Starting phenix.real_space_refine on Thu May 15 09:33:16 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8kia_37256/05_2025/8kia_37256.cif Found real_map, /net/cci-nas-00/data/ceres_data/8kia_37256/05_2025/8kia_37256.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8kia_37256/05_2025/8kia_37256.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8kia_37256/05_2025/8kia_37256.map" model { file = "/net/cci-nas-00/data/ceres_data/8kia_37256/05_2025/8kia_37256.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8kia_37256/05_2025/8kia_37256.cif" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.002 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: 4 Type Number sf(0) Gaussians S 90 5.16 5 C 8140 2.51 5 N 2090 2.21 5 O 2397 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 56 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 12717 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 12717 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1580, 12717 Classifications: {'peptide': 1580} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 44, 'TRANS': 1535} Chain breaks: 11 Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 2, 'ARG:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 24 Time building chain proxies: 7.86, per 1000 atoms: 0.62 Number of scatterers: 12717 At special positions: 0 Unit cell: (112.32, 109.2, 114.4, 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 90 16.00 O 2397 8.00 N 2090 7.00 C 8140 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 3.14 Conformation dependent library (CDL) restraints added in 1.7 seconds 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3048 Finding SS restraints... Secondary structure from input PDB file: 75 helices and 7 sheets defined 59.9% alpha, 5.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.57 Creating SS restraints... Processing helix chain 'A' and resid 337 through 347 removed outlier: 4.575A pdb=" N ARG A 341 " --> pdb=" O GLU A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 352 through 363 Processing helix chain 'A' and resid 364 through 367 Processing helix chain 'A' and resid 372 through 390 Processing helix chain 'A' and resid 397 through 413 removed outlier: 4.856A pdb=" N GLN A 407 " --> pdb=" O ASP A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 432 removed outlier: 3.549A pdb=" N LYS A 418 " --> pdb=" O SER A 414 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 455 Processing helix chain 'A' and resid 462 through 466 removed outlier: 3.878A pdb=" N GLU A 465 " --> pdb=" O ASP A 462 " (cutoff:3.500A) Processing helix chain 'A' and resid 491 through 502 removed outlier: 3.692A pdb=" N ASN A 495 " --> pdb=" O ASN A 491 " (cutoff:3.500A) Processing helix chain 'A' and resid 521 through 536 Processing helix chain 'A' and resid 591 through 605 Processing helix chain 'A' and resid 663 through 682 Processing helix chain 'A' and resid 690 through 700 Processing helix chain 'A' and resid 701 through 706 removed outlier: 3.993A pdb=" N CYS A 704 " --> pdb=" O ASN A 701 " (cutoff:3.500A) Processing helix chain 'A' and resid 715 through 729 Processing helix chain 'A' and resid 730 through 749 Processing helix chain 'A' and resid 797 through 804 Processing helix chain 'A' and resid 828 through 837 Processing helix chain 'A' and resid 837 through 853 Proline residue: A 843 - end of helix Processing helix chain 'A' and resid 853 through 863 Processing helix chain 'A' and resid 874 through 893 Processing helix chain 'A' and resid 896 through 908 Processing helix chain 'A' and resid 921 through 927 Processing helix chain 'A' and resid 937 through 953 Processing helix chain 'A' and resid 991 through 1005 removed outlier: 3.933A pdb=" N LEU A 995 " --> pdb=" O THR A 991 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N MET A1005 " --> pdb=" O LEU A1001 " (cutoff:3.500A) Processing helix chain 'A' and resid 1012 through 1036 removed outlier: 3.888A pdb=" N ASN A1016 " --> pdb=" O ASN A1012 " (cutoff:3.500A) removed outlier: 5.067A pdb=" N THR A1018 " --> pdb=" O VAL A1014 " (cutoff:3.500A) Proline residue: A1024 - end of helix Processing helix chain 'A' and resid 1062 through 1075 Processing helix chain 'A' and resid 1077 through 1089 Processing helix chain 'A' and resid 1094 through 1097 Processing helix chain 'A' and resid 1098 through 1103 Processing helix chain 'A' and resid 1114 through 1124 removed outlier: 3.961A pdb=" N ILE A1118 " --> pdb=" O SER A1114 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ILE A1119 " --> pdb=" O THR A1115 " (cutoff:3.500A) Processing helix chain 'A' and resid 1126 through 1130 Processing helix chain 'A' and resid 1135 through 1151 removed outlier: 3.764A pdb=" N ALA A1139 " --> pdb=" O GLY A1135 " (cutoff:3.500A) Processing helix chain 'A' and resid 1151 through 1163 Processing helix chain 'A' and resid 1165 through 1178 Processing helix chain 'A' and resid 1190 through 1195 Processing helix chain 'A' and resid 1197 through 1209 removed outlier: 3.759A pdb=" N VAL A1201 " --> pdb=" O HIS A1197 " (cutoff:3.500A) Processing helix chain 'A' and resid 1223 through 1235 Processing helix chain 'A' and resid 1258 through 1272 removed outlier: 3.860A pdb=" N ASN A1272 " --> pdb=" O SER A1268 " (cutoff:3.500A) Processing helix chain 'A' and resid 1300 through 1314 Processing helix chain 'A' and resid 1331 through 1352 removed outlier: 3.614A pdb=" N ARG A1335 " --> pdb=" O ASP A1331 " (cutoff:3.500A) Processing helix chain 'A' and resid 1377 through 1385 removed outlier: 3.751A pdb=" N VAL A1381 " --> pdb=" O THR A1377 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LEU A1382 " --> pdb=" O TYR A1378 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N ILE A1385 " --> pdb=" O VAL A1381 " (cutoff:3.500A) Processing helix chain 'A' and resid 1393 through 1408 Processing helix chain 'A' and resid 1414 through 1428 Processing helix chain 'A' and resid 1439 through 1443 Processing helix chain 'A' and resid 1458 through 1478 removed outlier: 3.903A pdb=" N SER A1462 " --> pdb=" O LEU A1458 " (cutoff:3.500A) Processing helix chain 'A' and resid 1505 through 1513 Processing helix chain 'A' and resid 1517 through 1533 Processing helix chain 'A' and resid 1565 through 1575 removed outlier: 3.822A pdb=" N CYS A1573 " --> pdb=" O LEU A1569 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N GLU A1575 " --> pdb=" O ASN A1571 " (cutoff:3.500A) Processing helix chain 'A' and resid 1580 through 1598 Processing helix chain 'A' and resid 1603 through 1620 removed outlier: 4.639A pdb=" N PHE A1607 " --> pdb=" O GLU A1603 " (cutoff:3.500A) Processing helix chain 'A' and resid 1630 through 1638 Processing helix chain 'A' and resid 1642 through 1646 removed outlier: 3.614A pdb=" N GLU A1645 " --> pdb=" O LYS A1642 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ILE A1646 " --> pdb=" O SER A1643 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1642 through 1646' Processing helix chain 'A' and resid 1647 through 1651 Processing helix chain 'A' and resid 1657 through 1664 Processing helix chain 'A' and resid 1667 through 1682 Processing helix chain 'A' and resid 1686 through 1695 removed outlier: 3.766A pdb=" N ASP A1692 " --> pdb=" O GLU A1688 " (cutoff:3.500A) Processing helix chain 'A' and resid 1699 through 1714 Processing helix chain 'A' and resid 1717 through 1733 Processing helix chain 'A' and resid 1762 through 1769 removed outlier: 4.050A pdb=" N ASN A1765 " --> pdb=" O ILE A1762 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N LEU A1767 " --> pdb=" O GLU A1764 " (cutoff:3.500A) removed outlier: 4.902A pdb=" N ASN A1768 " --> pdb=" O ASN A1765 " (cutoff:3.500A) Processing helix chain 'A' and resid 1770 through 1780 Processing helix chain 'A' and resid 1781 through 1785 Processing helix chain 'A' and resid 1814 through 1829 removed outlier: 3.569A pdb=" N ASN A1829 " --> pdb=" O ILE A1825 " (cutoff:3.500A) Processing helix chain 'A' and resid 1830 through 1835 removed outlier: 3.732A pdb=" N ILE A1835 " --> pdb=" O GLU A1831 " (cutoff:3.500A) Processing helix chain 'A' and resid 1843 through 1850 Processing helix chain 'A' and resid 1870 through 1876 removed outlier: 4.199A pdb=" N LEU A1874 " --> pdb=" O LEU A1870 " (cutoff:3.500A) Processing helix chain 'A' and resid 1891 through 1905 removed outlier: 4.410A pdb=" N LYS A1905 " --> pdb=" O LEU A1901 " (cutoff:3.500A) Processing helix chain 'A' and resid 1910 through 1924 Processing helix chain 'A' and resid 1924 through 1936 Proline residue: A1932 - end of helix Processing helix chain 'A' and resid 1954 through 1965 Proline residue: A1960 - end of helix Processing helix chain 'A' and resid 1986 through 2008 Processing helix chain 'A' and resid 2018 through 2030 removed outlier: 4.368A pdb=" N ASN A2030 " --> pdb=" O PHE A2026 " (cutoff:3.500A) Processing helix chain 'A' and resid 2031 through 2043 removed outlier: 4.619A pdb=" N MET A2042 " --> pdb=" O ALA A2038 " (cutoff:3.500A) Processing helix chain 'A' and resid 2052 through 2058 removed outlier: 3.671A pdb=" N PHE A2056 " --> pdb=" O ILE A2052 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ARG A2058 " --> pdb=" O THR A2054 " (cutoff:3.500A) Processing helix chain 'A' and resid 2065 through 2069 removed outlier: 3.536A pdb=" N LEU A2069 " --> pdb=" O LYS A2066 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 508 through 509 removed outlier: 3.568A pdb=" N HIS A 790 " --> pdb=" O TYR A 820 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N MET A 822 " --> pdb=" O ALA A 788 " (cutoff:3.500A) removed outlier: 4.787A pdb=" N ALA A 788 " --> pdb=" O MET A 822 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 508 through 509 removed outlier: 3.568A pdb=" N HIS A 790 " --> pdb=" O TYR A 820 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N MET A 822 " --> pdb=" O ALA A 788 " (cutoff:3.500A) removed outlier: 4.787A pdb=" N ALA A 788 " --> pdb=" O MET A 822 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N TYR A 786 " --> pdb=" O GLN A 825 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N GLN A 825 " --> pdb=" O TYR A 786 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1109 through 1110 Processing sheet with id=AA4, first strand: chain 'A' and resid 1298 through 1299 removed outlier: 6.844A pdb=" N VAL A1281 " --> pdb=" O CYS A1412 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 1489 through 1492 removed outlier: 3.711A pdb=" N HIS A1492 " --> pdb=" O ASP A1495 " (cutoff:3.500A) removed outlier: 5.324A pdb=" N LYS A1541 " --> pdb=" O ASP A1367 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 1548 through 1549 Processing sheet with id=AA7, first strand: chain 'A' and resid 1973 through 1975 removed outlier: 3.740A pdb=" N ILE A2084 " --> pdb=" O VAL A1974 " (cutoff:3.500A) 666 hydrogen bonds defined for protein. 1920 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: 4.86 Time building geometry restraints manager: 3.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2888 1.33 - 1.45: 2781 1.45 - 1.58: 7134 1.58 - 1.70: 2 1.70 - 1.82: 147 Bond restraints: 12952 Sorted by residual: bond pdb=" C LEU A 912 " pdb=" N PRO A 913 " ideal model delta sigma weight residual 1.337 1.387 -0.050 9.80e-03 1.04e+04 2.61e+01 bond pdb=" CA PHE A1953 " pdb=" C PHE A1953 " ideal model delta sigma weight residual 1.523 1.466 0.056 1.41e-02 5.03e+03 1.59e+01 bond pdb=" CB TRP A 859 " pdb=" CG TRP A 859 " ideal model delta sigma weight residual 1.498 1.596 -0.098 3.10e-02 1.04e+03 1.01e+01 bond pdb=" CB ILE A 882 " pdb=" CG2 ILE A 882 " ideal model delta sigma weight residual 1.521 1.427 0.094 3.30e-02 9.18e+02 8.07e+00 bond pdb=" CB ASN A 919 " pdb=" CG ASN A 919 " ideal model delta sigma weight residual 1.516 1.581 -0.065 2.50e-02 1.60e+03 6.83e+00 ... (remaining 12947 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.74: 17048 3.74 - 7.48: 304 7.48 - 11.22: 67 11.22 - 14.97: 24 14.97 - 18.71: 4 Bond angle restraints: 17447 Sorted by residual: angle pdb=" CA LYS A1691 " pdb=" CB LYS A1691 " pdb=" CG LYS A1691 " ideal model delta sigma weight residual 114.10 127.49 -13.39 2.00e+00 2.50e-01 4.48e+01 angle pdb=" C LYS A 432 " pdb=" N LYS A 433 " pdb=" CA LYS A 433 " ideal model delta sigma weight residual 121.54 133.56 -12.02 1.91e+00 2.74e-01 3.96e+01 angle pdb=" CA MET A1509 " pdb=" CB MET A1509 " pdb=" CG MET A1509 " ideal model delta sigma weight residual 114.10 126.44 -12.34 2.00e+00 2.50e-01 3.81e+01 angle pdb=" CA GLU A1202 " pdb=" CB GLU A1202 " pdb=" CG GLU A1202 " ideal model delta sigma weight residual 114.10 125.81 -11.71 2.00e+00 2.50e-01 3.43e+01 angle pdb=" CA LYS A 433 " pdb=" CB LYS A 433 " pdb=" CG LYS A 433 " ideal model delta sigma weight residual 114.10 125.45 -11.35 2.00e+00 2.50e-01 3.22e+01 ... (remaining 17442 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 6735 17.97 - 35.95: 960 35.95 - 53.92: 193 53.92 - 71.90: 28 71.90 - 89.87: 7 Dihedral angle restraints: 7923 sinusoidal: 3238 harmonic: 4685 Sorted by residual: dihedral pdb=" CA VAL A1014 " pdb=" C VAL A1014 " pdb=" N HIS A1015 " pdb=" CA HIS A1015 " ideal model delta harmonic sigma weight residual 180.00 142.90 37.10 0 5.00e+00 4.00e-02 5.51e+01 dihedral pdb=" CA VAL A1962 " pdb=" C VAL A1962 " pdb=" N GLU A1963 " pdb=" CA GLU A1963 " ideal model delta harmonic sigma weight residual 180.00 153.10 26.90 0 5.00e+00 4.00e-02 2.89e+01 dihedral pdb=" CA ILE A1003 " pdb=" C ILE A1003 " pdb=" N TYR A1004 " pdb=" CA TYR A1004 " ideal model delta harmonic sigma weight residual -180.00 -153.86 -26.14 0 5.00e+00 4.00e-02 2.73e+01 ... (remaining 7920 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.091: 1723 0.091 - 0.182: 236 0.182 - 0.273: 21 0.273 - 0.364: 2 0.364 - 0.455: 1 Chirality restraints: 1983 Sorted by residual: chirality pdb=" CB VAL A1604 " pdb=" CA VAL A1604 " pdb=" CG1 VAL A1604 " pdb=" CG2 VAL A1604 " both_signs ideal model delta sigma weight residual False -2.63 -2.17 -0.45 2.00e-01 2.50e+01 5.18e+00 chirality pdb=" CB ILE A1240 " pdb=" CA ILE A1240 " pdb=" CG1 ILE A1240 " pdb=" CG2 ILE A1240 " both_signs ideal model delta sigma weight residual False 2.64 2.35 0.30 2.00e-01 2.50e+01 2.19e+00 chirality pdb=" CB VAL A1627 " pdb=" CA VAL A1627 " pdb=" CG1 VAL A1627 " pdb=" CG2 VAL A1627 " both_signs ideal model delta sigma weight residual False -2.63 -2.34 -0.29 2.00e-01 2.50e+01 2.09e+00 ... (remaining 1980 not shown) Planarity restraints: 2182 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A1704 " 0.024 2.00e-02 2.50e+03 3.46e-02 2.09e+01 pdb=" CG PHE A1704 " -0.079 2.00e-02 2.50e+03 pdb=" CD1 PHE A1704 " 0.028 2.00e-02 2.50e+03 pdb=" CD2 PHE A1704 " 0.029 2.00e-02 2.50e+03 pdb=" CE1 PHE A1704 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE A1704 " -0.002 2.00e-02 2.50e+03 pdb=" CZ PHE A1704 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 859 " -0.027 2.00e-02 2.50e+03 2.34e-02 1.37e+01 pdb=" CG TRP A 859 " 0.061 2.00e-02 2.50e+03 pdb=" CD1 TRP A 859 " -0.028 2.00e-02 2.50e+03 pdb=" CD2 TRP A 859 " 0.005 2.00e-02 2.50e+03 pdb=" NE1 TRP A 859 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP A 859 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A 859 " -0.007 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 859 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 859 " 0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP A 859 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A1363 " -0.000 2.00e-02 2.50e+03 2.39e-02 1.00e+01 pdb=" CG PHE A1363 " 0.040 2.00e-02 2.50e+03 pdb=" CD1 PHE A1363 " -0.016 2.00e-02 2.50e+03 pdb=" CD2 PHE A1363 " -0.041 2.00e-02 2.50e+03 pdb=" CE1 PHE A1363 " -0.007 2.00e-02 2.50e+03 pdb=" CE2 PHE A1363 " 0.018 2.00e-02 2.50e+03 pdb=" CZ PHE A1363 " 0.006 2.00e-02 2.50e+03 ... (remaining 2179 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 660 2.72 - 3.26: 12785 3.26 - 3.81: 21629 3.81 - 4.35: 25959 4.35 - 4.90: 42704 Nonbonded interactions: 103737 Sorted by model distance: nonbonded pdb=" OG1 THR A 718 " pdb=" OE2 GLU A1603 " model vdw 2.171 3.040 nonbonded pdb=" O LYS A1440 " pdb=" OG1 THR A1443 " model vdw 2.190 3.040 nonbonded pdb=" O ASN A1538 " pdb=" OG SER A1542 " model vdw 2.216 3.040 nonbonded pdb=" O VAL A 889 " pdb=" OG1 THR A 893 " model vdw 2.256 3.040 nonbonded pdb=" OG SER A 742 " pdb=" O LEU A 832 " model vdw 2.268 3.040 ... (remaining 103732 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: 2.500 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.560 Check model and map are aligned: 0.110 Set scattering table: 0.140 Process input model: 32.140 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.050 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:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7237 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 : 0.006 0.098 12952 Z= 0.279 Angle : 1.338 18.708 17447 Z= 0.679 Chirality : 0.063 0.455 1983 Planarity : 0.007 0.076 2182 Dihedral : 16.757 89.870 4875 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.32 % Allowed : 7.58 % Favored : 92.10 % Rotamer: Outliers : 2.34 % Allowed : 24.91 % Favored : 72.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.64 (0.19), residues: 1556 helix: -1.09 (0.16), residues: 869 sheet: -0.49 (0.72), residues: 59 loop : -2.79 (0.22), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.061 0.003 TRP A 859 HIS 0.020 0.002 HIS A1312 PHE 0.079 0.003 PHE A1704 TYR 0.050 0.003 TYR A2041 ARG 0.009 0.001 ARG A2034 Details of bonding type rmsd hydrogen bonds : bond 0.08465 ( 655) hydrogen bonds : angle 6.54821 ( 1920) covalent geometry : bond 0.00600 (12952) covalent geometry : angle 1.33771 (17447) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 304 time to evaluate : 1.423 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 371 MET cc_start: 0.7150 (mmm) cc_final: 0.6879 (mmm) REVERT: A 402 LYS cc_start: 0.7517 (mmtm) cc_final: 0.7280 (tptp) REVERT: A 481 ILE cc_start: 0.6036 (OUTLIER) cc_final: 0.5736 (mm) REVERT: A 525 ASP cc_start: 0.8256 (m-30) cc_final: 0.7643 (t0) REVERT: A 655 MET cc_start: 0.4136 (mtt) cc_final: 0.3783 (mtp) REVERT: A 749 ASP cc_start: 0.8118 (m-30) cc_final: 0.7881 (p0) REVERT: A 767 MET cc_start: 0.6948 (mmt) cc_final: 0.5238 (mmt) REVERT: A 822 MET cc_start: 0.7665 (mtt) cc_final: 0.7245 (mtt) REVERT: A 890 MET cc_start: 0.8471 (mmm) cc_final: 0.8172 (mmm) REVERT: A 946 LYS cc_start: 0.8405 (OUTLIER) cc_final: 0.8005 (mttp) REVERT: A 997 ASN cc_start: 0.8757 (m-40) cc_final: 0.8188 (m110) REVERT: A 1049 MET cc_start: 0.6608 (pmm) cc_final: 0.6367 (mpp) REVERT: A 1173 LEU cc_start: -0.5699 (OUTLIER) cc_final: -0.6263 (mp) REVERT: A 1238 MET cc_start: 0.7167 (pmm) cc_final: 0.5982 (tmm) REVERT: A 1243 ASP cc_start: 0.8591 (t70) cc_final: 0.8325 (t70) REVERT: A 1262 MET cc_start: 0.8060 (mmt) cc_final: 0.7585 (tpp) REVERT: A 1311 GLU cc_start: 0.8272 (tt0) cc_final: 0.7773 (tt0) REVERT: A 1315 LYS cc_start: 0.8879 (mtmt) cc_final: 0.8417 (mtmm) REVERT: A 1348 TYR cc_start: 0.7891 (t80) cc_final: 0.7277 (t80) REVERT: A 1447 TYR cc_start: 0.8341 (p90) cc_final: 0.8114 (p90) REVERT: A 1564 LEU cc_start: 0.8325 (OUTLIER) cc_final: 0.8069 (tt) REVERT: A 1622 MET cc_start: 0.7965 (mmt) cc_final: 0.7567 (mmp) REVERT: A 1664 LEU cc_start: 0.8724 (mt) cc_final: 0.8371 (mp) REVERT: A 1671 GLN cc_start: 0.8819 (tt0) cc_final: 0.8608 (tt0) REVERT: A 1770 MET cc_start: 0.8226 (mpp) cc_final: 0.7808 (mpp) REVERT: A 1845 LEU cc_start: 0.8822 (pt) cc_final: 0.8185 (mt) REVERT: A 1847 GLN cc_start: 0.8181 (mm-40) cc_final: 0.7821 (mm110) REVERT: A 1875 ARG cc_start: 0.7033 (mmt-90) cc_final: 0.6532 (mmt-90) REVERT: A 1962 VAL cc_start: 0.7131 (OUTLIER) cc_final: 0.6681 (t) REVERT: A 2021 PHE cc_start: 0.8660 (m-10) cc_final: 0.8368 (m-10) REVERT: A 2039 CYS cc_start: 0.9324 (m) cc_final: 0.9029 (t) REVERT: A 2048 ARG cc_start: 0.8451 (tpm170) cc_final: 0.7742 (mtt180) outliers start: 34 outliers final: 24 residues processed: 322 average time/residue: 0.2195 time to fit residues: 105.6842 Evaluate side-chains 312 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 283 time to evaluate : 1.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 321 TRP Chi-restraints excluded: chain A residue 415 LEU Chi-restraints excluded: chain A residue 470 PHE Chi-restraints excluded: chain A residue 481 ILE Chi-restraints excluded: chain A residue 725 LEU Chi-restraints excluded: chain A residue 742 SER Chi-restraints excluded: chain A residue 840 SER Chi-restraints excluded: chain A residue 935 VAL Chi-restraints excluded: chain A residue 937 ASP Chi-restraints excluded: chain A residue 946 LYS Chi-restraints excluded: chain A residue 982 CYS Chi-restraints excluded: chain A residue 995 LEU Chi-restraints excluded: chain A residue 1173 LEU Chi-restraints excluded: chain A residue 1245 VAL Chi-restraints excluded: chain A residue 1246 MET Chi-restraints excluded: chain A residue 1415 THR Chi-restraints excluded: chain A residue 1463 SER Chi-restraints excluded: chain A residue 1541 LYS Chi-restraints excluded: chain A residue 1545 SER Chi-restraints excluded: chain A residue 1564 LEU Chi-restraints excluded: chain A residue 1590 ILE Chi-restraints excluded: chain A residue 1648 THR Chi-restraints excluded: chain A residue 1897 GLU Chi-restraints excluded: chain A residue 1908 LEU Chi-restraints excluded: chain A residue 1917 CYS Chi-restraints excluded: chain A residue 1962 VAL Chi-restraints excluded: chain A residue 1998 LEU Chi-restraints excluded: chain A residue 2026 PHE Chi-restraints excluded: chain A residue 2052 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 133 optimal weight: 3.9990 chunk 119 optimal weight: 0.6980 chunk 66 optimal weight: 0.1980 chunk 40 optimal weight: 4.9990 chunk 80 optimal weight: 0.8980 chunk 63 optimal weight: 0.7980 chunk 123 optimal weight: 0.9990 chunk 47 optimal weight: 0.9980 chunk 75 optimal weight: 5.9990 chunk 92 optimal weight: 4.9990 chunk 143 optimal weight: 0.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 409 GLN A1496 ASN ** A1571 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.121488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.098935 restraints weight = 35346.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.101478 restraints weight = 22396.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.103232 restraints weight = 15901.641| |-----------------------------------------------------------------------------| r_work (final): 0.3741 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7302 moved from start: 0.1185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 12952 Z= 0.146 Angle : 0.758 11.688 17447 Z= 0.385 Chirality : 0.045 0.195 1983 Planarity : 0.004 0.047 2182 Dihedral : 7.372 59.772 1740 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 13.63 Ramachandran Plot: Outliers : 0.32 % Allowed : 7.01 % Favored : 92.67 % Rotamer: Outliers : 3.03 % Allowed : 20.99 % Favored : 75.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -1.62 (0.21), residues: 1556 helix: -0.07 (0.17), residues: 876 sheet: -0.29 (0.68), residues: 64 loop : -2.68 (0.23), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP A 859 HIS 0.012 0.001 HIS A1312 PHE 0.030 0.002 PHE A 741 TYR 0.048 0.002 TYR A2041 ARG 0.005 0.000 ARG A2034 Details of bonding type rmsd hydrogen bonds : bond 0.04267 ( 655) hydrogen bonds : angle 5.19979 ( 1920) covalent geometry : bond 0.00325 (12952) covalent geometry : angle 0.75819 (17447) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 297 time to evaluate : 1.434 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 402 LYS cc_start: 0.7440 (mmtm) cc_final: 0.7132 (tptp) REVERT: A 525 ASP cc_start: 0.8201 (m-30) cc_final: 0.7765 (t0) REVERT: A 655 MET cc_start: 0.4167 (mtt) cc_final: 0.3880 (mtp) REVERT: A 738 MET cc_start: 0.7878 (mmt) cc_final: 0.7616 (mmt) REVERT: A 767 MET cc_start: 0.7275 (mmt) cc_final: 0.5649 (mmt) REVERT: A 768 MET cc_start: 0.6837 (mtp) cc_final: 0.6477 (mtp) REVERT: A 890 MET cc_start: 0.8508 (mmm) cc_final: 0.8220 (mmm) REVERT: A 1049 MET cc_start: 0.6728 (OUTLIER) cc_final: 0.6492 (mpp) REVERT: A 1238 MET cc_start: 0.7043 (pmm) cc_final: 0.6148 (tmm) REVERT: A 1262 MET cc_start: 0.8131 (mmt) cc_final: 0.7638 (tpp) REVERT: A 1315 LYS cc_start: 0.8891 (mtmt) cc_final: 0.8263 (mtpt) REVERT: A 1350 ASP cc_start: 0.8502 (m-30) cc_final: 0.8201 (p0) REVERT: A 1418 PHE cc_start: 0.8178 (t80) cc_final: 0.7848 (t80) REVERT: A 1461 LEU cc_start: 0.8723 (OUTLIER) cc_final: 0.7793 (tt) REVERT: A 1509 MET cc_start: 0.8054 (ppp) cc_final: 0.7650 (ppp) REVERT: A 1620 TYR cc_start: 0.6333 (OUTLIER) cc_final: 0.5284 (t80) REVERT: A 1622 MET cc_start: 0.8134 (mmt) cc_final: 0.7735 (mmp) REVERT: A 1770 MET cc_start: 0.8137 (mpp) cc_final: 0.7762 (mpp) REVERT: A 1780 TYR cc_start: 0.8541 (m-10) cc_final: 0.8236 (m-10) REVERT: A 1819 MET cc_start: 0.8081 (mmm) cc_final: 0.7824 (mmm) REVERT: A 1845 LEU cc_start: 0.8716 (pt) cc_final: 0.8151 (mt) REVERT: A 1851 TYR cc_start: 0.6651 (m-80) cc_final: 0.6302 (m-80) REVERT: A 1875 ARG cc_start: 0.7220 (mmt-90) cc_final: 0.6776 (mmt-90) REVERT: A 2008 MET cc_start: 0.5724 (pmm) cc_final: 0.4349 (ppp) REVERT: A 2021 PHE cc_start: 0.8612 (m-10) cc_final: 0.8349 (t80) REVERT: A 2048 ARG cc_start: 0.8490 (tpm170) cc_final: 0.7812 (mtt180) outliers start: 44 outliers final: 24 residues processed: 322 average time/residue: 0.2104 time to fit residues: 102.8242 Evaluate side-chains 301 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 274 time to evaluate : 1.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 378 ASP Chi-restraints excluded: chain A residue 470 PHE Chi-restraints excluded: chain A residue 718 THR Chi-restraints excluded: chain A residue 742 SER Chi-restraints excluded: chain A residue 874 THR Chi-restraints excluded: chain A residue 935 VAL Chi-restraints excluded: chain A residue 1005 MET Chi-restraints excluded: chain A residue 1049 MET Chi-restraints excluded: chain A residue 1085 ILE Chi-restraints excluded: chain A residue 1230 LEU Chi-restraints excluded: chain A residue 1245 VAL Chi-restraints excluded: chain A residue 1303 VAL Chi-restraints excluded: chain A residue 1317 VAL Chi-restraints excluded: chain A residue 1402 ILE Chi-restraints excluded: chain A residue 1411 VAL Chi-restraints excluded: chain A residue 1461 LEU Chi-restraints excluded: chain A residue 1566 CYS Chi-restraints excluded: chain A residue 1579 ILE Chi-restraints excluded: chain A residue 1596 LEU Chi-restraints excluded: chain A residue 1605 ILE Chi-restraints excluded: chain A residue 1620 TYR Chi-restraints excluded: chain A residue 1648 THR Chi-restraints excluded: chain A residue 1661 LEU Chi-restraints excluded: chain A residue 1908 LEU Chi-restraints excluded: chain A residue 1998 LEU Chi-restraints excluded: chain A residue 2026 PHE Chi-restraints excluded: chain A residue 2056 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 120 optimal weight: 3.9990 chunk 52 optimal weight: 0.6980 chunk 95 optimal weight: 0.8980 chunk 9 optimal weight: 3.9990 chunk 29 optimal weight: 3.9990 chunk 22 optimal weight: 3.9990 chunk 153 optimal weight: 4.9990 chunk 108 optimal weight: 2.9990 chunk 131 optimal weight: 0.7980 chunk 93 optimal weight: 0.5980 chunk 34 optimal weight: 2.9990 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 374 GLN ** A 790 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 997 ASN ** A 998 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1015 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1452 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.118642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.095652 restraints weight = 36514.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.098111 restraints weight = 23212.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.099663 restraints weight = 16717.886| |-----------------------------------------------------------------------------| r_work (final): 0.3685 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7413 moved from start: 0.1834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 12952 Z= 0.170 Angle : 0.732 12.265 17447 Z= 0.375 Chirality : 0.045 0.194 1983 Planarity : 0.004 0.039 2182 Dihedral : 6.120 51.792 1699 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 14.37 Ramachandran Plot: Outliers : 0.26 % Allowed : 7.65 % Favored : 92.10 % Rotamer: Outliers : 3.79 % Allowed : 21.13 % Favored : 75.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -1.11 (0.21), residues: 1556 helix: 0.40 (0.18), residues: 876 sheet: -0.29 (0.64), residues: 71 loop : -2.53 (0.24), residues: 609 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 859 HIS 0.010 0.001 HIS A1312 PHE 0.037 0.002 PHE A1363 TYR 0.034 0.002 TYR A1620 ARG 0.003 0.000 ARG A2034 Details of bonding type rmsd hydrogen bonds : bond 0.04148 ( 655) hydrogen bonds : angle 5.01115 ( 1920) covalent geometry : bond 0.00376 (12952) covalent geometry : angle 0.73161 (17447) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 292 time to evaluate : 1.504 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 374 GLN cc_start: 0.7412 (OUTLIER) cc_final: 0.6377 (tt0) REVERT: A 525 ASP cc_start: 0.8238 (m-30) cc_final: 0.7656 (t0) REVERT: A 527 THR cc_start: 0.9015 (m) cc_final: 0.8772 (p) REVERT: A 655 MET cc_start: 0.4189 (mtt) cc_final: 0.3885 (mtp) REVERT: A 738 MET cc_start: 0.7796 (mmt) cc_final: 0.7360 (mmt) REVERT: A 767 MET cc_start: 0.7561 (mmt) cc_final: 0.5857 (mmt) REVERT: A 875 MET cc_start: 0.8196 (tpp) cc_final: 0.7954 (tpp) REVERT: A 890 MET cc_start: 0.8534 (mmm) cc_final: 0.8177 (mmm) REVERT: A 1049 MET cc_start: 0.6902 (OUTLIER) cc_final: 0.6690 (mpp) REVERT: A 1105 LYS cc_start: 0.8532 (ptpt) cc_final: 0.8284 (ptpt) REVERT: A 1238 MET cc_start: 0.7029 (pmm) cc_final: 0.6180 (tmm) REVERT: A 1262 MET cc_start: 0.8226 (mmt) cc_final: 0.7680 (tpp) REVERT: A 1315 LYS cc_start: 0.8904 (mtmt) cc_final: 0.8461 (mtpt) REVERT: A 1350 ASP cc_start: 0.8588 (m-30) cc_final: 0.8294 (p0) REVERT: A 1404 MET cc_start: 0.7978 (mmt) cc_final: 0.7730 (mmt) REVERT: A 1566 CYS cc_start: 0.8193 (OUTLIER) cc_final: 0.7900 (m) REVERT: A 1620 TYR cc_start: 0.6294 (OUTLIER) cc_final: 0.5202 (t80) REVERT: A 1622 MET cc_start: 0.8217 (mmt) cc_final: 0.7856 (mmp) REVERT: A 1770 MET cc_start: 0.8114 (mpp) cc_final: 0.7841 (mpp) REVERT: A 1780 TYR cc_start: 0.8680 (m-10) cc_final: 0.8475 (m-10) REVERT: A 1819 MET cc_start: 0.8188 (mmm) cc_final: 0.7931 (mmm) REVERT: A 1845 LEU cc_start: 0.8796 (pt) cc_final: 0.8366 (mp) REVERT: A 1875 ARG cc_start: 0.7285 (mmt-90) cc_final: 0.6864 (mmt-90) REVERT: A 2021 PHE cc_start: 0.8679 (m-10) cc_final: 0.8442 (m-10) REVERT: A 2048 ARG cc_start: 0.8543 (tpm170) cc_final: 0.7790 (mtt180) outliers start: 55 outliers final: 30 residues processed: 323 average time/residue: 0.2225 time to fit residues: 108.7517 Evaluate side-chains 299 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 265 time to evaluate : 1.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 374 GLN Chi-restraints excluded: chain A residue 378 ASP Chi-restraints excluded: chain A residue 470 PHE Chi-restraints excluded: chain A residue 718 THR Chi-restraints excluded: chain A residue 725 LEU Chi-restraints excluded: chain A residue 791 ILE Chi-restraints excluded: chain A residue 833 LEU Chi-restraints excluded: chain A residue 911 PHE Chi-restraints excluded: chain A residue 935 VAL Chi-restraints excluded: chain A residue 984 ILE Chi-restraints excluded: chain A residue 995 LEU Chi-restraints excluded: chain A residue 1005 MET Chi-restraints excluded: chain A residue 1049 MET Chi-restraints excluded: chain A residue 1230 LEU Chi-restraints excluded: chain A residue 1245 VAL Chi-restraints excluded: chain A residue 1303 VAL Chi-restraints excluded: chain A residue 1317 VAL Chi-restraints excluded: chain A residue 1411 VAL Chi-restraints excluded: chain A residue 1464 VAL Chi-restraints excluded: chain A residue 1482 ASP Chi-restraints excluded: chain A residue 1562 ILE Chi-restraints excluded: chain A residue 1566 CYS Chi-restraints excluded: chain A residue 1579 ILE Chi-restraints excluded: chain A residue 1590 ILE Chi-restraints excluded: chain A residue 1596 LEU Chi-restraints excluded: chain A residue 1605 ILE Chi-restraints excluded: chain A residue 1620 TYR Chi-restraints excluded: chain A residue 1648 THR Chi-restraints excluded: chain A residue 1661 LEU Chi-restraints excluded: chain A residue 1908 LEU Chi-restraints excluded: chain A residue 1917 CYS Chi-restraints excluded: chain A residue 1998 LEU Chi-restraints excluded: chain A residue 2026 PHE Chi-restraints excluded: chain A residue 2056 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 0 optimal weight: 6.9990 chunk 21 optimal weight: 7.9990 chunk 85 optimal weight: 0.6980 chunk 12 optimal weight: 1.9990 chunk 6 optimal weight: 4.9990 chunk 5 optimal weight: 5.9990 chunk 58 optimal weight: 0.9990 chunk 79 optimal weight: 2.9990 chunk 64 optimal weight: 0.4980 chunk 112 optimal weight: 4.9990 chunk 8 optimal weight: 0.0020 overall best weight: 0.8392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 374 GLN A 409 GLN ** A 790 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 997 ASN ** A 998 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1015 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1728 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.119114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.095703 restraints weight = 36008.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.098151 restraints weight = 22905.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.099699 restraints weight = 16561.245| |-----------------------------------------------------------------------------| r_work (final): 0.3686 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7408 moved from start: 0.2115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 12952 Z= 0.146 Angle : 0.730 13.995 17447 Z= 0.370 Chirality : 0.045 0.196 1983 Planarity : 0.004 0.064 2182 Dihedral : 5.982 53.321 1698 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 13.63 Ramachandran Plot: Outliers : 0.26 % Allowed : 7.39 % Favored : 92.35 % Rotamer: Outliers : 4.20 % Allowed : 23.12 % Favored : 72.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -1.08 (0.21), residues: 1556 helix: 0.48 (0.18), residues: 872 sheet: -0.38 (0.62), residues: 71 loop : -2.59 (0.24), residues: 613 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 859 HIS 0.007 0.001 HIS A1015 PHE 0.038 0.002 PHE A1363 TYR 0.033 0.002 TYR A1620 ARG 0.005 0.000 ARG A1335 Details of bonding type rmsd hydrogen bonds : bond 0.04045 ( 655) hydrogen bonds : angle 4.91666 ( 1920) covalent geometry : bond 0.00329 (12952) covalent geometry : angle 0.72984 (17447) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 284 time to evaluate : 1.554 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 374 GLN cc_start: 0.7440 (OUTLIER) cc_final: 0.6462 (tt0) REVERT: A 402 LYS cc_start: 0.7589 (tptp) cc_final: 0.6847 (tppt) REVERT: A 525 ASP cc_start: 0.8202 (m-30) cc_final: 0.7621 (t0) REVERT: A 527 THR cc_start: 0.9026 (m) cc_final: 0.8806 (p) REVERT: A 655 MET cc_start: 0.4085 (mtt) cc_final: 0.3780 (mtp) REVERT: A 738 MET cc_start: 0.7780 (mmt) cc_final: 0.7550 (mmt) REVERT: A 767 MET cc_start: 0.7508 (mmt) cc_final: 0.5753 (mmt) REVERT: A 890 MET cc_start: 0.8538 (mmm) cc_final: 0.8303 (mmm) REVERT: A 1049 MET cc_start: 0.6779 (OUTLIER) cc_final: 0.6577 (mpp) REVERT: A 1105 LYS cc_start: 0.8552 (ptpt) cc_final: 0.8267 (ptpt) REVERT: A 1173 LEU cc_start: -0.5352 (OUTLIER) cc_final: -0.6053 (mp) REVERT: A 1238 MET cc_start: 0.7054 (pmm) cc_final: 0.6279 (tmm) REVERT: A 1262 MET cc_start: 0.8201 (OUTLIER) cc_final: 0.7658 (tpp) REVERT: A 1315 LYS cc_start: 0.8966 (mtmt) cc_final: 0.8253 (mtmt) REVERT: A 1335 ARG cc_start: 0.8851 (mmp-170) cc_final: 0.8570 (mmp-170) REVERT: A 1350 ASP cc_start: 0.8572 (m-30) cc_final: 0.8324 (p0) REVERT: A 1461 LEU cc_start: 0.8829 (OUTLIER) cc_final: 0.7958 (tp) REVERT: A 1509 MET cc_start: 0.8041 (ppp) cc_final: 0.7709 (ppp) REVERT: A 1566 CYS cc_start: 0.8179 (OUTLIER) cc_final: 0.7930 (m) REVERT: A 1620 TYR cc_start: 0.6198 (OUTLIER) cc_final: 0.5221 (t80) REVERT: A 1622 MET cc_start: 0.8259 (mmt) cc_final: 0.7751 (mmp) REVERT: A 1770 MET cc_start: 0.8117 (mpp) cc_final: 0.7849 (mpp) REVERT: A 1845 LEU cc_start: 0.8770 (pt) cc_final: 0.8382 (mp) REVERT: A 1875 ARG cc_start: 0.7247 (mmt-90) cc_final: 0.6802 (mmt-90) REVERT: A 2021 PHE cc_start: 0.8716 (m-10) cc_final: 0.8499 (m-10) REVERT: A 2048 ARG cc_start: 0.8572 (tpm170) cc_final: 0.8306 (tpp-160) outliers start: 61 outliers final: 40 residues processed: 318 average time/residue: 0.2226 time to fit residues: 107.1794 Evaluate side-chains 316 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 269 time to evaluate : 1.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 332 GLU Chi-restraints excluded: chain A residue 374 GLN Chi-restraints excluded: chain A residue 378 ASP Chi-restraints excluded: chain A residue 470 PHE Chi-restraints excluded: chain A residue 718 THR Chi-restraints excluded: chain A residue 725 LEU Chi-restraints excluded: chain A residue 742 SER Chi-restraints excluded: chain A residue 749 ASP Chi-restraints excluded: chain A residue 766 SER Chi-restraints excluded: chain A residue 791 ILE Chi-restraints excluded: chain A residue 833 LEU Chi-restraints excluded: chain A residue 906 MET Chi-restraints excluded: chain A residue 935 VAL Chi-restraints excluded: chain A residue 982 CYS Chi-restraints excluded: chain A residue 984 ILE Chi-restraints excluded: chain A residue 995 LEU Chi-restraints excluded: chain A residue 1005 MET Chi-restraints excluded: chain A residue 1037 PHE Chi-restraints excluded: chain A residue 1049 MET Chi-restraints excluded: chain A residue 1173 LEU Chi-restraints excluded: chain A residue 1230 LEU Chi-restraints excluded: chain A residue 1245 VAL Chi-restraints excluded: chain A residue 1262 MET Chi-restraints excluded: chain A residue 1303 VAL Chi-restraints excluded: chain A residue 1317 VAL Chi-restraints excluded: chain A residue 1402 ILE Chi-restraints excluded: chain A residue 1411 VAL Chi-restraints excluded: chain A residue 1415 THR Chi-restraints excluded: chain A residue 1461 LEU Chi-restraints excluded: chain A residue 1482 ASP Chi-restraints excluded: chain A residue 1541 LYS Chi-restraints excluded: chain A residue 1566 CYS Chi-restraints excluded: chain A residue 1579 ILE Chi-restraints excluded: chain A residue 1590 ILE Chi-restraints excluded: chain A residue 1596 LEU Chi-restraints excluded: chain A residue 1605 ILE Chi-restraints excluded: chain A residue 1620 TYR Chi-restraints excluded: chain A residue 1648 THR Chi-restraints excluded: chain A residue 1661 LEU Chi-restraints excluded: chain A residue 1908 LEU Chi-restraints excluded: chain A residue 1917 CYS Chi-restraints excluded: chain A residue 1985 LEU Chi-restraints excluded: chain A residue 1988 ILE Chi-restraints excluded: chain A residue 1998 LEU Chi-restraints excluded: chain A residue 2026 PHE Chi-restraints excluded: chain A residue 2052 ILE Chi-restraints excluded: chain A residue 2056 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 115 optimal weight: 0.7980 chunk 45 optimal weight: 0.0050 chunk 110 optimal weight: 0.8980 chunk 18 optimal weight: 8.9990 chunk 102 optimal weight: 3.9990 chunk 44 optimal weight: 0.9990 chunk 144 optimal weight: 0.0470 chunk 103 optimal weight: 3.9990 chunk 84 optimal weight: 6.9990 chunk 98 optimal weight: 8.9990 chunk 141 optimal weight: 4.9990 overall best weight: 0.5494 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 363 ASN A 374 GLN A 409 GLN A 997 ASN ** A1015 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1420 ASN A1628 ASN A1829 ASN A1919 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.119668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.096236 restraints weight = 35919.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.098712 restraints weight = 23034.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.100448 restraints weight = 16679.811| |-----------------------------------------------------------------------------| r_work (final): 0.3700 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7383 moved from start: 0.2330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 12952 Z= 0.132 Angle : 0.729 11.724 17447 Z= 0.365 Chirality : 0.045 0.179 1983 Planarity : 0.004 0.059 2182 Dihedral : 5.925 53.877 1698 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 13.08 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.84 % Favored : 91.97 % Rotamer: Outliers : 4.13 % Allowed : 23.19 % Favored : 72.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -0.96 (0.22), residues: 1556 helix: 0.61 (0.18), residues: 865 sheet: -0.32 (0.63), residues: 71 loop : -2.56 (0.24), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A1958 HIS 0.007 0.001 HIS A1015 PHE 0.030 0.002 PHE A1363 TYR 0.031 0.002 TYR A1620 ARG 0.005 0.000 ARG A1335 Details of bonding type rmsd hydrogen bonds : bond 0.03889 ( 655) hydrogen bonds : angle 4.81730 ( 1920) covalent geometry : bond 0.00297 (12952) covalent geometry : angle 0.72900 (17447) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 276 time to evaluate : 1.591 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 374 GLN cc_start: 0.7572 (OUTLIER) cc_final: 0.6674 (tt0) REVERT: A 499 GLU cc_start: 0.8470 (pt0) cc_final: 0.8242 (pp20) REVERT: A 525 ASP cc_start: 0.8225 (m-30) cc_final: 0.7639 (t0) REVERT: A 655 MET cc_start: 0.4061 (mtt) cc_final: 0.3732 (mtp) REVERT: A 742 SER cc_start: 0.9134 (OUTLIER) cc_final: 0.8901 (p) REVERT: A 760 LEU cc_start: 0.8598 (tt) cc_final: 0.8381 (mp) REVERT: A 767 MET cc_start: 0.7486 (mmt) cc_final: 0.5681 (mmt) REVERT: A 768 MET cc_start: 0.7302 (ttm) cc_final: 0.6971 (ttm) REVERT: A 1105 LYS cc_start: 0.8558 (ptpt) cc_final: 0.8274 (ptpt) REVERT: A 1173 LEU cc_start: -0.5368 (OUTLIER) cc_final: -0.6073 (mp) REVERT: A 1238 MET cc_start: 0.6961 (pmm) cc_final: 0.6209 (tmm) REVERT: A 1262 MET cc_start: 0.8193 (OUTLIER) cc_final: 0.7634 (tpp) REVERT: A 1267 MET cc_start: 0.9091 (mmm) cc_final: 0.8819 (mmm) REVERT: A 1315 LYS cc_start: 0.9015 (mtmt) cc_final: 0.8311 (mtmt) REVERT: A 1350 ASP cc_start: 0.8549 (m-30) cc_final: 0.8309 (p0) REVERT: A 1461 LEU cc_start: 0.8829 (OUTLIER) cc_final: 0.8021 (tp) REVERT: A 1620 TYR cc_start: 0.6131 (OUTLIER) cc_final: 0.5325 (t80) REVERT: A 1770 MET cc_start: 0.8146 (mpp) cc_final: 0.7943 (mpp) REVERT: A 1780 TYR cc_start: 0.8367 (m-10) cc_final: 0.7978 (m-10) REVERT: A 1845 LEU cc_start: 0.8762 (pt) cc_final: 0.8325 (mt) REVERT: A 1875 ARG cc_start: 0.7131 (mmt-90) cc_final: 0.6680 (mmt-90) REVERT: A 1927 PHE cc_start: 0.8784 (t80) cc_final: 0.8499 (t80) REVERT: A 1963 GLU cc_start: 0.7919 (mm-30) cc_final: 0.7577 (pp20) REVERT: A 2008 MET cc_start: 0.5967 (pmm) cc_final: 0.4969 (ppp) REVERT: A 2021 PHE cc_start: 0.8627 (m-10) cc_final: 0.8370 (t80) REVERT: A 2049 LEU cc_start: 0.8547 (tp) cc_final: 0.7588 (mp) outliers start: 60 outliers final: 38 residues processed: 308 average time/residue: 0.2203 time to fit residues: 102.2054 Evaluate side-chains 305 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 261 time to evaluate : 1.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 321 TRP Chi-restraints excluded: chain A residue 374 GLN Chi-restraints excluded: chain A residue 378 ASP Chi-restraints excluded: chain A residue 470 PHE Chi-restraints excluded: chain A residue 680 LEU Chi-restraints excluded: chain A residue 718 THR Chi-restraints excluded: chain A residue 725 LEU Chi-restraints excluded: chain A residue 742 SER Chi-restraints excluded: chain A residue 749 ASP Chi-restraints excluded: chain A residue 770 LEU Chi-restraints excluded: chain A residue 791 ILE Chi-restraints excluded: chain A residue 833 LEU Chi-restraints excluded: chain A residue 906 MET Chi-restraints excluded: chain A residue 935 VAL Chi-restraints excluded: chain A residue 982 CYS Chi-restraints excluded: chain A residue 984 ILE Chi-restraints excluded: chain A residue 995 LEU Chi-restraints excluded: chain A residue 1005 MET Chi-restraints excluded: chain A residue 1037 PHE Chi-restraints excluded: chain A residue 1173 LEU Chi-restraints excluded: chain A residue 1230 LEU Chi-restraints excluded: chain A residue 1262 MET Chi-restraints excluded: chain A residue 1303 VAL Chi-restraints excluded: chain A residue 1317 VAL Chi-restraints excluded: chain A residue 1402 ILE Chi-restraints excluded: chain A residue 1411 VAL Chi-restraints excluded: chain A residue 1415 THR Chi-restraints excluded: chain A residue 1461 LEU Chi-restraints excluded: chain A residue 1541 LYS Chi-restraints excluded: chain A residue 1566 CYS Chi-restraints excluded: chain A residue 1579 ILE Chi-restraints excluded: chain A residue 1590 ILE Chi-restraints excluded: chain A residue 1592 VAL Chi-restraints excluded: chain A residue 1596 LEU Chi-restraints excluded: chain A residue 1605 ILE Chi-restraints excluded: chain A residue 1620 TYR Chi-restraints excluded: chain A residue 1661 LEU Chi-restraints excluded: chain A residue 1908 LEU Chi-restraints excluded: chain A residue 1917 CYS Chi-restraints excluded: chain A residue 1985 LEU Chi-restraints excluded: chain A residue 1998 LEU Chi-restraints excluded: chain A residue 2026 PHE Chi-restraints excluded: chain A residue 2052 ILE Chi-restraints excluded: chain A residue 2056 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 7 optimal weight: 1.9990 chunk 75 optimal weight: 5.9990 chunk 84 optimal weight: 6.9990 chunk 140 optimal weight: 5.9990 chunk 20 optimal weight: 8.9990 chunk 97 optimal weight: 2.9990 chunk 147 optimal weight: 8.9990 chunk 146 optimal weight: 6.9990 chunk 119 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 87 optimal weight: 0.0980 overall best weight: 1.8188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 374 GLN A 997 ASN ** A1015 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1628 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.113245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.090730 restraints weight = 37497.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.093131 restraints weight = 23346.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.094667 restraints weight = 16580.567| |-----------------------------------------------------------------------------| r_work (final): 0.3597 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7513 moved from start: 0.2915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 12952 Z= 0.220 Angle : 0.790 11.566 17447 Z= 0.405 Chirality : 0.048 0.324 1983 Planarity : 0.005 0.075 2182 Dihedral : 6.093 55.793 1696 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 17.74 Ramachandran Plot: Outliers : 0.19 % Allowed : 8.48 % Favored : 91.32 % Rotamer: Outliers : 4.54 % Allowed : 23.68 % Favored : 71.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -1.11 (0.21), residues: 1556 helix: 0.50 (0.18), residues: 868 sheet: -0.32 (0.58), residues: 75 loop : -2.69 (0.24), residues: 613 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.003 TRP A1958 HIS 0.006 0.001 HIS A1015 PHE 0.054 0.002 PHE A1363 TYR 0.030 0.002 TYR A1620 ARG 0.007 0.001 ARG A 899 Details of bonding type rmsd hydrogen bonds : bond 0.04292 ( 655) hydrogen bonds : angle 5.03340 ( 1920) covalent geometry : bond 0.00483 (12952) covalent geometry : angle 0.79025 (17447) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 272 time to evaluate : 1.627 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 359 PHE cc_start: 0.8538 (t80) cc_final: 0.8321 (t80) REVERT: A 374 GLN cc_start: 0.7819 (OUTLIER) cc_final: 0.7226 (tt0) REVERT: A 499 GLU cc_start: 0.8682 (pt0) cc_final: 0.8336 (pp20) REVERT: A 525 ASP cc_start: 0.8220 (m-30) cc_final: 0.7587 (t0) REVERT: A 655 MET cc_start: 0.4280 (mtt) cc_final: 0.3977 (mtp) REVERT: A 768 MET cc_start: 0.7495 (ttm) cc_final: 0.7124 (ttm) REVERT: A 809 TYR cc_start: 0.7408 (OUTLIER) cc_final: 0.6958 (t80) REVERT: A 890 MET cc_start: 0.8320 (mmm) cc_final: 0.8018 (mmm) REVERT: A 1105 LYS cc_start: 0.8617 (ptpt) cc_final: 0.7790 (tmtt) REVERT: A 1238 MET cc_start: 0.7058 (pmm) cc_final: 0.6277 (tmm) REVERT: A 1262 MET cc_start: 0.8272 (OUTLIER) cc_final: 0.7702 (tpp) REVERT: A 1315 LYS cc_start: 0.9022 (mtmt) cc_final: 0.8623 (mtpt) REVERT: A 1350 ASP cc_start: 0.8667 (m-30) cc_final: 0.8387 (p0) REVERT: A 1389 ILE cc_start: 0.8791 (mt) cc_final: 0.8533 (mt) REVERT: A 1418 PHE cc_start: 0.8427 (t80) cc_final: 0.7547 (t80) REVERT: A 1461 LEU cc_start: 0.9005 (OUTLIER) cc_final: 0.8328 (tp) REVERT: A 1620 TYR cc_start: 0.6614 (OUTLIER) cc_final: 0.5815 (t80) REVERT: A 1770 MET cc_start: 0.8149 (mpp) cc_final: 0.7936 (mpp) REVERT: A 1875 ARG cc_start: 0.7288 (mmt-90) cc_final: 0.6856 (mmt-90) REVERT: A 1927 PHE cc_start: 0.8867 (t80) cc_final: 0.8617 (t80) REVERT: A 2048 ARG cc_start: 0.8387 (tpp-160) cc_final: 0.7913 (mtt180) REVERT: A 2049 LEU cc_start: 0.8720 (tp) cc_final: 0.7900 (mp) outliers start: 66 outliers final: 46 residues processed: 311 average time/residue: 0.2267 time to fit residues: 105.8318 Evaluate side-chains 306 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 255 time to evaluate : 1.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 374 GLN Chi-restraints excluded: chain A residue 378 ASP Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 470 PHE Chi-restraints excluded: chain A residue 680 LEU Chi-restraints excluded: chain A residue 718 THR Chi-restraints excluded: chain A residue 725 LEU Chi-restraints excluded: chain A residue 742 SER Chi-restraints excluded: chain A residue 749 ASP Chi-restraints excluded: chain A residue 766 SER Chi-restraints excluded: chain A residue 770 LEU Chi-restraints excluded: chain A residue 791 ILE Chi-restraints excluded: chain A residue 809 TYR Chi-restraints excluded: chain A residue 833 LEU Chi-restraints excluded: chain A residue 906 MET Chi-restraints excluded: chain A residue 935 VAL Chi-restraints excluded: chain A residue 982 CYS Chi-restraints excluded: chain A residue 984 ILE Chi-restraints excluded: chain A residue 995 LEU Chi-restraints excluded: chain A residue 1005 MET Chi-restraints excluded: chain A residue 1037 PHE Chi-restraints excluded: chain A residue 1064 VAL Chi-restraints excluded: chain A residue 1085 ILE Chi-restraints excluded: chain A residue 1173 LEU Chi-restraints excluded: chain A residue 1230 LEU Chi-restraints excluded: chain A residue 1262 MET Chi-restraints excluded: chain A residue 1283 VAL Chi-restraints excluded: chain A residue 1303 VAL Chi-restraints excluded: chain A residue 1317 VAL Chi-restraints excluded: chain A residue 1335 ARG Chi-restraints excluded: chain A residue 1402 ILE Chi-restraints excluded: chain A residue 1411 VAL Chi-restraints excluded: chain A residue 1415 THR Chi-restraints excluded: chain A residue 1461 LEU Chi-restraints excluded: chain A residue 1482 ASP Chi-restraints excluded: chain A residue 1541 LYS Chi-restraints excluded: chain A residue 1566 CYS Chi-restraints excluded: chain A residue 1579 ILE Chi-restraints excluded: chain A residue 1590 ILE Chi-restraints excluded: chain A residue 1596 LEU Chi-restraints excluded: chain A residue 1605 ILE Chi-restraints excluded: chain A residue 1620 TYR Chi-restraints excluded: chain A residue 1661 LEU Chi-restraints excluded: chain A residue 1750 THR Chi-restraints excluded: chain A residue 1908 LEU Chi-restraints excluded: chain A residue 1917 CYS Chi-restraints excluded: chain A residue 1985 LEU Chi-restraints excluded: chain A residue 1998 LEU Chi-restraints excluded: chain A residue 2026 PHE Chi-restraints excluded: chain A residue 2052 ILE Chi-restraints excluded: chain A residue 2056 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 41 optimal weight: 1.9990 chunk 132 optimal weight: 0.7980 chunk 88 optimal weight: 3.9990 chunk 81 optimal weight: 3.9990 chunk 80 optimal weight: 0.9990 chunk 51 optimal weight: 5.9990 chunk 77 optimal weight: 4.9990 chunk 115 optimal weight: 4.9990 chunk 49 optimal weight: 6.9990 chunk 141 optimal weight: 3.9990 chunk 116 optimal weight: 0.5980 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 363 ASN A 374 GLN A 997 ASN ** A1015 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1452 ASN A1496 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.113126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.090551 restraints weight = 36547.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.092967 restraints weight = 22729.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.094645 restraints weight = 16240.047| |-----------------------------------------------------------------------------| r_work (final): 0.3597 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7524 moved from start: 0.3311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 12952 Z= 0.207 Angle : 0.804 12.106 17447 Z= 0.409 Chirality : 0.048 0.237 1983 Planarity : 0.004 0.073 2182 Dihedral : 6.115 57.280 1696 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 17.19 Ramachandran Plot: Outliers : 0.19 % Allowed : 8.42 % Favored : 91.39 % Rotamer: Outliers : 4.54 % Allowed : 24.98 % Favored : 70.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -1.21 (0.21), residues: 1556 helix: 0.40 (0.18), residues: 871 sheet: -0.37 (0.59), residues: 72 loop : -2.71 (0.24), residues: 613 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A1958 HIS 0.007 0.001 HIS A1312 PHE 0.033 0.002 PHE A 741 TYR 0.031 0.002 TYR A1620 ARG 0.006 0.001 ARG A 899 Details of bonding type rmsd hydrogen bonds : bond 0.04304 ( 655) hydrogen bonds : angle 5.05986 ( 1920) covalent geometry : bond 0.00461 (12952) covalent geometry : angle 0.80369 (17447) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 274 time to evaluate : 1.552 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 374 GLN cc_start: 0.7846 (OUTLIER) cc_final: 0.7301 (tt0) REVERT: A 499 GLU cc_start: 0.8667 (pt0) cc_final: 0.8456 (pp20) REVERT: A 525 ASP cc_start: 0.8220 (m-30) cc_final: 0.7503 (t0) REVERT: A 655 MET cc_start: 0.4336 (mtt) cc_final: 0.4027 (mtp) REVERT: A 767 MET cc_start: 0.7350 (mmt) cc_final: 0.5654 (mmt) REVERT: A 768 MET cc_start: 0.7575 (ttm) cc_final: 0.7201 (ttm) REVERT: A 809 TYR cc_start: 0.7433 (OUTLIER) cc_final: 0.6972 (t80) REVERT: A 836 PHE cc_start: 0.9113 (t80) cc_final: 0.8863 (t80) REVERT: A 873 MET cc_start: 0.8035 (mpp) cc_final: 0.7642 (mpp) REVERT: A 890 MET cc_start: 0.8263 (mmm) cc_final: 0.7868 (mmm) REVERT: A 1105 LYS cc_start: 0.8623 (ptpt) cc_final: 0.7801 (tmtt) REVERT: A 1262 MET cc_start: 0.8290 (OUTLIER) cc_final: 0.7726 (tpp) REVERT: A 1315 LYS cc_start: 0.9059 (mtmt) cc_final: 0.8401 (mtmt) REVERT: A 1335 ARG cc_start: 0.8944 (mmp-170) cc_final: 0.8714 (mmp80) REVERT: A 1350 ASP cc_start: 0.8675 (m-30) cc_final: 0.8391 (p0) REVERT: A 1389 ILE cc_start: 0.8762 (mt) cc_final: 0.8550 (mt) REVERT: A 1418 PHE cc_start: 0.8657 (t80) cc_final: 0.8306 (t80) REVERT: A 1620 TYR cc_start: 0.6683 (OUTLIER) cc_final: 0.5545 (t80) REVERT: A 1647 PRO cc_start: 0.8813 (Cg_exo) cc_final: 0.8377 (Cg_endo) REVERT: A 1650 MET cc_start: 0.8736 (OUTLIER) cc_final: 0.8179 (pmm) REVERT: A 1770 MET cc_start: 0.8218 (mpp) cc_final: 0.7993 (mpp) REVERT: A 1875 ARG cc_start: 0.7480 (mmt-90) cc_final: 0.6979 (mmt-90) REVERT: A 1919 ASN cc_start: 0.8860 (m-40) cc_final: 0.8582 (m110) REVERT: A 2021 PHE cc_start: 0.8781 (m-10) cc_final: 0.8489 (m-10) REVERT: A 2049 LEU cc_start: 0.8806 (tp) cc_final: 0.7956 (mp) outliers start: 66 outliers final: 50 residues processed: 311 average time/residue: 0.2191 time to fit residues: 103.1988 Evaluate side-chains 313 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 258 time to evaluate : 1.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 374 GLN Chi-restraints excluded: chain A residue 378 ASP Chi-restraints excluded: chain A residue 470 PHE Chi-restraints excluded: chain A residue 680 LEU Chi-restraints excluded: chain A residue 690 LYS Chi-restraints excluded: chain A residue 718 THR Chi-restraints excluded: chain A residue 725 LEU Chi-restraints excluded: chain A residue 742 SER Chi-restraints excluded: chain A residue 749 ASP Chi-restraints excluded: chain A residue 766 SER Chi-restraints excluded: chain A residue 791 ILE Chi-restraints excluded: chain A residue 809 TYR Chi-restraints excluded: chain A residue 833 LEU Chi-restraints excluded: chain A residue 902 ILE Chi-restraints excluded: chain A residue 906 MET Chi-restraints excluded: chain A residue 935 VAL Chi-restraints excluded: chain A residue 982 CYS Chi-restraints excluded: chain A residue 984 ILE Chi-restraints excluded: chain A residue 995 LEU Chi-restraints excluded: chain A residue 1005 MET Chi-restraints excluded: chain A residue 1037 PHE Chi-restraints excluded: chain A residue 1064 VAL Chi-restraints excluded: chain A residue 1085 ILE Chi-restraints excluded: chain A residue 1173 LEU Chi-restraints excluded: chain A residue 1230 LEU Chi-restraints excluded: chain A residue 1262 MET Chi-restraints excluded: chain A residue 1303 VAL Chi-restraints excluded: chain A residue 1317 VAL Chi-restraints excluded: chain A residue 1341 SER Chi-restraints excluded: chain A residue 1402 ILE Chi-restraints excluded: chain A residue 1415 THR Chi-restraints excluded: chain A residue 1452 ASN Chi-restraints excluded: chain A residue 1454 LEU Chi-restraints excluded: chain A residue 1482 ASP Chi-restraints excluded: chain A residue 1541 LYS Chi-restraints excluded: chain A residue 1566 CYS Chi-restraints excluded: chain A residue 1579 ILE Chi-restraints excluded: chain A residue 1590 ILE Chi-restraints excluded: chain A residue 1596 LEU Chi-restraints excluded: chain A residue 1605 ILE Chi-restraints excluded: chain A residue 1620 TYR Chi-restraints excluded: chain A residue 1648 THR Chi-restraints excluded: chain A residue 1650 MET Chi-restraints excluded: chain A residue 1661 LEU Chi-restraints excluded: chain A residue 1908 LEU Chi-restraints excluded: chain A residue 1917 CYS Chi-restraints excluded: chain A residue 1933 ILE Chi-restraints excluded: chain A residue 1985 LEU Chi-restraints excluded: chain A residue 1988 ILE Chi-restraints excluded: chain A residue 1998 LEU Chi-restraints excluded: chain A residue 2026 PHE Chi-restraints excluded: chain A residue 2040 ASN Chi-restraints excluded: chain A residue 2052 ILE Chi-restraints excluded: chain A residue 2056 PHE Chi-restraints excluded: chain A residue 2081 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 103 optimal weight: 0.0770 chunk 29 optimal weight: 0.6980 chunk 47 optimal weight: 0.9980 chunk 137 optimal weight: 6.9990 chunk 0 optimal weight: 6.9990 chunk 131 optimal weight: 0.6980 chunk 52 optimal weight: 0.6980 chunk 61 optimal weight: 1.9990 chunk 143 optimal weight: 0.0570 chunk 19 optimal weight: 0.9990 chunk 154 optimal weight: 0.9980 overall best weight: 0.4456 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 374 GLN A 997 ASN ** A1015 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1452 ASN A1571 ASN A1996 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.116280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.093357 restraints weight = 36426.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.095779 restraints weight = 22827.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.097372 restraints weight = 16247.374| |-----------------------------------------------------------------------------| r_work (final): 0.3641 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7446 moved from start: 0.3280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 12952 Z= 0.141 Angle : 0.796 13.162 17447 Z= 0.397 Chirality : 0.047 0.197 1983 Planarity : 0.004 0.065 2182 Dihedral : 6.000 57.759 1696 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 15.12 Ramachandran Plot: Outliers : 0.19 % Allowed : 8.35 % Favored : 91.45 % Rotamer: Outliers : 3.51 % Allowed : 26.50 % Favored : 69.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -1.06 (0.21), residues: 1556 helix: 0.46 (0.18), residues: 863 sheet: -0.13 (0.65), residues: 62 loop : -2.48 (0.24), residues: 631 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A1958 HIS 0.010 0.001 HIS A1312 PHE 0.036 0.002 PHE A2002 TYR 0.035 0.002 TYR A1620 ARG 0.005 0.000 ARG A 899 Details of bonding type rmsd hydrogen bonds : bond 0.04034 ( 655) hydrogen bonds : angle 4.90480 ( 1920) covalent geometry : bond 0.00319 (12952) covalent geometry : angle 0.79571 (17447) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 269 time to evaluate : 1.490 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 369 GLU cc_start: 0.7732 (pm20) cc_final: 0.7291 (pm20) REVERT: A 374 GLN cc_start: 0.7667 (OUTLIER) cc_final: 0.7284 (pt0) REVERT: A 402 LYS cc_start: 0.7294 (tptp) cc_final: 0.6573 (tppt) REVERT: A 499 GLU cc_start: 0.8712 (pt0) cc_final: 0.8475 (pp20) REVERT: A 525 ASP cc_start: 0.8264 (m-30) cc_final: 0.7622 (t0) REVERT: A 655 MET cc_start: 0.4052 (mtt) cc_final: 0.3752 (mtp) REVERT: A 767 MET cc_start: 0.7033 (mmt) cc_final: 0.5387 (mmt) REVERT: A 768 MET cc_start: 0.7525 (ttm) cc_final: 0.7212 (ttm) REVERT: A 809 TYR cc_start: 0.7384 (OUTLIER) cc_final: 0.6925 (t80) REVERT: A 836 PHE cc_start: 0.9057 (t80) cc_final: 0.8754 (t80) REVERT: A 873 MET cc_start: 0.8041 (mpp) cc_final: 0.7626 (mpp) REVERT: A 890 MET cc_start: 0.8358 (mmm) cc_final: 0.8085 (mmm) REVERT: A 1026 GLU cc_start: 0.8612 (tm-30) cc_final: 0.7642 (mp0) REVERT: A 1049 MET cc_start: 0.6668 (pmm) cc_final: 0.6372 (mpp) REVERT: A 1105 LYS cc_start: 0.8582 (ptpt) cc_final: 0.7704 (tmtt) REVERT: A 1262 MET cc_start: 0.8162 (OUTLIER) cc_final: 0.7588 (tpp) REVERT: A 1311 GLU cc_start: 0.8175 (tp30) cc_final: 0.7890 (tp30) REVERT: A 1315 LYS cc_start: 0.9024 (mtmt) cc_final: 0.8544 (mtmt) REVERT: A 1350 ASP cc_start: 0.8627 (m-30) cc_final: 0.8375 (p0) REVERT: A 1389 ILE cc_start: 0.8698 (mt) cc_final: 0.8494 (mt) REVERT: A 1398 MET cc_start: 0.8111 (mtm) cc_final: 0.7629 (ptp) REVERT: A 1418 PHE cc_start: 0.8802 (t80) cc_final: 0.8260 (t80) REVERT: A 1461 LEU cc_start: 0.8916 (OUTLIER) cc_final: 0.8288 (tp) REVERT: A 1620 TYR cc_start: 0.6497 (OUTLIER) cc_final: 0.5008 (t80) REVERT: A 1650 MET cc_start: 0.8687 (OUTLIER) cc_final: 0.8170 (pmm) REVERT: A 1770 MET cc_start: 0.8200 (mpp) cc_final: 0.7968 (mpp) REVERT: A 2008 MET cc_start: 0.6069 (pmm) cc_final: 0.5076 (ppp) REVERT: A 2021 PHE cc_start: 0.8782 (m-10) cc_final: 0.8396 (t80) REVERT: A 2049 LEU cc_start: 0.8736 (tp) cc_final: 0.7995 (mp) REVERT: A 2088 GLU cc_start: 0.6405 (tp30) cc_final: 0.6201 (tp30) outliers start: 51 outliers final: 40 residues processed: 297 average time/residue: 0.2229 time to fit residues: 99.4062 Evaluate side-chains 300 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 254 time to evaluate : 1.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 321 TRP Chi-restraints excluded: chain A residue 374 GLN Chi-restraints excluded: chain A residue 378 ASP Chi-restraints excluded: chain A residue 470 PHE Chi-restraints excluded: chain A residue 680 LEU Chi-restraints excluded: chain A residue 690 LYS Chi-restraints excluded: chain A residue 718 THR Chi-restraints excluded: chain A residue 725 LEU Chi-restraints excluded: chain A residue 742 SER Chi-restraints excluded: chain A residue 749 ASP Chi-restraints excluded: chain A residue 791 ILE Chi-restraints excluded: chain A residue 809 TYR Chi-restraints excluded: chain A residue 902 ILE Chi-restraints excluded: chain A residue 906 MET Chi-restraints excluded: chain A residue 935 VAL Chi-restraints excluded: chain A residue 982 CYS Chi-restraints excluded: chain A residue 984 ILE Chi-restraints excluded: chain A residue 995 LEU Chi-restraints excluded: chain A residue 1005 MET Chi-restraints excluded: chain A residue 1037 PHE Chi-restraints excluded: chain A residue 1085 ILE Chi-restraints excluded: chain A residue 1173 LEU Chi-restraints excluded: chain A residue 1230 LEU Chi-restraints excluded: chain A residue 1262 MET Chi-restraints excluded: chain A residue 1303 VAL Chi-restraints excluded: chain A residue 1317 VAL Chi-restraints excluded: chain A residue 1402 ILE Chi-restraints excluded: chain A residue 1415 THR Chi-restraints excluded: chain A residue 1452 ASN Chi-restraints excluded: chain A residue 1461 LEU Chi-restraints excluded: chain A residue 1482 ASP Chi-restraints excluded: chain A residue 1541 LYS Chi-restraints excluded: chain A residue 1566 CYS Chi-restraints excluded: chain A residue 1579 ILE Chi-restraints excluded: chain A residue 1590 ILE Chi-restraints excluded: chain A residue 1596 LEU Chi-restraints excluded: chain A residue 1605 ILE Chi-restraints excluded: chain A residue 1620 TYR Chi-restraints excluded: chain A residue 1650 MET Chi-restraints excluded: chain A residue 1661 LEU Chi-restraints excluded: chain A residue 1908 LEU Chi-restraints excluded: chain A residue 1985 LEU Chi-restraints excluded: chain A residue 1998 LEU Chi-restraints excluded: chain A residue 2026 PHE Chi-restraints excluded: chain A residue 2052 ILE Chi-restraints excluded: chain A residue 2056 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 20 optimal weight: 0.9980 chunk 107 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 155 optimal weight: 2.9990 chunk 96 optimal weight: 0.9990 chunk 131 optimal weight: 0.8980 chunk 2 optimal weight: 0.9990 chunk 70 optimal weight: 6.9990 chunk 77 optimal weight: 7.9990 chunk 118 optimal weight: 1.9990 chunk 5 optimal weight: 6.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 374 GLN A 997 ASN ** A1015 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1452 ASN A1496 ASN A1571 ASN ** A2068 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.114082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.091895 restraints weight = 36511.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.094241 restraints weight = 23102.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.095902 restraints weight = 16625.275| |-----------------------------------------------------------------------------| r_work (final): 0.3616 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7486 moved from start: 0.3496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 12952 Z= 0.172 Angle : 0.803 12.940 17447 Z= 0.405 Chirality : 0.048 0.216 1983 Planarity : 0.004 0.066 2182 Dihedral : 6.026 59.686 1696 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 17.86 Ramachandran Plot: Outliers : 0.19 % Allowed : 8.87 % Favored : 90.94 % Rotamer: Outliers : 3.85 % Allowed : 26.91 % Favored : 69.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -1.11 (0.21), residues: 1556 helix: 0.45 (0.18), residues: 863 sheet: -0.18 (0.64), residues: 62 loop : -2.55 (0.23), residues: 631 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A1958 HIS 0.008 0.001 HIS A1312 PHE 0.034 0.002 PHE A1927 TYR 0.033 0.002 TYR A1620 ARG 0.007 0.000 ARG A 899 Details of bonding type rmsd hydrogen bonds : bond 0.04182 ( 655) hydrogen bonds : angle 4.99812 ( 1920) covalent geometry : bond 0.00389 (12952) covalent geometry : angle 0.80304 (17447) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 261 time to evaluate : 1.529 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 369 GLU cc_start: 0.7760 (pm20) cc_final: 0.7192 (pm20) REVERT: A 374 GLN cc_start: 0.7735 (OUTLIER) cc_final: 0.7386 (pt0) REVERT: A 402 LYS cc_start: 0.7366 (tptp) cc_final: 0.6636 (tppt) REVERT: A 525 ASP cc_start: 0.8178 (m-30) cc_final: 0.7500 (t0) REVERT: A 655 MET cc_start: 0.4094 (mtt) cc_final: 0.3746 (mtp) REVERT: A 767 MET cc_start: 0.7209 (mmt) cc_final: 0.5558 (mmt) REVERT: A 768 MET cc_start: 0.7492 (ttm) cc_final: 0.7258 (ttm) REVERT: A 809 TYR cc_start: 0.7446 (OUTLIER) cc_final: 0.7048 (t80) REVERT: A 836 PHE cc_start: 0.9068 (t80) cc_final: 0.8773 (t80) REVERT: A 873 MET cc_start: 0.8071 (mpp) cc_final: 0.7669 (mpp) REVERT: A 890 MET cc_start: 0.8319 (mmm) cc_final: 0.7960 (mmm) REVERT: A 1011 HIS cc_start: 0.5313 (OUTLIER) cc_final: 0.4781 (p-80) REVERT: A 1049 MET cc_start: 0.6758 (pmm) cc_final: 0.6494 (mpp) REVERT: A 1105 LYS cc_start: 0.8587 (ptpt) cc_final: 0.7759 (tmtt) REVERT: A 1238 MET cc_start: 0.6990 (mmp) cc_final: 0.6374 (tmm) REVERT: A 1262 MET cc_start: 0.8103 (OUTLIER) cc_final: 0.7548 (tpp) REVERT: A 1311 GLU cc_start: 0.8189 (tp30) cc_final: 0.7653 (tp30) REVERT: A 1315 LYS cc_start: 0.9069 (mtmt) cc_final: 0.8659 (mtmt) REVERT: A 1350 ASP cc_start: 0.8636 (m-30) cc_final: 0.8395 (p0) REVERT: A 1389 ILE cc_start: 0.8709 (mt) cc_final: 0.8507 (mt) REVERT: A 1418 PHE cc_start: 0.8772 (t80) cc_final: 0.8301 (t80) REVERT: A 1620 TYR cc_start: 0.6552 (OUTLIER) cc_final: 0.4999 (t80) REVERT: A 1645 GLU cc_start: 0.8763 (OUTLIER) cc_final: 0.8022 (pm20) REVERT: A 1650 MET cc_start: 0.8776 (OUTLIER) cc_final: 0.8233 (pmm) REVERT: A 1770 MET cc_start: 0.8194 (mpp) cc_final: 0.7993 (mpp) REVERT: A 1919 ASN cc_start: 0.8846 (m-40) cc_final: 0.8496 (m110) REVERT: A 2021 PHE cc_start: 0.8689 (m-10) cc_final: 0.8403 (m-10) REVERT: A 2049 LEU cc_start: 0.8765 (tp) cc_final: 0.8039 (mp) REVERT: A 2088 GLU cc_start: 0.6452 (tp30) cc_final: 0.6202 (tp30) outliers start: 56 outliers final: 42 residues processed: 293 average time/residue: 0.2202 time to fit residues: 97.7214 Evaluate side-chains 305 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 256 time to evaluate : 2.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 374 GLN Chi-restraints excluded: chain A residue 378 ASP Chi-restraints excluded: chain A residue 470 PHE Chi-restraints excluded: chain A residue 680 LEU Chi-restraints excluded: chain A residue 690 LYS Chi-restraints excluded: chain A residue 718 THR Chi-restraints excluded: chain A residue 725 LEU Chi-restraints excluded: chain A residue 742 SER Chi-restraints excluded: chain A residue 749 ASP Chi-restraints excluded: chain A residue 770 LEU Chi-restraints excluded: chain A residue 791 ILE Chi-restraints excluded: chain A residue 809 TYR Chi-restraints excluded: chain A residue 906 MET Chi-restraints excluded: chain A residue 935 VAL Chi-restraints excluded: chain A residue 982 CYS Chi-restraints excluded: chain A residue 984 ILE Chi-restraints excluded: chain A residue 995 LEU Chi-restraints excluded: chain A residue 1005 MET Chi-restraints excluded: chain A residue 1011 HIS Chi-restraints excluded: chain A residue 1037 PHE Chi-restraints excluded: chain A residue 1085 ILE Chi-restraints excluded: chain A residue 1173 LEU Chi-restraints excluded: chain A residue 1230 LEU Chi-restraints excluded: chain A residue 1262 MET Chi-restraints excluded: chain A residue 1303 VAL Chi-restraints excluded: chain A residue 1317 VAL Chi-restraints excluded: chain A residue 1335 ARG Chi-restraints excluded: chain A residue 1341 SER Chi-restraints excluded: chain A residue 1402 ILE Chi-restraints excluded: chain A residue 1415 THR Chi-restraints excluded: chain A residue 1452 ASN Chi-restraints excluded: chain A residue 1482 ASP Chi-restraints excluded: chain A residue 1541 LYS Chi-restraints excluded: chain A residue 1579 ILE Chi-restraints excluded: chain A residue 1590 ILE Chi-restraints excluded: chain A residue 1596 LEU Chi-restraints excluded: chain A residue 1605 ILE Chi-restraints excluded: chain A residue 1620 TYR Chi-restraints excluded: chain A residue 1645 GLU Chi-restraints excluded: chain A residue 1650 MET Chi-restraints excluded: chain A residue 1896 MET Chi-restraints excluded: chain A residue 1908 LEU Chi-restraints excluded: chain A residue 1985 LEU Chi-restraints excluded: chain A residue 1988 ILE Chi-restraints excluded: chain A residue 1998 LEU Chi-restraints excluded: chain A residue 2026 PHE Chi-restraints excluded: chain A residue 2052 ILE Chi-restraints excluded: chain A residue 2056 PHE Chi-restraints excluded: chain A residue 2081 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 22 optimal weight: 3.9990 chunk 147 optimal weight: 6.9990 chunk 7 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 chunk 123 optimal weight: 0.9990 chunk 4 optimal weight: 0.5980 chunk 103 optimal weight: 1.9990 chunk 92 optimal weight: 5.9990 chunk 155 optimal weight: 2.9990 chunk 99 optimal weight: 0.5980 chunk 148 optimal weight: 3.9990 overall best weight: 1.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 374 GLN ** A1015 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1452 ASN A1496 ASN ** A2068 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.114640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.091513 restraints weight = 36680.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.093921 restraints weight = 23277.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.095624 restraints weight = 16757.624| |-----------------------------------------------------------------------------| r_work (final): 0.3612 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7489 moved from start: 0.3615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 12952 Z= 0.167 Angle : 0.819 13.304 17447 Z= 0.412 Chirality : 0.048 0.211 1983 Planarity : 0.004 0.065 2182 Dihedral : 6.007 57.007 1696 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 17.23 Ramachandran Plot: Outliers : 0.19 % Allowed : 8.35 % Favored : 91.45 % Rotamer: Outliers : 3.51 % Allowed : 26.91 % Favored : 69.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -1.09 (0.21), residues: 1556 helix: 0.45 (0.18), residues: 862 sheet: -0.24 (0.62), residues: 68 loop : -2.54 (0.24), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A1958 HIS 0.008 0.001 HIS A1312 PHE 0.036 0.002 PHE A2002 TYR 0.033 0.002 TYR A1620 ARG 0.006 0.000 ARG A 899 Details of bonding type rmsd hydrogen bonds : bond 0.04216 ( 655) hydrogen bonds : angle 5.00009 ( 1920) covalent geometry : bond 0.00380 (12952) covalent geometry : angle 0.81921 (17447) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 258 time to evaluate : 1.610 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 374 GLN cc_start: 0.7765 (OUTLIER) cc_final: 0.7447 (pt0) REVERT: A 402 LYS cc_start: 0.7405 (tptp) cc_final: 0.7059 (tppt) REVERT: A 525 ASP cc_start: 0.8209 (m-30) cc_final: 0.7499 (t0) REVERT: A 655 MET cc_start: 0.4071 (mtt) cc_final: 0.3732 (mtp) REVERT: A 767 MET cc_start: 0.7190 (mmt) cc_final: 0.5485 (mmt) REVERT: A 768 MET cc_start: 0.7544 (ttm) cc_final: 0.7280 (ttm) REVERT: A 809 TYR cc_start: 0.7435 (OUTLIER) cc_final: 0.7125 (t80) REVERT: A 836 PHE cc_start: 0.9073 (t80) cc_final: 0.8761 (t80) REVERT: A 873 MET cc_start: 0.8095 (mpp) cc_final: 0.7659 (mpp) REVERT: A 946 LYS cc_start: 0.8640 (OUTLIER) cc_final: 0.8363 (mttp) REVERT: A 1105 LYS cc_start: 0.8575 (ptpt) cc_final: 0.7746 (tmtt) REVERT: A 1238 MET cc_start: 0.7046 (mmp) cc_final: 0.6516 (tmm) REVERT: A 1262 MET cc_start: 0.8140 (OUTLIER) cc_final: 0.7640 (tpp) REVERT: A 1267 MET cc_start: 0.8987 (mmm) cc_final: 0.8706 (mmm) REVERT: A 1311 GLU cc_start: 0.8242 (tp30) cc_final: 0.7697 (tp30) REVERT: A 1315 LYS cc_start: 0.9024 (mtmt) cc_final: 0.8655 (mtmt) REVERT: A 1350 ASP cc_start: 0.8656 (m-30) cc_final: 0.8401 (p0) REVERT: A 1389 ILE cc_start: 0.8719 (mt) cc_final: 0.8510 (mt) REVERT: A 1404 MET cc_start: 0.7390 (mmt) cc_final: 0.7166 (mmp) REVERT: A 1418 PHE cc_start: 0.8887 (t80) cc_final: 0.8359 (t80) REVERT: A 1620 TYR cc_start: 0.6696 (OUTLIER) cc_final: 0.5122 (t80) REVERT: A 1645 GLU cc_start: 0.8752 (OUTLIER) cc_final: 0.8038 (pm20) REVERT: A 1647 PRO cc_start: 0.8798 (Cg_exo) cc_final: 0.8339 (Cg_endo) REVERT: A 1650 MET cc_start: 0.8770 (OUTLIER) cc_final: 0.8168 (pmm) REVERT: A 1770 MET cc_start: 0.8208 (mpp) cc_final: 0.7988 (mpp) REVERT: A 1820 GLU cc_start: 0.7950 (tp30) cc_final: 0.7622 (tp30) REVERT: A 1919 ASN cc_start: 0.8863 (m-40) cc_final: 0.8513 (m110) REVERT: A 2021 PHE cc_start: 0.8741 (m-10) cc_final: 0.8442 (m-10) REVERT: A 2022 GLU cc_start: 0.6612 (OUTLIER) cc_final: 0.6354 (mp0) REVERT: A 2049 LEU cc_start: 0.8795 (tp) cc_final: 0.8109 (mp) REVERT: A 2088 GLU cc_start: 0.6535 (tp30) cc_final: 0.6274 (tp30) outliers start: 51 outliers final: 43 residues processed: 288 average time/residue: 0.2291 time to fit residues: 99.0425 Evaluate side-chains 305 residues out of total 1462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 254 time to evaluate : 1.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 374 GLN Chi-restraints excluded: chain A residue 378 ASP Chi-restraints excluded: chain A residue 470 PHE Chi-restraints excluded: chain A residue 680 LEU Chi-restraints excluded: chain A residue 690 LYS Chi-restraints excluded: chain A residue 718 THR Chi-restraints excluded: chain A residue 725 LEU Chi-restraints excluded: chain A residue 742 SER Chi-restraints excluded: chain A residue 749 ASP Chi-restraints excluded: chain A residue 770 LEU Chi-restraints excluded: chain A residue 791 ILE Chi-restraints excluded: chain A residue 809 TYR Chi-restraints excluded: chain A residue 906 MET Chi-restraints excluded: chain A residue 935 VAL Chi-restraints excluded: chain A residue 946 LYS Chi-restraints excluded: chain A residue 982 CYS Chi-restraints excluded: chain A residue 984 ILE Chi-restraints excluded: chain A residue 995 LEU Chi-restraints excluded: chain A residue 1005 MET Chi-restraints excluded: chain A residue 1011 HIS Chi-restraints excluded: chain A residue 1037 PHE Chi-restraints excluded: chain A residue 1085 ILE Chi-restraints excluded: chain A residue 1173 LEU Chi-restraints excluded: chain A residue 1230 LEU Chi-restraints excluded: chain A residue 1262 MET Chi-restraints excluded: chain A residue 1303 VAL Chi-restraints excluded: chain A residue 1317 VAL Chi-restraints excluded: chain A residue 1335 ARG Chi-restraints excluded: chain A residue 1341 SER Chi-restraints excluded: chain A residue 1402 ILE Chi-restraints excluded: chain A residue 1415 THR Chi-restraints excluded: chain A residue 1452 ASN Chi-restraints excluded: chain A residue 1482 ASP Chi-restraints excluded: chain A residue 1541 LYS Chi-restraints excluded: chain A residue 1579 ILE Chi-restraints excluded: chain A residue 1590 ILE Chi-restraints excluded: chain A residue 1596 LEU Chi-restraints excluded: chain A residue 1605 ILE Chi-restraints excluded: chain A residue 1620 TYR Chi-restraints excluded: chain A residue 1645 GLU Chi-restraints excluded: chain A residue 1650 MET Chi-restraints excluded: chain A residue 1896 MET Chi-restraints excluded: chain A residue 1908 LEU Chi-restraints excluded: chain A residue 1985 LEU Chi-restraints excluded: chain A residue 1998 LEU Chi-restraints excluded: chain A residue 2022 GLU Chi-restraints excluded: chain A residue 2026 PHE Chi-restraints excluded: chain A residue 2040 ASN Chi-restraints excluded: chain A residue 2052 ILE Chi-restraints excluded: chain A residue 2056 PHE Chi-restraints excluded: chain A residue 2081 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 17 optimal weight: 3.9990 chunk 28 optimal weight: 0.5980 chunk 5 optimal weight: 3.9990 chunk 145 optimal weight: 0.0970 chunk 79 optimal weight: 1.9990 chunk 87 optimal weight: 0.6980 chunk 2 optimal weight: 0.0470 chunk 108 optimal weight: 0.3980 chunk 4 optimal weight: 0.9990 chunk 1 optimal weight: 0.8980 chunk 152 optimal weight: 0.9980 overall best weight: 0.3676 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1015 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1452 ASN ** A2068 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.116890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.094030 restraints weight = 36273.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.096481 restraints weight = 22793.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.098174 restraints weight = 16160.890| |-----------------------------------------------------------------------------| r_work (final): 0.3656 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7427 moved from start: 0.3613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12952 Z= 0.141 Angle : 0.814 13.736 17447 Z= 0.405 Chirality : 0.047 0.217 1983 Planarity : 0.004 0.061 2182 Dihedral : 5.886 57.091 1696 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 15.47 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.90 % Favored : 91.90 % Rotamer: Outliers : 3.17 % Allowed : 27.60 % Favored : 69.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -1.01 (0.22), residues: 1556 helix: 0.48 (0.18), residues: 864 sheet: -0.15 (0.63), residues: 68 loop : -2.44 (0.24), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A1958 HIS 0.007 0.001 HIS A1015 PHE 0.025 0.002 PHE A 741 TYR 0.032 0.001 TYR A1620 ARG 0.005 0.000 ARG A 899 Details of bonding type rmsd hydrogen bonds : bond 0.04054 ( 655) hydrogen bonds : angle 4.87777 ( 1920) covalent geometry : bond 0.00317 (12952) covalent geometry : angle 0.81430 (17447) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4234.65 seconds wall clock time: 75 minutes 30.62 seconds (4530.62 seconds total)