Starting phenix.real_space_refine on Mon May 12 14:49:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9j40_61129/05_2025/9j40_61129.cif Found real_map, /net/cci-nas-00/data/ceres_data/9j40_61129/05_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9j40_61129/05_2025/9j40_61129.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9j40_61129/05_2025/9j40_61129.map" model { file = "/net/cci-nas-00/data/ceres_data/9j40_61129/05_2025/9j40_61129.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9j40_61129/05_2025/9j40_61129.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: {'GLN:plan1': 5, 'HIS:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 5, 'TRP:plan': 1, 'ASP:plan': 3, 'PHE:plan': 2, 'GLU:plan': 4, 'ARG:plan': 3} 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: {'GLN:plan1': 5, 'HIS:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 5, 'TRP:plan': 1, 'ASP:plan': 3, 'PHE:plan': 2, 'GLU:plan': 4, 'ARG:plan': 3} 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: 5.91, per 1000 atoms: 0.65 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: 2.46 Conformation dependent library (CDL) restraints added in 1.0 seconds 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: 0.81 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: 2.46 Time building geometry restraints manager: 2.81 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: 0.04 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: 0.680 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: 0.310 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 22.950 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.040 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:3.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.450 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.49 (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 TRP 0.022 0.002 TRP A 363 HIS 0.012 0.003 HIS B 412 PHE 0.031 0.002 PHE A 114 TYR 0.037 0.002 TYR A 104 ARG 0.003 0.000 ARG A 295 Details of bonding type rmsd link_NAG-ASN : bond 0.02533 ( 2) link_NAG-ASN : angle 6.73602 ( 6) hydrogen bonds : bond 0.24518 ( 626) hydrogen bonds : angle 6.07941 ( 1866) covalent geometry : bond 0.00912 ( 9254) covalent geometry : angle 1.36522 (12576) *********************** 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 : 0.901 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: 0.1752 time to fit residues: 31.6893 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 : 0.915 ------------------------------------------------------------------------------- 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 96 optimal weight: 3.9990 chunk 86 optimal weight: 2.9990 chunk 47 optimal weight: 8.9990 chunk 29 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 chunk 46 optimal weight: 6.9990 chunk 89 optimal weight: 0.8980 chunk 34 optimal weight: 0.7980 chunk 54 optimal weight: 7.9990 chunk 66 optimal weight: 0.3980 chunk 103 optimal weight: 9.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- 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 A 658 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4476 r_free = 0.4476 target = 0.230935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.186750 restraints weight = 10390.943| |-----------------------------------------------------------------------------| r_work (start): 0.4062 rms_B_bonded: 1.87 r_work: 0.3766 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.3766 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7447 moved from start: 0.2159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 9256 Z= 0.208 Angle : 0.767 12.027 12582 Z= 0.384 Chirality : 0.046 0.309 1514 Planarity : 0.007 0.089 1488 Dihedral : 15.038 106.397 1624 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.12 % Favored : 95.62 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.86 (0.26), residues: 1142 helix: 2.11 (0.18), residues: 886 sheet: None (None), residues: 0 loop : -2.04 (0.40), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 363 HIS 0.004 0.001 HIS A 658 PHE 0.026 0.002 PHE B 114 TYR 0.010 0.002 TYR B 451 ARG 0.004 0.001 ARG B 213 Details of bonding type rmsd link_NAG-ASN : bond 0.01751 ( 2) link_NAG-ASN : angle 6.31410 ( 6) hydrogen bonds : bond 0.07525 ( 626) hydrogen bonds : angle 4.28554 ( 1866) covalent geometry : bond 0.00467 ( 9254) covalent geometry : angle 0.75486 (12576) *********************** 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 158 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 123 time to evaluate : 0.922 Fit side-chains REVERT: B 39 ILE cc_start: 0.7909 (OUTLIER) cc_final: 0.7404 (mt) REVERT: A 79 ARG cc_start: 0.8309 (mtp85) cc_final: 0.8030 (mtt90) REVERT: A 93 LEU cc_start: 0.7101 (OUTLIER) cc_final: 0.6315 (mp) REVERT: A 180 LEU cc_start: 0.6947 (OUTLIER) cc_final: 0.6636 (mt) outliers start: 35 outliers final: 18 residues processed: 152 average time/residue: 0.1616 time to fit residues: 36.6144 Evaluate side-chains 139 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 118 time to evaluate : 0.918 ------------------------------------------------------------------------------- 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 445 LEU Chi-restraints excluded: chain B residue 457 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 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 666 ILE Chi-restraints excluded: chain A residue 670 PHE 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 65 optimal weight: 1.9990 chunk 45 optimal weight: 3.9990 chunk 28 optimal weight: 0.5980 chunk 41 optimal weight: 1.9990 chunk 12 optimal weight: 0.9980 chunk 70 optimal weight: 2.9990 chunk 58 optimal weight: 0.8980 chunk 37 optimal weight: 0.8980 chunk 48 optimal weight: 20.0000 chunk 44 optimal weight: 30.0000 chunk 53 optimal weight: 9.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- 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 = 0.4456 r_free = 0.4456 target = 0.229324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.181436 restraints weight = 10610.350| |-----------------------------------------------------------------------------| r_work (start): 0.4012 rms_B_bonded: 3.15 r_work: 0.3703 rms_B_bonded: 4.48 restraints_weight: 0.5000 r_work (final): 0.3703 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7450 moved from start: 0.2612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9256 Z= 0.165 Angle : 0.631 9.770 12582 Z= 0.320 Chirality : 0.042 0.195 1514 Planarity : 0.006 0.070 1488 Dihedral : 13.926 101.965 1624 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.35 % Allowed : 3.77 % Favored : 95.88 % Rotamer: Outliers : 4.17 % Allowed : 20.27 % Favored : 75.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.00 (0.26), residues: 1142 helix: 2.17 (0.18), residues: 888 sheet: None (None), residues: 0 loop : -1.87 (0.38), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 363 HIS 0.003 0.001 HIS A 310 PHE 0.018 0.001 PHE A 352 TYR 0.008 0.001 TYR B 451 ARG 0.003 0.000 ARG A 657 Details of bonding type rmsd link_NAG-ASN : bond 0.01618 ( 2) link_NAG-ASN : angle 5.68180 ( 6) hydrogen bonds : bond 0.06627 ( 626) hydrogen bonds : angle 3.98352 ( 1866) covalent geometry : bond 0.00357 ( 9254) covalent geometry : angle 0.61868 (12576) *********************** 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 159 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 122 time to evaluate : 0.870 Fit side-chains REVERT: B 93 LEU cc_start: 0.7102 (OUTLIER) cc_final: 0.6155 (mp) REVERT: A 93 LEU cc_start: 0.7002 (OUTLIER) cc_final: 0.6156 (mp) REVERT: A 180 LEU cc_start: 0.6750 (OUTLIER) cc_final: 0.6446 (mt) REVERT: A 339 GLU cc_start: 0.7337 (mt-10) cc_final: 0.6785 (mt-10) REVERT: A 392 ILE cc_start: 0.8209 (mm) cc_final: 0.7818 (mt) outliers start: 37 outliers final: 20 residues processed: 149 average time/residue: 0.1678 time to fit residues: 36.8701 Evaluate side-chains 143 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 120 time to evaluate : 0.844 ------------------------------------------------------------------------------- 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 395 ILE Chi-restraints excluded: chain B residue 666 ILE Chi-restraints excluded: chain A residue 39 ILE Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 164 GLU Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 241 VAL 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 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 705 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 29 optimal weight: 1.9990 chunk 15 optimal weight: 0.9990 chunk 109 optimal weight: 0.9980 chunk 64 optimal weight: 2.9990 chunk 89 optimal weight: 0.7980 chunk 36 optimal weight: 0.7980 chunk 28 optimal weight: 0.9980 chunk 111 optimal weight: 8.9990 chunk 63 optimal weight: 0.6980 chunk 12 optimal weight: 1.9990 chunk 76 optimal weight: 5.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 = 0.231414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.186511 restraints weight = 10223.943| |-----------------------------------------------------------------------------| r_work (start): 0.4053 rms_B_bonded: 2.63 r_work: 0.3740 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.3740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7427 moved from start: 0.2952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9256 Z= 0.147 Angle : 0.600 10.426 12582 Z= 0.303 Chirality : 0.041 0.200 1514 Planarity : 0.006 0.059 1488 Dihedral : 13.688 98.414 1622 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.35 % Allowed : 3.77 % Favored : 95.88 % Rotamer: Outliers : 4.62 % Allowed : 19.71 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.11 (0.26), residues: 1142 helix: 2.26 (0.18), residues: 888 sheet: None (None), residues: 0 loop : -1.89 (0.38), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 679 HIS 0.003 0.001 HIS A 310 PHE 0.017 0.001 PHE A 114 TYR 0.006 0.001 TYR B 451 ARG 0.002 0.000 ARG A 657 Details of bonding type rmsd link_NAG-ASN : bond 0.01275 ( 2) link_NAG-ASN : angle 4.97223 ( 6) hydrogen bonds : bond 0.05699 ( 626) hydrogen bonds : angle 3.85115 ( 1866) covalent geometry : bond 0.00312 ( 9254) covalent geometry : angle 0.59046 (12576) *********************** 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 159 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 118 time to evaluate : 0.810 Fit side-chains REVERT: B 93 LEU cc_start: 0.6978 (OUTLIER) cc_final: 0.6254 (mp) REVERT: B 180 LEU cc_start: 0.6752 (OUTLIER) cc_final: 0.6465 (mt) REVERT: B 222 MET cc_start: 0.7670 (mmm) cc_final: 0.7378 (mmm) REVERT: B 234 ASP cc_start: 0.6527 (t0) cc_final: 0.6309 (t0) REVERT: A 93 LEU cc_start: 0.6944 (OUTLIER) cc_final: 0.6154 (mp) REVERT: A 180 LEU cc_start: 0.6754 (OUTLIER) cc_final: 0.6444 (mt) REVERT: A 339 GLU cc_start: 0.7297 (mt-10) cc_final: 0.6770 (mt-10) REVERT: A 392 ILE cc_start: 0.8238 (mm) cc_final: 0.7857 (mt) outliers start: 41 outliers final: 27 residues processed: 146 average time/residue: 0.1545 time to fit residues: 34.3659 Evaluate side-chains 150 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 119 time to evaluate : 0.944 ------------------------------------------------------------------------------- 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 180 LEU Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 286 LYS Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 331 ILE 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 484 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 93 LEU Chi-restraints excluded: chain A residue 164 GLU Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 296 GLU 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 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 67 optimal weight: 1.9990 chunk 52 optimal weight: 3.9990 chunk 13 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 chunk 23 optimal weight: 4.9990 chunk 21 optimal weight: 3.9990 chunk 34 optimal weight: 3.9990 chunk 83 optimal weight: 0.9990 chunk 9 optimal weight: 2.9990 chunk 4 optimal weight: 0.3980 chunk 80 optimal weight: 3.9990 overall best weight: 1.6788 ------------------------------------------------------------------------------- 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 = 0.4408 r_free = 0.4408 target = 0.224145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.177916 restraints weight = 10472.443| |-----------------------------------------------------------------------------| r_work (start): 0.3972 rms_B_bonded: 1.83 r_work: 0.3719 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3719 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7491 moved from start: 0.3283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 9256 Z= 0.205 Angle : 0.663 12.541 12582 Z= 0.334 Chirality : 0.044 0.240 1514 Planarity : 0.006 0.056 1488 Dihedral : 13.775 97.112 1622 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.35 % Allowed : 4.29 % Favored : 95.36 % Rotamer: Outliers : 4.73 % Allowed : 19.48 % Favored : 75.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.79 (0.26), residues: 1142 helix: 2.01 (0.18), residues: 888 sheet: None (None), residues: 0 loop : -1.93 (0.38), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 679 HIS 0.003 0.001 HIS A 310 PHE 0.023 0.002 PHE A 352 TYR 0.009 0.001 TYR A 170 ARG 0.003 0.001 ARG A 235 Details of bonding type rmsd link_NAG-ASN : bond 0.01420 ( 2) link_NAG-ASN : angle 4.97858 ( 6) hydrogen bonds : bond 0.06893 ( 626) hydrogen bonds : angle 4.09215 ( 1866) covalent geometry : bond 0.00481 ( 9254) covalent geometry : angle 0.65394 (12576) *********************** 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 159 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 117 time to evaluate : 0.895 Fit side-chains REVERT: B 93 LEU cc_start: 0.7270 (OUTLIER) cc_final: 0.6289 (mp) REVERT: B 233 LEU cc_start: 0.7720 (OUTLIER) cc_final: 0.7324 (mt) REVERT: A 93 LEU cc_start: 0.7180 (OUTLIER) cc_final: 0.6321 (mp) REVERT: A 180 LEU cc_start: 0.6964 (OUTLIER) cc_final: 0.6683 (mt) REVERT: A 339 GLU cc_start: 0.7214 (mt-10) cc_final: 0.6756 (mt-10) REVERT: A 392 ILE cc_start: 0.8182 (mm) cc_final: 0.7781 (mt) outliers start: 42 outliers final: 30 residues processed: 147 average time/residue: 0.1577 time to fit residues: 35.2651 Evaluate side-chains 149 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 115 time to evaluate : 0.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 39 ILE Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 132 SER Chi-restraints excluded: chain B residue 164 GLU Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 233 LEU 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 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 93 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 237 VAL Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 296 GLU Chi-restraints excluded: chain A residue 307 VAL 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 484 ILE 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 107 optimal weight: 40.0000 chunk 68 optimal weight: 0.6980 chunk 18 optimal weight: 0.6980 chunk 93 optimal weight: 0.5980 chunk 49 optimal weight: 10.0000 chunk 45 optimal weight: 0.0870 chunk 113 optimal weight: 1.9990 chunk 54 optimal weight: 0.0370 chunk 47 optimal weight: 50.0000 chunk 74 optimal weight: 0.9980 chunk 56 optimal weight: 1.9990 overall best weight: 0.4236 ------------------------------------------------------------------------------- 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 = 0.4470 r_free = 0.4470 target = 0.231314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.185454 restraints weight = 10175.522| |-----------------------------------------------------------------------------| r_work (start): 0.4063 rms_B_bonded: 1.83 r_work: 0.3777 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.3777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7408 moved from start: 0.3445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 9256 Z= 0.127 Angle : 0.570 10.681 12582 Z= 0.287 Chirality : 0.040 0.198 1514 Planarity : 0.005 0.057 1488 Dihedral : 13.147 93.804 1622 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.35 % Allowed : 3.68 % Favored : 95.97 % Rotamer: Outliers : 3.72 % Allowed : 20.05 % Favored : 76.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.25 (0.26), residues: 1142 helix: 2.40 (0.18), residues: 886 sheet: None (None), residues: 0 loop : -1.98 (0.38), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 679 HIS 0.003 0.001 HIS B 310 PHE 0.015 0.001 PHE A 352 TYR 0.008 0.001 TYR B 104 ARG 0.001 0.000 ARG A 657 Details of bonding type rmsd link_NAG-ASN : bond 0.01105 ( 2) link_NAG-ASN : angle 4.48980 ( 6) hydrogen bonds : bond 0.04909 ( 626) hydrogen bonds : angle 3.73789 ( 1866) covalent geometry : bond 0.00247 ( 9254) covalent geometry : angle 0.56201 (12576) *********************** 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 153 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 120 time to evaluate : 0.838 Fit side-chains REVERT: B 93 LEU cc_start: 0.6839 (OUTLIER) cc_final: 0.6162 (mp) REVERT: B 233 LEU cc_start: 0.7708 (OUTLIER) cc_final: 0.7439 (mt) REVERT: A 93 LEU cc_start: 0.6827 (OUTLIER) cc_final: 0.6122 (mp) REVERT: A 180 LEU cc_start: 0.6753 (OUTLIER) cc_final: 0.6440 (mt) REVERT: A 339 GLU cc_start: 0.7127 (mt-10) cc_final: 0.6541 (mt-10) REVERT: A 392 ILE cc_start: 0.8206 (mm) cc_final: 0.7840 (mt) outliers start: 33 outliers final: 23 residues processed: 142 average time/residue: 0.1547 time to fit residues: 33.4635 Evaluate side-chains 139 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 112 time to evaluate : 0.817 ------------------------------------------------------------------------------- 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 132 SER 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 307 VAL Chi-restraints excluded: chain B residue 331 ILE Chi-restraints excluded: chain B residue 400 ILE 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 164 GLU Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 296 GLU Chi-restraints excluded: chain A residue 331 ILE Chi-restraints excluded: chain A residue 367 PHE Chi-restraints excluded: chain A residue 400 ILE Chi-restraints excluded: chain A residue 425 VAL Chi-restraints excluded: chain A residue 468 LEU 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 39 optimal weight: 4.9990 chunk 27 optimal weight: 7.9990 chunk 106 optimal weight: 8.9990 chunk 35 optimal weight: 0.6980 chunk 43 optimal weight: 0.6980 chunk 12 optimal weight: 1.9990 chunk 112 optimal weight: 2.9990 chunk 14 optimal weight: 0.6980 chunk 15 optimal weight: 0.6980 chunk 94 optimal weight: 0.0470 chunk 26 optimal weight: 1.9990 overall best weight: 0.5678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 412 HIS B 716 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4468 r_free = 0.4468 target = 0.230983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.185588 restraints weight = 10440.696| |-----------------------------------------------------------------------------| r_work (start): 0.4045 rms_B_bonded: 1.85 r_work: 0.3793 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3793 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7368 moved from start: 0.3550 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= 0.128 Angle : 0.573 10.283 12582 Z= 0.285 Chirality : 0.040 0.198 1514 Planarity : 0.005 0.056 1488 Dihedral : 12.860 92.516 1622 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.35 % Allowed : 3.59 % Favored : 96.06 % Rotamer: Outliers : 5.07 % Allowed : 18.81 % Favored : 76.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.36 (0.26), residues: 1142 helix: 2.49 (0.18), residues: 888 sheet: None (None), residues: 0 loop : -2.00 (0.38), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 679 HIS 0.003 0.001 HIS A 310 PHE 0.015 0.001 PHE A 352 TYR 0.010 0.001 TYR A 104 ARG 0.001 0.000 ARG B 657 Details of bonding type rmsd link_NAG-ASN : bond 0.01113 ( 2) link_NAG-ASN : angle 4.38480 ( 6) hydrogen bonds : bond 0.04851 ( 626) hydrogen bonds : angle 3.71704 ( 1866) covalent geometry : bond 0.00262 ( 9254) covalent geometry : angle 0.56479 (12576) *********************** 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 157 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 112 time to evaluate : 0.849 Fit side-chains REVERT: B 48 GLU cc_start: 0.7835 (OUTLIER) cc_final: 0.7604 (tt0) REVERT: B 93 LEU cc_start: 0.6757 (OUTLIER) cc_final: 0.6181 (mp) REVERT: B 233 LEU cc_start: 0.7677 (OUTLIER) cc_final: 0.7444 (mt) REVERT: B 268 ILE cc_start: 0.8552 (OUTLIER) cc_final: 0.8130 (tt) REVERT: A 48 GLU cc_start: 0.7916 (OUTLIER) cc_final: 0.7716 (tt0) REVERT: A 93 LEU cc_start: 0.6778 (OUTLIER) cc_final: 0.6063 (mp) REVERT: A 180 LEU cc_start: 0.6950 (OUTLIER) cc_final: 0.6632 (mt) REVERT: A 339 GLU cc_start: 0.7067 (mt-10) cc_final: 0.6528 (mt-10) REVERT: A 392 ILE cc_start: 0.8094 (mm) cc_final: 0.7735 (mt) outliers start: 45 outliers final: 31 residues processed: 144 average time/residue: 0.1479 time to fit residues: 32.9001 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 : 0.916 ------------------------------------------------------------------------------- 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 132 SER Chi-restraints excluded: chain B residue 233 LEU Chi-restraints excluded: chain B residue 268 ILE 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 331 ILE Chi-restraints excluded: chain B residue 337 ASN 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 695 PHE Chi-restraints excluded: chain A residue 39 ILE Chi-restraints excluded: chain A residue 48 GLU Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 94 ASN Chi-restraints excluded: chain A residue 132 SER Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 296 GLU Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 331 ILE 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 468 LEU 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 695 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 79 optimal weight: 0.2980 chunk 19 optimal weight: 4.9990 chunk 89 optimal weight: 0.7980 chunk 106 optimal weight: 10.0000 chunk 49 optimal weight: 10.0000 chunk 77 optimal weight: 0.8980 chunk 93 optimal weight: 1.9990 chunk 62 optimal weight: 0.8980 chunk 33 optimal weight: 4.9990 chunk 44 optimal weight: 20.0000 chunk 25 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 412 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4458 r_free = 0.4458 target = 0.229770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.184101 restraints weight = 10625.053| |-----------------------------------------------------------------------------| r_work (start): 0.4029 rms_B_bonded: 1.85 r_work: 0.3774 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3774 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7395 moved from start: 0.3701 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= 0.136 Angle : 0.585 9.665 12582 Z= 0.289 Chirality : 0.041 0.208 1514 Planarity : 0.005 0.053 1488 Dihedral : 12.825 91.177 1622 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.35 % Allowed : 3.68 % Favored : 95.97 % Rotamer: Outliers : 4.95 % Allowed : 19.14 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.33 (0.26), residues: 1142 helix: 2.45 (0.18), residues: 890 sheet: None (None), residues: 0 loop : -2.02 (0.38), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 679 HIS 0.004 0.001 HIS A 412 PHE 0.018 0.001 PHE A 352 TYR 0.009 0.001 TYR A 104 ARG 0.002 0.000 ARG B 657 Details of bonding type rmsd link_NAG-ASN : bond 0.01131 ( 2) link_NAG-ASN : angle 4.32697 ( 6) hydrogen bonds : bond 0.05042 ( 626) hydrogen bonds : angle 3.75816 ( 1866) covalent geometry : bond 0.00291 ( 9254) covalent geometry : angle 0.57734 (12576) *********************** 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 161 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 117 time to evaluate : 0.942 Fit side-chains REVERT: B 93 LEU cc_start: 0.6820 (OUTLIER) cc_final: 0.6420 (mp) REVERT: B 233 LEU cc_start: 0.7728 (OUTLIER) cc_final: 0.7482 (mt) REVERT: A 93 LEU cc_start: 0.6833 (OUTLIER) cc_final: 0.6116 (mp) REVERT: A 180 LEU cc_start: 0.7022 (OUTLIER) cc_final: 0.6700 (mt) REVERT: A 339 GLU cc_start: 0.7047 (mt-10) cc_final: 0.6533 (mt-10) REVERT: A 392 ILE cc_start: 0.8077 (mm) cc_final: 0.7726 (mt) outliers start: 44 outliers final: 34 residues processed: 147 average time/residue: 0.1528 time to fit residues: 34.4368 Evaluate side-chains 151 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 113 time to evaluate : 0.914 ------------------------------------------------------------------------------- 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 132 SER 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 331 ILE 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 666 ILE Chi-restraints excluded: chain B residue 669 LEU Chi-restraints excluded: chain B residue 670 PHE Chi-restraints excluded: chain B residue 695 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 132 SER Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 296 GLU 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 468 LEU 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 695 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 58 optimal weight: 0.9990 chunk 83 optimal weight: 0.9980 chunk 53 optimal weight: 6.9990 chunk 73 optimal weight: 20.0000 chunk 47 optimal weight: 30.0000 chunk 109 optimal weight: 0.7980 chunk 98 optimal weight: 9.9990 chunk 30 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 42 optimal weight: 5.9990 chunk 101 optimal weight: 0.6980 overall best weight: 1.0984 ------------------------------------------------------------------------------- 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 = 0.4435 r_free = 0.4435 target = 0.227253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.180527 restraints weight = 10182.302| |-----------------------------------------------------------------------------| r_work (start): 0.3991 rms_B_bonded: 1.78 r_work: 0.3752 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7431 moved from start: 0.3802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9256 Z= 0.156 Angle : 0.621 11.268 12582 Z= 0.306 Chirality : 0.042 0.221 1514 Planarity : 0.005 0.057 1488 Dihedral : 12.804 90.068 1622 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.35 % Allowed : 3.94 % Favored : 95.71 % Rotamer: Outliers : 4.73 % Allowed : 19.59 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.17 (0.26), residues: 1142 helix: 2.35 (0.18), residues: 890 sheet: None (None), residues: 0 loop : -2.10 (0.37), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 679 HIS 0.008 0.002 HIS A 412 PHE 0.024 0.001 PHE A 352 TYR 0.011 0.001 TYR A 104 ARG 0.002 0.000 ARG B 657 Details of bonding type rmsd link_NAG-ASN : bond 0.01191 ( 2) link_NAG-ASN : angle 4.37895 ( 6) hydrogen bonds : bond 0.05591 ( 626) hydrogen bonds : angle 3.83182 ( 1866) covalent geometry : bond 0.00351 ( 9254) covalent geometry : angle 0.61325 (12576) *********************** 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 156 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 114 time to evaluate : 0.939 Fit side-chains revert: symmetry clash REVERT: B 48 GLU cc_start: 0.7962 (OUTLIER) cc_final: 0.7720 (tt0) REVERT: B 93 LEU cc_start: 0.6928 (OUTLIER) cc_final: 0.6579 (mp) REVERT: B 233 LEU cc_start: 0.7762 (OUTLIER) cc_final: 0.7508 (mt) REVERT: A 93 LEU cc_start: 0.6938 (OUTLIER) cc_final: 0.6171 (mp) REVERT: A 180 LEU cc_start: 0.7102 (OUTLIER) cc_final: 0.6791 (mt) REVERT: A 268 ILE cc_start: 0.8569 (OUTLIER) cc_final: 0.8158 (tt) REVERT: A 339 GLU cc_start: 0.7115 (mt-10) cc_final: 0.6574 (mt-10) REVERT: A 392 ILE cc_start: 0.8155 (mm) cc_final: 0.7788 (mt) outliers start: 42 outliers final: 34 residues processed: 146 average time/residue: 0.1557 time to fit residues: 35.0319 Evaluate side-chains 150 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 110 time to evaluate : 0.811 ------------------------------------------------------------------------------- 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 132 SER 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 337 ASN Chi-restraints excluded: chain B residue 395 ILE Chi-restraints excluded: chain B residue 400 ILE Chi-restraints excluded: chain B residue 425 VAL 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 695 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 132 SER Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 268 ILE Chi-restraints excluded: chain A residue 296 GLU Chi-restraints excluded: chain A residue 307 VAL 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 468 LEU 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 695 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 63 optimal weight: 0.2980 chunk 106 optimal weight: 10.0000 chunk 75 optimal weight: 0.5980 chunk 9 optimal weight: 2.9990 chunk 104 optimal weight: 30.0000 chunk 8 optimal weight: 0.9980 chunk 67 optimal weight: 0.5980 chunk 62 optimal weight: 0.9990 chunk 45 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- 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 = 0.4456 r_free = 0.4456 target = 0.229720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.187868 restraints weight = 10294.789| |-----------------------------------------------------------------------------| r_work (start): 0.4062 rms_B_bonded: 1.71 r_work: 0.3773 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7389 moved from start: 0.3883 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= 0.133 Angle : 0.603 11.009 12582 Z= 0.294 Chirality : 0.041 0.210 1514 Planarity : 0.005 0.056 1488 Dihedral : 12.619 89.146 1622 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.35 % Allowed : 3.85 % Favored : 95.80 % Rotamer: Outliers : 4.62 % Allowed : 19.93 % Favored : 75.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.27 (0.26), residues: 1142 helix: 2.43 (0.18), residues: 890 sheet: None (None), residues: 0 loop : -2.14 (0.37), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 679 HIS 0.005 0.001 HIS A 412 PHE 0.021 0.001 PHE A 352 TYR 0.011 0.001 TYR B 104 ARG 0.002 0.000 ARG A 657 Details of bonding type rmsd link_NAG-ASN : bond 0.01077 ( 2) link_NAG-ASN : angle 4.32484 ( 6) hydrogen bonds : bond 0.04913 ( 626) hydrogen bonds : angle 3.73925 ( 1866) covalent geometry : bond 0.00281 ( 9254) covalent geometry : angle 0.59534 (12576) ********************** 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 156 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 115 time to evaluate : 0.904 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 48 GLU cc_start: 0.7864 (OUTLIER) cc_final: 0.7631 (tt0) REVERT: B 233 LEU cc_start: 0.7926 (OUTLIER) cc_final: 0.7481 (mt) REVERT: A 93 LEU cc_start: 0.6771 (OUTLIER) cc_final: 0.6054 (mp) REVERT: A 180 LEU cc_start: 0.6990 (OUTLIER) cc_final: 0.6686 (mt) REVERT: A 185 PHE cc_start: 0.7049 (m-10) cc_final: 0.6831 (m-80) REVERT: A 234 ASP cc_start: 0.6058 (t0) cc_final: 0.5857 (t0) REVERT: A 268 ILE cc_start: 0.8551 (OUTLIER) cc_final: 0.8128 (tt) REVERT: A 339 GLU cc_start: 0.7088 (mt-10) cc_final: 0.6560 (mt-10) REVERT: A 392 ILE cc_start: 0.8181 (mm) cc_final: 0.7824 (mt) outliers start: 41 outliers final: 34 residues processed: 143 average time/residue: 0.1429 time to fit residues: 31.7667 Evaluate side-chains 151 residues out of total 1004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 112 time to evaluate : 0.846 ------------------------------------------------------------------------------- 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 132 SER 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 331 ILE Chi-restraints excluded: chain B residue 334 THR 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 666 ILE Chi-restraints excluded: chain B residue 669 LEU Chi-restraints excluded: chain B residue 670 PHE Chi-restraints excluded: chain B residue 695 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 132 SER Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 268 ILE Chi-restraints excluded: chain A residue 296 GLU Chi-restraints excluded: chain A residue 307 VAL 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 468 LEU 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 695 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 56 optimal weight: 3.9990 chunk 62 optimal weight: 0.8980 chunk 103 optimal weight: 20.0000 chunk 84 optimal weight: 5.9990 chunk 4 optimal weight: 0.4980 chunk 45 optimal weight: 1.9990 chunk 9 optimal weight: 0.7980 chunk 104 optimal weight: 30.0000 chunk 49 optimal weight: 10.0000 chunk 69 optimal weight: 2.9990 chunk 106 optimal weight: 9.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- 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 = 0.4420 r_free = 0.4420 target = 0.225294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.178019 restraints weight = 10282.353| |-----------------------------------------------------------------------------| r_work (start): 0.3964 rms_B_bonded: 1.80 r_work: 0.3727 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7464 moved from start: 0.3960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 9256 Z= 0.181 Angle : 0.647 10.232 12582 Z= 0.318 Chirality : 0.043 0.233 1514 Planarity : 0.005 0.056 1488 Dihedral : 12.693 88.626 1622 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.35 % Allowed : 4.03 % Favored : 95.62 % Rotamer: Outliers : 4.95 % Allowed : 20.05 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.98 (0.26), residues: 1142 helix: 2.22 (0.18), residues: 890 sheet: None (None), residues: 0 loop : -2.23 (0.36), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 679 HIS 0.004 0.001 HIS A 412 PHE 0.029 0.002 PHE A 352 TYR 0.012 0.001 TYR A 104 ARG 0.003 0.000 ARG A 657 Details of bonding type rmsd link_NAG-ASN : bond 0.01189 ( 2) link_NAG-ASN : angle 4.46296 ( 6) hydrogen bonds : bond 0.06038 ( 626) hydrogen bonds : angle 3.93823 ( 1866) covalent geometry : bond 0.00426 ( 9254) covalent geometry : angle 0.63977 (12576) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4057.52 seconds wall clock time: 71 minutes 1.92 seconds (4261.92 seconds total)