Starting phenix.real_space_refine on Thu Jun 12 02:23:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wd8_37457/06_2025/8wd8_37457.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wd8_37457/06_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_37457/06_2025/8wd8_37457.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wd8_37457/06_2025/8wd8_37457.map" model { file = "/net/cci-nas-00/data/ceres_data/8wd8_37457/06_2025/8wd8_37457.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wd8_37457/06_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-5710/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: 3.32 Conformation dependent library (CDL) restraints added in 1.6 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: 5.03 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: 5.62 Time building geometry restraints manager: 3.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2292 1.32 - 1.44: 3816 1.44 - 1.57: 7788 1.57 - 1.69: 124 1.69 - 1.81: 52 Bond restraints: 14072 Sorted by residual: bond pdb=" CA HIS B 546 " pdb=" C HIS B 546 " ideal model delta sigma weight residual 1.526 1.484 0.042 1.11e-02 8.12e+03 1.43e+01 bond pdb=" CA HIS A 546 " pdb=" C HIS A 546 " ideal model delta sigma weight residual 1.526 1.484 0.042 1.11e-02 8.12e+03 1.43e+01 bond pdb=" C PRO B 541 " pdb=" O PRO B 541 " ideal model delta sigma weight residual 1.233 1.203 0.030 1.18e-02 7.18e+03 6.31e+00 bond pdb=" C PRO A 541 " pdb=" O PRO A 541 " ideal model delta sigma weight residual 1.233 1.204 0.029 1.18e-02 7.18e+03 6.17e+00 bond pdb=" C ARG A 736 " pdb=" O ARG A 736 " ideal model delta sigma weight residual 1.234 1.206 0.028 1.22e-02 6.72e+03 5.17e+00 ... (remaining 14067 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.93: 18789 1.93 - 3.86: 436 3.86 - 5.79: 38 5.79 - 7.72: 13 7.72 - 9.65: 8 Bond angle restraints: 19284 Sorted by residual: angle pdb=" N ARG A 736 " pdb=" CA ARG A 736 " pdb=" C ARG A 736 " ideal model delta sigma weight residual 109.23 116.66 -7.43 1.55e+00 4.16e-01 2.30e+01 angle pdb=" N GLU B 739 " pdb=" CA GLU B 739 " pdb=" C GLU B 739 " ideal model delta sigma weight residual 111.14 116.28 -5.14 1.08e+00 8.57e-01 2.26e+01 angle pdb=" N GLU A 739 " pdb=" CA GLU A 739 " pdb=" C GLU A 739 " ideal model delta sigma weight residual 111.14 115.78 -4.64 1.08e+00 8.57e-01 1.85e+01 angle pdb=" N LYS A 543 " pdb=" CA LYS A 543 " pdb=" C LYS A 543 " ideal model delta sigma weight residual 111.14 115.66 -4.52 1.08e+00 8.57e-01 1.75e+01 angle pdb=" CB ILE A 17 " pdb=" CG1 ILE A 17 " pdb=" CD1 ILE A 17 " ideal model delta sigma weight residual 113.80 122.54 -8.74 2.10e+00 2.27e-01 1.73e+01 ... (remaining 19279 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.46: 7618 28.46 - 56.92: 703 56.92 - 85.38: 58 85.38 - 113.84: 5 113.84 - 142.30: 4 Dihedral angle restraints: 8388 sinusoidal: 3946 harmonic: 4442 Sorted by residual: dihedral pdb=" CA TYR B 561 " pdb=" C TYR B 561 " pdb=" N ILE B 562 " pdb=" CA ILE B 562 " ideal model delta harmonic sigma weight residual -180.00 -159.28 -20.72 0 5.00e+00 4.00e-02 1.72e+01 dihedral pdb=" CA TYR A 561 " pdb=" C TYR A 561 " pdb=" N ILE A 562 " pdb=" CA ILE A 562 " ideal model delta harmonic sigma weight residual -180.00 -159.30 -20.70 0 5.00e+00 4.00e-02 1.71e+01 dihedral pdb=" C4' DA T 2 " pdb=" C3' DA T 2 " pdb=" O3' DA T 2 " pdb=" P DA T 3 " ideal model delta sinusoidal sigma weight residual 220.00 77.70 142.30 1 3.50e+01 8.16e-04 1.40e+01 ... (remaining 8385 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 1652 0.049 - 0.097: 358 0.097 - 0.146: 153 0.146 - 0.194: 17 0.194 - 0.243: 2 Chirality restraints: 2182 Sorted by residual: chirality pdb=" CB VAL B 728 " pdb=" CA VAL B 728 " pdb=" CG1 VAL B 728 " pdb=" CG2 VAL B 728 " both_signs ideal model delta sigma weight residual False -2.63 -2.39 -0.24 2.00e-01 2.50e+01 1.47e+00 chirality pdb=" CB VAL A 728 " pdb=" CA VAL A 728 " pdb=" CG1 VAL A 728 " pdb=" CG2 VAL A 728 " both_signs ideal model delta sigma weight residual False -2.63 -2.39 -0.24 2.00e-01 2.50e+01 1.44e+00 chirality pdb=" CA ASN B 487 " pdb=" N ASN B 487 " pdb=" C ASN B 487 " pdb=" CB ASN B 487 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.90e-01 ... (remaining 2179 not shown) Planarity restraints: 2210 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS B 29 " 0.064 5.00e-02 4.00e+02 9.67e-02 1.50e+01 pdb=" N PRO B 30 " -0.167 5.00e-02 4.00e+02 pdb=" CA PRO B 30 " 0.051 5.00e-02 4.00e+02 pdb=" CD PRO B 30 " 0.052 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS A 29 " -0.064 5.00e-02 4.00e+02 9.65e-02 1.49e+01 pdb=" N PRO A 30 " 0.167 5.00e-02 4.00e+02 pdb=" CA PRO A 30 " -0.051 5.00e-02 4.00e+02 pdb=" CD PRO A 30 " -0.052 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLY A 734 " -0.016 2.00e-02 2.50e+03 3.14e-02 9.85e+00 pdb=" C GLY A 734 " 0.054 2.00e-02 2.50e+03 pdb=" O GLY A 734 " -0.020 2.00e-02 2.50e+03 pdb=" N TRP A 735 " -0.019 2.00e-02 2.50e+03 ... (remaining 2207 not shown) Histogram of nonbonded interaction distances: 1.85 - 2.46: 37 2.46 - 3.07: 7396 3.07 - 3.68: 19820 3.68 - 4.29: 31258 4.29 - 4.90: 51892 Nonbonded interactions: 110403 Sorted by model distance: nonbonded pdb=" ND1 HIS A 546 " pdb="ZN ZN A 801 " model vdw 1.852 2.310 nonbonded pdb=" ND1 HIS B 546 " pdb="ZN ZN A 801 " model vdw 1.870 2.310 nonbonded pdb=" O VAL B 750 " pdb="MG MG B 801 " model vdw 2.095 2.170 nonbonded pdb=" O VAL A 750 " pdb="MG MG A 802 " model vdw 2.095 2.170 nonbonded pdb=" OP1 DT U 6 " pdb="MG MG B 802 " model vdw 2.108 2.170 ... (remaining 110398 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 750 or resid 802 through 803)) selection = (chain 'B' and (resid 1 through 750 or resid 802 through 803)) } ncs_group { reference = chain 'G' selection = chain 'H' } ncs_group { reference = (chain 'T' and resid 0 through 15) selection = chain 'U' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.010 Normalize map: mean=0, sd=1: 0.710 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: 0.570 Check model and map are aligned: 0.110 Set scattering table: 0.140 Process input model: 37.710 Find NCS groups from input model: 0.610 Set up NCS constraints: 0.050 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:12.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.630 ------------------------------------------------------------------------------- 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 : 1.456 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: 1.3558 time to fit residues: 299.2533 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 : 1.480 ------------------------------------------------------------------------------- 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 = 0.099276 restraints weight = 15863.921| |-----------------------------------------------------------------------------| r_work (start): 0.2987 rms_B_bonded: 1.59 r_work: 0.2856 rms_B_bonded: 2.13 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 3.91507 ( 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 : 1.521 Fit side-chains REVERT: A 29 LYS cc_start: 0.7351 (mptt) cc_final: 0.6435 (mmtp) REVERT: A 42 ARG cc_start: 0.8075 (OUTLIER) cc_final: 0.7848 (mpp80) REVERT: A 200 GLU cc_start: 0.8052 (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: 0.7495 (ttt) REVERT: A 624 LYS cc_start: 0.7960 (tttp) cc_final: 0.7380 (ttpp) REVERT: A 702 LEU cc_start: 0.8632 (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: 0.6622 (mptp) REVERT: B 448 MET cc_start: 0.7905 (OUTLIER) cc_final: 0.7499 (ttt) REVERT: B 624 LYS cc_start: 0.7951 (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: 1.3551 time to fit residues: 259.9126 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 : 1.434 ------------------------------------------------------------------------------- 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: 6.9990 chunk 64 optimal weight: 4.9990 chunk 108 optimal weight: 1.9990 chunk 77 optimal weight: 5.9990 chunk 62 optimal weight: 4.9990 chunk 130 optimal weight: 3.9990 chunk 28 optimal weight: 0.8980 chunk 135 optimal weight: 0.9990 chunk 6 optimal weight: 9.9990 chunk 15 optimal weight: 8.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.121511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.097346 restraints weight = 15963.962| |-----------------------------------------------------------------------------| r_work (start): 0.2983 rms_B_bonded: 1.52 r_work: 0.2857 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.2725 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.2725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8677 moved from start: 0.2101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 14072 Z= 0.201 Angle : 0.564 9.281 19284 Z= 0.302 Chirality : 0.046 0.141 2182 Planarity : 0.005 0.054 2210 Dihedral : 16.297 160.290 2350 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 2.89 % Allowed : 23.19 % Favored : 73.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.11 (0.23), residues: 548 sheet: 0.69 (0.26), residues: 374 loop : -1.29 (0.24), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 413 HIS 0.005 0.001 HIS A 722 PHE 0.009 0.001 PHE A 67 TYR 0.012 0.001 TYR A 548 ARG 0.006 0.000 ARG B 145 Details of bonding type rmsd hydrogen bonds : bond 0.04656 ( 604) hydrogen bonds : angle 3.88313 ( 1744) covalent geometry : bond 0.00486 (14072) covalent geometry : angle 0.56428 (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 208 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 168 time to evaluate : 1.449 Fit side-chains REVERT: A 29 LYS cc_start: 0.7433 (mptt) cc_final: 0.6817 (mttp) REVERT: A 99 HIS cc_start: 0.7753 (t-90) cc_final: 0.7334 (t-90) REVERT: A 202 ASN cc_start: 0.8129 (m-40) cc_final: 0.7819 (m-40) REVERT: A 225 LYS cc_start: 0.8267 (mmmt) cc_final: 0.7414 (ttpp) REVERT: A 373 LYS cc_start: 0.7297 (mttt) cc_final: 0.6751 (mptp) REVERT: A 448 MET cc_start: 0.7980 (OUTLIER) cc_final: 0.7515 (ttt) REVERT: A 482 ILE cc_start: 0.8738 (OUTLIER) cc_final: 0.8095 (mm) REVERT: A 624 LYS cc_start: 0.7952 (tttp) cc_final: 0.7417 (ttpp) REVERT: A 702 LEU cc_start: 0.8671 (OUTLIER) cc_final: 0.8426 (mt) REVERT: B 29 LYS cc_start: 0.7436 (mptt) cc_final: 0.6783 (mttp) REVERT: B 99 HIS cc_start: 0.7762 (t-90) cc_final: 0.7345 (t-90) REVERT: B 202 ASN cc_start: 0.8144 (m-40) cc_final: 0.7836 (m-40) REVERT: B 225 LYS cc_start: 0.8261 (mmmt) cc_final: 0.7427 (ttpp) REVERT: B 373 LYS cc_start: 0.7292 (mttt) cc_final: 0.6749 (mptp) REVERT: B 448 MET cc_start: 0.7975 (OUTLIER) cc_final: 0.7509 (ttt) REVERT: B 482 ILE cc_start: 0.8738 (OUTLIER) cc_final: 0.8098 (mm) REVERT: B 542 MET cc_start: 0.8858 (mtt) cc_final: 0.8551 (mtt) REVERT: B 624 LYS cc_start: 0.7938 (tttp) cc_final: 0.7401 (ttpp) REVERT: B 702 LEU cc_start: 0.8665 (OUTLIER) cc_final: 0.8415 (mt) outliers start: 40 outliers final: 8 residues processed: 196 average time/residue: 1.4200 time to fit residues: 302.0789 Evaluate side-chains 178 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 164 time to evaluate : 1.597 ------------------------------------------------------------------------------- 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 686 THR Chi-restraints excluded: chain A residue 702 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 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: 0.7980 chunk 41 optimal weight: 0.0670 chunk 67 optimal weight: 2.9990 chunk 18 optimal weight: 0.5980 chunk 108 optimal weight: 0.0070 chunk 26 optimal weight: 5.9990 chunk 142 optimal weight: 2.9990 chunk 76 optimal weight: 3.9990 chunk 95 optimal weight: 0.9990 overall best weight: 0.4938 ------------------------------------------------------------------------------- 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 = 0.3380 r_free = 0.3380 target = 0.127540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.104033 restraints weight = 15893.226| |-----------------------------------------------------------------------------| r_work (start): 0.3074 rms_B_bonded: 1.60 r_work: 0.2938 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2807 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.2807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8646 moved from start: 0.1952 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= 0.100 Angle : 0.451 7.920 19284 Z= 0.251 Chirality : 0.042 0.138 2182 Planarity : 0.004 0.052 2210 Dihedral : 16.091 159.454 2346 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 1.95 % Allowed : 24.71 % Favored : 73.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.73 (0.22), residues: 1496 helix: 1.80 (0.23), residues: 536 sheet: 0.78 (0.26), residues: 372 loop : -0.95 (0.24), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 413 HIS 0.003 0.001 HIS A 256 PHE 0.010 0.001 PHE A 227 TYR 0.010 0.001 TYR A 650 ARG 0.006 0.000 ARG A 145 Details of bonding type rmsd hydrogen bonds : bond 0.03065 ( 604) hydrogen bonds : angle 3.55073 ( 1744) covalent geometry : bond 0.00220 (14072) covalent geometry : angle 0.45068 (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 201 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 174 time to evaluate : 1.573 Fit side-chains REVERT: A 29 LYS cc_start: 0.7563 (mptt) cc_final: 0.6888 (mttp) REVERT: A 202 ASN cc_start: 0.8174 (m-40) cc_final: 0.7882 (m-40) REVERT: A 225 LYS cc_start: 0.8271 (mmmt) cc_final: 0.7409 (ttpp) REVERT: A 373 LYS cc_start: 0.7197 (mttt) cc_final: 0.6729 (mptp) REVERT: A 448 MET cc_start: 0.7815 (OUTLIER) cc_final: 0.7416 (ttt) REVERT: A 487 ASN cc_start: 0.7832 (p0) cc_final: 0.7506 (p0) REVERT: A 499 GLU cc_start: 0.7263 (mp0) cc_final: 0.6921 (tm-30) REVERT: A 702 LEU cc_start: 0.8715 (OUTLIER) cc_final: 0.8493 (mt) REVERT: B 29 LYS cc_start: 0.7538 (mptt) cc_final: 0.6871 (mttp) REVERT: B 42 ARG cc_start: 0.8008 (mtt-85) cc_final: 0.7790 (mpp80) REVERT: B 202 ASN cc_start: 0.8160 (m-40) cc_final: 0.7857 (m-40) REVERT: B 225 LYS cc_start: 0.8229 (mmmt) cc_final: 0.7385 (ttpp) REVERT: B 373 LYS cc_start: 0.7195 (mttt) cc_final: 0.6717 (mptp) REVERT: B 448 MET cc_start: 0.7831 (OUTLIER) cc_final: 0.7430 (ttt) REVERT: B 487 ASN cc_start: 0.7834 (p0) cc_final: 0.7514 (p0) REVERT: B 499 GLU cc_start: 0.7236 (mp0) cc_final: 0.6906 (tm-30) REVERT: B 702 LEU cc_start: 0.8722 (OUTLIER) cc_final: 0.8495 (mt) outliers start: 27 outliers final: 4 residues processed: 193 average time/residue: 1.4060 time to fit residues: 294.8382 Evaluate side-chains 176 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 168 time to evaluate : 1.560 ------------------------------------------------------------------------------- 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 122 GLU 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: 9.9990 chunk 29 optimal weight: 4.9990 chunk 115 optimal weight: 7.9990 chunk 54 optimal weight: 0.0030 chunk 123 optimal weight: 4.9990 chunk 49 optimal weight: 8.9990 chunk 41 optimal weight: 2.9990 chunk 122 optimal weight: 0.9980 chunk 65 optimal weight: 5.9990 chunk 27 optimal weight: 0.5980 overall best weight: 1.5194 ------------------------------------------------------------------------------- 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 = 0.3328 r_free = 0.3328 target = 0.123207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.098697 restraints weight = 15824.742| |-----------------------------------------------------------------------------| r_work (start): 0.3002 rms_B_bonded: 1.66 r_work: 0.2866 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2733 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.2733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8652 moved from start: 0.2099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 14072 Z= 0.141 Angle : 0.497 8.536 19284 Z= 0.270 Chirality : 0.044 0.141 2182 Planarity : 0.004 0.048 2210 Dihedral : 16.134 161.355 2346 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 2.75 % Allowed : 23.63 % Favored : 73.63 % 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: 0.76 (0.22), residues: 1496 helix: 1.77 (0.23), residues: 552 sheet: 0.83 (0.26), residues: 374 loop : -1.00 (0.25), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 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 A 282 ARG 0.006 0.000 ARG A 145 Details of bonding type rmsd hydrogen bonds : bond 0.03719 ( 604) hydrogen bonds : angle 3.60476 ( 1744) covalent geometry : bond 0.00333 (14072) covalent geometry : angle 0.49659 (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 207 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 169 time to evaluate : 1.488 Fit side-chains REVERT: A 20 GLU cc_start: 0.7818 (OUTLIER) cc_final: 0.6465 (pp20) REVERT: A 29 LYS cc_start: 0.7459 (mptt) cc_final: 0.6790 (mttp) REVERT: A 99 HIS cc_start: 0.7805 (t-90) cc_final: 0.7313 (t-90) REVERT: A 202 ASN cc_start: 0.8173 (m-40) cc_final: 0.7877 (m-40) REVERT: A 373 LYS cc_start: 0.7131 (mttt) cc_final: 0.6652 (mptp) REVERT: A 448 MET cc_start: 0.7904 (OUTLIER) cc_final: 0.7443 (ttt) REVERT: A 482 ILE cc_start: 0.8705 (OUTLIER) cc_final: 0.7996 (mm) REVERT: A 624 LYS cc_start: 0.7958 (tttp) cc_final: 0.7389 (ttpp) REVERT: A 702 LEU cc_start: 0.8619 (OUTLIER) cc_final: 0.8366 (mt) REVERT: B 19 ASN cc_start: 0.7046 (OUTLIER) cc_final: 0.6108 (OUTLIER) REVERT: B 20 GLU cc_start: 0.7905 (OUTLIER) cc_final: 0.6976 (pm20) REVERT: B 29 LYS cc_start: 0.7434 (mptt) cc_final: 0.6640 (mttp) REVERT: B 42 ARG cc_start: 0.8078 (mtt-85) cc_final: 0.7801 (mpp80) REVERT: B 202 ASN cc_start: 0.8145 (m-40) cc_final: 0.7828 (m-40) REVERT: B 373 LYS cc_start: 0.7138 (mttt) cc_final: 0.6656 (mptp) REVERT: B 448 MET cc_start: 0.7921 (OUTLIER) cc_final: 0.7460 (ttt) REVERT: B 624 LYS cc_start: 0.7944 (tttp) cc_final: 0.7368 (ttpp) REVERT: B 702 LEU cc_start: 0.8627 (OUTLIER) cc_final: 0.8368 (mt) outliers start: 38 outliers final: 11 residues processed: 192 average time/residue: 1.4118 time to fit residues: 294.8100 Evaluate side-chains 183 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 165 time to evaluate : 1.766 ------------------------------------------------------------------------------- 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 B residue 19 ASN Chi-restraints excluded: chain B residue 20 GLU Chi-restraints excluded: chain B residue 122 GLU Chi-restraints excluded: chain B residue 410 LEU Chi-restraints excluded: chain B residue 448 MET Chi-restraints excluded: chain B residue 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: 9.9990 chunk 144 optimal weight: 4.9990 chunk 71 optimal weight: 0.6980 chunk 107 optimal weight: 0.8980 chunk 82 optimal weight: 10.0000 chunk 140 optimal weight: 2.9990 chunk 29 optimal weight: 3.9990 chunk 12 optimal weight: 2.9990 chunk 20 optimal weight: 6.9990 chunk 39 optimal weight: 4.9990 chunk 105 optimal weight: 2.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- 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 = 0.3314 r_free = 0.3314 target = 0.121984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.097363 restraints weight = 16043.384| |-----------------------------------------------------------------------------| r_work (start): 0.2986 rms_B_bonded: 1.67 r_work: 0.2853 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2718 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.2718 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8702 moved from start: 0.2260 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= 0.174 Angle : 0.533 9.254 19284 Z= 0.287 Chirality : 0.045 0.137 2182 Planarity : 0.004 0.044 2210 Dihedral : 16.276 161.908 2346 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 2.89 % Allowed : 24.49 % 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: 0.73 (0.22), residues: 1496 helix: 1.76 (0.23), residues: 550 sheet: 0.83 (0.27), residues: 366 loop : -1.01 (0.24), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 218 HIS 0.005 0.001 HIS B 722 PHE 0.010 0.001 PHE A 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 0.04169 ( 604) hydrogen bonds : angle 3.68333 ( 1744) covalent geometry : bond 0.00420 (14072) covalent geometry : angle 0.53340 (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 210 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 170 time to evaluate : 1.676 Fit side-chains REVERT: A 20 GLU cc_start: 0.7855 (OUTLIER) cc_final: 0.6493 (pp20) REVERT: A 29 LYS cc_start: 0.7481 (mptt) cc_final: 0.6725 (mttp) REVERT: A 42 ARG cc_start: 0.8046 (mtp85) cc_final: 0.7620 (ttp80) REVERT: A 99 HIS cc_start: 0.7884 (t-90) cc_final: 0.7408 (t-90) REVERT: A 202 ASN cc_start: 0.8149 (m-40) cc_final: 0.7854 (m-40) REVERT: A 225 LYS cc_start: 0.8161 (mmmt) cc_final: 0.7261 (ttpp) REVERT: A 373 LYS cc_start: 0.7204 (mttt) cc_final: 0.6692 (mptp) REVERT: A 448 MET cc_start: 0.7987 (OUTLIER) cc_final: 0.7524 (ttt) REVERT: A 482 ILE cc_start: 0.8776 (OUTLIER) cc_final: 0.8108 (mm) REVERT: A 624 LYS cc_start: 0.8015 (tttp) cc_final: 0.7475 (ttpp) REVERT: A 702 LEU cc_start: 0.8662 (OUTLIER) cc_final: 0.8408 (mt) REVERT: B 19 ASN cc_start: 0.7057 (OUTLIER) cc_final: 0.6154 (OUTLIER) REVERT: B 20 GLU cc_start: 0.7943 (OUTLIER) cc_final: 0.7058 (pm20) REVERT: B 29 LYS cc_start: 0.7357 (mptt) cc_final: 0.6627 (mttm) REVERT: B 42 ARG cc_start: 0.8122 (mtt-85) cc_final: 0.7574 (ttp80) REVERT: B 99 HIS cc_start: 0.7841 (t-90) cc_final: 0.7364 (t-90) REVERT: B 202 ASN cc_start: 0.8154 (m-40) cc_final: 0.7838 (m-40) REVERT: B 225 LYS cc_start: 0.8157 (mmmt) cc_final: 0.7270 (ttpp) REVERT: B 373 LYS cc_start: 0.7204 (mttt) cc_final: 0.6683 (mptp) REVERT: B 448 MET cc_start: 0.7989 (OUTLIER) cc_final: 0.7526 (ttt) REVERT: B 482 ILE cc_start: 0.8783 (OUTLIER) cc_final: 0.8133 (mm) REVERT: B 624 LYS cc_start: 0.7997 (tttp) cc_final: 0.7455 (ttpp) REVERT: B 702 LEU cc_start: 0.8664 (OUTLIER) cc_final: 0.8403 (mt) outliers start: 40 outliers final: 15 residues processed: 197 average time/residue: 1.5572 time to fit residues: 335.5673 Evaluate side-chains 188 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 165 time to evaluate : 1.756 ------------------------------------------------------------------------------- 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 566 ILE Chi-restraints excluded: chain A residue 593 LYS Chi-restraints excluded: chain A residue 688 THR Chi-restraints excluded: chain A residue 702 LEU Chi-restraints excluded: chain A residue 714 ASP Chi-restraints excluded: chain B residue 3 MET Chi-restraints excluded: chain B residue 19 ASN Chi-restraints excluded: chain B residue 20 GLU Chi-restraints excluded: chain B residue 122 GLU Chi-restraints excluded: chain B residue 410 LEU Chi-restraints excluded: chain B residue 448 MET Chi-restraints excluded: chain B residue 482 ILE Chi-restraints excluded: chain B residue 511 LEU Chi-restraints excluded: chain B residue 566 ILE Chi-restraints excluded: chain B residue 593 LYS Chi-restraints excluded: chain B residue 688 THR 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: 0.3980 chunk 69 optimal weight: 7.9990 chunk 35 optimal weight: 9.9990 chunk 80 optimal weight: 5.9990 chunk 36 optimal weight: 4.9990 chunk 17 optimal weight: 8.9990 chunk 148 optimal weight: 4.9990 chunk 91 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 103 optimal weight: 1.9990 overall best weight: 2.6788 ------------------------------------------------------------------------------- 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 = 0.3295 r_free = 0.3295 target = 0.120507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.095797 restraints weight = 15968.477| |-----------------------------------------------------------------------------| r_work (start): 0.2965 rms_B_bonded: 1.67 r_work: 0.2832 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2698 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.2698 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8690 moved from start: 0.2398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 14072 Z= 0.207 Angle : 0.565 9.843 19284 Z= 0.302 Chirality : 0.046 0.147 2182 Planarity : 0.004 0.042 2210 Dihedral : 16.359 162.097 2346 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 3.11 % Allowed : 24.42 % Favored : 72.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.62 (0.22), residues: 1496 helix: 1.73 (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 A 218 HIS 0.005 0.001 HIS A 722 PHE 0.010 0.001 PHE A 227 TYR 0.011 0.001 TYR B 548 ARG 0.008 0.000 ARG A 145 Details of bonding type rmsd hydrogen bonds : bond 0.04594 ( 604) hydrogen bonds : angle 3.77379 ( 1744) covalent geometry : bond 0.00503 (14072) covalent geometry : angle 0.56525 (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 205 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 162 time to evaluate : 1.830 Fit side-chains REVERT: A 20 GLU cc_start: 0.7849 (OUTLIER) cc_final: 0.6534 (pp20) REVERT: A 29 LYS cc_start: 0.7481 (mptt) cc_final: 0.6758 (mttp) REVERT: A 42 ARG cc_start: 0.8061 (mtp85) cc_final: 0.7592 (ttp80) REVERT: A 99 HIS cc_start: 0.7878 (t-90) cc_final: 0.7318 (t-90) REVERT: A 202 ASN cc_start: 0.8160 (m-40) cc_final: 0.7852 (m-40) REVERT: A 225 LYS cc_start: 0.8176 (mmmt) cc_final: 0.7298 (ttpp) REVERT: A 373 LYS cc_start: 0.7180 (mttt) cc_final: 0.6659 (mptp) REVERT: A 448 MET cc_start: 0.8008 (OUTLIER) cc_final: 0.7522 (ttt) REVERT: A 482 ILE cc_start: 0.8757 (OUTLIER) cc_final: 0.8108 (mm) REVERT: A 624 LYS cc_start: 0.7940 (tttp) cc_final: 0.7402 (ttpp) REVERT: A 702 LEU cc_start: 0.8636 (OUTLIER) cc_final: 0.8421 (mt) REVERT: B 19 ASN cc_start: 0.7097 (OUTLIER) cc_final: 0.6254 (OUTLIER) REVERT: B 20 GLU cc_start: 0.7921 (OUTLIER) cc_final: 0.7079 (pm20) REVERT: B 29 LYS cc_start: 0.7282 (mptt) cc_final: 0.6454 (mttp) REVERT: B 42 ARG cc_start: 0.8102 (mtt-85) cc_final: 0.7531 (ttp80) REVERT: B 99 HIS cc_start: 0.7852 (t-90) cc_final: 0.7321 (t-90) REVERT: B 202 ASN cc_start: 0.8137 (m-40) cc_final: 0.7809 (m-40) REVERT: B 225 LYS cc_start: 0.8177 (mmmt) cc_final: 0.7301 (ttpp) REVERT: B 373 LYS cc_start: 0.7174 (mttt) cc_final: 0.6645 (mptp) REVERT: B 448 MET cc_start: 0.8006 (OUTLIER) cc_final: 0.7522 (ttt) REVERT: B 482 ILE cc_start: 0.8752 (OUTLIER) cc_final: 0.8110 (mm) REVERT: B 624 LYS cc_start: 0.7925 (tttp) cc_final: 0.7387 (ttpp) outliers start: 43 outliers final: 21 residues processed: 195 average time/residue: 1.9534 time to fit residues: 414.7487 Evaluate side-chains 187 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 159 time to evaluate : 1.532 ------------------------------------------------------------------------------- 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 525 LEU 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 702 LEU Chi-restraints excluded: chain A residue 714 ASP Chi-restraints excluded: chain B residue 3 MET Chi-restraints excluded: chain B residue 19 ASN Chi-restraints excluded: chain B residue 20 GLU Chi-restraints excluded: chain B residue 122 GLU Chi-restraints excluded: chain B residue 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 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 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: 7.9990 chunk 68 optimal weight: 1.9990 chunk 108 optimal weight: 8.9990 chunk 120 optimal weight: 6.9990 chunk 79 optimal weight: 9.9990 chunk 109 optimal weight: 1.9990 chunk 89 optimal weight: 4.9990 chunk 95 optimal weight: 2.9990 chunk 19 optimal weight: 7.9990 chunk 17 optimal weight: 8.9990 chunk 147 optimal weight: 5.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- 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 = 0.3279 r_free = 0.3279 target = 0.119216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.094864 restraints weight = 16000.101| |-----------------------------------------------------------------------------| r_work (start): 0.2952 rms_B_bonded: 1.54 r_work: 0.2823 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.2693 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.2693 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8707 moved from start: 0.2515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.071 14072 Z= 0.260 Angle : 0.613 10.617 19284 Z= 0.323 Chirality : 0.049 0.157 2182 Planarity : 0.005 0.041 2210 Dihedral : 16.419 161.917 2346 Min Nonbonded Distance : 1.862 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 2.67 % Allowed : 25.00 % Favored : 72.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.42 (0.22), residues: 1496 helix: 1.59 (0.23), residues: 550 sheet: 0.58 (0.26), residues: 374 loop : -1.25 (0.24), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 218 HIS 0.006 0.001 HIS A 722 PHE 0.012 0.002 PHE B 67 TYR 0.014 0.002 TYR A 548 ARG 0.009 0.000 ARG A 145 Details of bonding type rmsd hydrogen bonds : bond 0.05112 ( 604) hydrogen bonds : angle 3.85614 ( 1744) covalent geometry : bond 0.00640 (14072) covalent geometry : angle 0.61342 (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 194 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 157 time to evaluate : 3.464 Fit side-chains REVERT: A 20 GLU cc_start: 0.7915 (OUTLIER) cc_final: 0.6598 (pp20) REVERT: A 29 LYS cc_start: 0.7475 (mptt) cc_final: 0.6696 (mttp) REVERT: A 42 ARG cc_start: 0.8074 (mtp85) cc_final: 0.7623 (ttp80) REVERT: A 99 HIS cc_start: 0.7892 (t-90) cc_final: 0.7336 (t-90) REVERT: A 202 ASN cc_start: 0.8161 (m-40) cc_final: 0.7849 (m-40) REVERT: A 225 LYS cc_start: 0.8186 (mmmt) cc_final: 0.7317 (ttpp) REVERT: A 373 LYS cc_start: 0.7187 (mttt) cc_final: 0.6647 (mptp) REVERT: A 448 MET cc_start: 0.7999 (OUTLIER) cc_final: 0.7500 (ttt) REVERT: A 482 ILE cc_start: 0.8750 (OUTLIER) cc_final: 0.8117 (mm) REVERT: A 624 LYS cc_start: 0.7966 (tttp) cc_final: 0.7469 (ttpp) REVERT: A 738 ARG cc_start: 0.7834 (mtm110) cc_final: 0.7518 (mtm110) REVERT: A 740 GLU cc_start: 0.8068 (OUTLIER) cc_final: 0.7641 (pm20) REVERT: B 19 ASN cc_start: 0.7094 (OUTLIER) cc_final: 0.6231 (OUTLIER) REVERT: B 20 GLU cc_start: 0.7933 (OUTLIER) cc_final: 0.7030 (pm20) REVERT: B 29 LYS cc_start: 0.7319 (mptt) cc_final: 0.6449 (mttp) REVERT: B 42 ARG cc_start: 0.8135 (mtt-85) cc_final: 0.7570 (ttp80) REVERT: B 99 HIS cc_start: 0.7835 (t-90) cc_final: 0.7300 (t-90) REVERT: B 202 ASN cc_start: 0.8144 (m-40) cc_final: 0.7814 (m-40) REVERT: B 225 LYS cc_start: 0.8182 (mmmt) cc_final: 0.7315 (ttpp) REVERT: B 373 LYS cc_start: 0.7183 (mttt) cc_final: 0.6639 (mptp) REVERT: B 448 MET cc_start: 0.7996 (OUTLIER) cc_final: 0.7497 (ttt) REVERT: B 482 ILE cc_start: 0.8750 (OUTLIER) cc_final: 0.8134 (mm) REVERT: B 624 LYS cc_start: 0.7951 (tttp) cc_final: 0.7461 (ttpp) outliers start: 37 outliers final: 20 residues processed: 186 average time/residue: 2.4029 time to fit residues: 490.2087 Evaluate side-chains 184 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 157 time to evaluate : 1.590 ------------------------------------------------------------------------------- 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 448 MET Chi-restraints excluded: chain A residue 482 ILE Chi-restraints excluded: chain A residue 511 LEU 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 A residue 740 GLU Chi-restraints excluded: chain B residue 3 MET Chi-restraints excluded: chain B residue 19 ASN Chi-restraints excluded: chain B residue 20 GLU Chi-restraints excluded: chain B residue 122 GLU Chi-restraints excluded: chain B residue 234 VAL Chi-restraints excluded: chain B residue 448 MET Chi-restraints excluded: chain B residue 482 ILE Chi-restraints excluded: chain B residue 511 LEU 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 Chi-restraints excluded: chain B residue 740 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 94 optimal weight: 2.9990 chunk 53 optimal weight: 3.9990 chunk 109 optimal weight: 0.5980 chunk 57 optimal weight: 3.9990 chunk 147 optimal weight: 6.9990 chunk 99 optimal weight: 2.9990 chunk 16 optimal weight: 7.9990 chunk 151 optimal weight: 5.9990 chunk 41 optimal weight: 0.1980 chunk 80 optimal weight: 3.9990 chunk 146 optimal weight: 0.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 573 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.122243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.098311 restraints weight = 15856.626| |-----------------------------------------------------------------------------| r_work (start): 0.3002 rms_B_bonded: 1.48 r_work: 0.2877 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.2748 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.2748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8646 moved from start: 0.2389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 14072 Z= 0.145 Angle : 0.508 9.920 19284 Z= 0.276 Chirality : 0.044 0.137 2182 Planarity : 0.004 0.043 2210 Dihedral : 16.283 162.444 2346 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 2.17 % Allowed : 25.43 % Favored : 72.40 % 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: 1.83 (0.23), residues: 548 sheet: 0.74 (0.27), residues: 366 loop : -1.06 (0.25), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 413 HIS 0.004 0.001 HIS A 722 PHE 0.011 0.001 PHE A 227 TYR 0.010 0.001 TYR B 650 ARG 0.008 0.000 ARG A 145 Details of bonding type rmsd hydrogen bonds : bond 0.03814 ( 604) hydrogen bonds : angle 3.66760 ( 1744) covalent geometry : bond 0.00339 (14072) covalent geometry : angle 0.50845 (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 195 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 165 time to evaluate : 2.236 Fit side-chains REVERT: A 20 GLU cc_start: 0.7869 (OUTLIER) cc_final: 0.7536 (pm20) REVERT: A 29 LYS cc_start: 0.7502 (mptt) cc_final: 0.6699 (mttp) REVERT: A 42 ARG cc_start: 0.8025 (mtp85) cc_final: 0.7612 (ttp80) REVERT: A 99 HIS cc_start: 0.7817 (t-90) cc_final: 0.7266 (t-90) REVERT: A 202 ASN cc_start: 0.8149 (m-40) cc_final: 0.7835 (m-40) REVERT: A 225 LYS cc_start: 0.8153 (mmmt) cc_final: 0.7294 (ttpp) REVERT: A 373 LYS cc_start: 0.7139 (mttt) cc_final: 0.6617 (mptp) REVERT: A 448 MET cc_start: 0.7927 (OUTLIER) cc_final: 0.7459 (ttt) REVERT: A 586 ASP cc_start: 0.7972 (p0) cc_final: 0.7426 (m-30) REVERT: A 624 LYS cc_start: 0.7898 (tttp) cc_final: 0.7355 (ttpp) REVERT: A 740 GLU cc_start: 0.8083 (OUTLIER) cc_final: 0.7778 (pm20) REVERT: B 19 ASN cc_start: 0.7052 (OUTLIER) cc_final: 0.6140 (OUTLIER) REVERT: B 20 GLU cc_start: 0.7877 (OUTLIER) cc_final: 0.6998 (pm20) REVERT: B 29 LYS cc_start: 0.7332 (mptt) cc_final: 0.6434 (mttp) REVERT: B 42 ARG cc_start: 0.8059 (mtt-85) cc_final: 0.7803 (mpp80) REVERT: B 99 HIS cc_start: 0.7806 (t-90) cc_final: 0.7262 (t-90) REVERT: B 202 ASN cc_start: 0.8124 (m-40) cc_final: 0.7795 (m-40) REVERT: B 225 LYS cc_start: 0.8136 (mmmt) cc_final: 0.7282 (ttpp) REVERT: B 373 LYS cc_start: 0.7144 (mttt) cc_final: 0.6614 (mptp) REVERT: B 448 MET cc_start: 0.7925 (OUTLIER) cc_final: 0.7454 (ttt) REVERT: B 482 ILE cc_start: 0.8742 (OUTLIER) cc_final: 0.8091 (mm) REVERT: B 624 LYS cc_start: 0.7885 (tttp) cc_final: 0.7342 (ttpp) outliers start: 30 outliers final: 16 residues processed: 188 average time/residue: 2.5258 time to fit residues: 529.4929 Evaluate side-chains 187 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 165 time to evaluate : 2.632 ------------------------------------------------------------------------------- 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 448 MET Chi-restraints excluded: chain A residue 525 LEU 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 A residue 740 GLU Chi-restraints excluded: chain B residue 3 MET Chi-restraints excluded: chain B residue 19 ASN Chi-restraints excluded: chain B residue 20 GLU Chi-restraints excluded: chain B residue 122 GLU Chi-restraints excluded: chain B residue 234 VAL Chi-restraints excluded: chain B residue 320 PHE Chi-restraints excluded: chain B residue 448 MET Chi-restraints excluded: chain B residue 482 ILE Chi-restraints excluded: chain B residue 525 LEU Chi-restraints excluded: chain B residue 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 59 optimal weight: 0.8980 chunk 52 optimal weight: 9.9990 chunk 128 optimal weight: 4.9990 chunk 74 optimal weight: 0.8980 chunk 60 optimal weight: 4.9990 chunk 85 optimal weight: 0.9990 chunk 148 optimal weight: 0.0370 chunk 127 optimal weight: 3.9990 chunk 95 optimal weight: 2.9990 chunk 7 optimal weight: 7.9990 chunk 83 optimal weight: 9.9990 overall best weight: 1.1662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.123696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.099646 restraints weight = 15830.369| |-----------------------------------------------------------------------------| r_work (start): 0.2986 rms_B_bonded: 1.54 r_work: 0.2856 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.2726 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.2726 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8627 moved from start: 0.2325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14072 Z= 0.125 Angle : 0.491 9.594 19284 Z= 0.267 Chirality : 0.043 0.148 2182 Planarity : 0.004 0.045 2210 Dihedral : 16.191 162.223 2346 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 1.66 % Allowed : 25.87 % Favored : 72.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.91 (0.22), residues: 1496 helix: 2.01 (0.23), residues: 548 sheet: 0.83 (0.27), residues: 366 loop : -0.93 (0.25), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 413 HIS 0.004 0.001 HIS B 722 PHE 0.011 0.001 PHE B 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 0.03485 ( 604) hydrogen bonds : angle 3.54306 ( 1744) covalent geometry : bond 0.00290 (14072) covalent geometry : angle 0.49081 (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 196 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 173 time to evaluate : 1.572 Fit side-chains revert: symmetry clash REVERT: A 20 GLU cc_start: 0.7798 (OUTLIER) cc_final: 0.7499 (pm20) REVERT: A 29 LYS cc_start: 0.7536 (mptt) cc_final: 0.6751 (mttp) REVERT: A 42 ARG cc_start: 0.8007 (mtp85) cc_final: 0.7593 (ttp80) REVERT: A 99 HIS cc_start: 0.7802 (t-90) cc_final: 0.7288 (t-90) REVERT: A 145 ARG cc_start: 0.8640 (mtt90) cc_final: 0.8436 (mtt90) REVERT: A 202 ASN cc_start: 0.8174 (m-40) cc_final: 0.7856 (m-40) REVERT: A 225 LYS cc_start: 0.8112 (mmmt) cc_final: 0.7235 (ttpp) REVERT: A 373 LYS cc_start: 0.7105 (mttt) cc_final: 0.6615 (mptp) REVERT: A 448 MET cc_start: 0.7896 (OUTLIER) cc_final: 0.7463 (ttt) REVERT: A 487 ASN cc_start: 0.7821 (p0) cc_final: 0.7609 (p0) REVERT: A 586 ASP cc_start: 0.7813 (p0) cc_final: 0.7475 (m-30) REVERT: A 624 LYS cc_start: 0.7928 (tttp) cc_final: 0.7364 (ttpp) REVERT: B 19 ASN cc_start: 0.7009 (OUTLIER) cc_final: 0.6095 (OUTLIER) REVERT: B 20 GLU cc_start: 0.7853 (OUTLIER) cc_final: 0.7010 (pm20) REVERT: B 29 LYS cc_start: 0.7329 (mptt) cc_final: 0.6426 (mttp) REVERT: B 42 ARG cc_start: 0.8061 (mtt-85) cc_final: 0.7814 (mpp80) REVERT: B 99 HIS cc_start: 0.7798 (t-90) cc_final: 0.7311 (t-90) REVERT: B 202 ASN cc_start: 0.8136 (m-40) cc_final: 0.7806 (m-40) REVERT: B 225 LYS cc_start: 0.8102 (mmmt) cc_final: 0.7234 (ttpp) REVERT: B 373 LYS cc_start: 0.7119 (mttt) cc_final: 0.6620 (mptp) REVERT: B 448 MET cc_start: 0.7906 (OUTLIER) cc_final: 0.7466 (ttt) REVERT: B 482 ILE cc_start: 0.8736 (OUTLIER) cc_final: 0.8053 (mm) REVERT: B 624 LYS cc_start: 0.7861 (tttp) cc_final: 0.7294 (ttpp) outliers start: 23 outliers final: 17 residues processed: 188 average time/residue: 1.5703 time to fit residues: 320.6595 Evaluate side-chains 190 residues out of total 1384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 168 time to evaluate : 2.576 ------------------------------------------------------------------------------- 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 566 ILE 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 122 GLU Chi-restraints excluded: chain B residue 234 VAL Chi-restraints excluded: chain B residue 320 PHE Chi-restraints excluded: chain B residue 448 MET Chi-restraints excluded: chain B residue 482 ILE Chi-restraints excluded: chain B residue 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 Chi-restraints excluded: chain B residue 740 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 54 optimal weight: 4.9990 chunk 104 optimal weight: 0.2980 chunk 112 optimal weight: 0.0060 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: 9.9990 chunk 11 optimal weight: 4.9990 chunk 106 optimal weight: 0.9980 chunk 98 optimal weight: 3.9990 overall best weight: 0.6398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 480 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.126927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.103008 restraints weight = 15827.198| |-----------------------------------------------------------------------------| r_work (start): 0.3066 rms_B_bonded: 1.54 r_work: 0.2929 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2798 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.2798 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8595 moved from start: 0.2230 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= 0.103 Angle : 0.461 9.034 19284 Z= 0.253 Chirality : 0.042 0.145 2182 Planarity : 0.004 0.045 2210 Dihedral : 16.083 161.464 2346 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 1.66 % Allowed : 25.87 % Favored : 72.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.12 (0.22), residues: 1496 helix: 2.19 (0.23), residues: 548 sheet: 0.96 (0.27), residues: 368 loop : -0.84 (0.25), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 151 HIS 0.003 0.000 HIS A 722 PHE 0.011 0.001 PHE B 227 TYR 0.009 0.001 TYR B 650 ARG 0.008 0.000 ARG A 145 Details of bonding type rmsd hydrogen bonds : bond 0.03023 ( 604) hydrogen bonds : angle 3.43970 ( 1744) covalent geometry : bond 0.00228 (14072) covalent geometry : angle 0.46117 (19284) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10154.40 seconds wall clock time: 182 minutes 57.22 seconds (10977.22 seconds total)