Starting phenix.real_space_refine on Thu Feb 5 02:32:11 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9nje_49481/02_2026/9nje_49481.cif Found real_map, /net/cci-nas-00/data/ceres_data/9nje_49481/02_2026/9nje_49481.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.44 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9nje_49481/02_2026/9nje_49481.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9nje_49481/02_2026/9nje_49481.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9nje_49481/02_2026/9nje_49481.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9nje_49481/02_2026/9nje_49481.map" } resolution = 2.44 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 3 5.49 5 S 60 5.16 5 C 8992 2.51 5 N 2423 2.21 5 O 2764 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14242 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 4788 Number of conformers: 1 Conformer: "" Number of residues, atoms: 624, 4788 Classifications: {'peptide': 624} Link IDs: {'PTRANS': 31, 'TRANS': 592} Chain: "B" Number of atoms: 4769 Number of conformers: 1 Conformer: "" Number of residues, atoms: 621, 4769 Classifications: {'peptide': 621} Link IDs: {'PTRANS': 31, 'TRANS': 589} Chain breaks: 1 Chain: "C" Number of atoms: 4670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 610, 4670 Classifications: {'peptide': 610} Link IDs: {'PTRANS': 30, 'TRANS': 579} Chain breaks: 1 Chain: "A" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Unusual residues: {'PO4': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Unusual residues: {'PO4': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Unusual residues: {'PO4': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.93, per 1000 atoms: 0.21 Number of scatterers: 14242 At special positions: 0 Unit cell: (107.862, 107.862, 106.275, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 60 16.00 P 3 15.00 O 2764 8.00 N 2423 7.00 C 8992 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: 1.22 Conformation dependent library (CDL) restraints added in 524.3 milliseconds 3690 Ramachandran restraints generated. 1845 Oldfield, 0 Emsley, 1845 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3456 Finding SS restraints... Secondary structure from input PDB file: 56 helices and 12 sheets defined 42.7% alpha, 22.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.48 Creating SS restraints... Processing helix chain 'A' and resid 115 through 119 Processing helix chain 'A' and resid 124 through 139 Processing helix chain 'A' and resid 140 through 142 No H-bonds generated for 'chain 'A' and resid 140 through 142' Processing helix chain 'A' and resid 164 through 180 removed outlier: 4.268A pdb=" N LEU A 168 " --> pdb=" O GLU A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 205 through 210 Processing helix chain 'A' and resid 237 through 266 removed outlier: 3.711A pdb=" N GLN A 254 " --> pdb=" O LYS A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 300 removed outlier: 6.171A pdb=" N GLU A 293 " --> pdb=" O LYS A 289 " (cutoff:3.500A) removed outlier: 5.642A pdb=" N ARG A 294 " --> pdb=" O LEU A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 328 removed outlier: 3.578A pdb=" N GLU A 322 " --> pdb=" O LEU A 318 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLN A 323 " --> pdb=" O ASP A 319 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLU A 326 " --> pdb=" O GLU A 322 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 356 removed outlier: 3.796A pdb=" N VAL A 352 " --> pdb=" O PHE A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 401 through 405 Processing helix chain 'A' and resid 409 through 414 removed outlier: 3.698A pdb=" N THR A 413 " --> pdb=" O ASP A 409 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 435 Processing helix chain 'A' and resid 444 through 459 Processing helix chain 'A' and resid 460 through 462 No H-bonds generated for 'chain 'A' and resid 460 through 462' Processing helix chain 'A' and resid 482 through 499 Processing helix chain 'A' and resid 534 through 540 removed outlier: 3.570A pdb=" N ASP A 538 " --> pdb=" O LEU A 534 " (cutoff:3.500A) Processing helix chain 'A' and resid 567 through 593 removed outlier: 3.591A pdb=" N VAL A 571 " --> pdb=" O PRO A 567 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LYS A 591 " --> pdb=" O GLN A 587 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N THR A 592 " --> pdb=" O ILE A 588 " (cutoff:3.500A) Processing helix chain 'A' and resid 616 through 622 Processing helix chain 'A' and resid 625 through 636 Processing helix chain 'A' and resid 653 through 669 Processing helix chain 'B' and resid 124 through 139 Processing helix chain 'B' and resid 140 through 142 No H-bonds generated for 'chain 'B' and resid 140 through 142' Processing helix chain 'B' and resid 164 through 180 removed outlier: 4.284A pdb=" N LEU B 168 " --> pdb=" O GLU B 164 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 210 removed outlier: 3.534A pdb=" N SER B 210 " --> pdb=" O ARG B 206 " (cutoff:3.500A) Processing helix chain 'B' and resid 237 through 267 removed outlier: 3.769A pdb=" N GLN B 254 " --> pdb=" O LYS B 250 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 300 removed outlier: 5.551A pdb=" N GLU B 293 " --> pdb=" O LYS B 289 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N ARG B 294 " --> pdb=" O LEU B 290 " (cutoff:3.500A) Processing helix chain 'B' and resid 305 through 328 removed outlier: 3.721A pdb=" N GLN B 323 " --> pdb=" O ASP B 319 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LYS B 325 " --> pdb=" O GLU B 321 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N GLU B 326 " --> pdb=" O GLU B 322 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N LYS B 327 " --> pdb=" O GLN B 323 " (cutoff:3.500A) Processing helix chain 'B' and resid 332 through 356 removed outlier: 3.524A pdb=" N PHE B 340 " --> pdb=" O ILE B 336 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N VAL B 352 " --> pdb=" O PHE B 348 " (cutoff:3.500A) Processing helix chain 'B' and resid 402 through 406 Processing helix chain 'B' and resid 430 through 435 Processing helix chain 'B' and resid 445 through 459 Processing helix chain 'B' and resid 460 through 462 No H-bonds generated for 'chain 'B' and resid 460 through 462' Processing helix chain 'B' and resid 482 through 498 removed outlier: 3.679A pdb=" N ALA B 488 " --> pdb=" O SER B 484 " (cutoff:3.500A) Processing helix chain 'B' and resid 534 through 541 Processing helix chain 'B' and resid 567 through 593 removed outlier: 3.637A pdb=" N THR B 592 " --> pdb=" O ILE B 588 " (cutoff:3.500A) Processing helix chain 'B' and resid 613 through 622 removed outlier: 4.682A pdb=" N ALA B 618 " --> pdb=" O LEU B 614 " (cutoff:3.500A) removed outlier: 5.394A pdb=" N LYS B 619 " --> pdb=" O SER B 615 " (cutoff:3.500A) Processing helix chain 'B' and resid 625 through 635 Processing helix chain 'B' and resid 653 through 668 Processing helix chain 'C' and resid 124 through 139 Processing helix chain 'C' and resid 140 through 142 No H-bonds generated for 'chain 'C' and resid 140 through 142' Processing helix chain 'C' and resid 164 through 180 removed outlier: 4.329A pdb=" N LEU C 168 " --> pdb=" O GLU C 164 " (cutoff:3.500A) Processing helix chain 'C' and resid 205 through 211 removed outlier: 3.857A pdb=" N SER C 211 " --> pdb=" O LYS C 207 " (cutoff:3.500A) Processing helix chain 'C' and resid 222 through 224 No H-bonds generated for 'chain 'C' and resid 222 through 224' Processing helix chain 'C' and resid 237 through 267 removed outlier: 3.668A pdb=" N GLN C 254 " --> pdb=" O LYS C 250 " (cutoff:3.500A) Processing helix chain 'C' and resid 280 through 300 removed outlier: 6.565A pdb=" N GLU C 293 " --> pdb=" O LYS C 289 " (cutoff:3.500A) removed outlier: 5.240A pdb=" N ARG C 294 " --> pdb=" O LEU C 290 " (cutoff:3.500A) Processing helix chain 'C' and resid 305 through 328 removed outlier: 3.677A pdb=" N GLU C 322 " --> pdb=" O LEU C 318 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLN C 323 " --> pdb=" O ASP C 319 " (cutoff:3.500A) Processing helix chain 'C' and resid 332 through 356 removed outlier: 3.569A pdb=" N ILE C 337 " --> pdb=" O PRO C 333 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N VAL C 352 " --> pdb=" O PHE C 348 " (cutoff:3.500A) Processing helix chain 'C' and resid 430 through 435 Processing helix chain 'C' and resid 444 through 459 Processing helix chain 'C' and resid 460 through 462 No H-bonds generated for 'chain 'C' and resid 460 through 462' Processing helix chain 'C' and resid 482 through 499 Processing helix chain 'C' and resid 534 through 540 Processing helix chain 'C' and resid 567 through 593 removed outlier: 3.513A pdb=" N VAL C 571 " --> pdb=" O PRO C 567 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N THR C 592 " --> pdb=" O ILE C 588 " (cutoff:3.500A) Processing helix chain 'C' and resid 613 through 622 removed outlier: 4.702A pdb=" N ALA C 618 " --> pdb=" O LEU C 614 " (cutoff:3.500A) removed outlier: 5.664A pdb=" N LYS C 619 " --> pdb=" O SER C 615 " (cutoff:3.500A) Processing helix chain 'C' and resid 625 through 635 Processing helix chain 'C' and resid 653 through 668 removed outlier: 3.520A pdb=" N ILE C 664 " --> pdb=" O ALA C 660 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 47 through 51 removed outlier: 6.442A pdb=" N ALA A 79 " --> pdb=" O LEU A 157 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 199 through 202 removed outlier: 4.067A pdb=" N ILE A 195 " --> pdb=" O LEU A 214 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N LEU A 214 " --> pdb=" O ILE A 195 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N ALA A 221 " --> pdb=" O ILE A 226 " (cutoff:3.500A) removed outlier: 5.798A pdb=" N ILE A 226 " --> pdb=" O ALA A 221 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N VAL A 227 " --> pdb=" O ILE A 561 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N ILE A 561 " --> pdb=" O VAL A 227 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LEU A 229 " --> pdb=" O ALA A 559 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N THR A 555 " --> pdb=" O ALA A 233 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ALA A 556 " --> pdb=" O ALA A 548 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N MET A 543 " --> pdb=" O LEU A 513 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N LEU A 513 " --> pdb=" O MET A 543 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N ALA A 510 " --> pdb=" O THR A 531 " (cutoff:3.500A) removed outlier: 5.077A pdb=" N THR A 531 " --> pdb=" O ALA A 510 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N GLY A 512 " --> pdb=" O LEU A 529 " (cutoff:3.500A) removed outlier: 4.782A pdb=" N LEU A 529 " --> pdb=" O GLY A 512 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N VAL A 514 " --> pdb=" O TYR A 527 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N TYR A 527 " --> pdb=" O VAL A 514 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N LYS A 516 " --> pdb=" O GLU A 525 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 370 through 371 removed outlier: 6.245A pdb=" N GLN A 392 " --> pdb=" O LEU A 477 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 606 through 611 Processing sheet with id=AA5, first strand: chain 'B' and resid 47 through 51 removed outlier: 6.282A pdb=" N ALA B 79 " --> pdb=" O LEU B 157 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N VAL B 99 " --> pdb=" O VAL B 152 " (cutoff:3.500A) removed outlier: 8.110A pdb=" N CYS B 154 " --> pdb=" O VAL B 99 " (cutoff:3.500A) removed outlier: 7.281A pdb=" N ASP B 101 " --> pdb=" O CYS B 154 " (cutoff:3.500A) removed outlier: 8.209A pdb=" N LEU B 156 " --> pdb=" O ASP B 101 " (cutoff:3.500A) removed outlier: 8.674A pdb=" N ARG B 103 " --> pdb=" O LEU B 156 " (cutoff:3.500A) removed outlier: 9.036A pdb=" N ALA B 158 " --> pdb=" O ARG B 103 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 199 through 202 removed outlier: 4.134A pdb=" N ILE B 195 " --> pdb=" O LEU B 214 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N LEU B 214 " --> pdb=" O ILE B 195 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N ASN B 215 " --> pdb=" O ALA B 231 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N ALA B 231 " --> pdb=" O ASN B 215 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N VAL B 217 " --> pdb=" O LEU B 229 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N LEU B 229 " --> pdb=" O VAL B 217 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N ALA B 219 " --> pdb=" O VAL B 227 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N GLN B 225 " --> pdb=" O ALA B 221 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N VAL B 227 " --> pdb=" O ILE B 561 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N ILE B 561 " --> pdb=" O VAL B 227 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N LEU B 229 " --> pdb=" O ALA B 559 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N THR B 555 " --> pdb=" O ALA B 233 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N MET B 543 " --> pdb=" O LEU B 513 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N LEU B 513 " --> pdb=" O MET B 543 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N ALA B 510 " --> pdb=" O THR B 531 " (cutoff:3.500A) removed outlier: 5.116A pdb=" N THR B 531 " --> pdb=" O ALA B 510 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N GLY B 512 " --> pdb=" O LEU B 529 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N LEU B 529 " --> pdb=" O GLY B 512 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N VAL B 514 " --> pdb=" O TYR B 527 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N TYR B 527 " --> pdb=" O VAL B 514 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N LYS B 516 " --> pdb=" O GLU B 525 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 370 through 374 removed outlier: 6.271A pdb=" N GLN B 392 " --> pdb=" O LEU B 477 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 606 through 611 Processing sheet with id=AA9, first strand: chain 'C' and resid 47 through 51 removed outlier: 6.370A pdb=" N ALA C 79 " --> pdb=" O LEU C 157 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N LEU C 156 " --> pdb=" O ARG C 103 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 199 through 202 removed outlier: 4.066A pdb=" N ILE C 195 " --> pdb=" O LEU C 214 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N LEU C 214 " --> pdb=" O ILE C 195 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N ASN C 215 " --> pdb=" O ALA C 231 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N ALA C 231 " --> pdb=" O ASN C 215 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N VAL C 217 " --> pdb=" O LEU C 229 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N LEU C 229 " --> pdb=" O VAL C 217 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N ALA C 219 " --> pdb=" O VAL C 227 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLN C 225 " --> pdb=" O ALA C 221 " (cutoff:3.500A) removed outlier: 7.335A pdb=" N VAL C 227 " --> pdb=" O ILE C 561 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N ILE C 561 " --> pdb=" O VAL C 227 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LEU C 229 " --> pdb=" O ALA C 559 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N THR C 555 " --> pdb=" O ALA C 233 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N MET C 543 " --> pdb=" O LEU C 513 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N LEU C 513 " --> pdb=" O MET C 543 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ASP C 526 " --> pdb=" O LYS C 516 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 370 through 371 removed outlier: 3.549A pdb=" N GLY C 382 " --> pdb=" O VAL C 397 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N GLN C 392 " --> pdb=" O LEU C 477 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 606 through 611 824 hydrogen bonds defined for protein. 2322 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.73 Time building geometry restraints manager: 1.56 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: 4739 1.34 - 1.46: 2835 1.46 - 1.58: 6796 1.58 - 1.70: 0 1.70 - 1.82: 99 Bond restraints: 14469 Sorted by residual: bond pdb=" CA ALA B 660 " pdb=" CB ALA B 660 " ideal model delta sigma weight residual 1.528 1.490 0.039 1.56e-02 4.11e+03 6.21e+00 bond pdb=" CA ALA B 656 " pdb=" CB ALA B 656 " ideal model delta sigma weight residual 1.528 1.492 0.037 1.56e-02 4.11e+03 5.60e+00 bond pdb=" N HIS B 658 " pdb=" CA HIS B 658 " ideal model delta sigma weight residual 1.459 1.487 -0.028 1.20e-02 6.94e+03 5.41e+00 bond pdb=" N GLU B 659 " pdb=" CA GLU B 659 " ideal model delta sigma weight residual 1.459 1.478 -0.019 1.21e-02 6.83e+03 2.38e+00 bond pdb=" CG HIS B 658 " pdb=" CD2 HIS B 658 " ideal model delta sigma weight residual 1.354 1.337 0.017 1.10e-02 8.26e+03 2.34e+00 ... (remaining 14464 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.69: 19207 1.69 - 3.38: 315 3.38 - 5.08: 58 5.08 - 6.77: 10 6.77 - 8.46: 2 Bond angle restraints: 19592 Sorted by residual: angle pdb=" N GLU B 659 " pdb=" CA GLU B 659 " pdb=" CB GLU B 659 " ideal model delta sigma weight residual 110.12 105.03 5.09 1.47e+00 4.63e-01 1.20e+01 angle pdb=" CB GLU B 659 " pdb=" CG GLU B 659 " pdb=" CD GLU B 659 " ideal model delta sigma weight residual 112.60 106.93 5.67 1.70e+00 3.46e-01 1.11e+01 angle pdb=" CB GLU C 330 " pdb=" CG GLU C 330 " pdb=" CD GLU C 330 " ideal model delta sigma weight residual 112.60 118.22 -5.62 1.70e+00 3.46e-01 1.09e+01 angle pdb=" CA LYS C 439 " pdb=" CB LYS C 439 " pdb=" CG LYS C 439 " ideal model delta sigma weight residual 114.10 120.49 -6.39 2.00e+00 2.50e-01 1.02e+01 angle pdb=" CB GLU A 322 " pdb=" CG GLU A 322 " pdb=" CD GLU A 322 " ideal model delta sigma weight residual 112.60 118.02 -5.42 1.70e+00 3.46e-01 1.01e+01 ... (remaining 19587 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 7722 17.94 - 35.89: 866 35.89 - 53.83: 241 53.83 - 71.78: 53 71.78 - 89.72: 26 Dihedral angle restraints: 8908 sinusoidal: 3552 harmonic: 5356 Sorted by residual: dihedral pdb=" CD ARG B 661 " pdb=" NE ARG B 661 " pdb=" CZ ARG B 661 " pdb=" NH1 ARG B 661 " ideal model delta sinusoidal sigma weight residual 0.00 89.72 -89.72 1 1.00e+01 1.00e-02 9.55e+01 dihedral pdb=" CA LYS A 105 " pdb=" C LYS A 105 " pdb=" N ALA A 106 " pdb=" CA ALA A 106 " ideal model delta harmonic sigma weight residual 180.00 -157.03 -22.97 0 5.00e+00 4.00e-02 2.11e+01 dihedral pdb=" CA THR B 114 " pdb=" C THR B 114 " pdb=" N ASN B 115 " pdb=" CA ASN B 115 " ideal model delta harmonic sigma weight residual 180.00 -158.92 -21.08 0 5.00e+00 4.00e-02 1.78e+01 ... (remaining 8905 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 1684 0.047 - 0.095: 469 0.095 - 0.142: 136 0.142 - 0.189: 4 0.189 - 0.236: 2 Chirality restraints: 2295 Sorted by residual: chirality pdb=" CA GLU B 659 " pdb=" N GLU B 659 " pdb=" C GLU B 659 " pdb=" CB GLU B 659 " both_signs ideal model delta sigma weight residual False 2.51 2.75 -0.24 2.00e-01 2.50e+01 1.40e+00 chirality pdb=" CB THR C 272 " pdb=" CA THR C 272 " pdb=" OG1 THR C 272 " pdb=" CG2 THR C 272 " both_signs ideal model delta sigma weight residual False 2.55 2.34 0.21 2.00e-01 2.50e+01 1.07e+00 chirality pdb=" CA PRO A 113 " pdb=" N PRO A 113 " pdb=" C PRO A 113 " pdb=" CB PRO A 113 " both_signs ideal model delta sigma weight residual False 2.72 2.55 0.17 2.00e-01 2.50e+01 7.16e-01 ... (remaining 2292 not shown) Planarity restraints: 2536 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 661 " 1.110 9.50e-02 1.11e+02 4.98e-01 1.49e+02 pdb=" NE ARG B 661 " -0.067 2.00e-02 2.50e+03 pdb=" CZ ARG B 661 " -0.011 2.00e-02 2.50e+03 pdb=" NH1 ARG B 661 " 0.014 2.00e-02 2.50e+03 pdb=" NH2 ARG B 661 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP B 643 " -0.012 2.00e-02 2.50e+03 2.49e-02 6.18e+00 pdb=" CG ASP B 643 " 0.043 2.00e-02 2.50e+03 pdb=" OD1 ASP B 643 " -0.016 2.00e-02 2.50e+03 pdb=" OD2 ASP B 643 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP C 332 " -0.032 5.00e-02 4.00e+02 4.79e-02 3.67e+00 pdb=" N PRO C 333 " 0.083 5.00e-02 4.00e+02 pdb=" CA PRO C 333 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO C 333 " -0.027 5.00e-02 4.00e+02 ... (remaining 2533 not shown) Histogram of nonbonded interaction distances: 2.46 - 2.95: 6320 2.95 - 3.43: 14284 3.43 - 3.92: 24023 3.92 - 4.41: 28583 4.41 - 4.90: 45902 Nonbonded interactions: 119112 Sorted by model distance: nonbonded pdb=" N GLU C 330 " pdb=" OE1 GLU C 330 " model vdw 2.457 3.120 nonbonded pdb=" OD1 ASP B 643 " pdb=" N GLU B 644 " model vdw 2.492 3.120 nonbonded pdb=" N GLU B 326 " pdb=" OE1 GLU B 326 " model vdw 2.508 3.120 nonbonded pdb=" N GLU A 322 " pdb=" OE1 GLU A 322 " model vdw 2.517 3.120 nonbonded pdb=" O ARG C 464 " pdb=" OD1 ASP C 465 " model vdw 2.526 3.040 ... (remaining 119107 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 46 through 108 or resid 122 through 440 or resid 444 throu \ gh 668 or resid 901)) selection = (chain 'B' and (resid 46 through 108 or resid 122 through 668 or resid 901)) selection = (chain 'C' and (resid 46 through 440 or resid 444 through 901)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.130 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.160 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 13.310 Find NCS groups from input model: 0.270 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:10.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8734 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 : 0.006 0.042 14469 Z= 0.256 Angle : 0.574 8.458 19592 Z= 0.309 Chirality : 0.047 0.236 2295 Planarity : 0.011 0.498 2536 Dihedral : 17.131 89.721 5452 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 2.22 % Allowed : 23.79 % Favored : 73.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.63 (0.20), residues: 1845 helix: 0.44 (0.18), residues: 702 sheet: 1.21 (0.26), residues: 436 loop : 0.07 (0.25), residues: 707 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG B 617 TYR 0.025 0.002 TYR B 116 PHE 0.015 0.002 PHE A 620 TRP 0.004 0.001 TRP A 184 HIS 0.007 0.001 HIS B 426 Details of bonding type rmsd covalent geometry : bond 0.00574 (14469) covalent geometry : angle 0.57433 (19592) hydrogen bonds : bond 0.21530 ( 824) hydrogen bonds : angle 7.85620 ( 2322) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3690 Ramachandran restraints generated. 1845 Oldfield, 0 Emsley, 1845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3690 Ramachandran restraints generated. 1845 Oldfield, 0 Emsley, 1845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 137 time to evaluate : 0.571 Fit side-chains revert: symmetry clash REVERT: A 387 GLN cc_start: 0.9230 (OUTLIER) cc_final: 0.8649 (tp40) REVERT: A 428 GLU cc_start: 0.8686 (mm-30) cc_final: 0.8385 (mm-30) REVERT: A 550 THR cc_start: 0.9219 (m) cc_final: 0.8962 (p) REVERT: A 552 LYS cc_start: 0.8863 (pttp) cc_final: 0.8504 (ptpp) REVERT: A 645 GLU cc_start: 0.6999 (OUTLIER) cc_final: 0.5911 (pm20) REVERT: A 663 PHE cc_start: 0.7314 (m-80) cc_final: 0.6604 (t80) REVERT: B 89 LYS cc_start: 0.8597 (tppp) cc_final: 0.8324 (mmmt) REVERT: B 111 ARG cc_start: 0.6751 (OUTLIER) cc_final: 0.6245 (mpt180) REVERT: B 199 GLU cc_start: 0.8652 (mm-30) cc_final: 0.8188 (mp0) REVERT: B 206 ARG cc_start: 0.8682 (mtp180) cc_final: 0.8353 (tmm-80) REVERT: B 308 SER cc_start: 0.9058 (m) cc_final: 0.8846 (p) REVERT: B 378 LYS cc_start: 0.8795 (mtpm) cc_final: 0.8409 (tttm) REVERT: B 516 LYS cc_start: 0.8655 (OUTLIER) cc_final: 0.8141 (ttmm) REVERT: B 552 LYS cc_start: 0.8349 (pttm) cc_final: 0.7898 (mtpp) REVERT: B 560 ASP cc_start: 0.8103 (m-30) cc_final: 0.7674 (t70) REVERT: C 55 LYS cc_start: 0.9047 (tptp) cc_final: 0.8739 (ttmt) REVERT: C 89 LYS cc_start: 0.8932 (tppt) cc_final: 0.8609 (ttpp) REVERT: C 199 GLU cc_start: 0.8437 (mm-30) cc_final: 0.8064 (tp30) REVERT: C 207 LYS cc_start: 0.8968 (mmmm) cc_final: 0.8739 (mttm) REVERT: C 311 GLU cc_start: 0.8541 (pt0) cc_final: 0.8153 (pp20) REVERT: C 319 ASP cc_start: 0.8627 (m-30) cc_final: 0.8050 (t0) REVERT: C 322 GLU cc_start: 0.8727 (mp0) cc_final: 0.8063 (tp30) REVERT: C 455 GLU cc_start: 0.8922 (OUTLIER) cc_final: 0.8628 (tt0) outliers start: 35 outliers final: 23 residues processed: 160 average time/residue: 0.6736 time to fit residues: 116.3761 Evaluate side-chains 156 residues out of total 1576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 128 time to evaluate : 0.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 LYS Chi-restraints excluded: chain A residue 111 ARG Chi-restraints excluded: chain A residue 210 SER Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 371 SER Chi-restraints excluded: chain A residue 387 GLN Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 645 GLU Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 59 SER Chi-restraints excluded: chain B residue 96 MET Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 111 ARG Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 376 MET Chi-restraints excluded: chain B residue 516 LYS Chi-restraints excluded: chain B residue 644 GLU Chi-restraints excluded: chain B residue 658 HIS Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 257 GLN Chi-restraints excluded: chain C residue 372 CYS Chi-restraints excluded: chain C residue 376 MET Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain C residue 443 LEU Chi-restraints excluded: chain C residue 455 GLU Chi-restraints excluded: chain C residue 483 SER Chi-restraints excluded: chain C residue 638 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 98 optimal weight: 5.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 0.0040 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 0.0020 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 chunk 149 optimal weight: 6.9990 overall best weight: 1.6006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 369 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.103086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.080198 restraints weight = 21416.119| |-----------------------------------------------------------------------------| r_work (start): 0.3027 rms_B_bonded: 2.23 r_work: 0.2889 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2764 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.2764 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8656 moved from start: 0.0856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 14469 Z= 0.185 Angle : 0.544 6.249 19592 Z= 0.299 Chirality : 0.046 0.178 2295 Planarity : 0.004 0.045 2536 Dihedral : 7.127 68.514 2045 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 4.82 % Allowed : 20.37 % Favored : 74.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.64 (0.20), residues: 1845 helix: 1.98 (0.18), residues: 707 sheet: 1.32 (0.25), residues: 442 loop : 0.06 (0.25), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 617 TYR 0.023 0.002 TYR C 334 PHE 0.016 0.001 PHE B 620 TRP 0.004 0.001 TRP C 184 HIS 0.006 0.001 HIS B 426 Details of bonding type rmsd covalent geometry : bond 0.00404 (14469) covalent geometry : angle 0.54445 (19592) hydrogen bonds : bond 0.06453 ( 824) hydrogen bonds : angle 5.44122 ( 2322) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3690 Ramachandran restraints generated. 1845 Oldfield, 0 Emsley, 1845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3690 Ramachandran restraints generated. 1845 Oldfield, 0 Emsley, 1845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 140 time to evaluate : 0.533 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 228 MET cc_start: 0.9091 (OUTLIER) cc_final: 0.8566 (tmm) REVERT: A 419 LYS cc_start: 0.6923 (OUTLIER) cc_final: 0.5373 (mmmt) REVERT: A 428 GLU cc_start: 0.8628 (mm-30) cc_final: 0.8336 (mm-30) REVERT: A 550 THR cc_start: 0.9173 (m) cc_final: 0.8899 (p) REVERT: A 552 LYS cc_start: 0.8847 (pttp) cc_final: 0.8462 (ptpp) REVERT: A 632 GLN cc_start: 0.8266 (tt0) cc_final: 0.7916 (tm-30) REVERT: A 645 GLU cc_start: 0.6946 (OUTLIER) cc_final: 0.5877 (pm20) REVERT: A 663 PHE cc_start: 0.7206 (m-80) cc_final: 0.6847 (t80) REVERT: B 111 ARG cc_start: 0.6703 (OUTLIER) cc_final: 0.6229 (mpt180) REVERT: B 199 GLU cc_start: 0.8569 (mm-30) cc_final: 0.8038 (mp0) REVERT: B 206 ARG cc_start: 0.8650 (OUTLIER) cc_final: 0.8302 (tmm-80) REVERT: B 378 LYS cc_start: 0.8746 (mtpm) cc_final: 0.8477 (tttp) REVERT: B 552 LYS cc_start: 0.8365 (pttm) cc_final: 0.7872 (mtpp) REVERT: B 560 ASP cc_start: 0.7979 (m-30) cc_final: 0.7525 (t70) REVERT: C 55 LYS cc_start: 0.8977 (tptp) cc_final: 0.8676 (ttmt) REVERT: C 89 LYS cc_start: 0.8934 (tppt) cc_final: 0.8585 (ttpp) REVERT: C 199 GLU cc_start: 0.8466 (mm-30) cc_final: 0.8098 (tp30) REVERT: C 311 GLU cc_start: 0.8320 (pt0) cc_final: 0.7992 (pp20) REVERT: C 406 ILE cc_start: 0.7710 (OUTLIER) cc_final: 0.7214 (pp) outliers start: 76 outliers final: 33 residues processed: 201 average time/residue: 0.5999 time to fit residues: 131.4291 Evaluate side-chains 164 residues out of total 1576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 125 time to evaluate : 0.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 LYS Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 111 ARG Chi-restraints excluded: chain A residue 228 MET Chi-restraints excluded: chain A residue 257 GLN Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 326 GLU Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 419 LYS Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 484 SER Chi-restraints excluded: chain A residue 523 GLU Chi-restraints excluded: chain A residue 606 VAL Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 630 LYS Chi-restraints excluded: chain A residue 645 GLU Chi-restraints excluded: chain B residue 59 SER Chi-restraints excluded: chain B residue 111 ARG Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 206 ARG Chi-restraints excluded: chain B residue 269 THR Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 371 SER Chi-restraints excluded: chain B residue 376 MET Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain B residue 547 ILE Chi-restraints excluded: chain B residue 568 ILE Chi-restraints excluded: chain B residue 644 GLU Chi-restraints excluded: chain B residue 658 HIS Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 257 GLN Chi-restraints excluded: chain C residue 269 THR Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain C residue 406 ILE Chi-restraints excluded: chain C residue 434 THR Chi-restraints excluded: chain C residue 562 LYS Chi-restraints excluded: chain C residue 637 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 146 optimal weight: 3.9990 chunk 140 optimal weight: 0.6980 chunk 59 optimal weight: 6.9990 chunk 167 optimal weight: 3.9990 chunk 45 optimal weight: 2.9990 chunk 19 optimal weight: 3.9990 chunk 97 optimal weight: 1.9990 chunk 46 optimal weight: 0.9990 chunk 121 optimal weight: 0.2980 chunk 44 optimal weight: 0.9990 chunk 52 optimal weight: 0.0030 overall best weight: 0.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 369 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.105759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.082918 restraints weight = 21434.561| |-----------------------------------------------------------------------------| r_work (start): 0.3076 rms_B_bonded: 2.25 r_work: 0.2940 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2817 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8608 moved from start: 0.1278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 14469 Z= 0.120 Angle : 0.486 6.664 19592 Z= 0.265 Chirality : 0.044 0.150 2295 Planarity : 0.004 0.047 2536 Dihedral : 5.884 65.841 2018 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 3.62 % Allowed : 21.57 % Favored : 74.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.94 (0.20), residues: 1845 helix: 2.34 (0.18), residues: 712 sheet: 1.30 (0.25), residues: 447 loop : 0.20 (0.25), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 617 TYR 0.026 0.001 TYR C 334 PHE 0.017 0.001 PHE B 620 TRP 0.008 0.001 TRP A 184 HIS 0.005 0.001 HIS B 426 Details of bonding type rmsd covalent geometry : bond 0.00243 (14469) covalent geometry : angle 0.48573 (19592) hydrogen bonds : bond 0.05025 ( 824) hydrogen bonds : angle 4.97345 ( 2322) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3690 Ramachandran restraints generated. 1845 Oldfield, 0 Emsley, 1845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3690 Ramachandran restraints generated. 1845 Oldfield, 0 Emsley, 1845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 145 time to evaluate : 0.572 Fit side-chains revert: symmetry clash REVERT: A 419 LYS cc_start: 0.6735 (OUTLIER) cc_final: 0.5078 (mmmt) REVERT: A 428 GLU cc_start: 0.8600 (mm-30) cc_final: 0.8340 (mm-30) REVERT: A 550 THR cc_start: 0.9070 (m) cc_final: 0.8739 (p) REVERT: A 552 LYS cc_start: 0.8807 (pttp) cc_final: 0.8240 (mttt) REVERT: A 632 GLN cc_start: 0.8229 (tt0) cc_final: 0.7894 (tm-30) REVERT: A 663 PHE cc_start: 0.7186 (m-80) cc_final: 0.6847 (t80) REVERT: B 111 ARG cc_start: 0.6680 (OUTLIER) cc_final: 0.6099 (mpt180) REVERT: B 118 ARG cc_start: 0.3525 (OUTLIER) cc_final: 0.2314 (mtt180) REVERT: B 199 GLU cc_start: 0.8544 (mm-30) cc_final: 0.8010 (mp0) REVERT: B 378 LYS cc_start: 0.8661 (mtpm) cc_final: 0.8386 (tttp) REVERT: B 523 GLU cc_start: 0.8100 (OUTLIER) cc_final: 0.7691 (mm-30) REVERT: B 552 LYS cc_start: 0.8371 (pttm) cc_final: 0.7854 (mtpp) REVERT: B 560 ASP cc_start: 0.7962 (m-30) cc_final: 0.7521 (t70) REVERT: B 616 LYS cc_start: 0.8699 (OUTLIER) cc_final: 0.8301 (ttmt) REVERT: B 644 GLU cc_start: 0.7777 (OUTLIER) cc_final: 0.7202 (pm20) REVERT: C 55 LYS cc_start: 0.8942 (tptp) cc_final: 0.8653 (ttmt) REVERT: C 89 LYS cc_start: 0.8920 (tppt) cc_final: 0.8553 (ttpp) REVERT: C 199 GLU cc_start: 0.8464 (mm-30) cc_final: 0.8122 (tp30) REVERT: C 207 LYS cc_start: 0.8705 (mmmm) cc_final: 0.8497 (mttm) REVERT: C 237 LEU cc_start: 0.8442 (OUTLIER) cc_final: 0.8123 (mt) REVERT: C 257 GLN cc_start: 0.8662 (OUTLIER) cc_final: 0.8261 (pt0) REVERT: C 311 GLU cc_start: 0.8231 (pt0) cc_final: 0.7967 (pp20) REVERT: C 322 GLU cc_start: 0.8461 (mp0) cc_final: 0.7708 (tp30) REVERT: C 406 ILE cc_start: 0.7637 (OUTLIER) cc_final: 0.7327 (pp) REVERT: C 426 HIS cc_start: 0.8239 (t70) cc_final: 0.7775 (m90) outliers start: 57 outliers final: 20 residues processed: 193 average time/residue: 0.6080 time to fit residues: 128.2607 Evaluate side-chains 161 residues out of total 1576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 132 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 LYS Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 111 ARG Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 351 ILE Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 419 LYS Chi-restraints excluded: chain A residue 484 SER Chi-restraints excluded: chain A residue 523 GLU Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 614 LEU Chi-restraints excluded: chain B residue 111 ARG Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 118 ARG Chi-restraints excluded: chain B residue 257 GLN Chi-restraints excluded: chain B residue 269 THR Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 371 SER Chi-restraints excluded: chain B residue 523 GLU Chi-restraints excluded: chain B residue 547 ILE Chi-restraints excluded: chain B residue 616 LYS Chi-restraints excluded: chain B residue 644 GLU Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain C residue 257 GLN Chi-restraints excluded: chain C residue 269 THR Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain C residue 406 ILE Chi-restraints excluded: chain C residue 562 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 94 optimal weight: 3.9990 chunk 42 optimal weight: 5.9990 chunk 165 optimal weight: 5.9990 chunk 41 optimal weight: 0.0970 chunk 151 optimal weight: 8.9990 chunk 108 optimal weight: 4.9990 chunk 14 optimal weight: 7.9990 chunk 23 optimal weight: 2.9990 chunk 132 optimal weight: 0.7980 chunk 7 optimal weight: 0.0270 chunk 175 optimal weight: 1.9990 overall best weight: 1.1840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 155 ASN C 155 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.104693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.081818 restraints weight = 21338.539| |-----------------------------------------------------------------------------| r_work (start): 0.3057 rms_B_bonded: 2.23 r_work: 0.2923 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2801 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.2801 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8629 moved from start: 0.1294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14469 Z= 0.148 Angle : 0.494 7.184 19592 Z= 0.269 Chirality : 0.044 0.153 2295 Planarity : 0.004 0.049 2536 Dihedral : 5.416 58.987 2006 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 4.12 % Allowed : 21.07 % Favored : 74.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.00 (0.20), residues: 1845 helix: 2.45 (0.18), residues: 713 sheet: 1.33 (0.25), residues: 447 loop : 0.17 (0.25), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 617 TYR 0.027 0.002 TYR C 334 PHE 0.012 0.001 PHE C 340 TRP 0.005 0.001 TRP C 184 HIS 0.004 0.001 HIS B 426 Details of bonding type rmsd covalent geometry : bond 0.00322 (14469) covalent geometry : angle 0.49442 (19592) hydrogen bonds : bond 0.04997 ( 824) hydrogen bonds : angle 4.90565 ( 2322) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3690 Ramachandran restraints generated. 1845 Oldfield, 0 Emsley, 1845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3690 Ramachandran restraints generated. 1845 Oldfield, 0 Emsley, 1845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 136 time to evaluate : 0.557 Fit side-chains REVERT: A 228 MET cc_start: 0.9094 (OUTLIER) cc_final: 0.8610 (tmm) REVERT: A 419 LYS cc_start: 0.6803 (OUTLIER) cc_final: 0.5063 (mmmt) REVERT: A 428 GLU cc_start: 0.8611 (mm-30) cc_final: 0.8335 (mm-30) REVERT: A 550 THR cc_start: 0.9097 (m) cc_final: 0.8870 (p) REVERT: A 552 LYS cc_start: 0.8817 (pttp) cc_final: 0.8402 (pmmt) REVERT: A 617 ARG cc_start: 0.8637 (mtm110) cc_final: 0.8243 (mmm-85) REVERT: A 632 GLN cc_start: 0.8250 (tt0) cc_final: 0.7905 (tm-30) REVERT: A 663 PHE cc_start: 0.7175 (m-80) cc_final: 0.6866 (t80) REVERT: B 111 ARG cc_start: 0.6652 (OUTLIER) cc_final: 0.6054 (mpt180) REVERT: B 118 ARG cc_start: 0.3644 (OUTLIER) cc_final: 0.2114 (mtt180) REVERT: B 199 GLU cc_start: 0.8566 (mm-30) cc_final: 0.8081 (mp0) REVERT: B 378 LYS cc_start: 0.8693 (mtpm) cc_final: 0.8423 (tttp) REVERT: B 523 GLU cc_start: 0.8121 (OUTLIER) cc_final: 0.7715 (mm-30) REVERT: B 552 LYS cc_start: 0.8354 (pttm) cc_final: 0.7866 (mtpp) REVERT: B 560 ASP cc_start: 0.7988 (m-30) cc_final: 0.7534 (t70) REVERT: B 643 ASP cc_start: 0.7288 (t0) cc_final: 0.6752 (t0) REVERT: B 644 GLU cc_start: 0.7730 (OUTLIER) cc_final: 0.7261 (pm20) REVERT: C 55 LYS cc_start: 0.8961 (OUTLIER) cc_final: 0.8698 (ttmt) REVERT: C 89 LYS cc_start: 0.8921 (tppt) cc_final: 0.8558 (ttpp) REVERT: C 105 LYS cc_start: 0.7953 (OUTLIER) cc_final: 0.7477 (ptpt) REVERT: C 199 GLU cc_start: 0.8466 (mm-30) cc_final: 0.8112 (tp30) REVERT: C 207 LYS cc_start: 0.8734 (mmmm) cc_final: 0.8532 (mttm) REVERT: C 237 LEU cc_start: 0.8466 (OUTLIER) cc_final: 0.8115 (mt) REVERT: C 257 GLN cc_start: 0.8632 (OUTLIER) cc_final: 0.8282 (pt0) REVERT: C 311 GLU cc_start: 0.8237 (pt0) cc_final: 0.7914 (pp20) REVERT: C 322 GLU cc_start: 0.8470 (mp0) cc_final: 0.7697 (tp30) REVERT: C 406 ILE cc_start: 0.7561 (OUTLIER) cc_final: 0.7113 (pp) outliers start: 65 outliers final: 30 residues processed: 189 average time/residue: 0.5903 time to fit residues: 121.9833 Evaluate side-chains 168 residues out of total 1576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 127 time to evaluate : 0.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 LYS Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 111 ARG Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 228 MET Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 326 GLU Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 419 LYS Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 484 SER Chi-restraints excluded: chain A residue 523 GLU Chi-restraints excluded: chain A residue 547 ILE Chi-restraints excluded: chain A residue 606 VAL Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 614 LEU Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 111 ARG Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 118 ARG Chi-restraints excluded: chain B residue 257 GLN Chi-restraints excluded: chain B residue 269 THR Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 371 SER Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 424 MET Chi-restraints excluded: chain B residue 523 GLU Chi-restraints excluded: chain B residue 547 ILE Chi-restraints excluded: chain B residue 644 GLU Chi-restraints excluded: chain C residue 55 LYS Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 105 LYS Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain C residue 257 GLN Chi-restraints excluded: chain C residue 269 THR Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain C residue 406 ILE Chi-restraints excluded: chain C residue 434 THR Chi-restraints excluded: chain C residue 562 LYS Chi-restraints excluded: chain C residue 637 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 171 optimal weight: 4.9990 chunk 97 optimal weight: 0.7980 chunk 25 optimal weight: 4.9990 chunk 2 optimal weight: 6.9990 chunk 18 optimal weight: 4.9990 chunk 7 optimal weight: 1.9990 chunk 163 optimal weight: 2.9990 chunk 31 optimal weight: 3.9990 chunk 41 optimal weight: 3.9990 chunk 12 optimal weight: 0.9980 chunk 121 optimal weight: 0.0870 overall best weight: 1.3762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.104639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.081481 restraints weight = 21378.646| |-----------------------------------------------------------------------------| r_work (start): 0.3046 rms_B_bonded: 2.21 r_work: 0.2915 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2793 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.2793 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8666 moved from start: 0.1283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 14469 Z= 0.159 Angle : 0.503 7.542 19592 Z= 0.273 Chirality : 0.045 0.149 2295 Planarity : 0.004 0.048 2536 Dihedral : 5.370 59.642 2006 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 4.31 % Allowed : 20.94 % Favored : 74.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.01 (0.20), residues: 1845 helix: 2.47 (0.18), residues: 709 sheet: 1.30 (0.25), residues: 450 loop : 0.18 (0.25), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 617 TYR 0.028 0.002 TYR C 334 PHE 0.013 0.001 PHE A 545 TRP 0.005 0.001 TRP C 184 HIS 0.005 0.001 HIS B 426 Details of bonding type rmsd covalent geometry : bond 0.00349 (14469) covalent geometry : angle 0.50304 (19592) hydrogen bonds : bond 0.05064 ( 824) hydrogen bonds : angle 4.88121 ( 2322) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3690 Ramachandran restraints generated. 1845 Oldfield, 0 Emsley, 1845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3690 Ramachandran restraints generated. 1845 Oldfield, 0 Emsley, 1845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 136 time to evaluate : 0.620 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 228 MET cc_start: 0.9107 (OUTLIER) cc_final: 0.8659 (tmm) REVERT: A 318 LEU cc_start: 0.8786 (OUTLIER) cc_final: 0.8413 (mm) REVERT: A 419 LYS cc_start: 0.6876 (OUTLIER) cc_final: 0.5160 (mmmt) REVERT: A 428 GLU cc_start: 0.8555 (mm-30) cc_final: 0.8303 (mm-30) REVERT: A 550 THR cc_start: 0.9134 (m) cc_final: 0.8920 (p) REVERT: A 552 LYS cc_start: 0.8791 (pttp) cc_final: 0.8450 (pmmt) REVERT: A 617 ARG cc_start: 0.8656 (mtm110) cc_final: 0.8239 (mmm-85) REVERT: A 632 GLN cc_start: 0.8291 (tt0) cc_final: 0.7976 (tm-30) REVERT: A 645 GLU cc_start: 0.6942 (OUTLIER) cc_final: 0.5878 (pm20) REVERT: A 663 PHE cc_start: 0.7160 (m-80) cc_final: 0.6911 (t80) REVERT: B 111 ARG cc_start: 0.6756 (OUTLIER) cc_final: 0.6180 (mpt180) REVERT: B 118 ARG cc_start: 0.3776 (OUTLIER) cc_final: 0.2404 (mtt180) REVERT: B 199 GLU cc_start: 0.8588 (mm-30) cc_final: 0.8059 (mp0) REVERT: B 209 MET cc_start: 0.8245 (mmm) cc_final: 0.7990 (mtt) REVERT: B 230 GLU cc_start: 0.8577 (OUTLIER) cc_final: 0.8196 (tm-30) REVERT: B 285 LYS cc_start: 0.8313 (ttpp) cc_final: 0.7840 (tptt) REVERT: B 378 LYS cc_start: 0.8715 (mtpm) cc_final: 0.8440 (tttp) REVERT: B 552 LYS cc_start: 0.8412 (pttm) cc_final: 0.7954 (mtpp) REVERT: B 560 ASP cc_start: 0.8038 (OUTLIER) cc_final: 0.7572 (t70) REVERT: B 632 GLN cc_start: 0.8146 (mt0) cc_final: 0.7946 (mt0) REVERT: C 55 LYS cc_start: 0.8947 (OUTLIER) cc_final: 0.8726 (ttmt) REVERT: C 89 LYS cc_start: 0.8939 (tppt) cc_final: 0.8607 (ttpp) REVERT: C 199 GLU cc_start: 0.8457 (mm-30) cc_final: 0.8131 (tp30) REVERT: C 237 LEU cc_start: 0.8571 (OUTLIER) cc_final: 0.8243 (mt) REVERT: C 257 GLN cc_start: 0.8696 (tt0) cc_final: 0.8395 (pt0) REVERT: C 311 GLU cc_start: 0.8192 (pt0) cc_final: 0.7903 (pp20) REVERT: C 406 ILE cc_start: 0.7640 (OUTLIER) cc_final: 0.7138 (pp) REVERT: C 418 ILE cc_start: 0.7366 (OUTLIER) cc_final: 0.7105 (mt) REVERT: C 426 HIS cc_start: 0.8206 (t70) cc_final: 0.7884 (m90) outliers start: 68 outliers final: 36 residues processed: 192 average time/residue: 0.6330 time to fit residues: 132.7653 Evaluate side-chains 176 residues out of total 1576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 128 time to evaluate : 0.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 LYS Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 111 ARG Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 166 ASP Chi-restraints excluded: chain A residue 228 MET Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 419 LYS Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 484 SER Chi-restraints excluded: chain A residue 523 GLU Chi-restraints excluded: chain A residue 606 VAL Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 645 GLU Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 111 ARG Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 118 ARG Chi-restraints excluded: chain B residue 230 GLU Chi-restraints excluded: chain B residue 257 GLN Chi-restraints excluded: chain B residue 269 THR Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 371 SER Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 424 MET Chi-restraints excluded: chain B residue 547 ILE Chi-restraints excluded: chain B residue 560 ASP Chi-restraints excluded: chain B residue 568 ILE Chi-restraints excluded: chain B residue 644 GLU Chi-restraints excluded: chain B residue 658 HIS Chi-restraints excluded: chain C residue 55 LYS Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain C residue 269 THR Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain C residue 406 ILE Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 434 THR Chi-restraints excluded: chain C residue 484 SER Chi-restraints excluded: chain C residue 562 LYS Chi-restraints excluded: chain C residue 587 GLN Chi-restraints excluded: chain C residue 603 ASN Chi-restraints excluded: chain C residue 637 VAL Chi-restraints excluded: chain C residue 667 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 160 optimal weight: 5.9990 chunk 167 optimal weight: 5.9990 chunk 75 optimal weight: 0.5980 chunk 183 optimal weight: 4.9990 chunk 39 optimal weight: 9.9990 chunk 41 optimal weight: 0.9980 chunk 90 optimal weight: 3.9990 chunk 133 optimal weight: 4.9990 chunk 128 optimal weight: 3.9990 chunk 64 optimal weight: 5.9990 chunk 154 optimal weight: 0.9980 overall best weight: 2.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 155 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.103353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.080248 restraints weight = 21411.443| |-----------------------------------------------------------------------------| r_work (start): 0.3026 rms_B_bonded: 2.20 r_work: 0.2894 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2772 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8688 moved from start: 0.1213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 14469 Z= 0.212 Angle : 0.540 7.865 19592 Z= 0.293 Chirality : 0.046 0.158 2295 Planarity : 0.004 0.055 2536 Dihedral : 5.503 65.630 2003 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 4.82 % Allowed : 21.00 % Favored : 74.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.91 (0.20), residues: 1845 helix: 2.38 (0.18), residues: 709 sheet: 1.35 (0.25), residues: 445 loop : 0.07 (0.25), residues: 691 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG B 617 TYR 0.027 0.002 TYR C 334 PHE 0.015 0.001 PHE A 545 TRP 0.004 0.001 TRP C 184 HIS 0.005 0.001 HIS B 426 Details of bonding type rmsd covalent geometry : bond 0.00480 (14469) covalent geometry : angle 0.54028 (19592) hydrogen bonds : bond 0.05462 ( 824) hydrogen bonds : angle 4.96372 ( 2322) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3690 Ramachandran restraints generated. 1845 Oldfield, 0 Emsley, 1845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3690 Ramachandran restraints generated. 1845 Oldfield, 0 Emsley, 1845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 127 time to evaluate : 0.395 Fit side-chains REVERT: A 228 MET cc_start: 0.9117 (OUTLIER) cc_final: 0.8718 (tmm) REVERT: A 419 LYS cc_start: 0.7004 (OUTLIER) cc_final: 0.5441 (mmmt) REVERT: A 428 GLU cc_start: 0.8577 (mm-30) cc_final: 0.8321 (mm-30) REVERT: A 550 THR cc_start: 0.9184 (m) cc_final: 0.8973 (p) REVERT: A 552 LYS cc_start: 0.8812 (pttp) cc_final: 0.8497 (ptpp) REVERT: A 617 ARG cc_start: 0.8646 (mtm110) cc_final: 0.8242 (mmm-85) REVERT: A 632 GLN cc_start: 0.8295 (tt0) cc_final: 0.7967 (tm-30) REVERT: A 645 GLU cc_start: 0.7014 (OUTLIER) cc_final: 0.5957 (pm20) REVERT: A 663 PHE cc_start: 0.7117 (m-80) cc_final: 0.6887 (t80) REVERT: B 111 ARG cc_start: 0.6714 (OUTLIER) cc_final: 0.6179 (mpt180) REVERT: B 118 ARG cc_start: 0.3852 (OUTLIER) cc_final: 0.2185 (mtt180) REVERT: B 199 GLU cc_start: 0.8599 (mm-30) cc_final: 0.8065 (mp0) REVERT: B 206 ARG cc_start: 0.8686 (OUTLIER) cc_final: 0.8330 (tmm-80) REVERT: B 378 LYS cc_start: 0.8762 (mtpm) cc_final: 0.8488 (tttp) REVERT: B 552 LYS cc_start: 0.8408 (pttm) cc_final: 0.7955 (mtpp) REVERT: B 560 ASP cc_start: 0.8050 (OUTLIER) cc_final: 0.7580 (t70) REVERT: B 616 LYS cc_start: 0.8770 (OUTLIER) cc_final: 0.8364 (ttmt) REVERT: B 632 GLN cc_start: 0.8171 (mt0) cc_final: 0.7968 (mt0) REVERT: B 644 GLU cc_start: 0.7811 (OUTLIER) cc_final: 0.7261 (pm20) REVERT: C 55 LYS cc_start: 0.8961 (OUTLIER) cc_final: 0.8744 (ttmt) REVERT: C 89 LYS cc_start: 0.8944 (tppt) cc_final: 0.8616 (ttpp) REVERT: C 199 GLU cc_start: 0.8467 (mm-30) cc_final: 0.8129 (tp30) REVERT: C 237 LEU cc_start: 0.8652 (OUTLIER) cc_final: 0.8338 (mt) REVERT: C 257 GLN cc_start: 0.8702 (tt0) cc_final: 0.8393 (pt0) REVERT: C 311 GLU cc_start: 0.8217 (pt0) cc_final: 0.7912 (pp20) REVERT: C 322 GLU cc_start: 0.8445 (mp0) cc_final: 0.7829 (tp30) REVERT: C 406 ILE cc_start: 0.7736 (OUTLIER) cc_final: 0.7197 (pp) REVERT: C 418 ILE cc_start: 0.7378 (OUTLIER) cc_final: 0.7128 (mt) REVERT: C 426 HIS cc_start: 0.8283 (t70) cc_final: 0.7956 (m90) REVERT: C 617 ARG cc_start: 0.8264 (OUTLIER) cc_final: 0.7820 (tpp80) outliers start: 76 outliers final: 41 residues processed: 187 average time/residue: 0.5547 time to fit residues: 113.4833 Evaluate side-chains 182 residues out of total 1576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 127 time to evaluate : 0.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 LYS Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain A residue 111 ARG Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 228 MET Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 326 GLU Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 419 LYS Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 484 SER Chi-restraints excluded: chain A residue 606 VAL Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 616 LYS Chi-restraints excluded: chain A residue 645 GLU Chi-restraints excluded: chain B residue 50 ASP Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 111 ARG Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 118 ARG Chi-restraints excluded: chain B residue 206 ARG Chi-restraints excluded: chain B residue 257 GLN Chi-restraints excluded: chain B residue 269 THR Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 371 SER Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 424 MET Chi-restraints excluded: chain B residue 547 ILE Chi-restraints excluded: chain B residue 560 ASP Chi-restraints excluded: chain B residue 568 ILE Chi-restraints excluded: chain B residue 616 LYS Chi-restraints excluded: chain B residue 644 GLU Chi-restraints excluded: chain B residue 658 HIS Chi-restraints excluded: chain C residue 55 LYS Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain C residue 269 THR Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain C residue 404 SER Chi-restraints excluded: chain C residue 406 ILE Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 434 THR Chi-restraints excluded: chain C residue 484 SER Chi-restraints excluded: chain C residue 562 LYS Chi-restraints excluded: chain C residue 587 GLN Chi-restraints excluded: chain C residue 603 ASN Chi-restraints excluded: chain C residue 617 ARG Chi-restraints excluded: chain C residue 637 VAL Chi-restraints excluded: chain C residue 667 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 159 optimal weight: 10.0000 chunk 106 optimal weight: 0.9990 chunk 110 optimal weight: 0.9990 chunk 68 optimal weight: 3.9990 chunk 111 optimal weight: 3.9990 chunk 184 optimal weight: 0.9980 chunk 93 optimal weight: 0.9980 chunk 147 optimal weight: 2.9990 chunk 87 optimal weight: 0.9980 chunk 166 optimal weight: 3.9990 chunk 97 optimal weight: 1.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 323 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.105358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.082225 restraints weight = 21287.567| |-----------------------------------------------------------------------------| r_work (start): 0.3059 rms_B_bonded: 2.21 r_work: 0.2928 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2806 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.2806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8657 moved from start: 0.1362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14469 Z= 0.139 Angle : 0.506 8.592 19592 Z= 0.273 Chirality : 0.044 0.150 2295 Planarity : 0.004 0.053 2536 Dihedral : 5.355 61.479 2003 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 4.70 % Allowed : 21.19 % Favored : 74.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.01 (0.20), residues: 1845 helix: 2.50 (0.18), residues: 711 sheet: 1.27 (0.25), residues: 450 loop : 0.18 (0.25), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG B 617 TYR 0.027 0.001 TYR C 334 PHE 0.016 0.001 PHE B 620 TRP 0.006 0.001 TRP B 184 HIS 0.004 0.001 HIS B 426 Details of bonding type rmsd covalent geometry : bond 0.00302 (14469) covalent geometry : angle 0.50629 (19592) hydrogen bonds : bond 0.04849 ( 824) hydrogen bonds : angle 4.80564 ( 2322) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3690 Ramachandran restraints generated. 1845 Oldfield, 0 Emsley, 1845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3690 Ramachandran restraints generated. 1845 Oldfield, 0 Emsley, 1845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 133 time to evaluate : 0.378 Fit side-chains revert: symmetry clash REVERT: A 228 MET cc_start: 0.9106 (OUTLIER) cc_final: 0.8652 (tmm) REVERT: A 419 LYS cc_start: 0.6855 (OUTLIER) cc_final: 0.5124 (mmmt) REVERT: A 428 GLU cc_start: 0.8550 (mm-30) cc_final: 0.8299 (mm-30) REVERT: A 550 THR cc_start: 0.9131 (m) cc_final: 0.8878 (p) REVERT: A 552 LYS cc_start: 0.8774 (pttp) cc_final: 0.8281 (mttt) REVERT: A 632 GLN cc_start: 0.8303 (tt0) cc_final: 0.7941 (tm-30) REVERT: A 645 GLU cc_start: 0.6941 (OUTLIER) cc_final: 0.5881 (pm20) REVERT: A 663 PHE cc_start: 0.7170 (m-80) cc_final: 0.6952 (t80) REVERT: B 111 ARG cc_start: 0.6741 (OUTLIER) cc_final: 0.6160 (mpt180) REVERT: B 118 ARG cc_start: 0.3769 (OUTLIER) cc_final: 0.2310 (mtt180) REVERT: B 199 GLU cc_start: 0.8597 (mm-30) cc_final: 0.8058 (mp0) REVERT: B 206 ARG cc_start: 0.8629 (OUTLIER) cc_final: 0.8264 (tmm-80) REVERT: B 285 LYS cc_start: 0.8310 (ttpp) cc_final: 0.7842 (tptt) REVERT: B 378 LYS cc_start: 0.8695 (mtpm) cc_final: 0.8428 (tttp) REVERT: B 552 LYS cc_start: 0.8426 (pttm) cc_final: 0.7956 (mtpp) REVERT: B 560 ASP cc_start: 0.8038 (OUTLIER) cc_final: 0.7594 (t70) REVERT: B 616 LYS cc_start: 0.8693 (OUTLIER) cc_final: 0.8292 (ttmt) REVERT: B 632 GLN cc_start: 0.8129 (mt0) cc_final: 0.7919 (mt0) REVERT: B 644 GLU cc_start: 0.7708 (OUTLIER) cc_final: 0.7271 (pm20) REVERT: C 55 LYS cc_start: 0.8933 (OUTLIER) cc_final: 0.8701 (ttmt) REVERT: C 89 LYS cc_start: 0.8936 (tppt) cc_final: 0.8594 (ttpp) REVERT: C 199 GLU cc_start: 0.8473 (mm-30) cc_final: 0.8161 (tp30) REVERT: C 237 LEU cc_start: 0.8508 (OUTLIER) cc_final: 0.8166 (mt) REVERT: C 257 GLN cc_start: 0.8701 (tt0) cc_final: 0.8383 (pt0) REVERT: C 311 GLU cc_start: 0.8170 (pt0) cc_final: 0.7865 (pp20) REVERT: C 322 GLU cc_start: 0.8500 (mp0) cc_final: 0.7830 (tp30) REVERT: C 406 ILE cc_start: 0.7681 (OUTLIER) cc_final: 0.7161 (pp) REVERT: C 418 ILE cc_start: 0.7351 (OUTLIER) cc_final: 0.7092 (mt) REVERT: C 426 HIS cc_start: 0.8238 (t70) cc_final: 0.7928 (m90) REVERT: C 617 ARG cc_start: 0.8272 (OUTLIER) cc_final: 0.7809 (tpp80) outliers start: 74 outliers final: 42 residues processed: 191 average time/residue: 0.5431 time to fit residues: 113.6089 Evaluate side-chains 183 residues out of total 1576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 127 time to evaluate : 0.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 LYS Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 111 ARG Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 166 ASP Chi-restraints excluded: chain A residue 228 MET Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 326 GLU Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 419 LYS Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 484 SER Chi-restraints excluded: chain A residue 523 GLU Chi-restraints excluded: chain A residue 606 VAL Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 614 LEU Chi-restraints excluded: chain A residue 645 GLU Chi-restraints excluded: chain A residue 667 ILE Chi-restraints excluded: chain B residue 50 ASP Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 111 ARG Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 118 ARG Chi-restraints excluded: chain B residue 206 ARG Chi-restraints excluded: chain B residue 257 GLN Chi-restraints excluded: chain B residue 269 THR Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 371 SER Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 424 MET Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain B residue 547 ILE Chi-restraints excluded: chain B residue 560 ASP Chi-restraints excluded: chain B residue 568 ILE Chi-restraints excluded: chain B residue 616 LYS Chi-restraints excluded: chain B residue 644 GLU Chi-restraints excluded: chain B residue 658 HIS Chi-restraints excluded: chain C residue 55 LYS Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain C residue 269 THR Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain C residue 404 SER Chi-restraints excluded: chain C residue 406 ILE Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 434 THR Chi-restraints excluded: chain C residue 484 SER Chi-restraints excluded: chain C residue 562 LYS Chi-restraints excluded: chain C residue 587 GLN Chi-restraints excluded: chain C residue 603 ASN Chi-restraints excluded: chain C residue 617 ARG Chi-restraints excluded: chain C residue 667 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 58 optimal weight: 8.9990 chunk 113 optimal weight: 3.9990 chunk 99 optimal weight: 3.9990 chunk 82 optimal weight: 1.9990 chunk 62 optimal weight: 6.9990 chunk 116 optimal weight: 0.9990 chunk 130 optimal weight: 9.9990 chunk 132 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 79 optimal weight: 3.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 155 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.102948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.079775 restraints weight = 21301.091| |-----------------------------------------------------------------------------| r_work (start): 0.3017 rms_B_bonded: 2.20 r_work: 0.2885 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2762 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.2762 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8696 moved from start: 0.1198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 14469 Z= 0.235 Angle : 0.575 8.629 19592 Z= 0.308 Chirality : 0.047 0.238 2295 Planarity : 0.005 0.056 2536 Dihedral : 5.561 59.796 2003 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 4.57 % Allowed : 21.51 % Favored : 73.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.86 (0.20), residues: 1845 helix: 2.34 (0.18), residues: 709 sheet: 1.31 (0.25), residues: 447 loop : 0.04 (0.25), residues: 689 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG B 617 TYR 0.029 0.002 TYR C 334 PHE 0.016 0.002 PHE A 545 TRP 0.005 0.001 TRP A 184 HIS 0.006 0.001 HIS B 426 Details of bonding type rmsd covalent geometry : bond 0.00534 (14469) covalent geometry : angle 0.57524 (19592) hydrogen bonds : bond 0.05660 ( 824) hydrogen bonds : angle 5.00966 ( 2322) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3690 Ramachandran restraints generated. 1845 Oldfield, 0 Emsley, 1845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3690 Ramachandran restraints generated. 1845 Oldfield, 0 Emsley, 1845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 128 time to evaluate : 0.570 Fit side-chains revert: symmetry clash REVERT: A 228 MET cc_start: 0.9123 (OUTLIER) cc_final: 0.8726 (tmm) REVERT: A 419 LYS cc_start: 0.7034 (OUTLIER) cc_final: 0.5613 (mmmt) REVERT: A 428 GLU cc_start: 0.8628 (mm-30) cc_final: 0.8325 (mm-30) REVERT: A 552 LYS cc_start: 0.8814 (pttp) cc_final: 0.8501 (ptpp) REVERT: A 632 GLN cc_start: 0.8317 (tt0) cc_final: 0.7980 (tm-30) REVERT: A 645 GLU cc_start: 0.7023 (OUTLIER) cc_final: 0.5929 (pm20) REVERT: A 663 PHE cc_start: 0.7180 (m-80) cc_final: 0.6841 (t80) REVERT: B 111 ARG cc_start: 0.6752 (OUTLIER) cc_final: 0.6231 (mpt180) REVERT: B 199 GLU cc_start: 0.8638 (mm-30) cc_final: 0.8096 (mp0) REVERT: B 378 LYS cc_start: 0.8772 (mtpm) cc_final: 0.8497 (tttp) REVERT: B 552 LYS cc_start: 0.8428 (pttm) cc_final: 0.7967 (mtpp) REVERT: B 560 ASP cc_start: 0.8063 (OUTLIER) cc_final: 0.7596 (t70) REVERT: B 616 LYS cc_start: 0.8777 (OUTLIER) cc_final: 0.8372 (ttmt) REVERT: B 644 GLU cc_start: 0.7765 (OUTLIER) cc_final: 0.7296 (pm20) REVERT: C 55 LYS cc_start: 0.8982 (OUTLIER) cc_final: 0.8763 (ttmt) REVERT: C 89 LYS cc_start: 0.8934 (tppt) cc_final: 0.8616 (ttpp) REVERT: C 199 GLU cc_start: 0.8475 (mm-30) cc_final: 0.8129 (tp30) REVERT: C 237 LEU cc_start: 0.8715 (OUTLIER) cc_final: 0.8409 (mt) REVERT: C 257 GLN cc_start: 0.8717 (tt0) cc_final: 0.8385 (pt0) REVERT: C 319 ASP cc_start: 0.8552 (m-30) cc_final: 0.8085 (t0) REVERT: C 322 GLU cc_start: 0.8556 (mp0) cc_final: 0.7846 (tp30) REVERT: C 358 ARG cc_start: 0.8371 (OUTLIER) cc_final: 0.7879 (mtp180) REVERT: C 426 HIS cc_start: 0.8282 (t70) cc_final: 0.7957 (m90) REVERT: C 617 ARG cc_start: 0.8380 (OUTLIER) cc_final: 0.7883 (tpp80) outliers start: 72 outliers final: 43 residues processed: 184 average time/residue: 0.5839 time to fit residues: 117.3133 Evaluate side-chains 178 residues out of total 1576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 124 time to evaluate : 0.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 LYS Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain A residue 111 ARG Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 166 ASP Chi-restraints excluded: chain A residue 228 MET Chi-restraints excluded: chain A residue 257 GLN Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 326 GLU Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 419 LYS Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 484 SER Chi-restraints excluded: chain A residue 606 VAL Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 645 GLU Chi-restraints excluded: chain A residue 667 ILE Chi-restraints excluded: chain B residue 50 ASP Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 96 MET Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 111 ARG Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 257 GLN Chi-restraints excluded: chain B residue 269 THR Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 371 SER Chi-restraints excluded: chain B residue 376 MET Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 424 MET Chi-restraints excluded: chain B residue 547 ILE Chi-restraints excluded: chain B residue 560 ASP Chi-restraints excluded: chain B residue 568 ILE Chi-restraints excluded: chain B residue 616 LYS Chi-restraints excluded: chain B residue 644 GLU Chi-restraints excluded: chain C residue 55 LYS Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain C residue 269 THR Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain C residue 358 ARG Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain C residue 404 SER Chi-restraints excluded: chain C residue 434 THR Chi-restraints excluded: chain C residue 484 SER Chi-restraints excluded: chain C residue 562 LYS Chi-restraints excluded: chain C residue 603 ASN Chi-restraints excluded: chain C residue 617 ARG Chi-restraints excluded: chain C residue 637 VAL Chi-restraints excluded: chain C residue 667 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 7 optimal weight: 5.9990 chunk 29 optimal weight: 5.9990 chunk 152 optimal weight: 4.9990 chunk 10 optimal weight: 6.9990 chunk 170 optimal weight: 0.3980 chunk 86 optimal weight: 3.9990 chunk 112 optimal weight: 0.8980 chunk 121 optimal weight: 0.0980 chunk 130 optimal weight: 0.7980 chunk 90 optimal weight: 2.9990 chunk 6 optimal weight: 0.4980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.105986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.083258 restraints weight = 21296.038| |-----------------------------------------------------------------------------| r_work (start): 0.3080 rms_B_bonded: 2.20 r_work: 0.2949 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2828 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.2828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8636 moved from start: 0.1524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 14469 Z= 0.123 Angle : 0.517 8.963 19592 Z= 0.278 Chirality : 0.045 0.269 2295 Planarity : 0.004 0.058 2536 Dihedral : 5.317 58.288 2003 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 3.30 % Allowed : 22.97 % Favored : 73.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.04 (0.20), residues: 1845 helix: 2.54 (0.19), residues: 711 sheet: 1.24 (0.25), residues: 450 loop : 0.21 (0.26), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG B 617 TYR 0.029 0.001 TYR C 334 PHE 0.013 0.001 PHE C 340 TRP 0.012 0.002 TRP A 184 HIS 0.008 0.001 HIS A 304 Details of bonding type rmsd covalent geometry : bond 0.00261 (14469) covalent geometry : angle 0.51693 (19592) hydrogen bonds : bond 0.04543 ( 824) hydrogen bonds : angle 4.72115 ( 2322) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3690 Ramachandran restraints generated. 1845 Oldfield, 0 Emsley, 1845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3690 Ramachandran restraints generated. 1845 Oldfield, 0 Emsley, 1845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 135 time to evaluate : 0.350 Fit side-chains revert: symmetry clash REVERT: A 228 MET cc_start: 0.9098 (OUTLIER) cc_final: 0.8498 (tmm) REVERT: A 419 LYS cc_start: 0.6785 (OUTLIER) cc_final: 0.5134 (mmmt) REVERT: A 428 GLU cc_start: 0.8528 (mm-30) cc_final: 0.8274 (mm-30) REVERT: A 552 LYS cc_start: 0.8800 (pttp) cc_final: 0.8513 (ptpp) REVERT: A 632 GLN cc_start: 0.8291 (tt0) cc_final: 0.7984 (tm-30) REVERT: A 645 GLU cc_start: 0.6906 (OUTLIER) cc_final: 0.5851 (pm20) REVERT: A 663 PHE cc_start: 0.7141 (m-80) cc_final: 0.6874 (t80) REVERT: B 111 ARG cc_start: 0.6658 (OUTLIER) cc_final: 0.6224 (mpt180) REVERT: B 118 ARG cc_start: 0.3695 (OUTLIER) cc_final: 0.2273 (mtt180) REVERT: B 199 GLU cc_start: 0.8574 (mm-30) cc_final: 0.8087 (mp0) REVERT: B 378 LYS cc_start: 0.8678 (mtpm) cc_final: 0.8408 (tttp) REVERT: B 552 LYS cc_start: 0.8423 (pttm) cc_final: 0.7945 (mtpp) REVERT: B 560 ASP cc_start: 0.8036 (OUTLIER) cc_final: 0.7589 (t70) REVERT: B 616 LYS cc_start: 0.8691 (OUTLIER) cc_final: 0.8275 (ttmt) REVERT: B 643 ASP cc_start: 0.7107 (t0) cc_final: 0.6678 (t0) REVERT: B 644 GLU cc_start: 0.7609 (OUTLIER) cc_final: 0.7218 (pm20) REVERT: B 663 PHE cc_start: 0.7697 (m-80) cc_final: 0.7434 (m-80) REVERT: C 55 LYS cc_start: 0.8896 (OUTLIER) cc_final: 0.8655 (ttmt) REVERT: C 89 LYS cc_start: 0.8945 (tppt) cc_final: 0.8603 (ttpp) REVERT: C 199 GLU cc_start: 0.8466 (mm-30) cc_final: 0.8143 (tp30) REVERT: C 237 LEU cc_start: 0.8437 (OUTLIER) cc_final: 0.8124 (mt) REVERT: C 257 GLN cc_start: 0.8681 (tt0) cc_final: 0.8349 (pt0) REVERT: C 319 ASP cc_start: 0.8481 (m-30) cc_final: 0.8019 (t0) REVERT: C 322 GLU cc_start: 0.8566 (mp0) cc_final: 0.7861 (tp30) REVERT: C 406 ILE cc_start: 0.7795 (pt) cc_final: 0.7488 (pp) REVERT: C 426 HIS cc_start: 0.8191 (t70) cc_final: 0.7883 (m90) REVERT: C 603 ASN cc_start: 0.8364 (OUTLIER) cc_final: 0.8129 (p0) REVERT: C 617 ARG cc_start: 0.8345 (OUTLIER) cc_final: 0.7877 (ttp80) outliers start: 52 outliers final: 28 residues processed: 173 average time/residue: 0.5671 time to fit residues: 107.0433 Evaluate side-chains 174 residues out of total 1576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 134 time to evaluate : 0.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 LYS Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 111 ARG Chi-restraints excluded: chain A residue 228 MET Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 326 GLU Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 419 LYS Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 484 SER Chi-restraints excluded: chain A residue 523 GLU Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 645 GLU Chi-restraints excluded: chain A residue 667 ILE Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 111 ARG Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 118 ARG Chi-restraints excluded: chain B residue 257 GLN Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 371 SER Chi-restraints excluded: chain B residue 424 MET Chi-restraints excluded: chain B residue 547 ILE Chi-restraints excluded: chain B residue 560 ASP Chi-restraints excluded: chain B residue 568 ILE Chi-restraints excluded: chain B residue 606 VAL Chi-restraints excluded: chain B residue 616 LYS Chi-restraints excluded: chain B residue 644 GLU Chi-restraints excluded: chain B residue 658 HIS Chi-restraints excluded: chain C residue 55 LYS Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain C residue 484 SER Chi-restraints excluded: chain C residue 587 GLN Chi-restraints excluded: chain C residue 603 ASN Chi-restraints excluded: chain C residue 617 ARG Chi-restraints excluded: chain C residue 667 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 126 optimal weight: 8.9990 chunk 88 optimal weight: 0.9980 chunk 64 optimal weight: 6.9990 chunk 179 optimal weight: 9.9990 chunk 167 optimal weight: 6.9990 chunk 122 optimal weight: 0.8980 chunk 43 optimal weight: 5.9990 chunk 99 optimal weight: 5.9990 chunk 117 optimal weight: 2.9990 chunk 134 optimal weight: 0.9990 chunk 29 optimal weight: 3.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.103672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.080491 restraints weight = 21299.962| |-----------------------------------------------------------------------------| r_work (start): 0.3031 rms_B_bonded: 2.21 r_work: 0.2900 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2778 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2778 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8682 moved from start: 0.1328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 14469 Z= 0.201 Angle : 0.564 8.522 19592 Z= 0.302 Chirality : 0.046 0.293 2295 Planarity : 0.004 0.060 2536 Dihedral : 5.457 57.676 2003 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 2.92 % Allowed : 23.48 % Favored : 73.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.94 (0.20), residues: 1845 helix: 2.45 (0.18), residues: 706 sheet: 1.33 (0.25), residues: 439 loop : 0.09 (0.25), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG B 617 TYR 0.029 0.002 TYR C 334 PHE 0.031 0.002 PHE B 620 TRP 0.004 0.001 TRP C 184 HIS 0.006 0.001 HIS B 426 Details of bonding type rmsd covalent geometry : bond 0.00455 (14469) covalent geometry : angle 0.56370 (19592) hydrogen bonds : bond 0.05329 ( 824) hydrogen bonds : angle 4.90127 ( 2322) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3690 Ramachandran restraints generated. 1845 Oldfield, 0 Emsley, 1845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3690 Ramachandran restraints generated. 1845 Oldfield, 0 Emsley, 1845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 132 time to evaluate : 0.511 Fit side-chains revert: symmetry clash REVERT: A 228 MET cc_start: 0.9115 (OUTLIER) cc_final: 0.8715 (tmm) REVERT: A 419 LYS cc_start: 0.6975 (OUTLIER) cc_final: 0.5365 (mmmt) REVERT: A 428 GLU cc_start: 0.8578 (mm-30) cc_final: 0.8319 (mm-30) REVERT: A 552 LYS cc_start: 0.8818 (pttp) cc_final: 0.8511 (ptpp) REVERT: A 632 GLN cc_start: 0.8310 (tt0) cc_final: 0.7969 (tm-30) REVERT: A 645 GLU cc_start: 0.7000 (OUTLIER) cc_final: 0.5914 (pm20) REVERT: A 663 PHE cc_start: 0.7067 (m-80) cc_final: 0.6821 (t80) REVERT: B 111 ARG cc_start: 0.6684 (OUTLIER) cc_final: 0.6111 (mpt180) REVERT: B 199 GLU cc_start: 0.8617 (mm-30) cc_final: 0.8084 (mp0) REVERT: B 378 LYS cc_start: 0.8764 (mtpm) cc_final: 0.8489 (tttp) REVERT: B 552 LYS cc_start: 0.8426 (pttm) cc_final: 0.7949 (mtpp) REVERT: B 560 ASP cc_start: 0.8056 (OUTLIER) cc_final: 0.7605 (t70) REVERT: B 616 LYS cc_start: 0.8698 (OUTLIER) cc_final: 0.8287 (ttmt) REVERT: B 643 ASP cc_start: 0.7254 (t0) cc_final: 0.6829 (t0) REVERT: B 644 GLU cc_start: 0.7706 (OUTLIER) cc_final: 0.7282 (pm20) REVERT: C 55 LYS cc_start: 0.8961 (OUTLIER) cc_final: 0.8746 (ttmt) REVERT: C 89 LYS cc_start: 0.8947 (tppt) cc_final: 0.8613 (ttpp) REVERT: C 199 GLU cc_start: 0.8484 (mm-30) cc_final: 0.8148 (tp30) REVERT: C 237 LEU cc_start: 0.8646 (OUTLIER) cc_final: 0.8344 (mt) REVERT: C 257 GLN cc_start: 0.8705 (tt0) cc_final: 0.8359 (pt0) REVERT: C 322 GLU cc_start: 0.8582 (mp0) cc_final: 0.7846 (tp30) REVERT: C 426 HIS cc_start: 0.8272 (t70) cc_final: 0.7960 (m90) REVERT: C 562 LYS cc_start: 0.8630 (OUTLIER) cc_final: 0.8283 (mptt) REVERT: C 617 ARG cc_start: 0.8416 (OUTLIER) cc_final: 0.7924 (tpp80) outliers start: 46 outliers final: 32 residues processed: 168 average time/residue: 0.5854 time to fit residues: 107.1403 Evaluate side-chains 168 residues out of total 1576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 125 time to evaluate : 0.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 LYS Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain A residue 111 ARG Chi-restraints excluded: chain A residue 228 MET Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 284 VAL Chi-restraints excluded: chain A residue 326 GLU Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 419 LYS Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 484 SER Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 645 GLU Chi-restraints excluded: chain A residue 667 ILE Chi-restraints excluded: chain B residue 50 ASP Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 111 ARG Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 257 GLN Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 371 SER Chi-restraints excluded: chain B residue 376 MET Chi-restraints excluded: chain B residue 424 MET Chi-restraints excluded: chain B residue 547 ILE Chi-restraints excluded: chain B residue 560 ASP Chi-restraints excluded: chain B residue 568 ILE Chi-restraints excluded: chain B residue 616 LYS Chi-restraints excluded: chain B residue 644 GLU Chi-restraints excluded: chain B residue 658 HIS Chi-restraints excluded: chain C residue 55 LYS Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain C residue 269 THR Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain C residue 484 SER Chi-restraints excluded: chain C residue 562 LYS Chi-restraints excluded: chain C residue 617 ARG Chi-restraints excluded: chain C residue 667 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 65 optimal weight: 8.9990 chunk 119 optimal weight: 1.9990 chunk 178 optimal weight: 0.6980 chunk 18 optimal weight: 2.9990 chunk 7 optimal weight: 6.9990 chunk 12 optimal weight: 0.7980 chunk 17 optimal weight: 0.9990 chunk 63 optimal weight: 1.9990 chunk 44 optimal weight: 6.9990 chunk 106 optimal weight: 0.7980 chunk 33 optimal weight: 2.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.104989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.082289 restraints weight = 21143.204| |-----------------------------------------------------------------------------| r_work (start): 0.3063 rms_B_bonded: 2.17 r_work: 0.2934 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2813 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8653 moved from start: 0.1441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 14469 Z= 0.146 Angle : 0.538 9.635 19592 Z= 0.289 Chirality : 0.045 0.294 2295 Planarity : 0.004 0.061 2536 Dihedral : 5.376 57.484 2003 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 2.86 % Allowed : 23.54 % Favored : 73.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.01 (0.20), residues: 1845 helix: 2.50 (0.19), residues: 709 sheet: 1.27 (0.25), residues: 450 loop : 0.19 (0.25), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG B 617 TYR 0.029 0.001 TYR C 334 PHE 0.013 0.001 PHE C 340 TRP 0.007 0.001 TRP B 184 HIS 0.005 0.001 HIS B 426 Details of bonding type rmsd covalent geometry : bond 0.00322 (14469) covalent geometry : angle 0.53791 (19592) hydrogen bonds : bond 0.04814 ( 824) hydrogen bonds : angle 4.78513 ( 2322) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4598.14 seconds wall clock time: 79 minutes 15.96 seconds (4755.96 seconds total)