Starting phenix.real_space_refine on Wed Mar 4 00:37:02 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7p4i_13193/03_2026/7p4i_13193.cif Found real_map, /net/cci-nas-00/data/ceres_data/7p4i_13193/03_2026/7p4i_13193.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7p4i_13193/03_2026/7p4i_13193.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7p4i_13193/03_2026/7p4i_13193.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7p4i_13193/03_2026/7p4i_13193.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7p4i_13193/03_2026/7p4i_13193.map" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.023 sd= 0.073 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: 4 Type Number sf(0) Gaussians S 48 5.16 5 C 6198 2.51 5 N 1572 2.21 5 O 1692 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9510 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 3170 Number of conformers: 1 Conformer: "" Number of residues, atoms: 428, 3170 Classifications: {'peptide': 428} Link IDs: {'PTRANS': 15, 'TRANS': 412} Chain breaks: 1 Restraints were copied for chains: B, C Time building chain proxies: 2.42, per 1000 atoms: 0.25 Number of scatterers: 9510 At special positions: 0 Unit cell: (120.146, 119.294, 86.9142, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 48 16.00 O 1692 8.00 N 1572 7.00 C 6198 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.77 Conformation dependent library (CDL) restraints added in 372.6 milliseconds 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2328 Finding SS restraints... Secondary structure from input PDB file: 75 helices and 3 sheets defined 79.7% alpha, 3.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.23 Creating SS restraints... Processing helix chain 'A' and resid 37 through 41 removed outlier: 3.664A pdb=" N ARG A 40 " --> pdb=" O GLY A 37 " (cutoff:3.500A) Processing helix chain 'A' and resid 42 through 60 removed outlier: 3.578A pdb=" N LEU A 46 " --> pdb=" O GLN A 42 " (cutoff:3.500A) Processing helix chain 'A' and resid 68 through 74 removed outlier: 4.150A pdb=" N TYR A 74 " --> pdb=" O THR A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 89 removed outlier: 3.597A pdb=" N GLU A 80 " --> pdb=" O ALA A 76 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N ILE A 89 " --> pdb=" O MET A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 105 removed outlier: 3.617A pdb=" N LEU A 93 " --> pdb=" O ILE A 89 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N LEU A 98 " --> pdb=" O VAL A 94 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N VAL A 99 " --> pdb=" O VAL A 95 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N SER A 104 " --> pdb=" O SER A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 140 removed outlier: 4.054A pdb=" N ALA A 117 " --> pdb=" O LEU A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 169 No H-bonds generated for 'chain 'A' and resid 167 through 169' Processing helix chain 'A' and resid 170 through 179 removed outlier: 3.587A pdb=" N LEU A 174 " --> pdb=" O SER A 170 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N PHE A 179 " --> pdb=" O ALA A 175 " (cutoff:3.500A) Processing helix chain 'A' and resid 184 through 187 Processing helix chain 'A' and resid 223 through 240 removed outlier: 4.257A pdb=" N LEU A 228 " --> pdb=" O LEU A 224 " (cutoff:3.500A) removed outlier: 5.174A pdb=" N PHE A 229 " --> pdb=" O GLY A 225 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LYS A 238 " --> pdb=" O GLY A 234 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LEU A 240 " --> pdb=" O ALA A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 243 No H-bonds generated for 'chain 'A' and resid 241 through 243' Processing helix chain 'A' and resid 244 through 285 removed outlier: 3.996A pdb=" N ILE A 248 " --> pdb=" O GLY A 244 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N SER A 253 " --> pdb=" O ARG A 249 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ASN A 255 " --> pdb=" O PHE A 251 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N GLU A 256 " --> pdb=" O ASN A 252 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N VAL A 260 " --> pdb=" O GLU A 256 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N LEU A 261 " --> pdb=" O ALA A 257 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N VAL A 262 " --> pdb=" O THR A 258 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N SER A 263 " --> pdb=" O MET A 259 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N TRP A 264 " --> pdb=" O VAL A 260 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N TYR A 268 " --> pdb=" O TRP A 264 " (cutoff:3.500A) Proline residue: A 270 - end of helix removed outlier: 4.109A pdb=" N MET A 274 " --> pdb=" O PRO A 270 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N PHE A 275 " --> pdb=" O VAL A 271 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LEU A 276 " --> pdb=" O GLY A 272 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N GLY A 278 " --> pdb=" O MET A 274 " (cutoff:3.500A) removed outlier: 4.997A pdb=" N GLU A 283 " --> pdb=" O SER A 279 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N MET A 284 " --> pdb=" O LYS A 280 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LYS A 285 " --> pdb=" O ILE A 281 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 322 removed outlier: 5.087A pdb=" N LEU A 313 " --> pdb=" O GLY A 309 " (cutoff:3.500A) Proline residue: A 314 - end of helix removed outlier: 3.528A pdb=" N PHE A 320 " --> pdb=" O ILE A 316 " (cutoff:3.500A) Processing helix chain 'A' and resid 325 through 330 removed outlier: 3.869A pdb=" N LEU A 329 " --> pdb=" O PRO A 325 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LEU A 330 " --> pdb=" O PHE A 326 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 325 through 330' Processing helix chain 'A' and resid 332 through 343 removed outlier: 3.653A pdb=" N CYS A 343 " --> pdb=" O ALA A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 348 through 360 removed outlier: 3.876A pdb=" N MET A 352 " --> pdb=" O THR A 348 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N MET A 353 " --> pdb=" O LEU A 349 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N GLU A 358 " --> pdb=" O LYS A 354 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 369 Processing helix chain 'A' and resid 370 through 378 removed outlier: 4.082A pdb=" N THR A 376 " --> pdb=" O PRO A 372 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N VAL A 377 " --> pdb=" O ILE A 373 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 398 removed outlier: 3.655A pdb=" N ILE A 384 " --> pdb=" O ASP A 380 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 416 Processing helix chain 'A' and resid 417 through 419 No H-bonds generated for 'chain 'A' and resid 417 through 419' Processing helix chain 'A' and resid 427 through 439 removed outlier: 3.569A pdb=" N ILE A 438 " --> pdb=" O ILE A 434 " (cutoff:3.500A) Processing helix chain 'A' and resid 441 through 444 removed outlier: 4.369A pdb=" N ASP A 444 " --> pdb=" O PRO A 441 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 441 through 444' Processing helix chain 'A' and resid 445 through 450 removed outlier: 4.156A pdb=" N LEU A 449 " --> pdb=" O LEU A 445 " (cutoff:3.500A) Processing helix chain 'A' and resid 451 through 480 removed outlier: 3.948A pdb=" N VAL A 455 " --> pdb=" O VAL A 451 " (cutoff:3.500A) removed outlier: 4.821A pdb=" N ARG A 457 " --> pdb=" O TRP A 453 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N VAL A 461 " --> pdb=" O ARG A 457 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N VAL A 462 " --> pdb=" O THR A 458 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ASP A 467 " --> pdb=" O ASN A 463 " (cutoff:3.500A) Processing helix chain 'B' and resid 37 through 41 removed outlier: 3.663A pdb=" N ARG B 40 " --> pdb=" O GLY B 37 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 60 removed outlier: 3.578A pdb=" N LEU B 46 " --> pdb=" O GLN B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 68 through 74 removed outlier: 4.150A pdb=" N TYR B 74 " --> pdb=" O THR B 70 " (cutoff:3.500A) Processing helix chain 'B' and resid 76 through 89 removed outlier: 3.597A pdb=" N GLU B 80 " --> pdb=" O ALA B 76 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N ILE B 89 " --> pdb=" O MET B 85 " (cutoff:3.500A) Processing helix chain 'B' and resid 89 through 105 removed outlier: 3.617A pdb=" N LEU B 93 " --> pdb=" O ILE B 89 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N LEU B 98 " --> pdb=" O VAL B 94 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N VAL B 99 " --> pdb=" O VAL B 95 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N SER B 104 " --> pdb=" O SER B 100 " (cutoff:3.500A) Processing helix chain 'B' and resid 113 through 140 removed outlier: 4.053A pdb=" N ALA B 117 " --> pdb=" O LEU B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 169 No H-bonds generated for 'chain 'B' and resid 167 through 169' Processing helix chain 'B' and resid 170 through 179 removed outlier: 3.588A pdb=" N LEU B 174 " --> pdb=" O SER B 170 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N PHE B 179 " --> pdb=" O ALA B 175 " (cutoff:3.500A) Processing helix chain 'B' and resid 184 through 187 Processing helix chain 'B' and resid 223 through 240 removed outlier: 4.257A pdb=" N LEU B 228 " --> pdb=" O LEU B 224 " (cutoff:3.500A) removed outlier: 5.172A pdb=" N PHE B 229 " --> pdb=" O GLY B 225 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LYS B 238 " --> pdb=" O GLY B 234 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LEU B 240 " --> pdb=" O ALA B 236 " (cutoff:3.500A) Processing helix chain 'B' and resid 241 through 243 No H-bonds generated for 'chain 'B' and resid 241 through 243' Processing helix chain 'B' and resid 244 through 285 removed outlier: 3.996A pdb=" N ILE B 248 " --> pdb=" O GLY B 244 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N SER B 253 " --> pdb=" O ARG B 249 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ASN B 255 " --> pdb=" O PHE B 251 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N GLU B 256 " --> pdb=" O ASN B 252 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N VAL B 260 " --> pdb=" O GLU B 256 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N LEU B 261 " --> pdb=" O ALA B 257 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N VAL B 262 " --> pdb=" O THR B 258 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N SER B 263 " --> pdb=" O MET B 259 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N TRP B 264 " --> pdb=" O VAL B 260 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N TYR B 268 " --> pdb=" O TRP B 264 " (cutoff:3.500A) Proline residue: B 270 - end of helix removed outlier: 4.109A pdb=" N MET B 274 " --> pdb=" O PRO B 270 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N PHE B 275 " --> pdb=" O VAL B 271 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LEU B 276 " --> pdb=" O GLY B 272 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N GLY B 278 " --> pdb=" O MET B 274 " (cutoff:3.500A) removed outlier: 4.997A pdb=" N GLU B 283 " --> pdb=" O SER B 279 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N MET B 284 " --> pdb=" O LYS B 280 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LYS B 285 " --> pdb=" O ILE B 281 " (cutoff:3.500A) Processing helix chain 'B' and resid 287 through 322 removed outlier: 5.088A pdb=" N LEU B 313 " --> pdb=" O GLY B 309 " (cutoff:3.500A) Proline residue: B 314 - end of helix removed outlier: 3.528A pdb=" N PHE B 320 " --> pdb=" O ILE B 316 " (cutoff:3.500A) Processing helix chain 'B' and resid 325 through 330 removed outlier: 3.869A pdb=" N LEU B 329 " --> pdb=" O PRO B 325 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LEU B 330 " --> pdb=" O PHE B 326 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 325 through 330' Processing helix chain 'B' and resid 332 through 343 removed outlier: 3.653A pdb=" N CYS B 343 " --> pdb=" O ALA B 339 " (cutoff:3.500A) Processing helix chain 'B' and resid 348 through 360 removed outlier: 3.876A pdb=" N MET B 352 " --> pdb=" O THR B 348 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N MET B 353 " --> pdb=" O LEU B 349 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N GLU B 358 " --> pdb=" O LYS B 354 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 369 Processing helix chain 'B' and resid 370 through 378 removed outlier: 4.081A pdb=" N THR B 376 " --> pdb=" O PRO B 372 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N VAL B 377 " --> pdb=" O ILE B 373 " (cutoff:3.500A) Processing helix chain 'B' and resid 380 through 398 removed outlier: 3.655A pdb=" N ILE B 384 " --> pdb=" O ASP B 380 " (cutoff:3.500A) Processing helix chain 'B' and resid 402 through 416 Processing helix chain 'B' and resid 417 through 419 No H-bonds generated for 'chain 'B' and resid 417 through 419' Processing helix chain 'B' and resid 427 through 439 removed outlier: 3.570A pdb=" N ILE B 438 " --> pdb=" O ILE B 434 " (cutoff:3.500A) Processing helix chain 'B' and resid 441 through 444 removed outlier: 4.370A pdb=" N ASP B 444 " --> pdb=" O PRO B 441 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 441 through 444' Processing helix chain 'B' and resid 445 through 450 removed outlier: 4.157A pdb=" N LEU B 449 " --> pdb=" O LEU B 445 " (cutoff:3.500A) Processing helix chain 'B' and resid 451 through 480 removed outlier: 3.949A pdb=" N VAL B 455 " --> pdb=" O VAL B 451 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N ARG B 457 " --> pdb=" O TRP B 453 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N VAL B 461 " --> pdb=" O ARG B 457 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N VAL B 462 " --> pdb=" O THR B 458 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ASP B 467 " --> pdb=" O ASN B 463 " (cutoff:3.500A) Processing helix chain 'C' and resid 37 through 41 removed outlier: 3.665A pdb=" N ARG C 40 " --> pdb=" O GLY C 37 " (cutoff:3.500A) Processing helix chain 'C' and resid 42 through 60 removed outlier: 3.578A pdb=" N LEU C 46 " --> pdb=" O GLN C 42 " (cutoff:3.500A) Processing helix chain 'C' and resid 68 through 74 removed outlier: 4.150A pdb=" N TYR C 74 " --> pdb=" O THR C 70 " (cutoff:3.500A) Processing helix chain 'C' and resid 76 through 89 removed outlier: 3.597A pdb=" N GLU C 80 " --> pdb=" O ALA C 76 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N ILE C 89 " --> pdb=" O MET C 85 " (cutoff:3.500A) Processing helix chain 'C' and resid 89 through 105 removed outlier: 3.617A pdb=" N LEU C 93 " --> pdb=" O ILE C 89 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N LEU C 98 " --> pdb=" O VAL C 94 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N VAL C 99 " --> pdb=" O VAL C 95 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N SER C 104 " --> pdb=" O SER C 100 " (cutoff:3.500A) Processing helix chain 'C' and resid 113 through 140 removed outlier: 4.053A pdb=" N ALA C 117 " --> pdb=" O LEU C 113 " (cutoff:3.500A) Processing helix chain 'C' and resid 167 through 169 No H-bonds generated for 'chain 'C' and resid 167 through 169' Processing helix chain 'C' and resid 170 through 179 removed outlier: 3.587A pdb=" N LEU C 174 " --> pdb=" O SER C 170 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N PHE C 179 " --> pdb=" O ALA C 175 " (cutoff:3.500A) Processing helix chain 'C' and resid 184 through 187 Processing helix chain 'C' and resid 223 through 240 removed outlier: 4.258A pdb=" N LEU C 228 " --> pdb=" O LEU C 224 " (cutoff:3.500A) removed outlier: 5.173A pdb=" N PHE C 229 " --> pdb=" O GLY C 225 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LYS C 238 " --> pdb=" O GLY C 234 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LEU C 240 " --> pdb=" O ALA C 236 " (cutoff:3.500A) Processing helix chain 'C' and resid 241 through 243 No H-bonds generated for 'chain 'C' and resid 241 through 243' Processing helix chain 'C' and resid 244 through 285 removed outlier: 3.997A pdb=" N ILE C 248 " --> pdb=" O GLY C 244 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N SER C 253 " --> pdb=" O ARG C 249 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ASN C 255 " --> pdb=" O PHE C 251 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N GLU C 256 " --> pdb=" O ASN C 252 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N VAL C 260 " --> pdb=" O GLU C 256 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N LEU C 261 " --> pdb=" O ALA C 257 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N VAL C 262 " --> pdb=" O THR C 258 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N SER C 263 " --> pdb=" O MET C 259 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N TRP C 264 " --> pdb=" O VAL C 260 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N TYR C 268 " --> pdb=" O TRP C 264 " (cutoff:3.500A) Proline residue: C 270 - end of helix removed outlier: 4.108A pdb=" N MET C 274 " --> pdb=" O PRO C 270 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N PHE C 275 " --> pdb=" O VAL C 271 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LEU C 276 " --> pdb=" O GLY C 272 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N GLY C 278 " --> pdb=" O MET C 274 " (cutoff:3.500A) removed outlier: 4.996A pdb=" N GLU C 283 " --> pdb=" O SER C 279 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N MET C 284 " --> pdb=" O LYS C 280 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LYS C 285 " --> pdb=" O ILE C 281 " (cutoff:3.500A) Processing helix chain 'C' and resid 287 through 322 removed outlier: 5.087A pdb=" N LEU C 313 " --> pdb=" O GLY C 309 " (cutoff:3.500A) Proline residue: C 314 - end of helix removed outlier: 3.527A pdb=" N PHE C 320 " --> pdb=" O ILE C 316 " (cutoff:3.500A) Processing helix chain 'C' and resid 325 through 330 removed outlier: 3.870A pdb=" N LEU C 329 " --> pdb=" O PRO C 325 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LEU C 330 " --> pdb=" O PHE C 326 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 325 through 330' Processing helix chain 'C' and resid 332 through 343 removed outlier: 3.652A pdb=" N CYS C 343 " --> pdb=" O ALA C 339 " (cutoff:3.500A) Processing helix chain 'C' and resid 348 through 360 removed outlier: 3.876A pdb=" N MET C 352 " --> pdb=" O THR C 348 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N MET C 353 " --> pdb=" O LEU C 349 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N GLU C 358 " --> pdb=" O LYS C 354 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 369 Processing helix chain 'C' and resid 370 through 378 removed outlier: 4.081A pdb=" N THR C 376 " --> pdb=" O PRO C 372 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N VAL C 377 " --> pdb=" O ILE C 373 " (cutoff:3.500A) Processing helix chain 'C' and resid 380 through 398 removed outlier: 3.656A pdb=" N ILE C 384 " --> pdb=" O ASP C 380 " (cutoff:3.500A) Processing helix chain 'C' and resid 402 through 416 Processing helix chain 'C' and resid 417 through 419 No H-bonds generated for 'chain 'C' and resid 417 through 419' Processing helix chain 'C' and resid 427 through 439 removed outlier: 3.568A pdb=" N ILE C 438 " --> pdb=" O ILE C 434 " (cutoff:3.500A) Processing helix chain 'C' and resid 441 through 444 removed outlier: 4.369A pdb=" N ASP C 444 " --> pdb=" O PRO C 441 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 441 through 444' Processing helix chain 'C' and resid 445 through 450 removed outlier: 4.156A pdb=" N LEU C 449 " --> pdb=" O LEU C 445 " (cutoff:3.500A) Processing helix chain 'C' and resid 451 through 480 removed outlier: 3.948A pdb=" N VAL C 455 " --> pdb=" O VAL C 451 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N ARG C 457 " --> pdb=" O TRP C 453 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N VAL C 461 " --> pdb=" O ARG C 457 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N VAL C 462 " --> pdb=" O THR C 458 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ASP C 467 " --> pdb=" O ASN C 463 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 189 through 196 Processing sheet with id=AA2, first strand: chain 'B' and resid 189 through 196 Processing sheet with id=AA3, first strand: chain 'C' and resid 189 through 196 594 hydrogen bonds defined for protein. 1737 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.33 Time building geometry restraints manager: 1.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2999 1.34 - 1.46: 1178 1.46 - 1.57: 5414 1.57 - 1.69: 0 1.69 - 1.81: 81 Bond restraints: 9672 Sorted by residual: bond pdb=" C PHE B 77 " pdb=" N PRO B 78 " ideal model delta sigma weight residual 1.335 1.354 -0.019 1.28e-02 6.10e+03 2.26e+00 bond pdb=" C PHE C 77 " pdb=" N PRO C 78 " ideal model delta sigma weight residual 1.335 1.353 -0.019 1.28e-02 6.10e+03 2.12e+00 bond pdb=" C PHE A 77 " pdb=" N PRO A 78 " ideal model delta sigma weight residual 1.335 1.353 -0.019 1.28e-02 6.10e+03 2.10e+00 bond pdb=" C ALA A 334 " pdb=" N PRO A 335 " ideal model delta sigma weight residual 1.335 1.352 -0.016 1.36e-02 5.41e+03 1.46e+00 bond pdb=" C ALA C 334 " pdb=" N PRO C 335 " ideal model delta sigma weight residual 1.335 1.351 -0.016 1.36e-02 5.41e+03 1.39e+00 ... (remaining 9667 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.04: 12834 2.04 - 4.07: 249 4.07 - 6.11: 60 6.11 - 8.15: 9 8.15 - 10.18: 6 Bond angle restraints: 13158 Sorted by residual: angle pdb=" C ALA B 76 " pdb=" N PHE B 77 " pdb=" CA PHE B 77 " ideal model delta sigma weight residual 120.26 124.54 -4.28 1.34e+00 5.57e-01 1.02e+01 angle pdb=" C ALA A 76 " pdb=" N PHE A 77 " pdb=" CA PHE A 77 " ideal model delta sigma weight residual 120.26 124.53 -4.27 1.34e+00 5.57e-01 1.02e+01 angle pdb=" C ALA C 76 " pdb=" N PHE C 77 " pdb=" CA PHE C 77 " ideal model delta sigma weight residual 120.26 124.53 -4.27 1.34e+00 5.57e-01 1.02e+01 angle pdb=" CA LEU B 313 " pdb=" CB LEU B 313 " pdb=" CG LEU B 313 " ideal model delta sigma weight residual 116.30 126.48 -10.18 3.50e+00 8.16e-02 8.46e+00 angle pdb=" CA LEU C 313 " pdb=" CB LEU C 313 " pdb=" CG LEU C 313 " ideal model delta sigma weight residual 116.30 126.47 -10.17 3.50e+00 8.16e-02 8.44e+00 ... (remaining 13153 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.89: 4786 11.89 - 23.79: 625 23.79 - 35.68: 226 35.68 - 47.57: 57 47.57 - 59.46: 15 Dihedral angle restraints: 5709 sinusoidal: 2082 harmonic: 3627 Sorted by residual: dihedral pdb=" CA LEU B 62 " pdb=" C LEU B 62 " pdb=" N ARG B 63 " pdb=" CA ARG B 63 " ideal model delta harmonic sigma weight residual -180.00 -151.18 -28.82 0 5.00e+00 4.00e-02 3.32e+01 dihedral pdb=" CA LEU C 62 " pdb=" C LEU C 62 " pdb=" N ARG C 63 " pdb=" CA ARG C 63 " ideal model delta harmonic sigma weight residual -180.00 -151.19 -28.81 0 5.00e+00 4.00e-02 3.32e+01 dihedral pdb=" CA LEU A 62 " pdb=" C LEU A 62 " pdb=" N ARG A 63 " pdb=" CA ARG A 63 " ideal model delta harmonic sigma weight residual -180.00 -151.21 -28.79 0 5.00e+00 4.00e-02 3.32e+01 ... (remaining 5706 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 1018 0.032 - 0.064: 460 0.064 - 0.096: 137 0.096 - 0.128: 41 0.128 - 0.160: 3 Chirality restraints: 1659 Sorted by residual: chirality pdb=" CA LEU C 313 " pdb=" N LEU C 313 " pdb=" C LEU C 313 " pdb=" CB LEU C 313 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.37e-01 chirality pdb=" CA LEU A 313 " pdb=" N LEU A 313 " pdb=" C LEU A 313 " pdb=" CB LEU A 313 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.04e-01 chirality pdb=" CA LEU B 313 " pdb=" N LEU B 313 " pdb=" C LEU B 313 " pdb=" CB LEU B 313 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.90e-01 ... (remaining 1656 not shown) Planarity restraints: 1626 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA B 334 " -0.026 5.00e-02 4.00e+02 3.90e-02 2.44e+00 pdb=" N PRO B 335 " 0.067 5.00e-02 4.00e+02 pdb=" CA PRO B 335 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO B 335 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A 334 " -0.026 5.00e-02 4.00e+02 3.90e-02 2.43e+00 pdb=" N PRO A 335 " 0.067 5.00e-02 4.00e+02 pdb=" CA PRO A 335 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 335 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA C 334 " -0.026 5.00e-02 4.00e+02 3.89e-02 2.42e+00 pdb=" N PRO C 335 " 0.067 5.00e-02 4.00e+02 pdb=" CA PRO C 335 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO C 335 " -0.022 5.00e-02 4.00e+02 ... (remaining 1623 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.71: 364 2.71 - 3.26: 10712 3.26 - 3.81: 15044 3.81 - 4.35: 18140 4.35 - 4.90: 28741 Nonbonded interactions: 73001 Sorted by model distance: nonbonded pdb=" O VAL B 260 " pdb=" OG SER B 263 " model vdw 2.168 3.040 nonbonded pdb=" O VAL A 260 " pdb=" OG SER A 263 " model vdw 2.168 3.040 nonbonded pdb=" O VAL C 260 " pdb=" OG SER C 263 " model vdw 2.168 3.040 nonbonded pdb=" OG1 THR C 167 " pdb=" OH TYR C 195 " model vdw 2.232 3.040 nonbonded pdb=" OG1 THR A 167 " pdb=" OH TYR A 195 " model vdw 2.232 3.040 ... (remaining 72996 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.570 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.130 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 9.800 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 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:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9672 Z= 0.143 Angle : 0.765 10.183 13158 Z= 0.410 Chirality : 0.039 0.160 1659 Planarity : 0.004 0.039 1626 Dihedral : 13.104 59.464 3381 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 11.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.54 (0.24), residues: 1272 helix: 0.56 (0.19), residues: 780 sheet: -2.19 (0.48), residues: 48 loop : -1.74 (0.31), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 368 TYR 0.011 0.001 TYR A 191 PHE 0.007 0.001 PHE C 250 TRP 0.002 0.000 TRP B 267 HIS 0.004 0.001 HIS C 476 Details of bonding type rmsd covalent geometry : bond 0.00271 ( 9672) covalent geometry : angle 0.76478 (13158) hydrogen bonds : bond 0.16431 ( 594) hydrogen bonds : angle 6.67139 ( 1737) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 33 time to evaluate : 0.383 Fit side-chains REVERT: A 85 MET cc_start: 0.8983 (mtm) cc_final: 0.8667 (ptp) REVERT: A 266 MET cc_start: 0.9299 (mmm) cc_final: 0.8938 (mmm) REVERT: B 85 MET cc_start: 0.9152 (mtm) cc_final: 0.8852 (mtm) REVERT: C 221 MET cc_start: 0.8992 (ptp) cc_final: 0.8637 (ptp) outliers start: 0 outliers final: 0 residues processed: 33 average time/residue: 0.0780 time to fit residues: 4.3243 Evaluate side-chains 33 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 33 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 108 optimal weight: 5.9990 chunk 49 optimal weight: 0.5980 chunk 97 optimal weight: 7.9990 chunk 113 optimal weight: 50.0000 chunk 53 optimal weight: 20.0000 chunk 5 optimal weight: 9.9990 chunk 33 optimal weight: 10.0000 chunk 123 optimal weight: 0.7980 chunk 65 optimal weight: 4.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 6.9990 overall best weight: 3.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 475 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 475 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 475 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.031371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2857 r_free = 0.2857 target = 0.025681 restraints weight = 162975.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.026364 restraints weight = 87578.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.026837 restraints weight = 57249.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.027168 restraints weight = 42380.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.027389 restraints weight = 34440.110| |-----------------------------------------------------------------------------| r_work (final): 0.2932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8527 moved from start: 0.1006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 9672 Z= 0.120 Angle : 0.631 9.673 13158 Z= 0.315 Chirality : 0.040 0.147 1659 Planarity : 0.004 0.037 1626 Dihedral : 4.562 29.037 1344 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 0.29 % Allowed : 8.36 % Favored : 91.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.17 (0.25), residues: 1272 helix: 0.86 (0.19), residues: 804 sheet: -1.77 (0.58), residues: 48 loop : -1.79 (0.32), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 322 TYR 0.011 0.002 TYR B 191 PHE 0.009 0.001 PHE A 250 TRP 0.003 0.001 TRP B 267 HIS 0.003 0.001 HIS A 476 Details of bonding type rmsd covalent geometry : bond 0.00249 ( 9672) covalent geometry : angle 0.63097 (13158) hydrogen bonds : bond 0.03755 ( 594) hydrogen bonds : angle 4.60580 ( 1737) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 33 time to evaluate : 0.369 Fit side-chains REVERT: A 85 MET cc_start: 0.8913 (mtm) cc_final: 0.8576 (ptp) REVERT: A 266 MET cc_start: 0.9077 (mmm) cc_final: 0.8769 (mmm) REVERT: B 85 MET cc_start: 0.8967 (mtm) cc_final: 0.8761 (mtm) REVERT: C 221 MET cc_start: 0.9168 (ptp) cc_final: 0.8784 (ptp) REVERT: C 266 MET cc_start: 0.9080 (mmm) cc_final: 0.8778 (mmm) outliers start: 3 outliers final: 0 residues processed: 36 average time/residue: 0.0777 time to fit residues: 4.6639 Evaluate side-chains 33 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 33 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 44 optimal weight: 9.9990 chunk 0 optimal weight: 50.0000 chunk 60 optimal weight: 0.9990 chunk 72 optimal weight: 30.0000 chunk 116 optimal weight: 0.0670 chunk 125 optimal weight: 9.9990 chunk 23 optimal weight: 20.0000 chunk 31 optimal weight: 0.8980 chunk 98 optimal weight: 10.0000 chunk 94 optimal weight: 30.0000 chunk 118 optimal weight: 7.9990 overall best weight: 3.9924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 397 ASN ** A 475 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 397 ASN ** B 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 475 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 397 ASN ** C 475 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.031174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2851 r_free = 0.2851 target = 0.025550 restraints weight = 163443.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.026232 restraints weight = 87461.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.026707 restraints weight = 56986.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.027029 restraints weight = 42195.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.027250 restraints weight = 34306.176| |-----------------------------------------------------------------------------| r_work (final): 0.2916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8547 moved from start: 0.1440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9672 Z= 0.119 Angle : 0.647 8.674 13158 Z= 0.321 Chirality : 0.041 0.149 1659 Planarity : 0.003 0.033 1626 Dihedral : 4.449 28.277 1344 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 0.00 % Allowed : 6.49 % Favored : 93.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.01 (0.24), residues: 1272 helix: 0.94 (0.19), residues: 801 sheet: -1.88 (0.51), residues: 48 loop : -1.54 (0.33), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 322 TYR 0.009 0.001 TYR C 74 PHE 0.019 0.001 PHE A 250 TRP 0.003 0.000 TRP B 453 HIS 0.003 0.001 HIS B 475 Details of bonding type rmsd covalent geometry : bond 0.00255 ( 9672) covalent geometry : angle 0.64704 (13158) hydrogen bonds : bond 0.03438 ( 594) hydrogen bonds : angle 4.24155 ( 1737) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 33 time to evaluate : 0.373 Fit side-chains REVERT: A 85 MET cc_start: 0.8934 (mtm) cc_final: 0.8617 (ptp) REVERT: A 379 MET cc_start: 0.8755 (ptp) cc_final: 0.8316 (mpp) REVERT: B 85 MET cc_start: 0.8974 (mtm) cc_final: 0.8565 (ptp) REVERT: B 259 MET cc_start: 0.8811 (tmm) cc_final: 0.8609 (tmm) REVERT: B 353 MET cc_start: 0.9139 (ptp) cc_final: 0.8905 (ptp) REVERT: C 85 MET cc_start: 0.9027 (mtm) cc_final: 0.8668 (ptp) REVERT: C 88 MET cc_start: 0.8807 (mmt) cc_final: 0.8517 (tpp) REVERT: C 221 MET cc_start: 0.9167 (ptp) cc_final: 0.8791 (ptp) REVERT: C 379 MET cc_start: 0.8892 (ptp) cc_final: 0.8323 (mpp) outliers start: 0 outliers final: 0 residues processed: 33 average time/residue: 0.0785 time to fit residues: 4.3296 Evaluate side-chains 33 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 33 time to evaluate : 0.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 82 optimal weight: 8.9990 chunk 102 optimal weight: 30.0000 chunk 67 optimal weight: 50.0000 chunk 6 optimal weight: 6.9990 chunk 50 optimal weight: 1.9990 chunk 80 optimal weight: 50.0000 chunk 17 optimal weight: 7.9990 chunk 13 optimal weight: 10.0000 chunk 39 optimal weight: 0.3980 chunk 91 optimal weight: 20.0000 chunk 84 optimal weight: 50.0000 overall best weight: 5.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 397 ASN ** A 475 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 397 ASN ** B 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 475 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 397 ASN ** C 475 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.035903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.026671 restraints weight = 129999.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.027262 restraints weight = 89481.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.027708 restraints weight = 69016.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.027976 restraints weight = 57398.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.028205 restraints weight = 50857.346| |-----------------------------------------------------------------------------| r_work (final): 0.2880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8603 moved from start: 0.1811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9672 Z= 0.135 Angle : 0.630 8.316 13158 Z= 0.316 Chirality : 0.040 0.147 1659 Planarity : 0.003 0.030 1626 Dihedral : 4.461 27.057 1344 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 0.00 % Allowed : 6.88 % Favored : 93.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.22 (0.25), residues: 1272 helix: 1.11 (0.19), residues: 804 sheet: -2.14 (0.49), residues: 48 loop : -1.42 (0.33), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 322 TYR 0.009 0.001 TYR C 74 PHE 0.018 0.001 PHE A 250 TRP 0.004 0.001 TRP B 267 HIS 0.003 0.001 HIS B 475 Details of bonding type rmsd covalent geometry : bond 0.00302 ( 9672) covalent geometry : angle 0.62953 (13158) hydrogen bonds : bond 0.03319 ( 594) hydrogen bonds : angle 4.14771 ( 1737) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 33 time to evaluate : 0.373 Fit side-chains REVERT: A 85 MET cc_start: 0.8885 (mtm) cc_final: 0.8619 (ptp) REVERT: A 379 MET cc_start: 0.8848 (ptp) cc_final: 0.8393 (mpp) REVERT: B 81 MET cc_start: 0.9635 (mmt) cc_final: 0.9382 (mmm) REVERT: B 85 MET cc_start: 0.8837 (mtm) cc_final: 0.8605 (ptp) REVERT: B 259 MET cc_start: 0.8777 (tmm) cc_final: 0.8559 (tmm) REVERT: B 266 MET cc_start: 0.9079 (mmm) cc_final: 0.8854 (mmm) REVERT: C 88 MET cc_start: 0.8768 (tpp) cc_final: 0.8546 (mmt) REVERT: C 266 MET cc_start: 0.9104 (mmm) cc_final: 0.8894 (mmm) REVERT: C 379 MET cc_start: 0.8859 (ptp) cc_final: 0.8316 (mpp) outliers start: 0 outliers final: 0 residues processed: 33 average time/residue: 0.0809 time to fit residues: 4.4407 Evaluate side-chains 33 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 33 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 116 optimal weight: 30.0000 chunk 83 optimal weight: 30.0000 chunk 95 optimal weight: 30.0000 chunk 80 optimal weight: 30.0000 chunk 47 optimal weight: 0.0050 chunk 76 optimal weight: 6.9990 chunk 104 optimal weight: 10.0000 chunk 65 optimal weight: 0.7980 chunk 96 optimal weight: 0.9990 chunk 45 optimal weight: 5.9990 chunk 125 optimal weight: 20.0000 overall best weight: 2.9600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 397 ASN ** A 475 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 397 ASN ** B 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 475 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 397 ASN ** C 475 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.035772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.026810 restraints weight = 129409.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.027407 restraints weight = 88323.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.027847 restraints weight = 67794.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.028144 restraints weight = 56205.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.028282 restraints weight = 49406.658| |-----------------------------------------------------------------------------| r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8592 moved from start: 0.1945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 9672 Z= 0.111 Angle : 0.660 9.063 13158 Z= 0.319 Chirality : 0.040 0.148 1659 Planarity : 0.003 0.028 1626 Dihedral : 4.451 28.931 1344 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.31 (0.25), residues: 1272 helix: 1.14 (0.19), residues: 813 sheet: -1.99 (0.50), residues: 48 loop : -1.35 (0.34), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 327 TYR 0.009 0.001 TYR B 191 PHE 0.019 0.001 PHE A 250 TRP 0.002 0.000 TRP B 453 HIS 0.002 0.001 HIS C 475 Details of bonding type rmsd covalent geometry : bond 0.00237 ( 9672) covalent geometry : angle 0.65968 (13158) hydrogen bonds : bond 0.03114 ( 594) hydrogen bonds : angle 4.05143 ( 1737) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 33 time to evaluate : 0.348 Fit side-chains REVERT: A 81 MET cc_start: 0.9661 (mmt) cc_final: 0.9380 (mmm) REVERT: A 379 MET cc_start: 0.8846 (ptp) cc_final: 0.8308 (mpp) REVERT: B 81 MET cc_start: 0.9606 (mmt) cc_final: 0.9335 (mmm) REVERT: B 85 MET cc_start: 0.8800 (mtm) cc_final: 0.8595 (ptp) REVERT: B 274 MET cc_start: 0.9461 (ppp) cc_final: 0.9251 (ppp) REVERT: C 266 MET cc_start: 0.9027 (mmm) cc_final: 0.8823 (mmm) REVERT: C 274 MET cc_start: 0.9484 (ppp) cc_final: 0.9273 (ppp) REVERT: C 379 MET cc_start: 0.8877 (ptp) cc_final: 0.8296 (mpp) outliers start: 0 outliers final: 0 residues processed: 33 average time/residue: 0.0778 time to fit residues: 4.2969 Evaluate side-chains 33 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 33 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 96 optimal weight: 6.9990 chunk 27 optimal weight: 8.9990 chunk 73 optimal weight: 8.9990 chunk 83 optimal weight: 9.9990 chunk 28 optimal weight: 20.0000 chunk 59 optimal weight: 7.9990 chunk 53 optimal weight: 0.6980 chunk 47 optimal weight: 3.9990 chunk 120 optimal weight: 0.9990 chunk 39 optimal weight: 30.0000 chunk 69 optimal weight: 6.9990 overall best weight: 3.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 397 ASN ** A 475 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 397 ASN ** B 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 475 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 397 ASN ** C 475 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.035716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.026756 restraints weight = 128865.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.027340 restraints weight = 88432.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.027760 restraints weight = 68091.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.028064 restraints weight = 56780.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.028259 restraints weight = 49973.076| |-----------------------------------------------------------------------------| r_work (final): 0.2888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8599 moved from start: 0.2091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9672 Z= 0.117 Angle : 0.656 8.698 13158 Z= 0.319 Chirality : 0.040 0.149 1659 Planarity : 0.003 0.025 1626 Dihedral : 4.437 28.504 1344 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.44 (0.25), residues: 1272 helix: 1.23 (0.19), residues: 810 sheet: -2.70 (0.49), residues: 60 loop : -1.09 (0.35), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 327 TYR 0.008 0.001 TYR C 74 PHE 0.017 0.001 PHE A 250 TRP 0.002 0.000 TRP A 264 HIS 0.002 0.001 HIS B 475 Details of bonding type rmsd covalent geometry : bond 0.00260 ( 9672) covalent geometry : angle 0.65582 (13158) hydrogen bonds : bond 0.03076 ( 594) hydrogen bonds : angle 4.02121 ( 1737) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 35 time to evaluate : 0.337 Fit side-chains REVERT: A 274 MET cc_start: 0.9426 (ppp) cc_final: 0.9218 (ppp) REVERT: A 379 MET cc_start: 0.8887 (ptp) cc_final: 0.8332 (mpp) REVERT: B 81 MET cc_start: 0.9639 (mmt) cc_final: 0.9357 (mmm) REVERT: B 85 MET cc_start: 0.8817 (mtm) cc_final: 0.8606 (ptp) REVERT: C 353 MET cc_start: 0.8796 (ptp) cc_final: 0.8461 (pmm) REVERT: C 379 MET cc_start: 0.8870 (ptp) cc_final: 0.8321 (mpp) outliers start: 0 outliers final: 0 residues processed: 35 average time/residue: 0.0811 time to fit residues: 4.6495 Evaluate side-chains 33 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 33 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 93 optimal weight: 7.9990 chunk 107 optimal weight: 0.8980 chunk 28 optimal weight: 30.0000 chunk 37 optimal weight: 0.0570 chunk 122 optimal weight: 40.0000 chunk 52 optimal weight: 30.0000 chunk 99 optimal weight: 0.0980 chunk 53 optimal weight: 9.9990 chunk 75 optimal weight: 6.9990 chunk 69 optimal weight: 8.9990 chunk 86 optimal weight: 30.0000 overall best weight: 3.2102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 209 HIS A 397 ASN ** A 475 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 209 HIS B 397 ASN ** B 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 475 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 209 HIS C 397 ASN ** C 475 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.030876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2859 r_free = 0.2859 target = 0.025780 restraints weight = 162419.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2886 r_free = 0.2886 target = 0.026300 restraints weight = 99201.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.026667 restraints weight = 69539.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.026935 restraints weight = 54254.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.027084 restraints weight = 45409.075| |-----------------------------------------------------------------------------| r_work (final): 0.2906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8568 moved from start: 0.2257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 9672 Z= 0.112 Angle : 0.656 8.733 13158 Z= 0.318 Chirality : 0.040 0.162 1659 Planarity : 0.003 0.047 1626 Dihedral : 4.449 29.187 1344 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.52 (0.25), residues: 1272 helix: 1.26 (0.19), residues: 810 sheet: -2.70 (0.50), residues: 60 loop : -0.97 (0.35), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 322 TYR 0.008 0.001 TYR C 74 PHE 0.018 0.001 PHE A 250 TRP 0.002 0.000 TRP A 264 HIS 0.001 0.001 HIS C 476 Details of bonding type rmsd covalent geometry : bond 0.00247 ( 9672) covalent geometry : angle 0.65555 (13158) hydrogen bonds : bond 0.03029 ( 594) hydrogen bonds : angle 3.95033 ( 1737) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 34 time to evaluate : 0.373 Fit side-chains REVERT: A 81 MET cc_start: 0.9696 (mmt) cc_final: 0.9438 (mmm) REVERT: A 353 MET cc_start: 0.9029 (ptp) cc_final: 0.8729 (pmm) REVERT: A 379 MET cc_start: 0.8781 (ptp) cc_final: 0.8277 (mpp) REVERT: B 81 MET cc_start: 0.9700 (mmt) cc_final: 0.9416 (mmm) REVERT: B 85 MET cc_start: 0.8920 (mtm) cc_final: 0.8641 (ptp) REVERT: B 259 MET cc_start: 0.8718 (tmm) cc_final: 0.8475 (tmm) REVERT: B 274 MET cc_start: 0.9362 (ppp) cc_final: 0.9098 (ppp) REVERT: B 353 MET cc_start: 0.9027 (ptp) cc_final: 0.8313 (pmm) REVERT: C 379 MET cc_start: 0.8799 (ptp) cc_final: 0.8288 (mpp) outliers start: 0 outliers final: 0 residues processed: 34 average time/residue: 0.0760 time to fit residues: 4.3379 Evaluate side-chains 33 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 33 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 19 optimal weight: 4.9990 chunk 58 optimal weight: 20.0000 chunk 41 optimal weight: 10.0000 chunk 72 optimal weight: 7.9990 chunk 64 optimal weight: 6.9990 chunk 51 optimal weight: 6.9990 chunk 115 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 90 optimal weight: 0.9980 chunk 18 optimal weight: 0.8980 chunk 59 optimal weight: 7.9990 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 475 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 475 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 475 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.035712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.026807 restraints weight = 128646.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.027373 restraints weight = 89136.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.027769 restraints weight = 68801.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.028074 restraints weight = 57629.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.028239 restraints weight = 50730.451| |-----------------------------------------------------------------------------| r_work (final): 0.2895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8584 moved from start: 0.2342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 9672 Z= 0.109 Angle : 0.656 9.133 13158 Z= 0.319 Chirality : 0.040 0.160 1659 Planarity : 0.003 0.028 1626 Dihedral : 4.395 28.790 1344 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.49 (0.25), residues: 1272 helix: 1.22 (0.19), residues: 813 sheet: -2.65 (0.50), residues: 60 loop : -0.96 (0.35), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 322 TYR 0.008 0.001 TYR C 74 PHE 0.018 0.001 PHE A 250 TRP 0.002 0.000 TRP A 264 HIS 0.002 0.001 HIS B 308 Details of bonding type rmsd covalent geometry : bond 0.00233 ( 9672) covalent geometry : angle 0.65639 (13158) hydrogen bonds : bond 0.02976 ( 594) hydrogen bonds : angle 3.96458 ( 1737) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 33 time to evaluate : 0.375 Fit side-chains REVERT: A 274 MET cc_start: 0.9413 (ppp) cc_final: 0.9206 (ppp) REVERT: A 353 MET cc_start: 0.9001 (ptp) cc_final: 0.8722 (pmm) REVERT: A 379 MET cc_start: 0.8881 (ptp) cc_final: 0.8349 (mpp) REVERT: B 81 MET cc_start: 0.9642 (mmt) cc_final: 0.9344 (mmm) REVERT: B 259 MET cc_start: 0.8630 (tmm) cc_final: 0.8394 (tmm) REVERT: B 353 MET cc_start: 0.8981 (ptp) cc_final: 0.8263 (pmm) REVERT: B 379 MET cc_start: 0.8971 (ptp) cc_final: 0.8490 (mpp) REVERT: C 221 MET cc_start: 0.8898 (ptp) cc_final: 0.8568 (ptp) REVERT: C 266 MET cc_start: 0.9125 (mmt) cc_final: 0.8801 (mmm) REVERT: C 353 MET cc_start: 0.8811 (ptp) cc_final: 0.8207 (pmm) REVERT: C 379 MET cc_start: 0.8901 (ptp) cc_final: 0.8369 (mpp) outliers start: 0 outliers final: 0 residues processed: 33 average time/residue: 0.0719 time to fit residues: 3.9161 Evaluate side-chains 33 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 33 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 20 optimal weight: 1.9990 chunk 106 optimal weight: 2.9990 chunk 64 optimal weight: 0.8980 chunk 124 optimal weight: 8.9990 chunk 118 optimal weight: 4.9990 chunk 4 optimal weight: 7.9990 chunk 6 optimal weight: 7.9990 chunk 62 optimal weight: 8.9990 chunk 7 optimal weight: 30.0000 chunk 44 optimal weight: 6.9990 chunk 73 optimal weight: 6.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 475 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 475 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 475 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.030843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2859 r_free = 0.2859 target = 0.025756 restraints weight = 162188.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2883 r_free = 0.2883 target = 0.026268 restraints weight = 98965.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.026641 restraints weight = 69812.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.026867 restraints weight = 54848.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.027062 restraints weight = 46848.977| |-----------------------------------------------------------------------------| r_work (final): 0.2903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8578 moved from start: 0.2462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9672 Z= 0.115 Angle : 0.674 9.971 13158 Z= 0.325 Chirality : 0.041 0.156 1659 Planarity : 0.003 0.024 1626 Dihedral : 4.415 29.115 1344 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.51 (0.25), residues: 1272 helix: 1.23 (0.19), residues: 813 sheet: -2.64 (0.51), residues: 60 loop : -0.95 (0.35), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 322 TYR 0.012 0.001 TYR C 74 PHE 0.017 0.001 PHE A 250 TRP 0.003 0.000 TRP C 267 HIS 0.002 0.001 HIS B 475 Details of bonding type rmsd covalent geometry : bond 0.00254 ( 9672) covalent geometry : angle 0.67360 (13158) hydrogen bonds : bond 0.03031 ( 594) hydrogen bonds : angle 3.97576 ( 1737) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 33 time to evaluate : 0.316 Fit side-chains REVERT: B 259 MET cc_start: 0.8769 (tmm) cc_final: 0.8484 (tmm) REVERT: B 353 MET cc_start: 0.9066 (ptp) cc_final: 0.8175 (pmm) REVERT: B 379 MET cc_start: 0.8853 (ptp) cc_final: 0.8395 (mpp) REVERT: C 259 MET cc_start: 0.8760 (tmm) cc_final: 0.8543 (tmm) REVERT: C 353 MET cc_start: 0.8869 (ptp) cc_final: 0.8142 (pmm) outliers start: 0 outliers final: 0 residues processed: 33 average time/residue: 0.0757 time to fit residues: 4.1403 Evaluate side-chains 33 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 33 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 110 optimal weight: 8.9990 chunk 38 optimal weight: 7.9990 chunk 14 optimal weight: 30.0000 chunk 93 optimal weight: 6.9990 chunk 78 optimal weight: 0.4980 chunk 94 optimal weight: 8.9990 chunk 63 optimal weight: 4.9990 chunk 68 optimal weight: 4.9990 chunk 80 optimal weight: 9.9990 chunk 96 optimal weight: 7.9990 chunk 59 optimal weight: 2.9990 overall best weight: 4.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 475 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 475 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 475 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.035655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2896 r_free = 0.2896 target = 0.026720 restraints weight = 128091.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.027266 restraints weight = 88800.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.027682 restraints weight = 68971.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.027969 restraints weight = 57551.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.028170 restraints weight = 50861.571| |-----------------------------------------------------------------------------| r_work (final): 0.2886 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8609 moved from start: 0.2620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9672 Z= 0.120 Angle : 0.682 9.811 13158 Z= 0.330 Chirality : 0.041 0.155 1659 Planarity : 0.003 0.022 1626 Dihedral : 4.464 29.451 1344 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 0.00 % Allowed : 0.49 % Favored : 99.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.56 (0.25), residues: 1272 helix: 1.23 (0.19), residues: 813 sheet: -2.69 (0.50), residues: 60 loop : -0.82 (0.36), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 322 TYR 0.008 0.001 TYR C 74 PHE 0.016 0.001 PHE A 250 TRP 0.005 0.001 TRP C 267 HIS 0.003 0.001 HIS B 475 Details of bonding type rmsd covalent geometry : bond 0.00267 ( 9672) covalent geometry : angle 0.68180 (13158) hydrogen bonds : bond 0.03082 ( 594) hydrogen bonds : angle 3.99128 ( 1737) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 33 time to evaluate : 0.272 Fit side-chains REVERT: A 274 MET cc_start: 0.9436 (ppp) cc_final: 0.9208 (ppp) REVERT: A 353 MET cc_start: 0.8800 (ptp) cc_final: 0.8309 (pmm) REVERT: A 379 MET cc_start: 0.8980 (ptp) cc_final: 0.8411 (mpp) REVERT: B 259 MET cc_start: 0.8701 (tmm) cc_final: 0.8436 (tmm) REVERT: B 379 MET cc_start: 0.8930 (ptp) cc_final: 0.8342 (mpp) REVERT: C 353 MET cc_start: 0.8776 (ptp) cc_final: 0.8136 (pmm) REVERT: C 379 MET cc_start: 0.8990 (ptp) cc_final: 0.8410 (mpp) outliers start: 0 outliers final: 0 residues processed: 33 average time/residue: 0.0737 time to fit residues: 4.0990 Evaluate side-chains 33 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 33 time to evaluate : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 122 optimal weight: 50.0000 chunk 31 optimal weight: 0.0980 chunk 119 optimal weight: 5.9990 chunk 104 optimal weight: 0.8980 chunk 68 optimal weight: 5.9990 chunk 71 optimal weight: 2.9990 chunk 32 optimal weight: 6.9990 chunk 87 optimal weight: 6.9990 chunk 3 optimal weight: 6.9990 chunk 59 optimal weight: 6.9990 chunk 111 optimal weight: 4.9990 overall best weight: 2.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 475 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 475 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 475 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.030732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2855 r_free = 0.2855 target = 0.025687 restraints weight = 162311.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2879 r_free = 0.2879 target = 0.026207 restraints weight = 99614.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2896 r_free = 0.2896 target = 0.026581 restraints weight = 70699.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.026838 restraints weight = 55282.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.027009 restraints weight = 46533.981| |-----------------------------------------------------------------------------| r_work (final): 0.2899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8579 moved from start: 0.2698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 9672 Z= 0.111 Angle : 0.677 10.040 13158 Z= 0.325 Chirality : 0.041 0.158 1659 Planarity : 0.003 0.023 1626 Dihedral : 4.439 29.543 1344 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 0.00 % Allowed : 0.29 % Favored : 99.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.63 (0.25), residues: 1272 helix: 1.27 (0.19), residues: 813 sheet: -2.65 (0.51), residues: 60 loop : -0.77 (0.36), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 322 TYR 0.010 0.001 TYR A 74 PHE 0.017 0.001 PHE A 250 TRP 0.003 0.000 TRP C 267 HIS 0.002 0.001 HIS B 475 Details of bonding type rmsd covalent geometry : bond 0.00243 ( 9672) covalent geometry : angle 0.67651 (13158) hydrogen bonds : bond 0.02997 ( 594) hydrogen bonds : angle 3.94982 ( 1737) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1562.22 seconds wall clock time: 27 minutes 46.03 seconds (1666.03 seconds total)