Starting phenix.real_space_refine on Fri Mar 15 02:03:20 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uvk_26812/03_2024/7uvk_26812.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uvk_26812/03_2024/7uvk_26812.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.28 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uvk_26812/03_2024/7uvk_26812.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uvk_26812/03_2024/7uvk_26812.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uvk_26812/03_2024/7uvk_26812.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uvk_26812/03_2024/7uvk_26812.pdb" } resolution = 3.28 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= 0.001 sd= 0.045 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 19 5.16 5 C 6536 2.51 5 N 1750 2.21 5 O 2045 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 932": "OE1" <-> "OE2" Residue "A TYR 957": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1048": "OD1" <-> "OD2" Residue "A GLU 1189": "OE1" <-> "OE2" Residue "A PHE 1236": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1250": "OE1" <-> "OE2" Residue "A GLU 1253": "OE1" <-> "OE2" Residue "A ASP 1303": "OD1" <-> "OD2" Residue "A ASP 1310": "OD1" <-> "OD2" Residue "A GLU 1312": "OE1" <-> "OE2" Residue "A GLU 1313": "OE1" <-> "OE2" Residue "A GLU 1320": "OE1" <-> "OE2" Residue "A GLU 1340": "OE1" <-> "OE2" Residue "A GLU 1349": "OE1" <-> "OE2" Residue "A GLU 1370": "OE1" <-> "OE2" Residue "A TYR 1376": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1503": "OE1" <-> "OE2" Residue "A ASP 1507": "OD1" <-> "OD2" Residue "A PHE 1510": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1528": "OD1" <-> "OD2" Residue "A ASP 1583": "OD1" <-> "OD2" Residue "A GLU 1627": "OE1" <-> "OE2" Residue "A PHE 1711": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1731": "OE1" <-> "OE2" Residue "A GLU 1744": "OE1" <-> "OE2" Residue "A GLU 1767": "OE1" <-> "OE2" Residue "A GLU 1791": "OE1" <-> "OE2" Residue "A GLU 1848": "OE1" <-> "OE2" Residue "A GLU 1856": "OE1" <-> "OE2" Residue "A PHE 1872": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1899": "OD1" <-> "OD2" Residue "A TYR 1933": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1965": "OD1" <-> "OD2" Residue "A GLU 1984": "OE1" <-> "OE2" Residue "A GLU 1996": "OE1" <-> "OE2" Residue "A GLU 2010": "OE1" <-> "OE2" Residue "A TYR 2016": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 2119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 2153": "OE1" <-> "OE2" Residue "A PHE 2193": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 10350 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 10350 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1295, 10350 Classifications: {'peptide': 1295} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 30, 'TRANS': 1264} Time building chain proxies: 5.52, per 1000 atoms: 0.53 Number of scatterers: 10350 At special positions: 0 Unit cell: (87.15, 110.39, 144.42, 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 19 16.00 O 2045 8.00 N 1750 7.00 C 6536 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.78 Conformation dependent library (CDL) restraints added in 1.8 seconds 2586 Ramachandran restraints generated. 1293 Oldfield, 0 Emsley, 1293 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2440 Finding SS restraints... Secondary structure from input PDB file: 44 helices and 16 sheets defined 34.3% alpha, 11.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.32 Creating SS restraints... Processing helix chain 'A' and resid 1025 through 1036 Processing helix chain 'A' and resid 1253 through 1257 Processing helix chain 'A' and resid 1318 through 1323 Processing helix chain 'A' and resid 1324 through 1326 No H-bonds generated for 'chain 'A' and resid 1324 through 1326' Processing helix chain 'A' and resid 1359 through 1361 No H-bonds generated for 'chain 'A' and resid 1359 through 1361' Processing helix chain 'A' and resid 1362 through 1373 removed outlier: 4.176A pdb=" N LYS A1371 " --> pdb=" O LYS A1367 " (cutoff:3.500A) Processing helix chain 'A' and resid 1377 through 1387 Processing helix chain 'A' and resid 1392 through 1396 removed outlier: 3.775A pdb=" N TYR A1395 " --> pdb=" O ASN A1392 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N THR A1396 " --> pdb=" O THR A1393 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1392 through 1396' Processing helix chain 'A' and resid 1412 through 1417 Processing helix chain 'A' and resid 1468 through 1481 removed outlier: 4.688A pdb=" N ASN A1477 " --> pdb=" O LYS A1473 " (cutoff:3.500A) removed outlier: 5.005A pdb=" N ASP A1478 " --> pdb=" O ALA A1474 " (cutoff:3.500A) Processing helix chain 'A' and resid 1486 through 1493 removed outlier: 3.632A pdb=" N ARG A1490 " --> pdb=" O SER A1486 " (cutoff:3.500A) Processing helix chain 'A' and resid 1500 through 1505 removed outlier: 4.393A pdb=" N GLU A1503 " --> pdb=" O LYS A1500 " (cutoff:3.500A) Processing helix chain 'A' and resid 1506 through 1516 removed outlier: 4.350A pdb=" N THR A1511 " --> pdb=" O ASP A1507 " (cutoff:3.500A) Processing helix chain 'A' and resid 1516 through 1529 removed outlier: 3.924A pdb=" N SER A1520 " --> pdb=" O ASN A1516 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N ALA A1529 " --> pdb=" O LEU A1525 " (cutoff:3.500A) Processing helix chain 'A' and resid 1537 through 1550 removed outlier: 3.833A pdb=" N TYR A1542 " --> pdb=" O ILE A1538 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ASN A1550 " --> pdb=" O LYS A1546 " (cutoff:3.500A) Processing helix chain 'A' and resid 1550 through 1565 removed outlier: 3.502A pdb=" N TYR A1565 " --> pdb=" O LEU A1561 " (cutoff:3.500A) Processing helix chain 'A' and resid 1573 through 1580 removed outlier: 3.848A pdb=" N LEU A1577 " --> pdb=" O SER A1573 " (cutoff:3.500A) Processing helix chain 'A' and resid 1581 through 1586 removed outlier: 4.269A pdb=" N PHE A1585 " --> pdb=" O LEU A1582 " (cutoff:3.500A) Processing helix chain 'A' and resid 1591 through 1601 Processing helix chain 'A' and resid 1608 through 1610 No H-bonds generated for 'chain 'A' and resid 1608 through 1610' Processing helix chain 'A' and resid 1611 through 1619 Processing helix chain 'A' and resid 1628 through 1640 Processing helix chain 'A' and resid 1645 through 1654 Processing helix chain 'A' and resid 1665 through 1673 Processing helix chain 'A' and resid 1682 through 1688 Processing helix chain 'A' and resid 1694 through 1696 No H-bonds generated for 'chain 'A' and resid 1694 through 1696' Processing helix chain 'A' and resid 1697 through 1703 Processing helix chain 'A' and resid 1723 through 1727 Processing helix chain 'A' and resid 1737 through 1764 Processing helix chain 'A' and resid 1768 through 1772 Processing helix chain 'A' and resid 1801 through 1807 Processing helix chain 'A' and resid 1838 through 1853 removed outlier: 3.920A pdb=" N ALA A1842 " --> pdb=" O ASP A1838 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N VAL A1843 " --> pdb=" O LYS A1839 " (cutoff:3.500A) Processing helix chain 'A' and resid 1869 through 1875 removed outlier: 4.216A pdb=" N TYR A1873 " --> pdb=" O GLY A1869 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N ALA A1874 " --> pdb=" O PRO A1870 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N LYS A1875 " --> pdb=" O GLU A1871 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1869 through 1875' Processing helix chain 'A' and resid 1910 through 1915 removed outlier: 3.780A pdb=" N PHE A1915 " --> pdb=" O PRO A1911 " (cutoff:3.500A) Processing helix chain 'A' and resid 1917 through 1944 removed outlier: 3.553A pdb=" N ALA A1942 " --> pdb=" O LEU A1938 " (cutoff:3.500A) Processing helix chain 'A' and resid 1947 through 1954 Processing helix chain 'A' and resid 1981 through 1988 Processing helix chain 'A' and resid 1990 through 1997 removed outlier: 3.714A pdb=" N LEU A1994 " --> pdb=" O SER A1990 " (cutoff:3.500A) Processing helix chain 'A' and resid 2039 through 2052 Processing helix chain 'A' and resid 2066 through 2073 Processing helix chain 'A' and resid 2088 through 2097 Processing helix chain 'A' and resid 2103 through 2120 Processing helix chain 'A' and resid 2144 through 2161 removed outlier: 4.091A pdb=" N LEU A2148 " --> pdb=" O ASN A2144 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLU A2161 " --> pdb=" O ARG A2157 " (cutoff:3.500A) Processing helix chain 'A' and resid 2173 through 2190 removed outlier: 3.506A pdb=" N LYS A2177 " --> pdb=" O SER A2173 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 923 through 924 removed outlier: 6.419A pdb=" N LEU A 923 " --> pdb=" O ILE A 997 " (cutoff:3.500A) removed outlier: 7.972A pdb=" N HIS A 999 " --> pdb=" O LEU A 923 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 942 through 944 removed outlier: 3.548A pdb=" N ARG A 942 " --> pdb=" O THR A 935 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N LEU A 933 " --> pdb=" O VAL A 944 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N PHE A 958 " --> pdb=" O TYR A 934 " (cutoff:3.500A) removed outlier: 7.330A pdb=" N VAL A 990 " --> pdb=" O LYS A 974 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 978 through 980 removed outlier: 7.330A pdb=" N VAL A 990 " --> pdb=" O LYS A 974 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1047 through 1048 removed outlier: 6.963A pdb=" N MET A1047 " --> pdb=" O TYR A1082 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 1105 through 1109 removed outlier: 5.719A pdb=" N ALA A1105 " --> pdb=" O VAL A1134 " (cutoff:3.500A) removed outlier: 7.504A pdb=" N ALA A1136 " --> pdb=" O ALA A1105 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N VAL A1107 " --> pdb=" O ALA A1136 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N PHE A1158 " --> pdb=" O SER A1194 " (cutoff:3.500A) removed outlier: 7.460A pdb=" N ASP A1196 " --> pdb=" O PHE A1158 " (cutoff:3.500A) removed outlier: 7.393A pdb=" N GLY A1160 " --> pdb=" O ASP A1196 " (cutoff:3.500A) removed outlier: 8.277A pdb=" N ALA A1198 " --> pdb=" O GLY A1160 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N ILE A1162 " --> pdb=" O ALA A1198 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 1113 through 1114 removed outlier: 6.389A pdb=" N ALA A1113 " --> pdb=" O GLY A1142 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 1117 through 1120 removed outlier: 6.949A pdb=" N LYS A1118 " --> pdb=" O ILE A1145 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 1152 through 1154 Processing sheet with id=AA9, first strand: chain 'A' and resid 1178 through 1181 removed outlier: 6.846A pdb=" N GLY A1179 " --> pdb=" O ALA A1212 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N VAL A1214 " --> pdb=" O GLY A1179 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N GLY A1213 " --> pdb=" O VAL A1243 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ASN A1245 " --> pdb=" O GLY A1213 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 1220 through 1222 removed outlier: 6.023A pdb=" N ILE A1221 " --> pdb=" O THR A1261 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'A' and resid 1299 through 1300 Processing sheet with id=AB3, first strand: chain 'A' and resid 1424 through 1427 Processing sheet with id=AB4, first strand: chain 'A' and resid 1438 through 1442 removed outlier: 7.513A pdb=" N GLU A1449 " --> pdb=" O LEU A1441 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 1657 through 1660 removed outlier: 3.690A pdb=" N THR A1718 " --> pdb=" O ASN A1715 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 1973 through 1978 Processing sheet with id=AB7, first strand: chain 'A' and resid 2076 through 2079 321 hydrogen bonds defined for protein. 918 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: 3.78 Time building geometry restraints manager: 4.13 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: 2120 1.33 - 1.45: 2435 1.45 - 1.57: 5939 1.57 - 1.69: 1 1.69 - 1.81: 38 Bond restraints: 10533 Sorted by residual: bond pdb=" CG PRO A 954 " pdb=" CD PRO A 954 " ideal model delta sigma weight residual 1.503 1.208 0.295 3.40e-02 8.65e+02 7.54e+01 bond pdb=" N PRO A 954 " pdb=" CD PRO A 954 " ideal model delta sigma weight residual 1.473 1.545 -0.072 1.40e-02 5.10e+03 2.62e+01 bond pdb=" CB PRO A 954 " pdb=" CG PRO A 954 " ideal model delta sigma weight residual 1.492 1.681 -0.189 5.00e-02 4.00e+02 1.43e+01 bond pdb=" N PRO A 954 " pdb=" CA PRO A 954 " ideal model delta sigma weight residual 1.469 1.443 0.026 1.28e-02 6.10e+03 4.05e+00 bond pdb=" CA ILE A1071 " pdb=" CB ILE A1071 " ideal model delta sigma weight residual 1.528 1.546 -0.018 1.34e-02 5.57e+03 1.77e+00 ... (remaining 10528 not shown) Histogram of bond angle deviations from ideal: 86.83 - 97.68: 3 97.68 - 108.54: 400 108.54 - 119.40: 8291 119.40 - 130.25: 5508 130.25 - 141.11: 26 Bond angle restraints: 14228 Sorted by residual: angle pdb=" CA PRO A 954 " pdb=" N PRO A 954 " pdb=" CD PRO A 954 " ideal model delta sigma weight residual 112.00 96.05 15.95 1.40e+00 5.10e-01 1.30e+02 angle pdb=" N PRO A 954 " pdb=" CD PRO A 954 " pdb=" CG PRO A 954 " ideal model delta sigma weight residual 103.20 86.83 16.37 1.50e+00 4.44e-01 1.19e+02 angle pdb=" CA PRO A 954 " pdb=" CB PRO A 954 " pdb=" CG PRO A 954 " ideal model delta sigma weight residual 104.50 91.55 12.95 1.90e+00 2.77e-01 4.65e+01 angle pdb=" N VAL A1318 " pdb=" CA VAL A1318 " pdb=" C VAL A1318 " ideal model delta sigma weight residual 111.91 106.85 5.06 8.90e-01 1.26e+00 3.23e+01 angle pdb=" C ASN A 953 " pdb=" N PRO A 954 " pdb=" CD PRO A 954 " ideal model delta sigma weight residual 125.00 141.11 -16.11 4.10e+00 5.95e-02 1.54e+01 ... (remaining 14223 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.39: 5716 17.39 - 34.77: 574 34.77 - 52.16: 87 52.16 - 69.54: 10 69.54 - 86.93: 5 Dihedral angle restraints: 6392 sinusoidal: 2582 harmonic: 3810 Sorted by residual: dihedral pdb=" CA SER A1055 " pdb=" C SER A1055 " pdb=" N ASP A1056 " pdb=" CA ASP A1056 " ideal model delta harmonic sigma weight residual 180.00 145.58 34.42 0 5.00e+00 4.00e-02 4.74e+01 dihedral pdb=" CA LYS A2191 " pdb=" C LYS A2191 " pdb=" N ASP A2192 " pdb=" CA ASP A2192 " ideal model delta harmonic sigma weight residual 180.00 156.06 23.94 0 5.00e+00 4.00e-02 2.29e+01 dihedral pdb=" CA PRO A1705 " pdb=" C PRO A1705 " pdb=" N GLU A1706 " pdb=" CA GLU A1706 " ideal model delta harmonic sigma weight residual 180.00 -157.26 -22.74 0 5.00e+00 4.00e-02 2.07e+01 ... (remaining 6389 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 1323 0.060 - 0.121: 234 0.121 - 0.181: 21 0.181 - 0.241: 2 0.241 - 0.302: 1 Chirality restraints: 1581 Sorted by residual: chirality pdb=" CB ILE A1071 " pdb=" CA ILE A1071 " pdb=" CG1 ILE A1071 " pdb=" CG2 ILE A1071 " both_signs ideal model delta sigma weight residual False 2.64 2.34 0.30 2.00e-01 2.50e+01 2.28e+00 chirality pdb=" CA PRO A1966 " pdb=" N PRO A1966 " pdb=" C PRO A1966 " pdb=" CB PRO A1966 " both_signs ideal model delta sigma weight residual False 2.72 2.52 0.20 2.00e-01 2.50e+01 9.53e-01 chirality pdb=" CB VAL A1475 " pdb=" CA VAL A1475 " pdb=" CG1 VAL A1475 " pdb=" CG2 VAL A1475 " both_signs ideal model delta sigma weight residual False -2.63 -2.43 -0.19 2.00e-01 2.50e+01 9.48e-01 ... (remaining 1578 not shown) Planarity restraints: 1841 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A1829 " -0.008 2.00e-02 2.50e+03 1.53e-02 4.09e+00 pdb=" CG PHE A1829 " 0.032 2.00e-02 2.50e+03 pdb=" CD1 PHE A1829 " -0.020 2.00e-02 2.50e+03 pdb=" CD2 PHE A1829 " -0.007 2.00e-02 2.50e+03 pdb=" CE1 PHE A1829 " 0.008 2.00e-02 2.50e+03 pdb=" CE2 PHE A1829 " -0.005 2.00e-02 2.50e+03 pdb=" CZ PHE A1829 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP A1965 " -0.009 2.00e-02 2.50e+03 1.86e-02 3.47e+00 pdb=" CG ASP A1965 " 0.032 2.00e-02 2.50e+03 pdb=" OD1 ASP A1965 " -0.012 2.00e-02 2.50e+03 pdb=" OD2 ASP A1965 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN A 953 " -0.034 5.00e-02 4.00e+02 4.55e-02 3.31e+00 pdb=" N PRO A 954 " 0.078 5.00e-02 4.00e+02 pdb=" CA PRO A 954 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 954 " -0.025 5.00e-02 4.00e+02 ... (remaining 1838 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.71: 445 2.71 - 3.26: 10615 3.26 - 3.81: 15755 3.81 - 4.35: 20937 4.35 - 4.90: 35527 Nonbonded interactions: 83279 Sorted by model distance: nonbonded pdb=" O GLY A1204 " pdb=" NZ LYS A1238 " model vdw 2.168 2.520 nonbonded pdb=" OG SER A2031 " pdb=" O GLY A2034 " model vdw 2.189 2.440 nonbonded pdb=" OE2 GLU A1370 " pdb=" NH1 ARG A1378 " model vdw 2.202 2.520 nonbonded pdb=" O SER A1663 " pdb=" OG SER A1669 " model vdw 2.219 2.440 nonbonded pdb=" NH2 ARG A2073 " pdb=" OE2 GLU A2094 " model vdw 2.240 2.520 ... (remaining 83274 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.090 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 10.150 Check model and map are aligned: 0.150 Set scattering table: 0.100 Process input model: 30.310 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.040 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:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7420 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.295 10533 Z= 0.332 Angle : 0.741 16.372 14228 Z= 0.432 Chirality : 0.046 0.302 1581 Planarity : 0.004 0.045 1841 Dihedral : 13.598 86.927 3952 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.05 % Favored : 90.95 % Rotamer: Outliers : 0.00 % Allowed : 0.26 % Favored : 99.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -3.16 (0.21), residues: 1293 helix: -0.34 (0.26), residues: 402 sheet: -3.39 (0.34), residues: 180 loop : -2.91 (0.19), residues: 711 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A1247 HIS 0.008 0.001 HIS A1847 PHE 0.032 0.002 PHE A1829 TYR 0.024 0.001 TYR A1172 ARG 0.010 0.000 ARG A1139 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2586 Ramachandran restraints generated. 1293 Oldfield, 0 Emsley, 1293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2586 Ramachandran restraints generated. 1293 Oldfield, 0 Emsley, 1293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 1148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 263 time to evaluate : 1.113 Fit side-chains REVERT: A 922 LYS cc_start: 0.7116 (mmtp) cc_final: 0.6678 (mmtm) REVERT: A 939 ASN cc_start: 0.6680 (t0) cc_final: 0.6247 (t0) REVERT: A 940 LYS cc_start: 0.7893 (ptmm) cc_final: 0.7631 (ptmm) REVERT: A 1034 ASN cc_start: 0.7371 (m-40) cc_final: 0.7128 (m-40) REVERT: A 1050 ARG cc_start: 0.7375 (ptp-170) cc_final: 0.6883 (mtt180) REVERT: A 1077 LYS cc_start: 0.6487 (ttpt) cc_final: 0.6217 (ptpp) REVERT: A 1195 ILE cc_start: 0.8254 (pt) cc_final: 0.7816 (pt) REVERT: A 1266 ASP cc_start: 0.7104 (t0) cc_final: 0.6844 (t0) REVERT: A 1294 ASN cc_start: 0.7379 (m-40) cc_final: 0.7087 (m-40) REVERT: A 1406 LYS cc_start: 0.7331 (mttt) cc_final: 0.6763 (mtmm) REVERT: A 1407 ASP cc_start: 0.6877 (m-30) cc_final: 0.6633 (m-30) REVERT: A 1473 LYS cc_start: 0.7569 (ptmm) cc_final: 0.7350 (pttt) REVERT: A 1478 ASP cc_start: 0.7380 (m-30) cc_final: 0.7140 (m-30) REVERT: A 1498 ASN cc_start: 0.7990 (t0) cc_final: 0.7703 (p0) REVERT: A 1546 LYS cc_start: 0.7934 (ttpt) cc_final: 0.7733 (ttmm) REVERT: A 1583 ASP cc_start: 0.8350 (p0) cc_final: 0.8108 (p0) REVERT: A 1594 ASP cc_start: 0.7509 (m-30) cc_final: 0.7182 (m-30) REVERT: A 1646 ASN cc_start: 0.7837 (p0) cc_final: 0.7474 (p0) REVERT: A 1662 LYS cc_start: 0.8613 (mttp) cc_final: 0.8404 (mtmt) REVERT: A 1703 THR cc_start: 0.8526 (m) cc_final: 0.8040 (p) REVERT: A 1725 ASP cc_start: 0.7397 (m-30) cc_final: 0.7142 (t0) REVERT: A 1832 MET cc_start: 0.8452 (mmm) cc_final: 0.8236 (mmt) REVERT: A 1855 ARG cc_start: 0.7163 (mtm-85) cc_final: 0.6936 (mtm180) REVERT: A 1856 GLU cc_start: 0.7723 (mm-30) cc_final: 0.7480 (mm-30) REVERT: A 1953 ASP cc_start: 0.6904 (t0) cc_final: 0.6538 (m-30) outliers start: 0 outliers final: 0 residues processed: 263 average time/residue: 0.2643 time to fit residues: 92.7138 Evaluate side-chains 157 residues out of total 1148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 157 time to evaluate : 1.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 108 optimal weight: 2.9990 chunk 97 optimal weight: 1.9990 chunk 54 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 52 optimal weight: 0.5980 chunk 101 optimal weight: 3.9990 chunk 39 optimal weight: 4.9990 chunk 61 optimal weight: 2.9990 chunk 75 optimal weight: 0.7980 chunk 117 optimal weight: 1.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1007 ASN A1206 GLN A1229 ASN A1368 ASN A1415 ASN ** A1715 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1817 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1969 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1987 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7732 moved from start: 0.3192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 10533 Z= 0.339 Angle : 0.712 9.683 14228 Z= 0.383 Chirality : 0.048 0.182 1581 Planarity : 0.005 0.051 1841 Dihedral : 6.143 37.223 1419 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 13.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.74 % Favored : 90.26 % Rotamer: Outliers : 2.26 % Allowed : 9.93 % Favored : 87.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -2.98 (0.21), residues: 1293 helix: -0.36 (0.26), residues: 409 sheet: -3.31 (0.36), residues: 151 loop : -2.75 (0.19), residues: 733 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A1247 HIS 0.007 0.002 HIS A1847 PHE 0.036 0.003 PHE A2119 TYR 0.029 0.002 TYR A1172 ARG 0.006 0.001 ARG A1774 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2586 Ramachandran restraints generated. 1293 Oldfield, 0 Emsley, 1293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2586 Ramachandran restraints generated. 1293 Oldfield, 0 Emsley, 1293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 172 time to evaluate : 1.332 Fit side-chains REVERT: A 922 LYS cc_start: 0.7759 (mmtp) cc_final: 0.7460 (mmtm) REVERT: A 1050 ARG cc_start: 0.7638 (ptp-170) cc_final: 0.7159 (mtm-85) REVERT: A 1073 GLU cc_start: 0.6927 (mp0) cc_final: 0.6710 (mp0) REVERT: A 1098 GLN cc_start: 0.8146 (tt0) cc_final: 0.7719 (tt0) REVERT: A 1100 LEU cc_start: 0.8299 (tp) cc_final: 0.7329 (tp) REVERT: A 1266 ASP cc_start: 0.7157 (t0) cc_final: 0.6782 (t0) REVERT: A 1294 ASN cc_start: 0.7496 (m-40) cc_final: 0.7274 (m-40) REVERT: A 1298 LYS cc_start: 0.7657 (mmtt) cc_final: 0.7413 (mmtt) REVERT: A 1335 LYS cc_start: 0.7956 (mtpt) cc_final: 0.7691 (mptt) REVERT: A 1406 LYS cc_start: 0.7552 (mttt) cc_final: 0.6932 (mtmm) REVERT: A 1477 ASN cc_start: 0.7807 (t0) cc_final: 0.7504 (t0) REVERT: A 1478 ASP cc_start: 0.7616 (m-30) cc_final: 0.7385 (m-30) REVERT: A 1583 ASP cc_start: 0.8115 (p0) cc_final: 0.7855 (p0) REVERT: A 1594 ASP cc_start: 0.7552 (m-30) cc_final: 0.7312 (m-30) REVERT: A 1662 LYS cc_start: 0.8804 (mttp) cc_final: 0.8565 (mtmt) REVERT: A 1725 ASP cc_start: 0.7734 (m-30) cc_final: 0.7340 (m-30) REVERT: A 1757 TYR cc_start: 0.7977 (m-80) cc_final: 0.7344 (m-80) REVERT: A 1770 GLU cc_start: 0.7354 (mt-10) cc_final: 0.6884 (mm-30) REVERT: A 1855 ARG cc_start: 0.7632 (mtm-85) cc_final: 0.7419 (mtt90) REVERT: A 1856 GLU cc_start: 0.7861 (mm-30) cc_final: 0.7584 (mm-30) REVERT: A 1927 ASN cc_start: 0.7755 (m110) cc_final: 0.7550 (m110) REVERT: A 1953 ASP cc_start: 0.7134 (t0) cc_final: 0.6642 (m-30) REVERT: A 1988 LEU cc_start: 0.6833 (OUTLIER) cc_final: 0.6218 (mp) REVERT: A 2033 ILE cc_start: 0.8152 (mm) cc_final: 0.7948 (mt) REVERT: A 2124 ARG cc_start: 0.6459 (mmp80) cc_final: 0.6176 (mmp80) REVERT: A 2172 ASN cc_start: 0.8074 (t0) cc_final: 0.7806 (t0) outliers start: 26 outliers final: 16 residues processed: 192 average time/residue: 0.2424 time to fit residues: 64.8411 Evaluate side-chains 153 residues out of total 1148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 136 time to evaluate : 1.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 952 THR Chi-restraints excluded: chain A residue 990 VAL Chi-restraints excluded: chain A residue 1009 THR Chi-restraints excluded: chain A residue 1109 SER Chi-restraints excluded: chain A residue 1165 THR Chi-restraints excluded: chain A residue 1174 ILE Chi-restraints excluded: chain A residue 1184 VAL Chi-restraints excluded: chain A residue 1257 SER Chi-restraints excluded: chain A residue 1267 VAL Chi-restraints excluded: chain A residue 1403 VAL Chi-restraints excluded: chain A residue 1430 ASP Chi-restraints excluded: chain A residue 1588 SER Chi-restraints excluded: chain A residue 1777 LEU Chi-restraints excluded: chain A residue 1789 ASN Chi-restraints excluded: chain A residue 1794 GLU Chi-restraints excluded: chain A residue 1988 LEU Chi-restraints excluded: chain A residue 2088 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 65 optimal weight: 0.7980 chunk 36 optimal weight: 0.9990 chunk 97 optimal weight: 0.0870 chunk 79 optimal weight: 0.9990 chunk 32 optimal weight: 3.9990 chunk 117 optimal weight: 5.9990 chunk 126 optimal weight: 2.9990 chunk 104 optimal weight: 4.9990 chunk 116 optimal weight: 0.6980 chunk 40 optimal weight: 3.9990 chunk 94 optimal weight: 2.9990 overall best weight: 0.7162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1229 ASN A1391 ASN A1415 ASN A1768 ASN A1817 HIS ** A1969 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7694 moved from start: 0.3462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10533 Z= 0.191 Angle : 0.580 7.195 14228 Z= 0.314 Chirality : 0.044 0.182 1581 Planarity : 0.004 0.048 1841 Dihedral : 5.650 33.967 1419 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 11.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.58 % Favored : 91.42 % Rotamer: Outliers : 2.79 % Allowed : 12.54 % Favored : 84.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -2.77 (0.22), residues: 1293 helix: -0.05 (0.26), residues: 408 sheet: -2.88 (0.32), residues: 218 loop : -2.70 (0.20), residues: 667 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A1247 HIS 0.007 0.001 HIS A1847 PHE 0.029 0.002 PHE A2119 TYR 0.022 0.001 TYR A1831 ARG 0.005 0.000 ARG A2157 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2586 Ramachandran restraints generated. 1293 Oldfield, 0 Emsley, 1293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2586 Ramachandran restraints generated. 1293 Oldfield, 0 Emsley, 1293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 140 time to evaluate : 1.246 Fit side-chains REVERT: A 922 LYS cc_start: 0.7871 (mmtp) cc_final: 0.7533 (mmtm) REVERT: A 1050 ARG cc_start: 0.7637 (ptp-170) cc_final: 0.7263 (mtm-85) REVERT: A 1073 GLU cc_start: 0.7040 (mp0) cc_final: 0.6636 (mp0) REVERT: A 1098 GLN cc_start: 0.8097 (tt0) cc_final: 0.7109 (tt0) REVERT: A 1119 GLU cc_start: 0.7551 (mt-10) cc_final: 0.7165 (tt0) REVERT: A 1132 SER cc_start: 0.8882 (m) cc_final: 0.8603 (t) REVERT: A 1266 ASP cc_start: 0.7087 (t0) cc_final: 0.6735 (t0) REVERT: A 1294 ASN cc_start: 0.7381 (m-40) cc_final: 0.7169 (m-40) REVERT: A 1335 LYS cc_start: 0.7896 (mtpt) cc_final: 0.7620 (mptt) REVERT: A 1406 LYS cc_start: 0.7316 (mttt) cc_final: 0.6704 (mtmm) REVERT: A 1407 ASP cc_start: 0.6773 (m-30) cc_final: 0.6466 (m-30) REVERT: A 1416 LYS cc_start: 0.6581 (mttm) cc_final: 0.5881 (mttt) REVERT: A 1422 ASN cc_start: 0.7902 (m110) cc_final: 0.7670 (m110) REVERT: A 1477 ASN cc_start: 0.7837 (t0) cc_final: 0.7528 (t0) REVERT: A 1478 ASP cc_start: 0.7709 (m-30) cc_final: 0.7478 (m-30) REVERT: A 1583 ASP cc_start: 0.8082 (p0) cc_final: 0.7840 (p0) REVERT: A 1594 ASP cc_start: 0.7582 (m-30) cc_final: 0.7326 (m-30) REVERT: A 1757 TYR cc_start: 0.7973 (m-80) cc_final: 0.7076 (m-80) REVERT: A 1770 GLU cc_start: 0.7322 (mt-10) cc_final: 0.6855 (mm-30) REVERT: A 1846 THR cc_start: 0.8090 (m) cc_final: 0.7727 (p) REVERT: A 1855 ARG cc_start: 0.7602 (mtm-85) cc_final: 0.7330 (mtt90) REVERT: A 1856 GLU cc_start: 0.7928 (mm-30) cc_final: 0.7416 (mm-30) REVERT: A 1927 ASN cc_start: 0.7707 (m110) cc_final: 0.7479 (m110) REVERT: A 1953 ASP cc_start: 0.7104 (t0) cc_final: 0.6630 (m-30) REVERT: A 2058 MET cc_start: 0.8213 (ttt) cc_final: 0.7898 (ttt) REVERT: A 2124 ARG cc_start: 0.6279 (mmp80) cc_final: 0.6044 (mmp80) outliers start: 32 outliers final: 25 residues processed: 163 average time/residue: 0.2296 time to fit residues: 53.6383 Evaluate side-chains 154 residues out of total 1148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 129 time to evaluate : 1.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 952 THR Chi-restraints excluded: chain A residue 990 VAL Chi-restraints excluded: chain A residue 1003 ILE Chi-restraints excluded: chain A residue 1063 ASN Chi-restraints excluded: chain A residue 1109 SER Chi-restraints excluded: chain A residue 1112 ASP Chi-restraints excluded: chain A residue 1116 ILE Chi-restraints excluded: chain A residue 1165 THR Chi-restraints excluded: chain A residue 1174 ILE Chi-restraints excluded: chain A residue 1184 VAL Chi-restraints excluded: chain A residue 1255 SER Chi-restraints excluded: chain A residue 1257 SER Chi-restraints excluded: chain A residue 1267 VAL Chi-restraints excluded: chain A residue 1269 VAL Chi-restraints excluded: chain A residue 1286 THR Chi-restraints excluded: chain A residue 1580 TYR Chi-restraints excluded: chain A residue 1588 SER Chi-restraints excluded: chain A residue 1646 ASN Chi-restraints excluded: chain A residue 1777 LEU Chi-restraints excluded: chain A residue 1779 TYR Chi-restraints excluded: chain A residue 1789 ASN Chi-restraints excluded: chain A residue 1794 GLU Chi-restraints excluded: chain A residue 1894 VAL Chi-restraints excluded: chain A residue 1920 ASP Chi-restraints excluded: chain A residue 1950 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 115 optimal weight: 3.9990 chunk 88 optimal weight: 4.9990 chunk 60 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 chunk 78 optimal weight: 2.9990 chunk 117 optimal weight: 0.9990 chunk 124 optimal weight: 3.9990 chunk 61 optimal weight: 0.9990 chunk 111 optimal weight: 0.9980 chunk 33 optimal weight: 0.0870 overall best weight: 1.2164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1001 ASN A1083 ASN A1415 ASN A1817 HIS ** A1969 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7749 moved from start: 0.3893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 10533 Z= 0.277 Angle : 0.629 12.165 14228 Z= 0.337 Chirality : 0.046 0.198 1581 Planarity : 0.004 0.052 1841 Dihedral : 5.748 32.599 1419 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 11.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.51 % Favored : 90.49 % Rotamer: Outliers : 4.01 % Allowed : 13.76 % Favored : 82.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -2.73 (0.21), residues: 1293 helix: -0.14 (0.26), residues: 415 sheet: -2.74 (0.38), residues: 164 loop : -2.72 (0.19), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A1247 HIS 0.007 0.001 HIS A1847 PHE 0.030 0.002 PHE A2119 TYR 0.022 0.002 TYR A1831 ARG 0.005 0.001 ARG A1774 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2586 Ramachandran restraints generated. 1293 Oldfield, 0 Emsley, 1293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2586 Ramachandran restraints generated. 1293 Oldfield, 0 Emsley, 1293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 135 time to evaluate : 1.161 Fit side-chains REVERT: A 966 PHE cc_start: 0.7658 (p90) cc_final: 0.7451 (p90) REVERT: A 1050 ARG cc_start: 0.7797 (ptp-170) cc_final: 0.7368 (mtt180) REVERT: A 1100 LEU cc_start: 0.8177 (OUTLIER) cc_final: 0.7862 (mt) REVERT: A 1119 GLU cc_start: 0.7545 (mt-10) cc_final: 0.7118 (tt0) REVERT: A 1132 SER cc_start: 0.9069 (m) cc_final: 0.8765 (t) REVERT: A 1225 TYR cc_start: 0.6969 (OUTLIER) cc_final: 0.6340 (t80) REVERT: A 1266 ASP cc_start: 0.7164 (t0) cc_final: 0.6784 (t0) REVERT: A 1294 ASN cc_start: 0.7408 (m-40) cc_final: 0.7195 (m-40) REVERT: A 1335 LYS cc_start: 0.7898 (mtpt) cc_final: 0.7606 (mptt) REVERT: A 1397 LYS cc_start: 0.7817 (tppt) cc_final: 0.6934 (mtmt) REVERT: A 1406 LYS cc_start: 0.7387 (mttt) cc_final: 0.6737 (mtmm) REVERT: A 1416 LYS cc_start: 0.6711 (mttm) cc_final: 0.5951 (mttt) REVERT: A 1422 ASN cc_start: 0.8000 (m110) cc_final: 0.7751 (m-40) REVERT: A 1477 ASN cc_start: 0.7724 (t0) cc_final: 0.7373 (t0) REVERT: A 1594 ASP cc_start: 0.7573 (m-30) cc_final: 0.7271 (m-30) REVERT: A 1757 TYR cc_start: 0.8223 (m-80) cc_final: 0.7362 (m-80) REVERT: A 1770 GLU cc_start: 0.7375 (mt-10) cc_final: 0.6986 (mm-30) REVERT: A 1794 GLU cc_start: 0.8040 (OUTLIER) cc_final: 0.7788 (tt0) REVERT: A 1855 ARG cc_start: 0.7662 (mtm-85) cc_final: 0.7412 (mtt90) REVERT: A 1856 GLU cc_start: 0.7869 (mm-30) cc_final: 0.7347 (mm-30) REVERT: A 1953 ASP cc_start: 0.7122 (t0) cc_final: 0.6718 (m-30) REVERT: A 2007 ASP cc_start: 0.5617 (t70) cc_final: 0.5068 (t0) REVERT: A 2153 GLU cc_start: 0.7806 (tm-30) cc_final: 0.7439 (tt0) outliers start: 46 outliers final: 34 residues processed: 165 average time/residue: 0.2154 time to fit residues: 51.2701 Evaluate side-chains 167 residues out of total 1148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 130 time to evaluate : 1.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 952 THR Chi-restraints excluded: chain A residue 953 ASN Chi-restraints excluded: chain A residue 990 VAL Chi-restraints excluded: chain A residue 1003 ILE Chi-restraints excluded: chain A residue 1100 LEU Chi-restraints excluded: chain A residue 1109 SER Chi-restraints excluded: chain A residue 1112 ASP Chi-restraints excluded: chain A residue 1116 ILE Chi-restraints excluded: chain A residue 1123 ASP Chi-restraints excluded: chain A residue 1165 THR Chi-restraints excluded: chain A residue 1174 ILE Chi-restraints excluded: chain A residue 1184 VAL Chi-restraints excluded: chain A residue 1220 THR Chi-restraints excluded: chain A residue 1225 TYR Chi-restraints excluded: chain A residue 1255 SER Chi-restraints excluded: chain A residue 1257 SER Chi-restraints excluded: chain A residue 1269 VAL Chi-restraints excluded: chain A residue 1286 THR Chi-restraints excluded: chain A residue 1403 VAL Chi-restraints excluded: chain A residue 1430 ASP Chi-restraints excluded: chain A residue 1500 LYS Chi-restraints excluded: chain A residue 1580 TYR Chi-restraints excluded: chain A residue 1588 SER Chi-restraints excluded: chain A residue 1641 LEU Chi-restraints excluded: chain A residue 1646 ASN Chi-restraints excluded: chain A residue 1659 VAL Chi-restraints excluded: chain A residue 1709 MET Chi-restraints excluded: chain A residue 1777 LEU Chi-restraints excluded: chain A residue 1779 TYR Chi-restraints excluded: chain A residue 1789 ASN Chi-restraints excluded: chain A residue 1794 GLU Chi-restraints excluded: chain A residue 1840 SER Chi-restraints excluded: chain A residue 1862 TYR Chi-restraints excluded: chain A residue 1894 VAL Chi-restraints excluded: chain A residue 1918 VAL Chi-restraints excluded: chain A residue 1920 ASP Chi-restraints excluded: chain A residue 1950 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 103 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 chunk 1 optimal weight: 4.9990 chunk 92 optimal weight: 0.5980 chunk 51 optimal weight: 2.9990 chunk 106 optimal weight: 4.9990 chunk 86 optimal weight: 0.5980 chunk 0 optimal weight: 5.9990 chunk 63 optimal weight: 2.9990 chunk 111 optimal weight: 0.9990 chunk 31 optimal weight: 4.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 999 HIS A1028 ASN A1415 ASN ** A1817 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1927 ASN ** A1969 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.4292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 10533 Z= 0.346 Angle : 0.675 12.549 14228 Z= 0.360 Chirality : 0.048 0.183 1581 Planarity : 0.005 0.057 1841 Dihedral : 6.007 32.951 1419 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 12.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.82 % Favored : 90.18 % Rotamer: Outliers : 4.97 % Allowed : 14.37 % Favored : 80.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -2.78 (0.21), residues: 1293 helix: -0.20 (0.26), residues: 412 sheet: -2.65 (0.38), residues: 163 loop : -2.76 (0.19), residues: 718 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A1247 HIS 0.007 0.001 HIS A1847 PHE 0.031 0.002 PHE A2119 TYR 0.023 0.002 TYR A1172 ARG 0.005 0.001 ARG A2124 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2586 Ramachandran restraints generated. 1293 Oldfield, 0 Emsley, 1293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2586 Ramachandran restraints generated. 1293 Oldfield, 0 Emsley, 1293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 141 time to evaluate : 1.258 Fit side-chains REVERT: A 939 ASN cc_start: 0.7183 (t0) cc_final: 0.6750 (t0) REVERT: A 1073 GLU cc_start: 0.7017 (mp0) cc_final: 0.6813 (mp0) REVERT: A 1132 SER cc_start: 0.9110 (m) cc_final: 0.8792 (t) REVERT: A 1202 ASN cc_start: 0.8150 (t0) cc_final: 0.7582 (t0) REVERT: A 1225 TYR cc_start: 0.7302 (OUTLIER) cc_final: 0.6439 (t80) REVERT: A 1266 ASP cc_start: 0.7192 (t0) cc_final: 0.6713 (t0) REVERT: A 1335 LYS cc_start: 0.7935 (mtpt) cc_final: 0.7628 (mptt) REVERT: A 1338 LYS cc_start: 0.5223 (ptmm) cc_final: 0.4614 (mmtm) REVERT: A 1397 LYS cc_start: 0.7861 (tppt) cc_final: 0.6854 (mtpt) REVERT: A 1406 LYS cc_start: 0.7381 (mttt) cc_final: 0.6734 (mtmm) REVERT: A 1416 LYS cc_start: 0.6770 (mttm) cc_final: 0.6002 (mttt) REVERT: A 1422 ASN cc_start: 0.8025 (m110) cc_final: 0.7815 (m-40) REVERT: A 1477 ASN cc_start: 0.7735 (t0) cc_final: 0.7379 (t0) REVERT: A 1594 ASP cc_start: 0.7584 (m-30) cc_final: 0.7248 (m-30) REVERT: A 1770 GLU cc_start: 0.7417 (mt-10) cc_final: 0.7020 (mm-30) REVERT: A 1780 ASP cc_start: 0.8741 (OUTLIER) cc_final: 0.7781 (t0) REVERT: A 1794 GLU cc_start: 0.8112 (OUTLIER) cc_final: 0.7884 (tt0) REVERT: A 1819 LYS cc_start: 0.7862 (tppt) cc_final: 0.7150 (pttp) REVERT: A 1829 PHE cc_start: 0.8772 (OUTLIER) cc_final: 0.8396 (t80) REVERT: A 1855 ARG cc_start: 0.7725 (mtm-85) cc_final: 0.7517 (mtt90) REVERT: A 1856 GLU cc_start: 0.7865 (mm-30) cc_final: 0.7587 (mm-30) REVERT: A 1953 ASP cc_start: 0.7142 (t0) cc_final: 0.6718 (m-30) REVERT: A 2124 ARG cc_start: 0.6371 (mmp80) cc_final: 0.6073 (mmp-170) REVERT: A 2153 GLU cc_start: 0.7781 (tm-30) cc_final: 0.7411 (tt0) outliers start: 57 outliers final: 43 residues processed: 180 average time/residue: 0.2112 time to fit residues: 55.0144 Evaluate side-chains 180 residues out of total 1148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 133 time to evaluate : 1.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 944 VAL Chi-restraints excluded: chain A residue 952 THR Chi-restraints excluded: chain A residue 953 ASN Chi-restraints excluded: chain A residue 990 VAL Chi-restraints excluded: chain A residue 997 ILE Chi-restraints excluded: chain A residue 1003 ILE Chi-restraints excluded: chain A residue 1009 THR Chi-restraints excluded: chain A residue 1022 VAL Chi-restraints excluded: chain A residue 1109 SER Chi-restraints excluded: chain A residue 1112 ASP Chi-restraints excluded: chain A residue 1116 ILE Chi-restraints excluded: chain A residue 1123 ASP Chi-restraints excluded: chain A residue 1165 THR Chi-restraints excluded: chain A residue 1174 ILE Chi-restraints excluded: chain A residue 1184 VAL Chi-restraints excluded: chain A residue 1220 THR Chi-restraints excluded: chain A residue 1225 TYR Chi-restraints excluded: chain A residue 1255 SER Chi-restraints excluded: chain A residue 1257 SER Chi-restraints excluded: chain A residue 1269 VAL Chi-restraints excluded: chain A residue 1273 ASN Chi-restraints excluded: chain A residue 1286 THR Chi-restraints excluded: chain A residue 1403 VAL Chi-restraints excluded: chain A residue 1430 ASP Chi-restraints excluded: chain A residue 1500 LYS Chi-restraints excluded: chain A residue 1580 TYR Chi-restraints excluded: chain A residue 1588 SER Chi-restraints excluded: chain A residue 1641 LEU Chi-restraints excluded: chain A residue 1646 ASN Chi-restraints excluded: chain A residue 1659 VAL Chi-restraints excluded: chain A residue 1718 THR Chi-restraints excluded: chain A residue 1777 LEU Chi-restraints excluded: chain A residue 1779 TYR Chi-restraints excluded: chain A residue 1780 ASP Chi-restraints excluded: chain A residue 1789 ASN Chi-restraints excluded: chain A residue 1794 GLU Chi-restraints excluded: chain A residue 1825 THR Chi-restraints excluded: chain A residue 1827 ASP Chi-restraints excluded: chain A residue 1829 PHE Chi-restraints excluded: chain A residue 1840 SER Chi-restraints excluded: chain A residue 1862 TYR Chi-restraints excluded: chain A residue 1894 VAL Chi-restraints excluded: chain A residue 1918 VAL Chi-restraints excluded: chain A residue 1920 ASP Chi-restraints excluded: chain A residue 1950 GLU Chi-restraints excluded: chain A residue 1965 ASP Chi-restraints excluded: chain A residue 2084 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 41 optimal weight: 4.9990 chunk 112 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 73 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.8980 chunk 57 optimal weight: 0.6980 chunk 10 optimal weight: 4.9990 chunk 65 optimal weight: 0.6980 chunk 120 optimal weight: 0.8980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1083 ASN ** A1817 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1969 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7759 moved from start: 0.4365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 10533 Z= 0.240 Angle : 0.610 11.216 14228 Z= 0.327 Chirality : 0.045 0.182 1581 Planarity : 0.004 0.057 1841 Dihedral : 5.721 30.994 1419 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 11.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.97 % Favored : 91.03 % Rotamer: Outliers : 4.97 % Allowed : 15.33 % Favored : 79.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -2.67 (0.21), residues: 1293 helix: -0.13 (0.26), residues: 418 sheet: -2.48 (0.39), residues: 161 loop : -2.73 (0.19), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A1247 HIS 0.006 0.001 HIS A1847 PHE 0.027 0.002 PHE A2119 TYR 0.018 0.002 TYR A1172 ARG 0.004 0.000 ARG A2124 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2586 Ramachandran restraints generated. 1293 Oldfield, 0 Emsley, 1293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2586 Ramachandran restraints generated. 1293 Oldfield, 0 Emsley, 1293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 142 time to evaluate : 1.211 Fit side-chains REVERT: A 929 SER cc_start: 0.8710 (t) cc_final: 0.8423 (p) REVERT: A 939 ASN cc_start: 0.7199 (t0) cc_final: 0.6752 (t0) REVERT: A 1073 GLU cc_start: 0.7092 (mp0) cc_final: 0.6836 (mp0) REVERT: A 1098 GLN cc_start: 0.8135 (tt0) cc_final: 0.7593 (tt0) REVERT: A 1119 GLU cc_start: 0.7567 (mt-10) cc_final: 0.7173 (tt0) REVERT: A 1132 SER cc_start: 0.9029 (m) cc_final: 0.8729 (t) REVERT: A 1225 TYR cc_start: 0.7288 (OUTLIER) cc_final: 0.6297 (t80) REVERT: A 1266 ASP cc_start: 0.7187 (t0) cc_final: 0.6712 (t0) REVERT: A 1335 LYS cc_start: 0.7886 (mtpt) cc_final: 0.7486 (mptt) REVERT: A 1338 LYS cc_start: 0.5186 (ptmm) cc_final: 0.4647 (mmtm) REVERT: A 1397 LYS cc_start: 0.7772 (tppt) cc_final: 0.6790 (mtpt) REVERT: A 1406 LYS cc_start: 0.7350 (mttt) cc_final: 0.6706 (mtmm) REVERT: A 1416 LYS cc_start: 0.6620 (mttm) cc_final: 0.5866 (mttt) REVERT: A 1477 ASN cc_start: 0.7704 (t0) cc_final: 0.7328 (t0) REVERT: A 1583 ASP cc_start: 0.8297 (p0) cc_final: 0.8083 (p0) REVERT: A 1594 ASP cc_start: 0.7579 (m-30) cc_final: 0.7237 (m-30) REVERT: A 1770 GLU cc_start: 0.7374 (mt-10) cc_final: 0.7005 (mm-30) REVERT: A 1780 ASP cc_start: 0.8589 (OUTLIER) cc_final: 0.7594 (t0) REVERT: A 1794 GLU cc_start: 0.8087 (OUTLIER) cc_final: 0.7864 (tt0) REVERT: A 1819 LYS cc_start: 0.7835 (tppt) cc_final: 0.7126 (pttp) REVERT: A 1829 PHE cc_start: 0.8674 (OUTLIER) cc_final: 0.8345 (t80) REVERT: A 1855 ARG cc_start: 0.7803 (mtm-85) cc_final: 0.7567 (mtt90) REVERT: A 1856 GLU cc_start: 0.7916 (mm-30) cc_final: 0.7664 (mm-30) REVERT: A 1925 MET cc_start: 0.8399 (mmt) cc_final: 0.7977 (mmt) REVERT: A 1953 ASP cc_start: 0.7127 (t0) cc_final: 0.6745 (m-30) REVERT: A 2113 LYS cc_start: 0.7360 (tttm) cc_final: 0.6986 (ttmm) REVERT: A 2124 ARG cc_start: 0.6355 (mmp80) cc_final: 0.6036 (mmp-170) REVERT: A 2153 GLU cc_start: 0.7750 (tm-30) cc_final: 0.7398 (tt0) outliers start: 57 outliers final: 38 residues processed: 178 average time/residue: 0.2247 time to fit residues: 57.3987 Evaluate side-chains 177 residues out of total 1148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 135 time to evaluate : 1.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 944 VAL Chi-restraints excluded: chain A residue 952 THR Chi-restraints excluded: chain A residue 953 ASN Chi-restraints excluded: chain A residue 990 VAL Chi-restraints excluded: chain A residue 1003 ILE Chi-restraints excluded: chain A residue 1009 THR Chi-restraints excluded: chain A residue 1022 VAL Chi-restraints excluded: chain A residue 1109 SER Chi-restraints excluded: chain A residue 1112 ASP Chi-restraints excluded: chain A residue 1116 ILE Chi-restraints excluded: chain A residue 1165 THR Chi-restraints excluded: chain A residue 1174 ILE Chi-restraints excluded: chain A residue 1184 VAL Chi-restraints excluded: chain A residue 1220 THR Chi-restraints excluded: chain A residue 1225 TYR Chi-restraints excluded: chain A residue 1255 SER Chi-restraints excluded: chain A residue 1269 VAL Chi-restraints excluded: chain A residue 1273 ASN Chi-restraints excluded: chain A residue 1286 THR Chi-restraints excluded: chain A residue 1403 VAL Chi-restraints excluded: chain A residue 1430 ASP Chi-restraints excluded: chain A residue 1500 LYS Chi-restraints excluded: chain A residue 1580 TYR Chi-restraints excluded: chain A residue 1588 SER Chi-restraints excluded: chain A residue 1641 LEU Chi-restraints excluded: chain A residue 1646 ASN Chi-restraints excluded: chain A residue 1659 VAL Chi-restraints excluded: chain A residue 1718 THR Chi-restraints excluded: chain A residue 1777 LEU Chi-restraints excluded: chain A residue 1779 TYR Chi-restraints excluded: chain A residue 1780 ASP Chi-restraints excluded: chain A residue 1789 ASN Chi-restraints excluded: chain A residue 1794 GLU Chi-restraints excluded: chain A residue 1825 THR Chi-restraints excluded: chain A residue 1827 ASP Chi-restraints excluded: chain A residue 1829 PHE Chi-restraints excluded: chain A residue 1840 SER Chi-restraints excluded: chain A residue 1862 TYR Chi-restraints excluded: chain A residue 1894 VAL Chi-restraints excluded: chain A residue 1918 VAL Chi-restraints excluded: chain A residue 1920 ASP Chi-restraints excluded: chain A residue 1965 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 14 optimal weight: 4.9990 chunk 71 optimal weight: 0.5980 chunk 91 optimal weight: 0.6980 chunk 70 optimal weight: 0.6980 chunk 105 optimal weight: 0.9980 chunk 69 optimal weight: 0.8980 chunk 124 optimal weight: 1.9990 chunk 77 optimal weight: 0.0870 chunk 75 optimal weight: 2.9990 chunk 57 optimal weight: 2.9990 chunk 76 optimal weight: 1.9990 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1605 ASN A1817 HIS A1960 ASN ** A1969 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7702 moved from start: 0.4413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10533 Z= 0.167 Angle : 0.561 10.027 14228 Z= 0.301 Chirality : 0.044 0.179 1581 Planarity : 0.004 0.058 1841 Dihedral : 5.309 27.550 1419 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.12 % Favored : 91.88 % Rotamer: Outliers : 4.09 % Allowed : 16.38 % Favored : 79.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.44 (0.22), residues: 1293 helix: 0.16 (0.26), residues: 406 sheet: -2.31 (0.34), residues: 211 loop : -2.59 (0.20), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1247 HIS 0.007 0.001 HIS A1847 PHE 0.025 0.002 PHE A2119 TYR 0.013 0.001 TYR A1225 ARG 0.004 0.000 ARG A2124 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2586 Ramachandran restraints generated. 1293 Oldfield, 0 Emsley, 1293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2586 Ramachandran restraints generated. 1293 Oldfield, 0 Emsley, 1293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 143 time to evaluate : 1.270 Fit side-chains REVERT: A 929 SER cc_start: 0.8737 (t) cc_final: 0.8472 (p) REVERT: A 939 ASN cc_start: 0.7243 (t0) cc_final: 0.6781 (t0) REVERT: A 1073 GLU cc_start: 0.7065 (mp0) cc_final: 0.6846 (mp0) REVERT: A 1119 GLU cc_start: 0.7490 (mt-10) cc_final: 0.7156 (tt0) REVERT: A 1121 LYS cc_start: 0.7693 (mmmm) cc_final: 0.7478 (mtpp) REVERT: A 1132 SER cc_start: 0.8971 (m) cc_final: 0.8708 (t) REVERT: A 1225 TYR cc_start: 0.7152 (OUTLIER) cc_final: 0.6220 (t80) REVERT: A 1266 ASP cc_start: 0.7195 (t0) cc_final: 0.6738 (t0) REVERT: A 1335 LYS cc_start: 0.7826 (mtpt) cc_final: 0.7443 (mptt) REVERT: A 1338 LYS cc_start: 0.5090 (ptmm) cc_final: 0.4531 (mmtm) REVERT: A 1406 LYS cc_start: 0.7190 (mttt) cc_final: 0.6627 (mtmm) REVERT: A 1416 LYS cc_start: 0.6668 (mttm) cc_final: 0.5898 (mttt) REVERT: A 1477 ASN cc_start: 0.7666 (t0) cc_final: 0.7281 (t0) REVERT: A 1583 ASP cc_start: 0.8316 (p0) cc_final: 0.8013 (p0) REVERT: A 1594 ASP cc_start: 0.7549 (m-30) cc_final: 0.7244 (m-30) REVERT: A 1638 LYS cc_start: 0.7663 (mttm) cc_final: 0.7429 (mttt) REVERT: A 1757 TYR cc_start: 0.8119 (m-80) cc_final: 0.7191 (m-80) REVERT: A 1770 GLU cc_start: 0.7388 (mt-10) cc_final: 0.7010 (mm-30) REVERT: A 1780 ASP cc_start: 0.8345 (OUTLIER) cc_final: 0.7746 (m-30) REVERT: A 1794 GLU cc_start: 0.7992 (OUTLIER) cc_final: 0.7653 (tt0) REVERT: A 1855 ARG cc_start: 0.7685 (mtm-85) cc_final: 0.7433 (mtt90) REVERT: A 1856 GLU cc_start: 0.8008 (mm-30) cc_final: 0.7557 (mm-30) REVERT: A 1953 ASP cc_start: 0.7132 (t0) cc_final: 0.6730 (m-30) REVERT: A 2113 LYS cc_start: 0.7293 (tttm) cc_final: 0.6979 (ttmm) REVERT: A 2153 GLU cc_start: 0.7711 (tm-30) cc_final: 0.7382 (tt0) outliers start: 47 outliers final: 29 residues processed: 173 average time/residue: 0.2272 time to fit residues: 56.0231 Evaluate side-chains 167 residues out of total 1148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 135 time to evaluate : 1.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 952 THR Chi-restraints excluded: chain A residue 990 VAL Chi-restraints excluded: chain A residue 1009 THR Chi-restraints excluded: chain A residue 1022 VAL Chi-restraints excluded: chain A residue 1109 SER Chi-restraints excluded: chain A residue 1112 ASP Chi-restraints excluded: chain A residue 1116 ILE Chi-restraints excluded: chain A residue 1165 THR Chi-restraints excluded: chain A residue 1174 ILE Chi-restraints excluded: chain A residue 1184 VAL Chi-restraints excluded: chain A residue 1220 THR Chi-restraints excluded: chain A residue 1225 TYR Chi-restraints excluded: chain A residue 1257 SER Chi-restraints excluded: chain A residue 1269 VAL Chi-restraints excluded: chain A residue 1294 ASN Chi-restraints excluded: chain A residue 1403 VAL Chi-restraints excluded: chain A residue 1430 ASP Chi-restraints excluded: chain A residue 1580 TYR Chi-restraints excluded: chain A residue 1588 SER Chi-restraints excluded: chain A residue 1641 LEU Chi-restraints excluded: chain A residue 1646 ASN Chi-restraints excluded: chain A residue 1718 THR Chi-restraints excluded: chain A residue 1779 TYR Chi-restraints excluded: chain A residue 1780 ASP Chi-restraints excluded: chain A residue 1794 GLU Chi-restraints excluded: chain A residue 1825 THR Chi-restraints excluded: chain A residue 1827 ASP Chi-restraints excluded: chain A residue 1862 TYR Chi-restraints excluded: chain A residue 1894 VAL Chi-restraints excluded: chain A residue 1918 VAL Chi-restraints excluded: chain A residue 1920 ASP Chi-restraints excluded: chain A residue 1965 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 49 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 chunk 37 optimal weight: 0.9990 chunk 24 optimal weight: 4.9990 chunk 79 optimal weight: 0.6980 chunk 84 optimal weight: 3.9990 chunk 61 optimal weight: 3.9990 chunk 11 optimal weight: 0.9980 chunk 97 optimal weight: 0.0670 chunk 113 optimal weight: 4.9990 chunk 119 optimal weight: 0.9980 overall best weight: 0.7520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1817 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1969 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7721 moved from start: 0.4493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10533 Z= 0.193 Angle : 0.579 10.982 14228 Z= 0.309 Chirality : 0.045 0.231 1581 Planarity : 0.004 0.057 1841 Dihedral : 5.316 26.223 1419 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.74 % Favored : 91.26 % Rotamer: Outliers : 4.09 % Allowed : 16.81 % Favored : 79.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.41 (0.22), residues: 1293 helix: 0.15 (0.26), residues: 407 sheet: -2.33 (0.39), residues: 166 loop : -2.57 (0.19), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1247 HIS 0.007 0.001 HIS A1847 PHE 0.025 0.002 PHE A2119 TYR 0.016 0.001 TYR A1172 ARG 0.005 0.000 ARG A2124 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2586 Ramachandran restraints generated. 1293 Oldfield, 0 Emsley, 1293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2586 Ramachandran restraints generated. 1293 Oldfield, 0 Emsley, 1293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 133 time to evaluate : 1.244 Fit side-chains REVERT: A 929 SER cc_start: 0.8736 (t) cc_final: 0.8458 (p) REVERT: A 989 ILE cc_start: 0.8246 (OUTLIER) cc_final: 0.8007 (mt) REVERT: A 1073 GLU cc_start: 0.7048 (mp0) cc_final: 0.6213 (mp0) REVERT: A 1098 GLN cc_start: 0.8005 (tt0) cc_final: 0.6856 (tt0) REVERT: A 1119 GLU cc_start: 0.7512 (mt-10) cc_final: 0.7167 (tt0) REVERT: A 1121 LYS cc_start: 0.7692 (mmmm) cc_final: 0.7466 (mtpp) REVERT: A 1132 SER cc_start: 0.9019 (m) cc_final: 0.8729 (t) REVERT: A 1225 TYR cc_start: 0.7154 (OUTLIER) cc_final: 0.6199 (t80) REVERT: A 1266 ASP cc_start: 0.7269 (t0) cc_final: 0.6756 (t0) REVERT: A 1335 LYS cc_start: 0.7850 (mtpt) cc_final: 0.7461 (mptt) REVERT: A 1338 LYS cc_start: 0.5102 (ptmm) cc_final: 0.4528 (mmtm) REVERT: A 1406 LYS cc_start: 0.7208 (mttt) cc_final: 0.6607 (mtmm) REVERT: A 1416 LYS cc_start: 0.6666 (mttm) cc_final: 0.5884 (mttt) REVERT: A 1477 ASN cc_start: 0.7682 (t0) cc_final: 0.7297 (t0) REVERT: A 1583 ASP cc_start: 0.8273 (p0) cc_final: 0.8017 (p0) REVERT: A 1594 ASP cc_start: 0.7543 (m-30) cc_final: 0.7249 (m-30) REVERT: A 1638 LYS cc_start: 0.7748 (mttm) cc_final: 0.7528 (mttt) REVERT: A 1770 GLU cc_start: 0.7406 (mt-10) cc_final: 0.7015 (mm-30) REVERT: A 1780 ASP cc_start: 0.8561 (OUTLIER) cc_final: 0.7607 (t0) REVERT: A 1794 GLU cc_start: 0.7965 (OUTLIER) cc_final: 0.7726 (tt0) REVERT: A 1855 ARG cc_start: 0.7707 (mtm-85) cc_final: 0.7458 (mtt90) REVERT: A 1856 GLU cc_start: 0.7988 (mm-30) cc_final: 0.7734 (mm-30) REVERT: A 1953 ASP cc_start: 0.7131 (t0) cc_final: 0.6733 (m-30) REVERT: A 2113 LYS cc_start: 0.7314 (tttm) cc_final: 0.6994 (ttmm) REVERT: A 2153 GLU cc_start: 0.7710 (tm-30) cc_final: 0.7397 (tt0) outliers start: 47 outliers final: 41 residues processed: 162 average time/residue: 0.2253 time to fit residues: 52.1508 Evaluate side-chains 177 residues out of total 1148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 132 time to evaluate : 1.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 952 THR Chi-restraints excluded: chain A residue 953 ASN Chi-restraints excluded: chain A residue 989 ILE Chi-restraints excluded: chain A residue 990 VAL Chi-restraints excluded: chain A residue 1003 ILE Chi-restraints excluded: chain A residue 1009 THR Chi-restraints excluded: chain A residue 1022 VAL Chi-restraints excluded: chain A residue 1063 ASN Chi-restraints excluded: chain A residue 1109 SER Chi-restraints excluded: chain A residue 1112 ASP Chi-restraints excluded: chain A residue 1116 ILE Chi-restraints excluded: chain A residue 1165 THR Chi-restraints excluded: chain A residue 1174 ILE Chi-restraints excluded: chain A residue 1184 VAL Chi-restraints excluded: chain A residue 1220 THR Chi-restraints excluded: chain A residue 1225 TYR Chi-restraints excluded: chain A residue 1255 SER Chi-restraints excluded: chain A residue 1257 SER Chi-restraints excluded: chain A residue 1269 VAL Chi-restraints excluded: chain A residue 1273 ASN Chi-restraints excluded: chain A residue 1294 ASN Chi-restraints excluded: chain A residue 1403 VAL Chi-restraints excluded: chain A residue 1430 ASP Chi-restraints excluded: chain A residue 1500 LYS Chi-restraints excluded: chain A residue 1580 TYR Chi-restraints excluded: chain A residue 1588 SER Chi-restraints excluded: chain A residue 1641 LEU Chi-restraints excluded: chain A residue 1646 ASN Chi-restraints excluded: chain A residue 1659 VAL Chi-restraints excluded: chain A residue 1709 MET Chi-restraints excluded: chain A residue 1718 THR Chi-restraints excluded: chain A residue 1777 LEU Chi-restraints excluded: chain A residue 1779 TYR Chi-restraints excluded: chain A residue 1780 ASP Chi-restraints excluded: chain A residue 1788 THR Chi-restraints excluded: chain A residue 1789 ASN Chi-restraints excluded: chain A residue 1794 GLU Chi-restraints excluded: chain A residue 1825 THR Chi-restraints excluded: chain A residue 1827 ASP Chi-restraints excluded: chain A residue 1862 TYR Chi-restraints excluded: chain A residue 1894 VAL Chi-restraints excluded: chain A residue 1918 VAL Chi-restraints excluded: chain A residue 1920 ASP Chi-restraints excluded: chain A residue 1965 ASP Chi-restraints excluded: chain A residue 2059 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 108 optimal weight: 2.9990 chunk 115 optimal weight: 3.9990 chunk 119 optimal weight: 0.8980 chunk 69 optimal weight: 0.4980 chunk 50 optimal weight: 2.9990 chunk 90 optimal weight: 0.7980 chunk 35 optimal weight: 2.9990 chunk 104 optimal weight: 4.9990 chunk 109 optimal weight: 2.9990 chunk 76 optimal weight: 0.6980 chunk 122 optimal weight: 4.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1817 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 moved from start: 0.4648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 10533 Z= 0.263 Angle : 0.626 11.959 14228 Z= 0.333 Chirality : 0.046 0.230 1581 Planarity : 0.004 0.060 1841 Dihedral : 5.600 26.020 1419 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 11.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.67 % Favored : 90.33 % Rotamer: Outliers : 4.27 % Allowed : 16.64 % Favored : 79.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.44 (0.22), residues: 1293 helix: 0.12 (0.26), residues: 406 sheet: -2.38 (0.39), residues: 168 loop : -2.57 (0.20), residues: 719 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A1247 HIS 0.007 0.001 HIS A1847 PHE 0.027 0.002 PHE A2119 TYR 0.020 0.002 TYR A1172 ARG 0.005 0.000 ARG A1774 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2586 Ramachandran restraints generated. 1293 Oldfield, 0 Emsley, 1293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2586 Ramachandran restraints generated. 1293 Oldfield, 0 Emsley, 1293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 132 time to evaluate : 1.121 Fit side-chains REVERT: A 989 ILE cc_start: 0.8271 (OUTLIER) cc_final: 0.8020 (mt) REVERT: A 1073 GLU cc_start: 0.7072 (mp0) cc_final: 0.6324 (mp0) REVERT: A 1098 GLN cc_start: 0.8026 (tt0) cc_final: 0.6873 (tt0) REVERT: A 1132 SER cc_start: 0.9059 (m) cc_final: 0.8732 (t) REVERT: A 1225 TYR cc_start: 0.7397 (OUTLIER) cc_final: 0.6217 (t80) REVERT: A 1266 ASP cc_start: 0.7317 (t0) cc_final: 0.6749 (t0) REVERT: A 1335 LYS cc_start: 0.7876 (mtpt) cc_final: 0.7490 (mptt) REVERT: A 1338 LYS cc_start: 0.5117 (ptmm) cc_final: 0.4506 (mmtm) REVERT: A 1397 LYS cc_start: 0.7831 (tppt) cc_final: 0.6797 (mtpt) REVERT: A 1406 LYS cc_start: 0.7248 (mttt) cc_final: 0.6621 (mtmm) REVERT: A 1416 LYS cc_start: 0.6727 (mttm) cc_final: 0.5945 (mttt) REVERT: A 1477 ASN cc_start: 0.7701 (t0) cc_final: 0.7311 (t0) REVERT: A 1583 ASP cc_start: 0.8232 (p0) cc_final: 0.7991 (p0) REVERT: A 1594 ASP cc_start: 0.7587 (m-30) cc_final: 0.7223 (m-30) REVERT: A 1770 GLU cc_start: 0.7395 (mt-10) cc_final: 0.7023 (mm-30) REVERT: A 1780 ASP cc_start: 0.8727 (OUTLIER) cc_final: 0.7845 (t0) REVERT: A 1794 GLU cc_start: 0.8068 (OUTLIER) cc_final: 0.7835 (tt0) REVERT: A 1829 PHE cc_start: 0.8708 (OUTLIER) cc_final: 0.8282 (t80) REVERT: A 1856 GLU cc_start: 0.7954 (mm-30) cc_final: 0.7712 (mm-30) REVERT: A 1945 LYS cc_start: 0.7559 (mtmt) cc_final: 0.7088 (ptmt) REVERT: A 1953 ASP cc_start: 0.7139 (t0) cc_final: 0.6746 (m-30) REVERT: A 2113 LYS cc_start: 0.7397 (tttm) cc_final: 0.7149 (ttmm) REVERT: A 2124 ARG cc_start: 0.6371 (mmp80) cc_final: 0.6021 (mmt180) REVERT: A 2153 GLU cc_start: 0.7739 (tm-30) cc_final: 0.7427 (tt0) outliers start: 49 outliers final: 42 residues processed: 164 average time/residue: 0.2139 time to fit residues: 50.8263 Evaluate side-chains 178 residues out of total 1148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 131 time to evaluate : 0.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 944 VAL Chi-restraints excluded: chain A residue 952 THR Chi-restraints excluded: chain A residue 953 ASN Chi-restraints excluded: chain A residue 989 ILE Chi-restraints excluded: chain A residue 990 VAL Chi-restraints excluded: chain A residue 1009 THR Chi-restraints excluded: chain A residue 1022 VAL Chi-restraints excluded: chain A residue 1063 ASN Chi-restraints excluded: chain A residue 1109 SER Chi-restraints excluded: chain A residue 1112 ASP Chi-restraints excluded: chain A residue 1116 ILE Chi-restraints excluded: chain A residue 1165 THR Chi-restraints excluded: chain A residue 1174 ILE Chi-restraints excluded: chain A residue 1184 VAL Chi-restraints excluded: chain A residue 1220 THR Chi-restraints excluded: chain A residue 1225 TYR Chi-restraints excluded: chain A residue 1255 SER Chi-restraints excluded: chain A residue 1257 SER Chi-restraints excluded: chain A residue 1269 VAL Chi-restraints excluded: chain A residue 1273 ASN Chi-restraints excluded: chain A residue 1294 ASN Chi-restraints excluded: chain A residue 1403 VAL Chi-restraints excluded: chain A residue 1430 ASP Chi-restraints excluded: chain A residue 1500 LYS Chi-restraints excluded: chain A residue 1580 TYR Chi-restraints excluded: chain A residue 1588 SER Chi-restraints excluded: chain A residue 1641 LEU Chi-restraints excluded: chain A residue 1646 ASN Chi-restraints excluded: chain A residue 1659 VAL Chi-restraints excluded: chain A residue 1709 MET Chi-restraints excluded: chain A residue 1718 THR Chi-restraints excluded: chain A residue 1777 LEU Chi-restraints excluded: chain A residue 1779 TYR Chi-restraints excluded: chain A residue 1780 ASP Chi-restraints excluded: chain A residue 1788 THR Chi-restraints excluded: chain A residue 1789 ASN Chi-restraints excluded: chain A residue 1794 GLU Chi-restraints excluded: chain A residue 1825 THR Chi-restraints excluded: chain A residue 1827 ASP Chi-restraints excluded: chain A residue 1829 PHE Chi-restraints excluded: chain A residue 1862 TYR Chi-restraints excluded: chain A residue 1894 VAL Chi-restraints excluded: chain A residue 1918 VAL Chi-restraints excluded: chain A residue 1920 ASP Chi-restraints excluded: chain A residue 1965 ASP Chi-restraints excluded: chain A residue 2035 THR Chi-restraints excluded: chain A residue 2059 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 74 optimal weight: 1.9990 chunk 58 optimal weight: 0.8980 chunk 85 optimal weight: 0.9980 chunk 128 optimal weight: 0.2980 chunk 118 optimal weight: 3.9990 chunk 102 optimal weight: 0.5980 chunk 10 optimal weight: 0.9990 chunk 79 optimal weight: 0.0070 chunk 62 optimal weight: 2.9990 chunk 81 optimal weight: 1.9990 chunk 109 optimal weight: 0.2980 overall best weight: 0.4198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 943 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1817 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7674 moved from start: 0.4623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 10533 Z= 0.143 Angle : 0.547 9.186 14228 Z= 0.293 Chirality : 0.043 0.233 1581 Planarity : 0.004 0.056 1841 Dihedral : 5.108 24.548 1419 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.97 % Favored : 92.03 % Rotamer: Outliers : 3.75 % Allowed : 17.51 % Favored : 78.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.33 (0.22), residues: 1293 helix: 0.29 (0.26), residues: 407 sheet: -2.33 (0.34), residues: 216 loop : -2.53 (0.20), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A1247 HIS 0.006 0.001 HIS A1847 PHE 0.024 0.001 PHE A2119 TYR 0.013 0.001 TYR A1225 ARG 0.004 0.000 ARG A2124 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2586 Ramachandran restraints generated. 1293 Oldfield, 0 Emsley, 1293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2586 Ramachandran restraints generated. 1293 Oldfield, 0 Emsley, 1293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 138 time to evaluate : 1.230 Fit side-chains REVERT: A 929 SER cc_start: 0.8679 (t) cc_final: 0.8451 (p) REVERT: A 939 ASN cc_start: 0.7330 (t0) cc_final: 0.6982 (t0) REVERT: A 989 ILE cc_start: 0.8197 (OUTLIER) cc_final: 0.7946 (mt) REVERT: A 1063 ASN cc_start: 0.7832 (OUTLIER) cc_final: 0.7043 (m-40) REVERT: A 1073 GLU cc_start: 0.7001 (mp0) cc_final: 0.6369 (mp0) REVERT: A 1098 GLN cc_start: 0.7937 (tt0) cc_final: 0.6850 (tt0) REVERT: A 1119 GLU cc_start: 0.7416 (mt-10) cc_final: 0.7079 (tt0) REVERT: A 1132 SER cc_start: 0.8953 (m) cc_final: 0.8695 (t) REVERT: A 1225 TYR cc_start: 0.7248 (OUTLIER) cc_final: 0.6049 (t80) REVERT: A 1266 ASP cc_start: 0.7293 (t0) cc_final: 0.6768 (t0) REVERT: A 1321 ASN cc_start: 0.7407 (t0) cc_final: 0.6586 (m-40) REVERT: A 1335 LYS cc_start: 0.7790 (mtpt) cc_final: 0.7430 (mptt) REVERT: A 1338 LYS cc_start: 0.4834 (ptmm) cc_final: 0.4331 (mmtm) REVERT: A 1407 ASP cc_start: 0.6936 (m-30) cc_final: 0.6235 (m-30) REVERT: A 1416 LYS cc_start: 0.6740 (mttm) cc_final: 0.5989 (mttt) REVERT: A 1477 ASN cc_start: 0.7657 (t0) cc_final: 0.7277 (t0) REVERT: A 1583 ASP cc_start: 0.8208 (p0) cc_final: 0.7946 (p0) REVERT: A 1594 ASP cc_start: 0.7585 (m-30) cc_final: 0.7289 (m-30) REVERT: A 1638 LYS cc_start: 0.7728 (mttm) cc_final: 0.7509 (mttt) REVERT: A 1757 TYR cc_start: 0.8170 (m-80) cc_final: 0.7257 (m-80) REVERT: A 1770 GLU cc_start: 0.7383 (mt-10) cc_final: 0.7003 (mm-30) REVERT: A 1780 ASP cc_start: 0.8336 (OUTLIER) cc_final: 0.7352 (t0) REVERT: A 1794 GLU cc_start: 0.7980 (OUTLIER) cc_final: 0.7740 (tt0) REVERT: A 1856 GLU cc_start: 0.8012 (mm-30) cc_final: 0.7783 (mm-30) REVERT: A 1953 ASP cc_start: 0.7070 (t0) cc_final: 0.6732 (m-30) REVERT: A 2058 MET cc_start: 0.8265 (ttt) cc_final: 0.7908 (ttt) REVERT: A 2113 LYS cc_start: 0.7292 (tttm) cc_final: 0.6981 (ttmm) REVERT: A 2124 ARG cc_start: 0.6314 (mmp80) cc_final: 0.5962 (mmt180) REVERT: A 2153 GLU cc_start: 0.7683 (tm-30) cc_final: 0.7374 (tt0) outliers start: 43 outliers final: 31 residues processed: 166 average time/residue: 0.2354 time to fit residues: 56.0249 Evaluate side-chains 167 residues out of total 1148 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 131 time to evaluate : 1.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 952 THR Chi-restraints excluded: chain A residue 989 ILE Chi-restraints excluded: chain A residue 990 VAL Chi-restraints excluded: chain A residue 997 ILE Chi-restraints excluded: chain A residue 1009 THR Chi-restraints excluded: chain A residue 1022 VAL Chi-restraints excluded: chain A residue 1063 ASN Chi-restraints excluded: chain A residue 1109 SER Chi-restraints excluded: chain A residue 1112 ASP Chi-restraints excluded: chain A residue 1116 ILE Chi-restraints excluded: chain A residue 1165 THR Chi-restraints excluded: chain A residue 1174 ILE Chi-restraints excluded: chain A residue 1184 VAL Chi-restraints excluded: chain A residue 1220 THR Chi-restraints excluded: chain A residue 1225 TYR Chi-restraints excluded: chain A residue 1255 SER Chi-restraints excluded: chain A residue 1269 VAL Chi-restraints excluded: chain A residue 1294 ASN Chi-restraints excluded: chain A residue 1403 VAL Chi-restraints excluded: chain A residue 1580 TYR Chi-restraints excluded: chain A residue 1588 SER Chi-restraints excluded: chain A residue 1646 ASN Chi-restraints excluded: chain A residue 1659 VAL Chi-restraints excluded: chain A residue 1718 THR Chi-restraints excluded: chain A residue 1779 TYR Chi-restraints excluded: chain A residue 1780 ASP Chi-restraints excluded: chain A residue 1794 GLU Chi-restraints excluded: chain A residue 1825 THR Chi-restraints excluded: chain A residue 1827 ASP Chi-restraints excluded: chain A residue 1862 TYR Chi-restraints excluded: chain A residue 1894 VAL Chi-restraints excluded: chain A residue 1918 VAL Chi-restraints excluded: chain A residue 1920 ASP Chi-restraints excluded: chain A residue 1965 ASP Chi-restraints excluded: chain A residue 2035 THR Chi-restraints excluded: chain A residue 2059 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 31 optimal weight: 4.9990 chunk 94 optimal weight: 3.9990 chunk 15 optimal weight: 3.9990 chunk 28 optimal weight: 2.9990 chunk 102 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 105 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 18 optimal weight: 0.0980 chunk 89 optimal weight: 0.9990 chunk 5 optimal weight: 3.9990 overall best weight: 1.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1922 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.125027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.105412 restraints weight = 12367.301| |-----------------------------------------------------------------------------| r_work (start): 0.3047 rms_B_bonded: 1.39 r_work: 0.2939 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.2808 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8511 moved from start: 0.4853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 10533 Z= 0.348 Angle : 0.679 16.117 14228 Z= 0.359 Chirality : 0.048 0.247 1581 Planarity : 0.004 0.064 1841 Dihedral : 5.828 26.315 1419 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 12.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.44 % Favored : 89.56 % Rotamer: Outliers : 3.57 % Allowed : 17.68 % Favored : 78.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.42 (0.22), residues: 1293 helix: 0.05 (0.26), residues: 405 sheet: -2.13 (0.39), residues: 163 loop : -2.57 (0.19), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A1247 HIS 0.007 0.001 HIS A1847 PHE 0.028 0.002 PHE A2119 TYR 0.022 0.002 TYR A1172 ARG 0.006 0.001 ARG A1774 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2463.10 seconds wall clock time: 45 minutes 8.38 seconds (2708.38 seconds total)