Starting phenix.real_space_refine on Wed Sep 17 14:16:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9j40_61129/09_2025/9j40_61129.cif Found real_map, /net/cci-nas-00/data/ceres_data/9j40_61129/09_2025/9j40_61129.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9j40_61129/09_2025/9j40_61129.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9j40_61129/09_2025/9j40_61129.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9j40_61129/09_2025/9j40_61129.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9j40_61129/09_2025/9j40_61129.map" } resolution = 3.4 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= 0.000 sd= 0.047 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: 5 Type Number sf(0) Gaussians P 6 5.49 5 S 52 5.16 5 C 6104 2.51 5 N 1354 2.21 5 O 1534 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9050 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 4310 Number of conformers: 1 Conformer: "" Number of residues, atoms: 575, 4310 Classifications: {'peptide': 575} Incomplete info: {'truncation_to_alanine': 58} Link IDs: {'PTRANS': 21, 'TRANS': 553} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 212 Unresolved non-hydrogen angles: 266 Unresolved non-hydrogen dihedrals: 178 Unresolved non-hydrogen chiralities: 16 Planarities with less than four sites: {'TRP:plan': 1, 'ASP:plan': 3, 'GLN:plan1': 5, 'ASN:plan1': 5, 'GLU:plan': 4, 'ARG:plan': 3, 'HIS:plan': 1, 'PHE:plan': 2, 'TYR:plan': 2} Unresolved non-hydrogen planarities: 115 Chain: "A" Number of atoms: 4310 Number of conformers: 1 Conformer: "" Number of residues, atoms: 575, 4310 Classifications: {'peptide': 575} Incomplete info: {'truncation_to_alanine': 58} Link IDs: {'PTRANS': 21, 'TRANS': 553} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 212 Unresolved non-hydrogen angles: 266 Unresolved non-hydrogen dihedrals: 178 Unresolved non-hydrogen chiralities: 16 Planarities with less than four sites: {'TRP:plan': 1, 'ASP:plan': 3, 'GLN:plan1': 5, 'ASN:plan1': 5, 'GLU:plan': 4, 'ARG:plan': 3, 'HIS:plan': 1, 'PHE:plan': 2, 'TYR:plan': 2} Unresolved non-hydrogen planarities: 115 Chain: "B" Number of atoms: 215 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 215 Unusual residues: {'CLR': 1, 'IOS': 1, 'NAG': 1, 'POV': 3} Classifications: {'peptide': 1, 'undetermined': 6} Modifications used: {'COO': 1} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 215 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 215 Unusual residues: {'CLR': 1, 'IOS': 1, 'NAG': 1, 'POV': 3} Classifications: {'peptide': 1, 'undetermined': 6} Modifications used: {'COO': 1} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 2.49, per 1000 atoms: 0.28 Number of scatterers: 9050 At special positions: 0 Unit cell: (126.5, 91.3, 75.9, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 52 16.00 P 6 15.00 O 1534 8.00 N 1354 7.00 C 6104 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 Links applied NAG-ASN " NAG A1106 " - " ASN A 309 " " NAG B1106 " - " ASN B 309 " Time building additional restraints: 1.00 Conformation dependent library (CDL) restraints added in 361.8 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2156 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 0 sheets defined 85.9% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.27 Creating SS restraints... Processing helix chain 'B' and resid 38 through 41 Processing helix chain 'B' and resid 42 through 62 removed outlier: 3.658A pdb=" N CYS B 49 " --> pdb=" O ALA B 45 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N PHE B 50 " --> pdb=" O LEU B 46 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N VAL B 53 " --> pdb=" O CYS B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 66 through 80 removed outlier: 4.143A pdb=" N GLY B 72 " --> pdb=" O THR B 68 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N LEU B 73 " --> pdb=" O GLN B 69 " (cutoff:3.500A) Processing helix chain 'B' and resid 80 through 93 removed outlier: 3.574A pdb=" N ALA B 84 " --> pdb=" O PHE B 80 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N VAL B 92 " --> pdb=" O LYS B 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 99 through 125 removed outlier: 3.531A pdb=" N LEU B 103 " --> pdb=" O ASP B 99 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LEU B 107 " --> pdb=" O LEU B 103 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU B 123 " --> pdb=" O VAL B 119 " (cutoff:3.500A) Processing helix chain 'B' and resid 130 through 141 removed outlier: 3.584A pdb=" N LEU B 136 " --> pdb=" O SER B 132 " (cutoff:3.500A) Proline residue: B 138 - end of helix Processing helix chain 'B' and resid 149 through 159 removed outlier: 3.693A pdb=" N ILE B 153 " --> pdb=" O LEU B 149 " (cutoff:3.500A) Processing helix chain 'B' and resid 162 through 167 removed outlier: 3.559A pdb=" N LEU B 166 " --> pdb=" O PRO B 163 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLN B 167 " --> pdb=" O GLU B 164 " (cutoff:3.500A) Processing helix chain 'B' and resid 168 through 196 Proline residue: B 174 - end of helix removed outlier: 3.544A pdb=" N ASN B 181 " --> pdb=" O LEU B 177 " (cutoff:3.500A) Proline residue: B 182 - end of helix Processing helix chain 'B' and resid 202 through 216 removed outlier: 3.556A pdb=" N ILE B 206 " --> pdb=" O ASN B 202 " (cutoff:3.500A) Processing helix chain 'B' and resid 219 through 233 removed outlier: 3.823A pdb=" N PHE B 231 " --> pdb=" O ILE B 227 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ILE B 232 " --> pdb=" O ALA B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 251 removed outlier: 4.475A pdb=" N ASN B 243 " --> pdb=" O VAL B 239 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N PHE B 244 " --> pdb=" O TYR B 240 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LEU B 248 " --> pdb=" O PHE B 244 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N SER B 251 " --> pdb=" O GLY B 247 " (cutoff:3.500A) Processing helix chain 'B' and resid 251 through 264 removed outlier: 3.647A pdb=" N SER B 255 " --> pdb=" O SER B 251 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU B 257 " --> pdb=" O SER B 253 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N MET B 264 " --> pdb=" O LEU B 260 " (cutoff:3.500A) Processing helix chain 'B' and resid 272 through 288 removed outlier: 3.606A pdb=" N PHE B 276 " --> pdb=" O LYS B 272 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N VAL B 278 " --> pdb=" O SER B 274 " (cutoff:3.500A) Processing helix chain 'B' and resid 288 through 302 removed outlier: 3.796A pdb=" N LEU B 292 " --> pdb=" O LEU B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 322 removed outlier: 3.508A pdb=" N PHE B 318 " --> pdb=" O SER B 314 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N GLY B 321 " --> pdb=" O ALA B 317 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N VAL B 322 " --> pdb=" O PHE B 318 " (cutoff:3.500A) Processing helix chain 'B' and resid 327 through 337 removed outlier: 3.654A pdb=" N ILE B 331 " --> pdb=" O PRO B 327 " (cutoff:3.500A) Processing helix chain 'B' and resid 339 through 366 removed outlier: 3.750A pdb=" N PHE B 352 " --> pdb=" O VAL B 348 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ALA B 355 " --> pdb=" O THR B 351 " (cutoff:3.500A) Proline residue: B 356 - end of helix removed outlier: 3.603A pdb=" N TYR B 359 " --> pdb=" O ALA B 355 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N THR B 366 " --> pdb=" O ALA B 362 " (cutoff:3.500A) Processing helix chain 'B' and resid 372 through 404 removed outlier: 3.698A pdb=" N ALA B 376 " --> pdb=" O PRO B 372 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N TYR B 377 " --> pdb=" O LYS B 373 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ALA B 378 " --> pdb=" O PRO B 374 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N VAL B 389 " --> pdb=" O ASP B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 408 removed outlier: 3.752A pdb=" N LYS B 408 " --> pdb=" O LYS B 405 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 405 through 408' Processing helix chain 'B' and resid 409 through 436 removed outlier: 3.654A pdb=" N MET B 413 " --> pdb=" O GLN B 409 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N LEU B 414 " --> pdb=" O LEU B 410 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N THR B 415 " --> pdb=" O PRO B 411 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ALA B 421 " --> pdb=" O ASN B 417 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N MET B 430 " --> pdb=" O CYS B 426 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ILE B 431 " --> pdb=" O ALA B 427 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N PHE B 434 " --> pdb=" O MET B 430 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N VAL B 435 " --> pdb=" O ILE B 431 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N LYS B 436 " --> pdb=" O TRP B 432 " (cutoff:3.500A) Processing helix chain 'B' and resid 439 through 473 removed outlier: 3.575A pdb=" N GLN B 443 " --> pdb=" O ASN B 439 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ILE B 444 " --> pdb=" O PHE B 440 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LEU B 445 " --> pdb=" O VAL B 441 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL B 446 " --> pdb=" O GLY B 442 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLY B 462 " --> pdb=" O TYR B 458 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LYS B 472 " --> pdb=" O LEU B 468 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N LYS B 473 " --> pdb=" O PHE B 469 " (cutoff:3.500A) Processing helix chain 'B' and resid 480 through 502 removed outlier: 3.517A pdb=" N ILE B 491 " --> pdb=" O SER B 487 " (cutoff:3.500A) Proline residue: B 492 - end of helix Processing helix chain 'B' and resid 511 through 515 removed outlier: 3.688A pdb=" N PHE B 514 " --> pdb=" O ASP B 511 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N PHE B 515 " --> pdb=" O SER B 512 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 511 through 515' Processing helix chain 'B' and resid 517 through 545 removed outlier: 3.813A pdb=" N MET B 521 " --> pdb=" O GLY B 517 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ALA B 525 " --> pdb=" O MET B 521 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N SER B 538 " --> pdb=" O ILE B 534 " (cutoff:3.500A) Processing helix chain 'B' and resid 655 through 682 removed outlier: 5.179A pdb=" N LEU B 660 " --> pdb=" O THR B 656 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LEU B 661 " --> pdb=" O ARG B 657 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N TRP B 679 " --> pdb=" O SER B 675 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU B 680 " --> pdb=" O CYS B 676 " (cutoff:3.500A) Processing helix chain 'B' and resid 688 through 702 Processing helix chain 'B' and resid 702 through 712 removed outlier: 3.693A pdb=" N ILE B 706 " --> pdb=" O GLY B 702 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ILE B 710 " --> pdb=" O ILE B 706 " (cutoff:3.500A) Processing helix chain 'A' and resid 38 through 41 Processing helix chain 'A' and resid 42 through 62 removed outlier: 3.635A pdb=" N CYS A 49 " --> pdb=" O ALA A 45 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N PHE A 50 " --> pdb=" O LEU A 46 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N VAL A 53 " --> pdb=" O CYS A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 66 through 93 removed outlier: 3.956A pdb=" N GLY A 72 " --> pdb=" O THR A 68 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N LEU A 73 " --> pdb=" O GLN A 69 " (cutoff:3.500A) removed outlier: 5.438A pdb=" N LEU A 82 " --> pdb=" O SER A 78 " (cutoff:3.500A) Proline residue: A 83 - end of helix Processing helix chain 'A' and resid 99 through 125 removed outlier: 4.006A pdb=" N LEU A 103 " --> pdb=" O ASP A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 130 through 141 Proline residue: A 138 - end of helix Processing helix chain 'A' and resid 149 through 159 removed outlier: 3.588A pdb=" N ILE A 153 " --> pdb=" O LEU A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 167 removed outlier: 3.591A pdb=" N LEU A 166 " --> pdb=" O PRO A 163 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N GLN A 167 " --> pdb=" O GLU A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 196 removed outlier: 3.573A pdb=" N ALA A 173 " --> pdb=" O ILE A 169 " (cutoff:3.500A) Proline residue: A 174 - end of helix Proline residue: A 182 - end of helix Processing helix chain 'A' and resid 202 through 216 removed outlier: 3.721A pdb=" N ILE A 206 " --> pdb=" O ASN A 202 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N VAL A 207 " --> pdb=" O LYS A 203 " (cutoff:3.500A) Processing helix chain 'A' and resid 219 through 233 removed outlier: 3.618A pdb=" N PHE A 231 " --> pdb=" O ILE A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 251 removed outlier: 4.541A pdb=" N ASN A 243 " --> pdb=" O VAL A 239 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N PHE A 244 " --> pdb=" O TYR A 240 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LEU A 248 " --> pdb=" O PHE A 244 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N SER A 251 " --> pdb=" O GLY A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 264 removed outlier: 3.816A pdb=" N SER A 255 " --> pdb=" O SER A 251 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N MET A 264 " --> pdb=" O LEU A 260 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 302 Proline residue: A 291 - end of helix Processing helix chain 'A' and resid 306 through 322 removed outlier: 3.860A pdb=" N GLY A 321 " --> pdb=" O ALA A 317 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N VAL A 322 " --> pdb=" O PHE A 318 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 337 removed outlier: 3.579A pdb=" N ILE A 331 " --> pdb=" O PRO A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 366 removed outlier: 3.910A pdb=" N ALA A 355 " --> pdb=" O THR A 351 " (cutoff:3.500A) Proline residue: A 356 - end of helix removed outlier: 3.854A pdb=" N TYR A 359 " --> pdb=" O ALA A 355 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 404 removed outlier: 3.548A pdb=" N LEU A 375 " --> pdb=" O ASP A 371 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ILE A 388 " --> pdb=" O PHE A 384 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N VAL A 389 " --> pdb=" O ASP A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 408 removed outlier: 3.880A pdb=" N LYS A 408 " --> pdb=" O LYS A 405 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 405 through 408' Processing helix chain 'A' and resid 409 through 434 removed outlier: 4.006A pdb=" N MET A 413 " --> pdb=" O GLN A 409 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N LEU A 414 " --> pdb=" O LEU A 410 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N THR A 415 " --> pdb=" O PRO A 411 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N PHE A 434 " --> pdb=" O MET A 430 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 473 removed outlier: 3.625A pdb=" N GLN A 443 " --> pdb=" O ASN A 439 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N ILE A 444 " --> pdb=" O PHE A 440 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N LEU A 445 " --> pdb=" O VAL A 441 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLY A 462 " --> pdb=" O TYR A 458 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N LYS A 472 " --> pdb=" O LEU A 468 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N LYS A 473 " --> pdb=" O PHE A 469 " (cutoff:3.500A) Processing helix chain 'A' and resid 480 through 502 Proline residue: A 492 - end of helix Processing helix chain 'A' and resid 511 through 515 removed outlier: 3.684A pdb=" N PHE A 514 " --> pdb=" O ASP A 511 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N PHE A 515 " --> pdb=" O SER A 512 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 511 through 515' Processing helix chain 'A' and resid 517 through 545 removed outlier: 3.809A pdb=" N MET A 521 " --> pdb=" O GLY A 517 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ALA A 525 " --> pdb=" O MET A 521 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N SER A 538 " --> pdb=" O ILE A 534 " (cutoff:3.500A) Processing helix chain 'A' and resid 655 through 682 removed outlier: 5.177A pdb=" N LEU A 660 " --> pdb=" O THR A 656 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LEU A 661 " --> pdb=" O ARG A 657 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N TRP A 679 " --> pdb=" O SER A 675 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU A 680 " --> pdb=" O CYS A 676 " (cutoff:3.500A) Processing helix chain 'A' and resid 688 through 702 Processing helix chain 'A' and resid 702 through 712 removed outlier: 3.604A pdb=" N ILE A 706 " --> pdb=" O GLY A 702 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ILE A 710 " --> pdb=" O ILE A 706 " (cutoff:3.500A) 626 hydrogen bonds defined for protein. 1866 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.27 Time building geometry restraints manager: 1.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.90 - 1.08: 1 1.08 - 1.26: 1319 1.26 - 1.44: 2471 1.44 - 1.63: 5375 1.63 - 1.81: 88 Bond restraints: 9254 Sorted by residual: bond pdb=" CB PRO B 182 " pdb=" CG PRO B 182 " ideal model delta sigma weight residual 1.492 0.895 0.597 5.00e-02 4.00e+02 1.42e+02 bond pdb=" CG PRO B 182 " pdb=" CD PRO B 182 " ideal model delta sigma weight residual 1.503 1.224 0.279 3.40e-02 8.65e+02 6.76e+01 bond pdb=" C8 IOS A1102 " pdb=" N1 IOS A1102 " ideal model delta sigma weight residual 1.364 1.504 -0.140 2.00e-02 2.50e+03 4.89e+01 bond pdb=" C8 IOS B1102 " pdb=" N1 IOS B1102 " ideal model delta sigma weight residual 1.364 1.503 -0.139 2.00e-02 2.50e+03 4.83e+01 bond pdb=" C1 IOS A1102 " pdb=" C2 IOS A1102 " ideal model delta sigma weight residual 1.366 1.269 0.097 2.00e-02 2.50e+03 2.38e+01 ... (remaining 9249 not shown) Histogram of bond angle deviations from ideal: 0.00 - 9.64: 12550 9.64 - 19.27: 23 19.27 - 28.91: 1 28.91 - 38.54: 1 38.54 - 48.18: 1 Bond angle restraints: 12576 Sorted by residual: angle pdb=" CA PRO B 182 " pdb=" CB PRO B 182 " pdb=" CG PRO B 182 " ideal model delta sigma weight residual 104.50 69.66 34.84 1.90e+00 2.77e-01 3.36e+02 angle pdb=" N PRO B 182 " pdb=" CD PRO B 182 " pdb=" CG PRO B 182 " ideal model delta sigma weight residual 103.20 75.81 27.39 1.50e+00 4.44e-01 3.34e+02 angle pdb=" CB PRO B 182 " pdb=" CG PRO B 182 " pdb=" CD PRO B 182 " ideal model delta sigma weight residual 106.10 154.28 -48.18 3.20e+00 9.77e-02 2.27e+02 angle pdb=" CA PRO B 182 " pdb=" N PRO B 182 " pdb=" CD PRO B 182 " ideal model delta sigma weight residual 112.00 101.04 10.96 1.40e+00 5.10e-01 6.13e+01 angle pdb=" CA PRO B 368 " pdb=" N PRO B 368 " pdb=" CD PRO B 368 " ideal model delta sigma weight residual 112.00 103.15 8.85 1.40e+00 5.10e-01 4.00e+01 ... (remaining 12571 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.09: 4977 23.09 - 46.17: 443 46.17 - 69.26: 79 69.26 - 92.35: 15 92.35 - 115.43: 30 Dihedral angle restraints: 5544 sinusoidal: 2206 harmonic: 3338 Sorted by residual: dihedral pdb=" N PRO B 182 " pdb=" CG PRO B 182 " pdb=" CD PRO B 182 " pdb=" CB PRO B 182 " ideal model delta sinusoidal sigma weight residual 30.00 113.51 -83.51 1 1.50e+01 4.44e-03 3.78e+01 dihedral pdb=" N ASN A 337 " pdb=" C ASN A 337 " pdb=" CA ASN A 337 " pdb=" CB ASN A 337 " ideal model delta harmonic sigma weight residual 122.80 134.39 -11.59 0 2.50e+00 1.60e-01 2.15e+01 dihedral pdb=" CA PRO B 182 " pdb=" CB PRO B 182 " pdb=" CG PRO B 182 " pdb=" CD PRO B 182 " ideal model delta sinusoidal sigma weight residual 38.00 121.45 -83.45 1 2.00e+01 2.50e-03 2.13e+01 ... (remaining 5541 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.078: 1312 0.078 - 0.156: 174 0.156 - 0.233: 21 0.233 - 0.311: 4 0.311 - 0.389: 3 Chirality restraints: 1514 Sorted by residual: chirality pdb=" C1 NAG A1106 " pdb=" ND2 ASN A 309 " pdb=" C2 NAG A1106 " pdb=" O5 NAG A1106 " both_signs ideal model delta sigma weight residual False -2.40 -2.01 -0.39 2.00e-01 2.50e+01 3.78e+00 chirality pdb=" C1 NAG B1106 " pdb=" ND2 ASN B 309 " pdb=" C2 NAG B1106 " pdb=" O5 NAG B1106 " both_signs ideal model delta sigma weight residual False -2.40 -2.04 -0.36 2.00e-01 2.50e+01 3.31e+00 chirality pdb=" CA ASN A 337 " pdb=" N ASN A 337 " pdb=" C ASN A 337 " pdb=" CB ASN A 337 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.68e+00 ... (remaining 1511 not shown) Planarity restraints: 1490 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE A 147 " 0.030 2.00e-02 2.50e+03 6.09e-02 3.71e+01 pdb=" C PHE A 147 " -0.105 2.00e-02 2.50e+03 pdb=" O PHE A 147 " 0.040 2.00e-02 2.50e+03 pdb=" N ALA A 148 " 0.036 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN B 217 " 0.087 5.00e-02 4.00e+02 1.29e-01 2.67e+01 pdb=" N PRO B 218 " -0.223 5.00e-02 4.00e+02 pdb=" CA PRO B 218 " 0.068 5.00e-02 4.00e+02 pdb=" CD PRO B 218 " 0.069 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE A 137 " 0.084 5.00e-02 4.00e+02 1.22e-01 2.39e+01 pdb=" N PRO A 138 " -0.211 5.00e-02 4.00e+02 pdb=" CA PRO A 138 " 0.062 5.00e-02 4.00e+02 pdb=" CD PRO A 138 " 0.066 5.00e-02 4.00e+02 ... (remaining 1487 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 2137 2.80 - 3.33: 8861 3.33 - 3.85: 13824 3.85 - 4.38: 15171 4.38 - 4.90: 27124 Nonbonded interactions: 67117 Sorted by model distance: nonbonded pdb=" O MET B 413 " pdb=" OG1 THR B 416 " model vdw 2.278 3.040 nonbonded pdb=" O GLN B 520 " pdb=" OG1 THR B 523 " model vdw 2.278 3.040 nonbonded pdb=" O GLN A 520 " pdb=" OG1 THR A 523 " model vdw 2.279 3.040 nonbonded pdb=" O VAL A 340 " pdb=" OG1 THR A 344 " model vdw 2.290 3.040 nonbonded pdb=" O SER B 383 " pdb=" OG SER B 387 " model vdw 2.324 3.040 ... (remaining 67112 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.880 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: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 9.820 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7311 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.597 9256 Z= 0.336 Angle : 1.373 48.180 12582 Z= 0.734 Chirality : 0.058 0.389 1514 Planarity : 0.011 0.129 1488 Dihedral : 19.900 115.433 3388 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.62 % Favored : 92.21 % Rotamer: Outliers : 0.68 % Allowed : 24.32 % Favored : 75.00 % Cbeta Deviations : 0.09 % 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 aren not related in a simple way. whole: 1.49 (0.26), residues: 1142 helix: 1.95 (0.18), residues: 856 sheet: None (None), residues: 0 loop : -2.11 (0.39), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 295 TYR 0.037 0.002 TYR A 104 PHE 0.031 0.002 PHE A 114 TRP 0.022 0.002 TRP A 363 HIS 0.012 0.003 HIS B 412 Details of bonding type rmsd covalent geometry : bond 0.00912 ( 9254) covalent geometry : angle 1.36522 (12576) hydrogen bonds : bond 0.24518 ( 626) hydrogen bonds : angle 6.07941 ( 1866) link_NAG-ASN : bond 0.02533 ( 2) link_NAG-ASN : angle 6.73602 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 115 time to evaluate : 0.313 Fit side-chains revert: symmetry clash REVERT: B 39 ILE cc_start: 0.6930 (OUTLIER) cc_final: 0.6534 (mt) REVERT: A 39 ILE cc_start: 0.6828 (OUTLIER) cc_final: 0.6605 (mt) REVERT: A 146 ASP cc_start: 0.8175 (m-30) cc_final: 0.7889 (m-30) REVERT: A 337 ASN cc_start: 0.6435 (p0) cc_final: 0.5357 (t0) outliers start: 6 outliers final: 1 residues processed: 121 average time/residue: 0.0749 time to fit residues: 13.7850 Evaluate side-chains 107 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 104 time to evaluate : 0.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 39 ILE Chi-restraints excluded: chain B residue 445 LEU Chi-restraints excluded: chain A residue 39 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 108 optimal weight: 7.9990 chunk 49 optimal weight: 6.9990 chunk 97 optimal weight: 9.9990 chunk 113 optimal weight: 0.6980 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 0.6980 chunk 33 optimal weight: 0.7980 chunk 65 optimal weight: 0.8980 chunk 62 optimal weight: 0.6980 chunk 51 optimal weight: 10.0000 chunk 100 optimal weight: 5.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 145 ASN A 145 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4525 r_free = 0.4525 target = 0.236477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.183331 restraints weight = 10319.554| |-----------------------------------------------------------------------------| r_work (start): 0.4021 rms_B_bonded: 2.14 r_work: 0.3817 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.3817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7241 moved from start: 0.1886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 9256 Z= 0.173 Angle : 0.732 10.447 12582 Z= 0.365 Chirality : 0.044 0.300 1514 Planarity : 0.007 0.097 1488 Dihedral : 14.597 104.466 1624 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.94 % Favored : 95.80 % Rotamer: Outliers : 3.60 % Allowed : 20.50 % Favored : 75.90 % 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 aren not related in a simple way. whole: 2.06 (0.26), residues: 1142 helix: 2.27 (0.18), residues: 886 sheet: None (None), residues: 0 loop : -2.05 (0.40), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 235 TYR 0.009 0.001 TYR B 451 PHE 0.025 0.002 PHE B 114 TRP 0.017 0.001 TRP B 363 HIS 0.005 0.001 HIS B 310 Details of bonding type rmsd covalent geometry : bond 0.00366 ( 9254) covalent geometry : angle 0.71858 (12576) hydrogen bonds : bond 0.07013 ( 626) hydrogen bonds : angle 4.16745 ( 1866) link_NAG-ASN : bond 0.01609 ( 2) link_NAG-ASN : angle 6.33764 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 116 time to evaluate : 0.320 Fit side-chains REVERT: B 39 ILE cc_start: 0.7667 (OUTLIER) cc_final: 0.7263 (mt) REVERT: B 93 LEU cc_start: 0.6953 (OUTLIER) cc_final: 0.6163 (mp) REVERT: A 93 LEU cc_start: 0.6740 (OUTLIER) cc_final: 0.6089 (mp) REVERT: A 180 LEU cc_start: 0.6535 (OUTLIER) cc_final: 0.6236 (mt) outliers start: 32 outliers final: 15 residues processed: 140 average time/residue: 0.0704 time to fit residues: 14.9970 Evaluate side-chains 130 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 111 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 39 ILE Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 164 GLU Chi-restraints excluded: chain B residue 286 LYS Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 334 THR Chi-restraints excluded: chain B residue 445 LEU Chi-restraints excluded: chain B residue 457 THR Chi-restraints excluded: chain A residue 39 ILE Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 400 ILE Chi-restraints excluded: chain A residue 425 VAL Chi-restraints excluded: chain A residue 457 THR Chi-restraints excluded: chain A residue 705 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 20 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 61 optimal weight: 0.1980 chunk 50 optimal weight: 10.0000 chunk 21 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 46 optimal weight: 20.0000 chunk 58 optimal weight: 0.9980 chunk 91 optimal weight: 0.7980 chunk 19 optimal weight: 1.9990 chunk 42 optimal weight: 0.7980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 682 ASN A 682 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4463 r_free = 0.4463 target = 0.236248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.194296 restraints weight = 10063.294| |-----------------------------------------------------------------------------| r_work (start): 0.4058 rms_B_bonded: 1.59 r_work: 0.3772 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7319 moved from start: 0.2507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9256 Z= 0.160 Angle : 0.629 10.084 12582 Z= 0.317 Chirality : 0.042 0.178 1514 Planarity : 0.006 0.080 1488 Dihedral : 13.550 100.413 1624 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.12 % Favored : 95.62 % Rotamer: Outliers : 3.60 % Allowed : 19.93 % Favored : 76.46 % 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 aren not related in a simple way. whole: 2.13 (0.26), residues: 1142 helix: 2.29 (0.18), residues: 888 sheet: None (None), residues: 0 loop : -1.93 (0.38), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 657 TYR 0.007 0.001 TYR B 451 PHE 0.018 0.001 PHE A 114 TRP 0.016 0.001 TRP A 363 HIS 0.003 0.001 HIS A 310 Details of bonding type rmsd covalent geometry : bond 0.00339 ( 9254) covalent geometry : angle 0.61879 (12576) hydrogen bonds : bond 0.06356 ( 626) hydrogen bonds : angle 3.91873 ( 1866) link_NAG-ASN : bond 0.01674 ( 2) link_NAG-ASN : angle 5.29595 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 120 time to evaluate : 0.327 Fit side-chains REVERT: B 39 ILE cc_start: 0.8017 (OUTLIER) cc_final: 0.7370 (mt) REVERT: A 93 LEU cc_start: 0.6838 (OUTLIER) cc_final: 0.6055 (mp) REVERT: A 180 LEU cc_start: 0.6847 (OUTLIER) cc_final: 0.6560 (mt) REVERT: A 339 GLU cc_start: 0.7265 (mt-10) cc_final: 0.6827 (mt-10) REVERT: A 392 ILE cc_start: 0.8076 (mm) cc_final: 0.7694 (mt) REVERT: A 413 MET cc_start: 0.5312 (OUTLIER) cc_final: 0.5005 (ptm) outliers start: 32 outliers final: 18 residues processed: 143 average time/residue: 0.0740 time to fit residues: 15.9344 Evaluate side-chains 136 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 114 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 39 ILE Chi-restraints excluded: chain B residue 164 GLU Chi-restraints excluded: chain B residue 286 LYS Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 334 THR Chi-restraints excluded: chain B residue 666 ILE Chi-restraints excluded: chain B residue 670 PHE Chi-restraints excluded: chain A residue 39 ILE Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 94 ASN Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 367 PHE Chi-restraints excluded: chain A residue 400 ILE Chi-restraints excluded: chain A residue 413 MET Chi-restraints excluded: chain A residue 425 VAL Chi-restraints excluded: chain A residue 655 LEU Chi-restraints excluded: chain A residue 666 ILE Chi-restraints excluded: chain A residue 670 PHE Chi-restraints excluded: chain A residue 705 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 78 optimal weight: 2.9990 chunk 71 optimal weight: 0.3980 chunk 100 optimal weight: 1.9990 chunk 19 optimal weight: 0.5980 chunk 37 optimal weight: 3.9990 chunk 79 optimal weight: 0.9990 chunk 107 optimal weight: 20.0000 chunk 76 optimal weight: 0.2980 chunk 57 optimal weight: 0.4980 chunk 45 optimal weight: 0.6980 chunk 47 optimal weight: 20.0000 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4478 r_free = 0.4478 target = 0.238432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.193527 restraints weight = 10223.438| |-----------------------------------------------------------------------------| r_work (start): 0.4058 rms_B_bonded: 2.50 r_work: 0.3781 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.3781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7274 moved from start: 0.2856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9256 Z= 0.127 Angle : 0.569 10.716 12582 Z= 0.285 Chirality : 0.040 0.200 1514 Planarity : 0.005 0.066 1488 Dihedral : 13.181 96.971 1622 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.35 % Allowed : 3.68 % Favored : 95.97 % Rotamer: Outliers : 4.05 % Allowed : 19.59 % Favored : 76.35 % 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 aren not related in a simple way. whole: 2.36 (0.26), residues: 1142 helix: 2.46 (0.18), residues: 888 sheet: None (None), residues: 0 loop : -1.91 (0.38), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 657 TYR 0.014 0.001 TYR A 104 PHE 0.014 0.001 PHE A 114 TRP 0.013 0.001 TRP B 679 HIS 0.003 0.001 HIS A 310 Details of bonding type rmsd covalent geometry : bond 0.00251 ( 9254) covalent geometry : angle 0.56077 (12576) hydrogen bonds : bond 0.04963 ( 626) hydrogen bonds : angle 3.71636 ( 1866) link_NAG-ASN : bond 0.01132 ( 2) link_NAG-ASN : angle 4.53439 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 118 time to evaluate : 0.326 Fit side-chains REVERT: B 93 LEU cc_start: 0.6650 (OUTLIER) cc_final: 0.6047 (mp) REVERT: B 222 MET cc_start: 0.7313 (mmm) cc_final: 0.6995 (mmm) REVERT: A 180 LEU cc_start: 0.6750 (OUTLIER) cc_final: 0.6455 (mt) REVERT: A 339 GLU cc_start: 0.7197 (mt-10) cc_final: 0.6774 (mt-10) REVERT: A 392 ILE cc_start: 0.8031 (mm) cc_final: 0.7679 (mt) outliers start: 36 outliers final: 20 residues processed: 145 average time/residue: 0.0654 time to fit residues: 14.4625 Evaluate side-chains 133 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 111 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 39 ILE Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 94 ASN Chi-restraints excluded: chain B residue 164 GLU Chi-restraints excluded: chain B residue 286 LYS Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 395 ILE Chi-restraints excluded: chain B residue 666 ILE Chi-restraints excluded: chain B residue 669 LEU Chi-restraints excluded: chain B residue 670 PHE Chi-restraints excluded: chain A residue 39 ILE Chi-restraints excluded: chain A residue 94 ASN Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 367 PHE Chi-restraints excluded: chain A residue 395 ILE Chi-restraints excluded: chain A residue 400 ILE Chi-restraints excluded: chain A residue 425 VAL Chi-restraints excluded: chain A residue 666 ILE Chi-restraints excluded: chain A residue 670 PHE Chi-restraints excluded: chain A residue 705 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 18 optimal weight: 0.9980 chunk 100 optimal weight: 0.8980 chunk 61 optimal weight: 1.9990 chunk 103 optimal weight: 30.0000 chunk 29 optimal weight: 0.8980 chunk 82 optimal weight: 0.8980 chunk 95 optimal weight: 3.9990 chunk 5 optimal weight: 0.9990 chunk 36 optimal weight: 0.2980 chunk 7 optimal weight: 2.9990 chunk 3 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4451 r_free = 0.4451 target = 0.235305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.189807 restraints weight = 10133.497| |-----------------------------------------------------------------------------| r_work (start): 0.4022 rms_B_bonded: 1.98 r_work: 0.3753 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7333 moved from start: 0.3080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9256 Z= 0.139 Angle : 0.581 10.493 12582 Z= 0.291 Chirality : 0.041 0.194 1514 Planarity : 0.005 0.056 1488 Dihedral : 13.097 94.990 1622 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.35 % Allowed : 4.03 % Favored : 95.62 % Rotamer: Outliers : 3.94 % Allowed : 20.05 % Favored : 76.01 % 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 aren not related in a simple way. whole: 2.38 (0.26), residues: 1142 helix: 2.46 (0.18), residues: 890 sheet: None (None), residues: 0 loop : -1.87 (0.38), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 657 TYR 0.006 0.001 TYR A 170 PHE 0.021 0.001 PHE A 701 TRP 0.014 0.001 TRP A 679 HIS 0.006 0.001 HIS B 412 Details of bonding type rmsd covalent geometry : bond 0.00296 ( 9254) covalent geometry : angle 0.57324 (12576) hydrogen bonds : bond 0.05249 ( 626) hydrogen bonds : angle 3.72952 ( 1866) link_NAG-ASN : bond 0.01177 ( 2) link_NAG-ASN : angle 4.39112 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 114 time to evaluate : 0.308 Fit side-chains REVERT: B 93 LEU cc_start: 0.6866 (OUTLIER) cc_final: 0.6281 (mp) REVERT: B 222 MET cc_start: 0.7493 (mmm) cc_final: 0.7200 (mmm) REVERT: B 234 ASP cc_start: 0.6489 (t0) cc_final: 0.6250 (t0) REVERT: A 93 LEU cc_start: 0.6458 (OUTLIER) cc_final: 0.5230 (mp) REVERT: A 180 LEU cc_start: 0.6892 (OUTLIER) cc_final: 0.6597 (mt) REVERT: A 222 MET cc_start: 0.7433 (mmt) cc_final: 0.7160 (mmm) REVERT: A 339 GLU cc_start: 0.7285 (mt-10) cc_final: 0.6894 (mt-10) REVERT: A 392 ILE cc_start: 0.8047 (mm) cc_final: 0.7687 (mt) outliers start: 35 outliers final: 26 residues processed: 137 average time/residue: 0.0733 time to fit residues: 15.5155 Evaluate side-chains 139 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 110 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 39 ILE Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 94 ASN Chi-restraints excluded: chain B residue 164 GLU Chi-restraints excluded: chain B residue 286 LYS Chi-restraints excluded: chain B residue 296 GLU Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 334 THR Chi-restraints excluded: chain B residue 395 ILE Chi-restraints excluded: chain B residue 400 ILE Chi-restraints excluded: chain B residue 666 ILE Chi-restraints excluded: chain B residue 669 LEU Chi-restraints excluded: chain B residue 670 PHE Chi-restraints excluded: chain B residue 705 PHE Chi-restraints excluded: chain A residue 39 ILE Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 94 ASN Chi-restraints excluded: chain A residue 164 GLU Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 367 PHE Chi-restraints excluded: chain A residue 395 ILE Chi-restraints excluded: chain A residue 400 ILE Chi-restraints excluded: chain A residue 425 VAL Chi-restraints excluded: chain A residue 655 LEU Chi-restraints excluded: chain A residue 666 ILE Chi-restraints excluded: chain A residue 670 PHE Chi-restraints excluded: chain A residue 705 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 90 optimal weight: 3.9990 chunk 15 optimal weight: 0.7980 chunk 65 optimal weight: 0.8980 chunk 79 optimal weight: 0.9980 chunk 99 optimal weight: 5.9990 chunk 47 optimal weight: 40.0000 chunk 78 optimal weight: 1.9990 chunk 85 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 67 optimal weight: 0.3980 chunk 34 optimal weight: 2.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4447 r_free = 0.4447 target = 0.234678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.190058 restraints weight = 10215.228| |-----------------------------------------------------------------------------| r_work (start): 0.4028 rms_B_bonded: 1.60 r_work: 0.3788 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7323 moved from start: 0.3284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9256 Z= 0.137 Angle : 0.585 13.285 12582 Z= 0.291 Chirality : 0.041 0.238 1514 Planarity : 0.005 0.056 1488 Dihedral : 13.055 93.521 1622 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.35 % Allowed : 3.94 % Favored : 95.71 % Rotamer: Outliers : 4.28 % Allowed : 19.71 % Favored : 76.01 % 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 aren not related in a simple way. whole: 2.38 (0.26), residues: 1142 helix: 2.47 (0.18), residues: 890 sheet: None (None), residues: 0 loop : -1.89 (0.39), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 657 TYR 0.006 0.001 TYR A 170 PHE 0.018 0.001 PHE A 701 TRP 0.016 0.001 TRP A 679 HIS 0.003 0.001 HIS A 310 Details of bonding type rmsd covalent geometry : bond 0.00295 ( 9254) covalent geometry : angle 0.57822 (12576) hydrogen bonds : bond 0.05126 ( 626) hydrogen bonds : angle 3.74247 ( 1866) link_NAG-ASN : bond 0.01118 ( 2) link_NAG-ASN : angle 4.25502 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 111 time to evaluate : 0.328 Fit side-chains REVERT: B 48 GLU cc_start: 0.7819 (OUTLIER) cc_final: 0.7597 (tt0) REVERT: B 93 LEU cc_start: 0.6841 (OUTLIER) cc_final: 0.6527 (mp) REVERT: B 222 MET cc_start: 0.7563 (mmm) cc_final: 0.7324 (mmm) REVERT: A 48 GLU cc_start: 0.7874 (OUTLIER) cc_final: 0.7672 (tt0) REVERT: A 180 LEU cc_start: 0.6906 (OUTLIER) cc_final: 0.6604 (mt) REVERT: A 339 GLU cc_start: 0.7201 (mt-10) cc_final: 0.6759 (mt-10) REVERT: A 392 ILE cc_start: 0.8041 (mm) cc_final: 0.7683 (mt) outliers start: 38 outliers final: 30 residues processed: 139 average time/residue: 0.0746 time to fit residues: 16.0436 Evaluate side-chains 140 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 106 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 39 ILE Chi-restraints excluded: chain B residue 48 GLU Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 94 ASN Chi-restraints excluded: chain B residue 164 GLU Chi-restraints excluded: chain B residue 286 LYS Chi-restraints excluded: chain B residue 296 GLU Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 334 THR Chi-restraints excluded: chain B residue 395 ILE Chi-restraints excluded: chain B residue 400 ILE Chi-restraints excluded: chain B residue 666 ILE Chi-restraints excluded: chain B residue 669 LEU Chi-restraints excluded: chain B residue 670 PHE Chi-restraints excluded: chain B residue 705 PHE Chi-restraints excluded: chain A residue 39 ILE Chi-restraints excluded: chain A residue 48 GLU Chi-restraints excluded: chain A residue 94 ASN Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 132 SER Chi-restraints excluded: chain A residue 164 GLU Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 331 ILE Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 367 PHE Chi-restraints excluded: chain A residue 395 ILE Chi-restraints excluded: chain A residue 400 ILE Chi-restraints excluded: chain A residue 425 VAL Chi-restraints excluded: chain A residue 655 LEU Chi-restraints excluded: chain A residue 666 ILE Chi-restraints excluded: chain A residue 670 PHE Chi-restraints excluded: chain A residue 705 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 1 optimal weight: 0.7980 chunk 41 optimal weight: 0.9980 chunk 70 optimal weight: 0.7980 chunk 65 optimal weight: 0.7980 chunk 93 optimal weight: 3.9990 chunk 20 optimal weight: 0.9980 chunk 87 optimal weight: 1.9990 chunk 85 optimal weight: 0.0000 chunk 102 optimal weight: 0.9990 chunk 60 optimal weight: 0.7980 chunk 9 optimal weight: 2.9990 overall best weight: 0.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 672 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4461 r_free = 0.4461 target = 0.235928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.193080 restraints weight = 10167.677| |-----------------------------------------------------------------------------| r_work (start): 0.4051 rms_B_bonded: 1.56 r_work: 0.3796 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7331 moved from start: 0.3463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9256 Z= 0.127 Angle : 0.573 11.001 12582 Z= 0.284 Chirality : 0.040 0.199 1514 Planarity : 0.005 0.056 1488 Dihedral : 12.864 91.256 1622 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.35 % Allowed : 3.59 % Favored : 96.06 % Rotamer: Outliers : 4.39 % Allowed : 19.71 % Favored : 75.90 % 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 aren not related in a simple way. whole: 2.42 (0.26), residues: 1142 helix: 2.54 (0.18), residues: 888 sheet: None (None), residues: 0 loop : -2.01 (0.38), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 657 TYR 0.005 0.001 TYR A 170 PHE 0.020 0.001 PHE A 701 TRP 0.013 0.001 TRP B 679 HIS 0.003 0.001 HIS A 310 Details of bonding type rmsd covalent geometry : bond 0.00265 ( 9254) covalent geometry : angle 0.56600 (12576) hydrogen bonds : bond 0.04755 ( 626) hydrogen bonds : angle 3.71228 ( 1866) link_NAG-ASN : bond 0.01054 ( 2) link_NAG-ASN : angle 4.23282 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 110 time to evaluate : 0.352 Fit side-chains REVERT: B 48 GLU cc_start: 0.7823 (OUTLIER) cc_final: 0.7588 (tt0) REVERT: B 222 MET cc_start: 0.7564 (mmm) cc_final: 0.7339 (mmm) REVERT: A 48 GLU cc_start: 0.7835 (OUTLIER) cc_final: 0.7616 (tt0) REVERT: A 180 LEU cc_start: 0.6897 (OUTLIER) cc_final: 0.6598 (mt) REVERT: A 339 GLU cc_start: 0.7090 (mt-10) cc_final: 0.6587 (mt-10) REVERT: A 392 ILE cc_start: 0.8084 (mm) cc_final: 0.7717 (mt) outliers start: 39 outliers final: 25 residues processed: 139 average time/residue: 0.0776 time to fit residues: 16.3622 Evaluate side-chains 132 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 104 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 39 ILE Chi-restraints excluded: chain B residue 48 GLU Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 94 ASN Chi-restraints excluded: chain B residue 164 GLU Chi-restraints excluded: chain B residue 286 LYS Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 395 ILE Chi-restraints excluded: chain B residue 400 ILE Chi-restraints excluded: chain B residue 666 ILE Chi-restraints excluded: chain B residue 669 LEU Chi-restraints excluded: chain B residue 670 PHE Chi-restraints excluded: chain A residue 39 ILE Chi-restraints excluded: chain A residue 48 GLU Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 132 SER Chi-restraints excluded: chain A residue 164 GLU Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 331 ILE Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 367 PHE Chi-restraints excluded: chain A residue 395 ILE Chi-restraints excluded: chain A residue 400 ILE Chi-restraints excluded: chain A residue 425 VAL Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 670 PHE Chi-restraints excluded: chain A residue 705 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 17 optimal weight: 0.9980 chunk 108 optimal weight: 7.9990 chunk 94 optimal weight: 0.9990 chunk 96 optimal weight: 0.6980 chunk 56 optimal weight: 3.9990 chunk 19 optimal weight: 0.8980 chunk 110 optimal weight: 6.9990 chunk 49 optimal weight: 9.9990 chunk 14 optimal weight: 1.9990 chunk 24 optimal weight: 0.9990 chunk 90 optimal weight: 0.0270 overall best weight: 0.7240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 422 GLN A 658 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4447 r_free = 0.4447 target = 0.234314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.189007 restraints weight = 10143.814| |-----------------------------------------------------------------------------| r_work (start): 0.4019 rms_B_bonded: 1.60 r_work: 0.3789 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7299 moved from start: 0.3575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9256 Z= 0.131 Angle : 0.585 11.645 12582 Z= 0.288 Chirality : 0.041 0.206 1514 Planarity : 0.005 0.052 1488 Dihedral : 12.770 90.031 1622 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.35 % Allowed : 3.68 % Favored : 95.97 % Rotamer: Outliers : 3.94 % Allowed : 20.38 % Favored : 75.68 % 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 aren not related in a simple way. whole: 2.42 (0.26), residues: 1142 helix: 2.54 (0.18), residues: 888 sheet: None (None), residues: 0 loop : -2.04 (0.38), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 657 TYR 0.006 0.001 TYR A 170 PHE 0.019 0.001 PHE A 701 TRP 0.011 0.001 TRP A 679 HIS 0.003 0.001 HIS A 310 Details of bonding type rmsd covalent geometry : bond 0.00280 ( 9254) covalent geometry : angle 0.57818 (12576) hydrogen bonds : bond 0.04874 ( 626) hydrogen bonds : angle 3.72810 ( 1866) link_NAG-ASN : bond 0.01055 ( 2) link_NAG-ASN : angle 4.14930 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 110 time to evaluate : 0.327 Fit side-chains REVERT: B 48 GLU cc_start: 0.7816 (OUTLIER) cc_final: 0.7580 (tt0) REVERT: B 233 LEU cc_start: 0.7702 (OUTLIER) cc_final: 0.7329 (mt) REVERT: A 48 GLU cc_start: 0.7832 (OUTLIER) cc_final: 0.7618 (tt0) REVERT: A 180 LEU cc_start: 0.6898 (OUTLIER) cc_final: 0.6604 (mt) REVERT: A 339 GLU cc_start: 0.7018 (mt-10) cc_final: 0.6507 (mt-10) REVERT: A 392 ILE cc_start: 0.8015 (mm) cc_final: 0.7668 (mt) outliers start: 35 outliers final: 25 residues processed: 134 average time/residue: 0.0702 time to fit residues: 14.6550 Evaluate side-chains 140 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 111 time to evaluate : 0.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 39 ILE Chi-restraints excluded: chain B residue 48 GLU Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 94 ASN Chi-restraints excluded: chain B residue 164 GLU Chi-restraints excluded: chain B residue 233 LEU Chi-restraints excluded: chain B residue 286 LYS Chi-restraints excluded: chain B residue 296 GLU Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 337 ASN Chi-restraints excluded: chain B residue 395 ILE Chi-restraints excluded: chain B residue 400 ILE Chi-restraints excluded: chain B residue 669 LEU Chi-restraints excluded: chain B residue 670 PHE Chi-restraints excluded: chain A residue 39 ILE Chi-restraints excluded: chain A residue 48 GLU Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 132 SER Chi-restraints excluded: chain A residue 164 GLU Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 331 ILE Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 395 ILE Chi-restraints excluded: chain A residue 400 ILE Chi-restraints excluded: chain A residue 425 VAL Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 670 PHE Chi-restraints excluded: chain A residue 705 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 78 optimal weight: 2.9990 chunk 15 optimal weight: 0.6980 chunk 68 optimal weight: 0.9980 chunk 42 optimal weight: 5.9990 chunk 57 optimal weight: 0.7980 chunk 71 optimal weight: 1.9990 chunk 79 optimal weight: 0.7980 chunk 7 optimal weight: 1.9990 chunk 104 optimal weight: 40.0000 chunk 16 optimal weight: 0.0770 chunk 19 optimal weight: 4.9990 overall best weight: 0.6738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4428 r_free = 0.4428 target = 0.231135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.186459 restraints weight = 9965.450| |-----------------------------------------------------------------------------| r_work (start): 0.4026 rms_B_bonded: 1.53 r_work: 0.3806 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.3806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7287 moved from start: 0.3686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9256 Z= 0.128 Angle : 0.589 13.970 12582 Z= 0.286 Chirality : 0.041 0.206 1514 Planarity : 0.005 0.056 1488 Dihedral : 12.603 88.511 1622 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.35 % Allowed : 3.50 % Favored : 96.15 % Rotamer: Outliers : 3.49 % Allowed : 20.50 % Favored : 76.01 % 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 aren not related in a simple way. whole: 2.46 (0.26), residues: 1142 helix: 2.56 (0.18), residues: 890 sheet: None (None), residues: 0 loop : -2.04 (0.38), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 657 TYR 0.005 0.001 TYR A 170 PHE 0.018 0.001 PHE A 352 TRP 0.011 0.001 TRP A 679 HIS 0.003 0.001 HIS A 310 Details of bonding type rmsd covalent geometry : bond 0.00271 ( 9254) covalent geometry : angle 0.58250 (12576) hydrogen bonds : bond 0.04704 ( 626) hydrogen bonds : angle 3.69875 ( 1866) link_NAG-ASN : bond 0.01014 ( 2) link_NAG-ASN : angle 4.15001 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 109 time to evaluate : 0.462 Fit side-chains REVERT: B 48 GLU cc_start: 0.7785 (OUTLIER) cc_final: 0.7577 (tt0) REVERT: B 233 LEU cc_start: 0.7769 (OUTLIER) cc_final: 0.7448 (mt) REVERT: A 180 LEU cc_start: 0.6883 (OUTLIER) cc_final: 0.6607 (mt) REVERT: A 339 GLU cc_start: 0.7022 (mt-10) cc_final: 0.6638 (mt-10) REVERT: A 392 ILE cc_start: 0.8013 (mm) cc_final: 0.7669 (mt) outliers start: 31 outliers final: 24 residues processed: 130 average time/residue: 0.0735 time to fit residues: 14.8003 Evaluate side-chains 134 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 107 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 39 ILE Chi-restraints excluded: chain B residue 48 GLU Chi-restraints excluded: chain B residue 94 ASN Chi-restraints excluded: chain B residue 164 GLU Chi-restraints excluded: chain B residue 233 LEU Chi-restraints excluded: chain B residue 286 LYS Chi-restraints excluded: chain B residue 296 GLU Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 395 ILE Chi-restraints excluded: chain B residue 400 ILE Chi-restraints excluded: chain B residue 468 LEU Chi-restraints excluded: chain B residue 669 LEU Chi-restraints excluded: chain B residue 670 PHE Chi-restraints excluded: chain A residue 39 ILE Chi-restraints excluded: chain A residue 132 SER Chi-restraints excluded: chain A residue 164 GLU Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 331 ILE Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 367 PHE Chi-restraints excluded: chain A residue 395 ILE Chi-restraints excluded: chain A residue 400 ILE Chi-restraints excluded: chain A residue 425 VAL Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 670 PHE Chi-restraints excluded: chain A residue 705 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 83 optimal weight: 0.9980 chunk 69 optimal weight: 0.7980 chunk 12 optimal weight: 0.9980 chunk 61 optimal weight: 0.1980 chunk 8 optimal weight: 0.7980 chunk 94 optimal weight: 2.9990 chunk 36 optimal weight: 0.9980 chunk 45 optimal weight: 0.3980 chunk 41 optimal weight: 1.9990 chunk 64 optimal weight: 0.9980 chunk 80 optimal weight: 0.7980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4458 r_free = 0.4458 target = 0.235620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.190481 restraints weight = 10059.547| |-----------------------------------------------------------------------------| r_work (start): 0.4030 rms_B_bonded: 1.60 r_work: 0.3766 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3766 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7266 moved from start: 0.3744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9256 Z= 0.126 Angle : 0.596 13.739 12582 Z= 0.287 Chirality : 0.040 0.205 1514 Planarity : 0.005 0.056 1488 Dihedral : 12.424 87.766 1622 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.35 % Allowed : 3.68 % Favored : 95.97 % Rotamer: Outliers : 3.60 % Allowed : 20.38 % Favored : 76.01 % 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 aren not related in a simple way. whole: 2.48 (0.26), residues: 1142 helix: 2.58 (0.18), residues: 890 sheet: None (None), residues: 0 loop : -2.03 (0.38), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 213 TYR 0.005 0.001 TYR A 170 PHE 0.017 0.001 PHE A 352 TRP 0.010 0.001 TRP B 679 HIS 0.005 0.001 HIS A 412 Details of bonding type rmsd covalent geometry : bond 0.00265 ( 9254) covalent geometry : angle 0.58889 (12576) hydrogen bonds : bond 0.04571 ( 626) hydrogen bonds : angle 3.67993 ( 1866) link_NAG-ASN : bond 0.00991 ( 2) link_NAG-ASN : angle 4.10409 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 108 time to evaluate : 0.337 Fit side-chains REVERT: B 48 GLU cc_start: 0.7755 (OUTLIER) cc_final: 0.7544 (tt0) REVERT: B 233 LEU cc_start: 0.7721 (OUTLIER) cc_final: 0.7387 (mt) REVERT: A 180 LEU cc_start: 0.6835 (OUTLIER) cc_final: 0.6550 (mt) REVERT: A 339 GLU cc_start: 0.6968 (mt-10) cc_final: 0.6566 (mt-10) REVERT: A 392 ILE cc_start: 0.7935 (mm) cc_final: 0.7602 (mt) REVERT: A 406 LYS cc_start: 0.8139 (tmtt) cc_final: 0.7899 (tttm) outliers start: 32 outliers final: 27 residues processed: 127 average time/residue: 0.0724 time to fit residues: 14.3669 Evaluate side-chains 138 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 108 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 39 ILE Chi-restraints excluded: chain B residue 48 GLU Chi-restraints excluded: chain B residue 94 ASN Chi-restraints excluded: chain B residue 164 GLU Chi-restraints excluded: chain B residue 233 LEU Chi-restraints excluded: chain B residue 286 LYS Chi-restraints excluded: chain B residue 296 GLU Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 334 THR Chi-restraints excluded: chain B residue 395 ILE Chi-restraints excluded: chain B residue 400 ILE Chi-restraints excluded: chain B residue 468 LEU Chi-restraints excluded: chain B residue 669 LEU Chi-restraints excluded: chain B residue 670 PHE Chi-restraints excluded: chain A residue 39 ILE Chi-restraints excluded: chain A residue 94 ASN Chi-restraints excluded: chain A residue 132 SER Chi-restraints excluded: chain A residue 164 GLU Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 331 ILE Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 337 ASN Chi-restraints excluded: chain A residue 367 PHE Chi-restraints excluded: chain A residue 395 ILE Chi-restraints excluded: chain A residue 400 ILE Chi-restraints excluded: chain A residue 425 VAL Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 670 PHE Chi-restraints excluded: chain A residue 705 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 22 optimal weight: 0.0970 chunk 62 optimal weight: 0.9990 chunk 112 optimal weight: 3.9990 chunk 42 optimal weight: 5.9990 chunk 10 optimal weight: 0.7980 chunk 48 optimal weight: 8.9990 chunk 73 optimal weight: 0.3980 chunk 19 optimal weight: 0.5980 chunk 41 optimal weight: 0.8980 chunk 110 optimal weight: 7.9990 chunk 56 optimal weight: 1.9990 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 412 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4462 r_free = 0.4462 target = 0.236187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.192255 restraints weight = 9983.613| |-----------------------------------------------------------------------------| r_work (start): 0.4045 rms_B_bonded: 1.70 r_work: 0.3777 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7266 moved from start: 0.3841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9256 Z= 0.122 Angle : 0.594 13.604 12582 Z= 0.285 Chirality : 0.040 0.204 1514 Planarity : 0.005 0.057 1488 Dihedral : 12.257 86.851 1622 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.35 % Allowed : 3.77 % Favored : 95.88 % Rotamer: Outliers : 3.83 % Allowed : 20.50 % Favored : 75.68 % 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 aren not related in a simple way. whole: 2.50 (0.26), residues: 1142 helix: 2.60 (0.18), residues: 892 sheet: None (None), residues: 0 loop : -2.09 (0.38), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 657 TYR 0.005 0.001 TYR A 170 PHE 0.017 0.001 PHE A 352 TRP 0.010 0.001 TRP B 679 HIS 0.003 0.001 HIS B 412 Details of bonding type rmsd covalent geometry : bond 0.00254 ( 9254) covalent geometry : angle 0.58714 (12576) hydrogen bonds : bond 0.04419 ( 626) hydrogen bonds : angle 3.64873 ( 1866) link_NAG-ASN : bond 0.00962 ( 2) link_NAG-ASN : angle 4.08599 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2036.88 seconds wall clock time: 35 minutes 43.62 seconds (2143.62 seconds total)