Starting phenix.real_space_refine on Wed Jun 11 12:03:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9mot_48481/06_2025/9mot_48481_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9mot_48481/06_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_48481/06_2025/9mot_48481.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9mot_48481/06_2025/9mot_48481.map" model { file = "/net/cci-nas-00/data/ceres_data/9mot_48481/06_2025/9mot_48481_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9mot_48481/06_2025/9mot_48481_neut.cif" } resolution = 3.15 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 8.18, per 1000 atoms: 0.64 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: 3.12 Conformation dependent library (CDL) restraints added in 1.7 seconds 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: 1.57 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: 4.64 Time building geometry restraints manager: 3.78 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: 18.290 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: 0.020 Extract box with map and model: 0.580 Check model and map are aligned: 0.110 Set scattering table: 0.150 Process input model: 32.760 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.320 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.027 0.002 TRP B1934 HIS 0.006 0.001 HIS B2159 PHE 0.020 0.002 PHE A 154 TYR 0.016 0.002 TYR A 418 ARG 0.019 0.001 ARG B1606 Details of bonding type rmsd link_NAG-ASN : bond 0.00861 ( 8) link_NAG-ASN : angle 5.10579 ( 24) hydrogen bonds : bond 0.16191 ( 200) hydrogen bonds : angle 8.67720 ( 492) SS BOND : bond 0.00268 ( 10) SS BOND : angle 1.22261 ( 20) covalent geometry : bond 0.00373 (13037) covalent geometry : angle 0.77413 (17662) *********************** 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 : 1.386 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: 0.5578 (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: 0.3225 time to fit residues: 122.4263 Evaluate side-chains 227 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 226 time to evaluate : 1.305 ------------------------------------------------------------------------------- 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 131 optimal weight: 1.9990 chunk 118 optimal weight: 0.9980 chunk 65 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 79 optimal weight: 0.3980 chunk 63 optimal weight: 0.6980 chunk 122 optimal weight: 1.9990 chunk 47 optimal weight: 0.9980 chunk 74 optimal weight: 3.9990 chunk 91 optimal weight: 0.7980 chunk 141 optimal weight: 3.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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** ** 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 ** B1864 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1955 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2031 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2159 HIS ** 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 = 0.4577 r_free = 0.4577 target = 0.173521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4396 r_free = 0.4396 target = 0.158170 restraints weight = 22754.393| |-----------------------------------------------------------------------------| r_work (start): 0.4396 rms_B_bonded: 2.80 r_work: 0.4299 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.4299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6072 moved from start: 0.1179 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= 0.199 Angle : 0.756 14.716 17706 Z= 0.386 Chirality : 0.051 0.393 1895 Planarity : 0.006 0.068 2258 Dihedral : 8.253 106.566 1872 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 20.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.15 % Favored : 87.85 % Rotamer: Outliers : 1.08 % Allowed : 9.38 % Favored : 89.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.35 (0.19), residues: 1555 helix: -2.60 (0.54), residues: 64 sheet: -1.79 (0.27), residues: 345 loop : -2.53 (0.17), residues: 1146 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B1934 HIS 0.009 0.001 HIS A 609 PHE 0.022 0.002 PHE A 651 TYR 0.023 0.002 TYR A 144 ARG 0.008 0.001 ARG D 312 Details of bonding type rmsd link_NAG-ASN : bond 0.00975 ( 8) link_NAG-ASN : angle 4.54092 ( 24) hydrogen bonds : bond 0.04138 ( 200) hydrogen bonds : angle 7.88319 ( 492) SS BOND : bond 0.00462 ( 10) SS BOND : angle 1.37624 ( 20) covalent geometry : bond 0.00450 (13037) covalent geometry : angle 0.73650 (17662) *********************** 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 250 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 235 time to evaluate : 1.384 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 ASP cc_start: 0.7033 (t0) cc_final: 0.6764 (t0) REVERT: A 453 TYR cc_start: 0.5926 (t80) cc_final: 0.5722 (t80) REVERT: A 516 GLN cc_start: 0.5972 (OUTLIER) cc_final: 0.5663 (pm20) REVERT: A 523 PHE cc_start: 0.7048 (m-80) cc_final: 0.6541 (m-80) REVERT: A 618 MET cc_start: 0.7123 (mpp) cc_final: 0.6850 (mpp) REVERT: B 1736 MET cc_start: 0.7795 (ttm) cc_final: 0.6548 (mtt) REVERT: B 2003 GLN cc_start: 0.8215 (tm-30) cc_final: 0.7920 (tm-30) REVERT: B 2174 ARG cc_start: 0.6418 (ttm170) cc_final: 0.5758 (mtp180) REVERT: D 193 LYS cc_start: 0.7432 (mtpp) cc_final: 0.6911 (tmtt) REVERT: D 323 ILE cc_start: 0.6081 (tp) cc_final: 0.5877 (tp) REVERT: D 390 TYR cc_start: 0.7069 (m-80) cc_final: 0.5793 (m-80) outliers start: 15 outliers final: 10 residues processed: 240 average time/residue: 0.3536 time to fit residues: 122.2919 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 : 1.452 ------------------------------------------------------------------------------- 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 108 optimal weight: 4.9990 chunk 103 optimal weight: 0.4980 chunk 146 optimal weight: 0.9980 chunk 116 optimal weight: 0.6980 chunk 71 optimal weight: 2.9990 chunk 72 optimal weight: 1.9990 chunk 123 optimal weight: 2.9990 chunk 131 optimal weight: 0.5980 chunk 119 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 94 optimal weight: 2.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- 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** ** 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** ** B1955 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2031 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 328 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4545 r_free = 0.4545 target = 0.170853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4358 r_free = 0.4358 target = 0.155285 restraints weight = 22943.195| |-----------------------------------------------------------------------------| r_work (start): 0.4357 rms_B_bonded: 2.82 r_work: 0.4258 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.4258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6168 moved from start: 0.1784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 13055 Z= 0.222 Angle : 0.771 14.762 17706 Z= 0.396 Chirality : 0.051 0.409 1895 Planarity : 0.006 0.081 2258 Dihedral : 8.373 107.040 1872 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 21.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.05 % Favored : 86.95 % Rotamer: Outliers : 2.45 % Allowed : 13.42 % Favored : 84.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.50 (0.19), residues: 1555 helix: -2.45 (0.58), residues: 58 sheet: -2.02 (0.26), residues: 366 loop : -2.61 (0.17), residues: 1131 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B1920 HIS 0.011 0.002 HIS A 609 PHE 0.025 0.002 PHE A 651 TYR 0.026 0.002 TYR A 144 ARG 0.011 0.001 ARG D 312 Details of bonding type rmsd link_NAG-ASN : bond 0.01052 ( 8) link_NAG-ASN : angle 4.64591 ( 24) hydrogen bonds : bond 0.04152 ( 200) hydrogen bonds : angle 7.75852 ( 492) SS BOND : bond 0.00937 ( 10) SS BOND : angle 1.28213 ( 20) covalent geometry : bond 0.00498 (13037) covalent geometry : angle 0.75199 (17662) *********************** 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 268 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 234 time to evaluate : 1.960 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: 0.7145 (t0) cc_final: 0.6860 (t0) REVERT: A 330 GLU cc_start: 0.5754 (tm-30) cc_final: 0.5430 (tm-30) REVERT: A 516 GLN cc_start: 0.6246 (OUTLIER) cc_final: 0.5954 (pm20) REVERT: A 523 PHE cc_start: 0.7179 (m-80) cc_final: 0.6674 (m-80) REVERT: A 596 ILE cc_start: 0.6848 (pt) cc_final: 0.6640 (pt) REVERT: B 1681 VAL cc_start: 0.7720 (OUTLIER) cc_final: 0.7518 (p) REVERT: B 1736 MET cc_start: 0.7811 (ttm) cc_final: 0.6551 (mtt) REVERT: B 1738 MET cc_start: 0.7625 (tmm) cc_final: 0.7174 (tmm) REVERT: B 1875 MET cc_start: 0.7104 (mpp) cc_final: 0.6828 (mpp) REVERT: B 2003 GLN cc_start: 0.8294 (tm-30) cc_final: 0.7976 (tm-30) REVERT: B 2026 LEU cc_start: 0.5055 (OUTLIER) cc_final: 0.4692 (pp) REVERT: B 2174 ARG cc_start: 0.6416 (ttm170) cc_final: 0.5769 (mtm180) REVERT: B 2180 TRP cc_start: 0.3307 (m100) cc_final: 0.1928 (m100) outliers start: 34 outliers final: 25 residues processed: 249 average time/residue: 0.4034 time to fit residues: 148.6340 Evaluate side-chains 251 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 223 time to evaluate : 2.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 LEU 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 1590 VAL Chi-restraints excluded: chain B residue 1681 VAL Chi-restraints excluded: chain B residue 1858 THR Chi-restraints excluded: chain B residue 1870 THR Chi-restraints excluded: chain B residue 1946 THR Chi-restraints excluded: chain B residue 1960 CYS Chi-restraints excluded: chain B residue 2026 LEU Chi-restraints excluded: chain B residue 2110 THR Chi-restraints excluded: chain B residue 2169 ILE Chi-restraints excluded: chain D residue 199 VAL 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 139 optimal weight: 0.7980 chunk 134 optimal weight: 0.6980 chunk 114 optimal weight: 0.8980 chunk 47 optimal weight: 0.9990 chunk 43 optimal weight: 0.0970 chunk 91 optimal weight: 0.6980 chunk 148 optimal weight: 0.9980 chunk 77 optimal weight: 0.9980 chunk 136 optimal weight: 1.9990 chunk 128 optimal weight: 0.9990 chunk 35 optimal weight: 0.1980 overall best weight: 0.4978 ------------------------------------------------------------------------------- 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 242 HIS ** B1724 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1819 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1826 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1955 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2031 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 406 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4571 r_free = 0.4571 target = 0.172954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4389 r_free = 0.4389 target = 0.157533 restraints weight = 22771.444| |-----------------------------------------------------------------------------| r_work (start): 0.4389 rms_B_bonded: 2.83 r_work: 0.4291 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.4291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6091 moved from start: 0.1919 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= 0.158 Angle : 0.703 14.328 17706 Z= 0.361 Chirality : 0.049 0.392 1895 Planarity : 0.005 0.072 2258 Dihedral : 8.090 104.392 1872 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 20.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.90 % Favored : 88.10 % Rotamer: Outliers : 3.25 % Allowed : 15.01 % Favored : 81.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.40 (0.19), residues: 1555 helix: -2.30 (0.59), residues: 58 sheet: -1.95 (0.27), residues: 368 loop : -2.55 (0.17), residues: 1129 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B1920 HIS 0.006 0.001 HIS D 406 PHE 0.024 0.002 PHE A 651 TYR 0.025 0.002 TYR A 144 ARG 0.008 0.001 ARG D 312 Details of bonding type rmsd link_NAG-ASN : bond 0.00888 ( 8) link_NAG-ASN : angle 4.28894 ( 24) hydrogen bonds : bond 0.03605 ( 200) hydrogen bonds : angle 7.44477 ( 492) SS BOND : bond 0.00247 ( 10) SS BOND : angle 1.23918 ( 20) covalent geometry : bond 0.00356 (13037) covalent geometry : angle 0.68485 (17662) *********************** 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 271 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 226 time to evaluate : 1.452 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 ARG cc_start: 0.6414 (mmm-85) cc_final: 0.6197 (mmm160) REVERT: A 135 ASP cc_start: 0.7061 (t0) cc_final: 0.6826 (t0) REVERT: A 330 GLU cc_start: 0.5832 (tm-30) cc_final: 0.5571 (tm-30) REVERT: A 516 GLN cc_start: 0.6232 (OUTLIER) cc_final: 0.5868 (pm20) REVERT: A 523 PHE cc_start: 0.7118 (m-80) cc_final: 0.6640 (m-80) REVERT: A 596 ILE cc_start: 0.6799 (pt) cc_final: 0.6507 (pt) REVERT: B 1736 MET cc_start: 0.7869 (ttm) cc_final: 0.6527 (mtt) REVERT: B 1875 MET cc_start: 0.6989 (mpp) cc_final: 0.6732 (mpp) REVERT: B 1883 MET cc_start: 0.4241 (tmm) cc_final: 0.3561 (tmm) REVERT: B 1939 MET cc_start: 0.4930 (mmt) cc_final: 0.3699 (mpp) REVERT: B 2003 GLN cc_start: 0.8265 (tm-30) cc_final: 0.7898 (tm-30) REVERT: B 2026 LEU cc_start: 0.5062 (OUTLIER) cc_final: 0.4739 (pp) REVERT: B 2054 ILE cc_start: 0.0742 (OUTLIER) cc_final: 0.0205 (mt) REVERT: B 2174 ARG cc_start: 0.6424 (ttm170) cc_final: 0.5716 (mtm180) REVERT: B 2180 TRP cc_start: 0.3325 (m100) cc_final: 0.1908 (m100) REVERT: D 205 TRP cc_start: 0.5547 (m-10) cc_final: 0.4772 (m-10) outliers start: 45 outliers final: 27 residues processed: 248 average time/residue: 0.2683 time to fit residues: 96.6900 Evaluate side-chains 250 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 220 time to evaluate : 1.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 LEU 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 171 THR 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 1553 ASN 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 1870 THR Chi-restraints excluded: chain B residue 1946 THR Chi-restraints excluded: chain B residue 1960 CYS 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 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 130 optimal weight: 1.9990 chunk 80 optimal weight: 0.7980 chunk 131 optimal weight: 1.9990 chunk 96 optimal weight: 0.8980 chunk 22 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 117 optimal weight: 0.5980 chunk 134 optimal weight: 0.5980 chunk 21 optimal weight: 0.4980 chunk 94 optimal weight: 0.7980 chunk 35 optimal weight: 0.5980 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** ** B1670 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1724 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1733 ASN ** B1819 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1829 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1955 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2031 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 388 HIS D 404 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4561 r_free = 0.4561 target = 0.172113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4376 r_free = 0.4376 target = 0.156526 restraints weight = 22595.860| |-----------------------------------------------------------------------------| r_work (start): 0.4375 rms_B_bonded: 2.85 r_work: 0.4277 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.4277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6111 moved from start: 0.2129 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= 0.171 Angle : 0.718 14.340 17706 Z= 0.365 Chirality : 0.049 0.397 1895 Planarity : 0.005 0.068 2258 Dihedral : 8.067 104.595 1872 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 20.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.35 % Favored : 87.65 % Rotamer: Outliers : 3.68 % Allowed : 15.95 % Favored : 80.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.42 (0.19), residues: 1555 helix: -2.25 (0.58), residues: 58 sheet: -1.99 (0.27), residues: 374 loop : -2.55 (0.17), residues: 1123 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B1920 HIS 0.005 0.001 HIS A 609 PHE 0.024 0.002 PHE A 651 TYR 0.026 0.002 TYR A 144 ARG 0.006 0.001 ARG D 312 Details of bonding type rmsd link_NAG-ASN : bond 0.00909 ( 8) link_NAG-ASN : angle 4.25369 ( 24) hydrogen bonds : bond 0.03599 ( 200) hydrogen bonds : angle 7.35152 ( 492) SS BOND : bond 0.00291 ( 10) SS BOND : angle 1.15324 ( 20) covalent geometry : bond 0.00385 (13037) covalent geometry : angle 0.70098 (17662) *********************** 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 274 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 223 time to evaluate : 1.396 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 ASP cc_start: 0.7069 (t0) cc_final: 0.6841 (t0) REVERT: A 330 GLU cc_start: 0.5844 (tm-30) cc_final: 0.5569 (tm-30) REVERT: A 516 GLN cc_start: 0.6263 (OUTLIER) cc_final: 0.5935 (pm20) REVERT: A 523 PHE cc_start: 0.7123 (m-80) cc_final: 0.6596 (m-80) REVERT: A 596 ILE cc_start: 0.6860 (pt) cc_final: 0.6599 (pt) REVERT: B 1691 GLU cc_start: 0.4631 (OUTLIER) cc_final: 0.4137 (pt0) REVERT: B 1736 MET cc_start: 0.7755 (ttm) cc_final: 0.6327 (mtt) REVERT: B 1810 ASP cc_start: 0.6049 (p0) cc_final: 0.5687 (p0) REVERT: B 1875 MET cc_start: 0.6985 (mpp) cc_final: 0.6727 (mpp) REVERT: B 2026 LEU cc_start: 0.5076 (OUTLIER) cc_final: 0.4764 (pp) REVERT: B 2054 ILE cc_start: 0.0839 (OUTLIER) cc_final: 0.0281 (mt) REVERT: B 2174 ARG cc_start: 0.6511 (ttm170) cc_final: 0.5861 (mtm180) REVERT: B 2180 TRP cc_start: 0.3282 (m100) cc_final: 0.1881 (m100) REVERT: D 205 TRP cc_start: 0.5638 (m-10) cc_final: 0.4864 (m-10) REVERT: D 213 MET cc_start: 0.4434 (OUTLIER) cc_final: 0.3420 (tmm) REVERT: D 273 ILE cc_start: 0.6022 (mm) cc_final: 0.5773 (mt) REVERT: D 323 ILE cc_start: 0.5931 (tp) cc_final: 0.5719 (tp) REVERT: D 371 THR cc_start: 0.6903 (OUTLIER) cc_final: 0.6557 (p) outliers start: 51 outliers final: 29 residues processed: 256 average time/residue: 0.2660 time to fit residues: 98.8106 Evaluate side-chains 256 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 221 time to evaluate : 1.294 ------------------------------------------------------------------------------- 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 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 1590 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 1946 THR Chi-restraints excluded: chain B residue 1960 CYS 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 D residue 213 MET Chi-restraints excluded: chain D residue 220 LEU Chi-restraints excluded: chain D residue 354 ASP 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 78 optimal weight: 1.9990 chunk 114 optimal weight: 0.7980 chunk 43 optimal weight: 0.6980 chunk 136 optimal weight: 4.9990 chunk 80 optimal weight: 1.9990 chunk 77 optimal weight: 0.0770 chunk 129 optimal weight: 2.9990 chunk 119 optimal weight: 0.0470 chunk 104 optimal weight: 2.9990 chunk 26 optimal weight: 0.7980 chunk 32 optimal weight: 0.5980 overall best weight: 0.4436 ------------------------------------------------------------------------------- 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** B1733 ASN ** B1819 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1955 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2031 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 369 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4579 r_free = 0.4579 target = 0.173581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4393 r_free = 0.4393 target = 0.157973 restraints weight = 22889.774| |-----------------------------------------------------------------------------| r_work (start): 0.4395 rms_B_bonded: 2.89 r_work: 0.4293 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.4293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6076 moved from start: 0.2308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 13055 Z= 0.149 Angle : 0.706 14.119 17706 Z= 0.358 Chirality : 0.049 0.389 1895 Planarity : 0.005 0.066 2258 Dihedral : 7.942 103.159 1872 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 18.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.70 % Favored : 88.30 % Rotamer: Outliers : 3.46 % Allowed : 17.17 % Favored : 79.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.39 (0.19), residues: 1555 helix: -2.30 (0.56), residues: 64 sheet: -1.94 (0.27), residues: 374 loop : -2.53 (0.17), residues: 1117 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B1920 HIS 0.008 0.001 HIS D 369 PHE 0.023 0.002 PHE A 651 TYR 0.027 0.002 TYR A 144 ARG 0.005 0.000 ARG D 312 Details of bonding type rmsd link_NAG-ASN : bond 0.00856 ( 8) link_NAG-ASN : angle 4.08817 ( 24) hydrogen bonds : bond 0.03404 ( 200) hydrogen bonds : angle 7.18892 ( 492) SS BOND : bond 0.00480 ( 10) SS BOND : angle 1.48580 ( 20) covalent geometry : bond 0.00337 (13037) covalent geometry : angle 0.68912 (17662) *********************** 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 272 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 224 time to evaluate : 1.425 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 165 CYS cc_start: 0.4492 (m) cc_final: 0.4160 (m) REVERT: A 330 GLU cc_start: 0.5856 (tm-30) cc_final: 0.5610 (tm-30) REVERT: A 458 ASN cc_start: 0.7007 (t0) cc_final: 0.6757 (t0) REVERT: A 485 ARG cc_start: 0.8158 (tpt-90) cc_final: 0.7143 (tmm160) REVERT: A 516 GLN cc_start: 0.6278 (OUTLIER) cc_final: 0.5870 (pm20) REVERT: A 523 PHE cc_start: 0.7104 (m-80) cc_final: 0.6572 (m-80) REVERT: A 596 ILE cc_start: 0.6767 (pt) cc_final: 0.6517 (pt) REVERT: B 1736 MET cc_start: 0.7567 (ttm) cc_final: 0.6217 (mtt) REVERT: B 1810 ASP cc_start: 0.6145 (p0) cc_final: 0.5796 (p0) REVERT: B 1875 MET cc_start: 0.7049 (mpp) cc_final: 0.6748 (mpp) REVERT: B 1939 MET cc_start: 0.4585 (mmt) cc_final: 0.3797 (mmt) REVERT: B 2026 LEU cc_start: 0.5067 (OUTLIER) cc_final: 0.4784 (pp) REVERT: B 2054 ILE cc_start: 0.0640 (OUTLIER) cc_final: 0.0123 (mt) REVERT: B 2174 ARG cc_start: 0.6456 (ttm170) cc_final: 0.5804 (mtm180) REVERT: B 2180 TRP cc_start: 0.3252 (m100) cc_final: 0.1851 (m100) REVERT: D 213 MET cc_start: 0.4400 (OUTLIER) cc_final: 0.3483 (tmm) REVERT: D 273 ILE cc_start: 0.6041 (OUTLIER) cc_final: 0.5815 (mt) REVERT: D 323 ILE cc_start: 0.5903 (tp) cc_final: 0.5701 (tp) REVERT: D 371 THR cc_start: 0.6831 (OUTLIER) cc_final: 0.6490 (p) outliers start: 48 outliers final: 34 residues processed: 253 average time/residue: 0.2634 time to fit residues: 96.6563 Evaluate side-chains 253 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 213 time to evaluate : 1.387 ------------------------------------------------------------------------------- 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 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 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 1630 VAL Chi-restraints excluded: chain B residue 1647 LEU Chi-restraints excluded: chain B residue 1665 TRP 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 1946 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 B residue 2169 ILE Chi-restraints excluded: chain D residue 213 MET Chi-restraints excluded: chain D residue 273 ILE Chi-restraints excluded: chain D residue 354 ASP 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 85 optimal weight: 0.3980 chunk 22 optimal weight: 0.9980 chunk 97 optimal weight: 0.8980 chunk 96 optimal weight: 0.9980 chunk 21 optimal weight: 0.7980 chunk 11 optimal weight: 0.9990 chunk 115 optimal weight: 1.9990 chunk 121 optimal weight: 0.9980 chunk 12 optimal weight: 0.6980 chunk 128 optimal weight: 0.1980 chunk 123 optimal weight: 0.0010 overall best weight: 0.4186 ------------------------------------------------------------------------------- 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 ** 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** ** B2031 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2089 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2159 HIS ** 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 = 0.4580 r_free = 0.4580 target = 0.173581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4397 r_free = 0.4397 target = 0.158183 restraints weight = 22579.496| |-----------------------------------------------------------------------------| r_work (start): 0.4398 rms_B_bonded: 2.85 r_work: 0.4299 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.4299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6061 moved from start: 0.2426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13055 Z= 0.148 Angle : 0.707 14.028 17706 Z= 0.359 Chirality : 0.049 0.387 1895 Planarity : 0.005 0.063 2258 Dihedral : 7.901 103.388 1872 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 18.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.51 % Favored : 88.49 % Rotamer: Outliers : 3.54 % Allowed : 18.18 % Favored : 78.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.37 (0.19), residues: 1555 helix: -2.31 (0.54), residues: 64 sheet: -1.94 (0.26), residues: 379 loop : -2.51 (0.17), residues: 1112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP A 333 HIS 0.014 0.001 HIS D 369 PHE 0.023 0.002 PHE A 651 TYR 0.029 0.002 TYR D 390 ARG 0.016 0.001 ARG D 314 Details of bonding type rmsd link_NAG-ASN : bond 0.00852 ( 8) link_NAG-ASN : angle 4.02560 ( 24) hydrogen bonds : bond 0.03327 ( 200) hydrogen bonds : angle 7.18404 ( 492) SS BOND : bond 0.00279 ( 10) SS BOND : angle 1.44510 ( 20) covalent geometry : bond 0.00336 (13037) covalent geometry : angle 0.69032 (17662) *********************** 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 264 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 215 time to evaluate : 1.326 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 332 ILE cc_start: 0.7146 (mp) cc_final: 0.6806 (tt) REVERT: A 458 ASN cc_start: 0.7021 (t0) cc_final: 0.6775 (t0) REVERT: A 516 GLN cc_start: 0.6257 (tt0) cc_final: 0.5850 (pm20) REVERT: A 523 PHE cc_start: 0.7067 (m-80) cc_final: 0.6565 (m-80) REVERT: A 596 ILE cc_start: 0.6741 (pt) cc_final: 0.6482 (pt) REVERT: B 1736 MET cc_start: 0.7591 (ttm) cc_final: 0.6194 (mtt) REVERT: B 1810 ASP cc_start: 0.6053 (p0) cc_final: 0.5729 (p0) REVERT: B 1875 MET cc_start: 0.7026 (mpp) cc_final: 0.6736 (mpp) REVERT: B 1890 ILE cc_start: 0.8055 (mm) cc_final: 0.7667 (mm) REVERT: B 1939 MET cc_start: 0.4604 (mmt) cc_final: 0.3539 (mmt) REVERT: B 2026 LEU cc_start: 0.5049 (OUTLIER) cc_final: 0.4767 (pp) REVERT: B 2054 ILE cc_start: 0.0639 (OUTLIER) cc_final: 0.0125 (mt) REVERT: B 2174 ARG cc_start: 0.6424 (ttm170) cc_final: 0.5756 (mtm180) REVERT: B 2180 TRP cc_start: 0.3241 (m100) cc_final: 0.1875 (m100) REVERT: D 213 MET cc_start: 0.4503 (OUTLIER) cc_final: 0.3603 (tmm) REVERT: D 273 ILE cc_start: 0.6015 (mm) cc_final: 0.5783 (mt) REVERT: D 323 ILE cc_start: 0.5909 (tp) cc_final: 0.5701 (tp) REVERT: D 371 THR cc_start: 0.6832 (OUTLIER) cc_final: 0.6518 (p) outliers start: 49 outliers final: 34 residues processed: 247 average time/residue: 0.2459 time to fit residues: 88.3788 Evaluate side-chains 249 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 211 time to evaluate : 1.324 ------------------------------------------------------------------------------- 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 353 ASP 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 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 1630 VAL Chi-restraints excluded: chain B residue 1647 LEU Chi-restraints excluded: chain B residue 1665 TRP 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 1946 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 D residue 213 MET Chi-restraints excluded: chain D residue 354 ASP Chi-restraints excluded: chain D residue 367 SER 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 104 optimal weight: 2.9990 chunk 123 optimal weight: 0.0010 chunk 43 optimal weight: 0.9990 chunk 118 optimal weight: 0.0570 chunk 132 optimal weight: 0.8980 chunk 37 optimal weight: 2.9990 chunk 46 optimal weight: 0.7980 chunk 125 optimal weight: 1.9990 chunk 107 optimal weight: 0.3980 chunk 139 optimal weight: 0.8980 chunk 86 optimal weight: 0.0980 overall best weight: 0.2704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 HIS A 182 GLN A 207 ASN ** A 597 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 639 ASN ** B1643 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** ** B1973 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2031 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2089 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2159 HIS ** 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 = 0.4603 r_free = 0.4603 target = 0.175598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4424 r_free = 0.4424 target = 0.160269 restraints weight = 22842.508| |-----------------------------------------------------------------------------| r_work (start): 0.4423 rms_B_bonded: 2.87 r_work: 0.4324 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.4324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6004 moved from start: 0.2566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13055 Z= 0.132 Angle : 0.692 13.823 17706 Z= 0.351 Chirality : 0.048 0.377 1895 Planarity : 0.005 0.063 2258 Dihedral : 7.737 104.103 1872 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 17.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.19 % Favored : 88.81 % Rotamer: Outliers : 3.17 % Allowed : 18.69 % Favored : 78.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.31 (0.19), residues: 1555 helix: -2.33 (0.54), residues: 64 sheet: -1.84 (0.27), residues: 375 loop : -2.49 (0.17), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP A 333 HIS 0.008 0.001 HIS D 369 PHE 0.022 0.002 PHE A 651 TYR 0.027 0.001 TYR A 144 ARG 0.006 0.000 ARG D 314 Details of bonding type rmsd link_NAG-ASN : bond 0.00813 ( 8) link_NAG-ASN : angle 3.86987 ( 24) hydrogen bonds : bond 0.03176 ( 200) hydrogen bonds : angle 7.05817 ( 492) SS BOND : bond 0.00253 ( 10) SS BOND : angle 1.36731 ( 20) covalent geometry : bond 0.00300 (13037) covalent geometry : angle 0.67646 (17662) *********************** 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 267 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 223 time to evaluate : 1.287 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 332 ILE cc_start: 0.7141 (mp) cc_final: 0.6758 (tt) REVERT: A 458 ASN cc_start: 0.6917 (t0) cc_final: 0.6705 (t0) REVERT: A 485 ARG cc_start: 0.7954 (tpt-90) cc_final: 0.6810 (ttp-170) REVERT: A 516 GLN cc_start: 0.6239 (tt0) cc_final: 0.5869 (pm20) REVERT: A 523 PHE cc_start: 0.7040 (m-80) cc_final: 0.6545 (m-80) REVERT: A 558 MET cc_start: 0.6786 (pmm) cc_final: 0.6564 (ptp) REVERT: A 596 ILE cc_start: 0.6643 (pt) cc_final: 0.6371 (pt) REVERT: A 618 MET cc_start: 0.6972 (mpp) cc_final: 0.6770 (mpp) REVERT: A 624 THR cc_start: 0.7441 (m) cc_final: 0.7096 (t) REVERT: B 1736 MET cc_start: 0.7413 (ttm) cc_final: 0.6126 (mtt) REVERT: B 1738 MET cc_start: 0.7237 (tmt) cc_final: 0.6793 (tmt) REVERT: B 1810 ASP cc_start: 0.5993 (p0) cc_final: 0.5662 (p0) REVERT: B 1883 MET cc_start: 0.4222 (tmm) cc_final: 0.3904 (tmm) REVERT: B 1939 MET cc_start: 0.4532 (mmt) cc_final: 0.3182 (mpp) REVERT: B 2015 ILE cc_start: 0.5507 (OUTLIER) cc_final: 0.4801 (pt) REVERT: B 2054 ILE cc_start: 0.0398 (OUTLIER) cc_final: -0.0084 (mt) REVERT: B 2174 ARG cc_start: 0.6420 (ttm170) cc_final: 0.5637 (mtp180) REVERT: B 2180 TRP cc_start: 0.3157 (m100) cc_final: 0.1796 (m100) REVERT: D 213 MET cc_start: 0.4517 (OUTLIER) cc_final: 0.3659 (tmm) outliers start: 44 outliers final: 34 residues processed: 255 average time/residue: 0.2593 time to fit residues: 94.8181 Evaluate side-chains 250 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 213 time to evaluate : 1.409 ------------------------------------------------------------------------------- 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 353 ASP Chi-restraints excluded: chain A residue 380 THR 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 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 B residue 1590 VAL Chi-restraints excluded: chain B residue 1630 VAL Chi-restraints excluded: chain B residue 1647 LEU Chi-restraints excluded: chain B residue 1665 TRP Chi-restraints excluded: chain B residue 1813 VAL Chi-restraints excluded: chain B residue 1817 HIS Chi-restraints excluded: chain B residue 1841 PHE Chi-restraints excluded: chain B residue 1858 THR Chi-restraints excluded: chain B residue 1945 ILE Chi-restraints excluded: chain B residue 1960 CYS Chi-restraints excluded: chain B residue 2013 ILE Chi-restraints excluded: chain B residue 2015 ILE Chi-restraints excluded: chain B residue 2016 SER Chi-restraints excluded: chain B residue 2054 ILE Chi-restraints excluded: chain B residue 2110 THR 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 369 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 76 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 115 optimal weight: 2.9990 chunk 99 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 chunk 23 optimal weight: 0.6980 chunk 65 optimal weight: 2.9990 chunk 103 optimal weight: 0.8980 chunk 4 optimal weight: 3.9990 chunk 153 optimal weight: 1.9990 chunk 88 optimal weight: 1.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 ASN ** 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** ** B1857 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1955 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2031 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2089 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4505 r_free = 0.4505 target = 0.167297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4315 r_free = 0.4315 target = 0.151761 restraints weight = 22710.796| |-----------------------------------------------------------------------------| r_work (start): 0.4313 rms_B_bonded: 2.79 r_work: 0.4212 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.4212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6256 moved from start: 0.2916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.061 13055 Z= 0.292 Angle : 0.877 14.467 17706 Z= 0.449 Chirality : 0.054 0.423 1895 Planarity : 0.006 0.063 2258 Dihedral : 8.507 107.423 1872 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 24.87 Ramachandran Plot: Outliers : 0.06 % Allowed : 13.31 % Favored : 86.62 % Rotamer: Outliers : 3.46 % Allowed : 18.83 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.51 (0.19), residues: 1555 helix: -2.30 (0.56), residues: 58 sheet: -1.90 (0.27), residues: 372 loop : -2.68 (0.16), residues: 1125 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.003 TRP A 333 HIS 0.009 0.002 HIS B1829 PHE 0.031 0.003 PHE A 424 TYR 0.028 0.003 TYR A 418 ARG 0.008 0.001 ARG D 314 Details of bonding type rmsd link_NAG-ASN : bond 0.01241 ( 8) link_NAG-ASN : angle 4.57484 ( 24) hydrogen bonds : bond 0.04294 ( 200) hydrogen bonds : angle 7.75702 ( 492) SS BOND : bond 0.01218 ( 10) SS BOND : angle 1.83486 ( 20) covalent geometry : bond 0.00658 (13037) covalent geometry : angle 0.85913 (17662) *********************** 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 282 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 234 time to evaluate : 1.316 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 GLU cc_start: 0.7045 (mt-10) cc_final: 0.6678 (mt-10) REVERT: A 270 MET cc_start: 0.7092 (OUTLIER) cc_final: 0.6149 (tmm) REVERT: A 330 GLU cc_start: 0.5882 (tm-30) cc_final: 0.5634 (tm-30) REVERT: A 332 ILE cc_start: 0.7175 (mp) cc_final: 0.6755 (tt) REVERT: A 516 GLN cc_start: 0.6309 (OUTLIER) cc_final: 0.5854 (pm20) REVERT: A 523 PHE cc_start: 0.7099 (m-80) cc_final: 0.6585 (m-80) REVERT: A 596 ILE cc_start: 0.6649 (pt) cc_final: 0.6403 (pt) REVERT: A 624 THR cc_start: 0.7499 (m) cc_final: 0.7112 (t) REVERT: B 1711 ASP cc_start: 0.5744 (t0) cc_final: 0.5437 (t0) REVERT: B 1736 MET cc_start: 0.7160 (ttm) cc_final: 0.6216 (mtt) REVERT: B 1738 MET cc_start: 0.7428 (tmt) cc_final: 0.6893 (tmt) REVERT: B 1810 ASP cc_start: 0.6091 (p0) cc_final: 0.5864 (p0) REVERT: B 1883 MET cc_start: 0.4673 (tmm) cc_final: 0.3915 (tmm) REVERT: B 2026 LEU cc_start: 0.5274 (OUTLIER) cc_final: 0.4872 (pp) REVERT: B 2053 GLN cc_start: 0.3693 (pp30) cc_final: 0.3321 (pp30) REVERT: B 2054 ILE cc_start: 0.1379 (OUTLIER) cc_final: 0.0678 (mt) REVERT: B 2174 ARG cc_start: 0.6514 (ttm170) cc_final: 0.5770 (mtp180) REVERT: D 170 LEU cc_start: 0.7486 (OUTLIER) cc_final: 0.7224 (mt) REVERT: D 213 MET cc_start: 0.4720 (OUTLIER) cc_final: 0.3814 (tmm) REVERT: D 286 ARG cc_start: 0.3921 (ttt-90) cc_final: 0.2411 (mtp180) outliers start: 48 outliers final: 38 residues processed: 264 average time/residue: 0.2478 time to fit residues: 94.6476 Evaluate side-chains 269 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 225 time to evaluate : 1.304 ------------------------------------------------------------------------------- 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 171 THR 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 270 MET 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 1630 VAL Chi-restraints excluded: chain B residue 1647 LEU Chi-restraints excluded: chain B residue 1665 TRP Chi-restraints excluded: chain B residue 1813 VAL Chi-restraints excluded: chain B residue 1817 HIS 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 2063 TRP Chi-restraints excluded: chain B residue 2110 THR Chi-restraints excluded: chain B residue 2173 ILE Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain D residue 199 VAL Chi-restraints excluded: chain D residue 213 MET Chi-restraints excluded: chain D residue 343 MET Chi-restraints excluded: chain D residue 354 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 39 optimal weight: 0.2980 chunk 35 optimal weight: 0.0770 chunk 34 optimal weight: 0.6980 chunk 43 optimal weight: 0.8980 chunk 11 optimal weight: 2.9990 chunk 78 optimal weight: 0.8980 chunk 152 optimal weight: 0.7980 chunk 84 optimal weight: 0.9980 chunk 116 optimal weight: 0.8980 chunk 50 optimal weight: 0.9990 chunk 144 optimal weight: 0.9990 overall best weight: 0.5538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 ASN ** A 562 ASN ** 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** ** B1864 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2089 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2159 HIS ** 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 = 0.4556 r_free = 0.4556 target = 0.171545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4372 r_free = 0.4372 target = 0.155997 restraints weight = 22663.874| |-----------------------------------------------------------------------------| r_work (start): 0.4368 rms_B_bonded: 2.82 r_work: 0.4268 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.4268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6128 moved from start: 0.2914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 13055 Z= 0.174 Angle : 0.764 13.978 17706 Z= 0.389 Chirality : 0.051 0.402 1895 Planarity : 0.005 0.065 2258 Dihedral : 8.228 104.816 1872 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 21.11 Ramachandran Plot: Outliers : 0.06 % Allowed : 11.51 % Favored : 88.42 % Rotamer: Outliers : 3.03 % Allowed : 19.62 % Favored : 77.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.48 (0.19), residues: 1555 helix: -2.28 (0.55), residues: 64 sheet: -1.98 (0.27), residues: 378 loop : -2.62 (0.17), residues: 1113 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 333 HIS 0.007 0.001 HIS A 609 PHE 0.025 0.002 PHE A 651 TYR 0.034 0.002 TYR A 415 ARG 0.011 0.001 ARG D 314 Details of bonding type rmsd link_NAG-ASN : bond 0.00878 ( 8) link_NAG-ASN : angle 4.10095 ( 24) hydrogen bonds : bond 0.03514 ( 200) hydrogen bonds : angle 7.47314 ( 492) SS BOND : bond 0.00304 ( 10) SS BOND : angle 1.47339 ( 20) covalent geometry : bond 0.00400 (13037) covalent geometry : angle 0.74784 (17662) ********************** 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 270 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 228 time to evaluate : 1.512 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 330 GLU cc_start: 0.5860 (tm-30) cc_final: 0.5653 (tm-30) REVERT: A 332 ILE cc_start: 0.7104 (mp) cc_final: 0.6772 (tt) REVERT: A 367 MET cc_start: 0.5653 (mmt) cc_final: 0.4707 (mmt) REVERT: A 458 ASN cc_start: 0.7101 (t0) cc_final: 0.6877 (t0) REVERT: A 516 GLN cc_start: 0.6201 (tt0) cc_final: 0.5823 (pm20) REVERT: A 523 PHE cc_start: 0.6960 (m-80) cc_final: 0.6442 (m-80) REVERT: A 596 ILE cc_start: 0.6509 (pt) cc_final: 0.6270 (pt) REVERT: A 624 THR cc_start: 0.7404 (m) cc_final: 0.7130 (t) REVERT: B 1736 MET cc_start: 0.7014 (ttm) cc_final: 0.6115 (mtt) REVERT: B 1738 MET cc_start: 0.7376 (tmt) cc_final: 0.6967 (tmt) REVERT: B 1810 ASP cc_start: 0.6027 (p0) cc_final: 0.5798 (p0) REVERT: B 2026 LEU cc_start: 0.5093 (OUTLIER) cc_final: 0.4708 (pp) REVERT: B 2053 GLN cc_start: 0.3760 (pp30) cc_final: 0.3479 (pp30) REVERT: B 2054 ILE cc_start: 0.1051 (OUTLIER) cc_final: 0.0436 (mt) REVERT: B 2174 ARG cc_start: 0.6522 (ttm170) cc_final: 0.6097 (mtm180) REVERT: D 213 MET cc_start: 0.4720 (OUTLIER) cc_final: 0.3909 (tmm) REVERT: D 218 LYS cc_start: 0.6979 (tttt) cc_final: 0.6751 (mtmm) outliers start: 42 outliers final: 34 residues processed: 256 average time/residue: 0.2612 time to fit residues: 96.4247 Evaluate side-chains 262 residues out of total 1386 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 225 time to evaluate : 1.484 ------------------------------------------------------------------------------- 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 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 1630 VAL Chi-restraints excluded: chain B residue 1647 LEU Chi-restraints excluded: chain B residue 1665 TRP Chi-restraints excluded: chain B residue 1813 VAL Chi-restraints excluded: chain B residue 1817 HIS 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 2173 ILE Chi-restraints excluded: chain D residue 213 MET Chi-restraints excluded: chain D residue 354 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 99 optimal weight: 0.8980 chunk 19 optimal weight: 0.5980 chunk 78 optimal weight: 0.6980 chunk 125 optimal weight: 1.9990 chunk 145 optimal weight: 1.9990 chunk 80 optimal weight: 0.5980 chunk 0 optimal weight: 2.9990 chunk 103 optimal weight: 0.7980 chunk 135 optimal weight: 0.9990 chunk 8 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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** ** B1724 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1819 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1829 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1864 GLN ** 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** ** B2159 HIS ** 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 = 0.4543 r_free = 0.4543 target = 0.170517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4359 r_free = 0.4359 target = 0.155079 restraints weight = 22590.364| |-----------------------------------------------------------------------------| r_work (start): 0.4360 rms_B_bonded: 2.80 r_work: 0.4257 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.4257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6165 moved from start: 0.3052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 13055 Z= 0.195 Angle : 0.786 14.084 17706 Z= 0.399 Chirality : 0.051 0.405 1895 Planarity : 0.005 0.063 2258 Dihedral : 8.278 105.047 1872 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 22.15 Ramachandran Plot: Outliers : 0.06 % Allowed : 12.41 % Favored : 87.52 % Rotamer: Outliers : 3.17 % Allowed : 19.48 % Favored : 77.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.48 (0.19), residues: 1555 helix: -2.22 (0.57), residues: 64 sheet: -1.95 (0.27), residues: 364 loop : -2.63 (0.16), residues: 1127 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 333 HIS 0.007 0.001 HIS A 609 PHE 0.025 0.002 PHE A 651 TYR 0.026 0.002 TYR A 144 ARG 0.010 0.001 ARG D 314 Details of bonding type rmsd link_NAG-ASN : bond 0.00938 ( 8) link_NAG-ASN : angle 4.11294 ( 24) hydrogen bonds : bond 0.03589 ( 200) hydrogen bonds : angle 7.54386 ( 492) SS BOND : bond 0.00338 ( 10) SS BOND : angle 1.58105 ( 20) covalent geometry : bond 0.00447 (13037) covalent geometry : angle 0.77033 (17662) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8082.66 seconds wall clock time: 143 minutes 16.00 seconds (8596.00 seconds total)