Starting phenix.real_space_refine on Thu May 15 18:14:21 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wd8_37457/05_2025/8wd8_37457.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wd8_37457/05_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_37457/05_2025/8wd8_37457.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wd8_37457/05_2025/8wd8_37457.map" model { file = "/net/cci-nas-00/data/ceres_data/8wd8_37457/05_2025/8wd8_37457.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wd8_37457/05_2025/8wd8_37457.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 8.49, per 1000 atoms: 0.62 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: 3.01 Conformation dependent library (CDL) restraints added in 1.5 seconds 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: 4.81 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: 5.64 Time building geometry restraints manager: 3.59 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.820 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: 0.460 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 36.010 Find NCS groups from input model: 0.570 Set up NCS constraints: 0.060 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:13.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.360 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.013 0.001 TRP B 151 HIS 0.005 0.001 HIS A 639 PHE 0.011 0.001 PHE A 164 TYR 0.015 0.001 TYR A 650 ARG 0.010 0.001 ARG A 563 Details of bonding type rmsd hydrogen bonds : bond 0.14046 ( 604) hydrogen bonds : angle 5.52099 ( 1744) covalent geometry : bond 0.00402 (14072) covalent geometry : angle 0.70309 (19284) *********************** 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 : 1.576 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: 1.2910 time to fit residues: 285.9165 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 : 1.508 ------------------------------------------------------------------------------- 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 130 optimal weight: 2.9990 chunk 116 optimal weight: 7.9990 chunk 64 optimal weight: 0.0170 chunk 39 optimal weight: 7.9990 chunk 78 optimal weight: 2.9990 chunk 62 optimal weight: 6.9990 chunk 120 optimal weight: 8.9990 chunk 46 optimal weight: 0.9980 chunk 73 optimal weight: 3.9990 chunk 89 optimal weight: 6.9990 chunk 139 optimal weight: 4.9990 overall best weight: 2.2024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 ASN A 99 HIS ** A 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 573 GLN B 94 ASN B 99 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 = 0.3339 r_free = 0.3339 target = 0.123908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.099277 restraints weight = 15863.893| |-----------------------------------------------------------------------------| r_work (start): 0.2987 rms_B_bonded: 1.59 r_work: 0.2855 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.2721 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.2721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8640 moved from start: 0.1732 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= 0.182 Angle : 0.561 8.679 19284 Z= 0.303 Chirality : 0.046 0.143 2182 Planarity : 0.005 0.063 2210 Dihedral : 16.377 157.377 2358 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 2.17 % Allowed : 24.35 % Favored : 73.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.21), residues: 1496 helix: 0.41 (0.22), residues: 538 sheet: 0.60 (0.26), residues: 378 loop : -1.28 (0.23), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 413 HIS 0.006 0.001 HIS B 99 PHE 0.013 0.001 PHE B 584 TYR 0.012 0.001 TYR A 282 ARG 0.007 0.001 ARG B 563 Details of bonding type rmsd hydrogen bonds : bond 0.04566 ( 604) hydrogen bonds : angle 3.91506 ( 1744) covalent geometry : bond 0.00436 (14072) covalent geometry : angle 0.56122 (19284) *********************** 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 192 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 162 time to evaluate : 1.365 Fit side-chains REVERT: A 29 LYS cc_start: 0.7350 (mptt) cc_final: 0.6435 (mmtp) REVERT: A 42 ARG cc_start: 0.8074 (OUTLIER) cc_final: 0.7848 (mpp80) REVERT: A 200 GLU cc_start: 0.8053 (mt-10) cc_final: 0.7841 (mp0) REVERT: A 373 LYS cc_start: 0.7264 (mttt) cc_final: 0.6625 (mptp) REVERT: A 448 MET cc_start: 0.7899 (OUTLIER) cc_final: 0.7494 (ttt) REVERT: A 624 LYS cc_start: 0.7960 (tttp) cc_final: 0.7380 (ttpp) REVERT: A 702 LEU cc_start: 0.8633 (OUTLIER) cc_final: 0.8353 (mt) REVERT: B 42 ARG cc_start: 0.8051 (OUTLIER) cc_final: 0.7830 (mpp80) REVERT: B 373 LYS cc_start: 0.7261 (mttt) cc_final: 0.6623 (mptp) REVERT: B 448 MET cc_start: 0.7904 (OUTLIER) cc_final: 0.7498 (ttt) REVERT: B 624 LYS cc_start: 0.7952 (tttp) cc_final: 0.7376 (ttpp) REVERT: B 702 LEU cc_start: 0.8620 (OUTLIER) cc_final: 0.8337 (mt) outliers start: 30 outliers final: 4 residues processed: 176 average time/residue: 1.3024 time to fit residues: 250.2771 Evaluate side-chains 170 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 160 time to evaluate : 1.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ILE Chi-restraints excluded: chain A residue 42 ARG Chi-restraints excluded: chain A residue 448 MET Chi-restraints excluded: chain A residue 525 LEU Chi-restraints excluded: chain A residue 702 LEU Chi-restraints excluded: chain B residue 17 ILE Chi-restraints excluded: chain B residue 42 ARG Chi-restraints excluded: chain B residue 448 MET Chi-restraints excluded: chain B residue 525 LEU Chi-restraints excluded: chain B residue 702 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 153 optimal weight: 4.9990 chunk 13 optimal weight: 5.9990 chunk 64 optimal weight: 4.9990 chunk 108 optimal weight: 0.9990 chunk 77 optimal weight: 5.9990 chunk 62 optimal weight: 4.9990 chunk 130 optimal weight: 3.9990 chunk 28 optimal weight: 0.9980 chunk 135 optimal weight: 0.9990 chunk 6 optimal weight: 9.9990 chunk 15 optimal weight: 8.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- 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 = 0.3316 r_free = 0.3316 target = 0.122129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.098298 restraints weight = 15966.688| |-----------------------------------------------------------------------------| r_work (start): 0.2996 rms_B_bonded: 1.48 r_work: 0.2868 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.2737 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.2737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8662 moved from start: 0.2042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 14072 Z= 0.190 Angle : 0.550 9.023 19284 Z= 0.296 Chirality : 0.046 0.141 2182 Planarity : 0.004 0.055 2210 Dihedral : 16.273 160.267 2350 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 2.89 % Allowed : 23.34 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.21), residues: 1496 helix: 1.09 (0.23), residues: 548 sheet: 0.63 (0.26), residues: 378 loop : -1.24 (0.24), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 413 HIS 0.005 0.001 HIS B 722 PHE 0.009 0.001 PHE A 227 TYR 0.011 0.001 TYR A 548 ARG 0.005 0.000 ARG B 145 Details of bonding type rmsd hydrogen bonds : bond 0.04491 ( 604) hydrogen bonds : angle 3.85489 ( 1744) covalent geometry : bond 0.00457 (14072) covalent geometry : angle 0.54997 (19284) *********************** 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 210 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 170 time to evaluate : 1.381 Fit side-chains REVERT: A 29 LYS cc_start: 0.7518 (mptt) cc_final: 0.6818 (mttp) REVERT: A 99 HIS cc_start: 0.7748 (t-90) cc_final: 0.7500 (t-90) REVERT: A 200 GLU cc_start: 0.8108 (mt-10) cc_final: 0.7860 (mp0) REVERT: A 202 ASN cc_start: 0.8132 (m-40) cc_final: 0.7824 (m-40) REVERT: A 225 LYS cc_start: 0.8261 (mmmt) cc_final: 0.7390 (ttpp) REVERT: A 373 LYS cc_start: 0.7310 (mttt) cc_final: 0.6759 (mptp) REVERT: A 448 MET cc_start: 0.7956 (OUTLIER) cc_final: 0.7491 (ttt) REVERT: A 482 ILE cc_start: 0.8727 (OUTLIER) cc_final: 0.8080 (mm) REVERT: A 593 LYS cc_start: 0.8496 (OUTLIER) cc_final: 0.8188 (ptpt) REVERT: A 624 LYS cc_start: 0.7926 (tttp) cc_final: 0.7387 (ttpp) REVERT: A 702 LEU cc_start: 0.8657 (OUTLIER) cc_final: 0.8409 (mt) REVERT: A 740 GLU cc_start: 0.8106 (OUTLIER) cc_final: 0.7864 (pm20) REVERT: B 29 LYS cc_start: 0.7448 (mptt) cc_final: 0.6771 (mttp) REVERT: B 42 ARG cc_start: 0.8131 (mtt-85) cc_final: 0.7891 (mpp80) REVERT: B 99 HIS cc_start: 0.7732 (t-90) cc_final: 0.7482 (t-90) REVERT: B 202 ASN cc_start: 0.8162 (m-40) cc_final: 0.7859 (m-40) REVERT: B 225 LYS cc_start: 0.8253 (mmmt) cc_final: 0.7388 (ttpp) REVERT: B 373 LYS cc_start: 0.7304 (mttt) cc_final: 0.6749 (mptp) REVERT: B 448 MET cc_start: 0.7961 (OUTLIER) cc_final: 0.7498 (ttt) REVERT: B 482 ILE cc_start: 0.8743 (OUTLIER) cc_final: 0.8096 (mm) REVERT: B 593 LYS cc_start: 0.8503 (OUTLIER) cc_final: 0.8192 (ptpt) REVERT: B 624 LYS cc_start: 0.7914 (tttp) cc_final: 0.7372 (ttpp) REVERT: B 702 LEU cc_start: 0.8651 (OUTLIER) cc_final: 0.8397 (mt) outliers start: 40 outliers final: 8 residues processed: 198 average time/residue: 1.3045 time to fit residues: 280.9246 Evaluate side-chains 179 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 162 time to evaluate : 1.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 448 MET Chi-restraints excluded: chain A residue 482 ILE Chi-restraints excluded: chain A residue 511 LEU Chi-restraints excluded: chain A residue 566 ILE Chi-restraints excluded: chain A residue 593 LYS Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 702 LEU Chi-restraints excluded: chain A residue 740 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 84 optimal weight: 10.0000 chunk 29 optimal weight: 4.9990 chunk 27 optimal weight: 0.8980 chunk 41 optimal weight: 0.4980 chunk 67 optimal weight: 2.9990 chunk 18 optimal weight: 0.4980 chunk 108 optimal weight: 0.0870 chunk 26 optimal weight: 0.9990 chunk 142 optimal weight: 3.9990 chunk 76 optimal weight: 3.9990 chunk 95 optimal weight: 6.9990 overall best weight: 0.5960 ------------------------------------------------------------------------------- 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 = 0.3382 r_free = 0.3382 target = 0.127650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.103833 restraints weight = 15843.366| |-----------------------------------------------------------------------------| r_work (start): 0.3061 rms_B_bonded: 1.53 r_work: 0.2937 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.2809 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.2809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8586 moved from start: 0.1936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 14072 Z= 0.102 Angle : 0.455 8.029 19284 Z= 0.253 Chirality : 0.042 0.140 2182 Planarity : 0.004 0.052 2210 Dihedral : 16.105 159.758 2346 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 2.10 % Allowed : 24.93 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.22), residues: 1496 helix: 1.76 (0.23), residues: 538 sheet: 0.75 (0.26), residues: 372 loop : -0.95 (0.24), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 413 HIS 0.003 0.001 HIS B 722 PHE 0.010 0.001 PHE A 227 TYR 0.009 0.001 TYR A 650 ARG 0.006 0.000 ARG A 145 Details of bonding type rmsd hydrogen bonds : bond 0.03130 ( 604) hydrogen bonds : angle 3.57401 ( 1744) covalent geometry : bond 0.00224 (14072) covalent geometry : angle 0.45546 (19284) *********************** 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 205 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 176 time to evaluate : 1.576 Fit side-chains REVERT: A 29 LYS cc_start: 0.7521 (mptt) cc_final: 0.6859 (mttp) REVERT: A 200 GLU cc_start: 0.8120 (mt-10) cc_final: 0.7856 (mp0) REVERT: A 202 ASN cc_start: 0.8164 (m-40) cc_final: 0.7860 (m-40) REVERT: A 225 LYS cc_start: 0.8164 (mmmt) cc_final: 0.7289 (ttpp) REVERT: A 373 LYS cc_start: 0.7175 (mttt) cc_final: 0.6660 (mptp) REVERT: A 448 MET cc_start: 0.7788 (OUTLIER) cc_final: 0.7370 (ttt) REVERT: A 487 ASN cc_start: 0.7766 (p0) cc_final: 0.7483 (p0) REVERT: A 499 GLU cc_start: 0.7207 (mp0) cc_final: 0.6863 (tm-30) REVERT: A 702 LEU cc_start: 0.8639 (OUTLIER) cc_final: 0.8412 (mt) REVERT: B 29 LYS cc_start: 0.7502 (mptt) cc_final: 0.6831 (mttp) REVERT: B 42 ARG cc_start: 0.8003 (mtt-85) cc_final: 0.7760 (mpp80) REVERT: B 202 ASN cc_start: 0.8151 (m-40) cc_final: 0.7845 (m-40) REVERT: B 225 LYS cc_start: 0.8219 (mmmt) cc_final: 0.7394 (ttpp) REVERT: B 373 LYS cc_start: 0.7155 (mttt) cc_final: 0.6662 (mptp) REVERT: B 448 MET cc_start: 0.7795 (OUTLIER) cc_final: 0.7370 (ttt) REVERT: B 487 ASN cc_start: 0.7771 (p0) cc_final: 0.7494 (p0) REVERT: B 499 GLU cc_start: 0.7195 (mp0) cc_final: 0.6867 (tm-30) REVERT: B 702 LEU cc_start: 0.8646 (OUTLIER) cc_final: 0.8415 (mt) outliers start: 29 outliers final: 3 residues processed: 195 average time/residue: 1.3070 time to fit residues: 279.0004 Evaluate side-chains 177 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 170 time to evaluate : 1.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 448 MET Chi-restraints excluded: chain A residue 702 LEU Chi-restraints excluded: chain A residue 714 ASP Chi-restraints excluded: chain B residue 448 MET 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 11 optimal weight: 2.9990 chunk 40 optimal weight: 8.9990 chunk 29 optimal weight: 3.9990 chunk 115 optimal weight: 7.9990 chunk 54 optimal weight: 0.7980 chunk 123 optimal weight: 5.9990 chunk 49 optimal weight: 5.9990 chunk 41 optimal weight: 2.9990 chunk 122 optimal weight: 0.9990 chunk 65 optimal weight: 5.9990 chunk 27 optimal weight: 0.5980 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 143 GLN 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 = 0.123451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.099396 restraints weight = 15823.797| |-----------------------------------------------------------------------------| r_work (start): 0.3013 rms_B_bonded: 1.53 r_work: 0.2886 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.2754 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.2754 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8642 moved from start: 0.2089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 14072 Z= 0.148 Angle : 0.500 8.674 19284 Z= 0.271 Chirality : 0.044 0.141 2182 Planarity : 0.004 0.047 2210 Dihedral : 16.150 161.293 2346 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.22), residues: 1496 helix: 1.72 (0.23), residues: 552 sheet: 0.80 (0.26), residues: 374 loop : -0.99 (0.25), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 413 HIS 0.004 0.001 HIS A 722 PHE 0.010 0.001 PHE B 227 TYR 0.009 0.001 TYR B 282 ARG 0.007 0.000 ARG A 145 Details of bonding type rmsd hydrogen bonds : bond 0.03804 ( 604) hydrogen bonds : angle 3.60915 ( 1744) covalent geometry : bond 0.00352 (14072) covalent geometry : angle 0.50032 (19284) *********************** 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 204 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 168 time to evaluate : 1.589 Fit side-chains REVERT: A 20 GLU cc_start: 0.7825 (OUTLIER) cc_final: 0.6465 (pp20) REVERT: A 29 LYS cc_start: 0.7442 (mptt) cc_final: 0.6910 (mttm) REVERT: A 99 HIS cc_start: 0.7788 (t-90) cc_final: 0.7313 (t-90) REVERT: A 202 ASN cc_start: 0.8142 (m-40) cc_final: 0.7826 (m-40) REVERT: A 373 LYS cc_start: 0.7173 (mttt) cc_final: 0.6656 (mptp) REVERT: A 448 MET cc_start: 0.7906 (OUTLIER) cc_final: 0.7444 (ttt) REVERT: A 482 ILE cc_start: 0.8709 (OUTLIER) cc_final: 0.8022 (mm) REVERT: A 624 LYS cc_start: 0.7965 (tttp) cc_final: 0.7402 (ttpp) REVERT: A 702 LEU cc_start: 0.8600 (OUTLIER) cc_final: 0.8344 (mt) REVERT: A 740 GLU cc_start: 0.8035 (OUTLIER) cc_final: 0.7780 (pm20) REVERT: B 20 GLU cc_start: 0.7832 (OUTLIER) cc_final: 0.6471 (pp20) REVERT: B 29 LYS cc_start: 0.7445 (mptt) cc_final: 0.6805 (mttp) REVERT: B 42 ARG cc_start: 0.8060 (mtt-85) cc_final: 0.7794 (mpp80) REVERT: B 99 HIS cc_start: 0.7768 (t-90) cc_final: 0.7293 (t-90) REVERT: B 202 ASN cc_start: 0.8149 (m-40) cc_final: 0.7839 (m-40) REVERT: B 373 LYS cc_start: 0.7180 (mttt) cc_final: 0.6659 (mptp) REVERT: B 448 MET cc_start: 0.7914 (OUTLIER) cc_final: 0.7454 (ttt) REVERT: B 482 ILE cc_start: 0.8734 (OUTLIER) cc_final: 0.8043 (mm) REVERT: B 624 LYS cc_start: 0.7947 (tttp) cc_final: 0.7374 (ttpp) REVERT: B 702 LEU cc_start: 0.8612 (OUTLIER) cc_final: 0.8351 (mt) outliers start: 36 outliers final: 10 residues processed: 189 average time/residue: 1.3014 time to fit residues: 268.2763 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 : 1.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 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 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 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 593 LYS 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 7 optimal weight: 5.9990 chunk 144 optimal weight: 4.9990 chunk 71 optimal weight: 0.9980 chunk 107 optimal weight: 9.9990 chunk 82 optimal weight: 8.9990 chunk 140 optimal weight: 3.9990 chunk 29 optimal weight: 6.9990 chunk 12 optimal weight: 0.8980 chunk 20 optimal weight: 0.0040 chunk 39 optimal weight: 10.0000 chunk 105 optimal weight: 3.9990 overall best weight: 1.9796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 208 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.121805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.097282 restraints weight = 16037.288| |-----------------------------------------------------------------------------| r_work (start): 0.2972 rms_B_bonded: 1.66 r_work: 0.2834 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2699 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.2699 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8726 moved from start: 0.2223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 14072 Z= 0.165 Angle : 0.523 9.215 19284 Z= 0.282 Chirality : 0.045 0.135 2182 Planarity : 0.004 0.044 2210 Dihedral : 16.257 161.672 2346 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 2.82 % Allowed : 23.99 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.22), residues: 1496 helix: 1.75 (0.23), residues: 550 sheet: 0.82 (0.26), residues: 366 loop : -0.95 (0.25), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 413 HIS 0.005 0.001 HIS A 722 PHE 0.010 0.001 PHE B 227 TYR 0.010 0.001 TYR B 548 ARG 0.007 0.000 ARG A 145 Details of bonding type rmsd hydrogen bonds : bond 0.04059 ( 604) hydrogen bonds : angle 3.66688 ( 1744) covalent geometry : bond 0.00397 (14072) covalent geometry : angle 0.52273 (19284) *********************** 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 208 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 169 time to evaluate : 1.365 Fit side-chains REVERT: A 20 GLU cc_start: 0.7888 (OUTLIER) cc_final: 0.6570 (pp20) REVERT: A 29 LYS cc_start: 0.7500 (mptt) cc_final: 0.6748 (mttp) REVERT: A 42 ARG cc_start: 0.8132 (mtp85) cc_final: 0.7682 (ttp80) REVERT: A 99 HIS cc_start: 0.7884 (t-90) cc_final: 0.7424 (t-90) REVERT: A 202 ASN cc_start: 0.8155 (m-40) cc_final: 0.7860 (m-40) REVERT: A 225 LYS cc_start: 0.8197 (mmmt) cc_final: 0.7299 (ttpp) REVERT: A 373 LYS cc_start: 0.7224 (mttt) cc_final: 0.6709 (mptp) REVERT: A 448 MET cc_start: 0.7998 (OUTLIER) cc_final: 0.7541 (ttt) REVERT: A 482 ILE cc_start: 0.8800 (OUTLIER) cc_final: 0.8140 (mm) REVERT: A 624 LYS cc_start: 0.8023 (tttp) cc_final: 0.7508 (ttpp) REVERT: A 702 LEU cc_start: 0.8685 (OUTLIER) cc_final: 0.8431 (mt) REVERT: B 20 GLU cc_start: 0.7907 (OUTLIER) cc_final: 0.6598 (pp20) REVERT: B 29 LYS cc_start: 0.7513 (mptt) cc_final: 0.6757 (mttp) REVERT: B 42 ARG cc_start: 0.8123 (mtt-85) cc_final: 0.7864 (mpp80) REVERT: B 99 HIS cc_start: 0.7889 (t-90) cc_final: 0.7435 (t-90) REVERT: B 202 ASN cc_start: 0.8138 (m-40) cc_final: 0.7822 (m-40) REVERT: B 225 LYS cc_start: 0.8190 (mmmt) cc_final: 0.7302 (ttpp) REVERT: B 373 LYS cc_start: 0.7240 (mttt) cc_final: 0.6725 (mptp) REVERT: B 448 MET cc_start: 0.7988 (OUTLIER) cc_final: 0.7537 (ttt) REVERT: B 482 ILE cc_start: 0.8803 (OUTLIER) cc_final: 0.8148 (mm) REVERT: B 624 LYS cc_start: 0.8018 (tttp) cc_final: 0.7489 (ttpp) REVERT: B 702 LEU cc_start: 0.8687 (OUTLIER) cc_final: 0.8427 (mt) outliers start: 39 outliers final: 13 residues processed: 194 average time/residue: 1.3459 time to fit residues: 284.5009 Evaluate side-chains 187 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 166 time to evaluate : 1.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 MET Chi-restraints excluded: chain A residue 20 GLU Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 448 MET Chi-restraints excluded: chain A residue 482 ILE Chi-restraints excluded: chain A residue 511 LEU Chi-restraints excluded: chain A residue 566 ILE Chi-restraints excluded: chain A residue 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 20 GLU Chi-restraints excluded: chain B residue 32 ASP Chi-restraints excluded: chain B residue 410 LEU Chi-restraints excluded: chain B residue 448 MET Chi-restraints excluded: chain B residue 482 ILE Chi-restraints excluded: chain B residue 511 LEU Chi-restraints excluded: chain B residue 566 ILE Chi-restraints excluded: chain B residue 593 LYS Chi-restraints excluded: chain B residue 702 LEU Chi-restraints excluded: chain B residue 714 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 127 optimal weight: 8.9990 chunk 111 optimal weight: 0.0370 chunk 69 optimal weight: 8.9990 chunk 35 optimal weight: 9.9990 chunk 80 optimal weight: 8.9990 chunk 36 optimal weight: 7.9990 chunk 17 optimal weight: 10.0000 chunk 148 optimal weight: 0.0770 chunk 91 optimal weight: 9.9990 chunk 11 optimal weight: 2.9990 chunk 103 optimal weight: 3.9990 overall best weight: 3.0222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 208 HIS B 480 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.119565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.095174 restraints weight = 16039.706| |-----------------------------------------------------------------------------| r_work (start): 0.2963 rms_B_bonded: 1.62 r_work: 0.2825 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2691 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.2691 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8706 moved from start: 0.2408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 14072 Z= 0.225 Angle : 0.581 10.006 19284 Z= 0.309 Chirality : 0.047 0.151 2182 Planarity : 0.004 0.042 2210 Dihedral : 16.383 162.096 2346 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 2.89 % Allowed : 24.28 % Favored : 72.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.22), residues: 1496 helix: 1.68 (0.23), residues: 548 sheet: 0.68 (0.26), residues: 374 loop : -1.09 (0.25), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 218 HIS 0.005 0.001 HIS A 722 PHE 0.011 0.001 PHE A 67 TYR 0.012 0.002 TYR B 548 ARG 0.007 0.000 ARG A 145 Details of bonding type rmsd hydrogen bonds : bond 0.04800 ( 604) hydrogen bonds : angle 3.79391 ( 1744) covalent geometry : bond 0.00551 (14072) covalent geometry : angle 0.58148 (19284) *********************** 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 203 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 163 time to evaluate : 1.555 Fit side-chains REVERT: A 20 GLU cc_start: 0.7868 (OUTLIER) cc_final: 0.6569 (pp20) REVERT: A 29 LYS cc_start: 0.7480 (mptt) cc_final: 0.6809 (mttm) REVERT: A 42 ARG cc_start: 0.8065 (mtp85) cc_final: 0.7597 (ttp80) REVERT: A 99 HIS cc_start: 0.7878 (t-90) cc_final: 0.7357 (t-90) REVERT: A 202 ASN cc_start: 0.8157 (m-40) cc_final: 0.7848 (m-40) REVERT: A 225 LYS cc_start: 0.8214 (mmmt) cc_final: 0.7330 (ttpp) REVERT: A 373 LYS cc_start: 0.7206 (mttt) cc_final: 0.6682 (mptp) REVERT: A 448 MET cc_start: 0.8002 (OUTLIER) cc_final: 0.7510 (ttt) REVERT: A 482 ILE cc_start: 0.8755 (OUTLIER) cc_final: 0.8113 (mm) REVERT: A 562 ILE cc_start: 0.6219 (OUTLIER) cc_final: 0.5560 (mp) REVERT: A 624 LYS cc_start: 0.7958 (tttp) cc_final: 0.7444 (ttpp) REVERT: B 20 GLU cc_start: 0.7885 (OUTLIER) cc_final: 0.6589 (pp20) REVERT: B 29 LYS cc_start: 0.7486 (mptt) cc_final: 0.6820 (mttm) REVERT: B 42 ARG cc_start: 0.8123 (mtt-85) cc_final: 0.7533 (ttp80) REVERT: B 99 HIS cc_start: 0.7871 (t-90) cc_final: 0.7354 (t-90) REVERT: B 202 ASN cc_start: 0.8139 (m-40) cc_final: 0.7817 (m-40) REVERT: B 225 LYS cc_start: 0.8202 (mmmt) cc_final: 0.7325 (ttpp) REVERT: B 373 LYS cc_start: 0.7206 (mttt) cc_final: 0.6676 (mptp) REVERT: B 448 MET cc_start: 0.8004 (OUTLIER) cc_final: 0.7512 (ttt) REVERT: B 482 ILE cc_start: 0.8761 (OUTLIER) cc_final: 0.8125 (mm) REVERT: B 562 ILE cc_start: 0.6220 (OUTLIER) cc_final: 0.5573 (mp) REVERT: B 624 LYS cc_start: 0.7953 (tttp) cc_final: 0.7433 (ttpp) REVERT: B 702 LEU cc_start: 0.8649 (OUTLIER) cc_final: 0.8419 (mt) outliers start: 40 outliers final: 24 residues processed: 193 average time/residue: 1.2861 time to fit residues: 270.5521 Evaluate side-chains 189 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 156 time to evaluate : 1.549 ------------------------------------------------------------------------------- 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 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 688 THR 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 32 ASP 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 129 optimal weight: 3.9990 chunk 68 optimal weight: 0.6980 chunk 108 optimal weight: 0.2980 chunk 120 optimal weight: 6.9990 chunk 79 optimal weight: 10.0000 chunk 109 optimal weight: 4.9990 chunk 89 optimal weight: 4.9990 chunk 95 optimal weight: 2.9990 chunk 19 optimal weight: 7.9990 chunk 17 optimal weight: 7.9990 chunk 147 optimal weight: 5.9990 overall best weight: 2.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 325 ASN B 325 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.120641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.096413 restraints weight = 15973.680| |-----------------------------------------------------------------------------| r_work (start): 0.2970 rms_B_bonded: 1.54 r_work: 0.2842 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.2710 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.2710 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8689 moved from start: 0.2422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 14072 Z= 0.201 Angle : 0.561 10.190 19284 Z= 0.300 Chirality : 0.046 0.147 2182 Planarity : 0.004 0.042 2210 Dihedral : 16.357 162.217 2346 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 3.18 % Allowed : 24.13 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.22), residues: 1496 helix: 1.69 (0.23), residues: 548 sheet: 0.69 (0.26), residues: 366 loop : -1.11 (0.24), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 413 HIS 0.005 0.001 HIS A 722 PHE 0.011 0.001 PHE A 227 TYR 0.011 0.001 TYR A 548 ARG 0.008 0.000 ARG A 145 Details of bonding type rmsd hydrogen bonds : bond 0.04521 ( 604) hydrogen bonds : angle 3.77951 ( 1744) covalent geometry : bond 0.00489 (14072) covalent geometry : angle 0.56137 (19284) *********************** 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 202 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 158 time to evaluate : 1.597 Fit side-chains REVERT: A 20 GLU cc_start: 0.7859 (OUTLIER) cc_final: 0.6545 (pp20) REVERT: A 29 LYS cc_start: 0.7475 (mptt) cc_final: 0.6740 (mttp) REVERT: A 42 ARG cc_start: 0.8050 (mtp85) cc_final: 0.7594 (ttp80) REVERT: A 99 HIS cc_start: 0.7879 (t-90) cc_final: 0.7322 (t-90) REVERT: A 202 ASN cc_start: 0.8148 (m-40) cc_final: 0.7829 (m-40) REVERT: A 225 LYS cc_start: 0.8194 (mmmt) cc_final: 0.7316 (ttpp) REVERT: A 373 LYS cc_start: 0.7169 (mttt) cc_final: 0.6642 (mptp) REVERT: A 448 MET cc_start: 0.7988 (OUTLIER) cc_final: 0.7503 (ttt) REVERT: A 482 ILE cc_start: 0.8756 (OUTLIER) cc_final: 0.8115 (mm) REVERT: A 562 ILE cc_start: 0.6221 (OUTLIER) cc_final: 0.5555 (mp) REVERT: A 624 LYS cc_start: 0.7947 (tttp) cc_final: 0.7417 (ttpp) REVERT: B 20 GLU cc_start: 0.7889 (OUTLIER) cc_final: 0.6578 (pp20) REVERT: B 29 LYS cc_start: 0.7492 (mptt) cc_final: 0.6734 (mttp) REVERT: B 42 ARG cc_start: 0.8120 (mtt-85) cc_final: 0.7562 (ttp80) REVERT: B 99 HIS cc_start: 0.7869 (t-90) cc_final: 0.7314 (t-90) REVERT: B 202 ASN cc_start: 0.8134 (m-40) cc_final: 0.7808 (m-40) REVERT: B 225 LYS cc_start: 0.8184 (mmmt) cc_final: 0.7312 (ttpp) REVERT: B 373 LYS cc_start: 0.7168 (mttt) cc_final: 0.6635 (mptp) REVERT: B 448 MET cc_start: 0.7993 (OUTLIER) cc_final: 0.7509 (ttt) REVERT: B 482 ILE cc_start: 0.8766 (OUTLIER) cc_final: 0.8126 (mm) REVERT: B 562 ILE cc_start: 0.6211 (OUTLIER) cc_final: 0.5557 (mp) REVERT: B 624 LYS cc_start: 0.7939 (tttp) cc_final: 0.7411 (ttpp) outliers start: 44 outliers final: 23 residues processed: 190 average time/residue: 1.3161 time to fit residues: 273.4737 Evaluate side-chains 185 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 154 time to evaluate : 1.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 MET Chi-restraints excluded: chain A residue 20 GLU Chi-restraints excluded: chain A residue 254 LEU 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 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 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 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 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 714 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 94 optimal weight: 3.9990 chunk 53 optimal weight: 3.9990 chunk 109 optimal weight: 9.9990 chunk 57 optimal weight: 0.0870 chunk 147 optimal weight: 3.9990 chunk 99 optimal weight: 7.9990 chunk 16 optimal weight: 8.9990 chunk 151 optimal weight: 3.9990 chunk 41 optimal weight: 4.9990 chunk 80 optimal weight: 10.0000 chunk 146 optimal weight: 1.9990 overall best weight: 2.8166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 662 HIS B 662 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.120083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.096032 restraints weight = 15931.599| |-----------------------------------------------------------------------------| r_work (start): 0.2931 rms_B_bonded: 1.52 r_work: 0.2800 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.2670 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.2670 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8686 moved from start: 0.2474 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= 0.214 Angle : 0.572 10.371 19284 Z= 0.304 Chirality : 0.047 0.148 2182 Planarity : 0.004 0.041 2210 Dihedral : 16.390 162.360 2346 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 2.96 % Allowed : 24.06 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.22), residues: 1496 helix: 1.64 (0.23), residues: 550 sheet: 0.63 (0.26), residues: 374 loop : -1.17 (0.25), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 218 HIS 0.005 0.001 HIS A 722 PHE 0.011 0.001 PHE A 227 TYR 0.012 0.001 TYR B 548 ARG 0.009 0.000 ARG A 145 Details of bonding type rmsd hydrogen bonds : bond 0.04643 ( 604) hydrogen bonds : angle 3.78585 ( 1744) covalent geometry : bond 0.00522 (14072) covalent geometry : angle 0.57155 (19284) *********************** 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 196 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 155 time to evaluate : 1.409 Fit side-chains REVERT: A 20 GLU cc_start: 0.7893 (OUTLIER) cc_final: 0.6574 (pp20) REVERT: A 29 LYS cc_start: 0.7492 (mptt) cc_final: 0.6691 (mttp) REVERT: A 42 ARG cc_start: 0.8068 (mtp85) cc_final: 0.7597 (ttp80) REVERT: A 202 ASN cc_start: 0.8160 (m-40) cc_final: 0.7833 (m-40) REVERT: A 225 LYS cc_start: 0.8180 (mmmt) cc_final: 0.7311 (ttpp) REVERT: A 373 LYS cc_start: 0.7160 (mttt) cc_final: 0.6631 (mptp) REVERT: A 448 MET cc_start: 0.7973 (OUTLIER) cc_final: 0.7475 (ttt) REVERT: A 482 ILE cc_start: 0.8734 (OUTLIER) cc_final: 0.8099 (mm) REVERT: A 562 ILE cc_start: 0.6196 (OUTLIER) cc_final: 0.5548 (mp) REVERT: A 624 LYS cc_start: 0.7937 (tttp) cc_final: 0.7421 (ttpp) REVERT: B 20 GLU cc_start: 0.7957 (OUTLIER) cc_final: 0.6614 (pp20) REVERT: B 29 LYS cc_start: 0.7515 (mptt) cc_final: 0.6712 (mttp) REVERT: B 42 ARG cc_start: 0.8115 (mtt-85) cc_final: 0.7553 (ttp80) REVERT: B 202 ASN cc_start: 0.8141 (m-40) cc_final: 0.7806 (m-40) REVERT: B 225 LYS cc_start: 0.8171 (mmmt) cc_final: 0.7307 (ttpp) REVERT: B 373 LYS cc_start: 0.7157 (mttt) cc_final: 0.6619 (mptp) REVERT: B 410 LEU cc_start: 0.6347 (OUTLIER) cc_final: 0.6144 (mp) REVERT: B 448 MET cc_start: 0.7974 (OUTLIER) cc_final: 0.7474 (ttt) REVERT: B 482 ILE cc_start: 0.8751 (OUTLIER) cc_final: 0.8115 (mm) REVERT: B 562 ILE cc_start: 0.6244 (OUTLIER) cc_final: 0.5603 (mp) REVERT: B 624 LYS cc_start: 0.7931 (tttp) cc_final: 0.7416 (ttpp) outliers start: 41 outliers final: 26 residues processed: 186 average time/residue: 1.2738 time to fit residues: 260.3747 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 : 1.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 MET Chi-restraints excluded: chain A residue 20 GLU Chi-restraints excluded: chain A residue 254 LEU 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 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 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 32 ASP Chi-restraints excluded: chain B residue 122 GLU Chi-restraints excluded: chain B residue 234 VAL Chi-restraints excluded: chain B residue 320 PHE 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 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 59 optimal weight: 0.9980 chunk 52 optimal weight: 4.9990 chunk 128 optimal weight: 2.9990 chunk 74 optimal weight: 0.8980 chunk 60 optimal weight: 0.8980 chunk 85 optimal weight: 3.9990 chunk 148 optimal weight: 3.9990 chunk 127 optimal weight: 2.9990 chunk 95 optimal weight: 3.9990 chunk 7 optimal weight: 10.0000 chunk 83 optimal weight: 6.9990 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 662 HIS B 573 GLN B 662 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.121909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.097465 restraints weight = 15895.652| |-----------------------------------------------------------------------------| r_work (start): 0.2984 rms_B_bonded: 1.53 r_work: 0.2866 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.2734 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.2734 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8655 moved from start: 0.2390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 14072 Z= 0.155 Angle : 0.518 10.183 19284 Z= 0.279 Chirality : 0.045 0.143 2182 Planarity : 0.004 0.043 2210 Dihedral : 16.293 162.259 2346 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 2.31 % Allowed : 25.07 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.22), residues: 1496 helix: 1.82 (0.23), residues: 548 sheet: 0.77 (0.27), residues: 366 loop : -1.03 (0.25), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 413 HIS 0.004 0.001 HIS A 722 PHE 0.011 0.001 PHE A 227 TYR 0.010 0.001 TYR B 723 ARG 0.009 0.000 ARG A 145 Details of bonding type rmsd hydrogen bonds : bond 0.03901 ( 604) hydrogen bonds : angle 3.64932 ( 1744) covalent geometry : bond 0.00368 (14072) covalent geometry : angle 0.51750 (19284) ********************** 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 192 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 160 time to evaluate : 1.610 Fit side-chains REVERT: A 20 GLU cc_start: 0.7890 (OUTLIER) cc_final: 0.7561 (pm20) REVERT: A 29 LYS cc_start: 0.7509 (mptt) cc_final: 0.6688 (mttp) REVERT: A 42 ARG cc_start: 0.8014 (mtp85) cc_final: 0.7600 (ttp80) REVERT: A 202 ASN cc_start: 0.8171 (m-40) cc_final: 0.7842 (m-40) REVERT: A 225 LYS cc_start: 0.8119 (mmmt) cc_final: 0.7275 (ttpp) REVERT: A 373 LYS cc_start: 0.7150 (mttt) cc_final: 0.6626 (mptp) REVERT: A 448 MET cc_start: 0.7937 (OUTLIER) cc_final: 0.7467 (ttt) REVERT: A 562 ILE cc_start: 0.6152 (OUTLIER) cc_final: 0.5482 (mp) REVERT: A 624 LYS cc_start: 0.7906 (tttp) cc_final: 0.7373 (ttpp) REVERT: B 20 GLU cc_start: 0.7872 (OUTLIER) cc_final: 0.6555 (pp20) REVERT: B 29 LYS cc_start: 0.7504 (mptt) cc_final: 0.6680 (mttp) REVERT: B 42 ARG cc_start: 0.8078 (mtt-85) cc_final: 0.7545 (ttp80) REVERT: B 202 ASN cc_start: 0.8133 (m-40) cc_final: 0.7802 (m-40) REVERT: B 225 LYS cc_start: 0.8125 (mmmt) cc_final: 0.7279 (ttpp) REVERT: B 373 LYS cc_start: 0.7147 (mttt) cc_final: 0.6620 (mptp) REVERT: B 448 MET cc_start: 0.7935 (OUTLIER) cc_final: 0.7468 (ttt) REVERT: B 562 ILE cc_start: 0.6144 (OUTLIER) cc_final: 0.5470 (mp) REVERT: B 624 LYS cc_start: 0.7895 (tttp) cc_final: 0.7359 (ttpp) outliers start: 32 outliers final: 21 residues processed: 185 average time/residue: 1.2949 time to fit residues: 261.8697 Evaluate side-chains 189 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 162 time to evaluate : 1.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 MET Chi-restraints excluded: chain A residue 20 GLU Chi-restraints excluded: chain A residue 320 PHE 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 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 701 LEU Chi-restraints excluded: chain A residue 714 ASP Chi-restraints excluded: chain B residue 3 MET Chi-restraints excluded: chain B residue 20 GLU 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 320 PHE Chi-restraints excluded: chain B residue 410 LEU 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 593 LYS Chi-restraints excluded: chain B residue 688 THR 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 54 optimal weight: 0.7980 chunk 104 optimal weight: 0.6980 chunk 112 optimal weight: 0.0570 chunk 119 optimal weight: 3.9990 chunk 105 optimal weight: 0.8980 chunk 35 optimal weight: 0.9990 chunk 9 optimal weight: 0.9990 chunk 134 optimal weight: 0.5980 chunk 11 optimal weight: 4.9990 chunk 106 optimal weight: 1.9990 chunk 98 optimal weight: 3.9990 overall best weight: 0.6098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 139 HIS A 304 ASN B 480 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.127565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.103899 restraints weight = 15826.935| |-----------------------------------------------------------------------------| r_work (start): 0.3047 rms_B_bonded: 1.53 r_work: 0.2922 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.2792 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.2792 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8575 moved from start: 0.2250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 14072 Z= 0.101 Angle : 0.457 9.110 19284 Z= 0.251 Chirality : 0.042 0.144 2182 Planarity : 0.004 0.046 2210 Dihedral : 16.108 160.862 2346 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 1.81 % Allowed : 25.29 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.08 (0.22), residues: 1496 helix: 2.10 (0.23), residues: 548 sheet: 1.00 (0.27), residues: 368 loop : -0.86 (0.25), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 151 HIS 0.002 0.000 HIS A 722 PHE 0.010 0.001 PHE A 227 TYR 0.009 0.001 TYR A 650 ARG 0.008 0.000 ARG A 145 Details of bonding type rmsd hydrogen bonds : bond 0.02980 ( 604) hydrogen bonds : angle 3.43860 ( 1744) covalent geometry : bond 0.00225 (14072) covalent geometry : angle 0.45693 (19284) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8613.09 seconds wall clock time: 149 minutes 5.84 seconds (8945.84 seconds total)