Starting phenix.real_space_refine on Sun Aug 24 22:11:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tag_41134/08_2025/8tag_41134_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tag_41134/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/8tag_41134/08_2025/8tag_41134_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tag_41134/08_2025/8tag_41134_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8tag_41134/08_2025/8tag_41134.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tag_41134/08_2025/8tag_41134.map" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.007 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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, 'ARG:plan': 2, 'TYR:plan': 2, 'GLU:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 2, 'PHE:plan': 1, 'HIS: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: {'ARG:plan': 1, 'GLU:plan': 2} 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: 4.74, per 1000 atoms: 0.20 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: 2.22 Conformation dependent library (CDL) restraints added in 759.0 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.68 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: 5.26 Time building geometry restraints manager: 3.04 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: 1.210 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: 0.160 Extract box with map and model: 0.300 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 22.930 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.450 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.005 0.001 ARG A 289 TYR 0.030 0.001 TYR A 668 PHE 0.017 0.002 PHE A 560 TRP 0.026 0.002 TRP B 132 HIS 0.004 0.001 HIS B 275 Details of bonding type rmsd covalent geometry : bond 0.00443 (12236) covalent geometry : angle 0.62907 (16607) SS BOND : bond 0.00305 ( 10) SS BOND : angle 1.29797 ( 20) hydrogen bonds : bond 0.12032 ( 694) hydrogen bonds : angle 5.52743 ( 2040) link_NAG-ASN : bond 0.03284 ( 2) link_NAG-ASN : angle 10.72923 ( 6) *********************** 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 : 0.639 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: 0.2624 time to fit residues: 54.5904 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 : 0.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 8.9990 chunk 10 optimal weight: 10.0000 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 9.9990 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 1.9990 chunk 55 optimal weight: 9.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- 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 = 0.4330 r_free = 0.4330 target = 0.203037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.135479 restraints weight = 38056.447| |-----------------------------------------------------------------------------| r_work (start): 0.3605 rms_B_bonded: 2.43 r_work: 0.3442 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3303 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.0932 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= 0.144 Angle : 0.546 7.470 16633 Z= 0.298 Chirality : 0.045 0.408 1821 Planarity : 0.005 0.058 2064 Dihedral : 5.581 57.276 1722 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 0.40 % Allowed : 4.29 % Favored : 95.32 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.84 (0.22), residues: 1426 helix: 1.83 (0.17), residues: 823 sheet: -1.40 (0.72), residues: 48 loop : -1.26 (0.26), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 200 TYR 0.020 0.001 TYR A 668 PHE 0.012 0.001 PHE A 560 TRP 0.016 0.001 TRP B 132 HIS 0.003 0.001 HIS B 830 Details of bonding type rmsd covalent geometry : bond 0.00317 (12236) covalent geometry : angle 0.54448 (16607) SS BOND : bond 0.00277 ( 10) SS BOND : angle 1.07259 ( 20) hydrogen bonds : bond 0.05059 ( 694) hydrogen bonds : angle 4.70952 ( 2040) link_NAG-ASN : bond 0.00321 ( 2) link_NAG-ASN : angle 1.68595 ( 6) *********************** 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 131 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 126 time to evaluate : 0.585 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: 0.4653 (mpp) cc_final: 0.4264 (mmm) REVERT: B 132 TRP cc_start: 0.5852 (t-100) cc_final: 0.5574 (t-100) outliers start: 5 outliers final: 4 residues processed: 129 average time/residue: 0.2377 time to fit residues: 44.1971 Evaluate side-chains 126 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 122 time to evaluate : 0.401 ------------------------------------------------------------------------------- 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 24 optimal weight: 0.8980 chunk 125 optimal weight: 1.9990 chunk 87 optimal weight: 0.9990 chunk 123 optimal weight: 3.9990 chunk 122 optimal weight: 0.9990 chunk 101 optimal weight: 3.9990 chunk 133 optimal weight: 1.9990 chunk 32 optimal weight: 3.9990 chunk 58 optimal weight: 2.9990 chunk 117 optimal weight: 1.9990 chunk 96 optimal weight: 2.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- 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 = 0.4326 r_free = 0.4326 target = 0.202650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.141115 restraints weight = 37833.088| |-----------------------------------------------------------------------------| r_work (start): 0.3674 rms_B_bonded: 2.91 r_work: 0.3419 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.3287 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.1184 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= 0.134 Angle : 0.513 7.683 16633 Z= 0.279 Chirality : 0.045 0.411 1821 Planarity : 0.005 0.051 2064 Dihedral : 4.949 51.087 1722 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 0.71 % Allowed : 5.24 % Favored : 94.05 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.98 (0.22), residues: 1426 helix: 1.96 (0.17), residues: 825 sheet: -1.28 (0.71), residues: 48 loop : -1.24 (0.26), residues: 553 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 200 TYR 0.015 0.001 TYR A 668 PHE 0.011 0.001 PHE B 300 TRP 0.014 0.001 TRP B 132 HIS 0.003 0.001 HIS A 108 Details of bonding type rmsd covalent geometry : bond 0.00302 (12236) covalent geometry : angle 0.51151 (16607) SS BOND : bond 0.00230 ( 10) SS BOND : angle 0.79913 ( 20) hydrogen bonds : bond 0.04766 ( 694) hydrogen bonds : angle 4.48812 ( 2040) link_NAG-ASN : bond 0.00057 ( 2) link_NAG-ASN : angle 1.58459 ( 6) *********************** 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: 9 poor density : 134 time to evaluate : 0.658 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: A 631 MET cc_start: 0.4534 (mpp) cc_final: 0.4226 (mmm) REVERT: A 721 ASP cc_start: 0.6632 (t0) cc_final: 0.5848 (p0) REVERT: B 235 ARG cc_start: 0.8532 (ttt180) cc_final: 0.8220 (ttt180) outliers start: 9 outliers final: 6 residues processed: 141 average time/residue: 0.2608 time to fit residues: 53.1681 Evaluate side-chains 134 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 128 time to evaluate : 0.632 ------------------------------------------------------------------------------- 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 141 ILE Chi-restraints excluded: chain B residue 223 GLN Chi-restraints excluded: chain B residue 531 VAL 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 142 optimal weight: 3.9990 chunk 13 optimal weight: 0.5980 chunk 89 optimal weight: 3.9990 chunk 7 optimal weight: 0.9980 chunk 44 optimal weight: 2.9990 chunk 2 optimal weight: 6.9990 chunk 30 optimal weight: 20.0000 chunk 12 optimal weight: 10.0000 chunk 72 optimal weight: 4.9990 chunk 67 optimal weight: 1.9990 chunk 22 optimal weight: 4.9990 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 = 0.4309 r_free = 0.4309 target = 0.200952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.135943 restraints weight = 38033.808| |-----------------------------------------------------------------------------| r_work (start): 0.3609 rms_B_bonded: 2.89 r_work: 0.3394 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.3258 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.1495 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= 0.170 Angle : 0.531 7.827 16633 Z= 0.291 Chirality : 0.045 0.414 1821 Planarity : 0.005 0.052 2064 Dihedral : 4.805 51.154 1722 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 0.79 % Allowed : 6.67 % Favored : 92.54 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.86 (0.22), residues: 1426 helix: 1.86 (0.17), residues: 824 sheet: -1.36 (0.72), residues: 48 loop : -1.28 (0.26), residues: 554 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 289 TYR 0.014 0.001 TYR A 668 PHE 0.013 0.001 PHE B 560 TRP 0.009 0.001 TRP A 397 HIS 0.004 0.001 HIS B 830 Details of bonding type rmsd covalent geometry : bond 0.00399 (12236) covalent geometry : angle 0.52914 (16607) SS BOND : bond 0.00231 ( 10) SS BOND : angle 0.76147 ( 20) hydrogen bonds : bond 0.04910 ( 694) hydrogen bonds : angle 4.45846 ( 2040) link_NAG-ASN : bond 0.00143 ( 2) link_NAG-ASN : angle 1.89889 ( 6) *********************** 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 146 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 136 time to evaluate : 0.660 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: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 7 residues processed: 142 average time/residue: 0.2755 time to fit residues: 55.5320 Evaluate side-chains 136 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 129 time to evaluate : 0.667 ------------------------------------------------------------------------------- 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 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 51 optimal weight: 1.9990 chunk 36 optimal weight: 4.9990 chunk 86 optimal weight: 0.9980 chunk 33 optimal weight: 6.9990 chunk 78 optimal weight: 4.9990 chunk 47 optimal weight: 30.0000 chunk 91 optimal weight: 0.9980 chunk 49 optimal weight: 0.0010 chunk 101 optimal weight: 3.9990 chunk 87 optimal weight: 0.5980 chunk 53 optimal weight: 4.9990 overall best weight: 0.9188 ------------------------------------------------------------------------------- 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 = 0.4328 r_free = 0.4328 target = 0.202838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.137148 restraints weight = 37852.785| |-----------------------------------------------------------------------------| r_work (start): 0.3620 rms_B_bonded: 2.82 r_work: 0.3427 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3290 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.1682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 12248 Z= 0.111 Angle : 0.492 7.853 16633 Z= 0.267 Chirality : 0.044 0.411 1821 Planarity : 0.004 0.051 2064 Dihedral : 4.534 50.354 1722 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 0.71 % Allowed : 8.10 % Favored : 91.19 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.13 (0.22), residues: 1426 helix: 2.10 (0.17), residues: 824 sheet: -1.65 (0.68), residues: 58 loop : -1.15 (0.26), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 200 TYR 0.013 0.001 TYR A 668 PHE 0.018 0.001 PHE A 461 TRP 0.010 0.001 TRP A 397 HIS 0.002 0.001 HIS A 108 Details of bonding type rmsd covalent geometry : bond 0.00241 (12236) covalent geometry : angle 0.49097 (16607) SS BOND : bond 0.00180 ( 10) SS BOND : angle 0.66743 ( 20) hydrogen bonds : bond 0.04421 ( 694) hydrogen bonds : angle 4.30990 ( 2040) link_NAG-ASN : bond 0.00054 ( 2) link_NAG-ASN : angle 1.75599 ( 6) *********************** 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: 9 poor density : 135 time to evaluate : 0.799 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: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 8 residues processed: 142 average time/residue: 0.2768 time to fit residues: 55.9400 Evaluate side-chains 140 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 132 time to evaluate : 0.650 ------------------------------------------------------------------------------- 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 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 43 optimal weight: 0.3980 chunk 80 optimal weight: 3.9990 chunk 24 optimal weight: 0.8980 chunk 66 optimal weight: 1.9990 chunk 126 optimal weight: 0.9980 chunk 137 optimal weight: 6.9990 chunk 82 optimal weight: 5.9990 chunk 71 optimal weight: 1.9990 chunk 12 optimal weight: 20.0000 chunk 123 optimal weight: 2.9990 chunk 26 optimal weight: 0.3980 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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 = 0.4328 r_free = 0.4328 target = 0.203102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.142928 restraints weight = 37976.408| |-----------------------------------------------------------------------------| r_work (start): 0.3702 rms_B_bonded: 2.61 r_work: 0.3455 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3322 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3322 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.1852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 12248 Z= 0.110 Angle : 0.481 7.890 16633 Z= 0.261 Chirality : 0.044 0.410 1821 Planarity : 0.004 0.051 2064 Dihedral : 4.357 49.076 1722 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 0.63 % Allowed : 8.49 % Favored : 90.87 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.24 (0.22), residues: 1426 helix: 2.23 (0.17), residues: 819 sheet: -1.50 (0.69), residues: 58 loop : -1.15 (0.26), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 200 TYR 0.014 0.001 TYR A 668 PHE 0.011 0.001 PHE A 538 TRP 0.015 0.001 TRP B 132 HIS 0.003 0.001 HIS A 108 Details of bonding type rmsd covalent geometry : bond 0.00244 (12236) covalent geometry : angle 0.48013 (16607) SS BOND : bond 0.00176 ( 10) SS BOND : angle 0.62149 ( 20) hydrogen bonds : bond 0.04268 ( 694) hydrogen bonds : angle 4.23443 ( 2040) link_NAG-ASN : bond 0.00039 ( 2) link_NAG-ASN : angle 1.78692 ( 6) *********************** 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 139 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 131 time to evaluate : 0.680 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: symmetry clash REVERT: A 108 HIS cc_start: 0.6336 (t-90) cc_final: 0.5560 (m-70) REVERT: A 258 GLU cc_start: 0.4005 (mp0) cc_final: 0.3425 (pm20) REVERT: A 339 ASP cc_start: 0.7224 (m-30) cc_final: 0.6883 (m-30) REVERT: A 790 LYS cc_start: 0.7238 (mmmt) cc_final: 0.6763 (tttp) outliers start: 8 outliers final: 6 residues processed: 137 average time/residue: 0.2724 time to fit residues: 53.4585 Evaluate side-chains 132 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 126 time to evaluate : 0.657 ------------------------------------------------------------------------------- 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 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 85 optimal weight: 10.0000 chunk 94 optimal weight: 3.9990 chunk 18 optimal weight: 2.9990 chunk 63 optimal weight: 6.9990 chunk 93 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 65 optimal weight: 0.9990 chunk 135 optimal weight: 1.9990 chunk 26 optimal weight: 0.3980 chunk 52 optimal weight: 1.9990 chunk 17 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 = 0.4317 r_free = 0.4317 target = 0.201881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.141318 restraints weight = 38038.889| |-----------------------------------------------------------------------------| r_work (start): 0.3681 rms_B_bonded: 2.61 r_work: 0.3435 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3304 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.1909 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 8.036 16633 Z= 0.270 Chirality : 0.045 0.413 1821 Planarity : 0.004 0.051 2064 Dihedral : 4.388 49.241 1722 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 0.87 % Allowed : 9.05 % Favored : 90.08 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.19 (0.22), residues: 1426 helix: 2.20 (0.17), residues: 818 sheet: -1.58 (0.69), residues: 58 loop : -1.18 (0.26), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 200 TYR 0.017 0.001 TYR A 668 PHE 0.022 0.001 PHE A 461 TRP 0.018 0.001 TRP B 132 HIS 0.004 0.001 HIS A 108 Details of bonding type rmsd covalent geometry : bond 0.00304 (12236) covalent geometry : angle 0.49734 (16607) SS BOND : bond 0.00180 ( 10) SS BOND : angle 0.60751 ( 20) hydrogen bonds : bond 0.04411 ( 694) hydrogen bonds : angle 4.23425 ( 2040) link_NAG-ASN : bond 0.00067 ( 2) link_NAG-ASN : angle 1.84839 ( 6) *********************** 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: 11 poor density : 130 time to evaluate : 0.633 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: symmetry clash REVERT: A 108 HIS cc_start: 0.6347 (t-90) cc_final: 0.5576 (m-70) REVERT: A 258 GLU cc_start: 0.4045 (mp0) cc_final: 0.3473 (pm20) REVERT: A 339 ASP cc_start: 0.7237 (m-30) cc_final: 0.6892 (m-30) REVERT: A 604 GLU cc_start: 0.8110 (OUTLIER) cc_final: 0.7826 (pt0) REVERT: A 790 LYS cc_start: 0.7270 (mmmt) cc_final: 0.6812 (tttp) outliers start: 11 outliers final: 8 residues processed: 138 average time/residue: 0.2759 time to fit residues: 54.1442 Evaluate side-chains 136 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 127 time to evaluate : 0.536 ------------------------------------------------------------------------------- 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 12 optimal weight: 9.9990 chunk 2 optimal weight: 10.0000 chunk 17 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 chunk 77 optimal weight: 5.9990 chunk 83 optimal weight: 3.9990 chunk 50 optimal weight: 3.9990 chunk 58 optimal weight: 0.7980 chunk 66 optimal weight: 0.7980 chunk 11 optimal weight: 10.0000 chunk 13 optimal weight: 7.9990 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 559 GLN B 674 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4292 r_free = 0.4292 target = 0.199312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.138743 restraints weight = 38111.408| |-----------------------------------------------------------------------------| r_work (start): 0.3651 rms_B_bonded: 2.54 r_work: 0.3399 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3265 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3265 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.2013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 12248 Z= 0.190 Angle : 0.539 8.135 16633 Z= 0.296 Chirality : 0.046 0.416 1821 Planarity : 0.005 0.062 2064 Dihedral : 4.665 50.710 1722 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 0.71 % Allowed : 8.89 % Favored : 90.40 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.88 (0.22), residues: 1426 helix: 1.90 (0.17), residues: 819 sheet: -1.75 (0.68), residues: 58 loop : -1.23 (0.26), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 712 TYR 0.015 0.001 TYR A 668 PHE 0.015 0.001 PHE B 300 TRP 0.019 0.001 TRP B 132 HIS 0.004 0.001 HIS A 108 Details of bonding type rmsd covalent geometry : bond 0.00447 (12236) covalent geometry : angle 0.53774 (16607) SS BOND : bond 0.00223 ( 10) SS BOND : angle 0.68289 ( 20) hydrogen bonds : bond 0.04929 ( 694) hydrogen bonds : angle 4.34666 ( 2040) link_NAG-ASN : bond 0.00169 ( 2) link_NAG-ASN : angle 2.02181 ( 6) *********************** 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 137 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 128 time to evaluate : 0.747 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: 0.6425 (t-90) cc_final: 0.5655 (m-70) REVERT: A 203 PHE cc_start: 0.6380 (t80) cc_final: 0.5801 (t80) REVERT: A 258 GLU cc_start: 0.4115 (mp0) cc_final: 0.3536 (pm20) REVERT: A 339 ASP cc_start: 0.7211 (m-30) cc_final: 0.6900 (m-30) REVERT: A 604 GLU cc_start: 0.8261 (OUTLIER) cc_final: 0.7987 (pt0) REVERT: A 790 LYS cc_start: 0.7309 (mmmt) cc_final: 0.6866 (tttp) outliers start: 9 outliers final: 8 residues processed: 135 average time/residue: 0.2683 time to fit residues: 51.8757 Evaluate side-chains 136 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 127 time to evaluate : 0.679 ------------------------------------------------------------------------------- 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 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 111 optimal weight: 0.9980 chunk 58 optimal weight: 2.9990 chunk 81 optimal weight: 9.9990 chunk 119 optimal weight: 1.9990 chunk 116 optimal weight: 4.9990 chunk 59 optimal weight: 0.9980 chunk 46 optimal weight: 7.9990 chunk 57 optimal weight: 1.9990 chunk 123 optimal weight: 1.9990 chunk 134 optimal weight: 4.9990 chunk 108 optimal weight: 0.9980 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 559 GLN B 674 GLN B 695 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4309 r_free = 0.4309 target = 0.201090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.136031 restraints weight = 37951.991| |-----------------------------------------------------------------------------| r_work (start): 0.3600 rms_B_bonded: 2.99 r_work: 0.3392 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work: 0.3255 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.2067 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= 0.126 Angle : 0.502 8.046 16633 Z= 0.272 Chirality : 0.045 0.414 1821 Planarity : 0.005 0.052 2064 Dihedral : 4.523 50.769 1722 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 0.87 % Allowed : 9.37 % Favored : 89.76 % Cbeta Deviations : 0.15 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.04 (0.22), residues: 1426 helix: 2.07 (0.17), residues: 818 sheet: -1.73 (0.67), residues: 58 loop : -1.23 (0.26), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 289 TYR 0.012 0.001 TYR A 668 PHE 0.020 0.001 PHE A 461 TRP 0.019 0.001 TRP B 132 HIS 0.003 0.001 HIS A 108 Details of bonding type rmsd covalent geometry : bond 0.00281 (12236) covalent geometry : angle 0.50134 (16607) SS BOND : bond 0.00165 ( 10) SS BOND : angle 0.60268 ( 20) hydrogen bonds : bond 0.04489 ( 694) hydrogen bonds : angle 4.25806 ( 2040) link_NAG-ASN : bond 0.00088 ( 2) link_NAG-ASN : angle 1.75703 ( 6) *********************** 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 : 0.635 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: 0.6367 (t-90) cc_final: 0.5625 (m-70) REVERT: A 203 PHE cc_start: 0.6380 (t80) cc_final: 0.5802 (t80) REVERT: A 339 ASP cc_start: 0.7257 (m-30) cc_final: 0.6940 (m-30) REVERT: A 604 GLU cc_start: 0.8241 (OUTLIER) cc_final: 0.7994 (pt0) REVERT: A 790 LYS cc_start: 0.7299 (mmmt) cc_final: 0.6844 (tttp) outliers start: 11 outliers final: 8 residues processed: 134 average time/residue: 0.2778 time to fit residues: 52.7670 Evaluate side-chains 137 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 128 time to evaluate : 0.601 ------------------------------------------------------------------------------- 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 2 optimal weight: 4.9990 chunk 33 optimal weight: 7.9990 chunk 10 optimal weight: 7.9990 chunk 7 optimal weight: 10.0000 chunk 92 optimal weight: 1.9990 chunk 39 optimal weight: 3.9990 chunk 138 optimal weight: 1.9990 chunk 137 optimal weight: 0.0980 chunk 25 optimal weight: 4.9990 chunk 104 optimal weight: 9.9990 chunk 6 optimal weight: 5.9990 overall best weight: 2.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 559 GLN B 674 GLN B 695 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4299 r_free = 0.4299 target = 0.199629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.136855 restraints weight = 38273.165| |-----------------------------------------------------------------------------| r_work (start): 0.3615 rms_B_bonded: 2.69 r_work: 0.3362 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3225 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.2157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 12248 Z= 0.201 Angle : 0.550 8.156 16633 Z= 0.302 Chirality : 0.046 0.419 1821 Planarity : 0.005 0.052 2064 Dihedral : 4.801 52.150 1722 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 0.95 % Allowed : 9.13 % Favored : 89.92 % Cbeta Deviations : 0.15 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.76 (0.22), residues: 1426 helix: 1.81 (0.17), residues: 818 sheet: -1.91 (0.65), residues: 58 loop : -1.27 (0.26), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 712 TYR 0.015 0.001 TYR A 668 PHE 0.016 0.001 PHE B 300 TRP 0.025 0.001 TRP B 132 HIS 0.005 0.001 HIS A 108 Details of bonding type rmsd covalent geometry : bond 0.00475 (12236) covalent geometry : angle 0.54884 (16607) SS BOND : bond 0.00222 ( 10) SS BOND : angle 0.70459 ( 20) hydrogen bonds : bond 0.05035 ( 694) hydrogen bonds : angle 4.38472 ( 2040) link_NAG-ASN : bond 0.00186 ( 2) link_NAG-ASN : angle 1.89739 ( 6) ********************** 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 143 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 131 time to evaluate : 0.646 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: 0.6470 (t-90) cc_final: 0.5691 (m-70) REVERT: A 339 ASP cc_start: 0.7236 (m-30) cc_final: 0.6938 (m-30) REVERT: A 604 GLU cc_start: 0.8347 (OUTLIER) cc_final: 0.8102 (pt0) outliers start: 12 outliers final: 8 residues processed: 140 average time/residue: 0.2774 time to fit residues: 55.3516 Evaluate side-chains 135 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 126 time to evaluate : 0.639 ------------------------------------------------------------------------------- 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 74 optimal weight: 10.0000 chunk 47 optimal weight: 20.0000 chunk 15 optimal weight: 9.9990 chunk 10 optimal weight: 7.9990 chunk 56 optimal weight: 1.9990 chunk 115 optimal weight: 1.9990 chunk 131 optimal weight: 1.9990 chunk 49 optimal weight: 3.9990 chunk 85 optimal weight: 1.9990 chunk 114 optimal weight: 0.9980 chunk 37 optimal weight: 5.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 559 GLN B 544 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4293 r_free = 0.4293 target = 0.199548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.137947 restraints weight = 38040.056| |-----------------------------------------------------------------------------| r_work (start): 0.3646 rms_B_bonded: 2.65 r_work: 0.3394 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3255 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.2239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12248 Z= 0.150 Angle : 0.528 10.226 16633 Z= 0.285 Chirality : 0.045 0.416 1821 Planarity : 0.005 0.052 2064 Dihedral : 4.727 52.891 1722 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 0.79 % Allowed : 9.44 % Favored : 89.76 % Cbeta Deviations : 0.15 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.85 (0.22), residues: 1426 helix: 1.90 (0.17), residues: 818 sheet: -1.85 (0.66), residues: 58 loop : -1.27 (0.26), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 542 TYR 0.013 0.001 TYR A 668 PHE 0.018 0.001 PHE A 461 TRP 0.021 0.001 TRP B 132 HIS 0.003 0.001 HIS A 108 Details of bonding type rmsd covalent geometry : bond 0.00347 (12236) covalent geometry : angle 0.52683 (16607) SS BOND : bond 0.00174 ( 10) SS BOND : angle 0.62629 ( 20) hydrogen bonds : bond 0.04704 ( 694) hydrogen bonds : angle 4.33328 ( 2040) link_NAG-ASN : bond 0.00126 ( 2) link_NAG-ASN : angle 1.72118 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7126.07 seconds wall clock time: 121 minutes 36.63 seconds (7296.63 seconds total)