Starting phenix.real_space_refine on Fri Jul 3 02:33:35 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7lgw_23331/07_2026/7lgw_23331.cif Found real_map, /net/cci-nas-00/data/ceres_data/7lgw_23331/07_2026/7lgw_23331.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7lgw_23331/07_2026/7lgw_23331.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7lgw_23331/07_2026/7lgw_23331.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7lgw_23331/07_2026/7lgw_23331.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7lgw_23331/07_2026/7lgw_23331.cif" model { file = "/net/cci-nas-00/data/ceres_data/7lgw_23331/07_2026/7lgw_23331.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7lgw_23331/07_2026/7lgw_23331.cif" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 sd= 0.037 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: 5 Type Number sf(0) Gaussians S 48 5.16 5 Cl 2 4.86 5 C 7766 2.51 5 N 1690 2.21 5 O 1884 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 30 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 11390 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 5226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 680, 5226 Classifications: {'peptide': 680} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 34, 'TRANS': 645} Chain breaks: 1 Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASN:plan1': 2, 'GLU:plan': 2, 'GLN:plan1': 1, 'ARG:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 29 Chain: "B" Number of atoms: 5226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 680, 5226 Classifications: {'peptide': 680} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 34, 'TRANS': 645} Chain breaks: 1 Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASN:plan1': 2, 'GLU:plan': 2, 'GLN:plan1': 1, 'ARG:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 29 Chain: "A" Number of atoms: 459 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 459 Unusual residues: {' CL': 1, 'C14': 2, 'CLR': 1, 'D10': 17, 'D12': 5, 'HEX': 1, 'HP6': 2, 'OCT': 19} Classifications: {'undetermined': 48} Link IDs: {None: 47} Chain: "B" Number of atoms: 449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 449 Unusual residues: {' CL': 1, 'C14': 2, 'CLR': 1, 'D10': 16, 'D12': 5, 'HEX': 1, 'HP6': 2, 'OCT': 19} Classifications: {'undetermined': 47} Link IDs: {None: 46} Chain: "A" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 15 Classifications: {'water': 15} Link IDs: {None: 14} Chain: "B" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 15 Classifications: {'water': 15} Link IDs: {None: 14} Time building chain proxies: 2.41, per 1000 atoms: 0.21 Number of scatterers: 11390 At special positions: 0 Unit cell: (102.16, 117.777, 113.872, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Cl 2 17.00 S 48 16.00 O 1884 8.00 N 1690 7.00 C 7766 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.84 Conformation dependent library (CDL) restraints added in 385.0 milliseconds 2704 Ramachandran restraints generated. 1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2512 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 5 sheets defined 72.4% alpha, 4.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.32 Creating SS restraints... Processing helix chain 'A' and resid 24 through 32 removed outlier: 3.752A pdb=" N ARG A 31 " --> pdb=" O VAL A 27 " (cutoff:3.500A) Processing helix chain 'A' and resid 41 through 50 Processing helix chain 'A' and resid 53 through 65 Processing helix chain 'A' and resid 66 through 71 Processing helix chain 'A' and resid 75 through 105 removed outlier: 5.545A pdb=" N LEU A 81 " --> pdb=" O LYS A 77 " (cutoff:3.500A) removed outlier: 5.366A pdb=" N GLY A 82 " --> pdb=" O GLU A 78 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N LEU A 93 " --> pdb=" O SER A 89 " (cutoff:3.500A) Proline residue: A 96 - end of helix Processing helix chain 'A' and resid 108 through 116 removed outlier: 3.838A pdb=" N GLY A 112 " --> pdb=" O PRO A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 127 removed outlier: 3.505A pdb=" N PHE A 125 " --> pdb=" O ILE A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 152 Processing helix chain 'A' and resid 168 through 196 Processing helix chain 'A' and resid 197 through 205 removed outlier: 3.818A pdb=" N PHE A 200 " --> pdb=" O ARG A 197 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 225 Processing helix chain 'A' and resid 225 through 231 Processing helix chain 'A' and resid 241 through 254 Processing helix chain 'A' and resid 255 through 257 No H-bonds generated for 'chain 'A' and resid 255 through 257' Processing helix chain 'A' and resid 258 through 282 Processing helix chain 'A' and resid 291 through 308 removed outlier: 3.893A pdb=" N PHE A 295 " --> pdb=" O PRO A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 313 Processing helix chain 'A' and resid 332 through 334 No H-bonds generated for 'chain 'A' and resid 332 through 334' Processing helix chain 'A' and resid 335 through 363 removed outlier: 6.071A pdb=" N VAL A 341 " --> pdb=" O HIS A 337 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N ASP A 342 " --> pdb=" O LEU A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 388 removed outlier: 3.792A pdb=" N LEU A 387 " --> pdb=" O SER A 383 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N PHE A 388 " --> pdb=" O ILE A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 397 through 406 Processing helix chain 'A' and resid 411 through 427 Processing helix chain 'A' and resid 428 through 433 removed outlier: 3.591A pdb=" N GLU A 433 " --> pdb=" O PHE A 430 " (cutoff:3.500A) Processing helix chain 'A' and resid 436 through 448 removed outlier: 3.647A pdb=" N LEU A 440 " --> pdb=" O PRO A 436 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 453 Processing helix chain 'A' and resid 456 through 465 removed outlier: 3.743A pdb=" N PHE A 460 " --> pdb=" O SER A 456 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 482 Processing helix chain 'A' and resid 485 through 505 removed outlier: 3.530A pdb=" N ILE A 489 " --> pdb=" O ASP A 485 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N VAL A 499 " --> pdb=" O ALA A 495 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ILE A 500 " --> pdb=" O LEU A 496 " (cutoff:3.500A) Processing helix chain 'A' and resid 523 through 527 removed outlier: 4.420A pdb=" N GLU A 527 " --> pdb=" O ILE A 523 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 523 through 527' Processing helix chain 'A' and resid 545 through 560 removed outlier: 4.823A pdb=" N ASP A 550 " --> pdb=" O TYR A 546 " (cutoff:3.500A) removed outlier: 5.866A pdb=" N LEU A 551 " --> pdb=" O ALA A 547 " (cutoff:3.500A) Processing helix chain 'A' and resid 563 through 579 removed outlier: 3.562A pdb=" N ALA A 579 " --> pdb=" O MET A 575 " (cutoff:3.500A) Processing helix chain 'A' and resid 626 through 631 Processing helix chain 'A' and resid 653 through 670 removed outlier: 3.704A pdb=" N VAL A 670 " --> pdb=" O GLU A 666 " (cutoff:3.500A) Processing helix chain 'A' and resid 680 through 690 Processing helix chain 'A' and resid 691 through 700 removed outlier: 3.772A pdb=" N GLU A 694 " --> pdb=" O ARG A 691 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N ASN A 695 " --> pdb=" O PHE A 692 " (cutoff:3.500A) Proline residue: A 696 - end of helix Processing helix chain 'A' and resid 705 through 725 removed outlier: 3.710A pdb=" N SER A 725 " --> pdb=" O GLU A 721 " (cutoff:3.500A) Processing helix chain 'B' and resid 24 through 32 removed outlier: 3.752A pdb=" N ARG B 31 " --> pdb=" O VAL B 27 " (cutoff:3.500A) Processing helix chain 'B' and resid 41 through 50 Processing helix chain 'B' and resid 53 through 65 Processing helix chain 'B' and resid 66 through 71 Processing helix chain 'B' and resid 75 through 105 removed outlier: 5.544A pdb=" N LEU B 81 " --> pdb=" O LYS B 77 " (cutoff:3.500A) removed outlier: 5.366A pdb=" N GLY B 82 " --> pdb=" O GLU B 78 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N LEU B 93 " --> pdb=" O SER B 89 " (cutoff:3.500A) Proline residue: B 96 - end of helix Processing helix chain 'B' and resid 108 through 116 removed outlier: 3.838A pdb=" N GLY B 112 " --> pdb=" O PRO B 108 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 127 removed outlier: 3.505A pdb=" N PHE B 125 " --> pdb=" O ILE B 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 152 Processing helix chain 'B' and resid 168 through 196 Processing helix chain 'B' and resid 197 through 205 removed outlier: 3.818A pdb=" N PHE B 200 " --> pdb=" O ARG B 197 " (cutoff:3.500A) Processing helix chain 'B' and resid 206 through 225 Processing helix chain 'B' and resid 225 through 231 Processing helix chain 'B' and resid 241 through 254 Processing helix chain 'B' and resid 255 through 257 No H-bonds generated for 'chain 'B' and resid 255 through 257' Processing helix chain 'B' and resid 258 through 282 Processing helix chain 'B' and resid 291 through 308 removed outlier: 3.894A pdb=" N PHE B 295 " --> pdb=" O PRO B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 313 Processing helix chain 'B' and resid 332 through 334 No H-bonds generated for 'chain 'B' and resid 332 through 334' Processing helix chain 'B' and resid 335 through 363 removed outlier: 6.070A pdb=" N VAL B 341 " --> pdb=" O HIS B 337 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N ASP B 342 " --> pdb=" O LEU B 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 370 through 388 removed outlier: 3.793A pdb=" N LEU B 387 " --> pdb=" O SER B 383 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N PHE B 388 " --> pdb=" O ILE B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 397 through 406 Processing helix chain 'B' and resid 411 through 427 Processing helix chain 'B' and resid 428 through 433 removed outlier: 3.591A pdb=" N GLU B 433 " --> pdb=" O PHE B 430 " (cutoff:3.500A) Processing helix chain 'B' and resid 436 through 448 removed outlier: 3.647A pdb=" N LEU B 440 " --> pdb=" O PRO B 436 " (cutoff:3.500A) Processing helix chain 'B' and resid 448 through 453 Processing helix chain 'B' and resid 456 through 465 removed outlier: 3.743A pdb=" N PHE B 460 " --> pdb=" O SER B 456 " (cutoff:3.500A) Processing helix chain 'B' and resid 465 through 482 Processing helix chain 'B' and resid 485 through 505 removed outlier: 3.530A pdb=" N ILE B 489 " --> pdb=" O ASP B 485 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N VAL B 499 " --> pdb=" O ALA B 495 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ILE B 500 " --> pdb=" O LEU B 496 " (cutoff:3.500A) Processing helix chain 'B' and resid 523 through 527 removed outlier: 4.420A pdb=" N GLU B 527 " --> pdb=" O ILE B 523 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 523 through 527' Processing helix chain 'B' and resid 545 through 560 removed outlier: 4.823A pdb=" N ASP B 550 " --> pdb=" O TYR B 546 " (cutoff:3.500A) removed outlier: 5.866A pdb=" N LEU B 551 " --> pdb=" O ALA B 547 " (cutoff:3.500A) Processing helix chain 'B' and resid 563 through 579 removed outlier: 3.561A pdb=" N ALA B 579 " --> pdb=" O MET B 575 " (cutoff:3.500A) Processing helix chain 'B' and resid 626 through 631 Processing helix chain 'B' and resid 653 through 670 removed outlier: 3.704A pdb=" N VAL B 670 " --> pdb=" O GLU B 666 " (cutoff:3.500A) Processing helix chain 'B' and resid 680 through 690 Processing helix chain 'B' and resid 691 through 700 removed outlier: 3.772A pdb=" N GLU B 694 " --> pdb=" O ARG B 691 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N ASN B 695 " --> pdb=" O PHE B 692 " (cutoff:3.500A) Proline residue: B 696 - end of helix Processing helix chain 'B' and resid 705 through 725 removed outlier: 3.710A pdb=" N SER B 725 " --> pdb=" O GLU B 721 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 15 through 21 Processing sheet with id=AA2, first strand: chain 'A' and resid 133 through 135 removed outlier: 4.633A pdb=" N SER A 133 " --> pdb=" O SER A 396 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 520 through 522 removed outlier: 4.618A pdb=" N ILE A 537 " --> pdb=" O LEU A 511 " (cutoff:3.500A) removed outlier: 8.555A pdb=" N LYS A 513 " --> pdb=" O ILE A 535 " (cutoff:3.500A) removed outlier: 12.218A pdb=" N ILE A 535 " --> pdb=" O LYS A 513 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N LYS A 536 " --> pdb=" O ILE A 643 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N ASP A 645 " --> pdb=" O LYS A 536 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N PHE A 538 " --> pdb=" O ASP A 645 " (cutoff:3.500A) removed outlier: 8.261A pdb=" N PHE A 703 " --> pdb=" O VAL A 674 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N LEU A 676 " --> pdb=" O PHE A 703 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 133 through 135 removed outlier: 4.633A pdb=" N SER B 133 " --> pdb=" O SER B 396 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 520 through 522 removed outlier: 4.618A pdb=" N ILE B 537 " --> pdb=" O LEU B 511 " (cutoff:3.500A) removed outlier: 8.554A pdb=" N LYS B 513 " --> pdb=" O ILE B 535 " (cutoff:3.500A) removed outlier: 12.217A pdb=" N ILE B 535 " --> pdb=" O LYS B 513 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N LYS B 536 " --> pdb=" O ILE B 643 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N ASP B 645 " --> pdb=" O LYS B 536 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N PHE B 538 " --> pdb=" O ASP B 645 " (cutoff:3.500A) removed outlier: 8.262A pdb=" N PHE B 703 " --> pdb=" O VAL B 674 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N LEU B 676 " --> pdb=" O PHE B 703 " (cutoff:3.500A) 672 hydrogen bonds defined for protein. 1950 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.89 Time building geometry restraints manager: 1.06 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3238 1.34 - 1.46: 2221 1.46 - 1.58: 5972 1.58 - 1.69: 0 1.69 - 1.81: 78 Bond restraints: 11509 Sorted by residual: bond pdb=" CB GLU B 721 " pdb=" CG GLU B 721 " ideal model delta sigma weight residual 1.520 1.569 -0.049 3.00e-02 1.11e+03 2.62e+00 bond pdb=" CB GLU A 721 " pdb=" CG GLU A 721 " ideal model delta sigma weight residual 1.520 1.568 -0.048 3.00e-02 1.11e+03 2.60e+00 bond pdb=" C3 CLR A 802 " pdb=" O1 CLR A 802 " ideal model delta sigma weight residual 1.413 1.435 -0.022 2.00e-02 2.50e+03 1.16e+00 bond pdb=" C3 CLR B 802 " pdb=" O1 CLR B 802 " ideal model delta sigma weight residual 1.413 1.434 -0.021 2.00e-02 2.50e+03 1.15e+00 bond pdb=" CG GLU B 721 " pdb=" CD GLU B 721 " ideal model delta sigma weight residual 1.516 1.540 -0.024 2.50e-02 1.60e+03 9.20e-01 ... (remaining 11504 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.61: 14310 1.61 - 3.21: 337 3.21 - 4.82: 629 4.82 - 6.42: 18 6.42 - 8.03: 2 Bond angle restraints: 15296 Sorted by residual: angle pdb=" N GLU B 527 " pdb=" CA GLU B 527 " pdb=" CB GLU B 527 " ideal model delta sigma weight residual 114.27 108.71 5.56 1.64e+00 3.72e-01 1.15e+01 angle pdb=" N GLU A 527 " pdb=" CA GLU A 527 " pdb=" CB GLU A 527 " ideal model delta sigma weight residual 114.27 108.72 5.55 1.64e+00 3.72e-01 1.14e+01 angle pdb=" N ASN A 548 " pdb=" CA ASN A 548 " pdb=" C ASN A 548 " ideal model delta sigma weight residual 114.75 110.90 3.85 1.26e+00 6.30e-01 9.33e+00 angle pdb=" N ASN B 548 " pdb=" CA ASN B 548 " pdb=" C ASN B 548 " ideal model delta sigma weight residual 114.75 110.92 3.83 1.26e+00 6.30e-01 9.25e+00 angle pdb=" CB MET A 575 " pdb=" CG MET A 575 " pdb=" SD MET A 575 " ideal model delta sigma weight residual 112.70 120.73 -8.03 3.00e+00 1.11e-01 7.16e+00 ... (remaining 15291 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.35: 6380 16.35 - 32.70: 432 32.70 - 49.05: 87 49.05 - 65.40: 30 65.40 - 81.75: 4 Dihedral angle restraints: 6933 sinusoidal: 3009 harmonic: 3924 Sorted by residual: dihedral pdb=" CA GLU A 527 " pdb=" C GLU A 527 " pdb=" N GLU A 528 " pdb=" CA GLU A 528 " ideal model delta harmonic sigma weight residual 180.00 155.17 24.83 0 5.00e+00 4.00e-02 2.47e+01 dihedral pdb=" CA GLU B 527 " pdb=" C GLU B 527 " pdb=" N GLU B 528 " pdb=" CA GLU B 528 " ideal model delta harmonic sigma weight residual 180.00 155.23 24.77 0 5.00e+00 4.00e-02 2.45e+01 dihedral pdb=" CA PHE B 23 " pdb=" C PHE B 23 " pdb=" N SER B 24 " pdb=" CA SER B 24 " ideal model delta harmonic sigma weight residual 180.00 160.59 19.41 0 5.00e+00 4.00e-02 1.51e+01 ... (remaining 6930 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 936 0.028 - 0.056: 507 0.056 - 0.084: 188 0.084 - 0.112: 90 0.112 - 0.140: 23 Chirality restraints: 1744 Sorted by residual: chirality pdb=" C17 CLR A 802 " pdb=" C13 CLR A 802 " pdb=" C16 CLR A 802 " pdb=" C20 CLR A 802 " both_signs ideal model delta sigma weight residual False 2.55 2.41 0.14 2.00e-01 2.50e+01 4.88e-01 chirality pdb=" CA LEU A 271 " pdb=" N LEU A 271 " pdb=" C LEU A 271 " pdb=" CB LEU A 271 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.75e-01 chirality pdb=" CA LEU B 271 " pdb=" N LEU B 271 " pdb=" C LEU B 271 " pdb=" CB LEU B 271 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.14 2.00e-01 2.50e+01 4.56e-01 ... (remaining 1741 not shown) Planarity restraints: 1808 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASP A 686 " -0.008 2.00e-02 2.50e+03 1.62e-02 2.63e+00 pdb=" CG ASP A 686 " 0.028 2.00e-02 2.50e+03 pdb=" OD1 ASP A 686 " -0.010 2.00e-02 2.50e+03 pdb=" OD2 ASP A 686 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP B 686 " 0.008 2.00e-02 2.50e+03 1.59e-02 2.52e+00 pdb=" CG ASP B 686 " -0.027 2.00e-02 2.50e+03 pdb=" OD1 ASP B 686 " 0.010 2.00e-02 2.50e+03 pdb=" OD2 ASP B 686 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR B 53 " -0.023 5.00e-02 4.00e+02 3.42e-02 1.87e+00 pdb=" N PRO B 54 " 0.059 5.00e-02 4.00e+02 pdb=" CA PRO B 54 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO B 54 " -0.019 5.00e-02 4.00e+02 ... (remaining 1805 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.73: 473 2.73 - 3.27: 11237 3.27 - 3.81: 18423 3.81 - 4.36: 23731 4.36 - 4.90: 39842 Nonbonded interactions: 93706 Sorted by model distance: nonbonded pdb=" O ALA B 495 " pdb=" OG1 THR B 498 " model vdw 2.184 3.040 nonbonded pdb=" O ALA A 495 " pdb=" OG1 THR A 498 " model vdw 2.184 3.040 nonbonded pdb=" OD1 ASP A 645 " pdb=" OG1 THR A 647 " model vdw 2.232 3.040 nonbonded pdb=" OD1 ASP B 645 " pdb=" OG1 THR B 647 " model vdw 2.232 3.040 nonbonded pdb=" O VAL B 402 " pdb=" OG1 THR B 406 " model vdw 2.257 3.040 ... (remaining 93701 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 13 through 835 or resid 841 through 847)) selection = (chain 'B' and (resid 13 through 835 or resid 841 through 847)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.040 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: 0.270 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.180 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 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 : 0.003 0.049 11509 Z= 0.155 Angle : 0.955 8.029 15296 Z= 0.403 Chirality : 0.042 0.140 1744 Planarity : 0.004 0.034 1808 Dihedral : 12.205 81.749 4421 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 0.71 % Allowed : 0.71 % Favored : 98.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.33 (0.23), residues: 1352 helix: 1.36 (0.17), residues: 904 sheet: 1.54 (0.72), residues: 50 loop : -0.18 (0.32), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 716 TYR 0.020 0.001 TYR A 79 PHE 0.014 0.001 PHE A 625 TRP 0.010 0.001 TRP B 472 HIS 0.004 0.001 HIS B 707 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.15 (11509) covalent geometry : angle 0.95492 / 0.40 (15296) hydrogen bonds : bond 0.12828 / 8.51 ( 672) hydrogen bonds : angle 6.13507 / 4.48 ( 1950) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2704 Ramachandran restraints generated. 1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2704 Ramachandran restraints generated. 1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 135 time to evaluate : 0.253 Fit side-chains REVERT: A 316 ASP cc_start: 0.8311 (m-30) cc_final: 0.8035 (m-30) REVERT: A 463 ARG cc_start: 0.7706 (mtm-85) cc_final: 0.7484 (mtp180) REVERT: B 316 ASP cc_start: 0.8308 (m-30) cc_final: 0.8030 (m-30) REVERT: B 463 ARG cc_start: 0.7690 (mtm-85) cc_final: 0.7458 (mtp180) outliers start: 8 outliers final: 0 residues processed: 137 average time/residue: 0.5092 time to fit residues: 75.3785 Evaluate side-chains 100 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 100 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 98 optimal weight: 10.0000 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 0.5980 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 0.1980 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 55 optimal weight: 4.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 14 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.147031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.111161 restraints weight = 12630.918| |-----------------------------------------------------------------------------| r_work (start): 0.3342 rms_B_bonded: 1.86 r_work: 0.3238 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3118 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.0938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 11509 Z= 0.128 Angle : 0.510 6.529 15296 Z= 0.262 Chirality : 0.042 0.136 1744 Planarity : 0.004 0.037 1808 Dihedral : 6.782 57.376 2051 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 0.88 % Allowed : 7.14 % Favored : 91.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.83 (0.23), residues: 1352 helix: 1.81 (0.18), residues: 890 sheet: 3.00 (0.71), residues: 38 loop : -0.16 (0.31), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 31 TYR 0.016 0.001 TYR A 16 PHE 0.014 0.001 PHE A 111 TRP 0.011 0.001 TRP B 70 HIS 0.004 0.001 HIS A 337 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.13 (11509) covalent geometry : angle 0.50976 / 0.26 (15296) hydrogen bonds : bond 0.04093 / 2.63 ( 672) hydrogen bonds : angle 4.66367 / 3.43 ( 1950) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2704 Ramachandran restraints generated. 1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2704 Ramachandran restraints generated. 1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 105 time to evaluate : 0.292 Fit side-chains REVERT: A 267 MET cc_start: 0.7727 (ttp) cc_final: 0.7524 (ttp) REVERT: A 271 LEU cc_start: 0.7771 (mt) cc_final: 0.7519 (mp) REVERT: A 316 ASP cc_start: 0.8704 (m-30) cc_final: 0.8268 (m-30) REVERT: A 463 ARG cc_start: 0.7799 (mtm-85) cc_final: 0.7452 (mtp180) REVERT: A 572 ARG cc_start: 0.7008 (mtm110) cc_final: 0.6755 (mtm110) REVERT: B 267 MET cc_start: 0.7797 (ttp) cc_final: 0.7596 (ttp) REVERT: B 271 LEU cc_start: 0.7876 (mt) cc_final: 0.7647 (mp) REVERT: B 316 ASP cc_start: 0.8668 (m-30) cc_final: 0.8219 (m-30) REVERT: B 463 ARG cc_start: 0.7750 (mtm-85) cc_final: 0.7455 (mtp180) REVERT: B 682 GLN cc_start: 0.7976 (OUTLIER) cc_final: 0.7181 (tt0) outliers start: 10 outliers final: 5 residues processed: 106 average time/residue: 0.4479 time to fit residues: 51.9185 Evaluate side-chains 99 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 93 time to evaluate : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain A residue 474 THR Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 36 ASP Chi-restraints excluded: chain B residue 474 THR Chi-restraints excluded: chain B residue 682 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 106 optimal weight: 6.9990 chunk 115 optimal weight: 7.9990 chunk 91 optimal weight: 4.9990 chunk 77 optimal weight: 2.9990 chunk 121 optimal weight: 0.6980 chunk 26 optimal weight: 10.0000 chunk 113 optimal weight: 2.9990 chunk 109 optimal weight: 3.9990 chunk 28 optimal weight: 7.9990 chunk 111 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 14 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.143959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.107855 restraints weight = 12779.959| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 1.86 r_work: 0.3196 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3075 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.1330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 11509 Z= 0.150 Angle : 0.512 7.059 15296 Z= 0.263 Chirality : 0.042 0.132 1744 Planarity : 0.004 0.046 1808 Dihedral : 7.107 57.705 2051 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 1.23 % Allowed : 8.29 % Favored : 90.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.69 (0.23), residues: 1352 helix: 1.81 (0.18), residues: 888 sheet: 2.85 (0.69), residues: 38 loop : -0.50 (0.29), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 31 TYR 0.015 0.002 TYR A 16 PHE 0.017 0.001 PHE A 241 TRP 0.011 0.002 TRP A 70 HIS 0.003 0.001 HIS B 640 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.15 (11509) covalent geometry : angle 0.51204 / 0.26 (15296) hydrogen bonds : bond 0.04215 / 2.74 ( 672) hydrogen bonds : angle 4.49614 / 3.31 ( 1950) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2704 Ramachandran restraints generated. 1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2704 Ramachandran restraints generated. 1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 111 time to evaluate : 0.406 Fit side-chains REVERT: A 122 MET cc_start: 0.7984 (mtm) cc_final: 0.7702 (mtp) REVERT: A 316 ASP cc_start: 0.8730 (m-30) cc_final: 0.8285 (m-30) REVERT: A 357 MET cc_start: 0.8565 (tpt) cc_final: 0.7920 (tpt) REVERT: A 463 ARG cc_start: 0.7763 (mtm-85) cc_final: 0.7314 (mtp180) REVERT: A 682 GLN cc_start: 0.8031 (OUTLIER) cc_final: 0.7099 (tt0) REVERT: B 122 MET cc_start: 0.7959 (mtm) cc_final: 0.7667 (mtp) REVERT: B 267 MET cc_start: 0.7750 (ttp) cc_final: 0.7395 (tmm) REVERT: B 316 ASP cc_start: 0.8710 (m-30) cc_final: 0.8233 (m-30) REVERT: B 357 MET cc_start: 0.8569 (tpt) cc_final: 0.8060 (tpt) REVERT: B 463 ARG cc_start: 0.7757 (mtm-85) cc_final: 0.7381 (mtp180) REVERT: B 615 LYS cc_start: 0.7931 (tptm) cc_final: 0.7673 (tppp) REVERT: B 682 GLN cc_start: 0.8006 (OUTLIER) cc_final: 0.7081 (tt0) outliers start: 14 outliers final: 5 residues processed: 112 average time/residue: 0.4763 time to fit residues: 58.0804 Evaluate side-chains 103 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 96 time to evaluate : 0.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain A residue 474 THR Chi-restraints excluded: chain A residue 682 GLN Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 36 ASP Chi-restraints excluded: chain B residue 474 THR Chi-restraints excluded: chain B residue 682 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 13 optimal weight: 0.8980 chunk 120 optimal weight: 0.9990 chunk 73 optimal weight: 3.9990 chunk 67 optimal weight: 7.9990 chunk 33 optimal weight: 6.9990 chunk 82 optimal weight: 0.0670 chunk 53 optimal weight: 8.9990 chunk 14 optimal weight: 5.9990 chunk 110 optimal weight: 7.9990 chunk 107 optimal weight: 10.0000 chunk 17 optimal weight: 2.9990 overall best weight: 1.7924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 389 GLN B 389 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.144441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.108732 restraints weight = 12799.395| |-----------------------------------------------------------------------------| r_work (start): 0.3310 rms_B_bonded: 1.85 r_work: 0.3205 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3083 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.1494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 11509 Z= 0.129 Angle : 0.491 7.285 15296 Z= 0.250 Chirality : 0.042 0.128 1744 Planarity : 0.004 0.046 1808 Dihedral : 7.030 59.985 2051 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 1.59 % Allowed : 9.44 % Favored : 88.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.68 (0.23), residues: 1352 helix: 1.81 (0.18), residues: 890 sheet: 2.72 (0.69), residues: 38 loop : -0.51 (0.29), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 31 TYR 0.014 0.001 TYR B 16 PHE 0.014 0.001 PHE A 111 TRP 0.012 0.002 TRP B 70 HIS 0.003 0.001 HIS B 640 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.13 (11509) covalent geometry : angle 0.49089 / 0.25 (15296) hydrogen bonds : bond 0.03905 / 2.53 ( 672) hydrogen bonds : angle 4.39282 / 3.23 ( 1950) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2704 Ramachandran restraints generated. 1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2704 Ramachandran restraints generated. 1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 99 time to evaluate : 0.274 Fit side-chains REVERT: A 122 MET cc_start: 0.7984 (mtm) cc_final: 0.7689 (mtp) REVERT: A 271 LEU cc_start: 0.7728 (mt) cc_final: 0.7520 (mp) REVERT: A 316 ASP cc_start: 0.8735 (m-30) cc_final: 0.8271 (m-30) REVERT: A 357 MET cc_start: 0.8562 (tpt) cc_final: 0.8027 (tpt) REVERT: A 463 ARG cc_start: 0.7799 (mtm-85) cc_final: 0.7419 (mtp180) REVERT: A 682 GLN cc_start: 0.8022 (OUTLIER) cc_final: 0.7177 (tt0) REVERT: B 316 ASP cc_start: 0.8720 (m-30) cc_final: 0.8252 (m-30) REVERT: B 357 MET cc_start: 0.8581 (tpt) cc_final: 0.8114 (tpt) REVERT: B 463 ARG cc_start: 0.7740 (mtm-85) cc_final: 0.7350 (mtp180) REVERT: B 615 LYS cc_start: 0.7961 (tptm) cc_final: 0.7730 (tppp) REVERT: B 682 GLN cc_start: 0.7995 (OUTLIER) cc_final: 0.7157 (tt0) outliers start: 18 outliers final: 7 residues processed: 104 average time/residue: 0.4673 time to fit residues: 52.9929 Evaluate side-chains 106 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 97 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain A residue 36 ASP Chi-restraints excluded: chain A residue 474 THR Chi-restraints excluded: chain A residue 682 GLN Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 180 MET Chi-restraints excluded: chain B residue 348 ILE Chi-restraints excluded: chain B residue 474 THR Chi-restraints excluded: chain B residue 682 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 23 optimal weight: 6.9990 chunk 93 optimal weight: 10.0000 chunk 84 optimal weight: 10.0000 chunk 109 optimal weight: 4.9990 chunk 53 optimal weight: 7.9990 chunk 51 optimal weight: 0.0020 chunk 48 optimal weight: 8.9990 chunk 87 optimal weight: 4.9990 chunk 68 optimal weight: 0.9980 chunk 132 optimal weight: 2.9990 chunk 50 optimal weight: 0.7980 overall best weight: 1.9592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 389 GLN B 389 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.143851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.108074 restraints weight = 12759.961| |-----------------------------------------------------------------------------| r_work (start): 0.3300 rms_B_bonded: 1.85 r_work: 0.3194 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3073 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.1605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 11509 Z= 0.137 Angle : 0.493 8.279 15296 Z= 0.251 Chirality : 0.042 0.128 1744 Planarity : 0.004 0.047 1808 Dihedral : 7.069 57.737 2051 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 1.59 % Allowed : 9.96 % Favored : 88.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.65 (0.23), residues: 1352 helix: 1.81 (0.18), residues: 888 sheet: 2.65 (0.69), residues: 38 loop : -0.56 (0.29), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 31 TYR 0.014 0.001 TYR B 16 PHE 0.015 0.001 PHE A 111 TRP 0.012 0.002 TRP A 70 HIS 0.003 0.001 HIS B 640 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.14 (11509) covalent geometry : angle 0.49268 / 0.25 (15296) hydrogen bonds : bond 0.03975 / 2.58 ( 672) hydrogen bonds : angle 4.36708 / 3.21 ( 1950) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2704 Ramachandran restraints generated. 1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2704 Ramachandran restraints generated. 1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 99 time to evaluate : 0.429 Fit side-chains REVERT: A 122 MET cc_start: 0.8015 (mtm) cc_final: 0.7704 (mtp) REVERT: A 271 LEU cc_start: 0.7802 (mt) cc_final: 0.7581 (mp) REVERT: A 316 ASP cc_start: 0.8754 (m-30) cc_final: 0.8293 (m-30) REVERT: A 463 ARG cc_start: 0.7827 (mtm-85) cc_final: 0.7425 (mtp180) REVERT: A 615 LYS cc_start: 0.7975 (tptm) cc_final: 0.7661 (tppp) REVERT: A 682 GLN cc_start: 0.8026 (OUTLIER) cc_final: 0.7208 (tt0) REVERT: B 122 MET cc_start: 0.7994 (mtm) cc_final: 0.7682 (mtp) REVERT: B 316 ASP cc_start: 0.8735 (m-30) cc_final: 0.8264 (m-30) REVERT: B 357 MET cc_start: 0.8595 (tpt) cc_final: 0.8137 (tpt) REVERT: B 463 ARG cc_start: 0.7788 (mtm-85) cc_final: 0.7371 (mtp180) REVERT: B 615 LYS cc_start: 0.7921 (tptm) cc_final: 0.7720 (tppp) REVERT: B 682 GLN cc_start: 0.7976 (OUTLIER) cc_final: 0.7164 (tt0) outliers start: 18 outliers final: 7 residues processed: 105 average time/residue: 0.5357 time to fit residues: 61.1862 Evaluate side-chains 102 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 93 time to evaluate : 0.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain A residue 474 THR Chi-restraints excluded: chain A residue 682 GLN Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 36 ASP Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 180 MET Chi-restraints excluded: chain B residue 474 THR Chi-restraints excluded: chain B residue 682 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 96 optimal weight: 9.9990 chunk 56 optimal weight: 5.9990 chunk 82 optimal weight: 0.1980 chunk 73 optimal weight: 5.9990 chunk 17 optimal weight: 8.9990 chunk 27 optimal weight: 9.9990 chunk 112 optimal weight: 6.9990 chunk 52 optimal weight: 0.9990 chunk 123 optimal weight: 2.9990 chunk 119 optimal weight: 0.8980 chunk 74 optimal weight: 0.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 389 GLN B 389 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.144573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.108704 restraints weight = 12758.916| |-----------------------------------------------------------------------------| r_work (start): 0.3328 rms_B_bonded: 1.86 r_work: 0.3222 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3101 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.1713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 11509 Z= 0.107 Angle : 0.463 8.353 15296 Z= 0.236 Chirality : 0.041 0.127 1744 Planarity : 0.004 0.045 1808 Dihedral : 6.710 57.260 2051 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 1.32 % Allowed : 10.41 % Favored : 88.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.82 (0.23), residues: 1352 helix: 1.89 (0.18), residues: 892 sheet: 2.57 (0.70), residues: 36 loop : -0.35 (0.30), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 31 TYR 0.013 0.001 TYR A 16 PHE 0.013 0.001 PHE A 111 TRP 0.012 0.002 TRP A 70 HIS 0.002 0.001 HIS A 337 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.11 (11509) covalent geometry : angle 0.46260 / 0.24 (15296) hydrogen bonds : bond 0.03583 / 2.32 ( 672) hydrogen bonds : angle 4.25502 / 3.13 ( 1950) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2704 Ramachandran restraints generated. 1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2704 Ramachandran restraints generated. 1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 106 time to evaluate : 0.417 Fit side-chains REVERT: A 122 MET cc_start: 0.7975 (mtm) cc_final: 0.7666 (mtp) REVERT: A 169 GLU cc_start: 0.7578 (OUTLIER) cc_final: 0.7096 (OUTLIER) REVERT: A 271 LEU cc_start: 0.7799 (mt) cc_final: 0.7576 (mp) REVERT: A 316 ASP cc_start: 0.8736 (m-30) cc_final: 0.8270 (m-30) REVERT: A 357 MET cc_start: 0.8544 (tpt) cc_final: 0.8166 (tpt) REVERT: A 463 ARG cc_start: 0.7818 (mtm-85) cc_final: 0.7403 (mtp180) REVERT: A 615 LYS cc_start: 0.8003 (tptm) cc_final: 0.7711 (tppp) REVERT: A 682 GLN cc_start: 0.8007 (OUTLIER) cc_final: 0.7696 (tt0) REVERT: B 316 ASP cc_start: 0.8755 (m-30) cc_final: 0.8454 (m-30) REVERT: B 357 MET cc_start: 0.8555 (tpt) cc_final: 0.8200 (tpt) REVERT: B 463 ARG cc_start: 0.7795 (mtm-85) cc_final: 0.7377 (mtp180) REVERT: B 682 GLN cc_start: 0.7968 (OUTLIER) cc_final: 0.7639 (tt0) outliers start: 15 outliers final: 6 residues processed: 111 average time/residue: 0.4924 time to fit residues: 59.8360 Evaluate side-chains 107 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 99 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 GLU Chi-restraints excluded: chain A residue 474 THR Chi-restraints excluded: chain A residue 682 GLN Chi-restraints excluded: chain B residue 36 ASP Chi-restraints excluded: chain B residue 261 SER Chi-restraints excluded: chain B residue 348 ILE Chi-restraints excluded: chain B residue 474 THR Chi-restraints excluded: chain B residue 682 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 133 optimal weight: 3.9990 chunk 128 optimal weight: 3.9990 chunk 64 optimal weight: 7.9990 chunk 129 optimal weight: 0.9980 chunk 32 optimal weight: 10.0000 chunk 103 optimal weight: 7.9990 chunk 118 optimal weight: 0.0970 chunk 45 optimal weight: 8.9990 chunk 29 optimal weight: 10.0000 chunk 43 optimal weight: 4.9990 chunk 97 optimal weight: 9.9990 overall best weight: 2.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 389 GLN A 648 GLN B 389 GLN B 648 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.141888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.106210 restraints weight = 12802.572| |-----------------------------------------------------------------------------| r_work (start): 0.3278 rms_B_bonded: 1.82 r_work: 0.3172 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3051 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.1810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 11509 Z= 0.179 Angle : 0.539 9.156 15296 Z= 0.273 Chirality : 0.044 0.132 1744 Planarity : 0.005 0.050 1808 Dihedral : 7.485 59.877 2051 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 2.20 % Allowed : 10.23 % Favored : 87.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.54 (0.23), residues: 1352 helix: 1.66 (0.18), residues: 898 sheet: 2.48 (0.73), residues: 36 loop : -0.46 (0.30), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 211 TYR 0.016 0.001 TYR A 16 PHE 0.016 0.001 PHE A 111 TRP 0.011 0.002 TRP A 70 HIS 0.004 0.001 HIS B 640 Details of bonding type rmsd/Z covalent geometry : bond 0.00439 / 0.18 (11509) covalent geometry : angle 0.53878 / 0.27 (15296) hydrogen bonds : bond 0.04338 / 2.82 ( 672) hydrogen bonds : angle 4.41988 / 3.25 ( 1950) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2704 Ramachandran restraints generated. 1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2704 Ramachandran restraints generated. 1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 96 time to evaluate : 0.427 Fit side-chains REVERT: A 122 MET cc_start: 0.8044 (mtm) cc_final: 0.7738 (mtp) REVERT: A 267 MET cc_start: 0.7717 (ttp) cc_final: 0.7435 (tmm) REVERT: A 271 LEU cc_start: 0.7880 (mt) cc_final: 0.7657 (mp) REVERT: A 310 LYS cc_start: 0.7074 (tttt) cc_final: 0.6585 (tptt) REVERT: A 316 ASP cc_start: 0.8688 (m-30) cc_final: 0.8257 (m-30) REVERT: A 463 ARG cc_start: 0.7835 (mtm-85) cc_final: 0.7405 (mtp180) REVERT: A 615 LYS cc_start: 0.8050 (tptm) cc_final: 0.7794 (tppp) REVERT: A 682 GLN cc_start: 0.7923 (OUTLIER) cc_final: 0.7121 (tt0) REVERT: B 122 MET cc_start: 0.8004 (mtm) cc_final: 0.7690 (mtp) REVERT: B 310 LYS cc_start: 0.7098 (tttt) cc_final: 0.6621 (tptt) REVERT: B 316 ASP cc_start: 0.8700 (m-30) cc_final: 0.8266 (m-30) REVERT: B 463 ARG cc_start: 0.7793 (mtm-85) cc_final: 0.7361 (mtp180) REVERT: B 682 GLN cc_start: 0.7899 (OUTLIER) cc_final: 0.7596 (tt0) outliers start: 25 outliers final: 9 residues processed: 109 average time/residue: 0.5408 time to fit residues: 64.0113 Evaluate side-chains 101 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 90 time to evaluate : 0.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain A residue 180 MET Chi-restraints excluded: chain A residue 233 LYS Chi-restraints excluded: chain A residue 474 THR Chi-restraints excluded: chain A residue 682 GLN Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 36 ASP Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 261 SER Chi-restraints excluded: chain B residue 474 THR Chi-restraints excluded: chain B residue 682 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 69 optimal weight: 2.9990 chunk 43 optimal weight: 0.9980 chunk 116 optimal weight: 2.9990 chunk 7 optimal weight: 0.9980 chunk 131 optimal weight: 5.9990 chunk 81 optimal weight: 0.5980 chunk 32 optimal weight: 8.9990 chunk 109 optimal weight: 8.9990 chunk 35 optimal weight: 0.9980 chunk 86 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 389 GLN B 389 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.145040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.109746 restraints weight = 12676.615| |-----------------------------------------------------------------------------| r_work (start): 0.3316 rms_B_bonded: 1.83 r_work: 0.3212 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3091 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.1870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 11509 Z= 0.108 Angle : 0.480 9.804 15296 Z= 0.242 Chirality : 0.041 0.127 1744 Planarity : 0.004 0.045 1808 Dihedral : 6.912 57.574 2051 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 1.32 % Allowed : 11.38 % Favored : 87.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.74 (0.23), residues: 1352 helix: 1.85 (0.18), residues: 890 sheet: 2.38 (0.70), residues: 36 loop : -0.42 (0.29), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 31 TYR 0.013 0.001 TYR A 16 PHE 0.014 0.001 PHE A 269 TRP 0.013 0.002 TRP A 70 HIS 0.002 0.001 HIS A 337 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.11 (11509) covalent geometry : angle 0.47953 / 0.24 (15296) hydrogen bonds : bond 0.03648 / 2.36 ( 672) hydrogen bonds : angle 4.27550 / 3.15 ( 1950) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2704 Ramachandran restraints generated. 1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2704 Ramachandran restraints generated. 1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 97 time to evaluate : 0.263 Fit side-chains REVERT: A 122 MET cc_start: 0.7990 (mtm) cc_final: 0.7684 (mtp) REVERT: A 310 LYS cc_start: 0.7085 (tttt) cc_final: 0.6644 (tptt) REVERT: A 316 ASP cc_start: 0.8711 (m-30) cc_final: 0.8285 (m-30) REVERT: A 463 ARG cc_start: 0.7846 (mtm-85) cc_final: 0.7414 (mtp180) REVERT: A 615 LYS cc_start: 0.8040 (tptm) cc_final: 0.7806 (tppp) REVERT: B 122 MET cc_start: 0.8011 (mtm) cc_final: 0.7705 (mtp) REVERT: B 310 LYS cc_start: 0.7098 (tttt) cc_final: 0.6654 (tptt) REVERT: B 316 ASP cc_start: 0.8713 (m-30) cc_final: 0.8254 (m-30) REVERT: B 463 ARG cc_start: 0.7808 (mtm-85) cc_final: 0.7381 (mtp180) outliers start: 15 outliers final: 4 residues processed: 103 average time/residue: 0.4554 time to fit residues: 51.2595 Evaluate side-chains 99 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 95 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 180 MET Chi-restraints excluded: chain A residue 474 THR Chi-restraints excluded: chain B residue 261 SER Chi-restraints excluded: chain B residue 474 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 32 optimal weight: 10.0000 chunk 3 optimal weight: 8.9990 chunk 11 optimal weight: 9.9990 chunk 60 optimal weight: 0.5980 chunk 21 optimal weight: 6.9990 chunk 46 optimal weight: 0.8980 chunk 23 optimal weight: 7.9990 chunk 100 optimal weight: 9.9990 chunk 131 optimal weight: 8.9990 chunk 90 optimal weight: 10.0000 chunk 42 optimal weight: 7.9990 overall best weight: 4.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 389 GLN A 454 GLN B 389 GLN B 454 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.139400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.103630 restraints weight = 12706.016| |-----------------------------------------------------------------------------| r_work (start): 0.3227 rms_B_bonded: 1.81 r_work: 0.3120 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3000 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.2023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.050 11509 Z= 0.276 Angle : 0.612 10.358 15296 Z= 0.312 Chirality : 0.047 0.135 1744 Planarity : 0.005 0.053 1808 Dihedral : 8.380 59.867 2051 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 1.41 % Allowed : 11.64 % Favored : 86.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.17 (0.23), residues: 1352 helix: 1.43 (0.17), residues: 894 sheet: 2.29 (0.75), residues: 36 loop : -0.71 (0.29), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 211 TYR 0.019 0.002 TYR A 16 PHE 0.020 0.002 PHE A 111 TRP 0.010 0.002 TRP A 70 HIS 0.006 0.001 HIS A 640 Details of bonding type rmsd/Z covalent geometry : bond 0.00688 / 0.28 (11509) covalent geometry : angle 0.61238 / 0.31 (15296) hydrogen bonds : bond 0.05069 / 3.31 ( 672) hydrogen bonds : angle 4.57354 / 3.36 ( 1950) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2704 Ramachandran restraints generated. 1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2704 Ramachandran restraints generated. 1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 90 time to evaluate : 0.368 Fit side-chains REVERT: A 122 MET cc_start: 0.8103 (mtm) cc_final: 0.7804 (mtp) REVERT: A 310 LYS cc_start: 0.7081 (tttt) cc_final: 0.6615 (tptt) REVERT: A 316 ASP cc_start: 0.8737 (m-30) cc_final: 0.8318 (m-30) REVERT: A 463 ARG cc_start: 0.7840 (mtm-85) cc_final: 0.7378 (mtp180) REVERT: A 615 LYS cc_start: 0.8060 (tptm) cc_final: 0.7831 (tppp) REVERT: B 122 MET cc_start: 0.8084 (mtm) cc_final: 0.7785 (mtp) REVERT: B 310 LYS cc_start: 0.7113 (tttt) cc_final: 0.6631 (tptt) REVERT: B 316 ASP cc_start: 0.8696 (m-30) cc_final: 0.8262 (m-30) REVERT: B 463 ARG cc_start: 0.7829 (mtm-85) cc_final: 0.7381 (mtp180) outliers start: 16 outliers final: 5 residues processed: 98 average time/residue: 0.5376 time to fit residues: 56.9471 Evaluate side-chains 95 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 90 time to evaluate : 0.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 233 LYS Chi-restraints excluded: chain A residue 474 THR Chi-restraints excluded: chain B residue 261 SER Chi-restraints excluded: chain B residue 390 THR Chi-restraints excluded: chain B residue 474 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 101 optimal weight: 3.9990 chunk 43 optimal weight: 1.9990 chunk 40 optimal weight: 5.9990 chunk 135 optimal weight: 0.9990 chunk 56 optimal weight: 8.9990 chunk 106 optimal weight: 0.7980 chunk 119 optimal weight: 0.9980 chunk 111 optimal weight: 2.9990 chunk 35 optimal weight: 5.9990 chunk 124 optimal weight: 6.9990 chunk 64 optimal weight: 3.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 389 GLN B 389 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.143171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.107507 restraints weight = 12755.348| |-----------------------------------------------------------------------------| r_work (start): 0.3290 rms_B_bonded: 1.84 r_work: 0.3186 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3065 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.2013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 11509 Z= 0.127 Angle : 0.496 10.527 15296 Z= 0.252 Chirality : 0.042 0.128 1744 Planarity : 0.004 0.049 1808 Dihedral : 7.524 59.684 2051 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 0.88 % Allowed : 11.99 % Favored : 87.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.52 (0.23), residues: 1352 helix: 1.69 (0.18), residues: 892 sheet: 2.24 (0.72), residues: 36 loop : -0.54 (0.29), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 211 TYR 0.014 0.001 TYR A 16 PHE 0.014 0.001 PHE A 269 TRP 0.013 0.002 TRP A 70 HIS 0.003 0.001 HIS A 640 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.13 (11509) covalent geometry : angle 0.49645 / 0.25 (15296) hydrogen bonds : bond 0.03913 / 2.53 ( 672) hydrogen bonds : angle 4.36417 / 3.21 ( 1950) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2704 Ramachandran restraints generated. 1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2704 Ramachandran restraints generated. 1352 Oldfield, 0 Emsley, 1352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 92 time to evaluate : 0.421 Fit side-chains REVERT: A 122 MET cc_start: 0.7931 (mtm) cc_final: 0.7621 (mtp) REVERT: A 310 LYS cc_start: 0.7056 (tttt) cc_final: 0.6590 (tptt) REVERT: A 316 ASP cc_start: 0.8725 (m-30) cc_final: 0.8265 (m-30) REVERT: A 463 ARG cc_start: 0.7805 (mtm-85) cc_final: 0.7352 (mtp180) REVERT: A 615 LYS cc_start: 0.8063 (tptm) cc_final: 0.7846 (tppp) REVERT: B 122 MET cc_start: 0.7943 (mtm) cc_final: 0.7634 (mtp) REVERT: B 310 LYS cc_start: 0.7093 (tttt) cc_final: 0.6615 (tptt) REVERT: B 316 ASP cc_start: 0.8697 (m-30) cc_final: 0.8405 (m-30) REVERT: B 463 ARG cc_start: 0.7752 (mtm-85) cc_final: 0.7297 (mtp180) outliers start: 10 outliers final: 4 residues processed: 98 average time/residue: 0.4475 time to fit residues: 48.0538 Evaluate side-chains 96 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 92 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain A residue 474 THR Chi-restraints excluded: chain B residue 261 SER Chi-restraints excluded: chain B residue 474 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 122 optimal weight: 3.9990 chunk 113 optimal weight: 2.9990 chunk 128 optimal weight: 6.9990 chunk 100 optimal weight: 8.9990 chunk 42 optimal weight: 7.9990 chunk 117 optimal weight: 2.9990 chunk 47 optimal weight: 6.9990 chunk 26 optimal weight: 10.0000 chunk 125 optimal weight: 0.9990 chunk 38 optimal weight: 10.0000 chunk 114 optimal weight: 2.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 389 GLN B 389 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.141276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.105609 restraints weight = 12684.153| |-----------------------------------------------------------------------------| r_work (start): 0.3258 rms_B_bonded: 1.82 r_work: 0.3151 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3031 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.2071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 11509 Z= 0.175 Angle : 0.537 10.592 15296 Z= 0.273 Chirality : 0.043 0.128 1744 Planarity : 0.004 0.049 1808 Dihedral : 7.824 58.128 2051 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 1.23 % Allowed : 11.73 % Favored : 87.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.45 (0.23), residues: 1352 helix: 1.63 (0.18), residues: 888 sheet: 2.30 (0.74), residues: 36 loop : -0.52 (0.29), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 211 TYR 0.016 0.001 TYR A 16 PHE 0.017 0.001 PHE B 111 TRP 0.012 0.002 TRP A 70 HIS 0.004 0.001 HIS B 640 Details of bonding type rmsd/Z covalent geometry : bond 0.00425 / 0.17 (11509) covalent geometry : angle 0.53694 / 0.27 (15296) hydrogen bonds : bond 0.04335 / 2.82 ( 672) hydrogen bonds : angle 4.42580 / 3.25 ( 1950) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3404.54 seconds wall clock time: 58 minutes 50.18 seconds (3530.18 seconds total)