Starting phenix.real_space_refine on Fri Jul 3 11:48:17 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9mov_48439/07_2026/9mov_48439_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9mov_48439/07_2026/9mov_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 { model { file = "/net/cci-nas-00/data/ceres_data/9mov_48439/07_2026/9mov_48439_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9mov_48439/07_2026/9mov_48439_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9mov_48439/07_2026/9mov_48439.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9mov_48439/07_2026/9mov_48439.map" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/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, 14 Ad-hoc single atom residues: {' CA': 7} Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Chain breaks: 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: 2.89, per 1000 atoms: 0.21 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: 1.26 Conformation dependent library (CDL) restraints added in 662.3 milliseconds 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: 0.34 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: 2.35 Time building geometry restraints manager: 1.67 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: 7.150 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: 0.260 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 12.730 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.020 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:9.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4841 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.022 0.001 ARG C 9 TYR 0.016 0.002 TYR A 418 PHE 0.020 0.002 PHE A 154 TRP 0.027 0.002 TRP B1934 HIS 0.006 0.001 HIS B2159 Details of bonding type rmsd/Z covalent geometry : bond 0.00441 / 0.22 (14249) covalent geometry : angle 0.83260 / 0.44 (19308) SS BOND : bond 0.07410 / 5.97 ( 19) SS BOND : angle 2.10103 / 1.27 ( 38) hydrogen bonds : bond 0.16887 / 10.47 ( 231) hydrogen bonds : angle 8.57370 / 5.94 ( 564) Misc. bond : bond 0.13426 / 7.07 ( 1) link_NAG-ASN : bond 0.00833 / 0.37 ( 9) link_NAG-ASN : angle 4.83322 / 2.21 ( 27) *********************** 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 : 0.471 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: 0.6233 (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: 0.5447 (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: 0.6236 (m100) outliers start: 5 outliers final: 2 residues processed: 324 average time/residue: 0.4441 time to fit residues: 160.1726 Evaluate side-chains 198 residues out of total 1504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 196 time to evaluate : 0.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 98 optimal weight: 0.0970 chunk 107 optimal weight: 0.6980 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 0.0270 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 4.9990 chunk 91 optimal weight: 0.7980 chunk 149 optimal weight: 7.9990 overall best weight: 0.9238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 73 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** 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 B1955 HIS ** 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 = 0.5011 r_free = 0.5011 target = 0.171964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.4665 r_free = 0.4665 target = 0.140918 restraints weight = 34919.055| |-----------------------------------------------------------------------------| r_work (start): 0.4612 rms_B_bonded: 6.09 r_work (final): 0.4612 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4612 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4612 r_free = 0.4612 target_work(ls_wunit_k1) = 0.138 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4612 r_free = 0.4612 target_work(ls_wunit_k1) = 0.138 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (9 function evaluations) r_final: 0.4612 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6174 moved from start: 0.2401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 14278 Z= 0.190 Angle : 0.805 13.986 19373 Z= 0.405 Chirality : 0.051 0.360 2061 Planarity : 0.006 0.091 2479 Dihedral : 8.882 106.238 2077 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 22.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.96 % Favored : 89.04 % Rotamer: Outliers : 2.73 % Allowed : 13.50 % Favored : 83.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.10 (0.19), residues: 1679 helix: -2.04 (0.53), residues: 79 sheet: -1.97 (0.25), residues: 384 loop : -2.24 (0.17), residues: 1216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG D 286 TYR 0.036 0.002 TYR A 38 PHE 0.023 0.002 PHE A 424 TRP 0.025 0.002 TRP D 231 HIS 0.008 0.001 HIS A 609 Details of bonding type rmsd/Z covalent geometry : bond 0.00432 / 0.19 (14249) covalent geometry : angle 0.78771 / 0.40 (19308) SS BOND : bond 0.00472 / 0.25 ( 19) SS BOND : angle 1.98495 / 1.13 ( 38) hydrogen bonds : bond 0.04223 / 2.68 ( 231) hydrogen bonds : angle 7.78363 / 5.44 ( 564) Misc. bond : bond 0.00291 / 0.15 ( 1) link_NAG-ASN : bond 0.00763 / 0.29 ( 9) link_NAG-ASN : angle 4.02480 / 1.87 ( 27) *********************** 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 257 residues out of total 1504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 216 time to evaluate : 0.393 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 70 ILE cc_start: 0.6441 (OUTLIER) cc_final: 0.6065 (mp) REVERT: A 237 GLU cc_start: 0.3228 (mm-30) cc_final: 0.2471 (mm-30) REVERT: B 1654 GLU cc_start: 0.7633 (tt0) cc_final: 0.5971 (pm20) REVERT: B 1657 THR cc_start: 0.7904 (t) cc_final: 0.7564 (m) REVERT: B 1658 TYR cc_start: 0.6862 (p90) cc_final: 0.6506 (p90) REVERT: B 1736 MET cc_start: 0.7443 (ttm) cc_final: 0.6170 (mpt) REVERT: B 1752 LYS cc_start: 0.7274 (mmpt) cc_final: 0.7025 (mmpt) REVERT: B 1783 MET cc_start: 0.7115 (mpt) cc_final: 0.6526 (mmt) outliers start: 41 outliers final: 13 residues processed: 242 average time/residue: 0.4568 time to fit residues: 123.8171 Evaluate side-chains 190 residues out of total 1504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 176 time to evaluate : 0.487 ------------------------------------------------------------------------------- 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 519 VAL Chi-restraints excluded: chain A residue 614 THR Chi-restraints excluded: chain B residue 1793 TYR Chi-restraints excluded: chain B residue 2063 TRP Chi-restraints excluded: chain B residue 2117 SER 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 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 41 optimal weight: 0.8980 chunk 9 optimal weight: 0.2980 chunk 110 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 158 optimal weight: 3.9990 chunk 84 optimal weight: 0.9990 chunk 136 optimal weight: 20.0000 chunk 121 optimal weight: 2.9990 chunk 144 optimal weight: 0.8980 chunk 164 optimal weight: 5.9990 chunk 87 optimal weight: 0.5980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 73 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** B1670 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** B1863 ASN ** B1864 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2085 GLN ** B2091 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2162 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 = 0.4987 r_free = 0.4987 target = 0.170009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.4639 r_free = 0.4639 target = 0.141942 restraints weight = 34538.054| |-----------------------------------------------------------------------------| r_work (start): 0.4608 rms_B_bonded: 5.40 r_work (final): 0.4608 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6185 moved from start: 0.2936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 14278 Z= 0.171 Angle : 0.773 13.752 19373 Z= 0.386 Chirality : 0.050 0.359 2061 Planarity : 0.005 0.080 2479 Dihedral : 8.685 105.942 2075 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 22.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.77 % Favored : 90.23 % Rotamer: Outliers : 3.12 % Allowed : 16.02 % Favored : 80.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.09 (0.19), residues: 1679 helix: -2.10 (0.51), residues: 81 sheet: -2.01 (0.25), residues: 388 loop : -2.20 (0.17), residues: 1210 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 286 TYR 0.024 0.002 TYR A 38 PHE 0.022 0.002 PHE A 154 TRP 0.031 0.002 TRP D 234 HIS 0.011 0.001 HIS A 609 Details of bonding type rmsd/Z covalent geometry : bond 0.00397 / 0.17 (14249) covalent geometry : angle 0.75995 / 0.38 (19308) SS BOND : bond 0.00257 / 0.17 ( 19) SS BOND : angle 1.33566 / 0.78 ( 38) hydrogen bonds : bond 0.03879 / 2.45 ( 231) hydrogen bonds : angle 7.49035 / 5.16 ( 564) Misc. bond : bond 0.00209 / 0.11 ( 1) link_NAG-ASN : bond 0.00775 / 0.31 ( 9) link_NAG-ASN : angle 3.70368 / 1.70 ( 27) *********************** 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 248 residues out of total 1504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 201 time to evaluate : 0.599 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 237 GLU cc_start: 0.3169 (mm-30) cc_final: 0.2480 (mm-30) REVERT: B 1593 ARG cc_start: 0.6330 (OUTLIER) cc_final: 0.6106 (mtp85) REVERT: B 1654 GLU cc_start: 0.7755 (tt0) cc_final: 0.6186 (pm20) REVERT: B 1657 THR cc_start: 0.7889 (t) cc_final: 0.7583 (m) REVERT: B 1658 TYR cc_start: 0.6867 (p90) cc_final: 0.6531 (p90) REVERT: B 1736 MET cc_start: 0.7398 (ttm) cc_final: 0.6138 (mmt) REVERT: B 1783 MET cc_start: 0.7249 (OUTLIER) cc_final: 0.6581 (mmt) REVERT: B 1811 ILE cc_start: 0.7854 (tp) cc_final: 0.7386 (mp) REVERT: D 187 LEU cc_start: 0.9033 (mt) cc_final: 0.8810 (mp) REVERT: D 231 TRP cc_start: 0.7397 (t60) cc_final: 0.7151 (t60) outliers start: 47 outliers final: 18 residues processed: 230 average time/residue: 0.4997 time to fit residues: 128.7102 Evaluate side-chains 191 residues out of total 1504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 171 time to evaluate : 0.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 B residue 1590 VAL Chi-restraints excluded: chain B residue 1593 ARG Chi-restraints excluded: chain B residue 1783 MET Chi-restraints excluded: chain B residue 1793 TYR Chi-restraints excluded: chain B residue 1899 GLU Chi-restraints excluded: chain B residue 2029 GLU 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 141 optimal weight: 0.0570 chunk 32 optimal weight: 2.9990 chunk 50 optimal weight: 5.9990 chunk 120 optimal weight: 0.3980 chunk 51 optimal weight: 0.9990 chunk 107 optimal weight: 2.9990 chunk 104 optimal weight: 0.3980 chunk 7 optimal weight: 2.9990 chunk 136 optimal weight: 20.0000 chunk 118 optimal weight: 5.9990 chunk 128 optimal weight: 0.6980 overall best weight: 0.5100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 517 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 597 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** B1863 ASN ** B1864 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2085 GLN ** 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 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 = 0.4997 r_free = 0.4997 target = 0.170801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.4645 r_free = 0.4645 target = 0.142330 restraints weight = 34712.721| |-----------------------------------------------------------------------------| r_work (start): 0.4617 rms_B_bonded: 5.46 r_work (final): 0.4617 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6164 moved from start: 0.3371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 14278 Z= 0.148 Angle : 0.741 13.421 19373 Z= 0.368 Chirality : 0.049 0.354 2061 Planarity : 0.005 0.067 2479 Dihedral : 8.466 105.652 2075 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 21.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.01 % Favored : 89.99 % Rotamer: Outliers : 3.39 % Allowed : 18.42 % Favored : 78.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.06 (0.19), residues: 1679 helix: -2.10 (0.50), residues: 86 sheet: -2.07 (0.25), residues: 394 loop : -2.14 (0.17), residues: 1199 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 608 TYR 0.018 0.002 TYR A 7 PHE 0.020 0.002 PHE A 651 TRP 0.032 0.002 TRP D 205 HIS 0.010 0.001 HIS A 609 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.15 (14249) covalent geometry : angle 0.72884 / 0.37 (19308) SS BOND : bond 0.00473 / 0.25 ( 19) SS BOND : angle 1.03030 / 0.62 ( 38) hydrogen bonds : bond 0.03474 / 2.17 ( 231) hydrogen bonds : angle 7.26958 / 5.00 ( 564) Misc. bond : bond 0.00186 / 0.10 ( 1) link_NAG-ASN : bond 0.00773 / 0.32 ( 9) link_NAG-ASN : angle 3.54202 / 1.62 ( 27) *********************** 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 249 residues out of total 1504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 198 time to evaluate : 0.455 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: 0.5504 (m) cc_final: 0.4815 (p) REVERT: A 237 GLU cc_start: 0.3138 (mm-30) cc_final: 0.2759 (mm-30) REVERT: A 599 THR cc_start: 0.7727 (m) cc_final: 0.7330 (p) REVERT: B 1654 GLU cc_start: 0.7830 (tt0) cc_final: 0.6101 (pm20) REVERT: B 1658 TYR cc_start: 0.6829 (p90) cc_final: 0.6467 (p90) REVERT: B 1736 MET cc_start: 0.7277 (ttm) cc_final: 0.6126 (mmt) REVERT: B 1783 MET cc_start: 0.7272 (mpt) cc_final: 0.6564 (mmt) REVERT: B 1811 ILE cc_start: 0.7991 (tp) cc_final: 0.7499 (mp) REVERT: B 1883 MET cc_start: 0.4095 (ppp) cc_final: 0.3538 (ppp) REVERT: B 1944 ILE cc_start: 0.6409 (mt) cc_final: 0.6152 (mt) REVERT: B 2034 GLU cc_start: 0.7680 (mm-30) cc_final: 0.7450 (mm-30) REVERT: D 187 LEU cc_start: 0.9072 (mt) cc_final: 0.8828 (mp) REVERT: D 231 TRP cc_start: 0.7479 (t60) cc_final: 0.7208 (t60) REVERT: D 343 MET cc_start: 0.6866 (OUTLIER) cc_final: 0.6582 (ppp) outliers start: 51 outliers final: 22 residues processed: 230 average time/residue: 0.4496 time to fit residues: 116.5828 Evaluate side-chains 199 residues out of total 1504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 176 time to evaluate : 0.536 ------------------------------------------------------------------------------- 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 335 TYR Chi-restraints excluded: chain A residue 431 VAL Chi-restraints excluded: chain A residue 621 GLU Chi-restraints excluded: chain B residue 1590 VAL Chi-restraints excluded: chain B residue 1793 TYR Chi-restraints excluded: chain B residue 1899 GLU Chi-restraints excluded: chain B residue 2016 SER 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 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 65 optimal weight: 0.7980 chunk 149 optimal weight: 1.9990 chunk 162 optimal weight: 9.9990 chunk 154 optimal weight: 2.9990 chunk 83 optimal weight: 2.9990 chunk 81 optimal weight: 0.0570 chunk 164 optimal weight: 8.9990 chunk 89 optimal weight: 0.0970 chunk 151 optimal weight: 6.9990 chunk 71 optimal weight: 2.9990 chunk 119 optimal weight: 7.9990 overall best weight: 1.1900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 51 GLN A 73 HIS ** A 85 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 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 251 ASN A 315 GLN ** A 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 509 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 517 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** B1829 HIS 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 303 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4935 r_free = 0.4935 target = 0.165269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4570 r_free = 0.4570 target = 0.136639 restraints weight = 34827.557| |-----------------------------------------------------------------------------| r_work (start): 0.4544 rms_B_bonded: 5.51 r_work (final): 0.4544 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6301 moved from start: 0.3848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 14278 Z= 0.204 Angle : 0.786 12.946 19373 Z= 0.394 Chirality : 0.049 0.344 2061 Planarity : 0.005 0.061 2479 Dihedral : 8.476 106.565 2073 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 24.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.38 % Favored : 88.62 % Rotamer: Outliers : 4.06 % Allowed : 20.15 % Favored : 75.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.13 (0.19), residues: 1679 helix: -2.27 (0.48), residues: 87 sheet: -2.15 (0.25), residues: 389 loop : -2.17 (0.17), residues: 1203 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 317 TYR 0.019 0.002 TYR A 120 PHE 0.022 0.002 PHE A 651 TRP 0.035 0.002 TRP D 372 HIS 0.008 0.001 HIS B1817 Details of bonding type rmsd/Z covalent geometry : bond 0.00464 / 0.20 (14249) covalent geometry : angle 0.77514 / 0.39 (19308) SS BOND : bond 0.00426 / 0.24 ( 19) SS BOND : angle 1.11274 / 0.65 ( 38) hydrogen bonds : bond 0.03744 / 2.36 ( 231) hydrogen bonds : angle 7.31250 / 5.05 ( 564) Misc. bond : bond 0.00157 / 0.08 ( 1) link_NAG-ASN : bond 0.00750 / 0.30 ( 9) link_NAG-ASN : angle 3.48361 / 1.60 ( 27) *********************** 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 260 residues out of total 1504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 199 time to evaluate : 0.428 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: 0.3192 (mm-30) cc_final: 0.1621 (mt-10) REVERT: A 599 THR cc_start: 0.7702 (m) cc_final: 0.7361 (p) REVERT: B 1584 ASP cc_start: 0.8409 (t0) cc_final: 0.7608 (m-30) REVERT: B 1654 GLU cc_start: 0.8102 (tt0) cc_final: 0.6285 (pm20) REVERT: B 1658 TYR cc_start: 0.6911 (p90) cc_final: 0.6402 (p90) REVERT: B 1709 GLU cc_start: 0.6764 (tp30) cc_final: 0.6489 (mp0) REVERT: B 1736 MET cc_start: 0.7142 (ttm) cc_final: 0.5981 (mmt) REVERT: B 1752 LYS cc_start: 0.7337 (mmpt) cc_final: 0.7056 (mmpt) REVERT: B 1811 ILE cc_start: 0.8008 (tp) cc_final: 0.7550 (mp) REVERT: B 1817 HIS cc_start: 0.7672 (OUTLIER) cc_final: 0.7429 (m90) REVERT: B 1855 LEU cc_start: 0.7145 (tp) cc_final: 0.6935 (tp) REVERT: B 1939 MET cc_start: 0.5784 (OUTLIER) cc_final: 0.4672 (mpt) REVERT: B 1944 ILE cc_start: 0.6384 (mt) cc_final: 0.6079 (mt) REVERT: B 2034 GLU cc_start: 0.8046 (mm-30) cc_final: 0.7808 (mm-30) REVERT: D 177 ARG cc_start: 0.7446 (mpt90) cc_final: 0.7218 (mmp80) REVERT: D 231 TRP cc_start: 0.7519 (t60) cc_final: 0.7227 (t60) REVERT: D 343 MET cc_start: 0.7037 (OUTLIER) cc_final: 0.6818 (ppp) outliers start: 61 outliers final: 25 residues processed: 240 average time/residue: 0.4380 time to fit residues: 119.2803 Evaluate side-chains 203 residues out of total 1504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 175 time to evaluate : 0.533 ------------------------------------------------------------------------------- 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 335 TYR Chi-restraints excluded: chain A residue 431 VAL Chi-restraints excluded: chain A residue 444 ILE Chi-restraints excluded: chain A residue 565 VAL 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 1939 MET Chi-restraints excluded: chain B residue 1967 VAL Chi-restraints excluded: chain B residue 2016 SER 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 2184 ILE Chi-restraints excluded: chain B residue 2186 LEU Chi-restraints excluded: chain D residue 256 ASN 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 53 optimal weight: 0.6980 chunk 98 optimal weight: 0.6980 chunk 130 optimal weight: 1.9990 chunk 142 optimal weight: 5.9990 chunk 55 optimal weight: 8.9990 chunk 38 optimal weight: 3.9990 chunk 107 optimal weight: 0.7980 chunk 168 optimal weight: 2.9990 chunk 74 optimal weight: 0.9990 chunk 140 optimal weight: 20.0000 chunk 166 optimal weight: 0.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 85 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 420 HIS ** A 509 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 517 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 581 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** ** 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** ** C 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 303 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4959 r_free = 0.4959 target = 0.166558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4602 r_free = 0.4602 target = 0.138586 restraints weight = 34817.843| |-----------------------------------------------------------------------------| r_work (start): 0.4547 rms_B_bonded: 5.45 r_work (final): 0.4547 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6260 moved from start: 0.4135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 14278 Z= 0.172 Angle : 0.768 12.773 19373 Z= 0.384 Chirality : 0.049 0.341 2061 Planarity : 0.005 0.055 2479 Dihedral : 8.343 105.708 2073 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 22.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.54 % Favored : 89.46 % Rotamer: Outliers : 3.26 % Allowed : 22.54 % Favored : 74.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.14 (0.19), residues: 1679 helix: -2.08 (0.49), residues: 86 sheet: -2.24 (0.25), residues: 395 loop : -2.16 (0.17), residues: 1198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 286 TYR 0.022 0.002 TYR A 120 PHE 0.023 0.002 PHE A 651 TRP 0.035 0.002 TRP D 372 HIS 0.010 0.001 HIS B1817 Details of bonding type rmsd/Z covalent geometry : bond 0.00401 / 0.17 (14249) covalent geometry : angle 0.75755 / 0.38 (19308) SS BOND : bond 0.00382 / 0.21 ( 19) SS BOND : angle 1.11758 / 0.65 ( 38) hydrogen bonds : bond 0.03555 / 2.26 ( 231) hydrogen bonds : angle 7.26151 / 5.03 ( 564) Misc. bond : bond 0.00121 / 0.06 ( 1) link_NAG-ASN : bond 0.00720 / 0.28 ( 9) link_NAG-ASN : angle 3.39908 / 1.56 ( 27) *********************** 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 239 residues out of total 1504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 190 time to evaluate : 0.455 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 192 GLU cc_start: 0.7444 (OUTLIER) cc_final: 0.7240 (mm-30) REVERT: A 233 SER cc_start: 0.5387 (m) cc_final: 0.4778 (p) REVERT: A 237 GLU cc_start: 0.3039 (mm-30) cc_final: 0.1763 (mt-10) REVERT: A 270 MET cc_start: 0.6075 (OUTLIER) cc_final: 0.5843 (tpp) REVERT: A 599 THR cc_start: 0.7620 (m) cc_final: 0.7307 (p) REVERT: B 1584 ASP cc_start: 0.8462 (t0) cc_final: 0.7565 (m-30) REVERT: B 1654 GLU cc_start: 0.8079 (tt0) cc_final: 0.6256 (pm20) REVERT: B 1658 TYR cc_start: 0.6844 (p90) cc_final: 0.6387 (p90) REVERT: B 1709 GLU cc_start: 0.6767 (tp30) cc_final: 0.6475 (mp0) REVERT: B 1736 MET cc_start: 0.6773 (ttm) cc_final: 0.5940 (mmt) REVERT: B 1811 ILE cc_start: 0.7953 (tp) cc_final: 0.7537 (mp) REVERT: B 1817 HIS cc_start: 0.7638 (OUTLIER) cc_final: 0.7399 (m90) REVERT: B 1883 MET cc_start: 0.3772 (ppp) cc_final: 0.3026 (ppp) REVERT: B 1939 MET cc_start: 0.5757 (OUTLIER) cc_final: 0.4918 (mpt) REVERT: B 1944 ILE cc_start: 0.6303 (mt) cc_final: 0.5895 (mt) REVERT: B 2034 GLU cc_start: 0.8020 (mm-30) cc_final: 0.7788 (mm-30) REVERT: B 2074 ARG cc_start: 0.5212 (mmt180) cc_final: 0.4931 (mmt-90) REVERT: D 177 ARG cc_start: 0.7507 (mpt90) cc_final: 0.7232 (mmp80) REVERT: D 192 LYS cc_start: 0.9167 (mmpt) cc_final: 0.8958 (mmpt) REVERT: D 231 TRP cc_start: 0.7545 (t60) cc_final: 0.7221 (t60) REVERT: D 239 ASP cc_start: 0.6842 (t0) cc_final: 0.6624 (t0) outliers start: 49 outliers final: 26 residues processed: 223 average time/residue: 0.3851 time to fit residues: 97.5376 Evaluate side-chains 203 residues out of total 1504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 173 time to evaluate : 0.477 ------------------------------------------------------------------------------- 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 192 GLU 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 447 VAL Chi-restraints excluded: chain A residue 565 VAL 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 1869 GLN Chi-restraints excluded: chain B residue 1889 ILE 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 B residue 2184 ILE 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 165 optimal weight: 8.9990 chunk 84 optimal weight: 2.9990 chunk 125 optimal weight: 2.9990 chunk 48 optimal weight: 0.8980 chunk 83 optimal weight: 3.9990 chunk 43 optimal weight: 4.9990 chunk 128 optimal weight: 0.6980 chunk 19 optimal weight: 0.3980 chunk 96 optimal weight: 0.9990 chunk 53 optimal weight: 1.9990 chunk 58 optimal weight: 0.8980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 85 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 517 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 581 GLN ** 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** ** 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** ** C 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4957 r_free = 0.4957 target = 0.166333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4595 r_free = 0.4595 target = 0.138017 restraints weight = 35007.131| |-----------------------------------------------------------------------------| r_work (start): 0.4550 rms_B_bonded: 5.52 r_work (final): 0.4550 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6284 moved from start: 0.4302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 14278 Z= 0.169 Angle : 0.784 12.475 19373 Z= 0.391 Chirality : 0.049 0.338 2061 Planarity : 0.005 0.053 2479 Dihedral : 8.281 105.907 2073 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 22.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.54 % Favored : 89.46 % Rotamer: Outliers : 3.06 % Allowed : 23.94 % Favored : 73.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.16 (0.19), residues: 1679 helix: -1.95 (0.51), residues: 81 sheet: -2.37 (0.24), residues: 389 loop : -2.14 (0.17), residues: 1209 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG D 286 TYR 0.021 0.002 TYR A 120 PHE 0.023 0.002 PHE A 651 TRP 0.059 0.002 TRP B1665 HIS 0.010 0.001 HIS B1817 Details of bonding type rmsd/Z covalent geometry : bond 0.00393 / 0.17 (14249) covalent geometry : angle 0.77262 / 0.39 (19308) SS BOND : bond 0.00371 / 0.26 ( 19) SS BOND : angle 1.41886 / 0.87 ( 38) hydrogen bonds : bond 0.03395 / 2.15 ( 231) hydrogen bonds : angle 7.20203 / 4.98 ( 564) Misc. bond : bond 0.00131 / 0.07 ( 1) link_NAG-ASN : bond 0.00708 / 0.28 ( 9) link_NAG-ASN : angle 3.30906 / 1.52 ( 27) *********************** 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 233 residues out of total 1504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 187 time to evaluate : 0.523 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: 0.3193 (mm-30) cc_final: 0.1739 (mt-10) REVERT: A 270 MET cc_start: 0.6088 (OUTLIER) cc_final: 0.5801 (tpp) REVERT: A 292 MET cc_start: 0.6739 (tpt) cc_final: 0.6313 (tpp) REVERT: A 593 ILE cc_start: 0.8963 (OUTLIER) cc_final: 0.8716 (tp) REVERT: B 1584 ASP cc_start: 0.8364 (t0) cc_final: 0.7527 (m-30) REVERT: B 1654 GLU cc_start: 0.8106 (tt0) cc_final: 0.6422 (pm20) REVERT: B 1658 TYR cc_start: 0.6913 (p90) cc_final: 0.6574 (p90) REVERT: B 1709 GLU cc_start: 0.6732 (tp30) cc_final: 0.6485 (mp0) REVERT: B 1736 MET cc_start: 0.6805 (ttm) cc_final: 0.6023 (mmt) REVERT: B 1752 LYS cc_start: 0.7238 (mmpt) cc_final: 0.6970 (mmpt) REVERT: B 1810 ASP cc_start: 0.7340 (p0) cc_final: 0.7137 (p0) REVERT: B 1811 ILE cc_start: 0.7848 (tp) cc_final: 0.7426 (mp) REVERT: B 1817 HIS cc_start: 0.7743 (OUTLIER) cc_final: 0.7538 (m90) REVERT: B 1883 MET cc_start: 0.4030 (ppp) cc_final: 0.3344 (ppp) REVERT: B 1939 MET cc_start: 0.5699 (OUTLIER) cc_final: 0.4653 (mpt) REVERT: B 1944 ILE cc_start: 0.6268 (mt) cc_final: 0.5867 (mt) REVERT: B 2034 GLU cc_start: 0.7987 (mm-30) cc_final: 0.7782 (mm-30) REVERT: D 177 ARG cc_start: 0.7532 (mpt90) cc_final: 0.7301 (mmp80) REVERT: D 192 LYS cc_start: 0.9138 (mmpt) cc_final: 0.8900 (mmpt) REVERT: D 231 TRP cc_start: 0.7581 (t60) cc_final: 0.7244 (t60) REVERT: D 239 ASP cc_start: 0.6761 (t0) cc_final: 0.6542 (t0) REVERT: D 300 TRP cc_start: 0.4943 (OUTLIER) cc_final: 0.3790 (m100) REVERT: D 343 MET cc_start: 0.7189 (OUTLIER) cc_final: 0.6931 (ppp) outliers start: 46 outliers final: 27 residues processed: 218 average time/residue: 0.4302 time to fit residues: 106.0596 Evaluate side-chains 204 residues out of total 1504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 171 time to evaluate : 0.477 ------------------------------------------------------------------------------- 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 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 1793 TYR Chi-restraints excluded: chain B residue 1817 HIS Chi-restraints excluded: chain B residue 1869 GLN Chi-restraints excluded: chain B residue 1889 ILE Chi-restraints excluded: chain B residue 1939 MET 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 B residue 2184 ILE Chi-restraints excluded: chain B residue 2186 LEU Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 273 ILE Chi-restraints excluded: chain D residue 297 VAL Chi-restraints excluded: chain D residue 300 TRP 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 155 optimal weight: 5.9990 chunk 88 optimal weight: 0.1980 chunk 25 optimal weight: 1.9990 chunk 124 optimal weight: 6.9990 chunk 70 optimal weight: 2.9990 chunk 126 optimal weight: 0.9990 chunk 80 optimal weight: 0.9990 chunk 165 optimal weight: 0.7980 chunk 74 optimal weight: 1.9990 chunk 3 optimal weight: 0.5980 chunk 23 optimal weight: 0.6980 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 85 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 517 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 581 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** ** 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** ** C 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4960 r_free = 0.4960 target = 0.166839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.4602 r_free = 0.4602 target = 0.138583 restraints weight = 35100.266| |-----------------------------------------------------------------------------| r_work (start): 0.4563 rms_B_bonded: 5.34 r_work (final): 0.4563 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6248 moved from start: 0.4471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 14278 Z= 0.159 Angle : 0.778 12.244 19373 Z= 0.389 Chirality : 0.049 0.337 2061 Planarity : 0.005 0.058 2479 Dihedral : 8.154 105.855 2073 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 22.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.48 % Favored : 89.52 % Rotamer: Outliers : 3.12 % Allowed : 24.07 % Favored : 72.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.16 (0.19), residues: 1679 helix: -1.94 (0.54), residues: 75 sheet: -2.36 (0.24), residues: 391 loop : -2.15 (0.17), residues: 1213 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 286 TYR 0.020 0.002 TYR A 38 PHE 0.023 0.002 PHE A 651 TRP 0.037 0.002 TRP D 234 HIS 0.010 0.001 HIS B1817 Details of bonding type rmsd/Z covalent geometry : bond 0.00373 / 0.16 (14249) covalent geometry : angle 0.76696 / 0.39 (19308) SS BOND : bond 0.00276 / 0.18 ( 19) SS BOND : angle 1.40049 / 0.84 ( 38) hydrogen bonds : bond 0.03363 / 2.10 ( 231) hydrogen bonds : angle 7.17396 / 4.96 ( 564) Misc. bond : bond 0.00162 / 0.09 ( 1) link_NAG-ASN : bond 0.00702 / 0.28 ( 9) link_NAG-ASN : angle 3.23556 / 1.48 ( 27) *********************** 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 229 residues out of total 1504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 182 time to evaluate : 0.367 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 233 SER cc_start: 0.5363 (m) cc_final: 0.4902 (p) REVERT: A 237 GLU cc_start: 0.3130 (mm-30) cc_final: 0.1889 (mt-10) REVERT: A 292 MET cc_start: 0.6665 (tpt) cc_final: 0.6339 (tpp) REVERT: A 410 MET cc_start: 0.7129 (mmm) cc_final: 0.6519 (mtm) REVERT: A 593 ILE cc_start: 0.8961 (OUTLIER) cc_final: 0.8682 (tp) REVERT: B 1584 ASP cc_start: 0.8265 (t0) cc_final: 0.7531 (m-30) REVERT: B 1654 GLU cc_start: 0.8053 (tt0) cc_final: 0.6196 (pm20) REVERT: B 1658 TYR cc_start: 0.6827 (p90) cc_final: 0.6464 (p90) REVERT: B 1709 GLU cc_start: 0.6599 (tp30) cc_final: 0.6387 (mp0) REVERT: B 1736 MET cc_start: 0.6775 (ttm) cc_final: 0.5907 (mmt) REVERT: B 1811 ILE cc_start: 0.7943 (tp) cc_final: 0.7504 (mp) REVERT: B 1817 HIS cc_start: 0.7682 (OUTLIER) cc_final: 0.7460 (m90) REVERT: B 1883 MET cc_start: 0.3952 (ppp) cc_final: 0.3427 (ppp) REVERT: B 1944 ILE cc_start: 0.6266 (OUTLIER) cc_final: 0.5893 (mt) REVERT: B 2074 ARG cc_start: 0.5139 (mmt180) cc_final: 0.4886 (mmt-90) REVERT: C 145 TRP cc_start: 0.4351 (p-90) cc_final: 0.3985 (p-90) REVERT: D 177 ARG cc_start: 0.7676 (mpt90) cc_final: 0.7381 (mmp80) REVERT: D 192 LYS cc_start: 0.9228 (mmpt) cc_final: 0.9002 (mmpt) REVERT: D 231 TRP cc_start: 0.7621 (t60) cc_final: 0.7300 (t60) REVERT: D 239 ASP cc_start: 0.7249 (t0) cc_final: 0.7017 (t0) REVERT: D 300 TRP cc_start: 0.4894 (OUTLIER) cc_final: 0.3847 (m100) REVERT: D 343 MET cc_start: 0.7147 (OUTLIER) cc_final: 0.6859 (ppp) outliers start: 47 outliers final: 28 residues processed: 209 average time/residue: 0.4036 time to fit residues: 95.8172 Evaluate side-chains 202 residues out of total 1504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 169 time to evaluate : 0.375 ------------------------------------------------------------------------------- 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 158 LEU 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 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 1793 TYR Chi-restraints excluded: chain B residue 1813 VAL Chi-restraints excluded: chain B residue 1817 HIS Chi-restraints excluded: chain B residue 1858 THR Chi-restraints excluded: chain B residue 1869 GLN Chi-restraints excluded: chain B residue 1889 ILE Chi-restraints excluded: chain B residue 1944 ILE Chi-restraints excluded: chain B residue 2033 CYS Chi-restraints excluded: chain B residue 2068 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 2184 ILE Chi-restraints excluded: chain B residue 2186 LEU Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 273 ILE Chi-restraints excluded: chain D residue 297 VAL Chi-restraints excluded: chain D residue 300 TRP 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 38 optimal weight: 6.9990 chunk 51 optimal weight: 0.0980 chunk 149 optimal weight: 0.9990 chunk 93 optimal weight: 0.0980 chunk 127 optimal weight: 0.8980 chunk 121 optimal weight: 4.9990 chunk 140 optimal weight: 5.9990 chunk 50 optimal weight: 0.9980 chunk 142 optimal weight: 4.9990 chunk 130 optimal weight: 2.9990 chunk 17 optimal weight: 0.5980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 85 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 517 GLN ** A 581 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** ** B1857 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1863 ASN ** B1864 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1894 GLN ** 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** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4959 r_free = 0.4959 target = 0.167080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.4596 r_free = 0.4596 target = 0.138698 restraints weight = 34985.614| |-----------------------------------------------------------------------------| r_work (start): 0.4565 rms_B_bonded: 5.48 r_work (final): 0.4565 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6236 moved from start: 0.4610 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= 0.152 Angle : 0.800 15.225 19373 Z= 0.395 Chirality : 0.049 0.327 2061 Planarity : 0.005 0.053 2479 Dihedral : 8.073 106.162 2073 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 21.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.30 % Favored : 89.70 % Rotamer: Outliers : 2.66 % Allowed : 25.07 % Favored : 72.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.12 (0.19), residues: 1679 helix: -1.94 (0.53), residues: 81 sheet: -2.34 (0.24), residues: 390 loop : -2.11 (0.17), residues: 1208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B1907 TYR 0.018 0.002 TYR A 38 PHE 0.022 0.002 PHE A 651 TRP 0.046 0.002 TRP D 234 HIS 0.011 0.001 HIS B1817 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.15 (14249) covalent geometry : angle 0.78993 / 0.39 (19308) SS BOND : bond 0.00291 / 0.20 ( 19) SS BOND : angle 1.40300 / 0.86 ( 38) hydrogen bonds : bond 0.03264 / 2.07 ( 231) hydrogen bonds : angle 7.08147 / 4.90 ( 564) Misc. bond : bond 0.00144 / 0.08 ( 1) link_NAG-ASN : bond 0.00680 / 0.28 ( 9) link_NAG-ASN : angle 3.18079 / 1.47 ( 27) *********************** 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 224 residues out of total 1504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 184 time to evaluate : 0.528 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 233 SER cc_start: 0.5354 (m) cc_final: 0.4938 (p) REVERT: A 237 GLU cc_start: 0.3092 (mm-30) cc_final: 0.1872 (mt-10) REVERT: A 292 MET cc_start: 0.6665 (tpt) cc_final: 0.6369 (tpp) REVERT: A 410 MET cc_start: 0.7113 (mmm) cc_final: 0.6747 (mtm) REVERT: A 593 ILE cc_start: 0.8942 (OUTLIER) cc_final: 0.8660 (tp) REVERT: B 1584 ASP cc_start: 0.8247 (t0) cc_final: 0.7555 (m-30) REVERT: B 1654 GLU cc_start: 0.8042 (tt0) cc_final: 0.6313 (pm20) REVERT: B 1658 TYR cc_start: 0.6766 (p90) cc_final: 0.6419 (p90) REVERT: B 1736 MET cc_start: 0.6975 (ttm) cc_final: 0.5828 (mmt) REVERT: B 1752 LYS cc_start: 0.7217 (mmpt) cc_final: 0.7002 (mmpt) REVERT: B 1811 ILE cc_start: 0.7938 (tp) cc_final: 0.7490 (mp) REVERT: B 1817 HIS cc_start: 0.7798 (OUTLIER) cc_final: 0.7570 (m90) REVERT: B 1846 MET cc_start: 0.7095 (tpp) cc_final: 0.5314 (mpp) REVERT: B 1883 MET cc_start: 0.3947 (ppp) cc_final: 0.3421 (ppp) REVERT: B 1944 ILE cc_start: 0.6206 (OUTLIER) cc_final: 0.5877 (mt) REVERT: B 2074 ARG cc_start: 0.5204 (mmt180) cc_final: 0.4958 (mmt-90) REVERT: C 145 TRP cc_start: 0.4465 (p-90) cc_final: 0.4053 (p-90) REVERT: D 177 ARG cc_start: 0.7624 (mpt90) cc_final: 0.7344 (mmp80) REVERT: D 192 LYS cc_start: 0.9219 (mmpt) cc_final: 0.8992 (mmpt) REVERT: D 231 TRP cc_start: 0.7639 (t60) cc_final: 0.7334 (t60) REVERT: D 239 ASP cc_start: 0.7314 (t0) cc_final: 0.7020 (t0) REVERT: D 300 TRP cc_start: 0.5002 (OUTLIER) cc_final: 0.3998 (m100) REVERT: D 343 MET cc_start: 0.7075 (OUTLIER) cc_final: 0.6794 (ppp) REVERT: D 404 HIS cc_start: 0.8796 (m-70) cc_final: 0.8585 (m-70) outliers start: 40 outliers final: 27 residues processed: 210 average time/residue: 0.3858 time to fit residues: 92.0842 Evaluate side-chains 200 residues out of total 1504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 168 time to evaluate : 0.523 ------------------------------------------------------------------------------- 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 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 1793 TYR Chi-restraints excluded: chain B residue 1813 VAL Chi-restraints excluded: chain B residue 1817 HIS Chi-restraints excluded: chain B residue 1858 THR Chi-restraints excluded: chain B residue 1869 GLN Chi-restraints excluded: chain B residue 1889 ILE 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 B residue 2184 ILE Chi-restraints excluded: chain B residue 2186 LEU Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 273 ILE Chi-restraints excluded: chain D residue 297 VAL Chi-restraints excluded: chain D residue 300 TRP Chi-restraints excluded: chain D residue 343 MET 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 7 optimal weight: 4.9990 chunk 87 optimal weight: 0.7980 chunk 12 optimal weight: 0.7980 chunk 14 optimal weight: 2.9990 chunk 26 optimal weight: 0.9990 chunk 37 optimal weight: 0.0770 chunk 34 optimal weight: 5.9990 chunk 161 optimal weight: 0.8980 chunk 160 optimal weight: 6.9990 chunk 103 optimal weight: 4.9990 chunk 129 optimal weight: 1.9990 overall best weight: 0.7140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 85 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 581 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** ** 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** ** C 102 ASN ** 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 = 0.4956 r_free = 0.4956 target = 0.166560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4590 r_free = 0.4590 target = 0.137925 restraints weight = 34949.556| |-----------------------------------------------------------------------------| r_work (start): 0.4554 rms_B_bonded: 5.49 r_work (final): 0.4554 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6260 moved from start: 0.4788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 14278 Z= 0.164 Angle : 0.806 13.758 19373 Z= 0.400 Chirality : 0.049 0.320 2061 Planarity : 0.005 0.055 2479 Dihedral : 8.076 106.775 2073 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 22.44 Ramachandran Plot: Outliers : 0.06 % Allowed : 10.66 % Favored : 89.28 % Rotamer: Outliers : 2.79 % Allowed : 25.07 % Favored : 72.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.13 (0.19), residues: 1679 helix: -2.12 (0.53), residues: 81 sheet: -2.37 (0.24), residues: 395 loop : -2.09 (0.17), residues: 1203 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B1907 TYR 0.020 0.002 TYR A 120 PHE 0.022 0.002 PHE A 651 TRP 0.051 0.002 TRP D 234 HIS 0.011 0.001 HIS B1817 Details of bonding type rmsd/Z covalent geometry : bond 0.00383 / 0.16 (14249) covalent geometry : angle 0.79665 / 0.40 (19308) SS BOND : bond 0.00294 / 0.20 ( 19) SS BOND : angle 1.21188 / 0.72 ( 38) hydrogen bonds : bond 0.03286 / 2.08 ( 231) hydrogen bonds : angle 7.04000 / 4.88 ( 564) Misc. bond : bond 0.00130 / 0.07 ( 1) link_NAG-ASN : bond 0.00670 / 0.27 ( 9) link_NAG-ASN : angle 3.11828 / 1.45 ( 27) ********************** 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 215 residues out of total 1504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 173 time to evaluate : 0.535 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 233 SER cc_start: 0.5358 (m) cc_final: 0.4936 (p) REVERT: A 237 GLU cc_start: 0.3106 (mm-30) cc_final: 0.2894 (mm-30) REVERT: A 292 MET cc_start: 0.6760 (tpt) cc_final: 0.6476 (tpp) REVERT: A 410 MET cc_start: 0.7118 (mmm) cc_final: 0.6830 (mtm) REVERT: A 593 ILE cc_start: 0.8947 (OUTLIER) cc_final: 0.8663 (tp) REVERT: B 1584 ASP cc_start: 0.8261 (t0) cc_final: 0.7576 (m-30) REVERT: B 1654 GLU cc_start: 0.8083 (tt0) cc_final: 0.6288 (pm20) REVERT: B 1658 TYR cc_start: 0.6818 (p90) cc_final: 0.6460 (p90) REVERT: B 1736 MET cc_start: 0.6987 (ttm) cc_final: 0.5808 (mmt) REVERT: B 1810 ASP cc_start: 0.7304 (p0) cc_final: 0.7094 (p0) REVERT: B 1811 ILE cc_start: 0.7907 (tp) cc_final: 0.7449 (mp) REVERT: B 1817 HIS cc_start: 0.7833 (OUTLIER) cc_final: 0.7621 (m90) REVERT: B 1846 MET cc_start: 0.7242 (tpp) cc_final: 0.5185 (mpp) REVERT: B 1883 MET cc_start: 0.3944 (ppp) cc_final: 0.3355 (ppp) REVERT: B 1944 ILE cc_start: 0.6374 (OUTLIER) cc_final: 0.6065 (mt) REVERT: B 2074 ARG cc_start: 0.5219 (mmt180) cc_final: 0.4976 (mmt-90) REVERT: C 145 TRP cc_start: 0.4323 (p-90) cc_final: 0.4002 (p-90) REVERT: D 177 ARG cc_start: 0.7618 (mpt90) cc_final: 0.7357 (mmp80) REVERT: D 192 LYS cc_start: 0.9193 (mmpt) cc_final: 0.8961 (mmpt) REVERT: D 231 TRP cc_start: 0.7684 (t60) cc_final: 0.7406 (t60) REVERT: D 239 ASP cc_start: 0.7188 (t0) cc_final: 0.6869 (t0) REVERT: D 343 MET cc_start: 0.7100 (OUTLIER) cc_final: 0.6860 (ppp) outliers start: 42 outliers final: 26 residues processed: 200 average time/residue: 0.3932 time to fit residues: 90.1294 Evaluate side-chains 199 residues out of total 1504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 169 time to evaluate : 0.607 ------------------------------------------------------------------------------- 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 1813 VAL Chi-restraints excluded: chain B residue 1817 HIS Chi-restraints excluded: chain B residue 1858 THR Chi-restraints excluded: chain B residue 1869 GLN Chi-restraints excluded: chain B residue 1889 ILE Chi-restraints excluded: chain B residue 1944 ILE Chi-restraints excluded: chain B residue 2033 CYS Chi-restraints excluded: chain B residue 2068 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 219 LEU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 113 optimal weight: 0.9980 chunk 68 optimal weight: 0.4980 chunk 153 optimal weight: 2.9990 chunk 151 optimal weight: 0.9990 chunk 8 optimal weight: 0.5980 chunk 141 optimal weight: 1.9990 chunk 61 optimal weight: 0.9980 chunk 54 optimal weight: 0.0980 chunk 25 optimal weight: 0.7980 chunk 149 optimal weight: 0.9990 chunk 37 optimal weight: 0.0370 overall best weight: 0.4058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 85 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 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** ** 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** ** C 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4979 r_free = 0.4979 target = 0.168308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4616 r_free = 0.4616 target = 0.140509 restraints weight = 34667.524| |-----------------------------------------------------------------------------| r_work (start): 0.4575 rms_B_bonded: 5.39 r_work (final): 0.4575 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6178 moved from start: 0.4874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14278 Z= 0.141 Angle : 0.785 13.481 19373 Z= 0.388 Chirality : 0.049 0.317 2061 Planarity : 0.005 0.089 2479 Dihedral : 7.908 106.645 2073 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 20.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.77 % Favored : 90.23 % Rotamer: Outliers : 2.19 % Allowed : 25.80 % Favored : 72.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.14 (0.19), residues: 1679 helix: -2.13 (0.50), residues: 87 sheet: -2.33 (0.24), residues: 411 loop : -2.10 (0.17), residues: 1181 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 81 TYR 0.021 0.002 TYR B1565 PHE 0.021 0.002 PHE A 651 TRP 0.052 0.002 TRP D 234 HIS 0.011 0.001 HIS B1817 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.14 (14249) covalent geometry : angle 0.77674 / 0.39 (19308) SS BOND : bond 0.00289 / 0.18 ( 19) SS BOND : angle 1.03577 / 0.59 ( 38) hydrogen bonds : bond 0.03220 / 2.04 ( 231) hydrogen bonds : angle 6.92210 / 4.79 ( 564) Misc. bond : bond 0.00126 / 0.07 ( 1) link_NAG-ASN : bond 0.00658 / 0.27 ( 9) link_NAG-ASN : angle 3.02644 / 1.40 ( 27) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4629.24 seconds wall clock time: 80 minutes 3.61 seconds (4803.61 seconds total)