Starting phenix.real_space_refine on Fri Jul 3 09:42:34 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8wd8_37457/07_2026/8wd8_37457.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wd8_37457/07_2026/8wd8_37457.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/8wd8_37457/07_2026/8wd8_37457.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8wd8_37457/07_2026/8wd8_37457.cif" model { file = "/net/cci-nas-00/data/ceres_data/8wd8_37457/07_2026/8wd8_37457.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wd8_37457/07_2026/8wd8_37457.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8wd8_37457/07_2026/8wd8_37457.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wd8_37457/07_2026/8wd8_37457.map" } 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-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 13667 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 6174 Number of conformers: 1 Conformer: "" Number of residues, atoms: 750, 6174 Classifications: {'peptide': 750} Link IDs: {'PTRANS': 29, 'TRANS': 720} Chain: "T" Number of atoms: 317 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 317 Classifications: {'DNA': 16} Link IDs: {'rna3p': 15} Chain: "G" Number of atoms: 339 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 339 Classifications: {'DNA': 16} Link IDs: {'rna3p': 15} Chain: "B" Number of atoms: 6174 Number of conformers: 1 Conformer: "" Number of residues, atoms: 750, 6174 Classifications: {'peptide': 750} Link IDs: {'PTRANS': 29, 'TRANS': 720} Chain: "U" Number of atoms: 317 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 317 Classifications: {'DNA': 16} Link IDs: {'rna3p': 15} Chain: "H" Number of atoms: 339 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 339 Classifications: {'DNA': 16} Link IDs: {'rna3p': 15} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 2, ' ZN': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "T" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 2.64, per 1000 atoms: 0.19 Number of scatterers: 13667 At special positions: 0 Unit cell: (111.35, 89.25, 101.15, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 1 29.99 S 26 16.00 P 64 15.00 Mg 6 11.99 O 2612 8.00 N 2334 7.00 C 8624 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.90 Conformation dependent library (CDL) restraints added in 516.5 milliseconds 2992 Ramachandran restraints generated. 1496 Oldfield, 0 Emsley, 1496 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2872 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 18 sheets defined 37.5% alpha, 25.3% beta 27 base pairs and 46 stacking pairs defined. Time for finding SS restraints: 1.62 Creating SS restraints... Processing helix chain 'A' and resid 35 through 43 Processing helix chain 'A' and resid 76 through 78 No H-bonds generated for 'chain 'A' and resid 76 through 78' Processing helix chain 'A' and resid 79 through 94 Processing helix chain 'A' and resid 97 through 106 Processing helix chain 'A' and resid 149 through 154 removed outlier: 3.546A pdb=" N VAL A 154 " --> pdb=" O LEU A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 168 Processing helix chain 'A' and resid 204 through 218 removed outlier: 3.853A pdb=" N TYR A 217 " --> pdb=" O HIS A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 220 through 231 Processing helix chain 'A' and resid 267 through 271 removed outlier: 3.669A pdb=" N LEU A 271 " --> pdb=" O ALA A 268 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 284 removed outlier: 3.503A pdb=" N LYS A 284 " --> pdb=" O LEU A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 303 removed outlier: 3.888A pdb=" N THR A 303 " --> pdb=" O ASN A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 326 removed outlier: 3.549A pdb=" N ASP A 326 " --> pdb=" O ASP A 323 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 323 through 326' Processing helix chain 'A' and resid 346 through 350 removed outlier: 3.867A pdb=" N ARG A 349 " --> pdb=" O SER A 346 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N LEU A 350 " --> pdb=" O LYS A 347 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 346 through 350' Processing helix chain 'A' and resid 368 through 374 removed outlier: 3.544A pdb=" N LYS A 372 " --> pdb=" O PRO A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 388 through 412 Processing helix chain 'A' and resid 422 through 424 No H-bonds generated for 'chain 'A' and resid 422 through 424' Processing helix chain 'A' and resid 433 through 448 Processing helix chain 'A' and resid 465 through 478 Processing helix chain 'A' and resid 487 through 492 Processing helix chain 'A' and resid 503 through 518 removed outlier: 3.693A pdb=" N LEU A 518 " --> pdb=" O ILE A 514 " (cutoff:3.500A) Processing helix chain 'A' and resid 579 through 594 Processing helix chain 'A' and resid 612 through 626 Processing helix chain 'A' and resid 693 through 704 removed outlier: 3.632A pdb=" N ILE A 697 " --> pdb=" O THR A 693 " (cutoff:3.500A) Processing helix chain 'A' and resid 718 through 733 removed outlier: 3.642A pdb=" N LYS A 733 " --> pdb=" O ARG A 729 " (cutoff:3.500A) Processing helix chain 'A' and resid 738 through 744 Processing helix chain 'B' and resid 35 through 43 Processing helix chain 'B' and resid 76 through 78 No H-bonds generated for 'chain 'B' and resid 76 through 78' Processing helix chain 'B' and resid 79 through 94 Processing helix chain 'B' and resid 97 through 106 Processing helix chain 'B' and resid 149 through 154 removed outlier: 3.546A pdb=" N VAL B 154 " --> pdb=" O LEU B 150 " (cutoff:3.500A) Processing helix chain 'B' and resid 157 through 168 Processing helix chain 'B' and resid 204 through 218 removed outlier: 3.854A pdb=" N TYR B 217 " --> pdb=" O HIS B 213 " (cutoff:3.500A) Processing helix chain 'B' and resid 220 through 231 Processing helix chain 'B' and resid 267 through 271 removed outlier: 3.669A pdb=" N LEU B 271 " --> pdb=" O ALA B 268 " (cutoff:3.500A) Processing helix chain 'B' and resid 272 through 284 removed outlier: 3.502A pdb=" N LYS B 284 " --> pdb=" O LEU B 280 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 303 removed outlier: 3.889A pdb=" N THR B 303 " --> pdb=" O ASN B 299 " (cutoff:3.500A) Processing helix chain 'B' and resid 323 through 326 removed outlier: 3.549A pdb=" N ASP B 326 " --> pdb=" O ASP B 323 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 323 through 326' Processing helix chain 'B' and resid 346 through 350 removed outlier: 3.867A pdb=" N ARG B 349 " --> pdb=" O SER B 346 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N LEU B 350 " --> pdb=" O LYS B 347 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 346 through 350' Processing helix chain 'B' and resid 368 through 374 removed outlier: 3.544A pdb=" N LYS B 372 " --> pdb=" O PRO B 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 388 through 412 Processing helix chain 'B' and resid 422 through 424 No H-bonds generated for 'chain 'B' and resid 422 through 424' Processing helix chain 'B' and resid 433 through 448 Processing helix chain 'B' and resid 465 through 478 Processing helix chain 'B' and resid 487 through 492 Processing helix chain 'B' and resid 503 through 518 removed outlier: 3.694A pdb=" N LEU B 518 " --> pdb=" O ILE B 514 " (cutoff:3.500A) Processing helix chain 'B' and resid 579 through 594 Processing helix chain 'B' and resid 612 through 626 Processing helix chain 'B' and resid 693 through 704 removed outlier: 3.632A pdb=" N ILE B 697 " --> pdb=" O THR B 693 " (cutoff:3.500A) Processing helix chain 'B' and resid 718 through 733 removed outlier: 3.641A pdb=" N LYS B 733 " --> pdb=" O ARG B 729 " (cutoff:3.500A) Processing helix chain 'B' and resid 738 through 744 Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 6 removed outlier: 7.183A pdb=" N GLU A 316 " --> pdb=" O ARG A 652 " (cutoff:3.500A) removed outlier: 5.170A pdb=" N ARG A 652 " --> pdb=" O GLU A 316 " (cutoff:3.500A) removed outlier: 5.580A pdb=" N LEU A 676 " --> pdb=" O VAL A 636 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N VAL A 636 " --> pdb=" O LEU A 676 " (cutoff:3.500A) removed outlier: 5.451A pdb=" N GLU A 678 " --> pdb=" O ASN A 634 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N ASN A 634 " --> pdb=" O GLU A 678 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ARG A 607 " --> pdb=" O PHE A 633 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ILE A 635 " --> pdb=" O ARG A 607 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N TYR A 533 " --> pdb=" O LEU A 604 " (cutoff:3.500A) removed outlier: 7.754A pdb=" N LEU A 606 " --> pdb=" O TYR A 533 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N VAL A 535 " --> pdb=" O LEU A 606 " (cutoff:3.500A) removed outlier: 7.630A pdb=" N ASP A 608 " --> pdb=" O VAL A 535 " (cutoff:3.500A) removed outlier: 7.348A pdb=" N ILE A 537 " --> pdb=" O ASP A 608 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 3 through 6 removed outlier: 7.183A pdb=" N GLU A 316 " --> pdb=" O ARG A 652 " (cutoff:3.500A) removed outlier: 5.170A pdb=" N ARG A 652 " --> pdb=" O GLU A 316 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 9 through 11 Processing sheet with id=AA4, first strand: chain 'A' and resid 46 through 49 removed outlier: 5.411A pdb=" N VAL A 47 " --> pdb=" O ALA A 56 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N ALA A 56 " --> pdb=" O VAL A 47 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N ILE A 21 " --> pdb=" O GLU A 72 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N GLU A 72 " --> pdb=" O ILE A 21 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N LEU A 23 " --> pdb=" O GLU A 70 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 198 through 199 Processing sheet with id=AA6, first strand: chain 'A' and resid 198 through 199 Processing sheet with id=AA7, first strand: chain 'A' and resid 337 through 339 Processing sheet with id=AA8, first strand: chain 'A' and resid 418 through 420 removed outlier: 8.313A pdb=" N PHE A 427 " --> pdb=" O VAL A 379 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N ILE A 381 " --> pdb=" O PHE A 427 " (cutoff:3.500A) removed outlier: 7.270A pdb=" N ILE A 429 " --> pdb=" O ILE A 381 " (cutoff:3.500A) removed outlier: 5.664A pdb=" N VAL A 383 " --> pdb=" O ILE A 429 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 418 through 420 removed outlier: 6.570A pdb=" N GLY A 454 " --> pdb=" O ILE A 482 " (cutoff:3.500A) removed outlier: 8.190A pdb=" N GLN A 484 " --> pdb=" O GLY A 454 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N ALA A 456 " --> pdb=" O GLN A 484 " (cutoff:3.500A) removed outlier: 7.800A pdb=" N VAL A 486 " --> pdb=" O ALA A 456 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N ILE A 458 " --> pdb=" O VAL A 486 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 3 through 6 removed outlier: 7.184A pdb=" N GLU B 316 " --> pdb=" O ARG B 652 " (cutoff:3.500A) removed outlier: 5.170A pdb=" N ARG B 652 " --> pdb=" O GLU B 316 " (cutoff:3.500A) removed outlier: 5.580A pdb=" N LEU B 676 " --> pdb=" O VAL B 636 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N VAL B 636 " --> pdb=" O LEU B 676 " (cutoff:3.500A) removed outlier: 5.450A pdb=" N GLU B 678 " --> pdb=" O ASN B 634 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N ASN B 634 " --> pdb=" O GLU B 678 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ARG B 607 " --> pdb=" O PHE B 633 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ILE B 635 " --> pdb=" O ARG B 607 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N TYR B 533 " --> pdb=" O LEU B 604 " (cutoff:3.500A) removed outlier: 7.755A pdb=" N LEU B 606 " --> pdb=" O TYR B 533 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N VAL B 535 " --> pdb=" O LEU B 606 " (cutoff:3.500A) removed outlier: 7.629A pdb=" N ASP B 608 " --> pdb=" O VAL B 535 " (cutoff:3.500A) removed outlier: 7.347A pdb=" N ILE B 537 " --> pdb=" O ASP B 608 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 3 through 6 removed outlier: 7.184A pdb=" N GLU B 316 " --> pdb=" O ARG B 652 " (cutoff:3.500A) removed outlier: 5.170A pdb=" N ARG B 652 " --> pdb=" O GLU B 316 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 9 through 11 Processing sheet with id=AB4, first strand: chain 'B' and resid 46 through 49 removed outlier: 5.411A pdb=" N VAL B 47 " --> pdb=" O ALA B 56 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N ALA B 56 " --> pdb=" O VAL B 47 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N ILE B 21 " --> pdb=" O GLU B 72 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N GLU B 72 " --> pdb=" O ILE B 21 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N LEU B 23 " --> pdb=" O GLU B 70 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 198 through 199 Processing sheet with id=AB6, first strand: chain 'B' and resid 198 through 199 Processing sheet with id=AB7, first strand: chain 'B' and resid 337 through 339 Processing sheet with id=AB8, first strand: chain 'B' and resid 418 through 420 removed outlier: 8.313A pdb=" N PHE B 427 " --> pdb=" O VAL B 379 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N ILE B 381 " --> pdb=" O PHE B 427 " (cutoff:3.500A) removed outlier: 7.270A pdb=" N ILE B 429 " --> pdb=" O ILE B 381 " (cutoff:3.500A) removed outlier: 5.663A pdb=" N VAL B 383 " --> pdb=" O ILE B 429 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 418 through 420 removed outlier: 6.570A pdb=" N GLY B 454 " --> pdb=" O ILE B 482 " (cutoff:3.500A) removed outlier: 8.191A pdb=" N GLN B 484 " --> pdb=" O GLY B 454 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N ALA B 456 " --> pdb=" O GLN B 484 " (cutoff:3.500A) removed outlier: 7.800A pdb=" N VAL B 486 " --> pdb=" O ALA B 456 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N ILE B 458 " --> pdb=" O VAL B 486 " (cutoff:3.500A) 578 hydrogen bonds defined for protein. 1608 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 68 hydrogen bonds 136 hydrogen bond angles 0 basepair planarities 27 basepair parallelities 46 stacking parallelities Total time for adding SS restraints: 2.67 Time building geometry restraints manager: 1.30 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2292 1.32 - 1.44: 3816 1.44 - 1.57: 7788 1.57 - 1.69: 124 1.69 - 1.81: 52 Bond restraints: 14072 Sorted by residual: bond pdb=" C1' DC U 8 " pdb=" N1 DC U 8 " ideal model delta sigma weight residual 1.468 1.536 -0.068 1.40e-02 5.10e+03 2.32e+01 bond pdb=" C1' DC T 8 " pdb=" N1 DC T 8 " ideal model delta sigma weight residual 1.468 1.535 -0.067 1.40e-02 5.10e+03 2.30e+01 bond pdb=" C1' DT U 6 " pdb=" N1 DT U 6 " ideal model delta sigma weight residual 1.468 1.530 -0.062 1.40e-02 5.10e+03 1.97e+01 bond pdb=" C1' DT T 6 " pdb=" N1 DT T 6 " ideal model delta sigma weight residual 1.468 1.530 -0.062 1.40e-02 5.10e+03 1.97e+01 bond pdb=" CA HIS B 546 " pdb=" C HIS B 546 " ideal model delta sigma weight residual 1.526 1.484 0.042 1.11e-02 8.12e+03 1.43e+01 ... (remaining 14067 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.93: 18708 1.93 - 3.86: 515 3.86 - 5.79: 40 5.79 - 7.72: 13 7.72 - 9.65: 8 Bond angle restraints: 19284 Sorted by residual: angle pdb=" N ARG A 736 " pdb=" CA ARG A 736 " pdb=" C ARG A 736 " ideal model delta sigma weight residual 109.23 116.66 -7.43 1.55e+00 4.16e-01 2.30e+01 angle pdb=" N GLU B 739 " pdb=" CA GLU B 739 " pdb=" C GLU B 739 " ideal model delta sigma weight residual 111.14 116.28 -5.14 1.08e+00 8.57e-01 2.26e+01 angle pdb=" N3 DT T 6 " pdb=" C4 DT T 6 " pdb=" O4 DT T 6 " ideal model delta sigma weight residual 119.90 122.62 -2.72 6.00e-01 2.78e+00 2.05e+01 angle pdb=" N3 DT U 6 " pdb=" C4 DT U 6 " pdb=" O4 DT U 6 " ideal model delta sigma weight residual 119.90 122.59 -2.69 6.00e-01 2.78e+00 2.01e+01 angle pdb=" N GLU A 739 " pdb=" CA GLU A 739 " pdb=" C GLU A 739 " ideal model delta sigma weight residual 111.14 115.78 -4.64 1.08e+00 8.57e-01 1.85e+01 ... (remaining 19279 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.46: 7618 28.46 - 56.92: 703 56.92 - 85.38: 58 85.38 - 113.84: 5 113.84 - 142.30: 4 Dihedral angle restraints: 8388 sinusoidal: 3946 harmonic: 4442 Sorted by residual: dihedral pdb=" CA TYR B 561 " pdb=" C TYR B 561 " pdb=" N ILE B 562 " pdb=" CA ILE B 562 " ideal model delta harmonic sigma weight residual -180.00 -159.28 -20.72 0 5.00e+00 4.00e-02 1.72e+01 dihedral pdb=" CA TYR A 561 " pdb=" C TYR A 561 " pdb=" N ILE A 562 " pdb=" CA ILE A 562 " ideal model delta harmonic sigma weight residual -180.00 -159.30 -20.70 0 5.00e+00 4.00e-02 1.71e+01 dihedral pdb=" C4' DA T 2 " pdb=" C3' DA T 2 " pdb=" O3' DA T 2 " pdb=" P DA T 3 " ideal model delta sinusoidal sigma weight residual 220.00 77.70 142.30 1 3.50e+01 8.16e-04 1.40e+01 ... (remaining 8385 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 1589 0.049 - 0.097: 395 0.097 - 0.146: 177 0.146 - 0.194: 19 0.194 - 0.243: 2 Chirality restraints: 2182 Sorted by residual: chirality pdb=" CB VAL B 728 " pdb=" CA VAL B 728 " pdb=" CG1 VAL B 728 " pdb=" CG2 VAL B 728 " both_signs ideal model delta sigma weight residual False -2.63 -2.39 -0.24 2.00e-01 2.50e+01 1.47e+00 chirality pdb=" CB VAL A 728 " pdb=" CA VAL A 728 " pdb=" CG1 VAL A 728 " pdb=" CG2 VAL A 728 " both_signs ideal model delta sigma weight residual False -2.63 -2.39 -0.24 2.00e-01 2.50e+01 1.44e+00 chirality pdb=" P DA T 3 " pdb=" OP1 DA T 3 " pdb=" OP2 DA T 3 " pdb=" O5' DA T 3 " both_signs ideal model delta sigma weight residual True 2.34 -2.53 -0.19 2.00e-01 2.50e+01 9.42e-01 ... (remaining 2179 not shown) Planarity restraints: 2210 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS B 29 " 0.064 5.00e-02 4.00e+02 9.67e-02 1.50e+01 pdb=" N PRO B 30 " -0.167 5.00e-02 4.00e+02 pdb=" CA PRO B 30 " 0.051 5.00e-02 4.00e+02 pdb=" CD PRO B 30 " 0.052 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS A 29 " -0.064 5.00e-02 4.00e+02 9.65e-02 1.49e+01 pdb=" N PRO A 30 " 0.167 5.00e-02 4.00e+02 pdb=" CA PRO A 30 " -0.051 5.00e-02 4.00e+02 pdb=" CD PRO A 30 " -0.052 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLY A 734 " -0.016 2.00e-02 2.50e+03 3.14e-02 9.85e+00 pdb=" C GLY A 734 " 0.054 2.00e-02 2.50e+03 pdb=" O GLY A 734 " -0.020 2.00e-02 2.50e+03 pdb=" N TRP A 735 " -0.019 2.00e-02 2.50e+03 ... (remaining 2207 not shown) Histogram of nonbonded interaction distances: 1.85 - 2.46: 37 2.46 - 3.07: 7396 3.07 - 3.68: 19820 3.68 - 4.29: 31258 4.29 - 4.90: 51892 Nonbonded interactions: 110403 Sorted by model distance: nonbonded pdb=" ND1 HIS A 546 " pdb="ZN ZN A 801 " model vdw 1.852 2.310 nonbonded pdb=" ND1 HIS B 546 " pdb="ZN ZN A 801 " model vdw 1.870 2.310 nonbonded pdb=" O VAL B 750 " pdb="MG MG B 801 " model vdw 2.095 2.170 nonbonded pdb=" O VAL A 750 " pdb="MG MG A 802 " model vdw 2.095 2.170 nonbonded pdb=" OP1 DT U 6 " pdb="MG MG B 802 " model vdw 2.108 2.170 ... (remaining 110398 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 750 or resid 802 through 803)) selection = (chain 'B' and (resid 1 through 750 or resid 802 through 803)) } ncs_group { reference = chain 'G' selection = chain 'H' } ncs_group { reference = (chain 'T' and resid 0 through 15) selection = chain 'U' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.120 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: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 13.780 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8889 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 14072 Z= 0.340 Angle : 0.733 9.649 19284 Z= 0.494 Chirality : 0.051 0.243 2182 Planarity : 0.007 0.097 2210 Dihedral : 19.785 142.302 5516 Min Nonbonded Distance : 1.852 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 0.65 % Allowed : 24.64 % Favored : 74.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.91 (0.18), residues: 1496 helix: -1.83 (0.17), residues: 528 sheet: 0.31 (0.26), residues: 360 loop : -1.59 (0.21), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 563 TYR 0.015 0.001 TYR A 650 PHE 0.011 0.001 PHE A 164 TRP 0.013 0.001 TRP B 151 HIS 0.005 0.001 HIS A 639 Details of bonding type rmsd/Z covalent geometry : bond 0.00465 / 0.34 (14072) covalent geometry : angle 0.73259 / 0.49 (19284) hydrogen bonds : bond 0.14046 / 9.18 ( 604) hydrogen bonds : angle 5.52099 / 3.78 ( 1744) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2992 Ramachandran restraints generated. 1496 Oldfield, 0 Emsley, 1496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2992 Ramachandran restraints generated. 1496 Oldfield, 0 Emsley, 1496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 198 time to evaluate : 0.469 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: 0.5955 time to fit residues: 131.7610 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 : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ILE Chi-restraints excluded: chain A residue 543 LYS Chi-restraints excluded: chain B residue 17 ILE Chi-restraints excluded: chain B residue 543 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 0.5980 chunk 10 optimal weight: 8.9990 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 10.0000 chunk 122 optimal weight: 0.7980 chunk 91 optimal weight: 5.9990 chunk 149 optimal weight: 0.6980 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 99 HIS A 181 HIS B 99 HIS B 181 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.129752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.105455 restraints weight = 15879.564| |-----------------------------------------------------------------------------| r_work (start): 0.3087 rms_B_bonded: 1.62 r_work: 0.2946 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2813 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.2813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8859 moved from start: 0.1034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 14072 Z= 0.143 Angle : 0.523 6.149 19284 Z= 0.297 Chirality : 0.044 0.149 2182 Planarity : 0.005 0.064 2210 Dihedral : 16.032 151.424 2358 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 1.59 % Allowed : 25.22 % 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 are not related in a simple way. whole: -0.44 (0.20), residues: 1496 helix: 0.26 (0.21), residues: 538 sheet: 0.47 (0.25), residues: 390 loop : -1.31 (0.23), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 563 TYR 0.011 0.001 TYR A 282 PHE 0.015 0.001 PHE B 584 TRP 0.008 0.001 TRP A 735 HIS 0.007 0.001 HIS B 99 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.14 (14072) covalent geometry : angle 0.52284 / 0.30 (19284) hydrogen bonds : bond 0.04289 / 2.73 ( 604) hydrogen bonds : angle 4.00209 / 2.73 ( 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: 22 poor density : 161 time to evaluate : 0.480 Fit side-chains REVERT: A 29 LYS cc_start: 0.7446 (mptt) cc_final: 0.6989 (mttm) REVERT: A 99 HIS cc_start: 0.7367 (t-90) cc_final: 0.6824 (t-90) REVERT: A 103 ARG cc_start: 0.7377 (mtm180) cc_final: 0.6706 (mtt180) REVERT: A 373 LYS cc_start: 0.7405 (mttt) cc_final: 0.6708 (mptp) REVERT: A 448 MET cc_start: 0.7766 (OUTLIER) cc_final: 0.7410 (ttt) REVERT: A 499 GLU cc_start: 0.7180 (mp0) cc_final: 0.6828 (tp30) REVERT: B 99 HIS cc_start: 0.7339 (t-90) cc_final: 0.6762 (t-90) REVERT: B 103 ARG cc_start: 0.7392 (mtm180) cc_final: 0.6684 (mtt180) REVERT: B 373 LYS cc_start: 0.7405 (mttt) cc_final: 0.6711 (mptp) REVERT: B 448 MET cc_start: 0.7795 (OUTLIER) cc_final: 0.7452 (ttt) REVERT: B 543 LYS cc_start: 0.9078 (OUTLIER) cc_final: 0.8736 (ttmm) outliers start: 22 outliers final: 3 residues processed: 172 average time/residue: 0.5756 time to fit residues: 108.3201 Evaluate side-chains 158 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 152 time to evaluate : 0.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 448 MET Chi-restraints excluded: chain A residue 525 LEU Chi-restraints excluded: chain B residue 17 ILE Chi-restraints excluded: chain B residue 448 MET Chi-restraints excluded: chain B residue 525 LEU Chi-restraints excluded: chain B residue 543 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 146 optimal weight: 7.9990 chunk 119 optimal weight: 1.9990 chunk 75 optimal weight: 9.9990 chunk 8 optimal weight: 3.9990 chunk 101 optimal weight: 9.9990 chunk 91 optimal weight: 6.9990 chunk 7 optimal weight: 0.9990 chunk 71 optimal weight: 10.0000 chunk 56 optimal weight: 5.9990 chunk 51 optimal weight: 6.9990 chunk 21 optimal weight: 4.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 480 ASN B 335 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.122071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.097741 restraints weight = 16108.768| |-----------------------------------------------------------------------------| r_work (start): 0.2941 rms_B_bonded: 1.59 r_work: 0.2806 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.2673 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.2673 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8920 moved from start: 0.1843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.076 14072 Z= 0.241 Angle : 0.651 8.851 19284 Z= 0.351 Chirality : 0.049 0.183 2182 Planarity : 0.005 0.056 2210 Dihedral : 16.274 158.220 2352 Min Nonbonded Distance : 1.866 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 2.38 % Allowed : 25.00 % Favored : 72.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.02 (0.21), residues: 1496 helix: 0.95 (0.22), residues: 552 sheet: 0.59 (0.26), residues: 374 loop : -1.29 (0.24), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 738 TYR 0.014 0.002 TYR A 282 PHE 0.021 0.002 PHE B 584 TRP 0.004 0.001 TRP A 735 HIS 0.007 0.001 HIS B 722 Details of bonding type rmsd/Z covalent geometry : bond 0.00569 / 0.24 (14072) covalent geometry : angle 0.65117 / 0.35 (19284) hydrogen bonds : bond 0.05484 / 3.45 ( 604) hydrogen bonds : angle 3.96022 / 2.70 ( 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 188 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 155 time to evaluate : 0.477 Fit side-chains revert: symmetry clash REVERT: A 29 LYS cc_start: 0.7409 (mptt) cc_final: 0.6768 (mttp) REVERT: A 373 LYS cc_start: 0.7367 (mttt) cc_final: 0.6686 (mptp) REVERT: A 448 MET cc_start: 0.7886 (OUTLIER) cc_final: 0.7430 (ttt) REVERT: A 624 LYS cc_start: 0.8100 (tttp) cc_final: 0.7532 (ttpp) REVERT: A 702 LEU cc_start: 0.8638 (OUTLIER) cc_final: 0.8396 (mt) REVERT: B 29 LYS cc_start: 0.7475 (mptt) cc_final: 0.6843 (mttp) REVERT: B 103 ARG cc_start: 0.7360 (mtm180) cc_final: 0.7157 (mtt180) REVERT: B 373 LYS cc_start: 0.7372 (mttt) cc_final: 0.6699 (mptp) REVERT: B 448 MET cc_start: 0.7892 (OUTLIER) cc_final: 0.7488 (ttt) REVERT: B 495 ASP cc_start: 0.7210 (t0) cc_final: 0.6917 (t0) REVERT: B 499 GLU cc_start: 0.7590 (mm-30) cc_final: 0.6849 (mp0) REVERT: B 624 LYS cc_start: 0.8034 (tttp) cc_final: 0.7462 (ttpp) REVERT: B 702 LEU cc_start: 0.8638 (mm) cc_final: 0.8413 (mt) outliers start: 33 outliers final: 11 residues processed: 176 average time/residue: 0.6045 time to fit residues: 115.7512 Evaluate side-chains 167 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 153 time to evaluate : 0.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 448 MET Chi-restraints excluded: chain A residue 483 SER Chi-restraints excluded: chain A residue 511 LEU Chi-restraints excluded: chain A residue 525 LEU Chi-restraints excluded: chain A residue 662 HIS Chi-restraints excluded: chain A residue 688 THR Chi-restraints excluded: chain A residue 702 LEU Chi-restraints excluded: chain B residue 448 MET Chi-restraints excluded: chain B residue 483 SER Chi-restraints excluded: chain B residue 511 LEU Chi-restraints excluded: chain B residue 525 LEU Chi-restraints excluded: chain B residue 662 HIS Chi-restraints excluded: chain B residue 688 THR Chi-restraints excluded: chain B residue 740 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 15 optimal weight: 0.9980 chunk 6 optimal weight: 8.9990 chunk 109 optimal weight: 7.9990 chunk 149 optimal weight: 1.9990 chunk 24 optimal weight: 3.9990 chunk 96 optimal weight: 0.9990 chunk 141 optimal weight: 3.9990 chunk 88 optimal weight: 2.9990 chunk 42 optimal weight: 0.6980 chunk 60 optimal weight: 3.9990 chunk 43 optimal weight: 0.9980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 573 GLN B 335 ASN B 573 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.124191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.099692 restraints weight = 15946.726| |-----------------------------------------------------------------------------| r_work (start): 0.2992 rms_B_bonded: 1.57 r_work: 0.2849 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2717 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.2717 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8924 moved from start: 0.1793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 14072 Z= 0.124 Angle : 0.502 8.427 19284 Z= 0.287 Chirality : 0.044 0.191 2182 Planarity : 0.004 0.049 2210 Dihedral : 16.283 159.756 2346 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 1.88 % Allowed : 26.08 % Favored : 72.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.44 (0.22), residues: 1496 helix: 1.43 (0.23), residues: 552 sheet: 0.61 (0.26), residues: 380 loop : -1.05 (0.25), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 145 TYR 0.010 0.001 TYR A 650 PHE 0.010 0.001 PHE A 227 TRP 0.006 0.001 TRP A 413 HIS 0.003 0.001 HIS A 722 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.12 (14072) covalent geometry : angle 0.50222 / 0.29 (19284) hydrogen bonds : bond 0.03895 / 2.48 ( 604) hydrogen bonds : angle 3.76485 / 2.55 ( 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 187 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 161 time to evaluate : 0.498 Fit side-chains REVERT: A 29 LYS cc_start: 0.7572 (mptt) cc_final: 0.6999 (mttm) REVERT: A 180 GLU cc_start: 0.8239 (tt0) cc_final: 0.7971 (tt0) REVERT: A 373 LYS cc_start: 0.7363 (mttt) cc_final: 0.6799 (mptp) REVERT: A 448 MET cc_start: 0.7899 (OUTLIER) cc_final: 0.7534 (ttt) REVERT: A 624 LYS cc_start: 0.7963 (tttp) cc_final: 0.7413 (ttpp) REVERT: A 702 LEU cc_start: 0.8724 (mm) cc_final: 0.8512 (mt) REVERT: B 29 LYS cc_start: 0.7518 (mptt) cc_final: 0.6975 (mttm) REVERT: B 373 LYS cc_start: 0.7378 (mttt) cc_final: 0.6809 (mptp) REVERT: B 448 MET cc_start: 0.7879 (OUTLIER) cc_final: 0.7488 (ttt) REVERT: B 499 GLU cc_start: 0.7608 (mm-30) cc_final: 0.6927 (mp0) REVERT: B 702 LEU cc_start: 0.8730 (OUTLIER) cc_final: 0.8495 (mt) outliers start: 26 outliers final: 7 residues processed: 176 average time/residue: 0.5628 time to fit residues: 108.0890 Evaluate side-chains 168 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 158 time to evaluate : 0.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 448 MET Chi-restraints excluded: chain A residue 525 LEU Chi-restraints excluded: chain A residue 566 ILE Chi-restraints excluded: chain A residue 593 LYS Chi-restraints excluded: chain B residue 16 ILE 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: 0.9980 chunk 35 optimal weight: 8.9990 chunk 88 optimal weight: 0.4980 chunk 150 optimal weight: 3.9990 chunk 135 optimal weight: 5.9990 chunk 16 optimal weight: 4.9990 chunk 123 optimal weight: 3.9990 chunk 120 optimal weight: 0.0470 chunk 26 optimal weight: 6.9990 chunk 110 optimal weight: 8.9990 chunk 108 optimal weight: 0.3980 overall best weight: 1.1880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.124816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.100334 restraints weight = 16047.557| |-----------------------------------------------------------------------------| r_work (start): 0.3028 rms_B_bonded: 1.58 r_work: 0.2888 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2754 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.2754 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8885 moved from start: 0.1841 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= 0.124 Angle : 0.490 8.229 19284 Z= 0.279 Chirality : 0.044 0.199 2182 Planarity : 0.004 0.045 2210 Dihedral : 16.154 159.527 2346 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 1.81 % Allowed : 25.65 % Favored : 72.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.67 (0.22), residues: 1496 helix: 1.67 (0.23), residues: 552 sheet: 0.64 (0.26), residues: 386 loop : -0.94 (0.25), residues: 558 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 0.000 TRP A 413 HIS 0.003 0.001 HIS A 722 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.12 (14072) covalent geometry : angle 0.49039 / 0.28 (19284) hydrogen bonds : bond 0.03684 / 2.34 ( 604) hydrogen bonds : angle 3.63986 / 2.45 ( 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 191 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 166 time to evaluate : 0.506 Fit side-chains REVERT: A 29 LYS cc_start: 0.7573 (mptt) cc_final: 0.6984 (mttm) REVERT: A 180 GLU cc_start: 0.8242 (tt0) cc_final: 0.7945 (tt0) REVERT: A 373 LYS cc_start: 0.7261 (mttt) cc_final: 0.6681 (mptp) REVERT: A 448 MET cc_start: 0.7862 (OUTLIER) cc_final: 0.7438 (ttt) REVERT: A 702 LEU cc_start: 0.8679 (mm) cc_final: 0.8458 (mt) REVERT: B 29 LYS cc_start: 0.7535 (mptt) cc_final: 0.6951 (mttm) REVERT: B 180 GLU cc_start: 0.8217 (tt0) cc_final: 0.7929 (tt0) REVERT: B 225 LYS cc_start: 0.8137 (mmmt) cc_final: 0.7660 (mmtt) REVERT: B 373 LYS cc_start: 0.7288 (mttt) cc_final: 0.6710 (mptp) REVERT: B 448 MET cc_start: 0.7862 (OUTLIER) cc_final: 0.7474 (ttt) REVERT: B 499 GLU cc_start: 0.7611 (mm-30) cc_final: 0.6942 (mp0) REVERT: B 702 LEU cc_start: 0.8692 (OUTLIER) cc_final: 0.8457 (mt) outliers start: 25 outliers final: 11 residues processed: 179 average time/residue: 0.5507 time to fit residues: 108.0072 Evaluate side-chains 171 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 157 time to evaluate : 0.423 ------------------------------------------------------------------------------- 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 587 MET Chi-restraints excluded: chain A residue 593 LYS Chi-restraints excluded: chain A residue 714 ASP Chi-restraints excluded: chain B residue 16 ILE 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 587 MET Chi-restraints excluded: chain B residue 593 LYS Chi-restraints excluded: chain B residue 702 LEU Chi-restraints excluded: chain B residue 714 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 126 optimal weight: 7.9990 chunk 134 optimal weight: 0.0470 chunk 87 optimal weight: 6.9990 chunk 51 optimal weight: 6.9990 chunk 119 optimal weight: 5.9990 chunk 73 optimal weight: 6.9990 chunk 141 optimal weight: 5.9990 chunk 17 optimal weight: 8.9990 chunk 54 optimal weight: 0.8980 chunk 69 optimal weight: 8.9990 chunk 39 optimal weight: 9.9990 overall best weight: 3.9884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.119812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.095506 restraints weight = 16029.882| |-----------------------------------------------------------------------------| r_work (start): 0.2921 rms_B_bonded: 1.57 r_work: 0.2786 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.2654 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.2654 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8944 moved from start: 0.2180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.080 14072 Z= 0.260 Angle : 0.642 10.259 19284 Z= 0.343 Chirality : 0.050 0.280 2182 Planarity : 0.005 0.043 2210 Dihedral : 16.333 163.362 2346 Min Nonbonded Distance : 1.858 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 3.32 % Allowed : 23.70 % Favored : 72.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.41 (0.22), residues: 1496 helix: 1.51 (0.23), residues: 548 sheet: 0.53 (0.26), residues: 378 loop : -1.12 (0.25), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 145 TYR 0.013 0.002 TYR A 548 PHE 0.013 0.002 PHE A 67 TRP 0.005 0.001 TRP A 735 HIS 0.007 0.001 HIS A 722 Details of bonding type rmsd/Z covalent geometry : bond 0.00626 / 0.26 (14072) covalent geometry : angle 0.64166 / 0.34 (19284) hydrogen bonds : bond 0.05365 / 3.38 ( 604) hydrogen bonds : angle 3.88139 / 2.63 ( 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 206 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 160 time to evaluate : 0.636 Fit side-chains REVERT: A 29 LYS cc_start: 0.7436 (mptt) cc_final: 0.6781 (mttp) REVERT: A 99 HIS cc_start: 0.7804 (t-90) cc_final: 0.7573 (t-90) REVERT: A 180 GLU cc_start: 0.8237 (tt0) cc_final: 0.7958 (tt0) REVERT: A 225 LYS cc_start: 0.8298 (mmmt) cc_final: 0.7379 (ttpp) REVERT: A 373 LYS cc_start: 0.7245 (mttt) cc_final: 0.6693 (mptp) REVERT: A 375 GLU cc_start: 0.7956 (OUTLIER) cc_final: 0.7644 (tp30) REVERT: A 448 MET cc_start: 0.7990 (OUTLIER) cc_final: 0.7534 (ttt) REVERT: A 482 ILE cc_start: 0.8735 (OUTLIER) cc_final: 0.8136 (mm) REVERT: A 499 GLU cc_start: 0.7205 (OUTLIER) cc_final: 0.6982 (mp0) REVERT: A 624 LYS cc_start: 0.8003 (tttp) cc_final: 0.7471 (ttpp) REVERT: A 702 LEU cc_start: 0.8611 (OUTLIER) cc_final: 0.8354 (mt) REVERT: A 740 GLU cc_start: 0.8042 (OUTLIER) cc_final: 0.7789 (pm20) REVERT: B 29 LYS cc_start: 0.7445 (mptt) cc_final: 0.6783 (mttp) REVERT: B 99 HIS cc_start: 0.7843 (t-90) cc_final: 0.7476 (t-90) REVERT: B 202 ASN cc_start: 0.8161 (m-40) cc_final: 0.7851 (m-40) REVERT: B 373 LYS cc_start: 0.7241 (mttt) cc_final: 0.6688 (mptp) REVERT: B 448 MET cc_start: 0.8011 (OUTLIER) cc_final: 0.7558 (ttt) REVERT: B 482 ILE cc_start: 0.8739 (OUTLIER) cc_final: 0.8145 (mm) REVERT: B 499 GLU cc_start: 0.7569 (mm-30) cc_final: 0.6906 (mp0) REVERT: B 624 LYS cc_start: 0.7988 (tttp) cc_final: 0.7457 (ttpp) REVERT: B 702 LEU cc_start: 0.8603 (OUTLIER) cc_final: 0.8338 (mt) outliers start: 46 outliers final: 14 residues processed: 188 average time/residue: 0.6321 time to fit residues: 129.5519 Evaluate side-chains 176 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 153 time to evaluate : 0.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 MET Chi-restraints excluded: chain A residue 19 ASN Chi-restraints excluded: chain A residue 122 GLU Chi-restraints excluded: chain A residue 375 GLU Chi-restraints excluded: chain A residue 448 MET Chi-restraints excluded: chain A residue 482 ILE Chi-restraints excluded: chain A residue 499 GLU Chi-restraints excluded: chain A residue 511 LEU Chi-restraints excluded: chain A residue 587 MET Chi-restraints excluded: chain A residue 593 LYS Chi-restraints excluded: chain A residue 702 LEU Chi-restraints excluded: chain A residue 714 ASP Chi-restraints excluded: chain A residue 740 GLU Chi-restraints excluded: chain B residue 3 MET Chi-restraints excluded: chain B residue 19 ASN Chi-restraints excluded: chain B residue 122 GLU Chi-restraints excluded: chain B residue 448 MET Chi-restraints excluded: chain B residue 482 ILE Chi-restraints excluded: chain B residue 511 LEU Chi-restraints excluded: chain B residue 525 LEU Chi-restraints excluded: chain B residue 593 LYS Chi-restraints excluded: chain B residue 702 LEU Chi-restraints excluded: chain B residue 714 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 86 optimal weight: 0.9990 chunk 137 optimal weight: 2.9990 chunk 82 optimal weight: 0.8980 chunk 73 optimal weight: 0.9980 chunk 18 optimal weight: 0.5980 chunk 6 optimal weight: 8.9990 chunk 23 optimal weight: 1.9990 chunk 61 optimal weight: 0.9990 chunk 114 optimal weight: 2.9990 chunk 105 optimal weight: 5.9990 chunk 63 optimal weight: 0.9980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 480 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.124478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.100082 restraints weight = 15869.458| |-----------------------------------------------------------------------------| r_work (start): 0.2998 rms_B_bonded: 1.57 r_work: 0.2857 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2725 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.2725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8888 moved from start: 0.2082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 14072 Z= 0.119 Angle : 0.489 8.756 19284 Z= 0.281 Chirality : 0.044 0.271 2182 Planarity : 0.004 0.044 2210 Dihedral : 16.339 165.935 2346 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 2.17 % Allowed : 25.07 % Favored : 72.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.78 (0.22), residues: 1496 helix: 1.85 (0.23), residues: 548 sheet: 0.71 (0.26), residues: 380 loop : -0.95 (0.25), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 145 TYR 0.011 0.001 TYR A 650 PHE 0.012 0.001 PHE B 227 TRP 0.006 0.001 TRP A 413 HIS 0.002 0.001 HIS B 722 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.12 (14072) covalent geometry : angle 0.48926 / 0.28 (19284) hydrogen bonds : bond 0.03655 / 2.34 ( 604) hydrogen bonds : angle 3.65354 / 2.46 ( 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 197 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 167 time to evaluate : 0.366 Fit side-chains REVERT: A 29 LYS cc_start: 0.7486 (mptt) cc_final: 0.6824 (mttp) REVERT: A 180 GLU cc_start: 0.8222 (tt0) cc_final: 0.7954 (tt0) REVERT: A 202 ASN cc_start: 0.8180 (m-40) cc_final: 0.7858 (m-40) REVERT: A 225 LYS cc_start: 0.8240 (mmmt) cc_final: 0.7392 (ttpp) REVERT: A 337 LYS cc_start: 0.7742 (mttp) cc_final: 0.7400 (mttt) REVERT: A 373 LYS cc_start: 0.7178 (mttt) cc_final: 0.6597 (mptp) REVERT: A 448 MET cc_start: 0.7838 (OUTLIER) cc_final: 0.7428 (ttt) REVERT: A 482 ILE cc_start: 0.8728 (OUTLIER) cc_final: 0.8074 (mm) REVERT: A 702 LEU cc_start: 0.8650 (OUTLIER) cc_final: 0.8436 (mt) REVERT: B 29 LYS cc_start: 0.7449 (mptt) cc_final: 0.6809 (mttp) REVERT: B 42 ARG cc_start: 0.7940 (mtt-85) cc_final: 0.7716 (mtp85) REVERT: B 202 ASN cc_start: 0.8166 (m-40) cc_final: 0.7851 (m-40) REVERT: B 225 LYS cc_start: 0.8135 (mmmt) cc_final: 0.7675 (mmtt) REVERT: B 373 LYS cc_start: 0.7169 (mttt) cc_final: 0.6587 (mptp) REVERT: B 448 MET cc_start: 0.7828 (OUTLIER) cc_final: 0.7432 (ttt) REVERT: B 482 ILE cc_start: 0.8737 (OUTLIER) cc_final: 0.8091 (mm) REVERT: B 499 GLU cc_start: 0.7542 (mm-30) cc_final: 0.6917 (mp0) REVERT: B 702 LEU cc_start: 0.8685 (OUTLIER) cc_final: 0.8461 (mt) outliers start: 30 outliers final: 11 residues processed: 190 average time/residue: 0.5981 time to fit residues: 124.5081 Evaluate side-chains 175 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 158 time to evaluate : 0.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 482 ILE 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 122 GLU Chi-restraints excluded: chain B residue 234 VAL Chi-restraints excluded: chain B residue 448 MET Chi-restraints excluded: chain B residue 482 ILE Chi-restraints excluded: chain B residue 566 ILE Chi-restraints excluded: chain B residue 593 LYS Chi-restraints excluded: chain B residue 702 LEU Chi-restraints excluded: chain B residue 714 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 16 optimal weight: 0.8980 chunk 136 optimal weight: 3.9990 chunk 111 optimal weight: 2.9990 chunk 56 optimal weight: 0.0060 chunk 153 optimal weight: 10.0000 chunk 117 optimal weight: 10.0000 chunk 107 optimal weight: 0.9990 chunk 115 optimal weight: 0.5980 chunk 30 optimal weight: 0.7980 chunk 78 optimal weight: 5.9990 chunk 95 optimal weight: 6.9990 overall best weight: 0.6598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.125271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.101271 restraints weight = 15843.053| |-----------------------------------------------------------------------------| r_work (start): 0.3039 rms_B_bonded: 1.53 r_work: 0.2904 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2773 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.2773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8894 moved from start: 0.2065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 14072 Z= 0.109 Angle : 0.473 8.503 19284 Z= 0.271 Chirality : 0.043 0.258 2182 Planarity : 0.004 0.045 2210 Dihedral : 16.111 164.213 2346 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 2.17 % Allowed : 24.78 % Favored : 73.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.98 (0.22), residues: 1496 helix: 2.01 (0.23), residues: 550 sheet: 0.79 (0.26), residues: 380 loop : -0.83 (0.25), residues: 566 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 145 TYR 0.010 0.001 TYR B 650 PHE 0.011 0.001 PHE B 227 TRP 0.004 0.000 TRP A 413 HIS 0.003 0.001 HIS B 722 Details of bonding type rmsd/Z covalent geometry : bond 0.00216 / 0.11 (14072) covalent geometry : angle 0.47333 / 0.27 (19284) hydrogen bonds : bond 0.03354 / 2.14 ( 604) hydrogen bonds : angle 3.52737 / 2.37 ( 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 194 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 164 time to evaluate : 0.525 Fit side-chains REVERT: A 29 LYS cc_start: 0.7483 (mptt) cc_final: 0.6946 (mttm) REVERT: A 202 ASN cc_start: 0.8190 (m-40) cc_final: 0.7880 (m-40) REVERT: A 225 LYS cc_start: 0.8243 (mmmt) cc_final: 0.7390 (ttpp) REVERT: A 337 LYS cc_start: 0.7780 (mttp) cc_final: 0.7432 (mttt) REVERT: A 373 LYS cc_start: 0.7102 (mttt) cc_final: 0.6606 (mptp) REVERT: A 448 MET cc_start: 0.7889 (OUTLIER) cc_final: 0.7460 (ttt) REVERT: A 482 ILE cc_start: 0.8752 (OUTLIER) cc_final: 0.8080 (mm) REVERT: A 702 LEU cc_start: 0.8688 (OUTLIER) cc_final: 0.8472 (mt) REVERT: B 19 ASN cc_start: 0.7181 (OUTLIER) cc_final: 0.6970 (p0) REVERT: B 29 LYS cc_start: 0.7473 (mptt) cc_final: 0.6825 (mttp) REVERT: B 42 ARG cc_start: 0.7911 (mtt-85) cc_final: 0.7703 (mpp80) REVERT: B 202 ASN cc_start: 0.8181 (m-40) cc_final: 0.7872 (m-40) REVERT: B 225 LYS cc_start: 0.8129 (mmmt) cc_final: 0.7344 (ttpp) REVERT: B 373 LYS cc_start: 0.7102 (mttt) cc_final: 0.6597 (mptp) REVERT: B 448 MET cc_start: 0.7893 (OUTLIER) cc_final: 0.7478 (ttt) REVERT: B 482 ILE cc_start: 0.8761 (OUTLIER) cc_final: 0.8088 (mm) REVERT: B 499 GLU cc_start: 0.7553 (mm-30) cc_final: 0.6950 (mp0) REVERT: B 702 LEU cc_start: 0.8700 (OUTLIER) cc_final: 0.8473 (mt) outliers start: 30 outliers final: 8 residues processed: 183 average time/residue: 0.5855 time to fit residues: 117.7122 Evaluate side-chains 176 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 161 time to evaluate : 0.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 MET Chi-restraints excluded: chain A residue 122 GLU Chi-restraints excluded: chain A residue 448 MET Chi-restraints excluded: chain A residue 482 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 32 ASP Chi-restraints excluded: chain B residue 122 GLU Chi-restraints excluded: chain B residue 234 VAL Chi-restraints excluded: chain B residue 448 MET Chi-restraints excluded: chain B residue 482 ILE Chi-restraints excluded: chain B residue 702 LEU Chi-restraints excluded: chain B residue 714 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 6 optimal weight: 10.0000 chunk 60 optimal weight: 5.9990 chunk 57 optimal weight: 5.9990 chunk 117 optimal weight: 8.9990 chunk 149 optimal weight: 5.9990 chunk 136 optimal weight: 1.9990 chunk 36 optimal weight: 0.3980 chunk 142 optimal weight: 5.9990 chunk 33 optimal weight: 0.9980 chunk 11 optimal weight: 3.9990 chunk 108 optimal weight: 5.9990 overall best weight: 2.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.121502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.097335 restraints weight = 16016.432| |-----------------------------------------------------------------------------| r_work (start): 0.2967 rms_B_bonded: 1.55 r_work: 0.2838 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.2707 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.2707 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8940 moved from start: 0.2228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 14072 Z= 0.193 Angle : 0.564 9.732 19284 Z= 0.308 Chirality : 0.047 0.309 2182 Planarity : 0.004 0.044 2210 Dihedral : 16.175 165.980 2346 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 1.88 % Allowed : 25.43 % Favored : 72.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.80 (0.22), residues: 1496 helix: 1.86 (0.23), residues: 550 sheet: 0.78 (0.26), residues: 376 loop : -0.98 (0.25), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 145 TYR 0.011 0.001 TYR A 548 PHE 0.010 0.001 PHE A 67 TRP 0.005 0.001 TRP A 735 HIS 0.005 0.001 HIS B 722 Details of bonding type rmsd/Z covalent geometry : bond 0.00456 / 0.19 (14072) covalent geometry : angle 0.56442 / 0.31 (19284) hydrogen bonds : bond 0.04492 / 2.85 ( 604) hydrogen bonds : angle 3.67776 / 2.48 ( 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 187 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 161 time to evaluate : 0.554 Fit side-chains REVERT: A 29 LYS cc_start: 0.7453 (mptt) cc_final: 0.6873 (mttm) REVERT: A 99 HIS cc_start: 0.7818 (t-90) cc_final: 0.7433 (t-90) REVERT: A 202 ASN cc_start: 0.8172 (m-40) cc_final: 0.7853 (m-40) REVERT: A 225 LYS cc_start: 0.8211 (mmmt) cc_final: 0.7333 (ttpp) REVERT: A 337 LYS cc_start: 0.7796 (mttp) cc_final: 0.7441 (mttt) REVERT: A 373 LYS cc_start: 0.7135 (mttt) cc_final: 0.6607 (mptp) REVERT: A 448 MET cc_start: 0.7975 (OUTLIER) cc_final: 0.7538 (ttt) REVERT: A 482 ILE cc_start: 0.8762 (OUTLIER) cc_final: 0.8121 (mm) REVERT: A 702 LEU cc_start: 0.8656 (OUTLIER) cc_final: 0.8417 (mt) REVERT: B 29 LYS cc_start: 0.7481 (mptt) cc_final: 0.6900 (mttm) REVERT: B 42 ARG cc_start: 0.8013 (mtt-85) cc_final: 0.7810 (mtp85) REVERT: B 99 HIS cc_start: 0.7842 (t-90) cc_final: 0.7420 (t-90) REVERT: B 202 ASN cc_start: 0.8160 (m-40) cc_final: 0.7845 (m-40) REVERT: B 225 LYS cc_start: 0.8175 (mmmt) cc_final: 0.7289 (ttpp) REVERT: B 373 LYS cc_start: 0.7147 (mttt) cc_final: 0.6611 (mptp) REVERT: B 448 MET cc_start: 0.7991 (OUTLIER) cc_final: 0.7544 (ttt) REVERT: B 482 ILE cc_start: 0.8784 (OUTLIER) cc_final: 0.8140 (mm) REVERT: B 499 GLU cc_start: 0.7507 (mm-30) cc_final: 0.6915 (mp0) REVERT: B 624 LYS cc_start: 0.8005 (tttp) cc_final: 0.7461 (ttpp) REVERT: B 702 LEU cc_start: 0.8643 (OUTLIER) cc_final: 0.8379 (mt) REVERT: B 738 ARG cc_start: 0.7794 (mtm110) cc_final: 0.7569 (mmm-85) outliers start: 26 outliers final: 12 residues processed: 178 average time/residue: 0.6662 time to fit residues: 129.3084 Evaluate side-chains 176 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 158 time to evaluate : 0.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 MET 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 572 GLU Chi-restraints excluded: chain A residue 593 LYS Chi-restraints excluded: chain A residue 702 LEU Chi-restraints excluded: chain A residue 714 ASP Chi-restraints excluded: chain B residue 3 MET Chi-restraints excluded: chain B residue 32 ASP Chi-restraints excluded: chain B residue 122 GLU Chi-restraints excluded: chain B residue 234 VAL Chi-restraints excluded: chain B residue 410 LEU Chi-restraints excluded: chain B residue 448 MET Chi-restraints excluded: chain B residue 482 ILE Chi-restraints excluded: chain B residue 702 LEU Chi-restraints excluded: chain B residue 714 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 35 optimal weight: 8.9990 chunk 89 optimal weight: 7.9990 chunk 14 optimal weight: 1.9990 chunk 86 optimal weight: 0.8980 chunk 118 optimal weight: 3.9990 chunk 152 optimal weight: 9.9990 chunk 16 optimal weight: 1.9990 chunk 90 optimal weight: 2.9990 chunk 109 optimal weight: 10.0000 chunk 110 optimal weight: 0.9990 chunk 84 optimal weight: 9.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.122017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.097714 restraints weight = 15938.736| |-----------------------------------------------------------------------------| r_work (start): 0.3000 rms_B_bonded: 1.67 r_work: 0.2865 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2731 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.2731 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8914 moved from start: 0.2224 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= 0.149 Angle : 0.521 9.269 19284 Z= 0.292 Chirality : 0.045 0.307 2182 Planarity : 0.004 0.044 2210 Dihedral : 16.138 167.272 2346 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 1.37 % Allowed : 25.87 % Favored : 72.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.84 (0.22), residues: 1496 helix: 1.89 (0.23), residues: 550 sheet: 0.79 (0.26), residues: 376 loop : -0.94 (0.25), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 145 TYR 0.009 0.001 TYR B 723 PHE 0.011 0.001 PHE B 227 TRP 0.003 0.001 TRP A 413 HIS 0.004 0.001 HIS A 722 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.15 (14072) covalent geometry : angle 0.52122 / 0.29 (19284) hydrogen bonds : bond 0.04041 / 2.57 ( 604) hydrogen bonds : angle 3.64143 / 2.46 ( 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 187 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 168 time to evaluate : 0.368 Fit side-chains REVERT: A 29 LYS cc_start: 0.7456 (mptt) cc_final: 0.6714 (mttp) REVERT: A 99 HIS cc_start: 0.7769 (t-90) cc_final: 0.7356 (t-90) REVERT: A 202 ASN cc_start: 0.8169 (m-40) cc_final: 0.7848 (m-40) REVERT: A 225 LYS cc_start: 0.8167 (mmmt) cc_final: 0.7291 (ttpp) REVERT: A 337 LYS cc_start: 0.7781 (mttp) cc_final: 0.7426 (mttt) REVERT: A 373 LYS cc_start: 0.7110 (mttt) cc_final: 0.6586 (mptp) REVERT: A 448 MET cc_start: 0.7931 (OUTLIER) cc_final: 0.7472 (ttt) REVERT: A 482 ILE cc_start: 0.8741 (OUTLIER) cc_final: 0.8089 (mm) REVERT: A 624 LYS cc_start: 0.7975 (tttp) cc_final: 0.7418 (ttpp) REVERT: A 702 LEU cc_start: 0.8668 (OUTLIER) cc_final: 0.8446 (mt) REVERT: B 29 LYS cc_start: 0.7469 (mptt) cc_final: 0.6735 (mttp) REVERT: B 42 ARG cc_start: 0.7948 (mtt-85) cc_final: 0.7488 (ttp80) REVERT: B 99 HIS cc_start: 0.7825 (t-90) cc_final: 0.7365 (t-90) REVERT: B 202 ASN cc_start: 0.8185 (m-40) cc_final: 0.7869 (m-40) REVERT: B 225 LYS cc_start: 0.8154 (mmmt) cc_final: 0.7283 (ttpp) REVERT: B 373 LYS cc_start: 0.7122 (mttt) cc_final: 0.6589 (mptp) REVERT: B 448 MET cc_start: 0.7937 (OUTLIER) cc_final: 0.7475 (ttt) REVERT: B 482 ILE cc_start: 0.8759 (OUTLIER) cc_final: 0.8106 (mm) REVERT: B 499 GLU cc_start: 0.7508 (mm-30) cc_final: 0.6867 (mp0) REVERT: B 624 LYS cc_start: 0.7948 (tttp) cc_final: 0.7385 (ttpp) REVERT: B 738 ARG cc_start: 0.7746 (mtm110) cc_final: 0.7512 (mmm-85) outliers start: 19 outliers final: 13 residues processed: 180 average time/residue: 0.6203 time to fit residues: 122.2803 Evaluate side-chains 186 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 168 time to evaluate : 0.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 MET 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 593 LYS Chi-restraints excluded: chain A residue 702 LEU Chi-restraints excluded: chain A residue 714 ASP Chi-restraints excluded: chain B residue 3 MET Chi-restraints excluded: chain B residue 32 ASP Chi-restraints excluded: chain B residue 122 GLU Chi-restraints excluded: chain B residue 234 VAL Chi-restraints excluded: chain B residue 410 LEU Chi-restraints excluded: chain B residue 448 MET Chi-restraints excluded: chain B residue 482 ILE Chi-restraints excluded: chain B residue 511 LEU Chi-restraints excluded: chain B residue 525 LEU Chi-restraints excluded: chain B residue 714 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 39 optimal weight: 10.0000 chunk 90 optimal weight: 4.9990 chunk 95 optimal weight: 3.9990 chunk 56 optimal weight: 3.9990 chunk 58 optimal weight: 0.7980 chunk 18 optimal weight: 0.7980 chunk 112 optimal weight: 9.9990 chunk 67 optimal weight: 3.9990 chunk 142 optimal weight: 5.9990 chunk 37 optimal weight: 0.9990 chunk 140 optimal weight: 5.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.122161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.098261 restraints weight = 16070.700| |-----------------------------------------------------------------------------| r_work (start): 0.2957 rms_B_bonded: 1.72 r_work: 0.2812 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2679 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.2679 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8956 moved from start: 0.2253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 14072 Z= 0.165 Angle : 0.536 9.399 19284 Z= 0.297 Chirality : 0.046 0.311 2182 Planarity : 0.004 0.044 2210 Dihedral : 16.127 167.191 2346 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 1.59 % Allowed : 25.43 % Favored : 72.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.81 (0.22), residues: 1496 helix: 1.86 (0.23), residues: 550 sheet: 0.78 (0.26), residues: 376 loop : -0.96 (0.25), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 526 TYR 0.010 0.001 TYR B 723 PHE 0.010 0.001 PHE B 227 TRP 0.003 0.001 TRP A 735 HIS 0.005 0.001 HIS A 722 Details of bonding type rmsd/Z covalent geometry : bond 0.00377 / 0.16 (14072) covalent geometry : angle 0.53556 / 0.30 (19284) hydrogen bonds : bond 0.04191 / 2.66 ( 604) hydrogen bonds : angle 3.65359 / 2.46 ( 1744) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3868.01 seconds wall clock time: 66 minutes 48.26 seconds (4008.26 seconds total)