Starting phenix.real_space_refine on Fri Feb 14 18:58:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7uvk_26812/02_2025/7uvk_26812.cif Found real_map, /net/cci-nas-00/data/ceres_data/7uvk_26812/02_2025/7uvk_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_26812/02_2025/7uvk_26812.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7uvk_26812/02_2025/7uvk_26812.map" model { file = "/net/cci-nas-00/data/ceres_data/7uvk_26812/02_2025/7uvk_26812.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7uvk_26812/02_2025/7uvk_26812.cif" } resolution = 3.28 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.045 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 19 5.16 5 C 6536 2.51 5 N 1750 2.21 5 O 2045 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 40 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 10350 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 10350 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1295, 10350 Classifications: {'peptide': 1295} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 30, 'TRANS': 1264} Time building chain proxies: 6.39, per 1000 atoms: 0.62 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: 2.55 Conformation dependent library (CDL) restraints added in 1.3 seconds 2586 Ramachandran restraints generated. 1293 Oldfield, 0 Emsley, 1293 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2440 Finding SS restraints... Secondary structure from input PDB file: 44 helices and 16 sheets defined 34.3% alpha, 11.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.23 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: 4.02 Time building geometry restraints manager: 2.98 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: 2.730 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: 0.430 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 26.570 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7420 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.295 10533 Z= 0.332 Angle : 0.741 16.372 14228 Z= 0.432 Chirality : 0.046 0.302 1581 Planarity : 0.004 0.045 1841 Dihedral : 13.598 86.927 3952 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.05 % Favored : 90.95 % Rotamer: Outliers : 0.00 % Allowed : 0.26 % Favored : 99.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.16 (0.21), residues: 1293 helix: -0.34 (0.26), residues: 402 sheet: -3.39 (0.34), residues: 180 loop : -2.91 (0.19), residues: 711 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A1247 HIS 0.008 0.001 HIS A1847 PHE 0.032 0.002 PHE A1829 TYR 0.024 0.001 TYR A1172 ARG 0.010 0.000 ARG A1139 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2586 Ramachandran restraints generated. 1293 Oldfield, 0 Emsley, 1293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2586 Ramachandran restraints generated. 1293 Oldfield, 0 Emsley, 1293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 263 time to evaluate : 1.111 Fit side-chains REVERT: A 922 LYS cc_start: 0.7116 (mmtp) cc_final: 0.6678 (mmtm) REVERT: A 939 ASN cc_start: 0.6680 (t0) cc_final: 0.6247 (t0) REVERT: A 940 LYS cc_start: 0.7893 (ptmm) cc_final: 0.7631 (ptmm) REVERT: A 1034 ASN cc_start: 0.7371 (m-40) cc_final: 0.7128 (m-40) REVERT: A 1050 ARG cc_start: 0.7375 (ptp-170) cc_final: 0.6883 (mtt180) REVERT: A 1077 LYS cc_start: 0.6487 (ttpt) cc_final: 0.6217 (ptpp) REVERT: A 1195 ILE cc_start: 0.8254 (pt) cc_final: 0.7816 (pt) REVERT: A 1266 ASP cc_start: 0.7104 (t0) cc_final: 0.6844 (t0) REVERT: A 1294 ASN cc_start: 0.7379 (m-40) cc_final: 0.7087 (m-40) REVERT: A 1406 LYS cc_start: 0.7331 (mttt) cc_final: 0.6763 (mtmm) REVERT: A 1407 ASP cc_start: 0.6877 (m-30) cc_final: 0.6633 (m-30) REVERT: A 1473 LYS cc_start: 0.7569 (ptmm) cc_final: 0.7350 (pttt) REVERT: A 1478 ASP cc_start: 0.7380 (m-30) cc_final: 0.7140 (m-30) REVERT: A 1498 ASN cc_start: 0.7990 (t0) cc_final: 0.7703 (p0) REVERT: A 1546 LYS cc_start: 0.7934 (ttpt) cc_final: 0.7733 (ttmm) REVERT: A 1583 ASP cc_start: 0.8350 (p0) cc_final: 0.8108 (p0) REVERT: A 1594 ASP cc_start: 0.7509 (m-30) cc_final: 0.7182 (m-30) REVERT: A 1646 ASN cc_start: 0.7837 (p0) cc_final: 0.7474 (p0) REVERT: A 1662 LYS cc_start: 0.8613 (mttp) cc_final: 0.8404 (mtmt) REVERT: A 1703 THR cc_start: 0.8526 (m) cc_final: 0.8040 (p) REVERT: A 1725 ASP cc_start: 0.7397 (m-30) cc_final: 0.7142 (t0) REVERT: A 1832 MET cc_start: 0.8452 (mmm) cc_final: 0.8236 (mmt) REVERT: A 1855 ARG cc_start: 0.7163 (mtm-85) cc_final: 0.6936 (mtm180) REVERT: A 1856 GLU cc_start: 0.7723 (mm-30) cc_final: 0.7480 (mm-30) REVERT: A 1953 ASP cc_start: 0.6904 (t0) cc_final: 0.6538 (m-30) outliers start: 0 outliers final: 0 residues processed: 263 average time/residue: 0.2788 time to fit residues: 97.7366 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 : 1.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 108 optimal weight: 2.9990 chunk 97 optimal weight: 0.0970 chunk 54 optimal weight: 2.9990 chunk 33 optimal weight: 0.0030 chunk 65 optimal weight: 1.9990 chunk 52 optimal weight: 0.7980 chunk 101 optimal weight: 3.9990 chunk 39 optimal weight: 4.9990 chunk 61 optimal weight: 3.9990 chunk 75 optimal weight: 0.9990 chunk 117 optimal weight: 0.7980 overall best weight: 0.5390 ------------------------------------------------------------------------------- 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 = 0.3545 r_free = 0.3545 target = 0.144457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.126172 restraints weight = 12240.365| |-----------------------------------------------------------------------------| r_work (start): 0.3331 rms_B_bonded: 1.36 r_work: 0.3179 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3045 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.2088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 10533 Z= 0.187 Angle : 0.596 7.562 14228 Z= 0.324 Chirality : 0.044 0.183 1581 Planarity : 0.004 0.046 1841 Dihedral : 5.467 32.280 1419 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.66 % Favored : 91.34 % Rotamer: Outliers : 1.48 % Allowed : 8.62 % Favored : 89.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.77 (0.22), residues: 1293 helix: -0.04 (0.26), residues: 411 sheet: -3.03 (0.33), residues: 205 loop : -2.67 (0.20), residues: 677 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A1247 HIS 0.007 0.001 HIS A1847 PHE 0.029 0.002 PHE A2119 TYR 0.021 0.001 TYR A1831 ARG 0.005 0.000 ARG A1139 *********************** 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 190 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 173 time to evaluate : 1.116 Fit side-chains REVERT: A 922 LYS cc_start: 0.8453 (mmtp) cc_final: 0.8200 (mmtt) REVERT: A 939 ASN cc_start: 0.7102 (t0) cc_final: 0.6760 (t0) REVERT: A 1050 ARG cc_start: 0.7935 (ptp-170) cc_final: 0.7490 (mtm-85) REVERT: A 1098 GLN cc_start: 0.8428 (tt0) cc_final: 0.7914 (tt0) REVERT: A 1266 ASP cc_start: 0.7732 (t0) cc_final: 0.7200 (t0) REVERT: A 1406 LYS cc_start: 0.7877 (mttt) cc_final: 0.7431 (mtmm) REVERT: A 1478 ASP cc_start: 0.8388 (m-30) cc_final: 0.8187 (m-30) REVERT: A 1583 ASP cc_start: 0.8525 (p0) cc_final: 0.8299 (p0) REVERT: A 1757 TYR cc_start: 0.8219 (m-80) cc_final: 0.7514 (m-80) REVERT: A 2084 ILE cc_start: 0.8255 (tt) cc_final: 0.7991 (tt) REVERT: A 2124 ARG cc_start: 0.6835 (mmp80) cc_final: 0.6184 (mmp80) REVERT: A 2172 ASN cc_start: 0.8371 (t0) cc_final: 0.7987 (t0) outliers start: 17 outliers final: 12 residues processed: 182 average time/residue: 0.2601 time to fit residues: 66.3211 Evaluate side-chains 144 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 132 time to evaluate : 1.119 ------------------------------------------------------------------------------- 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 1588 SER Chi-restraints excluded: chain A residue 1736 ASP Chi-restraints excluded: chain A residue 1777 LEU Chi-restraints excluded: chain A residue 1779 TYR Chi-restraints excluded: chain A residue 1789 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 35 optimal weight: 6.9990 chunk 115 optimal weight: 2.9990 chunk 126 optimal weight: 4.9990 chunk 117 optimal weight: 0.8980 chunk 106 optimal weight: 2.9990 chunk 109 optimal weight: 0.9990 chunk 14 optimal weight: 6.9990 chunk 95 optimal weight: 2.9990 chunk 73 optimal weight: 0.0030 chunk 22 optimal weight: 0.1980 chunk 47 optimal weight: 1.9990 overall best weight: 0.8194 ------------------------------------------------------------------------------- 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 ** A1715 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1817 HIS A1927 ASN ** 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 = 0.3441 r_free = 0.3441 target = 0.135664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.115540 restraints weight = 12500.387| |-----------------------------------------------------------------------------| r_work (start): 0.3196 rms_B_bonded: 1.49 r_work: 0.3082 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2952 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.3197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 10533 Z= 0.226 Angle : 0.608 10.948 14228 Z= 0.329 Chirality : 0.045 0.183 1581 Planarity : 0.004 0.049 1841 Dihedral : 5.502 31.955 1419 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.89 % Favored : 91.11 % Rotamer: Outliers : 2.44 % Allowed : 12.72 % Favored : 84.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.68 (0.22), residues: 1293 helix: 0.01 (0.26), residues: 413 sheet: -2.82 (0.31), residues: 223 loop : -2.63 (0.20), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A1247 HIS 0.006 0.001 HIS A1847 PHE 0.030 0.002 PHE A2119 TYR 0.023 0.002 TYR A1831 ARG 0.005 0.001 ARG A1774 *********************** 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: 28 poor density : 155 time to evaluate : 1.145 Fit side-chains REVERT: A 1050 ARG cc_start: 0.8117 (ptp-170) cc_final: 0.7630 (mtm-85) REVERT: A 1266 ASP cc_start: 0.7762 (t0) cc_final: 0.7270 (t0) REVERT: A 1298 LYS cc_start: 0.8034 (tptm) cc_final: 0.7578 (tptt) REVERT: A 1335 LYS cc_start: 0.8492 (mptt) cc_final: 0.8228 (mptt) REVERT: A 1406 LYS cc_start: 0.7838 (mttt) cc_final: 0.7413 (mtmm) REVERT: A 1478 ASP cc_start: 0.8470 (m-30) cc_final: 0.8228 (m-30) REVERT: A 1757 TYR cc_start: 0.8719 (m-80) cc_final: 0.8027 (m-80) REVERT: A 1770 GLU cc_start: 0.7936 (mt-10) cc_final: 0.7598 (mm-30) REVERT: A 2032 LYS cc_start: 0.8428 (mttm) cc_final: 0.8064 (mptt) outliers start: 28 outliers final: 23 residues processed: 171 average time/residue: 0.2435 time to fit residues: 58.7357 Evaluate side-chains 148 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 125 time to evaluate : 1.135 ------------------------------------------------------------------------------- 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 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 1286 THR Chi-restraints excluded: chain A residue 1299 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 1709 MET Chi-restraints excluded: chain A residue 1777 LEU Chi-restraints excluded: chain A residue 1779 TYR Chi-restraints excluded: chain A residue 1789 ASN Chi-restraints excluded: chain A residue 1894 VAL Chi-restraints excluded: chain A residue 1965 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 4 optimal weight: 0.4980 chunk 39 optimal weight: 6.9990 chunk 69 optimal weight: 0.7980 chunk 83 optimal weight: 2.9990 chunk 96 optimal weight: 0.5980 chunk 108 optimal weight: 2.9990 chunk 122 optimal weight: 0.0010 chunk 66 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 chunk 116 optimal weight: 3.9990 chunk 63 optimal weight: 0.6980 overall best weight: 0.5186 ------------------------------------------------------------------------------- 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** A1391 ASN A1415 ASN A1817 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 = 0.3447 r_free = 0.3447 target = 0.136281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.116475 restraints weight = 12317.281| |-----------------------------------------------------------------------------| r_work (start): 0.3222 rms_B_bonded: 1.45 r_work: 0.3113 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2982 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.3526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10533 Z= 0.169 Angle : 0.557 9.594 14228 Z= 0.302 Chirality : 0.044 0.195 1581 Planarity : 0.004 0.044 1841 Dihedral : 5.235 29.491 1419 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.51 % Favored : 91.49 % Rotamer: Outliers : 3.05 % Allowed : 13.85 % Favored : 83.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.51 (0.22), residues: 1293 helix: 0.21 (0.26), residues: 409 sheet: -2.57 (0.32), residues: 224 loop : -2.63 (0.20), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A1247 HIS 0.005 0.001 HIS A1847 PHE 0.028 0.002 PHE A2119 TYR 0.019 0.001 TYR A1831 ARG 0.006 0.000 ARG A2157 *********************** 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 172 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 137 time to evaluate : 1.441 Fit side-chains REVERT: A 1050 ARG cc_start: 0.8114 (ptp-170) cc_final: 0.7609 (mtm-85) REVERT: A 1100 LEU cc_start: 0.7841 (OUTLIER) cc_final: 0.7526 (mt) REVERT: A 1119 GLU cc_start: 0.8352 (mt-10) cc_final: 0.8046 (tt0) REVERT: A 1266 ASP cc_start: 0.7886 (t0) cc_final: 0.7400 (t0) REVERT: A 1286 THR cc_start: 0.6933 (OUTLIER) cc_final: 0.6720 (t) REVERT: A 1298 LYS cc_start: 0.8062 (tptm) cc_final: 0.7460 (mmtm) REVERT: A 1406 LYS cc_start: 0.7805 (mttt) cc_final: 0.7362 (mtmm) REVERT: A 1416 LYS cc_start: 0.7302 (mttm) cc_final: 0.6822 (mttt) REVERT: A 1757 TYR cc_start: 0.8648 (m-80) cc_final: 0.7940 (m-80) REVERT: A 1770 GLU cc_start: 0.7921 (mt-10) cc_final: 0.7619 (mm-30) REVERT: A 1829 PHE cc_start: 0.8853 (OUTLIER) cc_final: 0.8649 (t80) REVERT: A 1988 LEU cc_start: 0.7997 (OUTLIER) cc_final: 0.7291 (mp) REVERT: A 2032 LYS cc_start: 0.8404 (mttm) cc_final: 0.8098 (mptt) outliers start: 35 outliers final: 23 residues processed: 159 average time/residue: 0.2525 time to fit residues: 57.1776 Evaluate side-chains 151 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 124 time to evaluate : 1.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 952 THR Chi-restraints excluded: chain A residue 990 VAL Chi-restraints excluded: chain A residue 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 1220 THR 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 1403 VAL Chi-restraints excluded: chain A residue 1430 ASP Chi-restraints excluded: chain A residue 1500 LYS Chi-restraints excluded: chain A residue 1588 SER Chi-restraints excluded: chain A residue 1641 LEU Chi-restraints excluded: chain A residue 1709 MET Chi-restraints excluded: chain A residue 1777 LEU Chi-restraints excluded: chain A residue 1779 TYR Chi-restraints excluded: chain A residue 1789 ASN Chi-restraints excluded: chain A residue 1829 PHE Chi-restraints excluded: chain A residue 1862 TYR Chi-restraints excluded: chain A residue 1894 VAL Chi-restraints excluded: chain A residue 1920 ASP Chi-restraints excluded: chain A residue 1965 ASP Chi-restraints excluded: chain A residue 1988 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 19 optimal weight: 4.9990 chunk 78 optimal weight: 0.0770 chunk 69 optimal weight: 1.9990 chunk 125 optimal weight: 7.9990 chunk 5 optimal weight: 3.9990 chunk 98 optimal weight: 3.9990 chunk 43 optimal weight: 3.9990 chunk 128 optimal weight: 2.9990 chunk 97 optimal weight: 1.9990 chunk 44 optimal weight: 0.9990 chunk 126 optimal weight: 2.9990 overall best weight: 1.6146 ------------------------------------------------------------------------------- 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** ** A1001 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1262 ASN A1415 ASN A1550 ASN A1768 ASN ** A1817 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1907 GLN ** A1969 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.126148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.106287 restraints weight = 12290.960| |-----------------------------------------------------------------------------| r_work (start): 0.3101 rms_B_bonded: 1.41 r_work: 0.2989 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2859 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8503 moved from start: 0.4225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 10533 Z= 0.351 Angle : 0.700 13.239 14228 Z= 0.375 Chirality : 0.049 0.181 1581 Planarity : 0.005 0.059 1841 Dihedral : 5.972 31.679 1419 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.74 % Favored : 90.26 % Rotamer: Outliers : 3.83 % Allowed : 14.29 % Favored : 81.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.74 (0.21), residues: 1293 helix: -0.23 (0.25), residues: 418 sheet: -2.70 (0.36), residues: 178 loop : -2.67 (0.19), residues: 697 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A1247 HIS 0.005 0.001 HIS A1847 PHE 0.032 0.003 PHE A2119 TYR 0.027 0.002 TYR A1172 ARG 0.006 0.001 ARG A1774 *********************** 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 176 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 132 time to evaluate : 1.076 Fit side-chains REVERT: A 1073 GLU cc_start: 0.7488 (mp0) cc_final: 0.7080 (mp0) REVERT: A 1225 TYR cc_start: 0.7753 (OUTLIER) cc_final: 0.6946 (t80) REVERT: A 1266 ASP cc_start: 0.7882 (t0) cc_final: 0.7563 (t0) REVERT: A 1298 LYS cc_start: 0.7969 (tptm) cc_final: 0.7355 (mmtm) REVERT: A 1321 ASN cc_start: 0.7369 (t0) cc_final: 0.6730 (m-40) REVERT: A 1338 LYS cc_start: 0.6107 (ptmm) cc_final: 0.5319 (mmtm) REVERT: A 1406 LYS cc_start: 0.8076 (mttt) cc_final: 0.7634 (mtmm) REVERT: A 1416 LYS cc_start: 0.7562 (mttm) cc_final: 0.7029 (mttt) REVERT: A 1422 ASN cc_start: 0.8454 (m-40) cc_final: 0.8100 (m110) REVERT: A 1583 ASP cc_start: 0.8540 (p0) cc_final: 0.8283 (p0) REVERT: A 1757 TYR cc_start: 0.8852 (m-80) cc_final: 0.8213 (m-80) REVERT: A 1829 PHE cc_start: 0.9221 (OUTLIER) cc_final: 0.8860 (t80) REVERT: A 2153 GLU cc_start: 0.8703 (tm-30) cc_final: 0.8109 (tt0) outliers start: 44 outliers final: 33 residues processed: 162 average time/residue: 0.2297 time to fit residues: 53.3673 Evaluate side-chains 155 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 120 time to evaluate : 1.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 952 THR Chi-restraints excluded: chain A residue 953 ASN Chi-restraints excluded: chain A residue 990 VAL Chi-restraints excluded: chain A residue 1003 ILE Chi-restraints excluded: chain A residue 1009 THR Chi-restraints excluded: chain A residue 1109 SER Chi-restraints excluded: chain A residue 1134 VAL Chi-restraints excluded: chain A residue 1165 THR 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 1294 ASN Chi-restraints excluded: chain A residue 1403 VAL Chi-restraints excluded: chain A residue 1430 ASP Chi-restraints excluded: chain A residue 1500 LYS Chi-restraints excluded: chain A residue 1580 TYR Chi-restraints excluded: chain A residue 1588 SER Chi-restraints excluded: chain A residue 1641 LEU Chi-restraints excluded: chain A residue 1646 ASN Chi-restraints excluded: chain A residue 1659 VAL Chi-restraints excluded: chain A residue 1709 MET Chi-restraints excluded: chain A residue 1718 THR Chi-restraints excluded: chain A residue 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 1827 ASP Chi-restraints excluded: chain A residue 1829 PHE Chi-restraints excluded: chain A residue 1918 VAL Chi-restraints excluded: chain A residue 1950 GLU Chi-restraints excluded: chain A residue 1965 ASP Chi-restraints excluded: chain A residue 2142 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 96 optimal weight: 1.9990 chunk 119 optimal weight: 0.9990 chunk 44 optimal weight: 6.9990 chunk 26 optimal weight: 0.7980 chunk 106 optimal weight: 0.0980 chunk 71 optimal weight: 0.4980 chunk 56 optimal weight: 2.9990 chunk 85 optimal weight: 1.9990 chunk 46 optimal weight: 0.6980 chunk 39 optimal weight: 0.8980 chunk 123 optimal weight: 3.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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** A1001 ASN A1028 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 = 0.3396 r_free = 0.3396 target = 0.132282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.114122 restraints weight = 12332.693| |-----------------------------------------------------------------------------| r_work (start): 0.3222 rms_B_bonded: 1.29 r_work: 0.3086 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2963 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.4254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10533 Z= 0.182 Angle : 0.574 9.440 14228 Z= 0.311 Chirality : 0.044 0.198 1581 Planarity : 0.004 0.053 1841 Dihedral : 5.405 28.931 1419 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.28 % Favored : 91.72 % Rotamer: Outliers : 4.01 % Allowed : 15.42 % Favored : 80.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.53 (0.22), residues: 1293 helix: 0.07 (0.26), residues: 413 sheet: -2.49 (0.31), residues: 229 loop : -2.59 (0.21), residues: 651 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1760 HIS 0.005 0.001 HIS A1847 PHE 0.026 0.002 PHE A2119 TYR 0.015 0.001 TYR A1172 ARG 0.005 0.000 ARG A2157 *********************** 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 184 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 138 time to evaluate : 1.235 Fit side-chains REVERT: A 1050 ARG cc_start: 0.8224 (ptp-170) cc_final: 0.7745 (mtt180) REVERT: A 1100 LEU cc_start: 0.8138 (OUTLIER) cc_final: 0.7589 (tp) REVERT: A 1119 GLU cc_start: 0.8425 (mt-10) cc_final: 0.8198 (tt0) REVERT: A 1225 TYR cc_start: 0.7646 (OUTLIER) cc_final: 0.6932 (t80) REVERT: A 1243 VAL cc_start: 0.9057 (t) cc_final: 0.8774 (p) REVERT: A 1266 ASP cc_start: 0.7912 (t0) cc_final: 0.7393 (t0) REVERT: A 1298 LYS cc_start: 0.7950 (tptm) cc_final: 0.7322 (mmtm) REVERT: A 1321 ASN cc_start: 0.7374 (t0) cc_final: 0.6757 (m-40) REVERT: A 1338 LYS cc_start: 0.6027 (ptmm) cc_final: 0.5347 (mmtm) REVERT: A 1416 LYS cc_start: 0.7537 (mttm) cc_final: 0.7074 (mttt) REVERT: A 1422 ASN cc_start: 0.8375 (m-40) cc_final: 0.8038 (m110) REVERT: A 1757 TYR cc_start: 0.8713 (m-80) cc_final: 0.8041 (m-80) REVERT: A 1770 GLU cc_start: 0.8244 (tp30) cc_final: 0.7669 (mm-30) REVERT: A 1829 PHE cc_start: 0.9006 (OUTLIER) cc_final: 0.8709 (t80) REVERT: A 2033 ILE cc_start: 0.8795 (mm) cc_final: 0.8558 (mt) REVERT: A 2153 GLU cc_start: 0.8699 (tm-30) cc_final: 0.8117 (tt0) outliers start: 46 outliers final: 29 residues processed: 167 average time/residue: 0.2245 time to fit residues: 54.2387 Evaluate side-chains 162 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 130 time to evaluate : 1.239 ------------------------------------------------------------------------------- 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 1100 LEU Chi-restraints excluded: chain A residue 1109 SER Chi-restraints excluded: chain A residue 1116 ILE Chi-restraints excluded: chain A residue 1165 THR 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 1403 VAL Chi-restraints excluded: chain A residue 1430 ASP Chi-restraints excluded: chain A residue 1500 LYS 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 1827 ASP Chi-restraints excluded: chain A residue 1829 PHE Chi-restraints excluded: chain A residue 1862 TYR Chi-restraints excluded: chain A residue 1894 VAL Chi-restraints excluded: chain A residue 1918 VAL Chi-restraints excluded: chain A residue 1965 ASP Chi-restraints excluded: chain A residue 2142 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 59 optimal weight: 0.0870 chunk 101 optimal weight: 3.9990 chunk 74 optimal weight: 1.9990 chunk 73 optimal weight: 0.7980 chunk 15 optimal weight: 0.7980 chunk 102 optimal weight: 0.9980 chunk 122 optimal weight: 2.9990 chunk 83 optimal weight: 1.9990 chunk 72 optimal weight: 2.9990 chunk 27 optimal weight: 4.9990 chunk 55 optimal weight: 0.8980 overall best weight: 0.7158 ------------------------------------------------------------------------------- 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** A1415 ASN A1422 ASN A1605 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 = 0.3397 r_free = 0.3397 target = 0.132202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.113843 restraints weight = 12398.540| |-----------------------------------------------------------------------------| r_work (start): 0.3194 rms_B_bonded: 1.28 r_work: 0.3062 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2937 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.4366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10533 Z= 0.197 Angle : 0.584 10.635 14228 Z= 0.314 Chirality : 0.045 0.188 1581 Planarity : 0.004 0.052 1841 Dihedral : 5.344 27.148 1419 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.89 % Favored : 91.11 % Rotamer: Outliers : 4.01 % Allowed : 16.11 % Favored : 79.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.46 (0.22), residues: 1293 helix: 0.13 (0.26), residues: 413 sheet: -2.44 (0.31), residues: 229 loop : -2.56 (0.21), residues: 651 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1760 HIS 0.005 0.001 HIS A1847 PHE 0.026 0.002 PHE A2119 TYR 0.017 0.001 TYR A1172 ARG 0.004 0.000 ARG A2157 *********************** 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 181 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 135 time to evaluate : 0.988 Fit side-chains REVERT: A 1050 ARG cc_start: 0.8244 (ptp-170) cc_final: 0.7781 (mtt180) REVERT: A 1225 TYR cc_start: 0.7615 (OUTLIER) cc_final: 0.6894 (t80) REVERT: A 1266 ASP cc_start: 0.7864 (t0) cc_final: 0.7357 (t0) REVERT: A 1298 LYS cc_start: 0.7918 (tptm) cc_final: 0.7282 (mmtm) REVERT: A 1321 ASN cc_start: 0.7411 (t0) cc_final: 0.6791 (m-40) REVERT: A 1338 LYS cc_start: 0.6048 (ptmm) cc_final: 0.5313 (mmtm) REVERT: A 1406 LYS cc_start: 0.7879 (mttt) cc_final: 0.7413 (mtmm) REVERT: A 1416 LYS cc_start: 0.7493 (mttm) cc_final: 0.7045 (mttt) REVERT: A 1422 ASN cc_start: 0.8228 (m110) cc_final: 0.7858 (m110) REVERT: A 1583 ASP cc_start: 0.8588 (p0) cc_final: 0.8268 (p0) REVERT: A 1757 TYR cc_start: 0.8726 (m-80) cc_final: 0.8016 (m-80) REVERT: A 1770 GLU cc_start: 0.8321 (tp30) cc_final: 0.8079 (mm-30) REVERT: A 1780 ASP cc_start: 0.8551 (OUTLIER) cc_final: 0.8116 (m-30) REVERT: A 1783 ARG cc_start: 0.8943 (mtt-85) cc_final: 0.8623 (mtt180) REVERT: A 1829 PHE cc_start: 0.9022 (OUTLIER) cc_final: 0.8702 (t80) REVERT: A 2153 GLU cc_start: 0.8655 (tm-30) cc_final: 0.8090 (tt0) outliers start: 46 outliers final: 35 residues processed: 164 average time/residue: 0.2229 time to fit residues: 53.0879 Evaluate side-chains 164 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 126 time to evaluate : 1.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 952 THR Chi-restraints excluded: chain A residue 953 ASN Chi-restraints excluded: chain A residue 990 VAL Chi-restraints excluded: chain A residue 1003 ILE Chi-restraints excluded: chain A residue 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 1165 THR 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 1294 ASN Chi-restraints excluded: chain A residue 1403 VAL Chi-restraints excluded: chain A residue 1430 ASP Chi-restraints excluded: chain A residue 1500 LYS Chi-restraints excluded: chain A residue 1580 TYR Chi-restraints excluded: chain A residue 1588 SER Chi-restraints excluded: chain A residue 1641 LEU Chi-restraints excluded: chain A residue 1646 ASN Chi-restraints excluded: chain A residue 1659 VAL Chi-restraints excluded: chain A residue 1709 MET Chi-restraints excluded: chain A residue 1718 THR Chi-restraints excluded: chain A residue 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 1827 ASP Chi-restraints excluded: chain A residue 1829 PHE Chi-restraints excluded: chain A residue 1862 TYR Chi-restraints excluded: chain A residue 1894 VAL Chi-restraints excluded: chain A residue 1918 VAL Chi-restraints excluded: chain A residue 1965 ASP Chi-restraints excluded: chain A residue 2142 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 116 optimal weight: 3.9990 chunk 84 optimal weight: 3.9990 chunk 128 optimal weight: 0.8980 chunk 35 optimal weight: 3.9990 chunk 118 optimal weight: 2.9990 chunk 81 optimal weight: 2.9990 chunk 97 optimal weight: 0.0980 chunk 79 optimal weight: 0.3980 chunk 16 optimal weight: 3.9990 chunk 14 optimal weight: 0.6980 chunk 29 optimal weight: 4.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- 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** ** 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 = 0.130024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.110929 restraints weight = 12273.362| |-----------------------------------------------------------------------------| r_work (start): 0.3130 rms_B_bonded: 1.41 r_work: 0.3002 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2876 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.2876 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 moved from start: 0.4506 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= 0.247 Angle : 0.617 11.177 14228 Z= 0.330 Chirality : 0.046 0.190 1581 Planarity : 0.004 0.056 1841 Dihedral : 5.494 26.883 1419 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.82 % Favored : 91.18 % Rotamer: Outliers : 4.18 % Allowed : 16.29 % Favored : 79.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.50 (0.21), residues: 1293 helix: 0.10 (0.26), residues: 412 sheet: -2.59 (0.36), residues: 182 loop : -2.58 (0.20), residues: 699 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1247 HIS 0.005 0.001 HIS A1847 PHE 0.027 0.002 PHE A2119 TYR 0.019 0.001 TYR A1172 ARG 0.004 0.000 ARG A1774 *********************** 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 177 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 129 time to evaluate : 1.184 Fit side-chains REVERT: A 939 ASN cc_start: 0.7487 (t0) cc_final: 0.7076 (t0) REVERT: A 1050 ARG cc_start: 0.8224 (ptp-170) cc_final: 0.7771 (mtt180) REVERT: A 1225 TYR cc_start: 0.7697 (OUTLIER) cc_final: 0.6882 (t80) REVERT: A 1266 ASP cc_start: 0.7904 (t0) cc_final: 0.7318 (t0) REVERT: A 1298 LYS cc_start: 0.7880 (tptm) cc_final: 0.7254 (mmtm) REVERT: A 1338 LYS cc_start: 0.6101 (ptmm) cc_final: 0.5350 (mmtm) REVERT: A 1406 LYS cc_start: 0.7836 (mttt) cc_final: 0.7362 (mtmm) REVERT: A 1416 LYS cc_start: 0.7524 (mttm) cc_final: 0.7034 (mttt) REVERT: A 1422 ASN cc_start: 0.8320 (m110) cc_final: 0.7949 (m110) REVERT: A 1583 ASP cc_start: 0.8601 (p0) cc_final: 0.8307 (p0) REVERT: A 1757 TYR cc_start: 0.8750 (m-80) cc_final: 0.8098 (m-80) REVERT: A 1780 ASP cc_start: 0.8727 (OUTLIER) cc_final: 0.8325 (m-30) REVERT: A 1829 PHE cc_start: 0.9120 (OUTLIER) cc_final: 0.8808 (t80) REVERT: A 2084 ILE cc_start: 0.8889 (OUTLIER) cc_final: 0.8625 (pp) REVERT: A 2153 GLU cc_start: 0.8668 (tm-30) cc_final: 0.8120 (tt0) outliers start: 48 outliers final: 37 residues processed: 156 average time/residue: 0.2412 time to fit residues: 53.3321 Evaluate side-chains 167 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 126 time to evaluate : 1.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 952 THR Chi-restraints excluded: chain A residue 953 ASN Chi-restraints excluded: chain A residue 990 VAL Chi-restraints excluded: chain A residue 1003 ILE Chi-restraints excluded: chain A residue 1009 THR Chi-restraints excluded: chain A residue 1022 VAL Chi-restraints excluded: chain A residue 1075 LYS Chi-restraints excluded: chain A residue 1109 SER Chi-restraints excluded: chain A residue 1116 ILE Chi-restraints excluded: chain A residue 1165 THR 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 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 1827 ASP Chi-restraints excluded: chain A residue 1829 PHE Chi-restraints excluded: chain A residue 1862 TYR Chi-restraints excluded: chain A residue 1894 VAL Chi-restraints excluded: chain A residue 1918 VAL Chi-restraints excluded: chain A residue 1920 ASP Chi-restraints excluded: chain A residue 1965 ASP Chi-restraints excluded: chain A residue 2058 MET Chi-restraints excluded: chain A residue 2084 ILE Chi-restraints excluded: chain A residue 2142 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 42 optimal weight: 6.9990 chunk 128 optimal weight: 0.5980 chunk 80 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 12 optimal weight: 3.9990 chunk 96 optimal weight: 2.9990 chunk 125 optimal weight: 4.9990 chunk 90 optimal weight: 0.0980 chunk 68 optimal weight: 3.9990 chunk 21 optimal weight: 3.9990 chunk 18 optimal weight: 0.6980 overall best weight: 1.2784 ------------------------------------------------------------------------------- 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** A1415 ASN ** A1817 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1969 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.127959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.108787 restraints weight = 12497.682| |-----------------------------------------------------------------------------| r_work (start): 0.3126 rms_B_bonded: 1.43 r_work: 0.2989 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2857 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.2857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.4685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 10533 Z= 0.291 Angle : 0.654 11.873 14228 Z= 0.349 Chirality : 0.047 0.196 1581 Planarity : 0.004 0.060 1841 Dihedral : 5.733 26.936 1419 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.59 % Favored : 90.41 % Rotamer: Outliers : 3.75 % Allowed : 17.16 % Favored : 79.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.51 (0.21), residues: 1293 helix: 0.00 (0.25), residues: 412 sheet: -2.44 (0.37), residues: 174 loop : -2.58 (0.20), residues: 707 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A1247 HIS 0.005 0.001 HIS A1847 PHE 0.029 0.002 PHE A2119 TYR 0.021 0.002 TYR A1172 ARG 0.005 0.000 ARG A1774 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2586 Ramachandran restraints generated. 1293 Oldfield, 0 Emsley, 1293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2586 Ramachandran restraints generated. 1293 Oldfield, 0 Emsley, 1293 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 126 time to evaluate : 1.228 Fit side-chains REVERT: A 939 ASN cc_start: 0.7583 (t0) cc_final: 0.7095 (t0) REVERT: A 1225 TYR cc_start: 0.7849 (OUTLIER) cc_final: 0.6960 (t80) REVERT: A 1266 ASP cc_start: 0.7892 (t0) cc_final: 0.7578 (t0) REVERT: A 1298 LYS cc_start: 0.7888 (tptm) cc_final: 0.7285 (mmtm) REVERT: A 1338 LYS cc_start: 0.6111 (ptmm) cc_final: 0.5384 (mmtm) REVERT: A 1406 LYS cc_start: 0.7976 (mttt) cc_final: 0.7486 (mtmm) REVERT: A 1416 LYS cc_start: 0.7624 (mttm) cc_final: 0.7158 (mttt) REVERT: A 1422 ASN cc_start: 0.8357 (m110) cc_final: 0.7984 (m110) REVERT: A 1757 TYR cc_start: 0.8804 (m-80) cc_final: 0.8186 (m-80) REVERT: A 1829 PHE cc_start: 0.9195 (OUTLIER) cc_final: 0.8866 (t80) REVERT: A 1965 ASP cc_start: 0.7921 (OUTLIER) cc_final: 0.7262 (t0) REVERT: A 2071 LYS cc_start: 0.8295 (mtmt) cc_final: 0.8034 (tttm) REVERT: A 2084 ILE cc_start: 0.8877 (OUTLIER) cc_final: 0.8643 (pp) REVERT: A 2153 GLU cc_start: 0.8704 (tm-30) cc_final: 0.8157 (tt0) outliers start: 43 outliers final: 34 residues processed: 154 average time/residue: 0.2355 time to fit residues: 52.6479 Evaluate side-chains 161 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 123 time to evaluate : 1.266 ------------------------------------------------------------------------------- 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 1165 THR 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 1827 ASP Chi-restraints excluded: chain A residue 1829 PHE Chi-restraints excluded: chain A residue 1862 TYR Chi-restraints excluded: chain A residue 1894 VAL Chi-restraints excluded: chain A residue 1918 VAL Chi-restraints excluded: chain A residue 1920 ASP Chi-restraints excluded: chain A residue 1965 ASP Chi-restraints excluded: chain A residue 2058 MET Chi-restraints excluded: chain A residue 2084 ILE Chi-restraints excluded: chain A residue 2142 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 5 optimal weight: 2.9990 chunk 4 optimal weight: 0.8980 chunk 34 optimal weight: 0.6980 chunk 51 optimal weight: 0.8980 chunk 95 optimal weight: 2.9990 chunk 90 optimal weight: 1.9990 chunk 122 optimal weight: 4.9990 chunk 93 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 109 optimal weight: 0.1980 chunk 107 optimal weight: 2.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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** ** 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 = 0.3365 r_free = 0.3365 target = 0.129678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.111796 restraints weight = 12316.297| |-----------------------------------------------------------------------------| r_work (start): 0.3188 rms_B_bonded: 1.22 r_work: 0.3053 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2928 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 moved from start: 0.4719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 10533 Z= 0.235 Angle : 0.617 10.771 14228 Z= 0.329 Chirality : 0.045 0.207 1581 Planarity : 0.004 0.060 1841 Dihedral : 5.585 26.239 1419 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.20 % Favored : 90.80 % Rotamer: Outliers : 3.48 % Allowed : 17.42 % Favored : 79.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.48 (0.21), residues: 1293 helix: 0.05 (0.25), residues: 412 sheet: -2.45 (0.36), residues: 179 loop : -2.57 (0.20), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1247 HIS 0.005 0.001 HIS A1847 PHE 0.027 0.002 PHE A2119 TYR 0.018 0.001 TYR A1172 ARG 0.004 0.000 ARG A1774 ********************** 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 163 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 123 time to evaluate : 1.216 Fit side-chains REVERT: A 939 ASN cc_start: 0.7609 (t0) cc_final: 0.7180 (t0) REVERT: A 1050 ARG cc_start: 0.8235 (ptp-170) cc_final: 0.7817 (mtt180) REVERT: A 1225 TYR cc_start: 0.7748 (OUTLIER) cc_final: 0.6881 (t80) REVERT: A 1243 VAL cc_start: 0.9118 (t) cc_final: 0.8870 (p) REVERT: A 1266 ASP cc_start: 0.7889 (t0) cc_final: 0.7372 (t0) REVERT: A 1298 LYS cc_start: 0.7836 (tptm) cc_final: 0.7275 (mmtm) REVERT: A 1338 LYS cc_start: 0.6007 (ptmm) cc_final: 0.5351 (mmtm) REVERT: A 1406 LYS cc_start: 0.7966 (mttt) cc_final: 0.7499 (mtmm) REVERT: A 1416 LYS cc_start: 0.7632 (mttm) cc_final: 0.7204 (mttt) REVERT: A 1422 ASN cc_start: 0.8323 (m110) cc_final: 0.7964 (m110) REVERT: A 1583 ASP cc_start: 0.8649 (p0) cc_final: 0.8354 (p0) REVERT: A 1757 TYR cc_start: 0.8752 (m-80) cc_final: 0.8097 (m-80) REVERT: A 1780 ASP cc_start: 0.8701 (OUTLIER) cc_final: 0.8328 (m-30) REVERT: A 1783 ARG cc_start: 0.8944 (mtt-85) cc_final: 0.8620 (mtt180) REVERT: A 1829 PHE cc_start: 0.9116 (OUTLIER) cc_final: 0.8759 (t80) REVERT: A 2153 GLU cc_start: 0.8677 (tm-30) cc_final: 0.8136 (tt0) outliers start: 40 outliers final: 35 residues processed: 148 average time/residue: 0.2419 time to fit residues: 51.0941 Evaluate side-chains 159 residues out of total 1148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 121 time to evaluate : 1.164 ------------------------------------------------------------------------------- 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 1165 THR 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 1253 GLU Chi-restraints excluded: chain A residue 1255 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 1827 ASP Chi-restraints excluded: chain A residue 1829 PHE Chi-restraints excluded: chain A residue 1862 TYR Chi-restraints excluded: chain A residue 1894 VAL Chi-restraints excluded: chain A residue 1918 VAL Chi-restraints excluded: chain A residue 1920 ASP Chi-restraints excluded: chain A residue 1965 ASP Chi-restraints excluded: chain A residue 2058 MET Chi-restraints excluded: chain A residue 2142 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 66 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 106 optimal weight: 0.9980 chunk 14 optimal weight: 2.9990 chunk 28 optimal weight: 0.8980 chunk 6 optimal weight: 0.8980 chunk 115 optimal weight: 0.9980 chunk 85 optimal weight: 0.9980 chunk 88 optimal weight: 5.9990 chunk 69 optimal weight: 0.5980 chunk 72 optimal weight: 2.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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** A1415 ASN ** A1817 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1969 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.130450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.111372 restraints weight = 12273.366| |-----------------------------------------------------------------------------| r_work (start): 0.3171 rms_B_bonded: 1.43 r_work: 0.3036 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2905 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.2905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 moved from start: 0.4753 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= 0.224 Angle : 0.610 10.854 14228 Z= 0.326 Chirality : 0.045 0.199 1581 Planarity : 0.004 0.060 1841 Dihedral : 5.513 25.948 1419 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.67 % Favored : 90.33 % Rotamer: Outliers : 3.66 % Allowed : 17.42 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.42 (0.22), residues: 1293 helix: 0.09 (0.26), residues: 412 sheet: -2.38 (0.37), residues: 174 loop : -2.54 (0.20), residues: 707 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1247 HIS 0.005 0.001 HIS A1847 PHE 0.026 0.002 PHE A2119 TYR 0.017 0.001 TYR A1172 ARG 0.004 0.000 ARG A1774 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5352.10 seconds wall clock time: 95 minutes 59.78 seconds (5759.78 seconds total)