Starting phenix.real_space_refine on Thu Mar 5 10:12:58 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7yij_33860/03_2026/7yij_33860.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yij_33860/03_2026/7yij_33860.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7yij_33860/03_2026/7yij_33860.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yij_33860/03_2026/7yij_33860.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7yij_33860/03_2026/7yij_33860.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yij_33860/03_2026/7yij_33860.map" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.029 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 K 1 8.98 5 S 128 5.16 5 C 13796 2.51 5 N 3544 2.21 5 O 3844 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 28 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 21313 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 5328 Number of conformers: 1 Conformer: "" Number of residues, atoms: 660, 5328 Classifications: {'peptide': 660} Link IDs: {'PTRANS': 19, 'TRANS': 640} Chain breaks: 2 Chain: "B" Number of atoms: 5328 Number of conformers: 1 Conformer: "" Number of residues, atoms: 660, 5328 Classifications: {'peptide': 660} Link IDs: {'PTRANS': 19, 'TRANS': 640} Chain breaks: 2 Chain: "C" Number of atoms: 5328 Number of conformers: 1 Conformer: "" Number of residues, atoms: 660, 5328 Classifications: {'peptide': 660} Link IDs: {'PTRANS': 19, 'TRANS': 640} Chain breaks: 2 Chain: "D" Number of atoms: 5328 Number of conformers: 1 Conformer: "" Number of residues, atoms: 660, 5328 Classifications: {'peptide': 660} Link IDs: {'PTRANS': 19, 'TRANS': 640} Chain breaks: 2 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' K': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.69, per 1000 atoms: 0.22 Number of scatterers: 21313 At special positions: 0 Unit cell: (146.877, 146.877, 129.897, 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) K 1 19.00 S 128 16.00 O 3844 8.00 N 3544 7.00 C 13796 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.72 Conformation dependent library (CDL) restraints added in 986.3 milliseconds 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5048 Finding SS restraints... Secondary structure from input PDB file: 88 helices and 8 sheets defined 43.8% alpha, 3.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.64 Creating SS restraints... Processing helix chain 'A' and resid 74 through 79 removed outlier: 3.598A pdb=" N GLU A 79 " --> pdb=" O LYS A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 154 removed outlier: 4.142A pdb=" N THR A 153 " --> pdb=" O ALA A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 178 Processing helix chain 'A' and resid 183 through 187 Processing helix chain 'A' and resid 211 through 238 removed outlier: 3.500A pdb=" N THR A 215 " --> pdb=" O CYS A 211 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N THR A 216 " --> pdb=" O ALA A 212 " (cutoff:3.500A) Proline residue: A 233 - end of helix Processing helix chain 'A' and resid 245 through 265 removed outlier: 3.523A pdb=" N VAL A 249 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N ASP A 251 " --> pdb=" O TRP A 247 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N SER A 252 " --> pdb=" O LEU A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 300 removed outlier: 3.959A pdb=" N PHE A 293 " --> pdb=" O LEU A 289 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N VAL A 294 " --> pdb=" O LYS A 290 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N ILE A 295 " --> pdb=" O THR A 291 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N ASP A 296 " --> pdb=" O TRP A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 326 Processing helix chain 'A' and resid 327 through 330 Processing helix chain 'A' and resid 331 through 337 removed outlier: 3.561A pdb=" N LYS A 337 " --> pdb=" O ARG A 333 " (cutoff:3.500A) Processing helix chain 'A' and resid 347 through 375 removed outlier: 4.061A pdb=" N VAL A 353 " --> pdb=" O LEU A 349 " (cutoff:3.500A) Processing helix chain 'A' and resid 387 through 397 removed outlier: 3.608A pdb=" N GLN A 391 " --> pdb=" O SER A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 431 Processing helix chain 'A' and resid 442 through 463 removed outlier: 3.860A pdb=" N LYS A 446 " --> pdb=" O THR A 442 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ALA A 451 " --> pdb=" O MET A 447 " (cutoff:3.500A) Processing helix chain 'A' and resid 464 through 494 removed outlier: 4.170A pdb=" N THR A 469 " --> pdb=" O GLY A 465 " (cutoff:3.500A) Processing helix chain 'A' and resid 498 through 514 removed outlier: 3.847A pdb=" N SER A 502 " --> pdb=" O PRO A 498 " (cutoff:3.500A) Processing helix chain 'A' and resid 524 through 528 removed outlier: 3.790A pdb=" N ILE A 527 " --> pdb=" O VAL A 524 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N CYS A 528 " --> pdb=" O LEU A 525 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 524 through 528' Processing helix chain 'A' and resid 529 through 542 removed outlier: 3.895A pdb=" N ASN A 541 " --> pdb=" O CYS A 537 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N ARG A 542 " --> pdb=" O VAL A 538 " (cutoff:3.500A) Processing helix chain 'A' and resid 557 through 563 Processing helix chain 'A' and resid 643 through 653 removed outlier: 3.961A pdb=" N LYS A 648 " --> pdb=" O GLU A 644 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N VAL A 649 " --> pdb=" O ALA A 645 " (cutoff:3.500A) Processing helix chain 'A' and resid 654 through 658 removed outlier: 3.799A pdb=" N ASN A 658 " --> pdb=" O ALA A 655 " (cutoff:3.500A) Processing helix chain 'A' and resid 681 through 691 removed outlier: 3.715A pdb=" N ARG A 691 " --> pdb=" O GLU A 687 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 79 removed outlier: 3.598A pdb=" N GLU B 79 " --> pdb=" O LYS B 75 " (cutoff:3.500A) Processing helix chain 'B' and resid 150 through 154 removed outlier: 4.142A pdb=" N THR B 153 " --> pdb=" O ALA B 150 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 178 Processing helix chain 'B' and resid 183 through 187 Processing helix chain 'B' and resid 211 through 238 removed outlier: 3.500A pdb=" N THR B 215 " --> pdb=" O CYS B 211 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N THR B 216 " --> pdb=" O ALA B 212 " (cutoff:3.500A) Proline residue: B 233 - end of helix Processing helix chain 'B' and resid 245 through 265 removed outlier: 3.523A pdb=" N VAL B 249 " --> pdb=" O ILE B 245 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N ASP B 251 " --> pdb=" O TRP B 247 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N SER B 252 " --> pdb=" O LEU B 248 " (cutoff:3.500A) Processing helix chain 'B' and resid 282 through 300 removed outlier: 3.959A pdb=" N PHE B 293 " --> pdb=" O LEU B 289 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N VAL B 294 " --> pdb=" O LYS B 290 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N ILE B 295 " --> pdb=" O THR B 291 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N ASP B 296 " --> pdb=" O TRP B 292 " (cutoff:3.500A) Processing helix chain 'B' and resid 321 through 326 Processing helix chain 'B' and resid 327 through 330 Processing helix chain 'B' and resid 331 through 337 removed outlier: 3.561A pdb=" N LYS B 337 " --> pdb=" O ARG B 333 " (cutoff:3.500A) Processing helix chain 'B' and resid 347 through 375 removed outlier: 4.061A pdb=" N VAL B 353 " --> pdb=" O LEU B 349 " (cutoff:3.500A) Processing helix chain 'B' and resid 387 through 397 removed outlier: 3.608A pdb=" N GLN B 391 " --> pdb=" O SER B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 414 through 431 Processing helix chain 'B' and resid 442 through 463 removed outlier: 3.860A pdb=" N LYS B 446 " --> pdb=" O THR B 442 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ALA B 451 " --> pdb=" O MET B 447 " (cutoff:3.500A) Processing helix chain 'B' and resid 464 through 494 removed outlier: 4.171A pdb=" N THR B 469 " --> pdb=" O GLY B 465 " (cutoff:3.500A) Processing helix chain 'B' and resid 498 through 514 removed outlier: 3.847A pdb=" N SER B 502 " --> pdb=" O PRO B 498 " (cutoff:3.500A) Processing helix chain 'B' and resid 524 through 528 removed outlier: 3.790A pdb=" N ILE B 527 " --> pdb=" O VAL B 524 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N CYS B 528 " --> pdb=" O LEU B 525 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 524 through 528' Processing helix chain 'B' and resid 529 through 542 removed outlier: 3.895A pdb=" N ASN B 541 " --> pdb=" O CYS B 537 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N ARG B 542 " --> pdb=" O VAL B 538 " (cutoff:3.500A) Processing helix chain 'B' and resid 557 through 563 Processing helix chain 'B' and resid 643 through 653 removed outlier: 3.961A pdb=" N LYS B 648 " --> pdb=" O GLU B 644 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N VAL B 649 " --> pdb=" O ALA B 645 " (cutoff:3.500A) Processing helix chain 'B' and resid 654 through 658 removed outlier: 3.799A pdb=" N ASN B 658 " --> pdb=" O ALA B 655 " (cutoff:3.500A) Processing helix chain 'B' and resid 681 through 691 removed outlier: 3.715A pdb=" N ARG B 691 " --> pdb=" O GLU B 687 " (cutoff:3.500A) Processing helix chain 'C' and resid 74 through 79 removed outlier: 3.598A pdb=" N GLU C 79 " --> pdb=" O LYS C 75 " (cutoff:3.500A) Processing helix chain 'C' and resid 150 through 154 removed outlier: 4.142A pdb=" N THR C 153 " --> pdb=" O ALA C 150 " (cutoff:3.500A) Processing helix chain 'C' and resid 172 through 178 Processing helix chain 'C' and resid 183 through 187 Processing helix chain 'C' and resid 211 through 238 removed outlier: 3.500A pdb=" N THR C 215 " --> pdb=" O CYS C 211 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N THR C 216 " --> pdb=" O ALA C 212 " (cutoff:3.500A) Proline residue: C 233 - end of helix Processing helix chain 'C' and resid 245 through 265 removed outlier: 3.523A pdb=" N VAL C 249 " --> pdb=" O ILE C 245 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N ASP C 251 " --> pdb=" O TRP C 247 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N SER C 252 " --> pdb=" O LEU C 248 " (cutoff:3.500A) Processing helix chain 'C' and resid 282 through 300 removed outlier: 3.959A pdb=" N PHE C 293 " --> pdb=" O LEU C 289 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N VAL C 294 " --> pdb=" O LYS C 290 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N ILE C 295 " --> pdb=" O THR C 291 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N ASP C 296 " --> pdb=" O TRP C 292 " (cutoff:3.500A) Processing helix chain 'C' and resid 321 through 326 Processing helix chain 'C' and resid 327 through 330 Processing helix chain 'C' and resid 331 through 337 removed outlier: 3.561A pdb=" N LYS C 337 " --> pdb=" O ARG C 333 " (cutoff:3.500A) Processing helix chain 'C' and resid 347 through 375 removed outlier: 4.061A pdb=" N VAL C 353 " --> pdb=" O LEU C 349 " (cutoff:3.500A) Processing helix chain 'C' and resid 387 through 397 removed outlier: 3.608A pdb=" N GLN C 391 " --> pdb=" O SER C 387 " (cutoff:3.500A) Processing helix chain 'C' and resid 414 through 431 Processing helix chain 'C' and resid 442 through 463 removed outlier: 3.860A pdb=" N LYS C 446 " --> pdb=" O THR C 442 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ALA C 451 " --> pdb=" O MET C 447 " (cutoff:3.500A) Processing helix chain 'C' and resid 464 through 494 removed outlier: 4.171A pdb=" N THR C 469 " --> pdb=" O GLY C 465 " (cutoff:3.500A) Processing helix chain 'C' and resid 498 through 514 removed outlier: 3.847A pdb=" N SER C 502 " --> pdb=" O PRO C 498 " (cutoff:3.500A) Processing helix chain 'C' and resid 524 through 528 removed outlier: 3.790A pdb=" N ILE C 527 " --> pdb=" O VAL C 524 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N CYS C 528 " --> pdb=" O LEU C 525 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 524 through 528' Processing helix chain 'C' and resid 529 through 542 removed outlier: 3.895A pdb=" N ASN C 541 " --> pdb=" O CYS C 537 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N ARG C 542 " --> pdb=" O VAL C 538 " (cutoff:3.500A) Processing helix chain 'C' and resid 557 through 563 Processing helix chain 'C' and resid 643 through 653 removed outlier: 3.961A pdb=" N LYS C 648 " --> pdb=" O GLU C 644 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N VAL C 649 " --> pdb=" O ALA C 645 " (cutoff:3.500A) Processing helix chain 'C' and resid 654 through 658 removed outlier: 3.799A pdb=" N ASN C 658 " --> pdb=" O ALA C 655 " (cutoff:3.500A) Processing helix chain 'C' and resid 681 through 691 removed outlier: 3.715A pdb=" N ARG C 691 " --> pdb=" O GLU C 687 " (cutoff:3.500A) Processing helix chain 'D' and resid 74 through 79 removed outlier: 3.597A pdb=" N GLU D 79 " --> pdb=" O LYS D 75 " (cutoff:3.500A) Processing helix chain 'D' and resid 150 through 154 removed outlier: 4.142A pdb=" N THR D 153 " --> pdb=" O ALA D 150 " (cutoff:3.500A) Processing helix chain 'D' and resid 172 through 178 Processing helix chain 'D' and resid 183 through 187 Processing helix chain 'D' and resid 211 through 238 removed outlier: 3.500A pdb=" N THR D 215 " --> pdb=" O CYS D 211 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N THR D 216 " --> pdb=" O ALA D 212 " (cutoff:3.500A) Proline residue: D 233 - end of helix Processing helix chain 'D' and resid 245 through 265 removed outlier: 3.523A pdb=" N VAL D 249 " --> pdb=" O ILE D 245 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N ASP D 251 " --> pdb=" O TRP D 247 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N SER D 252 " --> pdb=" O LEU D 248 " (cutoff:3.500A) Processing helix chain 'D' and resid 282 through 300 removed outlier: 3.959A pdb=" N PHE D 293 " --> pdb=" O LEU D 289 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N VAL D 294 " --> pdb=" O LYS D 290 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N ILE D 295 " --> pdb=" O THR D 291 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N ASP D 296 " --> pdb=" O TRP D 292 " (cutoff:3.500A) Processing helix chain 'D' and resid 321 through 326 Processing helix chain 'D' and resid 327 through 330 Processing helix chain 'D' and resid 331 through 337 removed outlier: 3.561A pdb=" N LYS D 337 " --> pdb=" O ARG D 333 " (cutoff:3.500A) Processing helix chain 'D' and resid 347 through 375 removed outlier: 4.061A pdb=" N VAL D 353 " --> pdb=" O LEU D 349 " (cutoff:3.500A) Processing helix chain 'D' and resid 387 through 397 removed outlier: 3.608A pdb=" N GLN D 391 " --> pdb=" O SER D 387 " (cutoff:3.500A) Processing helix chain 'D' and resid 414 through 431 Processing helix chain 'D' and resid 442 through 463 removed outlier: 3.860A pdb=" N LYS D 446 " --> pdb=" O THR D 442 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ALA D 451 " --> pdb=" O MET D 447 " (cutoff:3.500A) Processing helix chain 'D' and resid 464 through 494 removed outlier: 4.171A pdb=" N THR D 469 " --> pdb=" O GLY D 465 " (cutoff:3.500A) Processing helix chain 'D' and resid 498 through 514 removed outlier: 3.847A pdb=" N SER D 502 " --> pdb=" O PRO D 498 " (cutoff:3.500A) Processing helix chain 'D' and resid 524 through 528 removed outlier: 3.790A pdb=" N ILE D 527 " --> pdb=" O VAL D 524 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N CYS D 528 " --> pdb=" O LEU D 525 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 524 through 528' Processing helix chain 'D' and resid 529 through 542 removed outlier: 3.895A pdb=" N ASN D 541 " --> pdb=" O CYS D 537 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N ARG D 542 " --> pdb=" O VAL D 538 " (cutoff:3.500A) Processing helix chain 'D' and resid 557 through 563 Processing helix chain 'D' and resid 643 through 653 removed outlier: 3.961A pdb=" N LYS D 648 " --> pdb=" O GLU D 644 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N VAL D 649 " --> pdb=" O ALA D 645 " (cutoff:3.500A) Processing helix chain 'D' and resid 654 through 658 removed outlier: 3.799A pdb=" N ASN D 658 " --> pdb=" O ALA D 655 " (cutoff:3.500A) Processing helix chain 'D' and resid 681 through 691 removed outlier: 3.715A pdb=" N ARG D 691 " --> pdb=" O GLU D 687 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 567 through 570 removed outlier: 6.770A pdb=" N ASP A 637 " --> pdb=" O VAL A 591 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ILE A 641 " --> pdb=" O LEU A 587 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LEU A 587 " --> pdb=" O ILE A 641 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 603 through 606 removed outlier: 4.108A pdb=" N ALA A 605 " --> pdb=" O VAL A 597 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 567 through 570 removed outlier: 6.770A pdb=" N ASP B 637 " --> pdb=" O VAL B 591 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ILE B 641 " --> pdb=" O LEU B 587 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LEU B 587 " --> pdb=" O ILE B 641 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 603 through 606 removed outlier: 4.108A pdb=" N ALA B 605 " --> pdb=" O VAL B 597 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 567 through 570 removed outlier: 6.770A pdb=" N ASP C 637 " --> pdb=" O VAL C 591 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ILE C 641 " --> pdb=" O LEU C 587 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LEU C 587 " --> pdb=" O ILE C 641 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 603 through 606 removed outlier: 4.108A pdb=" N ALA C 605 " --> pdb=" O VAL C 597 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 567 through 570 removed outlier: 6.770A pdb=" N ASP D 637 " --> pdb=" O VAL D 591 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ILE D 641 " --> pdb=" O LEU D 587 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LEU D 587 " --> pdb=" O ILE D 641 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 603 through 606 removed outlier: 4.108A pdb=" N ALA D 605 " --> pdb=" O VAL D 597 " (cutoff:3.500A) 756 hydrogen bonds defined for protein. 2184 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: 3.42 Time building geometry restraints manager: 2.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6668 1.34 - 1.46: 5264 1.46 - 1.58: 9680 1.58 - 1.70: 0 1.70 - 1.82: 192 Bond restraints: 21804 Sorted by residual: bond pdb=" CA ASP C 37 " pdb=" C ASP C 37 " ideal model delta sigma weight residual 1.519 1.544 -0.025 1.01e-02 9.80e+03 6.04e+00 bond pdb=" CA ASP B 37 " pdb=" C ASP B 37 " ideal model delta sigma weight residual 1.519 1.544 -0.025 1.01e-02 9.80e+03 6.04e+00 bond pdb=" CA ASP D 37 " pdb=" C ASP D 37 " ideal model delta sigma weight residual 1.519 1.544 -0.025 1.01e-02 9.80e+03 6.04e+00 bond pdb=" CA ASP A 37 " pdb=" C ASP A 37 " ideal model delta sigma weight residual 1.519 1.544 -0.025 1.01e-02 9.80e+03 6.04e+00 bond pdb=" CB THR B 468 " pdb=" CG2 THR B 468 " ideal model delta sigma weight residual 1.521 1.443 0.078 3.30e-02 9.18e+02 5.59e+00 ... (remaining 21799 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.78: 29004 2.78 - 5.57: 496 5.57 - 8.35: 60 8.35 - 11.14: 16 11.14 - 13.92: 8 Bond angle restraints: 29584 Sorted by residual: angle pdb=" CA TRP C 38 " pdb=" CB TRP C 38 " pdb=" CG TRP C 38 " ideal model delta sigma weight residual 113.60 125.80 -12.20 1.90e+00 2.77e-01 4.12e+01 angle pdb=" CA TRP D 38 " pdb=" CB TRP D 38 " pdb=" CG TRP D 38 " ideal model delta sigma weight residual 113.60 125.80 -12.20 1.90e+00 2.77e-01 4.12e+01 angle pdb=" CA TRP A 38 " pdb=" CB TRP A 38 " pdb=" CG TRP A 38 " ideal model delta sigma weight residual 113.60 125.80 -12.20 1.90e+00 2.77e-01 4.12e+01 angle pdb=" CA TRP B 38 " pdb=" CB TRP B 38 " pdb=" CG TRP B 38 " ideal model delta sigma weight residual 113.60 125.80 -12.20 1.90e+00 2.77e-01 4.12e+01 angle pdb=" C GLU B 378 " pdb=" N VAL B 379 " pdb=" CA VAL B 379 " ideal model delta sigma weight residual 121.97 132.45 -10.48 1.80e+00 3.09e-01 3.39e+01 ... (remaining 29579 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.36: 11310 16.36 - 32.72: 1318 32.72 - 49.08: 244 49.08 - 65.43: 36 65.43 - 81.79: 24 Dihedral angle restraints: 12932 sinusoidal: 5144 harmonic: 7788 Sorted by residual: dihedral pdb=" CA GLN B 34 " pdb=" C GLN B 34 " pdb=" N ILE B 35 " pdb=" CA ILE B 35 " ideal model delta harmonic sigma weight residual -180.00 -133.57 -46.43 0 5.00e+00 4.00e-02 8.62e+01 dihedral pdb=" CA GLN D 34 " pdb=" C GLN D 34 " pdb=" N ILE D 35 " pdb=" CA ILE D 35 " ideal model delta harmonic sigma weight residual 180.00 -133.57 -46.43 0 5.00e+00 4.00e-02 8.62e+01 dihedral pdb=" CA GLN A 34 " pdb=" C GLN A 34 " pdb=" N ILE A 35 " pdb=" CA ILE A 35 " ideal model delta harmonic sigma weight residual -180.00 -133.57 -46.43 0 5.00e+00 4.00e-02 8.62e+01 ... (remaining 12929 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.089: 3144 0.089 - 0.177: 212 0.177 - 0.266: 40 0.266 - 0.355: 4 0.355 - 0.443: 4 Chirality restraints: 3404 Sorted by residual: chirality pdb=" CB THR D 468 " pdb=" CA THR D 468 " pdb=" OG1 THR D 468 " pdb=" CG2 THR D 468 " both_signs ideal model delta sigma weight residual False 2.55 2.11 0.44 2.00e-01 2.50e+01 4.91e+00 chirality pdb=" CB THR A 468 " pdb=" CA THR A 468 " pdb=" OG1 THR A 468 " pdb=" CG2 THR A 468 " both_signs ideal model delta sigma weight residual False 2.55 2.11 0.44 2.00e-01 2.50e+01 4.91e+00 chirality pdb=" CB THR B 468 " pdb=" CA THR B 468 " pdb=" OG1 THR B 468 " pdb=" CG2 THR B 468 " both_signs ideal model delta sigma weight residual False 2.55 2.11 0.44 2.00e-01 2.50e+01 4.91e+00 ... (remaining 3401 not shown) Planarity restraints: 3668 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE B 676 " 0.031 2.00e-02 2.50e+03 3.32e-02 1.92e+01 pdb=" CG PHE B 676 " -0.076 2.00e-02 2.50e+03 pdb=" CD1 PHE B 676 " 0.026 2.00e-02 2.50e+03 pdb=" CD2 PHE B 676 " 0.009 2.00e-02 2.50e+03 pdb=" CE1 PHE B 676 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 PHE B 676 " 0.013 2.00e-02 2.50e+03 pdb=" CZ PHE B 676 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 676 " -0.031 2.00e-02 2.50e+03 3.32e-02 1.92e+01 pdb=" CG PHE C 676 " 0.076 2.00e-02 2.50e+03 pdb=" CD1 PHE C 676 " -0.026 2.00e-02 2.50e+03 pdb=" CD2 PHE C 676 " -0.009 2.00e-02 2.50e+03 pdb=" CE1 PHE C 676 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 PHE C 676 " -0.013 2.00e-02 2.50e+03 pdb=" CZ PHE C 676 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE D 676 " -0.031 2.00e-02 2.50e+03 3.31e-02 1.92e+01 pdb=" CG PHE D 676 " 0.076 2.00e-02 2.50e+03 pdb=" CD1 PHE D 676 " -0.026 2.00e-02 2.50e+03 pdb=" CD2 PHE D 676 " -0.010 2.00e-02 2.50e+03 pdb=" CE1 PHE D 676 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 PHE D 676 " -0.012 2.00e-02 2.50e+03 pdb=" CZ PHE D 676 " -0.001 2.00e-02 2.50e+03 ... (remaining 3665 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.74: 1803 2.74 - 3.34: 25854 3.34 - 3.94: 39922 3.94 - 4.54: 51246 4.54 - 5.14: 78234 Nonbonded interactions: 197059 Sorted by model distance: nonbonded pdb=" O GLY A 465 " pdb=" OG1 THR A 468 " model vdw 2.135 3.040 nonbonded pdb=" O GLY D 465 " pdb=" OG1 THR D 468 " model vdw 2.136 3.040 nonbonded pdb=" O GLY C 465 " pdb=" OG1 THR C 468 " model vdw 2.136 3.040 nonbonded pdb=" O GLY B 465 " pdb=" OG1 THR B 468 " model vdw 2.136 3.040 nonbonded pdb=" O THR D 512 " pdb=" OG SER D 516 " model vdw 2.144 3.040 ... (remaining 197054 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 11 through 692) selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.850 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: 0.340 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 18.810 Find NCS groups from input model: 0.410 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6917 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 : 0.004 0.078 21804 Z= 0.219 Angle : 0.925 13.920 29584 Z= 0.526 Chirality : 0.054 0.443 3404 Planarity : 0.006 0.068 3668 Dihedral : 14.448 81.792 7884 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 19.41 Ramachandran Plot: Outliers : 1.38 % Allowed : 13.30 % Favored : 85.32 % Rotamer: Outliers : 0.00 % Allowed : 0.34 % Favored : 99.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.31 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.71 (0.16), residues: 2616 helix: 0.10 (0.16), residues: 1076 sheet: -1.98 (0.58), residues: 88 loop : -3.50 (0.14), residues: 1452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 677 TYR 0.038 0.002 TYR C 195 PHE 0.076 0.002 PHE C 676 TRP 0.053 0.002 TRP C 38 HIS 0.008 0.001 HIS D 539 Details of bonding type rmsd covalent geometry : bond 0.00441 (21804) covalent geometry : angle 0.92458 (29584) hydrogen bonds : bond 0.17041 ( 756) hydrogen bonds : angle 5.69413 ( 2184) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 316 time to evaluate : 0.777 Fit side-chains REVERT: A 376 ILE cc_start: 0.5143 (tt) cc_final: 0.4832 (mt) REVERT: A 442 THR cc_start: 0.8832 (p) cc_final: 0.8561 (t) REVERT: A 513 TRP cc_start: 0.7390 (m-10) cc_final: 0.7140 (m-10) REVERT: A 647 LEU cc_start: 0.8750 (pp) cc_final: 0.8478 (mt) REVERT: A 658 ASN cc_start: 0.6591 (t0) cc_final: 0.6361 (t0) REVERT: B 376 ILE cc_start: 0.5113 (tt) cc_final: 0.4811 (mt) REVERT: B 442 THR cc_start: 0.8738 (p) cc_final: 0.8502 (t) REVERT: B 513 TRP cc_start: 0.7396 (m-10) cc_final: 0.7143 (m-10) REVERT: B 647 LEU cc_start: 0.8740 (pp) cc_final: 0.8471 (mt) REVERT: B 658 ASN cc_start: 0.6599 (t0) cc_final: 0.6370 (t0) REVERT: C 376 ILE cc_start: 0.5141 (tt) cc_final: 0.4839 (mt) REVERT: C 442 THR cc_start: 0.8723 (p) cc_final: 0.8455 (t) REVERT: C 513 TRP cc_start: 0.7408 (m-10) cc_final: 0.7154 (m-10) REVERT: C 647 LEU cc_start: 0.8739 (pp) cc_final: 0.8472 (mt) REVERT: C 658 ASN cc_start: 0.6583 (t0) cc_final: 0.6350 (t0) REVERT: D 376 ILE cc_start: 0.5168 (tt) cc_final: 0.4858 (mt) REVERT: D 442 THR cc_start: 0.8746 (p) cc_final: 0.8472 (t) REVERT: D 513 TRP cc_start: 0.7407 (m-10) cc_final: 0.7153 (m-10) REVERT: D 647 LEU cc_start: 0.8752 (pp) cc_final: 0.8482 (mt) REVERT: D 658 ASN cc_start: 0.6578 (t0) cc_final: 0.6347 (t0) outliers start: 0 outliers final: 0 residues processed: 316 average time/residue: 0.1240 time to fit residues: 66.3293 Evaluate side-chains 240 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 240 time to evaluate : 0.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 197 optimal weight: 10.0000 chunk 215 optimal weight: 7.9990 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 8.9990 chunk 261 optimal weight: 9.9990 chunk 248 optimal weight: 10.0000 chunk 207 optimal weight: 8.9990 chunk 155 optimal weight: 10.0000 chunk 244 optimal weight: 7.9990 chunk 183 optimal weight: 1.9990 chunk 111 optimal weight: 6.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 91 ASN ** A 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 482 HIS ** A 639 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 669 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 91 ASN ** B 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 482 HIS ** B 639 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 669 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 91 ASN ** C 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 482 HIS ** C 639 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 669 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 91 ASN ** D 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 482 HIS ** D 639 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 669 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4530 r_free = 0.4530 target = 0.209394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.166889 restraints weight = 39086.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.163234 restraints weight = 55420.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.161955 restraints weight = 43332.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.159879 restraints weight = 43307.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.159071 restraints weight = 39760.402| |-----------------------------------------------------------------------------| r_work (final): 0.3945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7017 moved from start: 0.3329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.099 21804 Z= 0.498 Angle : 1.169 18.784 29584 Z= 0.609 Chirality : 0.064 0.381 3404 Planarity : 0.008 0.096 3668 Dihedral : 7.781 42.694 2864 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 27.43 Ramachandran Plot: Outliers : 1.38 % Allowed : 16.90 % Favored : 81.73 % Rotamer: Outliers : 4.20 % Allowed : 14.79 % Favored : 81.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.31 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.38 (0.15), residues: 2616 helix: -0.85 (0.15), residues: 1124 sheet: -1.95 (0.49), residues: 112 loop : -3.66 (0.15), residues: 1380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 677 TYR 0.024 0.003 TYR C 424 PHE 0.036 0.004 PHE A 613 TRP 0.046 0.004 TRP C 618 HIS 0.016 0.003 HIS D 267 Details of bonding type rmsd covalent geometry : bond 0.01164 (21804) covalent geometry : angle 1.16895 (29584) hydrogen bonds : bond 0.07658 ( 756) hydrogen bonds : angle 5.97588 ( 2184) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 252 time to evaluate : 0.915 Fit side-chains revert: symmetry clash REVERT: A 207 ILE cc_start: 0.8280 (mp) cc_final: 0.7980 (mm) REVERT: A 341 TYR cc_start: 0.8197 (OUTLIER) cc_final: 0.7719 (p90) REVERT: A 506 MET cc_start: 0.7635 (tmm) cc_final: 0.7422 (tmm) REVERT: A 509 ILE cc_start: 0.8770 (pt) cc_final: 0.8444 (mm) REVERT: A 513 TRP cc_start: 0.7599 (m-10) cc_final: 0.7094 (m-10) REVERT: A 522 GLU cc_start: 0.7887 (mm-30) cc_final: 0.6821 (pm20) REVERT: A 676 PHE cc_start: 0.5190 (p90) cc_final: 0.4472 (p90) REVERT: B 207 ILE cc_start: 0.8270 (mp) cc_final: 0.7969 (mm) REVERT: B 341 TYR cc_start: 0.8200 (OUTLIER) cc_final: 0.7726 (p90) REVERT: B 506 MET cc_start: 0.7639 (tmm) cc_final: 0.7424 (tmm) REVERT: B 509 ILE cc_start: 0.8771 (pt) cc_final: 0.8445 (mm) REVERT: B 513 TRP cc_start: 0.7595 (m-10) cc_final: 0.7096 (m-10) REVERT: B 522 GLU cc_start: 0.7877 (mm-30) cc_final: 0.6816 (pm20) REVERT: B 676 PHE cc_start: 0.5181 (p90) cc_final: 0.4512 (p90) REVERT: C 207 ILE cc_start: 0.8274 (mp) cc_final: 0.7972 (mm) REVERT: C 341 TYR cc_start: 0.8193 (OUTLIER) cc_final: 0.7716 (p90) REVERT: C 506 MET cc_start: 0.7642 (tmm) cc_final: 0.7427 (tmm) REVERT: C 509 ILE cc_start: 0.8769 (pt) cc_final: 0.8449 (mm) REVERT: C 513 TRP cc_start: 0.7603 (m-10) cc_final: 0.7100 (m-10) REVERT: C 522 GLU cc_start: 0.7878 (mm-30) cc_final: 0.6820 (pm20) REVERT: C 676 PHE cc_start: 0.5172 (p90) cc_final: 0.4506 (p90) REVERT: D 38 TRP cc_start: 0.4022 (OUTLIER) cc_final: 0.3795 (p-90) REVERT: D 207 ILE cc_start: 0.8273 (mp) cc_final: 0.7974 (mm) REVERT: D 341 TYR cc_start: 0.8194 (OUTLIER) cc_final: 0.7720 (p90) REVERT: D 506 MET cc_start: 0.7636 (tmm) cc_final: 0.7418 (tmm) REVERT: D 509 ILE cc_start: 0.8770 (pt) cc_final: 0.8444 (mm) REVERT: D 513 TRP cc_start: 0.7603 (m-10) cc_final: 0.7103 (m-10) REVERT: D 522 GLU cc_start: 0.7866 (mm-30) cc_final: 0.6812 (pm20) REVERT: D 676 PHE cc_start: 0.5181 (p90) cc_final: 0.4513 (p90) outliers start: 100 outliers final: 56 residues processed: 320 average time/residue: 0.1269 time to fit residues: 67.0230 Evaluate side-chains 297 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 236 time to evaluate : 0.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 257 ILE Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 341 TYR Chi-restraints excluded: chain A residue 377 ASP Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 482 HIS Chi-restraints excluded: chain A residue 558 CYS Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 621 THR Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain B residue 257 ILE Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 334 VAL Chi-restraints excluded: chain B residue 341 TYR Chi-restraints excluded: chain B residue 377 ASP Chi-restraints excluded: chain B residue 379 VAL Chi-restraints excluded: chain B residue 482 HIS Chi-restraints excluded: chain B residue 558 CYS Chi-restraints excluded: chain B residue 564 VAL Chi-restraints excluded: chain B residue 621 THR Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 225 THR Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain C residue 257 ILE Chi-restraints excluded: chain C residue 260 VAL Chi-restraints excluded: chain C residue 326 VAL Chi-restraints excluded: chain C residue 334 VAL Chi-restraints excluded: chain C residue 341 TYR Chi-restraints excluded: chain C residue 377 ASP Chi-restraints excluded: chain C residue 379 VAL Chi-restraints excluded: chain C residue 482 HIS Chi-restraints excluded: chain C residue 558 CYS Chi-restraints excluded: chain C residue 564 VAL Chi-restraints excluded: chain C residue 621 THR Chi-restraints excluded: chain D residue 38 TRP Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 220 VAL Chi-restraints excluded: chain D residue 225 THR Chi-restraints excluded: chain D residue 256 VAL Chi-restraints excluded: chain D residue 257 ILE Chi-restraints excluded: chain D residue 260 VAL Chi-restraints excluded: chain D residue 326 VAL Chi-restraints excluded: chain D residue 334 VAL Chi-restraints excluded: chain D residue 341 TYR Chi-restraints excluded: chain D residue 377 ASP Chi-restraints excluded: chain D residue 379 VAL Chi-restraints excluded: chain D residue 482 HIS Chi-restraints excluded: chain D residue 558 CYS Chi-restraints excluded: chain D residue 564 VAL Chi-restraints excluded: chain D residue 621 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 44 optimal weight: 5.9990 chunk 204 optimal weight: 0.2980 chunk 88 optimal weight: 0.6980 chunk 173 optimal weight: 0.7980 chunk 230 optimal weight: 1.9990 chunk 119 optimal weight: 0.9990 chunk 162 optimal weight: 0.9980 chunk 197 optimal weight: 9.9990 chunk 124 optimal weight: 4.9990 chunk 30 optimal weight: 0.9990 chunk 146 optimal weight: 3.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 32 ASN ** A 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 209 HIS A 477 ASN A 482 HIS ** A 639 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 32 ASN ** B 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 209 HIS B 477 ASN B 482 HIS ** B 639 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 32 ASN ** C 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 209 HIS C 477 ASN C 482 HIS ** C 639 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 32 ASN ** D 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 209 HIS D 477 ASN D 482 HIS ** D 639 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4619 r_free = 0.4619 target = 0.217910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.175410 restraints weight = 38329.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.165222 restraints weight = 47621.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.164172 restraints weight = 40396.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.164544 restraints weight = 31155.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.164855 restraints weight = 28698.916| |-----------------------------------------------------------------------------| r_work (final): 0.4050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6844 moved from start: 0.3092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.130 21804 Z= 0.172 Angle : 0.806 18.833 29584 Z= 0.421 Chirality : 0.047 0.247 3404 Planarity : 0.005 0.057 3668 Dihedral : 6.634 48.986 2864 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 16.97 Ramachandran Plot: Outliers : 1.38 % Allowed : 13.00 % Favored : 85.63 % Rotamer: Outliers : 2.52 % Allowed : 18.82 % Favored : 78.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.73 (0.16), residues: 2616 helix: -0.18 (0.15), residues: 1152 sheet: -1.68 (0.48), residues: 108 loop : -3.48 (0.15), residues: 1356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 333 TYR 0.022 0.002 TYR C 88 PHE 0.033 0.002 PHE A 676 TRP 0.025 0.002 TRP D 38 HIS 0.011 0.001 HIS B 482 Details of bonding type rmsd covalent geometry : bond 0.00376 (21804) covalent geometry : angle 0.80572 (29584) hydrogen bonds : bond 0.05359 ( 756) hydrogen bonds : angle 4.73564 ( 2184) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 297 time to evaluate : 0.816 Fit side-chains REVERT: A 509 ILE cc_start: 0.8734 (pt) cc_final: 0.8415 (mm) REVERT: A 513 TRP cc_start: 0.7423 (m-10) cc_final: 0.6977 (m-10) REVERT: A 522 GLU cc_start: 0.7686 (mm-30) cc_final: 0.6702 (pm20) REVERT: B 509 ILE cc_start: 0.8728 (pt) cc_final: 0.8418 (mm) REVERT: B 513 TRP cc_start: 0.7409 (m-10) cc_final: 0.6967 (m-10) REVERT: B 522 GLU cc_start: 0.7681 (mm-30) cc_final: 0.6699 (pm20) REVERT: C 509 ILE cc_start: 0.8725 (pt) cc_final: 0.8402 (mm) REVERT: C 513 TRP cc_start: 0.7411 (m-10) cc_final: 0.6972 (m-10) REVERT: C 522 GLU cc_start: 0.7700 (mm-30) cc_final: 0.6702 (pm20) REVERT: D 509 ILE cc_start: 0.8728 (pt) cc_final: 0.8410 (mm) REVERT: D 513 TRP cc_start: 0.7409 (m-10) cc_final: 0.6966 (m-10) REVERT: D 522 GLU cc_start: 0.7695 (mm-30) cc_final: 0.6702 (pm20) outliers start: 60 outliers final: 28 residues processed: 345 average time/residue: 0.1216 time to fit residues: 69.2196 Evaluate side-chains 285 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 257 time to evaluate : 0.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 482 HIS Chi-restraints excluded: chain A residue 558 CYS Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain B residue 277 VAL Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 379 VAL Chi-restraints excluded: chain B residue 482 HIS Chi-restraints excluded: chain B residue 558 CYS Chi-restraints excluded: chain B residue 564 VAL Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain C residue 277 VAL Chi-restraints excluded: chain C residue 326 VAL Chi-restraints excluded: chain C residue 379 VAL Chi-restraints excluded: chain C residue 482 HIS Chi-restraints excluded: chain C residue 558 CYS Chi-restraints excluded: chain C residue 564 VAL Chi-restraints excluded: chain C residue 650 LEU Chi-restraints excluded: chain D residue 277 VAL Chi-restraints excluded: chain D residue 326 VAL Chi-restraints excluded: chain D residue 379 VAL Chi-restraints excluded: chain D residue 482 HIS Chi-restraints excluded: chain D residue 558 CYS Chi-restraints excluded: chain D residue 564 VAL Chi-restraints excluded: chain D residue 650 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 28 optimal weight: 6.9990 chunk 246 optimal weight: 3.9990 chunk 245 optimal weight: 1.9990 chunk 239 optimal weight: 0.9980 chunk 62 optimal weight: 0.6980 chunk 148 optimal weight: 9.9990 chunk 44 optimal weight: 2.9990 chunk 202 optimal weight: 9.9990 chunk 139 optimal weight: 4.9990 chunk 96 optimal weight: 3.9990 chunk 131 optimal weight: 10.0000 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 158 ASN A 482 HIS ** A 639 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 158 ASN B 473 GLN B 482 HIS ** B 639 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 158 ASN ** C 473 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 482 HIS ** C 639 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 34 GLN ** D 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 158 ASN ** D 473 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 482 HIS ** D 639 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4588 r_free = 0.4588 target = 0.214682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.173301 restraints weight = 38899.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.166498 restraints weight = 53993.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.162592 restraints weight = 46283.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.162874 restraints weight = 38384.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.163018 restraints weight = 31327.779| |-----------------------------------------------------------------------------| r_work (final): 0.4001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6949 moved from start: 0.3689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.088 21804 Z= 0.227 Angle : 0.833 19.223 29584 Z= 0.438 Chirality : 0.049 0.289 3404 Planarity : 0.005 0.056 3668 Dihedral : 6.489 45.694 2864 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 18.38 Ramachandran Plot: Outliers : 1.22 % Allowed : 14.72 % Favored : 84.06 % Rotamer: Outliers : 3.53 % Allowed : 21.39 % Favored : 75.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.62 (0.16), residues: 2616 helix: -0.10 (0.16), residues: 1156 sheet: -1.66 (0.48), residues: 108 loop : -3.41 (0.16), residues: 1352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 333 TYR 0.018 0.002 TYR D 88 PHE 0.033 0.002 PHE D 676 TRP 0.021 0.002 TRP A 618 HIS 0.011 0.002 HIS A 482 Details of bonding type rmsd covalent geometry : bond 0.00514 (21804) covalent geometry : angle 0.83309 (29584) hydrogen bonds : bond 0.05735 ( 756) hydrogen bonds : angle 4.69967 ( 2184) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 292 time to evaluate : 0.774 Fit side-chains REVERT: A 28 PHE cc_start: 0.2979 (OUTLIER) cc_final: 0.1945 (m-80) REVERT: A 109 MET cc_start: 0.2796 (pmm) cc_final: -0.0982 (ptt) REVERT: A 509 ILE cc_start: 0.8757 (pt) cc_final: 0.8416 (mm) REVERT: A 513 TRP cc_start: 0.7537 (m-10) cc_final: 0.6942 (m-10) REVERT: A 522 GLU cc_start: 0.7716 (mm-30) cc_final: 0.6732 (pm20) REVERT: B 28 PHE cc_start: 0.2962 (OUTLIER) cc_final: 0.1934 (m-80) REVERT: B 109 MET cc_start: 0.2774 (pmm) cc_final: -0.0993 (ptt) REVERT: B 509 ILE cc_start: 0.8740 (pt) cc_final: 0.8402 (mm) REVERT: B 513 TRP cc_start: 0.7515 (m-10) cc_final: 0.6921 (m-10) REVERT: B 522 GLU cc_start: 0.7717 (mm-30) cc_final: 0.6731 (pm20) REVERT: C 28 PHE cc_start: 0.2990 (OUTLIER) cc_final: 0.1955 (m-80) REVERT: C 109 MET cc_start: 0.2767 (pmm) cc_final: -0.1016 (ptt) REVERT: C 509 ILE cc_start: 0.8743 (pt) cc_final: 0.8406 (mm) REVERT: C 513 TRP cc_start: 0.7533 (m-10) cc_final: 0.6933 (m-10) REVERT: C 522 GLU cc_start: 0.7721 (mm-30) cc_final: 0.6737 (pm20) REVERT: D 28 PHE cc_start: 0.2964 (OUTLIER) cc_final: 0.1935 (m-80) REVERT: D 109 MET cc_start: 0.2807 (pmm) cc_final: -0.0968 (ptt) REVERT: D 509 ILE cc_start: 0.8738 (pt) cc_final: 0.8393 (mm) REVERT: D 513 TRP cc_start: 0.7524 (m-10) cc_final: 0.6929 (m-10) REVERT: D 522 GLU cc_start: 0.7698 (mm-30) cc_final: 0.6733 (pm20) outliers start: 84 outliers final: 48 residues processed: 352 average time/residue: 0.1348 time to fit residues: 76.8147 Evaluate side-chains 327 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 275 time to evaluate : 0.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 PHE Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 257 ILE Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain A residue 377 ASP Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 482 HIS Chi-restraints excluded: chain A residue 483 GLU Chi-restraints excluded: chain A residue 558 CYS Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain B residue 28 PHE Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain B residue 257 ILE Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 377 ASP Chi-restraints excluded: chain B residue 379 VAL Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain B residue 482 HIS Chi-restraints excluded: chain B residue 483 GLU Chi-restraints excluded: chain B residue 558 CYS Chi-restraints excluded: chain B residue 612 VAL Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain C residue 28 PHE Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain C residue 257 ILE Chi-restraints excluded: chain C residue 260 VAL Chi-restraints excluded: chain C residue 326 VAL Chi-restraints excluded: chain C residue 377 ASP Chi-restraints excluded: chain C residue 379 VAL Chi-restraints excluded: chain C residue 450 VAL Chi-restraints excluded: chain C residue 482 HIS Chi-restraints excluded: chain C residue 483 GLU Chi-restraints excluded: chain C residue 558 CYS Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain C residue 650 LEU Chi-restraints excluded: chain D residue 28 PHE Chi-restraints excluded: chain D residue 256 VAL Chi-restraints excluded: chain D residue 257 ILE Chi-restraints excluded: chain D residue 260 VAL Chi-restraints excluded: chain D residue 326 VAL Chi-restraints excluded: chain D residue 377 ASP Chi-restraints excluded: chain D residue 379 VAL Chi-restraints excluded: chain D residue 450 VAL Chi-restraints excluded: chain D residue 482 HIS Chi-restraints excluded: chain D residue 483 GLU Chi-restraints excluded: chain D residue 558 CYS Chi-restraints excluded: chain D residue 612 VAL Chi-restraints excluded: chain D residue 650 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 83 optimal weight: 8.9990 chunk 234 optimal weight: 1.9990 chunk 199 optimal weight: 1.9990 chunk 88 optimal weight: 0.7980 chunk 206 optimal weight: 10.0000 chunk 258 optimal weight: 3.9990 chunk 246 optimal weight: 9.9990 chunk 15 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 245 optimal weight: 0.8980 chunk 205 optimal weight: 3.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 GLN ** A 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 158 ASN ** A 473 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 482 HIS ** A 599 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 639 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 34 GLN ** B 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 158 ASN B 473 GLN B 482 HIS ** B 599 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 639 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 34 GLN ** C 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 158 ASN ** C 473 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 482 HIS ** C 599 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 639 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 158 ASN ** D 473 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 482 HIS ** D 599 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 639 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4601 r_free = 0.4601 target = 0.215473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.175032 restraints weight = 39166.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.168135 restraints weight = 52244.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.165327 restraints weight = 47134.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.165719 restraints weight = 36418.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.165618 restraints weight = 30123.102| |-----------------------------------------------------------------------------| r_work (final): 0.4055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6862 moved from start: 0.4089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.084 21804 Z= 0.174 Angle : 0.771 18.526 29584 Z= 0.408 Chirality : 0.047 0.378 3404 Planarity : 0.005 0.057 3668 Dihedral : 6.227 46.841 2864 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 17.54 Ramachandran Plot: Outliers : 1.22 % Allowed : 14.18 % Favored : 84.59 % Rotamer: Outliers : 4.41 % Allowed : 22.82 % Favored : 72.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.49 (0.16), residues: 2616 helix: 0.04 (0.16), residues: 1152 sheet: -1.63 (0.50), residues: 108 loop : -3.37 (0.16), residues: 1356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 533 TYR 0.014 0.001 TYR C 508 PHE 0.023 0.002 PHE C 270 TRP 0.021 0.001 TRP C 38 HIS 0.010 0.001 HIS B 482 Details of bonding type rmsd covalent geometry : bond 0.00380 (21804) covalent geometry : angle 0.77108 (29584) hydrogen bonds : bond 0.05137 ( 756) hydrogen bonds : angle 4.48190 ( 2184) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 389 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 284 time to evaluate : 0.707 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 109 MET cc_start: 0.2936 (pmm) cc_final: -0.0905 (ptt) REVERT: A 341 TYR cc_start: 0.7984 (OUTLIER) cc_final: 0.7502 (p90) REVERT: A 358 LEU cc_start: 0.8522 (OUTLIER) cc_final: 0.8262 (mp) REVERT: A 474 MET cc_start: 0.4670 (tmm) cc_final: 0.4164 (ttt) REVERT: A 509 ILE cc_start: 0.8708 (pt) cc_final: 0.8501 (mm) REVERT: A 513 TRP cc_start: 0.7410 (m-10) cc_final: 0.6854 (m-10) REVERT: A 522 GLU cc_start: 0.7649 (mm-30) cc_final: 0.6830 (pm20) REVERT: A 532 MET cc_start: 0.5957 (ppp) cc_final: 0.5631 (ppp) REVERT: B 109 MET cc_start: 0.2936 (pmm) cc_final: -0.0894 (ptt) REVERT: B 341 TYR cc_start: 0.7987 (OUTLIER) cc_final: 0.7501 (p90) REVERT: B 358 LEU cc_start: 0.8522 (OUTLIER) cc_final: 0.8263 (mp) REVERT: B 509 ILE cc_start: 0.8690 (pt) cc_final: 0.8479 (mm) REVERT: B 513 TRP cc_start: 0.7384 (m-10) cc_final: 0.6822 (m-10) REVERT: B 522 GLU cc_start: 0.7640 (mm-30) cc_final: 0.6824 (pm20) REVERT: B 532 MET cc_start: 0.5962 (ppp) cc_final: 0.5640 (ppp) REVERT: C 109 MET cc_start: 0.2923 (pmm) cc_final: -0.0914 (ptt) REVERT: C 341 TYR cc_start: 0.7980 (OUTLIER) cc_final: 0.7500 (p90) REVERT: C 358 LEU cc_start: 0.8544 (OUTLIER) cc_final: 0.8293 (mp) REVERT: C 474 MET cc_start: 0.4665 (tmm) cc_final: 0.4155 (ttt) REVERT: C 509 ILE cc_start: 0.8694 (pt) cc_final: 0.8493 (mm) REVERT: C 513 TRP cc_start: 0.7407 (m-10) cc_final: 0.6843 (m-10) REVERT: C 522 GLU cc_start: 0.7660 (mm-30) cc_final: 0.6828 (pm20) REVERT: C 532 MET cc_start: 0.5946 (ppp) cc_final: 0.5629 (ppp) REVERT: D 109 MET cc_start: 0.2941 (pmm) cc_final: -0.0883 (ptt) REVERT: D 341 TYR cc_start: 0.7975 (OUTLIER) cc_final: 0.7494 (p90) REVERT: D 358 LEU cc_start: 0.8528 (OUTLIER) cc_final: 0.8263 (mp) REVERT: D 474 MET cc_start: 0.4687 (tmm) cc_final: 0.4155 (ttt) REVERT: D 509 ILE cc_start: 0.8705 (pt) cc_final: 0.8493 (mm) REVERT: D 513 TRP cc_start: 0.7410 (m-10) cc_final: 0.6845 (m-10) REVERT: D 522 GLU cc_start: 0.7662 (mm-30) cc_final: 0.6838 (pm20) REVERT: D 532 MET cc_start: 0.5937 (ppp) cc_final: 0.5618 (ppp) outliers start: 105 outliers final: 49 residues processed: 365 average time/residue: 0.1310 time to fit residues: 77.9726 Evaluate side-chains 325 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 268 time to evaluate : 0.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 TYR Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain A residue 341 TYR Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 482 HIS Chi-restraints excluded: chain A residue 483 GLU Chi-restraints excluded: chain A residue 521 THR Chi-restraints excluded: chain A residue 558 CYS Chi-restraints excluded: chain A residue 566 PHE Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain B residue 98 TYR Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 341 TYR Chi-restraints excluded: chain B residue 358 LEU Chi-restraints excluded: chain B residue 379 VAL Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain B residue 473 GLN Chi-restraints excluded: chain B residue 482 HIS Chi-restraints excluded: chain B residue 483 GLU Chi-restraints excluded: chain B residue 521 THR Chi-restraints excluded: chain B residue 558 CYS Chi-restraints excluded: chain B residue 566 PHE Chi-restraints excluded: chain B residue 612 VAL Chi-restraints excluded: chain C residue 98 TYR Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain C residue 260 VAL Chi-restraints excluded: chain C residue 326 VAL Chi-restraints excluded: chain C residue 341 TYR Chi-restraints excluded: chain C residue 358 LEU Chi-restraints excluded: chain C residue 379 VAL Chi-restraints excluded: chain C residue 450 VAL Chi-restraints excluded: chain C residue 482 HIS Chi-restraints excluded: chain C residue 483 GLU Chi-restraints excluded: chain C residue 521 THR Chi-restraints excluded: chain C residue 558 CYS Chi-restraints excluded: chain C residue 566 PHE Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain D residue 98 TYR Chi-restraints excluded: chain D residue 256 VAL Chi-restraints excluded: chain D residue 260 VAL Chi-restraints excluded: chain D residue 326 VAL Chi-restraints excluded: chain D residue 341 TYR Chi-restraints excluded: chain D residue 358 LEU Chi-restraints excluded: chain D residue 379 VAL Chi-restraints excluded: chain D residue 450 VAL Chi-restraints excluded: chain D residue 482 HIS Chi-restraints excluded: chain D residue 483 GLU Chi-restraints excluded: chain D residue 521 THR Chi-restraints excluded: chain D residue 558 CYS Chi-restraints excluded: chain D residue 566 PHE Chi-restraints excluded: chain D residue 612 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 197 optimal weight: 8.9990 chunk 142 optimal weight: 5.9990 chunk 36 optimal weight: 0.6980 chunk 121 optimal weight: 0.8980 chunk 153 optimal weight: 1.9990 chunk 40 optimal weight: 0.7980 chunk 59 optimal weight: 4.9990 chunk 96 optimal weight: 0.9990 chunk 25 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 101 optimal weight: 4.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 118 HIS ** A 473 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 482 HIS ** A 599 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 639 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 118 HIS B 473 GLN B 482 HIS ** B 599 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 639 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 118 HIS ** C 473 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 482 HIS ** C 599 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 639 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 118 HIS ** D 473 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 482 HIS ** D 599 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 639 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4609 r_free = 0.4609 target = 0.216676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.175635 restraints weight = 39135.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.173178 restraints weight = 49957.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.170283 restraints weight = 37675.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.168395 restraints weight = 37591.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.167787 restraints weight = 34321.611| |-----------------------------------------------------------------------------| r_work (final): 0.4094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6773 moved from start: 0.4320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 21804 Z= 0.163 Angle : 0.764 18.575 29584 Z= 0.401 Chirality : 0.047 0.330 3404 Planarity : 0.005 0.057 3668 Dihedral : 6.045 45.664 2864 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 16.25 Ramachandran Plot: Outliers : 1.22 % Allowed : 13.99 % Favored : 84.79 % Rotamer: Outliers : 3.78 % Allowed : 23.91 % Favored : 72.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.29 (0.16), residues: 2616 helix: 0.14 (0.15), residues: 1152 sheet: -1.44 (0.51), residues: 108 loop : -3.19 (0.16), residues: 1356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 533 TYR 0.017 0.001 TYR D 88 PHE 0.027 0.002 PHE A 491 TRP 0.033 0.002 TRP A 618 HIS 0.008 0.001 HIS B 482 Details of bonding type rmsd covalent geometry : bond 0.00353 (21804) covalent geometry : angle 0.76440 (29584) hydrogen bonds : bond 0.04939 ( 756) hydrogen bonds : angle 4.42305 ( 2184) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 280 time to evaluate : 0.776 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 107 PHE cc_start: -0.0175 (OUTLIER) cc_final: -0.1138 (m-80) REVERT: A 109 MET cc_start: 0.3052 (pmm) cc_final: -0.1095 (ptt) REVERT: A 341 TYR cc_start: 0.8036 (OUTLIER) cc_final: 0.7557 (p90) REVERT: A 358 LEU cc_start: 0.8512 (OUTLIER) cc_final: 0.8298 (mp) REVERT: A 447 MET cc_start: 0.8358 (mtm) cc_final: 0.8133 (mtm) REVERT: A 513 TRP cc_start: 0.7330 (m-10) cc_final: 0.6799 (m-10) REVERT: A 522 GLU cc_start: 0.7536 (mm-30) cc_final: 0.6807 (pm20) REVERT: B 107 PHE cc_start: -0.0160 (OUTLIER) cc_final: -0.1134 (m-80) REVERT: B 109 MET cc_start: 0.3036 (pmm) cc_final: -0.1121 (ptt) REVERT: B 341 TYR cc_start: 0.8031 (OUTLIER) cc_final: 0.7553 (p90) REVERT: B 358 LEU cc_start: 0.8523 (OUTLIER) cc_final: 0.8295 (mp) REVERT: B 447 MET cc_start: 0.8369 (mtm) cc_final: 0.8156 (mtm) REVERT: B 513 TRP cc_start: 0.7315 (m-10) cc_final: 0.6786 (m-10) REVERT: B 522 GLU cc_start: 0.7536 (mm-30) cc_final: 0.6806 (pm20) REVERT: C 107 PHE cc_start: -0.0175 (OUTLIER) cc_final: -0.1147 (m-80) REVERT: C 109 MET cc_start: 0.3003 (pmm) cc_final: -0.1127 (ptt) REVERT: C 341 TYR cc_start: 0.8046 (OUTLIER) cc_final: 0.7568 (p90) REVERT: C 358 LEU cc_start: 0.8528 (OUTLIER) cc_final: 0.8294 (mp) REVERT: C 447 MET cc_start: 0.8358 (mtm) cc_final: 0.8151 (mtm) REVERT: C 474 MET cc_start: 0.4645 (tmm) cc_final: 0.4317 (ttt) REVERT: C 513 TRP cc_start: 0.7327 (m-10) cc_final: 0.6793 (m-10) REVERT: C 522 GLU cc_start: 0.7545 (mm-30) cc_final: 0.6806 (pm20) REVERT: D 107 PHE cc_start: -0.0172 (OUTLIER) cc_final: -0.1143 (m-80) REVERT: D 109 MET cc_start: 0.3027 (pmm) cc_final: -0.1110 (ptt) REVERT: D 341 TYR cc_start: 0.8054 (OUTLIER) cc_final: 0.7575 (p90) REVERT: D 358 LEU cc_start: 0.8516 (OUTLIER) cc_final: 0.8297 (mp) REVERT: D 447 MET cc_start: 0.8373 (mtm) cc_final: 0.8157 (mtm) REVERT: D 513 TRP cc_start: 0.7330 (m-10) cc_final: 0.6796 (m-10) REVERT: D 522 GLU cc_start: 0.7558 (mm-30) cc_final: 0.6812 (pm20) outliers start: 90 outliers final: 49 residues processed: 354 average time/residue: 0.1199 time to fit residues: 70.7213 Evaluate side-chains 317 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 256 time to evaluate : 0.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 TYR Chi-restraints excluded: chain A residue 107 PHE Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 257 ILE Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain A residue 341 TYR Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 482 HIS Chi-restraints excluded: chain A residue 521 THR Chi-restraints excluded: chain A residue 558 CYS Chi-restraints excluded: chain A residue 566 PHE Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain B residue 98 TYR Chi-restraints excluded: chain B residue 107 PHE Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain B residue 257 ILE Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 341 TYR Chi-restraints excluded: chain B residue 358 LEU Chi-restraints excluded: chain B residue 379 VAL Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain B residue 473 GLN Chi-restraints excluded: chain B residue 482 HIS Chi-restraints excluded: chain B residue 521 THR Chi-restraints excluded: chain B residue 558 CYS Chi-restraints excluded: chain B residue 566 PHE Chi-restraints excluded: chain B residue 612 VAL Chi-restraints excluded: chain C residue 98 TYR Chi-restraints excluded: chain C residue 107 PHE Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain C residue 257 ILE Chi-restraints excluded: chain C residue 326 VAL Chi-restraints excluded: chain C residue 341 TYR Chi-restraints excluded: chain C residue 358 LEU Chi-restraints excluded: chain C residue 379 VAL Chi-restraints excluded: chain C residue 450 VAL Chi-restraints excluded: chain C residue 482 HIS Chi-restraints excluded: chain C residue 521 THR Chi-restraints excluded: chain C residue 558 CYS Chi-restraints excluded: chain C residue 566 PHE Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain D residue 98 TYR Chi-restraints excluded: chain D residue 107 PHE Chi-restraints excluded: chain D residue 240 THR Chi-restraints excluded: chain D residue 256 VAL Chi-restraints excluded: chain D residue 257 ILE Chi-restraints excluded: chain D residue 326 VAL Chi-restraints excluded: chain D residue 341 TYR Chi-restraints excluded: chain D residue 358 LEU Chi-restraints excluded: chain D residue 379 VAL Chi-restraints excluded: chain D residue 450 VAL Chi-restraints excluded: chain D residue 482 HIS Chi-restraints excluded: chain D residue 521 THR Chi-restraints excluded: chain D residue 558 CYS Chi-restraints excluded: chain D residue 566 PHE Chi-restraints excluded: chain D residue 612 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 89 optimal weight: 0.0970 chunk 71 optimal weight: 6.9990 chunk 78 optimal weight: 10.0000 chunk 162 optimal weight: 5.9990 chunk 28 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 119 optimal weight: 2.9990 chunk 116 optimal weight: 6.9990 chunk 190 optimal weight: 6.9990 chunk 239 optimal weight: 0.7980 chunk 10 optimal weight: 3.9990 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 473 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 482 HIS ** A 599 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 477 ASN B 482 HIS ** B 599 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 473 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 482 HIS ** C 599 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 473 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 482 HIS ** D 599 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4590 r_free = 0.4590 target = 0.214818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.173914 restraints weight = 38855.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.169042 restraints weight = 49757.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.168170 restraints weight = 35395.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.165765 restraints weight = 35334.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.164166 restraints weight = 37173.673| |-----------------------------------------------------------------------------| r_work (final): 0.4031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6897 moved from start: 0.4659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 21804 Z= 0.195 Angle : 0.780 18.322 29584 Z= 0.410 Chirality : 0.048 0.310 3404 Planarity : 0.005 0.057 3668 Dihedral : 6.062 44.406 2864 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 16.86 Ramachandran Plot: Outliers : 1.22 % Allowed : 14.45 % Favored : 84.33 % Rotamer: Outliers : 3.66 % Allowed : 24.50 % Favored : 71.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.40 (0.16), residues: 2616 helix: 0.04 (0.15), residues: 1152 sheet: -1.20 (0.55), residues: 108 loop : -3.27 (0.16), residues: 1356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 333 TYR 0.017 0.002 TYR D 88 PHE 0.026 0.002 PHE B 491 TRP 0.045 0.002 TRP C 618 HIS 0.009 0.001 HIS C 482 Details of bonding type rmsd covalent geometry : bond 0.00438 (21804) covalent geometry : angle 0.77974 (29584) hydrogen bonds : bond 0.05259 ( 756) hydrogen bonds : angle 4.58192 ( 2184) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 282 time to evaluate : 0.730 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 107 PHE cc_start: -0.0063 (OUTLIER) cc_final: -0.1221 (m-80) REVERT: A 109 MET cc_start: 0.3092 (pmm) cc_final: -0.0979 (ptt) REVERT: A 207 ILE cc_start: 0.7895 (mp) cc_final: 0.7631 (mm) REVERT: A 341 TYR cc_start: 0.7972 (OUTLIER) cc_final: 0.7533 (p90) REVERT: A 358 LEU cc_start: 0.8528 (OUTLIER) cc_final: 0.8292 (mp) REVERT: A 509 ILE cc_start: 0.9283 (mm) cc_final: 0.8762 (pt) REVERT: A 513 TRP cc_start: 0.7093 (m-10) cc_final: 0.6794 (m-10) REVERT: A 522 GLU cc_start: 0.7435 (mm-30) cc_final: 0.6878 (pm20) REVERT: A 523 LYS cc_start: 0.8166 (ttpt) cc_final: 0.7762 (ttpt) REVERT: A 674 ILE cc_start: 0.3046 (OUTLIER) cc_final: 0.2506 (mt) REVERT: B 107 PHE cc_start: -0.0032 (OUTLIER) cc_final: -0.1204 (m-80) REVERT: B 109 MET cc_start: 0.3070 (pmm) cc_final: -0.0996 (ptt) REVERT: B 207 ILE cc_start: 0.7883 (mp) cc_final: 0.7619 (mm) REVERT: B 341 TYR cc_start: 0.7981 (OUTLIER) cc_final: 0.7545 (p90) REVERT: B 358 LEU cc_start: 0.8533 (OUTLIER) cc_final: 0.8287 (mp) REVERT: B 509 ILE cc_start: 0.9288 (mm) cc_final: 0.8765 (pt) REVERT: B 513 TRP cc_start: 0.7094 (m-10) cc_final: 0.6789 (m-10) REVERT: B 522 GLU cc_start: 0.7420 (mm-30) cc_final: 0.6867 (pm20) REVERT: B 523 LYS cc_start: 0.8165 (ttpt) cc_final: 0.7761 (ttpt) REVERT: B 674 ILE cc_start: 0.3154 (OUTLIER) cc_final: 0.2609 (mt) REVERT: C 107 PHE cc_start: -0.0106 (OUTLIER) cc_final: -0.1277 (m-80) REVERT: C 109 MET cc_start: 0.3039 (pmm) cc_final: -0.1019 (ptt) REVERT: C 207 ILE cc_start: 0.7884 (mp) cc_final: 0.7618 (mm) REVERT: C 341 TYR cc_start: 0.7967 (OUTLIER) cc_final: 0.7533 (p90) REVERT: C 358 LEU cc_start: 0.8559 (OUTLIER) cc_final: 0.8315 (mp) REVERT: C 474 MET cc_start: 0.4654 (tmm) cc_final: 0.4341 (ttt) REVERT: C 509 ILE cc_start: 0.9284 (mm) cc_final: 0.8759 (pt) REVERT: C 513 TRP cc_start: 0.7103 (m-10) cc_final: 0.6798 (m-10) REVERT: C 522 GLU cc_start: 0.7406 (mm-30) cc_final: 0.6848 (pm20) REVERT: C 523 LYS cc_start: 0.8166 (ttpt) cc_final: 0.7760 (ttpt) REVERT: C 674 ILE cc_start: 0.3150 (OUTLIER) cc_final: 0.2606 (mt) REVERT: D 107 PHE cc_start: -0.0051 (OUTLIER) cc_final: -0.1216 (m-80) REVERT: D 109 MET cc_start: 0.3029 (pmm) cc_final: -0.1015 (ptt) REVERT: D 207 ILE cc_start: 0.7883 (mp) cc_final: 0.7618 (mm) REVERT: D 341 TYR cc_start: 0.7984 (OUTLIER) cc_final: 0.7550 (p90) REVERT: D 358 LEU cc_start: 0.8561 (OUTLIER) cc_final: 0.8324 (mp) REVERT: D 509 ILE cc_start: 0.9280 (mm) cc_final: 0.8761 (pt) REVERT: D 513 TRP cc_start: 0.7107 (m-10) cc_final: 0.6804 (m-10) REVERT: D 522 GLU cc_start: 0.7434 (mm-30) cc_final: 0.6863 (pm20) REVERT: D 523 LYS cc_start: 0.8169 (ttpt) cc_final: 0.7763 (ttpt) REVERT: D 674 ILE cc_start: 0.3163 (OUTLIER) cc_final: 0.2617 (mt) outliers start: 87 outliers final: 52 residues processed: 353 average time/residue: 0.1245 time to fit residues: 73.2443 Evaluate side-chains 325 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 257 time to evaluate : 0.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 TYR Chi-restraints excluded: chain A residue 107 PHE Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 257 ILE Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain A residue 341 TYR Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 482 HIS Chi-restraints excluded: chain A residue 483 GLU Chi-restraints excluded: chain A residue 521 THR Chi-restraints excluded: chain A residue 558 CYS Chi-restraints excluded: chain A residue 584 VAL Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 674 ILE Chi-restraints excluded: chain B residue 98 TYR Chi-restraints excluded: chain B residue 107 PHE Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain B residue 257 ILE Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 341 TYR Chi-restraints excluded: chain B residue 358 LEU Chi-restraints excluded: chain B residue 379 VAL Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain B residue 482 HIS Chi-restraints excluded: chain B residue 483 GLU Chi-restraints excluded: chain B residue 521 THR Chi-restraints excluded: chain B residue 558 CYS Chi-restraints excluded: chain B residue 584 VAL Chi-restraints excluded: chain B residue 612 VAL Chi-restraints excluded: chain B residue 674 ILE Chi-restraints excluded: chain C residue 98 TYR Chi-restraints excluded: chain C residue 107 PHE Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain C residue 257 ILE Chi-restraints excluded: chain C residue 326 VAL Chi-restraints excluded: chain C residue 341 TYR Chi-restraints excluded: chain C residue 358 LEU Chi-restraints excluded: chain C residue 379 VAL Chi-restraints excluded: chain C residue 450 VAL Chi-restraints excluded: chain C residue 482 HIS Chi-restraints excluded: chain C residue 483 GLU Chi-restraints excluded: chain C residue 521 THR Chi-restraints excluded: chain C residue 558 CYS Chi-restraints excluded: chain C residue 584 VAL Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain C residue 674 ILE Chi-restraints excluded: chain D residue 98 TYR Chi-restraints excluded: chain D residue 107 PHE Chi-restraints excluded: chain D residue 240 THR Chi-restraints excluded: chain D residue 256 VAL Chi-restraints excluded: chain D residue 257 ILE Chi-restraints excluded: chain D residue 326 VAL Chi-restraints excluded: chain D residue 341 TYR Chi-restraints excluded: chain D residue 358 LEU Chi-restraints excluded: chain D residue 379 VAL Chi-restraints excluded: chain D residue 450 VAL Chi-restraints excluded: chain D residue 482 HIS Chi-restraints excluded: chain D residue 483 GLU Chi-restraints excluded: chain D residue 521 THR Chi-restraints excluded: chain D residue 558 CYS Chi-restraints excluded: chain D residue 584 VAL Chi-restraints excluded: chain D residue 612 VAL Chi-restraints excluded: chain D residue 674 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 200 optimal weight: 5.9990 chunk 238 optimal weight: 0.3980 chunk 124 optimal weight: 1.9990 chunk 209 optimal weight: 0.3980 chunk 92 optimal weight: 0.0770 chunk 99 optimal weight: 0.8980 chunk 74 optimal weight: 9.9990 chunk 210 optimal weight: 2.9990 chunk 230 optimal weight: 0.9990 chunk 227 optimal weight: 3.9990 chunk 116 optimal weight: 7.9990 overall best weight: 0.5540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 118 HIS ** A 473 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 599 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 599 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 473 GLN ** C 599 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 473 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 599 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4621 r_free = 0.4621 target = 0.218001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.177611 restraints weight = 39047.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.173171 restraints weight = 50749.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.171831 restraints weight = 34971.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.169975 restraints weight = 35162.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 53)----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.168823 restraints weight = 32323.170| |-----------------------------------------------------------------------------| r_work (final): 0.4083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6756 moved from start: 0.4846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.084 21804 Z= 0.146 Angle : 0.747 18.446 29584 Z= 0.391 Chirality : 0.046 0.285 3404 Planarity : 0.005 0.057 3668 Dihedral : 5.803 43.346 2864 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 15.57 Ramachandran Plot: Outliers : 1.22 % Allowed : 13.80 % Favored : 84.98 % Rotamer: Outliers : 3.03 % Allowed : 25.29 % Favored : 71.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.23 (0.17), residues: 2616 helix: 0.25 (0.15), residues: 1156 sheet: -0.97 (0.58), residues: 108 loop : -3.28 (0.16), residues: 1352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 333 TYR 0.015 0.001 TYR A 508 PHE 0.032 0.002 PHE C 491 TRP 0.048 0.002 TRP D 618 HIS 0.011 0.001 HIS C 482 Details of bonding type rmsd covalent geometry : bond 0.00307 (21804) covalent geometry : angle 0.74685 (29584) hydrogen bonds : bond 0.04726 ( 756) hydrogen bonds : angle 4.39730 ( 2184) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 293 time to evaluate : 0.716 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 107 PHE cc_start: -0.0040 (OUTLIER) cc_final: -0.1266 (m-80) REVERT: A 109 MET cc_start: 0.2726 (pmm) cc_final: -0.1149 (ptt) REVERT: A 207 ILE cc_start: 0.7974 (mp) cc_final: 0.7598 (mm) REVERT: A 513 TRP cc_start: 0.7028 (m-10) cc_final: 0.6728 (m-10) REVERT: A 522 GLU cc_start: 0.7476 (mm-30) cc_final: 0.6807 (pm20) REVERT: A 674 ILE cc_start: 0.3049 (OUTLIER) cc_final: 0.2507 (mt) REVERT: B 107 PHE cc_start: -0.0009 (OUTLIER) cc_final: -0.1246 (m-80) REVERT: B 109 MET cc_start: 0.2688 (pmm) cc_final: -0.1175 (ptt) REVERT: B 207 ILE cc_start: 0.7975 (mp) cc_final: 0.7598 (mm) REVERT: B 513 TRP cc_start: 0.7023 (m-10) cc_final: 0.6718 (m-10) REVERT: B 522 GLU cc_start: 0.7485 (mm-30) cc_final: 0.6808 (pm20) REVERT: B 674 ILE cc_start: 0.3047 (OUTLIER) cc_final: 0.2506 (mt) REVERT: C 107 PHE cc_start: -0.0035 (OUTLIER) cc_final: -0.1275 (m-80) REVERT: C 109 MET cc_start: 0.2673 (pmm) cc_final: -0.1182 (ptt) REVERT: C 207 ILE cc_start: 0.7981 (mp) cc_final: 0.7600 (mm) REVERT: C 513 TRP cc_start: 0.7026 (m-10) cc_final: 0.6723 (m-10) REVERT: C 522 GLU cc_start: 0.7460 (mm-30) cc_final: 0.6802 (pm20) REVERT: C 674 ILE cc_start: 0.3038 (OUTLIER) cc_final: 0.2503 (mt) REVERT: D 107 PHE cc_start: -0.0036 (OUTLIER) cc_final: -0.1258 (m-80) REVERT: D 109 MET cc_start: 0.2686 (pmm) cc_final: -0.1171 (ptt) REVERT: D 207 ILE cc_start: 0.7974 (mp) cc_final: 0.7594 (mm) REVERT: D 513 TRP cc_start: 0.7047 (m-10) cc_final: 0.6744 (m-10) REVERT: D 522 GLU cc_start: 0.7478 (mm-30) cc_final: 0.6811 (pm20) REVERT: D 674 ILE cc_start: 0.3042 (OUTLIER) cc_final: 0.2509 (mt) outliers start: 72 outliers final: 41 residues processed: 357 average time/residue: 0.1221 time to fit residues: 72.7467 Evaluate side-chains 309 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 260 time to evaluate : 0.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 TYR Chi-restraints excluded: chain A residue 107 PHE Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 482 HIS Chi-restraints excluded: chain A residue 483 GLU Chi-restraints excluded: chain A residue 521 THR Chi-restraints excluded: chain A residue 558 CYS Chi-restraints excluded: chain A residue 584 VAL Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 630 VAL Chi-restraints excluded: chain A residue 674 ILE Chi-restraints excluded: chain B residue 98 TYR Chi-restraints excluded: chain B residue 107 PHE Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 379 VAL Chi-restraints excluded: chain B residue 482 HIS Chi-restraints excluded: chain B residue 483 GLU Chi-restraints excluded: chain B residue 521 THR Chi-restraints excluded: chain B residue 558 CYS Chi-restraints excluded: chain B residue 584 VAL Chi-restraints excluded: chain B residue 612 VAL Chi-restraints excluded: chain B residue 674 ILE Chi-restraints excluded: chain C residue 98 TYR Chi-restraints excluded: chain C residue 107 PHE Chi-restraints excluded: chain C residue 225 THR Chi-restraints excluded: chain C residue 326 VAL Chi-restraints excluded: chain C residue 379 VAL Chi-restraints excluded: chain C residue 482 HIS Chi-restraints excluded: chain C residue 483 GLU Chi-restraints excluded: chain C residue 521 THR Chi-restraints excluded: chain C residue 558 CYS Chi-restraints excluded: chain C residue 584 VAL Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain C residue 674 ILE Chi-restraints excluded: chain D residue 98 TYR Chi-restraints excluded: chain D residue 107 PHE Chi-restraints excluded: chain D residue 225 THR Chi-restraints excluded: chain D residue 326 VAL Chi-restraints excluded: chain D residue 379 VAL Chi-restraints excluded: chain D residue 482 HIS Chi-restraints excluded: chain D residue 483 GLU Chi-restraints excluded: chain D residue 521 THR Chi-restraints excluded: chain D residue 558 CYS Chi-restraints excluded: chain D residue 584 VAL Chi-restraints excluded: chain D residue 612 VAL Chi-restraints excluded: chain D residue 674 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 172 optimal weight: 2.9990 chunk 190 optimal weight: 7.9990 chunk 132 optimal weight: 9.9990 chunk 119 optimal weight: 3.9990 chunk 38 optimal weight: 0.5980 chunk 107 optimal weight: 0.9990 chunk 149 optimal weight: 20.0000 chunk 35 optimal weight: 0.9990 chunk 73 optimal weight: 0.0670 chunk 187 optimal weight: 3.9990 chunk 99 optimal weight: 2.9990 overall best weight: 1.1324 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 158 ASN ** A 473 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 599 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 158 ASN B 473 GLN ** B 599 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 158 ASN C 473 GLN C 477 ASN ** C 599 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 158 ASN ** D 473 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 477 ASN ** D 599 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4602 r_free = 0.4602 target = 0.215719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4170 r_free = 0.4170 target = 0.174454 restraints weight = 38820.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.174217 restraints weight = 47612.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 59)----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.170260 restraints weight = 37130.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.168929 restraints weight = 38633.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.167028 restraints weight = 35416.153| |-----------------------------------------------------------------------------| r_work (final): 0.4075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6804 moved from start: 0.5109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 21804 Z= 0.162 Angle : 0.756 17.894 29584 Z= 0.398 Chirality : 0.047 0.305 3404 Planarity : 0.005 0.057 3668 Dihedral : 5.739 41.957 2864 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 15.90 Ramachandran Plot: Outliers : 1.22 % Allowed : 13.95 % Favored : 84.82 % Rotamer: Outliers : 2.73 % Allowed : 24.96 % Favored : 72.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.15 (0.17), residues: 2616 helix: 0.39 (0.16), residues: 1128 sheet: -1.09 (0.57), residues: 108 loop : -3.22 (0.16), residues: 1380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 333 TYR 0.016 0.001 TYR A 508 PHE 0.032 0.002 PHE B 491 TRP 0.051 0.002 TRP D 618 HIS 0.005 0.001 HIS C 539 Details of bonding type rmsd covalent geometry : bond 0.00350 (21804) covalent geometry : angle 0.75649 (29584) hydrogen bonds : bond 0.04947 ( 756) hydrogen bonds : angle 4.39781 ( 2184) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 289 time to evaluate : 0.748 Fit side-chains revert: symmetry clash REVERT: A 107 PHE cc_start: 0.0204 (OUTLIER) cc_final: -0.1152 (m-80) REVERT: A 109 MET cc_start: 0.2811 (pmm) cc_final: -0.0541 (ptt) REVERT: A 207 ILE cc_start: 0.7874 (mp) cc_final: 0.7525 (mm) REVERT: A 341 TYR cc_start: 0.7934 (OUTLIER) cc_final: 0.7439 (p90) REVERT: A 513 TRP cc_start: 0.6811 (m-10) cc_final: 0.6607 (m-10) REVERT: A 522 GLU cc_start: 0.7261 (mm-30) cc_final: 0.6844 (pm20) REVERT: A 625 HIS cc_start: 0.6817 (m-70) cc_final: 0.6305 (m-70) REVERT: A 674 ILE cc_start: 0.2969 (OUTLIER) cc_final: 0.2405 (mt) REVERT: B 107 PHE cc_start: 0.0212 (OUTLIER) cc_final: -0.1151 (m-80) REVERT: B 109 MET cc_start: 0.2740 (pmm) cc_final: -0.0612 (ptt) REVERT: B 207 ILE cc_start: 0.7863 (mp) cc_final: 0.7520 (mm) REVERT: B 341 TYR cc_start: 0.7945 (OUTLIER) cc_final: 0.7446 (p90) REVERT: B 522 GLU cc_start: 0.7275 (mm-30) cc_final: 0.6849 (pm20) REVERT: B 625 HIS cc_start: 0.6837 (m-70) cc_final: 0.6283 (m-70) REVERT: B 674 ILE cc_start: 0.2956 (OUTLIER) cc_final: 0.2385 (mt) REVERT: C 107 PHE cc_start: 0.0152 (OUTLIER) cc_final: -0.1208 (m-80) REVERT: C 109 MET cc_start: 0.2725 (pmm) cc_final: -0.0633 (ptt) REVERT: C 207 ILE cc_start: 0.7893 (mp) cc_final: 0.7546 (mm) REVERT: C 341 TYR cc_start: 0.7931 (OUTLIER) cc_final: 0.7443 (p90) REVERT: C 513 TRP cc_start: 0.6826 (m-10) cc_final: 0.6622 (m-10) REVERT: C 522 GLU cc_start: 0.7275 (mm-30) cc_final: 0.6838 (pm20) REVERT: C 625 HIS cc_start: 0.6840 (m-70) cc_final: 0.6289 (m-70) REVERT: C 674 ILE cc_start: 0.2971 (OUTLIER) cc_final: 0.2400 (mt) REVERT: D 107 PHE cc_start: 0.0199 (OUTLIER) cc_final: -0.1157 (m-80) REVERT: D 109 MET cc_start: 0.2722 (pmm) cc_final: -0.0728 (ptt) REVERT: D 207 ILE cc_start: 0.7870 (mp) cc_final: 0.7521 (mm) REVERT: D 341 TYR cc_start: 0.7940 (OUTLIER) cc_final: 0.7447 (p90) REVERT: D 513 TRP cc_start: 0.6812 (m-10) cc_final: 0.6601 (m-10) REVERT: D 522 GLU cc_start: 0.7289 (mm-30) cc_final: 0.6849 (pm20) REVERT: D 625 HIS cc_start: 0.6852 (m-70) cc_final: 0.6299 (m-70) REVERT: D 674 ILE cc_start: 0.2976 (OUTLIER) cc_final: 0.2402 (mt) outliers start: 65 outliers final: 36 residues processed: 341 average time/residue: 0.1190 time to fit residues: 68.9444 Evaluate side-chains 324 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 276 time to evaluate : 0.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 PHE Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain A residue 341 TYR Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 482 HIS Chi-restraints excluded: chain A residue 558 CYS Chi-restraints excluded: chain A residue 584 VAL Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 630 VAL Chi-restraints excluded: chain A residue 674 ILE Chi-restraints excluded: chain B residue 107 PHE Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 341 TYR Chi-restraints excluded: chain B residue 379 VAL Chi-restraints excluded: chain B residue 473 GLN Chi-restraints excluded: chain B residue 482 HIS Chi-restraints excluded: chain B residue 558 CYS Chi-restraints excluded: chain B residue 584 VAL Chi-restraints excluded: chain B residue 612 VAL Chi-restraints excluded: chain B residue 630 VAL Chi-restraints excluded: chain B residue 674 ILE Chi-restraints excluded: chain C residue 107 PHE Chi-restraints excluded: chain C residue 225 THR Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 326 VAL Chi-restraints excluded: chain C residue 341 TYR Chi-restraints excluded: chain C residue 379 VAL Chi-restraints excluded: chain C residue 482 HIS Chi-restraints excluded: chain C residue 558 CYS Chi-restraints excluded: chain C residue 584 VAL Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain C residue 674 ILE Chi-restraints excluded: chain D residue 107 PHE Chi-restraints excluded: chain D residue 225 THR Chi-restraints excluded: chain D residue 230 ILE Chi-restraints excluded: chain D residue 240 THR Chi-restraints excluded: chain D residue 326 VAL Chi-restraints excluded: chain D residue 341 TYR Chi-restraints excluded: chain D residue 379 VAL Chi-restraints excluded: chain D residue 482 HIS Chi-restraints excluded: chain D residue 558 CYS Chi-restraints excluded: chain D residue 584 VAL Chi-restraints excluded: chain D residue 612 VAL Chi-restraints excluded: chain D residue 674 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 40 optimal weight: 0.0970 chunk 236 optimal weight: 0.6980 chunk 9 optimal weight: 10.0000 chunk 170 optimal weight: 0.9980 chunk 159 optimal weight: 0.9990 chunk 246 optimal weight: 0.0370 chunk 89 optimal weight: 4.9990 chunk 219 optimal weight: 0.8980 chunk 86 optimal weight: 1.9990 chunk 15 optimal weight: 7.9990 chunk 222 optimal weight: 1.9990 overall best weight: 0.5456 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 473 GLN ** A 599 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 477 ASN ** B 599 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 473 GLN ** C 599 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 473 GLN ** D 599 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4620 r_free = 0.4620 target = 0.217711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.175180 restraints weight = 39240.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.170454 restraints weight = 44801.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 59)----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.165442 restraints weight = 31693.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.165683 restraints weight = 32003.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.165206 restraints weight = 27807.527| |-----------------------------------------------------------------------------| r_work (final): 0.4042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6866 moved from start: 0.5381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 21804 Z= 0.149 Angle : 0.752 17.927 29584 Z= 0.396 Chirality : 0.047 0.277 3404 Planarity : 0.005 0.057 3668 Dihedral : 5.628 41.292 2864 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 14.36 Ramachandran Plot: Outliers : 1.38 % Allowed : 12.84 % Favored : 85.78 % Rotamer: Outliers : 1.85 % Allowed : 26.01 % Favored : 72.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.20 (0.17), residues: 2616 helix: 0.39 (0.16), residues: 1140 sheet: -1.41 (0.55), residues: 116 loop : -3.30 (0.16), residues: 1360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 333 TYR 0.053 0.002 TYR B 288 PHE 0.035 0.002 PHE C 491 TRP 0.050 0.002 TRP C 618 HIS 0.005 0.001 HIS D 539 Details of bonding type rmsd covalent geometry : bond 0.00315 (21804) covalent geometry : angle 0.75181 (29584) hydrogen bonds : bond 0.04681 ( 756) hydrogen bonds : angle 4.39918 ( 2184) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 286 time to evaluate : 0.665 Fit side-chains revert: symmetry clash REVERT: A 107 PHE cc_start: 0.0252 (OUTLIER) cc_final: -0.1119 (m-80) REVERT: A 109 MET cc_start: 0.2427 (pmm) cc_final: -0.0926 (ptt) REVERT: A 207 ILE cc_start: 0.8005 (mp) cc_final: 0.7644 (mm) REVERT: A 513 TRP cc_start: 0.6886 (m-10) cc_final: 0.6676 (m-10) REVERT: A 522 GLU cc_start: 0.7406 (mm-30) cc_final: 0.6828 (pm20) REVERT: A 658 ASN cc_start: 0.7089 (t0) cc_final: 0.6847 (t0) REVERT: A 674 ILE cc_start: 0.2803 (OUTLIER) cc_final: 0.2229 (mt) REVERT: B 107 PHE cc_start: 0.0236 (OUTLIER) cc_final: -0.1131 (m-80) REVERT: B 109 MET cc_start: 0.2567 (pmm) cc_final: -0.0949 (ptt) REVERT: B 207 ILE cc_start: 0.8005 (mp) cc_final: 0.7644 (mm) REVERT: B 522 GLU cc_start: 0.7402 (mm-30) cc_final: 0.6830 (pm20) REVERT: B 658 ASN cc_start: 0.7066 (t0) cc_final: 0.6823 (t0) REVERT: B 674 ILE cc_start: 0.2818 (OUTLIER) cc_final: 0.2243 (mt) REVERT: C 107 PHE cc_start: 0.0224 (OUTLIER) cc_final: -0.1132 (m-80) REVERT: C 109 MET cc_start: 0.2579 (pmm) cc_final: -0.0931 (ptt) REVERT: C 207 ILE cc_start: 0.8041 (mp) cc_final: 0.7687 (mm) REVERT: C 474 MET cc_start: 0.3823 (tpt) cc_final: 0.3609 (tpp) REVERT: C 513 TRP cc_start: 0.6903 (m-10) cc_final: 0.6685 (m-10) REVERT: C 522 GLU cc_start: 0.7400 (mm-30) cc_final: 0.6833 (pm20) REVERT: C 658 ASN cc_start: 0.7085 (t0) cc_final: 0.6842 (t0) REVERT: C 674 ILE cc_start: 0.2821 (OUTLIER) cc_final: 0.2244 (mt) REVERT: D 107 PHE cc_start: 0.0194 (OUTLIER) cc_final: -0.1167 (m-80) REVERT: D 109 MET cc_start: 0.2519 (pmm) cc_final: -0.0986 (ptt) REVERT: D 207 ILE cc_start: 0.8023 (mp) cc_final: 0.7657 (mm) REVERT: D 341 TYR cc_start: 0.7938 (OUTLIER) cc_final: 0.7422 (p90) REVERT: D 513 TRP cc_start: 0.6923 (m-10) cc_final: 0.6708 (m-10) REVERT: D 522 GLU cc_start: 0.7415 (mm-30) cc_final: 0.6830 (pm20) REVERT: D 658 ASN cc_start: 0.7075 (t0) cc_final: 0.6836 (t0) REVERT: D 674 ILE cc_start: 0.2812 (OUTLIER) cc_final: 0.2238 (mt) outliers start: 44 outliers final: 33 residues processed: 322 average time/residue: 0.1161 time to fit residues: 63.3798 Evaluate side-chains 316 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 274 time to evaluate : 0.871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 PHE Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 482 HIS Chi-restraints excluded: chain A residue 558 CYS Chi-restraints excluded: chain A residue 584 VAL Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 674 ILE Chi-restraints excluded: chain B residue 107 PHE Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 379 VAL Chi-restraints excluded: chain B residue 482 HIS Chi-restraints excluded: chain B residue 558 CYS Chi-restraints excluded: chain B residue 584 VAL Chi-restraints excluded: chain B residue 612 VAL Chi-restraints excluded: chain B residue 630 VAL Chi-restraints excluded: chain B residue 674 ILE Chi-restraints excluded: chain C residue 107 PHE Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 326 VAL Chi-restraints excluded: chain C residue 379 VAL Chi-restraints excluded: chain C residue 473 GLN Chi-restraints excluded: chain C residue 482 HIS Chi-restraints excluded: chain C residue 521 THR Chi-restraints excluded: chain C residue 558 CYS Chi-restraints excluded: chain C residue 584 VAL Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain C residue 674 ILE Chi-restraints excluded: chain D residue 107 PHE Chi-restraints excluded: chain D residue 230 ILE Chi-restraints excluded: chain D residue 240 THR Chi-restraints excluded: chain D residue 326 VAL Chi-restraints excluded: chain D residue 341 TYR Chi-restraints excluded: chain D residue 379 VAL Chi-restraints excluded: chain D residue 482 HIS Chi-restraints excluded: chain D residue 521 THR Chi-restraints excluded: chain D residue 558 CYS Chi-restraints excluded: chain D residue 584 VAL Chi-restraints excluded: chain D residue 612 VAL Chi-restraints excluded: chain D residue 674 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 130 optimal weight: 1.9990 chunk 42 optimal weight: 0.8980 chunk 236 optimal weight: 0.7980 chunk 217 optimal weight: 0.9990 chunk 14 optimal weight: 6.9990 chunk 258 optimal weight: 1.9990 chunk 96 optimal weight: 0.8980 chunk 90 optimal weight: 0.9980 chunk 235 optimal weight: 3.9990 chunk 202 optimal weight: 0.0870 chunk 229 optimal weight: 7.9990 overall best weight: 0.7358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 473 GLN ** A 599 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 599 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 473 GLN ** C 599 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 473 GLN D 477 ASN ** D 599 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4612 r_free = 0.4612 target = 0.217070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4188 r_free = 0.4188 target = 0.176358 restraints weight = 38664.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.172768 restraints weight = 49328.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.170345 restraints weight = 38306.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.170575 restraints weight = 38366.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.170163 restraints weight = 33190.008| |-----------------------------------------------------------------------------| r_work (final): 0.4109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6716 moved from start: 0.5601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 21804 Z= 0.152 Angle : 0.742 17.686 29584 Z= 0.391 Chirality : 0.047 0.265 3404 Planarity : 0.005 0.057 3668 Dihedral : 5.555 39.700 2864 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 14.52 Ramachandran Plot: Outliers : 1.07 % Allowed : 13.34 % Favored : 85.59 % Rotamer: Outliers : 2.35 % Allowed : 25.67 % Favored : 71.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.19 (0.17), residues: 2616 helix: 0.41 (0.16), residues: 1136 sheet: -1.39 (0.55), residues: 116 loop : -3.30 (0.16), residues: 1364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 542 TYR 0.050 0.002 TYR D 288 PHE 0.033 0.002 PHE C 491 TRP 0.044 0.002 TRP D 618 HIS 0.005 0.001 HIS D 539 Details of bonding type rmsd covalent geometry : bond 0.00326 (21804) covalent geometry : angle 0.74217 (29584) hydrogen bonds : bond 0.04745 ( 756) hydrogen bonds : angle 4.38011 ( 2184) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3810.44 seconds wall clock time: 66 minutes 55.12 seconds (4015.12 seconds total)