Starting phenix.real_space_refine on Wed Mar 4 03:34:23 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7uvk_26812/03_2026/7uvk_26812.cif Found real_map, /net/cci-nas-00/data/ceres_data/7uvk_26812/03_2026/7uvk_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/cci-nas-00/data/ceres_data/7uvk_26812/03_2026/7uvk_26812.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7uvk_26812/03_2026/7uvk_26812.map" model { file = "/net/cci-nas-00/data/ceres_data/7uvk_26812/03_2026/7uvk_26812.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7uvk_26812/03_2026/7uvk_26812.cif" } resolution = 3.28 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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. Time to flip 40 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/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: 2.64, per 1000 atoms: 0.26 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.86 Conformation dependent library (CDL) restraints added in 605.1 milliseconds 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: 0.46 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: 1.83 Time building geometry restraints manager: 1.22 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: 0.00 - 3.27: 14146 3.27 - 6.55: 70 6.55 - 9.82: 7 9.82 - 13.10: 2 13.10 - 16.37: 3 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 3.120 nonbonded pdb=" OG SER A2031 " pdb=" O GLY A2034 " model vdw 2.189 3.040 nonbonded pdb=" OE2 GLU A1370 " pdb=" NH1 ARG A1378 " model vdw 2.202 3.120 nonbonded pdb=" O SER A1663 " pdb=" OG SER A1669 " model vdw 2.219 3.040 nonbonded pdb=" NH2 ARG A2073 " pdb=" OE2 GLU A2094 " model vdw 2.240 3.120 ... (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: 3.980 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.210 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 11.830 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.460 ------------------------------------------------------------------------------- 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= 0.197 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 : 10.92 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.16 (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 ARG 0.010 0.000 ARG A1139 TYR 0.024 0.001 TYR A1172 PHE 0.032 0.002 PHE A1829 TRP 0.013 0.001 TRP A1247 HIS 0.008 0.001 HIS A1847 Details of bonding type rmsd covalent geometry : bond 0.00494 (10533) covalent geometry : angle 0.74124 (14228) hydrogen bonds : bond 0.17953 ( 320) hydrogen bonds : angle 7.07764 ( 918) *********************** 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 to be fit. rotamer outliers: 0 poor density : 263 time to evaluate : 0.381 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: 0.8107 (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: 0.6935 (mtm180) REVERT: A 1856 GLU cc_start: 0.7723 (mm-30) cc_final: 0.7481 (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: 0.1252 time to fit residues: 44.0732 Evaluate side-chains 157 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 157 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 98 optimal weight: 0.0060 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 2.9990 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 0.0670 chunk 91 optimal weight: 4.9990 chunk 55 optimal weight: 0.0170 chunk 35 optimal weight: 4.9990 overall best weight: 1.0176 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1007 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.135839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.115994 restraints weight = 12398.324| |-----------------------------------------------------------------------------| r_work (start): 0.3198 rms_B_bonded: 1.46 r_work: 0.3082 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2949 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.2675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 10533 Z= 0.171 Angle : 0.660 8.038 14228 Z= 0.357 Chirality : 0.047 0.183 1581 Planarity : 0.004 0.050 1841 Dihedral : 5.796 34.464 1419 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.13 % Favored : 90.87 % Rotamer: Outliers : 1.66 % Allowed : 9.84 % Favored : 88.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.81 (0.21), residues: 1293 helix: -0.24 (0.26), residues: 416 sheet: -3.08 (0.37), residues: 147 loop : -2.69 (0.19), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A1774 TYR 0.024 0.002 TYR A1172 PHE 0.033 0.002 PHE A2119 TRP 0.012 0.002 TRP A1247 HIS 0.007 0.001 HIS A1847 Details of bonding type rmsd covalent geometry : bond 0.00401 (10533) covalent geometry : angle 0.66020 (14228) hydrogen bonds : bond 0.04149 ( 320) hydrogen bonds : angle 5.19091 ( 918) *********************** 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 189 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 170 time to evaluate : 0.378 Fit side-chains revert: symmetry clash REVERT: A 922 LYS cc_start: 0.8655 (mmtp) cc_final: 0.8326 (mmtt) REVERT: A 966 PHE cc_start: 0.7460 (p90) cc_final: 0.7005 (p90) REVERT: A 1050 ARG cc_start: 0.8097 (ptp-170) cc_final: 0.7565 (mtm-85) REVERT: A 1098 GLN cc_start: 0.8505 (tt0) cc_final: 0.7765 (tt0) REVERT: A 1112 ASP cc_start: 0.8011 (p0) cc_final: 0.7646 (p0) REVERT: A 1266 ASP cc_start: 0.7698 (t0) cc_final: 0.7166 (t0) REVERT: A 1298 LYS cc_start: 0.8014 (mmtt) cc_final: 0.7802 (mmtt) REVERT: A 1406 LYS cc_start: 0.7931 (mttt) cc_final: 0.7458 (mtmm) REVERT: A 1478 ASP cc_start: 0.8369 (m-30) cc_final: 0.8152 (m-30) REVERT: A 1583 ASP cc_start: 0.8532 (p0) cc_final: 0.8289 (p0) REVERT: A 1757 TYR cc_start: 0.8466 (m-80) cc_final: 0.7950 (m-80) REVERT: A 1770 GLU cc_start: 0.7876 (mt-10) cc_final: 0.7592 (mm-30) REVERT: A 2084 ILE cc_start: 0.8328 (tt) cc_final: 0.8084 (tt) REVERT: A 2124 ARG cc_start: 0.6910 (mmp80) cc_final: 0.6707 (mmp80) REVERT: A 2172 ASN cc_start: 0.8387 (t0) cc_final: 0.8086 (t0) outliers start: 19 outliers final: 14 residues processed: 184 average time/residue: 0.1114 time to fit residues: 28.6934 Evaluate side-chains 144 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 130 time to evaluate : 0.405 ------------------------------------------------------------------------------- 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 1109 SER Chi-restraints excluded: chain A residue 1165 THR 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 1500 LYS Chi-restraints excluded: chain A residue 1588 SER 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 2088 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 59 optimal weight: 2.9990 chunk 85 optimal weight: 1.9990 chunk 69 optimal weight: 0.9990 chunk 97 optimal weight: 0.1980 chunk 113 optimal weight: 0.7980 chunk 27 optimal weight: 1.9990 chunk 0 optimal weight: 6.9990 chunk 104 optimal weight: 0.4980 chunk 20 optimal weight: 3.9990 chunk 88 optimal weight: 6.9990 chunk 75 optimal weight: 2.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- 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** A1001 ASN A1415 ASN ** A1715 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1817 HIS A1927 ASN ** A1960 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1969 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.133444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.113698 restraints weight = 12411.616| |-----------------------------------------------------------------------------| r_work (start): 0.3170 rms_B_bonded: 1.45 r_work: 0.3059 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2929 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.3382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 10533 Z= 0.152 Angle : 0.609 10.732 14228 Z= 0.328 Chirality : 0.045 0.183 1581 Planarity : 0.004 0.050 1841 Dihedral : 5.568 32.448 1419 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.74 % Favored : 91.26 % Rotamer: Outliers : 2.79 % Allowed : 12.72 % Favored : 84.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.74 (0.22), residues: 1293 helix: -0.09 (0.26), residues: 415 sheet: -2.86 (0.31), residues: 223 loop : -2.64 (0.20), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A2157 TYR 0.024 0.002 TYR A1831 PHE 0.031 0.002 PHE A2119 TRP 0.010 0.001 TRP A1247 HIS 0.007 0.001 HIS A1847 Details of bonding type rmsd covalent geometry : bond 0.00353 (10533) covalent geometry : angle 0.60853 (14228) hydrogen bonds : bond 0.03992 ( 320) hydrogen bonds : angle 4.89757 ( 918) *********************** 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 183 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 151 time to evaluate : 0.424 Fit side-chains REVERT: A 922 LYS cc_start: 0.8770 (mmtp) cc_final: 0.8545 (mmtm) REVERT: A 966 PHE cc_start: 0.7554 (p90) cc_final: 0.6921 (p90) REVERT: A 1050 ARG cc_start: 0.8152 (ptp-170) cc_final: 0.7686 (mtm-85) REVERT: A 1100 LEU cc_start: 0.8213 (OUTLIER) cc_final: 0.7352 (mt) REVERT: A 1266 ASP cc_start: 0.7702 (t0) cc_final: 0.7280 (t0) REVERT: A 1335 LYS cc_start: 0.8447 (mptt) cc_final: 0.8227 (mptt) REVERT: A 1406 LYS cc_start: 0.7870 (mttt) cc_final: 0.7441 (mtmm) REVERT: A 1416 LYS cc_start: 0.7457 (mttm) cc_final: 0.6943 (mttt) REVERT: A 1422 ASN cc_start: 0.8199 (m-40) cc_final: 0.7938 (m110) REVERT: A 1757 TYR cc_start: 0.8592 (m-80) cc_final: 0.7926 (m-80) REVERT: A 1770 GLU cc_start: 0.7959 (mt-10) cc_final: 0.7674 (mm-30) REVERT: A 1829 PHE cc_start: 0.9032 (OUTLIER) cc_final: 0.8710 (t80) REVERT: A 1843 VAL cc_start: 0.8794 (m) cc_final: 0.8292 (t) REVERT: A 1846 THR cc_start: 0.9096 (m) cc_final: 0.8823 (p) REVERT: A 1988 LEU cc_start: 0.8104 (OUTLIER) cc_final: 0.7433 (mp) outliers start: 32 outliers final: 21 residues processed: 172 average time/residue: 0.0994 time to fit residues: 24.5697 Evaluate side-chains 157 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 133 time to evaluate : 0.387 ------------------------------------------------------------------------------- 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 1009 THR Chi-restraints excluded: chain A residue 1100 LEU Chi-restraints excluded: chain A residue 1109 SER Chi-restraints excluded: chain A residue 1165 THR Chi-restraints excluded: chain A residue 1184 VAL Chi-restraints excluded: chain A residue 1257 SER 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 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 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 1829 PHE Chi-restraints excluded: chain A residue 1894 VAL Chi-restraints excluded: chain A residue 1950 GLU Chi-restraints excluded: chain A residue 1988 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 105 optimal weight: 3.9990 chunk 97 optimal weight: 0.7980 chunk 43 optimal weight: 0.0970 chunk 31 optimal weight: 4.9990 chunk 22 optimal weight: 2.9990 chunk 3 optimal weight: 0.0170 chunk 13 optimal weight: 2.9990 chunk 53 optimal weight: 0.9990 chunk 77 optimal weight: 4.9990 chunk 29 optimal weight: 5.9990 chunk 60 optimal weight: 3.9990 overall best weight: 0.9820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 999 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1262 ASN A1391 ASN A1415 ASN A1817 HIS ** A1969 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.131304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.111063 restraints weight = 12504.695| |-----------------------------------------------------------------------------| r_work (start): 0.3131 rms_B_bonded: 1.49 r_work: 0.3018 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2885 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.3827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 10533 Z= 0.158 Angle : 0.611 11.081 14228 Z= 0.329 Chirality : 0.045 0.183 1581 Planarity : 0.004 0.050 1841 Dihedral : 5.578 31.494 1419 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.44 % Favored : 90.56 % Rotamer: Outliers : 4.27 % Allowed : 12.98 % Favored : 82.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.69 (0.22), residues: 1293 helix: -0.05 (0.26), residues: 414 sheet: -2.72 (0.31), residues: 241 loop : -2.63 (0.21), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A1774 TYR 0.023 0.002 TYR A1172 PHE 0.030 0.002 PHE A2119 TRP 0.010 0.001 TRP A1247 HIS 0.007 0.001 HIS A1847 Details of bonding type rmsd covalent geometry : bond 0.00370 (10533) covalent geometry : angle 0.61141 (14228) hydrogen bonds : bond 0.03893 ( 320) hydrogen bonds : angle 4.87661 ( 918) *********************** 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 188 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 139 time to evaluate : 0.405 Fit side-chains REVERT: A 1050 ARG cc_start: 0.8302 (ptp-170) cc_final: 0.7715 (mtm-85) REVERT: A 1098 GLN cc_start: 0.8508 (tt0) cc_final: 0.8085 (tt0) REVERT: A 1100 LEU cc_start: 0.8130 (OUTLIER) cc_final: 0.7777 (mt) REVERT: A 1225 TYR cc_start: 0.7523 (OUTLIER) cc_final: 0.7032 (t80) REVERT: A 1266 ASP cc_start: 0.7751 (t0) cc_final: 0.7224 (t0) REVERT: A 1273 ASN cc_start: 0.8572 (m-40) cc_final: 0.8285 (m-40) REVERT: A 1286 THR cc_start: 0.7217 (OUTLIER) cc_final: 0.6986 (t) REVERT: A 1335 LYS cc_start: 0.8391 (mptt) cc_final: 0.8156 (mptt) REVERT: A 1406 LYS cc_start: 0.7925 (mttt) cc_final: 0.7469 (mtmm) REVERT: A 1416 LYS cc_start: 0.7505 (mttm) cc_final: 0.6955 (mttt) REVERT: A 1422 ASN cc_start: 0.8412 (m-40) cc_final: 0.8134 (m-40) REVERT: A 1757 TYR cc_start: 0.8744 (m-80) cc_final: 0.8074 (m-80) REVERT: A 1770 GLU cc_start: 0.7960 (mt-10) cc_final: 0.7701 (mm-30) REVERT: A 1780 ASP cc_start: 0.8712 (OUTLIER) cc_final: 0.7881 (t0) REVERT: A 1794 GLU cc_start: 0.8450 (OUTLIER) cc_final: 0.8197 (tt0) REVERT: A 1988 LEU cc_start: 0.8199 (OUTLIER) cc_final: 0.7537 (mp) REVERT: A 2032 LYS cc_start: 0.8493 (mttm) cc_final: 0.8228 (mttp) REVERT: A 2113 LYS cc_start: 0.8388 (tttm) cc_final: 0.8155 (ttmm) REVERT: A 2153 GLU cc_start: 0.8670 (tm-30) cc_final: 0.8071 (tt0) outliers start: 49 outliers final: 33 residues processed: 172 average time/residue: 0.0948 time to fit residues: 23.7473 Evaluate side-chains 169 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 130 time to evaluate : 0.341 ------------------------------------------------------------------------------- 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 1009 THR Chi-restraints excluded: chain A residue 1100 LEU Chi-restraints excluded: chain A residue 1109 SER Chi-restraints excluded: chain A residue 1116 ILE Chi-restraints excluded: chain A residue 1134 VAL 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 1205 ASP 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 1286 THR Chi-restraints excluded: chain A residue 1391 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 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 1789 ASN Chi-restraints excluded: chain A residue 1794 GLU 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 1965 ASP Chi-restraints excluded: chain A residue 1988 LEU Chi-restraints excluded: chain A residue 2190 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 7 optimal weight: 5.9990 chunk 30 optimal weight: 4.9990 chunk 50 optimal weight: 2.9990 chunk 40 optimal weight: 3.9990 chunk 95 optimal weight: 2.9990 chunk 33 optimal weight: 0.7980 chunk 98 optimal weight: 0.9980 chunk 73 optimal weight: 2.9990 chunk 78 optimal weight: 2.9990 chunk 71 optimal weight: 0.8980 chunk 28 optimal weight: 0.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 999 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1028 ASN A1415 ASN A1768 ASN A1817 HIS ** A1969 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.128328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.109461 restraints weight = 12392.435| |-----------------------------------------------------------------------------| r_work (start): 0.3106 rms_B_bonded: 1.41 r_work: 0.2972 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2843 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.2843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8486 moved from start: 0.4192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 10533 Z= 0.195 Angle : 0.653 12.034 14228 Z= 0.350 Chirality : 0.047 0.183 1581 Planarity : 0.005 0.055 1841 Dihedral : 5.769 31.790 1419 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.51 % Favored : 90.49 % Rotamer: Outliers : 4.88 % Allowed : 14.46 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.75 (0.21), residues: 1293 helix: -0.22 (0.25), residues: 420 sheet: -2.71 (0.36), residues: 176 loop : -2.70 (0.19), residues: 697 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A1774 TYR 0.023 0.002 TYR A1172 PHE 0.030 0.002 PHE A2119 TRP 0.011 0.002 TRP A1760 HIS 0.007 0.001 HIS A1847 Details of bonding type rmsd covalent geometry : bond 0.00464 (10533) covalent geometry : angle 0.65265 (14228) hydrogen bonds : bond 0.04193 ( 320) hydrogen bonds : angle 4.96388 ( 918) *********************** 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 191 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 135 time to evaluate : 0.443 Fit side-chains REVERT: A 1000 GLU cc_start: 0.6659 (mt-10) cc_final: 0.6332 (mt-10) REVERT: A 1202 ASN cc_start: 0.8200 (t0) cc_final: 0.7890 (t0) REVERT: A 1225 TYR cc_start: 0.7699 (OUTLIER) cc_final: 0.6989 (t80) REVERT: A 1266 ASP cc_start: 0.7774 (t0) cc_final: 0.7171 (t0) REVERT: A 1286 THR cc_start: 0.7263 (OUTLIER) cc_final: 0.7018 (t) REVERT: A 1338 LYS cc_start: 0.6105 (ptmm) cc_final: 0.5325 (mmtm) REVERT: A 1406 LYS cc_start: 0.7966 (mttt) cc_final: 0.7506 (mtmm) REVERT: A 1416 LYS cc_start: 0.7646 (mttm) cc_final: 0.7110 (mttt) REVERT: A 1422 ASN cc_start: 0.8451 (m-40) cc_final: 0.8113 (m110) REVERT: A 1757 TYR cc_start: 0.8767 (m-80) cc_final: 0.8089 (m-80) REVERT: A 1780 ASP cc_start: 0.8767 (OUTLIER) cc_final: 0.7926 (t0) REVERT: A 1794 GLU cc_start: 0.8497 (OUTLIER) cc_final: 0.8293 (tt0) REVERT: A 1829 PHE cc_start: 0.9075 (OUTLIER) cc_final: 0.8704 (t80) REVERT: A 2153 GLU cc_start: 0.8691 (tm-30) cc_final: 0.8122 (tt0) outliers start: 56 outliers final: 40 residues processed: 177 average time/residue: 0.0970 time to fit residues: 24.9025 Evaluate side-chains 166 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 121 time to evaluate : 0.330 ------------------------------------------------------------------------------- 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 1009 THR Chi-restraints excluded: chain A residue 1022 VAL Chi-restraints excluded: chain A residue 1109 SER Chi-restraints excluded: chain A residue 1116 ILE Chi-restraints excluded: chain A residue 1134 VAL 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 1205 ASP Chi-restraints excluded: chain A residue 1220 THR Chi-restraints excluded: chain A residue 1225 TYR Chi-restraints excluded: chain A residue 1253 GLU 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 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 1718 THR Chi-restraints excluded: chain A residue 1776 VAL 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 Chi-restraints excluded: chain A residue 2190 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 116 optimal weight: 3.9990 chunk 93 optimal weight: 0.6980 chunk 9 optimal weight: 4.9990 chunk 11 optimal weight: 0.9990 chunk 117 optimal weight: 0.8980 chunk 102 optimal weight: 0.8980 chunk 86 optimal weight: 0.9980 chunk 101 optimal weight: 0.9990 chunk 15 optimal weight: 0.5980 chunk 75 optimal weight: 2.9990 chunk 38 optimal weight: 5.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 999 HIS A1415 ASN A1442 GLN A1817 HIS ** A1969 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.131120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.112207 restraints weight = 12404.308| |-----------------------------------------------------------------------------| r_work (start): 0.3146 rms_B_bonded: 1.42 r_work: 0.3014 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2885 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.2885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.4328 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= 0.143 Angle : 0.602 10.309 14228 Z= 0.324 Chirality : 0.045 0.180 1581 Planarity : 0.004 0.055 1841 Dihedral : 5.500 29.463 1419 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.97 % Favored : 91.03 % Rotamer: Outliers : 4.53 % Allowed : 15.68 % Favored : 79.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.62 (0.21), residues: 1293 helix: 0.01 (0.26), residues: 413 sheet: -2.67 (0.36), residues: 178 loop : -2.67 (0.19), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1774 TYR 0.018 0.001 TYR A1172 PHE 0.027 0.002 PHE A2119 TRP 0.010 0.001 TRP A1247 HIS 0.007 0.001 HIS A1847 Details of bonding type rmsd covalent geometry : bond 0.00330 (10533) covalent geometry : angle 0.60152 (14228) hydrogen bonds : bond 0.03732 ( 320) hydrogen bonds : angle 4.79623 ( 918) *********************** 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 185 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 133 time to evaluate : 0.387 Fit side-chains REVERT: A 939 ASN cc_start: 0.7400 (t0) cc_final: 0.6940 (t0) REVERT: A 1050 ARG cc_start: 0.8242 (ptp-170) cc_final: 0.7802 (mtt180) REVERT: A 1225 TYR cc_start: 0.7638 (OUTLIER) cc_final: 0.6865 (t80) REVERT: A 1266 ASP cc_start: 0.7788 (t0) cc_final: 0.7187 (t0) REVERT: A 1273 ASN cc_start: 0.8603 (m-40) cc_final: 0.8319 (m-40) REVERT: A 1338 LYS cc_start: 0.6045 (ptmm) cc_final: 0.5337 (mmtm) REVERT: A 1391 ASN cc_start: 0.8537 (OUTLIER) cc_final: 0.7973 (m-40) REVERT: A 1406 LYS cc_start: 0.7906 (mttt) cc_final: 0.7461 (mtmm) REVERT: A 1416 LYS cc_start: 0.7528 (mttm) cc_final: 0.7041 (mttt) REVERT: A 1422 ASN cc_start: 0.8394 (m-40) cc_final: 0.8109 (m110) REVERT: A 1757 TYR cc_start: 0.8711 (m-80) cc_final: 0.8064 (m-80) REVERT: A 1794 GLU cc_start: 0.8433 (OUTLIER) cc_final: 0.8200 (tt0) REVERT: A 2153 GLU cc_start: 0.8670 (tm-30) cc_final: 0.8101 (tt0) outliers start: 52 outliers final: 38 residues processed: 168 average time/residue: 0.0974 time to fit residues: 23.6495 Evaluate side-chains 165 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 124 time to evaluate : 0.374 ------------------------------------------------------------------------------- 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 1009 THR Chi-restraints excluded: chain A residue 1022 VAL Chi-restraints excluded: chain A residue 1109 SER Chi-restraints excluded: chain A residue 1116 ILE Chi-restraints excluded: chain A residue 1134 VAL 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 1205 ASP Chi-restraints excluded: chain A residue 1220 THR Chi-restraints excluded: chain A residue 1225 TYR Chi-restraints excluded: chain A residue 1253 GLU 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 1391 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 1718 THR Chi-restraints excluded: chain A residue 1776 VAL 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 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 2190 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 83 optimal weight: 2.9990 chunk 88 optimal weight: 0.0770 chunk 8 optimal weight: 3.9990 chunk 68 optimal weight: 3.9990 chunk 75 optimal weight: 3.9990 chunk 93 optimal weight: 0.9980 chunk 77 optimal weight: 0.8980 chunk 57 optimal weight: 0.8980 chunk 53 optimal weight: 0.9980 chunk 117 optimal weight: 0.9990 chunk 102 optimal weight: 1.9990 overall best weight: 0.7738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1415 ASN A1817 HIS ** A1969 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.131280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.113907 restraints weight = 12259.516| |-----------------------------------------------------------------------------| r_work (start): 0.3166 rms_B_bonded: 1.42 r_work: 0.3060 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.2940 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.2940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.4444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10533 Z= 0.138 Angle : 0.593 10.573 14228 Z= 0.319 Chirality : 0.045 0.179 1581 Planarity : 0.004 0.057 1841 Dihedral : 5.406 27.762 1419 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.58 % Favored : 91.42 % Rotamer: Outliers : 4.44 % Allowed : 16.46 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.49 (0.21), residues: 1293 helix: 0.09 (0.26), residues: 412 sheet: -2.45 (0.36), residues: 174 loop : -2.61 (0.20), residues: 707 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A2124 TYR 0.018 0.001 TYR A1172 PHE 0.026 0.002 PHE A2119 TRP 0.009 0.001 TRP A1760 HIS 0.007 0.001 HIS A1847 Details of bonding type rmsd covalent geometry : bond 0.00316 (10533) covalent geometry : angle 0.59278 (14228) hydrogen bonds : bond 0.03683 ( 320) hydrogen bonds : angle 4.73274 ( 918) *********************** 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 179 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 128 time to evaluate : 0.388 Fit side-chains REVERT: A 939 ASN cc_start: 0.7437 (t0) cc_final: 0.7086 (t0) REVERT: A 1050 ARG cc_start: 0.8242 (ptp-170) cc_final: 0.7814 (mtt180) REVERT: A 1225 TYR cc_start: 0.7582 (OUTLIER) cc_final: 0.6833 (t80) REVERT: A 1266 ASP cc_start: 0.7871 (t0) cc_final: 0.7233 (t0) REVERT: A 1273 ASN cc_start: 0.8639 (m-40) cc_final: 0.8349 (m-40) REVERT: A 1338 LYS cc_start: 0.5975 (ptmm) cc_final: 0.5274 (mmtm) REVERT: A 1406 LYS cc_start: 0.7884 (mttt) cc_final: 0.7459 (mtmm) REVERT: A 1416 LYS cc_start: 0.7444 (mttm) cc_final: 0.6986 (mttt) REVERT: A 1422 ASN cc_start: 0.8333 (m-40) cc_final: 0.8008 (m110) REVERT: A 1757 TYR cc_start: 0.8680 (m-80) cc_final: 0.8009 (m-80) REVERT: A 1780 ASP cc_start: 0.8497 (OUTLIER) cc_final: 0.7625 (t0) REVERT: A 1829 PHE cc_start: 0.9003 (OUTLIER) cc_final: 0.8751 (t80) REVERT: A 1846 THR cc_start: 0.9075 (m) cc_final: 0.8814 (p) REVERT: A 2084 ILE cc_start: 0.8697 (OUTLIER) cc_final: 0.8469 (pp) REVERT: A 2153 GLU cc_start: 0.8563 (tm-30) cc_final: 0.8006 (tt0) outliers start: 51 outliers final: 39 residues processed: 163 average time/residue: 0.0970 time to fit residues: 22.8162 Evaluate side-chains 167 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 124 time to evaluate : 0.347 ------------------------------------------------------------------------------- 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 1009 THR Chi-restraints excluded: chain A residue 1022 VAL Chi-restraints excluded: chain A residue 1109 SER Chi-restraints excluded: chain A residue 1116 ILE Chi-restraints excluded: chain A residue 1134 VAL 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 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 1776 VAL 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 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 Chi-restraints excluded: chain A residue 2032 LYS Chi-restraints excluded: chain A residue 2035 THR Chi-restraints excluded: chain A residue 2084 ILE Chi-restraints excluded: chain A residue 2190 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 22 optimal weight: 0.9980 chunk 6 optimal weight: 0.9980 chunk 47 optimal weight: 0.9980 chunk 45 optimal weight: 0.0980 chunk 119 optimal weight: 1.9990 chunk 37 optimal weight: 4.9990 chunk 21 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 112 optimal weight: 2.9990 chunk 113 optimal weight: 0.9990 chunk 93 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1605 ASN A1817 HIS ** A1969 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.130886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.113686 restraints weight = 12298.478| |-----------------------------------------------------------------------------| r_work (start): 0.3162 rms_B_bonded: 1.38 r_work: 0.3055 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.2938 rms_B_bonded: 3.20 restraints_weight: 0.2500 r_work (final): 0.2938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.4539 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= 0.142 Angle : 0.596 10.523 14228 Z= 0.320 Chirality : 0.045 0.181 1581 Planarity : 0.004 0.058 1841 Dihedral : 5.404 26.892 1419 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.89 % Favored : 91.11 % Rotamer: Outliers : 4.36 % Allowed : 16.72 % Favored : 78.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.41 (0.22), residues: 1293 helix: 0.11 (0.26), residues: 412 sheet: -2.35 (0.37), residues: 174 loop : -2.55 (0.20), residues: 707 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1774 TYR 0.019 0.001 TYR A1172 PHE 0.026 0.002 PHE A2119 TRP 0.009 0.001 TRP A1760 HIS 0.007 0.001 HIS A1847 Details of bonding type rmsd covalent geometry : bond 0.00328 (10533) covalent geometry : angle 0.59646 (14228) hydrogen bonds : bond 0.03687 ( 320) hydrogen bonds : angle 4.69066 ( 918) *********************** 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 178 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 128 time to evaluate : 0.378 Fit side-chains REVERT: A 939 ASN cc_start: 0.7446 (t0) cc_final: 0.7082 (t0) REVERT: A 1050 ARG cc_start: 0.8227 (ptp-170) cc_final: 0.7797 (mtt180) REVERT: A 1119 GLU cc_start: 0.8357 (mt-10) cc_final: 0.8123 (tt0) REVERT: A 1225 TYR cc_start: 0.7609 (OUTLIER) cc_final: 0.6738 (t80) REVERT: A 1266 ASP cc_start: 0.7827 (t0) cc_final: 0.7193 (t0) REVERT: A 1338 LYS cc_start: 0.5969 (ptmm) cc_final: 0.5300 (mmtm) REVERT: A 1416 LYS cc_start: 0.7526 (mttm) cc_final: 0.7051 (mttt) REVERT: A 1422 ASN cc_start: 0.8338 (m-40) cc_final: 0.7998 (m110) REVERT: A 1757 TYR cc_start: 0.8686 (m-80) cc_final: 0.8079 (m-80) REVERT: A 1780 ASP cc_start: 0.8498 (OUTLIER) cc_final: 0.7593 (t0) REVERT: A 1829 PHE cc_start: 0.9015 (OUTLIER) cc_final: 0.8693 (t80) REVERT: A 2084 ILE cc_start: 0.8734 (OUTLIER) cc_final: 0.8513 (pp) REVERT: A 2153 GLU cc_start: 0.8548 (tm-30) cc_final: 0.8001 (tt0) outliers start: 50 outliers final: 39 residues processed: 163 average time/residue: 0.0921 time to fit residues: 21.9916 Evaluate side-chains 167 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 124 time to evaluate : 0.346 ------------------------------------------------------------------------------- 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 1009 THR Chi-restraints excluded: chain A residue 1022 VAL Chi-restraints excluded: chain A residue 1109 SER Chi-restraints excluded: chain A residue 1116 ILE Chi-restraints excluded: chain A residue 1134 VAL 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 1400 VAL 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 1776 VAL 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 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 1965 ASP Chi-restraints excluded: chain A residue 2032 LYS Chi-restraints excluded: chain A residue 2035 THR Chi-restraints excluded: chain A residue 2084 ILE Chi-restraints excluded: chain A residue 2190 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 107 optimal weight: 0.8980 chunk 90 optimal weight: 0.9990 chunk 104 optimal weight: 3.9990 chunk 14 optimal weight: 6.9990 chunk 9 optimal weight: 3.9990 chunk 6 optimal weight: 0.9990 chunk 36 optimal weight: 3.9990 chunk 52 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 7 optimal weight: 0.3980 chunk 68 optimal weight: 4.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- 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** A1415 ASN A1422 ASN ** A1817 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1922 HIS ** A1969 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.127805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.110507 restraints weight = 12333.184| |-----------------------------------------------------------------------------| r_work (start): 0.3118 rms_B_bonded: 1.38 r_work: 0.3013 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.2895 rms_B_bonded: 3.11 restraints_weight: 0.2500 r_work (final): 0.2895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.4708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 10533 Z= 0.189 Angle : 0.652 11.946 14228 Z= 0.347 Chirality : 0.047 0.191 1581 Planarity : 0.004 0.059 1841 Dihedral : 5.713 27.123 1419 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.67 % Favored : 90.33 % Rotamer: Outliers : 4.18 % Allowed : 16.72 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.47 (0.22), residues: 1293 helix: -0.04 (0.26), residues: 408 sheet: -2.36 (0.36), residues: 184 loop : -2.51 (0.20), residues: 701 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1774 TYR 0.022 0.002 TYR A1172 PHE 0.027 0.002 PHE A2119 TRP 0.011 0.002 TRP A1247 HIS 0.007 0.001 HIS A1847 Details of bonding type rmsd covalent geometry : bond 0.00449 (10533) covalent geometry : angle 0.65175 (14228) hydrogen bonds : bond 0.04097 ( 320) hydrogen bonds : angle 4.85677 ( 918) *********************** 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 170 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 122 time to evaluate : 0.414 Fit side-chains REVERT: A 939 ASN cc_start: 0.7476 (t0) cc_final: 0.7090 (t0) REVERT: A 1050 ARG cc_start: 0.8229 (ptp-170) cc_final: 0.7779 (mtt180) REVERT: A 1225 TYR cc_start: 0.7780 (OUTLIER) cc_final: 0.6805 (t80) REVERT: A 1243 VAL cc_start: 0.9111 (t) cc_final: 0.8872 (p) REVERT: A 1266 ASP cc_start: 0.7844 (t0) cc_final: 0.7543 (t0) REVERT: A 1338 LYS cc_start: 0.5911 (ptmm) cc_final: 0.5310 (mmtm) REVERT: A 1406 LYS cc_start: 0.7936 (mttt) cc_final: 0.7493 (mtmm) REVERT: A 1416 LYS cc_start: 0.7595 (mttm) cc_final: 0.7129 (mttt) REVERT: A 1422 ASN cc_start: 0.8255 (m110) cc_final: 0.7874 (m110) REVERT: A 1757 TYR cc_start: 0.8748 (m-80) cc_final: 0.8208 (m-80) REVERT: A 1829 PHE cc_start: 0.9120 (OUTLIER) cc_final: 0.8738 (t80) REVERT: A 1945 LYS cc_start: 0.8087 (mtmt) cc_final: 0.7768 (ptmt) REVERT: A 2071 LYS cc_start: 0.8233 (mtmt) cc_final: 0.7894 (tttm) REVERT: A 2153 GLU cc_start: 0.8566 (tm-30) cc_final: 0.8051 (tt0) outliers start: 48 outliers final: 40 residues processed: 156 average time/residue: 0.1047 time to fit residues: 23.0639 Evaluate side-chains 162 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 120 time to evaluate : 0.393 ------------------------------------------------------------------------------- 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 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 1070 LEU Chi-restraints excluded: chain A residue 1109 SER Chi-restraints excluded: chain A residue 1116 ILE Chi-restraints excluded: chain A residue 1134 VAL 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 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 1776 VAL 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 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 1965 ASP Chi-restraints excluded: chain A residue 2032 LYS Chi-restraints excluded: chain A residue 2035 THR Chi-restraints excluded: chain A residue 2190 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 45 optimal weight: 3.9990 chunk 56 optimal weight: 0.9980 chunk 23 optimal weight: 2.9990 chunk 47 optimal weight: 0.8980 chunk 57 optimal weight: 0.8980 chunk 104 optimal weight: 4.9990 chunk 102 optimal weight: 0.9980 chunk 51 optimal weight: 0.6980 chunk 71 optimal weight: 0.6980 chunk 118 optimal weight: 2.9990 chunk 88 optimal weight: 7.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1969 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.130388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.112224 restraints weight = 12149.401| |-----------------------------------------------------------------------------| r_work (start): 0.3146 rms_B_bonded: 1.28 r_work: 0.3028 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.2906 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.2906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.4721 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= 0.146 Angle : 0.608 10.409 14228 Z= 0.325 Chirality : 0.045 0.181 1581 Planarity : 0.004 0.060 1841 Dihedral : 5.506 26.194 1419 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.97 % Favored : 91.03 % Rotamer: Outliers : 4.01 % Allowed : 17.25 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.40 (0.22), residues: 1293 helix: 0.09 (0.26), residues: 406 sheet: -2.31 (0.38), residues: 172 loop : -2.51 (0.20), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1774 TYR 0.019 0.001 TYR A1172 PHE 0.026 0.002 PHE A2119 TRP 0.010 0.002 TRP A1247 HIS 0.006 0.001 HIS A1847 Details of bonding type rmsd covalent geometry : bond 0.00337 (10533) covalent geometry : angle 0.60757 (14228) hydrogen bonds : bond 0.03731 ( 320) hydrogen bonds : angle 4.72054 ( 918) ********************** 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 173 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 127 time to evaluate : 0.309 Fit side-chains REVERT: A 939 ASN cc_start: 0.7502 (t0) cc_final: 0.7096 (t0) REVERT: A 1050 ARG cc_start: 0.8202 (ptp-170) cc_final: 0.7783 (mtt180) REVERT: A 1119 GLU cc_start: 0.8457 (mt-10) cc_final: 0.8182 (tt0) REVERT: A 1225 TYR cc_start: 0.7783 (OUTLIER) cc_final: 0.6796 (t80) REVERT: A 1243 VAL cc_start: 0.9089 (t) cc_final: 0.8823 (p) REVERT: A 1266 ASP cc_start: 0.7886 (t0) cc_final: 0.7291 (t0) REVERT: A 1338 LYS cc_start: 0.5738 (ptmm) cc_final: 0.5144 (mmtm) REVERT: A 1406 LYS cc_start: 0.7766 (mttt) cc_final: 0.7302 (mtmm) REVERT: A 1416 LYS cc_start: 0.7583 (mttm) cc_final: 0.7136 (mttt) REVERT: A 1422 ASN cc_start: 0.8320 (m110) cc_final: 0.7934 (m110) REVERT: A 1757 TYR cc_start: 0.8714 (m-80) cc_final: 0.8117 (m-80) REVERT: A 1780 ASP cc_start: 0.8659 (OUTLIER) cc_final: 0.7817 (t0) REVERT: A 1829 PHE cc_start: 0.9034 (OUTLIER) cc_final: 0.8712 (t80) REVERT: A 1945 LYS cc_start: 0.8097 (mtmt) cc_final: 0.7822 (ptmt) REVERT: A 2076 LYS cc_start: 0.8036 (ptpp) cc_final: 0.7762 (ptmt) REVERT: A 2153 GLU cc_start: 0.8604 (tm-30) cc_final: 0.8080 (tt0) outliers start: 46 outliers final: 40 residues processed: 158 average time/residue: 0.1004 time to fit residues: 22.5446 Evaluate side-chains 167 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 124 time to evaluate : 0.384 ------------------------------------------------------------------------------- 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 990 VAL Chi-restraints excluded: chain A residue 1009 THR Chi-restraints excluded: chain A residue 1022 VAL Chi-restraints excluded: chain A residue 1070 LEU Chi-restraints excluded: chain A residue 1109 SER Chi-restraints excluded: chain A residue 1116 ILE Chi-restraints excluded: chain A residue 1134 VAL 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 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 1776 VAL 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 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 1965 ASP Chi-restraints excluded: chain A residue 2032 LYS Chi-restraints excluded: chain A residue 2035 THR Chi-restraints excluded: chain A residue 2190 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 104 optimal weight: 4.9990 chunk 9 optimal weight: 3.9990 chunk 86 optimal weight: 3.9990 chunk 46 optimal weight: 1.9990 chunk 106 optimal weight: 0.1980 chunk 89 optimal weight: 0.7980 chunk 53 optimal weight: 3.9990 chunk 55 optimal weight: 0.9990 chunk 68 optimal weight: 3.9990 chunk 84 optimal weight: 0.9980 chunk 90 optimal weight: 1.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1969 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.129578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.110966 restraints weight = 12260.247| |-----------------------------------------------------------------------------| r_work (start): 0.3128 rms_B_bonded: 1.30 r_work: 0.3015 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.2894 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.2894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 moved from start: 0.4799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 10533 Z= 0.161 Angle : 0.624 11.316 14228 Z= 0.333 Chirality : 0.046 0.181 1581 Planarity : 0.004 0.061 1841 Dihedral : 5.568 25.694 1419 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.44 % Favored : 90.56 % Rotamer: Outliers : 4.09 % Allowed : 17.33 % Favored : 78.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.41 (0.22), residues: 1293 helix: 0.04 (0.26), residues: 413 sheet: -2.33 (0.37), residues: 182 loop : -2.50 (0.20), residues: 698 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1774 TYR 0.020 0.002 TYR A1172 PHE 0.026 0.002 PHE A2119 TRP 0.011 0.002 TRP A1247 HIS 0.007 0.001 HIS A1847 Details of bonding type rmsd covalent geometry : bond 0.00379 (10533) covalent geometry : angle 0.62368 (14228) hydrogen bonds : bond 0.03860 ( 320) hydrogen bonds : angle 4.76413 ( 918) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2480.44 seconds wall clock time: 43 minutes 17.12 seconds (2597.12 seconds total)