Starting phenix.real_space_refine on Sun Aug 24 16:55:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7yij_33860/08_2025/7yij_33860.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yij_33860/08_2025/7yij_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_33860/08_2025/7yij_33860.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yij_33860/08_2025/7yij_33860.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7yij_33860/08_2025/7yij_33860.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yij_33860/08_2025/7yij_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): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 21313 Number of models: 1 Model: "" Number of chains: 2 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: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' K': 1} Classifications: {'undetermined': 1} Restraints were copied for chains: B, C, D Time building chain proxies: 5.94, per 1000 atoms: 0.28 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: 1.84 Conformation dependent library (CDL) restraints added in 899.4 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.69 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: 3.95 Time building geometry restraints manager: 2.42 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: 4.790 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.450 Check model and map are aligned: 0.080 Set scattering table: 0.080 Process input model: 21.170 Find NCS groups from input model: 0.470 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.460 ------------------------------------------------------------------------------- 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 aren 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 : 0.957 Fit side-chains REVERT: A 376 ILE cc_start: 0.5143 (tt) cc_final: 0.4833 (mt) REVERT: A 442 THR cc_start: 0.8832 (p) cc_final: 0.8562 (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: 0.5114 (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: 0.8739 (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: 0.4840 (mt) REVERT: C 442 THR cc_start: 0.8724 (p) cc_final: 0.8456 (t) REVERT: C 513 TRP cc_start: 0.7408 (m-10) cc_final: 0.7155 (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: 0.6579 (t0) cc_final: 0.6347 (t0) outliers start: 0 outliers final: 0 residues processed: 316 average time/residue: 0.1267 time to fit residues: 67.8218 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 : 0.816 ------------------------------------------------------------------------------- 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 = 0.3968 r_free = 0.3968 target = 0.159073 restraints weight = 39761.535| |-----------------------------------------------------------------------------| r_work (final): 0.3946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7021 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 aren 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 : 0.814 Fit side-chains revert: symmetry clash REVERT: A 207 ILE cc_start: 0.8268 (mp) cc_final: 0.7969 (mm) REVERT: A 341 TYR cc_start: 0.8190 (OUTLIER) cc_final: 0.7712 (p90) REVERT: A 506 MET cc_start: 0.7618 (tmm) cc_final: 0.7408 (tmm) REVERT: A 509 ILE cc_start: 0.8763 (pt) cc_final: 0.8435 (mm) REVERT: A 513 TRP cc_start: 0.7591 (m-10) cc_final: 0.7090 (m-10) REVERT: A 522 GLU cc_start: 0.7880 (mm-30) cc_final: 0.6822 (pm20) REVERT: A 676 PHE cc_start: 0.5186 (p90) cc_final: 0.4469 (p90) REVERT: B 207 ILE cc_start: 0.8257 (mp) cc_final: 0.7958 (mm) REVERT: B 341 TYR cc_start: 0.8193 (OUTLIER) cc_final: 0.7720 (p90) REVERT: B 506 MET cc_start: 0.7621 (tmm) cc_final: 0.7409 (tmm) REVERT: B 509 ILE cc_start: 0.8763 (pt) cc_final: 0.8435 (mm) REVERT: B 513 TRP cc_start: 0.7587 (m-10) cc_final: 0.7091 (m-10) REVERT: B 522 GLU cc_start: 0.7870 (mm-30) cc_final: 0.6817 (pm20) REVERT: B 676 PHE cc_start: 0.5176 (p90) cc_final: 0.4509 (p90) REVERT: C 207 ILE cc_start: 0.8263 (mp) cc_final: 0.7962 (mm) REVERT: C 341 TYR cc_start: 0.8186 (OUTLIER) cc_final: 0.7709 (p90) REVERT: C 506 MET cc_start: 0.7624 (tmm) cc_final: 0.7412 (tmm) REVERT: C 509 ILE cc_start: 0.8762 (pt) cc_final: 0.8440 (mm) REVERT: C 513 TRP cc_start: 0.7597 (m-10) cc_final: 0.7096 (m-10) REVERT: C 522 GLU cc_start: 0.7871 (mm-30) cc_final: 0.6821 (pm20) REVERT: C 676 PHE cc_start: 0.5166 (p90) cc_final: 0.4503 (p90) REVERT: D 38 TRP cc_start: 0.4019 (OUTLIER) cc_final: 0.3791 (p-90) REVERT: D 207 ILE cc_start: 0.8261 (mp) cc_final: 0.7963 (mm) REVERT: D 341 TYR cc_start: 0.8186 (OUTLIER) cc_final: 0.7714 (p90) REVERT: D 506 MET cc_start: 0.7618 (tmm) cc_final: 0.7402 (tmm) REVERT: D 509 ILE cc_start: 0.8762 (pt) cc_final: 0.8435 (mm) REVERT: D 513 TRP cc_start: 0.7596 (m-10) cc_final: 0.7099 (m-10) REVERT: D 522 GLU cc_start: 0.7859 (mm-30) cc_final: 0.6813 (pm20) REVERT: D 676 PHE cc_start: 0.5176 (p90) cc_final: 0.4510 (p90) outliers start: 100 outliers final: 56 residues processed: 320 average time/residue: 0.1348 time to fit residues: 70.7870 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 : 0.842 ------------------------------------------------------------------------------- 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 = 0.4620 r_free = 0.4620 target = 0.217916 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.175424 restraints weight = 38329.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 67)----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.165135 restraints weight = 47579.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.163661 restraints weight = 43146.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.163973 restraints weight = 31291.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.164001 restraints weight = 29220.891| |-----------------------------------------------------------------------------| r_work (final): 0.4044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6865 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 aren 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 : 0.831 Fit side-chains REVERT: A 509 ILE cc_start: 0.8746 (pt) cc_final: 0.8427 (mm) REVERT: A 513 TRP cc_start: 0.7440 (m-10) cc_final: 0.6988 (m-10) REVERT: A 522 GLU cc_start: 0.7700 (mm-30) cc_final: 0.6702 (pm20) REVERT: B 509 ILE cc_start: 0.8742 (pt) cc_final: 0.8432 (mm) REVERT: B 513 TRP cc_start: 0.7426 (m-10) cc_final: 0.6979 (m-10) REVERT: B 522 GLU cc_start: 0.7695 (mm-30) cc_final: 0.6699 (pm20) REVERT: C 509 ILE cc_start: 0.8736 (pt) cc_final: 0.8416 (mm) REVERT: C 513 TRP cc_start: 0.7422 (m-10) cc_final: 0.6979 (m-10) REVERT: C 522 GLU cc_start: 0.7711 (mm-30) cc_final: 0.6702 (pm20) REVERT: D 509 ILE cc_start: 0.8747 (pt) cc_final: 0.8429 (mm) REVERT: D 513 TRP cc_start: 0.7430 (m-10) cc_final: 0.6980 (m-10) REVERT: D 522 GLU cc_start: 0.7704 (mm-30) cc_final: 0.6699 (pm20) outliers start: 60 outliers final: 28 residues processed: 345 average time/residue: 0.1341 time to fit residues: 76.2519 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 : 0.836 ------------------------------------------------------------------------------- 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: 5.9990 chunk 246 optimal weight: 3.9990 chunk 245 optimal weight: 0.9980 chunk 239 optimal weight: 0.9980 chunk 62 optimal weight: 0.3980 chunk 148 optimal weight: 9.9990 chunk 44 optimal weight: 2.9990 chunk 202 optimal weight: 10.0000 chunk 139 optimal weight: 4.9990 chunk 96 optimal weight: 3.9990 chunk 131 optimal weight: 10.0000 overall best weight: 1.8784 ------------------------------------------------------------------------------- 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 482 HIS ** C 639 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 158 ASN D 482 HIS ** 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 = 0.4596 r_free = 0.4596 target = 0.215429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4233 r_free = 0.4233 target = 0.181104 restraints weight = 38912.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4212 r_free = 0.4212 target = 0.179323 restraints weight = 53123.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4198 r_free = 0.4198 target = 0.178143 restraints weight = 43625.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4184 r_free = 0.4184 target = 0.176895 restraints weight = 42257.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 56)----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.175626 restraints weight = 45419.922| |-----------------------------------------------------------------------------| r_work (final): 0.4176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6636 moved from start: 0.3636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.089 21804 Z= 0.210 Angle : 0.819 19.288 29584 Z= 0.431 Chirality : 0.048 0.288 3404 Planarity : 0.005 0.056 3668 Dihedral : 6.430 45.931 2864 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 17.68 Ramachandran Plot: Outliers : 1.22 % Allowed : 14.72 % Favored : 84.06 % Rotamer: Outliers : 3.45 % Allowed : 21.13 % Favored : 75.42 % 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 aren not related in a simple way. whole: -2.58 (0.16), residues: 2616 helix: -0.06 (0.16), residues: 1156 sheet: -1.68 (0.48), residues: 108 loop : -3.40 (0.16), residues: 1352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 333 TYR 0.017 0.002 TYR C 88 PHE 0.033 0.002 PHE D 676 TRP 0.021 0.002 TRP A 618 HIS 0.013 0.002 HIS A 482 Details of bonding type rmsd covalent geometry : bond 0.00473 (21804) covalent geometry : angle 0.81857 (29584) hydrogen bonds : bond 0.05607 ( 756) hydrogen bonds : angle 4.64860 ( 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 381 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 299 time to evaluate : 0.846 Fit side-chains REVERT: A 28 PHE cc_start: 0.3289 (OUTLIER) cc_final: 0.2219 (m-80) REVERT: A 109 MET cc_start: 0.2707 (pmm) cc_final: -0.1057 (ptt) REVERT: A 509 ILE cc_start: 0.8367 (pt) cc_final: 0.8017 (mm) REVERT: A 513 TRP cc_start: 0.7114 (m-10) cc_final: 0.6663 (m-10) REVERT: A 522 GLU cc_start: 0.7363 (mm-30) cc_final: 0.6785 (pm20) REVERT: B 28 PHE cc_start: 0.3297 (OUTLIER) cc_final: 0.2227 (m-80) REVERT: B 109 MET cc_start: 0.2731 (pmm) cc_final: -0.1048 (ptt) REVERT: B 509 ILE cc_start: 0.8361 (pt) cc_final: 0.8008 (mm) REVERT: B 513 TRP cc_start: 0.7105 (m-10) cc_final: 0.6658 (m-10) REVERT: B 522 GLU cc_start: 0.7359 (mm-30) cc_final: 0.6777 (pm20) REVERT: C 28 PHE cc_start: 0.3291 (OUTLIER) cc_final: 0.2223 (m-80) REVERT: C 109 MET cc_start: 0.2727 (pmm) cc_final: -0.1053 (ptt) REVERT: C 509 ILE cc_start: 0.8361 (pt) cc_final: 0.8000 (mm) REVERT: C 513 TRP cc_start: 0.7116 (m-10) cc_final: 0.6664 (m-10) REVERT: C 522 GLU cc_start: 0.7377 (mm-30) cc_final: 0.6784 (pm20) REVERT: D 28 PHE cc_start: 0.3248 (OUTLIER) cc_final: 0.2178 (m-80) REVERT: D 109 MET cc_start: 0.2703 (pmm) cc_final: -0.1089 (ptt) REVERT: D 509 ILE cc_start: 0.8363 (pt) cc_final: 0.8001 (mm) REVERT: D 513 TRP cc_start: 0.7106 (m-10) cc_final: 0.6657 (m-10) REVERT: D 522 GLU cc_start: 0.7371 (mm-30) cc_final: 0.6786 (pm20) outliers start: 82 outliers final: 52 residues processed: 357 average time/residue: 0.1391 time to fit residues: 80.4407 Evaluate side-chains 318 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 262 time to evaluate : 0.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 PHE Chi-restraints excluded: chain A residue 118 HIS 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 118 HIS 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 118 HIS 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 118 HIS 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: 10.0000 chunk 234 optimal weight: 0.4980 chunk 199 optimal weight: 1.9990 chunk 88 optimal weight: 0.9990 chunk 206 optimal weight: 0.6980 chunk 258 optimal weight: 0.7980 chunk 246 optimal weight: 9.9990 chunk 15 optimal weight: 9.9990 chunk 33 optimal weight: 0.6980 chunk 245 optimal weight: 0.9990 chunk 205 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 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 C 482 HIS ** C 599 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 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: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4624 r_free = 0.4624 target = 0.217713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4180 r_free = 0.4180 target = 0.175200 restraints weight = 39265.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.169816 restraints weight = 46752.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.166137 restraints weight = 39621.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.166572 restraints weight = 34975.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.165900 restraints weight = 29843.444| |-----------------------------------------------------------------------------| r_work (final): 0.4046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6872 moved from start: 0.3948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 21804 Z= 0.155 Angle : 0.753 18.609 29584 Z= 0.398 Chirality : 0.047 0.387 3404 Planarity : 0.004 0.057 3668 Dihedral : 6.102 47.203 2864 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 16.93 Ramachandran Plot: Outliers : 1.22 % Allowed : 13.49 % Favored : 85.28 % Rotamer: Outliers : 4.12 % Allowed : 22.44 % Favored : 73.45 % 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 aren not related in a simple way. whole: -2.31 (0.16), residues: 2616 helix: 0.15 (0.15), residues: 1164 sheet: -1.59 (0.49), residues: 108 loop : -3.25 (0.16), residues: 1344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 533 TYR 0.014 0.001 TYR D 508 PHE 0.022 0.002 PHE C 270 TRP 0.022 0.001 TRP C 38 HIS 0.011 0.001 HIS B 482 Details of bonding type rmsd covalent geometry : bond 0.00322 (21804) covalent geometry : angle 0.75284 (29584) hydrogen bonds : bond 0.04845 ( 756) hydrogen bonds : angle 4.40707 ( 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 391 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 293 time to evaluate : 1.249 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 109 MET cc_start: 0.3041 (pmm) cc_final: -0.0970 (ptt) REVERT: A 474 MET cc_start: 0.4495 (tmm) cc_final: 0.4245 (ttt) REVERT: A 513 TRP cc_start: 0.7463 (m-10) cc_final: 0.6898 (m-10) REVERT: A 522 GLU cc_start: 0.7649 (mm-30) cc_final: 0.6694 (pm20) REVERT: A 532 MET cc_start: 0.5856 (ppp) cc_final: 0.5494 (ppp) REVERT: B 109 MET cc_start: 0.3086 (pmm) cc_final: -0.0920 (ptt) REVERT: B 513 TRP cc_start: 0.7450 (m-10) cc_final: 0.6877 (m-10) REVERT: B 522 GLU cc_start: 0.7615 (mm-30) cc_final: 0.6679 (pm20) REVERT: B 532 MET cc_start: 0.5853 (ppp) cc_final: 0.5494 (ppp) REVERT: C 109 MET cc_start: 0.3051 (pmm) cc_final: -0.0934 (ptt) REVERT: C 474 MET cc_start: 0.4559 (tmm) cc_final: 0.4291 (ttt) REVERT: C 513 TRP cc_start: 0.7445 (m-10) cc_final: 0.6871 (m-10) REVERT: C 522 GLU cc_start: 0.7629 (mm-30) cc_final: 0.6682 (pm20) REVERT: C 532 MET cc_start: 0.5917 (ppp) cc_final: 0.5572 (ppp) REVERT: D 109 MET cc_start: 0.3075 (pmm) cc_final: -0.0929 (ptt) REVERT: D 513 TRP cc_start: 0.7450 (m-10) cc_final: 0.6886 (m-10) REVERT: D 522 GLU cc_start: 0.7639 (mm-30) cc_final: 0.6688 (pm20) REVERT: D 532 MET cc_start: 0.5916 (ppp) cc_final: 0.5570 (ppp) outliers start: 98 outliers final: 45 residues processed: 371 average time/residue: 0.1240 time to fit residues: 75.6143 Evaluate side-chains 309 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 264 time to evaluate : 0.806 ------------------------------------------------------------------------------- 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 326 VAL 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 326 VAL 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 326 VAL 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 326 VAL 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: 5.9990 chunk 142 optimal weight: 0.2980 chunk 36 optimal weight: 1.9990 chunk 121 optimal weight: 0.8980 chunk 153 optimal weight: 1.9990 chunk 40 optimal weight: 0.0570 chunk 59 optimal weight: 7.9990 chunk 96 optimal weight: 1.9990 chunk 25 optimal weight: 5.9990 chunk 41 optimal weight: 0.1980 chunk 101 optimal weight: 2.9990 overall best weight: 0.6900 ------------------------------------------------------------------------------- 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 473 GLN ** 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 473 GLN ** 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 473 GLN ** 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 473 GLN ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4633 r_free = 0.4633 target = 0.218933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4209 r_free = 0.4209 target = 0.178154 restraints weight = 38886.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.170179 restraints weight = 47841.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.168221 restraints weight = 43938.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.168777 restraints weight = 32250.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.169282 restraints weight = 27820.100| |-----------------------------------------------------------------------------| r_work (final): 0.4099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6775 moved from start: 0.4192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 21804 Z= 0.151 Angle : 0.745 18.502 29584 Z= 0.391 Chirality : 0.047 0.332 3404 Planarity : 0.004 0.057 3668 Dihedral : 5.902 46.336 2864 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 15.76 Ramachandran Plot: Outliers : 1.22 % Allowed : 13.34 % Favored : 85.44 % Rotamer: Outliers : 3.36 % Allowed : 24.08 % Favored : 72.56 % 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 aren not related in a simple way. whole: -2.18 (0.17), residues: 2616 helix: 0.25 (0.16), residues: 1152 sheet: -1.32 (0.53), residues: 108 loop : -3.15 (0.16), residues: 1356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 333 TYR 0.016 0.001 TYR D 88 PHE 0.028 0.002 PHE B 491 TRP 0.032 0.002 TRP D 618 HIS 0.009 0.001 HIS B 482 Details of bonding type rmsd covalent geometry : bond 0.00320 (21804) covalent geometry : angle 0.74450 (29584) hydrogen bonds : bond 0.04689 ( 756) hydrogen bonds : angle 4.43738 ( 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 354 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 274 time to evaluate : 0.704 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 109 MET cc_start: 0.2898 (pmm) cc_final: -0.1046 (ptt) REVERT: A 341 TYR cc_start: 0.7973 (OUTLIER) cc_final: 0.7443 (p90) REVERT: A 513 TRP cc_start: 0.7244 (m-10) cc_final: 0.6834 (m-10) REVERT: A 522 GLU cc_start: 0.7446 (mm-30) cc_final: 0.6638 (pm20) REVERT: B 109 MET cc_start: 0.2905 (pmm) cc_final: -0.1017 (ptt) REVERT: B 341 TYR cc_start: 0.7955 (OUTLIER) cc_final: 0.7431 (p90) REVERT: B 513 TRP cc_start: 0.7229 (m-10) cc_final: 0.6816 (m-10) REVERT: B 522 GLU cc_start: 0.7454 (mm-30) cc_final: 0.6643 (pm20) REVERT: C 109 MET cc_start: 0.2873 (pmm) cc_final: -0.1037 (ptt) REVERT: C 341 TYR cc_start: 0.7973 (OUTLIER) cc_final: 0.7448 (p90) REVERT: C 513 TRP cc_start: 0.7224 (m-10) cc_final: 0.6811 (m-10) REVERT: C 522 GLU cc_start: 0.7474 (mm-30) cc_final: 0.6653 (pm20) REVERT: D 109 MET cc_start: 0.2975 (pmm) cc_final: -0.1008 (ptt) REVERT: D 341 TYR cc_start: 0.7972 (OUTLIER) cc_final: 0.7445 (p90) REVERT: D 513 TRP cc_start: 0.7249 (m-10) cc_final: 0.6837 (m-10) REVERT: D 522 GLU cc_start: 0.7456 (mm-30) cc_final: 0.6645 (pm20) outliers start: 80 outliers final: 48 residues processed: 342 average time/residue: 0.1191 time to fit residues: 67.6215 Evaluate side-chains 325 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 273 time to evaluate : 0.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 TYR Chi-restraints excluded: chain A residue 202 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 450 VAL Chi-restraints excluded: chain A residue 473 GLN 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 202 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 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 202 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 450 VAL Chi-restraints excluded: chain C residue 473 GLN 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 202 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 450 VAL Chi-restraints excluded: chain D residue 473 GLN 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 89 optimal weight: 4.9990 chunk 71 optimal weight: 0.5980 chunk 78 optimal weight: 20.0000 chunk 162 optimal weight: 5.9990 chunk 28 optimal weight: 5.9990 chunk 21 optimal weight: 2.9990 chunk 119 optimal weight: 0.9990 chunk 116 optimal weight: 6.9990 chunk 190 optimal weight: 5.9990 chunk 239 optimal weight: 0.8980 chunk 10 optimal weight: 10.0000 overall best weight: 2.0986 ------------------------------------------------------------------------------- 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 473 GLN A 477 ASN ** 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 477 ASN ** 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 473 GLN C 477 ASN ** 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 473 GLN D 477 ASN ** 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4585 r_free = 0.4585 target = 0.214105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.172335 restraints weight = 38726.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.169300 restraints weight = 49567.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.166872 restraints weight = 41535.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.165996 restraints weight = 37655.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.164473 restraints weight = 32434.047| |-----------------------------------------------------------------------------| r_work (final): 0.4038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6860 moved from start: 0.4647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.078 21804 Z= 0.215 Angle : 0.801 18.121 29584 Z= 0.422 Chirality : 0.049 0.324 3404 Planarity : 0.005 0.057 3668 Dihedral : 6.079 44.730 2864 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 18.28 Ramachandran Plot: Outliers : 1.22 % Allowed : 14.45 % Favored : 84.33 % Rotamer: Outliers : 3.66 % Allowed : 23.99 % Favored : 72.35 % 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 aren not related in a simple way. whole: -2.35 (0.17), residues: 2616 helix: 0.05 (0.15), residues: 1172 sheet: -1.24 (0.55), residues: 108 loop : -3.26 (0.16), residues: 1336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 333 TYR 0.020 0.002 TYR A 419 PHE 0.028 0.002 PHE B 491 TRP 0.041 0.002 TRP D 618 HIS 0.005 0.001 HIS A 267 Details of bonding type rmsd covalent geometry : bond 0.00482 (21804) covalent geometry : angle 0.80064 (29584) hydrogen bonds : bond 0.05491 ( 756) hydrogen bonds : angle 4.64706 ( 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 349 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 262 time to evaluate : 0.548 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 107 PHE cc_start: -0.0138 (OUTLIER) cc_final: -0.1329 (m-80) REVERT: A 109 MET cc_start: 0.3058 (pmm) cc_final: -0.1072 (ptt) REVERT: A 207 ILE cc_start: 0.8036 (mp) cc_final: 0.7752 (mm) REVERT: A 226 PHE cc_start: 0.8813 (t80) cc_final: 0.8540 (t80) REVERT: A 341 TYR cc_start: 0.8115 (OUTLIER) cc_final: 0.7689 (p90) REVERT: A 513 TRP cc_start: 0.7160 (m-10) cc_final: 0.6747 (m-10) REVERT: A 522 GLU cc_start: 0.7474 (mm-30) cc_final: 0.6818 (pm20) REVERT: A 674 ILE cc_start: 0.3079 (OUTLIER) cc_final: 0.2534 (mt) REVERT: B 28 PHE cc_start: 0.2763 (OUTLIER) cc_final: 0.1966 (m-80) REVERT: B 107 PHE cc_start: -0.0115 (OUTLIER) cc_final: -0.1329 (m-80) REVERT: B 109 MET cc_start: 0.3069 (pmm) cc_final: -0.1067 (ptt) REVERT: B 207 ILE cc_start: 0.8043 (mp) cc_final: 0.7750 (mm) REVERT: B 226 PHE cc_start: 0.8809 (t80) cc_final: 0.8539 (t80) REVERT: B 341 TYR cc_start: 0.8133 (OUTLIER) cc_final: 0.7709 (p90) REVERT: B 513 TRP cc_start: 0.7156 (m-10) cc_final: 0.6737 (m-10) REVERT: B 522 GLU cc_start: 0.7479 (mm-30) cc_final: 0.6819 (pm20) REVERT: B 674 ILE cc_start: 0.3120 (OUTLIER) cc_final: 0.2591 (mt) REVERT: C 28 PHE cc_start: 0.2758 (OUTLIER) cc_final: 0.1960 (m-80) REVERT: C 107 PHE cc_start: -0.0123 (OUTLIER) cc_final: -0.1343 (m-80) REVERT: C 109 MET cc_start: 0.3055 (pmm) cc_final: -0.1073 (ptt) REVERT: C 207 ILE cc_start: 0.8035 (mp) cc_final: 0.7743 (mm) REVERT: C 226 PHE cc_start: 0.8819 (t80) cc_final: 0.8548 (t80) REVERT: C 341 TYR cc_start: 0.8118 (OUTLIER) cc_final: 0.7692 (p90) REVERT: C 513 TRP cc_start: 0.7148 (m-10) cc_final: 0.6733 (m-10) REVERT: C 522 GLU cc_start: 0.7517 (mm-30) cc_final: 0.6855 (pm20) REVERT: C 674 ILE cc_start: 0.3118 (OUTLIER) cc_final: 0.2593 (mt) REVERT: D 107 PHE cc_start: -0.0260 (OUTLIER) cc_final: -0.1410 (m-80) REVERT: D 109 MET cc_start: 0.3030 (pmm) cc_final: -0.1116 (ptt) REVERT: D 207 ILE cc_start: 0.8047 (mp) cc_final: 0.7756 (mm) REVERT: D 226 PHE cc_start: 0.8803 (t80) cc_final: 0.8534 (t80) REVERT: D 341 TYR cc_start: 0.8124 (OUTLIER) cc_final: 0.7698 (p90) REVERT: D 513 TRP cc_start: 0.7158 (m-10) cc_final: 0.6749 (m-10) REVERT: D 522 GLU cc_start: 0.7515 (mm-30) cc_final: 0.6860 (pm20) REVERT: D 559 LEU cc_start: 0.8719 (mt) cc_final: 0.8473 (mp) REVERT: D 674 ILE cc_start: 0.3124 (OUTLIER) cc_final: 0.2600 (mt) outliers start: 87 outliers final: 44 residues processed: 332 average time/residue: 0.1186 time to fit residues: 65.2492 Evaluate side-chains 306 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 248 time to evaluate : 0.788 ------------------------------------------------------------------------------- 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 257 ILE 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 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 584 VAL Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 674 ILE Chi-restraints excluded: chain B residue 28 PHE Chi-restraints excluded: chain B residue 98 TYR Chi-restraints excluded: chain B residue 107 PHE Chi-restraints excluded: chain B residue 257 ILE Chi-restraints excluded: chain B residue 286 MET 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 450 VAL 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 584 VAL Chi-restraints excluded: chain B residue 612 VAL Chi-restraints excluded: chain B residue 674 ILE Chi-restraints excluded: chain C residue 28 PHE Chi-restraints excluded: chain C residue 98 TYR Chi-restraints excluded: chain C residue 107 PHE Chi-restraints excluded: chain C residue 257 ILE Chi-restraints excluded: chain C residue 286 MET 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 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 584 VAL Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain C residue 674 ILE Chi-restraints excluded: chain D residue 94 GLU Chi-restraints excluded: chain D residue 98 TYR Chi-restraints excluded: chain D residue 107 PHE Chi-restraints excluded: chain D residue 257 ILE Chi-restraints excluded: chain D residue 286 MET 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 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 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: 2.9990 chunk 238 optimal weight: 0.0980 chunk 124 optimal weight: 0.8980 chunk 209 optimal weight: 5.9990 chunk 92 optimal weight: 0.1980 chunk 99 optimal weight: 0.6980 chunk 74 optimal weight: 9.9990 chunk 210 optimal weight: 6.9990 chunk 230 optimal weight: 0.6980 chunk 227 optimal weight: 0.7980 chunk 116 optimal weight: 5.9990 overall best weight: 0.4980 ------------------------------------------------------------------------------- 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 287 ASN A 473 GLN ** A 599 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 473 GLN ** 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 ** 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 = 0.4635 r_free = 0.4635 target = 0.219313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4215 r_free = 0.4215 target = 0.178659 restraints weight = 38927.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.171438 restraints weight = 48086.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.169321 restraints weight = 40715.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.169435 restraints weight = 33703.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.168983 restraints weight = 30291.037| |-----------------------------------------------------------------------------| r_work (final): 0.4088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6781 moved from start: 0.4833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.090 21804 Z= 0.147 Angle : 0.740 18.427 29584 Z= 0.389 Chirality : 0.046 0.279 3404 Planarity : 0.005 0.057 3668 Dihedral : 5.695 43.597 2864 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 14.45 Ramachandran Plot: Outliers : 1.38 % Allowed : 13.07 % Favored : 85.55 % Rotamer: Outliers : 2.23 % Allowed : 25.17 % Favored : 72.61 % 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 aren not related in a simple way. whole: -2.14 (0.17), residues: 2616 helix: 0.34 (0.15), residues: 1156 sheet: -1.03 (0.57), residues: 108 loop : -3.23 (0.16), residues: 1352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 333 TYR 0.015 0.001 TYR D 508 PHE 0.036 0.002 PHE D 491 TRP 0.041 0.002 TRP D 618 HIS 0.005 0.001 HIS B 539 Details of bonding type rmsd covalent geometry : bond 0.00314 (21804) covalent geometry : angle 0.73972 (29584) hydrogen bonds : bond 0.04636 ( 756) hydrogen bonds : angle 4.40979 ( 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 356 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 303 time to evaluate : 0.791 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: symmetry clash REVERT: A 76 LYS cc_start: 0.7135 (tptt) cc_final: 0.6530 (tptt) REVERT: A 107 PHE cc_start: -0.0075 (OUTLIER) cc_final: -0.1287 (m-80) REVERT: A 109 MET cc_start: 0.2632 (pmm) cc_final: -0.1329 (ptt) REVERT: A 207 ILE cc_start: 0.7779 (mp) cc_final: 0.7418 (mm) REVERT: A 341 TYR cc_start: 0.7929 (OUTLIER) cc_final: 0.7452 (p90) REVERT: A 513 TRP cc_start: 0.7035 (m-10) cc_final: 0.6781 (m-10) REVERT: A 522 GLU cc_start: 0.7420 (mm-30) cc_final: 0.6757 (pm20) REVERT: A 625 HIS cc_start: 0.6885 (m-70) cc_final: 0.6351 (m-70) REVERT: A 658 ASN cc_start: 0.6927 (t0) cc_final: 0.6678 (t0) REVERT: B 76 LYS cc_start: 0.7125 (tptt) cc_final: 0.6523 (tptt) REVERT: B 107 PHE cc_start: -0.0047 (OUTLIER) cc_final: -0.1267 (m-80) REVERT: B 109 MET cc_start: 0.2617 (pmm) cc_final: -0.1340 (ptt) REVERT: B 207 ILE cc_start: 0.7764 (mp) cc_final: 0.7401 (mm) REVERT: B 341 TYR cc_start: 0.7927 (OUTLIER) cc_final: 0.7441 (p90) REVERT: B 513 TRP cc_start: 0.7032 (m-10) cc_final: 0.6765 (m-10) REVERT: B 522 GLU cc_start: 0.7428 (mm-30) cc_final: 0.6755 (pm20) REVERT: B 625 HIS cc_start: 0.6885 (m-70) cc_final: 0.6356 (m-70) REVERT: B 658 ASN cc_start: 0.6908 (t0) cc_final: 0.6664 (t0) REVERT: C 76 LYS cc_start: 0.7160 (tptt) cc_final: 0.6574 (tptt) REVERT: C 107 PHE cc_start: -0.0080 (OUTLIER) cc_final: -0.1283 (m-80) REVERT: C 109 MET cc_start: 0.2645 (pmm) cc_final: -0.1315 (ptt) REVERT: C 207 ILE cc_start: 0.7773 (mp) cc_final: 0.7408 (mm) REVERT: C 341 TYR cc_start: 0.7921 (OUTLIER) cc_final: 0.7434 (p90) REVERT: C 513 TRP cc_start: 0.7012 (m-10) cc_final: 0.6765 (m-10) REVERT: C 522 GLU cc_start: 0.7422 (mm-30) cc_final: 0.6757 (pm20) REVERT: C 625 HIS cc_start: 0.6905 (m-70) cc_final: 0.6368 (m-70) REVERT: C 658 ASN cc_start: 0.6929 (t0) cc_final: 0.6693 (t0) REVERT: D 107 PHE cc_start: -0.0130 (OUTLIER) cc_final: -0.1269 (m-80) REVERT: D 109 MET cc_start: 0.2679 (pmm) cc_final: -0.1258 (ptt) REVERT: D 207 ILE cc_start: 0.7774 (mp) cc_final: 0.7408 (mm) REVERT: D 341 TYR cc_start: 0.7919 (OUTLIER) cc_final: 0.7432 (p90) REVERT: D 513 TRP cc_start: 0.7038 (m-10) cc_final: 0.6758 (m-10) REVERT: D 522 GLU cc_start: 0.7445 (mm-30) cc_final: 0.6764 (pm20) REVERT: D 625 HIS cc_start: 0.6911 (m-70) cc_final: 0.6372 (m-70) REVERT: D 658 ASN cc_start: 0.6935 (t0) cc_final: 0.6693 (t0) outliers start: 53 outliers final: 28 residues processed: 346 average time/residue: 0.1172 time to fit residues: 66.9190 Evaluate side-chains 297 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 261 time to evaluate : 0.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 PHE 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 473 GLN 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 584 VAL Chi-restraints excluded: chain B residue 107 PHE 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 521 THR Chi-restraints excluded: chain B residue 558 CYS Chi-restraints excluded: chain B residue 584 VAL Chi-restraints excluded: chain C residue 107 PHE 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 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 D residue 107 PHE 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 473 GLN 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 172 optimal weight: 0.0970 chunk 190 optimal weight: 0.8980 chunk 132 optimal weight: 10.0000 chunk 119 optimal weight: 0.9990 chunk 38 optimal weight: 0.6980 chunk 107 optimal weight: 0.7980 chunk 149 optimal weight: 20.0000 chunk 35 optimal weight: 3.9990 chunk 73 optimal weight: 7.9990 chunk 187 optimal weight: 0.9980 chunk 99 optimal weight: 1.9990 overall best weight: 0.6978 ------------------------------------------------------------------------------- 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 ** 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 599 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 158 ASN D 473 GLN ** 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 = 0.4629 r_free = 0.4629 target = 0.218795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4199 r_free = 0.4199 target = 0.177146 restraints weight = 39372.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.169976 restraints weight = 48905.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.168707 restraints weight = 39418.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.168811 restraints weight = 30483.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.168650 restraints weight = 31024.377| |-----------------------------------------------------------------------------| r_work (final): 0.4081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6788 moved from start: 0.5080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 21804 Z= 0.151 Angle : 0.728 17.852 29584 Z= 0.387 Chirality : 0.046 0.297 3404 Planarity : 0.005 0.057 3668 Dihedral : 5.616 42.233 2864 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 14.92 Ramachandran Plot: Outliers : 1.38 % Allowed : 13.23 % Favored : 85.40 % Rotamer: Outliers : 1.81 % Allowed : 25.84 % Favored : 72.35 % 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 aren not related in a simple way. whole: -2.05 (0.17), residues: 2616 helix: 0.54 (0.16), residues: 1136 sheet: -1.34 (0.55), residues: 116 loop : -3.24 (0.16), residues: 1364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 333 TYR 0.014 0.001 TYR B 508 PHE 0.038 0.002 PHE C 471 TRP 0.050 0.002 TRP D 618 HIS 0.005 0.001 HIS C 539 Details of bonding type rmsd covalent geometry : bond 0.00317 (21804) covalent geometry : angle 0.72792 (29584) hydrogen bonds : bond 0.04677 ( 756) hydrogen bonds : angle 4.34009 ( 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 324 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 281 time to evaluate : 0.741 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 107 PHE cc_start: -0.0122 (OUTLIER) cc_final: -0.1283 (m-80) REVERT: A 109 MET cc_start: 0.2419 (pmm) cc_final: -0.1133 (ptt) REVERT: A 207 ILE cc_start: 0.7827 (mp) cc_final: 0.7476 (mm) REVERT: A 341 TYR cc_start: 0.7951 (OUTLIER) cc_final: 0.7366 (p90) REVERT: A 513 TRP cc_start: 0.7003 (m-10) cc_final: 0.6775 (m-10) REVERT: A 522 GLU cc_start: 0.7447 (mm-30) cc_final: 0.6781 (pm20) REVERT: A 625 HIS cc_start: 0.6884 (m-70) cc_final: 0.6377 (m-70) REVERT: A 658 ASN cc_start: 0.6973 (t0) cc_final: 0.6699 (t0) REVERT: A 674 ILE cc_start: 0.2918 (OUTLIER) cc_final: 0.2361 (mt) REVERT: B 107 PHE cc_start: -0.0087 (OUTLIER) cc_final: -0.1259 (m-80) REVERT: B 109 MET cc_start: 0.2400 (pmm) cc_final: -0.1147 (ptt) REVERT: B 207 ILE cc_start: 0.7852 (mp) cc_final: 0.7498 (mm) REVERT: B 341 TYR cc_start: 0.7963 (OUTLIER) cc_final: 0.7376 (p90) REVERT: B 513 TRP cc_start: 0.7006 (m-10) cc_final: 0.6778 (m-10) REVERT: B 522 GLU cc_start: 0.7443 (mm-30) cc_final: 0.6779 (pm20) REVERT: B 625 HIS cc_start: 0.6890 (m-70) cc_final: 0.6381 (m-70) REVERT: B 658 ASN cc_start: 0.7002 (t0) cc_final: 0.6727 (t0) REVERT: B 674 ILE cc_start: 0.2844 (OUTLIER) cc_final: 0.2306 (mt) REVERT: C 107 PHE cc_start: -0.0113 (OUTLIER) cc_final: -0.1283 (m-80) REVERT: C 109 MET cc_start: 0.2397 (pmm) cc_final: -0.1147 (ptt) REVERT: C 207 ILE cc_start: 0.7866 (mp) cc_final: 0.7505 (mm) REVERT: C 341 TYR cc_start: 0.7930 (OUTLIER) cc_final: 0.7335 (p90) REVERT: C 513 TRP cc_start: 0.7002 (m-10) cc_final: 0.6773 (m-10) REVERT: C 522 GLU cc_start: 0.7421 (mm-30) cc_final: 0.6771 (pm20) REVERT: C 625 HIS cc_start: 0.6898 (m-70) cc_final: 0.6388 (m-70) REVERT: C 658 ASN cc_start: 0.7011 (t0) cc_final: 0.6734 (t0) REVERT: C 674 ILE cc_start: 0.2827 (OUTLIER) cc_final: 0.2289 (mt) REVERT: D 107 PHE cc_start: 0.0104 (OUTLIER) cc_final: -0.1183 (m-80) REVERT: D 109 MET cc_start: 0.2490 (pmm) cc_final: -0.1072 (ptt) REVERT: D 207 ILE cc_start: 0.7864 (mp) cc_final: 0.7505 (mm) REVERT: D 341 TYR cc_start: 0.7950 (OUTLIER) cc_final: 0.7361 (p90) REVERT: D 513 TRP cc_start: 0.7011 (m-10) cc_final: 0.6779 (m-10) REVERT: D 522 GLU cc_start: 0.7401 (mm-30) cc_final: 0.6756 (pm20) REVERT: D 625 HIS cc_start: 0.6900 (m-70) cc_final: 0.6386 (m-70) REVERT: D 658 ASN cc_start: 0.7032 (t0) cc_final: 0.6753 (t0) REVERT: D 674 ILE cc_start: 0.2823 (OUTLIER) cc_final: 0.2287 (mt) outliers start: 43 outliers final: 28 residues processed: 320 average time/residue: 0.1172 time to fit residues: 62.1410 Evaluate side-chains 308 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 268 time to evaluate : 0.852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 PHE Chi-restraints excluded: chain A residue 178 HIS 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 473 GLN 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 674 ILE Chi-restraints excluded: chain B residue 107 PHE Chi-restraints excluded: chain B residue 178 HIS 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 674 ILE Chi-restraints excluded: chain C residue 107 PHE Chi-restraints excluded: chain C residue 178 HIS 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 473 GLN 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 674 ILE Chi-restraints excluded: chain D residue 107 PHE Chi-restraints excluded: chain D residue 178 HIS 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 473 GLN 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 674 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 40 optimal weight: 1.9990 chunk 236 optimal weight: 0.5980 chunk 9 optimal weight: 9.9990 chunk 170 optimal weight: 0.5980 chunk 159 optimal weight: 0.9990 chunk 246 optimal weight: 10.0000 chunk 89 optimal weight: 5.9990 chunk 219 optimal weight: 0.6980 chunk 86 optimal weight: 3.9990 chunk 15 optimal weight: 8.9990 chunk 222 optimal weight: 1.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- 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** ** A 639 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 473 GLN ** B 599 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 639 HIS ** 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4617 r_free = 0.4617 target = 0.217066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.175226 restraints weight = 39224.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.171690 restraints weight = 50119.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.170285 restraints weight = 36764.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.168543 restraints weight = 34421.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.168430 restraints weight = 28526.750| |-----------------------------------------------------------------------------| r_work (final): 0.4083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6762 moved from start: 0.5308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 21804 Z= 0.161 Angle : 0.754 17.754 29584 Z= 0.399 Chirality : 0.047 0.280 3404 Planarity : 0.005 0.057 3668 Dihedral : 5.620 41.163 2864 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 15.38 Ramachandran Plot: Outliers : 1.38 % Allowed : 13.26 % Favored : 85.36 % Rotamer: Outliers : 2.18 % Allowed : 25.84 % 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 aren not related in a simple way. whole: -2.14 (0.17), residues: 2616 helix: 0.50 (0.16), residues: 1132 sheet: -1.44 (0.55), residues: 116 loop : -3.30 (0.16), residues: 1368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 333 TYR 0.052 0.001 TYR A 288 PHE 0.039 0.002 PHE C 471 TRP 0.049 0.002 TRP D 618 HIS 0.005 0.001 HIS D 539 Details of bonding type rmsd covalent geometry : bond 0.00349 (21804) covalent geometry : angle 0.75423 (29584) hydrogen bonds : bond 0.04879 ( 756) hydrogen bonds : angle 4.40950 ( 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 329 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 277 time to evaluate : 0.856 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 107 PHE cc_start: 0.0207 (OUTLIER) cc_final: -0.1163 (m-80) REVERT: A 109 MET cc_start: 0.2564 (pmm) cc_final: -0.0691 (ptt) REVERT: A 207 ILE cc_start: 0.7912 (mp) cc_final: 0.7542 (mm) REVERT: A 341 TYR cc_start: 0.8042 (OUTLIER) cc_final: 0.7534 (p90) REVERT: A 513 TRP cc_start: 0.7016 (m-10) cc_final: 0.6807 (m-10) REVERT: A 522 GLU cc_start: 0.7502 (mm-30) cc_final: 0.6857 (pm20) REVERT: A 620 GLU cc_start: 0.7938 (mm-30) cc_final: 0.7684 (tp30) REVERT: A 658 ASN cc_start: 0.7121 (t0) cc_final: 0.6876 (t0) REVERT: A 674 ILE cc_start: 0.2969 (OUTLIER) cc_final: 0.2405 (mt) REVERT: B 107 PHE cc_start: 0.0215 (OUTLIER) cc_final: -0.1160 (m-80) REVERT: B 109 MET cc_start: 0.2563 (pmm) cc_final: -0.0685 (ptt) REVERT: B 207 ILE cc_start: 0.7961 (mp) cc_final: 0.7584 (mm) REVERT: B 341 TYR cc_start: 0.8042 (OUTLIER) cc_final: 0.7531 (p90) REVERT: B 513 TRP cc_start: 0.7005 (m-10) cc_final: 0.6805 (m-10) REVERT: B 522 GLU cc_start: 0.7495 (mm-30) cc_final: 0.6854 (pm20) REVERT: B 620 GLU cc_start: 0.7959 (mm-30) cc_final: 0.7702 (tp30) REVERT: B 674 ILE cc_start: 0.2950 (OUTLIER) cc_final: 0.2386 (mt) REVERT: C 107 PHE cc_start: 0.0224 (OUTLIER) cc_final: -0.1161 (m-80) REVERT: C 109 MET cc_start: 0.2523 (pmm) cc_final: -0.0729 (ptt) REVERT: C 207 ILE cc_start: 0.7968 (mp) cc_final: 0.7591 (mm) REVERT: C 341 TYR cc_start: 0.8040 (OUTLIER) cc_final: 0.7531 (p90) REVERT: C 513 TRP cc_start: 0.7015 (m-10) cc_final: 0.6803 (m-10) REVERT: C 522 GLU cc_start: 0.7507 (mm-30) cc_final: 0.6861 (pm20) REVERT: C 620 GLU cc_start: 0.7965 (mm-30) cc_final: 0.7707 (tp30) REVERT: C 674 ILE cc_start: 0.2939 (OUTLIER) cc_final: 0.2381 (mt) REVERT: D 107 PHE cc_start: 0.0202 (OUTLIER) cc_final: -0.1157 (m-80) REVERT: D 109 MET cc_start: 0.2752 (pmm) cc_final: -0.0686 (ptt) REVERT: D 207 ILE cc_start: 0.7972 (mp) cc_final: 0.7593 (mm) REVERT: D 341 TYR cc_start: 0.8045 (OUTLIER) cc_final: 0.7536 (p90) REVERT: D 513 TRP cc_start: 0.7026 (m-10) cc_final: 0.6815 (m-10) REVERT: D 522 GLU cc_start: 0.7512 (mm-30) cc_final: 0.6862 (pm20) REVERT: D 620 GLU cc_start: 0.7970 (mm-30) cc_final: 0.7716 (tp30) REVERT: D 674 ILE cc_start: 0.2935 (OUTLIER) cc_final: 0.2377 (mt) outliers start: 52 outliers final: 36 residues processed: 325 average time/residue: 0.1032 time to fit residues: 56.6588 Evaluate side-chains 310 residues out of total 2380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 262 time to evaluate : 0.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 PHE Chi-restraints excluded: chain A residue 178 HIS 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 473 GLN 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 630 VAL Chi-restraints excluded: chain A residue 674 ILE Chi-restraints excluded: chain B residue 107 PHE Chi-restraints excluded: chain B residue 178 HIS 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 674 ILE Chi-restraints excluded: chain C residue 107 PHE Chi-restraints excluded: chain C residue 178 HIS 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 473 GLN 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 178 HIS 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 473 GLN 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 130 optimal weight: 3.9990 chunk 42 optimal weight: 1.9990 chunk 236 optimal weight: 0.9990 chunk 217 optimal weight: 0.0270 chunk 14 optimal weight: 30.0000 chunk 258 optimal weight: 2.9990 chunk 96 optimal weight: 1.9990 chunk 90 optimal weight: 0.7980 chunk 235 optimal weight: 3.9990 chunk 202 optimal weight: 0.0010 chunk 229 optimal weight: 8.9990 overall best weight: 0.7648 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 473 GLN A 477 ASN ** A 599 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 473 GLN B 477 ASN ** B 599 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 473 GLN C 477 ASN ** 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4619 r_free = 0.4619 target = 0.217847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.176284 restraints weight = 39194.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.169601 restraints weight = 51107.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.167847 restraints weight = 38531.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.167273 restraints weight = 33357.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.167578 restraints weight = 27300.859| |-----------------------------------------------------------------------------| r_work (final): 0.4070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6783 moved from start: 0.5521 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= 0.155 Angle : 0.742 17.604 29584 Z= 0.391 Chirality : 0.047 0.263 3404 Planarity : 0.005 0.057 3668 Dihedral : 5.572 40.195 2864 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 14.87 Ramachandran Plot: Outliers : 1.26 % Allowed : 13.91 % Favored : 84.82 % Rotamer: Outliers : 2.31 % Allowed : 25.67 % Favored : 72.02 % 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 aren not related in a simple way. whole: -2.10 (0.17), residues: 2616 helix: 0.54 (0.16), residues: 1132 sheet: -1.46 (0.56), residues: 116 loop : -3.29 (0.16), residues: 1368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 333 TYR 0.048 0.001 TYR A 288 PHE 0.038 0.002 PHE A 471 TRP 0.042 0.002 TRP D 618 HIS 0.005 0.001 HIS B 539 Details of bonding type rmsd covalent geometry : bond 0.00334 (21804) covalent geometry : angle 0.74190 (29584) hydrogen bonds : bond 0.04778 ( 756) hydrogen bonds : angle 4.37122 ( 2184) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3745.52 seconds wall clock time: 65 minutes 50.65 seconds (3950.65 seconds total)