Starting phenix.real_space_refine on Mon Apr 6 08:56:12 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ohe_70488/04_2026/9ohe_70488.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ohe_70488/04_2026/9ohe_70488.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.59 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ohe_70488/04_2026/9ohe_70488.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ohe_70488/04_2026/9ohe_70488.map" model { file = "/net/cci-nas-00/data/ceres_data/9ohe_70488/04_2026/9ohe_70488.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ohe_70488/04_2026/9ohe_70488.cif" } resolution = 3.59 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= 0.011 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 41 5.16 5 C 10214 2.51 5 N 2831 2.21 5 O 3466 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 16552 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 16552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2366, 16552 Classifications: {'peptide': 2366} Incomplete info: {'backbone_only': 534} Link IDs: {'PTRANS': 52, 'TRANS': 2313} Unresolved chain link angles: 12 Unresolved non-hydrogen bonds: 2610 Unresolved non-hydrogen angles: 3774 Unresolved non-hydrogen dihedrals: 1775 Unresolved non-hydrogen chiralities: 668 Planarities with less than four sites: {'TRP:plan': 8, 'ARG:plan': 14, 'GLU:plan': 52, 'HIS:plan': 9, 'ASP:plan': 60, 'PHE:plan': 45, 'TYR:plan': 51, 'GLN:plan1': 13, 'ASN:plan1': 44} Unresolved non-hydrogen planarities: 1603 Time building chain proxies: 3.32, per 1000 atoms: 0.20 Number of scatterers: 16552 At special positions: 0 Unit cell: (84.46, 140.08, 216.3, 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 41 16.00 O 3466 8.00 N 2831 7.00 C 10214 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: 1.08 Conformation dependent library (CDL) restraints added in 598.6 milliseconds 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3390 Finding SS restraints... Secondary structure from input PDB file: 65 helices and 43 sheets defined 33.3% alpha, 23.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.26 Creating SS restraints... Processing helix chain 'A' and resid 5 through 13 Processing helix chain 'A' and resid 21 through 35 Processing helix chain 'A' and resid 41 through 62 Processing helix chain 'A' and resid 68 through 89 removed outlier: 3.722A pdb=" N LYS A 74 " --> pdb=" O LYS A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 121 removed outlier: 3.500A pdb=" N GLN A 117 " --> pdb=" O ASN A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 158 Processing helix chain 'A' and resid 167 through 197 Processing helix chain 'A' and resid 201 through 215 Processing helix chain 'A' and resid 217 through 234 Processing helix chain 'A' and resid 243 through 248 Processing helix chain 'A' and resid 251 through 262 Processing helix chain 'A' and resid 264 through 281 removed outlier: 3.593A pdb=" N ILE A 274 " --> pdb=" O ASP A 270 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N SER A 275 " --> pdb=" O ILE A 271 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 325 Processing helix chain 'A' and resid 334 through 338 Processing helix chain 'A' and resid 339 through 353 Processing helix chain 'A' and resid 355 through 360 Processing helix chain 'A' and resid 393 through 419 Proline residue: A 416 - end of helix Processing helix chain 'A' and resid 423 through 437 Processing helix chain 'A' and resid 443 through 450 removed outlier: 3.508A pdb=" N GLU A 449 " --> pdb=" O ARG A 445 " (cutoff:3.500A) Processing helix chain 'A' and resid 451 through 456 removed outlier: 4.901A pdb=" N LEU A 454 " --> pdb=" O GLY A 451 " (cutoff:3.500A) Processing helix chain 'A' and resid 463 through 468 Processing helix chain 'A' and resid 470 through 483 removed outlier: 3.756A pdb=" N TYR A 474 " --> pdb=" O GLY A 470 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 499 Processing helix chain 'A' and resid 500 through 502 No H-bonds generated for 'chain 'A' and resid 500 through 502' Processing helix chain 'A' and resid 512 through 519 Processing helix chain 'A' and resid 523 through 539 removed outlier: 3.782A pdb=" N ALA A 529 " --> pdb=" O ALA A 525 " (cutoff:3.500A) Processing helix chain 'A' and resid 558 through 568 Processing helix chain 'A' and resid 587 through 600 Processing helix chain 'A' and resid 667 through 683 removed outlier: 3.614A pdb=" N LEU A 681 " --> pdb=" O ALA A 677 " (cutoff:3.500A) Processing helix chain 'A' and resid 706 through 709 Processing helix chain 'A' and resid 710 through 727 removed outlier: 4.877A pdb=" N ASP A 721 " --> pdb=" O LEU A 717 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N LYS A 722 " --> pdb=" O LYS A 718 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N SER A 724 " --> pdb=" O LYS A 720 " (cutoff:3.500A) Processing helix chain 'A' and resid 731 through 733 No H-bonds generated for 'chain 'A' and resid 731 through 733' Processing helix chain 'A' and resid 764 through 775 Processing helix chain 'A' and resid 793 through 809 Processing helix chain 'A' and resid 814 through 838 removed outlier: 3.666A pdb=" N ILE A 836 " --> pdb=" O ILE A 832 " (cutoff:3.500A) Processing helix chain 'A' and resid 846 through 875 removed outlier: 3.734A pdb=" N LYS A 860 " --> pdb=" O LYS A 856 " (cutoff:3.500A) Processing helix chain 'A' and resid 916 through 934 Processing helix chain 'A' and resid 951 through 971 Processing helix chain 'A' and resid 975 through 980 Processing helix chain 'A' and resid 980 through 995 Processing helix chain 'A' and resid 997 through 1001 Processing helix chain 'A' and resid 1003 through 1017 Processing helix chain 'A' and resid 1041 through 1051 Processing helix chain 'A' and resid 1053 through 1065 Processing helix chain 'A' and resid 1072 through 1082 Processing helix chain 'A' and resid 1085 through 1094 removed outlier: 6.727A pdb=" N ILE A1091 " --> pdb=" O GLY A1088 " (cutoff:3.500A) removed outlier: 5.636A pdb=" N LEU A1092 " --> pdb=" O PHE A1089 " (cutoff:3.500A) Processing helix chain 'A' and resid 1116 through 1134 removed outlier: 4.287A pdb=" N VAL A1130 " --> pdb=" O HIS A1126 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N GLU A1131 " --> pdb=" O VAL A1127 " (cutoff:3.500A) Processing helix chain 'A' and resid 1203 through 1206 Processing helix chain 'A' and resid 1239 through 1243 Processing helix chain 'A' and resid 1245 through 1257 Processing helix chain 'A' and resid 1305 through 1310 Processing helix chain 'A' and resid 1348 through 1352 Processing helix chain 'A' and resid 1370 through 1375 removed outlier: 3.807A pdb=" N THR A1374 " --> pdb=" O GLY A1370 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LEU A1375 " --> pdb=" O ILE A1371 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1370 through 1375' Processing helix chain 'A' and resid 1432 through 1439 Processing helix chain 'A' and resid 1439 through 1450 Processing helix chain 'A' and resid 1558 through 1573 Processing helix chain 'A' and resid 1577 through 1588 removed outlier: 3.935A pdb=" N LEU A1581 " --> pdb=" O THR A1577 " (cutoff:3.500A) Processing helix chain 'A' and resid 1589 through 1594 Processing helix chain 'A' and resid 1650 through 1654 removed outlier: 3.914A pdb=" N GLN A1653 " --> pdb=" O GLY A1650 " (cutoff:3.500A) Processing helix chain 'A' and resid 1684 through 1688 Processing helix chain 'A' and resid 1736 through 1738 No H-bonds generated for 'chain 'A' and resid 1736 through 1738' Processing helix chain 'A' and resid 1773 through 1779 removed outlier: 3.673A pdb=" N LYS A1779 " --> pdb=" O THR A1775 " (cutoff:3.500A) Processing helix chain 'A' and resid 1792 through 1799 Processing helix chain 'A' and resid 1804 through 1810 removed outlier: 3.759A pdb=" N GLY A1807 " --> pdb=" O TYR A1804 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N ILE A1809 " --> pdb=" O ASP A1806 " (cutoff:3.500A) Processing helix chain 'A' and resid 2103 through 2107 Processing sheet with id=AA1, first strand: chain 'A' and resid 92 through 93 Processing sheet with id=AA2, first strand: chain 'A' and resid 237 through 239 removed outlier: 6.671A pdb=" N ASN A 238 " --> pdb=" O VAL A 127 " (cutoff:3.500A) removed outlier: 5.565A pdb=" N VAL A 129 " --> pdb=" O ASN A 238 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N ASN A 97 " --> pdb=" O MET A 283 " (cutoff:3.500A) removed outlier: 7.481A pdb=" N LEU A 285 " --> pdb=" O ASN A 97 " (cutoff:3.500A) removed outlier: 5.915A pdb=" N HIS A 99 " --> pdb=" O LEU A 285 " (cutoff:3.500A) removed outlier: 8.632A pdb=" N ASN A 384 " --> pdb=" O ASN A 378 " (cutoff:3.500A) removed outlier: 10.001A pdb=" N ASN A 378 " --> pdb=" O ASN A 384 " (cutoff:3.500A) removed outlier: 5.332A pdb=" N GLY A 386 " --> pdb=" O ALA A 376 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 290 through 291 Processing sheet with id=AA4, first strand: chain 'A' and resid 627 through 631 removed outlier: 3.780A pdb=" N GLU A 627 " --> pdb=" O ASN A 622 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N TYR A 621 " --> pdb=" O SER A 605 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N SER A 605 " --> pdb=" O TYR A 621 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N ILE A 646 " --> pdb=" O GLU A 692 " (cutoff:3.500A) removed outlier: 7.668A pdb=" N ASN A 694 " --> pdb=" O ILE A 646 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N ILE A 735 " --> pdb=" O PHE A 780 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N PHE A 780 " --> pdb=" O ILE A 735 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 627 through 631 removed outlier: 3.780A pdb=" N GLU A 627 " --> pdb=" O ASN A 622 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N TYR A 621 " --> pdb=" O SER A 605 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N SER A 605 " --> pdb=" O TYR A 621 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N ILE A 735 " --> pdb=" O PHE A 780 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N PHE A 780 " --> pdb=" O ILE A 735 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 744 through 746 Processing sheet with id=AA7, first strand: chain 'A' and resid 882 through 892 removed outlier: 10.163A pdb=" N PHE A 886 " --> pdb=" O ILE A 901 " (cutoff:3.500A) removed outlier: 10.890A pdb=" N ILE A 901 " --> pdb=" O PHE A 886 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N ASP A 888 " --> pdb=" O ARG A 899 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ARG A 899 " --> pdb=" O ASP A 888 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 936 through 940 removed outlier: 3.618A pdb=" N ASP A 938 " --> pdb=" O VAL A 945 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 1035 through 1036 Processing sheet with id=AB1, first strand: chain 'A' and resid 1067 through 1068 removed outlier: 5.319A pdb=" N ASP A1515 " --> pdb=" O TYR A1530 " (cutoff:3.500A) removed outlier: 5.125A pdb=" N TYR A1530 " --> pdb=" O ASP A1515 " (cutoff:3.500A) removed outlier: 7.366A pdb=" N ASN A1525 " --> pdb=" O LEU A1544 " (cutoff:3.500A) removed outlier: 5.128A pdb=" N LEU A1544 " --> pdb=" O ASN A1525 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N LYS A1537 " --> pdb=" O LEU A1557 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N LEU A1557 " --> pdb=" O LYS A1537 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N SER A1539 " --> pdb=" O VAL A1555 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N VAL A1555 " --> pdb=" O SER A1539 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N SER A1541 " --> pdb=" O ASN A1553 " (cutoff:3.500A) removed outlier: 7.751A pdb=" N SER A1554 " --> pdb=" O ASP A1607 " (cutoff:3.500A) removed outlier: 10.825A pdb=" N ASN A1609 " --> pdb=" O SER A1554 " (cutoff:3.500A) removed outlier: 11.351A pdb=" N HIS A1556 " --> pdb=" O ASN A1609 " (cutoff:3.500A) removed outlier: 11.044A pdb=" N ILE A1611 " --> pdb=" O HIS A1556 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N PHE A1610 " --> pdb=" O CYS A1625 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N ILE A1624 " --> pdb=" O PRO A1633 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N VAL A1691 " --> pdb=" O ILE A1718 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 1105 through 1107 Processing sheet with id=AB3, first strand: chain 'A' and resid 1136 through 1140 removed outlier: 6.892A pdb=" N ILE A1143 " --> pdb=" O LEU A1139 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N MET A1220 " --> pdb=" O ILE A1299 " (cutoff:3.500A) removed outlier: 5.961A pdb=" N TYR A1323 " --> pdb=" O ILE A1345 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N ASP A1347 " --> pdb=" O TYR A1323 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N LEU A1325 " --> pdb=" O ASP A1347 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N TRP A1344 " --> pdb=" O PHE A1401 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N SER A1403 " --> pdb=" O VAL A1418 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N VAL A1418 " --> pdb=" O SER A1403 " (cutoff:3.500A) removed outlier: 5.442A pdb=" N THR A1405 " --> pdb=" O ILE A1416 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N ILE A1416 " --> pdb=" O THR A1405 " (cutoff:3.500A) removed outlier: 5.171A pdb=" N SER A1407 " --> pdb=" O ALA A1414 " (cutoff:3.500A) removed outlier: 5.909A pdb=" N ALA A1414 " --> pdb=" O SER A1407 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N LEU A1427 " --> pdb=" O ASN A1459 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N GLY A1431 " --> pdb=" O SER A1463 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N VAL A1465 " --> pdb=" O GLY A1431 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 1161 through 1164 removed outlier: 6.752A pdb=" N SER A1161 " --> pdb=" O ILE A1155 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N ILE A1155 " --> pdb=" O SER A1161 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N VAL A1163 " --> pdb=" O SER A1153 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N SER A1153 " --> pdb=" O ARG A1288 " (cutoff:3.500A) removed outlier: 8.158A pdb=" N ASN A1290 " --> pdb=" O SER A1153 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N ILE A1155 " --> pdb=" O ASN A1290 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N GLY A1333 " --> pdb=" O LEU A1312 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 1179 through 1181 removed outlier: 6.613A pdb=" N ASP A1185 " --> pdb=" O PHE A1267 " (cutoff:3.500A) removed outlier: 4.992A pdb=" N ILE A1275 " --> pdb=" O GLY A1235 " (cutoff:3.500A) removed outlier: 5.319A pdb=" N GLY A1235 " --> pdb=" O ILE A1275 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N GLU A1168 " --> pdb=" O PHE A1230 " (cutoff:3.500A) removed outlier: 7.678A pdb=" N TRP A1232 " --> pdb=" O GLU A1168 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 1172 through 1176 removed outlier: 3.750A pdb=" N GLY A1175 " --> pdb=" O ALA A1190 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N ALA A1190 " --> pdb=" O GLY A1175 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 1353 through 1358 removed outlier: 4.990A pdb=" N ASP A1354 " --> pdb=" O GLY A1365 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 1376 through 1378 Processing sheet with id=AB9, first strand: chain 'A' and resid 1673 through 1677 removed outlier: 6.137A pdb=" N ILE A1674 " --> pdb=" O ASN A1703 " (cutoff:3.500A) removed outlier: 7.524A pdb=" N THR A1705 " --> pdb=" O ILE A1674 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N PHE A1676 " --> pdb=" O THR A1705 " (cutoff:3.500A) removed outlier: 6.052A pdb=" N ILE A1729 " --> pdb=" O SER A1781 " (cutoff:3.500A) removed outlier: 7.236A pdb=" N ASN A1783 " --> pdb=" O ILE A1729 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N VAL A1731 " --> pdb=" O ASN A1783 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N PHE A1784 " --> pdb=" O GLN A1788 " (cutoff:3.500A) removed outlier: 5.029A pdb=" N GLN A1788 " --> pdb=" O PHE A1784 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 1814 through 1818 Processing sheet with id=AC2, first strand: chain 'A' and resid 1834 through 1837 Processing sheet with id=AC3, first strand: chain 'A' and resid 1855 through 1859 Processing sheet with id=AC4, first strand: chain 'A' and resid 1877 through 1881 Processing sheet with id=AC5, first strand: chain 'A' and resid 1897 through 1899 removed outlier: 3.643A pdb=" N GLU A1921 " --> pdb=" O ALA A1909 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'A' and resid 1927 through 1931 Processing sheet with id=AC7, first strand: chain 'A' and resid 1948 through 1951 Processing sheet with id=AC8, first strand: chain 'A' and resid 1968 through 1972 Processing sheet with id=AC9, first strand: chain 'A' and resid 1988 through 1992 Processing sheet with id=AD1, first strand: chain 'A' and resid 2010 through 2012 Processing sheet with id=AD2, first strand: chain 'A' and resid 2028 through 2030 Processing sheet with id=AD3, first strand: chain 'A' and resid 2058 through 2062 Processing sheet with id=AD4, first strand: chain 'A' and resid 2078 through 2081 Processing sheet with id=AD5, first strand: chain 'A' and resid 2100 through 2102 removed outlier: 4.586A pdb=" N TYR A2110 " --> pdb=" O GLN A2118 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'A' and resid 2120 through 2124 Processing sheet with id=AD7, first strand: chain 'A' and resid 2141 through 2144 Processing sheet with id=AD8, first strand: chain 'A' and resid 2160 through 2162 removed outlier: 3.589A pdb=" N GLN A2184 " --> pdb=" O ALA A2172 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'A' and resid 2191 through 2192 Processing sheet with id=AE1, first strand: chain 'A' and resid 2210 through 2212 Processing sheet with id=AE2, first strand: chain 'A' and resid 2234 through 2238 Processing sheet with id=AE3, first strand: chain 'A' and resid 2254 through 2258 removed outlier: 4.447A pdb=" N TYR A2264 " --> pdb=" O GLN A2272 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'A' and resid 2274 through 2278 Processing sheet with id=AE5, first strand: chain 'A' and resid 2294 through 2298 Processing sheet with id=AE6, first strand: chain 'A' and resid 2324 through 2327 Processing sheet with id=AE7, first strand: chain 'A' and resid 2344 through 2348 removed outlier: 4.701A pdb=" N TYR A2354 " --> pdb=" O VAL A2363 " (cutoff:3.500A) 876 hydrogen bonds defined for protein. 2313 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: 6.32 Time building geometry restraints manager: 1.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 5814 1.34 - 1.46: 2983 1.46 - 1.57: 7920 1.57 - 1.69: 0 1.69 - 1.81: 74 Bond restraints: 16791 Sorted by residual: bond pdb=" C GLU A1197 " pdb=" N PRO A1198 " ideal model delta sigma weight residual 1.334 1.355 -0.021 2.34e-02 1.83e+03 8.38e-01 bond pdb=" CG LEU A 959 " pdb=" CD1 LEU A 959 " ideal model delta sigma weight residual 1.521 1.491 0.030 3.30e-02 9.18e+02 8.20e-01 bond pdb=" CB ARG A1309 " pdb=" CG ARG A1309 " ideal model delta sigma weight residual 1.520 1.497 0.023 3.00e-02 1.11e+03 6.01e-01 bond pdb=" CG1 ILE A1702 " pdb=" CD1 ILE A1702 " ideal model delta sigma weight residual 1.513 1.483 0.030 3.90e-02 6.57e+02 5.91e-01 bond pdb=" CB ILE A 841 " pdb=" CG2 ILE A 841 " ideal model delta sigma weight residual 1.521 1.496 0.025 3.30e-02 9.18e+02 5.61e-01 ... (remaining 16786 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.55: 21914 1.55 - 3.11: 511 3.11 - 4.66: 44 4.66 - 6.22: 7 6.22 - 7.77: 1 Bond angle restraints: 22477 Sorted by residual: angle pdb=" N GLU A1197 " pdb=" CA GLU A1197 " pdb=" C GLU A1197 " ideal model delta sigma weight residual 109.81 117.58 -7.77 2.21e+00 2.05e-01 1.24e+01 angle pdb=" N VAL A1741 " pdb=" CA VAL A1741 " pdb=" C VAL A1741 " ideal model delta sigma weight residual 108.90 103.60 5.30 1.66e+00 3.63e-01 1.02e+01 angle pdb=" C TYR A1740 " pdb=" N VAL A1741 " pdb=" CA VAL A1741 " ideal model delta sigma weight residual 122.69 127.02 -4.33 1.42e+00 4.96e-01 9.30e+00 angle pdb=" N TYR A1740 " pdb=" CA TYR A1740 " pdb=" C TYR A1740 " ideal model delta sigma weight residual 110.52 115.02 -4.50 1.48e+00 4.57e-01 9.25e+00 angle pdb=" N PRO A1847 " pdb=" CA PRO A1847 " pdb=" C PRO A1847 " ideal model delta sigma weight residual 110.70 113.64 -2.94 1.22e+00 6.72e-01 5.79e+00 ... (remaining 22472 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.23: 8638 17.23 - 34.45: 579 34.45 - 51.68: 92 51.68 - 68.91: 31 68.91 - 86.13: 14 Dihedral angle restraints: 9354 sinusoidal: 3516 harmonic: 5838 Sorted by residual: dihedral pdb=" CA SER A1755 " pdb=" C SER A1755 " pdb=" N GLU A1756 " pdb=" CA GLU A1756 " ideal model delta harmonic sigma weight residual 180.00 150.51 29.49 0 5.00e+00 4.00e-02 3.48e+01 dihedral pdb=" CA HIS A 35 " pdb=" C HIS A 35 " pdb=" N ASN A 36 " pdb=" CA ASN A 36 " ideal model delta harmonic sigma weight residual 180.00 -151.48 -28.52 0 5.00e+00 4.00e-02 3.25e+01 dihedral pdb=" CA PHE A1230 " pdb=" C PHE A1230 " pdb=" N ALA A1231 " pdb=" CA ALA A1231 " ideal model delta harmonic sigma weight residual 180.00 151.99 28.01 0 5.00e+00 4.00e-02 3.14e+01 ... (remaining 9351 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 1489 0.037 - 0.074: 506 0.074 - 0.112: 181 0.112 - 0.149: 58 0.149 - 0.186: 6 Chirality restraints: 2240 Sorted by residual: chirality pdb=" CA VAL A1741 " pdb=" N VAL A1741 " pdb=" C VAL A1741 " pdb=" CB VAL A1741 " both_signs ideal model delta sigma weight residual False 2.44 2.63 -0.19 2.00e-01 2.50e+01 8.66e-01 chirality pdb=" CB ILE A 612 " pdb=" CA ILE A 612 " pdb=" CG1 ILE A 612 " pdb=" CG2 ILE A 612 " both_signs ideal model delta sigma weight residual False 2.64 2.46 0.19 2.00e-01 2.50e+01 8.62e-01 chirality pdb=" CA TYR A1740 " pdb=" N TYR A1740 " pdb=" C TYR A1740 " pdb=" CB TYR A1740 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.73e-01 ... (remaining 2237 not shown) Planarity restraints: 3108 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 406 " 0.230 9.50e-02 1.11e+02 1.04e-01 8.06e+00 pdb=" NE ARG A 406 " -0.021 2.00e-02 2.50e+03 pdb=" CZ ARG A 406 " 0.019 2.00e-02 2.50e+03 pdb=" NH1 ARG A 406 " -0.009 2.00e-02 2.50e+03 pdb=" NH2 ARG A 406 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 643 " 0.190 9.50e-02 1.11e+02 8.57e-02 5.85e+00 pdb=" NE ARG A 643 " -0.018 2.00e-02 2.50e+03 pdb=" CZ ARG A 643 " 0.018 2.00e-02 2.50e+03 pdb=" NH1 ARG A 643 " -0.009 2.00e-02 2.50e+03 pdb=" NH2 ARG A 643 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A1114 " -0.186 9.50e-02 1.11e+02 8.40e-02 5.68e+00 pdb=" NE ARG A1114 " 0.018 2.00e-02 2.50e+03 pdb=" CZ ARG A1114 " -0.018 2.00e-02 2.50e+03 pdb=" NH1 ARG A1114 " 0.009 2.00e-02 2.50e+03 pdb=" NH2 ARG A1114 " 0.000 2.00e-02 2.50e+03 ... (remaining 3105 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1659 2.75 - 3.29: 17706 3.29 - 3.82: 26370 3.82 - 4.36: 31611 4.36 - 4.90: 52986 Nonbonded interactions: 130332 Sorted by model distance: nonbonded pdb=" OH TYR A 125 " pdb=" O GLY A 364 " model vdw 2.209 3.040 nonbonded pdb=" OD1 ASP A 270 " pdb=" NH1 ARG A 273 " model vdw 2.237 3.120 nonbonded pdb=" OG1 THR A1672 " pdb=" O TYR A1698 " model vdw 2.241 3.040 nonbonded pdb=" OE2 GLU A 258 " pdb=" OH TYR A 453 " model vdw 2.244 3.040 nonbonded pdb=" O ASN A1712 " pdb=" OG SER A1761 " model vdw 2.244 3.040 ... (remaining 130327 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.240 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: 0.250 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 18.150 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 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 0.030 16791 Z= 0.121 Angle : 0.571 7.769 22477 Z= 0.342 Chirality : 0.046 0.186 2240 Planarity : 0.005 0.104 3108 Dihedral : 12.665 86.132 5964 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 3.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % 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 are not related in a simple way. whole: -0.89 (0.16), residues: 2364 helix: -0.75 (0.17), residues: 676 sheet: -0.78 (0.23), residues: 478 loop : -0.25 (0.17), residues: 1210 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.004 ARG A 406 TYR 0.021 0.004 TYR A1740 PHE 0.022 0.001 PHE A1866 TRP 0.010 0.001 TRP A 118 HIS 0.003 0.001 HIS A1387 Details of bonding type rmsd covalent geometry : bond 0.00270 (16791) covalent geometry : angle 0.57104 (22477) hydrogen bonds : bond 0.20988 ( 856) hydrogen bonds : angle 8.83851 ( 2313) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 2137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 199 time to evaluate : 0.457 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.6565 (ttt) cc_final: 0.5522 (ptm) REVERT: A 258 GLU cc_start: 0.7938 (mm-30) cc_final: 0.7702 (mm-30) REVERT: A 327 ILE cc_start: 0.9275 (mt) cc_final: 0.8996 (mt) REVERT: A 467 ASN cc_start: 0.9096 (t0) cc_final: 0.8788 (t0) REVERT: A 495 GLU cc_start: 0.8108 (tt0) cc_final: 0.7855 (tt0) REVERT: A 696 LEU cc_start: 0.9017 (mt) cc_final: 0.8550 (mt) REVERT: A 755 LEU cc_start: 0.8829 (mt) cc_final: 0.8438 (mp) REVERT: A 833 ASP cc_start: 0.8345 (t70) cc_final: 0.7543 (t0) REVERT: A 1509 TYR cc_start: 0.7798 (m-80) cc_final: 0.7567 (m-10) REVERT: A 1582 MET cc_start: 0.9396 (mmm) cc_final: 0.9078 (mmm) outliers start: 0 outliers final: 0 residues processed: 199 average time/residue: 0.1379 time to fit residues: 41.0457 Evaluate side-chains 96 residues out of total 2137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 96 time to evaluate : 0.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 216 optimal weight: 4.9990 chunk 98 optimal weight: 6.9990 chunk 194 optimal weight: 30.0000 chunk 227 optimal weight: 6.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 0.0670 chunk 124 optimal weight: 0.0010 chunk 103 optimal weight: 0.9980 chunk 235 optimal weight: 50.0000 overall best weight: 0.7926 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 264 ASN A 653 HIS A 741 GLN A 876 ASN A1329 GLN A1380 ASN A1653 GLN A1711 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.065215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.050821 restraints weight = 67259.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.052795 restraints weight = 32245.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.054117 restraints weight = 20584.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.055011 restraints weight = 15271.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.055630 restraints weight = 12437.619| |-----------------------------------------------------------------------------| r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.2026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 16791 Z= 0.137 Angle : 0.552 7.067 22477 Z= 0.312 Chirality : 0.046 0.217 2240 Planarity : 0.003 0.038 3108 Dihedral : 5.285 24.776 2483 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 0.68 % Allowed : 5.41 % Favored : 93.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.33 (0.17), residues: 2364 helix: 1.19 (0.19), residues: 691 sheet: -0.87 (0.22), residues: 456 loop : 0.25 (0.18), residues: 1217 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 805 TYR 0.015 0.001 TYR A1645 PHE 0.023 0.001 PHE A 446 TRP 0.007 0.001 TRP A1344 HIS 0.003 0.001 HIS A 579 Details of bonding type rmsd covalent geometry : bond 0.00298 (16791) covalent geometry : angle 0.55214 (22477) hydrogen bonds : bond 0.03870 ( 856) hydrogen bonds : angle 5.74410 ( 2313) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 2137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 126 time to evaluate : 0.664 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.6744 (ttt) cc_final: 0.5687 (ptm) REVERT: A 314 MET cc_start: 0.8630 (mtp) cc_final: 0.7993 (ttm) REVERT: A 467 ASN cc_start: 0.9084 (t0) cc_final: 0.8801 (t0) REVERT: A 696 LEU cc_start: 0.8923 (mt) cc_final: 0.8508 (tt) REVERT: A 755 LEU cc_start: 0.9012 (mt) cc_final: 0.8577 (mp) REVERT: A 756 ASP cc_start: 0.8463 (t70) cc_final: 0.8018 (p0) REVERT: A 833 ASP cc_start: 0.8510 (t70) cc_final: 0.7978 (t0) REVERT: A 839 GLU cc_start: 0.8221 (mp0) cc_final: 0.7705 (mp0) REVERT: A 985 MET cc_start: 0.9132 (mmm) cc_final: 0.8863 (mmm) REVERT: A 1150 LEU cc_start: 0.9060 (tp) cc_final: 0.8697 (tp) REVERT: A 1569 MET cc_start: 0.8797 (mmp) cc_final: 0.8452 (mmp) REVERT: A 1582 MET cc_start: 0.9339 (mmm) cc_final: 0.8683 (tpt) REVERT: A 1785 SER cc_start: 0.8696 (m) cc_final: 0.8486 (p) outliers start: 11 outliers final: 3 residues processed: 137 average time/residue: 0.1129 time to fit residues: 24.9079 Evaluate side-chains 95 residues out of total 2137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 92 time to evaluate : 0.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1352 VAL Chi-restraints excluded: chain A residue 1819 TYR Chi-restraints excluded: chain A residue 1898 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 182 optimal weight: 3.9990 chunk 22 optimal weight: 0.6980 chunk 203 optimal weight: 8.9990 chunk 214 optimal weight: 20.0000 chunk 187 optimal weight: 9.9990 chunk 88 optimal weight: 4.9990 chunk 157 optimal weight: 5.9990 chunk 81 optimal weight: 0.0980 chunk 63 optimal weight: 0.9990 chunk 154 optimal weight: 3.9990 chunk 49 optimal weight: 3.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 802 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1545 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.061776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.047979 restraints weight = 69362.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.049761 restraints weight = 34530.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.050948 restraints weight = 22442.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.051768 restraints weight = 16867.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.052292 restraints weight = 13802.322| |-----------------------------------------------------------------------------| r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.2591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 16791 Z= 0.233 Angle : 0.575 7.126 22477 Z= 0.315 Chirality : 0.046 0.196 2240 Planarity : 0.003 0.037 3108 Dihedral : 4.987 25.631 2483 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 1.29 % Allowed : 7.38 % Favored : 91.33 % 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 are not related in a simple way. whole: 0.48 (0.17), residues: 2364 helix: 1.69 (0.20), residues: 678 sheet: -1.02 (0.22), residues: 469 loop : 0.22 (0.18), residues: 1217 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 805 TYR 0.017 0.002 TYR A1864 PHE 0.017 0.002 PHE A 424 TRP 0.007 0.001 TRP A1344 HIS 0.006 0.001 HIS A1126 Details of bonding type rmsd covalent geometry : bond 0.00520 (16791) covalent geometry : angle 0.57487 (22477) hydrogen bonds : bond 0.03800 ( 856) hydrogen bonds : angle 5.43033 ( 2313) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 2137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 94 time to evaluate : 0.623 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.6900 (ttt) cc_final: 0.5858 (ptm) REVERT: A 289 MET cc_start: 0.8897 (mmm) cc_final: 0.8599 (mmm) REVERT: A 314 MET cc_start: 0.8731 (mtp) cc_final: 0.8251 (mtp) REVERT: A 327 ILE cc_start: 0.8952 (mt) cc_final: 0.8691 (mm) REVERT: A 342 VAL cc_start: 0.8894 (t) cc_final: 0.8555 (p) REVERT: A 467 ASN cc_start: 0.9168 (t0) cc_final: 0.8833 (t0) REVERT: A 1150 LEU cc_start: 0.9044 (tp) cc_final: 0.8652 (tp) REVERT: A 1569 MET cc_start: 0.8791 (mmp) cc_final: 0.8458 (mmp) REVERT: A 1819 TYR cc_start: 0.8598 (OUTLIER) cc_final: 0.7977 (m-80) outliers start: 21 outliers final: 9 residues processed: 112 average time/residue: 0.1052 time to fit residues: 19.8855 Evaluate side-chains 90 residues out of total 2137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 80 time to evaluate : 0.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 187 ILE Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain A residue 675 ILE Chi-restraints excluded: chain A residue 744 VAL Chi-restraints excluded: chain A residue 1045 ILE Chi-restraints excluded: chain A residue 1352 VAL Chi-restraints excluded: chain A residue 1819 TYR Chi-restraints excluded: chain A residue 1870 ASN Chi-restraints excluded: chain A residue 1898 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 94 optimal weight: 4.9990 chunk 143 optimal weight: 1.9990 chunk 80 optimal weight: 0.9990 chunk 191 optimal weight: 10.0000 chunk 128 optimal weight: 20.0000 chunk 17 optimal weight: 0.6980 chunk 149 optimal weight: 5.9990 chunk 127 optimal weight: 50.0000 chunk 209 optimal weight: 0.0980 chunk 137 optimal weight: 0.8980 chunk 157 optimal weight: 2.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 802 GLN ** A1850 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 = 0.3432 r_free = 0.3432 target = 0.062694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.048883 restraints weight = 69344.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.050713 restraints weight = 34537.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.051949 restraints weight = 22429.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.052784 restraints weight = 16820.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.053363 restraints weight = 13723.932| |-----------------------------------------------------------------------------| r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.2944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 16791 Z= 0.130 Angle : 0.486 6.877 22477 Z= 0.268 Chirality : 0.044 0.186 2240 Planarity : 0.003 0.038 3108 Dihedral : 4.521 25.109 2483 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 0.92 % Allowed : 9.28 % Favored : 89.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.71 (0.18), residues: 2364 helix: 2.08 (0.20), residues: 678 sheet: -1.09 (0.22), residues: 486 loop : 0.35 (0.19), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 536 TYR 0.012 0.001 TYR A 255 PHE 0.014 0.001 PHE A 424 TRP 0.006 0.001 TRP A1344 HIS 0.004 0.001 HIS A1126 Details of bonding type rmsd covalent geometry : bond 0.00288 (16791) covalent geometry : angle 0.48649 (22477) hydrogen bonds : bond 0.03223 ( 856) hydrogen bonds : angle 4.93788 ( 2313) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 2137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 98 time to evaluate : 0.524 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.6850 (ttt) cc_final: 0.5811 (ptm) REVERT: A 176 MET cc_start: 0.9085 (tpp) cc_final: 0.8847 (tpp) REVERT: A 467 ASN cc_start: 0.9144 (t0) cc_final: 0.8828 (t0) REVERT: A 536 ARG cc_start: 0.9219 (ttm110) cc_final: 0.8710 (ttm110) REVERT: A 1129 LEU cc_start: 0.9639 (mt) cc_final: 0.9361 (tt) REVERT: A 1569 MET cc_start: 0.8767 (mmp) cc_final: 0.8425 (mmp) REVERT: A 1582 MET cc_start: 0.9290 (mmm) cc_final: 0.8555 (tpp) REVERT: A 1819 TYR cc_start: 0.8546 (OUTLIER) cc_final: 0.8068 (m-80) outliers start: 15 outliers final: 9 residues processed: 110 average time/residue: 0.1074 time to fit residues: 19.6698 Evaluate side-chains 97 residues out of total 2137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 87 time to evaluate : 0.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 ILE Chi-restraints excluded: chain A residue 377 PHE Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 696 LEU Chi-restraints excluded: chain A residue 744 VAL Chi-restraints excluded: chain A residue 791 SER Chi-restraints excluded: chain A residue 1045 ILE Chi-restraints excluded: chain A residue 1352 VAL Chi-restraints excluded: chain A residue 1819 TYR Chi-restraints excluded: chain A residue 1898 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 77 optimal weight: 1.9990 chunk 14 optimal weight: 3.9990 chunk 112 optimal weight: 0.9980 chunk 224 optimal weight: 10.0000 chunk 64 optimal weight: 1.9990 chunk 162 optimal weight: 3.9990 chunk 117 optimal weight: 50.0000 chunk 44 optimal weight: 2.9990 chunk 193 optimal weight: 9.9990 chunk 83 optimal weight: 0.8980 chunk 150 optimal weight: 3.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 802 GLN A 966 GLN A1570 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.061699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.047868 restraints weight = 70022.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.049671 restraints weight = 34933.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.050883 restraints weight = 22731.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.051695 restraints weight = 17049.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 17)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.052174 restraints weight = 13993.057| |-----------------------------------------------------------------------------| r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.3113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 16791 Z= 0.212 Angle : 0.543 8.796 22477 Z= 0.291 Chirality : 0.045 0.219 2240 Planarity : 0.003 0.035 3108 Dihedral : 4.536 24.351 2483 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 1.23 % Allowed : 10.20 % Favored : 88.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.68 (0.18), residues: 2364 helix: 2.06 (0.20), residues: 684 sheet: -1.04 (0.23), residues: 474 loop : 0.27 (0.18), residues: 1206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1353 TYR 0.024 0.001 TYR A 255 PHE 0.014 0.001 PHE A 377 TRP 0.006 0.001 TRP A1344 HIS 0.004 0.001 HIS A1126 Details of bonding type rmsd covalent geometry : bond 0.00474 (16791) covalent geometry : angle 0.54285 (22477) hydrogen bonds : bond 0.03374 ( 856) hydrogen bonds : angle 5.00604 ( 2313) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 2137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 87 time to evaluate : 0.705 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.6795 (ttt) cc_final: 0.5752 (ptm) REVERT: A 176 MET cc_start: 0.9038 (tpp) cc_final: 0.8780 (tpp) REVERT: A 289 MET cc_start: 0.9079 (mmm) cc_final: 0.8164 (mmm) REVERT: A 467 ASN cc_start: 0.9143 (t0) cc_final: 0.8787 (t0) REVERT: A 536 ARG cc_start: 0.9218 (ttm110) cc_final: 0.8650 (ttm110) REVERT: A 1150 LEU cc_start: 0.8867 (tp) cc_final: 0.8495 (tp) REVERT: A 1569 MET cc_start: 0.8728 (mmp) cc_final: 0.8426 (mmp) REVERT: A 1819 TYR cc_start: 0.8594 (OUTLIER) cc_final: 0.8121 (m-80) outliers start: 20 outliers final: 13 residues processed: 103 average time/residue: 0.1018 time to fit residues: 17.7818 Evaluate side-chains 95 residues out of total 2137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 81 time to evaluate : 0.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 187 ILE Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 377 PHE Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain A residue 696 LEU Chi-restraints excluded: chain A residue 744 VAL Chi-restraints excluded: chain A residue 791 SER Chi-restraints excluded: chain A residue 1045 ILE Chi-restraints excluded: chain A residue 1352 VAL Chi-restraints excluded: chain A residue 1649 VAL Chi-restraints excluded: chain A residue 1795 ILE Chi-restraints excluded: chain A residue 1819 TYR Chi-restraints excluded: chain A residue 1898 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 33 optimal weight: 0.0030 chunk 120 optimal weight: 6.9990 chunk 76 optimal weight: 2.9990 chunk 228 optimal weight: 50.0000 chunk 93 optimal weight: 0.9990 chunk 47 optimal weight: 0.6980 chunk 230 optimal weight: 50.0000 chunk 28 optimal weight: 1.9990 chunk 206 optimal weight: 40.0000 chunk 109 optimal weight: 0.0270 chunk 102 optimal weight: 0.0050 overall best weight: 0.3464 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 ASN A1413 ASN ** A1850 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.063548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.049730 restraints weight = 69079.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.051688 restraints weight = 32784.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.052966 restraints weight = 20742.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.053844 restraints weight = 15333.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.054428 restraints weight = 12402.862| |-----------------------------------------------------------------------------| r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.3434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 16791 Z= 0.090 Angle : 0.461 9.260 22477 Z= 0.248 Chirality : 0.043 0.176 2240 Planarity : 0.003 0.039 3108 Dihedral : 4.116 22.879 2483 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 1.17 % Allowed : 10.51 % Favored : 88.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.82 (0.18), residues: 2364 helix: 2.23 (0.20), residues: 689 sheet: -1.08 (0.22), residues: 509 loop : 0.43 (0.19), residues: 1166 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1353 TYR 0.017 0.001 TYR A 255 PHE 0.011 0.001 PHE A 446 TRP 0.007 0.001 TRP A1344 HIS 0.002 0.001 HIS A1126 Details of bonding type rmsd covalent geometry : bond 0.00189 (16791) covalent geometry : angle 0.46137 (22477) hydrogen bonds : bond 0.02837 ( 856) hydrogen bonds : angle 4.59095 ( 2313) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 2137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 99 time to evaluate : 0.570 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.6842 (ttt) cc_final: 0.5899 (ptm) REVERT: A 176 MET cc_start: 0.8980 (tpp) cc_final: 0.8724 (tpp) REVERT: A 289 MET cc_start: 0.8997 (mmm) cc_final: 0.8084 (mmm) REVERT: A 467 ASN cc_start: 0.9173 (t0) cc_final: 0.8792 (t0) REVERT: A 536 ARG cc_start: 0.9286 (ttm110) cc_final: 0.8762 (ttm110) REVERT: A 985 MET cc_start: 0.9123 (mmm) cc_final: 0.8713 (mmm) REVERT: A 1145 MET cc_start: 0.9024 (tpp) cc_final: 0.8577 (tpp) REVERT: A 1150 LEU cc_start: 0.8924 (tp) cc_final: 0.8539 (tp) REVERT: A 1569 MET cc_start: 0.8759 (mmp) cc_final: 0.8428 (mmp) REVERT: A 1819 TYR cc_start: 0.8504 (OUTLIER) cc_final: 0.8005 (m-80) outliers start: 19 outliers final: 11 residues processed: 113 average time/residue: 0.0996 time to fit residues: 18.7172 Evaluate side-chains 95 residues out of total 2137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 83 time to evaluate : 0.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 187 ILE Chi-restraints excluded: chain A residue 314 MET Chi-restraints excluded: chain A residue 377 PHE Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 696 LEU Chi-restraints excluded: chain A residue 744 VAL Chi-restraints excluded: chain A residue 791 SER Chi-restraints excluded: chain A residue 1067 MET Chi-restraints excluded: chain A residue 1352 VAL Chi-restraints excluded: chain A residue 1819 TYR Chi-restraints excluded: chain A residue 1898 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 85 optimal weight: 0.6980 chunk 101 optimal weight: 3.9990 chunk 229 optimal weight: 4.9990 chunk 148 optimal weight: 2.9990 chunk 14 optimal weight: 3.9990 chunk 72 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 124 optimal weight: 0.9980 chunk 36 optimal weight: 5.9990 chunk 52 optimal weight: 4.9990 chunk 185 optimal weight: 3.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 960 ASN A1574 ASN A1870 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.061579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.047681 restraints weight = 69797.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.049536 restraints weight = 33931.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.050752 restraints weight = 21739.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.051592 restraints weight = 16233.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.052168 restraints weight = 13216.133| |-----------------------------------------------------------------------------| r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.3436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 16791 Z= 0.224 Angle : 0.539 9.740 22477 Z= 0.288 Chirality : 0.045 0.177 2240 Planarity : 0.003 0.034 3108 Dihedral : 4.319 21.933 2483 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 1.48 % Allowed : 11.37 % Favored : 87.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.81 (0.18), residues: 2364 helix: 2.23 (0.20), residues: 685 sheet: -0.95 (0.23), residues: 470 loop : 0.30 (0.19), residues: 1209 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1309 TYR 0.027 0.001 TYR A 255 PHE 0.015 0.002 PHE A 377 TRP 0.006 0.001 TRP A 118 HIS 0.004 0.001 HIS A1126 Details of bonding type rmsd covalent geometry : bond 0.00497 (16791) covalent geometry : angle 0.53900 (22477) hydrogen bonds : bond 0.03258 ( 856) hydrogen bonds : angle 4.87613 ( 2313) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 2137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 84 time to evaluate : 0.660 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.6858 (ttt) cc_final: 0.5792 (ptm) REVERT: A 289 MET cc_start: 0.9082 (mmm) cc_final: 0.8458 (mmm) REVERT: A 467 ASN cc_start: 0.9234 (t0) cc_final: 0.8878 (t0) REVERT: A 536 ARG cc_start: 0.9285 (ttm110) cc_final: 0.8824 (ttm110) REVERT: A 985 MET cc_start: 0.9127 (mmm) cc_final: 0.8843 (mmm) REVERT: A 1145 MET cc_start: 0.9050 (tpp) cc_final: 0.8678 (tpt) REVERT: A 1150 LEU cc_start: 0.9045 (tp) cc_final: 0.8676 (tp) REVERT: A 1569 MET cc_start: 0.8820 (mmp) cc_final: 0.8499 (mmp) REVERT: A 1582 MET cc_start: 0.9210 (mmm) cc_final: 0.8638 (tpp) REVERT: A 1819 TYR cc_start: 0.8622 (OUTLIER) cc_final: 0.8197 (m-80) outliers start: 24 outliers final: 16 residues processed: 104 average time/residue: 0.1005 time to fit residues: 17.6983 Evaluate side-chains 99 residues out of total 2137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 82 time to evaluate : 0.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 187 ILE Chi-restraints excluded: chain A residue 314 MET Chi-restraints excluded: chain A residue 377 PHE Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain A residue 696 LEU Chi-restraints excluded: chain A residue 744 VAL Chi-restraints excluded: chain A residue 788 THR Chi-restraints excluded: chain A residue 791 SER Chi-restraints excluded: chain A residue 1032 ILE Chi-restraints excluded: chain A residue 1045 ILE Chi-restraints excluded: chain A residue 1352 VAL Chi-restraints excluded: chain A residue 1649 VAL Chi-restraints excluded: chain A residue 1819 TYR Chi-restraints excluded: chain A residue 1870 ASN Chi-restraints excluded: chain A residue 1898 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 181 optimal weight: 0.9980 chunk 82 optimal weight: 2.9990 chunk 155 optimal weight: 0.7980 chunk 76 optimal weight: 0.9990 chunk 177 optimal weight: 1.9990 chunk 210 optimal weight: 0.9980 chunk 0 optimal weight: 5.9990 chunk 189 optimal weight: 0.9990 chunk 131 optimal weight: 2.9990 chunk 209 optimal weight: 30.0000 chunk 134 optimal weight: 0.9980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1870 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.062224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.048380 restraints weight = 69440.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.050282 restraints weight = 33437.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.051538 restraints weight = 21358.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.052391 restraints weight = 15877.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.052975 restraints weight = 12897.254| |-----------------------------------------------------------------------------| r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.3563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 16791 Z= 0.127 Angle : 0.475 8.960 22477 Z= 0.255 Chirality : 0.044 0.171 2240 Planarity : 0.003 0.039 3108 Dihedral : 4.132 21.203 2483 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 1.17 % Allowed : 11.86 % Favored : 86.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.91 (0.18), residues: 2364 helix: 2.34 (0.20), residues: 683 sheet: -0.92 (0.23), residues: 476 loop : 0.37 (0.19), residues: 1205 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1353 TYR 0.025 0.001 TYR A 255 PHE 0.012 0.001 PHE A 424 TRP 0.006 0.001 TRP A1344 HIS 0.002 0.001 HIS A1126 Details of bonding type rmsd covalent geometry : bond 0.00282 (16791) covalent geometry : angle 0.47477 (22477) hydrogen bonds : bond 0.02936 ( 856) hydrogen bonds : angle 4.64825 ( 2313) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 2137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 85 time to evaluate : 0.491 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.6820 (ttt) cc_final: 0.5780 (ptm) REVERT: A 37 MET cc_start: 0.8799 (ttp) cc_final: 0.8308 (ptm) REVERT: A 176 MET cc_start: 0.9065 (tpp) cc_final: 0.8828 (tpp) REVERT: A 467 ASN cc_start: 0.9192 (t0) cc_final: 0.8782 (t0) REVERT: A 985 MET cc_start: 0.9081 (mmm) cc_final: 0.8713 (mmm) REVERT: A 1145 MET cc_start: 0.9064 (tpp) cc_final: 0.8493 (tpp) REVERT: A 1150 LEU cc_start: 0.8882 (tp) cc_final: 0.8495 (tp) REVERT: A 1569 MET cc_start: 0.8802 (mmp) cc_final: 0.8478 (mmp) REVERT: A 1582 MET cc_start: 0.9212 (mmm) cc_final: 0.8594 (tpp) REVERT: A 1819 TYR cc_start: 0.8562 (OUTLIER) cc_final: 0.8074 (m-80) outliers start: 19 outliers final: 15 residues processed: 101 average time/residue: 0.1049 time to fit residues: 17.8852 Evaluate side-chains 99 residues out of total 2137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 83 time to evaluate : 0.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 ILE Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 187 ILE Chi-restraints excluded: chain A residue 314 MET Chi-restraints excluded: chain A residue 377 PHE Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain A residue 579 HIS Chi-restraints excluded: chain A residue 696 LEU Chi-restraints excluded: chain A residue 788 THR Chi-restraints excluded: chain A residue 791 SER Chi-restraints excluded: chain A residue 1352 VAL Chi-restraints excluded: chain A residue 1395 VAL Chi-restraints excluded: chain A residue 1649 VAL Chi-restraints excluded: chain A residue 1819 TYR Chi-restraints excluded: chain A residue 1898 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 157 optimal weight: 4.9990 chunk 91 optimal weight: 5.9990 chunk 127 optimal weight: 20.0000 chunk 122 optimal weight: 20.0000 chunk 163 optimal weight: 0.9980 chunk 215 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 139 optimal weight: 0.9990 chunk 92 optimal weight: 0.9990 chunk 100 optimal weight: 5.9990 chunk 27 optimal weight: 0.0970 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.063216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.049519 restraints weight = 69590.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.051400 restraints weight = 33324.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.052664 restraints weight = 21183.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.053521 restraints weight = 15667.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.054107 restraints weight = 12682.347| |-----------------------------------------------------------------------------| r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.3685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 16791 Z= 0.134 Angle : 0.483 10.466 22477 Z= 0.257 Chirality : 0.043 0.170 2240 Planarity : 0.003 0.034 3108 Dihedral : 4.065 21.087 2483 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 1.29 % Allowed : 12.11 % Favored : 86.60 % 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 are not related in a simple way. whole: 0.97 (0.18), residues: 2364 helix: 2.40 (0.20), residues: 683 sheet: -0.87 (0.23), residues: 464 loop : 0.37 (0.19), residues: 1217 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 536 TYR 0.020 0.001 TYR A 255 PHE 0.011 0.001 PHE A 377 TRP 0.007 0.001 TRP A1344 HIS 0.004 0.001 HIS A1126 Details of bonding type rmsd covalent geometry : bond 0.00298 (16791) covalent geometry : angle 0.48313 (22477) hydrogen bonds : bond 0.02933 ( 856) hydrogen bonds : angle 4.60484 ( 2313) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 2137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 85 time to evaluate : 0.646 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.6801 (ttt) cc_final: 0.5768 (ptm) REVERT: A 37 MET cc_start: 0.8791 (ttp) cc_final: 0.8442 (ptm) REVERT: A 289 MET cc_start: 0.9182 (mmm) cc_final: 0.8292 (mmm) REVERT: A 985 MET cc_start: 0.9087 (mmm) cc_final: 0.8726 (mmm) REVERT: A 1145 MET cc_start: 0.9056 (tpp) cc_final: 0.8495 (tpp) REVERT: A 1150 LEU cc_start: 0.8887 (tp) cc_final: 0.8513 (tp) REVERT: A 1569 MET cc_start: 0.8784 (mmp) cc_final: 0.8466 (mmp) REVERT: A 1582 MET cc_start: 0.9228 (mmm) cc_final: 0.8578 (tpp) REVERT: A 1819 TYR cc_start: 0.8560 (OUTLIER) cc_final: 0.8093 (m-80) outliers start: 21 outliers final: 17 residues processed: 103 average time/residue: 0.1038 time to fit residues: 18.2274 Evaluate side-chains 102 residues out of total 2137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 84 time to evaluate : 0.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 ILE Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 187 ILE Chi-restraints excluded: chain A residue 314 MET Chi-restraints excluded: chain A residue 377 PHE Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain A residue 579 HIS Chi-restraints excluded: chain A residue 696 LEU Chi-restraints excluded: chain A residue 788 THR Chi-restraints excluded: chain A residue 791 SER Chi-restraints excluded: chain A residue 1032 ILE Chi-restraints excluded: chain A residue 1045 ILE Chi-restraints excluded: chain A residue 1352 VAL Chi-restraints excluded: chain A residue 1395 VAL Chi-restraints excluded: chain A residue 1649 VAL Chi-restraints excluded: chain A residue 1819 TYR Chi-restraints excluded: chain A residue 1898 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 209 optimal weight: 7.9990 chunk 72 optimal weight: 0.2980 chunk 138 optimal weight: 0.9990 chunk 50 optimal weight: 0.0170 chunk 43 optimal weight: 0.9980 chunk 134 optimal weight: 3.9990 chunk 146 optimal weight: 0.9980 chunk 192 optimal weight: 30.0000 chunk 211 optimal weight: 0.4980 chunk 121 optimal weight: 0.0670 chunk 223 optimal weight: 20.0000 overall best weight: 0.3756 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 151 ASN A 492 HIS A 510 GLN ** A1850 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 = 0.3454 r_free = 0.3454 target = 0.063601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.050148 restraints weight = 69130.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.052025 restraints weight = 34137.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.053265 restraints weight = 21985.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.054119 restraints weight = 16388.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.054712 restraints weight = 13284.689| |-----------------------------------------------------------------------------| r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.3924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 16791 Z= 0.087 Angle : 0.461 10.428 22477 Z= 0.243 Chirality : 0.043 0.165 2240 Planarity : 0.003 0.038 3108 Dihedral : 3.826 20.753 2483 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 0.80 % Allowed : 12.48 % Favored : 86.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.04 (0.18), residues: 2364 helix: 2.50 (0.20), residues: 685 sheet: -0.92 (0.23), residues: 493 loop : 0.46 (0.19), residues: 1186 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 536 TYR 0.019 0.001 TYR A 255 PHE 0.012 0.001 PHE A 424 TRP 0.006 0.001 TRP A1344 HIS 0.004 0.001 HIS A1126 Details of bonding type rmsd covalent geometry : bond 0.00186 (16791) covalent geometry : angle 0.46100 (22477) hydrogen bonds : bond 0.02656 ( 856) hydrogen bonds : angle 4.35902 ( 2313) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 2137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 92 time to evaluate : 0.629 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.6806 (ttt) cc_final: 0.5800 (ptm) REVERT: A 289 MET cc_start: 0.9170 (mmm) cc_final: 0.8205 (mmm) REVERT: A 436 MET cc_start: 0.8567 (mmp) cc_final: 0.8365 (mmt) REVERT: A 1121 VAL cc_start: 0.9517 (t) cc_final: 0.9272 (p) REVERT: A 1145 MET cc_start: 0.9048 (tpp) cc_final: 0.8616 (tpp) REVERT: A 1569 MET cc_start: 0.8762 (mmp) cc_final: 0.8439 (mmp) REVERT: A 1582 MET cc_start: 0.9204 (mmm) cc_final: 0.8604 (tpp) REVERT: A 1819 TYR cc_start: 0.8481 (OUTLIER) cc_final: 0.7990 (m-80) outliers start: 13 outliers final: 8 residues processed: 104 average time/residue: 0.1012 time to fit residues: 18.1586 Evaluate side-chains 94 residues out of total 2137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 85 time to evaluate : 0.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 ILE Chi-restraints excluded: chain A residue 377 PHE Chi-restraints excluded: chain A residue 696 LEU Chi-restraints excluded: chain A residue 791 SER Chi-restraints excluded: chain A residue 1045 ILE Chi-restraints excluded: chain A residue 1352 VAL Chi-restraints excluded: chain A residue 1395 VAL Chi-restraints excluded: chain A residue 1819 TYR Chi-restraints excluded: chain A residue 1898 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 16 optimal weight: 2.9990 chunk 197 optimal weight: 10.0000 chunk 33 optimal weight: 0.3980 chunk 234 optimal weight: 50.0000 chunk 87 optimal weight: 4.9990 chunk 104 optimal weight: 3.9990 chunk 72 optimal weight: 0.7980 chunk 112 optimal weight: 0.7980 chunk 204 optimal weight: 0.1980 chunk 6 optimal weight: 0.5980 chunk 94 optimal weight: 2.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 579 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1850 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 = 0.3449 r_free = 0.3449 target = 0.063356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.049905 restraints weight = 68732.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.051761 restraints weight = 34054.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.053001 restraints weight = 21982.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.053841 restraints weight = 16362.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.054414 restraints weight = 13324.040| |-----------------------------------------------------------------------------| r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.3997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 16791 Z= 0.096 Angle : 0.456 10.812 22477 Z= 0.241 Chirality : 0.043 0.198 2240 Planarity : 0.003 0.034 3108 Dihedral : 3.768 20.751 2483 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 0.74 % Allowed : 12.60 % Favored : 86.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.06 (0.18), residues: 2364 helix: 2.47 (0.20), residues: 689 sheet: -0.92 (0.23), residues: 502 loop : 0.52 (0.19), residues: 1173 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 536 TYR 0.031 0.001 TYR A 255 PHE 0.011 0.001 PHE A 424 TRP 0.006 0.001 TRP A1344 HIS 0.004 0.001 HIS A1126 Details of bonding type rmsd covalent geometry : bond 0.00211 (16791) covalent geometry : angle 0.45583 (22477) hydrogen bonds : bond 0.02697 ( 856) hydrogen bonds : angle 4.37312 ( 2313) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2519.66 seconds wall clock time: 44 minutes 23.12 seconds (2663.12 seconds total)