Starting phenix.real_space_refine on Tue Aug 26 04:30:42 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8p1l_17353/08_2025/8p1l_17353.cif Found real_map, /net/cci-nas-00/data/ceres_data/8p1l_17353/08_2025/8p1l_17353.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8p1l_17353/08_2025/8p1l_17353.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8p1l_17353/08_2025/8p1l_17353.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8p1l_17353/08_2025/8p1l_17353.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8p1l_17353/08_2025/8p1l_17353.map" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.026 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: 5 Type Number sf(0) Gaussians S 87 5.16 5 C 10567 2.51 5 N 2770 2.21 5 O 3000 1.98 5 H 16512 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 26 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 32936 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 32936 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2036, 32936 Classifications: {'peptide': 2036} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 71, 'TRANS': 1964} Chain breaks: 4 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Time building chain proxies: 5.25, per 1000 atoms: 0.16 Number of scatterers: 32936 At special positions: 0 Unit cell: (120.228, 159.372, 128.616, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 87 16.00 O 3000 8.00 N 2770 7.00 C 10567 6.00 H 16512 1.00 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: 2.75 Conformation dependent library (CDL) restraints added in 707.9 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 4052 Ramachandran restraints generated. 2026 Oldfield, 0 Emsley, 2026 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3886 Finding SS restraints... Secondary structure from input PDB file: 94 helices and 19 sheets defined 56.5% alpha, 7.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.93 Creating SS restraints... Processing helix chain 'A' and resid 1 through 14 removed outlier: 3.758A pdb=" N GLU A 13 " --> pdb=" O ASN A 9 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N PHE A 14 " --> pdb=" O LYS A 10 " (cutoff:3.500A) Processing helix chain 'A' and resid 20 through 47 removed outlier: 3.616A pdb=" N VAL A 39 " --> pdb=" O ARG A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 56 through 65 Processing helix chain 'A' and resid 67 through 76 removed outlier: 3.956A pdb=" N ILE A 71 " --> pdb=" O PRO A 67 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N LYS A 76 " --> pdb=" O THR A 72 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 94 removed outlier: 3.730A pdb=" N LYS A 93 " --> pdb=" O LYS A 89 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N MET A 94 " --> pdb=" O ALA A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 145 removed outlier: 3.802A pdb=" N GLY A 120 " --> pdb=" O ASP A 116 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N ALA A 130 " --> pdb=" O LEU A 126 " (cutoff:3.500A) removed outlier: 4.942A pdb=" N GLY A 131 " --> pdb=" O LYS A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 172 Processing helix chain 'A' and resid 176 through 198 removed outlier: 3.593A pdb=" N VAL A 180 " --> pdb=" O ARG A 176 " (cutoff:3.500A) Processing helix chain 'A' and resid 200 through 202 No H-bonds generated for 'chain 'A' and resid 200 through 202' Processing helix chain 'A' and resid 203 through 215 removed outlier: 3.749A pdb=" N LEU A 213 " --> pdb=" O ALA A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 239 through 251 removed outlier: 3.880A pdb=" N LEU A 243 " --> pdb=" O ASN A 239 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 282 removed outlier: 3.570A pdb=" N PHE A 271 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ALA A 276 " --> pdb=" O ASN A 272 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N GLN A 280 " --> pdb=" O ALA A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 323 removed outlier: 3.546A pdb=" N GLN A 311 " --> pdb=" O THR A 307 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N ASN A 323 " --> pdb=" O SER A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 343 Processing helix chain 'A' and resid 345 through 353 removed outlier: 3.765A pdb=" N TYR A 353 " --> pdb=" O MET A 349 " (cutoff:3.500A) Processing helix chain 'A' and resid 374 through 378 Processing helix chain 'A' and resid 379 through 391 Processing helix chain 'A' and resid 409 through 427 removed outlier: 3.635A pdb=" N GLN A 413 " --> pdb=" O SER A 409 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 458 removed outlier: 3.952A pdb=" N PHE A 454 " --> pdb=" O VAL A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 458 through 463 removed outlier: 3.695A pdb=" N TYR A 462 " --> pdb=" O GLU A 458 " (cutoff:3.500A) Processing helix chain 'A' and resid 463 through 468 Processing helix chain 'A' and resid 470 through 490 removed outlier: 3.550A pdb=" N LEU A 486 " --> pdb=" O ILE A 482 " (cutoff:3.500A) Processing helix chain 'A' and resid 504 through 507 Processing helix chain 'A' and resid 563 through 572 removed outlier: 3.546A pdb=" N ALA A 569 " --> pdb=" O ASN A 565 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N LEU A 570 " --> pdb=" O ARG A 566 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 593 Processing helix chain 'A' and resid 597 through 613 Processing helix chain 'A' and resid 617 through 630 removed outlier: 3.556A pdb=" N ARG A 627 " --> pdb=" O PHE A 623 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N TYR A 628 " --> pdb=" O ASP A 624 " (cutoff:3.500A) Processing helix chain 'A' and resid 631 through 633 No H-bonds generated for 'chain 'A' and resid 631 through 633' Processing helix chain 'A' and resid 640 through 648 removed outlier: 3.547A pdb=" N PHE A 648 " --> pdb=" O ILE A 644 " (cutoff:3.500A) Processing helix chain 'A' and resid 654 through 674 removed outlier: 3.533A pdb=" N ASN A 674 " --> pdb=" O ALA A 670 " (cutoff:3.500A) Processing helix chain 'A' and resid 712 through 726 removed outlier: 4.119A pdb=" N LEU A 716 " --> pdb=" O HIS A 712 " (cutoff:3.500A) Processing helix chain 'A' and resid 734 through 759 Processing helix chain 'A' and resid 760 through 767 Processing helix chain 'A' and resid 769 through 777 removed outlier: 3.746A pdb=" N ALA A 775 " --> pdb=" O TRP A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 786 through 802 removed outlier: 3.813A pdb=" N VAL A 800 " --> pdb=" O GLU A 796 " (cutoff:3.500A) Processing helix chain 'A' and resid 804 through 814 Processing helix chain 'A' and resid 847 through 857 Processing helix chain 'A' and resid 864 through 872 Processing helix chain 'A' and resid 898 through 917 Processing helix chain 'A' and resid 932 through 947 Processing helix chain 'A' and resid 983 through 992 removed outlier: 3.776A pdb=" N ARG A 987 " --> pdb=" O ALA A 983 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N SER A 990 " --> pdb=" O ARG A 986 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N MET A 991 " --> pdb=" O ARG A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 999 through 1012 Processing helix chain 'A' and resid 1020 through 1029 Processing helix chain 'A' and resid 1034 through 1044 removed outlier: 3.563A pdb=" N GLN A1039 " --> pdb=" O PRO A1035 " (cutoff:3.500A) removed outlier: 4.870A pdb=" N PHE A1040 " --> pdb=" O HIS A1036 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N PHE A1044 " --> pdb=" O PHE A1040 " (cutoff:3.500A) Processing helix chain 'A' and resid 1061 through 1084 removed outlier: 3.601A pdb=" N SER A1065 " --> pdb=" O LEU A1061 " (cutoff:3.500A) Processing helix chain 'A' and resid 1114 through 1127 removed outlier: 3.662A pdb=" N SER A1121 " --> pdb=" O PHE A1117 " (cutoff:3.500A) Processing helix chain 'A' and resid 1128 through 1132 removed outlier: 3.681A pdb=" N PHE A1132 " --> pdb=" O LEU A1129 " (cutoff:3.500A) Processing helix chain 'A' and resid 1137 through 1153 removed outlier: 3.752A pdb=" N SER A1141 " --> pdb=" O GLU A1137 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU A1145 " --> pdb=" O SER A1141 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLY A1153 " --> pdb=" O ILE A1149 " (cutoff:3.500A) Processing helix chain 'A' and resid 1168 through 1179 removed outlier: 3.537A pdb=" N LEU A1172 " --> pdb=" O ASN A1168 " (cutoff:3.500A) Processing helix chain 'A' and resid 1184 through 1194 removed outlier: 4.040A pdb=" N ILE A1188 " --> pdb=" O PRO A1184 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N LEU A1193 " --> pdb=" O LEU A1189 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N SER A1194 " --> pdb=" O LEU A1190 " (cutoff:3.500A) Processing helix chain 'A' and resid 1201 through 1218 removed outlier: 3.770A pdb=" N LEU A1216 " --> pdb=" O CYS A1212 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU A1218 " --> pdb=" O LYS A1214 " (cutoff:3.500A) Processing helix chain 'A' and resid 1221 through 1240 removed outlier: 3.900A pdb=" N TYR A1240 " --> pdb=" O VAL A1236 " (cutoff:3.500A) Processing helix chain 'A' and resid 1249 through 1254 removed outlier: 4.064A pdb=" N TYR A1253 " --> pdb=" O HIS A1249 " (cutoff:3.500A) Processing helix chain 'A' and resid 1262 through 1266 Processing helix chain 'A' and resid 1273 through 1278 Processing helix chain 'A' and resid 1282 through 1299 removed outlier: 3.802A pdb=" N LYS A1286 " --> pdb=" O GLY A1282 " (cutoff:3.500A) Processing helix chain 'A' and resid 1301 through 1319 Processing helix chain 'A' and resid 1354 through 1365 Processing helix chain 'A' and resid 1366 through 1370 Processing helix chain 'A' and resid 1375 through 1388 removed outlier: 4.423A pdb=" N ILE A1381 " --> pdb=" O ASP A1377 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N TYR A1382 " --> pdb=" O ASN A1378 " (cutoff:3.500A) Processing helix chain 'A' and resid 1389 through 1397 removed outlier: 3.538A pdb=" N ALA A1395 " --> pdb=" O SER A1391 " (cutoff:3.500A) Processing helix chain 'A' and resid 1400 through 1409 Processing helix chain 'A' and resid 1425 through 1440 Processing helix chain 'A' and resid 1443 through 1456 Processing helix chain 'A' and resid 1458 through 1469 removed outlier: 3.588A pdb=" N TYR A1462 " --> pdb=" O PHE A1458 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N TRP A1464 " --> pdb=" O LYS A1460 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LYS A1465 " --> pdb=" O GLU A1461 " (cutoff:3.500A) Processing helix chain 'A' and resid 1501 through 1511 removed outlier: 4.171A pdb=" N ALA A1505 " --> pdb=" O ASN A1501 " (cutoff:3.500A) Processing helix chain 'A' and resid 1514 through 1525 Processing helix chain 'A' and resid 1527 through 1529 No H-bonds generated for 'chain 'A' and resid 1527 through 1529' Processing helix chain 'A' and resid 1530 through 1545 Processing helix chain 'A' and resid 1552 through 1564 Proline residue: A1561 - end of helix Processing helix chain 'A' and resid 1581 through 1592 Processing helix chain 'A' and resid 1602 through 1606 Processing helix chain 'A' and resid 1621 through 1643 Processing helix chain 'A' and resid 1645 through 1652 removed outlier: 3.546A pdb=" N GLN A1651 " --> pdb=" O ARG A1647 " (cutoff:3.500A) Processing helix chain 'A' and resid 1660 through 1671 Processing helix chain 'A' and resid 1678 through 1688 removed outlier: 3.997A pdb=" N LEU A1684 " --> pdb=" O GLN A1680 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ASP A1688 " --> pdb=" O LEU A1684 " (cutoff:3.500A) Processing helix chain 'A' and resid 1693 through 1702 removed outlier: 3.664A pdb=" N ARG A1702 " --> pdb=" O LEU A1698 " (cutoff:3.500A) Processing helix chain 'A' and resid 1759 through 1778 removed outlier: 3.653A pdb=" N CYS A1777 " --> pdb=" O GLU A1773 " (cutoff:3.500A) Processing helix chain 'A' and resid 1820 through 1823 Processing helix chain 'A' and resid 1867 through 1871 removed outlier: 3.999A pdb=" N ALA A1870 " --> pdb=" O ARG A1867 " (cutoff:3.500A) Processing helix chain 'A' and resid 1888 through 1895 removed outlier: 3.882A pdb=" N SER A1893 " --> pdb=" O ASN A1889 " (cutoff:3.500A) Processing helix chain 'A' and resid 1896 through 1903 Processing helix chain 'A' and resid 1909 through 1917 Processing helix chain 'A' and resid 1924 through 1937 removed outlier: 4.100A pdb=" N MET A1928 " --> pdb=" O VAL A1924 " (cutoff:3.500A) Processing helix chain 'A' and resid 2036 through 2042 Processing helix chain 'A' and resid 2045 through 2050 removed outlier: 3.901A pdb=" N ILE A2049 " --> pdb=" O GLY A2046 " (cutoff:3.500A) Processing helix chain 'A' and resid 2054 through 2069 Processing helix chain 'A' and resid 2075 through 2079 removed outlier: 3.509A pdb=" N LEU A2079 " --> pdb=" O VAL A2076 " (cutoff:3.500A) Processing helix chain 'A' and resid 2080 through 2091 Processing helix chain 'A' and resid 2095 through 2100 removed outlier: 4.564A pdb=" N ASP A2100 " --> pdb=" O GLU A2096 " (cutoff:3.500A) Processing helix chain 'A' and resid 2101 through 2116 removed outlier: 4.972A pdb=" N ARG A2107 " --> pdb=" O GLU A2103 " (cutoff:3.500A) Processing helix chain 'A' and resid 2119 through 2123 removed outlier: 3.752A pdb=" N VAL A2123 " --> pdb=" O PRO A2120 " (cutoff:3.500A) Processing helix chain 'A' and resid 2130 through 2142 Processing helix chain 'A' and resid 2145 through 2151 removed outlier: 3.512A pdb=" N PHE A2150 " --> pdb=" O SER A2146 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N TYR A2151 " --> pdb=" O ILE A2147 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 98 through 102 Processing sheet with id=AA2, first strand: chain 'A' and resid 260 through 261 Processing sheet with id=AA3, first strand: chain 'A' and resid 260 through 261 Processing sheet with id=AA4, first strand: chain 'A' and resid 284 through 285 Processing sheet with id=AA5, first strand: chain 'A' and resid 499 through 502 removed outlier: 3.809A pdb=" N SER A 499 " --> pdb=" O ILE A 512 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 499 through 502 removed outlier: 3.809A pdb=" N SER A 499 " --> pdb=" O ILE A 512 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 701 through 702 Processing sheet with id=AA8, first strand: chain 'A' and resid 895 through 897 removed outlier: 4.142A pdb=" N ALA A 877 " --> pdb=" O LYS A1014 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N ILE A 881 " --> pdb=" O PHE A1018 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 1095 through 1096 Processing sheet with id=AB1, first strand: chain 'A' and resid 1417 through 1419 Processing sheet with id=AB2, first strand: chain 'A' and resid 1475 through 1476 removed outlier: 3.949A pdb=" N THR A1598 " --> pdb=" O ILE A1476 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 1486 through 1489 Processing sheet with id=AB4, first strand: chain 'A' and resid 1658 through 1659 removed outlier: 3.950A pdb=" N LYS A1658 " --> pdb=" O PHE A1655 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 1717 through 1719 Processing sheet with id=AB6, first strand: chain 'A' and resid 1740 through 1741 Processing sheet with id=AB7, first strand: chain 'A' and resid 1744 through 1745 Processing sheet with id=AB8, first strand: chain 'A' and resid 1784 through 1786 removed outlier: 4.147A pdb=" N VAL A1786 " --> pdb=" O CYS A1810 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N CYS A1810 " --> pdb=" O VAL A1786 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 1796 through 1797 Processing sheet with id=AC1, first strand: chain 'A' and resid 1833 through 1837 removed outlier: 6.146A pdb=" N ALA A1845 " --> pdb=" O LEU A1855 " (cutoff:3.500A) removed outlier: 5.241A pdb=" N LEU A1855 " --> pdb=" O ALA A1845 " (cutoff:3.500A) 827 hydrogen bonds defined for protein. 2352 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: 7.53 Time building geometry restraints manager: 3.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 16481 1.03 - 1.23: 34 1.23 - 1.42: 7059 1.42 - 1.61: 9588 1.61 - 1.81: 143 Bond restraints: 33305 Sorted by residual: bond pdb=" C ASP A1676 " pdb=" N PRO A1677 " ideal model delta sigma weight residual 1.332 1.360 -0.028 8.20e-03 1.49e+04 1.13e+01 bond pdb=" CA PHE A1655 " pdb=" CB PHE A1655 " ideal model delta sigma weight residual 1.528 1.548 -0.019 1.13e-02 7.83e+03 2.95e+00 bond pdb=" N MET A 1 " pdb=" CA MET A 1 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.81e+00 bond pdb=" N MET A 1 " pdb=" H MET A 1 " ideal model delta sigma weight residual 0.860 0.890 -0.030 2.00e-02 2.50e+03 2.28e+00 bond pdb=" CD GLU A1656 " pdb=" OE1 GLU A1656 " ideal model delta sigma weight residual 1.249 1.224 0.025 1.90e-02 2.77e+03 1.74e+00 ... (remaining 33300 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.07: 60206 7.07 - 14.14: 3 14.14 - 21.21: 0 21.21 - 28.28: 2 28.28 - 35.35: 12 Bond angle restraints: 60223 Sorted by residual: angle pdb=" C LYS A 493 " pdb=" CA LYS A 493 " pdb=" HA LYS A 493 " ideal model delta sigma weight residual 109.00 73.65 35.35 3.00e+00 1.11e-01 1.39e+02 angle pdb=" C GLN A1323 " pdb=" CA GLN A1323 " pdb=" HA GLN A1323 " ideal model delta sigma weight residual 109.00 73.84 35.16 3.00e+00 1.11e-01 1.37e+02 angle pdb=" C VAL A1475 " pdb=" CA VAL A1475 " pdb=" HA VAL A1475 " ideal model delta sigma weight residual 109.00 73.97 35.03 3.00e+00 1.11e-01 1.36e+02 angle pdb=" N VAL A1475 " pdb=" CA VAL A1475 " pdb=" HA VAL A1475 " ideal model delta sigma weight residual 110.00 75.19 34.81 3.00e+00 1.11e-01 1.35e+02 angle pdb=" N LYS A 493 " pdb=" CA LYS A 493 " pdb=" HA LYS A 493 " ideal model delta sigma weight residual 110.00 75.39 34.61 3.00e+00 1.11e-01 1.33e+02 ... (remaining 60218 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.01: 14141 17.01 - 34.02: 1132 34.02 - 51.02: 292 51.02 - 68.03: 53 68.03 - 85.04: 14 Dihedral angle restraints: 15632 sinusoidal: 8424 harmonic: 7208 Sorted by residual: dihedral pdb=" CA ARG A 774 " pdb=" C ARG A 774 " pdb=" N ALA A 775 " pdb=" CA ALA A 775 " ideal model delta harmonic sigma weight residual 180.00 159.61 20.39 0 5.00e+00 4.00e-02 1.66e+01 dihedral pdb=" CA PRO A2125 " pdb=" C PRO A2125 " pdb=" N ASP A2126 " pdb=" CA ASP A2126 " ideal model delta harmonic sigma weight residual 180.00 159.95 20.05 0 5.00e+00 4.00e-02 1.61e+01 dihedral pdb=" C VAL A1475 " pdb=" N VAL A1475 " pdb=" CA VAL A1475 " pdb=" CB VAL A1475 " ideal model delta harmonic sigma weight residual -122.00 -131.74 9.74 0 2.50e+00 1.60e-01 1.52e+01 ... (remaining 15629 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.076: 2347 0.076 - 0.152: 178 0.152 - 0.227: 1 0.227 - 0.303: 0 0.303 - 0.379: 3 Chirality restraints: 2529 Sorted by residual: chirality pdb=" CA LYS A 493 " pdb=" N LYS A 493 " pdb=" C LYS A 493 " pdb=" CB LYS A 493 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.59e+00 chirality pdb=" CA GLN A1323 " pdb=" N GLN A1323 " pdb=" C GLN A1323 " pdb=" CB GLN A1323 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.01e+00 chirality pdb=" CA VAL A1475 " pdb=" N VAL A1475 " pdb=" C VAL A1475 " pdb=" CB VAL A1475 " both_signs ideal model delta sigma weight residual False 2.44 2.12 0.32 2.00e-01 2.50e+01 2.53e+00 ... (remaining 2526 not shown) Planarity restraints: 4826 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER A1165 " -0.048 5.00e-02 4.00e+02 7.30e-02 8.52e+00 pdb=" N PRO A1166 " 0.126 5.00e-02 4.00e+02 pdb=" CA PRO A1166 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO A1166 " -0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A1676 " -0.039 5.00e-02 4.00e+02 5.88e-02 5.53e+00 pdb=" N PRO A1677 " 0.102 5.00e-02 4.00e+02 pdb=" CA PRO A1677 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO A1677 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A2124 " -0.030 5.00e-02 4.00e+02 4.52e-02 3.27e+00 pdb=" N PRO A2125 " 0.078 5.00e-02 4.00e+02 pdb=" CA PRO A2125 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO A2125 " -0.025 5.00e-02 4.00e+02 ... (remaining 4823 not shown) Histogram of nonbonded interaction distances: 1.57 - 2.18: 1459 2.18 - 2.78: 66938 2.78 - 3.39: 92511 3.39 - 3.99: 117461 3.99 - 4.60: 184330 Nonbonded interactions: 462699 Sorted by model distance: nonbonded pdb=" HG SER A 297 " pdb=" O ARG A 532 " model vdw 1.569 2.450 nonbonded pdb=" HZ3 LYS A 616 " pdb=" OG SER A 654 " model vdw 1.589 2.450 nonbonded pdb=" OE2 GLU A 275 " pdb=" HH TYR A 661 " model vdw 1.593 2.450 nonbonded pdb=" OE1 GLU A1720 " pdb=" H GLU A1720 " model vdw 1.598 2.450 nonbonded pdb=" OE1 GLN A 586 " pdb=" H SER A1221 " model vdw 1.606 2.450 ... (remaining 462694 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=0.00 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: 1.940 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.010 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.230 Extract box with map and model: 0.590 Check model and map are aligned: 0.100 Set scattering table: 0.090 Process input model: 28.020 Find NCS groups from input model: 0.100 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: 0.000 Load rotamer database and sin/cos tables:1.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7671 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 16793 Z= 0.129 Angle : 0.527 9.602 22704 Z= 0.298 Chirality : 0.040 0.379 2529 Planarity : 0.004 0.073 2866 Dihedral : 13.714 85.038 6229 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.54 % Allowed : 6.91 % Favored : 92.55 % Rotamer: Outliers : 0.00 % Allowed : 0.06 % Favored : 99.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.97 (0.19), residues: 2026 helix: 0.65 (0.17), residues: 1003 sheet: -2.16 (0.41), residues: 147 loop : -1.94 (0.20), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1703 TYR 0.010 0.001 TYR A 503 PHE 0.022 0.001 PHE A1655 TRP 0.009 0.001 TRP A1636 HIS 0.007 0.001 HIS A1881 Details of bonding type rmsd covalent geometry : bond 0.00266 (16793) covalent geometry : angle 0.52712 (22704) hydrogen bonds : bond 0.17492 ( 812) hydrogen bonds : angle 7.30050 ( 2352) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4052 Ramachandran restraints generated. 2026 Oldfield, 0 Emsley, 2026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4052 Ramachandran restraints generated. 2026 Oldfield, 0 Emsley, 2026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 684 is missing expected H atoms. Skipping. Residue ILE 1476 is missing expected H atoms. Skipping. Evaluate side-chains 274 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 274 time to evaluate : 0.825 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 TYR cc_start: 0.8130 (m-80) cc_final: 0.7798 (m-10) REVERT: A 203 GLU cc_start: 0.7711 (mt-10) cc_final: 0.7510 (mt-10) REVERT: A 1246 MET cc_start: 0.8193 (mtt) cc_final: 0.7840 (mtp) REVERT: A 1868 TYR cc_start: 0.7309 (m-80) cc_final: 0.7062 (m-80) REVERT: A 1869 GLN cc_start: 0.7562 (mp10) cc_final: 0.6748 (tm-30) REVERT: A 1879 PHE cc_start: 0.6492 (t80) cc_final: 0.6161 (t80) outliers start: 0 outliers final: 0 residues processed: 274 average time/residue: 0.2587 time to fit residues: 108.8166 Evaluate side-chains 217 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 217 time to evaluate : 0.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 98 optimal weight: 2.9990 chunk 194 optimal weight: 20.0000 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 7.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 3.9990 chunk 200 optimal weight: 7.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 3.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 410 HIS A 542 ASN ** A 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 918 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4199 r_free = 0.4199 target = 0.162639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.113452 restraints weight = 83425.401| |-----------------------------------------------------------------------------| r_work (start): 0.3508 rms_B_bonded: 3.17 r_work: 0.3386 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3386 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 moved from start: 0.1139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 16793 Z= 0.233 Angle : 0.575 8.436 22704 Z= 0.312 Chirality : 0.042 0.394 2529 Planarity : 0.005 0.103 2866 Dihedral : 4.322 20.676 2212 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.54 % Allowed : 7.85 % Favored : 91.61 % Rotamer: Outliers : 0.39 % Allowed : 6.30 % Favored : 93.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.99 (0.19), residues: 2026 helix: 0.64 (0.16), residues: 1037 sheet: -2.50 (0.40), residues: 156 loop : -1.95 (0.20), residues: 833 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.028 0.000 ARG A1637 TYR 0.014 0.001 TYR A 503 PHE 0.015 0.001 PHE A 585 TRP 0.013 0.001 TRP A 473 HIS 0.010 0.001 HIS A 410 Details of bonding type rmsd covalent geometry : bond 0.00524 (16793) covalent geometry : angle 0.57516 (22704) hydrogen bonds : bond 0.04779 ( 812) hydrogen bonds : angle 5.58418 ( 2352) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4052 Ramachandran restraints generated. 2026 Oldfield, 0 Emsley, 2026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4052 Ramachandran restraints generated. 2026 Oldfield, 0 Emsley, 2026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 684 is missing expected H atoms. Skipping. Residue ILE 1476 is missing expected H atoms. Skipping. Evaluate side-chains 233 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 226 time to evaluate : 0.869 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 744 GLU cc_start: 0.8393 (tt0) cc_final: 0.8040 (mm-30) REVERT: A 1246 MET cc_start: 0.8616 (mtt) cc_final: 0.7990 (mtp) REVERT: A 1544 ARG cc_start: 0.8843 (ttt180) cc_final: 0.8306 (ttp-110) REVERT: A 1678 GLU cc_start: 0.8200 (mp0) cc_final: 0.7868 (mp0) REVERT: A 1868 TYR cc_start: 0.7763 (m-80) cc_final: 0.7520 (m-80) REVERT: A 1869 GLN cc_start: 0.7780 (mp10) cc_final: 0.6806 (tm-30) REVERT: A 2112 MET cc_start: 0.4007 (mmp) cc_final: 0.3416 (tpp) outliers start: 7 outliers final: 5 residues processed: 230 average time/residue: 0.2737 time to fit residues: 96.2778 Evaluate side-chains 213 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 208 time to evaluate : 0.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 688 LEU Chi-restraints excluded: chain A residue 723 CYS Chi-restraints excluded: chain A residue 1293 LEU Chi-restraints excluded: chain A residue 1533 VAL Chi-restraints excluded: chain A residue 1659 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 14 optimal weight: 1.9990 chunk 185 optimal weight: 9.9990 chunk 43 optimal weight: 2.9990 chunk 100 optimal weight: 9.9990 chunk 45 optimal weight: 2.9990 chunk 13 optimal weight: 7.9990 chunk 188 optimal weight: 1.9990 chunk 122 optimal weight: 3.9990 chunk 127 optimal weight: 6.9990 chunk 111 optimal weight: 0.9980 chunk 63 optimal weight: 1.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1388 ASN A1782 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4190 r_free = 0.4190 target = 0.155570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.111563 restraints weight = 81372.471| |-----------------------------------------------------------------------------| r_work (start): 0.3562 rms_B_bonded: 2.99 r_work: 0.3422 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.3422 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.1388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 16793 Z= 0.167 Angle : 0.522 7.839 22704 Z= 0.280 Chirality : 0.040 0.388 2529 Planarity : 0.004 0.067 2866 Dihedral : 4.252 20.740 2212 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.59 % Allowed : 6.71 % Favored : 92.69 % Rotamer: Outliers : 0.77 % Allowed : 7.63 % Favored : 91.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.81 (0.19), residues: 2026 helix: 0.88 (0.16), residues: 1034 sheet: -2.46 (0.39), residues: 162 loop : -1.99 (0.20), residues: 830 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1637 TYR 0.019 0.001 TYR A1751 PHE 0.025 0.001 PHE A 215 TRP 0.013 0.001 TRP A 473 HIS 0.004 0.001 HIS A 712 Details of bonding type rmsd covalent geometry : bond 0.00374 (16793) covalent geometry : angle 0.52168 (22704) hydrogen bonds : bond 0.04153 ( 812) hydrogen bonds : angle 5.17968 ( 2352) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4052 Ramachandran restraints generated. 2026 Oldfield, 0 Emsley, 2026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4052 Ramachandran restraints generated. 2026 Oldfield, 0 Emsley, 2026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 684 is missing expected H atoms. Skipping. Residue ILE 1476 is missing expected H atoms. Skipping. Evaluate side-chains 240 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 226 time to evaluate : 0.768 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 203 GLU cc_start: 0.7926 (mt-10) cc_final: 0.7670 (mt-10) REVERT: A 465 ASP cc_start: 0.8726 (t70) cc_final: 0.8361 (t0) REVERT: A 1246 MET cc_start: 0.8610 (mtt) cc_final: 0.8117 (mtp) REVERT: A 1544 ARG cc_start: 0.8818 (ttt180) cc_final: 0.8350 (ttp-110) REVERT: A 1678 GLU cc_start: 0.8367 (mp0) cc_final: 0.7953 (mp0) REVERT: A 1868 TYR cc_start: 0.7763 (m-80) cc_final: 0.7524 (m-80) REVERT: A 1869 GLN cc_start: 0.7787 (mp10) cc_final: 0.6933 (tm-30) REVERT: A 2112 MET cc_start: 0.3886 (OUTLIER) cc_final: 0.3345 (tpt) outliers start: 14 outliers final: 10 residues processed: 233 average time/residue: 0.2966 time to fit residues: 105.1754 Evaluate side-chains 222 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 211 time to evaluate : 0.851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 297 SER Chi-restraints excluded: chain A residue 688 LEU Chi-restraints excluded: chain A residue 723 CYS Chi-restraints excluded: chain A residue 1278 THR Chi-restraints excluded: chain A residue 1293 LEU Chi-restraints excluded: chain A residue 1402 LEU Chi-restraints excluded: chain A residue 1578 VAL Chi-restraints excluded: chain A residue 1626 LEU Chi-restraints excluded: chain A residue 1659 THR Chi-restraints excluded: chain A residue 1837 LYS Chi-restraints excluded: chain A residue 2112 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 129 optimal weight: 5.9990 chunk 27 optimal weight: 4.9990 chunk 193 optimal weight: 0.0470 chunk 48 optimal weight: 1.9990 chunk 6 optimal weight: 9.9990 chunk 10 optimal weight: 7.9990 chunk 47 optimal weight: 0.7980 chunk 105 optimal weight: 1.9990 chunk 141 optimal weight: 4.9990 chunk 172 optimal weight: 6.9990 chunk 35 optimal weight: 2.9990 overall best weight: 1.5684 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 842 HIS A1060 ASN A1388 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4194 r_free = 0.4194 target = 0.155972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.111877 restraints weight = 81278.180| |-----------------------------------------------------------------------------| r_work (start): 0.3568 rms_B_bonded: 3.00 r_work: 0.3432 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3298 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 0.1621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 16793 Z= 0.141 Angle : 0.501 7.118 22704 Z= 0.268 Chirality : 0.040 0.387 2529 Planarity : 0.004 0.082 2866 Dihedral : 4.146 20.694 2212 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.59 % Allowed : 7.31 % Favored : 92.10 % Rotamer: Outliers : 0.83 % Allowed : 8.84 % Favored : 90.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.64 (0.19), residues: 2026 helix: 1.04 (0.16), residues: 1043 sheet: -2.47 (0.39), residues: 162 loop : -1.95 (0.20), residues: 821 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1702 TYR 0.013 0.001 TYR A 503 PHE 0.017 0.001 PHE A 531 TRP 0.012 0.001 TRP A 473 HIS 0.004 0.001 HIS A 278 Details of bonding type rmsd covalent geometry : bond 0.00320 (16793) covalent geometry : angle 0.50143 (22704) hydrogen bonds : bond 0.03694 ( 812) hydrogen bonds : angle 4.91434 ( 2352) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4052 Ramachandran restraints generated. 2026 Oldfield, 0 Emsley, 2026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4052 Ramachandran restraints generated. 2026 Oldfield, 0 Emsley, 2026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 684 is missing expected H atoms. Skipping. Residue ILE 1476 is missing expected H atoms. Skipping. Evaluate side-chains 237 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 222 time to evaluate : 0.831 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 385 MET cc_start: 0.8322 (tmm) cc_final: 0.7897 (tmm) REVERT: A 465 ASP cc_start: 0.8981 (t70) cc_final: 0.8583 (t0) REVERT: A 1246 MET cc_start: 0.8839 (mtt) cc_final: 0.8260 (mtp) REVERT: A 1544 ARG cc_start: 0.8887 (ttt180) cc_final: 0.8453 (ttp-110) REVERT: A 1678 GLU cc_start: 0.8450 (mp0) cc_final: 0.7883 (mp0) REVERT: A 1772 LYS cc_start: 0.8702 (ttmm) cc_final: 0.8217 (ttpt) REVERT: A 1868 TYR cc_start: 0.7932 (m-80) cc_final: 0.7625 (m-80) REVERT: A 1869 GLN cc_start: 0.7866 (mp10) cc_final: 0.6850 (tm-30) REVERT: A 2112 MET cc_start: 0.3871 (OUTLIER) cc_final: 0.3246 (tpp) outliers start: 15 outliers final: 12 residues processed: 229 average time/residue: 0.2936 time to fit residues: 102.1472 Evaluate side-chains 223 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 210 time to evaluate : 0.896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 297 SER Chi-restraints excluded: chain A residue 688 LEU Chi-restraints excluded: chain A residue 723 CYS Chi-restraints excluded: chain A residue 769 MET Chi-restraints excluded: chain A residue 1278 THR Chi-restraints excluded: chain A residue 1293 LEU Chi-restraints excluded: chain A residue 1402 LEU Chi-restraints excluded: chain A residue 1408 MET Chi-restraints excluded: chain A residue 1626 LEU Chi-restraints excluded: chain A residue 1659 THR Chi-restraints excluded: chain A residue 1774 LEU Chi-restraints excluded: chain A residue 1837 LYS Chi-restraints excluded: chain A residue 2112 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 151 optimal weight: 7.9990 chunk 25 optimal weight: 2.9990 chunk 126 optimal weight: 6.9990 chunk 143 optimal weight: 4.9990 chunk 196 optimal weight: 9.9990 chunk 180 optimal weight: 4.9990 chunk 136 optimal weight: 0.7980 chunk 20 optimal weight: 5.9990 chunk 16 optimal weight: 9.9990 chunk 158 optimal weight: 9.9990 chunk 123 optimal weight: 3.9990 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 675 ASN ** A 692 GLN ** 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 = 0.4180 r_free = 0.4180 target = 0.160662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.111383 restraints weight = 83238.194| |-----------------------------------------------------------------------------| r_work (start): 0.3481 rms_B_bonded: 3.15 r_work: 0.3359 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3359 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.1847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 16793 Z= 0.259 Angle : 0.568 6.648 22704 Z= 0.308 Chirality : 0.042 0.395 2529 Planarity : 0.004 0.077 2866 Dihedral : 4.356 21.465 2212 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.59 % Allowed : 8.98 % Favored : 90.42 % Rotamer: Outliers : 1.22 % Allowed : 9.95 % Favored : 88.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.83 (0.18), residues: 2026 helix: 0.90 (0.16), residues: 1039 sheet: -2.72 (0.39), residues: 161 loop : -2.02 (0.20), residues: 826 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 566 TYR 0.019 0.002 TYR A 503 PHE 0.018 0.002 PHE A 585 TRP 0.015 0.001 TRP A 473 HIS 0.005 0.001 HIS A 712 Details of bonding type rmsd covalent geometry : bond 0.00587 (16793) covalent geometry : angle 0.56782 (22704) hydrogen bonds : bond 0.04016 ( 812) hydrogen bonds : angle 5.12946 ( 2352) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4052 Ramachandran restraints generated. 2026 Oldfield, 0 Emsley, 2026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4052 Ramachandran restraints generated. 2026 Oldfield, 0 Emsley, 2026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 684 is missing expected H atoms. Skipping. Residue ILE 1476 is missing expected H atoms. Skipping. Evaluate side-chains 231 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 209 time to evaluate : 0.829 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 465 ASP cc_start: 0.8851 (t70) cc_final: 0.8467 (t0) REVERT: A 1544 ARG cc_start: 0.8850 (ttt180) cc_final: 0.8468 (ttp-110) REVERT: A 1675 ILE cc_start: 0.7960 (mp) cc_final: 0.7731 (mp) REVERT: A 1678 GLU cc_start: 0.8433 (mp0) cc_final: 0.7710 (mp0) REVERT: A 1832 PHE cc_start: 0.8279 (m-10) cc_final: 0.8006 (m-10) REVERT: A 1868 TYR cc_start: 0.7561 (m-80) cc_final: 0.7320 (m-80) REVERT: A 1869 GLN cc_start: 0.7770 (mp10) cc_final: 0.6902 (tm-30) REVERT: A 2112 MET cc_start: 0.3909 (OUTLIER) cc_final: 0.3289 (tpp) outliers start: 22 outliers final: 16 residues processed: 222 average time/residue: 0.2598 time to fit residues: 88.5388 Evaluate side-chains 216 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 199 time to evaluate : 0.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 HIS Chi-restraints excluded: chain A residue 296 CYS Chi-restraints excluded: chain A residue 297 SER Chi-restraints excluded: chain A residue 688 LEU Chi-restraints excluded: chain A residue 723 CYS Chi-restraints excluded: chain A residue 769 MET Chi-restraints excluded: chain A residue 1278 THR Chi-restraints excluded: chain A residue 1370 TYR Chi-restraints excluded: chain A residue 1402 LEU Chi-restraints excluded: chain A residue 1408 MET Chi-restraints excluded: chain A residue 1491 THR Chi-restraints excluded: chain A residue 1578 VAL Chi-restraints excluded: chain A residue 1626 LEU Chi-restraints excluded: chain A residue 1659 THR Chi-restraints excluded: chain A residue 1774 LEU Chi-restraints excluded: chain A residue 1837 LYS Chi-restraints excluded: chain A residue 2112 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 192 optimal weight: 6.9990 chunk 34 optimal weight: 6.9990 chunk 166 optimal weight: 10.0000 chunk 127 optimal weight: 4.9990 chunk 74 optimal weight: 2.9990 chunk 27 optimal weight: 3.9990 chunk 141 optimal weight: 5.9990 chunk 119 optimal weight: 0.2980 chunk 47 optimal weight: 0.8980 chunk 197 optimal weight: 10.0000 chunk 159 optimal weight: 3.9990 overall best weight: 2.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1060 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.160877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.111422 restraints weight = 82061.794| |-----------------------------------------------------------------------------| r_work (start): 0.3503 rms_B_bonded: 3.14 r_work: 0.3381 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3381 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.1973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 16793 Z= 0.190 Angle : 0.531 7.245 22704 Z= 0.285 Chirality : 0.041 0.392 2529 Planarity : 0.004 0.073 2866 Dihedral : 4.296 21.221 2212 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.59 % Allowed : 7.70 % Favored : 91.71 % Rotamer: Outliers : 1.16 % Allowed : 10.78 % Favored : 88.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.72 (0.19), residues: 2026 helix: 1.00 (0.16), residues: 1039 sheet: -2.69 (0.39), residues: 161 loop : -1.96 (0.20), residues: 826 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 566 TYR 0.017 0.001 TYR A 503 PHE 0.034 0.001 PHE A1655 TRP 0.014 0.001 TRP A 473 HIS 0.005 0.001 HIS A1847 Details of bonding type rmsd covalent geometry : bond 0.00433 (16793) covalent geometry : angle 0.53125 (22704) hydrogen bonds : bond 0.03758 ( 812) hydrogen bonds : angle 4.93243 ( 2352) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4052 Ramachandran restraints generated. 2026 Oldfield, 0 Emsley, 2026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4052 Ramachandran restraints generated. 2026 Oldfield, 0 Emsley, 2026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 684 is missing expected H atoms. Skipping. Residue ILE 1476 is missing expected H atoms. Skipping. Evaluate side-chains 235 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 214 time to evaluate : 0.801 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 GLU cc_start: 0.9019 (pm20) cc_final: 0.8755 (pm20) REVERT: A 465 ASP cc_start: 0.8822 (t70) cc_final: 0.8435 (t0) REVERT: A 735 MET cc_start: 0.6842 (tmm) cc_final: 0.6623 (tmm) REVERT: A 1544 ARG cc_start: 0.8826 (ttt180) cc_final: 0.8468 (ttp-110) REVERT: A 1583 GLU cc_start: 0.6514 (OUTLIER) cc_final: 0.5689 (mt-10) REVERT: A 1678 GLU cc_start: 0.8445 (mp0) cc_final: 0.7741 (mp0) REVERT: A 1869 GLN cc_start: 0.7845 (mp10) cc_final: 0.6814 (tm-30) REVERT: A 2112 MET cc_start: 0.3997 (OUTLIER) cc_final: 0.3368 (tpp) outliers start: 21 outliers final: 16 residues processed: 226 average time/residue: 0.3242 time to fit residues: 110.7392 Evaluate side-chains 227 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 209 time to evaluate : 0.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 HIS Chi-restraints excluded: chain A residue 297 SER Chi-restraints excluded: chain A residue 688 LEU Chi-restraints excluded: chain A residue 723 CYS Chi-restraints excluded: chain A residue 769 MET Chi-restraints excluded: chain A residue 894 PHE Chi-restraints excluded: chain A residue 932 ILE Chi-restraints excluded: chain A residue 1278 THR Chi-restraints excluded: chain A residue 1402 LEU Chi-restraints excluded: chain A residue 1408 MET Chi-restraints excluded: chain A residue 1491 THR Chi-restraints excluded: chain A residue 1538 MET Chi-restraints excluded: chain A residue 1578 VAL Chi-restraints excluded: chain A residue 1583 GLU Chi-restraints excluded: chain A residue 1626 LEU Chi-restraints excluded: chain A residue 1659 THR Chi-restraints excluded: chain A residue 1837 LYS Chi-restraints excluded: chain A residue 2112 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 57 optimal weight: 0.6980 chunk 123 optimal weight: 1.9990 chunk 134 optimal weight: 0.5980 chunk 108 optimal weight: 0.9990 chunk 26 optimal weight: 2.9990 chunk 176 optimal weight: 9.9990 chunk 170 optimal weight: 9.9990 chunk 69 optimal weight: 0.9980 chunk 167 optimal weight: 5.9990 chunk 141 optimal weight: 4.9990 chunk 39 optimal weight: 4.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1036 HIS A1060 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.162059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.112879 restraints weight = 81624.418| |-----------------------------------------------------------------------------| r_work (start): 0.3539 rms_B_bonded: 3.14 r_work: 0.3417 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3417 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 moved from start: 0.2044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 16793 Z= 0.116 Angle : 0.499 7.591 22704 Z= 0.263 Chirality : 0.040 0.383 2529 Planarity : 0.004 0.065 2866 Dihedral : 4.152 21.464 2212 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.59 % Allowed : 6.71 % Favored : 92.69 % Rotamer: Outliers : 1.05 % Allowed : 11.00 % Favored : 87.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.48 (0.19), residues: 2026 helix: 1.23 (0.16), residues: 1043 sheet: -2.41 (0.39), residues: 162 loop : -1.95 (0.20), residues: 821 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 340 TYR 0.014 0.001 TYR A 503 PHE 0.033 0.001 PHE A1655 TRP 0.012 0.001 TRP A 473 HIS 0.004 0.001 HIS A 278 Details of bonding type rmsd covalent geometry : bond 0.00261 (16793) covalent geometry : angle 0.49934 (22704) hydrogen bonds : bond 0.03446 ( 812) hydrogen bonds : angle 4.68158 ( 2352) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4052 Ramachandran restraints generated. 2026 Oldfield, 0 Emsley, 2026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4052 Ramachandran restraints generated. 2026 Oldfield, 0 Emsley, 2026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 684 is missing expected H atoms. Skipping. Residue ILE 1476 is missing expected H atoms. Skipping. Evaluate side-chains 240 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 221 time to evaluate : 0.943 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 GLU cc_start: 0.8979 (pm20) cc_final: 0.8710 (pm20) REVERT: A 735 MET cc_start: 0.6787 (tmm) cc_final: 0.6570 (tmm) REVERT: A 1036 HIS cc_start: 0.8614 (t70) cc_final: 0.8150 (t-90) REVERT: A 1246 MET cc_start: 0.8726 (mtt) cc_final: 0.8131 (mtp) REVERT: A 1544 ARG cc_start: 0.8791 (ttt180) cc_final: 0.8427 (ttp-110) REVERT: A 1583 GLU cc_start: 0.6394 (OUTLIER) cc_final: 0.5611 (mt-10) REVERT: A 1678 GLU cc_start: 0.8403 (mp0) cc_final: 0.7679 (mp0) REVERT: A 1772 LYS cc_start: 0.8674 (ttmm) cc_final: 0.8221 (ttpt) REVERT: A 1869 GLN cc_start: 0.7810 (mp10) cc_final: 0.6837 (tm-30) REVERT: A 2112 MET cc_start: 0.3793 (OUTLIER) cc_final: 0.3269 (tpp) outliers start: 19 outliers final: 15 residues processed: 230 average time/residue: 0.3289 time to fit residues: 114.3831 Evaluate side-chains 225 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 208 time to evaluate : 0.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 HIS Chi-restraints excluded: chain A residue 211 PHE Chi-restraints excluded: chain A residue 297 SER Chi-restraints excluded: chain A residue 688 LEU Chi-restraints excluded: chain A residue 723 CYS Chi-restraints excluded: chain A residue 769 MET Chi-restraints excluded: chain A residue 894 PHE Chi-restraints excluded: chain A residue 932 ILE Chi-restraints excluded: chain A residue 1278 THR Chi-restraints excluded: chain A residue 1402 LEU Chi-restraints excluded: chain A residue 1408 MET Chi-restraints excluded: chain A residue 1491 THR Chi-restraints excluded: chain A residue 1583 GLU Chi-restraints excluded: chain A residue 1626 LEU Chi-restraints excluded: chain A residue 1659 THR Chi-restraints excluded: chain A residue 1837 LYS Chi-restraints excluded: chain A residue 2112 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 32 optimal weight: 5.9990 chunk 55 optimal weight: 2.9990 chunk 145 optimal weight: 3.9990 chunk 70 optimal weight: 2.9990 chunk 65 optimal weight: 9.9990 chunk 92 optimal weight: 6.9990 chunk 85 optimal weight: 4.9990 chunk 37 optimal weight: 0.8980 chunk 117 optimal weight: 0.6980 chunk 154 optimal weight: 3.9990 chunk 141 optimal weight: 5.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1060 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4196 r_free = 0.4196 target = 0.160995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.112097 restraints weight = 82230.059| |-----------------------------------------------------------------------------| r_work (start): 0.3511 rms_B_bonded: 3.14 r_work: 0.3389 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3389 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.2188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 16793 Z= 0.184 Angle : 0.525 7.583 22704 Z= 0.280 Chirality : 0.040 0.390 2529 Planarity : 0.004 0.065 2866 Dihedral : 4.178 21.362 2212 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.59 % Allowed : 8.19 % Favored : 91.21 % Rotamer: Outliers : 1.11 % Allowed : 11.77 % Favored : 87.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.52 (0.19), residues: 2026 helix: 1.19 (0.16), residues: 1047 sheet: -2.40 (0.38), residues: 174 loop : -1.97 (0.20), residues: 805 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 340 TYR 0.021 0.001 TYR A1462 PHE 0.026 0.001 PHE A1655 TRP 0.013 0.001 TRP A 473 HIS 0.004 0.001 HIS A 278 Details of bonding type rmsd covalent geometry : bond 0.00420 (16793) covalent geometry : angle 0.52504 (22704) hydrogen bonds : bond 0.03575 ( 812) hydrogen bonds : angle 4.77172 ( 2352) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4052 Ramachandran restraints generated. 2026 Oldfield, 0 Emsley, 2026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4052 Ramachandran restraints generated. 2026 Oldfield, 0 Emsley, 2026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 684 is missing expected H atoms. Skipping. Residue ILE 1476 is missing expected H atoms. Skipping. Evaluate side-chains 228 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 208 time to evaluate : 0.925 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 GLU cc_start: 0.9010 (pm20) cc_final: 0.8734 (pm20) REVERT: A 465 ASP cc_start: 0.8815 (t70) cc_final: 0.8451 (t0) REVERT: A 1036 HIS cc_start: 0.8647 (t70) cc_final: 0.8161 (t-90) REVERT: A 1246 MET cc_start: 0.8781 (mtt) cc_final: 0.8171 (mtp) REVERT: A 1544 ARG cc_start: 0.8786 (ttt180) cc_final: 0.8427 (ttp-110) REVERT: A 1583 GLU cc_start: 0.6557 (OUTLIER) cc_final: 0.5730 (mt-10) REVERT: A 1678 GLU cc_start: 0.8440 (mp0) cc_final: 0.7835 (mp0) REVERT: A 1685 MET cc_start: 0.6796 (ttp) cc_final: 0.6493 (tmm) REVERT: A 1772 LYS cc_start: 0.8683 (ttmm) cc_final: 0.8228 (ttpt) REVERT: A 1869 GLN cc_start: 0.7809 (mp10) cc_final: 0.6830 (tm-30) REVERT: A 2112 MET cc_start: 0.3832 (OUTLIER) cc_final: 0.3299 (tpp) outliers start: 20 outliers final: 17 residues processed: 219 average time/residue: 0.3343 time to fit residues: 110.4224 Evaluate side-chains 225 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 206 time to evaluate : 1.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 HIS Chi-restraints excluded: chain A residue 296 CYS Chi-restraints excluded: chain A residue 297 SER Chi-restraints excluded: chain A residue 688 LEU Chi-restraints excluded: chain A residue 723 CYS Chi-restraints excluded: chain A residue 769 MET Chi-restraints excluded: chain A residue 894 PHE Chi-restraints excluded: chain A residue 932 ILE Chi-restraints excluded: chain A residue 1278 THR Chi-restraints excluded: chain A residue 1289 LEU Chi-restraints excluded: chain A residue 1402 LEU Chi-restraints excluded: chain A residue 1408 MET Chi-restraints excluded: chain A residue 1491 THR Chi-restraints excluded: chain A residue 1583 GLU Chi-restraints excluded: chain A residue 1626 LEU Chi-restraints excluded: chain A residue 1659 THR Chi-restraints excluded: chain A residue 1709 GLN Chi-restraints excluded: chain A residue 1837 LYS Chi-restraints excluded: chain A residue 2112 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 109 optimal weight: 0.5980 chunk 86 optimal weight: 9.9990 chunk 118 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 4 optimal weight: 5.9990 chunk 177 optimal weight: 10.0000 chunk 65 optimal weight: 8.9990 chunk 165 optimal weight: 8.9990 chunk 95 optimal weight: 4.9990 chunk 77 optimal weight: 1.9990 chunk 50 optimal weight: 0.9980 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1060 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4216 r_free = 0.4216 target = 0.163115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.114743 restraints weight = 81509.274| |-----------------------------------------------------------------------------| r_work (start): 0.3532 rms_B_bonded: 3.11 r_work: 0.3413 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3413 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7747 moved from start: 0.2219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 16793 Z= 0.146 Angle : 0.509 7.884 22704 Z= 0.270 Chirality : 0.040 0.387 2529 Planarity : 0.004 0.063 2866 Dihedral : 4.136 21.211 2212 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.59 % Allowed : 7.45 % Favored : 91.95 % Rotamer: Outliers : 1.00 % Allowed : 12.38 % Favored : 86.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.41 (0.19), residues: 2026 helix: 1.27 (0.16), residues: 1050 sheet: -2.35 (0.39), residues: 174 loop : -1.92 (0.20), residues: 802 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 480 TYR 0.028 0.001 TYR A1887 PHE 0.026 0.001 PHE A1655 TRP 0.012 0.001 TRP A 473 HIS 0.004 0.001 HIS A 278 Details of bonding type rmsd covalent geometry : bond 0.00331 (16793) covalent geometry : angle 0.50903 (22704) hydrogen bonds : bond 0.03441 ( 812) hydrogen bonds : angle 4.66668 ( 2352) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4052 Ramachandran restraints generated. 2026 Oldfield, 0 Emsley, 2026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4052 Ramachandran restraints generated. 2026 Oldfield, 0 Emsley, 2026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 684 is missing expected H atoms. Skipping. Residue ILE 1476 is missing expected H atoms. Skipping. Evaluate side-chains 230 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 212 time to evaluate : 0.922 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 GLU cc_start: 0.8952 (pm20) cc_final: 0.8698 (pm20) REVERT: A 465 ASP cc_start: 0.8842 (t70) cc_final: 0.8455 (t0) REVERT: A 1036 HIS cc_start: 0.8637 (t70) cc_final: 0.8002 (t-90) REVERT: A 1246 MET cc_start: 0.8786 (mtt) cc_final: 0.8121 (mtp) REVERT: A 1544 ARG cc_start: 0.8772 (ttt180) cc_final: 0.8458 (ttp-110) REVERT: A 1546 LEU cc_start: 0.8988 (mt) cc_final: 0.8785 (mp) REVERT: A 1583 GLU cc_start: 0.6424 (OUTLIER) cc_final: 0.5607 (mt-10) REVERT: A 1678 GLU cc_start: 0.8431 (mp0) cc_final: 0.7848 (mp0) REVERT: A 1685 MET cc_start: 0.6783 (ttp) cc_final: 0.6496 (tmm) REVERT: A 1772 LYS cc_start: 0.8651 (ttmm) cc_final: 0.8196 (ttpt) REVERT: A 1869 GLN cc_start: 0.7805 (mp10) cc_final: 0.6806 (tm-30) REVERT: A 1917 MET cc_start: 0.6963 (mmp) cc_final: 0.6735 (mmp) REVERT: A 2112 MET cc_start: 0.3804 (OUTLIER) cc_final: 0.3314 (tpp) outliers start: 18 outliers final: 15 residues processed: 222 average time/residue: 0.3409 time to fit residues: 113.0797 Evaluate side-chains 225 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 208 time to evaluate : 0.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 HIS Chi-restraints excluded: chain A residue 297 SER Chi-restraints excluded: chain A residue 688 LEU Chi-restraints excluded: chain A residue 723 CYS Chi-restraints excluded: chain A residue 769 MET Chi-restraints excluded: chain A residue 894 PHE Chi-restraints excluded: chain A residue 932 ILE Chi-restraints excluded: chain A residue 1278 THR Chi-restraints excluded: chain A residue 1402 LEU Chi-restraints excluded: chain A residue 1408 MET Chi-restraints excluded: chain A residue 1491 THR Chi-restraints excluded: chain A residue 1583 GLU Chi-restraints excluded: chain A residue 1626 LEU Chi-restraints excluded: chain A residue 1659 THR Chi-restraints excluded: chain A residue 1709 GLN Chi-restraints excluded: chain A residue 1837 LYS Chi-restraints excluded: chain A residue 2112 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 31 optimal weight: 5.9990 chunk 87 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 chunk 194 optimal weight: 3.9990 chunk 70 optimal weight: 2.9990 chunk 28 optimal weight: 0.8980 chunk 83 optimal weight: 4.9990 chunk 193 optimal weight: 0.0370 chunk 110 optimal weight: 5.9990 chunk 134 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 overall best weight: 1.7864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 692 GLN ** 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 = 0.4206 r_free = 0.4206 target = 0.161922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.112667 restraints weight = 82011.903| |-----------------------------------------------------------------------------| r_work (start): 0.3521 rms_B_bonded: 3.16 r_work: 0.3400 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3400 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.2289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 16793 Z= 0.151 Angle : 0.513 8.377 22704 Z= 0.272 Chirality : 0.040 0.386 2529 Planarity : 0.004 0.062 2866 Dihedral : 4.112 21.270 2212 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.59 % Allowed : 8.00 % Favored : 91.41 % Rotamer: Outliers : 1.00 % Allowed : 12.44 % Favored : 86.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.35 (0.19), residues: 2026 helix: 1.32 (0.16), residues: 1049 sheet: -2.33 (0.39), residues: 174 loop : -1.88 (0.21), residues: 803 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 340 TYR 0.016 0.001 TYR A 503 PHE 0.025 0.001 PHE A1655 TRP 0.012 0.001 TRP A 473 HIS 0.005 0.001 HIS A2133 Details of bonding type rmsd covalent geometry : bond 0.00343 (16793) covalent geometry : angle 0.51313 (22704) hydrogen bonds : bond 0.03423 ( 812) hydrogen bonds : angle 4.64339 ( 2352) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4052 Ramachandran restraints generated. 2026 Oldfield, 0 Emsley, 2026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4052 Ramachandran restraints generated. 2026 Oldfield, 0 Emsley, 2026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 684 is missing expected H atoms. Skipping. Residue ILE 1476 is missing expected H atoms. Skipping. Evaluate side-chains 230 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 212 time to evaluate : 1.032 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 GLU cc_start: 0.8954 (pm20) cc_final: 0.8699 (pm20) REVERT: A 465 ASP cc_start: 0.8801 (t70) cc_final: 0.8467 (t0) REVERT: A 1203 ASP cc_start: 0.8369 (m-30) cc_final: 0.8160 (t0) REVERT: A 1246 MET cc_start: 0.8788 (mtt) cc_final: 0.8169 (mtp) REVERT: A 1544 ARG cc_start: 0.8782 (ttt180) cc_final: 0.8457 (ttp-110) REVERT: A 1546 LEU cc_start: 0.8997 (mt) cc_final: 0.8788 (mp) REVERT: A 1583 GLU cc_start: 0.6489 (OUTLIER) cc_final: 0.5669 (mt-10) REVERT: A 1678 GLU cc_start: 0.8460 (mp0) cc_final: 0.8032 (mp0) REVERT: A 1685 MET cc_start: 0.6850 (ttp) cc_final: 0.6591 (tmm) REVERT: A 1772 LYS cc_start: 0.8676 (ttmm) cc_final: 0.8234 (ttpt) REVERT: A 1869 GLN cc_start: 0.7776 (mp10) cc_final: 0.6812 (tm-30) REVERT: A 2112 MET cc_start: 0.3875 (OUTLIER) cc_final: 0.3377 (tpp) outliers start: 18 outliers final: 15 residues processed: 222 average time/residue: 0.3396 time to fit residues: 113.5011 Evaluate side-chains 224 residues out of total 1812 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 207 time to evaluate : 0.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 HIS Chi-restraints excluded: chain A residue 297 SER Chi-restraints excluded: chain A residue 688 LEU Chi-restraints excluded: chain A residue 723 CYS Chi-restraints excluded: chain A residue 769 MET Chi-restraints excluded: chain A residue 894 PHE Chi-restraints excluded: chain A residue 932 ILE Chi-restraints excluded: chain A residue 1278 THR Chi-restraints excluded: chain A residue 1402 LEU Chi-restraints excluded: chain A residue 1408 MET Chi-restraints excluded: chain A residue 1491 THR Chi-restraints excluded: chain A residue 1583 GLU Chi-restraints excluded: chain A residue 1626 LEU Chi-restraints excluded: chain A residue 1659 THR Chi-restraints excluded: chain A residue 1709 GLN Chi-restraints excluded: chain A residue 1837 LYS Chi-restraints excluded: chain A residue 2112 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 128 optimal weight: 3.9990 chunk 201 optimal weight: 9.9990 chunk 176 optimal weight: 9.9990 chunk 137 optimal weight: 2.9990 chunk 192 optimal weight: 4.9990 chunk 89 optimal weight: 0.9980 chunk 133 optimal weight: 0.9990 chunk 96 optimal weight: 1.9990 chunk 4 optimal weight: 10.0000 chunk 30 optimal weight: 2.9990 chunk 136 optimal weight: 0.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 816 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4211 r_free = 0.4211 target = 0.161707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.113459 restraints weight = 81534.684| |-----------------------------------------------------------------------------| r_work (start): 0.3533 rms_B_bonded: 3.09 r_work: 0.3410 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3410 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.2331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 16793 Z= 0.139 Angle : 0.508 8.526 22704 Z= 0.268 Chirality : 0.040 0.385 2529 Planarity : 0.004 0.061 2866 Dihedral : 4.081 21.204 2212 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.59 % Allowed : 7.31 % Favored : 92.10 % Rotamer: Outliers : 1.05 % Allowed : 12.66 % Favored : 86.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.30 (0.19), residues: 2026 helix: 1.36 (0.16), residues: 1048 sheet: -2.31 (0.39), residues: 174 loop : -1.85 (0.21), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 340 TYR 0.016 0.001 TYR A1887 PHE 0.025 0.001 PHE A1655 TRP 0.011 0.001 TRP A 473 HIS 0.003 0.001 HIS A 278 Details of bonding type rmsd covalent geometry : bond 0.00316 (16793) covalent geometry : angle 0.50779 (22704) hydrogen bonds : bond 0.03359 ( 812) hydrogen bonds : angle 4.58590 ( 2352) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7842.34 seconds wall clock time: 134 minutes 4.20 seconds (8044.20 seconds total)