Starting phenix.real_space_refine on Thu Sep 26 00:41:54 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lgw_23331/09_2024/7lgw_23331.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lgw_23331/09_2024/7lgw_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lgw_23331/09_2024/7lgw_23331.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lgw_23331/09_2024/7lgw_23331.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lgw_23331/09_2024/7lgw_23331.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lgw_23331/09_2024/7lgw_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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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: 7.47, per 1000 atoms: 0.66 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: 2.91 Conformation dependent library (CDL) restraints added in 1.4 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: 1.29 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: 3.34 Time building geometry restraints manager: 3.29 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: 0.880 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.460 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 27.580 Find NCS groups from input model: 0.500 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:12.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.160 ------------------------------------------------------------------------------- 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= 0.222 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 *********************** 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 fitting. rotamer outliers: 8 poor density : 135 time to evaluate : 1.161 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: 1.2571 time to fit residues: 186.8095 Evaluate side-chains 100 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 100 time to evaluate : 1.390 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 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= 0.352 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 *********************** 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 fitting. rotamer outliers: 12 poor density : 107 time to evaluate : 1.251 Fit side-chains REVERT: A 122 MET cc_start: 0.8014 (mtm) cc_final: 0.7779 (mtp) REVERT: A 271 LEU cc_start: 0.8245 (mt) cc_final: 0.8032 (mp) REVERT: A 316 ASP cc_start: 0.8338 (m-30) cc_final: 0.8008 (m-30) REVERT: A 463 ARG cc_start: 0.7770 (mtm-85) cc_final: 0.7427 (mtp180) REVERT: A 572 ARG cc_start: 0.7347 (mtm110) cc_final: 0.7085 (mtm110) REVERT: A 682 GLN cc_start: 0.7971 (OUTLIER) cc_final: 0.7126 (tt0) REVERT: B 122 MET cc_start: 0.7978 (mtm) cc_final: 0.7737 (mtp) REVERT: B 271 LEU cc_start: 0.8323 (mt) cc_final: 0.8113 (mp) REVERT: B 316 ASP cc_start: 0.8380 (m-30) cc_final: 0.8033 (m-30) REVERT: B 463 ARG cc_start: 0.7733 (mtm-85) cc_final: 0.7449 (mtp180) REVERT: B 682 GLN cc_start: 0.7968 (OUTLIER) cc_final: 0.7051 (tt0) outliers start: 12 outliers final: 5 residues processed: 108 average time/residue: 1.2389 time to fit residues: 145.7096 Evaluate side-chains 102 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 95 time to evaluate : 1.134 ------------------------------------------------------------------------------- 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 68 optimal weight: 0.9980 chunk 38 optimal weight: 4.9990 chunk 102 optimal weight: 5.9990 chunk 84 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 123 optimal weight: 1.9990 chunk 133 optimal weight: 0.9980 chunk 110 optimal weight: 1.9990 chunk 122 optimal weight: 2.9990 chunk 42 optimal weight: 0.9990 chunk 99 optimal weight: 9.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.1382 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= 0.174 Angle : 0.478 6.494 15296 Z= 0.246 Chirality : 0.041 0.129 1744 Planarity : 0.004 0.045 1808 Dihedral : 7.136 57.732 2163 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 5.56 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: 1.64 (0.23), residues: 1352 helix: 1.77 (0.18), residues: 884 sheet: 2.62 (0.70), residues: 38 loop : -0.47 (0.30), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 70 HIS 0.003 0.001 HIS A 337 PHE 0.020 0.001 PHE A 241 TYR 0.014 0.001 TYR A 16 ARG 0.001 0.000 ARG B 31 *********************** 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 121 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 105 time to evaluate : 1.135 Fit side-chains REVERT: A 316 ASP cc_start: 0.8353 (m-30) cc_final: 0.7997 (m-30) REVERT: A 463 ARG cc_start: 0.7779 (mtm-85) cc_final: 0.7415 (mtp180) REVERT: A 682 GLN cc_start: 0.7986 (OUTLIER) cc_final: 0.7071 (tt0) REVERT: B 122 MET cc_start: 0.7895 (mtm) cc_final: 0.7650 (mtp) REVERT: B 316 ASP cc_start: 0.8355 (m-30) cc_final: 0.7995 (m-30) REVERT: B 463 ARG cc_start: 0.7737 (mtm-85) cc_final: 0.7445 (mtp180) REVERT: B 682 GLN cc_start: 0.7977 (OUTLIER) cc_final: 0.7055 (tt0) outliers start: 16 outliers final: 6 residues processed: 108 average time/residue: 1.2184 time to fit residues: 143.4717 Evaluate side-chains 108 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 100 time to evaluate : 1.205 ------------------------------------------------------------------------------- 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 122 optimal weight: 3.9990 chunk 93 optimal weight: 8.9990 chunk 64 optimal weight: 1.9990 chunk 13 optimal weight: 0.6980 chunk 59 optimal weight: 5.9990 chunk 83 optimal weight: 0.0470 chunk 124 optimal weight: 0.1980 chunk 131 optimal weight: 6.9990 chunk 117 optimal weight: 0.6980 chunk 35 optimal weight: 4.9990 chunk 109 optimal weight: 4.9990 overall best weight: 0.7280 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.1571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 11509 Z= 0.135 Angle : 0.462 8.933 15296 Z= 0.234 Chirality : 0.040 0.127 1744 Planarity : 0.004 0.045 1808 Dihedral : 6.492 59.050 2163 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 1.15 % Allowed : 10.05 % Favored : 88.80 % 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: 1.78 (0.23), residues: 1352 helix: 1.87 (0.18), residues: 888 sheet: 2.64 (0.67), residues: 38 loop : -0.41 (0.29), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 70 HIS 0.003 0.001 HIS A 337 PHE 0.014 0.001 PHE A 269 TYR 0.012 0.001 TYR A 16 ARG 0.003 0.000 ARG A 31 *********************** 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 131 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 118 time to evaluate : 1.132 Fit side-chains REVERT: A 316 ASP cc_start: 0.8347 (m-30) cc_final: 0.7993 (m-30) REVERT: A 463 ARG cc_start: 0.7766 (mtm-85) cc_final: 0.7441 (mtp180) REVERT: A 682 GLN cc_start: 0.7992 (tm-30) cc_final: 0.7754 (tt0) REVERT: B 316 ASP cc_start: 0.8349 (m-30) cc_final: 0.7991 (m-30) REVERT: B 463 ARG cc_start: 0.7721 (mtm-85) cc_final: 0.7415 (mtp180) REVERT: B 682 GLN cc_start: 0.7961 (OUTLIER) cc_final: 0.7148 (tt0) outliers start: 13 outliers final: 4 residues processed: 123 average time/residue: 1.0826 time to fit residues: 146.8425 Evaluate side-chains 107 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 102 time to evaluate : 1.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ASP Chi-restraints excluded: chain A residue 474 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 74 optimal weight: 10.0000 chunk 1 optimal weight: 0.4980 chunk 97 optimal weight: 3.9990 chunk 54 optimal weight: 4.9990 chunk 112 optimal weight: 3.9990 chunk 90 optimal weight: 4.9990 chunk 0 optimal weight: 7.9990 chunk 67 optimal weight: 4.9990 chunk 117 optimal weight: 0.6980 chunk 33 optimal weight: 9.9990 chunk 44 optimal weight: 0.9990 overall best weight: 2.0386 ------------------------------------------------------------------------------- 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 B 648 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 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 0.029 11509 Z= 0.221 Angle : 0.500 7.848 15296 Z= 0.255 Chirality : 0.042 0.128 1744 Planarity : 0.004 0.047 1808 Dihedral : 6.887 57.936 2163 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 2.20 % Allowed : 10.05 % Favored : 87.74 % 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: 1.68 (0.23), residues: 1352 helix: 1.81 (0.18), residues: 890 sheet: 2.78 (0.68), residues: 38 loop : -0.51 (0.29), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 70 HIS 0.003 0.001 HIS B 640 PHE 0.018 0.001 PHE A 241 TYR 0.015 0.001 TYR B 16 ARG 0.002 0.000 ARG A 211 *********************** 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 126 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 101 time to evaluate : 1.231 Fit side-chains REVERT: A 122 MET cc_start: 0.7944 (mtm) cc_final: 0.7694 (mtp) REVERT: A 271 LEU cc_start: 0.8243 (mt) cc_final: 0.7971 (mp) REVERT: A 316 ASP cc_start: 0.8383 (m-30) cc_final: 0.8022 (m-30) REVERT: A 463 ARG cc_start: 0.7787 (mtm-85) cc_final: 0.7465 (mtp180) REVERT: A 682 GLN cc_start: 0.7946 (OUTLIER) cc_final: 0.7553 (tt0) REVERT: B 122 MET cc_start: 0.7916 (mtm) cc_final: 0.7668 (mtp) REVERT: B 169 GLU cc_start: 0.7415 (OUTLIER) cc_final: 0.7000 (OUTLIER) REVERT: B 316 ASP cc_start: 0.8381 (m-30) cc_final: 0.8013 (m-30) REVERT: B 463 ARG cc_start: 0.7739 (mtm-85) cc_final: 0.7412 (mtp180) REVERT: B 682 GLN cc_start: 0.7914 (OUTLIER) cc_final: 0.7144 (tt0) outliers start: 25 outliers final: 11 residues processed: 109 average time/residue: 1.2132 time to fit residues: 144.3314 Evaluate side-chains 112 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 99 time to evaluate : 1.564 ------------------------------------------------------------------------------- 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 169 GLU Chi-restraints excluded: chain B residue 261 SER Chi-restraints excluded: chain B residue 474 THR Chi-restraints excluded: chain B residue 528 GLU 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 118 optimal weight: 0.0060 chunk 25 optimal weight: 10.0000 chunk 77 optimal weight: 0.8980 chunk 32 optimal weight: 10.0000 chunk 131 optimal weight: 5.9990 chunk 109 optimal weight: 4.9990 chunk 60 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 chunk 43 optimal weight: 5.9990 chunk 69 optimal weight: 3.9990 chunk 126 optimal weight: 0.8980 overall best weight: 1.5600 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.1753 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= 0.183 Angle : 0.480 8.264 15296 Z= 0.244 Chirality : 0.041 0.128 1744 Planarity : 0.004 0.046 1808 Dihedral : 6.774 56.578 2163 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 2.29 % Allowed : 10.23 % Favored : 87.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.74 (0.23), residues: 1352 helix: 1.86 (0.18), residues: 888 sheet: 2.69 (0.67), residues: 38 loop : -0.49 (0.29), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 70 HIS 0.002 0.001 HIS B 640 PHE 0.013 0.001 PHE A 111 TYR 0.013 0.001 TYR B 16 ARG 0.002 0.000 ARG A 31 *********************** 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 125 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 99 time to evaluate : 1.210 Fit side-chains REVERT: A 122 MET cc_start: 0.7907 (mtm) cc_final: 0.7659 (mtp) REVERT: A 271 LEU cc_start: 0.8303 (mt) cc_final: 0.8047 (mp) REVERT: A 316 ASP cc_start: 0.8378 (m-30) cc_final: 0.8113 (m-30) REVERT: A 463 ARG cc_start: 0.7771 (mtm-85) cc_final: 0.7425 (mtp180) REVERT: A 577 LYS cc_start: 0.7612 (OUTLIER) cc_final: 0.7384 (ttpt) REVERT: A 682 GLN cc_start: 0.7926 (OUTLIER) cc_final: 0.7701 (tt0) REVERT: B 122 MET cc_start: 0.7904 (mtm) cc_final: 0.7659 (mtp) REVERT: B 316 ASP cc_start: 0.8378 (m-30) cc_final: 0.8116 (m-30) REVERT: B 463 ARG cc_start: 0.7748 (mtm-85) cc_final: 0.7415 (mtp180) REVERT: B 682 GLN cc_start: 0.7879 (OUTLIER) cc_final: 0.7603 (tt0) outliers start: 26 outliers final: 10 residues processed: 113 average time/residue: 1.1308 time to fit residues: 141.3525 Evaluate side-chains 111 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 98 time to evaluate : 1.058 ------------------------------------------------------------------------------- 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 261 SER 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 36 ASP Chi-restraints excluded: chain B residue 180 MET Chi-restraints excluded: chain B residue 474 THR Chi-restraints excluded: chain B residue 521 ILE 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 14 optimal weight: 0.0980 chunk 74 optimal weight: 0.6980 chunk 96 optimal weight: 8.9990 chunk 110 optimal weight: 6.9990 chunk 73 optimal weight: 0.8980 chunk 131 optimal weight: 6.9990 chunk 82 optimal weight: 4.9990 chunk 79 optimal weight: 9.9990 chunk 60 optimal weight: 2.9990 chunk 81 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.1822 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= 0.170 Angle : 0.478 8.751 15296 Z= 0.242 Chirality : 0.041 0.127 1744 Planarity : 0.004 0.045 1808 Dihedral : 6.646 58.708 2163 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 2.03 % Allowed : 10.85 % 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: 1.84 (0.23), residues: 1352 helix: 1.92 (0.18), residues: 890 sheet: 2.66 (0.70), residues: 36 loop : -0.37 (0.30), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 70 HIS 0.002 0.001 HIS A 640 PHE 0.017 0.001 PHE A 241 TYR 0.013 0.001 TYR A 16 ARG 0.002 0.000 ARG A 31 *********************** 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 123 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 100 time to evaluate : 1.254 Fit side-chains REVERT: A 122 MET cc_start: 0.7904 (mtm) cc_final: 0.7659 (mtp) REVERT: A 271 LEU cc_start: 0.8305 (mt) cc_final: 0.8098 (mp) REVERT: A 316 ASP cc_start: 0.8383 (m-30) cc_final: 0.8119 (m-30) REVERT: A 463 ARG cc_start: 0.7764 (mtm-85) cc_final: 0.7421 (mtp180) REVERT: A 682 GLN cc_start: 0.7869 (OUTLIER) cc_final: 0.7652 (tt0) REVERT: B 122 MET cc_start: 0.7909 (mtm) cc_final: 0.7666 (mtp) REVERT: B 316 ASP cc_start: 0.8387 (m-30) cc_final: 0.8131 (m-30) REVERT: B 463 ARG cc_start: 0.7757 (mtm-85) cc_final: 0.7423 (mtp180) outliers start: 23 outliers final: 11 residues processed: 110 average time/residue: 1.0861 time to fit residues: 131.4403 Evaluate side-chains 105 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 93 time to evaluate : 1.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 180 MET Chi-restraints excluded: chain A residue 233 LYS Chi-restraints excluded: chain A residue 261 SER Chi-restraints excluded: chain A residue 474 THR Chi-restraints excluded: chain A residue 521 ILE Chi-restraints excluded: chain A residue 682 GLN 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 474 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 78 optimal weight: 1.9990 chunk 39 optimal weight: 10.0000 chunk 25 optimal weight: 10.0000 chunk 83 optimal weight: 8.9990 chunk 89 optimal weight: 6.9990 chunk 64 optimal weight: 7.9990 chunk 12 optimal weight: 7.9990 chunk 103 optimal weight: 3.9990 chunk 119 optimal weight: 6.9990 chunk 125 optimal weight: 0.5980 chunk 114 optimal weight: 0.8980 overall best weight: 2.8986 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.1911 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= 0.293 Angle : 0.548 9.970 15296 Z= 0.277 Chirality : 0.044 0.131 1744 Planarity : 0.005 0.049 1808 Dihedral : 7.456 58.692 2163 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 2.38 % Allowed : 11.02 % Favored : 86.60 % 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: 1.55 (0.23), residues: 1352 helix: 1.68 (0.18), residues: 898 sheet: 2.57 (0.72), residues: 36 loop : -0.50 (0.30), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 70 HIS 0.004 0.001 HIS A 640 PHE 0.019 0.002 PHE A 241 TYR 0.016 0.001 TYR A 16 ARG 0.002 0.000 ARG B 211 *********************** 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 120 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 93 time to evaluate : 1.279 Fit side-chains REVERT: A 122 MET cc_start: 0.7968 (mtm) cc_final: 0.7724 (mtp) REVERT: A 271 LEU cc_start: 0.8317 (mt) cc_final: 0.8083 (mp) REVERT: A 310 LYS cc_start: 0.7111 (tttt) cc_final: 0.6909 (tptt) REVERT: A 316 ASP cc_start: 0.8358 (m-30) cc_final: 0.8092 (m-30) REVERT: A 463 ARG cc_start: 0.7779 (mtm-85) cc_final: 0.7432 (mtp180) REVERT: A 682 GLN cc_start: 0.7834 (OUTLIER) cc_final: 0.7610 (tt0) REVERT: B 122 MET cc_start: 0.7927 (mtm) cc_final: 0.7675 (mtp) REVERT: B 316 ASP cc_start: 0.8374 (m-30) cc_final: 0.8116 (m-30) REVERT: B 463 ARG cc_start: 0.7752 (mtm-85) cc_final: 0.7420 (mtp180) outliers start: 27 outliers final: 14 residues processed: 105 average time/residue: 1.1857 time to fit residues: 135.2449 Evaluate side-chains 107 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 92 time to evaluate : 0.834 ------------------------------------------------------------------------------- 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 261 SER Chi-restraints excluded: chain A residue 474 THR Chi-restraints excluded: chain A residue 521 ILE 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 261 SER Chi-restraints excluded: chain B residue 390 THR 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 122 optimal weight: 2.9990 chunk 125 optimal weight: 0.6980 chunk 73 optimal weight: 0.9990 chunk 53 optimal weight: 6.9990 chunk 95 optimal weight: 4.9990 chunk 37 optimal weight: 0.9990 chunk 110 optimal weight: 7.9990 chunk 115 optimal weight: 7.9990 chunk 121 optimal weight: 0.9980 chunk 80 optimal weight: 5.9990 chunk 129 optimal weight: 1.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.1962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 11509 Z= 0.162 Angle : 0.473 10.159 15296 Z= 0.241 Chirality : 0.041 0.127 1744 Planarity : 0.004 0.046 1808 Dihedral : 6.856 57.824 2163 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 1.68 % Allowed : 11.38 % 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: 1.80 (0.23), residues: 1352 helix: 1.91 (0.18), residues: 890 sheet: 2.49 (0.70), residues: 36 loop : -0.43 (0.30), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 70 HIS 0.002 0.001 HIS B 640 PHE 0.017 0.001 PHE A 241 TYR 0.013 0.001 TYR A 16 ARG 0.002 0.000 ARG A 31 *********************** 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 113 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 94 time to evaluate : 1.098 Fit side-chains REVERT: A 122 MET cc_start: 0.7886 (mtm) cc_final: 0.7647 (mtp) REVERT: A 271 LEU cc_start: 0.8322 (mt) cc_final: 0.8077 (mp) REVERT: A 316 ASP cc_start: 0.8366 (m-30) cc_final: 0.8103 (m-30) REVERT: A 463 ARG cc_start: 0.7764 (mtm-85) cc_final: 0.7426 (mtp180) REVERT: B 122 MET cc_start: 0.7887 (mtm) cc_final: 0.7648 (mtp) REVERT: B 316 ASP cc_start: 0.8411 (m-30) cc_final: 0.8155 (m-30) REVERT: B 463 ARG cc_start: 0.7735 (mtm-85) cc_final: 0.7410 (mtp180) outliers start: 19 outliers final: 10 residues processed: 104 average time/residue: 1.1129 time to fit residues: 127.0061 Evaluate side-chains 102 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 92 time to evaluate : 1.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 180 MET Chi-restraints excluded: chain A residue 233 LYS Chi-restraints excluded: chain A residue 261 SER Chi-restraints excluded: chain A residue 474 THR Chi-restraints excluded: chain A residue 521 ILE Chi-restraints excluded: chain B residue 34 THR 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 474 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 78 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 89 optimal weight: 5.9990 chunk 135 optimal weight: 8.9990 chunk 124 optimal weight: 7.9990 chunk 107 optimal weight: 1.9990 chunk 11 optimal weight: 10.0000 chunk 83 optimal weight: 7.9990 chunk 66 optimal weight: 1.9990 chunk 85 optimal weight: 8.9990 chunk 114 optimal weight: 0.8980 overall best weight: 1.7788 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.2009 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= 0.208 Angle : 0.499 10.497 15296 Z= 0.253 Chirality : 0.042 0.128 1744 Planarity : 0.004 0.046 1808 Dihedral : 6.937 58.555 2163 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % 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 (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: 1.77 (0.23), residues: 1352 helix: 1.88 (0.18), residues: 890 sheet: 2.56 (0.71), residues: 36 loop : -0.45 (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 A 640 PHE 0.018 0.001 PHE A 241 TYR 0.014 0.001 TYR A 16 ARG 0.002 0.000 ARG A 571 ********************** 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 104 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 88 time to evaluate : 1.188 Fit side-chains REVERT: A 122 MET cc_start: 0.7905 (mtm) cc_final: 0.7664 (mtp) REVERT: A 271 LEU cc_start: 0.8335 (mt) cc_final: 0.8094 (mp) REVERT: A 316 ASP cc_start: 0.8340 (m-30) cc_final: 0.8066 (m-30) REVERT: A 463 ARG cc_start: 0.7764 (mtm-85) cc_final: 0.7424 (mtp180) REVERT: B 122 MET cc_start: 0.7899 (mtm) cc_final: 0.7655 (mtp) REVERT: B 316 ASP cc_start: 0.8403 (m-30) cc_final: 0.8163 (m-30) REVERT: B 463 ARG cc_start: 0.7734 (mtm-85) cc_final: 0.7403 (mtp180) REVERT: B 682 GLN cc_start: 0.7893 (OUTLIER) cc_final: 0.7558 (tt0) outliers start: 16 outliers final: 10 residues processed: 96 average time/residue: 1.1262 time to fit residues: 118.8908 Evaluate side-chains 99 residues out of total 1154 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 88 time to evaluate : 1.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 180 MET Chi-restraints excluded: chain A residue 233 LYS Chi-restraints excluded: chain A residue 261 SER Chi-restraints excluded: chain A residue 474 THR Chi-restraints excluded: chain A residue 521 ILE Chi-restraints excluded: chain B residue 34 THR 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 474 THR Chi-restraints excluded: chain B residue 682 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 33 optimal weight: 9.9990 chunk 99 optimal weight: 0.0770 chunk 15 optimal weight: 8.9990 chunk 29 optimal weight: 5.9990 chunk 108 optimal weight: 8.9990 chunk 45 optimal weight: 2.9990 chunk 110 optimal weight: 7.9990 chunk 13 optimal weight: 2.9990 chunk 19 optimal weight: 0.6980 chunk 94 optimal weight: 9.9990 chunk 6 optimal weight: 4.9990 overall best weight: 2.3544 ------------------------------------------------------------------------------- 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 = 0.3659 r_free = 0.3659 target = 0.142340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.106786 restraints weight = 12570.369| |-----------------------------------------------------------------------------| r_work (start): 0.3275 rms_B_bonded: 1.82 r_work: 0.3168 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3046 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.2043 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= 0.249 Angle : 0.518 10.940 15296 Z= 0.263 Chirality : 0.042 0.127 1744 Planarity : 0.004 0.048 1808 Dihedral : 7.268 59.746 2163 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 1.41 % Allowed : 11.90 % Favored : 86.68 % 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: 1.69 (0.23), residues: 1352 helix: 1.80 (0.18), residues: 888 sheet: 2.50 (0.72), residues: 36 loop : -0.42 (0.29), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 70 HIS 0.004 0.001 HIS A 640 PHE 0.018 0.001 PHE A 241 TYR 0.015 0.001 TYR A 16 ARG 0.002 0.000 ARG A 576 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3702.16 seconds wall clock time: 69 minutes 42.78 seconds (4182.78 seconds total)