Starting phenix.real_space_refine on Thu May 22 20:21:52 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tag_41134/05_2025/8tag_41134_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tag_41134/05_2025/8tag_41134.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8tag_41134/05_2025/8tag_41134.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tag_41134/05_2025/8tag_41134.map" model { file = "/net/cci-nas-00/data/ceres_data/8tag_41134/05_2025/8tag_41134_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tag_41134/05_2025/8tag_41134_trim.cif" } resolution = 3.2 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= 0.007 sd= 0.097 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: 6 Type Number sf(0) Gaussians Ca 3 9.91 5 S 71 5.16 5 C 7824 2.51 5 N 1906 2.21 5 O 2105 1.98 5 H 11607 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 35 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 23516 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 11240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 705, 11240 Classifications: {'peptide': 705} Link IDs: {'PTRANS': 32, 'TRANS': 672} Chain breaks: 6 Unresolved non-hydrogen bonds: 132 Unresolved non-hydrogen angles: 165 Unresolved non-hydrogen dihedrals: 111 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 2, 'TYR:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 3, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 69 Chain: "B" Number of atoms: 12189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 743, 12189 Classifications: {'peptide': 743} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PTRANS': 33, 'TRANS': 709} Chain breaks: 3 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "A" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 43 Unusual residues: {' CA': 1, 'NAG': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "B" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 44 Unusual residues: {' CA': 2, 'NAG': 3} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 10.58, per 1000 atoms: 0.45 Number of scatterers: 23516 At special positions: 0 Unit cell: (135.918, 87.256, 120.816, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 3 19.99 S 71 16.00 O 2105 8.00 N 1906 7.00 C 7824 6.00 H 11607 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS A 331 " - pdb=" SG CYS A 372 " distance=2.03 Simple disulfide: pdb=" SG CYS A 338 " - pdb=" SG CYS A 365 " distance=2.03 Simple disulfide: pdb=" SG CYS A 349 " - pdb=" SG CYS A 807 " distance=2.03 Simple disulfide: pdb=" SG CYS A 352 " - pdb=" SG CYS A 356 " distance=2.03 Simple disulfide: pdb=" SG CYS A 596 " - pdb=" SG CYS A 601 " distance=2.03 Simple disulfide: pdb=" SG CYS B 331 " - pdb=" SG CYS B 372 " distance=2.03 Simple disulfide: pdb=" SG CYS B 338 " - pdb=" SG CYS B 365 " distance=2.03 Simple disulfide: pdb=" SG CYS B 349 " - pdb=" SG CYS B 807 " distance=2.04 Simple disulfide: pdb=" SG CYS B 352 " - pdb=" SG CYS B 356 " distance=2.03 Simple disulfide: pdb=" SG CYS B 596 " - pdb=" SG CYS B 601 " distance=2.03 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 Atom "HETATM23469 O5 NAG A 903 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 901 " - " ASN A 362 " " NAG B 901 " - " ASN B 362 " Time building additional restraints: 5.72 Conformation dependent library (CDL) restraints added in 1.8 seconds 2852 Ramachandran restraints generated. 1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2758 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 7 sheets defined 63.7% alpha, 3.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.03 Creating SS restraints... Processing helix chain 'A' and resid 92 through 108 Processing helix chain 'A' and resid 131 through 142 removed outlier: 3.797A pdb=" N MET A 142 " --> pdb=" O TYR A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 192 Processing helix chain 'A' and resid 205 through 220 Processing helix chain 'A' and resid 233 through 240 Processing helix chain 'A' and resid 264 through 274 Processing helix chain 'A' and resid 275 through 279 Processing helix chain 'A' and resid 284 through 292 Processing helix chain 'A' and resid 293 through 326 removed outlier: 3.985A pdb=" N LEU A 312 " --> pdb=" O GLN A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 339 Processing helix chain 'A' and resid 364 through 375 removed outlier: 3.797A pdb=" N ILE A 373 " --> pdb=" O LYS A 369 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N PHE A 374 " --> pdb=" O LYS A 370 " (cutoff:3.500A) Processing helix chain 'A' and resid 376 through 408 removed outlier: 3.597A pdb=" N LEU A 380 " --> pdb=" O SER A 376 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N VAL A 388 " --> pdb=" O VAL A 384 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N THR A 391 " --> pdb=" O GLY A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 458 through 486 Processing helix chain 'A' and resid 504 through 539 removed outlier: 4.009A pdb=" N THR A 526 " --> pdb=" O MET A 522 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N ILE A 527 " --> pdb=" O ILE A 523 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N GLU A 539 " --> pdb=" O ILE A 535 " (cutoff:3.500A) Processing helix chain 'A' and resid 544 through 573 removed outlier: 5.652A pdb=" N SER A 566 " --> pdb=" O ASN A 562 " (cutoff:3.500A) removed outlier: 4.871A pdb=" N CYS A 567 " --> pdb=" O TYR A 563 " (cutoff:3.500A) Processing helix chain 'A' and resid 601 through 625 Processing helix chain 'A' and resid 625 through 638 removed outlier: 4.678A pdb=" N TRP A 629 " --> pdb=" O VAL A 625 " (cutoff:3.500A) Processing helix chain 'A' and resid 648 through 656 removed outlier: 3.527A pdb=" N LEU A 656 " --> pdb=" O GLN A 652 " (cutoff:3.500A) Processing helix chain 'A' and resid 662 through 681 removed outlier: 4.056A pdb=" N PHE A 681 " --> pdb=" O PHE A 677 " (cutoff:3.500A) Processing helix chain 'A' and resid 687 through 710 removed outlier: 4.125A pdb=" N ARG A 701 " --> pdb=" O ILE A 697 " (cutoff:3.500A) Processing helix chain 'A' and resid 725 through 747 removed outlier: 3.990A pdb=" N VAL A 738 " --> pdb=" O ILE A 734 " (cutoff:3.500A) Processing helix chain 'A' and resid 749 through 760 Processing helix chain 'A' and resid 775 through 781 Processing helix chain 'A' and resid 787 through 789 No H-bonds generated for 'chain 'A' and resid 787 through 789' Processing helix chain 'A' and resid 825 through 856 removed outlier: 3.540A pdb=" N TRP A 829 " --> pdb=" O ASN A 825 " (cutoff:3.500A) Processing helix chain 'A' and resid 856 through 861 Processing helix chain 'A' and resid 861 through 871 removed outlier: 3.844A pdb=" N LYS A 865 " --> pdb=" O SER A 861 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N GLU A 871 " --> pdb=" O LYS A 867 " (cutoff:3.500A) Processing helix chain 'B' and resid 87 through 109 removed outlier: 3.605A pdb=" N ASN B 91 " --> pdb=" O LYS B 87 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 143 Processing helix chain 'B' and resid 188 through 195 removed outlier: 5.627A pdb=" N ASN B 193 " --> pdb=" O SER B 190 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ASP B 194 " --> pdb=" O ARG B 191 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N PHE B 195 " --> pdb=" O MET B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 199 through 204 Processing helix chain 'B' and resid 205 through 220 Processing helix chain 'B' and resid 232 through 239 removed outlier: 3.810A pdb=" N LEU B 236 " --> pdb=" O GLY B 232 " (cutoff:3.500A) Processing helix chain 'B' and resid 264 through 273 Processing helix chain 'B' and resid 275 through 279 Processing helix chain 'B' and resid 284 through 293 Processing helix chain 'B' and resid 293 through 327 removed outlier: 3.957A pdb=" N TYR B 299 " --> pdb=" O LYS B 295 " (cutoff:3.500A) Processing helix chain 'B' and resid 331 through 339 Processing helix chain 'B' and resid 364 through 375 Processing helix chain 'B' and resid 376 through 408 removed outlier: 3.789A pdb=" N LEU B 380 " --> pdb=" O SER B 376 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N THR B 391 " --> pdb=" O GLY B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 410 through 416 Processing helix chain 'B' and resid 456 through 488 removed outlier: 3.598A pdb=" N THR B 488 " --> pdb=" O VAL B 484 " (cutoff:3.500A) Processing helix chain 'B' and resid 504 through 539 removed outlier: 3.928A pdb=" N THR B 526 " --> pdb=" O MET B 522 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ILE B 527 " --> pdb=" O ILE B 523 " (cutoff:3.500A) Processing helix chain 'B' and resid 543 through 573 removed outlier: 5.262A pdb=" N SER B 566 " --> pdb=" O ASN B 562 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N CYS B 567 " --> pdb=" O TYR B 563 " (cutoff:3.500A) Processing helix chain 'B' and resid 601 through 638 Proline residue: B 628 - end of helix Processing helix chain 'B' and resid 648 through 655 removed outlier: 3.810A pdb=" N HIS B 655 " --> pdb=" O GLU B 651 " (cutoff:3.500A) Processing helix chain 'B' and resid 664 through 681 removed outlier: 3.908A pdb=" N PHE B 681 " --> pdb=" O PHE B 677 " (cutoff:3.500A) Processing helix chain 'B' and resid 687 through 710 removed outlier: 4.278A pdb=" N ARG B 701 " --> pdb=" O ILE B 697 " (cutoff:3.500A) Processing helix chain 'B' and resid 724 through 747 removed outlier: 4.060A pdb=" N ILE B 728 " --> pdb=" O ALA B 724 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N VAL B 737 " --> pdb=" O ALA B 733 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N VAL B 738 " --> pdb=" O ILE B 734 " (cutoff:3.500A) Processing helix chain 'B' and resid 749 through 760 Processing helix chain 'B' and resid 775 through 781 Processing helix chain 'B' and resid 787 through 789 No H-bonds generated for 'chain 'B' and resid 787 through 789' Processing helix chain 'B' and resid 825 through 857 Processing helix chain 'B' and resid 861 through 868 Processing sheet with id=AA1, first strand: chain 'A' and resid 112 through 116 removed outlier: 3.807A pdb=" N VAL A 124 " --> pdb=" O TYR A 77 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N TYR A 77 " --> pdb=" O VAL A 124 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N PHE A 246 " --> pdb=" O ILE A 74 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N VAL A 76 " --> pdb=" O ALA A 244 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ALA A 244 " --> pdb=" O VAL A 76 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 347 through 348 Processing sheet with id=AA3, first strand: chain 'A' and resid 782 through 785 removed outlier: 3.556A pdb=" N CYS A 807 " --> pdb=" O PHE A 784 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 123 through 127 removed outlier: 3.551A pdb=" N VAL B 124 " --> pdb=" O TYR B 77 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N PHE B 246 " --> pdb=" O ILE B 74 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ALA B 244 " --> pdb=" O VAL B 76 " (cutoff:3.500A) removed outlier: 7.437A pdb=" N GLU B 78 " --> pdb=" O TYR B 242 " (cutoff:3.500A) removed outlier: 7.855A pdb=" N TYR B 242 " --> pdb=" O GLU B 78 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 221 through 225 removed outlier: 3.802A pdb=" N GLN B 223 " --> pdb=" O LYS B 230 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N MET B 225 " --> pdb=" O VAL B 228 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 347 through 348 removed outlier: 3.765A pdb=" N TRP B 359 " --> pdb=" O MET B 348 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 782 through 785 694 hydrogen bonds defined for protein. 2040 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: 7.79 Time building geometry restraints manager: 7.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 11595 1.03 - 1.23: 290 1.23 - 1.43: 5062 1.43 - 1.63: 6784 1.63 - 1.83: 112 Bond restraints: 23843 Sorted by residual: bond pdb=" N PHE B 52 " pdb=" H1 PHE B 52 " ideal model delta sigma weight residual 0.960 0.860 0.100 2.00e-02 2.50e+03 2.50e+01 bond pdb=" C1 NAG B 902 " pdb=" O5 NAG B 902 " ideal model delta sigma weight residual 1.406 1.432 -0.026 2.00e-02 2.50e+03 1.65e+00 bond pdb=" C ASP B 339 " pdb=" N PRO B 340 " ideal model delta sigma weight residual 1.334 1.344 -0.011 8.40e-03 1.42e+04 1.63e+00 bond pdb=" C1 NAG A 903 " pdb=" O5 NAG A 903 " ideal model delta sigma weight residual 1.406 1.431 -0.025 2.00e-02 2.50e+03 1.56e+00 bond pdb=" C1 NAG A 901 " pdb=" O5 NAG A 901 " ideal model delta sigma weight residual 1.406 1.431 -0.025 2.00e-02 2.50e+03 1.52e+00 ... (remaining 23838 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.32: 42920 7.32 - 14.64: 4 14.64 - 21.96: 0 21.96 - 29.28: 0 29.28 - 36.60: 24 Bond angle restraints: 42948 Sorted by residual: angle pdb=" N ASP A 286 " pdb=" CA ASP A 286 " pdb=" HA ASP A 286 " ideal model delta sigma weight residual 110.00 73.40 36.60 3.00e+00 1.11e-01 1.49e+02 angle pdb=" CB GLN A 94 " pdb=" CA GLN A 94 " pdb=" HA GLN A 94 " ideal model delta sigma weight residual 109.00 73.15 35.85 3.00e+00 1.11e-01 1.43e+02 angle pdb=" N ILE B 141 " pdb=" CA ILE B 141 " pdb=" HA ILE B 141 " ideal model delta sigma weight residual 110.00 74.38 35.62 3.00e+00 1.11e-01 1.41e+02 angle pdb=" CB ASP A 286 " pdb=" CA ASP A 286 " pdb=" HA ASP A 286 " ideal model delta sigma weight residual 109.00 73.42 35.58 3.00e+00 1.11e-01 1.41e+02 angle pdb=" CB PHE B 215 " pdb=" CA PHE B 215 " pdb=" HA PHE B 215 " ideal model delta sigma weight residual 109.00 73.58 35.42 3.00e+00 1.11e-01 1.39e+02 ... (remaining 42943 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.52: 10195 17.52 - 35.05: 908 35.05 - 52.57: 228 52.57 - 70.09: 60 70.09 - 87.61: 31 Dihedral angle restraints: 11422 sinusoidal: 6018 harmonic: 5404 Sorted by residual: dihedral pdb=" CB CYS A 338 " pdb=" SG CYS A 338 " pdb=" SG CYS A 365 " pdb=" CB CYS A 365 " ideal model delta sinusoidal sigma weight residual -86.00 -166.42 80.42 1 1.00e+01 1.00e-02 8.00e+01 dihedral pdb=" CB CYS A 352 " pdb=" SG CYS A 352 " pdb=" SG CYS A 356 " pdb=" CB CYS A 356 " ideal model delta sinusoidal sigma weight residual -86.00 -145.77 59.77 1 1.00e+01 1.00e-02 4.77e+01 dihedral pdb=" CB CYS B 352 " pdb=" SG CYS B 352 " pdb=" SG CYS B 356 " pdb=" CB CYS B 356 " ideal model delta sinusoidal sigma weight residual -86.00 -136.14 50.14 1 1.00e+01 1.00e-02 3.45e+01 ... (remaining 11419 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.781: 1819 0.781 - 1.561: 1 1.561 - 2.342: 0 2.342 - 3.123: 0 3.123 - 3.904: 1 Chirality restraints: 1821 Sorted by residual: chirality pdb=" C1 NAG B 901 " pdb=" ND2 ASN B 362 " pdb=" C2 NAG B 901 " pdb=" O5 NAG B 901 " both_signs ideal model delta sigma weight residual False -2.40 1.50 -3.90 2.00e-01 2.50e+01 3.81e+02 chirality pdb=" C4 NAG A 901 " pdb=" C3 NAG A 901 " pdb=" C5 NAG A 901 " pdb=" O4 NAG A 901 " both_signs ideal model delta sigma weight residual False -2.53 -0.98 -1.55 2.00e-01 2.50e+01 6.03e+01 chirality pdb=" CA CYS A 356 " pdb=" N CYS A 356 " pdb=" C CYS A 356 " pdb=" CB CYS A 356 " both_signs ideal model delta sigma weight residual False 2.51 2.09 0.42 2.00e-01 2.50e+01 4.49e+00 ... (remaining 1818 not shown) Planarity restraints: 3437 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 362 " -0.081 2.00e-02 2.50e+03 1.95e-01 4.73e+02 pdb=" CG ASN B 362 " 0.058 2.00e-02 2.50e+03 pdb=" OD1 ASN B 362 " -0.103 2.00e-02 2.50e+03 pdb=" ND2 ASN B 362 " 0.346 2.00e-02 2.50e+03 pdb=" C1 NAG B 901 " -0.221 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU B 540 " -0.050 5.00e-02 4.00e+02 7.64e-02 9.35e+00 pdb=" N PRO B 541 " 0.132 5.00e-02 4.00e+02 pdb=" CA PRO B 541 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO B 541 " -0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 618 " -0.011 2.00e-02 2.50e+03 2.27e-02 5.17e+00 pdb=" C ILE A 618 " 0.039 2.00e-02 2.50e+03 pdb=" O ILE A 618 " -0.015 2.00e-02 2.50e+03 pdb=" N TRP A 619 " -0.013 2.00e-02 2.50e+03 ... (remaining 3434 not shown) Histogram of nonbonded interaction distances: 1.30 - 1.96: 145 1.96 - 2.62: 28470 2.62 - 3.28: 70344 3.28 - 3.94: 86455 3.94 - 4.60: 135851 Nonbonded interactions: 321265 Sorted by model distance: nonbonded pdb="HD21 ASN A 778 " pdb=" O5 NAG A 903 " model vdw 1.304 2.450 nonbonded pdb=" OD1 ASP A 286 " pdb="HH12 ARG A 289 " model vdw 1.390 2.450 nonbonded pdb=" OD1 ASN A 525 " pdb="HE22 GLN A 559 " model vdw 1.520 2.450 nonbonded pdb="HH11 ARG B 69 " pdb=" OE1 GLN B 111 " model vdw 1.527 2.450 nonbonded pdb=" OE1 GLN A 506 " pdb=" H GLN A 506 " model vdw 1.586 2.450 ... (remaining 321260 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 59 through 361 or (resid 362 and (name N or name CA or nam \ e C or name O or name CB or name CG or name OD1 or name ND2 or name H or name HA \ or name HB2 or name HB3)) or resid 363 through 868 or resid 901 through 902 or \ resid 904)) selection = (chain 'B' and (resid 59 through 82 or resid 91 through 93 or (resid 94 through \ 97 and (name N or name CA or name C or name O or name CB or name H or name HA )) \ or resid 98 or (resid 99 and (name N or name CA or name C or name O or name CB \ or name H or name HA )) or resid 100 or (resid 101 through 107 and (name N or na \ me CA or name C or name O or name CB or name H or name HA )) or resid 108 throug \ h 115 or (resid 116 through 126 and (name N or name CA or name C or name O or na \ me CB or name H or name HA )) or resid 127 through 128 or (resid 129 and (name N \ or name CA or name C or name O or name CB or name H or name HA )) or resid 130 \ through 134 or (resid 135 through 137 and (name N or name CA or name C or name O \ or name CB or name H or name HA )) or resid 138 through 140 or (resid 141 and ( \ name N or name CA or name C or name O or name CB or name H or name HA )) or resi \ d 142 or (resid 143 and (name N or name CA or name C or name O or name CB or nam \ e H or name HA )) or resid 144 through 147 or resid 185 through 222 or resid 232 \ through 235 or (resid 236 through 239 and (name N or name CA or name C or name \ O or name CB or name H or name HA )) or resid 240 or (resid 241 and (name N or n \ ame CA or name C or name O or name CB or name H or name HA )) or resid 242 throu \ gh 423 or resid 457 through 487 or resid 503 through 589 or (resid 590 and (name \ N or name CA or name C or name O or name CB or name H or name HA )) or resid 59 \ 1 through 638 or resid 645 through 660 or (resid 661 and (name N or name CA or n \ ame C or name O or name CB or name H or name HA )) or resid 662 through 784 or ( \ resid 785 and (name N or name CA or name C or name O or name CB or name CG or na \ me OD1 or name ND2 or name H or name HA or name HB2 or name HB3)) or resid 786 t \ hrough 857 or (resid 858 and (name N or name CA or name C or name O or name CB o \ r name CG or name CD )) or (resid 859 and (name N or name CA or name C or name O \ or name CB or name CG or name OD1 or name OD2)) or resid 860 through 868 or res \ id 902 through 903 or resid 905)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.260 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: 0.370 Extract box with map and model: 0.830 Check model and map are aligned: 0.150 Set scattering table: 0.210 Process input model: 48.300 Find NCS groups from input model: 0.780 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7711 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 12248 Z= 0.199 Angle : 0.662 22.391 16633 Z= 0.353 Chirality : 0.109 3.904 1821 Planarity : 0.005 0.076 2064 Dihedral : 14.053 86.586 4503 Min Nonbonded Distance : 1.622 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.22), residues: 1426 helix: 1.73 (0.17), residues: 821 sheet: -1.83 (0.79), residues: 40 loop : -1.19 (0.26), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B 132 HIS 0.004 0.001 HIS B 275 PHE 0.017 0.002 PHE A 560 TYR 0.030 0.001 TYR A 668 ARG 0.005 0.001 ARG A 289 Details of bonding type rmsd link_NAG-ASN : bond 0.03284 ( 2) link_NAG-ASN : angle 10.72923 ( 6) hydrogen bonds : bond 0.12032 ( 694) hydrogen bonds : angle 5.52743 ( 2040) SS BOND : bond 0.00305 ( 10) SS BOND : angle 1.29797 ( 20) covalent geometry : bond 0.00443 (12236) covalent geometry : angle 0.62907 (16607) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2852 Ramachandran restraints generated. 1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2852 Ramachandran restraints generated. 1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 95 is missing expected H atoms. Skipping. Residue LYS 97 is missing expected H atoms. Skipping. Residue TYR 101 is missing expected H atoms. Skipping. Residue SER 103 is missing expected H atoms. Skipping. Residue LEU 105 is missing expected H atoms. Skipping. Residue ILE 106 is missing expected H atoms. Skipping. Residue SER 117 is missing expected H atoms. Skipping. Residue VAL 118 is missing expected H atoms. Skipping. Residue SER 119 is missing expected H atoms. Skipping. Residue LYS 122 is missing expected H atoms. Skipping. Residue LEU 123 is missing expected H atoms. Skipping. Residue VAL 124 is missing expected H atoms. Skipping. Residue VAL 126 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue TYR 137 is missing expected H atoms. Skipping. Residue ILE 141 is missing expected H atoms. Skipping. Residue LEU 236 is missing expected H atoms. Skipping. Residue VAL 237 is missing expected H atoms. Skipping. Residue SER 238 is missing expected H atoms. Skipping. Residue SER 239 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue LYS 590 is missing expected H atoms. Skipping. Residue LYS 661 is missing expected H atoms. Skipping. Evaluate side-chains 146 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 146 time to evaluate : 1.659 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 145 LYS cc_start: 0.6560 (mtmt) cc_final: 0.6224 (ttpt) outliers start: 0 outliers final: 0 residues processed: 146 average time/residue: 0.5562 time to fit residues: 116.6900 Evaluate side-chains 121 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 121 time to evaluate : 1.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 121 optimal weight: 10.0000 chunk 109 optimal weight: 1.9990 chunk 60 optimal weight: 3.9990 chunk 37 optimal weight: 9.9990 chunk 73 optimal weight: 20.0000 chunk 58 optimal weight: 0.4980 chunk 112 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 68 optimal weight: 3.9990 chunk 84 optimal weight: 7.9990 chunk 130 optimal weight: 0.9990 overall best weight: 1.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 559 GLN A 695 ASN B 426 GLN B 621 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4317 r_free = 0.4317 target = 0.201680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.137977 restraints weight = 37695.035| |-----------------------------------------------------------------------------| r_work (start): 0.3647 rms_B_bonded: 2.74 r_work: 0.3410 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.3271 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.0909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 12248 Z= 0.167 Angle : 0.562 7.492 16633 Z= 0.309 Chirality : 0.046 0.408 1821 Planarity : 0.005 0.059 2064 Dihedral : 5.687 57.253 1722 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 0.40 % Allowed : 4.44 % Favored : 95.16 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.22), residues: 1426 helix: 1.74 (0.17), residues: 824 sheet: -1.48 (0.73), residues: 48 loop : -1.28 (0.26), residues: 554 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 650 HIS 0.004 0.001 HIS B 830 PHE 0.013 0.001 PHE A 560 TYR 0.021 0.001 TYR A 668 ARG 0.004 0.000 ARG A 289 Details of bonding type rmsd link_NAG-ASN : bond 0.00378 ( 2) link_NAG-ASN : angle 1.74290 ( 6) hydrogen bonds : bond 0.05260 ( 694) hydrogen bonds : angle 4.77388 ( 2040) SS BOND : bond 0.00307 ( 10) SS BOND : angle 1.04794 ( 20) covalent geometry : bond 0.00385 (12236) covalent geometry : angle 0.56073 (16607) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2852 Ramachandran restraints generated. 1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2852 Ramachandran restraints generated. 1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 95 is missing expected H atoms. Skipping. Residue LYS 97 is missing expected H atoms. Skipping. Residue TYR 101 is missing expected H atoms. Skipping. Residue SER 103 is missing expected H atoms. Skipping. Residue LEU 105 is missing expected H atoms. Skipping. Residue ILE 106 is missing expected H atoms. Skipping. Residue SER 117 is missing expected H atoms. Skipping. Residue VAL 118 is missing expected H atoms. Skipping. Residue SER 119 is missing expected H atoms. Skipping. Residue LYS 122 is missing expected H atoms. Skipping. Residue LEU 123 is missing expected H atoms. Skipping. Residue VAL 124 is missing expected H atoms. Skipping. Residue VAL 126 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue TYR 137 is missing expected H atoms. Skipping. Residue ILE 141 is missing expected H atoms. Skipping. Residue LEU 236 is missing expected H atoms. Skipping. Residue VAL 237 is missing expected H atoms. Skipping. Residue SER 238 is missing expected H atoms. Skipping. Residue SER 239 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue LYS 590 is missing expected H atoms. Skipping. Residue LYS 661 is missing expected H atoms. Skipping. Evaluate side-chains 132 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 127 time to evaluate : 1.746 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 631 MET cc_start: 0.4646 (mpp) cc_final: 0.4260 (mmm) outliers start: 5 outliers final: 4 residues processed: 130 average time/residue: 0.5329 time to fit residues: 100.5465 Evaluate side-chains 124 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 120 time to evaluate : 1.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain B residue 141 ILE Chi-restraints excluded: chain B residue 531 VAL Chi-restraints excluded: chain B residue 546 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 39 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 chunk 52 optimal weight: 0.8980 chunk 4 optimal weight: 10.0000 chunk 96 optimal weight: 3.9990 chunk 124 optimal weight: 1.9990 chunk 105 optimal weight: 2.9990 chunk 107 optimal weight: 7.9990 chunk 0 optimal weight: 20.0000 chunk 3 optimal weight: 20.0000 chunk 24 optimal weight: 0.9980 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 559 GLN A 674 GLN A 695 ASN B 785 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4309 r_free = 0.4309 target = 0.200939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.133164 restraints weight = 37734.755| |-----------------------------------------------------------------------------| r_work (start): 0.3576 rms_B_bonded: 2.49 r_work: 0.3413 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3286 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.1281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 12248 Z= 0.164 Angle : 0.535 7.723 16633 Z= 0.293 Chirality : 0.045 0.413 1821 Planarity : 0.005 0.053 2064 Dihedral : 5.109 52.409 1722 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 0.87 % Allowed : 6.19 % Favored : 92.94 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.22), residues: 1426 helix: 1.80 (0.17), residues: 824 sheet: -1.44 (0.72), residues: 48 loop : -1.32 (0.26), residues: 554 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 273 HIS 0.003 0.001 HIS A 108 PHE 0.015 0.001 PHE A 461 TYR 0.017 0.001 TYR A 668 ARG 0.006 0.000 ARG A 289 Details of bonding type rmsd link_NAG-ASN : bond 0.00087 ( 2) link_NAG-ASN : angle 1.73207 ( 6) hydrogen bonds : bond 0.05030 ( 694) hydrogen bonds : angle 4.53289 ( 2040) SS BOND : bond 0.00237 ( 10) SS BOND : angle 0.87853 ( 20) covalent geometry : bond 0.00379 (12236) covalent geometry : angle 0.53375 (16607) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2852 Ramachandran restraints generated. 1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2852 Ramachandran restraints generated. 1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 95 is missing expected H atoms. Skipping. Residue LYS 97 is missing expected H atoms. Skipping. Residue TYR 101 is missing expected H atoms. Skipping. Residue SER 103 is missing expected H atoms. Skipping. Residue LEU 105 is missing expected H atoms. Skipping. Residue ILE 106 is missing expected H atoms. Skipping. Residue SER 117 is missing expected H atoms. Skipping. Residue VAL 118 is missing expected H atoms. Skipping. Residue SER 119 is missing expected H atoms. Skipping. Residue LYS 122 is missing expected H atoms. Skipping. Residue LEU 123 is missing expected H atoms. Skipping. Residue VAL 124 is missing expected H atoms. Skipping. Residue VAL 126 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue TYR 137 is missing expected H atoms. Skipping. Residue ILE 141 is missing expected H atoms. Skipping. Residue LEU 236 is missing expected H atoms. Skipping. Residue VAL 237 is missing expected H atoms. Skipping. Residue SER 238 is missing expected H atoms. Skipping. Residue SER 239 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue LYS 590 is missing expected H atoms. Skipping. Residue LYS 661 is missing expected H atoms. Skipping. Evaluate side-chains 143 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 132 time to evaluate : 1.847 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 631 MET cc_start: 0.4536 (mpp) cc_final: 0.4232 (mmm) REVERT: B 235 ARG cc_start: 0.8487 (OUTLIER) cc_final: 0.8118 (ttt180) REVERT: B 258 GLU cc_start: 0.7229 (mp0) cc_final: 0.7025 (mp0) outliers start: 11 outliers final: 6 residues processed: 139 average time/residue: 0.5673 time to fit residues: 114.8504 Evaluate side-chains 131 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 124 time to evaluate : 1.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 523 ILE Chi-restraints excluded: chain B residue 132 TRP Chi-restraints excluded: chain B residue 141 ILE Chi-restraints excluded: chain B residue 223 GLN Chi-restraints excluded: chain B residue 235 ARG Chi-restraints excluded: chain B residue 546 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 111 optimal weight: 4.9990 chunk 104 optimal weight: 0.9990 chunk 119 optimal weight: 0.9980 chunk 60 optimal weight: 4.9990 chunk 66 optimal weight: 0.9990 chunk 52 optimal weight: 2.9990 chunk 38 optimal weight: 9.9990 chunk 92 optimal weight: 1.9990 chunk 86 optimal weight: 2.9990 chunk 49 optimal weight: 6.9990 chunk 123 optimal weight: 3.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 559 GLN B 820 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4313 r_free = 0.4313 target = 0.201372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.142456 restraints weight = 38363.040| |-----------------------------------------------------------------------------| r_work (start): 0.3700 rms_B_bonded: 2.56 r_work: 0.3411 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3281 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.1581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12248 Z= 0.140 Angle : 0.512 7.878 16633 Z= 0.280 Chirality : 0.045 0.412 1821 Planarity : 0.005 0.050 2064 Dihedral : 4.783 51.611 1722 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 0.79 % Allowed : 7.78 % Favored : 91.43 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.88 (0.22), residues: 1426 helix: 1.90 (0.17), residues: 824 sheet: -1.93 (0.65), residues: 58 loop : -1.25 (0.26), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 397 HIS 0.004 0.001 HIS A 108 PHE 0.011 0.001 PHE A 461 TYR 0.013 0.001 TYR A 528 ARG 0.003 0.000 ARG A 289 Details of bonding type rmsd link_NAG-ASN : bond 0.00127 ( 2) link_NAG-ASN : angle 1.78475 ( 6) hydrogen bonds : bond 0.04697 ( 694) hydrogen bonds : angle 4.39867 ( 2040) SS BOND : bond 0.00204 ( 10) SS BOND : angle 0.74767 ( 20) covalent geometry : bond 0.00318 (12236) covalent geometry : angle 0.51051 (16607) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2852 Ramachandran restraints generated. 1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2852 Ramachandran restraints generated. 1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 95 is missing expected H atoms. Skipping. Residue LYS 97 is missing expected H atoms. Skipping. Residue TYR 101 is missing expected H atoms. Skipping. Residue SER 103 is missing expected H atoms. Skipping. Residue LEU 105 is missing expected H atoms. Skipping. Residue ILE 106 is missing expected H atoms. Skipping. Residue SER 117 is missing expected H atoms. Skipping. Residue VAL 118 is missing expected H atoms. Skipping. Residue SER 119 is missing expected H atoms. Skipping. Residue LYS 122 is missing expected H atoms. Skipping. Residue LEU 123 is missing expected H atoms. Skipping. Residue VAL 124 is missing expected H atoms. Skipping. Residue VAL 126 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue TYR 137 is missing expected H atoms. Skipping. Residue ILE 141 is missing expected H atoms. Skipping. Residue LEU 236 is missing expected H atoms. Skipping. Residue VAL 237 is missing expected H atoms. Skipping. Residue SER 238 is missing expected H atoms. Skipping. Residue SER 239 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue LYS 590 is missing expected H atoms. Skipping. Residue LYS 661 is missing expected H atoms. Skipping. Evaluate side-chains 144 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 134 time to evaluate : 2.088 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 339 ASP cc_start: 0.7280 (m-30) cc_final: 0.6939 (m-30) REVERT: A 631 MET cc_start: 0.4667 (mpp) cc_final: 0.4383 (mmm) REVERT: B 258 GLU cc_start: 0.7274 (mp0) cc_final: 0.7017 (mp0) outliers start: 10 outliers final: 8 residues processed: 141 average time/residue: 0.5992 time to fit residues: 121.6569 Evaluate side-chains 139 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 131 time to evaluate : 1.852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 289 ARG Chi-restraints excluded: chain A residue 523 ILE Chi-restraints excluded: chain B residue 132 TRP Chi-restraints excluded: chain B residue 141 ILE Chi-restraints excluded: chain B residue 223 GLN Chi-restraints excluded: chain B residue 349 CYS Chi-restraints excluded: chain B residue 546 ASP Chi-restraints excluded: chain B residue 767 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 85 optimal weight: 10.0000 chunk 117 optimal weight: 0.8980 chunk 97 optimal weight: 0.9990 chunk 104 optimal weight: 3.9990 chunk 72 optimal weight: 2.9990 chunk 106 optimal weight: 3.9990 chunk 43 optimal weight: 0.4980 chunk 13 optimal weight: 10.0000 chunk 34 optimal weight: 9.9990 chunk 73 optimal weight: 9.9990 chunk 138 optimal weight: 0.7980 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 559 GLN A 674 GLN A 695 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4315 r_free = 0.4315 target = 0.201733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.142315 restraints weight = 38271.176| |-----------------------------------------------------------------------------| r_work (start): 0.3699 rms_B_bonded: 2.51 r_work: 0.3441 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3311 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.1727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 12248 Z= 0.123 Angle : 0.498 7.994 16633 Z= 0.270 Chirality : 0.045 0.413 1821 Planarity : 0.004 0.051 2064 Dihedral : 4.597 50.832 1722 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 0.87 % Allowed : 8.57 % Favored : 90.56 % Cbeta Deviations : 0.07 % 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: 1.03 (0.22), residues: 1426 helix: 2.04 (0.17), residues: 824 sheet: -1.84 (0.66), residues: 58 loop : -1.21 (0.26), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 397 HIS 0.003 0.001 HIS A 108 PHE 0.011 0.001 PHE A 538 TYR 0.014 0.001 TYR A 668 ARG 0.002 0.000 ARG A 289 Details of bonding type rmsd link_NAG-ASN : bond 0.00075 ( 2) link_NAG-ASN : angle 1.83804 ( 6) hydrogen bonds : bond 0.04509 ( 694) hydrogen bonds : angle 4.31677 ( 2040) SS BOND : bond 0.00178 ( 10) SS BOND : angle 0.65492 ( 20) covalent geometry : bond 0.00275 (12236) covalent geometry : angle 0.49658 (16607) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2852 Ramachandran restraints generated. 1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2852 Ramachandran restraints generated. 1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 95 is missing expected H atoms. Skipping. Residue LYS 97 is missing expected H atoms. Skipping. Residue TYR 101 is missing expected H atoms. Skipping. Residue SER 103 is missing expected H atoms. Skipping. Residue LEU 105 is missing expected H atoms. Skipping. Residue ILE 106 is missing expected H atoms. Skipping. Residue SER 117 is missing expected H atoms. Skipping. Residue VAL 118 is missing expected H atoms. Skipping. Residue SER 119 is missing expected H atoms. Skipping. Residue LYS 122 is missing expected H atoms. Skipping. Residue LEU 123 is missing expected H atoms. Skipping. Residue VAL 124 is missing expected H atoms. Skipping. Residue VAL 126 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue TYR 137 is missing expected H atoms. Skipping. Residue ILE 141 is missing expected H atoms. Skipping. Residue LEU 236 is missing expected H atoms. Skipping. Residue VAL 237 is missing expected H atoms. Skipping. Residue SER 238 is missing expected H atoms. Skipping. Residue SER 239 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue LYS 590 is missing expected H atoms. Skipping. Residue LYS 661 is missing expected H atoms. Skipping. Evaluate side-chains 144 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 133 time to evaluate : 1.870 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 258 GLU cc_start: 0.4762 (mp0) cc_final: 0.4053 (pm20) REVERT: A 339 ASP cc_start: 0.7225 (m-30) cc_final: 0.6891 (m-30) REVERT: A 631 MET cc_start: 0.4623 (mpp) cc_final: 0.4370 (mmm) REVERT: B 258 GLU cc_start: 0.7347 (mp0) cc_final: 0.7057 (mp0) outliers start: 11 outliers final: 10 residues processed: 142 average time/residue: 0.5819 time to fit residues: 119.9803 Evaluate side-chains 140 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 130 time to evaluate : 1.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 289 ARG Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 523 ILE Chi-restraints excluded: chain A residue 622 ILE Chi-restraints excluded: chain B residue 132 TRP Chi-restraints excluded: chain B residue 141 ILE Chi-restraints excluded: chain B residue 223 GLN Chi-restraints excluded: chain B residue 349 CYS Chi-restraints excluded: chain B residue 546 ASP Chi-restraints excluded: chain B residue 767 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 124 optimal weight: 2.9990 chunk 46 optimal weight: 8.9990 chunk 143 optimal weight: 7.9990 chunk 141 optimal weight: 0.8980 chunk 82 optimal weight: 4.9990 chunk 32 optimal weight: 3.9990 chunk 117 optimal weight: 2.9990 chunk 77 optimal weight: 5.9990 chunk 51 optimal weight: 2.9990 chunk 142 optimal weight: 0.6980 chunk 4 optimal weight: 5.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 559 GLN A 674 GLN A 695 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4315 r_free = 0.4315 target = 0.201131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.138404 restraints weight = 37978.631| |-----------------------------------------------------------------------------| r_work (start): 0.3633 rms_B_bonded: 2.67 r_work: 0.3383 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3246 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.1874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 12248 Z= 0.169 Angle : 0.522 8.097 16633 Z= 0.287 Chirality : 0.045 0.416 1821 Planarity : 0.005 0.052 2064 Dihedral : 4.725 51.296 1722 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 0.95 % Allowed : 9.05 % Favored : 90.00 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.84 (0.22), residues: 1426 helix: 1.93 (0.17), residues: 817 sheet: -1.98 (0.64), residues: 58 loop : -1.30 (0.26), residues: 551 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 397 HIS 0.004 0.001 HIS B 830 PHE 0.020 0.001 PHE A 461 TYR 0.014 0.001 TYR A 668 ARG 0.003 0.000 ARG B 712 Details of bonding type rmsd link_NAG-ASN : bond 0.00132 ( 2) link_NAG-ASN : angle 1.94248 ( 6) hydrogen bonds : bond 0.04829 ( 694) hydrogen bonds : angle 4.35686 ( 2040) SS BOND : bond 0.00212 ( 10) SS BOND : angle 0.68118 ( 20) covalent geometry : bond 0.00394 (12236) covalent geometry : angle 0.52075 (16607) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2852 Ramachandran restraints generated. 1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2852 Ramachandran restraints generated. 1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 95 is missing expected H atoms. Skipping. Residue LYS 97 is missing expected H atoms. Skipping. Residue TYR 101 is missing expected H atoms. Skipping. Residue SER 103 is missing expected H atoms. Skipping. Residue LEU 105 is missing expected H atoms. Skipping. Residue ILE 106 is missing expected H atoms. Skipping. Residue SER 117 is missing expected H atoms. Skipping. Residue VAL 118 is missing expected H atoms. Skipping. Residue SER 119 is missing expected H atoms. Skipping. Residue LYS 122 is missing expected H atoms. Skipping. Residue LEU 123 is missing expected H atoms. Skipping. Residue VAL 124 is missing expected H atoms. Skipping. Residue VAL 126 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue TYR 137 is missing expected H atoms. Skipping. Residue ILE 141 is missing expected H atoms. Skipping. Residue LEU 236 is missing expected H atoms. Skipping. Residue VAL 237 is missing expected H atoms. Skipping. Residue SER 238 is missing expected H atoms. Skipping. Residue SER 239 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue LYS 590 is missing expected H atoms. Skipping. Residue LYS 661 is missing expected H atoms. Skipping. Evaluate side-chains 141 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 129 time to evaluate : 1.674 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 203 PHE cc_start: 0.6503 (t80) cc_final: 0.5899 (t80) REVERT: A 258 GLU cc_start: 0.4703 (mp0) cc_final: 0.3825 (pm20) REVERT: A 339 ASP cc_start: 0.7276 (m-30) cc_final: 0.6961 (m-30) REVERT: A 604 GLU cc_start: 0.8249 (OUTLIER) cc_final: 0.7946 (pt0) REVERT: A 631 MET cc_start: 0.4503 (mpp) cc_final: 0.4253 (mmm) REVERT: A 790 LYS cc_start: 0.7265 (mmmt) cc_final: 0.6818 (tttp) outliers start: 12 outliers final: 9 residues processed: 139 average time/residue: 0.5474 time to fit residues: 109.0038 Evaluate side-chains 139 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 129 time to evaluate : 1.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 289 ARG Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 523 ILE Chi-restraints excluded: chain A residue 604 GLU Chi-restraints excluded: chain B residue 132 TRP Chi-restraints excluded: chain B residue 141 ILE Chi-restraints excluded: chain B residue 223 GLN Chi-restraints excluded: chain B residue 349 CYS Chi-restraints excluded: chain B residue 546 ASP Chi-restraints excluded: chain B residue 767 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 89 optimal weight: 1.9990 chunk 137 optimal weight: 3.9990 chunk 112 optimal weight: 2.9990 chunk 57 optimal weight: 2.9990 chunk 70 optimal weight: 0.4980 chunk 19 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 chunk 133 optimal weight: 0.0270 chunk 83 optimal weight: 5.9990 chunk 77 optimal weight: 0.9990 chunk 104 optimal weight: 8.9990 overall best weight: 1.3044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 559 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4309 r_free = 0.4309 target = 0.201074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.140852 restraints weight = 38162.110| |-----------------------------------------------------------------------------| r_work (start): 0.3686 rms_B_bonded: 2.53 r_work: 0.3408 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3272 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.1956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 12248 Z= 0.124 Angle : 0.496 8.082 16633 Z= 0.269 Chirality : 0.044 0.415 1821 Planarity : 0.004 0.051 2064 Dihedral : 4.576 51.041 1722 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 1.27 % Allowed : 9.29 % Favored : 89.44 % Cbeta Deviations : 0.07 % 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: 1.03 (0.22), residues: 1426 helix: 2.09 (0.17), residues: 817 sheet: -1.91 (0.65), residues: 58 loop : -1.24 (0.26), residues: 551 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 397 HIS 0.002 0.001 HIS B 830 PHE 0.012 0.001 PHE A 538 TYR 0.011 0.001 TYR A 668 ARG 0.002 0.000 ARG A 289 Details of bonding type rmsd link_NAG-ASN : bond 0.00083 ( 2) link_NAG-ASN : angle 1.78655 ( 6) hydrogen bonds : bond 0.04475 ( 694) hydrogen bonds : angle 4.26578 ( 2040) SS BOND : bond 0.00172 ( 10) SS BOND : angle 0.61371 ( 20) covalent geometry : bond 0.00276 (12236) covalent geometry : angle 0.49431 (16607) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2852 Ramachandran restraints generated. 1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2852 Ramachandran restraints generated. 1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 95 is missing expected H atoms. Skipping. Residue LYS 97 is missing expected H atoms. Skipping. Residue TYR 101 is missing expected H atoms. Skipping. Residue SER 103 is missing expected H atoms. Skipping. Residue LEU 105 is missing expected H atoms. Skipping. Residue ILE 106 is missing expected H atoms. Skipping. Residue SER 117 is missing expected H atoms. Skipping. Residue VAL 118 is missing expected H atoms. Skipping. Residue SER 119 is missing expected H atoms. Skipping. Residue LYS 122 is missing expected H atoms. Skipping. Residue LEU 123 is missing expected H atoms. Skipping. Residue VAL 124 is missing expected H atoms. Skipping. Residue VAL 126 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue TYR 137 is missing expected H atoms. Skipping. Residue ILE 141 is missing expected H atoms. Skipping. Residue LEU 236 is missing expected H atoms. Skipping. Residue VAL 237 is missing expected H atoms. Skipping. Residue SER 238 is missing expected H atoms. Skipping. Residue SER 239 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue LYS 590 is missing expected H atoms. Skipping. Residue LYS 661 is missing expected H atoms. Skipping. Evaluate side-chains 141 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 125 time to evaluate : 1.674 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 203 PHE cc_start: 0.6444 (t80) cc_final: 0.5863 (t80) REVERT: A 258 GLU cc_start: 0.4679 (mp0) cc_final: 0.3860 (pm20) REVERT: A 339 ASP cc_start: 0.7177 (m-30) cc_final: 0.6867 (m-30) REVERT: A 604 GLU cc_start: 0.8205 (OUTLIER) cc_final: 0.7929 (pt0) REVERT: A 631 MET cc_start: 0.4383 (mpp) cc_final: 0.4129 (mmm) REVERT: A 790 LYS cc_start: 0.7267 (mmmt) cc_final: 0.6830 (tttp) REVERT: B 258 GLU cc_start: 0.7342 (mp0) cc_final: 0.7036 (mp0) outliers start: 16 outliers final: 11 residues processed: 138 average time/residue: 0.5418 time to fit residues: 106.5181 Evaluate side-chains 134 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 122 time to evaluate : 1.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 289 ARG Chi-restraints excluded: chain A residue 365 CYS Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 523 ILE Chi-restraints excluded: chain A residue 604 GLU Chi-restraints excluded: chain B residue 132 TRP Chi-restraints excluded: chain B residue 141 ILE Chi-restraints excluded: chain B residue 223 GLN Chi-restraints excluded: chain B residue 349 CYS Chi-restraints excluded: chain B residue 546 ASP Chi-restraints excluded: chain B residue 585 VAL Chi-restraints excluded: chain B residue 767 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 14 optimal weight: 9.9990 chunk 82 optimal weight: 2.9990 chunk 143 optimal weight: 5.9990 chunk 118 optimal weight: 1.9990 chunk 112 optimal weight: 2.9990 chunk 99 optimal weight: 0.9990 chunk 70 optimal weight: 0.3980 chunk 64 optimal weight: 2.9990 chunk 16 optimal weight: 10.0000 chunk 136 optimal weight: 0.9990 chunk 78 optimal weight: 3.9990 overall best weight: 1.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 559 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4303 r_free = 0.4303 target = 0.200358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.133149 restraints weight = 38166.483| |-----------------------------------------------------------------------------| r_work (start): 0.3570 rms_B_bonded: 2.42 r_work: 0.3410 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3271 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.2075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 12248 Z= 0.133 Angle : 0.499 8.057 16633 Z= 0.272 Chirality : 0.045 0.414 1821 Planarity : 0.005 0.062 2064 Dihedral : 4.550 50.695 1722 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 0.87 % Allowed : 9.68 % Favored : 89.44 % Cbeta Deviations : 0.07 % 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: 1.03 (0.22), residues: 1426 helix: 2.08 (0.17), residues: 817 sheet: -1.92 (0.65), residues: 58 loop : -1.22 (0.26), residues: 551 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 397 HIS 0.003 0.001 HIS A 108 PHE 0.012 0.001 PHE A 538 TYR 0.016 0.001 TYR A 668 ARG 0.002 0.000 ARG A 701 Details of bonding type rmsd link_NAG-ASN : bond 0.00078 ( 2) link_NAG-ASN : angle 1.83929 ( 6) hydrogen bonds : bond 0.04484 ( 694) hydrogen bonds : angle 4.25025 ( 2040) SS BOND : bond 0.00171 ( 10) SS BOND : angle 0.60480 ( 20) covalent geometry : bond 0.00303 (12236) covalent geometry : angle 0.49803 (16607) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2852 Ramachandran restraints generated. 1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2852 Ramachandran restraints generated. 1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 95 is missing expected H atoms. Skipping. Residue LYS 97 is missing expected H atoms. Skipping. Residue TYR 101 is missing expected H atoms. Skipping. Residue SER 103 is missing expected H atoms. Skipping. Residue LEU 105 is missing expected H atoms. Skipping. Residue ILE 106 is missing expected H atoms. Skipping. Residue SER 117 is missing expected H atoms. Skipping. Residue VAL 118 is missing expected H atoms. Skipping. Residue SER 119 is missing expected H atoms. Skipping. Residue LYS 122 is missing expected H atoms. Skipping. Residue LEU 123 is missing expected H atoms. Skipping. Residue VAL 124 is missing expected H atoms. Skipping. Residue VAL 126 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue TYR 137 is missing expected H atoms. Skipping. Residue ILE 141 is missing expected H atoms. Skipping. Residue LEU 236 is missing expected H atoms. Skipping. Residue VAL 237 is missing expected H atoms. Skipping. Residue SER 238 is missing expected H atoms. Skipping. Residue SER 239 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue LYS 590 is missing expected H atoms. Skipping. Residue LYS 661 is missing expected H atoms. Skipping. Evaluate side-chains 140 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 129 time to evaluate : 1.676 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 HIS cc_start: 0.6350 (t-90) cc_final: 0.5607 (m-70) REVERT: A 203 PHE cc_start: 0.6388 (t80) cc_final: 0.5794 (t80) REVERT: A 258 GLU cc_start: 0.4660 (mp0) cc_final: 0.3853 (pm20) REVERT: A 339 ASP cc_start: 0.7157 (m-30) cc_final: 0.6873 (m-30) REVERT: A 604 GLU cc_start: 0.8229 (OUTLIER) cc_final: 0.7941 (pt0) REVERT: A 631 MET cc_start: 0.4384 (mpp) cc_final: 0.4137 (mmm) REVERT: A 790 LYS cc_start: 0.7312 (mmmt) cc_final: 0.6867 (tttp) REVERT: B 609 LEU cc_start: 0.8524 (tt) cc_final: 0.8303 (tp) REVERT: B 714 MET cc_start: 0.8435 (mtp) cc_final: 0.8166 (mtp) outliers start: 11 outliers final: 9 residues processed: 138 average time/residue: 0.5361 time to fit residues: 105.0324 Evaluate side-chains 138 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 128 time to evaluate : 1.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 289 ARG Chi-restraints excluded: chain A residue 365 CYS Chi-restraints excluded: chain A residue 523 ILE Chi-restraints excluded: chain A residue 604 GLU Chi-restraints excluded: chain B residue 132 TRP Chi-restraints excluded: chain B residue 141 ILE Chi-restraints excluded: chain B residue 223 GLN Chi-restraints excluded: chain B residue 349 CYS Chi-restraints excluded: chain B residue 546 ASP Chi-restraints excluded: chain B residue 767 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 109 optimal weight: 1.9990 chunk 92 optimal weight: 1.9990 chunk 1 optimal weight: 9.9990 chunk 131 optimal weight: 1.9990 chunk 48 optimal weight: 5.9990 chunk 136 optimal weight: 0.0070 chunk 102 optimal weight: 5.9990 chunk 89 optimal weight: 1.9990 chunk 123 optimal weight: 2.9990 chunk 90 optimal weight: 0.5980 chunk 41 optimal weight: 2.9990 overall best weight: 1.3204 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 559 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4306 r_free = 0.4306 target = 0.200704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.133476 restraints weight = 38059.560| |-----------------------------------------------------------------------------| r_work (start): 0.3581 rms_B_bonded: 2.43 r_work: 0.3420 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3280 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.2116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 12248 Z= 0.125 Angle : 0.498 8.077 16633 Z= 0.270 Chirality : 0.045 0.414 1821 Planarity : 0.005 0.054 2064 Dihedral : 4.487 50.564 1722 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 0.87 % Allowed : 9.76 % Favored : 89.37 % Cbeta Deviations : 0.07 % 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: 1.11 (0.22), residues: 1426 helix: 2.15 (0.17), residues: 818 sheet: -1.91 (0.65), residues: 58 loop : -1.20 (0.26), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 397 HIS 0.004 0.001 HIS A 108 PHE 0.021 0.001 PHE A 461 TYR 0.012 0.001 TYR A 668 ARG 0.002 0.000 ARG A 289 Details of bonding type rmsd link_NAG-ASN : bond 0.00093 ( 2) link_NAG-ASN : angle 1.76769 ( 6) hydrogen bonds : bond 0.04395 ( 694) hydrogen bonds : angle 4.22411 ( 2040) SS BOND : bond 0.00163 ( 10) SS BOND : angle 0.58443 ( 20) covalent geometry : bond 0.00282 (12236) covalent geometry : angle 0.49667 (16607) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2852 Ramachandran restraints generated. 1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2852 Ramachandran restraints generated. 1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 95 is missing expected H atoms. Skipping. Residue LYS 97 is missing expected H atoms. Skipping. Residue TYR 101 is missing expected H atoms. Skipping. Residue SER 103 is missing expected H atoms. Skipping. Residue LEU 105 is missing expected H atoms. Skipping. Residue ILE 106 is missing expected H atoms. Skipping. Residue SER 117 is missing expected H atoms. Skipping. Residue VAL 118 is missing expected H atoms. Skipping. Residue SER 119 is missing expected H atoms. Skipping. Residue LYS 122 is missing expected H atoms. Skipping. Residue LEU 123 is missing expected H atoms. Skipping. Residue VAL 124 is missing expected H atoms. Skipping. Residue VAL 126 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue TYR 137 is missing expected H atoms. Skipping. Residue ILE 141 is missing expected H atoms. Skipping. Residue LEU 236 is missing expected H atoms. Skipping. Residue VAL 237 is missing expected H atoms. Skipping. Residue SER 238 is missing expected H atoms. Skipping. Residue SER 239 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue LYS 590 is missing expected H atoms. Skipping. Residue LYS 661 is missing expected H atoms. Skipping. Evaluate side-chains 138 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 127 time to evaluate : 1.803 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 HIS cc_start: 0.6362 (t-90) cc_final: 0.5907 (m-70) REVERT: A 203 PHE cc_start: 0.6377 (t80) cc_final: 0.5785 (t80) REVERT: A 339 ASP cc_start: 0.7156 (m-30) cc_final: 0.6865 (m-30) REVERT: A 604 GLU cc_start: 0.8202 (OUTLIER) cc_final: 0.7926 (pt0) REVERT: A 631 MET cc_start: 0.4418 (mpp) cc_final: 0.4170 (mmm) REVERT: A 790 LYS cc_start: 0.7265 (mmmt) cc_final: 0.6816 (tttp) REVERT: B 258 GLU cc_start: 0.7346 (mp0) cc_final: 0.7063 (mp0) REVERT: B 609 LEU cc_start: 0.8533 (tt) cc_final: 0.8300 (tp) REVERT: B 714 MET cc_start: 0.8414 (mtp) cc_final: 0.8145 (mtp) outliers start: 11 outliers final: 9 residues processed: 137 average time/residue: 0.5513 time to fit residues: 108.7857 Evaluate side-chains 137 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 127 time to evaluate : 1.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 289 ARG Chi-restraints excluded: chain A residue 365 CYS Chi-restraints excluded: chain A residue 523 ILE Chi-restraints excluded: chain A residue 604 GLU Chi-restraints excluded: chain B residue 132 TRP Chi-restraints excluded: chain B residue 141 ILE Chi-restraints excluded: chain B residue 349 CYS Chi-restraints excluded: chain B residue 546 ASP Chi-restraints excluded: chain B residue 585 VAL Chi-restraints excluded: chain B residue 767 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 105 optimal weight: 0.7980 chunk 52 optimal weight: 1.9990 chunk 106 optimal weight: 0.6980 chunk 4 optimal weight: 4.9990 chunk 62 optimal weight: 7.9990 chunk 47 optimal weight: 3.9990 chunk 90 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 50 optimal weight: 0.5980 chunk 54 optimal weight: 7.9990 chunk 29 optimal weight: 7.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 559 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4310 r_free = 0.4310 target = 0.201118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.135574 restraints weight = 37998.721| |-----------------------------------------------------------------------------| r_work (start): 0.3611 rms_B_bonded: 2.82 r_work: 0.3404 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.3270 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.2177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 12248 Z= 0.121 Angle : 0.496 8.020 16633 Z= 0.268 Chirality : 0.044 0.413 1821 Planarity : 0.004 0.051 2064 Dihedral : 4.437 50.334 1722 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 0.71 % Allowed : 9.92 % Favored : 89.37 % Cbeta Deviations : 0.07 % 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: 1.16 (0.22), residues: 1426 helix: 2.18 (0.17), residues: 818 sheet: -1.87 (0.65), residues: 58 loop : -1.17 (0.26), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 397 HIS 0.004 0.001 HIS A 108 PHE 0.012 0.001 PHE A 538 TYR 0.013 0.001 TYR A 668 ARG 0.002 0.000 ARG A 289 Details of bonding type rmsd link_NAG-ASN : bond 0.00064 ( 2) link_NAG-ASN : angle 1.73322 ( 6) hydrogen bonds : bond 0.04333 ( 694) hydrogen bonds : angle 4.21789 ( 2040) SS BOND : bond 0.00162 ( 10) SS BOND : angle 0.57247 ( 20) covalent geometry : bond 0.00272 (12236) covalent geometry : angle 0.49484 (16607) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2852 Ramachandran restraints generated. 1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2852 Ramachandran restraints generated. 1426 Oldfield, 0 Emsley, 1426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 95 is missing expected H atoms. Skipping. Residue LYS 97 is missing expected H atoms. Skipping. Residue TYR 101 is missing expected H atoms. Skipping. Residue SER 103 is missing expected H atoms. Skipping. Residue LEU 105 is missing expected H atoms. Skipping. Residue ILE 106 is missing expected H atoms. Skipping. Residue SER 117 is missing expected H atoms. Skipping. Residue VAL 118 is missing expected H atoms. Skipping. Residue SER 119 is missing expected H atoms. Skipping. Residue LYS 122 is missing expected H atoms. Skipping. Residue LEU 123 is missing expected H atoms. Skipping. Residue VAL 124 is missing expected H atoms. Skipping. Residue VAL 126 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue TYR 137 is missing expected H atoms. Skipping. Residue ILE 141 is missing expected H atoms. Skipping. Residue LEU 236 is missing expected H atoms. Skipping. Residue VAL 237 is missing expected H atoms. Skipping. Residue SER 238 is missing expected H atoms. Skipping. Residue SER 239 is missing expected H atoms. Skipping. Residue ILE 241 is missing expected H atoms. Skipping. Residue LYS 590 is missing expected H atoms. Skipping. Residue LYS 661 is missing expected H atoms. Skipping. Evaluate side-chains 138 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 129 time to evaluate : 1.625 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 HIS cc_start: 0.6357 (t-90) cc_final: 0.5662 (m-70) REVERT: A 203 PHE cc_start: 0.6385 (t80) cc_final: 0.5795 (t80) REVERT: A 339 ASP cc_start: 0.7171 (m-30) cc_final: 0.6901 (m-30) REVERT: A 604 GLU cc_start: 0.8196 (OUTLIER) cc_final: 0.7923 (pt0) REVERT: A 631 MET cc_start: 0.4421 (mpp) cc_final: 0.4129 (mmm) REVERT: A 721 ASP cc_start: 0.6505 (t0) cc_final: 0.5849 (p0) REVERT: B 258 GLU cc_start: 0.7365 (mp0) cc_final: 0.7067 (mp0) REVERT: B 609 LEU cc_start: 0.8534 (tt) cc_final: 0.8301 (tp) REVERT: B 714 MET cc_start: 0.8416 (mtp) cc_final: 0.8151 (mtp) outliers start: 9 outliers final: 7 residues processed: 136 average time/residue: 0.5168 time to fit residues: 100.7061 Evaluate side-chains 135 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 127 time to evaluate : 1.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 289 ARG Chi-restraints excluded: chain A residue 365 CYS Chi-restraints excluded: chain A residue 523 ILE Chi-restraints excluded: chain A residue 604 GLU Chi-restraints excluded: chain B residue 132 TRP Chi-restraints excluded: chain B residue 349 CYS Chi-restraints excluded: chain B residue 546 ASP Chi-restraints excluded: chain B residue 767 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 88 optimal weight: 3.9990 chunk 32 optimal weight: 3.9990 chunk 125 optimal weight: 1.9990 chunk 138 optimal weight: 1.9990 chunk 73 optimal weight: 20.0000 chunk 72 optimal weight: 3.9990 chunk 104 optimal weight: 4.9990 chunk 140 optimal weight: 0.9990 chunk 4 optimal weight: 0.0970 chunk 40 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 559 GLN A 674 GLN A 695 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4305 r_free = 0.4305 target = 0.200795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.135070 restraints weight = 38081.600| |-----------------------------------------------------------------------------| r_work (start): 0.3593 rms_B_bonded: 2.91 r_work: 0.3382 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work: 0.3246 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.2218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 12248 Z= 0.130 Angle : 0.500 7.994 16633 Z= 0.271 Chirality : 0.045 0.413 1821 Planarity : 0.005 0.051 2064 Dihedral : 4.432 50.565 1722 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 0.63 % Allowed : 10.16 % Favored : 89.21 % Cbeta Deviations : 0.07 % 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: 1.17 (0.22), residues: 1426 helix: 2.16 (0.17), residues: 823 sheet: -1.86 (0.66), residues: 58 loop : -1.15 (0.26), residues: 545 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 397 HIS 0.003 0.001 HIS A 108 PHE 0.019 0.001 PHE A 461 TYR 0.015 0.001 TYR A 668 ARG 0.002 0.000 ARG A 289 Details of bonding type rmsd link_NAG-ASN : bond 0.00071 ( 2) link_NAG-ASN : angle 1.72092 ( 6) hydrogen bonds : bond 0.04388 ( 694) hydrogen bonds : angle 4.22222 ( 2040) SS BOND : bond 0.00172 ( 10) SS BOND : angle 0.57699 ( 20) covalent geometry : bond 0.00296 (12236) covalent geometry : angle 0.49862 (16607) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12959.45 seconds wall clock time: 222 minutes 19.54 seconds (13339.54 seconds total)