Starting phenix.real_space_refine on Thu Aug 6 15:50:43 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9yq8_73327/08_2026/9yq8_73327.cif Found real_map, /net/cci-nas-00/data/ceres_data/9yq8_73327/08_2026/9yq8_73327.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.84 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9yq8_73327/08_2026/9yq8_73327.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9yq8_73327/08_2026/9yq8_73327.map" model { file = "/net/cci-nas-00/data/ceres_data/9yq8_73327/08_2026/9yq8_73327.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9yq8_73327/08_2026/9yq8_73327.cif" } resolution = 3.84 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= 0.016 sd= 1.160 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 93 5.16 5 C 9807 2.51 5 N 2647 2.21 5 O 2905 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 15452 Number of models: 1 Model: "" Number of chains: 5 Chain: "E" Number of atoms: 2220 Number of conformers: 1 Conformer: "" Number of residues, atoms: 283, 2220 Classifications: {'peptide': 283} Link IDs: {'PTRANS': 9, 'TRANS': 273} Chain breaks: 4 Chain: "A" Number of atoms: 5137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 631, 5137 Classifications: {'peptide': 631} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 29, 'TRANS': 601} Chain breaks: 5 Chain: "L" Number of atoms: 908 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 908 Classifications: {'peptide': 116} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 109} Chain breaks: 8 Chain: "H" Number of atoms: 1849 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1849 Classifications: {'peptide': 229} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 214} Chain breaks: 12 Chain: "B" Number of atoms: 5338 Number of conformers: 1 Conformer: "" Number of residues, atoms: 662, 5338 Classifications: {'peptide': 662} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 36, 'TRANS': 625} Chain breaks: 4 Time building chain proxies: 2.35, per 1000 atoms: 0.15 Number of scatterers: 15452 At special positions: 0 Unit cell: (119.564, 117.038, 139.772, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 93 16.00 O 2905 8.00 N 2647 7.00 C 9807 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=21, symmetry=0 Simple disulfide: pdb=" SG CYS E 89 " - pdb=" SG CYS E 100 " distance=2.03 Simple disulfide: pdb=" SG CYS E 96 " - pdb=" SG CYS E 109 " distance=2.03 Simple disulfide: pdb=" SG CYS E 111 " - pdb=" SG CYS E 124 " distance=2.03 Simple disulfide: pdb=" SG CYS E 132 " - pdb=" SG CYS E 302 " distance=2.03 Simple disulfide: pdb=" SG CYS E 201 " - pdb=" SG CYS E 206 " distance=2.03 Simple disulfide: pdb=" SG CYS E 221 " - pdb=" SG CYS E 237 " distance=2.03 Simple disulfide: pdb=" SG CYS E 350 " - pdb=" SG CYS E 364 " distance=2.03 Simple disulfide: pdb=" SG CYS E 375 " - pdb=" SG CYS E 403 " distance=2.03 Simple disulfide: pdb=" SG CYS A1697 " - pdb=" SG CYS A1723 " distance=2.04 Simple disulfide: pdb=" SG CYS A1879 " - pdb=" SG CYS A2033 " distance=2.03 Simple disulfide: pdb=" SG CYS A2038 " - pdb=" SG CYS A2193 " distance=2.03 Simple disulfide: pdb=" SG CYS L 191 " - pdb=" SG CYS L 231 " distance=2.03 Simple disulfide: pdb=" SG CYS L 219 " - pdb=" SG CYS L 243 " distance=2.03 Simple disulfide: pdb=" SG CYS L 293 " - pdb=" SG CYS H 439 " distance=2.03 Simple disulfide: pdb=" SG CYS H 348 " - pdb=" SG CYS H 364 " distance=2.03 Simple disulfide: pdb=" SG CYS H 493 " - pdb=" SG CYS H 507 " distance=2.03 Simple disulfide: pdb=" SG CYS H 521 " - pdb=" SG CYS H 551 " distance=2.03 Simple disulfide: pdb=" SG CYS B 139 " - pdb=" SG CYS B 165 " distance=2.05 Simple disulfide: pdb=" SG CYS B 220 " - pdb=" SG CYS B 301 " distance=2.04 Simple disulfide: pdb=" SG CYS B 472 " - pdb=" SG CYS B 498 " distance=2.04 Simple disulfide: pdb=" SG CYS B 575 " - pdb=" SG CYS B 656 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.94 Conformation dependent library (CDL) restraints added in 454.5 milliseconds 3686 Ramachandran restraints generated. 1843 Oldfield, 0 Emsley, 1843 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3574 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 29 sheets defined 9.8% alpha, 16.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.30 Creating SS restraints... Processing helix chain 'E' and resid 92 through 96 Processing helix chain 'E' and resid 235 through 240 removed outlier: 3.525A pdb=" N TYR E 239 " --> pdb=" O HIS E 236 " (cutoff:3.500A) Processing helix chain 'E' and resid 306 through 313 Processing helix chain 'E' and resid 346 through 354 Processing helix chain 'E' and resid 418 through 426 Processing helix chain 'A' and resid 1607 through 1612 removed outlier: 3.898A pdb=" N HIS A1612 " --> pdb=" O GLU A1608 " (cutoff:3.500A) Processing helix chain 'A' and resid 1650 through 1654 removed outlier: 3.973A pdb=" N GLU A1654 " --> pdb=" O LYS A1651 " (cutoff:3.500A) Processing helix chain 'A' and resid 1663 through 1667 Processing helix chain 'A' and resid 1707 through 1712 Processing helix chain 'A' and resid 1713 through 1715 No H-bonds generated for 'chain 'A' and resid 1713 through 1715' Processing helix chain 'A' and resid 1860 through 1866 Processing helix chain 'A' and resid 1891 through 1893 No H-bonds generated for 'chain 'A' and resid 1891 through 1893' Processing helix chain 'A' and resid 1905 through 1909 Processing helix chain 'A' and resid 2069 through 2073 removed outlier: 3.780A pdb=" N ARG A2072 " --> pdb=" O GLU A2069 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N ALA A2073 " --> pdb=" O PRO A2070 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2069 through 2073' Processing helix chain 'A' and resid 2114 through 2118 removed outlier: 3.752A pdb=" N SER A2117 " --> pdb=" O LYS A2114 " (cutoff:3.500A) Processing helix chain 'L' and resid 172 through 176 Processing helix chain 'L' and resid 199 through 204 Processing helix chain 'L' and resid 308 through 318 Processing helix chain 'H' and resid 361 through 366 removed outlier: 3.719A pdb=" N LEU H 365 " --> pdb=" O ALA H 361 " (cutoff:3.500A) Processing helix chain 'H' and resid 442 through 450 Processing helix chain 'H' and resid 489 through 495 removed outlier: 4.363A pdb=" N ASP H 495 " --> pdb=" O PRO H 491 " (cutoff:3.500A) Processing helix chain 'H' and resid 569 through 575 removed outlier: 3.740A pdb=" N ASP H 575 " --> pdb=" O GLN H 571 " (cutoff:3.500A) Processing helix chain 'B' and resid 105 through 113 removed outlier: 5.624A pdb=" N MET B 110 " --> pdb=" O ALA B 107 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N ASP B 111 " --> pdb=" O GLU B 108 " (cutoff:3.500A) Processing helix chain 'B' and resid 149 through 156 Processing helix chain 'B' and resid 284 through 290 Processing helix chain 'B' and resid 301 through 305 Processing helix chain 'B' and resid 482 through 488 Processing helix chain 'B' and resid 530 through 537 removed outlier: 3.621A pdb=" N LYS B 537 " --> pdb=" O ASP B 533 " (cutoff:3.500A) Processing helix chain 'B' and resid 551 through 557 Processing sheet with id=AA1, first strand: chain 'E' and resid 115 through 116 Processing sheet with id=AA2, first strand: chain 'E' and resid 261 through 263 removed outlier: 3.568A pdb=" N CYS E 221 " --> pdb=" O LEU E 212 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N VAL E 267 " --> pdb=" O ARG E 287 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N PHE B 668 " --> pdb=" O VAL E 268 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 338 through 340 removed outlier: 3.849A pdb=" N LYS E 338 " --> pdb=" O GLY E 323 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N HIS E 383 " --> pdb=" O THR E 394 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N PHE E 392 " --> pdb=" O THR E 385 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ILE E 396 " --> pdb=" O THR E 413 " (cutoff:3.500A) removed outlier: 7.444A pdb=" N ILE E 411 " --> pdb=" O SER E 398 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N GLY E 410 " --> pdb=" O ALA E 365 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1589 through 1594 removed outlier: 3.781A pdb=" N ILE A1561 " --> pdb=" O LYS A1589 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N VAL A1591 " --> pdb=" O GLU A1559 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 1622 through 1623 removed outlier: 5.974A pdb=" N ALA A1622 " --> pdb=" O CYS A1723 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 1701 through 1702 removed outlier: 3.583A pdb=" N GLY A1718 " --> pdb=" O TYR A1702 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 1739 through 1744 removed outlier: 6.655A pdb=" N ARG A1739 " --> pdb=" O ARG A1799 " (cutoff:3.500A) removed outlier: 7.295A pdb=" N HIS A1801 " --> pdb=" O ARG A1739 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N PHE A1741 " --> pdb=" O HIS A1801 " (cutoff:3.500A) removed outlier: 7.350A pdb=" N LEU A1803 " --> pdb=" O PHE A1741 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N LEU A1743 " --> pdb=" O LEU A1803 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N LEU A1844 " --> pdb=" O LEU A1800 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU A1802 " --> pdb=" O LYS A1842 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LYS A1842 " --> pdb=" O LEU A1802 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N THR A1820 " --> pdb=" O LYS A1847 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 1746 through 1747 removed outlier: 3.836A pdb=" N MET A1746 " --> pdb=" O ALA A1779 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ALA A1779 " --> pdb=" O MET A1746 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'A' and resid 1791 through 1793 Processing sheet with id=AB1, first strand: chain 'A' and resid 1835 through 1836 Processing sheet with id=AB2, first strand: chain 'A' and resid 1895 through 1897 removed outlier: 4.411A pdb=" N LYS A1896 " --> pdb=" O GLN A1936 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N GLN A1936 " --> pdb=" O LYS A1896 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ILE A1935 " --> pdb=" O ILE A2015 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ILE A2013 " --> pdb=" O VAL A1937 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N GLU A1964 " --> pdb=" O THR A2018 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 1920 through 1921 removed outlier: 3.962A pdb=" N TRP A1920 " --> pdb=" O LEU A2026 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 2008 through 2009 removed outlier: 7.214A pdb=" N GLN A2031 " --> pdb=" O THR A1946 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 2055 through 2056 removed outlier: 3.523A pdb=" N PHE A2172 " --> pdb=" O SER A2130 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N TYR A2125 " --> pdb=" O PHE A2150 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 2161 through 2163 removed outlier: 3.558A pdb=" N ILE A2108 " --> pdb=" O ASN A2162 " (cutoff:3.500A) removed outlier: 5.484A pdb=" N ILE A2105 " --> pdb=" O CYS A2193 " (cutoff:3.500A) removed outlier: 7.512A pdb=" N CYS A2193 " --> pdb=" O ILE A2105 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ILE A2109 " --> pdb=" O GLU A2189 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'L' and resid 230 through 232 removed outlier: 3.883A pdb=" N CYS L 231 " --> pdb=" O GLY L 241 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N GLY L 241 " --> pdb=" O CYS L 231 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'H' and resid 335 through 337 Processing sheet with id=AB9, first strand: chain 'H' and resid 456 through 457 removed outlier: 3.699A pdb=" N LEU H 485 " --> pdb=" O GLY H 456 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'H' and resid 505 through 507 Processing sheet with id=AC2, first strand: chain 'H' and resid 529 through 533 removed outlier: 6.688A pdb=" N PHE H 529 " --> pdb=" O MET H 542 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ARG H 538 " --> pdb=" O SER H 533 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 39 through 40 removed outlier: 3.528A pdb=" N ARG B 39 " --> pdb=" O ALA B 9 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ARG B 4 " --> pdb=" O ILE B 69 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ILE B 70 " --> pdb=" O TRP B 124 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 63 through 65 removed outlier: 6.758A pdb=" N ALA B 64 " --> pdb=" O CYS B 165 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 181 through 188 removed outlier: 3.925A pdb=" N SER B 226 " --> pdb=" O LYS B 181 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ILE B 183 " --> pdb=" O SER B 226 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N MET B 232 " --> pdb=" O PHE B 187 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ALA B 268 " --> pdb=" O TRP B 227 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU B 229 " --> pdb=" O THR B 266 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ASN B 269 " --> pdb=" O GLU B 249 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLN B 250 " --> pdb=" O HIS B 253 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 217 through 219 removed outlier: 5.621A pdb=" N ILE B 217 " --> pdb=" O ASP B 297 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLY B 276 " --> pdb=" O ILE B 298 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 363 through 371 removed outlier: 3.541A pdb=" N LYS B 365 " --> pdb=" O VAL B 331 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N THR B 369 " --> pdb=" O ALA B 327 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ALA B 327 " --> pdb=" O THR B 369 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N PHE B 325 " --> pdb=" O TYR B 371 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N THR B 402 " --> pdb=" O TRP B 322 " (cutoff:3.500A) removed outlier: 7.897A pdb=" N TYR B 324 " --> pdb=" O THR B 402 " (cutoff:3.500A) removed outlier: 5.747A pdb=" N LYS B 404 " --> pdb=" O TYR B 324 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N ILE B 326 " --> pdb=" O LYS B 404 " (cutoff:3.500A) removed outlier: 5.518A pdb=" N VAL B 406 " --> pdb=" O ILE B 326 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N ALA B 328 " --> pdb=" O VAL B 406 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 391 through 397 removed outlier: 4.828A pdb=" N LEU B 494 " --> pdb=" O GLY B 392 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N ILE B 394 " --> pdb=" O LEU B 494 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N LEU B 496 " --> pdb=" O ILE B 394 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N ARG B 396 " --> pdb=" O LEU B 496 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ILE B 497 " --> pdb=" O LEU B 473 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N LEU B 473 " --> pdb=" O ILE B 497 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 518 through 519 removed outlier: 3.829A pdb=" N CYS B 585 " --> pdb=" O ALA B 518 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 572 through 575 removed outlier: 6.927A pdb=" N LEU B 572 " --> pdb=" O ARG B 652 " (cutoff:3.500A) removed outlier: 7.523A pdb=" N VAL B 654 " --> pdb=" O LEU B 572 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N PHE B 574 " --> pdb=" O VAL B 654 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N PHE B 651 " --> pdb=" O TRP B 633 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 596 through 598 removed outlier: 3.554A pdb=" N THR B 636 " --> pdb=" O HIS B 597 " (cutoff:3.500A) 238 hydrogen bonds defined for protein. 573 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: 2.17 Time building geometry restraints manager: 1.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.50: 9424 1.50 - 1.79: 6279 1.79 - 2.08: 114 2.08 - 2.37: 0 2.37 - 2.67: 1 Bond restraints: 15818 Sorted by residual: bond pdb=" C SER A2118 " pdb=" N MET A2120 " ideal model delta sigma weight residual 1.332 2.666 -1.333 1.40e-02 5.10e+03 9.07e+03 bond pdb=" N VAL B 422 " pdb=" CA VAL B 422 " ideal model delta sigma weight residual 1.457 1.495 -0.038 9.30e-03 1.16e+04 1.64e+01 bond pdb=" N VAL A1569 " pdb=" CA VAL A1569 " ideal model delta sigma weight residual 1.457 1.494 -0.037 9.30e-03 1.16e+04 1.57e+01 bond pdb=" CA TYR A1966 " pdb=" C TYR A1966 " ideal model delta sigma weight residual 1.524 1.478 0.046 1.24e-02 6.50e+03 1.37e+01 bond pdb=" N PRO H 408 " pdb=" CD PRO H 408 " ideal model delta sigma weight residual 1.473 1.421 0.052 1.40e-02 5.10e+03 1.35e+01 ... (remaining 15813 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.13: 21301 5.13 - 10.27: 56 10.27 - 15.40: 1 15.40 - 20.54: 1 20.54 - 25.67: 1 Bond angle restraints: 21360 Sorted by residual: angle pdb=" CA SER A2118 " pdb=" C SER A2118 " pdb=" N MET A2120 " ideal model delta sigma weight residual 115.78 141.45 -25.67 1.35e+00 5.49e-01 3.62e+02 angle pdb=" O SER A2118 " pdb=" C SER A2118 " pdb=" N MET A2120 " ideal model delta sigma weight residual 121.50 101.35 20.15 2.64e+00 1.43e-01 5.83e+01 angle pdb=" N VAL L 184 " pdb=" CA VAL L 184 " pdb=" CB VAL L 184 " ideal model delta sigma weight residual 111.93 102.71 9.22 1.85e+00 2.92e-01 2.48e+01 angle pdb=" N TYR H 367 " pdb=" CA TYR H 367 " pdb=" C TYR H 367 " ideal model delta sigma weight residual 109.81 98.89 10.92 2.21e+00 2.05e-01 2.44e+01 angle pdb=" CA PHE A1592 " pdb=" C PHE A1592 " pdb=" O PHE A1592 " ideal model delta sigma weight residual 121.19 115.78 5.41 1.10e+00 8.26e-01 2.42e+01 ... (remaining 21355 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 8591 17.94 - 35.89: 691 35.89 - 53.83: 143 53.83 - 71.78: 35 71.78 - 89.72: 22 Dihedral angle restraints: 9482 sinusoidal: 3937 harmonic: 5545 Sorted by residual: dihedral pdb=" CB CYS E 350 " pdb=" SG CYS E 350 " pdb=" SG CYS E 364 " pdb=" CB CYS E 364 " ideal model delta sinusoidal sigma weight residual 93.00 175.32 -82.32 1 1.00e+01 1.00e-02 8.32e+01 dihedral pdb=" CB CYS E 89 " pdb=" SG CYS E 89 " pdb=" SG CYS E 100 " pdb=" CB CYS E 100 " ideal model delta sinusoidal sigma weight residual -86.00 -148.83 62.83 1 1.00e+01 1.00e-02 5.22e+01 dihedral pdb=" CB CYS B 139 " pdb=" SG CYS B 139 " pdb=" SG CYS B 165 " pdb=" CB CYS B 165 " ideal model delta sinusoidal sigma weight residual 93.00 39.98 53.02 1 1.00e+01 1.00e-02 3.83e+01 ... (remaining 9479 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 1857 0.069 - 0.138: 341 0.138 - 0.208: 45 0.208 - 0.277: 13 0.277 - 0.346: 2 Chirality restraints: 2258 Sorted by residual: chirality pdb=" CA VAL L 184 " pdb=" N VAL L 184 " pdb=" C VAL L 184 " pdb=" CB VAL L 184 " both_signs ideal model delta sigma weight residual False 2.44 2.79 -0.35 2.00e-01 2.50e+01 2.99e+00 chirality pdb=" CB VAL L 184 " pdb=" CA VAL L 184 " pdb=" CG1 VAL L 184 " pdb=" CG2 VAL L 184 " both_signs ideal model delta sigma weight residual False -2.63 -2.32 -0.31 2.00e-01 2.50e+01 2.36e+00 chirality pdb=" CA MET A1746 " pdb=" N MET A1746 " pdb=" C MET A1746 " pdb=" CB MET A1746 " both_signs ideal model delta sigma weight residual False 2.51 2.76 -0.25 2.00e-01 2.50e+01 1.57e+00 ... (remaining 2255 not shown) Planarity restraints: 2740 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER A1886 " 0.021 2.00e-02 2.50e+03 4.14e-02 1.71e+01 pdb=" C SER A1886 " -0.072 2.00e-02 2.50e+03 pdb=" O SER A1886 " 0.027 2.00e-02 2.50e+03 pdb=" N THR A1887 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR H 367 " 0.021 2.00e-02 2.50e+03 4.12e-02 1.70e+01 pdb=" C TYR H 367 " -0.071 2.00e-02 2.50e+03 pdb=" O TYR H 367 " 0.026 2.00e-02 2.50e+03 pdb=" N PRO H 368 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A1621 " 0.232 9.50e-02 1.11e+02 1.08e-01 1.60e+01 pdb=" NE ARG A1621 " -0.032 2.00e-02 2.50e+03 pdb=" CZ ARG A1621 " 0.050 2.00e-02 2.50e+03 pdb=" NH1 ARG A1621 " -0.020 2.00e-02 2.50e+03 pdb=" NH2 ARG A1621 " -0.009 2.00e-02 2.50e+03 ... (remaining 2737 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.69: 572 2.69 - 3.24: 16223 3.24 - 3.79: 24363 3.79 - 4.35: 32687 4.35 - 4.90: 52253 Nonbonded interactions: 126098 Sorted by model distance: nonbonded pdb=" OE2 GLU A2034 " pdb=" NZ LYS A2161 " model vdw 2.135 3.120 nonbonded pdb=" OG SER B 146 " pdb=" OD2 ASP B 153 " model vdw 2.211 3.040 nonbonded pdb=" O PHE E 387 " pdb=" OG1 THR E 390 " model vdw 2.239 3.040 nonbonded pdb=" O LEU A2075 " pdb=" NH1 ARG A2187 " model vdw 2.243 3.120 nonbonded pdb=" OG1 THR B 599 " pdb=" O MET B 634 " model vdw 2.275 3.040 ... (remaining 126093 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 5.010 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: 0.000 Extract box with map and model: 0.210 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 11.080 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5461 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 : 0.012 1.333 15839 Z= 0.838 Angle : 0.955 25.672 21402 Z= 0.598 Chirality : 0.056 0.346 2258 Planarity : 0.007 0.108 2740 Dihedral : 14.188 89.721 5845 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 14.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.07 % Favored : 88.93 % Rotamer: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.15 (0.18), residues: 1843 helix: -1.39 (0.45), residues: 121 sheet: -1.78 (0.28), residues: 357 loop : -2.43 (0.15), residues: 1365 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.053 0.001 ARG A1621 TYR 0.024 0.002 TYR A1966 PHE 0.022 0.002 PHE H 506 TRP 0.031 0.002 TRP H 370 HIS 0.009 0.001 HIS A1812 Details of bonding type rmsd/Z covalent geometry : bond 0.01198 / 0.84 (15818) covalent geometry : angle 0.95284 / 0.60 (21360) SS BOND : bond 0.00589 / 0.34 ( 21) SS BOND : angle 1.79193 / 1.10 ( 42) hydrogen bonds : bond 0.27742 / 17.21 ( 238) hydrogen bonds : angle 12.26054 / 8.12 ( 573) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3686 Ramachandran restraints generated. 1843 Oldfield, 0 Emsley, 1843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3686 Ramachandran restraints generated. 1843 Oldfield, 0 Emsley, 1843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 381 residues out of total 1691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 381 time to evaluate : 0.333 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 134 LYS cc_start: 0.5792 (tptp) cc_final: 0.5569 (mmtt) REVERT: E 136 THR cc_start: 0.7357 (p) cc_final: 0.6933 (t) REVERT: E 281 PHE cc_start: 0.6495 (m-10) cc_final: 0.6246 (m-10) REVERT: E 316 GLN cc_start: 0.7445 (tp40) cc_final: 0.7007 (tm-30) REVERT: A 1640 TYR cc_start: 0.5764 (m-10) cc_final: 0.5349 (m-10) REVERT: A 1736 MET cc_start: 0.5554 (mmm) cc_final: 0.5322 (mmm) REVERT: A 1899 GLU cc_start: 0.6125 (mm-30) cc_final: 0.5917 (mm-30) REVERT: L 244 ASP cc_start: 0.6686 (p0) cc_final: 0.5665 (m-30) REVERT: H 332 SER cc_start: 0.7973 (p) cc_final: 0.7627 (t) REVERT: H 451 GLN cc_start: 0.7249 (tt0) cc_final: 0.6052 (tt0) REVERT: H 454 TYR cc_start: 0.6392 (m-80) cc_final: 0.5771 (m-80) REVERT: B 57 LEU cc_start: 0.6521 (mt) cc_final: 0.5901 (mt) REVERT: B 89 ILE cc_start: 0.7438 (mm) cc_final: 0.6990 (mm) REVERT: B 179 PHE cc_start: 0.8303 (m-80) cc_final: 0.7866 (m-80) REVERT: B 269 ASN cc_start: 0.4162 (t0) cc_final: 0.3548 (m-40) REVERT: B 322 TRP cc_start: 0.7864 (m-90) cc_final: 0.6933 (m-90) REVERT: B 415 TYR cc_start: 0.5464 (m-80) cc_final: 0.5229 (m-80) REVERT: B 441 ASN cc_start: 0.6149 (t0) cc_final: 0.5761 (t0) REVERT: B 443 MET cc_start: 0.1991 (ttp) cc_final: 0.1299 (mtp) REVERT: B 530 TYR cc_start: 0.7191 (m-80) cc_final: 0.6899 (m-80) outliers start: 0 outliers final: 0 residues processed: 381 average time/residue: 0.1018 time to fit residues: 57.9239 Evaluate side-chains 340 residues out of total 1691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 340 time to evaluate : 0.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 98 optimal weight: 0.0070 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 0.7980 chunk 149 optimal weight: 0.7980 overall best weight: 0.7198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 316 GLN E 371 GLN A1629 GLN A1670 ASN A1683 HIS A1713 HIS ** A1781 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1812 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1918 ASN A1977 GLN A2082 ASN A2162 ASN L 213 GLN H 335 GLN H 415 ASN H 451 GLN B 87 GLN B 358 GLN B 534 ASN B 583 HIS ** B 601 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4576 r_free = 0.4576 target = 0.186655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4353 r_free = 0.4353 target = 0.169775 restraints weight = 34851.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4404 r_free = 0.4404 target = 0.173931 restraints weight = 19940.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4440 r_free = 0.4440 target = 0.176723 restraints weight = 12589.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4463 r_free = 0.4463 target = 0.178617 restraints weight = 8591.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.4480 r_free = 0.4480 target = 0.179928 restraints weight = 6183.442| |-----------------------------------------------------------------------------| r_work (final): 0.4482 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5614 moved from start: 0.1978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 15839 Z= 0.168 Angle : 0.708 8.518 21402 Z= 0.367 Chirality : 0.048 0.252 2258 Planarity : 0.005 0.055 2740 Dihedral : 5.886 89.086 2070 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 15.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.05 % Favored : 90.95 % Rotamer: Outliers : 2.01 % Allowed : 11.89 % Favored : 86.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.88 (0.18), residues: 1845 helix: -0.96 (0.47), residues: 124 sheet: -1.70 (0.25), residues: 401 loop : -2.22 (0.16), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG L 296 TYR 0.027 0.002 TYR A1961 PHE 0.030 0.002 PHE A1965 TRP 0.022 0.002 TRP A2084 HIS 0.006 0.001 HIS B 362 Details of bonding type rmsd/Z covalent geometry : bond 0.00381 / 0.17 (15818) covalent geometry : angle 0.70650 / 0.37 (21360) SS BOND : bond 0.00578 / 0.30 ( 21) SS BOND : angle 1.19679 / 0.64 ( 42) hydrogen bonds : bond 0.04871 / 2.98 ( 238) hydrogen bonds : angle 9.02949 / 5.92 ( 573) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3690 Ramachandran restraints generated. 1845 Oldfield, 0 Emsley, 1845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3690 Ramachandran restraints generated. 1845 Oldfield, 0 Emsley, 1845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 406 residues out of total 1691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 372 time to evaluate : 0.411 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: E 134 LYS cc_start: 0.5976 (tptp) cc_final: 0.5730 (mmtt) REVERT: E 136 THR cc_start: 0.7464 (p) cc_final: 0.7037 (t) REVERT: E 373 ASP cc_start: 0.6550 (m-30) cc_final: 0.6150 (m-30) REVERT: A 1667 LYS cc_start: 0.6612 (pttt) cc_final: 0.5801 (ttmt) REVERT: A 1736 MET cc_start: 0.5720 (mmm) cc_final: 0.5247 (mmm) REVERT: A 1786 SER cc_start: 0.8175 (p) cc_final: 0.7956 (p) REVERT: A 1799 ARG cc_start: 0.7179 (tmm-80) cc_final: 0.6695 (ttp80) REVERT: A 1824 ASN cc_start: 0.6120 (t0) cc_final: 0.5746 (t0) REVERT: A 2021 TYR cc_start: 0.6946 (t80) cc_final: 0.6741 (t80) REVERT: A 2186 LEU cc_start: 0.8234 (tp) cc_final: 0.7994 (tp) REVERT: L 242 TYR cc_start: 0.4898 (OUTLIER) cc_final: 0.4554 (t80) REVERT: H 414 GLU cc_start: 0.5372 (tm-30) cc_final: 0.4756 (mt-10) REVERT: B 57 LEU cc_start: 0.6403 (mt) cc_final: 0.6111 (mt) REVERT: B 89 ILE cc_start: 0.7502 (mm) cc_final: 0.7103 (mm) REVERT: B 179 PHE cc_start: 0.8237 (m-80) cc_final: 0.7791 (m-80) REVERT: B 249 GLU cc_start: 0.6236 (mp0) cc_final: 0.5674 (mp0) REVERT: B 320 LYS cc_start: 0.6034 (mppt) cc_final: 0.5785 (ttpt) REVERT: B 322 TRP cc_start: 0.7814 (m-90) cc_final: 0.6703 (m-90) REVERT: B 407 PHE cc_start: 0.7059 (t80) cc_final: 0.6796 (t80) REVERT: B 443 MET cc_start: 0.1464 (ttp) cc_final: 0.1161 (mtp) REVERT: B 464 GLU cc_start: 0.6627 (tm-30) cc_final: 0.6119 (tm-30) REVERT: B 497 ILE cc_start: 0.6909 (mp) cc_final: 0.6528 (mp) outliers start: 34 outliers final: 23 residues processed: 384 average time/residue: 0.0978 time to fit residues: 56.7344 Evaluate side-chains 379 residues out of total 1691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 355 time to evaluate : 0.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 224 THR Chi-restraints excluded: chain E residue 361 ASN Chi-restraints excluded: chain E residue 419 LEU Chi-restraints excluded: chain A residue 1556 ILE Chi-restraints excluded: chain A residue 1681 VAL Chi-restraints excluded: chain A residue 1811 ILE Chi-restraints excluded: chain A residue 1836 LEU Chi-restraints excluded: chain A residue 1837 LEU Chi-restraints excluded: chain A residue 2030 LEU Chi-restraints excluded: chain A residue 2081 VAL Chi-restraints excluded: chain L residue 242 TYR Chi-restraints excluded: chain H residue 564 PHE Chi-restraints excluded: chain B residue 33 PHE Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 141 THR Chi-restraints excluded: chain B residue 164 ILE Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 262 SER Chi-restraints excluded: chain B residue 264 THR Chi-restraints excluded: chain B residue 296 ILE Chi-restraints excluded: chain B residue 367 MET Chi-restraints excluded: chain B residue 374 GLU Chi-restraints excluded: chain B residue 377 THR Chi-restraints excluded: chain B residue 379 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 15 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 chunk 71 optimal weight: 0.0370 chunk 13 optimal weight: 0.8980 chunk 72 optimal weight: 0.8980 chunk 144 optimal weight: 3.9990 chunk 66 optimal weight: 0.7980 chunk 19 optimal weight: 1.9990 chunk 149 optimal weight: 0.7980 chunk 21 optimal weight: 0.6980 chunk 96 optimal weight: 0.4980 overall best weight: 0.5658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 316 GLN ** A1645 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1683 HIS ** A1812 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1918 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1975 ASN ** L 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 476 GLN B 23 ASN B 244 ASN B 471 GLN B 534 ASN ** B 601 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4576 r_free = 0.4576 target = 0.187124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4348 r_free = 0.4348 target = 0.169821 restraints weight = 35068.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4401 r_free = 0.4401 target = 0.174157 restraints weight = 19870.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4436 r_free = 0.4436 target = 0.176984 restraints weight = 12543.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4460 r_free = 0.4460 target = 0.178968 restraints weight = 8535.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4477 r_free = 0.4477 target = 0.180367 restraints weight = 6137.297| |-----------------------------------------------------------------------------| r_work (final): 0.4468 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5643 moved from start: 0.2609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 15839 Z= 0.146 Angle : 0.665 9.596 21402 Z= 0.342 Chirality : 0.047 0.212 2258 Planarity : 0.005 0.057 2740 Dihedral : 5.672 83.167 2070 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 16.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.38 % Favored : 90.62 % Rotamer: Outliers : 2.19 % Allowed : 16.14 % Favored : 81.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.71 (0.18), residues: 1845 helix: -0.90 (0.47), residues: 124 sheet: -1.60 (0.25), residues: 400 loop : -2.09 (0.16), residues: 1321 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 386 TYR 0.020 0.002 TYR A1966 PHE 0.023 0.002 PHE E 281 TRP 0.018 0.001 TRP E 421 HIS 0.007 0.001 HIS B 362 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.15 (15818) covalent geometry : angle 0.66363 / 0.34 (21360) SS BOND : bond 0.00574 / 0.37 ( 21) SS BOND : angle 1.14388 / 0.61 ( 42) hydrogen bonds : bond 0.03793 / 2.33 ( 238) hydrogen bonds : angle 8.33204 / 5.47 ( 573) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3690 Ramachandran restraints generated. 1845 Oldfield, 0 Emsley, 1845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3690 Ramachandran restraints generated. 1845 Oldfield, 0 Emsley, 1845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 413 residues out of total 1691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 376 time to evaluate : 0.501 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: E 136 THR cc_start: 0.7495 (p) cc_final: 0.7057 (t) REVERT: E 373 ASP cc_start: 0.6775 (m-30) cc_final: 0.6339 (m-30) REVERT: A 1667 LYS cc_start: 0.6761 (pttt) cc_final: 0.5919 (tttm) REVERT: A 1736 MET cc_start: 0.5614 (mmm) cc_final: 0.5297 (mmm) REVERT: A 1744 LEU cc_start: 0.8095 (tp) cc_final: 0.7869 (tt) REVERT: A 1824 ASN cc_start: 0.6108 (t0) cc_final: 0.5633 (t0) REVERT: A 2162 ASN cc_start: 0.7592 (m110) cc_final: 0.7260 (m110) REVERT: A 2186 LEU cc_start: 0.8145 (tp) cc_final: 0.7883 (tp) REVERT: L 242 TYR cc_start: 0.5089 (OUTLIER) cc_final: 0.4789 (t80) REVERT: H 414 GLU cc_start: 0.5354 (tm-30) cc_final: 0.4868 (mt-10) REVERT: B 75 LYS cc_start: 0.6849 (mttm) cc_final: 0.6064 (pttt) REVERT: B 89 ILE cc_start: 0.7402 (mm) cc_final: 0.6974 (mm) REVERT: B 179 PHE cc_start: 0.8301 (m-80) cc_final: 0.7834 (m-80) REVERT: B 320 LYS cc_start: 0.6118 (mppt) cc_final: 0.5670 (ttpt) REVERT: B 322 TRP cc_start: 0.7757 (m-90) cc_final: 0.6457 (m-90) REVERT: B 407 PHE cc_start: 0.7043 (t80) cc_final: 0.6740 (t80) REVERT: B 441 ASN cc_start: 0.6002 (t0) cc_final: 0.5640 (t0) REVERT: B 455 TYR cc_start: 0.7139 (m-10) cc_final: 0.6615 (m-80) REVERT: B 544 GLU cc_start: 0.7962 (pm20) cc_final: 0.7619 (pm20) REVERT: B 634 MET cc_start: 0.2736 (mmp) cc_final: 0.2397 (mmm) outliers start: 37 outliers final: 28 residues processed: 389 average time/residue: 0.0944 time to fit residues: 55.8373 Evaluate side-chains 375 residues out of total 1691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 346 time to evaluate : 0.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 224 THR Chi-restraints excluded: chain E residue 236 HIS Chi-restraints excluded: chain E residue 271 HIS Chi-restraints excluded: chain E residue 361 ASN Chi-restraints excluded: chain E residue 419 LEU Chi-restraints excluded: chain A residue 1556 ILE Chi-restraints excluded: chain A residue 1588 LYS Chi-restraints excluded: chain A residue 1681 VAL Chi-restraints excluded: chain A residue 1742 VAL Chi-restraints excluded: chain A residue 1811 ILE Chi-restraints excluded: chain A residue 1836 LEU Chi-restraints excluded: chain A residue 1837 LEU Chi-restraints excluded: chain A residue 1856 LEU Chi-restraints excluded: chain A residue 2028 LEU Chi-restraints excluded: chain A residue 2081 VAL Chi-restraints excluded: chain A residue 2116 LEU Chi-restraints excluded: chain L residue 242 TYR Chi-restraints excluded: chain H residue 564 PHE Chi-restraints excluded: chain B residue 33 PHE Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 141 THR Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 264 THR Chi-restraints excluded: chain B residue 296 ILE Chi-restraints excluded: chain B residue 367 MET Chi-restraints excluded: chain B residue 374 GLU Chi-restraints excluded: chain B residue 377 THR Chi-restraints excluded: chain B residue 379 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 30 optimal weight: 0.9980 chunk 32 optimal weight: 1.9990 chunk 180 optimal weight: 1.9990 chunk 158 optimal weight: 9.9990 chunk 106 optimal weight: 0.9980 chunk 159 optimal weight: 4.9990 chunk 171 optimal weight: 0.9990 chunk 50 optimal weight: 0.9990 chunk 37 optimal weight: 2.9990 chunk 80 optimal weight: 2.9990 chunk 162 optimal weight: 1.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 217 ASN E 316 GLN A1550 ASN ** A1645 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1812 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1869 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1913 ASN A1918 ASN ** L 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 222 HIS B 242 HIS B 244 ASN B 350 GLN B 534 ASN B 556 ASN B 601 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4483 r_free = 0.4483 target = 0.178315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4258 r_free = 0.4258 target = 0.161921 restraints weight = 34887.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4310 r_free = 0.4310 target = 0.166011 restraints weight = 19809.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4346 r_free = 0.4346 target = 0.168764 restraints weight = 12490.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4369 r_free = 0.4369 target = 0.170613 restraints weight = 8502.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4386 r_free = 0.4386 target = 0.171911 restraints weight = 6137.200| |-----------------------------------------------------------------------------| r_work (final): 0.4384 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5828 moved from start: 0.3409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 15839 Z= 0.221 Angle : 0.747 9.914 21402 Z= 0.385 Chirality : 0.048 0.207 2258 Planarity : 0.005 0.059 2740 Dihedral : 6.035 74.075 2070 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 22.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.68 % Favored : 89.32 % Rotamer: Outliers : 4.14 % Allowed : 18.27 % Favored : 77.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.92 (0.18), residues: 1845 helix: -1.15 (0.45), residues: 129 sheet: -1.94 (0.24), residues: 417 loop : -2.15 (0.16), residues: 1299 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A1799 TYR 0.025 0.003 TYR A1966 PHE 0.026 0.002 PHE A2163 TRP 0.025 0.002 TRP B 633 HIS 0.007 0.002 HIS A1815 Details of bonding type rmsd/Z covalent geometry : bond 0.00501 / 0.22 (15818) covalent geometry : angle 0.74552 / 0.38 (21360) SS BOND : bond 0.00866 / 0.44 ( 21) SS BOND : angle 1.29334 / 0.73 ( 42) hydrogen bonds : bond 0.04157 / 2.54 ( 238) hydrogen bonds : angle 8.42180 / 5.54 ( 573) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3690 Ramachandran restraints generated. 1845 Oldfield, 0 Emsley, 1845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3690 Ramachandran restraints generated. 1845 Oldfield, 0 Emsley, 1845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 427 residues out of total 1691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 357 time to evaluate : 0.341 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: E 136 THR cc_start: 0.7336 (p) cc_final: 0.6983 (t) REVERT: E 282 ASP cc_start: 0.7070 (t0) cc_final: 0.6667 (p0) REVERT: E 373 ASP cc_start: 0.7194 (m-30) cc_final: 0.6614 (m-30) REVERT: E 421 TRP cc_start: 0.7828 (t60) cc_final: 0.7519 (t60) REVERT: A 1736 MET cc_start: 0.5658 (mmm) cc_final: 0.5345 (mmm) REVERT: A 1744 LEU cc_start: 0.8207 (tp) cc_final: 0.7939 (tt) REVERT: A 1824 ASN cc_start: 0.6018 (t0) cc_final: 0.5419 (t0) REVERT: A 1935 ILE cc_start: 0.4489 (OUTLIER) cc_final: 0.4285 (pt) REVERT: A 2044 MET cc_start: 0.7650 (tpp) cc_final: 0.6928 (tpt) REVERT: A 2154 THR cc_start: 0.8196 (m) cc_final: 0.7822 (p) REVERT: B 75 LYS cc_start: 0.7097 (mttm) cc_final: 0.6372 (pttt) REVERT: B 179 PHE cc_start: 0.8446 (m-80) cc_final: 0.8077 (m-80) REVERT: B 249 GLU cc_start: 0.6367 (mp0) cc_final: 0.5783 (mp0) REVERT: B 255 VAL cc_start: 0.8030 (m) cc_final: 0.7633 (m) REVERT: B 320 LYS cc_start: 0.6290 (mppt) cc_final: 0.5916 (ttpt) REVERT: B 475 ARG cc_start: 0.7696 (mmt180) cc_final: 0.7318 (mmt180) REVERT: B 544 GLU cc_start: 0.8001 (pm20) cc_final: 0.7670 (pm20) REVERT: B 634 MET cc_start: 0.3239 (mmp) cc_final: 0.2784 (mmm) outliers start: 70 outliers final: 43 residues processed: 391 average time/residue: 0.0976 time to fit residues: 58.4611 Evaluate side-chains 389 residues out of total 1691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 345 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 213 ILE Chi-restraints excluded: chain E residue 224 THR Chi-restraints excluded: chain E residue 236 HIS Chi-restraints excluded: chain E residue 271 HIS Chi-restraints excluded: chain E residue 285 VAL Chi-restraints excluded: chain E residue 293 THR Chi-restraints excluded: chain E residue 361 ASN Chi-restraints excluded: chain E residue 419 LEU Chi-restraints excluded: chain A residue 1550 ASN Chi-restraints excluded: chain A residue 1556 ILE Chi-restraints excluded: chain A residue 1588 LYS Chi-restraints excluded: chain A residue 1609 TYR Chi-restraints excluded: chain A residue 1630 VAL Chi-restraints excluded: chain A residue 1681 VAL Chi-restraints excluded: chain A residue 1742 VAL Chi-restraints excluded: chain A residue 1811 ILE Chi-restraints excluded: chain A residue 1836 LEU Chi-restraints excluded: chain A residue 1837 LEU Chi-restraints excluded: chain A residue 1856 LEU Chi-restraints excluded: chain A residue 1903 TYR Chi-restraints excluded: chain A residue 1935 ILE Chi-restraints excluded: chain A residue 1944 ILE Chi-restraints excluded: chain A residue 1998 THR Chi-restraints excluded: chain A residue 1999 ILE Chi-restraints excluded: chain A residue 2030 LEU Chi-restraints excluded: chain A residue 2081 VAL Chi-restraints excluded: chain A residue 2169 ILE Chi-restraints excluded: chain L residue 240 PHE Chi-restraints excluded: chain H residue 557 TYR Chi-restraints excluded: chain H residue 564 PHE Chi-restraints excluded: chain B residue 33 PHE Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 141 THR Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 254 LYS Chi-restraints excluded: chain B residue 264 THR Chi-restraints excluded: chain B residue 280 ILE Chi-restraints excluded: chain B residue 296 ILE Chi-restraints excluded: chain B residue 350 GLN Chi-restraints excluded: chain B residue 367 MET Chi-restraints excluded: chain B residue 374 GLU Chi-restraints excluded: chain B residue 377 THR Chi-restraints excluded: chain B residue 379 HIS Chi-restraints excluded: chain B residue 560 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 127 optimal weight: 0.9990 chunk 17 optimal weight: 0.9990 chunk 121 optimal weight: 3.9990 chunk 7 optimal weight: 5.9990 chunk 181 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 74 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 182 optimal weight: 0.9980 chunk 172 optimal weight: 0.9990 overall best weight: 1.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 316 GLN ** A1645 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1670 ASN A1683 HIS A1775 HIS ** A1781 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1812 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1918 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1975 ASN ** L 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 318 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 350 GLN B 516 GLN B 583 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4474 r_free = 0.4474 target = 0.177215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4251 r_free = 0.4251 target = 0.161169 restraints weight = 34813.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4303 r_free = 0.4303 target = 0.165214 restraints weight = 19746.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4338 r_free = 0.4338 target = 0.167928 restraints weight = 12401.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4362 r_free = 0.4362 target = 0.169721 restraints weight = 8404.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.4379 r_free = 0.4379 target = 0.170987 restraints weight = 6059.726| |-----------------------------------------------------------------------------| r_work (final): 0.4376 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5854 moved from start: 0.3834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 15839 Z= 0.217 Angle : 0.755 9.051 21402 Z= 0.388 Chirality : 0.049 0.231 2258 Planarity : 0.006 0.058 2740 Dihedral : 6.097 67.723 2070 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 23.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.84 % Favored : 89.16 % Rotamer: Outliers : 4.55 % Allowed : 19.34 % Favored : 76.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.01 (0.18), residues: 1845 helix: -1.17 (0.46), residues: 123 sheet: -2.02 (0.24), residues: 419 loop : -2.21 (0.16), residues: 1303 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 457 TYR 0.022 0.002 TYR B 477 PHE 0.032 0.002 PHE B 407 TRP 0.029 0.002 TRP B 633 HIS 0.006 0.001 HIS A1645 Details of bonding type rmsd/Z covalent geometry : bond 0.00489 / 0.22 (15818) covalent geometry : angle 0.75215 / 0.39 (21360) SS BOND : bond 0.00404 / 0.23 ( 21) SS BOND : angle 1.73288 / 1.07 ( 42) hydrogen bonds : bond 0.04005 / 2.50 ( 238) hydrogen bonds : angle 8.34807 / 5.50 ( 573) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3690 Ramachandran restraints generated. 1845 Oldfield, 0 Emsley, 1845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3690 Ramachandran restraints generated. 1845 Oldfield, 0 Emsley, 1845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 440 residues out of total 1691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 363 time to evaluate : 0.382 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: E 136 THR cc_start: 0.7310 (p) cc_final: 0.6894 (t) REVERT: E 270 LYS cc_start: 0.7420 (mtmm) cc_final: 0.7193 (mtmm) REVERT: E 282 ASP cc_start: 0.7004 (t0) cc_final: 0.6682 (p0) REVERT: E 373 ASP cc_start: 0.7332 (m-30) cc_final: 0.6742 (m-30) REVERT: A 1736 MET cc_start: 0.5732 (mmm) cc_final: 0.5435 (mmm) REVERT: A 1785 TYR cc_start: 0.7862 (OUTLIER) cc_final: 0.6937 (t80) REVERT: A 1824 ASN cc_start: 0.6144 (t0) cc_final: 0.5591 (t0) REVERT: A 1941 LYS cc_start: 0.8095 (ptpp) cc_final: 0.7753 (ptpp) REVERT: A 2044 MET cc_start: 0.7701 (tpp) cc_final: 0.7479 (tpt) REVERT: A 2098 ASP cc_start: 0.7243 (p0) cc_final: 0.6638 (p0) REVERT: A 2120 MET cc_start: 0.6084 (ptt) cc_final: 0.5813 (ptm) REVERT: A 2154 THR cc_start: 0.8178 (m) cc_final: 0.7837 (p) REVERT: B 75 LYS cc_start: 0.7097 (mttm) cc_final: 0.6300 (pttt) REVERT: B 179 PHE cc_start: 0.8420 (m-80) cc_final: 0.8037 (m-80) REVERT: B 249 GLU cc_start: 0.6387 (mp0) cc_final: 0.5854 (mp0) REVERT: B 255 VAL cc_start: 0.8027 (m) cc_final: 0.7659 (m) REVERT: B 320 LYS cc_start: 0.6260 (mppt) cc_final: 0.5605 (ttpt) REVERT: B 322 TRP cc_start: 0.7736 (m-90) cc_final: 0.6524 (m-90) REVERT: B 475 ARG cc_start: 0.7683 (mmt180) cc_final: 0.7376 (mmt180) REVERT: B 544 GLU cc_start: 0.7989 (pm20) cc_final: 0.7688 (pm20) REVERT: B 634 MET cc_start: 0.3201 (mmp) cc_final: 0.2883 (mmm) outliers start: 77 outliers final: 51 residues processed: 397 average time/residue: 0.0916 time to fit residues: 55.9486 Evaluate side-chains 402 residues out of total 1691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 350 time to evaluate : 0.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 111 CYS Chi-restraints excluded: chain E residue 213 ILE Chi-restraints excluded: chain E residue 224 THR Chi-restraints excluded: chain E residue 236 HIS Chi-restraints excluded: chain E residue 244 PHE Chi-restraints excluded: chain E residue 271 HIS Chi-restraints excluded: chain E residue 285 VAL Chi-restraints excluded: chain E residue 293 THR Chi-restraints excluded: chain E residue 361 ASN Chi-restraints excluded: chain E residue 413 THR Chi-restraints excluded: chain E residue 419 LEU Chi-restraints excluded: chain A residue 1556 ILE Chi-restraints excluded: chain A residue 1588 LYS Chi-restraints excluded: chain A residue 1609 TYR Chi-restraints excluded: chain A residue 1630 VAL Chi-restraints excluded: chain A residue 1681 VAL Chi-restraints excluded: chain A residue 1706 VAL Chi-restraints excluded: chain A residue 1742 VAL Chi-restraints excluded: chain A residue 1746 MET Chi-restraints excluded: chain A residue 1785 TYR Chi-restraints excluded: chain A residue 1798 VAL Chi-restraints excluded: chain A residue 1811 ILE Chi-restraints excluded: chain A residue 1836 LEU Chi-restraints excluded: chain A residue 1837 LEU Chi-restraints excluded: chain A residue 1856 LEU Chi-restraints excluded: chain A residue 1903 TYR Chi-restraints excluded: chain A residue 1917 TYR Chi-restraints excluded: chain A residue 2030 LEU Chi-restraints excluded: chain A residue 2081 VAL Chi-restraints excluded: chain A residue 2169 ILE Chi-restraints excluded: chain L residue 240 PHE Chi-restraints excluded: chain H residue 334 TRP Chi-restraints excluded: chain H residue 401 LEU Chi-restraints excluded: chain H residue 557 TYR Chi-restraints excluded: chain H residue 564 PHE Chi-restraints excluded: chain B residue 16 SER Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 141 THR Chi-restraints excluded: chain B residue 197 SER Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 241 ILE Chi-restraints excluded: chain B residue 254 LYS Chi-restraints excluded: chain B residue 296 ILE Chi-restraints excluded: chain B residue 367 MET Chi-restraints excluded: chain B residue 374 GLU Chi-restraints excluded: chain B residue 377 THR Chi-restraints excluded: chain B residue 379 HIS Chi-restraints excluded: chain B residue 483 ILE Chi-restraints excluded: chain B residue 560 THR Chi-restraints excluded: chain B residue 580 VAL Chi-restraints excluded: chain B residue 601 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 26 optimal weight: 0.9980 chunk 16 optimal weight: 1.9990 chunk 76 optimal weight: 0.0040 chunk 45 optimal weight: 1.9990 chunk 13 optimal weight: 0.8980 chunk 127 optimal weight: 0.0670 chunk 150 optimal weight: 2.9990 chunk 178 optimal weight: 0.7980 chunk 36 optimal weight: 0.7980 chunk 5 optimal weight: 4.9990 chunk 148 optimal weight: 0.6980 overall best weight: 0.4730 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 316 GLN A1550 ASN ** A1645 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1812 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1864 GLN A1918 ASN A1975 ASN H 537 ASN H 541 GLN B 358 GLN ** B 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 534 ASN B 556 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4518 r_free = 0.4518 target = 0.180860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4299 r_free = 0.4299 target = 0.164635 restraints weight = 34849.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4350 r_free = 0.4350 target = 0.168729 restraints weight = 19669.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4384 r_free = 0.4384 target = 0.171464 restraints weight = 12392.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.4408 r_free = 0.4408 target = 0.173289 restraints weight = 8403.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 53)----------------| | r_work = 0.4424 r_free = 0.4424 target = 0.174545 restraints weight = 6053.101| |-----------------------------------------------------------------------------| r_work (final): 0.4426 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5748 moved from start: 0.4003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 15839 Z= 0.145 Angle : 0.704 9.155 21402 Z= 0.358 Chirality : 0.047 0.294 2258 Planarity : 0.005 0.061 2740 Dihedral : 5.786 63.963 2070 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 19.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.24 % Favored : 89.76 % Rotamer: Outliers : 3.43 % Allowed : 21.05 % Favored : 75.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.82 (0.18), residues: 1845 helix: -0.85 (0.47), residues: 117 sheet: -1.92 (0.25), residues: 408 loop : -2.08 (0.16), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG E 336 TYR 0.029 0.002 TYR A1702 PHE 0.030 0.002 PHE B 407 TRP 0.015 0.002 TRP A1682 HIS 0.006 0.001 HIS B 362 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.14 (15818) covalent geometry : angle 0.70167 / 0.36 (21360) SS BOND : bond 0.00379 / 0.22 ( 21) SS BOND : angle 1.43252 / 0.85 ( 42) hydrogen bonds : bond 0.03403 / 2.14 ( 238) hydrogen bonds : angle 7.87220 / 5.20 ( 573) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3690 Ramachandran restraints generated. 1845 Oldfield, 0 Emsley, 1845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3690 Ramachandran restraints generated. 1845 Oldfield, 0 Emsley, 1845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 422 residues out of total 1691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 364 time to evaluate : 0.356 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: E 282 ASP cc_start: 0.6912 (t0) cc_final: 0.6653 (p0) REVERT: E 373 ASP cc_start: 0.7070 (m-30) cc_final: 0.6481 (m-30) REVERT: A 1785 TYR cc_start: 0.7731 (OUTLIER) cc_final: 0.6906 (t80) REVERT: A 1824 ASN cc_start: 0.6146 (t0) cc_final: 0.5662 (t0) REVERT: A 1846 MET cc_start: 0.7253 (tmm) cc_final: 0.6893 (tmm) REVERT: A 1868 MET cc_start: 0.6326 (mmt) cc_final: 0.5661 (mmt) REVERT: A 1869 GLN cc_start: 0.6377 (tm-30) cc_final: 0.6145 (tm-30) REVERT: A 1918 ASN cc_start: 0.7453 (OUTLIER) cc_final: 0.6966 (t0) REVERT: A 1941 LYS cc_start: 0.8135 (ptpp) cc_final: 0.7784 (ptpp) REVERT: A 2044 MET cc_start: 0.7228 (tpp) cc_final: 0.6875 (tpt) REVERT: A 2089 ASN cc_start: 0.7047 (p0) cc_final: 0.6352 (p0) REVERT: A 2098 ASP cc_start: 0.7061 (p0) cc_final: 0.6480 (p0) REVERT: A 2154 THR cc_start: 0.8107 (m) cc_final: 0.7742 (p) REVERT: H 414 GLU cc_start: 0.5820 (tm-30) cc_final: 0.5592 (mt-10) REVERT: B 75 LYS cc_start: 0.6947 (mttm) cc_final: 0.6102 (pttt) REVERT: B 89 ILE cc_start: 0.7394 (mm) cc_final: 0.7027 (mm) REVERT: B 158 LEU cc_start: 0.7801 (OUTLIER) cc_final: 0.7501 (tt) REVERT: B 179 PHE cc_start: 0.8306 (m-80) cc_final: 0.8049 (m-80) REVERT: B 255 VAL cc_start: 0.7966 (m) cc_final: 0.7678 (m) REVERT: B 320 LYS cc_start: 0.6193 (mppt) cc_final: 0.5854 (ttpt) REVERT: B 475 ARG cc_start: 0.7597 (mmt180) cc_final: 0.7374 (mmt180) REVERT: B 503 LEU cc_start: 0.5983 (pt) cc_final: 0.5461 (pt) REVERT: B 544 GLU cc_start: 0.7941 (pm20) cc_final: 0.7664 (pm20) outliers start: 58 outliers final: 43 residues processed: 389 average time/residue: 0.0937 time to fit residues: 55.4987 Evaluate side-chains 397 residues out of total 1691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 351 time to evaluate : 0.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 213 ILE Chi-restraints excluded: chain E residue 271 HIS Chi-restraints excluded: chain E residue 361 ASN Chi-restraints excluded: chain E residue 403 CYS Chi-restraints excluded: chain E residue 413 THR Chi-restraints excluded: chain E residue 419 LEU Chi-restraints excluded: chain A residue 1550 ASN Chi-restraints excluded: chain A residue 1556 ILE Chi-restraints excluded: chain A residue 1609 TYR Chi-restraints excluded: chain A residue 1630 VAL Chi-restraints excluded: chain A residue 1681 VAL Chi-restraints excluded: chain A residue 1706 VAL Chi-restraints excluded: chain A residue 1720 LEU Chi-restraints excluded: chain A residue 1742 VAL Chi-restraints excluded: chain A residue 1746 MET Chi-restraints excluded: chain A residue 1785 TYR Chi-restraints excluded: chain A residue 1798 VAL Chi-restraints excluded: chain A residue 1811 ILE Chi-restraints excluded: chain A residue 1836 LEU Chi-restraints excluded: chain A residue 1917 TYR Chi-restraints excluded: chain A residue 1918 ASN Chi-restraints excluded: chain A residue 1944 ILE Chi-restraints excluded: chain A residue 1998 THR Chi-restraints excluded: chain A residue 2030 LEU Chi-restraints excluded: chain A residue 2081 VAL Chi-restraints excluded: chain A residue 2116 LEU Chi-restraints excluded: chain A residue 2169 ILE Chi-restraints excluded: chain H residue 353 ILE Chi-restraints excluded: chain H residue 557 TYR Chi-restraints excluded: chain H residue 564 PHE Chi-restraints excluded: chain B residue 16 SER Chi-restraints excluded: chain B residue 33 PHE Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 141 THR Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 197 SER Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 241 ILE Chi-restraints excluded: chain B residue 254 LYS Chi-restraints excluded: chain B residue 264 THR Chi-restraints excluded: chain B residue 296 ILE Chi-restraints excluded: chain B residue 367 MET Chi-restraints excluded: chain B residue 377 THR Chi-restraints excluded: chain B residue 379 HIS Chi-restraints excluded: chain B residue 560 THR Chi-restraints excluded: chain B residue 601 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 120 optimal weight: 0.0870 chunk 48 optimal weight: 0.9990 chunk 128 optimal weight: 0.0970 chunk 100 optimal weight: 4.9990 chunk 79 optimal weight: 3.9990 chunk 12 optimal weight: 0.8980 chunk 119 optimal weight: 0.9990 chunk 3 optimal weight: 0.6980 chunk 142 optimal weight: 0.8980 chunk 91 optimal weight: 6.9990 chunk 45 optimal weight: 0.7980 overall best weight: 0.5156 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 316 GLN ** A1645 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1812 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1918 ASN A1977 GLN ** B 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 534 ASN B 556 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4514 r_free = 0.4514 target = 0.180557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4295 r_free = 0.4295 target = 0.164299 restraints weight = 34709.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4347 r_free = 0.4347 target = 0.168429 restraints weight = 19624.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4382 r_free = 0.4382 target = 0.171194 restraints weight = 12319.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.4405 r_free = 0.4405 target = 0.173020 restraints weight = 8322.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.4421 r_free = 0.4421 target = 0.174286 restraints weight = 5973.616| |-----------------------------------------------------------------------------| r_work (final): 0.4421 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5754 moved from start: 0.4194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15839 Z= 0.148 Angle : 0.708 9.601 21402 Z= 0.360 Chirality : 0.048 0.411 2258 Planarity : 0.005 0.056 2740 Dihedral : 5.684 64.902 2070 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 19.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.24 % Favored : 89.76 % Rotamer: Outliers : 3.37 % Allowed : 22.24 % Favored : 74.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.76 (0.19), residues: 1845 helix: -0.80 (0.48), residues: 117 sheet: -1.84 (0.25), residues: 414 loop : -2.06 (0.16), residues: 1314 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A1910 TYR 0.036 0.002 TYR H 454 PHE 0.031 0.002 PHE B 407 TRP 0.028 0.002 TRP A1682 HIS 0.008 0.001 HIS B 228 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.15 (15818) covalent geometry : angle 0.70632 / 0.36 (21360) SS BOND : bond 0.00387 / 0.23 ( 21) SS BOND : angle 1.42274 / 0.82 ( 42) hydrogen bonds : bond 0.03308 / 2.12 ( 238) hydrogen bonds : angle 7.74409 / 5.10 ( 573) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3690 Ramachandran restraints generated. 1845 Oldfield, 0 Emsley, 1845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3690 Ramachandran restraints generated. 1845 Oldfield, 0 Emsley, 1845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 408 residues out of total 1691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 351 time to evaluate : 0.414 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: E 329 GLU cc_start: 0.5788 (tm-30) cc_final: 0.5564 (tm-30) REVERT: E 373 ASP cc_start: 0.7185 (m-30) cc_final: 0.6545 (m-30) REVERT: A 1736 MET cc_start: 0.5575 (mmm) cc_final: 0.5223 (mmm) REVERT: A 1785 TYR cc_start: 0.7756 (OUTLIER) cc_final: 0.6877 (t80) REVERT: A 1786 SER cc_start: 0.8298 (p) cc_final: 0.8022 (p) REVERT: A 1824 ASN cc_start: 0.6101 (t0) cc_final: 0.5629 (t0) REVERT: A 1869 GLN cc_start: 0.6361 (tm-30) cc_final: 0.6005 (tm-30) REVERT: A 1918 ASN cc_start: 0.7563 (OUTLIER) cc_final: 0.7192 (t0) REVERT: A 1941 LYS cc_start: 0.8172 (ptpp) cc_final: 0.7788 (ptpp) REVERT: A 2089 ASN cc_start: 0.7042 (p0) cc_final: 0.6312 (p0) REVERT: A 2120 MET cc_start: 0.5841 (ptt) cc_final: 0.5519 (ptm) REVERT: A 2154 THR cc_start: 0.8112 (m) cc_final: 0.7753 (p) REVERT: H 414 GLU cc_start: 0.5800 (tm-30) cc_final: 0.5320 (mt-10) REVERT: B 75 LYS cc_start: 0.6949 (mttm) cc_final: 0.6098 (pttt) REVERT: B 89 ILE cc_start: 0.7395 (mm) cc_final: 0.7026 (mm) REVERT: B 158 LEU cc_start: 0.7636 (OUTLIER) cc_final: 0.7243 (tt) REVERT: B 179 PHE cc_start: 0.8329 (m-80) cc_final: 0.7969 (m-80) REVERT: B 249 GLU cc_start: 0.6232 (mp0) cc_final: 0.5706 (mp0) REVERT: B 255 VAL cc_start: 0.8067 (m) cc_final: 0.7830 (m) REVERT: B 320 LYS cc_start: 0.6186 (mppt) cc_final: 0.5834 (ttpt) REVERT: B 503 LEU cc_start: 0.6020 (pt) cc_final: 0.5540 (pt) REVERT: B 544 GLU cc_start: 0.7916 (pm20) cc_final: 0.7665 (pm20) outliers start: 57 outliers final: 42 residues processed: 379 average time/residue: 0.0988 time to fit residues: 56.9267 Evaluate side-chains 385 residues out of total 1691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 340 time to evaluate : 0.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 111 CYS Chi-restraints excluded: chain E residue 213 ILE Chi-restraints excluded: chain E residue 236 HIS Chi-restraints excluded: chain E residue 271 HIS Chi-restraints excluded: chain E residue 361 ASN Chi-restraints excluded: chain E residue 403 CYS Chi-restraints excluded: chain E residue 419 LEU Chi-restraints excluded: chain A residue 1556 ILE Chi-restraints excluded: chain A residue 1609 TYR Chi-restraints excluded: chain A residue 1630 VAL Chi-restraints excluded: chain A residue 1681 VAL Chi-restraints excluded: chain A residue 1706 VAL Chi-restraints excluded: chain A residue 1742 VAL Chi-restraints excluded: chain A residue 1746 MET Chi-restraints excluded: chain A residue 1785 TYR Chi-restraints excluded: chain A residue 1798 VAL Chi-restraints excluded: chain A residue 1811 ILE Chi-restraints excluded: chain A residue 1836 LEU Chi-restraints excluded: chain A residue 1856 LEU Chi-restraints excluded: chain A residue 1917 TYR Chi-restraints excluded: chain A residue 1918 ASN Chi-restraints excluded: chain A residue 2025 THR Chi-restraints excluded: chain A residue 2081 VAL Chi-restraints excluded: chain A residue 2116 LEU Chi-restraints excluded: chain A residue 2169 ILE Chi-restraints excluded: chain L residue 215 VAL Chi-restraints excluded: chain H residue 353 ILE Chi-restraints excluded: chain H residue 557 TYR Chi-restraints excluded: chain H residue 564 PHE Chi-restraints excluded: chain B residue 33 PHE Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 141 THR Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 197 SER Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 241 ILE Chi-restraints excluded: chain B residue 296 ILE Chi-restraints excluded: chain B residue 367 MET Chi-restraints excluded: chain B residue 377 THR Chi-restraints excluded: chain B residue 379 HIS Chi-restraints excluded: chain B residue 466 THR Chi-restraints excluded: chain B residue 534 ASN Chi-restraints excluded: chain B residue 560 THR Chi-restraints excluded: chain B residue 601 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 93 optimal weight: 1.9990 chunk 126 optimal weight: 0.2980 chunk 87 optimal weight: 3.9990 chunk 168 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 50 optimal weight: 0.5980 chunk 16 optimal weight: 1.9990 chunk 103 optimal weight: 0.3980 chunk 164 optimal weight: 0.8980 chunk 151 optimal weight: 2.9990 chunk 117 optimal weight: 0.9990 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 135 GLN E 316 GLN E 361 ASN ** A1645 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1670 ASN A1683 HIS ** A1812 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1918 ASN A1940 GLN L 205 HIS L 206 GLN ** B 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 441 ASN B 534 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4509 r_free = 0.4509 target = 0.180092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4290 r_free = 0.4290 target = 0.163903 restraints weight = 35103.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4342 r_free = 0.4342 target = 0.168021 restraints weight = 19824.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4377 r_free = 0.4377 target = 0.170798 restraints weight = 12481.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.4400 r_free = 0.4400 target = 0.172641 restraints weight = 8437.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4416 r_free = 0.4416 target = 0.173894 restraints weight = 6044.394| |-----------------------------------------------------------------------------| r_work (final): 0.4415 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5774 moved from start: 0.4389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 15839 Z= 0.156 Angle : 0.718 10.787 21402 Z= 0.364 Chirality : 0.047 0.265 2258 Planarity : 0.005 0.057 2740 Dihedral : 5.665 66.334 2070 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 19.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.46 % Favored : 89.54 % Rotamer: Outliers : 3.37 % Allowed : 23.30 % Favored : 73.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.79 (0.19), residues: 1845 helix: -0.93 (0.47), residues: 123 sheet: -1.82 (0.25), residues: 413 loop : -2.08 (0.16), residues: 1309 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1910 TYR 0.025 0.002 TYR A1702 PHE 0.029 0.002 PHE B 407 TRP 0.022 0.002 TRP B 633 HIS 0.008 0.001 HIS B 228 Details of bonding type rmsd/Z covalent geometry : bond 0.00361 / 0.16 (15818) covalent geometry : angle 0.71599 / 0.36 (21360) SS BOND : bond 0.00365 / 0.21 ( 21) SS BOND : angle 1.42131 / 0.83 ( 42) hydrogen bonds : bond 0.03292 / 2.09 ( 238) hydrogen bonds : angle 7.64859 / 5.07 ( 573) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3690 Ramachandran restraints generated. 1845 Oldfield, 0 Emsley, 1845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3690 Ramachandran restraints generated. 1845 Oldfield, 0 Emsley, 1845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 402 residues out of total 1691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 345 time to evaluate : 0.443 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: E 329 GLU cc_start: 0.5860 (tm-30) cc_final: 0.5655 (tm-30) REVERT: E 373 ASP cc_start: 0.7164 (m-30) cc_final: 0.6538 (m-30) REVERT: A 1785 TYR cc_start: 0.7672 (OUTLIER) cc_final: 0.7009 (t80) REVERT: A 1824 ASN cc_start: 0.6127 (t0) cc_final: 0.5606 (t0) REVERT: A 1868 MET cc_start: 0.6428 (mmt) cc_final: 0.5717 (mmt) REVERT: A 1869 GLN cc_start: 0.6353 (tm-30) cc_final: 0.5928 (tm-30) REVERT: A 1941 LYS cc_start: 0.8206 (ptpp) cc_final: 0.7836 (ptpp) REVERT: A 2089 ASN cc_start: 0.7028 (p0) cc_final: 0.6284 (p0) REVERT: A 2120 MET cc_start: 0.5907 (ptt) cc_final: 0.5646 (ptm) REVERT: A 2123 LYS cc_start: 0.6347 (mmmm) cc_final: 0.6105 (tptm) REVERT: A 2154 THR cc_start: 0.8139 (m) cc_final: 0.7791 (p) REVERT: H 414 GLU cc_start: 0.5473 (tm-30) cc_final: 0.5257 (mp0) REVERT: B 75 LYS cc_start: 0.7022 (mttm) cc_final: 0.6161 (pttt) REVERT: B 89 ILE cc_start: 0.7419 (mm) cc_final: 0.7057 (mm) REVERT: B 158 LEU cc_start: 0.7558 (tt) cc_final: 0.7186 (tt) REVERT: B 179 PHE cc_start: 0.8324 (m-80) cc_final: 0.7992 (m-80) REVERT: B 249 GLU cc_start: 0.6237 (mp0) cc_final: 0.5720 (mp0) REVERT: B 255 VAL cc_start: 0.8104 (m) cc_final: 0.7732 (p) REVERT: B 277 LYS cc_start: 0.6827 (mmmm) cc_final: 0.6607 (mmmm) REVERT: B 320 LYS cc_start: 0.6210 (mppt) cc_final: 0.5829 (ttpt) REVERT: B 475 ARG cc_start: 0.7612 (mmt180) cc_final: 0.7332 (mmt180) REVERT: B 503 LEU cc_start: 0.5987 (pt) cc_final: 0.5529 (pt) REVERT: B 544 GLU cc_start: 0.7936 (pm20) cc_final: 0.7394 (pm20) REVERT: B 574 PHE cc_start: 0.6999 (m-10) cc_final: 0.6767 (m-80) outliers start: 57 outliers final: 43 residues processed: 372 average time/residue: 0.0988 time to fit residues: 56.4071 Evaluate side-chains 383 residues out of total 1691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 339 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 111 CYS Chi-restraints excluded: chain E residue 213 ILE Chi-restraints excluded: chain E residue 224 THR Chi-restraints excluded: chain E residue 271 HIS Chi-restraints excluded: chain E residue 361 ASN Chi-restraints excluded: chain E residue 403 CYS Chi-restraints excluded: chain E residue 419 LEU Chi-restraints excluded: chain A residue 1609 TYR Chi-restraints excluded: chain A residue 1630 VAL Chi-restraints excluded: chain A residue 1681 VAL Chi-restraints excluded: chain A residue 1706 VAL Chi-restraints excluded: chain A residue 1742 VAL Chi-restraints excluded: chain A residue 1746 MET Chi-restraints excluded: chain A residue 1785 TYR Chi-restraints excluded: chain A residue 1798 VAL Chi-restraints excluded: chain A residue 1811 ILE Chi-restraints excluded: chain A residue 1836 LEU Chi-restraints excluded: chain A residue 1856 LEU Chi-restraints excluded: chain A residue 1917 TYR Chi-restraints excluded: chain A residue 2025 THR Chi-restraints excluded: chain A residue 2030 LEU Chi-restraints excluded: chain A residue 2040 THR Chi-restraints excluded: chain A residue 2081 VAL Chi-restraints excluded: chain A residue 2169 ILE Chi-restraints excluded: chain L residue 171 VAL Chi-restraints excluded: chain L residue 215 VAL Chi-restraints excluded: chain H residue 353 ILE Chi-restraints excluded: chain H residue 557 TYR Chi-restraints excluded: chain H residue 564 PHE Chi-restraints excluded: chain B residue 33 PHE Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 141 THR Chi-restraints excluded: chain B residue 197 SER Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 241 ILE Chi-restraints excluded: chain B residue 296 ILE Chi-restraints excluded: chain B residue 367 MET Chi-restraints excluded: chain B residue 377 THR Chi-restraints excluded: chain B residue 379 HIS Chi-restraints excluded: chain B residue 466 THR Chi-restraints excluded: chain B residue 534 ASN Chi-restraints excluded: chain B residue 560 THR Chi-restraints excluded: chain B residue 580 VAL Chi-restraints excluded: chain B residue 601 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 69 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 chunk 148 optimal weight: 0.7980 chunk 44 optimal weight: 0.7980 chunk 34 optimal weight: 0.5980 chunk 35 optimal weight: 1.9990 chunk 73 optimal weight: 0.4980 chunk 159 optimal weight: 2.9990 chunk 46 optimal weight: 0.7980 chunk 95 optimal weight: 5.9990 chunk 8 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 316 GLN E 361 ASN ** A1645 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1812 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1918 ASN A1993 ASN ** A2082 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 534 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4503 r_free = 0.4503 target = 0.179514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4285 r_free = 0.4285 target = 0.163479 restraints weight = 34622.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4336 r_free = 0.4336 target = 0.167540 restraints weight = 19660.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4373 r_free = 0.4373 target = 0.170340 restraints weight = 12383.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.4396 r_free = 0.4396 target = 0.172172 restraints weight = 8397.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.4412 r_free = 0.4412 target = 0.173419 restraints weight = 6013.941| |-----------------------------------------------------------------------------| r_work (final): 0.4410 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5792 moved from start: 0.4585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 15839 Z= 0.161 Angle : 0.738 10.768 21402 Z= 0.373 Chirality : 0.048 0.308 2258 Planarity : 0.005 0.057 2740 Dihedral : 5.640 67.434 2070 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 19.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.89 % Favored : 89.11 % Rotamer: Outliers : 3.67 % Allowed : 23.30 % Favored : 73.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.81 (0.19), residues: 1845 helix: -1.02 (0.47), residues: 123 sheet: -1.83 (0.25), residues: 420 loop : -2.09 (0.16), residues: 1302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1910 TYR 0.045 0.002 TYR L 316 PHE 0.034 0.002 PHE B 407 TRP 0.020 0.002 TRP B 633 HIS 0.008 0.001 HIS B 228 Details of bonding type rmsd/Z covalent geometry : bond 0.00372 / 0.16 (15818) covalent geometry : angle 0.73596 / 0.37 (21360) SS BOND : bond 0.00354 / 0.20 ( 21) SS BOND : angle 1.40437 / 0.82 ( 42) hydrogen bonds : bond 0.03450 / 2.21 ( 238) hydrogen bonds : angle 7.54448 / 5.04 ( 573) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3690 Ramachandran restraints generated. 1845 Oldfield, 0 Emsley, 1845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3690 Ramachandran restraints generated. 1845 Oldfield, 0 Emsley, 1845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 407 residues out of total 1691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 345 time to evaluate : 0.584 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: E 270 LYS cc_start: 0.7356 (mtmm) cc_final: 0.7148 (mtmm) REVERT: E 329 GLU cc_start: 0.5944 (tm-30) cc_final: 0.5728 (tm-30) REVERT: E 373 ASP cc_start: 0.7213 (m-30) cc_final: 0.6694 (m-30) REVERT: A 1628 ILE cc_start: 0.7932 (OUTLIER) cc_final: 0.7556 (tt) REVERT: A 1785 TYR cc_start: 0.7675 (OUTLIER) cc_final: 0.7133 (t80) REVERT: A 1824 ASN cc_start: 0.6133 (t0) cc_final: 0.5617 (t0) REVERT: A 1868 MET cc_start: 0.6468 (mmt) cc_final: 0.5866 (mmt) REVERT: A 1869 GLN cc_start: 0.6343 (tm-30) cc_final: 0.5945 (tm-30) REVERT: A 1918 ASN cc_start: 0.7606 (OUTLIER) cc_final: 0.7119 (t0) REVERT: A 1941 LYS cc_start: 0.8247 (ptpp) cc_final: 0.7873 (ptpp) REVERT: A 2089 ASN cc_start: 0.7066 (p0) cc_final: 0.6257 (p0) REVERT: A 2120 MET cc_start: 0.5927 (ptt) cc_final: 0.5691 (ptm) REVERT: A 2123 LYS cc_start: 0.6283 (mmmm) cc_final: 0.6063 (tptm) REVERT: A 2154 THR cc_start: 0.8172 (m) cc_final: 0.7857 (p) REVERT: H 414 GLU cc_start: 0.5644 (tm-30) cc_final: 0.5409 (mp0) REVERT: B 75 LYS cc_start: 0.7049 (mttm) cc_final: 0.6202 (pttt) REVERT: B 89 ILE cc_start: 0.7394 (mm) cc_final: 0.7057 (mm) REVERT: B 158 LEU cc_start: 0.7561 (tt) cc_final: 0.7119 (tt) REVERT: B 179 PHE cc_start: 0.8334 (m-80) cc_final: 0.8016 (m-80) REVERT: B 249 GLU cc_start: 0.6253 (mp0) cc_final: 0.5724 (mp0) REVERT: B 255 VAL cc_start: 0.8109 (m) cc_final: 0.7725 (m) REVERT: B 277 LYS cc_start: 0.6855 (mmmm) cc_final: 0.6624 (mmmm) REVERT: B 320 LYS cc_start: 0.6198 (mppt) cc_final: 0.5818 (ttpt) REVERT: B 474 THR cc_start: 0.8006 (m) cc_final: 0.7765 (m) REVERT: B 475 ARG cc_start: 0.7575 (mmt180) cc_final: 0.7273 (mmt180) REVERT: B 503 LEU cc_start: 0.5924 (pt) cc_final: 0.5472 (pt) REVERT: B 544 GLU cc_start: 0.7919 (pm20) cc_final: 0.7419 (pm20) REVERT: B 574 PHE cc_start: 0.7056 (m-10) cc_final: 0.6836 (m-80) outliers start: 62 outliers final: 50 residues processed: 377 average time/residue: 0.1002 time to fit residues: 57.5458 Evaluate side-chains 392 residues out of total 1691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 339 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 111 CYS Chi-restraints excluded: chain E residue 213 ILE Chi-restraints excluded: chain E residue 224 THR Chi-restraints excluded: chain E residue 271 HIS Chi-restraints excluded: chain E residue 293 THR Chi-restraints excluded: chain E residue 361 ASN Chi-restraints excluded: chain E residue 403 CYS Chi-restraints excluded: chain E residue 419 LEU Chi-restraints excluded: chain A residue 1556 ILE Chi-restraints excluded: chain A residue 1609 TYR Chi-restraints excluded: chain A residue 1628 ILE Chi-restraints excluded: chain A residue 1630 VAL Chi-restraints excluded: chain A residue 1681 VAL Chi-restraints excluded: chain A residue 1706 VAL Chi-restraints excluded: chain A residue 1738 MET Chi-restraints excluded: chain A residue 1742 VAL Chi-restraints excluded: chain A residue 1746 MET Chi-restraints excluded: chain A residue 1785 TYR Chi-restraints excluded: chain A residue 1798 VAL Chi-restraints excluded: chain A residue 1811 ILE Chi-restraints excluded: chain A residue 1836 LEU Chi-restraints excluded: chain A residue 1856 LEU Chi-restraints excluded: chain A residue 1917 TYR Chi-restraints excluded: chain A residue 1918 ASN Chi-restraints excluded: chain A residue 2025 THR Chi-restraints excluded: chain A residue 2030 LEU Chi-restraints excluded: chain A residue 2040 THR Chi-restraints excluded: chain A residue 2081 VAL Chi-restraints excluded: chain A residue 2169 ILE Chi-restraints excluded: chain L residue 171 VAL Chi-restraints excluded: chain L residue 215 VAL Chi-restraints excluded: chain H residue 334 TRP Chi-restraints excluded: chain H residue 353 ILE Chi-restraints excluded: chain H residue 411 ASN Chi-restraints excluded: chain H residue 557 TYR Chi-restraints excluded: chain H residue 564 PHE Chi-restraints excluded: chain B residue 33 PHE Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 141 THR Chi-restraints excluded: chain B residue 197 SER Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 241 ILE Chi-restraints excluded: chain B residue 296 ILE Chi-restraints excluded: chain B residue 367 MET Chi-restraints excluded: chain B residue 377 THR Chi-restraints excluded: chain B residue 379 HIS Chi-restraints excluded: chain B residue 391 LEU Chi-restraints excluded: chain B residue 466 THR Chi-restraints excluded: chain B residue 534 ASN Chi-restraints excluded: chain B residue 560 THR Chi-restraints excluded: chain B residue 580 VAL Chi-restraints excluded: chain B residue 601 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 14 optimal weight: 0.0970 chunk 102 optimal weight: 3.9990 chunk 8 optimal weight: 0.0870 chunk 55 optimal weight: 3.9990 chunk 95 optimal weight: 4.9990 chunk 37 optimal weight: 1.9990 chunk 135 optimal weight: 0.7980 chunk 109 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 86 optimal weight: 0.6980 chunk 139 optimal weight: 1.9990 overall best weight: 0.7358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 316 GLN E 361 ASN A1629 GLN ** A1812 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1918 ASN ** A2082 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 87 GLN ** B 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 534 ASN ** B 597 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4495 r_free = 0.4495 target = 0.178906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4277 r_free = 0.4277 target = 0.162792 restraints weight = 34813.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4329 r_free = 0.4329 target = 0.166895 restraints weight = 19847.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4365 r_free = 0.4365 target = 0.169686 restraints weight = 12495.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.4387 r_free = 0.4387 target = 0.171539 restraints weight = 8477.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.4404 r_free = 0.4404 target = 0.172821 restraints weight = 6072.260| |-----------------------------------------------------------------------------| r_work (final): 0.4402 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5804 moved from start: 0.4728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 15839 Z= 0.171 Angle : 0.756 12.995 21402 Z= 0.384 Chirality : 0.049 0.303 2258 Planarity : 0.005 0.057 2740 Dihedral : 5.713 67.987 2070 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 20.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.73 % Favored : 89.27 % Rotamer: Outliers : 3.19 % Allowed : 23.83 % Favored : 72.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.82 (0.19), residues: 1845 helix: -1.08 (0.47), residues: 124 sheet: -1.81 (0.25), residues: 415 loop : -2.11 (0.16), residues: 1306 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A1910 TYR 0.061 0.002 TYR B 453 PHE 0.032 0.002 PHE E 281 TRP 0.026 0.002 TRP B 278 HIS 0.008 0.001 HIS B 228 Details of bonding type rmsd/Z covalent geometry : bond 0.00391 / 0.17 (15818) covalent geometry : angle 0.75340 / 0.38 (21360) SS BOND : bond 0.00470 / 0.26 ( 21) SS BOND : angle 1.58447 / 0.92 ( 42) hydrogen bonds : bond 0.03626 / 2.34 ( 238) hydrogen bonds : angle 7.56570 / 5.07 ( 573) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3690 Ramachandran restraints generated. 1845 Oldfield, 0 Emsley, 1845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3690 Ramachandran restraints generated. 1845 Oldfield, 0 Emsley, 1845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 395 residues out of total 1691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 341 time to evaluate : 0.536 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 270 LYS cc_start: 0.7365 (mtmm) cc_final: 0.7144 (mtmm) REVERT: E 329 GLU cc_start: 0.6081 (tm-30) cc_final: 0.5877 (tm-30) REVERT: E 373 ASP cc_start: 0.7224 (m-30) cc_final: 0.6826 (m-30) REVERT: A 1628 ILE cc_start: 0.7940 (OUTLIER) cc_final: 0.7569 (tt) REVERT: A 1783 MET cc_start: 0.6349 (mpp) cc_final: 0.5721 (mmm) REVERT: A 1792 MET cc_start: 0.7029 (pmm) cc_final: 0.6787 (pmm) REVERT: A 1824 ASN cc_start: 0.6125 (t0) cc_final: 0.5604 (t0) REVERT: A 1868 MET cc_start: 0.6478 (mmt) cc_final: 0.5855 (mmt) REVERT: A 1869 GLN cc_start: 0.6297 (tm-30) cc_final: 0.5892 (tm-30) REVERT: A 1918 ASN cc_start: 0.7714 (OUTLIER) cc_final: 0.7508 (t160) REVERT: A 1941 LYS cc_start: 0.8269 (ptpp) cc_final: 0.7909 (ptpp) REVERT: A 2089 ASN cc_start: 0.7100 (p0) cc_final: 0.6313 (p0) REVERT: A 2120 MET cc_start: 0.5917 (ptt) cc_final: 0.5701 (ptm) REVERT: A 2154 THR cc_start: 0.8254 (m) cc_final: 0.7939 (p) REVERT: B 75 LYS cc_start: 0.7059 (mttm) cc_final: 0.6201 (pttt) REVERT: B 89 ILE cc_start: 0.7398 (mm) cc_final: 0.7047 (mm) REVERT: B 158 LEU cc_start: 0.7528 (tt) cc_final: 0.7074 (tt) REVERT: B 179 PHE cc_start: 0.8327 (m-80) cc_final: 0.8009 (m-80) REVERT: B 249 GLU cc_start: 0.6219 (mp0) cc_final: 0.5689 (mp0) REVERT: B 255 VAL cc_start: 0.8076 (m) cc_final: 0.7661 (m) REVERT: B 277 LYS cc_start: 0.6793 (mmmm) cc_final: 0.6559 (mmmm) REVERT: B 320 LYS cc_start: 0.6209 (mppt) cc_final: 0.5809 (ttpt) REVERT: B 474 THR cc_start: 0.8036 (m) cc_final: 0.7830 (m) REVERT: B 475 ARG cc_start: 0.7524 (mmt180) cc_final: 0.7309 (mmt180) REVERT: B 503 LEU cc_start: 0.5966 (pt) cc_final: 0.5523 (pt) REVERT: B 544 GLU cc_start: 0.7913 (pm20) cc_final: 0.7542 (pt0) REVERT: B 574 PHE cc_start: 0.7158 (m-10) cc_final: 0.6953 (m-80) REVERT: B 649 LEU cc_start: 0.7158 (mm) cc_final: 0.6945 (mm) outliers start: 54 outliers final: 47 residues processed: 366 average time/residue: 0.1008 time to fit residues: 56.5849 Evaluate side-chains 382 residues out of total 1691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 333 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 111 CYS Chi-restraints excluded: chain E residue 213 ILE Chi-restraints excluded: chain E residue 224 THR Chi-restraints excluded: chain E residue 271 HIS Chi-restraints excluded: chain E residue 293 THR Chi-restraints excluded: chain E residue 403 CYS Chi-restraints excluded: chain E residue 419 LEU Chi-restraints excluded: chain A residue 1556 ILE Chi-restraints excluded: chain A residue 1609 TYR Chi-restraints excluded: chain A residue 1628 ILE Chi-restraints excluded: chain A residue 1630 VAL Chi-restraints excluded: chain A residue 1681 VAL Chi-restraints excluded: chain A residue 1706 VAL Chi-restraints excluded: chain A residue 1738 MET Chi-restraints excluded: chain A residue 1742 VAL Chi-restraints excluded: chain A residue 1746 MET Chi-restraints excluded: chain A residue 1798 VAL Chi-restraints excluded: chain A residue 1811 ILE Chi-restraints excluded: chain A residue 1836 LEU Chi-restraints excluded: chain A residue 1856 LEU Chi-restraints excluded: chain A residue 1917 TYR Chi-restraints excluded: chain A residue 1918 ASN Chi-restraints excluded: chain A residue 2025 THR Chi-restraints excluded: chain A residue 2030 LEU Chi-restraints excluded: chain A residue 2081 VAL Chi-restraints excluded: chain A residue 2169 ILE Chi-restraints excluded: chain L residue 171 VAL Chi-restraints excluded: chain L residue 215 VAL Chi-restraints excluded: chain H residue 411 ASN Chi-restraints excluded: chain H residue 557 TYR Chi-restraints excluded: chain H residue 564 PHE Chi-restraints excluded: chain B residue 33 PHE Chi-restraints excluded: chain B residue 36 ILE Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 141 THR Chi-restraints excluded: chain B residue 197 SER Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 241 ILE Chi-restraints excluded: chain B residue 296 ILE Chi-restraints excluded: chain B residue 367 MET Chi-restraints excluded: chain B residue 377 THR Chi-restraints excluded: chain B residue 379 HIS Chi-restraints excluded: chain B residue 391 LEU Chi-restraints excluded: chain B residue 466 THR Chi-restraints excluded: chain B residue 534 ASN Chi-restraints excluded: chain B residue 560 THR Chi-restraints excluded: chain B residue 561 ILE Chi-restraints excluded: chain B residue 580 VAL Chi-restraints excluded: chain B residue 601 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 26 optimal weight: 3.9990 chunk 51 optimal weight: 0.0870 chunk 131 optimal weight: 0.8980 chunk 89 optimal weight: 0.4980 chunk 80 optimal weight: 0.5980 chunk 32 optimal weight: 0.9980 chunk 178 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 94 optimal weight: 0.9990 chunk 164 optimal weight: 2.9990 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 316 GLN ** A1812 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1918 ASN ** A2082 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 5 GLN ** B 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 534 ASN ** B 597 HIS ** 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 = 0.4504 r_free = 0.4504 target = 0.179668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4288 r_free = 0.4288 target = 0.163639 restraints weight = 34823.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4340 r_free = 0.4340 target = 0.167691 restraints weight = 19800.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4376 r_free = 0.4376 target = 0.170484 restraints weight = 12533.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.4399 r_free = 0.4399 target = 0.172323 restraints weight = 8514.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.4416 r_free = 0.4416 target = 0.173609 restraints weight = 6108.553| |-----------------------------------------------------------------------------| r_work (final): 0.4417 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5785 moved from start: 0.4839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 15839 Z= 0.158 Angle : 0.756 13.159 21402 Z= 0.382 Chirality : 0.049 0.274 2258 Planarity : 0.005 0.057 2740 Dihedral : 5.699 68.883 2070 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 21.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.00 % Favored : 89.00 % Rotamer: Outliers : 3.13 % Allowed : 24.01 % Favored : 72.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.84 (0.19), residues: 1845 helix: -1.12 (0.46), residues: 124 sheet: -1.82 (0.25), residues: 415 loop : -2.11 (0.16), residues: 1306 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1910 TYR 0.075 0.002 TYR B 453 PHE 0.042 0.002 PHE B 407 TRP 0.030 0.002 TRP A1682 HIS 0.009 0.001 HIS B 228 Details of bonding type rmsd/Z covalent geometry : bond 0.00369 / 0.16 (15818) covalent geometry : angle 0.75395 / 0.38 (21360) SS BOND : bond 0.00398 / 0.23 ( 21) SS BOND : angle 1.49669 / 0.87 ( 42) hydrogen bonds : bond 0.03572 / 2.30 ( 238) hydrogen bonds : angle 7.49480 / 5.02 ( 573) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2254.60 seconds wall clock time: 39 minutes 58.56 seconds (2398.56 seconds total)