Starting phenix.real_space_refine on Thu Jun 12 14:27:06 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9mov_48439/06_2025/9mov_48439_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9mov_48439/06_2025/9mov_48439.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9mov_48439/06_2025/9mov_48439.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9mov_48439/06_2025/9mov_48439.map" model { file = "/net/cci-nas-00/data/ceres_data/9mov_48439/06_2025/9mov_48439_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9mov_48439/06_2025/9mov_48439_neut.cif" } resolution = 3.0 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= -0.000 sd= 0.020 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Ca 7 9.91 5 S 83 5.16 5 C 8793 2.51 5 N 2366 2.21 5 O 2649 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: 13898 Number of models: 1 Model: "" Number of chains: 8 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: "C" Number of atoms: 1169 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1169 Classifications: {'peptide': 146} Link IDs: {'PTRANS': 6, 'TRANS': 139} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Planarities with less than four sites: {'CGU:plan-1': 9} Unresolved non-hydrogen planarities: 9 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: "C" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 21 Unusual residues: {' CA': 7, 'NAG': 1} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 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 Residues with excluded nonbonded symmetry interactions: 1 residue: pdb="CA CA C 204 " occ=0.40 Time building chain proxies: 9.59, per 1000 atoms: 0.69 Number of scatterers: 13898 At special positions: 0 Unit cell: (100.932, 142.696, 139.216, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 7 19.99 S 83 16.00 O 2649 8.00 N 2366 7.00 C 8793 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=19, 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 C 17 " - pdb=" SG CYS C 22 " distance=2.05 Simple disulfide: pdb=" SG CYS C 50 " - pdb=" SG CYS C 69 " distance=2.03 Simple disulfide: pdb=" SG CYS C 59 " - pdb=" SG CYS C 64 " distance=2.03 Simple disulfide: pdb=" SG CYS C 63 " - pdb=" SG CYS C 78 " distance=2.03 Simple disulfide: pdb=" SG CYS C 80 " - pdb=" SG CYS C 89 " distance=2.03 Simple disulfide: pdb=" SG CYS C 98 " - pdb=" SG CYS C 109 " distance=2.03 Simple disulfide: pdb=" SG CYS C 105 " - pdb=" SG CYS C 118 " distance=2.03 Simple disulfide: pdb=" SG CYS C 120 " - pdb=" SG CYS C 133 " distance=2.03 Simple disulfide: pdb=" SG CYS C 141 " - pdb=" SG CYS D 277 " distance=1.71 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=1, 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 C 201 " - " ASN C 97 " " NAG D 501 " - " ASN D 248 " " NAG D 502 " - " ASN D 329 " " NAG D 503 " - " ASN D 313 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.58 Conformation dependent library (CDL) restraints added in 1.6 seconds 3358 Ramachandran restraints generated. 1679 Oldfield, 0 Emsley, 1679 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3190 Finding SS restraints... Secondary structure from input PDB file: 21 helices and 30 sheets defined 8.6% alpha, 19.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.20 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 'C' and resid 5 through 9 Processing helix chain 'C' and resid 12 through 18 removed outlier: 3.506A pdb=" N ILE C 18 " --> pdb=" O CGU C 14 " (cutoff:3.500A) Processing helix chain 'C' and resid 23 through 32 Processing helix chain 'C' and resid 33 through 45 removed outlier: 3.670A pdb=" N LYS C 43 " --> pdb=" O ALA C 39 " (cutoff:3.500A) Processing helix chain 'C' and resid 100 through 105 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 'C' and resid 69 through 71 Processing sheet with id=AC8, first strand: chain 'C' and resid 84 through 85 Processing sheet with id=AC9, first strand: chain 'C' and resid 108 through 111 Processing sheet with id=AD1, first strand: chain 'C' and resid 124 through 126 Processing sheet with id=AD2, 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=AD3, 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) 233 hydrogen bonds defined for protein. 564 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.09 Time building geometry restraints manager: 4.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 4413 1.34 - 1.46: 3316 1.46 - 1.58: 6396 1.58 - 1.71: 0 1.71 - 1.83: 124 Bond restraints: 14249 Sorted by residual: bond pdb=" CG CGU C 26 " pdb=" CD2 CGU C 26 " ideal model delta sigma weight residual 1.544 1.470 0.074 2.00e-02 2.50e+03 1.37e+01 bond pdb=" CG CGU C 19 " pdb=" CD2 CGU C 19 " ideal model delta sigma weight residual 1.544 1.478 0.066 2.00e-02 2.50e+03 1.09e+01 bond pdb=" CG CGU C 25 " pdb=" CD2 CGU C 25 " ideal model delta sigma weight residual 1.544 1.481 0.063 2.00e-02 2.50e+03 9.93e+00 bond pdb=" N VAL C 45 " pdb=" CA VAL C 45 " ideal model delta sigma weight residual 1.459 1.497 -0.038 1.25e-02 6.40e+03 9.09e+00 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 ... (remaining 14244 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.58: 18962 2.58 - 5.16: 303 5.16 - 7.73: 29 7.73 - 10.31: 8 10.31 - 12.89: 6 Bond angle restraints: 19308 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=" CD1 CGU C 7 " pdb=" CG CGU C 7 " pdb=" CD2 CGU C 7 " ideal model delta sigma weight residual 106.66 117.94 -11.28 3.00e+00 1.11e-01 1.41e+01 angle pdb=" CD1 CGU C 14 " pdb=" CG CGU C 14 " pdb=" CD2 CGU C 14 " ideal model delta sigma weight residual 106.66 117.78 -11.12 3.00e+00 1.11e-01 1.37e+01 ... (remaining 19303 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.26: 8027 21.26 - 42.51: 533 42.51 - 63.77: 47 63.77 - 85.02: 27 85.02 - 106.28: 4 Dihedral angle restraints: 8638 sinusoidal: 3672 harmonic: 4966 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 8635 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.079: 1787 0.079 - 0.158: 248 0.158 - 0.237: 19 0.237 - 0.316: 2 0.316 - 0.395: 5 Chirality restraints: 2061 Sorted by residual: chirality pdb=" CA LEU C 5 " pdb=" N LEU C 5 " pdb=" C LEU C 5 " pdb=" CB LEU C 5 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.89e+00 chirality pdb=" CA CGU C 7 " pdb=" N CGU C 7 " pdb=" C CGU C 7 " pdb=" CB CGU C 7 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.72e+00 chirality pdb=" CA ILE C 21 " pdb=" N ILE C 21 " pdb=" C ILE C 21 " pdb=" CB ILE C 21 " both_signs ideal model delta sigma weight residual False 2.43 2.80 -0.37 2.00e-01 2.50e+01 3.44e+00 ... (remaining 2058 not shown) Planarity restraints: 2488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG D 501 " 0.266 2.00e-02 2.50e+03 2.23e-01 6.20e+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=" CG CGU C 26 " -0.015 2.00e-02 2.50e+03 2.99e-02 8.95e+00 pdb=" CD2 CGU C 26 " 0.052 2.00e-02 2.50e+03 pdb="OE21 CGU C 26 " -0.019 2.00e-02 2.50e+03 pdb="OE22 CGU C 26 " -0.018 2.00e-02 2.50e+03 ... (remaining 2485 not shown) Histogram of nonbonded interaction distances: 1.01 - 1.79: 4 1.79 - 2.57: 51 2.57 - 3.34: 18039 3.34 - 4.12: 34993 4.12 - 4.90: 61753 Nonbonded interactions: 114840 Sorted by model distance: nonbonded pdb=" O CYS C 98 " pdb=" NH1 ARG D 286 " model vdw 1.010 3.120 nonbonded pdb=" O CYS C 98 " pdb=" CZ ARG D 286 " model vdw 1.159 3.270 nonbonded pdb=" OH TYR C 108 " pdb=" O LEU D 278 " model vdw 1.278 3.040 nonbonded pdb=" C CYS C 98 " pdb=" NH1 ARG D 286 " model vdw 1.557 3.350 nonbonded pdb=" C CYS C 98 " pdb=" CZ ARG D 286 " model vdw 1.916 3.500 ... (remaining 114835 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=0.40 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.130 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.590 Check model and map are aligned: 0.110 Set scattering table: 0.140 Process input model: 36.510 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4825 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 : 0.005 0.322 14278 Z= 0.283 Angle : 0.856 14.813 19373 Z= 0.446 Chirality : 0.056 0.395 2061 Planarity : 0.007 0.223 2479 Dihedral : 13.825 106.278 5391 Min Nonbonded Distance : 1.010 Molprobity Statistics. All-atom Clashscore : 19.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.61 % Favored : 88.39 % Rotamer: Outliers : 0.33 % Allowed : 0.40 % Favored : 99.27 % 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: -3.02 (0.19), residues: 1679 helix: -2.52 (0.49), residues: 78 sheet: -1.82 (0.26), residues: 376 loop : -2.18 (0.17), residues: 1225 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 0.022 0.001 ARG C 9 Details of bonding type rmsd link_NAG-ASN : bond 0.00833 ( 9) link_NAG-ASN : angle 4.83322 ( 27) hydrogen bonds : bond 0.16887 ( 231) hydrogen bonds : angle 8.57370 ( 564) SS BOND : bond 0.07410 ( 19) SS BOND : angle 2.10103 ( 38) covalent geometry : bond 0.00441 (14249) covalent geometry : angle 0.83260 (19308) Misc. bond : bond 0.13426 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3358 Ramachandran restraints generated. 1679 Oldfield, 0 Emsley, 1679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3358 Ramachandran restraints generated. 1679 Oldfield, 0 Emsley, 1679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 1504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 319 time to evaluate : 1.495 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 158 LEU cc_start: 0.7152 (mt) cc_final: 0.6447 (mt) REVERT: A 237 GLU cc_start: 0.4422 (mm-30) cc_final: 0.3770 (mm-30) REVERT: A 562 ASN cc_start: 0.5671 (p0) cc_final: 0.5445 (p0) REVERT: B 1736 MET cc_start: 0.7726 (ttm) cc_final: 0.7154 (mpt) REVERT: B 1853 TRP cc_start: 0.6542 (m100) cc_final: 0.6232 (m100) outliers start: 5 outliers final: 3 residues processed: 324 average time/residue: 1.0633 time to fit residues: 384.1080 Evaluate side-chains 199 residues out of total 1504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 196 time to evaluate : 1.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 1620 ILE Chi-restraints excluded: chain B residue 2181 ASN Chi-restraints excluded: chain D residue 354 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 143 optimal weight: 5.9990 chunk 128 optimal weight: 1.9990 chunk 71 optimal weight: 0.6980 chunk 44 optimal weight: 0.1980 chunk 86 optimal weight: 2.9990 chunk 68 optimal weight: 0.9990 chunk 133 optimal weight: 8.9990 chunk 51 optimal weight: 6.9990 chunk 81 optimal weight: 0.0370 chunk 99 optimal weight: 0.6980 chunk 154 optimal weight: 4.9990 overall best weight: 0.5260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 420 HIS ** A 509 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1670 ASN ** B1724 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1815 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1817 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1819 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1824 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1863 ASN ** B2159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 303 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5040 r_free = 0.5040 target = 0.174925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.4702 r_free = 0.4702 target = 0.144487 restraints weight = 35159.841| |-----------------------------------------------------------------------------| r_work (start): 0.4648 rms_B_bonded: 6.11 r_work (final): 0.4648 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4648 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4648 r_free = 0.4648 target_work(ls_wunit_k1) = 0.141 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4648 r_free = 0.4648 target_work(ls_wunit_k1) = 0.141 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.4648 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6042 moved from start: 0.2249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 14278 Z= 0.162 Angle : 0.789 14.055 19373 Z= 0.396 Chirality : 0.051 0.360 2061 Planarity : 0.006 0.091 2479 Dihedral : 8.548 106.288 2079 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 20.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.36 % Favored : 89.64 % Rotamer: Outliers : 2.66 % Allowed : 13.63 % Favored : 83.71 % 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: -3.05 (0.19), residues: 1679 helix: -2.06 (0.53), residues: 80 sheet: -1.95 (0.25), residues: 398 loop : -2.18 (0.17), residues: 1201 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP D 231 HIS 0.009 0.001 HIS A 609 PHE 0.021 0.002 PHE A 424 TYR 0.040 0.002 TYR A 38 ARG 0.011 0.001 ARG D 286 Details of bonding type rmsd link_NAG-ASN : bond 0.00777 ( 9) link_NAG-ASN : angle 3.96248 ( 27) hydrogen bonds : bond 0.04096 ( 231) hydrogen bonds : angle 7.70274 ( 564) SS BOND : bond 0.00505 ( 19) SS BOND : angle 1.92428 ( 38) covalent geometry : bond 0.00368 (14249) covalent geometry : angle 0.77124 (19308) Misc. bond : bond 0.00282 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3358 Ramachandran restraints generated. 1679 Oldfield, 0 Emsley, 1679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3358 Ramachandran restraints generated. 1679 Oldfield, 0 Emsley, 1679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 1504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 220 time to evaluate : 1.430 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 ILE cc_start: 0.6331 (OUTLIER) cc_final: 0.6021 (mp) REVERT: A 158 LEU cc_start: 0.7490 (mt) cc_final: 0.6652 (mp) REVERT: A 233 SER cc_start: 0.5783 (m) cc_final: 0.5070 (p) REVERT: A 237 GLU cc_start: 0.3553 (mm-30) cc_final: 0.2932 (mm-30) REVERT: A 335 TYR cc_start: 0.5970 (OUTLIER) cc_final: 0.5635 (m-80) REVERT: A 415 TYR cc_start: 0.6306 (m-80) cc_final: 0.5883 (m-80) REVERT: B 1657 THR cc_start: 0.7867 (t) cc_final: 0.7499 (m) REVERT: B 1670 ASN cc_start: 0.4744 (m110) cc_final: 0.4453 (m-40) REVERT: B 1736 MET cc_start: 0.7458 (ttm) cc_final: 0.6256 (mpt) REVERT: B 1811 ILE cc_start: 0.7761 (tp) cc_final: 0.7347 (mp) REVERT: B 1892 ASP cc_start: 0.7279 (m-30) cc_final: 0.7074 (t70) REVERT: B 1990 PHE cc_start: 0.6642 (m-80) cc_final: 0.6302 (m-80) REVERT: B 2002 ASN cc_start: 0.7857 (m-40) cc_final: 0.7626 (m110) REVERT: D 231 TRP cc_start: 0.7460 (t60) cc_final: 0.7204 (t60) outliers start: 40 outliers final: 11 residues processed: 244 average time/residue: 1.0531 time to fit residues: 287.4644 Evaluate side-chains 191 residues out of total 1504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 178 time to evaluate : 1.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 ILE Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 240 SER Chi-restraints excluded: chain A residue 335 TYR Chi-restraints excluded: chain B residue 1899 GLU Chi-restraints excluded: chain B residue 2063 TRP Chi-restraints excluded: chain B residue 2117 SER Chi-restraints excluded: chain D residue 273 ILE Chi-restraints excluded: chain D residue 297 VAL Chi-restraints excluded: chain D residue 354 ASP Chi-restraints excluded: chain D residue 396 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 15 optimal weight: 0.9990 chunk 115 optimal weight: 0.9980 chunk 32 optimal weight: 2.9990 chunk 126 optimal weight: 8.9990 chunk 139 optimal weight: 4.9990 chunk 63 optimal weight: 3.9990 chunk 125 optimal weight: 1.9990 chunk 5 optimal weight: 3.9990 chunk 142 optimal weight: 0.9990 chunk 154 optimal weight: 3.9990 chunk 6 optimal weight: 0.8980 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 142 HIS ** A 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 242 HIS ** A 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 509 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 556 ASN ** B1815 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1817 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1819 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1824 ASN ** B1829 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1864 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2091 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 303 HIS D 328 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4969 r_free = 0.4969 target = 0.170328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.4613 r_free = 0.4613 target = 0.139121 restraints weight = 35456.506| |-----------------------------------------------------------------------------| r_work (start): 0.4554 rms_B_bonded: 5.94 r_work (final): 0.4554 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6202 moved from start: 0.3009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 14278 Z= 0.210 Angle : 0.795 13.643 19373 Z= 0.401 Chirality : 0.051 0.357 2061 Planarity : 0.006 0.080 2479 Dihedral : 8.626 106.262 2075 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 23.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.07 % Favored : 89.93 % Rotamer: Outliers : 3.32 % Allowed : 14.83 % Favored : 81.85 % 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: -3.14 (0.19), residues: 1679 helix: -2.14 (0.51), residues: 81 sheet: -2.01 (0.26), residues: 384 loop : -2.25 (0.16), residues: 1214 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP D 234 HIS 0.010 0.001 HIS A 609 PHE 0.022 0.002 PHE A 651 TYR 0.025 0.002 TYR A 38 ARG 0.010 0.001 ARG D 398 Details of bonding type rmsd link_NAG-ASN : bond 0.00760 ( 9) link_NAG-ASN : angle 3.74850 ( 27) hydrogen bonds : bond 0.04066 ( 231) hydrogen bonds : angle 7.55913 ( 564) SS BOND : bond 0.00287 ( 19) SS BOND : angle 1.38043 ( 38) covalent geometry : bond 0.00473 (14249) covalent geometry : angle 0.78189 (19308) Misc. bond : bond 0.00200 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3358 Ramachandran restraints generated. 1679 Oldfield, 0 Emsley, 1679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3358 Ramachandran restraints generated. 1679 Oldfield, 0 Emsley, 1679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 204 time to evaluate : 1.628 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 237 GLU cc_start: 0.3506 (mm-30) cc_final: 0.2750 (mm-30) REVERT: A 503 LEU cc_start: 0.7040 (OUTLIER) cc_final: 0.6648 (pt) REVERT: A 599 THR cc_start: 0.7866 (m) cc_final: 0.7468 (p) REVERT: B 1654 GLU cc_start: 0.7855 (tt0) cc_final: 0.6056 (pm20) REVERT: B 1691 GLU cc_start: 0.6415 (OUTLIER) cc_final: 0.6181 (tm-30) REVERT: B 1736 MET cc_start: 0.7365 (ttm) cc_final: 0.6205 (mpt) REVERT: B 1752 LYS cc_start: 0.7324 (mmpt) cc_final: 0.6966 (mmpt) REVERT: B 1811 ILE cc_start: 0.7826 (tp) cc_final: 0.7397 (mp) REVERT: B 1868 MET cc_start: 0.6817 (ttp) cc_final: 0.6389 (tpp) REVERT: B 1900 PHE cc_start: 0.7713 (OUTLIER) cc_final: 0.7472 (p90) REVERT: B 1939 MET cc_start: 0.5453 (OUTLIER) cc_final: 0.4274 (mpt) REVERT: B 2074 ARG cc_start: 0.5090 (mmt180) cc_final: 0.4691 (mmt-90) REVERT: D 177 ARG cc_start: 0.7537 (mpt90) cc_final: 0.7274 (mmp80) outliers start: 50 outliers final: 19 residues processed: 238 average time/residue: 1.0373 time to fit residues: 276.8467 Evaluate side-chains 197 residues out of total 1504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 174 time to evaluate : 1.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 ILE Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 240 SER Chi-restraints excluded: chain A residue 241 ILE Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 614 THR Chi-restraints excluded: chain A residue 621 GLU Chi-restraints excluded: chain B residue 1590 VAL Chi-restraints excluded: chain B residue 1691 GLU Chi-restraints excluded: chain B residue 1858 THR Chi-restraints excluded: chain B residue 1900 PHE Chi-restraints excluded: chain B residue 1939 MET Chi-restraints excluded: chain B residue 2063 TRP Chi-restraints excluded: chain B residue 2117 SER Chi-restraints excluded: chain B residue 2157 LYS Chi-restraints excluded: chain B residue 2186 LEU Chi-restraints excluded: chain D residue 256 ASN Chi-restraints excluded: chain D residue 273 ILE Chi-restraints excluded: chain D residue 297 VAL Chi-restraints excluded: chain D residue 354 ASP Chi-restraints excluded: chain D residue 392 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 105 optimal weight: 0.0770 chunk 10 optimal weight: 0.9980 chunk 153 optimal weight: 8.9990 chunk 75 optimal weight: 0.9980 chunk 114 optimal weight: 0.9990 chunk 3 optimal weight: 1.9990 chunk 112 optimal weight: 0.0670 chunk 128 optimal weight: 0.7980 chunk 109 optimal weight: 0.8980 chunk 168 optimal weight: 0.9990 chunk 121 optimal weight: 2.9990 overall best weight: 0.5676 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 73 HIS ** A 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 509 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 517 GLN ** B1815 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1817 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1819 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1829 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1863 ASN ** B1864 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2091 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 262 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 303 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4982 r_free = 0.4982 target = 0.169066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.4619 r_free = 0.4619 target = 0.141024 restraints weight = 35592.633| |-----------------------------------------------------------------------------| r_work (start): 0.4576 rms_B_bonded: 5.47 r_work (final): 0.4576 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6160 moved from start: 0.3342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 14278 Z= 0.159 Angle : 0.750 13.362 19373 Z= 0.373 Chirality : 0.049 0.353 2061 Planarity : 0.005 0.061 2479 Dihedral : 8.358 105.861 2075 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 22.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.24 % Favored : 89.76 % Rotamer: Outliers : 3.12 % Allowed : 18.55 % Favored : 78.32 % 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: -3.09 (0.19), residues: 1679 helix: -2.16 (0.49), residues: 86 sheet: -2.10 (0.25), residues: 391 loop : -2.16 (0.17), residues: 1202 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP B1665 HIS 0.009 0.001 HIS D 262 PHE 0.022 0.002 PHE A 651 TYR 0.022 0.002 TYR A 38 ARG 0.012 0.001 ARG D 398 Details of bonding type rmsd link_NAG-ASN : bond 0.00767 ( 9) link_NAG-ASN : angle 3.56710 ( 27) hydrogen bonds : bond 0.03608 ( 231) hydrogen bonds : angle 7.37929 ( 564) SS BOND : bond 0.00238 ( 19) SS BOND : angle 1.12340 ( 38) covalent geometry : bond 0.00369 (14249) covalent geometry : angle 0.73772 (19308) Misc. bond : bond 0.00185 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3358 Ramachandran restraints generated. 1679 Oldfield, 0 Emsley, 1679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3358 Ramachandran restraints generated. 1679 Oldfield, 0 Emsley, 1679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 204 time to evaluate : 1.483 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 233 SER cc_start: 0.5869 (m) cc_final: 0.5208 (p) REVERT: A 237 GLU cc_start: 0.3196 (mm-30) cc_final: 0.2813 (mm-30) REVERT: A 599 THR cc_start: 0.7627 (m) cc_final: 0.7297 (p) REVERT: B 1654 GLU cc_start: 0.7893 (tt0) cc_final: 0.6001 (pm20) REVERT: B 1736 MET cc_start: 0.7266 (ttm) cc_final: 0.6162 (mpt) REVERT: B 1811 ILE cc_start: 0.7959 (tp) cc_final: 0.7485 (mp) REVERT: B 1868 MET cc_start: 0.6711 (OUTLIER) cc_final: 0.6276 (tpp) REVERT: B 1883 MET cc_start: 0.4200 (ppp) cc_final: 0.3628 (ppp) REVERT: B 1939 MET cc_start: 0.5604 (OUTLIER) cc_final: 0.4561 (mpt) REVERT: B 1944 ILE cc_start: 0.6491 (mt) cc_final: 0.6192 (mt) REVERT: D 231 TRP cc_start: 0.7349 (t60) cc_final: 0.7099 (t60) REVERT: D 343 MET cc_start: 0.7148 (OUTLIER) cc_final: 0.6854 (ppp) outliers start: 47 outliers final: 17 residues processed: 234 average time/residue: 0.9828 time to fit residues: 260.3992 Evaluate side-chains 193 residues out of total 1504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 173 time to evaluate : 1.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 240 SER Chi-restraints excluded: chain A residue 241 ILE Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 289 GLN Chi-restraints excluded: chain A residue 431 VAL Chi-restraints excluded: chain A residue 517 GLN Chi-restraints excluded: chain B residue 1590 VAL Chi-restraints excluded: chain B residue 1868 MET Chi-restraints excluded: chain B residue 1939 MET Chi-restraints excluded: chain B residue 2033 CYS Chi-restraints excluded: chain B residue 2063 TRP Chi-restraints excluded: chain B residue 2110 THR Chi-restraints excluded: chain B residue 2117 SER Chi-restraints excluded: chain B residue 2157 LYS Chi-restraints excluded: chain B residue 2186 LEU Chi-restraints excluded: chain D residue 273 ILE Chi-restraints excluded: chain D residue 297 VAL Chi-restraints excluded: chain D residue 343 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 98 optimal weight: 0.9990 chunk 80 optimal weight: 0.6980 chunk 42 optimal weight: 1.9990 chunk 38 optimal weight: 0.0980 chunk 83 optimal weight: 0.3980 chunk 126 optimal weight: 5.9990 chunk 26 optimal weight: 0.9990 chunk 106 optimal weight: 0.6980 chunk 57 optimal weight: 0.9980 chunk 54 optimal weight: 2.9990 chunk 41 optimal weight: 0.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 HIS ** A 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 509 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 517 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1815 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1817 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1819 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1829 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1863 ASN ** B1864 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2091 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2093 GLN ** B2159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 262 HIS D 303 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4980 r_free = 0.4980 target = 0.169082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.4629 r_free = 0.4629 target = 0.141823 restraints weight = 35815.656| |-----------------------------------------------------------------------------| r_work (start): 0.4586 rms_B_bonded: 5.35 r_work (final): 0.4586 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6149 moved from start: 0.3638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 14278 Z= 0.151 Angle : 0.754 13.101 19373 Z= 0.372 Chirality : 0.049 0.349 2061 Planarity : 0.005 0.057 2479 Dihedral : 8.115 106.475 2073 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 21.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.07 % Favored : 89.93 % Rotamer: Outliers : 3.19 % Allowed : 20.01 % Favored : 76.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.06 (0.19), residues: 1679 helix: -2.16 (0.50), residues: 86 sheet: -2.07 (0.25), residues: 392 loop : -2.14 (0.17), residues: 1201 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP B1665 HIS 0.008 0.001 HIS A 242 PHE 0.021 0.002 PHE A 651 TYR 0.017 0.002 TYR A 120 ARG 0.009 0.001 ARG D 286 Details of bonding type rmsd link_NAG-ASN : bond 0.00742 ( 9) link_NAG-ASN : angle 3.43675 ( 27) hydrogen bonds : bond 0.03460 ( 231) hydrogen bonds : angle 7.19116 ( 564) SS BOND : bond 0.00222 ( 19) SS BOND : angle 0.99042 ( 38) covalent geometry : bond 0.00349 (14249) covalent geometry : angle 0.74321 (19308) Misc. bond : bond 0.00092 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3358 Ramachandran restraints generated. 1679 Oldfield, 0 Emsley, 1679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3358 Ramachandran restraints generated. 1679 Oldfield, 0 Emsley, 1679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 191 time to evaluate : 2.307 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 233 SER cc_start: 0.5575 (m) cc_final: 0.4936 (p) REVERT: A 237 GLU cc_start: 0.3092 (mm-30) cc_final: 0.2800 (mm-30) REVERT: A 367 MET cc_start: 0.5656 (mmt) cc_final: 0.5302 (mpp) REVERT: A 593 ILE cc_start: 0.8958 (OUTLIER) cc_final: 0.8753 (tp) REVERT: A 599 THR cc_start: 0.7587 (m) cc_final: 0.7320 (p) REVERT: B 1654 GLU cc_start: 0.7939 (tt0) cc_final: 0.6182 (pm20) REVERT: B 1658 TYR cc_start: 0.6371 (p90) cc_final: 0.5703 (p90) REVERT: B 1736 MET cc_start: 0.7159 (ttm) cc_final: 0.6034 (mmt) REVERT: B 1811 ILE cc_start: 0.7907 (tp) cc_final: 0.7449 (mp) REVERT: B 1868 MET cc_start: 0.6676 (OUTLIER) cc_final: 0.6378 (tpp) REVERT: B 1883 MET cc_start: 0.4134 (ppp) cc_final: 0.3775 (ppp) REVERT: B 1944 ILE cc_start: 0.6424 (mt) cc_final: 0.6073 (mt) REVERT: B 2074 ARG cc_start: 0.5277 (mmt180) cc_final: 0.4915 (mmt-90) REVERT: D 231 TRP cc_start: 0.7425 (t60) cc_final: 0.7126 (t60) REVERT: D 343 MET cc_start: 0.7109 (OUTLIER) cc_final: 0.6823 (ppp) outliers start: 48 outliers final: 26 residues processed: 220 average time/residue: 1.0042 time to fit residues: 249.4027 Evaluate side-chains 194 residues out of total 1504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 165 time to evaluate : 1.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 ILE Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 240 SER Chi-restraints excluded: chain A residue 241 ILE Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 289 GLN Chi-restraints excluded: chain A residue 431 VAL Chi-restraints excluded: chain A residue 519 VAL Chi-restraints excluded: chain A residue 565 VAL Chi-restraints excluded: chain A residue 593 ILE Chi-restraints excluded: chain B residue 1559 GLU Chi-restraints excluded: chain B residue 1590 VAL Chi-restraints excluded: chain B residue 1793 TYR Chi-restraints excluded: chain B residue 1817 HIS Chi-restraints excluded: chain B residue 1858 THR Chi-restraints excluded: chain B residue 1868 MET Chi-restraints excluded: chain B residue 2016 SER Chi-restraints excluded: chain B residue 2033 CYS Chi-restraints excluded: chain B residue 2063 TRP Chi-restraints excluded: chain B residue 2095 LEU Chi-restraints excluded: chain B residue 2110 THR Chi-restraints excluded: chain B residue 2117 SER Chi-restraints excluded: chain B residue 2157 LYS Chi-restraints excluded: chain B residue 2186 LEU Chi-restraints excluded: chain D residue 273 ILE Chi-restraints excluded: chain D residue 297 VAL Chi-restraints excluded: chain D residue 343 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 108 optimal weight: 0.0010 chunk 112 optimal weight: 1.9990 chunk 113 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 158 optimal weight: 4.9990 chunk 44 optimal weight: 0.7980 chunk 35 optimal weight: 0.9990 chunk 38 optimal weight: 5.9990 chunk 49 optimal weight: 2.9990 chunk 165 optimal weight: 4.9990 chunk 128 optimal weight: 1.9990 overall best weight: 1.1592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 509 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 517 GLN ** B1815 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1817 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1819 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1829 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1863 ASN ** B1864 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1913 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1940 GLN ** B2091 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4937 r_free = 0.4937 target = 0.165268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 85)----------------| | r_work = 0.4555 r_free = 0.4555 target = 0.136238 restraints weight = 35664.926| |-----------------------------------------------------------------------------| r_work (start): 0.4517 rms_B_bonded: 5.46 r_work (final): 0.4517 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6266 moved from start: 0.3954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 14278 Z= 0.198 Angle : 0.789 12.745 19373 Z= 0.393 Chirality : 0.050 0.342 2061 Planarity : 0.005 0.055 2479 Dihedral : 8.263 106.483 2073 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 24.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.78 % Favored : 89.22 % Rotamer: Outliers : 3.79 % Allowed : 21.01 % Favored : 75.20 % 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: -3.09 (0.19), residues: 1679 helix: -2.21 (0.48), residues: 86 sheet: -2.25 (0.25), residues: 391 loop : -2.10 (0.17), residues: 1202 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP B1665 HIS 0.006 0.001 HIS A 420 PHE 0.022 0.002 PHE A 651 TYR 0.020 0.002 TYR A 120 ARG 0.009 0.000 ARG D 286 Details of bonding type rmsd link_NAG-ASN : bond 0.00739 ( 9) link_NAG-ASN : angle 3.42618 ( 27) hydrogen bonds : bond 0.03558 ( 231) hydrogen bonds : angle 7.29503 ( 564) SS BOND : bond 0.00264 ( 19) SS BOND : angle 1.53553 ( 38) covalent geometry : bond 0.00458 (14249) covalent geometry : angle 0.77727 (19308) Misc. bond : bond 0.00127 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3358 Ramachandran restraints generated. 1679 Oldfield, 0 Emsley, 1679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3358 Ramachandran restraints generated. 1679 Oldfield, 0 Emsley, 1679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 188 time to evaluate : 1.438 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 237 GLU cc_start: 0.3110 (mm-30) cc_final: 0.1537 (mt-10) REVERT: A 270 MET cc_start: 0.6074 (OUTLIER) cc_final: 0.5747 (tpp) REVERT: A 447 VAL cc_start: 0.7173 (OUTLIER) cc_final: 0.6905 (p) REVERT: A 517 GLN cc_start: 0.7914 (OUTLIER) cc_final: 0.7672 (pm20) REVERT: A 581 GLN cc_start: 0.7266 (OUTLIER) cc_final: 0.6904 (tt0) REVERT: A 593 ILE cc_start: 0.8947 (OUTLIER) cc_final: 0.8715 (tp) REVERT: B 1654 GLU cc_start: 0.8093 (tt0) cc_final: 0.6283 (pm20) REVERT: B 1709 GLU cc_start: 0.6792 (tp30) cc_final: 0.6512 (mp0) REVERT: B 1736 MET cc_start: 0.7087 (ttm) cc_final: 0.5988 (mmt) REVERT: B 1752 LYS cc_start: 0.7280 (mmpt) cc_final: 0.7020 (mmpt) REVERT: B 1811 ILE cc_start: 0.7995 (tp) cc_final: 0.7567 (mp) REVERT: B 1868 MET cc_start: 0.6807 (OUTLIER) cc_final: 0.6488 (tpp) REVERT: B 1883 MET cc_start: 0.4102 (ppp) cc_final: 0.3523 (ppp) REVERT: B 1940 GLN cc_start: 0.8497 (tp40) cc_final: 0.8294 (tp-100) REVERT: B 1944 ILE cc_start: 0.6507 (OUTLIER) cc_final: 0.6168 (mt) REVERT: B 2074 ARG cc_start: 0.5313 (mmt180) cc_final: 0.4966 (mmt-90) REVERT: D 231 TRP cc_start: 0.7538 (t60) cc_final: 0.7291 (t60) outliers start: 57 outliers final: 31 residues processed: 226 average time/residue: 0.9792 time to fit residues: 250.9654 Evaluate side-chains 206 residues out of total 1504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 168 time to evaluate : 1.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 TRP Chi-restraints excluded: chain A residue 70 ILE Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 240 SER Chi-restraints excluded: chain A residue 241 ILE Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 270 MET Chi-restraints excluded: chain A residue 289 GLN Chi-restraints excluded: chain A residue 431 VAL Chi-restraints excluded: chain A residue 444 ILE Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 517 GLN Chi-restraints excluded: chain A residue 565 VAL Chi-restraints excluded: chain A residue 581 GLN Chi-restraints excluded: chain A residue 593 ILE Chi-restraints excluded: chain B residue 1559 GLU Chi-restraints excluded: chain B residue 1590 VAL Chi-restraints excluded: chain B residue 1793 TYR Chi-restraints excluded: chain B residue 1858 THR Chi-restraints excluded: chain B residue 1868 MET Chi-restraints excluded: chain B residue 1869 GLN Chi-restraints excluded: chain B residue 1889 ILE Chi-restraints excluded: chain B residue 1899 GLU Chi-restraints excluded: chain B residue 1939 MET Chi-restraints excluded: chain B residue 1944 ILE Chi-restraints excluded: chain B residue 2015 ILE Chi-restraints excluded: chain B residue 2016 SER Chi-restraints excluded: chain B residue 2033 CYS Chi-restraints excluded: chain B residue 2063 TRP Chi-restraints excluded: chain B residue 2110 THR Chi-restraints excluded: chain B residue 2117 SER Chi-restraints excluded: chain B residue 2157 LYS Chi-restraints excluded: chain B residue 2186 LEU Chi-restraints excluded: chain D residue 273 ILE Chi-restraints excluded: chain D residue 297 VAL Chi-restraints excluded: chain D residue 392 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 66 optimal weight: 0.3980 chunk 20 optimal weight: 1.9990 chunk 24 optimal weight: 0.5980 chunk 126 optimal weight: 4.9990 chunk 161 optimal weight: 1.9990 chunk 167 optimal weight: 0.0870 chunk 144 optimal weight: 0.8980 chunk 150 optimal weight: 8.9990 chunk 106 optimal weight: 0.5980 chunk 48 optimal weight: 0.0470 chunk 98 optimal weight: 0.5980 overall best weight: 0.3456 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 509 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 517 GLN ** A 639 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1815 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1817 HIS ** 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** B1863 ASN ** B1864 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2091 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4975 r_free = 0.4975 target = 0.168264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.4597 r_free = 0.4597 target = 0.138750 restraints weight = 35848.779| |-----------------------------------------------------------------------------| r_work (start): 0.4565 rms_B_bonded: 5.69 r_work (final): 0.4565 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6189 moved from start: 0.4112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 14278 Z= 0.143 Angle : 0.761 12.592 19373 Z= 0.376 Chirality : 0.049 0.341 2061 Planarity : 0.005 0.055 2479 Dihedral : 8.035 105.934 2073 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 21.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.01 % Favored : 89.99 % Rotamer: Outliers : 2.99 % Allowed : 23.07 % Favored : 73.94 % 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: -2.99 (0.19), residues: 1679 helix: -1.80 (0.54), residues: 74 sheet: -2.23 (0.25), residues: 396 loop : -2.03 (0.17), residues: 1209 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.060 0.002 TRP B1665 HIS 0.012 0.001 HIS B1817 PHE 0.024 0.002 PHE A 520 TYR 0.018 0.002 TYR A 120 ARG 0.009 0.000 ARG D 286 Details of bonding type rmsd link_NAG-ASN : bond 0.00723 ( 9) link_NAG-ASN : angle 3.31866 ( 27) hydrogen bonds : bond 0.03328 ( 231) hydrogen bonds : angle 7.12436 ( 564) SS BOND : bond 0.00323 ( 19) SS BOND : angle 1.33221 ( 38) covalent geometry : bond 0.00330 (14249) covalent geometry : angle 0.74974 (19308) Misc. bond : bond 0.00142 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3358 Ramachandran restraints generated. 1679 Oldfield, 0 Emsley, 1679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3358 Ramachandran restraints generated. 1679 Oldfield, 0 Emsley, 1679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 185 time to evaluate : 1.635 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 159 ILE cc_start: 0.7896 (OUTLIER) cc_final: 0.7600 (pp) REVERT: A 233 SER cc_start: 0.5250 (m) cc_final: 0.4698 (p) REVERT: A 237 GLU cc_start: 0.3024 (mm-30) cc_final: 0.1774 (mt-10) REVERT: A 292 MET cc_start: 0.6602 (tpt) cc_final: 0.6238 (tpp) REVERT: A 387 GLU cc_start: 0.6704 (pm20) cc_final: 0.6440 (pp20) REVERT: A 581 GLN cc_start: 0.7119 (tt0) cc_final: 0.6814 (tt0) REVERT: A 593 ILE cc_start: 0.8939 (OUTLIER) cc_final: 0.8685 (tp) REVERT: A 599 THR cc_start: 0.7458 (m) cc_final: 0.7151 (p) REVERT: A 607 LYS cc_start: 0.6988 (ttmt) cc_final: 0.6779 (tptm) REVERT: B 1584 ASP cc_start: 0.8368 (t0) cc_final: 0.7513 (m-30) REVERT: B 1654 GLU cc_start: 0.7997 (tt0) cc_final: 0.6181 (pm20) REVERT: B 1658 TYR cc_start: 0.6004 (p90) cc_final: 0.5559 (p90) REVERT: B 1736 MET cc_start: 0.7172 (ttm) cc_final: 0.5928 (mmt) REVERT: B 1783 MET cc_start: 0.6901 (mtt) cc_final: 0.6312 (mmt) REVERT: B 1811 ILE cc_start: 0.7922 (tp) cc_final: 0.7498 (mp) REVERT: B 1868 MET cc_start: 0.6704 (OUTLIER) cc_final: 0.6274 (tpp) REVERT: B 1883 MET cc_start: 0.3984 (ppp) cc_final: 0.3408 (ppp) REVERT: B 1900 PHE cc_start: 0.8031 (OUTLIER) cc_final: 0.7416 (p90) REVERT: B 1940 GLN cc_start: 0.8410 (tp40) cc_final: 0.8187 (tp-100) REVERT: B 1944 ILE cc_start: 0.6354 (OUTLIER) cc_final: 0.5966 (mt) REVERT: B 2015 ILE cc_start: 0.6570 (OUTLIER) cc_final: 0.6307 (pt) REVERT: B 2034 GLU cc_start: 0.8120 (mm-30) cc_final: 0.7878 (mm-30) REVERT: B 2074 ARG cc_start: 0.5160 (mmt180) cc_final: 0.4837 (mmt-90) REVERT: D 231 TRP cc_start: 0.7553 (t60) cc_final: 0.7305 (t60) REVERT: D 343 MET cc_start: 0.7199 (OUTLIER) cc_final: 0.6967 (ppp) outliers start: 45 outliers final: 25 residues processed: 215 average time/residue: 0.9897 time to fit residues: 241.3924 Evaluate side-chains 196 residues out of total 1504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 164 time to evaluate : 1.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 TRP Chi-restraints excluded: chain A residue 70 ILE Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 241 ILE Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 289 GLN Chi-restraints excluded: chain A residue 431 VAL Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 565 VAL Chi-restraints excluded: chain A residue 593 ILE Chi-restraints excluded: chain B residue 1559 GLU Chi-restraints excluded: chain B residue 1590 VAL Chi-restraints excluded: chain B residue 1691 GLU Chi-restraints excluded: chain B residue 1793 TYR Chi-restraints excluded: chain B residue 1817 HIS Chi-restraints excluded: chain B residue 1868 MET Chi-restraints excluded: chain B residue 1869 GLN Chi-restraints excluded: chain B residue 1889 ILE Chi-restraints excluded: chain B residue 1899 GLU Chi-restraints excluded: chain B residue 1900 PHE Chi-restraints excluded: chain B residue 1944 ILE Chi-restraints excluded: chain B residue 2015 ILE Chi-restraints excluded: chain B residue 2033 CYS Chi-restraints excluded: chain B residue 2110 THR Chi-restraints excluded: chain B residue 2117 SER Chi-restraints excluded: chain B residue 2157 LYS Chi-restraints excluded: chain D residue 273 ILE Chi-restraints excluded: chain D residue 297 VAL Chi-restraints excluded: chain D residue 343 MET Chi-restraints excluded: chain D residue 392 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 112 optimal weight: 3.9990 chunk 96 optimal weight: 0.0040 chunk 91 optimal weight: 1.9990 chunk 114 optimal weight: 0.7980 chunk 163 optimal weight: 2.9990 chunk 132 optimal weight: 7.9990 chunk 17 optimal weight: 0.4980 chunk 45 optimal weight: 0.4980 chunk 4 optimal weight: 2.9990 chunk 11 optimal weight: 0.8980 chunk 46 optimal weight: 2.9990 overall best weight: 0.5392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 51 GLN ** A 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 517 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 639 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1815 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1817 HIS ** 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** B1863 ASN ** B1864 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2091 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4974 r_free = 0.4974 target = 0.167729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.4616 r_free = 0.4616 target = 0.140131 restraints weight = 35038.143| |-----------------------------------------------------------------------------| r_work (start): 0.4568 rms_B_bonded: 5.30 r_work (final): 0.4568 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6166 moved from start: 0.4291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 14278 Z= 0.150 Angle : 0.780 12.354 19373 Z= 0.387 Chirality : 0.049 0.335 2061 Planarity : 0.005 0.057 2479 Dihedral : 7.998 106.661 2073 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 21.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.24 % Favored : 89.76 % Rotamer: Outliers : 2.73 % Allowed : 23.74 % Favored : 73.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -2.97 (0.19), residues: 1679 helix: -1.96 (0.51), residues: 80 sheet: -2.21 (0.25), residues: 394 loop : -2.00 (0.17), residues: 1205 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.002 TRP B1665 HIS 0.011 0.001 HIS B1817 PHE 0.022 0.002 PHE A 651 TYR 0.017 0.002 TYR A 120 ARG 0.009 0.000 ARG D 286 Details of bonding type rmsd link_NAG-ASN : bond 0.00702 ( 9) link_NAG-ASN : angle 3.22215 ( 27) hydrogen bonds : bond 0.03265 ( 231) hydrogen bonds : angle 7.04724 ( 564) SS BOND : bond 0.00261 ( 19) SS BOND : angle 1.40196 ( 38) covalent geometry : bond 0.00350 (14249) covalent geometry : angle 0.76946 (19308) Misc. bond : bond 0.00134 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3358 Ramachandran restraints generated. 1679 Oldfield, 0 Emsley, 1679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3358 Ramachandran restraints generated. 1679 Oldfield, 0 Emsley, 1679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 181 time to evaluate : 1.586 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 233 SER cc_start: 0.5179 (m) cc_final: 0.4667 (p) REVERT: A 237 GLU cc_start: 0.3131 (mm-30) cc_final: 0.1879 (mt-10) REVERT: A 387 GLU cc_start: 0.6671 (pm20) cc_final: 0.6402 (pp20) REVERT: A 581 GLN cc_start: 0.7104 (tt0) cc_final: 0.6829 (tt0) REVERT: A 593 ILE cc_start: 0.8935 (OUTLIER) cc_final: 0.8661 (tp) REVERT: A 607 LYS cc_start: 0.7094 (ttmt) cc_final: 0.6846 (tptm) REVERT: B 1584 ASP cc_start: 0.8341 (t0) cc_final: 0.7508 (m-30) REVERT: B 1654 GLU cc_start: 0.7952 (tt0) cc_final: 0.6291 (pm20) REVERT: B 1658 TYR cc_start: 0.5811 (p90) cc_final: 0.5582 (p90) REVERT: B 1736 MET cc_start: 0.7273 (ttm) cc_final: 0.5980 (mmt) REVERT: B 1752 LYS cc_start: 0.7228 (mmpt) cc_final: 0.6986 (mmpt) REVERT: B 1783 MET cc_start: 0.6764 (mtt) cc_final: 0.6222 (mmt) REVERT: B 1811 ILE cc_start: 0.7913 (tp) cc_final: 0.7509 (mp) REVERT: B 1868 MET cc_start: 0.6737 (OUTLIER) cc_final: 0.6445 (tpp) REVERT: B 1883 MET cc_start: 0.4231 (ppp) cc_final: 0.3613 (ppp) REVERT: B 1944 ILE cc_start: 0.6453 (mt) cc_final: 0.6054 (mt) REVERT: B 2063 TRP cc_start: 0.7567 (t-100) cc_final: 0.7114 (t60) REVERT: B 2074 ARG cc_start: 0.5183 (mmt180) cc_final: 0.4861 (mmt-90) REVERT: D 231 TRP cc_start: 0.7579 (t60) cc_final: 0.7315 (t60) REVERT: D 343 MET cc_start: 0.7208 (OUTLIER) cc_final: 0.6964 (ppp) outliers start: 41 outliers final: 26 residues processed: 211 average time/residue: 1.3162 time to fit residues: 317.1795 Evaluate side-chains 200 residues out of total 1504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 171 time to evaluate : 1.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 TRP Chi-restraints excluded: chain A residue 70 ILE Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 241 ILE Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 289 GLN Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 565 VAL Chi-restraints excluded: chain A residue 593 ILE Chi-restraints excluded: chain B residue 1559 GLU Chi-restraints excluded: chain B residue 1590 VAL Chi-restraints excluded: chain B residue 1691 GLU Chi-restraints excluded: chain B residue 1817 HIS Chi-restraints excluded: chain B residue 1868 MET Chi-restraints excluded: chain B residue 1869 GLN Chi-restraints excluded: chain B residue 1889 ILE Chi-restraints excluded: chain B residue 1899 GLU Chi-restraints excluded: chain B residue 1939 MET Chi-restraints excluded: chain B residue 2033 CYS Chi-restraints excluded: chain B residue 2110 THR Chi-restraints excluded: chain B residue 2117 SER Chi-restraints excluded: chain B residue 2157 LYS Chi-restraints excluded: chain C residue 119 SER Chi-restraints excluded: chain D residue 273 ILE Chi-restraints excluded: chain D residue 297 VAL Chi-restraints excluded: chain D residue 343 MET Chi-restraints excluded: chain D residue 392 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 88 optimal weight: 0.9990 chunk 23 optimal weight: 0.8980 chunk 29 optimal weight: 3.9990 chunk 28 optimal weight: 0.5980 chunk 167 optimal weight: 9.9990 chunk 93 optimal weight: 0.5980 chunk 26 optimal weight: 0.9990 chunk 124 optimal weight: 0.9980 chunk 71 optimal weight: 0.9980 chunk 125 optimal weight: 0.8980 chunk 104 optimal weight: 3.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 517 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 639 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1815 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1817 HIS ** 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** B1863 ASN ** B1864 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1913 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2091 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2159 HIS ** 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 = 0.4953 r_free = 0.4953 target = 0.166651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.4574 r_free = 0.4574 target = 0.137747 restraints weight = 35863.236| |-----------------------------------------------------------------------------| r_work (start): 0.4537 rms_B_bonded: 5.70 r_work (final): 0.4537 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6234 moved from start: 0.4448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 14278 Z= 0.168 Angle : 0.796 13.264 19373 Z= 0.394 Chirality : 0.049 0.330 2061 Planarity : 0.005 0.056 2479 Dihedral : 8.018 106.773 2073 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 22.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.48 % Favored : 89.52 % Rotamer: Outliers : 2.53 % Allowed : 24.40 % Favored : 73.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -2.96 (0.19), residues: 1679 helix: -1.97 (0.51), residues: 81 sheet: -2.21 (0.25), residues: 385 loop : -2.00 (0.17), residues: 1213 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.057 0.002 TRP B1665 HIS 0.011 0.001 HIS B1817 PHE 0.022 0.002 PHE A 651 TYR 0.018 0.002 TYR A 120 ARG 0.008 0.000 ARG D 286 Details of bonding type rmsd link_NAG-ASN : bond 0.00697 ( 9) link_NAG-ASN : angle 3.17772 ( 27) hydrogen bonds : bond 0.03375 ( 231) hydrogen bonds : angle 7.03576 ( 564) SS BOND : bond 0.00283 ( 19) SS BOND : angle 1.15684 ( 38) covalent geometry : bond 0.00389 (14249) covalent geometry : angle 0.78654 (19308) Misc. bond : bond 0.00125 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3358 Ramachandran restraints generated. 1679 Oldfield, 0 Emsley, 1679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3358 Ramachandran restraints generated. 1679 Oldfield, 0 Emsley, 1679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 177 time to evaluate : 1.592 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 LEU cc_start: 0.7315 (tm) cc_final: 0.7111 (tp) REVERT: A 233 SER cc_start: 0.5305 (m) cc_final: 0.4852 (p) REVERT: A 237 GLU cc_start: 0.3134 (mm-30) cc_final: 0.2924 (mm-30) REVERT: A 410 MET cc_start: 0.6946 (mmm) cc_final: 0.6322 (mtm) REVERT: A 581 GLN cc_start: 0.7151 (tt0) cc_final: 0.6870 (tt0) REVERT: A 593 ILE cc_start: 0.8941 (OUTLIER) cc_final: 0.8637 (tp) REVERT: A 607 LYS cc_start: 0.7105 (ttmt) cc_final: 0.6781 (tptm) REVERT: A 621 GLU cc_start: 0.6599 (tm-30) cc_final: 0.6168 (tt0) REVERT: B 1584 ASP cc_start: 0.8397 (t0) cc_final: 0.7587 (m-30) REVERT: B 1654 GLU cc_start: 0.8001 (tt0) cc_final: 0.6253 (pm20) REVERT: B 1658 TYR cc_start: 0.5936 (p90) cc_final: 0.5648 (p90) REVERT: B 1736 MET cc_start: 0.7125 (ttm) cc_final: 0.5997 (mpt) REVERT: B 1752 LYS cc_start: 0.7193 (mmpt) cc_final: 0.6925 (mmpt) REVERT: B 1783 MET cc_start: 0.6744 (mtt) cc_final: 0.6242 (mmt) REVERT: B 1810 ASP cc_start: 0.7336 (p0) cc_final: 0.7125 (p0) REVERT: B 1811 ILE cc_start: 0.7880 (tp) cc_final: 0.7437 (mp) REVERT: B 1817 HIS cc_start: 0.7817 (OUTLIER) cc_final: 0.7595 (m90) REVERT: B 1846 MET cc_start: 0.7193 (tpp) cc_final: 0.6846 (tpp) REVERT: B 1868 MET cc_start: 0.6712 (OUTLIER) cc_final: 0.6414 (tpp) REVERT: B 1883 MET cc_start: 0.4177 (ppp) cc_final: 0.3505 (ppp) REVERT: B 1940 GLN cc_start: 0.8236 (tp40) cc_final: 0.7956 (tp-100) REVERT: B 1944 ILE cc_start: 0.6386 (OUTLIER) cc_final: 0.6010 (mt) REVERT: B 2074 ARG cc_start: 0.5219 (mmt180) cc_final: 0.4915 (mmt-90) REVERT: D 175 MET cc_start: 0.8108 (mpp) cc_final: 0.7872 (tpp) REVERT: D 231 TRP cc_start: 0.7682 (t60) cc_final: 0.7404 (t60) outliers start: 38 outliers final: 28 residues processed: 204 average time/residue: 1.1108 time to fit residues: 256.2248 Evaluate side-chains 202 residues out of total 1504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 170 time to evaluate : 1.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 TRP Chi-restraints excluded: chain A residue 70 ILE Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 240 SER Chi-restraints excluded: chain A residue 241 ILE Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 289 GLN Chi-restraints excluded: chain A residue 380 THR Chi-restraints excluded: chain A residue 444 ILE Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 565 VAL Chi-restraints excluded: chain A residue 593 ILE Chi-restraints excluded: chain B residue 1559 GLU Chi-restraints excluded: chain B residue 1590 VAL Chi-restraints excluded: chain B residue 1691 GLU Chi-restraints excluded: chain B residue 1817 HIS Chi-restraints excluded: chain B residue 1868 MET Chi-restraints excluded: chain B residue 1869 GLN Chi-restraints excluded: chain B residue 1889 ILE Chi-restraints excluded: chain B residue 1899 GLU Chi-restraints excluded: chain B residue 1939 MET Chi-restraints excluded: chain B residue 1944 ILE Chi-restraints excluded: chain B residue 2033 CYS Chi-restraints excluded: chain B residue 2110 THR Chi-restraints excluded: chain B residue 2117 SER Chi-restraints excluded: chain B residue 2157 LYS Chi-restraints excluded: chain C residue 119 SER Chi-restraints excluded: chain D residue 273 ILE Chi-restraints excluded: chain D residue 297 VAL Chi-restraints excluded: chain D residue 392 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 128 optimal weight: 1.9990 chunk 137 optimal weight: 1.9990 chunk 102 optimal weight: 0.8980 chunk 28 optimal weight: 0.9980 chunk 136 optimal weight: 8.9990 chunk 26 optimal weight: 0.7980 chunk 81 optimal weight: 5.9990 chunk 118 optimal weight: 0.0000 chunk 116 optimal weight: 0.6980 chunk 142 optimal weight: 7.9990 chunk 41 optimal weight: 1.9990 overall best weight: 0.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 517 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 639 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1815 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1817 HIS ** 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** B1863 ASN ** B1864 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1913 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2091 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2159 HIS ** 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 = 0.4955 r_free = 0.4955 target = 0.166680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.4582 r_free = 0.4582 target = 0.138161 restraints weight = 35965.654| |-----------------------------------------------------------------------------| r_work (start): 0.4543 rms_B_bonded: 5.56 r_work (final): 0.4543 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6214 moved from start: 0.4617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 14278 Z= 0.161 Angle : 0.805 13.828 19373 Z= 0.398 Chirality : 0.049 0.323 2061 Planarity : 0.005 0.057 2479 Dihedral : 8.009 106.584 2073 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 22.25 Ramachandran Plot: Outliers : 0.06 % Allowed : 10.18 % Favored : 89.76 % Rotamer: Outliers : 2.46 % Allowed : 24.73 % Favored : 72.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -2.98 (0.19), residues: 1679 helix: -1.96 (0.51), residues: 81 sheet: -2.28 (0.25), residues: 384 loop : -1.99 (0.17), residues: 1214 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.059 0.002 TRP B1665 HIS 0.011 0.001 HIS B1817 PHE 0.023 0.002 PHE A 424 TYR 0.019 0.002 TYR A 120 ARG 0.009 0.001 ARG D 306 Details of bonding type rmsd link_NAG-ASN : bond 0.00679 ( 9) link_NAG-ASN : angle 3.15342 ( 27) hydrogen bonds : bond 0.03315 ( 231) hydrogen bonds : angle 7.02690 ( 564) SS BOND : bond 0.00331 ( 19) SS BOND : angle 1.42181 ( 38) covalent geometry : bond 0.00377 (14249) covalent geometry : angle 0.79496 (19308) Misc. bond : bond 0.00126 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3358 Ramachandran restraints generated. 1679 Oldfield, 0 Emsley, 1679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3358 Ramachandran restraints generated. 1679 Oldfield, 0 Emsley, 1679 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 177 time to evaluate : 1.445 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 233 SER cc_start: 0.5325 (m) cc_final: 0.4886 (p) REVERT: A 237 GLU cc_start: 0.3238 (mm-30) cc_final: 0.2999 (mm-30) REVERT: A 367 MET cc_start: 0.5706 (mmt) cc_final: 0.5253 (tpp) REVERT: A 410 MET cc_start: 0.6943 (mmm) cc_final: 0.6513 (mtm) REVERT: A 581 GLN cc_start: 0.7109 (tt0) cc_final: 0.6829 (tt0) REVERT: A 593 ILE cc_start: 0.8931 (OUTLIER) cc_final: 0.8645 (tp) REVERT: A 607 LYS cc_start: 0.7090 (ttmt) cc_final: 0.6737 (tptm) REVERT: A 621 GLU cc_start: 0.6571 (tm-30) cc_final: 0.6099 (tt0) REVERT: B 1584 ASP cc_start: 0.8360 (t0) cc_final: 0.7583 (m-30) REVERT: B 1654 GLU cc_start: 0.7995 (tt0) cc_final: 0.6265 (pm20) REVERT: B 1658 TYR cc_start: 0.5855 (p90) cc_final: 0.5534 (p90) REVERT: B 1736 MET cc_start: 0.7186 (ttm) cc_final: 0.5999 (mpt) REVERT: B 1783 MET cc_start: 0.6696 (mtt) cc_final: 0.6222 (mmt) REVERT: B 1810 ASP cc_start: 0.7278 (p0) cc_final: 0.7066 (p0) REVERT: B 1811 ILE cc_start: 0.7895 (tp) cc_final: 0.7448 (mp) REVERT: B 1817 HIS cc_start: 0.7762 (OUTLIER) cc_final: 0.7560 (m90) REVERT: B 1846 MET cc_start: 0.7276 (tpp) cc_final: 0.6942 (tpp) REVERT: B 1868 MET cc_start: 0.6696 (OUTLIER) cc_final: 0.6385 (tpp) REVERT: B 1883 MET cc_start: 0.4158 (ppp) cc_final: 0.3497 (ppp) REVERT: B 1900 PHE cc_start: 0.8030 (OUTLIER) cc_final: 0.7183 (p90) REVERT: B 1940 GLN cc_start: 0.8273 (tp40) cc_final: 0.8033 (tp-100) REVERT: B 1944 ILE cc_start: 0.6377 (OUTLIER) cc_final: 0.5998 (mt) REVERT: B 2074 ARG cc_start: 0.5254 (mmt180) cc_final: 0.4948 (mmt-90) REVERT: C 145 TRP cc_start: 0.4823 (p-90) cc_final: 0.4493 (p-90) REVERT: D 231 TRP cc_start: 0.7667 (t60) cc_final: 0.7450 (t60) REVERT: D 343 MET cc_start: 0.7213 (ppp) cc_final: 0.6243 (pp-130) outliers start: 37 outliers final: 26 residues processed: 202 average time/residue: 0.9031 time to fit residues: 207.1596 Evaluate side-chains 200 residues out of total 1504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 169 time to evaluate : 1.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 TRP Chi-restraints excluded: chain A residue 70 ILE Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 241 ILE Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 380 THR Chi-restraints excluded: chain A residue 444 ILE Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 565 VAL Chi-restraints excluded: chain A residue 593 ILE Chi-restraints excluded: chain B residue 1559 GLU Chi-restraints excluded: chain B residue 1590 VAL Chi-restraints excluded: chain B residue 1691 GLU Chi-restraints excluded: chain B residue 1817 HIS Chi-restraints excluded: chain B residue 1858 THR Chi-restraints excluded: chain B residue 1868 MET Chi-restraints excluded: chain B residue 1869 GLN Chi-restraints excluded: chain B residue 1889 ILE Chi-restraints excluded: chain B residue 1900 PHE Chi-restraints excluded: chain B residue 1944 ILE Chi-restraints excluded: chain B residue 2033 CYS Chi-restraints excluded: chain B residue 2110 THR Chi-restraints excluded: chain B residue 2117 SER Chi-restraints excluded: chain B residue 2157 LYS Chi-restraints excluded: chain C residue 119 SER Chi-restraints excluded: chain D residue 273 ILE Chi-restraints excluded: chain D residue 297 VAL Chi-restraints excluded: chain D residue 354 ASP Chi-restraints excluded: chain D residue 392 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 72 optimal weight: 0.9980 chunk 19 optimal weight: 0.8980 chunk 159 optimal weight: 0.4980 chunk 128 optimal weight: 0.9990 chunk 115 optimal weight: 0.6980 chunk 69 optimal weight: 3.9990 chunk 54 optimal weight: 0.9990 chunk 42 optimal weight: 2.9990 chunk 126 optimal weight: 0.8980 chunk 162 optimal weight: 3.9990 chunk 140 optimal weight: 9.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 517 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1645 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1815 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1817 HIS ** 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** B1863 ASN ** B1864 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1913 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2091 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 271 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4929 r_free = 0.4929 target = 0.165787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4560 r_free = 0.4560 target = 0.138245 restraints weight = 35587.849| |-----------------------------------------------------------------------------| r_work (start): 0.4529 rms_B_bonded: 5.30 r_work (final): 0.4529 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6207 moved from start: 0.4755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 14278 Z= 0.171 Angle : 0.806 11.866 19373 Z= 0.401 Chirality : 0.049 0.317 2061 Planarity : 0.005 0.066 2479 Dihedral : 8.000 106.626 2073 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 23.06 Ramachandran Plot: Outliers : 0.06 % Allowed : 10.54 % Favored : 89.40 % Rotamer: Outliers : 2.33 % Allowed : 24.60 % Favored : 73.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -2.99 (0.19), residues: 1679 helix: -1.97 (0.52), residues: 81 sheet: -2.28 (0.25), residues: 395 loop : -2.00 (0.17), residues: 1203 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.082 0.003 TRP B2180 HIS 0.011 0.001 HIS B1817 PHE 0.023 0.002 PHE A 424 TYR 0.021 0.002 TYR A 120 ARG 0.009 0.001 ARG D 286 Details of bonding type rmsd link_NAG-ASN : bond 0.00667 ( 9) link_NAG-ASN : angle 3.10803 ( 27) hydrogen bonds : bond 0.03387 ( 231) hydrogen bonds : angle 7.19031 ( 564) SS BOND : bond 0.00281 ( 19) SS BOND : angle 1.06162 ( 38) covalent geometry : bond 0.00398 (14249) covalent geometry : angle 0.79732 (19308) Misc. bond : bond 0.00125 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11329.01 seconds wall clock time: 199 minutes 11.65 seconds (11951.65 seconds total)