Starting phenix.real_space_refine on Tue Jul 29 20:09:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7lgw_23331/07_2025/7lgw_23331.cif Found real_map, /net/cci-nas-00/data/ceres_data/7lgw_23331/07_2025/7lgw_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_2025/7lgw_23331.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7lgw_23331/07_2025/7lgw_23331.map" model { file = "/net/cci-nas-00/data/ceres_data/7lgw_23331/07_2025/7lgw_23331.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7lgw_23331/07_2025/7lgw_23331.cif" } resolution = 2.7 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= 0.004 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: {'GLN:plan1': 1, 'GLU:plan': 2, 'ASN:plan1': 2, 'PHE:plan': 1, 'ARG: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: {'GLN:plan1': 1, 'GLU:plan': 2, 'ASN:plan1': 2, 'PHE:plan': 1, 'ARG: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: 8.00, per 1000 atoms: 0.70 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: 3.33 Conformation dependent library (CDL) restraints added in 1.5 seconds 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: 1.38 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: 3.40 Time building geometry restraints manager: 3.81 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: 6485 16.35 - 32.70: 439 32.70 - 49.05: 87 49.05 - 65.40: 30 65.40 - 81.75: 4 Dihedral angle restraints: 7045 sinusoidal: 3121 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 7042 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 725 or resid 801 through 835 or resid 841 throu \ gh 847)) selection = (chain 'B' and (resid 13 through 725 or resid 801 through 835 or resid 841 throu \ gh 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: 0.980 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: 0.090 Set scattering table: 0.120 Process input model: 30.290 Find NCS groups from input model: 0.520 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:12.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 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 : 12.091 81.749 4533 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 (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: 1.33 (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 TRP 0.010 0.001 TRP B 472 HIS 0.004 0.001 HIS B 707 PHE 0.014 0.001 PHE A 625 TYR 0.020 0.001 TYR A 79 ARG 0.006 0.001 ARG B 716 Details of bonding type rmsd hydrogen bonds : bond 0.12828 ( 672) hydrogen bonds : angle 6.13507 ( 1950) covalent geometry : bond 0.00342 (11509) covalent geometry : angle 0.95492 (15296) *********************** 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 : 1.240 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: 1.2572 time to fit residues: 186.9658 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 : 1.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 114 optimal weight: 8.9990 chunk 103 optimal weight: 2.9990 chunk 57 optimal weight: 4.9990 chunk 35 optimal weight: 10.0000 chunk 69 optimal weight: 4.9990 chunk 55 optimal weight: 4.9990 chunk 106 optimal weight: 0.9990 chunk 41 optimal weight: 3.9990 chunk 64 optimal weight: 8.9990 chunk 79 optimal weight: 7.9990 chunk 123 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 14 GLN A 454 GLN B 454 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.141982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.105914 restraints weight = 12591.183| |-----------------------------------------------------------------------------| r_work (start): 0.3272 rms_B_bonded: 1.82 r_work: 0.3163 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3038 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.1282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 11509 Z= 0.219 Angle : 0.607 7.143 15296 Z= 0.308 Chirality : 0.045 0.142 1744 Planarity : 0.005 0.051 1808 Dihedral : 7.827 55.307 2163 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 1.06 % Allowed : 7.23 % Favored : 91.71 % 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: 1.40 (0.23), residues: 1352 helix: 1.55 (0.17), residues: 886 sheet: 2.85 (0.75), residues: 38 loop : -0.52 (0.30), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 70 HIS 0.005 0.001 HIS B 640 PHE 0.020 0.002 PHE B 111 TYR 0.018 0.002 TYR B 16 ARG 0.004 0.001 ARG B 399 Details of bonding type rmsd hydrogen bonds : bond 0.04921 ( 672) hydrogen bonds : angle 4.82178 ( 1950) covalent geometry : bond 0.00537 (11509) covalent geometry : angle 0.60662 (15296) *********************** 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 119 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 107 time to evaluate : 1.201 Fit side-chains REVERT: A 122 MET cc_start: 0.8065 (mtm) cc_final: 0.7773 (mtp) REVERT: A 271 LEU cc_start: 0.7802 (mt) cc_final: 0.7573 (mp) REVERT: A 316 ASP cc_start: 0.8674 (m-30) cc_final: 0.8249 (m-30) REVERT: A 463 ARG cc_start: 0.7787 (mtm-85) cc_final: 0.7375 (mtp180) REVERT: A 572 ARG cc_start: 0.6962 (mtm110) cc_final: 0.6648 (mtm110) REVERT: A 682 GLN cc_start: 0.8008 (OUTLIER) cc_final: 0.7172 (tt0) REVERT: B 14 GLN cc_start: 0.7419 (pt0) cc_final: 0.7197 (pt0) REVERT: B 122 MET cc_start: 0.8042 (mtm) cc_final: 0.7750 (mtp) REVERT: B 271 LEU cc_start: 0.7892 (mt) cc_final: 0.7659 (mp) REVERT: B 316 ASP cc_start: 0.8703 (m-30) cc_final: 0.8257 (m-30) REVERT: B 463 ARG cc_start: 0.7756 (mtm-85) cc_final: 0.7393 (mtp180) REVERT: B 682 GLN cc_start: 0.7994 (OUTLIER) cc_final: 0.7088 (tt0) outliers start: 12 outliers final: 5 residues processed: 108 average time/residue: 1.2931 time to fit residues: 151.7238 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 : 1.246 ------------------------------------------------------------------------------- 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 36 optimal weight: 2.9990 chunk 39 optimal weight: 10.0000 chunk 22 optimal weight: 3.9990 chunk 95 optimal weight: 9.9990 chunk 104 optimal weight: 2.9990 chunk 37 optimal weight: 0.9990 chunk 66 optimal weight: 0.8980 chunk 82 optimal weight: 7.9990 chunk 77 optimal weight: 0.0970 chunk 67 optimal weight: 7.9990 chunk 10 optimal weight: 0.9980 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3692 r_free = 0.3692 target = 0.145262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.109323 restraints weight = 12829.231| |-----------------------------------------------------------------------------| r_work (start): 0.3316 rms_B_bonded: 1.85 r_work: 0.3211 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3089 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 moved from start: 0.1362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 11509 Z= 0.113 Angle : 0.476 6.973 15296 Z= 0.245 Chirality : 0.041 0.129 1744 Planarity : 0.004 0.044 1808 Dihedral : 7.087 57.633 2163 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 1.41 % Allowed : 8.91 % Favored : 89.68 % 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: 1.67 (0.23), residues: 1352 helix: 1.79 (0.18), residues: 884 sheet: 2.64 (0.70), residues: 38 loop : -0.45 (0.30), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 70 HIS 0.003 0.001 HIS A 337 PHE 0.016 0.001 PHE A 241 TYR 0.014 0.001 TYR B 16 ARG 0.002 0.000 ARG B 31 Details of bonding type rmsd hydrogen bonds : bond 0.03899 ( 672) hydrogen bonds : angle 4.50949 ( 1950) covalent geometry : bond 0.00251 (11509) covalent geometry : angle 0.47609 (15296) *********************** 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 119 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 103 time to evaluate : 1.222 Fit side-chains REVERT: A 316 ASP cc_start: 0.8693 (m-30) cc_final: 0.8225 (m-30) REVERT: A 463 ARG cc_start: 0.7789 (mtm-85) cc_final: 0.7353 (mtp180) REVERT: A 572 ARG cc_start: 0.6876 (mtm110) cc_final: 0.6578 (mtm110) REVERT: A 682 GLN cc_start: 0.8002 (OUTLIER) cc_final: 0.7079 (tt0) REVERT: B 316 ASP cc_start: 0.8672 (m-30) cc_final: 0.8186 (m-30) REVERT: B 463 ARG cc_start: 0.7763 (mtm-85) cc_final: 0.7393 (mtp180) REVERT: B 615 LYS cc_start: 0.7979 (tptm) cc_final: 0.7701 (tppp) REVERT: B 682 GLN cc_start: 0.8015 (OUTLIER) cc_final: 0.7087 (tt0) outliers start: 16 outliers final: 6 residues processed: 106 average time/residue: 1.2154 time to fit residues: 140.6145 Evaluate side-chains 103 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 95 time to evaluate : 1.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 GLU Chi-restraints excluded: chain A residue 180 MET Chi-restraints excluded: chain A residue 474 THR Chi-restraints excluded: chain A residue 682 GLN Chi-restraints excluded: chain B residue 169 GLU Chi-restraints excluded: chain B residue 233 LYS 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 110 optimal weight: 8.9990 chunk 13 optimal weight: 0.9990 chunk 65 optimal weight: 2.9990 chunk 29 optimal weight: 8.9990 chunk 80 optimal weight: 5.9990 chunk 123 optimal weight: 2.9990 chunk 135 optimal weight: 1.9990 chunk 120 optimal weight: 0.9990 chunk 57 optimal weight: 3.9990 chunk 115 optimal weight: 4.9990 chunk 75 optimal weight: 5.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 389 GLN B 14 GLN B 389 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.143534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.107847 restraints weight = 12572.718| |-----------------------------------------------------------------------------| r_work (start): 0.3297 rms_B_bonded: 1.83 r_work: 0.3192 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3071 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.1539 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= 0.141 Angle : 0.517 8.379 15296 Z= 0.260 Chirality : 0.042 0.129 1744 Planarity : 0.004 0.048 1808 Dihedral : 7.175 59.578 2163 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 1.68 % Allowed : 9.70 % Favored : 88.62 % 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: 1.54 (0.23), residues: 1352 helix: 1.72 (0.18), residues: 888 sheet: 2.66 (0.69), residues: 38 loop : -0.58 (0.29), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 70 HIS 0.003 0.001 HIS B 640 PHE 0.016 0.001 PHE A 111 TYR 0.015 0.001 TYR B 16 ARG 0.003 0.000 ARG A 31 Details of bonding type rmsd hydrogen bonds : bond 0.04088 ( 672) hydrogen bonds : angle 4.43606 ( 1950) covalent geometry : bond 0.00332 (11509) covalent geometry : angle 0.51669 (15296) *********************** 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 119 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 100 time to evaluate : 1.151 Fit side-chains REVERT: A 122 MET cc_start: 0.8065 (mtm) cc_final: 0.7772 (mtp) REVERT: A 316 ASP cc_start: 0.8737 (m-30) cc_final: 0.8277 (m-30) REVERT: A 463 ARG cc_start: 0.7837 (mtm-85) cc_final: 0.7444 (mtp180) REVERT: A 615 LYS cc_start: 0.7982 (tptm) cc_final: 0.7625 (tppp) REVERT: A 682 GLN cc_start: 0.8045 (OUTLIER) cc_final: 0.7213 (tt0) REVERT: B 122 MET cc_start: 0.8049 (mtm) cc_final: 0.7739 (mtp) REVERT: B 316 ASP cc_start: 0.8710 (m-30) cc_final: 0.8414 (m-30) REVERT: B 463 ARG cc_start: 0.7800 (mtm-85) cc_final: 0.7412 (mtp180) REVERT: B 615 LYS cc_start: 0.7945 (tptm) cc_final: 0.7733 (tppp) REVERT: B 682 GLN cc_start: 0.8055 (OUTLIER) cc_final: 0.7242 (tt0) outliers start: 19 outliers final: 8 residues processed: 107 average time/residue: 1.4103 time to fit residues: 163.4510 Evaluate side-chains 106 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 96 time to evaluate : 1.239 ------------------------------------------------------------------------------- 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 233 LYS 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 86 optimal weight: 8.9990 chunk 115 optimal weight: 1.9990 chunk 112 optimal weight: 2.9990 chunk 54 optimal weight: 3.9990 chunk 23 optimal weight: 2.9990 chunk 1 optimal weight: 0.7980 chunk 130 optimal weight: 0.4980 chunk 11 optimal weight: 10.0000 chunk 85 optimal weight: 6.9990 chunk 101 optimal weight: 10.0000 chunk 133 optimal weight: 0.9980 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3688 r_free = 0.3688 target = 0.144806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.109107 restraints weight = 12532.015| |-----------------------------------------------------------------------------| r_work (start): 0.3316 rms_B_bonded: 1.84 r_work: 0.3211 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3090 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.1657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 11509 Z= 0.117 Angle : 0.483 8.009 15296 Z= 0.245 Chirality : 0.041 0.128 1744 Planarity : 0.004 0.046 1808 Dihedral : 6.925 58.668 2163 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 1.68 % Allowed : 9.96 % Favored : 88.36 % 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: 1.65 (0.23), residues: 1352 helix: 1.81 (0.18), residues: 886 sheet: 2.58 (0.68), residues: 38 loop : -0.54 (0.29), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 70 HIS 0.002 0.001 HIS A 337 PHE 0.014 0.001 PHE A 269 TYR 0.013 0.001 TYR A 16 ARG 0.002 0.000 ARG A 31 Details of bonding type rmsd hydrogen bonds : bond 0.03762 ( 672) hydrogen bonds : angle 4.34202 ( 1950) covalent geometry : bond 0.00266 (11509) covalent geometry : angle 0.48332 (15296) *********************** 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 121 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 102 time to evaluate : 1.873 Fit side-chains REVERT: A 122 MET cc_start: 0.7967 (mtm) cc_final: 0.7649 (mtp) REVERT: A 316 ASP cc_start: 0.8708 (m-30) cc_final: 0.8222 (m-30) REVERT: A 463 ARG cc_start: 0.7789 (mtm-85) cc_final: 0.7386 (mtp180) REVERT: A 615 LYS cc_start: 0.7999 (tptm) cc_final: 0.7710 (tppp) REVERT: A 682 GLN cc_start: 0.7989 (OUTLIER) cc_final: 0.7483 (tt0) REVERT: B 122 MET cc_start: 0.7954 (mtm) cc_final: 0.7646 (mtp) REVERT: B 316 ASP cc_start: 0.8690 (m-30) cc_final: 0.8394 (m-30) REVERT: B 463 ARG cc_start: 0.7765 (mtm-85) cc_final: 0.7360 (mtp180) REVERT: B 615 LYS cc_start: 0.7934 (tptm) cc_final: 0.7718 (tppp) REVERT: B 682 GLN cc_start: 0.7932 (OUTLIER) cc_final: 0.7402 (tt0) outliers start: 19 outliers final: 7 residues processed: 109 average time/residue: 1.5676 time to fit residues: 187.1826 Evaluate side-chains 107 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 98 time to evaluate : 0.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ASP 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 36 ASP 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 130 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 27 optimal weight: 7.9990 chunk 45 optimal weight: 1.9990 chunk 132 optimal weight: 3.9990 chunk 88 optimal weight: 1.9990 chunk 121 optimal weight: 2.9990 chunk 81 optimal weight: 4.9990 chunk 135 optimal weight: 1.9990 chunk 74 optimal weight: 4.9990 chunk 97 optimal weight: 10.0000 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3674 r_free = 0.3674 target = 0.143564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.107695 restraints weight = 12738.650| |-----------------------------------------------------------------------------| r_work (start): 0.3298 rms_B_bonded: 1.85 r_work: 0.3191 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3069 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.1743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 11509 Z= 0.140 Angle : 0.508 8.342 15296 Z= 0.257 Chirality : 0.042 0.128 1744 Planarity : 0.004 0.047 1808 Dihedral : 7.120 56.707 2163 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 2.20 % Allowed : 9.88 % Favored : 87.92 % 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: 1.62 (0.23), residues: 1352 helix: 1.75 (0.18), residues: 892 sheet: 2.54 (0.72), residues: 36 loop : -0.48 (0.29), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 70 HIS 0.003 0.001 HIS B 640 PHE 0.018 0.001 PHE A 241 TYR 0.014 0.001 TYR B 16 ARG 0.002 0.000 ARG A 211 Details of bonding type rmsd hydrogen bonds : bond 0.04017 ( 672) hydrogen bonds : angle 4.37408 ( 1950) covalent geometry : bond 0.00333 (11509) covalent geometry : angle 0.50812 (15296) *********************** 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 127 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 102 time to evaluate : 1.150 Fit side-chains REVERT: A 122 MET cc_start: 0.8021 (mtm) cc_final: 0.7714 (mtp) REVERT: A 316 ASP cc_start: 0.8718 (m-30) cc_final: 0.8417 (m-30) REVERT: A 463 ARG cc_start: 0.7811 (mtm-85) cc_final: 0.7391 (mtp180) REVERT: A 577 LYS cc_start: 0.7179 (OUTLIER) cc_final: 0.6977 (ttpt) REVERT: A 615 LYS cc_start: 0.8086 (tptm) cc_final: 0.7790 (tppp) REVERT: A 682 GLN cc_start: 0.7936 (OUTLIER) cc_final: 0.7680 (tt0) REVERT: B 122 MET cc_start: 0.8004 (mtm) cc_final: 0.7692 (mtp) REVERT: B 310 LYS cc_start: 0.7080 (tttt) cc_final: 0.6593 (tptt) REVERT: B 316 ASP cc_start: 0.8713 (m-30) cc_final: 0.8428 (m-30) REVERT: B 463 ARG cc_start: 0.7810 (mtm-85) cc_final: 0.7391 (mtp180) REVERT: B 682 GLN cc_start: 0.7932 (OUTLIER) cc_final: 0.7612 (tt0) outliers start: 25 outliers final: 11 residues processed: 114 average time/residue: 1.2970 time to fit residues: 160.2978 Evaluate side-chains 108 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 94 time to evaluate : 1.259 ------------------------------------------------------------------------------- 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 180 MET Chi-restraints excluded: chain A residue 233 LYS Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 474 THR Chi-restraints excluded: chain A residue 577 LYS 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 180 MET Chi-restraints excluded: chain B residue 233 LYS 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 10 optimal weight: 2.9990 chunk 102 optimal weight: 2.9990 chunk 12 optimal weight: 3.9990 chunk 62 optimal weight: 0.9990 chunk 84 optimal weight: 1.9990 chunk 4 optimal weight: 4.9990 chunk 131 optimal weight: 5.9990 chunk 46 optimal weight: 7.9990 chunk 125 optimal weight: 4.9990 chunk 64 optimal weight: 7.9990 chunk 88 optimal weight: 2.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 389 GLN A 648 GLN B 389 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.142631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.106917 restraints weight = 12790.250| |-----------------------------------------------------------------------------| r_work (start): 0.3287 rms_B_bonded: 1.84 r_work: 0.3181 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3059 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.1824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 11509 Z= 0.157 Angle : 0.530 9.998 15296 Z= 0.266 Chirality : 0.043 0.128 1744 Planarity : 0.004 0.048 1808 Dihedral : 7.347 59.337 2163 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 2.29 % Allowed : 10.58 % 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 (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: 1.52 (0.23), residues: 1352 helix: 1.65 (0.18), residues: 894 sheet: 2.50 (0.72), residues: 36 loop : -0.47 (0.29), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 70 HIS 0.003 0.001 HIS B 640 PHE 0.016 0.001 PHE A 241 TYR 0.015 0.001 TYR A 16 ARG 0.002 0.000 ARG A 211 Details of bonding type rmsd hydrogen bonds : bond 0.04170 ( 672) hydrogen bonds : angle 4.41556 ( 1950) covalent geometry : bond 0.00379 (11509) covalent geometry : angle 0.53019 (15296) *********************** 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 120 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 94 time to evaluate : 1.323 Fit side-chains REVERT: A 122 MET cc_start: 0.8000 (mtm) cc_final: 0.7690 (mtp) REVERT: A 257 LEU cc_start: 0.8122 (OUTLIER) cc_final: 0.7899 (pt) REVERT: A 310 LYS cc_start: 0.7049 (tttt) cc_final: 0.6552 (tptt) REVERT: A 316 ASP cc_start: 0.8707 (m-30) cc_final: 0.8418 (m-30) REVERT: A 463 ARG cc_start: 0.7814 (mtm-85) cc_final: 0.7388 (mtp180) REVERT: A 615 LYS cc_start: 0.8069 (tptm) cc_final: 0.7800 (tppp) REVERT: A 682 GLN cc_start: 0.7889 (OUTLIER) cc_final: 0.7635 (tt0) REVERT: B 122 MET cc_start: 0.7962 (mtm) cc_final: 0.7648 (mtp) REVERT: B 310 LYS cc_start: 0.7038 (tttt) cc_final: 0.6579 (tptt) REVERT: B 316 ASP cc_start: 0.8703 (m-30) cc_final: 0.8422 (m-30) REVERT: B 463 ARG cc_start: 0.7776 (mtm-85) cc_final: 0.7340 (mtp180) REVERT: B 682 GLN cc_start: 0.7863 (OUTLIER) cc_final: 0.7615 (tt0) outliers start: 26 outliers final: 14 residues processed: 108 average time/residue: 1.4588 time to fit residues: 170.4991 Evaluate side-chains 109 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 92 time to evaluate : 1.269 ------------------------------------------------------------------------------- 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 180 MET Chi-restraints excluded: chain A residue 233 LYS Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 390 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 233 LYS Chi-restraints excluded: chain B residue 261 SER Chi-restraints excluded: chain B residue 390 THR 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 5 optimal weight: 3.9990 chunk 26 optimal weight: 9.9990 chunk 117 optimal weight: 0.9990 chunk 0 optimal weight: 7.9990 chunk 9 optimal weight: 2.9990 chunk 123 optimal weight: 3.9990 chunk 103 optimal weight: 3.9990 chunk 66 optimal weight: 0.9980 chunk 35 optimal weight: 1.9990 chunk 39 optimal weight: 9.9990 chunk 55 optimal weight: 3.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3664 r_free = 0.3664 target = 0.142675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.107145 restraints weight = 12751.656| |-----------------------------------------------------------------------------| r_work (start): 0.3287 rms_B_bonded: 1.83 r_work: 0.3182 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3060 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.1906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 11509 Z= 0.148 Angle : 0.533 11.729 15296 Z= 0.265 Chirality : 0.043 0.137 1744 Planarity : 0.004 0.048 1808 Dihedral : 7.349 58.873 2163 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 2.20 % Allowed : 10.76 % 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 (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: 1.52 (0.23), residues: 1352 helix: 1.65 (0.17), residues: 894 sheet: 2.47 (0.72), residues: 36 loop : -0.45 (0.29), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 70 HIS 0.003 0.001 HIS B 640 PHE 0.017 0.001 PHE A 241 TYR 0.014 0.001 TYR A 16 ARG 0.002 0.000 ARG A 211 Details of bonding type rmsd hydrogen bonds : bond 0.04109 ( 672) hydrogen bonds : angle 4.42287 ( 1950) covalent geometry : bond 0.00357 (11509) covalent geometry : angle 0.53271 (15296) *********************** 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 121 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 96 time to evaluate : 1.116 Fit side-chains REVERT: A 122 MET cc_start: 0.8028 (mtm) cc_final: 0.7720 (mtp) REVERT: A 257 LEU cc_start: 0.8152 (OUTLIER) cc_final: 0.7927 (pt) REVERT: A 310 LYS cc_start: 0.7072 (tttt) cc_final: 0.6576 (tptt) REVERT: A 316 ASP cc_start: 0.8725 (m-30) cc_final: 0.8439 (m-30) REVERT: A 463 ARG cc_start: 0.7819 (mtm-85) cc_final: 0.7394 (mtp180) REVERT: A 615 LYS cc_start: 0.8091 (tptm) cc_final: 0.7852 (tppp) REVERT: A 682 GLN cc_start: 0.7913 (OUTLIER) cc_final: 0.7655 (tt0) REVERT: B 122 MET cc_start: 0.7978 (mtm) cc_final: 0.7665 (mtp) REVERT: B 269 PHE cc_start: 0.6713 (t80) cc_final: 0.6443 (t80) REVERT: B 310 LYS cc_start: 0.7098 (tttt) cc_final: 0.6621 (tptt) REVERT: B 316 ASP cc_start: 0.8724 (m-30) cc_final: 0.8443 (m-30) REVERT: B 463 ARG cc_start: 0.7784 (mtm-85) cc_final: 0.7349 (mtp180) REVERT: B 682 GLN cc_start: 0.7899 (OUTLIER) cc_final: 0.7661 (tt0) outliers start: 25 outliers final: 13 residues processed: 107 average time/residue: 1.1850 time to fit residues: 138.1018 Evaluate side-chains 110 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 94 time to evaluate : 1.228 ------------------------------------------------------------------------------- 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 257 LEU Chi-restraints excluded: chain A residue 390 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 233 LYS Chi-restraints excluded: chain B residue 261 SER Chi-restraints excluded: chain B residue 390 THR Chi-restraints excluded: chain B residue 474 THR Chi-restraints excluded: chain B residue 682 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 114 optimal weight: 0.6980 chunk 132 optimal weight: 5.9990 chunk 18 optimal weight: 3.9990 chunk 107 optimal weight: 10.0000 chunk 14 optimal weight: 0.0770 chunk 48 optimal weight: 7.9990 chunk 62 optimal weight: 0.2980 chunk 42 optimal weight: 7.9990 chunk 36 optimal weight: 8.9990 chunk 58 optimal weight: 1.9990 chunk 76 optimal weight: 0.9990 overall best weight: 0.8142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 389 GLN A 454 GLN B 389 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.146524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.111183 restraints weight = 12653.645| |-----------------------------------------------------------------------------| r_work (start): 0.3343 rms_B_bonded: 1.84 r_work: 0.3240 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3119 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 0.1989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 11509 Z= 0.099 Angle : 0.485 13.536 15296 Z= 0.238 Chirality : 0.041 0.131 1744 Planarity : 0.004 0.044 1808 Dihedral : 6.573 59.437 2163 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 1.23 % Allowed : 11.82 % 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 (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: 1.82 (0.23), residues: 1352 helix: 1.89 (0.18), residues: 890 sheet: 2.52 (0.69), residues: 36 loop : -0.34 (0.30), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 70 HIS 0.002 0.001 HIS A 337 PHE 0.015 0.001 PHE A 241 TYR 0.012 0.001 TYR A 16 ARG 0.002 0.000 ARG A 31 Details of bonding type rmsd hydrogen bonds : bond 0.03425 ( 672) hydrogen bonds : angle 4.24328 ( 1950) covalent geometry : bond 0.00216 (11509) covalent geometry : angle 0.48529 (15296) *********************** 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 125 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 111 time to evaluate : 1.143 Fit side-chains REVERT: A 235 LYS cc_start: 0.7842 (mtpp) cc_final: 0.7404 (ttmm) REVERT: A 310 LYS cc_start: 0.7026 (tttt) cc_final: 0.6640 (tptt) REVERT: A 316 ASP cc_start: 0.8782 (m-30) cc_final: 0.8512 (m-30) REVERT: A 463 ARG cc_start: 0.7794 (mtm-85) cc_final: 0.7357 (mtp180) REVERT: A 615 LYS cc_start: 0.8092 (tptm) cc_final: 0.7878 (tppp) REVERT: B 122 MET cc_start: 0.7937 (mtm) cc_final: 0.7635 (mtp) REVERT: B 269 PHE cc_start: 0.6535 (t80) cc_final: 0.6302 (t80) REVERT: B 310 LYS cc_start: 0.7079 (tttt) cc_final: 0.6677 (tptt) REVERT: B 316 ASP cc_start: 0.8769 (m-30) cc_final: 0.8483 (m-30) REVERT: B 463 ARG cc_start: 0.7773 (mtm-85) cc_final: 0.7340 (mtp180) outliers start: 14 outliers final: 5 residues processed: 118 average time/residue: 1.0486 time to fit residues: 135.9324 Evaluate side-chains 110 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 105 time to evaluate : 1.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 267 MET Chi-restraints excluded: chain A residue 474 THR Chi-restraints excluded: chain B residue 180 MET 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 103 optimal weight: 0.3980 chunk 38 optimal weight: 9.9990 chunk 35 optimal weight: 3.9990 chunk 100 optimal weight: 0.9980 chunk 77 optimal weight: 0.0470 chunk 36 optimal weight: 7.9990 chunk 102 optimal weight: 6.9990 chunk 65 optimal weight: 0.9980 chunk 55 optimal weight: 4.9990 chunk 32 optimal weight: 9.9990 chunk 37 optimal weight: 0.8980 overall best weight: 0.6678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 389 GLN A 682 GLN B 389 GLN B 454 GLN B 648 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.147293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.112390 restraints weight = 12572.054| |-----------------------------------------------------------------------------| r_work (start): 0.3355 rms_B_bonded: 1.83 r_work: 0.3252 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3132 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.2094 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= 0.095 Angle : 0.487 13.456 15296 Z= 0.239 Chirality : 0.041 0.127 1744 Planarity : 0.004 0.044 1808 Dihedral : 6.231 59.496 2163 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 0.79 % Allowed : 12.96 % Favored : 86.24 % 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: 1.95 (0.23), residues: 1352 helix: 1.97 (0.18), residues: 892 sheet: 2.84 (0.68), residues: 36 loop : -0.28 (0.30), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 70 HIS 0.002 0.001 HIS B 704 PHE 0.015 0.001 PHE A 241 TYR 0.010 0.001 TYR A 16 ARG 0.002 0.000 ARG A 31 Details of bonding type rmsd hydrogen bonds : bond 0.03332 ( 672) hydrogen bonds : angle 4.17046 ( 1950) covalent geometry : bond 0.00205 (11509) covalent geometry : angle 0.48712 (15296) ********************** 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 114 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 105 time to evaluate : 1.150 Fit side-chains REVERT: A 122 MET cc_start: 0.7999 (mtm) cc_final: 0.7688 (mtp) REVERT: A 235 LYS cc_start: 0.7809 (mtpp) cc_final: 0.7390 (ttmm) REVERT: A 251 LEU cc_start: 0.7841 (mt) cc_final: 0.7541 (mm) REVERT: A 269 PHE cc_start: 0.6645 (t80) cc_final: 0.6415 (t80) REVERT: A 310 LYS cc_start: 0.7087 (tttt) cc_final: 0.6734 (tptt) REVERT: A 316 ASP cc_start: 0.8733 (m-30) cc_final: 0.8454 (m-30) REVERT: A 463 ARG cc_start: 0.7831 (mtm-85) cc_final: 0.7397 (mtp180) REVERT: A 666 GLU cc_start: 0.7634 (mt-10) cc_final: 0.7363 (pt0) REVERT: A 682 GLN cc_start: 0.8012 (OUTLIER) cc_final: 0.7698 (tt0) REVERT: B 122 MET cc_start: 0.7999 (mtm) cc_final: 0.7700 (mtp) REVERT: B 251 LEU cc_start: 0.7828 (mt) cc_final: 0.7523 (mm) REVERT: B 310 LYS cc_start: 0.7059 (tttt) cc_final: 0.6711 (tptt) REVERT: B 316 ASP cc_start: 0.8785 (m-30) cc_final: 0.8509 (m-30) REVERT: B 463 ARG cc_start: 0.7794 (mtm-85) cc_final: 0.7363 (mtp180) REVERT: B 666 GLU cc_start: 0.7619 (mt-10) cc_final: 0.7347 (pt0) outliers start: 9 outliers final: 5 residues processed: 110 average time/residue: 1.1364 time to fit residues: 137.3553 Evaluate side-chains 105 residues out of total 1154 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 99 time to evaluate : 1.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 267 MET Chi-restraints excluded: chain A residue 474 THR Chi-restraints excluded: chain A residue 682 GLN Chi-restraints excluded: chain B residue 180 MET 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 45 optimal weight: 5.9990 chunk 42 optimal weight: 0.9990 chunk 27 optimal weight: 0.8980 chunk 116 optimal weight: 2.9990 chunk 9 optimal weight: 0.0050 chunk 40 optimal weight: 9.9990 chunk 61 optimal weight: 7.9990 chunk 87 optimal weight: 0.3980 chunk 94 optimal weight: 3.9990 chunk 37 optimal weight: 3.9990 chunk 70 optimal weight: 20.0000 overall best weight: 1.0598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 389 GLN ** A 682 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 256 ASN B 389 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.146898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.111752 restraints weight = 12545.446| |-----------------------------------------------------------------------------| r_work (start): 0.3338 rms_B_bonded: 1.83 r_work: 0.3233 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3113 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.2114 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= 0.105 Angle : 0.497 13.706 15296 Z= 0.244 Chirality : 0.041 0.127 1744 Planarity : 0.004 0.043 1808 Dihedral : 6.246 59.599 2163 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 0.71 % Allowed : 13.76 % Favored : 85.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.96 (0.23), residues: 1352 helix: 1.97 (0.18), residues: 892 sheet: 2.87 (0.68), residues: 36 loop : -0.28 (0.30), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 70 HIS 0.002 0.001 HIS A 337 PHE 0.012 0.001 PHE B 111 TYR 0.011 0.001 TYR A 16 ARG 0.002 0.000 ARG A 31 Details of bonding type rmsd hydrogen bonds : bond 0.03373 ( 672) hydrogen bonds : angle 4.17869 ( 1950) covalent geometry : bond 0.00236 (11509) covalent geometry : angle 0.49670 (15296) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9502.24 seconds wall clock time: 164 minutes 45.95 seconds (9885.95 seconds total)