Starting phenix.real_space_refine on Sat Aug 23 16:55:06 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wd8_37457/08_2025/8wd8_37457.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wd8_37457/08_2025/8wd8_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8wd8_37457/08_2025/8wd8_37457.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wd8_37457/08_2025/8wd8_37457.map" model { file = "/net/cci-nas-00/data/ceres_data/8wd8_37457/08_2025/8wd8_37457.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wd8_37457/08_2025/8wd8_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-2.0-5787/lib/python3.9/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: 3.75, per 1000 atoms: 0.27 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: 1.18 Conformation dependent library (CDL) restraints added in 703.5 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 1.99 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: 3.31 Time building geometry restraints manager: 1.65 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=" 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 bond pdb=" CA HIS A 546 " pdb=" C HIS A 546 " ideal model delta sigma weight residual 1.526 1.484 0.042 1.11e-02 8.12e+03 1.43e+01 bond pdb=" C PRO B 541 " pdb=" O PRO B 541 " ideal model delta sigma weight residual 1.233 1.203 0.030 1.18e-02 7.18e+03 6.31e+00 bond pdb=" C PRO A 541 " pdb=" O PRO A 541 " ideal model delta sigma weight residual 1.233 1.204 0.029 1.18e-02 7.18e+03 6.17e+00 bond pdb=" C ARG A 736 " pdb=" O ARG A 736 " ideal model delta sigma weight residual 1.234 1.206 0.028 1.22e-02 6.72e+03 5.17e+00 ... (remaining 14067 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.93: 18789 1.93 - 3.86: 436 3.86 - 5.79: 38 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=" 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 angle pdb=" N LYS A 543 " pdb=" CA LYS A 543 " pdb=" C LYS A 543 " ideal model delta sigma weight residual 111.14 115.66 -4.52 1.08e+00 8.57e-01 1.75e+01 angle pdb=" CB ILE A 17 " pdb=" CG1 ILE A 17 " pdb=" CD1 ILE A 17 " ideal model delta sigma weight residual 113.80 122.54 -8.74 2.10e+00 2.27e-01 1.73e+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: 1652 0.049 - 0.097: 358 0.097 - 0.146: 153 0.146 - 0.194: 17 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=" CA ASN B 487 " pdb=" N ASN B 487 " pdb=" C ASN B 487 " pdb=" CB ASN B 487 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.90e-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: 1.570 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.180 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 17.020 Find NCS groups from input model: 0.280 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:8.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8625 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 14072 Z= 0.220 Angle : 0.703 9.649 19284 Z= 0.409 Chirality : 0.048 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 aren 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 covalent geometry : bond 0.00402 (14072) covalent geometry : angle 0.70309 (19284) hydrogen bonds : bond 0.14046 ( 604) hydrogen bonds : angle 5.52099 ( 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 : 0.559 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: 0.7099 time to fit residues: 156.2192 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 : 0.571 ------------------------------------------------------------------------------- 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: 5.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 4.9990 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... Flipped N/Q/H residues before XYZ refinement: A 99 HIS A 181 HIS ** A 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 573 GLN B 99 HIS B 181 HIS ** B 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.126471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.101744 restraints weight = 15894.849| |-----------------------------------------------------------------------------| r_work (start): 0.3030 rms_B_bonded: 1.67 r_work: 0.2892 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2757 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.2757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8642 moved from start: 0.1417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14072 Z= 0.138 Angle : 0.505 7.292 19284 Z= 0.277 Chirality : 0.044 0.138 2182 Planarity : 0.005 0.065 2210 Dihedral : 16.135 151.519 2358 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 1.88 % Allowed : 24.71 % 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 aren not related in a simple way. whole: -0.37 (0.21), residues: 1496 helix: 0.27 (0.21), residues: 552 sheet: 0.52 (0.25), residues: 384 loop : -1.23 (0.24), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 563 TYR 0.011 0.001 TYR A 282 PHE 0.010 0.001 PHE A 584 TRP 0.004 0.001 TRP A 413 HIS 0.005 0.001 HIS B 99 Details of bonding type rmsd covalent geometry : bond 0.00320 (14072) covalent geometry : angle 0.50506 (19284) hydrogen bonds : bond 0.03886 ( 604) hydrogen bonds : angle 3.83773 ( 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: 26 poor density : 157 time to evaluate : 0.560 Fit side-chains REVERT: A 29 LYS cc_start: 0.7438 (mptt) cc_final: 0.6980 (mttm) REVERT: A 99 HIS cc_start: 0.7496 (t-90) cc_final: 0.6790 (t-90) REVERT: A 103 ARG cc_start: 0.7498 (mtm180) cc_final: 0.6767 (mtt180) REVERT: A 269 GLU cc_start: 0.8366 (OUTLIER) cc_final: 0.8159 (mt-10) REVERT: A 373 LYS cc_start: 0.7344 (mttt) cc_final: 0.6657 (mptp) REVERT: A 448 MET cc_start: 0.7849 (OUTLIER) cc_final: 0.7472 (ttt) REVERT: B 99 HIS cc_start: 0.7506 (t-90) cc_final: 0.6792 (t-90) REVERT: B 103 ARG cc_start: 0.7513 (mtm180) cc_final: 0.6786 (mtt180) REVERT: B 373 LYS cc_start: 0.7322 (mttt) cc_final: 0.6623 (mptp) REVERT: B 448 MET cc_start: 0.7844 (OUTLIER) cc_final: 0.7467 (ttt) outliers start: 26 outliers final: 4 residues processed: 169 average time/residue: 0.6881 time to fit residues: 126.6019 Evaluate side-chains 161 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 154 time to evaluate : 0.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ILE Chi-restraints excluded: chain A residue 269 GLU 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: 8.9990 chunk 119 optimal weight: 0.5980 chunk 75 optimal weight: 4.9990 chunk 8 optimal weight: 2.9990 chunk 101 optimal weight: 10.0000 chunk 91 optimal weight: 6.9990 chunk 7 optimal weight: 5.9990 chunk 71 optimal weight: 8.9990 chunk 56 optimal weight: 0.7980 chunk 51 optimal weight: 5.9990 chunk 21 optimal weight: 8.9990 overall best weight: 3.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 208 HIS ** A 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 335 ASN ** B 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.120778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.096455 restraints weight = 16152.347| |-----------------------------------------------------------------------------| r_work (start): 0.2953 rms_B_bonded: 1.54 r_work: 0.2825 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.2694 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.2694 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8706 moved from start: 0.2116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.071 14072 Z= 0.231 Angle : 0.598 9.401 19284 Z= 0.318 Chirality : 0.047 0.149 2182 Planarity : 0.005 0.054 2210 Dihedral : 16.399 160.511 2350 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 2.60 % Allowed : 23.63 % Favored : 73.77 % 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 aren not related in a simple way. whole: 0.08 (0.21), residues: 1496 helix: 1.03 (0.23), residues: 548 sheet: 0.67 (0.26), residues: 372 loop : -1.31 (0.23), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 563 TYR 0.013 0.002 TYR B 548 PHE 0.012 0.001 PHE B 67 TRP 0.004 0.001 TRP B 413 HIS 0.005 0.001 HIS B 722 Details of bonding type rmsd covalent geometry : bond 0.00566 (14072) covalent geometry : angle 0.59775 (19284) hydrogen bonds : bond 0.05074 ( 604) hydrogen bonds : angle 3.92959 ( 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 203 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 167 time to evaluate : 0.643 Fit side-chains REVERT: A 29 LYS cc_start: 0.7467 (mptt) cc_final: 0.6816 (mttp) REVERT: A 202 ASN cc_start: 0.8122 (m-40) cc_final: 0.7819 (m-40) REVERT: A 373 LYS cc_start: 0.7327 (mttt) cc_final: 0.6764 (mptp) REVERT: A 448 MET cc_start: 0.7993 (OUTLIER) cc_final: 0.7564 (ttt) REVERT: A 474 LYS cc_start: 0.8893 (OUTLIER) cc_final: 0.8581 (tttt) REVERT: A 482 ILE cc_start: 0.8750 (OUTLIER) cc_final: 0.8111 (mm) REVERT: A 624 LYS cc_start: 0.7993 (tttp) cc_final: 0.7467 (ttpp) REVERT: A 702 LEU cc_start: 0.8732 (mm) cc_final: 0.8510 (mt) REVERT: B 29 LYS cc_start: 0.7498 (mptt) cc_final: 0.6821 (mttp) REVERT: B 202 ASN cc_start: 0.8131 (m-40) cc_final: 0.7829 (m-40) REVERT: B 225 LYS cc_start: 0.8242 (mmmt) cc_final: 0.7377 (ttpp) REVERT: B 373 LYS cc_start: 0.7323 (mttt) cc_final: 0.6757 (mptp) REVERT: B 448 MET cc_start: 0.7999 (OUTLIER) cc_final: 0.7537 (ttt) REVERT: B 474 LYS cc_start: 0.8901 (OUTLIER) cc_final: 0.8592 (tttt) REVERT: B 482 ILE cc_start: 0.8761 (OUTLIER) cc_final: 0.8133 (mm) REVERT: B 624 LYS cc_start: 0.7985 (tttp) cc_final: 0.7465 (ttpp) REVERT: B 702 LEU cc_start: 0.8708 (mm) cc_final: 0.8481 (mt) outliers start: 36 outliers final: 12 residues processed: 191 average time/residue: 0.7152 time to fit residues: 148.0299 Evaluate side-chains 180 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 162 time to evaluate : 0.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 MET Chi-restraints excluded: chain A residue 448 MET Chi-restraints excluded: chain A residue 474 LYS 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 566 ILE Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain B residue 3 MET Chi-restraints excluded: chain B residue 448 MET Chi-restraints excluded: chain B residue 474 LYS 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 566 ILE Chi-restraints excluded: chain B residue 686 THR Chi-restraints excluded: chain B residue 714 ASP 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: 7.9990 chunk 6 optimal weight: 9.9990 chunk 109 optimal weight: 8.9990 chunk 149 optimal weight: 0.8980 chunk 24 optimal weight: 0.0670 chunk 96 optimal weight: 7.9990 chunk 141 optimal weight: 3.9990 chunk 88 optimal weight: 2.9990 chunk 42 optimal weight: 0.0170 chunk 60 optimal weight: 5.9990 chunk 43 optimal weight: 4.9990 overall best weight: 1.5960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.123376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.098934 restraints weight = 15927.297| |-----------------------------------------------------------------------------| r_work (start): 0.2991 rms_B_bonded: 1.50 r_work: 0.2874 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.2744 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.2744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8616 moved from start: 0.2076 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= 0.145 Angle : 0.504 9.020 19284 Z= 0.275 Chirality : 0.044 0.132 2182 Planarity : 0.004 0.051 2210 Dihedral : 16.241 160.733 2346 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 2.31 % Allowed : 24.49 % Favored : 73.19 % 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 aren not related in a simple way. whole: 0.41 (0.22), residues: 1496 helix: 1.44 (0.23), residues: 548 sheet: 0.65 (0.26), residues: 372 loop : -1.12 (0.24), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 145 TYR 0.009 0.001 TYR A 650 PHE 0.010 0.001 PHE B 227 TRP 0.004 0.001 TRP A 413 HIS 0.004 0.001 HIS A 722 Details of bonding type rmsd covalent geometry : bond 0.00341 (14072) covalent geometry : angle 0.50445 (19284) hydrogen bonds : bond 0.03827 ( 604) hydrogen bonds : angle 3.71207 ( 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 203 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 171 time to evaluate : 0.541 Fit side-chains REVERT: A 29 LYS cc_start: 0.7408 (mptt) cc_final: 0.6754 (mttp) REVERT: A 202 ASN cc_start: 0.8131 (m-40) cc_final: 0.7815 (m-40) REVERT: A 225 LYS cc_start: 0.8266 (mmmt) cc_final: 0.7408 (ttpp) REVERT: A 373 LYS cc_start: 0.7243 (mttt) cc_final: 0.6686 (mptp) REVERT: A 448 MET cc_start: 0.7884 (OUTLIER) cc_final: 0.7422 (ttt) REVERT: A 624 LYS cc_start: 0.7886 (tttp) cc_final: 0.7327 (ttpp) REVERT: A 702 LEU cc_start: 0.8621 (OUTLIER) cc_final: 0.8398 (mt) REVERT: B 29 LYS cc_start: 0.7436 (mptt) cc_final: 0.6829 (mttp) REVERT: B 202 ASN cc_start: 0.8154 (m-40) cc_final: 0.7837 (m-40) REVERT: B 225 LYS cc_start: 0.8147 (mmmt) cc_final: 0.7307 (ttpp) REVERT: B 373 LYS cc_start: 0.7235 (mttt) cc_final: 0.6684 (mptp) REVERT: B 448 MET cc_start: 0.7891 (OUTLIER) cc_final: 0.7432 (ttt) REVERT: B 624 LYS cc_start: 0.7870 (tttp) cc_final: 0.7310 (ttpp) REVERT: B 702 LEU cc_start: 0.8613 (OUTLIER) cc_final: 0.8384 (mt) outliers start: 32 outliers final: 8 residues processed: 189 average time/residue: 0.7455 time to fit residues: 152.6152 Evaluate side-chains 179 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 167 time to evaluate : 0.588 ------------------------------------------------------------------------------- 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 566 ILE 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 122 GLU Chi-restraints excluded: chain B residue 448 MET 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: 0.4980 chunk 35 optimal weight: 8.9990 chunk 88 optimal weight: 1.9990 chunk 150 optimal weight: 2.9990 chunk 135 optimal weight: 4.9990 chunk 16 optimal weight: 9.9990 chunk 123 optimal weight: 0.0980 chunk 120 optimal weight: 8.9990 chunk 26 optimal weight: 8.9990 chunk 110 optimal weight: 9.9990 chunk 108 optimal weight: 2.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 480 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.123540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.099803 restraints weight = 16003.879| |-----------------------------------------------------------------------------| r_work (start): 0.3006 rms_B_bonded: 1.44 r_work: 0.2878 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.2748 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.2748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8643 moved from start: 0.2158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 14072 Z= 0.151 Angle : 0.507 9.103 19284 Z= 0.276 Chirality : 0.044 0.136 2182 Planarity : 0.004 0.048 2210 Dihedral : 16.220 161.357 2346 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 2.24 % Allowed : 24.71 % 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 aren not related in a simple way. whole: 0.60 (0.22), residues: 1496 helix: 1.65 (0.23), residues: 548 sheet: 0.77 (0.26), residues: 376 loop : -1.10 (0.24), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 145 TYR 0.009 0.001 TYR B 548 PHE 0.010 0.001 PHE B 227 TRP 0.004 0.001 TRP A 413 HIS 0.004 0.001 HIS A 722 Details of bonding type rmsd covalent geometry : bond 0.00360 (14072) covalent geometry : angle 0.50715 (19284) hydrogen bonds : bond 0.03891 ( 604) hydrogen bonds : angle 3.64987 ( 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 202 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 171 time to evaluate : 0.666 Fit side-chains REVERT: A 20 GLU cc_start: 0.7815 (OUTLIER) cc_final: 0.6512 (pp20) REVERT: A 29 LYS cc_start: 0.7449 (mptt) cc_final: 0.6749 (mttp) REVERT: A 202 ASN cc_start: 0.8130 (m-40) cc_final: 0.7813 (m-40) REVERT: A 225 LYS cc_start: 0.8306 (mmmt) cc_final: 0.7453 (ttpp) REVERT: A 373 LYS cc_start: 0.7220 (mttt) cc_final: 0.6663 (mptp) REVERT: A 448 MET cc_start: 0.7924 (OUTLIER) cc_final: 0.7450 (ttt) REVERT: A 624 LYS cc_start: 0.7922 (tttp) cc_final: 0.7379 (ttpp) REVERT: A 702 LEU cc_start: 0.8588 (OUTLIER) cc_final: 0.8335 (mt) REVERT: B 19 ASN cc_start: 0.7040 (OUTLIER) cc_final: 0.6473 (OUTLIER) REVERT: B 20 GLU cc_start: 0.7916 (OUTLIER) cc_final: 0.7405 (pm20) REVERT: B 29 LYS cc_start: 0.7470 (mptt) cc_final: 0.6605 (mttp) REVERT: B 202 ASN cc_start: 0.8130 (m-40) cc_final: 0.7816 (m-40) REVERT: B 373 LYS cc_start: 0.7213 (mttt) cc_final: 0.6654 (mptp) REVERT: B 448 MET cc_start: 0.7928 (OUTLIER) cc_final: 0.7457 (ttt) REVERT: B 624 LYS cc_start: 0.7914 (tttp) cc_final: 0.7369 (ttpp) REVERT: B 702 LEU cc_start: 0.8597 (OUTLIER) cc_final: 0.8338 (mt) outliers start: 31 outliers final: 13 residues processed: 195 average time/residue: 0.7466 time to fit residues: 157.7394 Evaluate side-chains 185 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 166 time to evaluate : 0.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 593 LYS Chi-restraints excluded: chain A residue 702 LEU Chi-restraints excluded: chain A residue 714 ASP Chi-restraints excluded: chain B residue 19 ASN Chi-restraints excluded: chain B residue 20 GLU 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 566 ILE Chi-restraints excluded: chain B residue 593 LYS Chi-restraints excluded: chain B residue 686 THR Chi-restraints excluded: chain B residue 702 LEU Chi-restraints excluded: chain B residue 714 ASP Chi-restraints excluded: chain B residue 740 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 126 optimal weight: 8.9990 chunk 134 optimal weight: 1.9990 chunk 87 optimal weight: 6.9990 chunk 51 optimal weight: 6.9990 chunk 119 optimal weight: 9.9990 chunk 73 optimal weight: 2.9990 chunk 141 optimal weight: 0.9980 chunk 17 optimal weight: 8.9990 chunk 54 optimal weight: 0.8980 chunk 69 optimal weight: 7.9990 chunk 39 optimal weight: 9.9990 overall best weight: 2.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.120519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.095720 restraints weight = 15954.842| |-----------------------------------------------------------------------------| r_work (start): 0.2958 rms_B_bonded: 1.54 r_work: 0.2840 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.2707 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.2707 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8694 moved from start: 0.2337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 14072 Z= 0.211 Angle : 0.567 9.829 19284 Z= 0.303 Chirality : 0.047 0.146 2182 Planarity : 0.004 0.044 2210 Dihedral : 16.360 161.991 2346 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 3.68 % Allowed : 23.12 % Favored : 73.19 % 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 aren not related in a simple way. whole: 0.50 (0.22), residues: 1496 helix: 1.60 (0.23), residues: 548 sheet: 0.66 (0.26), residues: 374 loop : -1.15 (0.25), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 145 TYR 0.012 0.001 TYR A 548 PHE 0.010 0.001 PHE A 227 TRP 0.003 0.001 TRP A 218 HIS 0.005 0.001 HIS B 722 Details of bonding type rmsd covalent geometry : bond 0.00515 (14072) covalent geometry : angle 0.56693 (19284) hydrogen bonds : bond 0.04633 ( 604) hydrogen bonds : angle 3.76831 ( 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 212 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 161 time to evaluate : 0.547 Fit side-chains REVERT: A 20 GLU cc_start: 0.7816 (OUTLIER) cc_final: 0.6553 (pp20) REVERT: A 29 LYS cc_start: 0.7446 (mptt) cc_final: 0.6797 (mttm) REVERT: A 202 ASN cc_start: 0.8141 (m-40) cc_final: 0.7820 (m-40) REVERT: A 373 LYS cc_start: 0.7246 (mttt) cc_final: 0.6682 (mptp) REVERT: A 448 MET cc_start: 0.7990 (OUTLIER) cc_final: 0.7496 (ttt) REVERT: A 482 ILE cc_start: 0.8744 (OUTLIER) cc_final: 0.8104 (mm) REVERT: A 562 ILE cc_start: 0.6175 (OUTLIER) cc_final: 0.5541 (mp) REVERT: A 624 LYS cc_start: 0.7951 (tttp) cc_final: 0.7436 (ttpp) REVERT: A 702 LEU cc_start: 0.8628 (OUTLIER) cc_final: 0.8415 (mt) REVERT: B 19 ASN cc_start: 0.7099 (OUTLIER) cc_final: 0.6541 (OUTLIER) REVERT: B 20 GLU cc_start: 0.7942 (OUTLIER) cc_final: 0.7407 (pm20) REVERT: B 29 LYS cc_start: 0.7308 (mptt) cc_final: 0.6598 (mttm) REVERT: B 202 ASN cc_start: 0.8146 (m-40) cc_final: 0.7819 (m-40) REVERT: B 225 LYS cc_start: 0.8184 (mmmt) cc_final: 0.7268 (ttpp) REVERT: B 373 LYS cc_start: 0.7235 (mttt) cc_final: 0.6669 (mptp) REVERT: B 448 MET cc_start: 0.7978 (OUTLIER) cc_final: 0.7489 (ttt) REVERT: B 482 ILE cc_start: 0.8770 (OUTLIER) cc_final: 0.8128 (mm) REVERT: B 562 ILE cc_start: 0.6157 (OUTLIER) cc_final: 0.5524 (mp) REVERT: B 624 LYS cc_start: 0.7937 (tttp) cc_final: 0.7420 (ttpp) REVERT: B 702 LEU cc_start: 0.8619 (OUTLIER) cc_final: 0.8401 (mt) outliers start: 51 outliers final: 25 residues processed: 196 average time/residue: 0.7040 time to fit residues: 149.7368 Evaluate side-chains 191 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 156 time to evaluate : 0.647 ------------------------------------------------------------------------------- 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 562 ILE Chi-restraints excluded: chain A residue 566 ILE Chi-restraints excluded: chain A residue 572 GLU Chi-restraints excluded: chain A residue 593 LYS Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 688 THR 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 20 GLU 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 511 LEU Chi-restraints excluded: chain B residue 525 LEU Chi-restraints excluded: chain B residue 562 ILE Chi-restraints excluded: chain B residue 566 ILE Chi-restraints excluded: chain B residue 572 GLU Chi-restraints excluded: chain B residue 593 LYS Chi-restraints excluded: chain B residue 686 THR Chi-restraints excluded: chain B residue 688 THR Chi-restraints excluded: chain B residue 702 LEU Chi-restraints excluded: chain B residue 714 ASP Chi-restraints excluded: chain B residue 740 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 86 optimal weight: 0.5980 chunk 137 optimal weight: 0.9990 chunk 82 optimal weight: 7.9990 chunk 73 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 6 optimal weight: 6.9990 chunk 23 optimal weight: 8.9990 chunk 61 optimal weight: 0.8980 chunk 114 optimal weight: 2.9990 chunk 105 optimal weight: 6.9990 chunk 63 optimal weight: 0.9980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.123027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.098236 restraints weight = 15856.838| |-----------------------------------------------------------------------------| r_work (start): 0.3006 rms_B_bonded: 1.68 r_work: 0.2878 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2744 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.2744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8707 moved from start: 0.2249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14072 Z= 0.123 Angle : 0.485 9.180 19284 Z= 0.266 Chirality : 0.043 0.136 2182 Planarity : 0.004 0.045 2210 Dihedral : 16.234 161.855 2346 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 2.89 % Allowed : 23.99 % Favored : 73.12 % 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 aren not related in a simple way. whole: 0.79 (0.22), residues: 1496 helix: 1.86 (0.23), residues: 548 sheet: 0.83 (0.26), residues: 368 loop : -1.01 (0.25), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 145 TYR 0.009 0.001 TYR A 650 PHE 0.011 0.001 PHE A 227 TRP 0.004 0.001 TRP A 413 HIS 0.004 0.001 HIS A 722 Details of bonding type rmsd covalent geometry : bond 0.00283 (14072) covalent geometry : angle 0.48516 (19284) hydrogen bonds : bond 0.03529 ( 604) hydrogen bonds : angle 3.58899 ( 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 208 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 168 time to evaluate : 0.473 Fit side-chains REVERT: A 19 ASN cc_start: 0.7236 (OUTLIER) cc_final: 0.6465 (OUTLIER) REVERT: A 29 LYS cc_start: 0.7504 (mptt) cc_final: 0.6758 (mttm) REVERT: A 42 ARG cc_start: 0.8043 (mtp85) cc_final: 0.7658 (ttp80) REVERT: A 202 ASN cc_start: 0.8141 (m-40) cc_final: 0.7818 (m-40) REVERT: A 225 LYS cc_start: 0.8224 (mmmt) cc_final: 0.7309 (ttpp) REVERT: A 373 LYS cc_start: 0.7194 (mttt) cc_final: 0.6682 (mptp) REVERT: A 448 MET cc_start: 0.7959 (OUTLIER) cc_final: 0.7530 (ttt) REVERT: A 487 ASN cc_start: 0.8021 (p0) cc_final: 0.7811 (p0) REVERT: A 562 ILE cc_start: 0.6124 (OUTLIER) cc_final: 0.5477 (mp) REVERT: A 740 GLU cc_start: 0.8200 (OUTLIER) cc_final: 0.7908 (pm20) REVERT: B 29 LYS cc_start: 0.7348 (mptt) cc_final: 0.6610 (mttm) REVERT: B 202 ASN cc_start: 0.8142 (m-40) cc_final: 0.7816 (m-40) REVERT: B 225 LYS cc_start: 0.8222 (mmmt) cc_final: 0.7349 (ttpp) REVERT: B 373 LYS cc_start: 0.7197 (mttt) cc_final: 0.6683 (mptp) REVERT: B 448 MET cc_start: 0.7958 (OUTLIER) cc_final: 0.7516 (ttt) REVERT: B 487 ASN cc_start: 0.8030 (p0) cc_final: 0.7823 (p0) REVERT: B 562 ILE cc_start: 0.6117 (OUTLIER) cc_final: 0.5468 (mp) REVERT: B 624 LYS cc_start: 0.7950 (tttp) cc_final: 0.7426 (ttpp) outliers start: 40 outliers final: 19 residues processed: 196 average time/residue: 0.5729 time to fit residues: 122.2830 Evaluate side-chains 190 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 166 time to evaluate : 0.374 ------------------------------------------------------------------------------- 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 448 MET Chi-restraints excluded: chain A residue 511 LEU Chi-restraints excluded: chain A residue 562 ILE Chi-restraints excluded: chain A residue 593 LYS Chi-restraints excluded: chain A residue 596 ILE Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 688 THR 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 122 GLU Chi-restraints excluded: chain B residue 448 MET Chi-restraints excluded: chain B residue 511 LEU Chi-restraints excluded: chain B residue 562 ILE Chi-restraints excluded: chain B residue 566 ILE Chi-restraints excluded: chain B residue 572 GLU Chi-restraints excluded: chain B residue 593 LYS Chi-restraints excluded: chain B residue 596 ILE Chi-restraints excluded: chain B residue 688 THR Chi-restraints excluded: chain B residue 714 ASP Chi-restraints excluded: chain B residue 740 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 16 optimal weight: 9.9990 chunk 136 optimal weight: 0.9980 chunk 111 optimal weight: 0.6980 chunk 56 optimal weight: 1.9990 chunk 153 optimal weight: 4.9990 chunk 117 optimal weight: 9.9990 chunk 107 optimal weight: 0.1980 chunk 115 optimal weight: 0.9990 chunk 30 optimal weight: 0.8980 chunk 78 optimal weight: 5.9990 chunk 95 optimal weight: 5.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.126619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.102759 restraints weight = 15726.717| |-----------------------------------------------------------------------------| r_work (start): 0.3052 rms_B_bonded: 1.52 r_work: 0.2931 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.2802 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.2802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8596 moved from start: 0.2195 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= 0.107 Angle : 0.466 8.497 19284 Z= 0.257 Chirality : 0.043 0.141 2182 Planarity : 0.004 0.045 2210 Dihedral : 16.104 161.190 2346 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 2.31 % Allowed : 24.57 % Favored : 73.12 % 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 aren not related in a simple way. whole: 1.01 (0.22), residues: 1496 helix: 2.01 (0.23), residues: 550 sheet: 0.97 (0.27), residues: 368 loop : -0.88 (0.25), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 145 TYR 0.010 0.001 TYR A 650 PHE 0.011 0.001 PHE B 227 TRP 0.004 0.000 TRP A 151 HIS 0.003 0.001 HIS B 722 Details of bonding type rmsd covalent geometry : bond 0.00242 (14072) covalent geometry : angle 0.46575 (19284) hydrogen bonds : bond 0.03128 ( 604) hydrogen bonds : angle 3.46269 ( 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 203 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 171 time to evaluate : 0.383 Fit side-chains REVERT: A 29 LYS cc_start: 0.7466 (mptt) cc_final: 0.6776 (mttp) REVERT: A 42 ARG cc_start: 0.7994 (mtp85) cc_final: 0.7572 (ttp80) REVERT: A 202 ASN cc_start: 0.8153 (m-40) cc_final: 0.7825 (m-40) REVERT: A 225 LYS cc_start: 0.8138 (mmmt) cc_final: 0.7239 (ttpp) REVERT: A 373 LYS cc_start: 0.7043 (mttt) cc_final: 0.6542 (mptp) REVERT: A 448 MET cc_start: 0.7854 (OUTLIER) cc_final: 0.7410 (ttt) REVERT: A 482 ILE cc_start: 0.8694 (OUTLIER) cc_final: 0.7974 (mm) REVERT: A 487 ASN cc_start: 0.7788 (p0) cc_final: 0.7518 (p0) REVERT: A 562 ILE cc_start: 0.5982 (OUTLIER) cc_final: 0.5293 (mp) REVERT: A 738 ARG cc_start: 0.7721 (mtm110) cc_final: 0.7471 (mtm110) REVERT: A 740 GLU cc_start: 0.8117 (OUTLIER) cc_final: 0.7724 (pm20) REVERT: B 19 ASN cc_start: 0.7014 (OUTLIER) cc_final: 0.6056 (OUTLIER) REVERT: B 20 GLU cc_start: 0.7841 (OUTLIER) cc_final: 0.6951 (pm20) REVERT: B 202 ASN cc_start: 0.8141 (m-40) cc_final: 0.7811 (m-40) REVERT: B 225 LYS cc_start: 0.8120 (mmmt) cc_final: 0.7285 (ttpp) REVERT: B 373 LYS cc_start: 0.7069 (mttt) cc_final: 0.6561 (mptp) REVERT: B 448 MET cc_start: 0.7855 (OUTLIER) cc_final: 0.7435 (ttt) REVERT: B 487 ASN cc_start: 0.7792 (p0) cc_final: 0.7526 (p0) REVERT: B 562 ILE cc_start: 0.5990 (OUTLIER) cc_final: 0.5292 (mp) outliers start: 32 outliers final: 12 residues processed: 191 average time/residue: 0.5453 time to fit residues: 113.2184 Evaluate side-chains 187 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 168 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 MET Chi-restraints excluded: chain A residue 320 PHE Chi-restraints excluded: chain A residue 448 MET Chi-restraints excluded: chain A residue 482 ILE Chi-restraints excluded: chain A residue 562 ILE Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 688 THR Chi-restraints excluded: chain A residue 701 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 20 GLU Chi-restraints excluded: chain B residue 320 PHE Chi-restraints excluded: chain B residue 448 MET Chi-restraints excluded: chain B residue 562 ILE Chi-restraints excluded: chain B residue 688 THR Chi-restraints excluded: chain B residue 714 ASP Chi-restraints excluded: chain B residue 740 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 6 optimal weight: 6.9990 chunk 60 optimal weight: 7.9990 chunk 57 optimal weight: 5.9990 chunk 117 optimal weight: 10.0000 chunk 149 optimal weight: 5.9990 chunk 136 optimal weight: 3.9990 chunk 36 optimal weight: 6.9990 chunk 142 optimal weight: 7.9990 chunk 33 optimal weight: 0.9990 chunk 11 optimal weight: 4.9990 chunk 108 optimal weight: 2.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 325 ASN B 208 HIS B 325 ASN B 480 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.119054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.094036 restraints weight = 16047.802| |-----------------------------------------------------------------------------| r_work (start): 0.2929 rms_B_bonded: 1.63 r_work: 0.2790 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2656 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.2656 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8769 moved from start: 0.2455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.069 14072 Z= 0.269 Angle : 0.618 9.787 19284 Z= 0.325 Chirality : 0.049 0.162 2182 Planarity : 0.005 0.042 2210 Dihedral : 16.402 161.897 2346 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 2.24 % Allowed : 24.64 % Favored : 73.12 % 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 aren not related in a simple way. whole: 0.59 (0.22), residues: 1496 helix: 1.68 (0.23), residues: 550 sheet: 0.69 (0.26), residues: 374 loop : -1.12 (0.25), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 145 TYR 0.014 0.002 TYR A 548 PHE 0.012 0.002 PHE A 67 TRP 0.006 0.001 TRP A 218 HIS 0.006 0.001 HIS B 722 Details of bonding type rmsd covalent geometry : bond 0.00665 (14072) covalent geometry : angle 0.61777 (19284) hydrogen bonds : bond 0.05094 ( 604) hydrogen bonds : angle 3.74684 ( 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 : 0.460 Fit side-chains REVERT: A 29 LYS cc_start: 0.7519 (mptt) cc_final: 0.6766 (mttp) REVERT: A 42 ARG cc_start: 0.8089 (mtp85) cc_final: 0.7668 (ttp80) REVERT: A 99 HIS cc_start: 0.7840 (t-90) cc_final: 0.7399 (t-90) REVERT: A 202 ASN cc_start: 0.8157 (m-40) cc_final: 0.7835 (m-40) REVERT: A 225 LYS cc_start: 0.8265 (mmmt) cc_final: 0.7359 (ttpp) REVERT: A 373 LYS cc_start: 0.7257 (mttt) cc_final: 0.6707 (mptp) REVERT: A 448 MET cc_start: 0.8054 (OUTLIER) cc_final: 0.7581 (ttt) REVERT: A 482 ILE cc_start: 0.8799 (OUTLIER) cc_final: 0.8167 (mm) REVERT: A 562 ILE cc_start: 0.6237 (OUTLIER) cc_final: 0.5594 (mp) REVERT: A 624 LYS cc_start: 0.8031 (tttp) cc_final: 0.7537 (ttpp) REVERT: A 740 GLU cc_start: 0.8209 (OUTLIER) cc_final: 0.7958 (pm20) REVERT: B 19 ASN cc_start: 0.7188 (OUTLIER) cc_final: 0.6356 (OUTLIER) REVERT: B 20 GLU cc_start: 0.7979 (OUTLIER) cc_final: 0.7098 (pm20) REVERT: B 29 LYS cc_start: 0.7380 (mptt) cc_final: 0.6517 (mttp) REVERT: B 99 HIS cc_start: 0.7864 (t-90) cc_final: 0.7434 (t-90) REVERT: B 202 ASN cc_start: 0.8162 (m-40) cc_final: 0.7838 (m-40) REVERT: B 225 LYS cc_start: 0.8244 (mmmt) cc_final: 0.7362 (ttpp) REVERT: B 373 LYS cc_start: 0.7261 (mttt) cc_final: 0.6711 (mptp) REVERT: B 448 MET cc_start: 0.8079 (OUTLIER) cc_final: 0.7594 (ttt) REVERT: B 482 ILE cc_start: 0.8814 (OUTLIER) cc_final: 0.8181 (mm) REVERT: B 562 ILE cc_start: 0.6212 (OUTLIER) cc_final: 0.5573 (mp) REVERT: B 624 LYS cc_start: 0.8021 (tttp) cc_final: 0.7523 (ttpp) outliers start: 31 outliers final: 18 residues processed: 180 average time/residue: 0.5956 time to fit residues: 116.2413 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 : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 MET Chi-restraints excluded: chain A residue 448 MET Chi-restraints excluded: chain A residue 449 LYS Chi-restraints excluded: chain A residue 482 ILE Chi-restraints excluded: chain A residue 511 LEU Chi-restraints excluded: chain A residue 562 ILE Chi-restraints excluded: chain A residue 572 GLU Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 688 THR Chi-restraints excluded: chain A residue 701 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 20 GLU Chi-restraints excluded: chain B residue 34 MET Chi-restraints excluded: chain B residue 320 PHE 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 562 ILE Chi-restraints excluded: chain B residue 572 GLU Chi-restraints excluded: chain B residue 686 THR Chi-restraints excluded: chain B residue 688 THR Chi-restraints excluded: chain B residue 714 ASP Chi-restraints excluded: chain B residue 740 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 35 optimal weight: 0.9980 chunk 89 optimal weight: 5.9990 chunk 14 optimal weight: 1.9990 chunk 86 optimal weight: 2.9990 chunk 118 optimal weight: 2.9990 chunk 152 optimal weight: 3.9990 chunk 16 optimal weight: 7.9990 chunk 90 optimal weight: 3.9990 chunk 109 optimal weight: 10.0000 chunk 110 optimal weight: 7.9990 chunk 84 optimal weight: 8.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.120673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.095939 restraints weight = 15941.846| |-----------------------------------------------------------------------------| r_work (start): 0.2962 rms_B_bonded: 1.54 r_work: 0.2845 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.2713 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.2713 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8677 moved from start: 0.2438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 14072 Z= 0.201 Angle : 0.568 10.043 19284 Z= 0.303 Chirality : 0.046 0.154 2182 Planarity : 0.004 0.051 2210 Dihedral : 16.357 162.162 2346 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 2.10 % Allowed : 24.78 % Favored : 73.12 % 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 aren not related in a simple way. whole: 0.58 (0.22), residues: 1496 helix: 1.67 (0.23), residues: 548 sheet: 0.71 (0.26), residues: 366 loop : -1.09 (0.24), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 738 TYR 0.012 0.001 TYR B 548 PHE 0.010 0.001 PHE A 227 TRP 0.003 0.001 TRP A 218 HIS 0.005 0.001 HIS B 722 Details of bonding type rmsd covalent geometry : bond 0.00491 (14072) covalent geometry : angle 0.56822 (19284) hydrogen bonds : bond 0.04470 ( 604) hydrogen bonds : angle 3.71434 ( 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 197 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 168 time to evaluate : 0.456 Fit side-chains REVERT: A 29 LYS cc_start: 0.7490 (mptt) cc_final: 0.6686 (mttp) REVERT: A 42 ARG cc_start: 0.8042 (mtp85) cc_final: 0.7598 (ttp80) REVERT: A 99 HIS cc_start: 0.7725 (t-90) cc_final: 0.7292 (t-90) REVERT: A 202 ASN cc_start: 0.8141 (m-40) cc_final: 0.7808 (m-40) REVERT: A 225 LYS cc_start: 0.8195 (mmmt) cc_final: 0.7294 (ttpp) REVERT: A 373 LYS cc_start: 0.7144 (mttt) cc_final: 0.6619 (mptp) REVERT: A 448 MET cc_start: 0.7977 (OUTLIER) cc_final: 0.7485 (ttt) REVERT: A 482 ILE cc_start: 0.8724 (OUTLIER) cc_final: 0.8099 (mm) REVERT: A 562 ILE cc_start: 0.6145 (OUTLIER) cc_final: 0.5507 (mp) REVERT: A 624 LYS cc_start: 0.7939 (tttp) cc_final: 0.7407 (ttpp) REVERT: B 19 ASN cc_start: 0.7100 (OUTLIER) cc_final: 0.6265 (OUTLIER) REVERT: B 20 GLU cc_start: 0.7912 (OUTLIER) cc_final: 0.7005 (pm20) REVERT: B 29 LYS cc_start: 0.7347 (mptt) cc_final: 0.6444 (mttp) REVERT: B 34 MET cc_start: 0.3835 (OUTLIER) cc_final: 0.3557 (tpt) REVERT: B 99 HIS cc_start: 0.7750 (t-90) cc_final: 0.7329 (t-90) REVERT: B 103 ARG cc_start: 0.7352 (mtm180) cc_final: 0.7058 (mtt180) REVERT: B 202 ASN cc_start: 0.8140 (m-40) cc_final: 0.7804 (m-40) REVERT: B 225 LYS cc_start: 0.8163 (mmmt) cc_final: 0.7298 (ttpp) REVERT: B 373 LYS cc_start: 0.7146 (mttt) cc_final: 0.6623 (mptp) REVERT: B 448 MET cc_start: 0.7988 (OUTLIER) cc_final: 0.7501 (ttt) REVERT: B 482 ILE cc_start: 0.8748 (OUTLIER) cc_final: 0.8113 (mm) REVERT: B 562 ILE cc_start: 0.6131 (OUTLIER) cc_final: 0.5501 (mp) REVERT: B 624 LYS cc_start: 0.7916 (tttp) cc_final: 0.7387 (ttpp) outliers start: 29 outliers final: 16 residues processed: 186 average time/residue: 0.6274 time to fit residues: 126.6209 Evaluate side-chains 188 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 164 time to evaluate : 0.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 MET Chi-restraints excluded: chain A residue 448 MET Chi-restraints excluded: chain A residue 449 LYS Chi-restraints excluded: chain A residue 482 ILE Chi-restraints excluded: chain A residue 562 ILE Chi-restraints excluded: chain A residue 572 GLU Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 688 THR Chi-restraints excluded: chain A residue 701 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 20 GLU Chi-restraints excluded: chain B residue 34 MET Chi-restraints excluded: chain B residue 320 PHE Chi-restraints excluded: chain B residue 448 MET Chi-restraints excluded: chain B residue 482 ILE Chi-restraints excluded: chain B residue 525 LEU Chi-restraints excluded: chain B residue 562 ILE Chi-restraints excluded: chain B residue 572 GLU Chi-restraints excluded: chain B residue 686 THR Chi-restraints excluded: chain B residue 688 THR Chi-restraints excluded: chain B residue 701 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: 5.9990 chunk 95 optimal weight: 4.9990 chunk 56 optimal weight: 0.8980 chunk 58 optimal weight: 0.6980 chunk 18 optimal weight: 2.9990 chunk 112 optimal weight: 4.9990 chunk 67 optimal weight: 0.5980 chunk 142 optimal weight: 1.9990 chunk 37 optimal weight: 0.9990 chunk 140 optimal weight: 2.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 304 ASN B 662 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.124140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.100244 restraints weight = 15966.147| |-----------------------------------------------------------------------------| r_work (start): 0.3008 rms_B_bonded: 1.64 r_work: 0.2875 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.2744 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.2744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8643 moved from start: 0.2320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14072 Z= 0.121 Angle : 0.492 9.199 19284 Z= 0.269 Chirality : 0.043 0.143 2182 Planarity : 0.004 0.045 2210 Dihedral : 16.242 162.536 2346 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 1.59 % Allowed : 25.51 % Favored : 72.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.86 (0.22), residues: 1496 helix: 1.91 (0.23), residues: 548 sheet: 0.86 (0.26), residues: 368 loop : -0.94 (0.25), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 145 TYR 0.010 0.001 TYR A 650 PHE 0.011 0.001 PHE A 227 TRP 0.004 0.001 TRP A 413 HIS 0.003 0.001 HIS A 722 Details of bonding type rmsd covalent geometry : bond 0.00277 (14072) covalent geometry : angle 0.49151 (19284) hydrogen bonds : bond 0.03420 ( 604) hydrogen bonds : angle 3.55415 ( 1744) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4286.73 seconds wall clock time: 73 minutes 55.23 seconds (4435.23 seconds total)