Starting phenix.real_space_refine on Thu Sep 18 04:26:42 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9mov_48439/09_2025/9mov_48439_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9mov_48439/09_2025/9mov_48439.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9mov_48439/09_2025/9mov_48439_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9mov_48439/09_2025/9mov_48439_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9mov_48439/09_2025/9mov_48439.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9mov_48439/09_2025/9mov_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-2.0-5805/lib/python3.9/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, 21 Unusual residues: {' CA': 7, 'NAG': 1} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Residues with excluded nonbonded symmetry interactions: 1 residue: pdb="CA CA C 204 " occ=0.40 Time building chain proxies: 3.38, per 1000 atoms: 0.24 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: 1.20 Conformation dependent library (CDL) restraints added in 605.2 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.53 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: 2.60 Time building geometry restraints manager: 1.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 4413 1.34 - 1.46: 3316 1.46 - 1.58: 6396 1.58 - 1.71: 0 1.71 - 1.83: 124 Bond restraints: 14249 Sorted by residual: bond pdb=" CG CGU C 26 " pdb=" CD2 CGU C 26 " ideal model delta sigma weight residual 1.544 1.470 0.074 2.00e-02 2.50e+03 1.37e+01 bond pdb=" CG CGU C 19 " pdb=" CD2 CGU C 19 " ideal model delta sigma weight residual 1.544 1.478 0.066 2.00e-02 2.50e+03 1.09e+01 bond pdb=" CG CGU C 25 " pdb=" CD2 CGU C 25 " ideal model delta sigma weight residual 1.544 1.481 0.063 2.00e-02 2.50e+03 9.93e+00 bond pdb=" N VAL C 45 " pdb=" CA VAL C 45 " ideal model delta sigma weight residual 1.459 1.497 -0.038 1.25e-02 6.40e+03 9.09e+00 bond pdb=" N LYS A 499 " pdb=" CA LYS A 499 " ideal model delta sigma weight residual 1.453 1.488 -0.035 1.22e-02 6.72e+03 8.17e+00 ... (remaining 14244 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.58: 18962 2.58 - 5.16: 303 5.16 - 7.73: 29 7.73 - 10.31: 8 10.31 - 12.89: 6 Bond angle restraints: 19308 Sorted by residual: angle pdb=" CA ASP A 504 " pdb=" CB ASP A 504 " pdb=" CG ASP A 504 " ideal model delta sigma weight residual 112.60 119.14 -6.54 1.00e+00 1.00e+00 4.28e+01 angle pdb=" C SER B2183 " pdb=" CA SER B2183 " pdb=" CB SER B2183 " ideal model delta sigma weight residual 115.79 110.38 5.41 1.19e+00 7.06e-01 2.07e+01 angle pdb=" C ASP B1661 " pdb=" N SER B1662 " pdb=" CA SER B1662 " ideal model delta sigma weight residual 120.97 133.86 -12.89 2.84e+00 1.24e-01 2.06e+01 angle pdb=" CD1 CGU C 7 " pdb=" CG CGU C 7 " pdb=" CD2 CGU C 7 " ideal model delta sigma weight residual 106.66 117.94 -11.28 3.00e+00 1.11e-01 1.41e+01 angle pdb=" CD1 CGU C 14 " pdb=" CG CGU C 14 " pdb=" CD2 CGU C 14 " ideal model delta sigma weight residual 106.66 117.78 -11.12 3.00e+00 1.11e-01 1.37e+01 ... (remaining 19303 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.26: 8027 21.26 - 42.51: 533 42.51 - 63.77: 47 63.77 - 85.02: 27 85.02 - 106.28: 4 Dihedral angle restraints: 8638 sinusoidal: 3672 harmonic: 4966 Sorted by residual: dihedral pdb=" CB CYS D 331 " pdb=" SG CYS D 331 " pdb=" SG CYS D 345 " pdb=" CB CYS D 345 " ideal model delta sinusoidal sigma weight residual 93.00 157.97 -64.97 1 1.00e+01 1.00e-02 5.54e+01 dihedral pdb=" CB CYS D 196 " pdb=" SG CYS D 196 " pdb=" SG CYS D 212 " pdb=" CB CYS D 212 " ideal model delta sinusoidal sigma weight residual 93.00 40.24 52.76 1 1.00e+01 1.00e-02 3.79e+01 dihedral pdb=" CA HIS A 362 " pdb=" C HIS A 362 " pdb=" N TYR A 363 " pdb=" CA TYR A 363 " ideal model delta harmonic sigma weight residual 180.00 -153.12 -26.88 0 5.00e+00 4.00e-02 2.89e+01 ... (remaining 8635 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.079: 1787 0.079 - 0.158: 248 0.158 - 0.237: 19 0.237 - 0.316: 2 0.316 - 0.395: 5 Chirality restraints: 2061 Sorted by residual: chirality pdb=" CA LEU C 5 " pdb=" N LEU C 5 " pdb=" C LEU C 5 " pdb=" CB LEU C 5 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.89e+00 chirality pdb=" CA CGU C 7 " pdb=" N CGU C 7 " pdb=" C CGU C 7 " pdb=" CB CGU C 7 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.72e+00 chirality pdb=" CA ILE C 21 " pdb=" N ILE C 21 " pdb=" C ILE C 21 " pdb=" CB ILE C 21 " both_signs ideal model delta sigma weight residual False 2.43 2.80 -0.37 2.00e-01 2.50e+01 3.44e+00 ... (remaining 2058 not shown) Planarity restraints: 2488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG D 501 " 0.266 2.00e-02 2.50e+03 2.23e-01 6.20e+02 pdb=" C7 NAG D 501 " -0.070 2.00e-02 2.50e+03 pdb=" C8 NAG D 501 " 0.176 2.00e-02 2.50e+03 pdb=" N2 NAG D 501 " -0.376 2.00e-02 2.50e+03 pdb=" O7 NAG D 501 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN D 248 " 0.015 2.00e-02 2.50e+03 8.92e-02 9.94e+01 pdb=" CG ASN D 248 " 0.029 2.00e-02 2.50e+03 pdb=" OD1 ASN D 248 " -0.085 2.00e-02 2.50e+03 pdb=" ND2 ASN D 248 " 0.144 2.00e-02 2.50e+03 pdb=" C1 NAG D 501 " -0.103 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG CGU C 26 " -0.015 2.00e-02 2.50e+03 2.99e-02 8.95e+00 pdb=" CD2 CGU C 26 " 0.052 2.00e-02 2.50e+03 pdb="OE21 CGU C 26 " -0.019 2.00e-02 2.50e+03 pdb="OE22 CGU C 26 " -0.018 2.00e-02 2.50e+03 ... (remaining 2485 not shown) Histogram of nonbonded interaction distances: 1.01 - 1.79: 4 1.79 - 2.57: 51 2.57 - 3.34: 18039 3.34 - 4.12: 34993 4.12 - 4.90: 61753 Nonbonded interactions: 114840 Sorted by model distance: nonbonded pdb=" O CYS C 98 " pdb=" NH1 ARG D 286 " model vdw 1.010 3.120 nonbonded pdb=" O CYS C 98 " pdb=" CZ ARG D 286 " model vdw 1.159 3.270 nonbonded pdb=" OH TYR C 108 " pdb=" O LEU D 278 " model vdw 1.278 3.040 nonbonded pdb=" C CYS C 98 " pdb=" NH1 ARG D 286 " model vdw 1.557 3.350 nonbonded pdb=" C CYS C 98 " pdb=" CZ ARG D 286 " model vdw 1.916 3.500 ... (remaining 114835 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.40 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.270 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: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 14.240 Find NCS groups from input model: 0.100 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: 0.010 Load rotamer database and sin/cos tables:6.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4825 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.322 14278 Z= 0.283 Angle : 0.856 14.813 19373 Z= 0.446 Chirality : 0.056 0.395 2061 Planarity : 0.007 0.223 2479 Dihedral : 13.825 106.278 5391 Min Nonbonded Distance : 1.010 Molprobity Statistics. All-atom Clashscore : 19.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.61 % Favored : 88.39 % Rotamer: Outliers : 0.33 % Allowed : 0.40 % Favored : 99.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.02 (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 covalent geometry : bond 0.00441 (14249) covalent geometry : angle 0.83260 (19308) SS BOND : bond 0.07410 ( 19) SS BOND : angle 2.10103 ( 38) hydrogen bonds : bond 0.16887 ( 231) hydrogen bonds : angle 8.57370 ( 564) Misc. bond : bond 0.13426 ( 1) link_NAG-ASN : bond 0.00833 ( 9) link_NAG-ASN : angle 4.83322 ( 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 : 0.530 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 158 LEU cc_start: 0.7152 (mt) cc_final: 0.6221 (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: 0.7144 (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: 0.5422 time to fit residues: 194.5624 Evaluate side-chains 200 residues out of total 1504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 198 time to evaluate : 0.491 ------------------------------------------------------------------------------- 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: 0.9990 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: 2.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 4.9990 chunk 91 optimal weight: 0.8980 chunk 149 optimal weight: 7.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 509 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 556 ASN 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1829 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1863 ASN ** B1955 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2091 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4940 r_free = 0.4940 target = 0.166413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4568 r_free = 0.4568 target = 0.137929 restraints weight = 35247.130| |-----------------------------------------------------------------------------| r_work (start): 0.4527 rms_B_bonded: 5.23 r_work (final): 0.4527 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4526 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4526 r_free = 0.4526 target_work(ls_wunit_k1) = 0.133 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4526 r_free = 0.4526 target_work(ls_wunit_k1) = 0.133 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.4526 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6249 moved from start: 0.2746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 14278 Z= 0.262 Angle : 0.851 13.847 19373 Z= 0.433 Chirality : 0.053 0.358 2061 Planarity : 0.006 0.095 2479 Dihedral : 8.898 106.361 2077 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 26.03 Ramachandran Plot: Outliers : 0.06 % Allowed : 11.79 % Favored : 88.15 % Rotamer: Outliers : 3.12 % Allowed : 13.70 % Favored : 83.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.24 (0.19), residues: 1679 helix: -2.24 (0.50), residues: 81 sheet: -2.13 (0.25), residues: 391 loop : -2.30 (0.16), residues: 1207 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 118 TYR 0.028 0.003 TYR A 38 PHE 0.024 0.003 PHE A 424 TRP 0.027 0.002 TRP B1665 HIS 0.009 0.002 HIS A 609 Details of bonding type rmsd covalent geometry : bond 0.00586 (14249) covalent geometry : angle 0.83569 (19308) SS BOND : bond 0.00522 ( 19) SS BOND : angle 1.73206 ( 38) hydrogen bonds : bond 0.04443 ( 231) hydrogen bonds : angle 8.00033 ( 564) Misc. bond : bond 0.00066 ( 1) link_NAG-ASN : bond 0.00823 ( 9) link_NAG-ASN : angle 4.06181 ( 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 265 residues out of total 1504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 218 time to evaluate : 0.623 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: 0.3543 (mm-30) cc_final: 0.2761 (mm-30) REVERT: B 1654 GLU cc_start: 0.7932 (tt0) cc_final: 0.6187 (pm20) REVERT: B 1658 TYR cc_start: 0.7149 (p90) cc_final: 0.6622 (p90) REVERT: B 1736 MET cc_start: 0.7452 (ttm) cc_final: 0.6299 (mpt) REVERT: B 1773 LYS cc_start: 0.3962 (OUTLIER) cc_final: 0.3741 (pmtt) REVERT: B 1783 MET cc_start: 0.7140 (OUTLIER) cc_final: 0.6548 (mmt) REVERT: B 1900 PHE cc_start: 0.7920 (OUTLIER) cc_final: 0.7403 (p90) REVERT: B 2035 VAL cc_start: 0.8168 (OUTLIER) cc_final: 0.7880 (t) outliers start: 47 outliers final: 17 residues processed: 247 average time/residue: 0.5504 time to fit residues: 151.0274 Evaluate side-chains 197 residues out of total 1504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 176 time to evaluate : 0.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 ILE Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 240 SER Chi-restraints excluded: chain A residue 241 ILE Chi-restraints excluded: chain A residue 519 VAL Chi-restraints excluded: chain A residue 614 THR Chi-restraints excluded: chain B residue 1773 LYS Chi-restraints excluded: chain B residue 1783 MET Chi-restraints excluded: chain B residue 1793 TYR Chi-restraints excluded: chain B residue 1870 THR Chi-restraints excluded: chain B residue 1900 PHE Chi-restraints excluded: chain B residue 2035 VAL 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 392 VAL 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: 0.0980 chunk 9 optimal weight: 0.9980 chunk 110 optimal weight: 2.9990 chunk 17 optimal weight: 0.9990 chunk 158 optimal weight: 8.9990 chunk 84 optimal weight: 3.9990 chunk 136 optimal weight: 10.0000 chunk 121 optimal weight: 0.0870 chunk 144 optimal weight: 0.1980 chunk 164 optimal weight: 0.7980 chunk 87 optimal weight: 0.8980 overall best weight: 0.4158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 73 HIS ** A 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 242 HIS ** A 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 420 HIS A 448 GLN ** A 509 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 ** B1829 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1863 ASN ** B1864 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2091 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 303 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4994 r_free = 0.4994 target = 0.170360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.4631 r_free = 0.4631 target = 0.141601 restraints weight = 35231.243| |-----------------------------------------------------------------------------| r_work (start): 0.4595 rms_B_bonded: 5.61 r_work (final): 0.4595 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6148 moved from start: 0.3144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 14278 Z= 0.151 Angle : 0.773 13.686 19373 Z= 0.387 Chirality : 0.050 0.358 2061 Planarity : 0.005 0.081 2479 Dihedral : 8.554 105.348 2075 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 22.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.42 % Favored : 89.58 % Rotamer: Outliers : 3.06 % Allowed : 16.62 % Favored : 80.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.13 (0.19), residues: 1679 helix: -2.15 (0.50), residues: 80 sheet: -2.09 (0.25), residues: 390 loop : -2.21 (0.17), residues: 1209 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 286 TYR 0.026 0.002 TYR A 38 PHE 0.023 0.002 PHE A 651 TRP 0.032 0.002 TRP D 234 HIS 0.010 0.001 HIS A 609 Details of bonding type rmsd covalent geometry : bond 0.00346 (14249) covalent geometry : angle 0.76015 (19308) SS BOND : bond 0.00318 ( 19) SS BOND : angle 1.27704 ( 38) hydrogen bonds : bond 0.03777 ( 231) hydrogen bonds : angle 7.49750 ( 564) Misc. bond : bond 0.00195 ( 1) link_NAG-ASN : bond 0.00765 ( 9) link_NAG-ASN : angle 3.66758 ( 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 260 residues out of total 1504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 214 time to evaluate : 0.560 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 171 THR cc_start: 0.8884 (p) cc_final: 0.7972 (p) REVERT: A 233 SER cc_start: 0.5777 (m) cc_final: 0.5103 (p) REVERT: A 237 GLU cc_start: 0.3274 (mm-30) cc_final: 0.2783 (mm-30) REVERT: A 385 MET cc_start: 0.4816 (ttt) cc_final: 0.4601 (ttt) REVERT: B 1654 GLU cc_start: 0.7829 (tt0) cc_final: 0.6154 (pm20) REVERT: B 1658 TYR cc_start: 0.6855 (p90) cc_final: 0.6607 (p90) REVERT: B 1736 MET cc_start: 0.7361 (ttm) cc_final: 0.6221 (mpt) REVERT: B 1783 MET cc_start: 0.7174 (OUTLIER) cc_final: 0.6522 (mmt) REVERT: B 1811 ILE cc_start: 0.7930 (tp) cc_final: 0.7483 (mp) REVERT: B 1868 MET cc_start: 0.6740 (OUTLIER) cc_final: 0.6355 (tpp) REVERT: D 175 MET cc_start: 0.8225 (mmp) cc_final: 0.7814 (mpp) REVERT: D 187 LEU cc_start: 0.9019 (mt) cc_final: 0.8798 (mp) REVERT: D 231 TRP cc_start: 0.7343 (t60) cc_final: 0.7096 (t60) REVERT: D 232 GLU cc_start: 0.7708 (OUTLIER) cc_final: 0.6717 (tm-30) outliers start: 46 outliers final: 15 residues processed: 242 average time/residue: 0.5467 time to fit residues: 147.6063 Evaluate side-chains 193 residues out of total 1504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 175 time to evaluate : 0.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 TYR 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 621 GLU Chi-restraints excluded: chain B residue 1783 MET Chi-restraints excluded: chain B residue 1793 TYR Chi-restraints excluded: chain B residue 1868 MET Chi-restraints excluded: chain B residue 1899 GLU Chi-restraints excluded: chain B residue 2063 TRP Chi-restraints excluded: chain B residue 2117 SER Chi-restraints excluded: chain B residue 2184 ILE Chi-restraints excluded: chain B residue 2186 LEU Chi-restraints excluded: chain D residue 232 GLU Chi-restraints excluded: chain D residue 273 ILE Chi-restraints excluded: chain D residue 297 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 141 optimal weight: 2.9990 chunk 32 optimal weight: 4.9990 chunk 50 optimal weight: 2.9990 chunk 120 optimal weight: 3.9990 chunk 51 optimal weight: 0.7980 chunk 107 optimal weight: 1.9990 chunk 104 optimal weight: 6.9990 chunk 7 optimal weight: 3.9990 chunk 136 optimal weight: 20.0000 chunk 118 optimal weight: 0.7980 chunk 128 optimal weight: 1.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 103 HIS A 142 HIS ** A 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 149 ASN ** A 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 509 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1815 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1817 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1819 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1829 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1863 ASN ** B1864 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1913 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1993 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2091 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4891 r_free = 0.4891 target = 0.162578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.4500 r_free = 0.4500 target = 0.132696 restraints weight = 35210.844| |-----------------------------------------------------------------------------| r_work (start): 0.4464 rms_B_bonded: 5.61 r_work (final): 0.4464 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6365 moved from start: 0.3921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.068 14278 Z= 0.267 Angle : 0.838 12.985 19373 Z= 0.425 Chirality : 0.051 0.348 2061 Planarity : 0.006 0.067 2479 Dihedral : 8.734 105.487 2073 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 27.28 Ramachandran Plot: Outliers : 0.06 % Allowed : 11.91 % Favored : 88.03 % Rotamer: Outliers : 4.72 % Allowed : 18.68 % Favored : 76.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.22 (0.19), residues: 1679 helix: -2.13 (0.50), residues: 80 sheet: -2.30 (0.26), residues: 373 loop : -2.23 (0.17), residues: 1226 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 286 TYR 0.025 0.002 TYR B2121 PHE 0.029 0.002 PHE A 424 TRP 0.035 0.003 TRP D 372 HIS 0.011 0.002 HIS A 609 Details of bonding type rmsd covalent geometry : bond 0.00603 (14249) covalent geometry : angle 0.82629 (19308) SS BOND : bond 0.00558 ( 19) SS BOND : angle 1.19203 ( 38) hydrogen bonds : bond 0.04032 ( 231) hydrogen bonds : angle 7.66576 ( 564) Misc. bond : bond 0.00146 ( 1) link_NAG-ASN : bond 0.00831 ( 9) link_NAG-ASN : angle 3.66815 ( 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 260 residues out of total 1504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 189 time to evaluate : 0.629 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 15 TRP cc_start: 0.5473 (OUTLIER) cc_final: 0.5033 (m-10) REVERT: A 237 GLU cc_start: 0.3283 (mm-30) cc_final: 0.2590 (mm-30) REVERT: A 593 ILE cc_start: 0.8957 (OUTLIER) cc_final: 0.8719 (tp) REVERT: B 1584 ASP cc_start: 0.8326 (t0) cc_final: 0.7551 (m-30) REVERT: B 1654 GLU cc_start: 0.8271 (tt0) cc_final: 0.6396 (pm20) REVERT: B 1658 TYR cc_start: 0.7003 (p90) cc_final: 0.6592 (p90) REVERT: B 1681 VAL cc_start: 0.8239 (OUTLIER) cc_final: 0.8002 (p) REVERT: B 1736 MET cc_start: 0.7206 (ttm) cc_final: 0.6091 (mmt) REVERT: B 1752 LYS cc_start: 0.7451 (mmpt) cc_final: 0.7169 (mmpt) REVERT: B 1811 ILE cc_start: 0.7933 (tp) cc_final: 0.7483 (mp) REVERT: B 1817 HIS cc_start: 0.7718 (OUTLIER) cc_final: 0.7455 (m90) REVERT: B 1847 LYS cc_start: 0.6691 (tttp) cc_final: 0.6485 (ttmm) REVERT: B 1855 LEU cc_start: 0.7132 (tp) cc_final: 0.6833 (tp) REVERT: B 1868 MET cc_start: 0.6907 (OUTLIER) cc_final: 0.6618 (tpp) REVERT: B 1873 LEU cc_start: 0.8023 (OUTLIER) cc_final: 0.7756 (tt) REVERT: B 1939 MET cc_start: 0.5786 (OUTLIER) cc_final: 0.4916 (mpt) REVERT: B 1940 GLN cc_start: 0.8334 (tp-100) cc_final: 0.8069 (tp-100) REVERT: D 187 LEU cc_start: 0.9056 (mt) cc_final: 0.8839 (mp) REVERT: D 192 LYS cc_start: 0.9260 (mmpt) cc_final: 0.9046 (mmpt) REVERT: D 231 TRP cc_start: 0.7484 (t60) cc_final: 0.7224 (t60) REVERT: D 343 MET cc_start: 0.7054 (OUTLIER) cc_final: 0.6744 (ppp) outliers start: 71 outliers final: 32 residues processed: 239 average time/residue: 0.4727 time to fit residues: 128.5176 Evaluate side-chains 207 residues out of total 1504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 167 time to evaluate : 0.665 ------------------------------------------------------------------------------- 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 82 LEU Chi-restraints excluded: chain A residue 110 MET 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 335 TYR Chi-restraints excluded: chain A residue 431 VAL Chi-restraints excluded: chain A residue 444 ILE Chi-restraints excluded: chain A residue 519 VAL Chi-restraints excluded: chain A residue 593 ILE Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 621 GLU Chi-restraints excluded: chain A residue 630 VAL Chi-restraints excluded: chain B residue 1559 GLU Chi-restraints excluded: chain B residue 1590 VAL Chi-restraints excluded: chain B residue 1681 VAL Chi-restraints excluded: chain B residue 1793 TYR Chi-restraints excluded: chain B residue 1817 HIS Chi-restraints excluded: chain B residue 1858 THR Chi-restraints excluded: chain B residue 1868 MET Chi-restraints excluded: chain B residue 1873 LEU Chi-restraints excluded: chain B residue 1939 MET 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 2148 LYS Chi-restraints excluded: chain B residue 2184 ILE Chi-restraints excluded: chain B residue 2186 LEU Chi-restraints excluded: chain D residue 232 GLU 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 343 MET Chi-restraints excluded: chain D residue 354 ASP Chi-restraints excluded: chain D residue 392 VAL 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: 4.9990 chunk 162 optimal weight: 10.0000 chunk 154 optimal weight: 1.9990 chunk 83 optimal weight: 2.9990 chunk 81 optimal weight: 1.9990 chunk 164 optimal weight: 4.9990 chunk 89 optimal weight: 0.0030 chunk 151 optimal weight: 4.9990 chunk 71 optimal weight: 0.7980 chunk 119 optimal weight: 0.9990 overall best weight: 0.9194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 149 ASN ** A 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1815 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1817 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1819 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1829 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1857 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1863 ASN ** B1864 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1993 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** D 262 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4922 r_free = 0.4922 target = 0.164784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.4529 r_free = 0.4529 target = 0.134351 restraints weight = 35344.218| |-----------------------------------------------------------------------------| r_work (start): 0.4492 rms_B_bonded: 5.49 r_work (final): 0.4492 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6309 moved from start: 0.4117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 14278 Z= 0.185 Angle : 0.782 12.837 19373 Z= 0.392 Chirality : 0.050 0.343 2061 Planarity : 0.005 0.058 2479 Dihedral : 8.460 105.165 2073 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 23.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.72 % Favored : 89.28 % Rotamer: Outliers : 4.12 % Allowed : 20.74 % Favored : 75.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.22 (0.19), residues: 1679 helix: -2.01 (0.51), residues: 80 sheet: -2.42 (0.25), residues: 388 loop : -2.18 (0.17), residues: 1211 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG D 286 TYR 0.026 0.002 TYR A 120 PHE 0.027 0.002 PHE A 651 TRP 0.041 0.002 TRP D 372 HIS 0.008 0.001 HIS B1817 Details of bonding type rmsd covalent geometry : bond 0.00427 (14249) covalent geometry : angle 0.77085 (19308) SS BOND : bond 0.00244 ( 19) SS BOND : angle 1.08513 ( 38) hydrogen bonds : bond 0.03669 ( 231) hydrogen bonds : angle 7.43243 ( 564) Misc. bond : bond 0.00132 ( 1) link_NAG-ASN : bond 0.00736 ( 9) link_NAG-ASN : angle 3.48631 ( 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 251 residues out of total 1504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 189 time to evaluate : 0.572 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 15 TRP cc_start: 0.5489 (OUTLIER) cc_final: 0.5080 (m-10) REVERT: A 237 GLU cc_start: 0.3046 (mm-30) cc_final: 0.1550 (mt-10) REVERT: A 593 ILE cc_start: 0.8972 (OUTLIER) cc_final: 0.8727 (tp) REVERT: A 599 THR cc_start: 0.7640 (m) cc_final: 0.7312 (p) REVERT: B 1584 ASP cc_start: 0.8310 (t0) cc_final: 0.7536 (m-30) REVERT: B 1654 GLU cc_start: 0.8202 (tt0) cc_final: 0.6296 (pm20) REVERT: B 1658 TYR cc_start: 0.6926 (p90) cc_final: 0.6430 (p90) REVERT: B 1681 VAL cc_start: 0.8116 (OUTLIER) cc_final: 0.7909 (p) REVERT: B 1736 MET cc_start: 0.7142 (ttm) cc_final: 0.6030 (mmt) REVERT: B 1811 ILE cc_start: 0.7930 (tp) cc_final: 0.7539 (mp) REVERT: B 1817 HIS cc_start: 0.7719 (OUTLIER) cc_final: 0.7453 (m90) REVERT: B 1855 LEU cc_start: 0.7102 (tp) cc_final: 0.6867 (tp) REVERT: B 1868 MET cc_start: 0.6620 (OUTLIER) cc_final: 0.6402 (tpp) REVERT: B 1939 MET cc_start: 0.5689 (OUTLIER) cc_final: 0.4656 (mpt) REVERT: B 1940 GLN cc_start: 0.8221 (tp-100) cc_final: 0.7983 (tp-100) REVERT: D 177 ARG cc_start: 0.7215 (mmp80) cc_final: 0.6826 (mmp80) REVERT: D 192 LYS cc_start: 0.9222 (mmpt) cc_final: 0.8999 (mmpt) REVERT: D 231 TRP cc_start: 0.7571 (t60) cc_final: 0.7299 (t60) REVERT: D 232 GLU cc_start: 0.7552 (OUTLIER) cc_final: 0.6524 (tm-30) outliers start: 62 outliers final: 31 residues processed: 235 average time/residue: 0.4649 time to fit residues: 124.2072 Evaluate side-chains 209 residues out of total 1504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 171 time to evaluate : 0.553 ------------------------------------------------------------------------------- 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 82 LEU Chi-restraints excluded: chain A residue 110 MET Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 240 SER Chi-restraints excluded: chain A residue 241 ILE Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 289 GLN Chi-restraints excluded: chain A residue 431 VAL Chi-restraints excluded: chain A residue 444 ILE Chi-restraints excluded: chain A residue 517 GLN 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 1681 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 1868 MET 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 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 2148 LYS Chi-restraints excluded: chain B residue 2184 ILE Chi-restraints excluded: chain B residue 2186 LEU Chi-restraints excluded: chain C residue 145 TRP Chi-restraints excluded: chain D residue 232 GLU Chi-restraints excluded: chain D residue 253 THR Chi-restraints excluded: chain D residue 273 ILE Chi-restraints excluded: chain D residue 297 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 53 optimal weight: 3.9990 chunk 98 optimal weight: 0.5980 chunk 130 optimal weight: 0.8980 chunk 142 optimal weight: 8.9990 chunk 55 optimal weight: 2.9990 chunk 38 optimal weight: 0.8980 chunk 107 optimal weight: 0.8980 chunk 168 optimal weight: 3.9990 chunk 74 optimal weight: 1.9990 chunk 140 optimal weight: 10.0000 chunk 166 optimal weight: 6.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 149 ASN ** A 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 597 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1645 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1815 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1817 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1819 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1829 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1863 ASN ** B1864 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1993 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** D 328 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4909 r_free = 0.4909 target = 0.163635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.4523 r_free = 0.4523 target = 0.133957 restraints weight = 35015.564| |-----------------------------------------------------------------------------| r_work (start): 0.4486 rms_B_bonded: 5.48 r_work (final): 0.4486 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6322 moved from start: 0.4403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 14278 Z= 0.195 Angle : 0.795 12.513 19373 Z= 0.400 Chirality : 0.050 0.339 2061 Planarity : 0.005 0.058 2479 Dihedral : 8.437 105.115 2073 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 24.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.14 % Favored : 88.86 % Rotamer: Outliers : 4.06 % Allowed : 22.14 % Favored : 73.80 % 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 aren not related in a simple way. whole: -3.16 (0.19), residues: 1679 helix: -1.67 (0.54), residues: 74 sheet: -2.44 (0.25), residues: 384 loop : -2.14 (0.17), residues: 1221 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 286 TYR 0.027 0.002 TYR A 120 PHE 0.026 0.002 PHE A 651 TRP 0.052 0.002 TRP B1665 HIS 0.009 0.001 HIS A 242 Details of bonding type rmsd covalent geometry : bond 0.00447 (14249) covalent geometry : angle 0.78457 (19308) SS BOND : bond 0.00353 ( 19) SS BOND : angle 1.09346 ( 38) hydrogen bonds : bond 0.03640 ( 231) hydrogen bonds : angle 7.40641 ( 564) Misc. bond : bond 0.00121 ( 1) link_NAG-ASN : bond 0.00728 ( 9) link_NAG-ASN : angle 3.39949 ( 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: 61 poor density : 178 time to evaluate : 0.568 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 186 LEU cc_start: 0.7183 (OUTLIER) cc_final: 0.6918 (tm) REVERT: A 237 GLU cc_start: 0.3227 (mm-30) cc_final: 0.1697 (mt-10) REVERT: A 482 ASP cc_start: 0.8447 (t0) cc_final: 0.8235 (t0) REVERT: A 593 ILE cc_start: 0.8986 (OUTLIER) cc_final: 0.8724 (tp) REVERT: A 599 THR cc_start: 0.7687 (m) cc_final: 0.7363 (p) REVERT: B 1584 ASP cc_start: 0.8353 (t0) cc_final: 0.7556 (m-30) REVERT: B 1654 GLU cc_start: 0.8255 (tt0) cc_final: 0.6277 (pm20) REVERT: B 1658 TYR cc_start: 0.6852 (p90) cc_final: 0.6352 (p90) REVERT: B 1681 VAL cc_start: 0.8148 (OUTLIER) cc_final: 0.7915 (p) REVERT: B 1691 GLU cc_start: 0.5635 (OUTLIER) cc_final: 0.5256 (pp20) REVERT: B 1736 MET cc_start: 0.6975 (ttm) cc_final: 0.5973 (mmt) REVERT: B 1811 ILE cc_start: 0.8005 (tp) cc_final: 0.7602 (mp) REVERT: B 1817 HIS cc_start: 0.7712 (OUTLIER) cc_final: 0.7471 (m90) REVERT: B 1855 LEU cc_start: 0.7000 (tp) cc_final: 0.6797 (tp) REVERT: B 1868 MET cc_start: 0.6749 (OUTLIER) cc_final: 0.6532 (tpp) REVERT: B 1907 ARG cc_start: 0.7472 (ttm110) cc_final: 0.7113 (ttm110) REVERT: B 1940 GLN cc_start: 0.8239 (tp-100) cc_final: 0.7999 (tp-100) REVERT: B 2030 LEU cc_start: 0.6682 (mm) cc_final: 0.6426 (mm) REVERT: D 177 ARG cc_start: 0.7235 (mmp80) cc_final: 0.6930 (mmp80) REVERT: D 192 LYS cc_start: 0.9220 (mmpt) cc_final: 0.8980 (mmpt) REVERT: D 231 TRP cc_start: 0.7590 (t60) cc_final: 0.7328 (t60) REVERT: D 232 GLU cc_start: 0.7502 (OUTLIER) cc_final: 0.6496 (tm-30) outliers start: 61 outliers final: 31 residues processed: 223 average time/residue: 0.4693 time to fit residues: 118.6314 Evaluate side-chains 207 residues out of total 1504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 169 time to evaluate : 0.535 ------------------------------------------------------------------------------- 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 82 LEU Chi-restraints excluded: chain A residue 110 MET 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 186 LEU Chi-restraints excluded: chain A residue 240 SER Chi-restraints excluded: chain A residue 241 ILE Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 289 GLN Chi-restraints excluded: chain A residue 380 THR Chi-restraints excluded: chain A residue 431 VAL Chi-restraints excluded: chain A residue 444 ILE Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 517 GLN Chi-restraints excluded: chain A residue 593 ILE Chi-restraints excluded: chain B residue 1590 VAL Chi-restraints excluded: chain B residue 1681 VAL Chi-restraints excluded: chain B residue 1691 GLU 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 1868 MET Chi-restraints excluded: chain B residue 1869 GLN Chi-restraints excluded: chain B residue 1889 ILE Chi-restraints excluded: chain B residue 1899 GLU Chi-restraints excluded: chain B residue 1967 VAL 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 2148 LYS Chi-restraints excluded: chain B residue 2186 LEU Chi-restraints excluded: chain D residue 232 GLU Chi-restraints excluded: chain D residue 253 THR Chi-restraints excluded: chain D residue 273 ILE Chi-restraints excluded: chain D residue 297 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 165 optimal weight: 2.9990 chunk 84 optimal weight: 1.9990 chunk 125 optimal weight: 2.9990 chunk 48 optimal weight: 0.9980 chunk 83 optimal weight: 0.5980 chunk 43 optimal weight: 1.9990 chunk 128 optimal weight: 0.9990 chunk 19 optimal weight: 0.2980 chunk 96 optimal weight: 0.6980 chunk 53 optimal weight: 4.9990 chunk 58 optimal weight: 2.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 149 ASN ** A 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 597 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1645 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1815 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1817 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1819 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1829 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1857 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1863 ASN ** B1864 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1993 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4925 r_free = 0.4925 target = 0.164923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.4537 r_free = 0.4537 target = 0.134992 restraints weight = 35321.423| |-----------------------------------------------------------------------------| r_work (start): 0.4500 rms_B_bonded: 5.45 r_work (final): 0.4500 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6290 moved from start: 0.4521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 14278 Z= 0.166 Angle : 0.794 12.289 19373 Z= 0.395 Chirality : 0.050 0.337 2061 Planarity : 0.005 0.058 2479 Dihedral : 8.301 105.151 2073 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 22.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.42 % Favored : 89.58 % Rotamer: Outliers : 3.79 % Allowed : 22.87 % Favored : 73.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.19 (0.19), residues: 1679 helix: -1.59 (0.55), residues: 74 sheet: -2.48 (0.25), residues: 388 loop : -2.15 (0.17), residues: 1217 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 286 TYR 0.024 0.002 TYR A 120 PHE 0.026 0.002 PHE A 651 TRP 0.033 0.002 TRP D 234 HIS 0.008 0.001 HIS B1817 Details of bonding type rmsd covalent geometry : bond 0.00386 (14249) covalent geometry : angle 0.78405 (19308) SS BOND : bond 0.00268 ( 19) SS BOND : angle 1.21157 ( 38) hydrogen bonds : bond 0.03517 ( 231) hydrogen bonds : angle 7.28706 ( 564) Misc. bond : bond 0.00129 ( 1) link_NAG-ASN : bond 0.00708 ( 9) link_NAG-ASN : angle 3.30596 ( 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 240 residues out of total 1504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 183 time to evaluate : 0.561 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 186 LEU cc_start: 0.7112 (OUTLIER) cc_final: 0.6852 (tm) REVERT: A 237 GLU cc_start: 0.3345 (mm-30) cc_final: 0.2756 (mm-30) REVERT: A 593 ILE cc_start: 0.8982 (OUTLIER) cc_final: 0.8690 (tp) REVERT: A 599 THR cc_start: 0.7611 (m) cc_final: 0.7340 (p) REVERT: B 1584 ASP cc_start: 0.8332 (t0) cc_final: 0.7551 (m-30) REVERT: B 1654 GLU cc_start: 0.8215 (tt0) cc_final: 0.6312 (pm20) REVERT: B 1658 TYR cc_start: 0.6833 (p90) cc_final: 0.6344 (p90) REVERT: B 1681 VAL cc_start: 0.8082 (OUTLIER) cc_final: 0.7881 (p) REVERT: B 1691 GLU cc_start: 0.5660 (OUTLIER) cc_final: 0.5265 (pp20) REVERT: B 1736 MET cc_start: 0.7074 (ttm) cc_final: 0.5944 (mmt) REVERT: B 1811 ILE cc_start: 0.8016 (tp) cc_final: 0.7582 (mp) REVERT: B 1817 HIS cc_start: 0.7701 (OUTLIER) cc_final: 0.7478 (m90) REVERT: B 1868 MET cc_start: 0.6614 (OUTLIER) cc_final: 0.6405 (tpp) REVERT: B 1900 PHE cc_start: 0.8048 (OUTLIER) cc_final: 0.7350 (p90) REVERT: B 1907 ARG cc_start: 0.7395 (ttm110) cc_final: 0.7147 (ttm110) REVERT: B 1940 GLN cc_start: 0.8235 (tp-100) cc_final: 0.7966 (tp-100) REVERT: D 177 ARG cc_start: 0.7209 (mmp80) cc_final: 0.6917 (mmp80) REVERT: D 192 LYS cc_start: 0.9250 (mmpt) cc_final: 0.9008 (mmpt) REVERT: D 231 TRP cc_start: 0.7631 (t60) cc_final: 0.7371 (t60) REVERT: D 232 GLU cc_start: 0.7531 (OUTLIER) cc_final: 0.6431 (tm-30) REVERT: D 300 TRP cc_start: 0.5001 (OUTLIER) cc_final: 0.3654 (m100) REVERT: D 343 MET cc_start: 0.7202 (ppp) cc_final: 0.6234 (pp-130) outliers start: 57 outliers final: 28 residues processed: 221 average time/residue: 0.4786 time to fit residues: 119.7188 Evaluate side-chains 207 residues out of total 1504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 170 time to evaluate : 0.548 ------------------------------------------------------------------------------- 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 82 LEU Chi-restraints excluded: chain A residue 110 MET 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 186 LEU Chi-restraints excluded: chain A residue 240 SER Chi-restraints excluded: chain A residue 241 ILE Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 289 GLN Chi-restraints excluded: chain A residue 380 THR Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 517 GLN Chi-restraints excluded: chain A residue 565 VAL Chi-restraints excluded: chain A residue 593 ILE Chi-restraints excluded: chain B residue 1590 VAL Chi-restraints excluded: chain B residue 1681 VAL Chi-restraints excluded: chain B residue 1691 GLU 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 1868 MET Chi-restraints excluded: chain B residue 1869 GLN Chi-restraints excluded: chain B residue 1889 ILE Chi-restraints excluded: chain B residue 1900 PHE Chi-restraints excluded: chain B residue 1967 VAL Chi-restraints excluded: chain B residue 2110 THR Chi-restraints excluded: chain B residue 2117 SER Chi-restraints excluded: chain B residue 2186 LEU Chi-restraints excluded: chain D residue 232 GLU Chi-restraints excluded: chain D residue 253 THR 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 392 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 155 optimal weight: 4.9990 chunk 88 optimal weight: 0.5980 chunk 25 optimal weight: 0.8980 chunk 124 optimal weight: 4.9990 chunk 70 optimal weight: 6.9990 chunk 126 optimal weight: 4.9990 chunk 80 optimal weight: 0.5980 chunk 165 optimal weight: 0.9990 chunk 74 optimal weight: 1.9990 chunk 3 optimal weight: 0.7980 chunk 23 optimal weight: 3.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 51 GLN ** A 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 149 ASN ** A 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 597 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1645 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1815 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1817 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1819 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1829 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1857 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1863 ASN ** B1864 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1993 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4928 r_free = 0.4928 target = 0.166624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4525 r_free = 0.4525 target = 0.132607 restraints weight = 35652.720| |-----------------------------------------------------------------------------| r_work (start): 0.4492 rms_B_bonded: 6.23 r_work (final): 0.4492 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6306 moved from start: 0.4656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 14278 Z= 0.175 Angle : 0.810 13.048 19373 Z= 0.402 Chirality : 0.049 0.335 2061 Planarity : 0.005 0.057 2479 Dihedral : 8.271 105.520 2073 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 23.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.48 % Favored : 89.52 % Rotamer: Outliers : 3.59 % Allowed : 23.87 % Favored : 72.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.19 (0.19), residues: 1679 helix: -1.65 (0.53), residues: 80 sheet: -2.49 (0.24), residues: 390 loop : -2.14 (0.17), residues: 1209 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 286 TYR 0.023 0.002 TYR A 120 PHE 0.025 0.002 PHE A 651 TRP 0.038 0.002 TRP D 234 HIS 0.008 0.001 HIS B1817 Details of bonding type rmsd covalent geometry : bond 0.00409 (14249) covalent geometry : angle 0.79897 (19308) SS BOND : bond 0.00327 ( 19) SS BOND : angle 1.71350 ( 38) hydrogen bonds : bond 0.03491 ( 231) hydrogen bonds : angle 7.21114 ( 564) Misc. bond : bond 0.00126 ( 1) link_NAG-ASN : bond 0.00706 ( 9) link_NAG-ASN : angle 3.23649 ( 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 235 residues out of total 1504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 181 time to evaluate : 0.564 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 180 ASP cc_start: 0.7651 (m-30) cc_final: 0.7295 (t0) REVERT: A 186 LEU cc_start: 0.7144 (OUTLIER) cc_final: 0.6877 (tm) REVERT: A 237 GLU cc_start: 0.3466 (mm-30) cc_final: 0.2896 (mm-30) REVERT: A 292 MET cc_start: 0.6828 (tpt) cc_final: 0.6395 (tpp) REVERT: A 593 ILE cc_start: 0.8984 (OUTLIER) cc_final: 0.8668 (tp) REVERT: A 599 THR cc_start: 0.7563 (m) cc_final: 0.7308 (p) REVERT: B 1584 ASP cc_start: 0.8426 (t0) cc_final: 0.7611 (m-30) REVERT: B 1654 GLU cc_start: 0.8220 (tt0) cc_final: 0.6175 (pm20) REVERT: B 1658 TYR cc_start: 0.6806 (p90) cc_final: 0.6297 (p90) REVERT: B 1681 VAL cc_start: 0.8057 (OUTLIER) cc_final: 0.7832 (p) REVERT: B 1736 MET cc_start: 0.7006 (ttm) cc_final: 0.5835 (mmt) REVERT: B 1811 ILE cc_start: 0.7974 (tp) cc_final: 0.7549 (mp) REVERT: B 1817 HIS cc_start: 0.7651 (OUTLIER) cc_final: 0.7421 (m90) REVERT: B 1868 MET cc_start: 0.6772 (OUTLIER) cc_final: 0.6532 (tpp) REVERT: B 1907 ARG cc_start: 0.7465 (ttm110) cc_final: 0.6980 (ttp80) REVERT: B 1940 GLN cc_start: 0.8249 (tp-100) cc_final: 0.7964 (tp-100) REVERT: D 192 LYS cc_start: 0.9178 (mmpt) cc_final: 0.8920 (mmpt) REVERT: D 231 TRP cc_start: 0.7690 (t60) cc_final: 0.7455 (t60) REVERT: D 343 MET cc_start: 0.7200 (ppp) cc_final: 0.6224 (pp-130) outliers start: 54 outliers final: 32 residues processed: 217 average time/residue: 0.4756 time to fit residues: 116.6982 Evaluate side-chains 202 residues out of total 1504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 165 time to evaluate : 0.563 ------------------------------------------------------------------------------- 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 82 LEU Chi-restraints excluded: chain A residue 110 MET 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 186 LEU 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 349 SER Chi-restraints excluded: chain A residue 380 THR Chi-restraints excluded: chain A residue 444 ILE Chi-restraints excluded: chain A residue 517 GLN Chi-restraints excluded: chain A residue 565 VAL Chi-restraints excluded: chain A residue 593 ILE Chi-restraints excluded: chain A residue 622 SER Chi-restraints excluded: chain A residue 634 MET Chi-restraints excluded: chain B residue 1590 VAL Chi-restraints excluded: chain B residue 1681 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 1868 MET Chi-restraints excluded: chain B residue 1869 GLN Chi-restraints excluded: chain B residue 1889 ILE Chi-restraints excluded: chain B residue 1967 VAL Chi-restraints excluded: chain B residue 2110 THR Chi-restraints excluded: chain B residue 2117 SER Chi-restraints excluded: chain B residue 2186 LEU Chi-restraints excluded: chain D residue 232 GLU Chi-restraints excluded: chain D residue 253 THR Chi-restraints excluded: chain D residue 273 ILE Chi-restraints excluded: chain D residue 297 VAL Chi-restraints excluded: chain D residue 392 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 38 optimal weight: 0.9990 chunk 51 optimal weight: 4.9990 chunk 149 optimal weight: 0.8980 chunk 93 optimal weight: 0.0970 chunk 127 optimal weight: 0.5980 chunk 121 optimal weight: 0.9980 chunk 140 optimal weight: 9.9990 chunk 50 optimal weight: 0.9980 chunk 142 optimal weight: 5.9990 chunk 130 optimal weight: 2.9990 chunk 17 optimal weight: 0.0470 overall best weight: 0.5276 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 149 ASN ** A 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 597 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1645 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1815 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1817 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1819 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1829 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1857 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1863 ASN ** B1864 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1993 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4938 r_free = 0.4938 target = 0.166531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.4545 r_free = 0.4545 target = 0.135924 restraints weight = 35259.984| |-----------------------------------------------------------------------------| r_work (start): 0.4526 rms_B_bonded: 5.60 r_work (final): 0.4526 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6246 moved from start: 0.4787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 14278 Z= 0.160 Angle : 0.807 11.852 19373 Z= 0.402 Chirality : 0.050 0.329 2061 Planarity : 0.005 0.055 2479 Dihedral : 8.168 105.699 2073 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 21.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.13 % Favored : 89.87 % Rotamer: Outliers : 2.86 % Allowed : 24.87 % Favored : 72.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.16 (0.19), residues: 1679 helix: -1.61 (0.52), residues: 80 sheet: -2.44 (0.24), residues: 391 loop : -2.14 (0.17), residues: 1208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 286 TYR 0.021 0.002 TYR A 120 PHE 0.025 0.002 PHE A 651 TRP 0.043 0.002 TRP D 234 HIS 0.009 0.001 HIS A 420 Details of bonding type rmsd covalent geometry : bond 0.00379 (14249) covalent geometry : angle 0.79716 (19308) SS BOND : bond 0.00271 ( 19) SS BOND : angle 1.30259 ( 38) hydrogen bonds : bond 0.03331 ( 231) hydrogen bonds : angle 7.11671 ( 564) Misc. bond : bond 0.00120 ( 1) link_NAG-ASN : bond 0.00689 ( 9) link_NAG-ASN : angle 3.14879 ( 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 230 residues out of total 1504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 187 time to evaluate : 0.553 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 159 ILE cc_start: 0.8004 (OUTLIER) cc_final: 0.7707 (pp) REVERT: A 180 ASP cc_start: 0.7679 (m-30) cc_final: 0.7362 (t0) REVERT: A 186 LEU cc_start: 0.7191 (OUTLIER) cc_final: 0.6957 (tm) REVERT: A 233 SER cc_start: 0.5381 (m) cc_final: 0.4774 (p) REVERT: A 237 GLU cc_start: 0.3147 (mm-30) cc_final: 0.1739 (mt-10) REVERT: A 292 MET cc_start: 0.6777 (tpt) cc_final: 0.6319 (tpp) REVERT: A 410 MET cc_start: 0.7071 (mmm) cc_final: 0.6447 (mtm) REVERT: A 593 ILE cc_start: 0.8961 (OUTLIER) cc_final: 0.8674 (tp) REVERT: A 599 THR cc_start: 0.7512 (m) cc_final: 0.7224 (p) REVERT: B 1584 ASP cc_start: 0.8467 (t0) cc_final: 0.7638 (m-30) REVERT: B 1654 GLU cc_start: 0.8196 (tt0) cc_final: 0.6221 (pm20) REVERT: B 1658 TYR cc_start: 0.6763 (p90) cc_final: 0.6304 (p90) REVERT: B 1681 VAL cc_start: 0.8051 (OUTLIER) cc_final: 0.7844 (p) REVERT: B 1736 MET cc_start: 0.6962 (ttm) cc_final: 0.5766 (mmt) REVERT: B 1810 ASP cc_start: 0.7426 (p0) cc_final: 0.7193 (p0) REVERT: B 1811 ILE cc_start: 0.8036 (tp) cc_final: 0.7582 (mp) REVERT: B 1817 HIS cc_start: 0.7733 (OUTLIER) cc_final: 0.7507 (m90) REVERT: B 1846 MET cc_start: 0.7199 (tpp) cc_final: 0.6949 (tpp) REVERT: B 1868 MET cc_start: 0.6754 (OUTLIER) cc_final: 0.6510 (tpp) REVERT: B 1907 ARG cc_start: 0.7526 (ttm110) cc_final: 0.7076 (ttp80) REVERT: C 145 TRP cc_start: 0.4440 (p-90) cc_final: 0.4078 (p-90) REVERT: D 177 ARG cc_start: 0.7029 (mpp-170) cc_final: 0.6521 (mmp80) REVERT: D 192 LYS cc_start: 0.9198 (mmpt) cc_final: 0.8945 (mmpt) REVERT: D 231 TRP cc_start: 0.7770 (t60) cc_final: 0.7513 (t60) REVERT: D 232 GLU cc_start: 0.7548 (OUTLIER) cc_final: 0.6486 (tm-30) REVERT: D 343 MET cc_start: 0.7237 (ppp) cc_final: 0.6236 (pp-130) outliers start: 43 outliers final: 26 residues processed: 214 average time/residue: 0.4450 time to fit residues: 108.2376 Evaluate side-chains 209 residues out of total 1504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 176 time to evaluate : 0.545 ------------------------------------------------------------------------------- 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 82 LEU 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 186 LEU 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 349 SER Chi-restraints excluded: chain A residue 380 THR Chi-restraints excluded: chain A residue 565 VAL Chi-restraints excluded: chain A residue 593 ILE Chi-restraints excluded: chain A residue 622 SER Chi-restraints excluded: chain A residue 634 MET Chi-restraints excluded: chain B residue 1590 VAL Chi-restraints excluded: chain B residue 1681 VAL Chi-restraints excluded: chain B residue 1813 VAL Chi-restraints excluded: chain B residue 1817 HIS Chi-restraints excluded: chain B residue 1868 MET Chi-restraints excluded: chain B residue 1869 GLN Chi-restraints excluded: chain B residue 1889 ILE Chi-restraints excluded: chain B residue 1899 GLU Chi-restraints excluded: chain B residue 1967 VAL 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 2186 LEU Chi-restraints excluded: chain D residue 232 GLU Chi-restraints excluded: chain D residue 273 ILE Chi-restraints excluded: chain D residue 297 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 7 optimal weight: 0.9990 chunk 87 optimal weight: 2.9990 chunk 12 optimal weight: 0.9980 chunk 14 optimal weight: 0.7980 chunk 26 optimal weight: 1.9990 chunk 37 optimal weight: 3.9990 chunk 34 optimal weight: 0.0010 chunk 161 optimal weight: 3.9990 chunk 160 optimal weight: 7.9990 chunk 103 optimal weight: 0.9980 chunk 129 optimal weight: 0.9980 overall best weight: 0.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 597 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1645 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1815 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1817 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1819 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1829 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1857 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1863 ASN ** B1864 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1993 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 = 0.4939 r_free = 0.4939 target = 0.165508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.4546 r_free = 0.4546 target = 0.135057 restraints weight = 35449.661| |-----------------------------------------------------------------------------| r_work (start): 0.4517 rms_B_bonded: 5.60 r_work (final): 0.4517 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6273 moved from start: 0.4896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 14278 Z= 0.174 Angle : 0.832 11.654 19373 Z= 0.414 Chirality : 0.050 0.323 2061 Planarity : 0.005 0.056 2479 Dihedral : 8.187 105.839 2073 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 22.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.90 % Favored : 89.10 % Rotamer: Outliers : 2.59 % Allowed : 25.80 % Favored : 71.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.13 (0.19), residues: 1679 helix: -1.62 (0.53), residues: 80 sheet: -2.41 (0.25), residues: 389 loop : -2.13 (0.17), residues: 1210 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG C 81 TYR 0.022 0.002 TYR A 120 PHE 0.024 0.002 PHE A 651 TRP 0.050 0.002 TRP D 234 HIS 0.011 0.001 HIS B2128 Details of bonding type rmsd covalent geometry : bond 0.00408 (14249) covalent geometry : angle 0.82277 (19308) SS BOND : bond 0.00462 ( 19) SS BOND : angle 1.54892 ( 38) hydrogen bonds : bond 0.03508 ( 231) hydrogen bonds : angle 7.10903 ( 564) Misc. bond : bond 0.00121 ( 1) link_NAG-ASN : bond 0.00681 ( 9) link_NAG-ASN : angle 3.10414 ( 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 217 residues out of total 1504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 178 time to evaluate : 0.521 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 159 ILE cc_start: 0.7969 (OUTLIER) cc_final: 0.7691 (pp) REVERT: A 180 ASP cc_start: 0.7674 (m-30) cc_final: 0.7346 (t0) REVERT: A 186 LEU cc_start: 0.7093 (OUTLIER) cc_final: 0.6873 (tm) REVERT: A 237 GLU cc_start: 0.3135 (mm-30) cc_final: 0.1550 (mt-10) REVERT: A 292 MET cc_start: 0.6826 (tpt) cc_final: 0.6398 (tpp) REVERT: A 378 LYS cc_start: 0.8028 (mmmt) cc_final: 0.7356 (tptt) REVERT: A 410 MET cc_start: 0.7108 (mmm) cc_final: 0.6659 (mtm) REVERT: A 593 ILE cc_start: 0.8962 (OUTLIER) cc_final: 0.8681 (tp) REVERT: B 1584 ASP cc_start: 0.8485 (t0) cc_final: 0.7665 (m-30) REVERT: B 1654 GLU cc_start: 0.8224 (tt0) cc_final: 0.6333 (pm20) REVERT: B 1657 THR cc_start: 0.8062 (t) cc_final: 0.7641 (m) REVERT: B 1658 TYR cc_start: 0.6808 (p90) cc_final: 0.6424 (p90) REVERT: B 1681 VAL cc_start: 0.8069 (OUTLIER) cc_final: 0.7854 (p) REVERT: B 1736 MET cc_start: 0.6925 (ttm) cc_final: 0.5768 (mmt) REVERT: B 1810 ASP cc_start: 0.7428 (p0) cc_final: 0.7198 (p0) REVERT: B 1811 ILE cc_start: 0.8046 (tp) cc_final: 0.7580 (mp) REVERT: B 1817 HIS cc_start: 0.7771 (OUTLIER) cc_final: 0.7550 (m90) REVERT: B 1846 MET cc_start: 0.7236 (tpp) cc_final: 0.6958 (tpp) REVERT: B 1868 MET cc_start: 0.6788 (OUTLIER) cc_final: 0.6525 (tpp) REVERT: B 1907 ARG cc_start: 0.7510 (ttm110) cc_final: 0.7080 (ttp80) REVERT: C 145 TRP cc_start: 0.4484 (p-90) cc_final: 0.4110 (p-90) REVERT: D 175 MET cc_start: 0.7855 (mpp) cc_final: 0.7607 (tpp) REVERT: D 177 ARG cc_start: 0.6978 (mpp-170) cc_final: 0.6470 (mmp80) REVERT: D 192 LYS cc_start: 0.9207 (mmpt) cc_final: 0.8953 (mmpt) REVERT: D 231 TRP cc_start: 0.7796 (t60) cc_final: 0.7554 (t60) REVERT: D 232 GLU cc_start: 0.7583 (OUTLIER) cc_final: 0.6495 (tm-30) REVERT: D 343 MET cc_start: 0.7302 (ppp) cc_final: 0.6317 (pp-130) outliers start: 39 outliers final: 29 residues processed: 203 average time/residue: 0.4583 time to fit residues: 105.4942 Evaluate side-chains 203 residues out of total 1504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 167 time to evaluate : 0.462 ------------------------------------------------------------------------------- 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 82 LEU Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 182 GLN Chi-restraints excluded: chain A residue 186 LEU 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 349 SER Chi-restraints excluded: chain A residue 380 THR Chi-restraints excluded: chain A residue 444 ILE Chi-restraints excluded: chain A residue 478 TYR Chi-restraints excluded: chain A residue 517 GLN Chi-restraints excluded: chain A residue 565 VAL Chi-restraints excluded: chain A residue 593 ILE Chi-restraints excluded: chain A residue 622 SER Chi-restraints excluded: chain A residue 634 MET Chi-restraints excluded: chain B residue 1590 VAL Chi-restraints excluded: chain B residue 1681 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 1868 MET Chi-restraints excluded: chain B residue 1869 GLN Chi-restraints excluded: chain B residue 1889 ILE Chi-restraints excluded: chain B residue 1967 VAL 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 2186 LEU Chi-restraints excluded: chain D residue 232 GLU Chi-restraints excluded: chain D residue 273 ILE Chi-restraints excluded: chain D residue 400 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 113 optimal weight: 1.9990 chunk 68 optimal weight: 0.5980 chunk 153 optimal weight: 0.0980 chunk 151 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 141 optimal weight: 0.6980 chunk 61 optimal weight: 2.9990 chunk 54 optimal weight: 5.9990 chunk 25 optimal weight: 0.9990 chunk 149 optimal weight: 0.9990 chunk 37 optimal weight: 3.9990 overall best weight: 0.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 597 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1645 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1815 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1817 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1819 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1829 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1857 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1863 ASN ** B1864 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1913 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1993 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** D 271 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4941 r_free = 0.4941 target = 0.165883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.4550 r_free = 0.4550 target = 0.135455 restraints weight = 35388.085| |-----------------------------------------------------------------------------| r_work (start): 0.4522 rms_B_bonded: 5.73 r_work (final): 0.4522 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6269 moved from start: 0.4968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 14278 Z= 0.167 Angle : 0.825 11.514 19373 Z= 0.411 Chirality : 0.050 0.320 2061 Planarity : 0.005 0.055 2479 Dihedral : 8.159 105.869 2073 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 22.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.36 % Favored : 89.64 % Rotamer: Outliers : 2.66 % Allowed : 25.80 % Favored : 71.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.10 (0.19), residues: 1679 helix: -1.41 (0.57), residues: 74 sheet: -2.32 (0.24), residues: 401 loop : -2.14 (0.17), residues: 1204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 286 TYR 0.023 0.002 TYR D 393 PHE 0.024 0.002 PHE A 651 TRP 0.054 0.002 TRP D 234 HIS 0.012 0.001 HIS B2128 Details of bonding type rmsd covalent geometry : bond 0.00391 (14249) covalent geometry : angle 0.81607 (19308) SS BOND : bond 0.00333 ( 19) SS BOND : angle 1.45391 ( 38) hydrogen bonds : bond 0.03428 ( 231) hydrogen bonds : angle 7.08012 ( 564) Misc. bond : bond 0.00122 ( 1) link_NAG-ASN : bond 0.00668 ( 9) link_NAG-ASN : angle 3.06558 ( 27) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5574.57 seconds wall clock time: 96 minutes 14.84 seconds (5774.84 seconds total)