Starting phenix.real_space_refine on Sat Jan 20 01:24:51 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eop_28451/01_2024/8eop_28451_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eop_28451/01_2024/8eop_28451.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eop_28451/01_2024/8eop_28451.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eop_28451/01_2024/8eop_28451.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eop_28451/01_2024/8eop_28451_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eop_28451/01_2024/8eop_28451_updated.pdb" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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: 6 Type Number sf(0) Gaussians P 6 5.49 5 Mg 2 5.21 5 S 63 5.16 5 C 8504 2.51 5 N 2320 2.21 5 O 2370 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/chem_data/mon_lib" Total number of atoms: 13265 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 13050 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1687, 13050 Classifications: {'peptide': 1687} Link IDs: {'PTRANS': 105, 'TRANS': 1581} Chain breaks: 9 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 148 Unusual residues: {' MG': 2, 'ATP': 2, 'NAG': 6} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Time building chain proxies: 7.22, per 1000 atoms: 0.54 Number of scatterers: 13265 At special positions: 0 Unit cell: (159.131, 147.574, 105.791, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 63 16.00 P 6 15.00 Mg 2 11.99 O 2370 8.00 N 2320 7.00 C 8504 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 81 " distance=2.03 Simple disulfide: pdb=" SG CYS A 75 " - pdb=" SG CYS A 225 " distance=2.03 Simple disulfide: pdb=" SG CYS A 267 " - pdb=" SG CYS A 406 " distance=2.03 Simple disulfide: pdb=" SG CYS A1347 " - pdb=" SG CYS A1359 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG B 1 " - " NAG B 2 " " NAG B 2 " - " BMA B 3 " " NAG C 1 " - " NAG C 2 " NAG-ASN " NAG A2201 " - " ASN A 78 " " NAG A2202 " - " ASN A 98 " " NAG A2203 " - " ASN A 312 " " NAG A2204 " - " ASN A 340 " " NAG A2205 " - " ASN A1518 " " NAG A2206 " - " ASN A1457 " " NAG B 1 " - " ASN A1386 " " NAG C 1 " - " ASN A1381 " Time building additional restraints: 5.54 Conformation dependent library (CDL) restraints added in 2.4 seconds 3334 Ramachandran restraints generated. 1667 Oldfield, 0 Emsley, 1667 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3094 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 72 helices and 9 sheets defined 53.1% alpha, 3.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.34 Creating SS restraints... Processing helix chain 'A' and resid 3 through 20 Processing helix chain 'A' and resid 22 through 45 Proline residue: A 32 - end of helix removed outlier: 5.807A pdb=" N LEU A 35 " --> pdb=" O TRP A 31 " (cutoff:3.500A) removed outlier: 5.379A pdb=" N PHE A 36 " --> pdb=" O PRO A 32 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N SER A 45 " --> pdb=" O ALA A 41 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 64 No H-bonds generated for 'chain 'A' and resid 62 through 64' Processing helix chain 'A' and resid 67 through 75 Processing helix chain 'A' and resid 87 through 89 No H-bonds generated for 'chain 'A' and resid 87 through 89' Processing helix chain 'A' and resid 101 through 115 Processing helix chain 'A' and resid 117 through 125 Processing helix chain 'A' and resid 183 through 193 Processing helix chain 'A' and resid 199 through 207 Processing helix chain 'A' and resid 216 through 224 Processing helix chain 'A' and resid 265 through 276 removed outlier: 4.201A pdb=" N SER A 276 " --> pdb=" O GLY A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 278 through 291 removed outlier: 4.777A pdb=" N LEU A 283 " --> pdb=" O LEU A 279 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N TRP A 284 " --> pdb=" O SER A 280 " (cutoff:3.500A) Proline residue: A 289 - end of helix Processing helix chain 'A' and resid 302 through 339 removed outlier: 3.746A pdb=" N ARG A 313 " --> pdb=" O ALA A 309 " (cutoff:3.500A) removed outlier: 5.201A pdb=" N THR A 314 " --> pdb=" O GLN A 310 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N PHE A 315 " --> pdb=" O VAL A 311 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N THR A 319 " --> pdb=" O PHE A 315 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N LEU A 320 " --> pdb=" O GLU A 316 " (cutoff:3.500A) removed outlier: 5.703A pdb=" N LEU A 321 " --> pdb=" O GLU A 317 " (cutoff:3.500A) removed outlier: 5.985A pdb=" N ARG A 322 " --> pdb=" O LEU A 318 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ASP A 323 " --> pdb=" O THR A 319 " (cutoff:3.500A) Proline residue: A 333 - end of helix Processing helix chain 'A' and resid 343 through 353 Processing helix chain 'A' and resid 373 through 378 Processing helix chain 'A' and resid 380 through 382 No H-bonds generated for 'chain 'A' and resid 380 through 382' Processing helix chain 'A' and resid 388 through 406 Processing helix chain 'A' and resid 418 through 431 removed outlier: 4.362A pdb=" N ALA A 430 " --> pdb=" O LEU A 426 " (cutoff:3.500A) removed outlier: 5.030A pdb=" N GLU A 431 " --> pdb=" O GLN A 427 " (cutoff:3.500A) Processing helix chain 'A' and resid 497 through 501 Processing helix chain 'A' and resid 503 through 519 Processing helix chain 'A' and resid 541 through 557 removed outlier: 3.674A pdb=" N ARG A 548 " --> pdb=" O ARG A 544 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N SER A 549 " --> pdb=" O VAL A 545 " (cutoff:3.500A) Proline residue: A 551 - end of helix Processing helix chain 'A' and resid 560 through 574 Processing helix chain 'A' and resid 577 through 584 removed outlier: 3.738A pdb=" N MET A 584 " --> pdb=" O THR A 580 " (cutoff:3.500A) Processing helix chain 'A' and resid 588 through 616 Proline residue: A 602 - end of helix Processing helix chain 'A' and resid 625 through 648 removed outlier: 4.035A pdb=" N ALA A 648 " --> pdb=" O PHE A 644 " (cutoff:3.500A) Processing helix chain 'A' and resid 653 through 658 Processing helix chain 'A' and resid 662 through 667 removed outlier: 3.911A pdb=" N LEU A 667 " --> pdb=" O ALA A 663 " (cutoff:3.500A) Processing helix chain 'A' and resid 669 through 676 Processing helix chain 'A' and resid 683 through 690 Processing helix chain 'A' and resid 693 through 709 Processing helix chain 'A' and resid 733 through 754 Processing helix chain 'A' and resid 847 through 854 Processing helix chain 'A' and resid 880 through 882 No H-bonds generated for 'chain 'A' and resid 880 through 882' Processing helix chain 'A' and resid 898 through 909 Processing helix chain 'A' and resid 917 through 927 Processing helix chain 'A' and resid 937 through 939 No H-bonds generated for 'chain 'A' and resid 937 through 939' Processing helix chain 'A' and resid 942 through 954 Processing helix chain 'A' and resid 972 through 985 removed outlier: 3.823A pdb=" N GLY A 977 " --> pdb=" O ALA A 973 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N TYR A 985 " --> pdb=" O LEU A 981 " (cutoff:3.500A) Processing helix chain 'A' and resid 998 through 1004 Processing helix chain 'A' and resid 1022 through 1026 Processing helix chain 'A' and resid 1140 through 1150 Processing helix chain 'A' and resid 1214 through 1234 removed outlier: 3.688A pdb=" N LEU A1221 " --> pdb=" O THR A1217 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LEU A1226 " --> pdb=" O GLN A1222 " (cutoff:3.500A) Processing helix chain 'A' and resid 1236 through 1243 Processing helix chain 'A' and resid 1245 through 1258 removed outlier: 3.579A pdb=" N VAL A1250 " --> pdb=" O PRO A1246 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLY A1251 " --> pdb=" O ALA A1247 " (cutoff:3.500A) Processing helix chain 'A' and resid 1273 through 1275 No H-bonds generated for 'chain 'A' and resid 1273 through 1275' Processing helix chain 'A' and resid 1291 through 1304 Processing helix chain 'A' and resid 1311 through 1313 No H-bonds generated for 'chain 'A' and resid 1311 through 1313' Processing helix chain 'A' and resid 1325 through 1333 Processing helix chain 'A' and resid 1389 through 1401 Proline residue: A1396 - end of helix Processing helix chain 'A' and resid 1429 through 1440 removed outlier: 3.791A pdb=" N GLY A1433 " --> pdb=" O GLY A1429 " (cutoff:3.500A) Processing helix chain 'A' and resid 1450 through 1466 removed outlier: 4.099A pdb=" N ASP A1466 " --> pdb=" O ALA A1462 " (cutoff:3.500A) Processing helix chain 'A' and resid 1483 through 1498 Processing helix chain 'A' and resid 1534 through 1562 removed outlier: 3.704A pdb=" N PHE A1548 " --> pdb=" O PHE A1544 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N VAL A1549 " --> pdb=" O ALA A1545 " (cutoff:3.500A) Proline residue: A1550 - end of helix removed outlier: 4.614A pdb=" N PHE A1553 " --> pdb=" O VAL A1549 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N THR A1554 " --> pdb=" O PRO A1550 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N LEU A1555 " --> pdb=" O ALA A1551 " (cutoff:3.500A) removed outlier: 4.925A pdb=" N VAL A1556 " --> pdb=" O SER A1552 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N LEU A1557 " --> pdb=" O PHE A1553 " (cutoff:3.500A) Processing helix chain 'A' and resid 1566 through 1572 Processing helix chain 'A' and resid 1576 through 1604 removed outlier: 3.766A pdb=" N LEU A1592 " --> pdb=" O MET A1588 " (cutoff:3.500A) removed outlier: 5.084A pdb=" N VAL A1593 " --> pdb=" O CYS A1589 " (cutoff:3.500A) Proline residue: A1594 - end of helix Processing helix chain 'A' and resid 1616 through 1633 removed outlier: 3.818A pdb=" N THR A1631 " --> pdb=" O GLY A1627 " (cutoff:3.500A) Proline residue: A1632 - end of helix Processing helix chain 'A' and resid 1636 through 1638 No H-bonds generated for 'chain 'A' and resid 1636 through 1638' Processing helix chain 'A' and resid 1644 through 1670 removed outlier: 3.771A pdb=" N GLY A1662 " --> pdb=" O ILE A1658 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N ALA A1665 " --> pdb=" O ASN A1661 " (cutoff:3.500A) Processing helix chain 'A' and resid 1677 through 1687 removed outlier: 3.856A pdb=" N GLN A1686 " --> pdb=" O ARG A1682 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N VAL A1687 " --> pdb=" O ILE A1683 " (cutoff:3.500A) Processing helix chain 'A' and resid 1694 through 1697 No H-bonds generated for 'chain 'A' and resid 1694 through 1697' Processing helix chain 'A' and resid 1699 through 1716 removed outlier: 3.624A pdb=" N MET A1703 " --> pdb=" O GLY A1699 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N VAL A1704 " --> pdb=" O LEU A1700 " (cutoff:3.500A) Processing helix chain 'A' and resid 1731 through 1752 Proline residue: A1742 - end of helix removed outlier: 4.295A pdb=" N LEU A1745 " --> pdb=" O GLY A1741 " (cutoff:3.500A) Processing helix chain 'A' and resid 1775 through 1785 Processing helix chain 'A' and resid 1833 through 1841 Processing helix chain 'A' and resid 1862 through 1867 Processing helix chain 'A' and resid 1884 through 1895 Processing helix chain 'A' and resid 1899 through 1912 removed outlier: 4.470A pdb=" N ALA A1903 " --> pdb=" O ALA A1900 " (cutoff:3.500A) Processing helix chain 'A' and resid 1923 through 1925 No H-bonds generated for 'chain 'A' and resid 1923 through 1925' Processing helix chain 'A' and resid 1928 through 1940 removed outlier: 3.741A pdb=" N ALA A1939 " --> pdb=" O ALA A1935 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N LEU A1940 " --> pdb=" O THR A1936 " (cutoff:3.500A) Processing helix chain 'A' and resid 1958 through 1974 Processing helix chain 'A' and resid 2009 through 2015 Processing helix chain 'A' and resid 2094 through 2103 Processing sheet with id= A, first strand: chain 'A' and resid 49 through 51 removed outlier: 3.641A pdb=" N LEU A 49 " --> pdb=" O ASP A 539 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N TYR A 537 " --> pdb=" O HIS A 51 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 58 through 60 Processing sheet with id= C, first strand: chain 'A' and resid 439 through 441 removed outlier: 3.787A pdb=" N ARG A 463 " --> pdb=" O LEU A 441 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 807 through 810 removed outlier: 3.511A pdb=" N ARG A 810 " --> pdb=" O SER A 864 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N SER A 864 " --> pdb=" O ARG A 810 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 992 through 994 removed outlier: 5.996A pdb=" N THR A 837 " --> pdb=" O LEU A 993 " (cutoff:3.500A) removed outlier: 7.248A pdb=" N ARG A1007 " --> pdb=" O ALA A 838 " (cutoff:3.500A) removed outlier: 8.239A pdb=" N LEU A 840 " --> pdb=" O ARG A1007 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N ALA A1009 " --> pdb=" O LEU A 840 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N CYS A1018 " --> pdb=" O VAL A1010 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N ALA A1012 " --> pdb=" O LEU A1016 " (cutoff:3.500A) removed outlier: 5.214A pdb=" N LEU A1016 " --> pdb=" O ALA A1012 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 1284 through 1286 removed outlier: 3.986A pdb=" N SER A1284 " --> pdb=" O PHE A1417 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 1850 through 1853 removed outlier: 4.026A pdb=" N LEU A1793 " --> pdb=" O ILE A1817 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N LEU A1815 " --> pdb=" O LEU A1795 " (cutoff:3.500A) removed outlier: 5.355A pdb=" N LEU A1813 " --> pdb=" O ASN A1797 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'A' and resid 1822 through 1824 removed outlier: 6.053A pdb=" N VAL A1978 " --> pdb=" O PHE A1823 " (cutoff:3.500A) No H-bonds generated for sheet with id= H Processing sheet with id= I, first strand: chain 'A' and resid 1870 through 1872 removed outlier: 3.937A pdb=" N CYS A1872 " --> pdb=" O PHE A1948 " (cutoff:3.500A) 566 hydrogen bonds defined for protein. 1659 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.02 Time building geometry restraints manager: 6.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4312 1.34 - 1.46: 2808 1.46 - 1.58: 6355 1.58 - 1.70: 8 1.70 - 1.82: 95 Bond restraints: 13578 Sorted by residual: bond pdb=" CA ALA A1919 " pdb=" CB ALA A1919 " ideal model delta sigma weight residual 1.530 1.489 0.041 1.54e-02 4.22e+03 7.25e+00 bond pdb=" N ASP A1920 " pdb=" CA ASP A1920 " ideal model delta sigma weight residual 1.457 1.490 -0.033 1.29e-02 6.01e+03 6.56e+00 bond pdb=" CA SER A1916 " pdb=" CB SER A1916 " ideal model delta sigma weight residual 1.530 1.490 0.040 1.69e-02 3.50e+03 5.69e+00 bond pdb=" N SER A1916 " pdb=" CA SER A1916 " ideal model delta sigma weight residual 1.457 1.488 -0.030 1.29e-02 6.01e+03 5.45e+00 bond pdb=" C ARG A 880 " pdb=" N PRO A 881 " ideal model delta sigma weight residual 1.334 1.352 -0.018 8.40e-03 1.42e+04 4.74e+00 ... (remaining 13573 not shown) Histogram of bond angle deviations from ideal: 99.63 - 107.67: 671 107.67 - 115.72: 8219 115.72 - 123.76: 9133 123.76 - 131.80: 414 131.80 - 139.84: 37 Bond angle restraints: 18474 Sorted by residual: angle pdb=" N ILE A 559 " pdb=" CA ILE A 559 " pdb=" C ILE A 559 " ideal model delta sigma weight residual 113.71 109.79 3.92 9.50e-01 1.11e+00 1.70e+01 angle pdb=" N ILE A 879 " pdb=" CA ILE A 879 " pdb=" C ILE A 879 " ideal model delta sigma weight residual 112.96 109.37 3.59 1.00e+00 1.00e+00 1.29e+01 angle pdb=" CB ARG A 350 " pdb=" CG ARG A 350 " pdb=" CD ARG A 350 " ideal model delta sigma weight residual 111.30 119.24 -7.94 2.30e+00 1.89e-01 1.19e+01 angle pdb=" N VAL A 915 " pdb=" CA VAL A 915 " pdb=" C VAL A 915 " ideal model delta sigma weight residual 106.21 109.07 -2.86 1.07e+00 8.73e-01 7.13e+00 angle pdb=" C ASN A 98 " pdb=" N ASP A 99 " pdb=" CA ASP A 99 " ideal model delta sigma weight residual 121.54 126.60 -5.06 1.91e+00 2.74e-01 7.01e+00 ... (remaining 18469 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.78: 7603 21.78 - 43.56: 556 43.56 - 65.34: 67 65.34 - 87.12: 26 87.12 - 108.89: 10 Dihedral angle restraints: 8262 sinusoidal: 3457 harmonic: 4805 Sorted by residual: dihedral pdb=" CB CYS A1347 " pdb=" SG CYS A1347 " pdb=" SG CYS A1359 " pdb=" CB CYS A1359 " ideal model delta sinusoidal sigma weight residual 93.00 165.23 -72.23 1 1.00e+01 1.00e-02 6.67e+01 dihedral pdb=" O4 BMA B 3 " pdb=" C4 BMA B 3 " pdb=" C5 BMA B 3 " pdb=" O5 BMA B 3 " ideal model delta sinusoidal sigma weight residual 288.71 179.82 108.89 1 3.00e+01 1.11e-03 1.41e+01 dihedral pdb=" C3 BMA B 3 " pdb=" C4 BMA B 3 " pdb=" C5 BMA B 3 " pdb=" O5 BMA B 3 " ideal model delta sinusoidal sigma weight residual 47.62 -59.41 107.03 1 3.00e+01 1.11e-03 1.38e+01 ... (remaining 8259 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.089: 2016 0.089 - 0.178: 107 0.178 - 0.266: 2 0.266 - 0.355: 1 0.355 - 0.444: 2 Chirality restraints: 2128 Sorted by residual: chirality pdb=" C1 NAG A2202 " pdb=" ND2 ASN A 98 " pdb=" C2 NAG A2202 " pdb=" O5 NAG A2202 " both_signs ideal model delta sigma weight residual False -2.40 -1.96 -0.44 2.00e-01 2.50e+01 4.93e+00 chirality pdb=" C1 NAG A2206 " pdb=" ND2 ASN A1457 " pdb=" C2 NAG A2206 " pdb=" O5 NAG A2206 " both_signs ideal model delta sigma weight residual False -2.40 -2.04 -0.36 2.00e-01 2.50e+01 3.29e+00 chirality pdb=" C5 BMA B 3 " pdb=" C4 BMA B 3 " pdb=" C6 BMA B 3 " pdb=" O5 BMA B 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.54 0.27 2.00e-01 2.50e+01 1.82e+00 ... (remaining 2125 not shown) Planarity restraints: 2352 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU A1915 " -0.017 2.00e-02 2.50e+03 3.37e-02 1.13e+01 pdb=" C LEU A1915 " 0.058 2.00e-02 2.50e+03 pdb=" O LEU A1915 " -0.022 2.00e-02 2.50e+03 pdb=" N SER A1916 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO A1366 " 0.049 5.00e-02 4.00e+02 7.27e-02 8.46e+00 pdb=" N PRO A1367 " -0.126 5.00e-02 4.00e+02 pdb=" CA PRO A1367 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO A1367 " 0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 979 " 0.016 2.00e-02 2.50e+03 1.32e-02 4.34e+00 pdb=" CG TRP A 979 " -0.035 2.00e-02 2.50e+03 pdb=" CD1 TRP A 979 " 0.014 2.00e-02 2.50e+03 pdb=" CD2 TRP A 979 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP A 979 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP A 979 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A 979 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 979 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 979 " 0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP A 979 " 0.003 2.00e-02 2.50e+03 ... (remaining 2349 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 96 2.58 - 3.16: 10804 3.16 - 3.74: 20128 3.74 - 4.32: 25058 4.32 - 4.90: 42687 Nonbonded interactions: 98773 Sorted by model distance: nonbonded pdb="MG MG A2208 " pdb=" O1B ATP A2210 " model vdw 2.001 2.170 nonbonded pdb="MG MG A2208 " pdb=" O1G ATP A2210 " model vdw 2.008 2.170 nonbonded pdb=" OE1 GLN A1874 " pdb="MG MG A2209 " model vdw 2.053 2.170 nonbonded pdb=" OG1 THR A1834 " pdb="MG MG A2209 " model vdw 2.057 2.170 nonbonded pdb=" O2G ATP A2207 " pdb="MG MG A2209 " model vdw 2.213 2.170 ... (remaining 98768 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 2.900 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 12.480 Check model and map are aligned: 0.180 Set scattering table: 0.130 Process input model: 38.780 Find NCS groups from input model: 0.530 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7466 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 : 0.003 0.044 13578 Z= 0.198 Angle : 0.616 8.301 18474 Z= 0.305 Chirality : 0.042 0.444 2128 Planarity : 0.004 0.073 2344 Dihedral : 15.217 108.895 5156 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.64 % Favored : 94.30 % Rotamer: Outliers : 0.00 % Allowed : 0.29 % Favored : 99.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.22), residues: 1667 helix: 1.69 (0.18), residues: 917 sheet: -1.72 (0.51), residues: 114 loop : -1.88 (0.24), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP A 979 HIS 0.003 0.001 HIS A 882 PHE 0.011 0.001 PHE A 866 TYR 0.010 0.001 TYR A 17 ARG 0.011 0.000 ARG A 350 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3334 Ramachandran restraints generated. 1667 Oldfield, 0 Emsley, 1667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3334 Ramachandran restraints generated. 1667 Oldfield, 0 Emsley, 1667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 245 time to evaluate : 1.420 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 16 MET cc_start: 0.8242 (mmp) cc_final: 0.7990 (mmp) REVERT: A 323 ASP cc_start: 0.6558 (m-30) cc_final: 0.6309 (t70) REVERT: A 386 TRP cc_start: 0.4469 (m-10) cc_final: 0.3752 (m-10) REVERT: A 615 LYS cc_start: 0.7122 (tptt) cc_final: 0.6675 (tptp) REVERT: A 975 ARG cc_start: 0.7136 (mtt180) cc_final: 0.6898 (mtt90) REVERT: A 1372 VAL cc_start: 0.6604 (t) cc_final: 0.6001 (m) REVERT: A 1615 ASN cc_start: 0.6762 (p0) cc_final: 0.6011 (m-40) REVERT: A 1686 GLN cc_start: 0.7534 (mm-40) cc_final: 0.6909 (mt0) REVERT: A 1739 ILE cc_start: 0.8281 (tp) cc_final: 0.8078 (tt) REVERT: A 1750 LEU cc_start: 0.7204 (tt) cc_final: 0.6289 (mt) REVERT: A 1799 THR cc_start: 0.8070 (t) cc_final: 0.7665 (m) REVERT: A 1962 ARG cc_start: 0.7895 (ttm110) cc_final: 0.7561 (ptp-170) outliers start: 0 outliers final: 0 residues processed: 245 average time/residue: 0.3286 time to fit residues: 112.7122 Evaluate side-chains 153 residues out of total 1390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 153 time to evaluate : 1.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 141 optimal weight: 1.9990 chunk 127 optimal weight: 0.9990 chunk 70 optimal weight: 0.6980 chunk 43 optimal weight: 0.0870 chunk 85 optimal weight: 10.0000 chunk 68 optimal weight: 2.9990 chunk 131 optimal weight: 0.6980 chunk 50 optimal weight: 1.9990 chunk 80 optimal weight: 3.9990 chunk 98 optimal weight: 0.1980 chunk 152 optimal weight: 5.9990 overall best weight: 0.5360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 192 GLN ** A 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 390 HIS A 395 HIS A 477 ASN A 718 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7498 moved from start: 0.1317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 13578 Z= 0.163 Angle : 0.575 8.996 18474 Z= 0.274 Chirality : 0.040 0.291 2128 Planarity : 0.005 0.096 2344 Dihedral : 9.804 80.397 2129 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 1.01 % Allowed : 8.27 % Favored : 90.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.22), residues: 1667 helix: 1.74 (0.18), residues: 920 sheet: -1.59 (0.52), residues: 114 loop : -1.85 (0.24), residues: 633 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 328 HIS 0.011 0.001 HIS A 395 PHE 0.023 0.001 PHE A 303 TYR 0.014 0.001 TYR A 832 ARG 0.005 0.000 ARG A1349 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3334 Ramachandran restraints generated. 1667 Oldfield, 0 Emsley, 1667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3334 Ramachandran restraints generated. 1667 Oldfield, 0 Emsley, 1667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 160 time to evaluate : 1.386 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 8 MET cc_start: 0.6968 (tmm) cc_final: 0.5117 (mmm) REVERT: A 16 MET cc_start: 0.8278 (mmp) cc_final: 0.8001 (mmp) REVERT: A 202 GLU cc_start: 0.7398 (pt0) cc_final: 0.7055 (mm-30) REVERT: A 291 ILE cc_start: 0.6180 (mm) cc_final: 0.5807 (mm) REVERT: A 292 LEU cc_start: 0.6513 (mt) cc_final: 0.6181 (mp) REVERT: A 323 ASP cc_start: 0.6649 (m-30) cc_final: 0.6187 (t70) REVERT: A 581 MET cc_start: 0.8296 (OUTLIER) cc_final: 0.8077 (mtp) REVERT: A 615 LYS cc_start: 0.6980 (tptt) cc_final: 0.6610 (tptp) REVERT: A 815 ARG cc_start: 0.7684 (tpt90) cc_final: 0.7408 (tpt90) REVERT: A 876 MET cc_start: 0.7258 (ppp) cc_final: 0.6980 (ppp) REVERT: A 1372 VAL cc_start: 0.6551 (t) cc_final: 0.5946 (m) REVERT: A 1615 ASN cc_start: 0.6758 (p0) cc_final: 0.5985 (m-40) REVERT: A 1686 GLN cc_start: 0.7462 (mm-40) cc_final: 0.6936 (mt0) REVERT: A 1799 THR cc_start: 0.8126 (t) cc_final: 0.7818 (m) REVERT: A 1962 ARG cc_start: 0.8069 (ttm110) cc_final: 0.7483 (ptp-170) REVERT: A 2011 HIS cc_start: 0.7044 (t70) cc_final: 0.6571 (t-90) outliers start: 14 outliers final: 8 residues processed: 169 average time/residue: 0.2818 time to fit residues: 68.1692 Evaluate side-chains 151 residues out of total 1390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 142 time to evaluate : 1.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 ASP Chi-restraints excluded: chain A residue 581 MET Chi-restraints excluded: chain A residue 754 VAL Chi-restraints excluded: chain A residue 839 PHE Chi-restraints excluded: chain A residue 961 VAL Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1668 VAL Chi-restraints excluded: chain A residue 1729 VAL Chi-restraints excluded: chain A residue 1910 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 84 optimal weight: 4.9990 chunk 47 optimal weight: 0.6980 chunk 126 optimal weight: 1.9990 chunk 103 optimal weight: 8.9990 chunk 42 optimal weight: 0.9980 chunk 152 optimal weight: 0.0470 chunk 165 optimal weight: 4.9990 chunk 136 optimal weight: 1.9990 chunk 151 optimal weight: 3.9990 chunk 52 optimal weight: 0.8980 chunk 122 optimal weight: 1.9990 overall best weight: 0.9280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 44 HIS A 353 GLN A 395 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7553 moved from start: 0.1731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13578 Z= 0.191 Angle : 0.564 9.609 18474 Z= 0.272 Chirality : 0.039 0.251 2128 Planarity : 0.004 0.052 2344 Dihedral : 7.578 73.041 2129 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 1.80 % Allowed : 12.01 % Favored : 86.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.21), residues: 1667 helix: 1.71 (0.18), residues: 917 sheet: -1.63 (0.53), residues: 114 loop : -1.83 (0.24), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP A 484 HIS 0.007 0.001 HIS A 44 PHE 0.018 0.001 PHE A 303 TYR 0.016 0.001 TYR A1926 ARG 0.005 0.000 ARG A1210 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3334 Ramachandran restraints generated. 1667 Oldfield, 0 Emsley, 1667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3334 Ramachandran restraints generated. 1667 Oldfield, 0 Emsley, 1667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 154 time to evaluate : 1.450 Fit side-chains REVERT: A 8 MET cc_start: 0.6946 (tmm) cc_final: 0.5028 (mmm) REVERT: A 16 MET cc_start: 0.8296 (mmp) cc_final: 0.7980 (mmt) REVERT: A 30 LEU cc_start: 0.8286 (OUTLIER) cc_final: 0.7545 (mp) REVERT: A 291 ILE cc_start: 0.6231 (mm) cc_final: 0.5978 (mm) REVERT: A 581 MET cc_start: 0.8379 (OUTLIER) cc_final: 0.8168 (mtp) REVERT: A 615 LYS cc_start: 0.6972 (tptt) cc_final: 0.6554 (tptp) REVERT: A 1372 VAL cc_start: 0.6465 (t) cc_final: 0.5862 (m) REVERT: A 1530 MET cc_start: 0.6550 (tpp) cc_final: 0.6232 (mmm) REVERT: A 1615 ASN cc_start: 0.6831 (p0) cc_final: 0.6092 (m-40) REVERT: A 1686 GLN cc_start: 0.7437 (mm-40) cc_final: 0.7059 (mt0) REVERT: A 1799 THR cc_start: 0.8229 (t) cc_final: 0.7776 (m) REVERT: A 1962 ARG cc_start: 0.8085 (ttm110) cc_final: 0.7529 (ptp-170) REVERT: A 2011 HIS cc_start: 0.6943 (t70) cc_final: 0.6536 (t-90) outliers start: 25 outliers final: 16 residues processed: 172 average time/residue: 0.2661 time to fit residues: 67.0624 Evaluate side-chains 154 residues out of total 1390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 136 time to evaluate : 1.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 99 ASP Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 519 SER Chi-restraints excluded: chain A residue 532 MET Chi-restraints excluded: chain A residue 581 MET Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 754 VAL Chi-restraints excluded: chain A residue 839 PHE Chi-restraints excluded: chain A residue 927 VAL Chi-restraints excluded: chain A residue 961 VAL Chi-restraints excluded: chain A residue 970 VAL Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1255 VAL Chi-restraints excluded: chain A residue 1435 SER Chi-restraints excluded: chain A residue 1668 VAL Chi-restraints excluded: chain A residue 1729 VAL Chi-restraints excluded: chain A residue 1739 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 151 optimal weight: 3.9990 chunk 114 optimal weight: 4.9990 chunk 79 optimal weight: 0.9980 chunk 16 optimal weight: 0.7980 chunk 72 optimal weight: 3.9990 chunk 102 optimal weight: 0.5980 chunk 153 optimal weight: 1.9990 chunk 162 optimal weight: 1.9990 chunk 80 optimal weight: 0.7980 chunk 145 optimal weight: 2.9990 chunk 43 optimal weight: 0.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 395 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7554 moved from start: 0.1974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 13578 Z= 0.176 Angle : 0.553 9.639 18474 Z= 0.266 Chirality : 0.039 0.307 2128 Planarity : 0.005 0.084 2344 Dihedral : 6.939 65.377 2129 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer: Outliers : 2.52 % Allowed : 13.45 % Favored : 84.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.21), residues: 1667 helix: 1.73 (0.18), residues: 913 sheet: -1.62 (0.53), residues: 114 loop : -1.82 (0.24), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 328 HIS 0.007 0.001 HIS A 395 PHE 0.016 0.001 PHE A 303 TYR 0.013 0.001 TYR A1926 ARG 0.006 0.000 ARG A 922 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3334 Ramachandran restraints generated. 1667 Oldfield, 0 Emsley, 1667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3334 Ramachandran restraints generated. 1667 Oldfield, 0 Emsley, 1667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 144 time to evaluate : 1.449 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 8 MET cc_start: 0.6954 (tmm) cc_final: 0.5054 (mmm) REVERT: A 16 MET cc_start: 0.8277 (mmp) cc_final: 0.7950 (mmt) REVERT: A 30 LEU cc_start: 0.8253 (OUTLIER) cc_final: 0.7558 (mp) REVERT: A 119 HIS cc_start: 0.6610 (m90) cc_final: 0.6166 (m90) REVERT: A 291 ILE cc_start: 0.6258 (mm) cc_final: 0.5972 (mm) REVERT: A 477 ASN cc_start: 0.7437 (OUTLIER) cc_final: 0.7020 (m110) REVERT: A 485 ASP cc_start: 0.6822 (t0) cc_final: 0.6482 (m-30) REVERT: A 615 LYS cc_start: 0.7033 (tptt) cc_final: 0.6715 (tptp) REVERT: A 876 MET cc_start: 0.7606 (ppp) cc_final: 0.7357 (ppp) REVERT: A 1210 ARG cc_start: 0.6470 (mtt-85) cc_final: 0.6207 (mmt90) REVERT: A 1372 VAL cc_start: 0.6528 (t) cc_final: 0.5828 (m) REVERT: A 1607 GLN cc_start: 0.7842 (tp40) cc_final: 0.7461 (tm-30) REVERT: A 1615 ASN cc_start: 0.6887 (p0) cc_final: 0.6139 (m-40) REVERT: A 1686 GLN cc_start: 0.7385 (mm-40) cc_final: 0.7044 (mt0) REVERT: A 1750 LEU cc_start: 0.7530 (OUTLIER) cc_final: 0.6853 (mt) REVERT: A 1799 THR cc_start: 0.8209 (t) cc_final: 0.7809 (m) REVERT: A 1962 ARG cc_start: 0.8116 (ttm110) cc_final: 0.7525 (ptp-170) REVERT: A 2011 HIS cc_start: 0.6855 (t70) cc_final: 0.6423 (t-90) outliers start: 35 outliers final: 22 residues processed: 166 average time/residue: 0.2532 time to fit residues: 62.7083 Evaluate side-chains 164 residues out of total 1390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 139 time to evaluate : 1.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 99 ASP Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 395 HIS Chi-restraints excluded: chain A residue 438 VAL Chi-restraints excluded: chain A residue 477 ASN Chi-restraints excluded: chain A residue 519 SER Chi-restraints excluded: chain A residue 609 LEU Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 754 VAL Chi-restraints excluded: chain A residue 839 PHE Chi-restraints excluded: chain A residue 894 ASP Chi-restraints excluded: chain A residue 927 VAL Chi-restraints excluded: chain A residue 961 VAL Chi-restraints excluded: chain A residue 970 VAL Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1255 VAL Chi-restraints excluded: chain A residue 1379 VAL Chi-restraints excluded: chain A residue 1432 LEU Chi-restraints excluded: chain A residue 1668 VAL Chi-restraints excluded: chain A residue 1729 VAL Chi-restraints excluded: chain A residue 1750 LEU Chi-restraints excluded: chain A residue 1837 PHE Chi-restraints excluded: chain A residue 1852 VAL Chi-restraints excluded: chain A residue 1969 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 135 optimal weight: 1.9990 chunk 92 optimal weight: 0.6980 chunk 2 optimal weight: 0.9990 chunk 120 optimal weight: 9.9990 chunk 67 optimal weight: 6.9990 chunk 138 optimal weight: 2.9990 chunk 112 optimal weight: 6.9990 chunk 0 optimal weight: 4.9990 chunk 82 optimal weight: 4.9990 chunk 145 optimal weight: 8.9990 chunk 40 optimal weight: 0.8980 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 44 HIS A 395 HIS ** A1797 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7618 moved from start: 0.2310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 13578 Z= 0.254 Angle : 0.585 9.740 18474 Z= 0.286 Chirality : 0.040 0.239 2128 Planarity : 0.005 0.072 2344 Dihedral : 6.833 61.418 2129 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.60 % Favored : 93.40 % Rotamer: Outliers : 3.24 % Allowed : 13.96 % Favored : 82.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.21), residues: 1667 helix: 1.62 (0.18), residues: 910 sheet: -1.83 (0.52), residues: 114 loop : -1.85 (0.23), residues: 643 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 558 HIS 0.021 0.001 HIS A 395 PHE 0.016 0.002 PHE A1486 TYR 0.016 0.001 TYR A1926 ARG 0.008 0.000 ARG A 922 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3334 Ramachandran restraints generated. 1667 Oldfield, 0 Emsley, 1667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3334 Ramachandran restraints generated. 1667 Oldfield, 0 Emsley, 1667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 145 time to evaluate : 1.413 Fit side-chains revert: symmetry clash REVERT: A 8 MET cc_start: 0.6970 (tmm) cc_final: 0.5065 (mmm) REVERT: A 30 LEU cc_start: 0.8318 (OUTLIER) cc_final: 0.7645 (mp) REVERT: A 119 HIS cc_start: 0.6588 (m90) cc_final: 0.6244 (m90) REVERT: A 291 ILE cc_start: 0.6338 (mm) cc_final: 0.6102 (mm) REVERT: A 477 ASN cc_start: 0.7420 (OUTLIER) cc_final: 0.6980 (m110) REVERT: A 485 ASP cc_start: 0.6957 (t0) cc_final: 0.6509 (m-30) REVERT: A 615 LYS cc_start: 0.7146 (tptt) cc_final: 0.6895 (tptp) REVERT: A 1372 VAL cc_start: 0.6566 (t) cc_final: 0.5876 (m) REVERT: A 1588 MET cc_start: 0.8308 (tpt) cc_final: 0.8035 (tpt) REVERT: A 1607 GLN cc_start: 0.7917 (tp40) cc_final: 0.7546 (tm-30) REVERT: A 1615 ASN cc_start: 0.6783 (p0) cc_final: 0.5971 (m-40) REVERT: A 1686 GLN cc_start: 0.7341 (mm-40) cc_final: 0.6764 (mt0) REVERT: A 1812 ARG cc_start: 0.7870 (mmt-90) cc_final: 0.6327 (mtm180) REVERT: A 1888 LEU cc_start: 0.8782 (OUTLIER) cc_final: 0.8308 (mm) REVERT: A 1962 ARG cc_start: 0.8117 (ttm110) cc_final: 0.7528 (ptp-170) outliers start: 45 outliers final: 28 residues processed: 178 average time/residue: 0.2546 time to fit residues: 67.1687 Evaluate side-chains 167 residues out of total 1390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 136 time to evaluate : 1.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 99 ASP Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 438 VAL Chi-restraints excluded: chain A residue 477 ASN Chi-restraints excluded: chain A residue 519 SER Chi-restraints excluded: chain A residue 532 MET Chi-restraints excluded: chain A residue 554 LEU Chi-restraints excluded: chain A residue 609 LEU Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 754 VAL Chi-restraints excluded: chain A residue 839 PHE Chi-restraints excluded: chain A residue 894 ASP Chi-restraints excluded: chain A residue 927 VAL Chi-restraints excluded: chain A residue 961 VAL Chi-restraints excluded: chain A residue 970 VAL Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1255 VAL Chi-restraints excluded: chain A residue 1379 VAL Chi-restraints excluded: chain A residue 1405 THR Chi-restraints excluded: chain A residue 1456 LYS Chi-restraints excluded: chain A residue 1458 LEU Chi-restraints excluded: chain A residue 1471 LEU Chi-restraints excluded: chain A residue 1599 VAL Chi-restraints excluded: chain A residue 1668 VAL Chi-restraints excluded: chain A residue 1729 VAL Chi-restraints excluded: chain A residue 1798 LEU Chi-restraints excluded: chain A residue 1837 PHE Chi-restraints excluded: chain A residue 1852 VAL Chi-restraints excluded: chain A residue 1888 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 54 optimal weight: 2.9990 chunk 146 optimal weight: 0.3980 chunk 32 optimal weight: 3.9990 chunk 95 optimal weight: 0.0980 chunk 40 optimal weight: 0.9990 chunk 162 optimal weight: 2.9990 chunk 134 optimal weight: 0.0970 chunk 75 optimal weight: 3.9990 chunk 13 optimal weight: 2.9990 chunk 53 optimal weight: 0.0670 chunk 85 optimal weight: 0.0060 overall best weight: 0.1332 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 395 HIS A1797 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7518 moved from start: 0.2325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 13578 Z= 0.136 Angle : 0.525 10.597 18474 Z= 0.253 Chirality : 0.038 0.239 2128 Planarity : 0.004 0.057 2344 Dihedral : 6.088 55.843 2129 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 1.87 % Allowed : 16.04 % Favored : 82.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.21), residues: 1667 helix: 1.90 (0.18), residues: 912 sheet: -1.51 (0.56), residues: 104 loop : -1.84 (0.23), residues: 651 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 558 HIS 0.010 0.001 HIS A 395 PHE 0.015 0.001 PHE A 303 TYR 0.012 0.001 TYR A 560 ARG 0.006 0.000 ARG A1349 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3334 Ramachandran restraints generated. 1667 Oldfield, 0 Emsley, 1667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3334 Ramachandran restraints generated. 1667 Oldfield, 0 Emsley, 1667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 146 time to evaluate : 1.512 Fit side-chains REVERT: A 16 MET cc_start: 0.8203 (mmp) cc_final: 0.7943 (tpp) REVERT: A 30 LEU cc_start: 0.8255 (OUTLIER) cc_final: 0.7584 (mp) REVERT: A 119 HIS cc_start: 0.6572 (m90) cc_final: 0.6248 (m90) REVERT: A 291 ILE cc_start: 0.6274 (mm) cc_final: 0.5972 (mm) REVERT: A 292 LEU cc_start: 0.6453 (mt) cc_final: 0.6000 (mp) REVERT: A 477 ASN cc_start: 0.7350 (OUTLIER) cc_final: 0.6942 (m110) REVERT: A 485 ASP cc_start: 0.6917 (t0) cc_final: 0.6486 (m-30) REVERT: A 876 MET cc_start: 0.7690 (ppp) cc_final: 0.7438 (ppp) REVERT: A 1372 VAL cc_start: 0.6480 (t) cc_final: 0.5810 (m) REVERT: A 1430 GLN cc_start: 0.6976 (tt0) cc_final: 0.6599 (pp30) REVERT: A 1607 GLN cc_start: 0.7859 (tp40) cc_final: 0.7512 (tm-30) REVERT: A 1615 ASN cc_start: 0.6956 (p0) cc_final: 0.6131 (m-40) REVERT: A 1686 GLN cc_start: 0.7339 (mm-40) cc_final: 0.6941 (mt0) REVERT: A 1750 LEU cc_start: 0.7482 (tp) cc_final: 0.6795 (mt) REVERT: A 1812 ARG cc_start: 0.7738 (mmt-90) cc_final: 0.6386 (mtm180) REVERT: A 1962 ARG cc_start: 0.8135 (ttm110) cc_final: 0.7538 (ptp-170) outliers start: 26 outliers final: 17 residues processed: 164 average time/residue: 0.2600 time to fit residues: 62.4802 Evaluate side-chains 149 residues out of total 1390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 130 time to evaluate : 1.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 99 ASP Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 438 VAL Chi-restraints excluded: chain A residue 477 ASN Chi-restraints excluded: chain A residue 519 SER Chi-restraints excluded: chain A residue 609 LEU Chi-restraints excluded: chain A residue 618 ASP Chi-restraints excluded: chain A residue 839 PHE Chi-restraints excluded: chain A residue 961 VAL Chi-restraints excluded: chain A residue 1405 THR Chi-restraints excluded: chain A residue 1423 ASP Chi-restraints excluded: chain A residue 1432 LEU Chi-restraints excluded: chain A residue 1541 CYS Chi-restraints excluded: chain A residue 1729 VAL Chi-restraints excluded: chain A residue 1793 LEU Chi-restraints excluded: chain A residue 1798 LEU Chi-restraints excluded: chain A residue 1837 PHE Chi-restraints excluded: chain A residue 1852 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 156 optimal weight: 0.9990 chunk 18 optimal weight: 0.8980 chunk 92 optimal weight: 1.9990 chunk 118 optimal weight: 3.9990 chunk 91 optimal weight: 0.0030 chunk 136 optimal weight: 3.9990 chunk 90 optimal weight: 0.8980 chunk 161 optimal weight: 0.2980 chunk 101 optimal weight: 0.0870 chunk 98 optimal weight: 3.9990 chunk 74 optimal weight: 0.9990 overall best weight: 0.4368 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 395 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7530 moved from start: 0.2428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 13578 Z= 0.144 Angle : 0.527 9.630 18474 Z= 0.253 Chirality : 0.038 0.230 2128 Planarity : 0.004 0.078 2344 Dihedral : 5.955 55.455 2129 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 1.94 % Allowed : 16.62 % Favored : 81.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.22), residues: 1667 helix: 1.96 (0.18), residues: 912 sheet: -1.63 (0.52), residues: 119 loop : -1.78 (0.24), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 558 HIS 0.009 0.001 HIS A 395 PHE 0.014 0.001 PHE A 303 TYR 0.012 0.001 TYR A1926 ARG 0.005 0.000 ARG A 198 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3334 Ramachandran restraints generated. 1667 Oldfield, 0 Emsley, 1667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3334 Ramachandran restraints generated. 1667 Oldfield, 0 Emsley, 1667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 138 time to evaluate : 1.636 Fit side-chains REVERT: A 8 MET cc_start: 0.7094 (tmm) cc_final: 0.5348 (mmm) REVERT: A 16 MET cc_start: 0.8217 (mmp) cc_final: 0.7951 (tpp) REVERT: A 30 LEU cc_start: 0.8277 (OUTLIER) cc_final: 0.7602 (mp) REVERT: A 119 HIS cc_start: 0.6464 (m90) cc_final: 0.6191 (m90) REVERT: A 291 ILE cc_start: 0.6248 (mm) cc_final: 0.5949 (mm) REVERT: A 292 LEU cc_start: 0.6472 (mt) cc_final: 0.6017 (mp) REVERT: A 477 ASN cc_start: 0.7397 (OUTLIER) cc_final: 0.6967 (m110) REVERT: A 485 ASP cc_start: 0.7000 (t0) cc_final: 0.6530 (m-30) REVERT: A 1372 VAL cc_start: 0.6462 (t) cc_final: 0.5800 (m) REVERT: A 1430 GLN cc_start: 0.6893 (tt0) cc_final: 0.6524 (pp30) REVERT: A 1607 GLN cc_start: 0.7830 (tp40) cc_final: 0.7479 (tm-30) REVERT: A 1615 ASN cc_start: 0.7032 (p0) cc_final: 0.6189 (m-40) REVERT: A 1686 GLN cc_start: 0.7348 (mm-40) cc_final: 0.6940 (mt0) REVERT: A 1750 LEU cc_start: 0.7486 (tp) cc_final: 0.6785 (mt) REVERT: A 1812 ARG cc_start: 0.7576 (mmt-90) cc_final: 0.6172 (mtm180) REVERT: A 1962 ARG cc_start: 0.8143 (ttm110) cc_final: 0.7550 (ptp-170) outliers start: 27 outliers final: 21 residues processed: 157 average time/residue: 0.2603 time to fit residues: 61.0258 Evaluate side-chains 155 residues out of total 1390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 132 time to evaluate : 1.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 99 ASP Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 395 HIS Chi-restraints excluded: chain A residue 438 VAL Chi-restraints excluded: chain A residue 477 ASN Chi-restraints excluded: chain A residue 519 SER Chi-restraints excluded: chain A residue 609 LEU Chi-restraints excluded: chain A residue 618 ASP Chi-restraints excluded: chain A residue 839 PHE Chi-restraints excluded: chain A residue 894 ASP Chi-restraints excluded: chain A residue 925 GLN Chi-restraints excluded: chain A residue 961 VAL Chi-restraints excluded: chain A residue 992 ILE Chi-restraints excluded: chain A residue 1142 ILE Chi-restraints excluded: chain A residue 1405 THR Chi-restraints excluded: chain A residue 1423 ASP Chi-restraints excluded: chain A residue 1432 LEU Chi-restraints excluded: chain A residue 1456 LYS Chi-restraints excluded: chain A residue 1541 CYS Chi-restraints excluded: chain A residue 1729 VAL Chi-restraints excluded: chain A residue 1837 PHE Chi-restraints excluded: chain A residue 1852 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 100 optimal weight: 2.9990 chunk 64 optimal weight: 0.4980 chunk 96 optimal weight: 7.9990 chunk 48 optimal weight: 0.5980 chunk 31 optimal weight: 0.7980 chunk 102 optimal weight: 6.9990 chunk 110 optimal weight: 2.9990 chunk 80 optimal weight: 0.9980 chunk 15 optimal weight: 6.9990 chunk 127 optimal weight: 0.5980 chunk 147 optimal weight: 6.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 395 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7543 moved from start: 0.2488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 13578 Z= 0.163 Angle : 0.536 9.625 18474 Z= 0.258 Chirality : 0.038 0.227 2128 Planarity : 0.004 0.063 2344 Dihedral : 5.961 55.331 2129 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer: Outliers : 2.37 % Allowed : 16.55 % Favored : 81.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.22), residues: 1667 helix: 1.98 (0.18), residues: 911 sheet: -1.68 (0.52), residues: 119 loop : -1.74 (0.24), residues: 637 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 979 HIS 0.013 0.001 HIS A 395 PHE 0.014 0.001 PHE A 303 TYR 0.012 0.001 TYR A1926 ARG 0.005 0.000 ARG A 922 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3334 Ramachandran restraints generated. 1667 Oldfield, 0 Emsley, 1667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3334 Ramachandran restraints generated. 1667 Oldfield, 0 Emsley, 1667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 142 time to evaluate : 1.386 Fit side-chains REVERT: A 8 MET cc_start: 0.7045 (tmm) cc_final: 0.5243 (mmm) REVERT: A 16 MET cc_start: 0.8222 (mmp) cc_final: 0.7961 (tpp) REVERT: A 30 LEU cc_start: 0.8302 (OUTLIER) cc_final: 0.7616 (mp) REVERT: A 119 HIS cc_start: 0.6557 (m90) cc_final: 0.6286 (m90) REVERT: A 291 ILE cc_start: 0.6261 (mm) cc_final: 0.6031 (mm) REVERT: A 477 ASN cc_start: 0.7345 (OUTLIER) cc_final: 0.6911 (m110) REVERT: A 485 ASP cc_start: 0.7047 (t0) cc_final: 0.6526 (m-30) REVERT: A 876 MET cc_start: 0.7732 (ppp) cc_final: 0.7446 (ppp) REVERT: A 1372 VAL cc_start: 0.6479 (t) cc_final: 0.5800 (m) REVERT: A 1430 GLN cc_start: 0.6919 (tt0) cc_final: 0.6495 (pp30) REVERT: A 1607 GLN cc_start: 0.7864 (tp40) cc_final: 0.7524 (tm-30) REVERT: A 1615 ASN cc_start: 0.7031 (p0) cc_final: 0.6184 (m-40) REVERT: A 1686 GLN cc_start: 0.7380 (mm-40) cc_final: 0.6750 (mt0) REVERT: A 1750 LEU cc_start: 0.7511 (tp) cc_final: 0.6799 (mt) REVERT: A 1812 ARG cc_start: 0.7508 (mmt-90) cc_final: 0.6260 (mtm180) REVERT: A 1962 ARG cc_start: 0.8146 (ttm110) cc_final: 0.7556 (ptp-170) outliers start: 33 outliers final: 24 residues processed: 168 average time/residue: 0.2473 time to fit residues: 61.9843 Evaluate side-chains 162 residues out of total 1390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 136 time to evaluate : 1.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 99 ASP Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 438 VAL Chi-restraints excluded: chain A residue 477 ASN Chi-restraints excluded: chain A residue 519 SER Chi-restraints excluded: chain A residue 541 VAL Chi-restraints excluded: chain A residue 609 LEU Chi-restraints excluded: chain A residue 618 ASP Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 839 PHE Chi-restraints excluded: chain A residue 894 ASP Chi-restraints excluded: chain A residue 961 VAL Chi-restraints excluded: chain A residue 992 ILE Chi-restraints excluded: chain A residue 1142 ILE Chi-restraints excluded: chain A residue 1405 THR Chi-restraints excluded: chain A residue 1423 ASP Chi-restraints excluded: chain A residue 1432 LEU Chi-restraints excluded: chain A residue 1435 SER Chi-restraints excluded: chain A residue 1456 LYS Chi-restraints excluded: chain A residue 1541 CYS Chi-restraints excluded: chain A residue 1668 VAL Chi-restraints excluded: chain A residue 1729 VAL Chi-restraints excluded: chain A residue 1798 LEU Chi-restraints excluded: chain A residue 1837 PHE Chi-restraints excluded: chain A residue 1852 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 155 optimal weight: 0.9980 chunk 141 optimal weight: 0.6980 chunk 150 optimal weight: 7.9990 chunk 90 optimal weight: 1.9990 chunk 65 optimal weight: 0.9980 chunk 118 optimal weight: 3.9990 chunk 46 optimal weight: 3.9990 chunk 136 optimal weight: 2.9990 chunk 142 optimal weight: 0.8980 chunk 99 optimal weight: 0.0010 chunk 159 optimal weight: 4.9990 overall best weight: 0.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 44 HIS A 395 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7553 moved from start: 0.2610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 13578 Z= 0.166 Angle : 0.544 9.622 18474 Z= 0.263 Chirality : 0.038 0.227 2128 Planarity : 0.004 0.051 2344 Dihedral : 5.958 56.106 2129 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Rotamer: Outliers : 2.30 % Allowed : 16.91 % Favored : 80.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.22), residues: 1667 helix: 1.98 (0.18), residues: 909 sheet: -1.70 (0.52), residues: 119 loop : -1.75 (0.24), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 979 HIS 0.003 0.001 HIS A 717 PHE 0.014 0.001 PHE A 303 TYR 0.013 0.001 TYR A1926 ARG 0.005 0.000 ARG A 922 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3334 Ramachandran restraints generated. 1667 Oldfield, 0 Emsley, 1667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3334 Ramachandran restraints generated. 1667 Oldfield, 0 Emsley, 1667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 140 time to evaluate : 1.401 Fit side-chains revert: symmetry clash REVERT: A 8 MET cc_start: 0.6981 (tmm) cc_final: 0.5191 (mmm) REVERT: A 16 MET cc_start: 0.8232 (mmp) cc_final: 0.7960 (tpp) REVERT: A 30 LEU cc_start: 0.8305 (OUTLIER) cc_final: 0.7616 (mp) REVERT: A 119 HIS cc_start: 0.6639 (m90) cc_final: 0.6349 (m90) REVERT: A 291 ILE cc_start: 0.6175 (mm) cc_final: 0.5831 (mm) REVERT: A 292 LEU cc_start: 0.6538 (mt) cc_final: 0.5937 (mt) REVERT: A 477 ASN cc_start: 0.7352 (OUTLIER) cc_final: 0.6917 (m110) REVERT: A 876 MET cc_start: 0.7745 (ppp) cc_final: 0.7489 (ppp) REVERT: A 1372 VAL cc_start: 0.6479 (t) cc_final: 0.5814 (m) REVERT: A 1430 GLN cc_start: 0.6906 (tt0) cc_final: 0.6448 (pp30) REVERT: A 1587 ASP cc_start: 0.7273 (m-30) cc_final: 0.6813 (m-30) REVERT: A 1588 MET cc_start: 0.8259 (tpt) cc_final: 0.7861 (tpt) REVERT: A 1607 GLN cc_start: 0.7859 (tp40) cc_final: 0.7515 (tm-30) REVERT: A 1686 GLN cc_start: 0.7339 (mm-40) cc_final: 0.6729 (mt0) REVERT: A 1747 PHE cc_start: 0.7942 (t80) cc_final: 0.7591 (t80) REVERT: A 1750 LEU cc_start: 0.7522 (tp) cc_final: 0.6815 (mt) REVERT: A 1812 ARG cc_start: 0.7431 (mmt-90) cc_final: 0.6127 (mtm180) REVERT: A 1962 ARG cc_start: 0.8155 (ttm110) cc_final: 0.7552 (ptp-170) outliers start: 32 outliers final: 24 residues processed: 163 average time/residue: 0.2654 time to fit residues: 65.1836 Evaluate side-chains 163 residues out of total 1390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 137 time to evaluate : 1.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 99 ASP Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 438 VAL Chi-restraints excluded: chain A residue 477 ASN Chi-restraints excluded: chain A residue 519 SER Chi-restraints excluded: chain A residue 541 VAL Chi-restraints excluded: chain A residue 609 LEU Chi-restraints excluded: chain A residue 618 ASP Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 839 PHE Chi-restraints excluded: chain A residue 894 ASP Chi-restraints excluded: chain A residue 927 VAL Chi-restraints excluded: chain A residue 961 VAL Chi-restraints excluded: chain A residue 992 ILE Chi-restraints excluded: chain A residue 1379 VAL Chi-restraints excluded: chain A residue 1405 THR Chi-restraints excluded: chain A residue 1423 ASP Chi-restraints excluded: chain A residue 1432 LEU Chi-restraints excluded: chain A residue 1435 SER Chi-restraints excluded: chain A residue 1456 LYS Chi-restraints excluded: chain A residue 1541 CYS Chi-restraints excluded: chain A residue 1668 VAL Chi-restraints excluded: chain A residue 1729 VAL Chi-restraints excluded: chain A residue 1837 PHE Chi-restraints excluded: chain A residue 1852 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 97 optimal weight: 0.9990 chunk 75 optimal weight: 0.0670 chunk 110 optimal weight: 0.6980 chunk 167 optimal weight: 9.9990 chunk 154 optimal weight: 1.9990 chunk 133 optimal weight: 3.9990 chunk 13 optimal weight: 2.9990 chunk 102 optimal weight: 2.9990 chunk 81 optimal weight: 2.9990 chunk 105 optimal weight: 2.9990 chunk 141 optimal weight: 0.7980 overall best weight: 0.9122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 395 HIS A 925 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7570 moved from start: 0.2700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13578 Z= 0.186 Angle : 0.575 14.114 18474 Z= 0.274 Chirality : 0.039 0.230 2128 Planarity : 0.004 0.050 2344 Dihedral : 6.013 56.764 2129 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Rotamer: Outliers : 2.09 % Allowed : 17.77 % Favored : 80.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.22), residues: 1667 helix: 1.96 (0.18), residues: 910 sheet: -1.76 (0.51), residues: 119 loop : -1.73 (0.24), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 328 HIS 0.003 0.001 HIS A 717 PHE 0.014 0.001 PHE A 303 TYR 0.013 0.001 TYR A1918 ARG 0.005 0.000 ARG A 922 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3334 Ramachandran restraints generated. 1667 Oldfield, 0 Emsley, 1667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3334 Ramachandran restraints generated. 1667 Oldfield, 0 Emsley, 1667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 141 time to evaluate : 1.374 Fit side-chains revert: symmetry clash REVERT: A 8 MET cc_start: 0.6992 (tmm) cc_final: 0.5209 (mmm) REVERT: A 16 MET cc_start: 0.8240 (mmp) cc_final: 0.7970 (tpp) REVERT: A 119 HIS cc_start: 0.6602 (m90) cc_final: 0.6305 (m90) REVERT: A 291 ILE cc_start: 0.6192 (mm) cc_final: 0.5905 (mm) REVERT: A 292 LEU cc_start: 0.6528 (mt) cc_final: 0.6217 (mt) REVERT: A 317 GLU cc_start: 0.5630 (tm-30) cc_final: 0.5343 (tm-30) REVERT: A 477 ASN cc_start: 0.7362 (OUTLIER) cc_final: 0.6924 (m110) REVERT: A 876 MET cc_start: 0.7765 (ppp) cc_final: 0.7522 (ppp) REVERT: A 1349 ARG cc_start: 0.5720 (mtt180) cc_final: 0.5309 (mtm180) REVERT: A 1372 VAL cc_start: 0.6463 (t) cc_final: 0.5797 (m) REVERT: A 1430 GLN cc_start: 0.6913 (tt0) cc_final: 0.6438 (pp30) REVERT: A 1587 ASP cc_start: 0.7276 (m-30) cc_final: 0.6809 (m-30) REVERT: A 1588 MET cc_start: 0.8276 (tpt) cc_final: 0.7917 (tpt) REVERT: A 1607 GLN cc_start: 0.7893 (tp40) cc_final: 0.7568 (tm-30) REVERT: A 1686 GLN cc_start: 0.7348 (mm-40) cc_final: 0.6732 (mt0) REVERT: A 1750 LEU cc_start: 0.7543 (tp) cc_final: 0.6815 (mt) REVERT: A 1812 ARG cc_start: 0.7426 (mmt-90) cc_final: 0.6139 (mtm180) REVERT: A 1962 ARG cc_start: 0.8111 (ttm110) cc_final: 0.7535 (ptp-170) outliers start: 29 outliers final: 27 residues processed: 164 average time/residue: 0.2453 time to fit residues: 60.2037 Evaluate side-chains 164 residues out of total 1390 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 136 time to evaluate : 1.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 TYR Chi-restraints excluded: chain A residue 99 ASP Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 438 VAL Chi-restraints excluded: chain A residue 477 ASN Chi-restraints excluded: chain A residue 519 SER Chi-restraints excluded: chain A residue 541 VAL Chi-restraints excluded: chain A residue 609 LEU Chi-restraints excluded: chain A residue 618 ASP Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 839 PHE Chi-restraints excluded: chain A residue 894 ASP Chi-restraints excluded: chain A residue 927 VAL Chi-restraints excluded: chain A residue 961 VAL Chi-restraints excluded: chain A residue 992 ILE Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1142 ILE Chi-restraints excluded: chain A residue 1379 VAL Chi-restraints excluded: chain A residue 1405 THR Chi-restraints excluded: chain A residue 1423 ASP Chi-restraints excluded: chain A residue 1432 LEU Chi-restraints excluded: chain A residue 1435 SER Chi-restraints excluded: chain A residue 1456 LYS Chi-restraints excluded: chain A residue 1541 CYS Chi-restraints excluded: chain A residue 1729 VAL Chi-restraints excluded: chain A residue 1798 LEU Chi-restraints excluded: chain A residue 1837 PHE Chi-restraints excluded: chain A residue 1852 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 40 optimal weight: 0.9980 chunk 122 optimal weight: 0.0070 chunk 19 optimal weight: 0.9980 chunk 37 optimal weight: 0.7980 chunk 133 optimal weight: 0.9980 chunk 55 optimal weight: 0.7980 chunk 137 optimal weight: 0.5980 chunk 16 optimal weight: 4.9990 chunk 24 optimal weight: 5.9990 chunk 117 optimal weight: 0.0970 chunk 7 optimal weight: 1.9990 overall best weight: 0.4596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 395 HIS A 843 ASN A 925 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.178021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.147061 restraints weight = 18972.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.145752 restraints weight = 23949.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.146990 restraints weight = 23097.613| |-----------------------------------------------------------------------------| r_work (final): 0.3727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7567 moved from start: 0.2737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 13578 Z= 0.151 Angle : 0.559 13.471 18474 Z= 0.264 Chirality : 0.038 0.231 2128 Planarity : 0.004 0.048 2344 Dihedral : 5.839 55.971 2129 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 2.09 % Allowed : 17.84 % Favored : 80.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.22), residues: 1667 helix: 2.05 (0.18), residues: 909 sheet: -1.67 (0.52), residues: 119 loop : -1.73 (0.24), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP A 979 HIS 0.002 0.000 HIS A 717 PHE 0.014 0.001 PHE A 303 TYR 0.012 0.001 TYR A1918 ARG 0.005 0.000 ARG A 922 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2773.20 seconds wall clock time: 50 minutes 59.47 seconds (3059.47 seconds total)