Starting phenix.real_space_refine on Sat May 17 21:03:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9l7m_62874/05_2025/9l7m_62874_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9l7m_62874/05_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_62874/05_2025/9l7m_62874.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9l7m_62874/05_2025/9l7m_62874.map" model { file = "/net/cci-nas-00/data/ceres_data/9l7m_62874/05_2025/9l7m_62874_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9l7m_62874/05_2025/9l7m_62874_neut.cif" } resolution = 3.48 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 11.54, per 1000 atoms: 0.71 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: 4.72 Conformation dependent library (CDL) restraints added in 2.3 seconds 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: 2.02 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: 5.18 Time building geometry restraints manager: 5.31 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: 0.610 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: 0.020 Extract box with map and model: 0.690 Check model and map are aligned: 0.110 Set scattering table: 0.160 Process input model: 40.390 Find NCS groups from input model: 0.500 Set up NCS constraints: 0.050 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: 0.010 Load rotamer database and sin/cos tables:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.390 ------------------------------------------------------------------------------- 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 : 27.17 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.019 0.004 TRP A 21 HIS 0.024 0.004 HIS A 283 PHE 0.045 0.006 PHE D 395 TYR 0.051 0.005 TYR K 77 ARG 0.016 0.002 ARG C 156 Details of bonding type rmsd hydrogen bonds : bond 0.19933 ( 536) hydrogen bonds : angle 8.70953 ( 1605) covalent geometry : bond 0.02595 (16529) covalent geometry : angle 1.53585 (22423) 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 : 1.741 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: 0.2945 time to fit residues: 307.5548 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 : 1.717 ------------------------------------------------------------------------------- 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 169 optimal weight: 1.9990 chunk 152 optimal weight: 2.9990 chunk 84 optimal weight: 1.9990 chunk 52 optimal weight: 4.9990 chunk 102 optimal weight: 0.9980 chunk 81 optimal weight: 0.9990 chunk 157 optimal weight: 5.9990 chunk 60 optimal weight: 2.9990 chunk 95 optimal weight: 0.8980 chunk 117 optimal weight: 1.9990 chunk 182 optimal weight: 0.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 8 HIS 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 ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.4022 r_free = 0.4022 target = 0.161475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.134557 restraints weight = 21617.264| |-----------------------------------------------------------------------------| r_work (start): 0.3693 rms_B_bonded: 2.39 r_work: 0.3576 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work (final): 0.3576 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7663 moved from start: 0.4243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.096 16531 Z= 0.174 Angle : 0.773 10.607 22423 Z= 0.401 Chirality : 0.048 0.176 2457 Planarity : 0.006 0.071 2919 Dihedral : 13.687 152.682 2317 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.52 % Favored : 95.38 % Rotamer: Outliers : 4.15 % Allowed : 16.79 % Favored : 79.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.10 (0.16), residues: 2035 helix: -2.50 (0.16), residues: 791 sheet: -2.22 (0.28), residues: 314 loop : -3.03 (0.17), residues: 930 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 21 HIS 0.006 0.001 HIS C 197 PHE 0.023 0.002 PHE C 49 TYR 0.019 0.002 TYR D 432 ARG 0.007 0.001 ARG A 105 Details of bonding type rmsd hydrogen bonds : bond 0.04592 ( 536) hydrogen bonds : angle 5.75710 ( 1605) covalent geometry : bond 0.00406 (16529) covalent geometry : angle 0.77285 (22423) Misc. bond : bond 0.00018 ( 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 479 residues out of total 1757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 406 time to evaluate : 2.337 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.5050 (OUTLIER) cc_final: 0.4729 (pmm) REVERT: A 84 ARG cc_start: 0.7376 (ttp-110) cc_final: 0.7027 (ptm160) REVERT: A 203 MET cc_start: 0.8085 (mtt) cc_final: 0.7870 (mtp) REVERT: A 265 ILE cc_start: 0.8969 (mt) cc_final: 0.8717 (mt) REVERT: A 430 LYS cc_start: 0.8591 (ttmm) cc_final: 0.8352 (ttpt) REVERT: B 119 LEU cc_start: 0.8845 (tp) cc_final: 0.8571 (mt) REVERT: B 127 GLU cc_start: 0.7813 (mm-30) cc_final: 0.7472 (mt-10) REVERT: B 283 TYR cc_start: 0.6793 (m-10) cc_final: 0.6201 (t80) REVERT: B 422 GLU cc_start: 0.7881 (tp30) cc_final: 0.7376 (tt0) REVERT: C 24 TYR cc_start: 0.8940 (m-10) cc_final: 0.8712 (m-10) REVERT: C 27 GLU cc_start: 0.8196 (mt-10) cc_final: 0.7967 (mt-10) REVERT: C 107 HIS cc_start: 0.8866 (OUTLIER) cc_final: 0.8548 (t-170) REVERT: C 123 ARG cc_start: 0.7972 (ptm160) cc_final: 0.7682 (ttm-80) REVERT: C 160 ASP cc_start: 0.7752 (t70) cc_final: 0.7315 (m-30) REVERT: C 301 GLN cc_start: 0.8478 (pm20) cc_final: 0.7561 (mm-40) REVERT: C 357 TYR cc_start: 0.7178 (m-80) cc_final: 0.6901 (m-80) REVERT: C 382 THR cc_start: 0.7659 (OUTLIER) cc_final: 0.7440 (m) REVERT: C 419 SER cc_start: 0.8782 (m) cc_final: 0.8409 (p) REVERT: C 425 MET cc_start: 0.8339 (mmm) cc_final: 0.7654 (tpp) REVERT: D 21 TRP cc_start: 0.8792 (m100) cc_final: 0.8516 (m100) REVERT: D 283 TYR cc_start: 0.4829 (t80) cc_final: 0.4149 (t80) REVERT: D 322 ARG cc_start: 0.7466 (mmm160) cc_final: 0.7227 (mmm160) REVERT: D 325 MET cc_start: 0.6567 (mpp) cc_final: 0.6337 (mpp) REVERT: D 334 ASN cc_start: 0.7957 (t0) cc_final: 0.7466 (t0) REVERT: D 352 LYS cc_start: 0.7576 (tptp) cc_final: 0.6567 (mmtt) REVERT: D 385 GLN cc_start: 0.8360 (tt0) cc_final: 0.8068 (pp30) REVERT: D 386 GLU cc_start: 0.7633 (tp30) cc_final: 0.7247 (tp30) REVERT: K 12 MET cc_start: 0.6785 (mmm) cc_final: 0.6575 (mmm) REVERT: K 25 ARG cc_start: 0.8516 (mtm180) cc_final: 0.8302 (mtm180) REVERT: K 50 ARG cc_start: 0.7333 (tpt170) cc_final: 0.6573 (mmm-85) REVERT: K 122 MET cc_start: 0.6534 (ttp) cc_final: 0.6117 (ttp) outliers start: 73 outliers final: 43 residues processed: 462 average time/residue: 0.3016 time to fit residues: 206.1325 Evaluate side-chains 365 residues out of total 1757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 319 time to evaluate : 1.872 ------------------------------------------------------------------------------- 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 329 ASN 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 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 361 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 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 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 43 optimal weight: 4.9990 chunk 137 optimal weight: 8.9990 chunk 115 optimal weight: 4.9990 chunk 89 optimal weight: 0.0870 chunk 173 optimal weight: 6.9990 chunk 26 optimal weight: 0.6980 chunk 106 optimal weight: 0.8980 chunk 33 optimal weight: 5.9990 chunk 199 optimal weight: 0.0980 chunk 182 optimal weight: 0.9990 chunk 42 optimal weight: 0.9980 overall best weight: 0.5558 ------------------------------------------------------------------------------- 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 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 394 GLN ** C 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 101 ASN D 294 GLN 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: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.170921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.144261 restraints weight = 21119.117| |-----------------------------------------------------------------------------| r_work (start): 0.3792 rms_B_bonded: 2.36 r_work: 0.3664 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work (final): 0.3664 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7702 moved from start: 0.5024 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= 0.124 Angle : 0.647 8.056 22423 Z= 0.334 Chirality : 0.045 0.158 2457 Planarity : 0.005 0.059 2919 Dihedral : 12.555 159.182 2292 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 3.87 % Allowed : 18.27 % Favored : 77.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.12 (0.17), residues: 2035 helix: -1.82 (0.17), residues: 797 sheet: -1.74 (0.29), residues: 314 loop : -2.34 (0.18), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 346 HIS 0.008 0.001 HIS C 107 PHE 0.018 0.001 PHE C 202 TYR 0.022 0.001 TYR D 36 ARG 0.006 0.000 ARG B 401 Details of bonding type rmsd hydrogen bonds : bond 0.03818 ( 536) hydrogen bonds : angle 5.12852 ( 1605) covalent geometry : bond 0.00287 (16529) covalent geometry : angle 0.64689 (22423) Misc. bond : bond 0.00103 ( 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 407 residues out of total 1757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 339 time to evaluate : 1.991 Fit side-chains revert: symmetry clash REVERT: A 430 LYS cc_start: 0.8646 (ttmm) cc_final: 0.8402 (ttpt) REVERT: B 44 LEU cc_start: 0.7832 (OUTLIER) cc_final: 0.7460 (tt) REVERT: B 119 LEU cc_start: 0.8886 (tp) cc_final: 0.8625 (mt) REVERT: B 127 GLU cc_start: 0.7788 (mm-30) cc_final: 0.7481 (mt-10) REVERT: B 235 MET cc_start: 0.8308 (mtt) cc_final: 0.8011 (mtt) REVERT: B 283 TYR cc_start: 0.6951 (m-10) cc_final: 0.6330 (t80) REVERT: B 291 LEU cc_start: 0.7626 (OUTLIER) cc_final: 0.7338 (mt) REVERT: B 422 GLU cc_start: 0.7425 (tp30) cc_final: 0.7185 (tt0) REVERT: C 24 TYR cc_start: 0.8888 (m-10) cc_final: 0.8600 (m-10) REVERT: C 123 ARG cc_start: 0.8144 (ptm160) cc_final: 0.7920 (ttm-80) REVERT: C 160 ASP cc_start: 0.7669 (t70) cc_final: 0.7212 (m-30) REVERT: C 301 GLN cc_start: 0.8384 (pm20) cc_final: 0.7493 (mm110) REVERT: C 357 TYR cc_start: 0.7285 (m-80) cc_final: 0.6957 (m-80) REVERT: C 419 SER cc_start: 0.8831 (m) cc_final: 0.8479 (p) REVERT: C 425 MET cc_start: 0.8480 (mmm) cc_final: 0.7474 (tpt) REVERT: D 322 ARG cc_start: 0.7785 (mmm160) cc_final: 0.7263 (mmm160) REVERT: D 352 LYS cc_start: 0.7387 (tptp) cc_final: 0.6404 (mmtt) REVERT: D 385 GLN cc_start: 0.8244 (tt0) cc_final: 0.8016 (pp30) REVERT: D 386 GLU cc_start: 0.7565 (tp30) cc_final: 0.7241 (tp30) REVERT: K 12 MET cc_start: 0.6890 (mmm) cc_final: 0.6571 (mmm) REVERT: K 122 MET cc_start: 0.6667 (ttp) cc_final: 0.6164 (ttp) REVERT: K 176 PRO cc_start: 0.8031 (Cg_exo) cc_final: 0.7823 (Cg_endo) REVERT: K 197 MET cc_start: 0.5806 (tpt) cc_final: 0.5592 (tpt) outliers start: 68 outliers final: 36 residues processed: 388 average time/residue: 0.2688 time to fit residues: 155.2044 Evaluate side-chains 338 residues out of total 1757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 300 time to evaluate : 1.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 SER Chi-restraints excluded: chain A residue 158 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 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 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 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 109 optimal weight: 5.9990 chunk 162 optimal weight: 0.0970 chunk 147 optimal weight: 3.9990 chunk 126 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 76 optimal weight: 4.9990 chunk 188 optimal weight: 4.9990 chunk 172 optimal weight: 9.9990 chunk 57 optimal weight: 2.9990 chunk 54 optimal weight: 0.8980 chunk 166 optimal weight: 0.7980 overall best weight: 1.3582 ------------------------------------------------------------------------------- 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** ** B 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 424 ASN ** C 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 128 GLN C 256 GLN D 101 ASN D 136 GLN D 336 GLN ** D 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 394 GLN K 214 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.162151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.137006 restraints weight = 21151.717| |-----------------------------------------------------------------------------| r_work (start): 0.3712 rms_B_bonded: 2.04 r_work: 0.3565 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3422 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3422 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.5669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.098 16531 Z= 0.157 Angle : 0.640 7.066 22423 Z= 0.329 Chirality : 0.045 0.152 2457 Planarity : 0.005 0.060 2919 Dihedral : 12.067 167.833 2286 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 4.04 % Allowed : 19.75 % Favored : 76.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.64 (0.17), residues: 2035 helix: -1.42 (0.17), residues: 816 sheet: -1.64 (0.28), residues: 340 loop : -1.99 (0.19), residues: 879 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 21 HIS 0.007 0.001 HIS A 88 PHE 0.014 0.002 PHE B 377 TYR 0.019 0.002 TYR D 36 ARG 0.007 0.001 ARG K 161 Details of bonding type rmsd hydrogen bonds : bond 0.03771 ( 536) hydrogen bonds : angle 4.91950 ( 1605) covalent geometry : bond 0.00376 (16529) covalent geometry : angle 0.64044 (22423) Misc. bond : bond 0.00193 ( 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 387 residues out of total 1757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 316 time to evaluate : 1.984 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 VAL cc_start: 0.8980 (t) cc_final: 0.8762 (p) REVERT: A 84 ARG cc_start: 0.7749 (ttp-110) cc_final: 0.7261 (ptm-80) REVERT: B 83 PHE cc_start: 0.8090 (m-80) cc_final: 0.7835 (m-80) REVERT: B 119 LEU cc_start: 0.9023 (tp) cc_final: 0.8707 (mt) REVERT: B 127 GLU cc_start: 0.7956 (mm-30) cc_final: 0.7743 (mt-10) REVERT: B 149 MET cc_start: 0.8476 (ttt) cc_final: 0.8117 (ttp) REVERT: B 235 MET cc_start: 0.8380 (mtt) cc_final: 0.8154 (mtt) REVERT: B 283 TYR cc_start: 0.7188 (m-10) cc_final: 0.6378 (t80) REVERT: B 290 GLU cc_start: 0.7418 (tp30) cc_final: 0.7047 (tp30) REVERT: B 291 LEU cc_start: 0.7747 (OUTLIER) cc_final: 0.6952 (mp) REVERT: C 3 GLU cc_start: 0.7195 (pm20) cc_final: 0.6926 (pm20) REVERT: C 24 TYR cc_start: 0.8986 (m-10) cc_final: 0.8567 (m-10) REVERT: C 123 ARG cc_start: 0.8372 (ptm160) cc_final: 0.8056 (ttm-80) REVERT: C 160 ASP cc_start: 0.8062 (t70) cc_final: 0.7468 (m-30) REVERT: C 357 TYR cc_start: 0.7795 (m-80) cc_final: 0.7299 (m-80) REVERT: C 390 ARG cc_start: 0.8441 (mtm-85) cc_final: 0.7923 (mtm110) REVERT: C 425 MET cc_start: 0.8720 (mmm) cc_final: 0.8073 (tpp) REVERT: D 103 TRP cc_start: 0.8560 (t60) cc_final: 0.8000 (t60) REVERT: D 133 GLN cc_start: 0.7594 (tp-100) cc_final: 0.7061 (tp-100) REVERT: D 164 ARG cc_start: 0.8346 (mmp80) cc_final: 0.8135 (mmp80) REVERT: D 322 ARG cc_start: 0.7831 (mmm160) cc_final: 0.7306 (mmm160) REVERT: D 385 GLN cc_start: 0.8467 (tt0) cc_final: 0.8223 (pp30) REVERT: D 425 MET cc_start: 0.8465 (tpp) cc_final: 0.8229 (tpp) REVERT: K 122 MET cc_start: 0.6977 (ttp) cc_final: 0.6447 (ttp) REVERT: K 157 GLU cc_start: 0.8049 (pm20) cc_final: 0.7629 (pm20) REVERT: K 197 MET cc_start: 0.6022 (tpt) cc_final: 0.5795 (tpt) REVERT: K 268 LEU cc_start: 0.8551 (mp) cc_final: 0.8294 (mt) outliers start: 71 outliers final: 54 residues processed: 371 average time/residue: 0.2716 time to fit residues: 149.4054 Evaluate side-chains 344 residues out of total 1757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 289 time to evaluate : 1.901 ------------------------------------------------------------------------------- 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 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 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 70 LEU 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 217 LEU 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 286 LEU 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 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 252 LEU Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 257 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 326 LYS Chi-restraints excluded: chain D residue 356 CYS 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 191 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 160 optimal weight: 1.9990 chunk 23 optimal weight: 5.9990 chunk 94 optimal weight: 4.9990 chunk 180 optimal weight: 0.9980 chunk 1 optimal weight: 4.9990 chunk 36 optimal weight: 1.9990 chunk 87 optimal weight: 0.6980 chunk 89 optimal weight: 9.9990 chunk 25 optimal weight: 0.9990 chunk 68 optimal weight: 0.6980 chunk 11 optimal weight: 0.9980 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 ** B 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 128 GLN D 336 GLN ** D 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 253 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.152941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.126775 restraints weight = 22244.989| |-----------------------------------------------------------------------------| r_work (start): 0.3595 rms_B_bonded: 2.14 r_work: 0.3450 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3307 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.6047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 16531 Z= 0.120 Angle : 0.598 6.914 22423 Z= 0.304 Chirality : 0.044 0.156 2457 Planarity : 0.004 0.062 2919 Dihedral : 11.712 174.765 2286 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 3.53 % Allowed : 21.80 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.19 (0.18), residues: 2035 helix: -1.08 (0.18), residues: 810 sheet: -1.36 (0.29), residues: 350 loop : -1.73 (0.20), residues: 875 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 21 HIS 0.006 0.001 HIS A 88 PHE 0.014 0.001 PHE C 49 TYR 0.016 0.001 TYR D 36 ARG 0.006 0.000 ARG A 339 Details of bonding type rmsd hydrogen bonds : bond 0.03303 ( 536) hydrogen bonds : angle 4.78095 ( 1605) covalent geometry : bond 0.00286 (16529) covalent geometry : angle 0.59814 (22423) Misc. bond : bond 0.00153 ( 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 379 residues out of total 1757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 317 time to evaluate : 1.810 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 339 ARG cc_start: 0.8269 (mmp80) cc_final: 0.7875 (mmp80) REVERT: B 83 PHE cc_start: 0.7897 (m-80) cc_final: 0.7616 (m-80) REVERT: B 119 LEU cc_start: 0.8965 (tp) cc_final: 0.8638 (mt) REVERT: B 149 MET cc_start: 0.8646 (ttt) cc_final: 0.8333 (ttp) REVERT: B 235 MET cc_start: 0.8466 (mtt) cc_final: 0.8223 (mtt) REVERT: B 283 TYR cc_start: 0.7277 (m-10) cc_final: 0.6403 (t80) REVERT: B 290 GLU cc_start: 0.7471 (tp30) cc_final: 0.7054 (tp30) REVERT: B 291 LEU cc_start: 0.7602 (OUTLIER) cc_final: 0.6792 (mp) REVERT: C 24 TYR cc_start: 0.8889 (m-10) cc_final: 0.8560 (m-10) REVERT: C 123 ARG cc_start: 0.8408 (ptm160) cc_final: 0.8045 (ttm-80) REVERT: C 160 ASP cc_start: 0.8331 (t70) cc_final: 0.7558 (m-30) REVERT: C 357 TYR cc_start: 0.8088 (m-80) cc_final: 0.7618 (m-80) REVERT: C 425 MET cc_start: 0.8557 (mmm) cc_final: 0.8126 (tpp) REVERT: D 103 TRP cc_start: 0.8251 (t60) cc_final: 0.7943 (t60) REVERT: D 133 GLN cc_start: 0.7669 (tp-100) cc_final: 0.7102 (tp-100) REVERT: D 385 GLN cc_start: 0.8417 (tt0) cc_final: 0.7966 (pp30) REVERT: D 386 GLU cc_start: 0.7925 (mt-10) cc_final: 0.7439 (mm-30) REVERT: D 425 MET cc_start: 0.8251 (tpp) cc_final: 0.8044 (tpp) REVERT: K 20 GLU cc_start: 0.8503 (mm-30) cc_final: 0.8287 (mm-30) REVERT: K 122 MET cc_start: 0.7004 (ttp) cc_final: 0.6714 (ttp) outliers start: 62 outliers final: 45 residues processed: 365 average time/residue: 0.2723 time to fit residues: 148.1630 Evaluate side-chains 317 residues out of total 1757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 271 time to evaluate : 1.901 ------------------------------------------------------------------------------- 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 181 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 420 GLU 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 177 VAL Chi-restraints excluded: chain B residue 217 LEU 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 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 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 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 D residue 326 LYS 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 191 HIS Chi-restraints excluded: chain K residue 241 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 3 optimal weight: 0.0370 chunk 2 optimal weight: 0.7980 chunk 127 optimal weight: 0.9980 chunk 178 optimal weight: 7.9990 chunk 40 optimal weight: 0.8980 chunk 25 optimal weight: 0.2980 chunk 12 optimal weight: 0.9990 chunk 185 optimal weight: 4.9990 chunk 94 optimal weight: 2.9990 chunk 154 optimal weight: 1.9990 chunk 144 optimal weight: 0.9980 overall best weight: 0.6058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 301 GLN ** B 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 128 GLN D 192 HIS D 247 GLN D 336 GLN ** D 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 34 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.153532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.125895 restraints weight = 21975.898| |-----------------------------------------------------------------------------| r_work (start): 0.3560 rms_B_bonded: 2.38 r_work: 0.3441 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3296 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3296 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.6281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 16531 Z= 0.109 Angle : 0.595 7.734 22423 Z= 0.300 Chirality : 0.044 0.217 2457 Planarity : 0.004 0.057 2919 Dihedral : 11.439 178.110 2286 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 3.70 % Allowed : 22.03 % Favored : 74.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.87 (0.18), residues: 2035 helix: -0.76 (0.18), residues: 806 sheet: -1.26 (0.28), residues: 350 loop : -1.55 (0.20), residues: 879 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 346 HIS 0.003 0.001 HIS C 88 PHE 0.014 0.001 PHE A 141 TYR 0.014 0.001 TYR D 36 ARG 0.010 0.000 ARG D 164 Details of bonding type rmsd hydrogen bonds : bond 0.03149 ( 536) hydrogen bonds : angle 4.67873 ( 1605) covalent geometry : bond 0.00259 (16529) covalent geometry : angle 0.59451 (22423) Misc. bond : bond 0.00142 ( 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 373 residues out of total 1757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 308 time to evaluate : 1.754 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 22 GLU cc_start: 0.7981 (OUTLIER) cc_final: 0.7763 (tt0) REVERT: A 221 ARG cc_start: 0.5950 (mmt180) cc_final: 0.5716 (mmt180) REVERT: B 83 PHE cc_start: 0.7837 (m-80) cc_final: 0.7539 (m-80) REVERT: B 119 LEU cc_start: 0.8979 (tp) cc_final: 0.8644 (mt) REVERT: B 149 MET cc_start: 0.8660 (ttt) cc_final: 0.8294 (ttp) REVERT: B 235 MET cc_start: 0.8510 (mtt) cc_final: 0.8249 (mtt) REVERT: B 283 TYR cc_start: 0.7251 (m-10) cc_final: 0.6495 (t80) REVERT: B 291 LEU cc_start: 0.7512 (OUTLIER) cc_final: 0.7157 (mt) REVERT: B 422 GLU cc_start: 0.8119 (tp30) cc_final: 0.7670 (tt0) REVERT: C 24 TYR cc_start: 0.8895 (m-10) cc_final: 0.8565 (m-10) REVERT: C 123 ARG cc_start: 0.8430 (ptm160) cc_final: 0.8052 (ttm-80) REVERT: C 160 ASP cc_start: 0.8115 (t70) cc_final: 0.7553 (m-30) REVERT: C 339 ARG cc_start: 0.7701 (OUTLIER) cc_final: 0.6902 (ttm110) REVERT: C 349 THR cc_start: 0.8992 (p) cc_final: 0.8761 (p) REVERT: C 357 TYR cc_start: 0.8146 (m-80) cc_final: 0.7644 (m-80) REVERT: C 390 ARG cc_start: 0.8543 (mtm-85) cc_final: 0.8188 (mtm110) REVERT: C 425 MET cc_start: 0.8571 (mmm) cc_final: 0.8247 (tpp) REVERT: D 103 TRP cc_start: 0.8251 (t60) cc_final: 0.7888 (t60) REVERT: D 133 GLN cc_start: 0.7778 (tp-100) cc_final: 0.7139 (tp-100) REVERT: D 291 LEU cc_start: 0.8213 (tp) cc_final: 0.7806 (tt) REVERT: D 385 GLN cc_start: 0.8483 (tt0) cc_final: 0.8103 (pp30) REVERT: K 157 GLU cc_start: 0.7567 (pm20) cc_final: 0.6949 (pt0) REVERT: K 302 CYS cc_start: 0.8218 (m) cc_final: 0.8014 (m) outliers start: 65 outliers final: 48 residues processed: 357 average time/residue: 0.2783 time to fit residues: 146.3337 Evaluate side-chains 335 residues out of total 1757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 284 time to evaluate : 2.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 GLU Chi-restraints excluded: chain A residue 147 SER Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 271 THR 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 177 VAL Chi-restraints excluded: chain B residue 217 LEU 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 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 140 SER Chi-restraints excluded: chain C residue 181 VAL Chi-restraints excluded: chain C residue 191 THR Chi-restraints excluded: chain C residue 196 GLU 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 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 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 136 optimal weight: 0.9980 chunk 141 optimal weight: 6.9990 chunk 25 optimal weight: 1.9990 chunk 50 optimal weight: 3.9990 chunk 73 optimal weight: 0.7980 chunk 101 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 172 optimal weight: 10.0000 chunk 192 optimal weight: 7.9990 chunk 26 optimal weight: 0.9980 chunk 47 optimal weight: 3.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 128 GLN B 309 HIS ** C 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 128 GLN D 247 GLN D 336 GLN ** D 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.149887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.121504 restraints weight = 22222.272| |-----------------------------------------------------------------------------| r_work (start): 0.3510 rms_B_bonded: 2.43 r_work: 0.3384 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work (final): 0.3384 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.6535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 16531 Z= 0.146 Angle : 0.624 9.091 22423 Z= 0.316 Chirality : 0.045 0.150 2457 Planarity : 0.004 0.060 2919 Dihedral : 11.350 176.877 2284 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 3.47 % Allowed : 22.82 % Favored : 73.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.74 (0.18), residues: 2035 helix: -0.72 (0.18), residues: 808 sheet: -0.98 (0.29), residues: 348 loop : -1.52 (0.21), residues: 879 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 407 HIS 0.010 0.001 HIS B 309 PHE 0.012 0.001 PHE B 377 TYR 0.015 0.001 TYR C 408 ARG 0.007 0.000 ARG D 164 Details of bonding type rmsd hydrogen bonds : bond 0.03361 ( 536) hydrogen bonds : angle 4.73281 ( 1605) covalent geometry : bond 0.00354 (16529) covalent geometry : angle 0.62434 (22423) Misc. bond : bond 0.00184 ( 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 354 residues out of total 1757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 293 time to evaluate : 1.827 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 22 GLU cc_start: 0.7873 (OUTLIER) cc_final: 0.7654 (tt0) REVERT: A 221 ARG cc_start: 0.6086 (mmt180) cc_final: 0.5879 (mmt180) REVERT: A 339 ARG cc_start: 0.8152 (mmp80) cc_final: 0.7501 (mmp80) REVERT: B 71 GLU cc_start: 0.7461 (pt0) cc_final: 0.7113 (pt0) REVERT: B 83 PHE cc_start: 0.7806 (m-80) cc_final: 0.7491 (m-80) REVERT: B 119 LEU cc_start: 0.8965 (tp) cc_final: 0.8697 (mt) REVERT: B 235 MET cc_start: 0.8524 (mtt) cc_final: 0.8299 (mtt) REVERT: B 283 TYR cc_start: 0.6933 (m-10) cc_final: 0.6646 (t80) REVERT: B 291 LEU cc_start: 0.7515 (OUTLIER) cc_final: 0.6822 (mp) REVERT: B 422 GLU cc_start: 0.7931 (tp30) cc_final: 0.7573 (tt0) REVERT: C 24 TYR cc_start: 0.8878 (m-10) cc_final: 0.8508 (m-10) REVERT: C 123 ARG cc_start: 0.8237 (ptm160) cc_final: 0.8008 (ttm-80) REVERT: C 160 ASP cc_start: 0.7941 (t70) cc_final: 0.7420 (m-30) REVERT: C 339 ARG cc_start: 0.7913 (OUTLIER) cc_final: 0.7194 (ttm110) REVERT: C 390 ARG cc_start: 0.8413 (mtm-85) cc_final: 0.8174 (mtm110) REVERT: C 425 MET cc_start: 0.8577 (mmm) cc_final: 0.8375 (tpp) REVERT: D 103 TRP cc_start: 0.8330 (t60) cc_final: 0.7951 (t60) REVERT: D 133 GLN cc_start: 0.7880 (tp-100) cc_final: 0.7307 (tp-100) REVERT: D 291 LEU cc_start: 0.8313 (tp) cc_final: 0.7904 (tt) REVERT: D 309 HIS cc_start: 0.7470 (m-70) cc_final: 0.7019 (m-70) REVERT: D 385 GLN cc_start: 0.8554 (tt0) cc_final: 0.8108 (pp30) REVERT: K 157 GLU cc_start: 0.7674 (pm20) cc_final: 0.7070 (pt0) REVERT: K 178 GLU cc_start: 0.8647 (mm-30) cc_final: 0.8406 (tp30) outliers start: 61 outliers final: 46 residues processed: 338 average time/residue: 0.2652 time to fit residues: 134.8992 Evaluate side-chains 326 residues out of total 1757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 277 time to evaluate : 1.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 GLU Chi-restraints excluded: chain A residue 140 SER Chi-restraints excluded: chain A residue 147 SER 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 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 177 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 430 SER Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain C residue 140 SER Chi-restraints excluded: chain C residue 181 VAL 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 257 THR 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 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 134 optimal weight: 5.9990 chunk 40 optimal weight: 5.9990 chunk 155 optimal weight: 0.4980 chunk 97 optimal weight: 0.4980 chunk 127 optimal weight: 2.9990 chunk 64 optimal weight: 0.1980 chunk 46 optimal weight: 0.8980 chunk 96 optimal weight: 0.8980 chunk 120 optimal weight: 0.9980 chunk 114 optimal weight: 5.9990 chunk 13 optimal weight: 0.9980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 128 GLN B 139 HIS B 309 HIS ** C 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 128 GLN D 336 GLN ** D 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 58 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 = 0.150034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.122307 restraints weight = 21822.743| |-----------------------------------------------------------------------------| r_work (start): 0.3549 rms_B_bonded: 2.36 r_work: 0.3426 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3284 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.6675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 16531 Z= 0.109 Angle : 0.604 10.691 22423 Z= 0.305 Chirality : 0.044 0.201 2457 Planarity : 0.004 0.061 2919 Dihedral : 11.162 178.475 2283 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 3.13 % Allowed : 22.65 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.56 (0.18), residues: 2035 helix: -0.60 (0.18), residues: 810 sheet: -0.84 (0.29), residues: 346 loop : -1.41 (0.21), residues: 879 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 21 HIS 0.003 0.001 HIS C 88 PHE 0.011 0.001 PHE B 377 TYR 0.013 0.001 TYR D 36 ARG 0.006 0.000 ARG D 164 Details of bonding type rmsd hydrogen bonds : bond 0.03064 ( 536) hydrogen bonds : angle 4.63373 ( 1605) covalent geometry : bond 0.00257 (16529) covalent geometry : angle 0.60363 (22423) Misc. bond : bond 0.00135 ( 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 353 residues out of total 1757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 298 time to evaluate : 1.852 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 214 ARG cc_start: 0.8324 (ptt180) cc_final: 0.8038 (ptt90) REVERT: A 221 ARG cc_start: 0.6037 (mmt180) cc_final: 0.5834 (mmt180) REVERT: A 339 ARG cc_start: 0.7729 (mmp80) cc_final: 0.7385 (mmp80) REVERT: B 83 PHE cc_start: 0.7797 (m-80) cc_final: 0.7517 (m-80) REVERT: B 119 LEU cc_start: 0.8973 (tp) cc_final: 0.8629 (mt) REVERT: B 149 MET cc_start: 0.8650 (ttt) cc_final: 0.8274 (ttp) REVERT: B 235 MET cc_start: 0.8512 (mtt) cc_final: 0.8270 (mtt) REVERT: B 283 TYR cc_start: 0.7007 (m-10) cc_final: 0.6696 (t80) REVERT: B 291 LEU cc_start: 0.7524 (OUTLIER) cc_final: 0.6802 (mp) REVERT: B 422 GLU cc_start: 0.8235 (tp30) cc_final: 0.7799 (tt0) REVERT: C 24 TYR cc_start: 0.8898 (m-10) cc_final: 0.8538 (m-10) REVERT: C 123 ARG cc_start: 0.8417 (ptm160) cc_final: 0.8117 (ttm-80) REVERT: C 160 ASP cc_start: 0.8078 (t70) cc_final: 0.7323 (m-30) REVERT: C 339 ARG cc_start: 0.7809 (OUTLIER) cc_final: 0.7068 (ttm110) REVERT: C 349 THR cc_start: 0.8954 (p) cc_final: 0.8745 (p) REVERT: C 357 TYR cc_start: 0.8502 (m-80) cc_final: 0.8268 (m-80) REVERT: C 390 ARG cc_start: 0.8533 (mtm-85) cc_final: 0.8253 (mtm110) REVERT: C 391 LEU cc_start: 0.8829 (tp) cc_final: 0.8518 (tp) REVERT: D 103 TRP cc_start: 0.8275 (t60) cc_final: 0.8012 (t60) REVERT: D 133 GLN cc_start: 0.8124 (tp-100) cc_final: 0.7532 (tp-100) REVERT: D 291 LEU cc_start: 0.8290 (tp) cc_final: 0.7836 (tt) REVERT: D 309 HIS cc_start: 0.7584 (m-70) cc_final: 0.7167 (m-70) REVERT: D 385 GLN cc_start: 0.8576 (tt0) cc_final: 0.8103 (pp30) REVERT: D 425 MET cc_start: 0.8422 (tpt) cc_final: 0.8109 (mmm) REVERT: K 8 ASN cc_start: 0.7120 (p0) cc_final: 0.6432 (m-40) REVERT: K 105 MET cc_start: 0.5206 (mtm) cc_final: 0.4979 (mtm) REVERT: K 178 GLU cc_start: 0.8674 (mm-30) cc_final: 0.8446 (tp30) outliers start: 55 outliers final: 41 residues processed: 340 average time/residue: 0.2681 time to fit residues: 137.2928 Evaluate side-chains 326 residues out of total 1757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 283 time to evaluate : 1.783 ------------------------------------------------------------------------------- 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 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 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 177 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 140 SER 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 257 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 318 VAL Chi-restraints excluded: chain D residue 432 TYR Chi-restraints excluded: chain K residue 162 VAL Chi-restraints excluded: chain K residue 177 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 167 optimal weight: 0.4980 chunk 83 optimal weight: 0.9980 chunk 157 optimal weight: 7.9990 chunk 21 optimal weight: 0.0000 chunk 125 optimal weight: 3.9990 chunk 22 optimal weight: 2.9990 chunk 146 optimal weight: 1.9990 chunk 200 optimal weight: 2.9990 chunk 8 optimal weight: 10.0000 chunk 190 optimal weight: 0.9990 chunk 45 optimal weight: 0.7980 overall best weight: 0.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 128 GLN ** C 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 128 GLN D 247 GLN D 336 GLN ** D 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 58 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.159120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.132500 restraints weight = 21462.348| |-----------------------------------------------------------------------------| r_work (start): 0.3647 rms_B_bonded: 2.27 r_work: 0.3520 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3376 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3376 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.6821 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= 0.112 Angle : 0.606 10.944 22423 Z= 0.305 Chirality : 0.044 0.155 2457 Planarity : 0.004 0.061 2919 Dihedral : 11.001 178.271 2282 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 2.68 % Allowed : 23.79 % Favored : 73.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.39 (0.19), residues: 2035 helix: -0.44 (0.18), residues: 806 sheet: -0.74 (0.29), residues: 346 loop : -1.35 (0.21), residues: 883 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 346 HIS 0.005 0.001 HIS B 309 PHE 0.017 0.001 PHE A 255 TYR 0.012 0.001 TYR D 36 ARG 0.005 0.000 ARG D 164 Details of bonding type rmsd hydrogen bonds : bond 0.03015 ( 536) hydrogen bonds : angle 4.60554 ( 1605) covalent geometry : bond 0.00266 (16529) covalent geometry : angle 0.60633 (22423) Misc. bond : bond 0.00149 ( 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 337 residues out of total 1757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 290 time to evaluate : 1.746 Fit side-chains revert: symmetry clash REVERT: A 214 ARG cc_start: 0.8335 (ptt180) cc_final: 0.8055 (ptt90) REVERT: A 339 ARG cc_start: 0.7947 (mmp80) cc_final: 0.7555 (mmp80) REVERT: A 417 GLU cc_start: 0.8189 (tt0) cc_final: 0.7944 (tt0) REVERT: B 83 PHE cc_start: 0.7800 (m-80) cc_final: 0.7494 (m-80) REVERT: B 119 LEU cc_start: 0.8980 (tp) cc_final: 0.8656 (mt) REVERT: B 149 MET cc_start: 0.8564 (ttt) cc_final: 0.8229 (ttp) REVERT: B 235 MET cc_start: 0.8479 (mtt) cc_final: 0.8228 (mtt) REVERT: B 283 TYR cc_start: 0.7024 (m-10) cc_final: 0.6719 (t80) REVERT: B 291 LEU cc_start: 0.7455 (OUTLIER) cc_final: 0.6642 (mp) REVERT: B 422 GLU cc_start: 0.8137 (tp30) cc_final: 0.7769 (tt0) REVERT: B 425 MET cc_start: 0.7493 (tmm) cc_final: 0.7263 (tmm) REVERT: C 24 TYR cc_start: 0.8941 (m-10) cc_final: 0.8580 (m-10) REVERT: C 123 ARG cc_start: 0.8450 (ptm160) cc_final: 0.8158 (ttm-80) REVERT: C 160 ASP cc_start: 0.8079 (t70) cc_final: 0.7338 (m-30) REVERT: C 339 ARG cc_start: 0.7838 (OUTLIER) cc_final: 0.7117 (ttm110) REVERT: C 357 TYR cc_start: 0.8523 (m-80) cc_final: 0.8298 (m-80) REVERT: C 390 ARG cc_start: 0.8467 (mtm-85) cc_final: 0.8234 (mtm110) REVERT: C 391 LEU cc_start: 0.8799 (tp) cc_final: 0.8571 (tp) REVERT: D 103 TRP cc_start: 0.8420 (t60) cc_final: 0.8080 (t60) REVERT: D 133 GLN cc_start: 0.8219 (tp-100) cc_final: 0.7687 (tp-100) REVERT: D 291 LEU cc_start: 0.8294 (tp) cc_final: 0.7897 (tt) REVERT: D 309 HIS cc_start: 0.7664 (m-70) cc_final: 0.7259 (m-70) REVERT: D 338 LYS cc_start: 0.9062 (mmtt) cc_final: 0.8828 (mmtt) REVERT: D 385 GLN cc_start: 0.8425 (tt0) cc_final: 0.8031 (pp30) REVERT: D 425 MET cc_start: 0.8458 (tpt) cc_final: 0.8212 (mmm) REVERT: K 8 ASN cc_start: 0.7122 (p0) cc_final: 0.6466 (m-40) REVERT: K 28 LYS cc_start: 0.8580 (mmmt) cc_final: 0.8348 (ttmm) REVERT: K 157 GLU cc_start: 0.7662 (pm20) cc_final: 0.7256 (pt0) REVERT: K 178 GLU cc_start: 0.8750 (mm-30) cc_final: 0.8549 (tp30) REVERT: K 264 VAL cc_start: 0.8555 (t) cc_final: 0.8272 (t) outliers start: 47 outliers final: 35 residues processed: 328 average time/residue: 0.2757 time to fit residues: 136.2116 Evaluate side-chains 323 residues out of total 1757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 286 time to evaluate : 1.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 SER 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 B residue 37 HIS Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 177 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 430 SER Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain C residue 140 SER 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 257 THR 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 247 GLN Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 432 TYR Chi-restraints excluded: chain K residue 162 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 116 optimal weight: 5.9990 chunk 144 optimal weight: 6.9990 chunk 82 optimal weight: 0.9980 chunk 169 optimal weight: 0.8980 chunk 29 optimal weight: 0.9980 chunk 161 optimal weight: 2.9990 chunk 75 optimal weight: 0.8980 chunk 33 optimal weight: 0.9990 chunk 125 optimal weight: 1.9990 chunk 98 optimal weight: 3.9990 chunk 173 optimal weight: 1.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- 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 ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 309 HIS ** C 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 128 GLN C 249 ASN D 101 ASN D 247 GLN D 336 GLN ** D 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 58 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.157946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.131071 restraints weight = 21611.094| |-----------------------------------------------------------------------------| r_work (start): 0.3633 rms_B_bonded: 2.29 r_work: 0.3507 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3358 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3358 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.6922 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= 0.124 Angle : 0.629 11.891 22423 Z= 0.315 Chirality : 0.044 0.158 2457 Planarity : 0.004 0.064 2919 Dihedral : 10.971 177.049 2281 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 2.79 % Allowed : 23.68 % Favored : 73.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.30 (0.19), residues: 2035 helix: -0.34 (0.18), residues: 806 sheet: -0.73 (0.29), residues: 346 loop : -1.30 (0.21), residues: 883 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 346 HIS 0.003 0.001 HIS C 88 PHE 0.016 0.001 PHE A 255 TYR 0.014 0.001 TYR D 185 ARG 0.005 0.000 ARG D 164 Details of bonding type rmsd hydrogen bonds : bond 0.03092 ( 536) hydrogen bonds : angle 4.61411 ( 1605) covalent geometry : bond 0.00297 (16529) covalent geometry : angle 0.62869 (22423) Misc. bond : bond 0.00163 ( 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 340 residues out of total 1757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 291 time to evaluate : 1.776 Fit side-chains revert: symmetry clash REVERT: A 214 ARG cc_start: 0.8345 (ptt180) cc_final: 0.8052 (ptt90) REVERT: A 285 GLN cc_start: 0.4932 (mm-40) cc_final: 0.4223 (pm20) REVERT: A 300 ASN cc_start: 0.8677 (m-40) cc_final: 0.7131 (t0) REVERT: A 337 THR cc_start: 0.8201 (t) cc_final: 0.7760 (t) REVERT: A 339 ARG cc_start: 0.7886 (mmp80) cc_final: 0.7490 (mmp80) REVERT: A 420 GLU cc_start: 0.7393 (OUTLIER) cc_final: 0.7174 (mt-10) REVERT: B 83 PHE cc_start: 0.7805 (m-80) cc_final: 0.7547 (m-80) REVERT: B 119 LEU cc_start: 0.8999 (tp) cc_final: 0.8678 (mt) REVERT: B 149 MET cc_start: 0.8623 (ttt) cc_final: 0.8283 (ttp) REVERT: B 235 MET cc_start: 0.8481 (mtt) cc_final: 0.8270 (mtt) REVERT: B 283 TYR cc_start: 0.7100 (m-10) cc_final: 0.6727 (t80) REVERT: B 291 LEU cc_start: 0.7501 (OUTLIER) cc_final: 0.6822 (mp) REVERT: B 422 GLU cc_start: 0.8156 (tp30) cc_final: 0.7772 (tt0) REVERT: B 425 MET cc_start: 0.7559 (tmm) cc_final: 0.7340 (tmm) REVERT: C 24 TYR cc_start: 0.8939 (m-10) cc_final: 0.8572 (m-10) REVERT: C 123 ARG cc_start: 0.8475 (ptm160) cc_final: 0.8209 (ttm-80) REVERT: C 160 ASP cc_start: 0.8068 (t70) cc_final: 0.7324 (m-30) REVERT: C 301 GLN cc_start: 0.8861 (pm20) cc_final: 0.8453 (pm20) REVERT: C 339 ARG cc_start: 0.7684 (OUTLIER) cc_final: 0.7001 (ttm110) REVERT: C 357 TYR cc_start: 0.8589 (m-80) cc_final: 0.8362 (m-80) REVERT: C 390 ARG cc_start: 0.8485 (mtm-85) cc_final: 0.8247 (mtm110) REVERT: D 103 TRP cc_start: 0.8508 (t60) cc_final: 0.8127 (t60) REVERT: D 291 LEU cc_start: 0.8259 (tp) cc_final: 0.7870 (tt) REVERT: D 309 HIS cc_start: 0.7654 (m-70) cc_final: 0.7227 (m-70) REVERT: D 385 GLN cc_start: 0.8500 (tt0) cc_final: 0.8057 (pp30) REVERT: D 425 MET cc_start: 0.8487 (tpt) cc_final: 0.8214 (tpt) REVERT: K 28 LYS cc_start: 0.8613 (mmmt) cc_final: 0.8345 (ttmm) REVERT: K 157 GLU cc_start: 0.7697 (pm20) cc_final: 0.7352 (pt0) REVERT: K 264 VAL cc_start: 0.8578 (t) cc_final: 0.8263 (t) outliers start: 49 outliers final: 42 residues processed: 331 average time/residue: 0.2586 time to fit residues: 129.5584 Evaluate side-chains 329 residues out of total 1757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 284 time to evaluate : 1.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 SER 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 328 VAL 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 420 GLU Chi-restraints excluded: chain B residue 37 HIS Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 131 CYS 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 309 HIS 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 428 LEU Chi-restraints excluded: chain B residue 430 SER Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain C residue 140 SER 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 257 THR 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 247 GLN Chi-restraints excluded: chain D residue 269 MET Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 432 TYR Chi-restraints excluded: chain K residue 162 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 159 optimal weight: 0.4980 chunk 162 optimal weight: 5.9990 chunk 193 optimal weight: 9.9990 chunk 43 optimal weight: 5.9990 chunk 103 optimal weight: 0.7980 chunk 112 optimal weight: 5.9990 chunk 70 optimal weight: 3.9990 chunk 45 optimal weight: 0.0570 chunk 177 optimal weight: 0.9980 chunk 194 optimal weight: 0.8980 chunk 198 optimal weight: 3.9990 overall best weight: 0.6498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 GLN ** A 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 128 GLN ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 128 GLN D 247 GLN D 294 GLN D 336 GLN ** D 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 58 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.158159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.131335 restraints weight = 21500.573| |-----------------------------------------------------------------------------| r_work (start): 0.3611 rms_B_bonded: 2.27 r_work: 0.3487 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3340 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3340 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.6940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.134 16531 Z= 0.199 Angle : 1.029 59.199 22423 Z= 0.644 Chirality : 0.045 0.342 2457 Planarity : 0.005 0.107 2919 Dihedral : 11.033 177.042 2281 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.83 % Favored : 96.12 % Rotamer: Outliers : 2.68 % Allowed : 23.90 % Favored : 73.42 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.31 (0.19), residues: 2035 helix: -0.33 (0.18), residues: 806 sheet: -0.73 (0.29), residues: 346 loop : -1.33 (0.21), residues: 883 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 346 HIS 0.160 0.003 HIS B 309 PHE 0.017 0.001 PHE A 296 TYR 0.014 0.001 TYR B 36 ARG 0.006 0.000 ARG D 164 Details of bonding type rmsd hydrogen bonds : bond 0.03112 ( 536) hydrogen bonds : angle 4.61409 ( 1605) covalent geometry : bond 0.00384 (16529) covalent geometry : angle 1.02860 (22423) Misc. bond : bond 0.00144 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7906.80 seconds wall clock time: 137 minutes 59.32 seconds (8279.32 seconds total)