Starting phenix.real_space_refine on Sat Aug 23 14:48:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9mot_48481/08_2025/9mot_48481_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9mot_48481/08_2025/9mot_48481.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.15 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9mot_48481/08_2025/9mot_48481.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9mot_48481/08_2025/9mot_48481.map" model { file = "/net/cci-nas-00/data/ceres_data/9mot_48481/08_2025/9mot_48481_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9mot_48481/08_2025/9mot_48481_neut.cif" } resolution = 3.15 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= 0.002 sd= 0.031 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: 4 Type Number sf(0) Gaussians S 66 5.16 5 C 8068 2.51 5 N 2166 2.21 5 O 2408 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 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: 12708 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 5402 Number of conformers: 1 Conformer: "" Number of residues, atoms: 670, 5402 Classifications: {'peptide': 670} Link IDs: {'PTRANS': 35, 'TRANS': 634} Chain: "B" Number of atoms: 5304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 651, 5304 Classifications: {'peptide': 651} Link IDs: {'PTRANS': 29, 'TRANS': 621} Chain: "D" Number of atoms: 1890 Number of conformers: 1 Conformer: "" Number of residues, atoms: 240, 1890 Classifications: {'peptide': 240} Link IDs: {'PTRANS': 9, 'TRANS': 230} Chain: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 3.20, per 1000 atoms: 0.25 Number of scatterers: 12708 At special positions: 0 Unit cell: (95.711, 108.763, 129.645, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 66 16.00 O 2408 8.00 N 2166 7.00 C 8068 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS A 139 " - pdb=" SG CYS A 165 " distance=2.03 Simple disulfide: pdb=" SG CYS A 220 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 472 " - pdb=" SG CYS A 498 " distance=2.03 Simple disulfide: pdb=" SG CYS A 575 " - pdb=" SG CYS A 656 " distance=2.04 Simple disulfide: pdb=" SG CYS B1697 " - pdb=" SG CYS B1723 " distance=2.03 Simple disulfide: pdb=" SG CYS B1879 " - pdb=" SG CYS B2033 " distance=2.03 Simple disulfide: pdb=" SG CYS B2038 " - pdb=" SG CYS B2193 " distance=2.03 Simple disulfide: pdb=" SG CYS D 196 " - pdb=" SG CYS D 212 " distance=2.03 Simple disulfide: pdb=" SG CYS D 331 " - pdb=" SG CYS D 345 " distance=2.03 Simple disulfide: pdb=" SG CYS D 356 " - pdb=" SG CYS D 384 " 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 Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A2201 " - " ASN A 269 " " NAG A2202 " - " ASN A 211 " " NAG A2203 " - " ASN A 432 " " NAG B2201 " - " ASN B1982 " " NAG B2202 " - " ASN B1675 " " NAG D 501 " - " ASN D 248 " " NAG D 502 " - " ASN D 329 " " NAG D 503 " - " ASN D 313 " Time building additional restraints: 1.02 Conformation dependent library (CDL) restraints added in 572.3 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2924 Finding SS restraints... Secondary structure from input PDB file: 16 helices and 26 sheets defined 6.7% alpha, 20.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.49 Creating SS restraints... Processing helix chain 'A' and resid 42 through 46 removed outlier: 3.833A pdb=" N LYS A 46 " --> pdb=" O PRO A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 105 through 113 Processing helix chain 'A' and resid 152 through 157 Processing helix chain 'A' and resid 284 through 290 removed outlier: 4.383A pdb=" N ALA A 290 " --> pdb=" O LYS A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 482 through 488 Processing helix chain 'A' and resid 528 through 539 removed outlier: 4.640A pdb=" N ASN A 534 " --> pdb=" O TYR A 530 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ILE A 535 " --> pdb=" O LEU A 531 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N ASN A 536 " --> pdb=" O GLU A 532 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N LYS A 537 " --> pdb=" O ASP A 533 " (cutoff:3.500A) Processing helix chain 'A' and resid 552 through 557 removed outlier: 3.926A pdb=" N ASN A 556 " --> pdb=" O PHE A 552 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ILE A 557 " --> pdb=" O TYR A 553 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 552 through 557' Processing helix chain 'B' and resid 1610 through 1614 removed outlier: 4.175A pdb=" N GLY B1614 " --> pdb=" O GLU B1611 " (cutoff:3.500A) Processing helix chain 'B' and resid 1663 through 1667 Processing helix chain 'B' and resid 1707 through 1712 Processing helix chain 'B' and resid 1860 through 1864 Processing helix chain 'B' and resid 1905 through 1909 Processing helix chain 'D' and resid 211 through 216 Processing helix chain 'D' and resid 280 through 285 removed outlier: 4.254A pdb=" N GLU D 285 " --> pdb=" O SER D 281 " (cutoff:3.500A) Processing helix chain 'D' and resid 327 through 335 removed outlier: 3.830A pdb=" N SER D 332 " --> pdb=" O HIS D 328 " (cutoff:3.500A) removed outlier: 5.740A pdb=" N GLU D 333 " --> pdb=" O ASN D 329 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N VAL D 334 " --> pdb=" O GLU D 330 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N MET D 335 " --> pdb=" O CYS D 331 " (cutoff:3.500A) Processing helix chain 'D' and resid 399 through 404 Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 6 removed outlier: 6.473A pdb=" N ARG A 4 " --> pdb=" O LYS A 71 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 33 through 40 removed outlier: 3.569A pdb=" N VAL A 37 " --> pdb=" O GLN A 11 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N VAL A 8 " --> pdb=" O LYS A 75 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 62 through 64 removed outlier: 6.247A pdb=" N LEU A 62 " --> pdb=" O LEU A 163 " (cutoff:3.500A) removed outlier: 7.440A pdb=" N CYS A 165 " --> pdb=" O LEU A 62 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N ALA A 64 " --> pdb=" O CYS A 165 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 209 through 210 Processing sheet with id=AA5, first strand: chain 'A' and resid 217 through 218 removed outlier: 6.161A pdb=" N ILE A 217 " --> pdb=" O ASP A 297 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 328 through 332 Processing sheet with id=AA7, first strand: chain 'A' and resid 395 through 397 removed outlier: 5.998A pdb=" N ILE A 395 " --> pdb=" O LEU A 496 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 402 through 407 removed outlier: 4.108A pdb=" N TYR A 453 " --> pdb=" O PHE A 407 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 417 through 418 removed outlier: 3.580A pdb=" N TYR A 478 " --> pdb=" O TYR A 418 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 514 through 515 removed outlier: 6.674A pdb=" N ILE A 514 " --> pdb=" O GLN A 581 " (cutoff:3.500A) removed outlier: 8.345A pdb=" N HIS A 583 " --> pdb=" O ILE A 514 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 520 through 522 Processing sheet with id=AB3, first strand: chain 'A' and resid 572 through 573 removed outlier: 6.274A pdb=" N LEU A 572 " --> pdb=" O ARG A 652 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'A' and resid 612 through 615 removed outlier: 3.901A pdb=" N LEU A 594 " --> pdb=" O LEU A 615 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 1586 through 1594 removed outlier: 3.645A pdb=" N TYR B1587 " --> pdb=" O TRP B1563 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N ARG B1552 " --> pdb=" O GLN B1629 " (cutoff:3.500A) removed outlier: 7.754A pdb=" N ARG B1631 " --> pdb=" O ARG B1552 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N TYR B1554 " --> pdb=" O ARG B1631 " (cutoff:3.500A) removed outlier: 8.615A pdb=" N LYS B1633 " --> pdb=" O TYR B1554 " (cutoff:3.500A) removed outlier: 7.156A pdb=" N ILE B1556 " --> pdb=" O LYS B1633 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 1620 through 1623 removed outlier: 5.813A pdb=" N ILE B1620 " --> pdb=" O LEU B1721 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N CYS B1723 " --> pdb=" O ILE B1620 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N ALA B1622 " --> pdb=" O CYS B1723 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LEU B1720 " --> pdb=" O TRP B1700 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 1740 through 1743 removed outlier: 3.508A pdb=" N LEU B1803 " --> pdb=" O LEU B1743 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU B1822 " --> pdb=" O GLU B1845 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 1746 through 1747 removed outlier: 3.943A pdb=" N MET B1746 " --> pdb=" O ALA B1779 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ALA B1779 " --> pdb=" O MET B1746 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'B' and resid 1791 through 1792 Processing sheet with id=AC1, first strand: chain 'B' and resid 1834 through 1836 removed outlier: 3.820A pdb=" N HIS B1812 " --> pdb=" O LEU B1836 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N HIS B1815 " --> pdb=" O ASN B1857 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N ASN B1857 " --> pdb=" O HIS B1815 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 1896 through 1897 removed outlier: 7.736A pdb=" N ARG B2011 " --> pdb=" O MET B1939 " (cutoff:3.500A) removed outlier: 10.270A pdb=" N LYS B1941 " --> pdb=" O VAL B2009 " (cutoff:3.500A) removed outlier: 9.236A pdb=" N VAL B2009 " --> pdb=" O LYS B1941 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N GLU B1964 " --> pdb=" O THR B2018 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N GLN B1977 " --> pdb=" O TYR B1969 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 1896 through 1897 Processing sheet with id=AC4, first strand: chain 'B' and resid 1949 through 1951 removed outlier: 4.098A pdb=" N GLN B1951 " --> pdb=" O ARG B2027 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 2095 through 2098 removed outlier: 3.592A pdb=" N LYS B2178 " --> pdb=" O SER B2124 " (cutoff:3.500A) removed outlier: 7.668A pdb=" N SER B2124 " --> pdb=" O LYS B2178 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 2162 through 2169 removed outlier: 12.285A pdb=" N PHE B2164 " --> pdb=" O ILE B2109 " (cutoff:3.500A) removed outlier: 12.478A pdb=" N ILE B2109 " --> pdb=" O PHE B2164 " (cutoff:3.500A) removed outlier: 8.421A pdb=" N ALA B2107 " --> pdb=" O PRO B2166 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N ILE B2168 " --> pdb=" O ILE B2105 " (cutoff:3.500A) removed outlier: 5.458A pdb=" N ILE B2105 " --> pdb=" O CYS B2193 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N CYS B2193 " --> pdb=" O ILE B2105 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ALA B2107 " --> pdb=" O PHE B2191 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ILE B2109 " --> pdb=" O GLU B2189 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 174 through 175 removed outlier: 3.688A pdb=" N THR D 298 " --> pdb=" O PRO D 363 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N MET D 364 " --> pdb=" O VAL D 375 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N PHE D 373 " --> pdb=" O ALA D 366 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N VAL D 378 " --> pdb=" O THR D 394 " (cutoff:3.500A) removed outlier: 5.791A pdb=" N THR D 394 " --> pdb=" O VAL D 378 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 220 through 222 removed outlier: 4.064A pdb=" N CYS D 196 " --> pdb=" O LEU D 187 " (cutoff:3.500A) removed outlier: 7.742A pdb=" N GLY D 197 " --> pdb=" O ALA D 209 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N ALA D 209 " --> pdb=" O GLY D 197 " (cutoff:3.500A) 202 hydrogen bonds defined for protein. 492 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: 2.47 Time building geometry restraints manager: 1.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4091 1.34 - 1.47: 3212 1.47 - 1.59: 5627 1.59 - 1.71: 0 1.71 - 1.83: 107 Bond restraints: 13037 Sorted by residual: bond pdb=" N LYS A 499 " pdb=" CA LYS A 499 " ideal model delta sigma weight residual 1.453 1.488 -0.035 1.22e-02 6.72e+03 8.17e+00 bond pdb=" N ILE D 407 " pdb=" CA ILE D 407 " ideal model delta sigma weight residual 1.461 1.494 -0.034 1.19e-02 7.06e+03 8.06e+00 bond pdb=" N LYS D 191 " pdb=" CA LYS D 191 " ideal model delta sigma weight residual 1.457 1.494 -0.037 1.32e-02 5.74e+03 7.87e+00 bond pdb=" N ASP D 354 " pdb=" CA ASP D 354 " ideal model delta sigma weight residual 1.457 1.488 -0.031 1.29e-02 6.01e+03 5.80e+00 bond pdb=" N LYS D 193 " pdb=" CA LYS D 193 " ideal model delta sigma weight residual 1.454 1.482 -0.029 1.23e-02 6.61e+03 5.45e+00 ... (remaining 13032 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.58: 17390 2.58 - 5.16: 248 5.16 - 7.73: 19 7.73 - 10.31: 4 10.31 - 12.89: 1 Bond angle restraints: 17662 Sorted by residual: angle pdb=" CA ASP A 504 " pdb=" CB ASP A 504 " pdb=" CG ASP A 504 " ideal model delta sigma weight residual 112.60 119.14 -6.54 1.00e+00 1.00e+00 4.28e+01 angle pdb=" C SER B2183 " pdb=" CA SER B2183 " pdb=" CB SER B2183 " ideal model delta sigma weight residual 115.79 110.38 5.41 1.19e+00 7.06e-01 2.07e+01 angle pdb=" C ASP B1661 " pdb=" N SER B1662 " pdb=" CA SER B1662 " ideal model delta sigma weight residual 120.97 133.86 -12.89 2.84e+00 1.24e-01 2.06e+01 angle pdb=" CA ASP D 354 " pdb=" CB ASP D 354 " pdb=" CG ASP D 354 " ideal model delta sigma weight residual 112.60 116.22 -3.62 1.00e+00 1.00e+00 1.31e+01 angle pdb=" N MET D 213 " pdb=" CA MET D 213 " pdb=" C MET D 213 " ideal model delta sigma weight residual 113.15 109.12 4.03 1.19e+00 7.06e-01 1.15e+01 ... (remaining 17657 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.26: 7334 21.26 - 42.51: 495 42.51 - 63.77: 43 63.77 - 85.02: 26 85.02 - 106.28: 4 Dihedral angle restraints: 7902 sinusoidal: 3349 harmonic: 4553 Sorted by residual: dihedral pdb=" CB CYS D 331 " pdb=" SG CYS D 331 " pdb=" SG CYS D 345 " pdb=" CB CYS D 345 " ideal model delta sinusoidal sigma weight residual 93.00 157.97 -64.97 1 1.00e+01 1.00e-02 5.54e+01 dihedral pdb=" CB CYS D 196 " pdb=" SG CYS D 196 " pdb=" SG CYS D 212 " pdb=" CB CYS D 212 " ideal model delta sinusoidal sigma weight residual 93.00 40.24 52.76 1 1.00e+01 1.00e-02 3.79e+01 dihedral pdb=" CA HIS A 362 " pdb=" C HIS A 362 " pdb=" N TYR A 363 " pdb=" CA TYR A 363 " ideal model delta harmonic sigma weight residual 180.00 -153.12 -26.88 0 5.00e+00 4.00e-02 2.89e+01 ... (remaining 7899 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 1621 0.074 - 0.147: 254 0.147 - 0.221: 18 0.221 - 0.295: 0 0.295 - 0.368: 2 Chirality restraints: 1895 Sorted by residual: chirality pdb=" C1 NAG A2203 " pdb=" ND2 ASN A 432 " pdb=" C2 NAG A2203 " pdb=" O5 NAG A2203 " both_signs ideal model delta sigma weight residual False -2.40 -2.03 -0.37 2.00e-01 2.50e+01 3.39e+00 chirality pdb=" C1 NAG D 501 " pdb=" ND2 ASN D 248 " pdb=" C2 NAG D 501 " pdb=" O5 NAG D 501 " both_signs ideal model delta sigma weight residual False -2.40 -2.03 -0.37 2.00e-01 2.50e+01 3.35e+00 chirality pdb=" CB ILE A 394 " pdb=" CA ILE A 394 " pdb=" CG1 ILE A 394 " pdb=" CG2 ILE A 394 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.22 2.00e-01 2.50e+01 1.17e+00 ... (remaining 1892 not shown) Planarity restraints: 2266 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG D 501 " 0.265 2.00e-02 2.50e+03 2.22e-01 6.19e+02 pdb=" C7 NAG D 501 " -0.070 2.00e-02 2.50e+03 pdb=" C8 NAG D 501 " 0.176 2.00e-02 2.50e+03 pdb=" N2 NAG D 501 " -0.376 2.00e-02 2.50e+03 pdb=" O7 NAG D 501 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN D 248 " 0.015 2.00e-02 2.50e+03 8.92e-02 9.94e+01 pdb=" CG ASN D 248 " 0.029 2.00e-02 2.50e+03 pdb=" OD1 ASN D 248 " -0.085 2.00e-02 2.50e+03 pdb=" ND2 ASN D 248 " 0.144 2.00e-02 2.50e+03 pdb=" C1 NAG D 501 " -0.103 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP B2005 " -0.046 5.00e-02 4.00e+02 6.95e-02 7.74e+00 pdb=" N PRO B2006 " 0.120 5.00e-02 4.00e+02 pdb=" CA PRO B2006 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO B2006 " -0.038 5.00e-02 4.00e+02 ... (remaining 2263 not shown) Histogram of nonbonded interaction distances: 2.45 - 2.94: 5718 2.94 - 3.43: 13302 3.43 - 3.92: 21411 3.92 - 4.41: 24874 4.41 - 4.90: 39855 Nonbonded interactions: 105160 Sorted by model distance: nonbonded pdb=" O ASP B1660 " pdb=" OD1 ASP B1661 " model vdw 2.447 3.040 nonbonded pdb=" O PHE A 584 " pdb=" CA GLY A 620 " model vdw 2.454 2.752 nonbonded pdb=" O ILE A 561 " pdb=" OD1 ASN A 562 " model vdw 2.506 3.040 nonbonded pdb=" O LEU A 238 " pdb=" O LEU A 260 " model vdw 2.556 3.040 nonbonded pdb=" O ASP B1810 " pdb=" OD1 ASP B1810 " model vdw 2.558 3.040 ... (remaining 105155 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 5.220 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 13.440 Find NCS groups from input model: 0.080 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: 20.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5973 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 0.044 13055 Z= 0.186 Angle : 0.797 14.813 17706 Z= 0.427 Chirality : 0.052 0.368 1895 Planarity : 0.007 0.222 2258 Dihedral : 13.941 106.278 4948 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 19.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.22 % Favored : 87.78 % Rotamer: Outliers : 0.29 % Allowed : 0.29 % Favored : 99.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.32 (0.19), residues: 1555 helix: -2.98 (0.51), residues: 62 sheet: -1.89 (0.26), residues: 364 loop : -2.44 (0.17), residues: 1129 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG B1606 TYR 0.016 0.002 TYR A 418 PHE 0.020 0.002 PHE A 154 TRP 0.027 0.002 TRP B1934 HIS 0.006 0.001 HIS B2159 Details of bonding type rmsd covalent geometry : bond 0.00373 (13037) covalent geometry : angle 0.77413 (17662) SS BOND : bond 0.00268 ( 10) SS BOND : angle 1.22261 ( 20) hydrogen bonds : bond 0.16191 ( 200) hydrogen bonds : angle 8.67720 ( 492) link_NAG-ASN : bond 0.00861 ( 8) link_NAG-ASN : angle 5.10579 ( 24) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 265 time to evaluate : 0.478 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 ASP cc_start: 0.6894 (t0) cc_final: 0.6671 (t0) REVERT: B 1722 ILE cc_start: 0.6093 (pt) cc_final: 0.5579 (mm) REVERT: B 1733 ASN cc_start: 0.6696 (m-40) cc_final: 0.5625 (m110) REVERT: B 1736 MET cc_start: 0.7796 (ttm) cc_final: 0.6572 (mtt) REVERT: B 1811 ILE cc_start: 0.7629 (tp) cc_final: 0.7287 (mp) REVERT: B 2003 GLN cc_start: 0.8128 (tm-30) cc_final: 0.7865 (tm-30) REVERT: B 2174 ARG cc_start: 0.6498 (ttm170) cc_final: 0.5576 (mtm180) REVERT: D 356 CYS cc_start: 0.6475 (t) cc_final: 0.6237 (t) REVERT: D 390 TYR cc_start: 0.7036 (m-80) cc_final: 0.5702 (m-80) outliers start: 4 outliers final: 1 residues processed: 267 average time/residue: 0.1299 time to fit residues: 49.0478 Evaluate side-chains 226 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 225 time to evaluate : 0.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 354 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 98 optimal weight: 0.7980 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 0.3980 chunk 124 optimal weight: 0.5980 chunk 103 optimal weight: 0.6980 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 0.7980 chunk 149 optimal weight: 2.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 597 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1645 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1724 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1815 HIS ** B1819 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1824 ASN ** B1955 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4590 r_free = 0.4590 target = 0.174684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4409 r_free = 0.4409 target = 0.159320 restraints weight = 22885.279| |-----------------------------------------------------------------------------| r_work (start): 0.4408 rms_B_bonded: 2.82 r_work: 0.4311 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.4311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6042 moved from start: 0.1109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 13055 Z= 0.178 Angle : 0.739 14.646 17706 Z= 0.377 Chirality : 0.050 0.387 1895 Planarity : 0.005 0.068 2258 Dihedral : 8.188 106.155 1872 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 20.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.03 % Favored : 87.97 % Rotamer: Outliers : 1.08 % Allowed : 8.95 % Favored : 89.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.32 (0.19), residues: 1555 helix: -2.57 (0.54), residues: 64 sheet: -1.76 (0.27), residues: 345 loop : -2.51 (0.17), residues: 1146 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 312 TYR 0.025 0.002 TYR A 144 PHE 0.021 0.002 PHE A 651 TRP 0.026 0.002 TRP B1934 HIS 0.007 0.001 HIS A 609 Details of bonding type rmsd covalent geometry : bond 0.00404 (13037) covalent geometry : angle 0.71895 (17662) SS BOND : bond 0.00302 ( 10) SS BOND : angle 1.36043 ( 20) hydrogen bonds : bond 0.04165 ( 200) hydrogen bonds : angle 7.83804 ( 492) link_NAG-ASN : bond 0.00904 ( 8) link_NAG-ASN : angle 4.55605 ( 24) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 239 time to evaluate : 0.477 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 ASP cc_start: 0.6998 (t0) cc_final: 0.6758 (t0) REVERT: A 453 TYR cc_start: 0.5892 (t80) cc_final: 0.5684 (t80) REVERT: A 516 GLN cc_start: 0.5969 (OUTLIER) cc_final: 0.5666 (pm20) REVERT: A 523 PHE cc_start: 0.7020 (m-80) cc_final: 0.6528 (m-80) REVERT: A 618 MET cc_start: 0.7100 (mpp) cc_final: 0.6824 (mpp) REVERT: B 1736 MET cc_start: 0.7781 (ttm) cc_final: 0.6519 (mtt) REVERT: B 2003 GLN cc_start: 0.8218 (tm-30) cc_final: 0.7932 (tm-30) REVERT: B 2174 ARG cc_start: 0.6433 (ttm170) cc_final: 0.5659 (mtm-85) REVERT: D 193 LYS cc_start: 0.7409 (mtpp) cc_final: 0.6864 (tmtt) REVERT: D 323 ILE cc_start: 0.5947 (tp) cc_final: 0.5744 (tp) REVERT: D 390 TYR cc_start: 0.7046 (m-80) cc_final: 0.5800 (m-80) outliers start: 15 outliers final: 10 residues processed: 244 average time/residue: 0.1314 time to fit residues: 45.8007 Evaluate side-chains 238 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 227 time to evaluate : 0.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 ILE Chi-restraints excluded: chain A residue 79 ASP Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 516 GLN Chi-restraints excluded: chain A residue 614 THR Chi-restraints excluded: chain B residue 1553 ASN Chi-restraints excluded: chain B residue 1858 THR Chi-restraints excluded: chain B residue 1870 THR Chi-restraints excluded: chain B residue 1960 CYS Chi-restraints excluded: chain D residue 354 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 48 optimal weight: 0.5980 chunk 146 optimal weight: 0.9990 chunk 85 optimal weight: 0.9980 chunk 109 optimal weight: 2.9990 chunk 116 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 chunk 68 optimal weight: 2.9990 chunk 101 optimal weight: 0.6980 chunk 123 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 110 optimal weight: 0.8980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 207 ASN ** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1724 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1819 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2031 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 328 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4558 r_free = 0.4558 target = 0.172016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4371 r_free = 0.4371 target = 0.156264 restraints weight = 23049.472| |-----------------------------------------------------------------------------| r_work (start): 0.4371 rms_B_bonded: 2.88 r_work: 0.4270 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.4270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6134 moved from start: 0.1613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 13055 Z= 0.203 Angle : 0.745 14.635 17706 Z= 0.382 Chirality : 0.050 0.400 1895 Planarity : 0.006 0.079 2258 Dihedral : 8.246 106.324 1872 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 21.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.48 % Favored : 87.52 % Rotamer: Outliers : 2.24 % Allowed : 13.20 % Favored : 84.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.42 (0.19), residues: 1555 helix: -2.34 (0.60), residues: 58 sheet: -1.95 (0.26), residues: 364 loop : -2.57 (0.17), residues: 1133 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 312 TYR 0.025 0.002 TYR A 144 PHE 0.023 0.002 PHE A 651 TRP 0.021 0.002 TRP B1920 HIS 0.007 0.001 HIS B1829 Details of bonding type rmsd covalent geometry : bond 0.00458 (13037) covalent geometry : angle 0.72575 (17662) SS BOND : bond 0.00295 ( 10) SS BOND : angle 1.29749 ( 20) hydrogen bonds : bond 0.04036 ( 200) hydrogen bonds : angle 7.55066 ( 492) link_NAG-ASN : bond 0.00989 ( 8) link_NAG-ASN : angle 4.52700 ( 24) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 231 time to evaluate : 0.484 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 ASP cc_start: 0.7099 (t0) cc_final: 0.6869 (t0) REVERT: A 516 GLN cc_start: 0.6292 (OUTLIER) cc_final: 0.5937 (pm20) REVERT: A 523 PHE cc_start: 0.7185 (m-80) cc_final: 0.6659 (m-80) REVERT: A 596 ILE cc_start: 0.6830 (pt) cc_final: 0.6618 (pt) REVERT: B 1736 MET cc_start: 0.7787 (ttm) cc_final: 0.6507 (mtt) REVERT: B 1875 MET cc_start: 0.7091 (mpp) cc_final: 0.6794 (mpp) REVERT: B 2003 GLN cc_start: 0.8270 (tm-30) cc_final: 0.7926 (tm-30) REVERT: B 2174 ARG cc_start: 0.6411 (ttm170) cc_final: 0.5460 (mtt90) REVERT: B 2180 TRP cc_start: 0.3245 (m100) cc_final: 0.1900 (m100) REVERT: D 390 TYR cc_start: 0.7147 (m-80) cc_final: 0.5835 (m-80) outliers start: 31 outliers final: 23 residues processed: 245 average time/residue: 0.1195 time to fit residues: 42.6584 Evaluate side-chains 243 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 219 time to evaluate : 0.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 ILE Chi-restraints excluded: chain A residue 79 ASP Chi-restraints excluded: chain A residue 110 MET Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 431 VAL Chi-restraints excluded: chain A residue 436 THR Chi-restraints excluded: chain A residue 514 ILE Chi-restraints excluded: chain A residue 516 GLN Chi-restraints excluded: chain A residue 565 VAL Chi-restraints excluded: chain A residue 614 THR Chi-restraints excluded: chain B residue 1553 ASN Chi-restraints excluded: chain B residue 1734 MET Chi-restraints excluded: chain B residue 1858 THR Chi-restraints excluded: chain B residue 1870 THR Chi-restraints excluded: chain B residue 1960 CYS Chi-restraints excluded: chain B residue 2013 ILE Chi-restraints excluded: chain B residue 2033 CYS Chi-restraints excluded: chain B residue 2110 THR Chi-restraints excluded: chain D residue 220 LEU Chi-restraints excluded: chain D residue 273 ILE Chi-restraints excluded: chain D residue 354 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 52 optimal weight: 0.9990 chunk 116 optimal weight: 1.9990 chunk 90 optimal weight: 2.9990 chunk 97 optimal weight: 0.8980 chunk 127 optimal weight: 2.9990 chunk 65 optimal weight: 0.7980 chunk 71 optimal weight: 2.9990 chunk 56 optimal weight: 0.7980 chunk 92 optimal weight: 0.6980 chunk 139 optimal weight: 0.9990 chunk 107 optimal weight: 0.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 142 HIS ** A 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 207 ASN ** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1670 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1724 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1819 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1826 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1829 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2031 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4539 r_free = 0.4539 target = 0.170180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4358 r_free = 0.4358 target = 0.155110 restraints weight = 22626.061| |-----------------------------------------------------------------------------| r_work (start): 0.4359 rms_B_bonded: 2.78 r_work: 0.4262 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.4262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6142 moved from start: 0.1956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 13055 Z= 0.203 Angle : 0.744 14.577 17706 Z= 0.383 Chirality : 0.050 0.403 1895 Planarity : 0.005 0.073 2258 Dihedral : 8.245 106.206 1872 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 21.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.12 % Favored : 86.88 % Rotamer: Outliers : 2.96 % Allowed : 15.73 % Favored : 81.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.51 (0.19), residues: 1555 helix: -2.38 (0.58), residues: 58 sheet: -2.09 (0.26), residues: 375 loop : -2.59 (0.17), residues: 1122 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 312 TYR 0.025 0.002 TYR A 144 PHE 0.025 0.002 PHE A 651 TRP 0.022 0.002 TRP B1920 HIS 0.007 0.001 HIS A 609 Details of bonding type rmsd covalent geometry : bond 0.00458 (13037) covalent geometry : angle 0.72489 (17662) SS BOND : bond 0.00621 ( 10) SS BOND : angle 1.33808 ( 20) hydrogen bonds : bond 0.03906 ( 200) hydrogen bonds : angle 7.56620 ( 492) link_NAG-ASN : bond 0.00987 ( 8) link_NAG-ASN : angle 4.51487 ( 24) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 229 time to evaluate : 0.499 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 ASP cc_start: 0.7132 (t0) cc_final: 0.6868 (t0) REVERT: A 330 GLU cc_start: 0.5860 (tm-30) cc_final: 0.5552 (tm-30) REVERT: A 516 GLN cc_start: 0.6263 (OUTLIER) cc_final: 0.5888 (pm20) REVERT: A 523 PHE cc_start: 0.7164 (m-80) cc_final: 0.6619 (m-80) REVERT: A 596 ILE cc_start: 0.6655 (pt) cc_final: 0.6405 (pt) REVERT: B 1736 MET cc_start: 0.7785 (ttm) cc_final: 0.6563 (mtt) REVERT: B 1810 ASP cc_start: 0.6006 (p0) cc_final: 0.5656 (p0) REVERT: B 1875 MET cc_start: 0.6963 (mpp) cc_final: 0.6732 (mpp) REVERT: B 2003 GLN cc_start: 0.8235 (tm-30) cc_final: 0.7894 (tm-30) REVERT: B 2026 LEU cc_start: 0.5072 (OUTLIER) cc_final: 0.4695 (pp) REVERT: B 2054 ILE cc_start: 0.1013 (OUTLIER) cc_final: 0.0210 (mt) REVERT: B 2174 ARG cc_start: 0.6488 (ttm170) cc_final: 0.5758 (mtm180) REVERT: B 2180 TRP cc_start: 0.3216 (m100) cc_final: 0.1862 (m100) REVERT: D 170 LEU cc_start: 0.7269 (OUTLIER) cc_final: 0.6952 (mt) REVERT: D 205 TRP cc_start: 0.5616 (m-10) cc_final: 0.4839 (m-10) REVERT: D 390 TYR cc_start: 0.7166 (m-80) cc_final: 0.5897 (m-80) outliers start: 41 outliers final: 26 residues processed: 253 average time/residue: 0.1186 time to fit residues: 44.0508 Evaluate side-chains 256 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 226 time to evaluate : 0.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 ILE Chi-restraints excluded: chain A residue 79 ASP Chi-restraints excluded: chain A residue 110 MET Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 431 VAL Chi-restraints excluded: chain A residue 436 THR Chi-restraints excluded: chain A residue 478 TYR Chi-restraints excluded: chain A residue 514 ILE Chi-restraints excluded: chain A residue 516 GLN Chi-restraints excluded: chain A residue 565 VAL Chi-restraints excluded: chain A residue 614 THR Chi-restraints excluded: chain B residue 1590 VAL Chi-restraints excluded: chain B residue 1593 ARG Chi-restraints excluded: chain B residue 1665 TRP Chi-restraints excluded: chain B residue 1734 MET Chi-restraints excluded: chain B residue 1841 PHE Chi-restraints excluded: chain B residue 1858 THR Chi-restraints excluded: chain B residue 1870 THR Chi-restraints excluded: chain B residue 1960 CYS Chi-restraints excluded: chain B residue 2013 ILE Chi-restraints excluded: chain B residue 2026 LEU Chi-restraints excluded: chain B residue 2054 ILE Chi-restraints excluded: chain B residue 2110 THR Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain D residue 220 LEU Chi-restraints excluded: chain D residue 273 ILE Chi-restraints excluded: chain D residue 354 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 78 optimal weight: 1.9990 chunk 71 optimal weight: 0.9980 chunk 150 optimal weight: 0.9980 chunk 11 optimal weight: 2.9990 chunk 126 optimal weight: 0.4980 chunk 134 optimal weight: 0.4980 chunk 27 optimal weight: 2.9990 chunk 57 optimal weight: 1.9990 chunk 123 optimal weight: 0.7980 chunk 52 optimal weight: 0.9990 chunk 39 optimal weight: 0.0470 overall best weight: 0.5678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 207 ASN ** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 581 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1670 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1724 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1819 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1826 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1829 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 369 HIS D 388 HIS D 404 HIS D 406 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4562 r_free = 0.4562 target = 0.172193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4376 r_free = 0.4376 target = 0.156496 restraints weight = 22851.204| |-----------------------------------------------------------------------------| r_work (start): 0.4377 rms_B_bonded: 2.88 r_work: 0.4275 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.4275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6117 moved from start: 0.2154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 13055 Z= 0.167 Angle : 0.722 14.310 17706 Z= 0.367 Chirality : 0.049 0.395 1895 Planarity : 0.005 0.069 2258 Dihedral : 8.089 104.416 1872 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 20.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.15 % Favored : 87.85 % Rotamer: Outliers : 3.61 % Allowed : 16.52 % Favored : 79.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.46 (0.19), residues: 1555 helix: -2.29 (0.59), residues: 58 sheet: -2.10 (0.26), residues: 386 loop : -2.54 (0.17), residues: 1111 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 312 TYR 0.027 0.002 TYR A 144 PHE 0.024 0.002 PHE A 651 TRP 0.022 0.002 TRP B1920 HIS 0.007 0.001 HIS A 609 Details of bonding type rmsd covalent geometry : bond 0.00376 (13037) covalent geometry : angle 0.70443 (17662) SS BOND : bond 0.00580 ( 10) SS BOND : angle 1.19930 ( 20) hydrogen bonds : bond 0.03644 ( 200) hydrogen bonds : angle 7.33639 ( 492) link_NAG-ASN : bond 0.00902 ( 8) link_NAG-ASN : angle 4.27636 ( 24) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 223 time to evaluate : 0.518 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 ASP cc_start: 0.7081 (t0) cc_final: 0.6846 (t0) REVERT: A 165 CYS cc_start: 0.4638 (m) cc_final: 0.4285 (m) REVERT: A 247 VAL cc_start: 0.8377 (OUTLIER) cc_final: 0.8166 (p) REVERT: A 330 GLU cc_start: 0.5861 (tm-30) cc_final: 0.5536 (tm-30) REVERT: A 516 GLN cc_start: 0.6306 (OUTLIER) cc_final: 0.5912 (pm20) REVERT: A 523 PHE cc_start: 0.7189 (m-80) cc_final: 0.6650 (m-80) REVERT: A 558 MET cc_start: 0.6990 (pmm) cc_final: 0.6690 (pmm) REVERT: A 596 ILE cc_start: 0.6617 (pt) cc_final: 0.6409 (pt) REVERT: B 1736 MET cc_start: 0.7754 (ttm) cc_final: 0.6439 (mtt) REVERT: B 1810 ASP cc_start: 0.6022 (p0) cc_final: 0.5697 (p0) REVERT: B 1875 MET cc_start: 0.6930 (mpp) cc_final: 0.6710 (mpp) REVERT: B 1883 MET cc_start: 0.4280 (tmm) cc_final: 0.3616 (tmm) REVERT: B 1939 MET cc_start: 0.4660 (mmt) cc_final: 0.3969 (mmt) REVERT: B 2003 GLN cc_start: 0.8255 (tm-30) cc_final: 0.7863 (tm-30) REVERT: B 2026 LEU cc_start: 0.5175 (OUTLIER) cc_final: 0.4793 (pp) REVERT: B 2054 ILE cc_start: 0.0850 (OUTLIER) cc_final: 0.0084 (mt) REVERT: B 2120 MET cc_start: 0.7020 (tpt) cc_final: 0.6760 (mtp) REVERT: B 2174 ARG cc_start: 0.6471 (ttm170) cc_final: 0.5981 (mtm180) REVERT: B 2180 TRP cc_start: 0.3277 (m100) cc_final: 0.1869 (m100) REVERT: D 205 TRP cc_start: 0.5631 (m-10) cc_final: 0.4858 (m-10) REVERT: D 213 MET cc_start: 0.4484 (OUTLIER) cc_final: 0.3451 (tmm) REVERT: D 273 ILE cc_start: 0.6034 (mm) cc_final: 0.5789 (mt) REVERT: D 371 THR cc_start: 0.6852 (OUTLIER) cc_final: 0.6520 (p) outliers start: 50 outliers final: 30 residues processed: 253 average time/residue: 0.1228 time to fit residues: 45.2156 Evaluate side-chains 252 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 216 time to evaluate : 0.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 ILE Chi-restraints excluded: chain A residue 79 ASP Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 110 MET Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 353 ASP Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 431 VAL Chi-restraints excluded: chain A residue 436 THR Chi-restraints excluded: chain A residue 459 ILE Chi-restraints excluded: chain A residue 478 TYR Chi-restraints excluded: chain A residue 514 ILE Chi-restraints excluded: chain A residue 516 GLN Chi-restraints excluded: chain A residue 565 VAL Chi-restraints excluded: chain A residue 614 THR Chi-restraints excluded: chain B residue 1553 ASN Chi-restraints excluded: chain B residue 1590 VAL Chi-restraints excluded: chain B residue 1593 ARG Chi-restraints excluded: chain B residue 1665 TRP Chi-restraints excluded: chain B residue 1841 PHE Chi-restraints excluded: chain B residue 1858 THR Chi-restraints excluded: chain B residue 1960 CYS Chi-restraints excluded: chain B residue 2013 ILE Chi-restraints excluded: chain B residue 2016 SER Chi-restraints excluded: chain B residue 2026 LEU Chi-restraints excluded: chain B residue 2054 ILE Chi-restraints excluded: chain B residue 2110 THR Chi-restraints excluded: chain B residue 2169 ILE Chi-restraints excluded: chain D residue 213 MET Chi-restraints excluded: chain D residue 354 ASP Chi-restraints excluded: chain D residue 364 MET Chi-restraints excluded: chain D residue 371 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 90 optimal weight: 1.9990 chunk 24 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 chunk 102 optimal weight: 0.0000 chunk 83 optimal weight: 2.9990 chunk 128 optimal weight: 0.5980 chunk 103 optimal weight: 0.5980 chunk 9 optimal weight: 0.0170 chunk 153 optimal weight: 3.9990 chunk 139 optimal weight: 0.8980 chunk 129 optimal weight: 2.9990 overall best weight: 0.4222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 HIS A 207 ASN ** A 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 581 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1670 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1724 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1819 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1829 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 369 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4575 r_free = 0.4575 target = 0.173471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4390 r_free = 0.4390 target = 0.157845 restraints weight = 22751.761| |-----------------------------------------------------------------------------| r_work (start): 0.4388 rms_B_bonded: 2.89 r_work: 0.4289 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.4289 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6072 moved from start: 0.2277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 13055 Z= 0.149 Angle : 0.706 14.142 17706 Z= 0.358 Chirality : 0.049 0.388 1895 Planarity : 0.005 0.067 2258 Dihedral : 7.950 103.012 1872 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 19.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.15 % Favored : 87.85 % Rotamer: Outliers : 3.68 % Allowed : 17.68 % Favored : 78.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.39 (0.19), residues: 1555 helix: -2.19 (0.59), residues: 58 sheet: -2.06 (0.26), residues: 390 loop : -2.49 (0.17), residues: 1107 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B1698 TYR 0.027 0.002 TYR A 144 PHE 0.024 0.002 PHE A 651 TRP 0.022 0.001 TRP B1920 HIS 0.008 0.001 HIS D 369 Details of bonding type rmsd covalent geometry : bond 0.00341 (13037) covalent geometry : angle 0.68867 (17662) SS BOND : bond 0.00303 ( 10) SS BOND : angle 1.39874 ( 20) hydrogen bonds : bond 0.03430 ( 200) hydrogen bonds : angle 7.22689 ( 492) link_NAG-ASN : bond 0.00859 ( 8) link_NAG-ASN : angle 4.12619 ( 24) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 222 time to evaluate : 0.482 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 247 VAL cc_start: 0.8352 (OUTLIER) cc_final: 0.8145 (p) REVERT: A 458 ASN cc_start: 0.7030 (t0) cc_final: 0.6770 (t0) REVERT: A 516 GLN cc_start: 0.6338 (tt0) cc_final: 0.5911 (pm20) REVERT: A 523 PHE cc_start: 0.7062 (m-80) cc_final: 0.6545 (m-80) REVERT: A 596 ILE cc_start: 0.6813 (pt) cc_final: 0.6514 (pt) REVERT: B 1691 GLU cc_start: 0.4584 (OUTLIER) cc_final: 0.4096 (pt0) REVERT: B 1736 MET cc_start: 0.7668 (ttm) cc_final: 0.6375 (mtt) REVERT: B 1810 ASP cc_start: 0.6018 (p0) cc_final: 0.5711 (p0) REVERT: B 1875 MET cc_start: 0.6931 (mpp) cc_final: 0.6569 (mpp) REVERT: B 1939 MET cc_start: 0.4596 (mmt) cc_final: 0.3844 (mmt) REVERT: B 2026 LEU cc_start: 0.5137 (OUTLIER) cc_final: 0.4772 (pp) REVERT: B 2054 ILE cc_start: 0.0678 (OUTLIER) cc_final: 0.0171 (mt) REVERT: B 2174 ARG cc_start: 0.6484 (ttm170) cc_final: 0.5705 (mtp180) REVERT: B 2180 TRP cc_start: 0.3194 (m100) cc_final: 0.1800 (m100) REVERT: D 213 MET cc_start: 0.4405 (OUTLIER) cc_final: 0.3454 (tmm) REVERT: D 273 ILE cc_start: 0.6024 (mm) cc_final: 0.5795 (mt) REVERT: D 371 THR cc_start: 0.6884 (OUTLIER) cc_final: 0.6542 (p) outliers start: 51 outliers final: 36 residues processed: 256 average time/residue: 0.1132 time to fit residues: 41.8038 Evaluate side-chains 253 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 211 time to evaluate : 0.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 ILE Chi-restraints excluded: chain A residue 79 ASP Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 110 MET Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 353 ASP Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 422 VAL Chi-restraints excluded: chain A residue 431 VAL Chi-restraints excluded: chain A residue 436 THR Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 459 ILE Chi-restraints excluded: chain A residue 478 TYR Chi-restraints excluded: chain A residue 514 ILE Chi-restraints excluded: chain A residue 565 VAL Chi-restraints excluded: chain A residue 614 THR Chi-restraints excluded: chain B residue 1553 ASN Chi-restraints excluded: chain B residue 1590 VAL Chi-restraints excluded: chain B residue 1593 ARG Chi-restraints excluded: chain B residue 1630 VAL Chi-restraints excluded: chain B residue 1665 TRP Chi-restraints excluded: chain B residue 1691 GLU Chi-restraints excluded: chain B residue 1813 VAL Chi-restraints excluded: chain B residue 1841 PHE Chi-restraints excluded: chain B residue 1858 THR Chi-restraints excluded: chain B residue 1960 CYS Chi-restraints excluded: chain B residue 2013 ILE Chi-restraints excluded: chain B residue 2016 SER Chi-restraints excluded: chain B residue 2026 LEU Chi-restraints excluded: chain B residue 2033 CYS Chi-restraints excluded: chain B residue 2054 ILE Chi-restraints excluded: chain B residue 2110 THR Chi-restraints excluded: chain D residue 213 MET Chi-restraints excluded: chain D residue 315 THR Chi-restraints excluded: chain D residue 354 ASP Chi-restraints excluded: chain D residue 364 MET Chi-restraints excluded: chain D residue 369 HIS Chi-restraints excluded: chain D residue 371 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 51 optimal weight: 2.9990 chunk 74 optimal weight: 0.8980 chunk 56 optimal weight: 0.6980 chunk 44 optimal weight: 0.8980 chunk 110 optimal weight: 0.9980 chunk 9 optimal weight: 0.5980 chunk 120 optimal weight: 2.9990 chunk 26 optimal weight: 0.5980 chunk 95 optimal weight: 2.9990 chunk 112 optimal weight: 0.8980 chunk 55 optimal weight: 0.0670 overall best weight: 0.5718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 HIS A 207 ASN ** A 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1670 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1724 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1819 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1829 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1973 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4567 r_free = 0.4567 target = 0.172717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4380 r_free = 0.4380 target = 0.157093 restraints weight = 22825.962| |-----------------------------------------------------------------------------| r_work (start): 0.4382 rms_B_bonded: 2.87 r_work: 0.4280 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.4280 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6109 moved from start: 0.2392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 13055 Z= 0.166 Angle : 0.717 14.153 17706 Z= 0.366 Chirality : 0.049 0.392 1895 Planarity : 0.005 0.064 2258 Dihedral : 7.967 104.104 1872 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 19.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.03 % Favored : 87.97 % Rotamer: Outliers : 3.54 % Allowed : 18.76 % Favored : 77.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -3.37 (0.19), residues: 1555 helix: -2.17 (0.59), residues: 58 sheet: -2.03 (0.26), residues: 387 loop : -2.49 (0.17), residues: 1110 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 312 TYR 0.027 0.002 TYR A 144 PHE 0.025 0.002 PHE A 424 TRP 0.022 0.002 TRP B1920 HIS 0.020 0.001 HIS D 369 Details of bonding type rmsd covalent geometry : bond 0.00377 (13037) covalent geometry : angle 0.69963 (17662) SS BOND : bond 0.00256 ( 10) SS BOND : angle 1.50052 ( 20) hydrogen bonds : bond 0.03493 ( 200) hydrogen bonds : angle 7.20688 ( 492) link_NAG-ASN : bond 0.00891 ( 8) link_NAG-ASN : angle 4.13599 ( 24) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 220 time to evaluate : 0.491 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 458 ASN cc_start: 0.7120 (t0) cc_final: 0.6859 (t0) REVERT: A 516 GLN cc_start: 0.6296 (OUTLIER) cc_final: 0.5909 (pm20) REVERT: A 523 PHE cc_start: 0.7104 (m-80) cc_final: 0.6594 (m-80) REVERT: A 596 ILE cc_start: 0.6807 (pt) cc_final: 0.6539 (pt) REVERT: B 1691 GLU cc_start: 0.4641 (OUTLIER) cc_final: 0.4125 (pt0) REVERT: B 1736 MET cc_start: 0.7671 (ttm) cc_final: 0.6328 (mtt) REVERT: B 1810 ASP cc_start: 0.6075 (p0) cc_final: 0.5823 (p0) REVERT: B 1875 MET cc_start: 0.6950 (mpp) cc_final: 0.6590 (mpp) REVERT: B 1883 MET cc_start: 0.4473 (tmm) cc_final: 0.3752 (tmm) REVERT: B 1890 ILE cc_start: 0.8149 (mm) cc_final: 0.7741 (mm) REVERT: B 1939 MET cc_start: 0.4583 (mmt) cc_final: 0.3670 (mmt) REVERT: B 1951 GLN cc_start: 0.6625 (mp10) cc_final: 0.6368 (mp10) REVERT: B 2026 LEU cc_start: 0.5105 (OUTLIER) cc_final: 0.4731 (pp) REVERT: B 2054 ILE cc_start: 0.0707 (OUTLIER) cc_final: 0.0157 (mt) REVERT: B 2174 ARG cc_start: 0.6460 (ttm170) cc_final: 0.5695 (mtp180) REVERT: B 2180 TRP cc_start: 0.3161 (m100) cc_final: 0.1758 (m100) REVERT: D 213 MET cc_start: 0.4557 (OUTLIER) cc_final: 0.3650 (tmm) REVERT: D 273 ILE cc_start: 0.6059 (mm) cc_final: 0.5840 (mt) REVERT: D 371 THR cc_start: 0.6936 (OUTLIER) cc_final: 0.6627 (p) outliers start: 49 outliers final: 35 residues processed: 252 average time/residue: 0.1111 time to fit residues: 41.2237 Evaluate side-chains 257 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 216 time to evaluate : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 ILE Chi-restraints excluded: chain A residue 79 ASP Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 110 MET Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 380 THR Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 431 VAL Chi-restraints excluded: chain A residue 436 THR Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 459 ILE Chi-restraints excluded: chain A residue 478 TYR Chi-restraints excluded: chain A residue 514 ILE Chi-restraints excluded: chain A residue 516 GLN Chi-restraints excluded: chain A residue 565 VAL Chi-restraints excluded: chain A residue 614 THR Chi-restraints excluded: chain B residue 1553 ASN Chi-restraints excluded: chain B residue 1590 VAL Chi-restraints excluded: chain B residue 1593 ARG Chi-restraints excluded: chain B residue 1630 VAL Chi-restraints excluded: chain B residue 1665 TRP Chi-restraints excluded: chain B residue 1691 GLU Chi-restraints excluded: chain B residue 1813 VAL Chi-restraints excluded: chain B residue 1841 PHE Chi-restraints excluded: chain B residue 1858 THR Chi-restraints excluded: chain B residue 1870 THR Chi-restraints excluded: chain B residue 1960 CYS Chi-restraints excluded: chain B residue 2013 ILE Chi-restraints excluded: chain B residue 2016 SER Chi-restraints excluded: chain B residue 2026 LEU Chi-restraints excluded: chain B residue 2033 CYS Chi-restraints excluded: chain B residue 2054 ILE Chi-restraints excluded: chain B residue 2110 THR Chi-restraints excluded: chain D residue 213 MET Chi-restraints excluded: chain D residue 315 THR Chi-restraints excluded: chain D residue 354 ASP Chi-restraints excluded: chain D residue 364 MET Chi-restraints excluded: chain D residue 371 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 10 optimal weight: 2.9990 chunk 142 optimal weight: 0.8980 chunk 87 optimal weight: 2.9990 chunk 144 optimal weight: 0.0980 chunk 49 optimal weight: 0.8980 chunk 68 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 121 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 0 optimal weight: 0.5980 chunk 21 optimal weight: 2.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 182 GLN A 207 ASN ** B1724 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1819 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1826 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1829 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1973 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2089 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 369 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4531 r_free = 0.4531 target = 0.169613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4342 r_free = 0.4342 target = 0.154113 restraints weight = 22667.613| |-----------------------------------------------------------------------------| r_work (start): 0.4338 rms_B_bonded: 2.81 r_work: 0.4239 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.4239 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6188 moved from start: 0.2678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 13055 Z= 0.217 Angle : 0.774 14.300 17706 Z= 0.395 Chirality : 0.051 0.408 1895 Planarity : 0.005 0.065 2258 Dihedral : 8.251 107.164 1872 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 22.11 Ramachandran Plot: Outliers : 0.06 % Allowed : 12.73 % Favored : 87.20 % Rotamer: Outliers : 3.61 % Allowed : 19.41 % Favored : 76.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.50 (0.19), residues: 1555 helix: -2.30 (0.58), residues: 58 sheet: -2.01 (0.26), residues: 373 loop : -2.62 (0.16), residues: 1124 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 286 TYR 0.026 0.002 TYR A 144 PHE 0.028 0.002 PHE A 424 TRP 0.024 0.002 TRP B1920 HIS 0.009 0.001 HIS A 609 Details of bonding type rmsd covalent geometry : bond 0.00492 (13037) covalent geometry : angle 0.75613 (17662) SS BOND : bond 0.00306 ( 10) SS BOND : angle 1.52369 ( 20) hydrogen bonds : bond 0.03813 ( 200) hydrogen bonds : angle 7.48423 ( 492) link_NAG-ASN : bond 0.00998 ( 8) link_NAG-ASN : angle 4.33689 ( 24) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 220 time to evaluate : 0.473 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 330 GLU cc_start: 0.5878 (tm-30) cc_final: 0.5626 (tm-30) REVERT: A 333 TRP cc_start: 0.6942 (t-100) cc_final: 0.6717 (t-100) REVERT: A 458 ASN cc_start: 0.7162 (t0) cc_final: 0.6925 (t0) REVERT: A 516 GLN cc_start: 0.6327 (OUTLIER) cc_final: 0.5928 (pm20) REVERT: A 523 PHE cc_start: 0.7043 (m-80) cc_final: 0.6554 (m-80) REVERT: A 596 ILE cc_start: 0.6608 (pt) cc_final: 0.6379 (pt) REVERT: B 1691 GLU cc_start: 0.4785 (OUTLIER) cc_final: 0.4209 (pt0) REVERT: B 1736 MET cc_start: 0.7679 (ttm) cc_final: 0.6389 (mtt) REVERT: B 1810 ASP cc_start: 0.6090 (p0) cc_final: 0.5887 (p0) REVERT: B 1875 MET cc_start: 0.7022 (mpp) cc_final: 0.6748 (mpp) REVERT: B 1883 MET cc_start: 0.4654 (tmm) cc_final: 0.4073 (tmm) REVERT: B 1951 GLN cc_start: 0.6850 (mp10) cc_final: 0.6531 (mp10) REVERT: B 2003 GLN cc_start: 0.8222 (tm-30) cc_final: 0.8020 (tm-30) REVERT: B 2026 LEU cc_start: 0.5285 (OUTLIER) cc_final: 0.4824 (pp) REVERT: B 2174 ARG cc_start: 0.6527 (ttm170) cc_final: 0.5854 (mtp180) REVERT: D 213 MET cc_start: 0.4660 (OUTLIER) cc_final: 0.3786 (tmm) outliers start: 50 outliers final: 39 residues processed: 253 average time/residue: 0.1205 time to fit residues: 44.2399 Evaluate side-chains 256 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 213 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 LYS Chi-restraints excluded: chain A residue 70 ILE Chi-restraints excluded: chain A residue 79 ASP Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 110 MET Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 380 THR Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 431 VAL Chi-restraints excluded: chain A residue 436 THR Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 459 ILE Chi-restraints excluded: chain A residue 478 TYR Chi-restraints excluded: chain A residue 514 ILE Chi-restraints excluded: chain A residue 516 GLN Chi-restraints excluded: chain A residue 565 VAL Chi-restraints excluded: chain A residue 614 THR Chi-restraints excluded: chain B residue 1553 ASN Chi-restraints excluded: chain B residue 1590 VAL Chi-restraints excluded: chain B residue 1593 ARG Chi-restraints excluded: chain B residue 1630 VAL Chi-restraints excluded: chain B residue 1665 TRP Chi-restraints excluded: chain B residue 1691 GLU Chi-restraints excluded: chain B residue 1734 MET Chi-restraints excluded: chain B residue 1813 VAL Chi-restraints excluded: chain B residue 1841 PHE Chi-restraints excluded: chain B residue 1858 THR Chi-restraints excluded: chain B residue 1870 THR Chi-restraints excluded: chain B residue 1960 CYS Chi-restraints excluded: chain B residue 2013 ILE Chi-restraints excluded: chain B residue 2016 SER Chi-restraints excluded: chain B residue 2026 LEU Chi-restraints excluded: chain B residue 2063 TRP Chi-restraints excluded: chain B residue 2110 THR Chi-restraints excluded: chain B residue 2148 LYS Chi-restraints excluded: chain B residue 2173 ILE Chi-restraints excluded: chain D residue 213 MET Chi-restraints excluded: chain D residue 315 THR Chi-restraints excluded: chain D residue 354 ASP Chi-restraints excluded: chain D residue 364 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 122 optimal weight: 0.8980 chunk 70 optimal weight: 3.9990 chunk 64 optimal weight: 0.7980 chunk 114 optimal weight: 0.5980 chunk 37 optimal weight: 0.9990 chunk 81 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 119 optimal weight: 0.9980 chunk 77 optimal weight: 0.4980 chunk 75 optimal weight: 1.9990 chunk 45 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 207 ASN ** A 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 581 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1670 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1724 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1819 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1829 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2089 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 369 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4542 r_free = 0.4542 target = 0.170315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4354 r_free = 0.4354 target = 0.154816 restraints weight = 22815.976| |-----------------------------------------------------------------------------| r_work (start): 0.4355 rms_B_bonded: 2.82 r_work: 0.4253 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.4253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6177 moved from start: 0.2786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 13055 Z= 0.194 Angle : 0.764 14.191 17706 Z= 0.390 Chirality : 0.051 0.406 1895 Planarity : 0.005 0.064 2258 Dihedral : 8.195 105.096 1872 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 22.11 Ramachandran Plot: Outliers : 0.06 % Allowed : 12.48 % Favored : 87.46 % Rotamer: Outliers : 3.54 % Allowed : 20.13 % Favored : 76.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.54 (0.19), residues: 1555 helix: -2.43 (0.54), residues: 64 sheet: -2.00 (0.26), residues: 369 loop : -2.66 (0.16), residues: 1122 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B2014 TYR 0.025 0.002 TYR A 144 PHE 0.026 0.002 PHE A 651 TRP 0.023 0.002 TRP B1920 HIS 0.008 0.001 HIS A 609 Details of bonding type rmsd covalent geometry : bond 0.00442 (13037) covalent geometry : angle 0.74761 (17662) SS BOND : bond 0.00298 ( 10) SS BOND : angle 1.49335 ( 20) hydrogen bonds : bond 0.03655 ( 200) hydrogen bonds : angle 7.42132 ( 492) link_NAG-ASN : bond 0.00945 ( 8) link_NAG-ASN : angle 4.20772 ( 24) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 223 time to evaluate : 0.476 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 237 GLU cc_start: 0.4867 (mm-30) cc_final: 0.4376 (mt-10) REVERT: A 330 GLU cc_start: 0.5835 (tm-30) cc_final: 0.5569 (tm-30) REVERT: A 333 TRP cc_start: 0.6987 (t-100) cc_final: 0.6665 (t-100) REVERT: A 458 ASN cc_start: 0.7172 (t0) cc_final: 0.6939 (t0) REVERT: A 516 GLN cc_start: 0.6270 (OUTLIER) cc_final: 0.5889 (pm20) REVERT: A 523 PHE cc_start: 0.7080 (m-80) cc_final: 0.6581 (m-80) REVERT: A 556 ASN cc_start: 0.7348 (m-40) cc_final: 0.6880 (m-40) REVERT: A 596 ILE cc_start: 0.6602 (pt) cc_final: 0.6330 (pt) REVERT: A 638 MET cc_start: 0.7976 (mtp) cc_final: 0.7613 (mtp) REVERT: B 1691 GLU cc_start: 0.4614 (OUTLIER) cc_final: 0.4079 (pt0) REVERT: B 1736 MET cc_start: 0.7645 (ttm) cc_final: 0.6321 (mtt) REVERT: B 1875 MET cc_start: 0.7030 (mpp) cc_final: 0.6742 (mpp) REVERT: B 1951 GLN cc_start: 0.6753 (mp10) cc_final: 0.6448 (mp10) REVERT: B 2003 GLN cc_start: 0.8189 (tm-30) cc_final: 0.7977 (tm-30) REVERT: B 2026 LEU cc_start: 0.5075 (OUTLIER) cc_final: 0.4677 (pp) REVERT: B 2174 ARG cc_start: 0.6541 (ttm170) cc_final: 0.6107 (mtm180) REVERT: D 213 MET cc_start: 0.4718 (OUTLIER) cc_final: 0.3872 (tmm) REVERT: D 371 THR cc_start: 0.6813 (OUTLIER) cc_final: 0.6493 (p) outliers start: 49 outliers final: 39 residues processed: 253 average time/residue: 0.1229 time to fit residues: 45.0469 Evaluate side-chains 263 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 219 time to evaluate : 0.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 LYS Chi-restraints excluded: chain A residue 70 ILE Chi-restraints excluded: chain A residue 79 ASP Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 110 MET Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 380 THR Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 431 VAL Chi-restraints excluded: chain A residue 436 THR Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 459 ILE Chi-restraints excluded: chain A residue 478 TYR Chi-restraints excluded: chain A residue 514 ILE Chi-restraints excluded: chain A residue 516 GLN Chi-restraints excluded: chain A residue 565 VAL Chi-restraints excluded: chain A residue 614 THR Chi-restraints excluded: chain B residue 1553 ASN Chi-restraints excluded: chain B residue 1590 VAL Chi-restraints excluded: chain B residue 1593 ARG Chi-restraints excluded: chain B residue 1630 VAL Chi-restraints excluded: chain B residue 1665 TRP Chi-restraints excluded: chain B residue 1691 GLU Chi-restraints excluded: chain B residue 1813 VAL Chi-restraints excluded: chain B residue 1841 PHE Chi-restraints excluded: chain B residue 1858 THR Chi-restraints excluded: chain B residue 1870 THR Chi-restraints excluded: chain B residue 1960 CYS Chi-restraints excluded: chain B residue 2013 ILE Chi-restraints excluded: chain B residue 2016 SER Chi-restraints excluded: chain B residue 2026 LEU Chi-restraints excluded: chain B residue 2033 CYS Chi-restraints excluded: chain B residue 2110 THR Chi-restraints excluded: chain B residue 2148 LYS Chi-restraints excluded: chain B residue 2173 ILE Chi-restraints excluded: chain D residue 213 MET Chi-restraints excluded: chain D residue 354 ASP Chi-restraints excluded: chain D residue 364 MET Chi-restraints excluded: chain D residue 369 HIS Chi-restraints excluded: chain D residue 371 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 148 optimal weight: 0.6980 chunk 58 optimal weight: 0.9990 chunk 135 optimal weight: 0.9980 chunk 121 optimal weight: 0.9990 chunk 31 optimal weight: 0.9980 chunk 90 optimal weight: 0.6980 chunk 100 optimal weight: 0.8980 chunk 34 optimal weight: 1.9990 chunk 134 optimal weight: 2.9990 chunk 88 optimal weight: 0.0870 chunk 20 optimal weight: 1.9990 overall best weight: 0.6758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 207 ASN A 639 ASN ** B1670 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1683 HIS ** B1724 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1819 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1829 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1973 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2082 ASN ** B2089 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 369 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4544 r_free = 0.4544 target = 0.170494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4358 r_free = 0.4358 target = 0.154982 restraints weight = 22919.274| |-----------------------------------------------------------------------------| r_work (start): 0.4357 rms_B_bonded: 2.83 r_work: 0.4255 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.4255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6168 moved from start: 0.2875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 13055 Z= 0.186 Angle : 0.766 14.143 17706 Z= 0.389 Chirality : 0.051 0.403 1895 Planarity : 0.005 0.063 2258 Dihedral : 8.209 105.060 1872 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 21.99 Ramachandran Plot: Outliers : 0.06 % Allowed : 12.22 % Favored : 87.72 % Rotamer: Outliers : 3.54 % Allowed : 20.20 % Favored : 76.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.55 (0.19), residues: 1555 helix: -2.47 (0.54), residues: 64 sheet: -2.02 (0.26), residues: 371 loop : -2.66 (0.16), residues: 1120 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 222 TYR 0.039 0.002 TYR A 415 PHE 0.026 0.002 PHE A 651 TRP 0.022 0.002 TRP B1920 HIS 0.008 0.001 HIS A 609 Details of bonding type rmsd covalent geometry : bond 0.00425 (13037) covalent geometry : angle 0.74998 (17662) SS BOND : bond 0.00298 ( 10) SS BOND : angle 1.47738 ( 20) hydrogen bonds : bond 0.03531 ( 200) hydrogen bonds : angle 7.38698 ( 492) link_NAG-ASN : bond 0.00927 ( 8) link_NAG-ASN : angle 4.16424 ( 24) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3110 Ramachandran restraints generated. 1555 Oldfield, 0 Emsley, 1555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 228 time to evaluate : 0.410 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 237 GLU cc_start: 0.4875 (mm-30) cc_final: 0.4376 (mt-10) REVERT: A 330 GLU cc_start: 0.5828 (tm-30) cc_final: 0.5566 (tm-30) REVERT: A 332 ILE cc_start: 0.7077 (mp) cc_final: 0.6687 (tt) REVERT: A 333 TRP cc_start: 0.6991 (t-100) cc_final: 0.6695 (t-100) REVERT: A 458 ASN cc_start: 0.7161 (t0) cc_final: 0.6921 (t0) REVERT: A 516 GLN cc_start: 0.6335 (OUTLIER) cc_final: 0.5929 (pm20) REVERT: A 523 PHE cc_start: 0.7083 (m-80) cc_final: 0.6581 (m-80) REVERT: A 596 ILE cc_start: 0.6580 (pt) cc_final: 0.6314 (pt) REVERT: A 624 THR cc_start: 0.7440 (m) cc_final: 0.7158 (t) REVERT: B 1691 GLU cc_start: 0.4617 (OUTLIER) cc_final: 0.4080 (pt0) REVERT: B 1711 ASP cc_start: 0.5236 (m-30) cc_final: 0.5008 (t0) REVERT: B 1736 MET cc_start: 0.7609 (ttm) cc_final: 0.6267 (mtt) REVERT: B 1875 MET cc_start: 0.7046 (mpp) cc_final: 0.6757 (mpp) REVERT: B 2026 LEU cc_start: 0.5104 (OUTLIER) cc_final: 0.4716 (pp) REVERT: B 2174 ARG cc_start: 0.6533 (ttm170) cc_final: 0.6095 (mtm180) REVERT: B 2180 TRP cc_start: 0.2926 (m100) cc_final: 0.1729 (m100) REVERT: D 213 MET cc_start: 0.4728 (OUTLIER) cc_final: 0.3888 (tmm) REVERT: D 371 THR cc_start: 0.6712 (OUTLIER) cc_final: 0.6416 (p) outliers start: 49 outliers final: 42 residues processed: 259 average time/residue: 0.1220 time to fit residues: 45.6352 Evaluate side-chains 268 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 221 time to evaluate : 0.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 LYS Chi-restraints excluded: chain A residue 70 ILE Chi-restraints excluded: chain A residue 79 ASP Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 110 MET Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 380 THR Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 431 VAL Chi-restraints excluded: chain A residue 436 THR Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 459 ILE Chi-restraints excluded: chain A residue 478 TYR Chi-restraints excluded: chain A residue 514 ILE Chi-restraints excluded: chain A residue 516 GLN Chi-restraints excluded: chain A residue 565 VAL Chi-restraints excluded: chain A residue 614 THR Chi-restraints excluded: chain B residue 1553 ASN Chi-restraints excluded: chain B residue 1590 VAL Chi-restraints excluded: chain B residue 1593 ARG Chi-restraints excluded: chain B residue 1630 VAL Chi-restraints excluded: chain B residue 1665 TRP Chi-restraints excluded: chain B residue 1683 HIS Chi-restraints excluded: chain B residue 1691 GLU Chi-restraints excluded: chain B residue 1813 VAL Chi-restraints excluded: chain B residue 1841 PHE Chi-restraints excluded: chain B residue 1858 THR Chi-restraints excluded: chain B residue 1870 THR Chi-restraints excluded: chain B residue 1960 CYS Chi-restraints excluded: chain B residue 2013 ILE Chi-restraints excluded: chain B residue 2016 SER Chi-restraints excluded: chain B residue 2026 LEU Chi-restraints excluded: chain B residue 2033 CYS Chi-restraints excluded: chain B residue 2110 THR Chi-restraints excluded: chain B residue 2148 LYS Chi-restraints excluded: chain B residue 2173 ILE Chi-restraints excluded: chain D residue 213 MET Chi-restraints excluded: chain D residue 343 MET Chi-restraints excluded: chain D residue 354 ASP Chi-restraints excluded: chain D residue 364 MET Chi-restraints excluded: chain D residue 369 HIS Chi-restraints excluded: chain D residue 371 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 126 optimal weight: 0.3980 chunk 20 optimal weight: 1.9990 chunk 76 optimal weight: 0.9990 chunk 4 optimal weight: 0.8980 chunk 47 optimal weight: 0.7980 chunk 15 optimal weight: 0.9990 chunk 77 optimal weight: 0.6980 chunk 69 optimal weight: 0.6980 chunk 121 optimal weight: 0.6980 chunk 0 optimal weight: 0.5980 chunk 55 optimal weight: 1.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 207 ASN ** A 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1670 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1683 HIS ** B1724 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1819 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1829 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1973 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2089 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 369 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4547 r_free = 0.4547 target = 0.170883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4362 r_free = 0.4362 target = 0.155393 restraints weight = 22913.844| |-----------------------------------------------------------------------------| r_work (start): 0.4361 rms_B_bonded: 2.84 r_work: 0.4260 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.4260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6154 moved from start: 0.2931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 13055 Z= 0.181 Angle : 0.764 14.078 17706 Z= 0.388 Chirality : 0.051 0.459 1895 Planarity : 0.005 0.065 2258 Dihedral : 8.191 104.718 1872 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 21.87 Ramachandran Plot: Outliers : 0.06 % Allowed : 12.22 % Favored : 87.72 % Rotamer: Outliers : 3.54 % Allowed : 20.35 % Favored : 76.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.53 (0.19), residues: 1555 helix: -2.18 (0.58), residues: 58 sheet: -2.09 (0.26), residues: 375 loop : -2.63 (0.16), residues: 1122 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 222 TYR 0.027 0.002 TYR A 144 PHE 0.026 0.002 PHE A 651 TRP 0.021 0.002 TRP B1920 HIS 0.010 0.001 HIS D 369 Details of bonding type rmsd covalent geometry : bond 0.00414 (13037) covalent geometry : angle 0.74782 (17662) SS BOND : bond 0.00292 ( 10) SS BOND : angle 1.46411 ( 20) hydrogen bonds : bond 0.03468 ( 200) hydrogen bonds : angle 7.39225 ( 492) link_NAG-ASN : bond 0.00910 ( 8) link_NAG-ASN : angle 4.11663 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3351.85 seconds wall clock time: 58 minutes 46.89 seconds (3526.89 seconds total)