Starting phenix.real_space_refine on Thu Aug 6 04:16:23 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8wd8_37457/08_2026/8wd8_37457.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wd8_37457/08_2026/8wd8_37457.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/8wd8_37457/08_2026/8wd8_37457.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8wd8_37457/08_2026/8wd8_37457.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8wd8_37457/08_2026/8wd8_37457.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wd8_37457/08_2026/8wd8_37457.map" model { file = "/net/cci-nas-00/data/ceres_data/8wd8_37457/08_2026/8wd8_37457.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wd8_37457/08_2026/8wd8_37457.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.145 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: 7 Type Number sf(0) Gaussians Zn 1 6.06 5 P 64 5.49 5 Mg 6 5.21 5 S 26 5.16 5 C 8624 2.51 5 N 2334 2.21 5 O 2612 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 13667 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 6174 Number of conformers: 1 Conformer: "" Number of residues, atoms: 750, 6174 Classifications: {'peptide': 750} Link IDs: {'PTRANS': 29, 'TRANS': 720} Chain: "T" Number of atoms: 317 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 317 Classifications: {'DNA': 16} Link IDs: {'rna3p': 15} Chain: "G" Number of atoms: 339 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 339 Classifications: {'DNA': 16} Link IDs: {'rna3p': 15} Chain: "B" Number of atoms: 6174 Number of conformers: 1 Conformer: "" Number of residues, atoms: 750, 6174 Classifications: {'peptide': 750} Link IDs: {'PTRANS': 29, 'TRANS': 720} Chain: "U" Number of atoms: 317 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 317 Classifications: {'DNA': 16} Link IDs: {'rna3p': 15} Chain: "H" Number of atoms: 339 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 339 Classifications: {'DNA': 16} Link IDs: {'rna3p': 15} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 2, ' ZN': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "T" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 2.91, per 1000 atoms: 0.21 Number of scatterers: 13667 At special positions: 0 Unit cell: (111.35, 89.25, 101.15, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 1 29.99 S 26 16.00 P 64 15.00 Mg 6 11.99 O 2612 8.00 N 2334 7.00 C 8624 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: 0.99 Conformation dependent library (CDL) restraints added in 504.2 milliseconds 2992 Ramachandran restraints generated. 1496 Oldfield, 0 Emsley, 1496 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2872 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 18 sheets defined 37.5% alpha, 25.3% beta 27 base pairs and 46 stacking pairs defined. Time for finding SS restraints: 1.50 Creating SS restraints... Processing helix chain 'A' and resid 35 through 43 Processing helix chain 'A' and resid 76 through 78 No H-bonds generated for 'chain 'A' and resid 76 through 78' Processing helix chain 'A' and resid 79 through 94 Processing helix chain 'A' and resid 97 through 106 Processing helix chain 'A' and resid 149 through 154 removed outlier: 3.546A pdb=" N VAL A 154 " --> pdb=" O LEU A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 168 Processing helix chain 'A' and resid 204 through 218 removed outlier: 3.853A pdb=" N TYR A 217 " --> pdb=" O HIS A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 220 through 231 Processing helix chain 'A' and resid 267 through 271 removed outlier: 3.669A pdb=" N LEU A 271 " --> pdb=" O ALA A 268 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 284 removed outlier: 3.503A pdb=" N LYS A 284 " --> pdb=" O LEU A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 303 removed outlier: 3.888A pdb=" N THR A 303 " --> pdb=" O ASN A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 326 removed outlier: 3.549A pdb=" N ASP A 326 " --> pdb=" O ASP A 323 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 323 through 326' Processing helix chain 'A' and resid 346 through 350 removed outlier: 3.867A pdb=" N ARG A 349 " --> pdb=" O SER A 346 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N LEU A 350 " --> pdb=" O LYS A 347 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 346 through 350' Processing helix chain 'A' and resid 368 through 374 removed outlier: 3.544A pdb=" N LYS A 372 " --> pdb=" O PRO A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 388 through 412 Processing helix chain 'A' and resid 422 through 424 No H-bonds generated for 'chain 'A' and resid 422 through 424' Processing helix chain 'A' and resid 433 through 448 Processing helix chain 'A' and resid 465 through 478 Processing helix chain 'A' and resid 487 through 492 Processing helix chain 'A' and resid 503 through 518 removed outlier: 3.693A pdb=" N LEU A 518 " --> pdb=" O ILE A 514 " (cutoff:3.500A) Processing helix chain 'A' and resid 579 through 594 Processing helix chain 'A' and resid 612 through 626 Processing helix chain 'A' and resid 693 through 704 removed outlier: 3.632A pdb=" N ILE A 697 " --> pdb=" O THR A 693 " (cutoff:3.500A) Processing helix chain 'A' and resid 718 through 733 removed outlier: 3.642A pdb=" N LYS A 733 " --> pdb=" O ARG A 729 " (cutoff:3.500A) Processing helix chain 'A' and resid 738 through 744 Processing helix chain 'B' and resid 35 through 43 Processing helix chain 'B' and resid 76 through 78 No H-bonds generated for 'chain 'B' and resid 76 through 78' Processing helix chain 'B' and resid 79 through 94 Processing helix chain 'B' and resid 97 through 106 Processing helix chain 'B' and resid 149 through 154 removed outlier: 3.546A pdb=" N VAL B 154 " --> pdb=" O LEU B 150 " (cutoff:3.500A) Processing helix chain 'B' and resid 157 through 168 Processing helix chain 'B' and resid 204 through 218 removed outlier: 3.854A pdb=" N TYR B 217 " --> pdb=" O HIS B 213 " (cutoff:3.500A) Processing helix chain 'B' and resid 220 through 231 Processing helix chain 'B' and resid 267 through 271 removed outlier: 3.669A pdb=" N LEU B 271 " --> pdb=" O ALA B 268 " (cutoff:3.500A) Processing helix chain 'B' and resid 272 through 284 removed outlier: 3.502A pdb=" N LYS B 284 " --> pdb=" O LEU B 280 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 303 removed outlier: 3.889A pdb=" N THR B 303 " --> pdb=" O ASN B 299 " (cutoff:3.500A) Processing helix chain 'B' and resid 323 through 326 removed outlier: 3.549A pdb=" N ASP B 326 " --> pdb=" O ASP B 323 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 323 through 326' Processing helix chain 'B' and resid 346 through 350 removed outlier: 3.867A pdb=" N ARG B 349 " --> pdb=" O SER B 346 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N LEU B 350 " --> pdb=" O LYS B 347 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 346 through 350' Processing helix chain 'B' and resid 368 through 374 removed outlier: 3.544A pdb=" N LYS B 372 " --> pdb=" O PRO B 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 388 through 412 Processing helix chain 'B' and resid 422 through 424 No H-bonds generated for 'chain 'B' and resid 422 through 424' Processing helix chain 'B' and resid 433 through 448 Processing helix chain 'B' and resid 465 through 478 Processing helix chain 'B' and resid 487 through 492 Processing helix chain 'B' and resid 503 through 518 removed outlier: 3.694A pdb=" N LEU B 518 " --> pdb=" O ILE B 514 " (cutoff:3.500A) Processing helix chain 'B' and resid 579 through 594 Processing helix chain 'B' and resid 612 through 626 Processing helix chain 'B' and resid 693 through 704 removed outlier: 3.632A pdb=" N ILE B 697 " --> pdb=" O THR B 693 " (cutoff:3.500A) Processing helix chain 'B' and resid 718 through 733 removed outlier: 3.641A pdb=" N LYS B 733 " --> pdb=" O ARG B 729 " (cutoff:3.500A) Processing helix chain 'B' and resid 738 through 744 Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 6 removed outlier: 7.183A pdb=" N GLU A 316 " --> pdb=" O ARG A 652 " (cutoff:3.500A) removed outlier: 5.170A pdb=" N ARG A 652 " --> pdb=" O GLU A 316 " (cutoff:3.500A) removed outlier: 5.580A pdb=" N LEU A 676 " --> pdb=" O VAL A 636 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N VAL A 636 " --> pdb=" O LEU A 676 " (cutoff:3.500A) removed outlier: 5.451A pdb=" N GLU A 678 " --> pdb=" O ASN A 634 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N ASN A 634 " --> pdb=" O GLU A 678 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ARG A 607 " --> pdb=" O PHE A 633 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ILE A 635 " --> pdb=" O ARG A 607 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N TYR A 533 " --> pdb=" O LEU A 604 " (cutoff:3.500A) removed outlier: 7.754A pdb=" N LEU A 606 " --> pdb=" O TYR A 533 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N VAL A 535 " --> pdb=" O LEU A 606 " (cutoff:3.500A) removed outlier: 7.630A pdb=" N ASP A 608 " --> pdb=" O VAL A 535 " (cutoff:3.500A) removed outlier: 7.348A pdb=" N ILE A 537 " --> pdb=" O ASP A 608 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 3 through 6 removed outlier: 7.183A pdb=" N GLU A 316 " --> pdb=" O ARG A 652 " (cutoff:3.500A) removed outlier: 5.170A pdb=" N ARG A 652 " --> pdb=" O GLU A 316 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 9 through 11 Processing sheet with id=AA4, first strand: chain 'A' and resid 46 through 49 removed outlier: 5.411A pdb=" N VAL A 47 " --> pdb=" O ALA A 56 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N ALA A 56 " --> pdb=" O VAL A 47 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N ILE A 21 " --> pdb=" O GLU A 72 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N GLU A 72 " --> pdb=" O ILE A 21 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N LEU A 23 " --> pdb=" O GLU A 70 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 198 through 199 Processing sheet with id=AA6, first strand: chain 'A' and resid 198 through 199 Processing sheet with id=AA7, first strand: chain 'A' and resid 337 through 339 Processing sheet with id=AA8, first strand: chain 'A' and resid 418 through 420 removed outlier: 8.313A pdb=" N PHE A 427 " --> pdb=" O VAL A 379 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N ILE A 381 " --> pdb=" O PHE A 427 " (cutoff:3.500A) removed outlier: 7.270A pdb=" N ILE A 429 " --> pdb=" O ILE A 381 " (cutoff:3.500A) removed outlier: 5.664A pdb=" N VAL A 383 " --> pdb=" O ILE A 429 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 418 through 420 removed outlier: 6.570A pdb=" N GLY A 454 " --> pdb=" O ILE A 482 " (cutoff:3.500A) removed outlier: 8.190A pdb=" N GLN A 484 " --> pdb=" O GLY A 454 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N ALA A 456 " --> pdb=" O GLN A 484 " (cutoff:3.500A) removed outlier: 7.800A pdb=" N VAL A 486 " --> pdb=" O ALA A 456 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N ILE A 458 " --> pdb=" O VAL A 486 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 3 through 6 removed outlier: 7.184A pdb=" N GLU B 316 " --> pdb=" O ARG B 652 " (cutoff:3.500A) removed outlier: 5.170A pdb=" N ARG B 652 " --> pdb=" O GLU B 316 " (cutoff:3.500A) removed outlier: 5.580A pdb=" N LEU B 676 " --> pdb=" O VAL B 636 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N VAL B 636 " --> pdb=" O LEU B 676 " (cutoff:3.500A) removed outlier: 5.450A pdb=" N GLU B 678 " --> pdb=" O ASN B 634 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N ASN B 634 " --> pdb=" O GLU B 678 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ARG B 607 " --> pdb=" O PHE B 633 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ILE B 635 " --> pdb=" O ARG B 607 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N TYR B 533 " --> pdb=" O LEU B 604 " (cutoff:3.500A) removed outlier: 7.755A pdb=" N LEU B 606 " --> pdb=" O TYR B 533 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N VAL B 535 " --> pdb=" O LEU B 606 " (cutoff:3.500A) removed outlier: 7.629A pdb=" N ASP B 608 " --> pdb=" O VAL B 535 " (cutoff:3.500A) removed outlier: 7.347A pdb=" N ILE B 537 " --> pdb=" O ASP B 608 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 3 through 6 removed outlier: 7.184A pdb=" N GLU B 316 " --> pdb=" O ARG B 652 " (cutoff:3.500A) removed outlier: 5.170A pdb=" N ARG B 652 " --> pdb=" O GLU B 316 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 9 through 11 Processing sheet with id=AB4, first strand: chain 'B' and resid 46 through 49 removed outlier: 5.411A pdb=" N VAL B 47 " --> pdb=" O ALA B 56 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N ALA B 56 " --> pdb=" O VAL B 47 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N ILE B 21 " --> pdb=" O GLU B 72 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N GLU B 72 " --> pdb=" O ILE B 21 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N LEU B 23 " --> pdb=" O GLU B 70 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 198 through 199 Processing sheet with id=AB6, first strand: chain 'B' and resid 198 through 199 Processing sheet with id=AB7, first strand: chain 'B' and resid 337 through 339 Processing sheet with id=AB8, first strand: chain 'B' and resid 418 through 420 removed outlier: 8.313A pdb=" N PHE B 427 " --> pdb=" O VAL B 379 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N ILE B 381 " --> pdb=" O PHE B 427 " (cutoff:3.500A) removed outlier: 7.270A pdb=" N ILE B 429 " --> pdb=" O ILE B 381 " (cutoff:3.500A) removed outlier: 5.663A pdb=" N VAL B 383 " --> pdb=" O ILE B 429 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 418 through 420 removed outlier: 6.570A pdb=" N GLY B 454 " --> pdb=" O ILE B 482 " (cutoff:3.500A) removed outlier: 8.191A pdb=" N GLN B 484 " --> pdb=" O GLY B 454 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N ALA B 456 " --> pdb=" O GLN B 484 " (cutoff:3.500A) removed outlier: 7.800A pdb=" N VAL B 486 " --> pdb=" O ALA B 456 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N ILE B 458 " --> pdb=" O VAL B 486 " (cutoff:3.500A) 578 hydrogen bonds defined for protein. 1608 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 68 hydrogen bonds 136 hydrogen bond angles 0 basepair planarities 27 basepair parallelities 46 stacking parallelities Total time for adding SS restraints: 2.36 Time building geometry restraints manager: 1.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2292 1.32 - 1.44: 3816 1.44 - 1.57: 7788 1.57 - 1.69: 124 1.69 - 1.81: 52 Bond restraints: 14072 Sorted by residual: bond pdb=" C1' DC U 8 " pdb=" N1 DC U 8 " ideal model delta sigma weight residual 1.468 1.536 -0.068 1.40e-02 5.10e+03 2.32e+01 bond pdb=" C1' DC T 8 " pdb=" N1 DC T 8 " ideal model delta sigma weight residual 1.468 1.535 -0.067 1.40e-02 5.10e+03 2.30e+01 bond pdb=" C1' DT U 6 " pdb=" N1 DT U 6 " ideal model delta sigma weight residual 1.468 1.530 -0.062 1.40e-02 5.10e+03 1.97e+01 bond pdb=" C1' DT T 6 " pdb=" N1 DT T 6 " ideal model delta sigma weight residual 1.468 1.530 -0.062 1.40e-02 5.10e+03 1.97e+01 bond pdb=" CA HIS B 546 " pdb=" C HIS B 546 " ideal model delta sigma weight residual 1.526 1.484 0.042 1.11e-02 8.12e+03 1.43e+01 ... (remaining 14067 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.93: 18708 1.93 - 3.86: 514 3.86 - 5.79: 41 5.79 - 7.72: 13 7.72 - 9.65: 8 Bond angle restraints: 19284 Sorted by residual: angle pdb=" N ARG A 736 " pdb=" CA ARG A 736 " pdb=" C ARG A 736 " ideal model delta sigma weight residual 109.23 116.66 -7.43 1.55e+00 4.16e-01 2.30e+01 angle pdb=" N GLU B 739 " pdb=" CA GLU B 739 " pdb=" C GLU B 739 " ideal model delta sigma weight residual 111.14 116.28 -5.14 1.08e+00 8.57e-01 2.26e+01 angle pdb=" N3 DT T 6 " pdb=" C4 DT T 6 " pdb=" O4 DT T 6 " ideal model delta sigma weight residual 119.90 122.62 -2.72 6.00e-01 2.78e+00 2.05e+01 angle pdb=" N3 DT U 6 " pdb=" C4 DT U 6 " pdb=" O4 DT U 6 " ideal model delta sigma weight residual 119.90 122.59 -2.69 6.00e-01 2.78e+00 2.01e+01 angle pdb=" N GLU A 739 " pdb=" CA GLU A 739 " pdb=" C GLU A 739 " ideal model delta sigma weight residual 111.14 115.78 -4.64 1.08e+00 8.57e-01 1.85e+01 ... (remaining 19279 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.46: 7618 28.46 - 56.92: 703 56.92 - 85.38: 58 85.38 - 113.84: 5 113.84 - 142.30: 4 Dihedral angle restraints: 8388 sinusoidal: 3946 harmonic: 4442 Sorted by residual: dihedral pdb=" CA TYR B 561 " pdb=" C TYR B 561 " pdb=" N ILE B 562 " pdb=" CA ILE B 562 " ideal model delta harmonic sigma weight residual -180.00 -159.28 -20.72 0 5.00e+00 4.00e-02 1.72e+01 dihedral pdb=" CA TYR A 561 " pdb=" C TYR A 561 " pdb=" N ILE A 562 " pdb=" CA ILE A 562 " ideal model delta harmonic sigma weight residual -180.00 -159.30 -20.70 0 5.00e+00 4.00e-02 1.71e+01 dihedral pdb=" C4' DA T 2 " pdb=" C3' DA T 2 " pdb=" O3' DA T 2 " pdb=" P DA T 3 " ideal model delta sinusoidal sigma weight residual 220.00 77.70 142.30 1 3.50e+01 8.16e-04 1.40e+01 ... (remaining 8385 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 1589 0.049 - 0.097: 395 0.097 - 0.146: 177 0.146 - 0.194: 19 0.194 - 0.243: 2 Chirality restraints: 2182 Sorted by residual: chirality pdb=" CB VAL B 728 " pdb=" CA VAL B 728 " pdb=" CG1 VAL B 728 " pdb=" CG2 VAL B 728 " both_signs ideal model delta sigma weight residual False -2.63 -2.39 -0.24 2.00e-01 2.50e+01 1.47e+00 chirality pdb=" CB VAL A 728 " pdb=" CA VAL A 728 " pdb=" CG1 VAL A 728 " pdb=" CG2 VAL A 728 " both_signs ideal model delta sigma weight residual False -2.63 -2.39 -0.24 2.00e-01 2.50e+01 1.44e+00 chirality pdb=" P DA T 3 " pdb=" OP1 DA T 3 " pdb=" OP2 DA T 3 " pdb=" O5' DA T 3 " both_signs ideal model delta sigma weight residual True 2.34 -2.53 -0.19 2.00e-01 2.50e+01 9.42e-01 ... (remaining 2179 not shown) Planarity restraints: 2210 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS B 29 " 0.064 5.00e-02 4.00e+02 9.67e-02 1.50e+01 pdb=" N PRO B 30 " -0.167 5.00e-02 4.00e+02 pdb=" CA PRO B 30 " 0.051 5.00e-02 4.00e+02 pdb=" CD PRO B 30 " 0.052 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS A 29 " -0.064 5.00e-02 4.00e+02 9.65e-02 1.49e+01 pdb=" N PRO A 30 " 0.167 5.00e-02 4.00e+02 pdb=" CA PRO A 30 " -0.051 5.00e-02 4.00e+02 pdb=" CD PRO A 30 " -0.052 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLY A 734 " -0.016 2.00e-02 2.50e+03 3.14e-02 9.85e+00 pdb=" C GLY A 734 " 0.054 2.00e-02 2.50e+03 pdb=" O GLY A 734 " -0.020 2.00e-02 2.50e+03 pdb=" N TRP A 735 " -0.019 2.00e-02 2.50e+03 ... (remaining 2207 not shown) Histogram of nonbonded interaction distances: 1.85 - 2.46: 37 2.46 - 3.07: 7396 3.07 - 3.68: 19820 3.68 - 4.29: 31258 4.29 - 4.90: 51892 Nonbonded interactions: 110403 Sorted by model distance: nonbonded pdb=" ND1 HIS A 546 " pdb="ZN ZN A 801 " model vdw 1.852 2.310 nonbonded pdb=" ND1 HIS B 546 " pdb="ZN ZN A 801 " model vdw 1.870 2.310 nonbonded pdb=" O VAL B 750 " pdb="MG MG B 801 " model vdw 2.095 2.170 nonbonded pdb=" O VAL A 750 " pdb="MG MG A 802 " model vdw 2.095 2.170 nonbonded pdb=" OP1 DT U 6 " pdb="MG MG B 802 " model vdw 2.108 2.170 ... (remaining 110398 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 1 through 750 or resid 802 through 803)) selection = (chain 'B' and (resid 1 through 750 or resid 802 through 803)) } ncs_group { reference = chain 'G' selection = chain 'H' } ncs_group { reference = (chain 'T' and resid 0 through 15) selection = chain 'U' } 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: 1.020 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 13.130 Find NCS groups from input model: 0.200 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: 0.000 Load rotamer database and sin/cos tables:6.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8889 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 : 0.005 0.068 14072 Z= 0.340 Angle : 0.734 9.649 19284 Z= 0.496 Chirality : 0.051 0.243 2182 Planarity : 0.007 0.097 2210 Dihedral : 19.785 142.302 5516 Min Nonbonded Distance : 1.852 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 0.65 % Allowed : 24.64 % Favored : 74.71 % 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 (0.18), residues: 1496 helix: -1.83 (0.17), residues: 528 sheet: 0.31 (0.26), residues: 360 loop : -1.59 (0.21), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 563 TYR 0.015 0.001 TYR A 650 PHE 0.011 0.001 PHE A 164 TRP 0.013 0.001 TRP B 151 HIS 0.005 0.001 HIS A 639 Details of bonding type rmsd/Z covalent geometry : bond 0.00465 / 0.34 (14072) covalent geometry : angle 0.73392 / 0.50 (19284) hydrogen bonds : bond 0.14046 / 9.18 ( 604) hydrogen bonds : angle 5.52099 / 3.78 ( 1744) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2992 Ramachandran restraints generated. 1496 Oldfield, 0 Emsley, 1496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2992 Ramachandran restraints generated. 1496 Oldfield, 0 Emsley, 1496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 198 time to evaluate : 0.433 Fit side-chains REVERT: A 229 LYS cc_start: 0.8527 (ttpt) cc_final: 0.8302 (ttmt) REVERT: A 543 LYS cc_start: 0.8991 (OUTLIER) cc_final: 0.8763 (ttmm) REVERT: B 229 LYS cc_start: 0.8548 (ttpt) cc_final: 0.8294 (ttmt) REVERT: B 543 LYS cc_start: 0.9043 (OUTLIER) cc_final: 0.8809 (ttmm) REVERT: B 574 MET cc_start: 0.8439 (ttm) cc_final: 0.8221 (ttp) outliers start: 9 outliers final: 2 residues processed: 203 average time/residue: 0.5522 time to fit residues: 122.1687 Evaluate side-chains 160 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 156 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ILE Chi-restraints excluded: chain A residue 543 LYS Chi-restraints excluded: chain B residue 17 ILE Chi-restraints excluded: chain B residue 543 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 0.5980 chunk 10 optimal weight: 8.9990 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 10.0000 chunk 122 optimal weight: 0.7980 chunk 91 optimal weight: 5.9990 chunk 149 optimal weight: 0.6980 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 99 HIS A 181 HIS B 99 HIS B 181 HIS ** B 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.130193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.105889 restraints weight = 15876.619| |-----------------------------------------------------------------------------| r_work (start): 0.3084 rms_B_bonded: 1.63 r_work: 0.2951 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2817 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.2817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8857 moved from start: 0.1064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 14072 Z= 0.143 Angle : 0.523 6.210 19284 Z= 0.297 Chirality : 0.044 0.177 2182 Planarity : 0.005 0.064 2210 Dihedral : 16.013 150.823 2358 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 1.52 % Allowed : 25.14 % Favored : 73.34 % 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: -0.40 (0.20), residues: 1496 helix: 0.36 (0.22), residues: 538 sheet: 0.44 (0.25), residues: 392 loop : -1.32 (0.23), residues: 566 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 563 TYR 0.011 0.001 TYR B 282 PHE 0.013 0.001 PHE B 584 TRP 0.008 0.001 TRP A 735 HIS 0.007 0.001 HIS B 99 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.14 (14072) covalent geometry : angle 0.52304 / 0.30 (19284) hydrogen bonds : bond 0.04123 / 2.62 ( 604) hydrogen bonds : angle 3.96735 / 2.71 ( 1744) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2992 Ramachandran restraints generated. 1496 Oldfield, 0 Emsley, 1496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2992 Ramachandran restraints generated. 1496 Oldfield, 0 Emsley, 1496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 162 time to evaluate : 0.473 Fit side-chains REVERT: A 29 LYS cc_start: 0.7439 (mptt) cc_final: 0.6980 (mttm) REVERT: A 99 HIS cc_start: 0.7361 (t-90) cc_final: 0.6807 (t-90) REVERT: A 103 ARG cc_start: 0.7407 (mtm180) cc_final: 0.6760 (mtt180) REVERT: A 373 LYS cc_start: 0.7413 (mttt) cc_final: 0.6721 (mptp) REVERT: A 448 MET cc_start: 0.7769 (OUTLIER) cc_final: 0.7410 (ttt) REVERT: B 99 HIS cc_start: 0.7345 (t-90) cc_final: 0.6762 (t-90) REVERT: B 103 ARG cc_start: 0.7371 (mtm180) cc_final: 0.6654 (mtt180) REVERT: B 373 LYS cc_start: 0.7392 (mttt) cc_final: 0.6701 (mptp) REVERT: B 448 MET cc_start: 0.7800 (OUTLIER) cc_final: 0.7451 (ttt) outliers start: 21 outliers final: 3 residues processed: 173 average time/residue: 0.5724 time to fit residues: 108.3597 Evaluate side-chains 156 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 151 time to evaluate : 0.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 448 MET Chi-restraints excluded: chain A residue 525 LEU Chi-restraints excluded: chain B residue 17 ILE Chi-restraints excluded: chain B residue 448 MET Chi-restraints excluded: chain B residue 525 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 146 optimal weight: 7.9990 chunk 119 optimal weight: 3.9990 chunk 75 optimal weight: 10.0000 chunk 8 optimal weight: 3.9990 chunk 101 optimal weight: 10.0000 chunk 91 optimal weight: 8.9990 chunk 7 optimal weight: 1.9990 chunk 71 optimal weight: 8.9990 chunk 56 optimal weight: 2.9990 chunk 51 optimal weight: 6.9990 chunk 21 optimal weight: 5.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 369 GLN B 335 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.121138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.096409 restraints weight = 16183.246| |-----------------------------------------------------------------------------| r_work (start): 0.2933 rms_B_bonded: 1.59 r_work: 0.2783 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2649 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.2649 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8985 moved from start: 0.1846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.078 14072 Z= 0.258 Angle : 0.657 9.148 19284 Z= 0.352 Chirality : 0.050 0.196 2182 Planarity : 0.005 0.055 2210 Dihedral : 16.222 156.907 2348 Min Nonbonded Distance : 1.862 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 2.24 % Allowed : 25.14 % Favored : 72.62 % 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: 0.04 (0.21), residues: 1496 helix: 0.97 (0.22), residues: 552 sheet: 0.59 (0.25), residues: 374 loop : -1.27 (0.24), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 145 TYR 0.014 0.002 TYR B 282 PHE 0.014 0.002 PHE B 584 TRP 0.004 0.001 TRP A 735 HIS 0.006 0.001 HIS B 722 Details of bonding type rmsd/Z covalent geometry : bond 0.00619 / 0.26 (14072) covalent geometry : angle 0.65744 / 0.35 (19284) hydrogen bonds : bond 0.05549 / 3.48 ( 604) hydrogen bonds : angle 3.97133 / 2.71 ( 1744) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2992 Ramachandran restraints generated. 1496 Oldfield, 0 Emsley, 1496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2992 Ramachandran restraints generated. 1496 Oldfield, 0 Emsley, 1496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 156 time to evaluate : 0.380 Fit side-chains revert: symmetry clash REVERT: A 29 LYS cc_start: 0.7470 (mptt) cc_final: 0.6811 (mttp) REVERT: A 373 LYS cc_start: 0.7436 (mttt) cc_final: 0.6751 (mptp) REVERT: A 448 MET cc_start: 0.7945 (OUTLIER) cc_final: 0.7495 (ttt) REVERT: A 499 GLU cc_start: 0.7667 (mm-30) cc_final: 0.6957 (mp0) REVERT: A 624 LYS cc_start: 0.8180 (tttp) cc_final: 0.7636 (ttpp) REVERT: A 702 LEU cc_start: 0.8735 (mm) cc_final: 0.8507 (mt) REVERT: A 738 ARG cc_start: 0.7688 (mtm110) cc_final: 0.7395 (mtm110) REVERT: B 29 LYS cc_start: 0.7534 (mptt) cc_final: 0.6890 (mttp) REVERT: B 103 ARG cc_start: 0.7452 (mtm180) cc_final: 0.7242 (mtt180) REVERT: B 225 LYS cc_start: 0.8258 (mmmt) cc_final: 0.7447 (ttpp) REVERT: B 373 LYS cc_start: 0.7435 (mttt) cc_final: 0.6759 (mptp) REVERT: B 448 MET cc_start: 0.7950 (OUTLIER) cc_final: 0.7503 (ttt) REVERT: B 499 GLU cc_start: 0.7646 (mm-30) cc_final: 0.6925 (mp0) REVERT: B 624 LYS cc_start: 0.8107 (tttp) cc_final: 0.7562 (ttpp) REVERT: B 702 LEU cc_start: 0.8726 (mm) cc_final: 0.8497 (mt) outliers start: 31 outliers final: 11 residues processed: 176 average time/residue: 0.6004 time to fit residues: 115.0037 Evaluate side-chains 166 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 153 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 448 MET Chi-restraints excluded: chain A residue 483 SER Chi-restraints excluded: chain A residue 511 LEU Chi-restraints excluded: chain A residue 525 LEU Chi-restraints excluded: chain A residue 662 HIS Chi-restraints excluded: chain A residue 688 THR Chi-restraints excluded: chain B residue 448 MET Chi-restraints excluded: chain B residue 483 SER Chi-restraints excluded: chain B residue 511 LEU Chi-restraints excluded: chain B residue 525 LEU Chi-restraints excluded: chain B residue 662 HIS Chi-restraints excluded: chain B residue 688 THR Chi-restraints excluded: chain B residue 740 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 15 optimal weight: 4.9990 chunk 6 optimal weight: 5.9990 chunk 109 optimal weight: 8.9990 chunk 149 optimal weight: 0.9990 chunk 24 optimal weight: 3.9990 chunk 96 optimal weight: 2.9990 chunk 141 optimal weight: 3.9990 chunk 88 optimal weight: 0.8980 chunk 42 optimal weight: 2.9990 chunk 60 optimal weight: 3.9990 chunk 43 optimal weight: 0.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 480 ASN A 573 GLN B 335 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.124012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.099892 restraints weight = 15920.772| |-----------------------------------------------------------------------------| r_work (start): 0.2983 rms_B_bonded: 1.53 r_work: 0.2854 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.2723 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.2723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8892 moved from start: 0.1868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 14072 Z= 0.155 Angle : 0.533 8.951 19284 Z= 0.299 Chirality : 0.045 0.213 2182 Planarity : 0.004 0.049 2210 Dihedral : 16.260 158.273 2346 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 1.95 % Allowed : 25.58 % Favored : 72.47 % 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: 0.36 (0.22), residues: 1496 helix: 1.36 (0.23), residues: 552 sheet: 0.56 (0.26), residues: 380 loop : -1.10 (0.24), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 145 TYR 0.010 0.001 TYR A 650 PHE 0.010 0.001 PHE B 227 TRP 0.006 0.001 TRP B 413 HIS 0.004 0.001 HIS A 722 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.16 (14072) covalent geometry : angle 0.53302 / 0.30 (19284) hydrogen bonds : bond 0.04241 / 2.69 ( 604) hydrogen bonds : angle 3.80606 / 2.57 ( 1744) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2992 Ramachandran restraints generated. 1496 Oldfield, 0 Emsley, 1496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2992 Ramachandran restraints generated. 1496 Oldfield, 0 Emsley, 1496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 164 time to evaluate : 0.460 Fit side-chains REVERT: A 29 LYS cc_start: 0.7568 (mptt) cc_final: 0.6967 (mttm) REVERT: A 373 LYS cc_start: 0.7319 (mttt) cc_final: 0.6642 (mptp) REVERT: A 448 MET cc_start: 0.7909 (OUTLIER) cc_final: 0.7498 (ttt) REVERT: A 499 GLU cc_start: 0.7624 (mm-30) cc_final: 0.6945 (mp0) REVERT: A 624 LYS cc_start: 0.7956 (tttp) cc_final: 0.7387 (ttpp) REVERT: A 702 LEU cc_start: 0.8636 (OUTLIER) cc_final: 0.8407 (mt) REVERT: B 29 LYS cc_start: 0.7530 (mptt) cc_final: 0.6955 (mttm) REVERT: B 103 ARG cc_start: 0.7340 (mtm180) cc_final: 0.7138 (mtt180) REVERT: B 373 LYS cc_start: 0.7331 (mttt) cc_final: 0.6655 (mptp) REVERT: B 448 MET cc_start: 0.7905 (OUTLIER) cc_final: 0.7488 (ttt) REVERT: B 499 GLU cc_start: 0.7614 (mm-30) cc_final: 0.6891 (mp0) REVERT: B 624 LYS cc_start: 0.7926 (tttp) cc_final: 0.7351 (ttpp) REVERT: B 702 LEU cc_start: 0.8633 (OUTLIER) cc_final: 0.8404 (mt) outliers start: 27 outliers final: 9 residues processed: 179 average time/residue: 0.5903 time to fit residues: 114.8203 Evaluate side-chains 173 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 160 time to evaluate : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 GLU Chi-restraints excluded: chain A residue 448 MET Chi-restraints excluded: chain A residue 525 LEU Chi-restraints excluded: chain A residue 566 ILE Chi-restraints excluded: chain A residue 593 LYS Chi-restraints excluded: chain A residue 702 LEU Chi-restraints excluded: chain B residue 122 GLU Chi-restraints excluded: chain B residue 448 MET Chi-restraints excluded: chain B residue 525 LEU Chi-restraints excluded: chain B residue 566 ILE Chi-restraints excluded: chain B residue 593 LYS Chi-restraints excluded: chain B residue 702 LEU Chi-restraints excluded: chain B residue 714 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 37 optimal weight: 0.9990 chunk 35 optimal weight: 8.9990 chunk 88 optimal weight: 0.9980 chunk 150 optimal weight: 2.9990 chunk 135 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 123 optimal weight: 0.8980 chunk 120 optimal weight: 0.0980 chunk 26 optimal weight: 6.9990 chunk 110 optimal weight: 7.9990 chunk 108 optimal weight: 0.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 335 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.126629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.102335 restraints weight = 15960.086| |-----------------------------------------------------------------------------| r_work (start): 0.3017 rms_B_bonded: 1.59 r_work: 0.2874 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2741 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.2741 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8874 moved from start: 0.1868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 14072 Z= 0.112 Angle : 0.479 8.091 19284 Z= 0.275 Chirality : 0.043 0.210 2182 Planarity : 0.004 0.045 2210 Dihedral : 16.169 158.234 2346 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 2.10 % Allowed : 25.58 % Favored : 72.33 % 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: 0.71 (0.22), residues: 1496 helix: 1.72 (0.23), residues: 550 sheet: 0.70 (0.26), residues: 380 loop : -0.94 (0.25), residues: 566 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 738 TYR 0.010 0.001 TYR B 650 PHE 0.011 0.001 PHE A 227 TRP 0.005 0.001 TRP B 413 HIS 0.002 0.001 HIS A 722 Details of bonding type rmsd/Z covalent geometry : bond 0.00222 / 0.11 (14072) covalent geometry : angle 0.47861 / 0.27 (19284) hydrogen bonds : bond 0.03440 / 2.19 ( 604) hydrogen bonds : angle 3.61069 / 2.43 ( 1744) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2992 Ramachandran restraints generated. 1496 Oldfield, 0 Emsley, 1496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2992 Ramachandran restraints generated. 1496 Oldfield, 0 Emsley, 1496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 168 time to evaluate : 0.583 Fit side-chains REVERT: A 29 LYS cc_start: 0.7579 (mptt) cc_final: 0.6973 (mttm) REVERT: A 180 GLU cc_start: 0.8228 (tt0) cc_final: 0.7940 (tt0) REVERT: A 225 LYS cc_start: 0.8192 (mmmt) cc_final: 0.6972 (ptmm) REVERT: A 373 LYS cc_start: 0.7235 (mttt) cc_final: 0.6661 (mptp) REVERT: A 448 MET cc_start: 0.7779 (OUTLIER) cc_final: 0.7399 (ttt) REVERT: A 482 ILE cc_start: 0.8687 (OUTLIER) cc_final: 0.8029 (mm) REVERT: A 487 ASN cc_start: 0.7867 (p0) cc_final: 0.7640 (p0) REVERT: A 499 GLU cc_start: 0.7609 (mm-30) cc_final: 0.7003 (mp0) REVERT: A 702 LEU cc_start: 0.8686 (OUTLIER) cc_final: 0.8465 (mt) REVERT: B 29 LYS cc_start: 0.7507 (mptt) cc_final: 0.6891 (mttp) REVERT: B 103 ARG cc_start: 0.7392 (mtm180) cc_final: 0.7190 (mtt180) REVERT: B 180 GLU cc_start: 0.8221 (tt0) cc_final: 0.7930 (tt0) REVERT: B 225 LYS cc_start: 0.8117 (mmmt) cc_final: 0.7661 (mmtt) REVERT: B 373 LYS cc_start: 0.7245 (mttt) cc_final: 0.6673 (mptp) REVERT: B 448 MET cc_start: 0.7797 (OUTLIER) cc_final: 0.7413 (ttt) REVERT: B 482 ILE cc_start: 0.8716 (OUTLIER) cc_final: 0.8055 (mm) REVERT: B 487 ASN cc_start: 0.7871 (p0) cc_final: 0.7641 (p0) REVERT: B 499 GLU cc_start: 0.7606 (mm-30) cc_final: 0.6986 (mp0) REVERT: B 702 LEU cc_start: 0.8685 (OUTLIER) cc_final: 0.8459 (mt) outliers start: 29 outliers final: 8 residues processed: 184 average time/residue: 0.5821 time to fit residues: 116.8718 Evaluate side-chains 172 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 158 time to evaluate : 0.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 448 MET Chi-restraints excluded: chain A residue 482 ILE Chi-restraints excluded: chain A residue 566 ILE Chi-restraints excluded: chain A residue 587 MET Chi-restraints excluded: chain A residue 593 LYS Chi-restraints excluded: chain A residue 702 LEU Chi-restraints excluded: chain A residue 714 ASP Chi-restraints excluded: chain B residue 410 LEU Chi-restraints excluded: chain B residue 448 MET Chi-restraints excluded: chain B residue 482 ILE Chi-restraints excluded: chain B residue 593 LYS Chi-restraints excluded: chain B residue 702 LEU Chi-restraints excluded: chain B residue 714 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 126 optimal weight: 7.9990 chunk 134 optimal weight: 0.0980 chunk 87 optimal weight: 4.9990 chunk 51 optimal weight: 7.9990 chunk 119 optimal weight: 0.0170 chunk 73 optimal weight: 6.9990 chunk 141 optimal weight: 5.9990 chunk 17 optimal weight: 10.0000 chunk 54 optimal weight: 3.9990 chunk 69 optimal weight: 8.9990 chunk 39 optimal weight: 9.9990 overall best weight: 3.0224 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 335 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.121327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.096641 restraints weight = 15998.709| |-----------------------------------------------------------------------------| r_work (start): 0.2938 rms_B_bonded: 1.54 r_work: 0.2816 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.2684 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.2684 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8928 moved from start: 0.2096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 14072 Z= 0.207 Angle : 0.576 9.490 19284 Z= 0.314 Chirality : 0.048 0.265 2182 Planarity : 0.004 0.044 2210 Dihedral : 16.189 160.383 2346 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 3.47 % Allowed : 23.12 % Favored : 73.41 % 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: 0.61 (0.22), residues: 1496 helix: 1.66 (0.23), residues: 550 sheet: 0.64 (0.26), residues: 380 loop : -1.01 (0.25), residues: 566 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 145 TYR 0.012 0.001 TYR B 548 PHE 0.010 0.001 PHE A 67 TRP 0.004 0.001 TRP A 735 HIS 0.006 0.001 HIS B 722 Details of bonding type rmsd/Z covalent geometry : bond 0.00485 / 0.21 (14072) covalent geometry : angle 0.57589 / 0.31 (19284) hydrogen bonds : bond 0.04658 / 2.94 ( 604) hydrogen bonds : angle 3.75282 / 2.53 ( 1744) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2992 Ramachandran restraints generated. 1496 Oldfield, 0 Emsley, 1496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2992 Ramachandran restraints generated. 1496 Oldfield, 0 Emsley, 1496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 157 time to evaluate : 0.503 Fit side-chains REVERT: A 29 LYS cc_start: 0.7527 (mptt) cc_final: 0.6835 (mttp) REVERT: A 99 HIS cc_start: 0.7780 (t-90) cc_final: 0.7439 (t-90) REVERT: A 180 GLU cc_start: 0.8237 (tt0) cc_final: 0.7957 (tt0) REVERT: A 225 LYS cc_start: 0.8257 (mmmt) cc_final: 0.7369 (ttpp) REVERT: A 373 LYS cc_start: 0.7253 (mttt) cc_final: 0.6674 (mptp) REVERT: A 448 MET cc_start: 0.7943 (OUTLIER) cc_final: 0.7503 (ttt) REVERT: A 482 ILE cc_start: 0.8735 (OUTLIER) cc_final: 0.8094 (mm) REVERT: A 499 GLU cc_start: 0.7564 (mm-30) cc_final: 0.6867 (mp0) REVERT: A 624 LYS cc_start: 0.8015 (tttp) cc_final: 0.7454 (ttpp) REVERT: A 702 LEU cc_start: 0.8619 (OUTLIER) cc_final: 0.8366 (mt) REVERT: A 740 GLU cc_start: 0.7966 (OUTLIER) cc_final: 0.7761 (pm20) REVERT: B 29 LYS cc_start: 0.7496 (mptt) cc_final: 0.6835 (mttp) REVERT: B 202 ASN cc_start: 0.8172 (m-40) cc_final: 0.7858 (m-40) REVERT: B 225 LYS cc_start: 0.8162 (mmmt) cc_final: 0.7257 (ttpp) REVERT: B 373 LYS cc_start: 0.7248 (mttt) cc_final: 0.6671 (mptp) REVERT: B 448 MET cc_start: 0.7983 (OUTLIER) cc_final: 0.7537 (ttt) REVERT: B 482 ILE cc_start: 0.8748 (OUTLIER) cc_final: 0.8111 (mm) REVERT: B 499 GLU cc_start: 0.7578 (mm-30) cc_final: 0.6893 (mp0) REVERT: B 624 LYS cc_start: 0.8008 (tttp) cc_final: 0.7450 (ttpp) REVERT: B 702 LEU cc_start: 0.8616 (OUTLIER) cc_final: 0.8363 (mt) outliers start: 48 outliers final: 17 residues processed: 188 average time/residue: 0.6017 time to fit residues: 123.2746 Evaluate side-chains 177 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 153 time to evaluate : 0.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 MET Chi-restraints excluded: chain A residue 19 ASN Chi-restraints excluded: chain A residue 122 GLU Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 448 MET Chi-restraints excluded: chain A residue 482 ILE Chi-restraints excluded: chain A residue 511 LEU Chi-restraints excluded: chain A residue 566 ILE Chi-restraints excluded: chain A residue 587 MET Chi-restraints excluded: chain A residue 593 LYS Chi-restraints excluded: chain A residue 702 LEU Chi-restraints excluded: chain A residue 714 ASP Chi-restraints excluded: chain A residue 740 GLU Chi-restraints excluded: chain B residue 3 MET Chi-restraints excluded: chain B residue 19 ASN Chi-restraints excluded: chain B residue 122 GLU Chi-restraints excluded: chain B residue 234 VAL Chi-restraints excluded: chain B residue 410 LEU Chi-restraints excluded: chain B residue 448 MET Chi-restraints excluded: chain B residue 482 ILE Chi-restraints excluded: chain B residue 511 LEU Chi-restraints excluded: chain B residue 593 LYS Chi-restraints excluded: chain B residue 702 LEU Chi-restraints excluded: chain B residue 714 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 86 optimal weight: 0.7980 chunk 137 optimal weight: 3.9990 chunk 82 optimal weight: 6.9990 chunk 73 optimal weight: 0.8980 chunk 18 optimal weight: 0.4980 chunk 6 optimal weight: 10.0000 chunk 23 optimal weight: 10.0000 chunk 61 optimal weight: 2.9990 chunk 114 optimal weight: 0.8980 chunk 105 optimal weight: 3.9990 chunk 63 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 480 ASN B 573 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.124600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.101075 restraints weight = 15892.886| |-----------------------------------------------------------------------------| r_work (start): 0.3011 rms_B_bonded: 1.61 r_work: 0.2870 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2736 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.2736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8905 moved from start: 0.2049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 14072 Z= 0.111 Angle : 0.479 8.674 19284 Z= 0.276 Chirality : 0.044 0.261 2182 Planarity : 0.004 0.044 2210 Dihedral : 16.189 162.218 2346 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 2.46 % Allowed : 24.57 % Favored : 72.98 % 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: 0.87 (0.22), residues: 1496 helix: 1.90 (0.23), residues: 548 sheet: 0.77 (0.26), residues: 380 loop : -0.88 (0.25), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 145 TYR 0.010 0.001 TYR A 650 PHE 0.011 0.001 PHE B 227 TRP 0.005 0.001 TRP A 413 HIS 0.004 0.001 HIS B 99 Details of bonding type rmsd/Z covalent geometry : bond 0.00219 / 0.11 (14072) covalent geometry : angle 0.47911 / 0.28 (19284) hydrogen bonds : bond 0.03511 / 2.25 ( 604) hydrogen bonds : angle 3.61310 / 2.42 ( 1744) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2992 Ramachandran restraints generated. 1496 Oldfield, 0 Emsley, 1496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2992 Ramachandran restraints generated. 1496 Oldfield, 0 Emsley, 1496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 165 time to evaluate : 0.525 Fit side-chains REVERT: A 19 ASN cc_start: 0.6957 (OUTLIER) cc_final: 0.6068 (OUTLIER) REVERT: A 20 GLU cc_start: 0.7893 (OUTLIER) cc_final: 0.6969 (pm20) REVERT: A 29 LYS cc_start: 0.7462 (mptt) cc_final: 0.6858 (mttp) REVERT: A 99 HIS cc_start: 0.7710 (t-90) cc_final: 0.7471 (t-90) REVERT: A 180 GLU cc_start: 0.8191 (tt0) cc_final: 0.7936 (tt0) REVERT: A 202 ASN cc_start: 0.8169 (m-40) cc_final: 0.7857 (m-40) REVERT: A 225 LYS cc_start: 0.8287 (mmmt) cc_final: 0.7474 (ttpp) REVERT: A 337 LYS cc_start: 0.7772 (mttp) cc_final: 0.7415 (mttt) REVERT: A 373 LYS cc_start: 0.7215 (mttt) cc_final: 0.6637 (mptp) REVERT: A 448 MET cc_start: 0.7819 (OUTLIER) cc_final: 0.7382 (ttt) REVERT: A 487 ASN cc_start: 0.7863 (p0) cc_final: 0.7607 (p0) REVERT: A 499 GLU cc_start: 0.7522 (mm-30) cc_final: 0.6917 (mp0) REVERT: A 702 LEU cc_start: 0.8696 (OUTLIER) cc_final: 0.8473 (mt) REVERT: B 29 LYS cc_start: 0.7534 (mptt) cc_final: 0.6847 (mttp) REVERT: B 202 ASN cc_start: 0.8171 (m-40) cc_final: 0.7859 (m-40) REVERT: B 225 LYS cc_start: 0.8193 (mmmt) cc_final: 0.7345 (ttpp) REVERT: B 373 LYS cc_start: 0.7149 (mttt) cc_final: 0.6612 (mptp) REVERT: B 448 MET cc_start: 0.7839 (OUTLIER) cc_final: 0.7400 (ttt) REVERT: B 482 ILE cc_start: 0.8760 (OUTLIER) cc_final: 0.8094 (mm) REVERT: B 487 ASN cc_start: 0.7862 (p0) cc_final: 0.7609 (p0) REVERT: B 499 GLU cc_start: 0.7568 (mm-30) cc_final: 0.6953 (mp0) REVERT: B 624 LYS cc_start: 0.7901 (tttp) cc_final: 0.7336 (ttpp) REVERT: B 702 LEU cc_start: 0.8706 (OUTLIER) cc_final: 0.8481 (mt) outliers start: 34 outliers final: 15 residues processed: 188 average time/residue: 0.5183 time to fit residues: 106.6653 Evaluate side-chains 180 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 159 time to evaluate : 0.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ASN Chi-restraints excluded: chain A residue 20 GLU Chi-restraints excluded: chain A residue 122 GLU Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 448 MET Chi-restraints excluded: chain A residue 566 ILE Chi-restraints excluded: chain A residue 587 MET Chi-restraints excluded: chain A residue 593 LYS Chi-restraints excluded: chain A residue 596 ILE Chi-restraints excluded: chain A residue 702 LEU Chi-restraints excluded: chain A residue 714 ASP Chi-restraints excluded: chain B residue 32 ASP Chi-restraints excluded: chain B residue 122 GLU Chi-restraints excluded: chain B residue 410 LEU Chi-restraints excluded: chain B residue 448 MET Chi-restraints excluded: chain B residue 482 ILE Chi-restraints excluded: chain B residue 566 ILE Chi-restraints excluded: chain B residue 593 LYS Chi-restraints excluded: chain B residue 596 ILE Chi-restraints excluded: chain B residue 702 LEU Chi-restraints excluded: chain B residue 714 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 16 optimal weight: 2.9990 chunk 136 optimal weight: 3.9990 chunk 111 optimal weight: 10.0000 chunk 56 optimal weight: 0.6980 chunk 153 optimal weight: 10.0000 chunk 117 optimal weight: 8.9990 chunk 107 optimal weight: 0.8980 chunk 115 optimal weight: 0.8980 chunk 30 optimal weight: 0.0870 chunk 78 optimal weight: 6.9990 chunk 95 optimal weight: 6.9990 overall best weight: 1.1160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 480 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.123948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.099696 restraints weight = 15905.539| |-----------------------------------------------------------------------------| r_work (start): 0.3028 rms_B_bonded: 1.55 r_work: 0.2892 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2760 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.2760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8909 moved from start: 0.2073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 14072 Z= 0.120 Angle : 0.489 8.784 19284 Z= 0.277 Chirality : 0.044 0.261 2182 Planarity : 0.004 0.056 2210 Dihedral : 16.038 161.139 2346 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 2.38 % Allowed : 24.57 % Favored : 73.05 % 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: 0.95 (0.22), residues: 1496 helix: 1.96 (0.23), residues: 550 sheet: 0.79 (0.26), residues: 380 loop : -0.83 (0.26), residues: 566 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 145 TYR 0.009 0.001 TYR B 650 PHE 0.010 0.001 PHE B 227 TRP 0.003 0.000 TRP B 413 HIS 0.005 0.001 HIS B 99 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.12 (14072) covalent geometry : angle 0.48865 / 0.28 (19284) hydrogen bonds : bond 0.03555 / 2.27 ( 604) hydrogen bonds : angle 3.55121 / 2.39 ( 1744) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2992 Ramachandran restraints generated. 1496 Oldfield, 0 Emsley, 1496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2992 Ramachandran restraints generated. 1496 Oldfield, 0 Emsley, 1496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 166 time to evaluate : 0.328 Fit side-chains REVERT: A 19 ASN cc_start: 0.7016 (OUTLIER) cc_final: 0.6094 (OUTLIER) REVERT: A 20 GLU cc_start: 0.7902 (OUTLIER) cc_final: 0.7004 (pm20) REVERT: A 29 LYS cc_start: 0.7476 (mptt) cc_final: 0.6846 (mttp) REVERT: A 202 ASN cc_start: 0.8183 (m-40) cc_final: 0.7875 (m-40) REVERT: A 225 LYS cc_start: 0.8237 (mmmt) cc_final: 0.7359 (ttpp) REVERT: A 337 LYS cc_start: 0.7786 (mttp) cc_final: 0.7428 (mttt) REVERT: A 373 LYS cc_start: 0.7118 (mttt) cc_final: 0.6614 (mptp) REVERT: A 448 MET cc_start: 0.7901 (OUTLIER) cc_final: 0.7483 (ttt) REVERT: A 482 ILE cc_start: 0.8739 (OUTLIER) cc_final: 0.8061 (mm) REVERT: A 487 ASN cc_start: 0.7924 (p0) cc_final: 0.7694 (p0) REVERT: A 499 GLU cc_start: 0.7539 (mm-30) cc_final: 0.6941 (mp0) REVERT: A 702 LEU cc_start: 0.8711 (OUTLIER) cc_final: 0.8486 (mt) REVERT: A 738 ARG cc_start: 0.7723 (mtm110) cc_final: 0.7481 (mmm-85) REVERT: B 29 LYS cc_start: 0.7457 (mptt) cc_final: 0.6842 (mttp) REVERT: B 202 ASN cc_start: 0.8190 (m-40) cc_final: 0.7874 (m-40) REVERT: B 225 LYS cc_start: 0.8166 (mmmt) cc_final: 0.7319 (ttpp) REVERT: B 373 LYS cc_start: 0.7118 (mttt) cc_final: 0.6618 (mptp) REVERT: B 448 MET cc_start: 0.7921 (OUTLIER) cc_final: 0.7507 (ttt) REVERT: B 482 ILE cc_start: 0.8754 (OUTLIER) cc_final: 0.8068 (mm) REVERT: B 487 ASN cc_start: 0.7931 (p0) cc_final: 0.7698 (p0) REVERT: B 499 GLU cc_start: 0.7559 (mm-30) cc_final: 0.6950 (mp0) REVERT: B 624 LYS cc_start: 0.7938 (tttp) cc_final: 0.7362 (ttpp) REVERT: B 702 LEU cc_start: 0.8713 (OUTLIER) cc_final: 0.8483 (mt) outliers start: 33 outliers final: 18 residues processed: 188 average time/residue: 0.5156 time to fit residues: 106.4943 Evaluate side-chains 190 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 165 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 MET Chi-restraints excluded: chain A residue 19 ASN Chi-restraints excluded: chain A residue 20 GLU Chi-restraints excluded: chain A residue 122 GLU Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 448 MET Chi-restraints excluded: chain A residue 482 ILE Chi-restraints excluded: chain A residue 511 LEU Chi-restraints excluded: chain A residue 587 MET Chi-restraints excluded: chain A residue 593 LYS Chi-restraints excluded: chain A residue 702 LEU Chi-restraints excluded: chain A residue 714 ASP Chi-restraints excluded: chain B residue 3 MET Chi-restraints excluded: chain B residue 19 ASN Chi-restraints excluded: chain B residue 32 ASP Chi-restraints excluded: chain B residue 122 GLU Chi-restraints excluded: chain B residue 234 VAL Chi-restraints excluded: chain B residue 410 LEU Chi-restraints excluded: chain B residue 448 MET Chi-restraints excluded: chain B residue 482 ILE Chi-restraints excluded: chain B residue 511 LEU Chi-restraints excluded: chain B residue 566 ILE Chi-restraints excluded: chain B residue 593 LYS Chi-restraints excluded: chain B residue 702 LEU Chi-restraints excluded: chain B residue 714 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 6 optimal weight: 10.0000 chunk 60 optimal weight: 5.9990 chunk 57 optimal weight: 5.9990 chunk 117 optimal weight: 10.0000 chunk 149 optimal weight: 5.9990 chunk 136 optimal weight: 4.9990 chunk 36 optimal weight: 1.9990 chunk 142 optimal weight: 5.9990 chunk 33 optimal weight: 10.0000 chunk 11 optimal weight: 3.9990 chunk 108 optimal weight: 5.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 208 HIS B 208 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.119233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.095322 restraints weight = 16085.808| |-----------------------------------------------------------------------------| r_work (start): 0.2955 rms_B_bonded: 1.54 r_work: 0.2826 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.2695 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.2695 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8951 moved from start: 0.2353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.091 14072 Z= 0.288 Angle : 0.675 10.559 19284 Z= 0.356 Chirality : 0.051 0.343 2182 Planarity : 0.005 0.042 2210 Dihedral : 16.253 163.790 2346 Min Nonbonded Distance : 1.844 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 2.24 % Allowed : 25.00 % Favored : 72.76 % 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: 0.50 (0.22), residues: 1496 helix: 1.59 (0.23), residues: 552 sheet: 0.63 (0.26), residues: 374 loop : -1.14 (0.25), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 145 TYR 0.015 0.002 TYR A 548 PHE 0.015 0.002 PHE A 67 TRP 0.007 0.002 TRP A 735 HIS 0.008 0.001 HIS B 99 Details of bonding type rmsd/Z covalent geometry : bond 0.00704 / 0.29 (14072) covalent geometry : angle 0.67458 / 0.36 (19284) hydrogen bonds : bond 0.05589 / 3.53 ( 604) hydrogen bonds : angle 3.86986 / 2.62 ( 1744) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2992 Ramachandran restraints generated. 1496 Oldfield, 0 Emsley, 1496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2992 Ramachandran restraints generated. 1496 Oldfield, 0 Emsley, 1496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 161 time to evaluate : 0.517 Fit side-chains REVERT: A 20 GLU cc_start: 0.7938 (OUTLIER) cc_final: 0.6996 (pm20) REVERT: A 29 LYS cc_start: 0.7393 (mptt) cc_final: 0.6779 (mttm) REVERT: A 99 HIS cc_start: 0.7817 (t-90) cc_final: 0.7355 (t-90) REVERT: A 202 ASN cc_start: 0.8146 (m-40) cc_final: 0.7838 (m-40) REVERT: A 373 LYS cc_start: 0.7197 (mttt) cc_final: 0.6613 (mptp) REVERT: A 448 MET cc_start: 0.8011 (OUTLIER) cc_final: 0.7556 (ttt) REVERT: A 482 ILE cc_start: 0.8747 (OUTLIER) cc_final: 0.8116 (mm) REVERT: A 499 GLU cc_start: 0.7498 (mm-30) cc_final: 0.6905 (mp0) REVERT: A 624 LYS cc_start: 0.8024 (tttp) cc_final: 0.7505 (ttpp) REVERT: A 702 LEU cc_start: 0.8628 (OUTLIER) cc_final: 0.8371 (mt) REVERT: A 738 ARG cc_start: 0.7828 (mtm110) cc_final: 0.7541 (mmm-85) REVERT: B 29 LYS cc_start: 0.7434 (mptt) cc_final: 0.6700 (mttp) REVERT: B 42 ARG cc_start: 0.8038 (mtt-85) cc_final: 0.7833 (mtp85) REVERT: B 202 ASN cc_start: 0.8173 (m-40) cc_final: 0.7857 (m-40) REVERT: B 373 LYS cc_start: 0.7197 (mttt) cc_final: 0.6613 (mptp) REVERT: B 448 MET cc_start: 0.8030 (OUTLIER) cc_final: 0.7577 (ttt) REVERT: B 482 ILE cc_start: 0.8768 (OUTLIER) cc_final: 0.8133 (mm) REVERT: B 499 GLU cc_start: 0.7491 (mm-30) cc_final: 0.6876 (mp0) REVERT: B 624 LYS cc_start: 0.7969 (tttp) cc_final: 0.7451 (ttpp) REVERT: B 702 LEU cc_start: 0.8625 (OUTLIER) cc_final: 0.8364 (mt) outliers start: 31 outliers final: 18 residues processed: 179 average time/residue: 0.6268 time to fit residues: 122.0081 Evaluate side-chains 178 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 153 time to evaluate : 0.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 MET Chi-restraints excluded: chain A residue 19 ASN Chi-restraints excluded: chain A residue 20 GLU Chi-restraints excluded: chain A residue 122 GLU Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 448 MET Chi-restraints excluded: chain A residue 482 ILE Chi-restraints excluded: chain A residue 511 LEU Chi-restraints excluded: chain A residue 525 LEU Chi-restraints excluded: chain A residue 593 LYS Chi-restraints excluded: chain A residue 702 LEU Chi-restraints excluded: chain A residue 714 ASP Chi-restraints excluded: chain B residue 3 MET Chi-restraints excluded: chain B residue 19 ASN Chi-restraints excluded: chain B residue 32 ASP Chi-restraints excluded: chain B residue 122 GLU Chi-restraints excluded: chain B residue 234 VAL Chi-restraints excluded: chain B residue 410 LEU Chi-restraints excluded: chain B residue 448 MET Chi-restraints excluded: chain B residue 482 ILE Chi-restraints excluded: chain B residue 511 LEU Chi-restraints excluded: chain B residue 525 LEU Chi-restraints excluded: chain B residue 593 LYS Chi-restraints excluded: chain B residue 702 LEU Chi-restraints excluded: chain B residue 714 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 35 optimal weight: 6.9990 chunk 89 optimal weight: 3.9990 chunk 14 optimal weight: 0.9980 chunk 86 optimal weight: 1.9990 chunk 118 optimal weight: 2.9990 chunk 152 optimal weight: 9.9990 chunk 16 optimal weight: 5.9990 chunk 90 optimal weight: 1.9990 chunk 109 optimal weight: 7.9990 chunk 110 optimal weight: 4.9990 chunk 84 optimal weight: 7.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.120602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.096061 restraints weight = 15975.158| |-----------------------------------------------------------------------------| r_work (start): 0.2943 rms_B_bonded: 1.63 r_work: 0.2804 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2670 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.2670 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8969 moved from start: 0.2322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 14072 Z= 0.184 Angle : 0.566 9.929 19284 Z= 0.311 Chirality : 0.046 0.325 2182 Planarity : 0.004 0.043 2210 Dihedral : 16.227 165.209 2346 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 1.81 % Allowed : 25.65 % Favored : 72.54 % 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: 0.60 (0.22), residues: 1496 helix: 1.70 (0.23), residues: 550 sheet: 0.66 (0.26), residues: 374 loop : -1.08 (0.25), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 145 TYR 0.011 0.001 TYR B 723 PHE 0.011 0.001 PHE A 227 TRP 0.004 0.001 TRP A 413 HIS 0.005 0.001 HIS A 722 Details of bonding type rmsd/Z covalent geometry : bond 0.00425 / 0.18 (14072) covalent geometry : angle 0.56614 / 0.31 (19284) hydrogen bonds : bond 0.04540 / 2.88 ( 604) hydrogen bonds : angle 3.77920 / 2.55 ( 1744) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2992 Ramachandran restraints generated. 1496 Oldfield, 0 Emsley, 1496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2992 Ramachandran restraints generated. 1496 Oldfield, 0 Emsley, 1496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 159 time to evaluate : 0.531 Fit side-chains REVERT: A 19 ASN cc_start: 0.7000 (OUTLIER) cc_final: 0.6173 (OUTLIER) REVERT: A 20 GLU cc_start: 0.7942 (OUTLIER) cc_final: 0.7091 (pm20) REVERT: A 29 LYS cc_start: 0.7488 (mptt) cc_final: 0.6698 (mttp) REVERT: A 99 HIS cc_start: 0.7881 (t-90) cc_final: 0.7428 (t-90) REVERT: A 202 ASN cc_start: 0.8167 (m-40) cc_final: 0.7859 (m-40) REVERT: A 225 LYS cc_start: 0.8223 (mmmt) cc_final: 0.7332 (ttpp) REVERT: A 337 LYS cc_start: 0.7827 (mttp) cc_final: 0.7467 (mttt) REVERT: A 373 LYS cc_start: 0.7227 (mttt) cc_final: 0.6653 (mptp) REVERT: A 448 MET cc_start: 0.8005 (OUTLIER) cc_final: 0.7542 (ttt) REVERT: A 482 ILE cc_start: 0.8782 (OUTLIER) cc_final: 0.8146 (mm) REVERT: A 499 GLU cc_start: 0.7527 (mm-30) cc_final: 0.6969 (mp0) REVERT: A 624 LYS cc_start: 0.7989 (tttp) cc_final: 0.7471 (ttpp) REVERT: A 702 LEU cc_start: 0.8701 (OUTLIER) cc_final: 0.8483 (mt) REVERT: A 729 ARG cc_start: 0.8986 (OUTLIER) cc_final: 0.8755 (ttt-90) REVERT: A 738 ARG cc_start: 0.7825 (mtm110) cc_final: 0.7545 (mmm-85) REVERT: B 29 LYS cc_start: 0.7516 (mptt) cc_final: 0.6735 (mttp) REVERT: B 42 ARG cc_start: 0.8018 (mtt-85) cc_final: 0.7559 (ttp80) REVERT: B 202 ASN cc_start: 0.8187 (m-40) cc_final: 0.7868 (m-40) REVERT: B 225 LYS cc_start: 0.8215 (mmmt) cc_final: 0.7285 (ttpp) REVERT: B 373 LYS cc_start: 0.7223 (mttt) cc_final: 0.6644 (mptp) REVERT: B 448 MET cc_start: 0.8028 (OUTLIER) cc_final: 0.7563 (ttt) REVERT: B 482 ILE cc_start: 0.8803 (OUTLIER) cc_final: 0.8159 (mm) REVERT: B 499 GLU cc_start: 0.7515 (mm-30) cc_final: 0.6924 (mp0) REVERT: B 624 LYS cc_start: 0.7965 (tttp) cc_final: 0.7438 (ttpp) REVERT: B 702 LEU cc_start: 0.8703 (OUTLIER) cc_final: 0.8479 (mt) outliers start: 25 outliers final: 18 residues processed: 178 average time/residue: 0.6198 time to fit residues: 120.6611 Evaluate side-chains 183 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 157 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 MET Chi-restraints excluded: chain A residue 19 ASN Chi-restraints excluded: chain A residue 20 GLU Chi-restraints excluded: chain A residue 122 GLU Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 448 MET Chi-restraints excluded: chain A residue 482 ILE Chi-restraints excluded: chain A residue 511 LEU Chi-restraints excluded: chain A residue 525 LEU Chi-restraints excluded: chain A residue 593 LYS Chi-restraints excluded: chain A residue 702 LEU Chi-restraints excluded: chain A residue 714 ASP Chi-restraints excluded: chain A residue 729 ARG Chi-restraints excluded: chain B residue 3 MET Chi-restraints excluded: chain B residue 32 ASP Chi-restraints excluded: chain B residue 122 GLU Chi-restraints excluded: chain B residue 234 VAL Chi-restraints excluded: chain B residue 410 LEU Chi-restraints excluded: chain B residue 448 MET Chi-restraints excluded: chain B residue 482 ILE Chi-restraints excluded: chain B residue 511 LEU Chi-restraints excluded: chain B residue 525 LEU Chi-restraints excluded: chain B residue 593 LYS Chi-restraints excluded: chain B residue 702 LEU Chi-restraints excluded: chain B residue 714 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 39 optimal weight: 9.9990 chunk 90 optimal weight: 4.9990 chunk 95 optimal weight: 6.9990 chunk 56 optimal weight: 2.9990 chunk 58 optimal weight: 0.6980 chunk 18 optimal weight: 2.9990 chunk 112 optimal weight: 0.0040 chunk 67 optimal weight: 6.9990 chunk 142 optimal weight: 4.9990 chunk 37 optimal weight: 0.8980 chunk 140 optimal weight: 0.9980 overall best weight: 1.1194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.122638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.098523 restraints weight = 16042.905| |-----------------------------------------------------------------------------| r_work (start): 0.3003 rms_B_bonded: 1.67 r_work: 0.2864 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2730 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.2730 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8900 moved from start: 0.2287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 14072 Z= 0.128 Angle : 0.522 9.612 19284 Z= 0.294 Chirality : 0.045 0.314 2182 Planarity : 0.004 0.043 2210 Dihedral : 16.154 165.292 2346 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 1.88 % Allowed : 25.58 % Favored : 72.54 % 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: 0.77 (0.22), residues: 1496 helix: 1.84 (0.23), residues: 550 sheet: 0.74 (0.26), residues: 376 loop : -0.98 (0.25), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 145 TYR 0.010 0.001 TYR A 650 PHE 0.011 0.001 PHE B 227 TRP 0.005 0.001 TRP A 413 HIS 0.004 0.001 HIS B 722 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.13 (14072) covalent geometry : angle 0.52205 / 0.29 (19284) hydrogen bonds : bond 0.03992 / 2.55 ( 604) hydrogen bonds : angle 3.70760 / 2.50 ( 1744) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3628.06 seconds wall clock time: 62 minutes 32.29 seconds (3752.29 seconds total)