resid 70 through 70 No H-bonds generated for 'chain 'K' and resid 70 through 70' Processing helix chain 'K' and resid 71 through 75 Processing helix chain 'K' and resid 90 through 95 Processing helix chain 'K' and resid 108 through 121 removed outlier: 4.543A pdb=" N ASP K 114 " --> pdb=" O ARG K 110 " (cutoff:3.500A) Processing helix chain 'K' and resid 175 through 188 Processing helix chain 'K' and resid 245 through 271 removed outlier: 3.633A pdb=" N ASP K 249 " --> pdb=" O GLY K 245 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLU K 250 " --> pdb=" O ALA K 246 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LYS K 256 " --> pdb=" O LYS K 252 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ASN K 263 " --> pdb=" O SER K 259 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N VAL K 264 " --> pdb=" O ALA K 260 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ALA K 269 " --> pdb=" O ILE K 265 " (cutoff:3.500A) Processing helix chain 'K' and resid 280 through 287 removed outlier: 3.576A pdb=" N ARG K 284 " --> pdb=" O SER K 280 " (cutoff:3.500A) Processing helix chain 'K' and resid 308 through 322 removed outlier: 4.371A pdb=" N SER K 314 " --> pdb=" O SER K 310 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N GLY K 319 " --> pdb=" O THR K 315 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ALA K 322 " --> pdb=" O PHE K 318 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 65 through 68 removed outlier: 9.097A pdb=" N VAL A 66 " --> pdb=" O CYS A 4 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N SER A 6 " --> pdb=" O VAL A 66 " (cutoff:3.500A) removed outlier: 7.736A pdb=" N VAL A 68 " --> pdb=" O SER A 6 " (cutoff:3.500A) removed outlier: 5.916A pdb=" N HIS A 8 " --> pdb=" O VAL A 68 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N GLU A 3 " --> pdb=" O LEU A 132 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N GLY A 134 " --> pdb=" O GLU A 3 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N SER A 140 " --> pdb=" O VAL A 9 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N SER A 165 " --> pdb=" O GLN A 133 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 65 through 68 removed outlier: 9.097A pdb=" N VAL A 66 " --> pdb=" O CYS A 4 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N SER A 6 " --> pdb=" O VAL A 66 " (cutoff:3.500A) removed outlier: 7.736A pdb=" N VAL A 68 " --> pdb=" O SER A 6 " (cutoff:3.500A) removed outlier: 5.916A pdb=" N HIS A 8 " --> pdb=" O VAL A 68 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N GLU A 3 " --> pdb=" O LEU A 132 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N GLY A 134 " --> pdb=" O GLU A 3 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N SER A 140 " --> pdb=" O VAL A 9 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N PHE A 169 " --> pdb=" O VAL A 137 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 55 through 56 Processing sheet with id=AA4, first strand: chain 'A' and resid 269 through 270 removed outlier: 3.968A pdb=" N LEU A 269 " --> pdb=" O SER A 379 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N SER A 379 " --> pdb=" O LEU A 269 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 317 through 318 Processing sheet with id=AA6, first strand: chain 'A' and resid 320 through 321 Processing sheet with id=AA7, first strand: chain 'B' and resid 93 through 94 removed outlier: 7.972A pdb=" N VAL B 93 " --> pdb=" O ALA B 65 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N LEU B 67 " --> pdb=" O VAL B 93 " (cutoff:3.500A) removed outlier: 9.031A pdb=" N ILE B 66 " --> pdb=" O ILE B 4 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N HIS B 6 " --> pdb=" O ILE B 66 " (cutoff:3.500A) removed outlier: 7.573A pdb=" N VAL B 68 " --> pdb=" O HIS B 6 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N GLN B 8 " --> pdb=" O VAL B 68 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N VAL B 5 " --> pdb=" O GLN B 136 " (cutoff:3.500A) removed outlier: 8.190A pdb=" N THR B 138 " --> pdb=" O VAL B 5 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N ILE B 7 " --> pdb=" O THR B 138 " (cutoff:3.500A) removed outlier: 8.623A pdb=" N SER B 140 " --> pdb=" O ILE B 7 " (cutoff:3.500A) removed outlier: 8.141A pdb=" N ALA B 9 " --> pdb=" O SER B 140 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 93 through 94 removed outlier: 7.972A pdb=" N VAL B 93 " --> pdb=" O ALA B 65 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N LEU B 67 " --> pdb=" O VAL B 93 " (cutoff:3.500A) removed outlier: 9.031A pdb=" N ILE B 66 " --> pdb=" O ILE B 4 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N HIS B 6 " --> pdb=" O ILE B 66 " (cutoff:3.500A) removed outlier: 7.573A pdb=" N VAL B 68 " --> pdb=" O HIS B 6 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N GLN B 8 " --> pdb=" O VAL B 68 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N VAL B 5 " --> pdb=" O GLN B 136 " (cutoff:3.500A) removed outlier: 8.190A pdb=" N THR B 138 " --> pdb=" O VAL B 5 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N ILE B 7 " --> pdb=" O THR B 138 " (cutoff:3.500A) removed outlier: 8.623A pdb=" N SER B 140 " --> pdb=" O ILE B 7 " (cutoff:3.500A) removed outlier: 8.141A pdb=" N ALA B 9 " --> pdb=" O SER B 140 " (cutoff:3.500A) removed outlier: 7.783A pdb=" N PHE B 169 " --> pdb=" O PHE B 135 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N LEU B 137 " --> pdb=" O PHE B 169 " (cutoff:3.500A) removed outlier: 7.549A pdb=" N VAL B 171 " --> pdb=" O LEU B 137 " (cutoff:3.500A) removed outlier: 7.327A pdb=" N HIS B 139 " --> pdb=" O VAL B 171 " (cutoff:3.500A) removed outlier: 8.606A pdb=" N ASP B 205 " --> pdb=" O PRO B 270 " (cutoff:3.500A) removed outlier: 12.033A pdb=" N PHE B 272 " --> pdb=" O ASP B 205 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N PHE B 267 " --> pdb=" O SER B 381 " (cutoff:3.500A) removed outlier: 5.207A pdb=" N SER B 381 " --> pdb=" O PHE B 267 " (cutoff:3.500A) removed outlier: 8.782A pdb=" N LYS B 352 " --> pdb=" O LEU B 313 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N VAL B 315 " --> pdb=" O LYS B 352 " (cutoff:3.500A) removed outlier: 8.546A pdb=" N ALA B 354 " --> pdb=" O VAL B 315 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N ALA B 317 " --> pdb=" O ALA B 354 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 53 through 56 Processing sheet with id=AB1, first strand: chain 'C' and resid 65 through 68 removed outlier: 9.097A pdb=" N VAL C 66 " --> pdb=" O CYS C 4 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N SER C 6 " --> pdb=" O VAL C 66 " (cutoff:3.500A) removed outlier: 7.735A pdb=" N VAL C 68 " --> pdb=" O SER C 6 " (cutoff:3.500A) removed outlier: 5.917A pdb=" N HIS C 8 " --> pdb=" O VAL C 68 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N GLU C 3 " --> pdb=" O LEU C 132 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N GLY C 134 " --> pdb=" O GLU C 3 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N SER C 140 " --> pdb=" O VAL C 9 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N SER C 165 " --> pdb=" O GLN C 133 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 65 through 68 removed outlier: 9.097A pdb=" N VAL C 66 " --> pdb=" O CYS C 4 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N SER C 6 " --> pdb=" O VAL C 66 " (cutoff:3.500A) removed outlier: 7.735A pdb=" N VAL C 68 " --> pdb=" O SER C 6 " (cutoff:3.500A) removed outlier: 5.917A pdb=" N HIS C 8 " --> pdb=" O VAL C 68 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N GLU C 3 " --> pdb=" O LEU C 132 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N GLY C 134 " --> pdb=" O GLU C 3 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N SER C 140 " --> pdb=" O VAL C 9 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N PHE C 169 " --> pdb=" O VAL C 137 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 55 through 56 Processing sheet with id=AB4, first strand: chain 'C' and resid 269 through 270 removed outlier: 3.967A pdb=" N LEU C 269 " --> pdb=" O SER C 379 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N SER C 379 " --> pdb=" O LEU C 269 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'C' and resid 317 through 318 Processing sheet with id=AB6, first strand: chain 'C' and resid 320 through 321 Processing sheet with id=AB7, first strand: chain 'D' and resid 93 through 94 removed outlier: 7.972A pdb=" N VAL D 93 " --> pdb=" O ALA D 65 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N LEU D 67 " --> pdb=" O VAL D 93 " (cutoff:3.500A) removed outlier: 9.032A pdb=" N ILE D 66 " --> pdb=" O ILE D 4 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N HIS D 6 " --> pdb=" O ILE D 66 " (cutoff:3.500A) removed outlier: 7.571A pdb=" N VAL D 68 " --> pdb=" O HIS D 6 " (cutoff:3.500A) removed outlier: 6.006A pdb=" N GLN D 8 " --> pdb=" O VAL D 68 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N VAL D 5 " --> pdb=" O GLN D 136 " (cutoff:3.500A) removed outlier: 8.189A pdb=" N THR D 138 " --> pdb=" O VAL D 5 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N ILE D 7 " --> pdb=" O THR D 138 " (cutoff:3.500A) removed outlier: 8.623A pdb=" N SER D 140 " --> pdb=" O ILE D 7 " (cutoff:3.500A) removed outlier: 8.141A pdb=" N ALA D 9 " --> pdb=" O SER D 140 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 93 through 94 removed outlier: 7.972A pdb=" N VAL D 93 " --> pdb=" O ALA D 65 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N LEU D 67 " --> pdb=" O VAL D 93 " (cutoff:3.500A) removed outlier: 9.032A pdb=" N ILE D 66 " --> pdb=" O ILE D 4 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N HIS D 6 " --> pdb=" O ILE D 66 " (cutoff:3.500A) removed outlier: 7.571A pdb=" N VAL D 68 " --> pdb=" O HIS D 6 " (cutoff:3.500A) removed outlier: 6.006A pdb=" N GLN D 8 " --> pdb=" O VAL D 68 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N VAL D 5 " --> pdb=" O GLN D 136 " (cutoff:3.500A) removed outlier: 8.189A pdb=" N THR D 138 " --> pdb=" O VAL D 5 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N ILE D 7 " --> pdb=" O THR D 138 " (cutoff:3.500A) removed outlier: 8.623A pdb=" N SER D 140 " --> pdb=" O ILE D 7 " (cutoff:3.500A) removed outlier: 8.141A pdb=" N ALA D 9 " --> pdb=" O SER D 140 " (cutoff:3.500A) removed outlier: 7.783A pdb=" N PHE D 169 " --> pdb=" O PHE D 135 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N LEU D 137 " --> pdb=" O PHE D 169 " (cutoff:3.500A) removed outlier: 7.550A pdb=" N VAL D 171 " --> pdb=" O LEU D 137 " (cutoff:3.500A) removed outlier: 7.326A pdb=" N HIS D 139 " --> pdb=" O VAL D 171 " (cutoff:3.500A) removed outlier: 8.605A pdb=" N ASP D 205 " --> pdb=" O PRO D 270 " (cutoff:3.500A) removed outlier: 12.033A pdb=" N PHE D 272 " --> pdb=" O ASP D 205 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N PHE D 267 " --> pdb=" O SER D 381 " (cutoff:3.500A) removed outlier: 5.206A pdb=" N SER D 381 " --> pdb=" O PHE D 267 " (cutoff:3.500A) removed outlier: 8.782A pdb=" N LYS D 352 " --> pdb=" O LEU D 313 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N VAL D 315 " --> pdb=" O LYS D 352 " (cutoff:3.500A) removed outlier: 8.546A pdb=" N ALA D 354 " --> pdb=" O VAL D 315 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N ALA D 317 " --> pdb=" O ALA D 354 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 53 through 56 Processing sheet with id=AC1, first strand: chain 'K' and resid 51 through 52 removed outlier: 6.784A pdb=" N LYS K 10 " --> pdb=" O ILE K 298 " (cutoff:3.500A) removed outlier: 7.968A pdb=" N ILE K 300 " --> pdb=" O LYS K 10 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N MET K 12 " --> pdb=" O ILE K 300 " (cutoff:3.500A) removed outlier: 7.423A pdb=" N CYS K 302 " --> pdb=" O MET K 12 " (cutoff:3.500A) removed outlier: 5.865A pdb=" N ARG K 14 " --> pdb=" O CYS K 302 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N GLY K 79 " --> pdb=" O TYR K 228 " (cutoff:3.500A) removed outlier: 8.108A pdb=" N VAL K 230 " --> pdb=" O GLY K 79 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N ILE K 81 " --> pdb=" O VAL K 230 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'K' and resid 51 through 52 removed outlier: 6.784A pdb=" N LYS K 10 " --> pdb=" O ILE K 298 " (cutoff:3.500A) removed outlier: 7.968A pdb=" N ILE K 300 " --> pdb=" O LYS K 10 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N MET K 12 " --> pdb=" O ILE K 300 " (cutoff:3.500A) removed outlier: 7.423A pdb=" N CYS K 302 " --> pdb=" O MET K 12 " (cutoff:3.500A) removed outlier: 5.865A pdb=" N ARG K 14 " --> pdb=" O CYS K 302 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N GLY K 79 " --> pdb=" O TYR K 228 " (cutoff:3.500A) removed outlier: 8.108A pdb=" N VAL K 230 " --> pdb=" O GLY K 79 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N ILE K 81 " --> pdb=" O VAL K 230 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N ILE K 130 " --> pdb=" O VAL K 173 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ARG K 171 " --> pdb=" O VAL K 132 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'K' and resid 33 through 34 removed outlier: 3.655A pdb=" N ILE K 41 " --> pdb=" O LYS K 44 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'K' and resid 155 through 156 removed outlier: 3.678A pdb=" N HIS K 156 " --> pdb=" O TYR K 164 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N TYR K 164 " --> pdb=" O HIS K 156 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 576 hydrogen bonds defined for protein. 1605 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: 2.07 Time building geometry restraints manager: 1.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 3366 1.31 - 1.44: 4103 1.44 - 1.56: 8855 1.56 - 1.68: 31 1.68 - 1.80: 174 Bond restraints: 16529 Sorted by residual: bond pdb=" CA SER C 236 " pdb=" C SER C 236 " ideal model delta sigma weight residual 1.523 1.343 0.179 1.41e-02 5.03e+03 1.62e+02 bond pdb=" CA SER A 236 " pdb=" C SER A 236 " ideal model delta sigma weight residual 1.523 1.344 0.178 1.41e-02 5.03e+03 1.60e+02 bond pdb=" CA LYS A 124 " pdb=" C LYS A 124 " ideal model delta sigma weight residual 1.523 1.384 0.140 1.56e-02 4.11e+03 8.00e+01 bond pdb=" CA LYS C 124 " pdb=" C LYS C 124 " ideal model delta sigma weight residual 1.523 1.385 0.139 1.56e-02 4.11e+03 7.90e+01 bond pdb=" C MET D 269 " pdb=" N PRO D 270 " ideal model delta sigma weight residual 1.334 1.208 0.126 2.34e-02 1.83e+03 2.89e+01 ... (remaining 16524 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.36: 21461 3.36 - 6.73: 831 6.73 - 10.09: 114 10.09 - 13.45: 15 13.45 - 16.82: 2 Bond angle restraints: 22423 Sorted by residual: angle pdb=" CA ARG K 203 " pdb=" C ARG K 203 " pdb=" N SER K 204 " ideal model delta sigma weight residual 116.84 126.73 -9.89 1.71e+00 3.42e-01 3.35e+01 angle pdb=" CA ARG K 203 " pdb=" C ARG K 203 " pdb=" O ARG K 203 " ideal model delta sigma weight residual 120.51 112.81 7.70 1.43e+00 4.89e-01 2.90e+01 angle pdb=" C ARG A 123 " pdb=" N LYS A 124 " pdb=" CA LYS A 124 " ideal model delta sigma weight residual 122.56 113.49 9.07 1.72e+00 3.38e-01 2.78e+01 angle pdb=" C ARG C 123 " pdb=" N LYS C 124 " pdb=" CA LYS C 124 " ideal model delta sigma weight residual 122.56 113.56 9.00 1.72e+00 3.38e-01 2.74e+01 angle pdb=" C VAL C 182 " pdb=" N GLU C 183 " pdb=" CA GLU C 183 " ideal model delta sigma weight residual 119.78 125.89 -6.11 1.24e+00 6.50e-01 2.43e+01 ... (remaining 22418 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.92: 9374 31.92 - 63.83: 451 63.83 - 95.75: 35 95.75 - 127.66: 8 127.66 - 159.58: 8 Dihedral angle restraints: 9876 sinusoidal: 3963 harmonic: 5913 Sorted by residual: dihedral pdb=" CA GLU D 431 " pdb=" C GLU D 431 " pdb=" N TYR D 432 " pdb=" CA TYR D 432 " ideal model delta harmonic sigma weight residual 180.00 143.07 36.93 0 5.00e+00 4.00e-02 5.45e+01 dihedral pdb=" CA GLU B 431 " pdb=" C GLU B 431 " pdb=" N TYR B 432 " pdb=" CA TYR B 432 " ideal model delta harmonic sigma weight residual 180.00 143.11 36.89 0 5.00e+00 4.00e-02 5.44e+01 dihedral pdb=" C5' GTP B 501 " pdb=" O5' GTP B 501 " pdb=" PA GTP B 501 " pdb=" O3A GTP B 501 " ideal model delta sinusoidal sigma weight residual 69.27 -90.31 159.58 1 2.00e+01 2.50e-03 4.65e+01 ... (remaining 9873 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.072: 1431 0.072 - 0.143: 822 0.143 - 0.215: 171 0.215 - 0.287: 24 0.287 - 0.358: 9 Chirality restraints: 2457 Sorted by residual: chirality pdb=" CA SER C 236 " pdb=" N SER C 236 " pdb=" C SER C 236 " pdb=" CB SER C 236 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.21e+00 chirality pdb=" CA SER A 236 " pdb=" N SER A 236 " pdb=" C SER A 236 " pdb=" CB SER A 236 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.10e+00 chirality pdb=" CA TRP B 21 " pdb=" N TRP B 21 " pdb=" C TRP B 21 " pdb=" CB TRP B 21 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.97e+00 ... (remaining 2454 not shown) Planarity restraints: 2919 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR K 77 " -0.036 2.00e-02 2.50e+03 2.46e-02 1.21e+01 pdb=" CG TYR K 77 " 0.051 2.00e-02 2.50e+03 pdb=" CD1 TYR K 77 " 0.018 2.00e-02 2.50e+03 pdb=" CD2 TYR K 77 " -0.009 2.00e-02 2.50e+03 pdb=" CE1 TYR K 77 " -0.020 2.00e-02 2.50e+03 pdb=" CE2 TYR K 77 " 0.006 2.00e-02 2.50e+03 pdb=" CZ TYR K 77 " -0.009 2.00e-02 2.50e+03 pdb=" OH TYR K 77 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE D 395 " 0.024 2.00e-02 2.50e+03 1.98e-02 6.85e+00 pdb=" CG PHE D 395 " -0.045 2.00e-02 2.50e+03 pdb=" CD1 PHE D 395 " 0.007 2.00e-02 2.50e+03 pdb=" CD2 PHE D 395 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE D 395 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE D 395 " 0.007 2.00e-02 2.50e+03 pdb=" CZ PHE D 395 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 395 " 0.023 2.00e-02 2.50e+03 1.96e-02 6.75e+00 pdb=" CG PHE B 395 " -0.045 2.00e-02 2.50e+03 pdb=" CD1 PHE B 395 " 0.008 2.00e-02 2.50e+03 pdb=" CD2 PHE B 395 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE B 395 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE B 395 " 0.007 2.00e-02 2.50e+03 pdb=" CZ PHE B 395 " 0.005 2.00e-02 2.50e+03 ... (remaining 2916 not shown) Histogram of nonbonded interaction distances: 1.62 - 2.27: 92 2.27 - 2.93: 9106 2.93 - 3.59: 21709 3.59 - 4.24: 35584 4.24 - 4.90: 58887 Nonbonded interactions: 125378 Sorted by model distance: nonbonded pdb=" O3G GTP C 501 " pdb="MG MG C 502 " model vdw 1.616 2.170 nonbonded pdb=" O3G GTP A 501 " pdb="MG MG A 502 " model vdw 1.617 2.170 nonbonded pdb=" O1B GTP D 501 " pdb="MG MG D 502 " model vdw 1.733 2.170 nonbonded pdb=" O1B GTP B 501 " pdb="MG MG B 502 " model vdw 1.734 2.170 nonbonded pdb=" OE1 GLU A 71 " pdb="MG MG A 502 " model vdw 1.855 2.170 ... (remaining 125373 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } ncs_group { reference = chain 'B' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.490 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: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 13.570 Find NCS groups from input model: 0.180 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:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7196 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 : 0.026 0.179 16531 Z= 1.129 Angle : 1.536 16.819 22423 Z= 0.811 Chirality : 0.085 0.358 2457 Planarity : 0.008 0.060 2919 Dihedral : 19.063 159.579 6086 Min Nonbonded Distance : 1.616 Molprobity Statistics. All-atom Clashscore : 27.14 Ramachandran Plot: Outliers : 0.59 % Allowed : 17.89 % Favored : 81.52 % Rotamer: Outliers : 6.83 % Allowed : 11.61 % Favored : 81.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 2.27 % Twisted General : 0.36 % 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 aren not related in a simple way. whole: -6.00 (0.13), residues: 2035 helix: -4.01 (0.11), residues: 742 sheet: -3.28 (0.25), residues: 320 loop : -4.22 (0.15), residues: 973 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.002 ARG C 156 TYR 0.051 0.005 TYR K 77 PHE 0.045 0.006 PHE D 395 TRP 0.019 0.004 TRP A 21 HIS 0.024 0.004 HIS A 283 Details of bonding type rmsd covalent geometry : bond 0.02595 (16529) covalent geometry : angle 1.53585 (22423) hydrogen bonds : bond 0.19933 ( 536) hydrogen bonds : angle 8.70953 ( 1605) Misc. bond : bond 0.00106 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4070 Ramachandran restraints generated. 2035 Oldfield, 0 Emsley, 2035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4070 Ramachandran restraints generated. 2035 Oldfield, 0 Emsley, 2035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 770 residues out of total 1757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 650 time to evaluate : 0.593 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 27 GLU cc_start: 0.8278 (mt-10) cc_final: 0.7956 (mt-10) REVERT: A 71 GLU cc_start: 0.7378 (mt-10) cc_final: 0.6063 (pm20) REVERT: A 110 ILE cc_start: 0.8243 (mm) cc_final: 0.7663 (mm) REVERT: A 112 LYS cc_start: 0.6181 (mttt) cc_final: 0.5701 (ttmt) REVERT: A 194 THR cc_start: 0.8765 (OUTLIER) cc_final: 0.8467 (p) REVERT: A 345 ASP cc_start: 0.7566 (p0) cc_final: 0.6800 (m-30) REVERT: A 425 MET cc_start: 0.8465 (tpt) cc_final: 0.8230 (tpt) REVERT: B 105 LYS cc_start: 0.8619 (mtpp) cc_final: 0.8261 (mtmt) REVERT: B 433 GLN cc_start: 0.7552 (tp40) cc_final: 0.7097 (tp40) REVERT: C 160 ASP cc_start: 0.7173 (t70) cc_final: 0.6804 (m-30) REVERT: C 194 THR cc_start: 0.8584 (OUTLIER) cc_final: 0.8347 (p) REVERT: C 327 ASP cc_start: 0.6856 (m-30) cc_final: 0.6454 (m-30) REVERT: C 332 ILE cc_start: 0.8237 (OUTLIER) cc_final: 0.7869 (mt) REVERT: C 424 ASP cc_start: 0.7315 (m-30) cc_final: 0.7108 (t0) REVERT: D 2 ARG cc_start: 0.6544 (mtp85) cc_final: 0.5979 (mpt180) REVERT: D 105 LYS cc_start: 0.8485 (mtpp) cc_final: 0.8006 (mtmt) REVERT: D 346 TRP cc_start: 0.6654 (p-90) cc_final: 0.6362 (p-90) REVERT: D 352 LYS cc_start: 0.7461 (tptp) cc_final: 0.6780 (mmtt) REVERT: D 385 GLN cc_start: 0.7748 (tt0) cc_final: 0.7452 (pp30) REVERT: D 417 GLU cc_start: 0.7402 (tm-30) cc_final: 0.7135 (tm-30) REVERT: K 12 MET cc_start: 0.6943 (mmm) cc_final: 0.6422 (mmm) REVERT: K 50 ARG cc_start: 0.6557 (tpt170) cc_final: 0.6182 (tpt90) REVERT: K 214 GLN cc_start: 0.6505 (pt0) cc_final: 0.5875 (pt0) REVERT: K 238 VAL cc_start: 0.7221 (t) cc_final: 0.6938 (t) REVERT: K 241 THR cc_start: 0.7233 (m) cc_final: 0.6614 (m) outliers start: 120 outliers final: 23 residues processed: 730 average time/residue: 0.1165 time to fit residues: 123.1933 Evaluate side-chains 363 residues out of total 1757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 337 time to evaluate : 0.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 LYS Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 409 THR Chi-restraints excluded: chain C residue 40 LYS Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 191 THR Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain C residue 194 THR Chi-restraints excluded: chain C residue 207 GLU Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 337 THR Chi-restraints excluded: chain C residue 382 THR Chi-restraints excluded: chain D residue 23 VAL Chi-restraints excluded: chain D residue 109 THR Chi-restraints excluded: chain D residue 128 SER Chi-restraints excluded: chain D residue 131 CYS Chi-restraints excluded: chain D residue 138 THR Chi-restraints excluded: chain D residue 213 CYS Chi-restraints excluded: chain D residue 286 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 98 optimal weight: 0.9990 chunk 194 optimal weight: 2.9990 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 0.7980 chunk 200 optimal weight: 0.9990 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 2.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 HIS A 101 ASN A 256 GLN A 329 ASN A 356 ASN B 11 GLN B 59 ASN ** B 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 192 HIS B 193 GLN B 247 GLN B 249 ASN B 294 GLN ** B 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 385 GLN B 436 GLN ** C 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 61 HIS C 101 ASN C 107 HIS C 197 HIS C 228 ASN C 256 GLN D 8 GLN D 11 GLN ** D 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 107 HIS D 193 GLN D 247 GLN D 249 ASN D 309 HIS D 336 GLN ** D 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 78 ASN K 156 HIS K 198 ASN K 214 GLN K 218 GLN K 253 ASN K 287 GLN Total number of N/Q/H flips: 35 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.164380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.139730 restraints weight = 21663.596| |-----------------------------------------------------------------------------| r_work (start): 0.3755 rms_B_bonded: 2.26 r_work: 0.3607 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3471 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3471 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 moved from start: 0.4284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.101 16531 Z= 0.166 Angle : 0.768 10.549 22423 Z= 0.398 Chirality : 0.048 0.176 2457 Planarity : 0.006 0.072 2919 Dihedral : 13.580 153.155 2317 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.28 % Favored : 95.63 % Rotamer: Outliers : 4.04 % Allowed : 16.85 % Favored : 79.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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 aren not related in a simple way. whole: -4.08 (0.16), residues: 2035 helix: -2.45 (0.16), residues: 785 sheet: -2.23 (0.28), residues: 314 loop : -3.06 (0.17), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 215 TYR 0.018 0.002 TYR D 432 PHE 0.023 0.002 PHE C 49 TRP 0.015 0.002 TRP C 21 HIS 0.006 0.001 HIS C 197 Details of bonding type rmsd covalent geometry : bond 0.00384 (16529) covalent geometry : angle 0.76829 (22423) hydrogen bonds : bond 0.04405 ( 536) hydrogen bonds : angle 5.70843 ( 1605) Misc. bond : bond 0.00047 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4070 Ramachandran restraints generated. 2035 Oldfield, 0 Emsley, 2035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4070 Ramachandran restraints generated. 2035 Oldfield, 0 Emsley, 2035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 483 residues out of total 1757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 412 time to evaluate : 0.515 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.5144 (OUTLIER) cc_final: 0.4730 (pmm) REVERT: A 71 GLU cc_start: 0.7298 (mt-10) cc_final: 0.7046 (mt-10) REVERT: A 84 ARG cc_start: 0.7527 (ttp-110) cc_final: 0.7147 (ptm160) REVERT: A 265 ILE cc_start: 0.8991 (mt) cc_final: 0.8740 (mt) REVERT: A 430 LYS cc_start: 0.8613 (ttmm) cc_final: 0.8375 (ttpt) REVERT: B 119 LEU cc_start: 0.8867 (tp) cc_final: 0.8516 (mt) REVERT: B 127 GLU cc_start: 0.7958 (mm-30) cc_final: 0.7604 (mt-10) REVERT: B 283 TYR cc_start: 0.6820 (m-10) cc_final: 0.6240 (t80) REVERT: B 290 GLU cc_start: 0.7715 (tt0) cc_final: 0.7469 (tp30) REVERT: B 422 GLU cc_start: 0.8075 (tp30) cc_final: 0.7539 (tt0) REVERT: B 425 MET cc_start: 0.7422 (ttp) cc_final: 0.7220 (tmm) REVERT: C 27 GLU cc_start: 0.8331 (mt-10) cc_final: 0.8092 (mt-10) REVERT: C 107 HIS cc_start: 0.8910 (OUTLIER) cc_final: 0.8588 (t-170) REVERT: C 123 ARG cc_start: 0.8156 (ptm160) cc_final: 0.7788 (ttm-80) REVERT: C 160 ASP cc_start: 0.8098 (t70) cc_final: 0.7518 (m-30) REVERT: C 194 THR cc_start: 0.8643 (OUTLIER) cc_final: 0.8436 (p) REVERT: C 301 GLN cc_start: 0.8588 (pm20) cc_final: 0.7595 (mm-40) REVERT: C 357 TYR cc_start: 0.7255 (m-80) cc_final: 0.6948 (m-80) REVERT: C 382 THR cc_start: 0.7662 (OUTLIER) cc_final: 0.7446 (p) REVERT: C 419 SER cc_start: 0.8764 (m) cc_final: 0.8333 (p) REVERT: C 425 MET cc_start: 0.8308 (mmm) cc_final: 0.7196 (tpt) REVERT: D 290 GLU cc_start: 0.7472 (mt-10) cc_final: 0.7236 (mt-10) REVERT: D 322 ARG cc_start: 0.7455 (mmm160) cc_final: 0.7217 (mmm160) REVERT: D 325 MET cc_start: 0.6747 (mpp) cc_final: 0.6522 (mpp) REVERT: D 334 ASN cc_start: 0.8020 (t0) cc_final: 0.7609 (t0) REVERT: D 352 LYS cc_start: 0.7450 (tptp) cc_final: 0.6518 (mmtt) REVERT: D 385 GLN cc_start: 0.8425 (tt0) cc_final: 0.8006 (pp30) REVERT: D 416 MET cc_start: 0.7950 (tpp) cc_final: 0.7640 (tmm) REVERT: K 50 ARG cc_start: 0.7360 (tpt170) cc_final: 0.6623 (mmm-85) REVERT: K 119 ILE cc_start: 0.7797 (mm) cc_final: 0.7416 (mt) REVERT: K 122 MET cc_start: 0.6590 (ttp) cc_final: 0.6107 (ttp) REVERT: K 295 ARG cc_start: 0.7532 (mmt90) cc_final: 0.7236 (ptt90) outliers start: 71 outliers final: 41 residues processed: 465 average time/residue: 0.1072 time to fit residues: 74.6191 Evaluate side-chains 360 residues out of total 1757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 315 time to evaluate : 0.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 140 SER Chi-restraints excluded: chain A residue 147 SER Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 196 GLU Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain A residue 420 GLU Chi-restraints excluded: chain B residue 23 VAL Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain B residue 409 THR Chi-restraints excluded: chain B residue 423 SER Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain C residue 107 HIS Chi-restraints excluded: chain C residue 113 GLU Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 181 VAL Chi-restraints excluded: chain C residue 191 THR Chi-restraints excluded: chain C residue 194 THR Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 276 ILE Chi-restraints excluded: chain C residue 328 VAL Chi-restraints excluded: chain C residue 337 THR Chi-restraints excluded: chain C residue 382 THR Chi-restraints excluded: chain D residue 23 VAL Chi-restraints excluded: chain D residue 109 THR Chi-restraints excluded: chain D residue 138 THR Chi-restraints excluded: chain D residue 181 VAL Chi-restraints excluded: chain D residue 276 THR Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 356 CYS Chi-restraints excluded: chain D residue 378 ILE Chi-restraints excluded: chain K residue 162 VAL Chi-restraints excluded: chain K residue 188 SER Chi-restraints excluded: chain K residue 221 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 119 optimal weight: 5.9990 chunk 71 optimal weight: 1.9990 chunk 188 optimal weight: 0.0170 chunk 160 optimal weight: 5.9990 chunk 137 optimal weight: 0.0270 chunk 166 optimal weight: 4.9990 chunk 83 optimal weight: 1.9990 chunk 64 optimal weight: 4.9990 chunk 144 optimal weight: 0.8980 chunk 152 optimal weight: 8.9990 chunk 62 optimal weight: 1.9990 overall best weight: 0.9880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 101 ASN ** B 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 394 GLN ** C 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 88 HIS C 256 GLN C 258 ASN D 136 GLN D 300 ASN D 336 GLN ** D 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 160 ASN K 214 GLN K 253 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.169013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.141773 restraints weight = 21452.336| |-----------------------------------------------------------------------------| r_work (start): 0.3761 rms_B_bonded: 2.40 r_work: 0.3629 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work (final): 0.3629 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 moved from start: 0.5032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 16531 Z= 0.143 Angle : 0.662 7.702 22423 Z= 0.342 Chirality : 0.045 0.150 2457 Planarity : 0.005 0.060 2919 Dihedral : 12.568 159.786 2292 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 4.15 % Allowed : 17.53 % Favored : 78.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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 aren not related in a simple way. whole: -3.15 (0.17), residues: 2035 helix: -1.82 (0.17), residues: 809 sheet: -1.79 (0.29), residues: 314 loop : -2.36 (0.18), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG K 25 TYR 0.024 0.001 TYR D 36 PHE 0.014 0.001 PHE C 49 TRP 0.012 0.001 TRP A 346 HIS 0.011 0.001 HIS C 107 Details of bonding type rmsd covalent geometry : bond 0.00335 (16529) covalent geometry : angle 0.66213 (22423) hydrogen bonds : bond 0.03968 ( 536) hydrogen bonds : angle 5.12289 ( 1605) Misc. bond : bond 0.00131 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4070 Ramachandran restraints generated. 2035 Oldfield, 0 Emsley, 2035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4070 Ramachandran restraints generated. 2035 Oldfield, 0 Emsley, 2035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 409 residues out of total 1757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 336 time to evaluate : 0.594 Fit side-chains revert: symmetry clash REVERT: A 430 LYS cc_start: 0.8642 (ttmm) cc_final: 0.8395 (ttpt) REVERT: B 119 LEU cc_start: 0.8921 (tp) cc_final: 0.8676 (mt) REVERT: B 127 GLU cc_start: 0.7826 (mm-30) cc_final: 0.7572 (mt-10) REVERT: B 235 MET cc_start: 0.8314 (mtt) cc_final: 0.8021 (mtt) REVERT: B 283 TYR cc_start: 0.6993 (m-10) cc_final: 0.6342 (t80) REVERT: B 291 LEU cc_start: 0.7675 (OUTLIER) cc_final: 0.7439 (mt) REVERT: B 422 GLU cc_start: 0.7631 (tp30) cc_final: 0.7357 (tt0) REVERT: C 24 TYR cc_start: 0.8761 (m-10) cc_final: 0.8459 (m-10) REVERT: C 27 GLU cc_start: 0.8263 (mt-10) cc_final: 0.8052 (mt-10) REVERT: C 123 ARG cc_start: 0.8090 (ptm160) cc_final: 0.7829 (ttm-80) REVERT: C 160 ASP cc_start: 0.7710 (t70) cc_final: 0.7234 (m-30) REVERT: C 214 ARG cc_start: 0.7645 (ttp-170) cc_final: 0.7208 (ttp-170) REVERT: C 301 GLN cc_start: 0.8383 (pm20) cc_final: 0.7494 (mm110) REVERT: C 357 TYR cc_start: 0.7380 (m-80) cc_final: 0.7020 (m-80) REVERT: C 419 SER cc_start: 0.8856 (m) cc_final: 0.8519 (p) REVERT: C 425 MET cc_start: 0.8544 (mmm) cc_final: 0.8018 (tpp) REVERT: D 322 ARG cc_start: 0.7805 (mmm160) cc_final: 0.7306 (mmm160) REVERT: D 325 MET cc_start: 0.6820 (mpp) cc_final: 0.6419 (mpp) REVERT: D 352 LYS cc_start: 0.7465 (tptp) cc_final: 0.6537 (mmtt) REVERT: D 385 GLN cc_start: 0.8257 (tt0) cc_final: 0.7875 (pp30) REVERT: D 386 GLU cc_start: 0.7615 (mt-10) cc_final: 0.7154 (mm-30) REVERT: D 416 MET cc_start: 0.7803 (tpp) cc_final: 0.7537 (tmm) REVERT: D 417 GLU cc_start: 0.7388 (tt0) cc_final: 0.7185 (tt0) REVERT: K 119 ILE cc_start: 0.7956 (mm) cc_final: 0.7578 (mt) REVERT: K 122 MET cc_start: 0.6629 (ttp) cc_final: 0.6149 (ttp) outliers start: 73 outliers final: 41 residues processed: 387 average time/residue: 0.1028 time to fit residues: 60.3550 Evaluate side-chains 339 residues out of total 1757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 297 time to evaluate : 0.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 SER Chi-restraints excluded: chain A residue 147 SER Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain A residue 420 GLU Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 291 LEU Chi-restraints excluded: chain B residue 374 SER Chi-restraints excluded: chain B residue 385 GLN Chi-restraints excluded: chain B residue 409 THR Chi-restraints excluded: chain B residue 423 SER Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain C residue 113 GLU Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 181 VAL Chi-restraints excluded: chain C residue 191 THR Chi-restraints excluded: chain C residue 245 ASP Chi-restraints excluded: chain C residue 250 VAL Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 276 ILE Chi-restraints excluded: chain C residue 361 THR Chi-restraints excluded: chain D residue 109 THR Chi-restraints excluded: chain D residue 128 SER Chi-restraints excluded: chain D residue 138 THR Chi-restraints excluded: chain D residue 181 VAL Chi-restraints excluded: chain D residue 214 PHE Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 356 CYS Chi-restraints excluded: chain D residue 425 MET Chi-restraints excluded: chain K residue 65 CYS Chi-restraints excluded: chain K residue 160 ASN Chi-restraints excluded: chain K residue 162 VAL Chi-restraints excluded: chain K residue 177 ASP Chi-restraints excluded: chain K residue 221 GLN Chi-restraints excluded: chain K residue 241 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 47 optimal weight: 4.9990 chunk 60 optimal weight: 0.9980 chunk 152 optimal weight: 5.9990 chunk 21 optimal weight: 0.0470 chunk 95 optimal weight: 6.9990 chunk 109 optimal weight: 5.9990 chunk 191 optimal weight: 5.9990 chunk 26 optimal weight: 0.0980 chunk 72 optimal weight: 0.9990 chunk 34 optimal weight: 0.0770 chunk 35 optimal weight: 1.9990 overall best weight: 0.4438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 139 HIS ** C 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 128 GLN D 101 ASN D 192 HIS ** D 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 336 GLN D 350 ASN K 214 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.158590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.131060 restraints weight = 21836.052| |-----------------------------------------------------------------------------| r_work (start): 0.3633 rms_B_bonded: 2.42 r_work: 0.3512 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work (final): 0.3512 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7695 moved from start: 0.5507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 16531 Z= 0.112 Angle : 0.605 8.760 22423 Z= 0.310 Chirality : 0.044 0.157 2457 Planarity : 0.004 0.059 2919 Dihedral : 11.962 169.036 2286 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 3.47 % Allowed : 19.86 % Favored : 76.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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 aren not related in a simple way. whole: -2.60 (0.17), residues: 2035 helix: -1.45 (0.17), residues: 824 sheet: -1.46 (0.30), residues: 314 loop : -1.97 (0.19), residues: 897 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 84 TYR 0.020 0.001 TYR C 103 PHE 0.010 0.001 PHE B 377 TRP 0.011 0.001 TRP A 346 HIS 0.007 0.001 HIS A 88 Details of bonding type rmsd covalent geometry : bond 0.00267 (16529) covalent geometry : angle 0.60548 (22423) hydrogen bonds : bond 0.03371 ( 536) hydrogen bonds : angle 4.89044 ( 1605) Misc. bond : bond 0.00138 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4070 Ramachandran restraints generated. 2035 Oldfield, 0 Emsley, 2035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4070 Ramachandran restraints generated. 2035 Oldfield, 0 Emsley, 2035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 1757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 325 time to evaluate : 0.555 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 84 ARG cc_start: 0.7367 (ttp-110) cc_final: 0.6987 (ptm160) REVERT: A 377 MET cc_start: 0.6620 (tpp) cc_final: 0.6409 (tpt) REVERT: B 37 HIS cc_start: 0.6996 (OUTLIER) cc_final: 0.6114 (p90) REVERT: B 44 LEU cc_start: 0.8008 (OUTLIER) cc_final: 0.7600 (tt) REVERT: B 119 LEU cc_start: 0.8953 (tp) cc_final: 0.8644 (mt) REVERT: B 127 GLU cc_start: 0.7794 (mm-30) cc_final: 0.7583 (mt-10) REVERT: B 235 MET cc_start: 0.8363 (mtt) cc_final: 0.8099 (mtt) REVERT: B 283 TYR cc_start: 0.6948 (m-10) cc_final: 0.6244 (t80) REVERT: B 291 LEU cc_start: 0.7421 (OUTLIER) cc_final: 0.7097 (mt) REVERT: B 385 GLN cc_start: 0.8016 (OUTLIER) cc_final: 0.7804 (tt0) REVERT: B 422 GLU cc_start: 0.7642 (tp30) cc_final: 0.7348 (tt0) REVERT: C 24 TYR cc_start: 0.8771 (m-10) cc_final: 0.8441 (m-10) REVERT: C 27 GLU cc_start: 0.8335 (mt-10) cc_final: 0.8129 (mt-10) REVERT: C 123 ARG cc_start: 0.8063 (ptm160) cc_final: 0.7863 (ttm-80) REVERT: C 160 ASP cc_start: 0.7840 (t70) cc_final: 0.7339 (m-30) REVERT: C 185 TYR cc_start: 0.8718 (m-80) cc_final: 0.8462 (m-80) REVERT: C 357 TYR cc_start: 0.7617 (m-80) cc_final: 0.7136 (m-80) REVERT: C 419 SER cc_start: 0.8862 (m) cc_final: 0.8532 (p) REVERT: C 425 MET cc_start: 0.8467 (mmm) cc_final: 0.7368 (tpt) REVERT: D 322 ARG cc_start: 0.7788 (mmm160) cc_final: 0.7232 (mmm160) REVERT: D 352 LYS cc_start: 0.7311 (tptp) cc_final: 0.6414 (mmtt) REVERT: D 385 GLN cc_start: 0.8303 (tt0) cc_final: 0.7738 (pp30) REVERT: D 386 GLU cc_start: 0.7653 (mt-10) cc_final: 0.7257 (mm-30) REVERT: D 416 MET cc_start: 0.7879 (tpp) cc_final: 0.7576 (tmm) REVERT: D 417 GLU cc_start: 0.7453 (tt0) cc_final: 0.7212 (tt0) REVERT: K 20 GLU cc_start: 0.8346 (mm-30) cc_final: 0.8110 (mm-30) REVERT: K 122 MET cc_start: 0.6565 (ttp) cc_final: 0.6284 (ttp) REVERT: K 197 MET cc_start: 0.5876 (tpt) cc_final: 0.5609 (tpt) outliers start: 61 outliers final: 40 residues processed: 366 average time/residue: 0.1010 time to fit residues: 55.7773 Evaluate side-chains 332 residues out of total 1757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 288 time to evaluate : 0.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 420 GLU Chi-restraints excluded: chain B residue 37 HIS Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 259 MET Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 291 LEU Chi-restraints excluded: chain B residue 374 SER Chi-restraints excluded: chain B residue 385 GLN Chi-restraints excluded: chain B residue 409 THR Chi-restraints excluded: chain B residue 423 SER Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain C residue 113 GLU Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 181 VAL Chi-restraints excluded: chain C residue 191 THR Chi-restraints excluded: chain C residue 223 THR Chi-restraints excluded: chain C residue 245 ASP Chi-restraints excluded: chain C residue 250 VAL Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 276 ILE Chi-restraints excluded: chain C residue 381 THR Chi-restraints excluded: chain D residue 109 THR Chi-restraints excluded: chain D residue 138 THR Chi-restraints excluded: chain D residue 181 VAL Chi-restraints excluded: chain D residue 214 PHE Chi-restraints excluded: chain D residue 217 LEU Chi-restraints excluded: chain D residue 276 THR Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 356 CYS Chi-restraints excluded: chain D residue 425 MET Chi-restraints excluded: chain K residue 162 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 40 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 185 optimal weight: 1.9990 chunk 114 optimal weight: 1.9990 chunk 74 optimal weight: 4.9990 chunk 91 optimal weight: 4.9990 chunk 166 optimal weight: 1.9990 chunk 122 optimal weight: 2.9990 chunk 11 optimal weight: 0.8980 chunk 147 optimal weight: 0.0570 chunk 98 optimal weight: 5.9990 overall best weight: 1.3904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 128 GLN C 258 ASN D 294 GLN D 336 GLN ** D 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 394 GLN K 160 ASN K 253 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.150631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.123799 restraints weight = 22171.605| |-----------------------------------------------------------------------------| r_work (start): 0.3552 rms_B_bonded: 2.25 r_work: 0.3406 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.3406 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.5944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 16531 Z= 0.156 Angle : 0.635 10.342 22423 Z= 0.322 Chirality : 0.045 0.169 2457 Planarity : 0.004 0.061 2919 Dihedral : 11.770 174.333 2286 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 4.44 % Allowed : 20.89 % Favored : 74.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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 aren not related in a simple way. whole: -2.27 (0.18), residues: 2035 helix: -1.11 (0.18), residues: 810 sheet: -1.49 (0.29), residues: 340 loop : -1.76 (0.20), residues: 885 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 164 TYR 0.017 0.002 TYR D 36 PHE 0.017 0.002 PHE C 296 TRP 0.013 0.001 TRP C 407 HIS 0.006 0.001 HIS A 88 Details of bonding type rmsd covalent geometry : bond 0.00378 (16529) covalent geometry : angle 0.63487 (22423) hydrogen bonds : bond 0.03636 ( 536) hydrogen bonds : angle 4.83464 ( 1605) Misc. bond : bond 0.00209 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4070 Ramachandran restraints generated. 2035 Oldfield, 0 Emsley, 2035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4070 Ramachandran restraints generated. 2035 Oldfield, 0 Emsley, 2035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 384 residues out of total 1757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 306 time to evaluate : 0.579 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 71 GLU cc_start: 0.7512 (pt0) cc_final: 0.7240 (tt0) REVERT: B 119 LEU cc_start: 0.8957 (tp) cc_final: 0.8689 (mt) REVERT: B 235 MET cc_start: 0.8484 (mtt) cc_final: 0.8273 (mtt) REVERT: B 283 TYR cc_start: 0.7080 (m-10) cc_final: 0.6328 (t80) REVERT: B 290 GLU cc_start: 0.7188 (tp30) cc_final: 0.6808 (tp30) REVERT: B 291 LEU cc_start: 0.7604 (OUTLIER) cc_final: 0.7315 (mt) REVERT: C 3 GLU cc_start: 0.6978 (pm20) cc_final: 0.6743 (pm20) REVERT: C 24 TYR cc_start: 0.8831 (m-10) cc_final: 0.8485 (m-10) REVERT: C 123 ARG cc_start: 0.8108 (ptm160) cc_final: 0.7890 (ttm-80) REVERT: C 160 ASP cc_start: 0.7997 (t70) cc_final: 0.7338 (m-30) REVERT: C 390 ARG cc_start: 0.8496 (ttm-80) cc_final: 0.8283 (mtm110) REVERT: C 425 MET cc_start: 0.8568 (mmm) cc_final: 0.7987 (tpp) REVERT: D 416 MET cc_start: 0.7933 (tpp) cc_final: 0.7660 (tmm) REVERT: K 122 MET cc_start: 0.6903 (ttp) cc_final: 0.6514 (ttp) REVERT: K 157 GLU cc_start: 0.7694 (pm20) cc_final: 0.6809 (pt0) REVERT: K 302 CYS cc_start: 0.8063 (m) cc_final: 0.7747 (m) outliers start: 78 outliers final: 49 residues processed: 365 average time/residue: 0.1025 time to fit residues: 56.9176 Evaluate side-chains 322 residues out of total 1757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 272 time to evaluate : 0.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 SER Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 420 GLU Chi-restraints excluded: chain B residue 37 HIS Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain B residue 291 LEU Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain B residue 326 LYS Chi-restraints excluded: chain B residue 374 SER Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 409 THR Chi-restraints excluded: chain B residue 423 SER Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain C residue 113 GLU Chi-restraints excluded: chain C residue 147 SER Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 181 VAL Chi-restraints excluded: chain C residue 191 THR Chi-restraints excluded: chain C residue 223 THR Chi-restraints excluded: chain C residue 245 ASP Chi-restraints excluded: chain C residue 250 VAL Chi-restraints excluded: chain C residue 252 LEU Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 381 THR Chi-restraints excluded: chain D residue 109 THR Chi-restraints excluded: chain D residue 138 THR Chi-restraints excluded: chain D residue 181 VAL Chi-restraints excluded: chain D residue 214 PHE Chi-restraints excluded: chain D residue 269 MET Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain K residue 155 VAL Chi-restraints excluded: chain K residue 162 VAL Chi-restraints excluded: chain K residue 174 CYS Chi-restraints excluded: chain K residue 177 ASP Chi-restraints excluded: chain K residue 212 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 109 optimal weight: 5.9990 chunk 61 optimal weight: 0.6980 chunk 141 optimal weight: 8.9990 chunk 159 optimal weight: 3.9990 chunk 18 optimal weight: 4.9990 chunk 146 optimal weight: 0.8980 chunk 9 optimal weight: 7.9990 chunk 0 optimal weight: 8.9990 chunk 179 optimal weight: 0.4980 chunk 145 optimal weight: 6.9990 chunk 152 optimal weight: 0.0670 overall best weight: 1.2320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 88 HIS A 301 GLN ** A 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 128 GLN ** D 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 247 GLN D 336 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.148901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.120899 restraints weight = 22032.289| |-----------------------------------------------------------------------------| r_work (start): 0.3510 rms_B_bonded: 2.40 r_work: 0.3386 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3243 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.6279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 16531 Z= 0.139 Angle : 0.625 11.264 22423 Z= 0.316 Chirality : 0.045 0.214 2457 Planarity : 0.004 0.060 2919 Dihedral : 11.537 177.096 2286 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 3.81 % Allowed : 21.29 % Favored : 74.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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 aren not related in a simple way. whole: -2.05 (0.18), residues: 2035 helix: -0.93 (0.18), residues: 808 sheet: -1.44 (0.28), residues: 342 loop : -1.60 (0.20), residues: 885 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 164 TYR 0.016 0.001 TYR D 36 PHE 0.017 0.001 PHE K 33 TRP 0.011 0.001 TRP C 21 HIS 0.005 0.001 HIS C 192 Details of bonding type rmsd covalent geometry : bond 0.00335 (16529) covalent geometry : angle 0.62485 (22423) hydrogen bonds : bond 0.03438 ( 536) hydrogen bonds : angle 4.82201 ( 1605) Misc. bond : bond 0.00170 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4070 Ramachandran restraints generated. 2035 Oldfield, 0 Emsley, 2035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4070 Ramachandran restraints generated. 2035 Oldfield, 0 Emsley, 2035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 363 residues out of total 1757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 296 time to evaluate : 0.543 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 71 GLU cc_start: 0.7710 (pt0) cc_final: 0.7325 (tt0) REVERT: B 119 LEU cc_start: 0.8980 (tp) cc_final: 0.8661 (mt) REVERT: B 235 MET cc_start: 0.8501 (mtt) cc_final: 0.8258 (mtt) REVERT: B 283 TYR cc_start: 0.7307 (m-10) cc_final: 0.6497 (t80) REVERT: B 291 LEU cc_start: 0.7563 (OUTLIER) cc_final: 0.7169 (mt) REVERT: B 309 HIS cc_start: 0.7537 (m170) cc_final: 0.7272 (m170) REVERT: C 3 GLU cc_start: 0.7307 (pm20) cc_final: 0.7098 (pm20) REVERT: C 24 TYR cc_start: 0.8854 (m-10) cc_final: 0.8511 (m-10) REVERT: C 123 ARG cc_start: 0.8407 (ptm160) cc_final: 0.8110 (ttm-80) REVERT: C 160 ASP cc_start: 0.8230 (t70) cc_final: 0.7562 (m-30) REVERT: C 290 GLU cc_start: 0.7428 (pt0) cc_final: 0.6957 (pt0) REVERT: C 301 GLN cc_start: 0.8805 (pm20) cc_final: 0.8508 (pm20) REVERT: C 357 TYR cc_start: 0.8460 (m-80) cc_final: 0.8195 (m-80) REVERT: C 390 ARG cc_start: 0.8585 (ttm-80) cc_final: 0.8306 (mtm110) REVERT: C 425 MET cc_start: 0.8706 (mmm) cc_final: 0.8282 (tpp) REVERT: D 322 ARG cc_start: 0.8335 (mmm160) cc_final: 0.7685 (mmm160) REVERT: D 386 GLU cc_start: 0.7770 (mt-10) cc_final: 0.7293 (mm-30) REVERT: D 416 MET cc_start: 0.8278 (tpp) cc_final: 0.7818 (tmm) REVERT: D 420 GLU cc_start: 0.7603 (mm-30) cc_final: 0.7084 (tp30) REVERT: K 105 MET cc_start: 0.5043 (mtm) cc_final: 0.4717 (mtm) outliers start: 67 outliers final: 52 residues processed: 344 average time/residue: 0.1081 time to fit residues: 56.3183 Evaluate side-chains 325 residues out of total 1757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 272 time to evaluate : 0.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 SER Chi-restraints excluded: chain A residue 147 SER Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 420 GLU Chi-restraints excluded: chain B residue 37 HIS Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain B residue 291 LEU Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain B residue 326 LYS Chi-restraints excluded: chain B residue 345 GLU Chi-restraints excluded: chain B residue 356 CYS Chi-restraints excluded: chain B residue 374 SER Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 423 SER Chi-restraints excluded: chain B residue 430 SER Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain C residue 181 VAL Chi-restraints excluded: chain C residue 191 THR Chi-restraints excluded: chain C residue 223 THR Chi-restraints excluded: chain C residue 245 ASP Chi-restraints excluded: chain C residue 250 VAL Chi-restraints excluded: chain C residue 252 LEU Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 381 THR Chi-restraints excluded: chain D residue 109 THR Chi-restraints excluded: chain D residue 138 THR Chi-restraints excluded: chain D residue 181 VAL Chi-restraints excluded: chain D residue 214 PHE Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 247 GLN Chi-restraints excluded: chain D residue 269 MET Chi-restraints excluded: chain D residue 276 THR Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain K residue 162 VAL Chi-restraints excluded: chain K residue 174 CYS Chi-restraints excluded: chain K residue 177 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 19 optimal weight: 0.8980 chunk 34 optimal weight: 0.0980 chunk 173 optimal weight: 5.9990 chunk 40 optimal weight: 0.8980 chunk 44 optimal weight: 1.9990 chunk 86 optimal weight: 4.9990 chunk 152 optimal weight: 9.9990 chunk 109 optimal weight: 0.4980 chunk 98 optimal weight: 0.9980 chunk 37 optimal weight: 4.9990 chunk 171 optimal weight: 10.0000 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 128 GLN A 329 ASN ** C 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 128 GLN C 258 ASN ** D 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 247 GLN D 336 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.150439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.123499 restraints weight = 21997.548| |-----------------------------------------------------------------------------| r_work (start): 0.3547 rms_B_bonded: 2.20 r_work: 0.3398 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3398 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.6501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 16531 Z= 0.112 Angle : 0.597 12.446 22423 Z= 0.301 Chirality : 0.044 0.160 2457 Planarity : 0.004 0.058 2919 Dihedral : 11.261 179.659 2284 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 3.19 % Allowed : 22.42 % Favored : 74.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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 aren not related in a simple way. whole: -1.80 (0.18), residues: 2035 helix: -0.71 (0.18), residues: 808 sheet: -1.23 (0.28), residues: 338 loop : -1.50 (0.20), residues: 889 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 164 TYR 0.013 0.001 TYR D 36 PHE 0.012 0.001 PHE K 33 TRP 0.011 0.001 TRP C 21 HIS 0.003 0.001 HIS D 192 Details of bonding type rmsd covalent geometry : bond 0.00265 (16529) covalent geometry : angle 0.59717 (22423) hydrogen bonds : bond 0.03122 ( 536) hydrogen bonds : angle 4.70342 ( 1605) Misc. bond : bond 0.00141 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4070 Ramachandran restraints generated. 2035 Oldfield, 0 Emsley, 2035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4070 Ramachandran restraints generated. 2035 Oldfield, 0 Emsley, 2035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 1757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 289 time to evaluate : 0.404 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 221 ARG cc_start: 0.5979 (mmt180) cc_final: 0.5731 (mmt180) REVERT: B 119 LEU cc_start: 0.8943 (tp) cc_final: 0.8672 (mt) REVERT: B 235 MET cc_start: 0.8471 (mtt) cc_final: 0.8263 (mtt) REVERT: B 283 TYR cc_start: 0.6810 (m-10) cc_final: 0.6589 (t80) REVERT: B 291 LEU cc_start: 0.7411 (OUTLIER) cc_final: 0.7095 (mt) REVERT: C 24 TYR cc_start: 0.8782 (m-10) cc_final: 0.8445 (m-10) REVERT: C 160 ASP cc_start: 0.7845 (t70) cc_final: 0.7373 (m-30) REVERT: C 290 GLU cc_start: 0.7261 (pt0) cc_final: 0.6858 (pt0) REVERT: C 301 GLN cc_start: 0.8856 (pm20) cc_final: 0.8486 (pm20) REVERT: C 339 ARG cc_start: 0.7807 (OUTLIER) cc_final: 0.7062 (ttm110) REVERT: C 357 TYR cc_start: 0.8328 (m-80) cc_final: 0.8048 (m-80) REVERT: D 103 TRP cc_start: 0.8344 (t60) cc_final: 0.7965 (t60) REVERT: D 166 MET cc_start: 0.7869 (tpp) cc_final: 0.7660 (ttt) REVERT: D 416 MET cc_start: 0.8097 (tpp) cc_final: 0.7717 (tmm) REVERT: D 425 MET cc_start: 0.8191 (tpp) cc_final: 0.7897 (tpp) REVERT: K 8 ASN cc_start: 0.6982 (p0) cc_final: 0.6363 (m-40) REVERT: K 105 MET cc_start: 0.5165 (mtm) cc_final: 0.4841 (mtm) REVERT: K 157 GLU cc_start: 0.7342 (pm20) cc_final: 0.6960 (pt0) outliers start: 56 outliers final: 42 residues processed: 328 average time/residue: 0.1022 time to fit residues: 51.1278 Evaluate side-chains 320 residues out of total 1757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 276 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 SER Chi-restraints excluded: chain A residue 147 SER Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 329 ASN Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 398 MET Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain B residue 291 LEU Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain B residue 326 LYS Chi-restraints excluded: chain B residue 356 CYS Chi-restraints excluded: chain B residue 374 SER Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 423 SER Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain C residue 181 VAL Chi-restraints excluded: chain C residue 223 THR Chi-restraints excluded: chain C residue 245 ASP Chi-restraints excluded: chain C residue 250 VAL Chi-restraints excluded: chain C residue 252 LEU Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 339 ARG Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 381 THR Chi-restraints excluded: chain D residue 109 THR Chi-restraints excluded: chain D residue 138 THR Chi-restraints excluded: chain D residue 181 VAL Chi-restraints excluded: chain D residue 214 PHE Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 247 GLN Chi-restraints excluded: chain D residue 269 MET Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain K residue 162 VAL Chi-restraints excluded: chain K residue 177 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 189 optimal weight: 7.9990 chunk 119 optimal weight: 5.9990 chunk 136 optimal weight: 0.5980 chunk 98 optimal weight: 4.9990 chunk 171 optimal weight: 9.9990 chunk 4 optimal weight: 7.9990 chunk 178 optimal weight: 2.9990 chunk 197 optimal weight: 0.0170 chunk 57 optimal weight: 7.9990 chunk 128 optimal weight: 0.8980 chunk 200 optimal weight: 0.9990 overall best weight: 1.1022 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 128 GLN ** A 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 128 GLN ** C 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 247 GLN D 336 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.148583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.121452 restraints weight = 22174.603| |-----------------------------------------------------------------------------| r_work (start): 0.3524 rms_B_bonded: 2.22 r_work: 0.3380 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3240 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.6654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 16531 Z= 0.131 Angle : 0.613 12.861 22423 Z= 0.308 Chirality : 0.045 0.161 2457 Planarity : 0.004 0.061 2919 Dihedral : 11.204 178.746 2283 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 3.07 % Allowed : 22.48 % Favored : 74.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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 aren not related in a simple way. whole: -1.66 (0.18), residues: 2035 helix: -0.61 (0.18), residues: 808 sheet: -1.01 (0.29), residues: 336 loop : -1.48 (0.21), residues: 891 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 390 TYR 0.013 0.001 TYR D 36 PHE 0.018 0.001 PHE A 255 TRP 0.010 0.001 TRP C 407 HIS 0.003 0.001 HIS K 205 Details of bonding type rmsd covalent geometry : bond 0.00315 (16529) covalent geometry : angle 0.61319 (22423) hydrogen bonds : bond 0.03249 ( 536) hydrogen bonds : angle 4.70005 ( 1605) Misc. bond : bond 0.00168 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4070 Ramachandran restraints generated. 2035 Oldfield, 0 Emsley, 2035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4070 Ramachandran restraints generated. 2035 Oldfield, 0 Emsley, 2035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 1757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 292 time to evaluate : 0.433 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 221 ARG cc_start: 0.6051 (mmt180) cc_final: 0.5830 (mmt180) REVERT: B 119 LEU cc_start: 0.8983 (tp) cc_final: 0.8646 (mt) REVERT: B 235 MET cc_start: 0.8485 (mtt) cc_final: 0.8284 (mtt) REVERT: B 283 TYR cc_start: 0.7039 (m-10) cc_final: 0.6680 (t80) REVERT: B 291 LEU cc_start: 0.7610 (OUTLIER) cc_final: 0.6940 (mp) REVERT: B 422 GLU cc_start: 0.8106 (tp30) cc_final: 0.7742 (tt0) REVERT: C 24 TYR cc_start: 0.8861 (m-10) cc_final: 0.8531 (m-10) REVERT: C 160 ASP cc_start: 0.8162 (t70) cc_final: 0.7467 (m-30) REVERT: C 290 GLU cc_start: 0.7392 (pt0) cc_final: 0.6915 (pt0) REVERT: C 301 GLN cc_start: 0.8999 (pm20) cc_final: 0.8712 (pm20) REVERT: C 339 ARG cc_start: 0.7833 (OUTLIER) cc_final: 0.7087 (ttm110) REVERT: C 349 THR cc_start: 0.9002 (p) cc_final: 0.8781 (p) REVERT: C 357 TYR cc_start: 0.8499 (m-80) cc_final: 0.8200 (m-80) REVERT: D 103 TRP cc_start: 0.8404 (t60) cc_final: 0.8021 (t60) REVERT: D 309 HIS cc_start: 0.7755 (m-70) cc_final: 0.7276 (m-70) REVERT: D 322 ARG cc_start: 0.8392 (mmm160) cc_final: 0.7780 (mmm160) REVERT: D 425 MET cc_start: 0.8289 (tpp) cc_final: 0.8015 (tpp) REVERT: K 8 ASN cc_start: 0.7090 (p0) cc_final: 0.6429 (m-40) REVERT: K 157 GLU cc_start: 0.7857 (pm20) cc_final: 0.7348 (pt0) REVERT: K 178 GLU cc_start: 0.8704 (tp30) cc_final: 0.8501 (mm-30) outliers start: 54 outliers final: 41 residues processed: 328 average time/residue: 0.1033 time to fit residues: 51.9943 Evaluate side-chains 316 residues out of total 1757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 273 time to evaluate : 0.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 SER Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 398 MET Chi-restraints excluded: chain B residue 37 HIS Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain B residue 291 LEU Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain B residue 326 LYS Chi-restraints excluded: chain B residue 356 CYS Chi-restraints excluded: chain B residue 374 SER Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain C residue 181 VAL Chi-restraints excluded: chain C residue 223 THR Chi-restraints excluded: chain C residue 250 VAL Chi-restraints excluded: chain C residue 252 LEU Chi-restraints excluded: chain C residue 288 VAL Chi-restraints excluded: chain C residue 339 ARG Chi-restraints excluded: chain C residue 381 THR Chi-restraints excluded: chain D residue 109 THR Chi-restraints excluded: chain D residue 138 THR Chi-restraints excluded: chain D residue 181 VAL Chi-restraints excluded: chain D residue 214 PHE Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 247 GLN Chi-restraints excluded: chain D residue 269 MET Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain K residue 43 SER Chi-restraints excluded: chain K residue 155 VAL Chi-restraints excluded: chain K residue 162 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 133 optimal weight: 0.9980 chunk 9 optimal weight: 10.0000 chunk 21 optimal weight: 0.0060 chunk 80 optimal weight: 5.9990 chunk 15 optimal weight: 0.3980 chunk 187 optimal weight: 5.9990 chunk 85 optimal weight: 8.9990 chunk 182 optimal weight: 0.0970 chunk 105 optimal weight: 0.9980 chunk 168 optimal weight: 2.9990 chunk 61 optimal weight: 0.8980 overall best weight: 0.4794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 128 GLN ** A 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 309 HIS ** C 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 128 GLN ** C 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 247 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.158000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.132025 restraints weight = 21332.740| |-----------------------------------------------------------------------------| r_work (start): 0.3680 rms_B_bonded: 2.08 r_work: 0.3532 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3388 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3388 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.6805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 16531 Z= 0.107 Angle : 0.600 12.514 22423 Z= 0.301 Chirality : 0.044 0.157 2457 Planarity : 0.004 0.061 2919 Dihedral : 10.973 179.940 2282 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 2.79 % Allowed : 22.88 % Favored : 74.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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 aren not related in a simple way. whole: -1.45 (0.18), residues: 2035 helix: -0.41 (0.18), residues: 808 sheet: -0.92 (0.29), residues: 336 loop : -1.39 (0.21), residues: 891 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 243 TYR 0.013 0.001 TYR C 103 PHE 0.015 0.001 PHE A 255 TRP 0.011 0.001 TRP C 21 HIS 0.004 0.001 HIS B 309 Details of bonding type rmsd covalent geometry : bond 0.00253 (16529) covalent geometry : angle 0.60014 (22423) hydrogen bonds : bond 0.03014 ( 536) hydrogen bonds : angle 4.64356 ( 1605) Misc. bond : bond 0.00137 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4070 Ramachandran restraints generated. 2035 Oldfield, 0 Emsley, 2035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4070 Ramachandran restraints generated. 2035 Oldfield, 0 Emsley, 2035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 1757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 292 time to evaluate : 0.431 Fit side-chains revert: symmetry clash REVERT: A 214 ARG cc_start: 0.8358 (ptt180) cc_final: 0.7988 (ptt90) REVERT: A 221 ARG cc_start: 0.5849 (mmt180) cc_final: 0.5636 (mmt180) REVERT: B 44 LEU cc_start: 0.8379 (OUTLIER) cc_final: 0.8079 (tt) REVERT: B 119 LEU cc_start: 0.8956 (tp) cc_final: 0.8643 (mt) REVERT: B 235 MET cc_start: 0.8446 (mtt) cc_final: 0.8166 (mtt) REVERT: B 283 TYR cc_start: 0.6938 (m-10) cc_final: 0.6682 (t80) REVERT: B 291 LEU cc_start: 0.7429 (OUTLIER) cc_final: 0.6711 (mp) REVERT: B 422 GLU cc_start: 0.8091 (tp30) cc_final: 0.7715 (tt0) REVERT: C 24 TYR cc_start: 0.8914 (m-10) cc_final: 0.8676 (m-10) REVERT: C 160 ASP cc_start: 0.7988 (t70) cc_final: 0.7301 (m-30) REVERT: C 290 GLU cc_start: 0.7432 (pt0) cc_final: 0.7012 (pt0) REVERT: C 301 GLN cc_start: 0.9046 (pm20) cc_final: 0.8735 (pm20) REVERT: C 339 ARG cc_start: 0.7792 (OUTLIER) cc_final: 0.7059 (ttm110) REVERT: C 349 THR cc_start: 0.8897 (p) cc_final: 0.8687 (p) REVERT: C 357 TYR cc_start: 0.8504 (m-80) cc_final: 0.8200 (m-80) REVERT: D 103 TRP cc_start: 0.8428 (t60) cc_final: 0.8030 (t60) REVERT: D 235 MET cc_start: 0.8087 (mtp) cc_final: 0.7769 (mtp) REVERT: D 309 HIS cc_start: 0.7612 (m-70) cc_final: 0.7185 (m-70) REVERT: D 322 ARG cc_start: 0.8345 (mmm160) cc_final: 0.7749 (mmm160) REVERT: D 338 LYS cc_start: 0.9081 (mmtt) cc_final: 0.8818 (mmtt) REVERT: D 386 GLU cc_start: 0.7695 (mt-10) cc_final: 0.7334 (mm-30) REVERT: K 8 ASN cc_start: 0.7213 (p0) cc_final: 0.6428 (m-40) REVERT: K 12 MET cc_start: 0.7280 (mmm) cc_final: 0.6868 (mmm) REVERT: K 122 MET cc_start: 0.6573 (ttm) cc_final: 0.6306 (ttm) REVERT: K 157 GLU cc_start: 0.7802 (pm20) cc_final: 0.7313 (pt0) REVERT: K 178 GLU cc_start: 0.8734 (tp30) cc_final: 0.8527 (mm-30) outliers start: 49 outliers final: 40 residues processed: 327 average time/residue: 0.1040 time to fit residues: 51.9385 Evaluate side-chains 318 residues out of total 1757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 275 time to evaluate : 0.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 SER Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 398 MET Chi-restraints excluded: chain B residue 37 HIS Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain B residue 291 LEU Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain B residue 326 LYS Chi-restraints excluded: chain B residue 356 CYS Chi-restraints excluded: chain B residue 374 SER Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 430 SER Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain C residue 113 GLU Chi-restraints excluded: chain C residue 181 VAL Chi-restraints excluded: chain C residue 223 THR Chi-restraints excluded: chain C residue 250 VAL Chi-restraints excluded: chain C residue 288 VAL Chi-restraints excluded: chain C residue 339 ARG Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 381 THR Chi-restraints excluded: chain D residue 138 THR Chi-restraints excluded: chain D residue 181 VAL Chi-restraints excluded: chain D residue 214 PHE Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 247 GLN Chi-restraints excluded: chain D residue 269 MET Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain K residue 43 SER Chi-restraints excluded: chain K residue 74 LEU Chi-restraints excluded: chain K residue 155 VAL Chi-restraints excluded: chain K residue 162 VAL Chi-restraints excluded: chain K residue 212 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 124 optimal weight: 0.7980 chunk 86 optimal weight: 3.9990 chunk 95 optimal weight: 6.9990 chunk 145 optimal weight: 0.0980 chunk 61 optimal weight: 2.9990 chunk 167 optimal weight: 4.9990 chunk 132 optimal weight: 0.8980 chunk 88 optimal weight: 0.2980 chunk 84 optimal weight: 0.7980 chunk 143 optimal weight: 6.9990 chunk 166 optimal weight: 0.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 128 GLN ** A 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 128 GLN C 258 ASN D 247 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.160166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.132692 restraints weight = 21457.733| |-----------------------------------------------------------------------------| r_work (start): 0.3654 rms_B_bonded: 2.32 r_work: 0.3528 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3381 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3381 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.6925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 16531 Z= 0.110 Angle : 0.612 13.862 22423 Z= 0.304 Chirality : 0.044 0.155 2457 Planarity : 0.004 0.063 2919 Dihedral : 10.874 179.142 2280 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 2.62 % Allowed : 23.16 % Favored : 74.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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 aren not related in a simple way. whole: -1.28 (0.19), residues: 2035 helix: -0.22 (0.18), residues: 808 sheet: -0.89 (0.29), residues: 336 loop : -1.32 (0.21), residues: 891 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 64 TYR 0.012 0.001 TYR C 103 PHE 0.016 0.001 PHE A 255 TRP 0.011 0.001 TRP C 346 HIS 0.004 0.001 HIS D 192 Details of bonding type rmsd covalent geometry : bond 0.00263 (16529) covalent geometry : angle 0.61213 (22423) hydrogen bonds : bond 0.02982 ( 536) hydrogen bonds : angle 4.60080 ( 1605) Misc. bond : bond 0.00135 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4070 Ramachandran restraints generated. 2035 Oldfield, 0 Emsley, 2035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4070 Ramachandran restraints generated. 2035 Oldfield, 0 Emsley, 2035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 1757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 295 time to evaluate : 0.412 Fit side-chains REVERT: A 214 ARG cc_start: 0.8342 (ptt180) cc_final: 0.8059 (ptt90) REVERT: B 44 LEU cc_start: 0.8411 (OUTLIER) cc_final: 0.8157 (tt) REVERT: B 119 LEU cc_start: 0.8975 (tp) cc_final: 0.8659 (mt) REVERT: B 283 TYR cc_start: 0.6978 (m-10) cc_final: 0.6710 (t80) REVERT: B 291 LEU cc_start: 0.7450 (OUTLIER) cc_final: 0.6655 (mp) REVERT: B 422 GLU cc_start: 0.8104 (tp30) cc_final: 0.7710 (tt0) REVERT: C 24 TYR cc_start: 0.8935 (m-10) cc_final: 0.8640 (m-10) REVERT: C 160 ASP cc_start: 0.8014 (t70) cc_final: 0.7171 (m-30) REVERT: C 339 ARG cc_start: 0.7545 (OUTLIER) cc_final: 0.6858 (ttm110) REVERT: C 349 THR cc_start: 0.8858 (p) cc_final: 0.8653 (p) REVERT: C 357 TYR cc_start: 0.8534 (m-80) cc_final: 0.8212 (m-80) REVERT: D 103 TRP cc_start: 0.8437 (t60) cc_final: 0.8030 (t60) REVERT: D 235 MET cc_start: 0.8028 (mtp) cc_final: 0.7725 (mtp) REVERT: D 309 HIS cc_start: 0.7589 (m-70) cc_final: 0.7170 (m-70) REVERT: D 322 ARG cc_start: 0.8433 (mmm160) cc_final: 0.7896 (mmm160) REVERT: D 385 GLN cc_start: 0.8303 (pp30) cc_final: 0.7911 (pm20) REVERT: D 416 MET cc_start: 0.8080 (tpp) cc_final: 0.7764 (tpt) REVERT: K 8 ASN cc_start: 0.7085 (p0) cc_final: 0.6433 (m-40) REVERT: K 12 MET cc_start: 0.7306 (mmm) cc_final: 0.6872 (mmm) REVERT: K 134 TYR cc_start: 0.7622 (t80) cc_final: 0.7267 (t80) REVERT: K 157 GLU cc_start: 0.7977 (pm20) cc_final: 0.7512 (pt0) REVERT: K 178 GLU cc_start: 0.8745 (tp30) cc_final: 0.8534 (mm-30) outliers start: 46 outliers final: 37 residues processed: 327 average time/residue: 0.1136 time to fit residues: 56.2309 Evaluate side-chains 316 residues out of total 1757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 276 time to evaluate : 0.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 SER Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 398 MET Chi-restraints excluded: chain B residue 37 HIS Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain B residue 291 LEU Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain B residue 356 CYS Chi-restraints excluded: chain B residue 374 SER Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 423 SER Chi-restraints excluded: chain B residue 430 SER Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain C residue 181 VAL Chi-restraints excluded: chain C residue 250 VAL Chi-restraints excluded: chain C residue 288 VAL Chi-restraints excluded: chain C residue 339 ARG Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 381 THR Chi-restraints excluded: chain D residue 138 THR Chi-restraints excluded: chain D residue 181 VAL Chi-restraints excluded: chain D residue 214 PHE Chi-restraints excluded: chain D residue 247 GLN Chi-restraints excluded: chain D residue 269 MET Chi-restraints excluded: chain D residue 432 TYR Chi-restraints excluded: chain K residue 43 SER Chi-restraints excluded: chain K residue 74 LEU Chi-restraints excluded: chain K residue 155 VAL Chi-restraints excluded: chain K residue 162 VAL Chi-restraints excluded: chain K residue 212 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 78 optimal weight: 0.4980 chunk 68 optimal weight: 0.5980 chunk 10 optimal weight: 6.9990 chunk 45 optimal weight: 0.7980 chunk 168 optimal weight: 0.6980 chunk 44 optimal weight: 2.9990 chunk 137 optimal weight: 0.9980 chunk 174 optimal weight: 3.9990 chunk 132 optimal weight: 7.9990 chunk 5 optimal weight: 6.9990 chunk 98 optimal weight: 4.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 128 GLN ** A 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 309 HIS ** C 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 128 GLN K 58 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.159878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.133032 restraints weight = 21459.552| |-----------------------------------------------------------------------------| r_work (start): 0.3632 rms_B_bonded: 2.18 r_work: 0.3508 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3365 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3365 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.7024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 16531 Z= 0.114 Angle : 0.627 13.479 22423 Z= 0.310 Chirality : 0.044 0.153 2457 Planarity : 0.004 0.063 2919 Dihedral : 10.835 178.071 2280 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 2.50 % Allowed : 23.51 % Favored : 73.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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 aren not related in a simple way. whole: -1.18 (0.19), residues: 2035 helix: -0.11 (0.18), residues: 808 sheet: -0.86 (0.29), residues: 336 loop : -1.28 (0.21), residues: 891 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 64 TYR 0.024 0.001 TYR K 118 PHE 0.017 0.001 PHE A 255 TRP 0.010 0.001 TRP C 346 HIS 0.002 0.001 HIS D 192 Details of bonding type rmsd covalent geometry : bond 0.00273 (16529) covalent geometry : angle 0.62689 (22423) hydrogen bonds : bond 0.02997 ( 536) hydrogen bonds : angle 4.56642 ( 1605) Misc. bond : bond 0.00141 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3166.24 seconds wall clock time: 55 minutes 10.13 seconds (3310.13 seconds total)