Starting phenix.real_space_refine on Fri Mar 6 08:23:20 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7zke_14762/03_2026/7zke_14762.cif Found real_map, /net/cci-nas-00/data/ceres_data/7zke_14762/03_2026/7zke_14762.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7zke_14762/03_2026/7zke_14762.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7zke_14762/03_2026/7zke_14762.map" model { file = "/net/cci-nas-00/data/ceres_data/7zke_14762/03_2026/7zke_14762.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7zke_14762/03_2026/7zke_14762.cif" } resolution = 3.6 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= 0.004 sd= 0.091 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: 9 Type Number sf(0) Gaussians P 22 5.49 5 Mg 1 5.21 5 S 73 5.16 5 Be 1 3.05 5 C 9225 2.51 5 N 2571 2.21 5 O 2728 1.98 5 F 3 1.80 5 H 14679 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 29303 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 315 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 315 Classifications: {'DNA': 10} Link IDs: {'rna3p': 9} Chain: "B" Number of atoms: 315 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 315 Classifications: {'DNA': 10} Link IDs: {'rna3p': 9} Chain: "D" Number of atoms: 2907 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 2907 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 8, 'TRANS': 169} Chain: "E" Number of atoms: 25734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1623, 25734 Classifications: {'peptide': 1623} Link IDs: {'PTRANS': 84, 'TRANS': 1538} Chain breaks: 7 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 4.63, per 1000 atoms: 0.16 Number of scatterers: 29303 At special positions: 0 Unit cell: (100.416, 121.336, 149.578, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 9 Type Number sf(0) S 73 16.00 P 22 15.00 Mg 1 11.99 F 3 9.00 O 2728 8.00 N 2571 7.00 C 9225 6.00 Be 1 4.00 H 14679 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.49 Conformation dependent library (CDL) restraints added in 709.0 milliseconds 3566 Ramachandran restraints generated. 1783 Oldfield, 0 Emsley, 1783 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3408 Finding SS restraints... Secondary structure from input PDB file: 104 helices and 4 sheets defined 68.7% alpha, 5.4% beta 9 base pairs and 13 stacking pairs defined. Time for finding SS restraints: 4.68 Creating SS restraints... Processing helix chain 'D' and resid 96 through 104 removed outlier: 3.818A pdb=" N ILE D 100 " --> pdb=" O ASP D 96 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ALA D 101 " --> pdb=" O LEU D 97 " (cutoff:3.500A) Processing helix chain 'D' and resid 143 through 161 Processing helix chain 'D' and resid 186 through 194 removed outlier: 3.594A pdb=" N LEU D 190 " --> pdb=" O ARG D 186 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N HIS D 194 " --> pdb=" O LEU D 190 " (cutoff:3.500A) Processing helix chain 'D' and resid 234 through 250 removed outlier: 3.711A pdb=" N ILE D 238 " --> pdb=" O VAL D 234 " (cutoff:3.500A) Proline residue: D 247 - end of helix Processing helix chain 'E' and resid 3 through 14 removed outlier: 3.931A pdb=" N LEU E 12 " --> pdb=" O LEU E 8 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N GLU E 13 " --> pdb=" O VAL E 9 " (cutoff:3.500A) Processing helix chain 'E' and resid 17 through 35 Processing helix chain 'E' and resid 38 through 47 removed outlier: 3.823A pdb=" N ARG E 45 " --> pdb=" O ASN E 41 " (cutoff:3.500A) Processing helix chain 'E' and resid 48 through 52 removed outlier: 3.562A pdb=" N ARG E 51 " --> pdb=" O PRO E 48 " (cutoff:3.500A) Processing helix chain 'E' and resid 54 through 72 removed outlier: 3.655A pdb=" N ASN E 71 " --> pdb=" O LYS E 67 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ALA E 72 " --> pdb=" O ILE E 68 " (cutoff:3.500A) Processing helix chain 'E' and resid 111 through 115 Processing helix chain 'E' and resid 116 through 123 removed outlier: 3.546A pdb=" N ILE E 120 " --> pdb=" O ASP E 116 " (cutoff:3.500A) Processing helix chain 'E' and resid 134 through 139 Processing helix chain 'E' and resid 141 through 157 removed outlier: 4.041A pdb=" N ASN E 154 " --> pdb=" O LYS E 150 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N GLY E 155 " --> pdb=" O LYS E 151 " (cutoff:3.500A) Processing helix chain 'E' and resid 165 through 169 Processing helix chain 'E' and resid 313 through 324 removed outlier: 3.764A pdb=" N VAL E 322 " --> pdb=" O GLU E 318 " (cutoff:3.500A) Processing helix chain 'E' and resid 328 through 347 Processing helix chain 'E' and resid 348 through 350 No H-bonds generated for 'chain 'E' and resid 348 through 350' Processing helix chain 'E' and resid 357 through 383 removed outlier: 3.538A pdb=" N ARG E 375 " --> pdb=" O ASP E 371 " (cutoff:3.500A) Processing helix chain 'E' and resid 395 through 412 removed outlier: 4.458A pdb=" N HIS E 411 " --> pdb=" O ALA E 407 " (cutoff:3.500A) Processing helix chain 'E' and resid 413 through 430 removed outlier: 3.807A pdb=" N HIS E 418 " --> pdb=" O VAL E 414 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ALA E 419 " --> pdb=" O GLU E 415 " (cutoff:3.500A) Processing helix chain 'E' and resid 438 through 457 removed outlier: 3.599A pdb=" N VAL E 442 " --> pdb=" O ASN E 438 " (cutoff:3.500A) Processing helix chain 'E' and resid 457 through 462 removed outlier: 3.934A pdb=" N LEU E 461 " --> pdb=" O ARG E 457 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LEU E 462 " --> pdb=" O LYS E 458 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 457 through 462' Processing helix chain 'E' and resid 464 through 480 removed outlier: 4.244A pdb=" N ILE E 468 " --> pdb=" O ASP E 464 " (cutoff:3.500A) Processing helix chain 'E' and resid 483 through 495 removed outlier: 3.707A pdb=" N LEU E 494 " --> pdb=" O SER E 490 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ILE E 495 " --> pdb=" O ALA E 491 " (cutoff:3.500A) Processing helix chain 'E' and resid 497 through 502 Processing helix chain 'E' and resid 505 through 522 removed outlier: 3.510A pdb=" N LEU E 509 " --> pdb=" O ARG E 505 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N LEU E 520 " --> pdb=" O VAL E 516 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ASN E 522 " --> pdb=" O GLU E 518 " (cutoff:3.500A) Processing helix chain 'E' and resid 530 through 542 Processing helix chain 'E' and resid 544 through 556 removed outlier: 3.550A pdb=" N LEU E 548 " --> pdb=" O PHE E 544 " (cutoff:3.500A) Processing helix chain 'E' and resid 558 through 561 Processing helix chain 'E' and resid 562 through 567 Processing helix chain 'E' and resid 568 through 574 Proline residue: E 572 - end of helix Processing helix chain 'E' and resid 578 through 594 Processing helix chain 'E' and resid 596 through 601 removed outlier: 3.594A pdb=" N SER E 600 " --> pdb=" O GLY E 596 " (cutoff:3.500A) Processing helix chain 'E' and resid 605 through 618 Processing helix chain 'E' and resid 621 through 643 removed outlier: 3.575A pdb=" N ARG E 642 " --> pdb=" O ARG E 638 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ASP E 643 " --> pdb=" O LEU E 639 " (cutoff:3.500A) Processing helix chain 'E' and resid 643 through 653 removed outlier: 4.726A pdb=" N ALA E 653 " --> pdb=" O ASP E 649 " (cutoff:3.500A) Processing helix chain 'E' and resid 654 through 663 Processing helix chain 'E' and resid 676 through 680 Processing helix chain 'E' and resid 744 through 766 removed outlier: 3.978A pdb=" N PHE E 765 " --> pdb=" O LEU E 761 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ILE E 766 " --> pdb=" O ILE E 762 " (cutoff:3.500A) Processing helix chain 'E' and resid 767 through 770 Processing helix chain 'E' and resid 771 through 783 removed outlier: 3.812A pdb=" N ALA E 781 " --> pdb=" O ALA E 777 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N SER E 783 " --> pdb=" O LEU E 779 " (cutoff:3.500A) Processing helix chain 'E' and resid 786 through 804 Processing helix chain 'E' and resid 806 through 811 removed outlier: 3.842A pdb=" N ALA E 810 " --> pdb=" O THR E 806 " (cutoff:3.500A) Processing helix chain 'E' and resid 813 through 823 removed outlier: 3.799A pdb=" N ILE E 820 " --> pdb=" O PRO E 816 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ILE E 821 " --> pdb=" O LEU E 817 " (cutoff:3.500A) Processing helix chain 'E' and resid 829 through 831 No H-bonds generated for 'chain 'E' and resid 829 through 831' Processing helix chain 'E' and resid 832 through 853 removed outlier: 3.529A pdb=" N VAL E 836 " --> pdb=" O LEU E 832 " (cutoff:3.500A) Processing helix chain 'E' and resid 880 through 890 Processing helix chain 'E' and resid 890 through 899 Processing helix chain 'E' and resid 903 through 947 Proline residue: E 909 - end of helix removed outlier: 4.858A pdb=" N GLU E 913 " --> pdb=" O PRO E 909 " (cutoff:3.500A) Processing helix chain 'E' and resid 954 through 968 Processing helix chain 'E' and resid 970 through 992 removed outlier: 3.580A pdb=" N GLN E 986 " --> pdb=" O ALA E 982 " (cutoff:3.500A) Processing helix chain 'E' and resid 993 through 1009 removed outlier: 3.913A pdb=" N ALA E 997 " --> pdb=" O ARG E 993 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N CYS E1009 " --> pdb=" O VAL E1005 " (cutoff:3.500A) Processing helix chain 'E' and resid 1017 through 1022 removed outlier: 3.700A pdb=" N HIS E1021 " --> pdb=" O GLU E1017 " (cutoff:3.500A) Processing helix chain 'E' and resid 1028 through 1033 removed outlier: 3.524A pdb=" N GLN E1032 " --> pdb=" O ILE E1028 " (cutoff:3.500A) Processing helix chain 'E' and resid 1044 through 1072 Processing helix chain 'E' and resid 1074 through 1079 Processing helix chain 'E' and resid 1079 through 1095 removed outlier: 3.862A pdb=" N ARG E1083 " --> pdb=" O VAL E1079 " (cutoff:3.500A) Proline residue: E1089 - end of helix Processing helix chain 'E' and resid 1099 through 1104 Processing helix chain 'E' and resid 1108 through 1124 Processing helix chain 'E' and resid 1128 through 1130 No H-bonds generated for 'chain 'E' and resid 1128 through 1130' Processing helix chain 'E' and resid 1131 through 1147 Proline residue: E1140 - end of helix removed outlier: 3.647A pdb=" N ARG E1147 " --> pdb=" O ILE E1143 " (cutoff:3.500A) Processing helix chain 'E' and resid 1150 through 1168 Processing helix chain 'E' and resid 1168 through 1180 removed outlier: 4.132A pdb=" N THR E1174 " --> pdb=" O VAL E1170 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ALA E1175 " --> pdb=" O ASP E1171 " (cutoff:3.500A) Processing helix chain 'E' and resid 1181 through 1184 Processing helix chain 'E' and resid 1189 through 1208 removed outlier: 4.115A pdb=" N ARG E1193 " --> pdb=" O ASP E1189 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLY E1208 " --> pdb=" O ILE E1204 " (cutoff:3.500A) Processing helix chain 'E' and resid 1211 through 1213 No H-bonds generated for 'chain 'E' and resid 1211 through 1213' Processing helix chain 'E' and resid 1214 through 1224 removed outlier: 3.944A pdb=" N VAL E1220 " --> pdb=" O ILE E1216 " (cutoff:3.500A) Proline residue: E1221 - end of helix Processing helix chain 'E' and resid 1230 through 1245 removed outlier: 3.532A pdb=" N THR E1243 " --> pdb=" O THR E1239 " (cutoff:3.500A) Processing helix chain 'E' and resid 1246 through 1251 Proline residue: E1249 - end of helix No H-bonds generated for 'chain 'E' and resid 1246 through 1251' Processing helix chain 'E' and resid 1261 through 1280 removed outlier: 3.522A pdb=" N LEU E1265 " --> pdb=" O SER E1261 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLU E1271 " --> pdb=" O GLY E1267 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N THR E1273 " --> pdb=" O ASP E1269 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N PHE E1274 " --> pdb=" O ARG E1270 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ASP E1280 " --> pdb=" O ALA E1276 " (cutoff:3.500A) Processing helix chain 'E' and resid 1281 through 1284 Processing helix chain 'E' and resid 1298 through 1315 Processing helix chain 'E' and resid 1327 through 1351 removed outlier: 3.610A pdb=" N GLN E1331 " --> pdb=" O GLY E1327 " (cutoff:3.500A) Processing helix chain 'E' and resid 1352 through 1356 Processing helix chain 'E' and resid 1365 through 1367 No H-bonds generated for 'chain 'E' and resid 1365 through 1367' Processing helix chain 'E' and resid 1368 through 1380 Processing helix chain 'E' and resid 1391 through 1398 Processing helix chain 'E' and resid 1400 through 1405 removed outlier: 4.026A pdb=" N ASP E1403 " --> pdb=" O ASP E1400 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N THR E1405 " --> pdb=" O LEU E1402 " (cutoff:3.500A) Processing helix chain 'E' and resid 1412 through 1418 Processing helix chain 'E' and resid 1418 through 1423 Processing helix chain 'E' and resid 1435 through 1439 Processing helix chain 'E' and resid 1443 through 1450 Processing helix chain 'E' and resid 1468 through 1471 Processing helix chain 'E' and resid 1472 through 1480 Processing helix chain 'E' and resid 1486 through 1494 Processing helix chain 'E' and resid 1494 through 1503 removed outlier: 4.245A pdb=" N TYR E1503 " --> pdb=" O ALA E1499 " (cutoff:3.500A) Processing helix chain 'E' and resid 1507 through 1526 Processing helix chain 'E' and resid 1533 through 1538 removed outlier: 4.091A pdb=" N VAL E1537 " --> pdb=" O LEU E1533 " (cutoff:3.500A) Processing helix chain 'E' and resid 1554 through 1568 Processing helix chain 'E' and resid 1568 through 1576 Processing helix chain 'E' and resid 1580 through 1600 Processing helix chain 'E' and resid 1600 through 1605 removed outlier: 4.468A pdb=" N VAL E1604 " --> pdb=" O SER E1600 " (cutoff:3.500A) Processing helix chain 'E' and resid 1611 through 1623 Processing helix chain 'E' and resid 1628 through 1631 Processing helix chain 'E' and resid 1632 through 1645 removed outlier: 3.632A pdb=" N GLY E1636 " --> pdb=" O ALA E1632 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ARG E1639 " --> pdb=" O LEU E1635 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N ASP E1640 " --> pdb=" O GLY E1636 " (cutoff:3.500A) Processing helix chain 'E' and resid 1673 through 1687 removed outlier: 4.020A pdb=" N LEU E1685 " --> pdb=" O GLN E1681 " (cutoff:3.500A) Processing helix chain 'E' and resid 1702 through 1716 removed outlier: 4.226A pdb=" N GLN E1707 " --> pdb=" O ALA E1703 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N ASP E1708 " --> pdb=" O ASN E1704 " (cutoff:3.500A) Processing helix chain 'E' and resid 1726 through 1730 Processing helix chain 'E' and resid 1749 through 1759 removed outlier: 3.653A pdb=" N ASP E1753 " --> pdb=" O ASN E1749 " (cutoff:3.500A) Processing helix chain 'E' and resid 1778 through 1785 removed outlier: 3.763A pdb=" N GLU E1781 " --> pdb=" O GLY E1778 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N LEU E1785 " --> pdb=" O GLU E1782 " (cutoff:3.500A) Processing helix chain 'E' and resid 1786 through 1791 removed outlier: 3.928A pdb=" N PHE E1790 " --> pdb=" O SER E1786 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LYS E1791 " --> pdb=" O LEU E1787 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 1786 through 1791' Processing helix chain 'E' and resid 1856 through 1860 Processing helix chain 'E' and resid 1869 through 1876 removed outlier: 3.509A pdb=" N SER E1875 " --> pdb=" O GLN E1871 " (cutoff:3.500A) Processing helix chain 'E' and resid 1877 through 1884 removed outlier: 3.585A pdb=" N THR E1884 " --> pdb=" O GLY E1880 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'D' and resid 117 through 121 removed outlier: 3.790A pdb=" N GLY D 140 " --> pdb=" O ILE D 85 " (cutoff:3.500A) removed outlier: 5.613A pdb=" N ILE D 85 " --> pdb=" O GLY D 140 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N LEU D 82 " --> pdb=" O GLY D 177 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N GLY D 177 " --> pdb=" O LEU D 82 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N ASN D 84 " --> pdb=" O ILE D 175 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N ILE D 175 " --> pdb=" O ASN D 84 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N VAL D 86 " --> pdb=" O GLN D 173 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N ILE D 175 " --> pdb=" O GLY D 231 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N GLY D 231 " --> pdb=" O ILE D 175 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'E' and resid 667 through 668 removed outlier: 3.789A pdb=" N VAL E 668 " --> pdb=" O HIS E 671 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 1385 through 1388 removed outlier: 4.684A pdb=" N SER E1411 " --> pdb=" O TYR E1388 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N LEU E1361 " --> pdb=" O VAL E1431 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N ASP E1433 " --> pdb=" O LEU E1361 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N ILE E1363 " --> pdb=" O ASP E1433 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N CYS E1430 " --> pdb=" O LEU E1458 " (cutoff:3.500A) removed outlier: 7.731A pdb=" N LEU E1460 " --> pdb=" O CYS E1430 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N LEU E1432 " --> pdb=" O LEU E1460 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N GLY E1318 " --> pdb=" O ARG E1457 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ILE E1459 " --> pdb=" O GLY E1318 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 1544 through 1551 removed outlier: 6.444A pdb=" N ILE E1545 " --> pdb=" O VAL E1771 " (cutoff:3.500A) removed outlier: 7.814A pdb=" N ARG E1773 " --> pdb=" O ILE E1545 " (cutoff:3.500A) removed outlier: 7.307A pdb=" N GLN E1547 " --> pdb=" O ARG E1773 " (cutoff:3.500A) removed outlier: 7.851A pdb=" N ILE E1775 " --> pdb=" O GLN E1547 " (cutoff:3.500A) removed outlier: 5.949A pdb=" N TYR E1549 " --> pdb=" O ILE E1775 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N VAL E1741 " --> pdb=" O TYR E1772 " (cutoff:3.500A) removed outlier: 7.292A pdb=" N ILE E1774 " --> pdb=" O VAL E1741 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N PHE E1743 " --> pdb=" O ILE E1774 " (cutoff:3.500A) removed outlier: 8.251A pdb=" N THR E1776 " --> pdb=" O PHE E1743 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N LEU E1668 " --> pdb=" O ILE E1742 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N ALA E1667 " --> pdb=" O LEU E1722 " (cutoff:3.500A) removed outlier: 7.833A pdb=" N LEU E1724 " --> pdb=" O ALA E1667 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N ILE E1669 " --> pdb=" O LEU E1724 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N LEU E1695 " --> pdb=" O LEU E1723 " (cutoff:3.500A) removed outlier: 8.517A pdb=" N THR E1725 " --> pdb=" O LEU E1695 " (cutoff:3.500A) removed outlier: 8.010A pdb=" N LEU E1697 " --> pdb=" O THR E1725 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 785 hydrogen bonds defined for protein. 2256 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 27 hydrogen bonds 54 hydrogen bond angles 0 basepair planarities 9 basepair parallelities 13 stacking parallelities Total time for adding SS restraints: 7.25 Time building geometry restraints manager: 3.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 14657 1.03 - 1.22: 22 1.22 - 1.42: 5999 1.42 - 1.62: 8805 1.62 - 1.81: 128 Bond restraints: 29611 Sorted by residual: bond pdb=" C1' ADP E1902 " pdb=" C2' ADP E1902 " ideal model delta sigma weight residual 1.524 1.302 0.222 2.00e-02 2.50e+03 1.23e+02 bond pdb=" C1' ADP E1902 " pdb=" O4' ADP E1902 " ideal model delta sigma weight residual 1.426 1.622 -0.196 2.00e-02 2.50e+03 9.58e+01 bond pdb=" C4 ADP E1902 " pdb=" C5 ADP E1902 " ideal model delta sigma weight residual 1.490 1.329 0.161 2.00e-02 2.50e+03 6.45e+01 bond pdb=" C4' ADP E1902 " pdb=" O4' ADP E1902 " ideal model delta sigma weight residual 1.426 1.303 0.123 2.00e-02 2.50e+03 3.81e+01 bond pdb=" C5 ADP E1902 " pdb=" C6 ADP E1902 " ideal model delta sigma weight residual 1.490 1.370 0.120 2.00e-02 2.50e+03 3.57e+01 ... (remaining 29606 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.70: 53609 3.70 - 7.39: 124 7.39 - 11.09: 9 11.09 - 14.78: 1 14.78 - 18.48: 2 Bond angle restraints: 53745 Sorted by residual: angle pdb=" N1 ADP E1902 " pdb=" C6 ADP E1902 " pdb=" N6 ADP E1902 " ideal model delta sigma weight residual 120.00 101.52 18.48 3.00e+00 1.11e-01 3.79e+01 angle pdb=" C5 ADP E1902 " pdb=" C6 ADP E1902 " pdb=" N6 ADP E1902 " ideal model delta sigma weight residual 120.00 138.32 -18.32 3.00e+00 1.11e-01 3.73e+01 angle pdb=" F2 BEF E1903 " pdb="BE BEF E1903 " pdb=" F3 BEF E1903 " ideal model delta sigma weight residual 119.96 107.32 12.64 3.00e+00 1.11e-01 1.78e+01 angle pdb=" O2B ADP E1902 " pdb=" PB ADP E1902 " pdb=" O3B ADP E1902 " ideal model delta sigma weight residual 119.90 109.05 10.85 3.00e+00 1.11e-01 1.31e+01 angle pdb=" O1A ADP E1902 " pdb=" PA ADP E1902 " pdb=" O2A ADP E1902 " ideal model delta sigma weight residual 119.90 109.81 10.09 3.00e+00 1.11e-01 1.13e+01 ... (remaining 53740 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.50: 12541 19.50 - 38.99: 861 38.99 - 58.49: 249 58.49 - 77.99: 36 77.99 - 97.48: 11 Dihedral angle restraints: 13698 sinusoidal: 7759 harmonic: 5939 Sorted by residual: dihedral pdb=" O1B ADP E1902 " pdb=" O3A ADP E1902 " pdb=" PB ADP E1902 " pdb=" PA ADP E1902 " ideal model delta sinusoidal sigma weight residual -60.00 -157.49 97.48 1 2.00e+01 2.50e-03 2.71e+01 dihedral pdb=" CA ALA E1667 " pdb=" C ALA E1667 " pdb=" N LEU E1668 " pdb=" CA LEU E1668 " ideal model delta harmonic sigma weight residual 180.00 157.59 22.41 0 5.00e+00 4.00e-02 2.01e+01 dihedral pdb=" CA ASP D 96 " pdb=" C ASP D 96 " pdb=" N LEU D 97 " pdb=" CA LEU D 97 " ideal model delta harmonic sigma weight residual -180.00 -158.20 -21.80 0 5.00e+00 4.00e-02 1.90e+01 ... (remaining 13695 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 1519 0.035 - 0.070: 579 0.070 - 0.106: 154 0.106 - 0.141: 79 0.141 - 0.176: 6 Chirality restraints: 2337 Sorted by residual: chirality pdb=" CA THR E1124 " pdb=" N THR E1124 " pdb=" C THR E1124 " pdb=" CB THR E1124 " both_signs ideal model delta sigma weight residual False 2.53 2.35 0.18 2.00e-01 2.50e+01 7.74e-01 chirality pdb=" CA ILE E 766 " pdb=" N ILE E 766 " pdb=" C ILE E 766 " pdb=" CB ILE E 766 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 6.89e-01 chirality pdb=" CA THR E 768 " pdb=" N THR E 768 " pdb=" C THR E 768 " pdb=" CB THR E 768 " both_signs ideal model delta sigma weight residual False 2.53 2.36 0.16 2.00e-01 2.50e+01 6.55e-01 ... (remaining 2334 not shown) Planarity restraints: 4246 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL E 567 " -0.034 5.00e-02 4.00e+02 5.11e-02 4.18e+00 pdb=" N PRO E 568 " 0.088 5.00e-02 4.00e+02 pdb=" CA PRO E 568 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO E 568 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS E1132 " 0.030 5.00e-02 4.00e+02 4.49e-02 3.23e+00 pdb=" N PRO E1133 " -0.078 5.00e-02 4.00e+02 pdb=" CA PRO E1133 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO E1133 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU E 815 " -0.029 5.00e-02 4.00e+02 4.38e-02 3.07e+00 pdb=" N PRO E 816 " 0.076 5.00e-02 4.00e+02 pdb=" CA PRO E 816 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO E 816 " -0.025 5.00e-02 4.00e+02 ... (remaining 4243 not shown) Histogram of nonbonded interaction distances: 1.64 - 2.24: 2563 2.24 - 2.83: 65257 2.83 - 3.42: 77746 3.42 - 4.01: 103969 4.01 - 4.60: 162492 Nonbonded interactions: 412027 Sorted by model distance: nonbonded pdb=" OE1 GLU E 619 " pdb=" H GLU E 619 " model vdw 1.644 2.450 nonbonded pdb="HH11 ARG D 105 " pdb=" OH TYR E1872 " model vdw 1.661 2.450 nonbonded pdb=" HE ARG E1395 " pdb=" OD2 ASP E1418 " model vdw 1.666 2.450 nonbonded pdb=" OE1 GLU E1017 " pdb=" H GLU E1017 " model vdw 1.671 2.450 nonbonded pdb=" O ASN D 90 " pdb=" HG1 THR D 168 " model vdw 1.682 2.450 ... (remaining 412022 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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: 1.370 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: 0.150 Extract box with map and model: 0.430 Check model and map are aligned: 0.080 Set scattering table: 0.080 Process input model: 30.510 Find NCS groups from input model: 0.100 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:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6607 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 : 0.006 0.222 14932 Z= 0.281 Angle : 0.788 18.475 20293 Z= 0.413 Chirality : 0.043 0.176 2337 Planarity : 0.005 0.051 2535 Dihedral : 13.108 97.485 5692 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 1.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 0.26 % Allowed : 2.92 % Favored : 96.82 % 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: 0.40 (0.20), residues: 1783 helix: 0.52 (0.16), residues: 997 sheet: -0.89 (0.43), residues: 114 loop : 0.36 (0.26), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E1595 TYR 0.016 0.002 TYR E1155 PHE 0.015 0.002 PHE E1192 TRP 0.014 0.002 TRP E 55 HIS 0.007 0.001 HIS E 333 Details of bonding type rmsd covalent geometry : bond 0.00614 (14932) covalent geometry : angle 0.78770 (20293) hydrogen bonds : bond 0.14576 ( 812) hydrogen bonds : angle 5.99887 ( 2310) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3566 Ramachandran restraints generated. 1783 Oldfield, 0 Emsley, 1783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3566 Ramachandran restraints generated. 1783 Oldfield, 0 Emsley, 1783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 507 is missing expected H atoms. Skipping. Evaluate side-chains 383 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 379 time to evaluate : 0.754 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 439 MET cc_start: 0.6073 (ttm) cc_final: 0.5531 (tpp) REVERT: E 493 THR cc_start: 0.5454 (m) cc_final: 0.5232 (m) REVERT: E 827 SER cc_start: 0.8011 (p) cc_final: 0.7755 (t) REVERT: E 1066 ILE cc_start: 0.8284 (mt) cc_final: 0.8030 (mt) REVERT: E 1491 LEU cc_start: 0.7548 (mt) cc_final: 0.6950 (tp) REVERT: E 1549 TYR cc_start: 0.6198 (t80) cc_final: 0.5755 (t80) REVERT: E 1707 GLN cc_start: 0.7951 (tp40) cc_final: 0.7708 (tp40) outliers start: 4 outliers final: 0 residues processed: 381 average time/residue: 0.3045 time to fit residues: 165.3679 Evaluate side-chains 214 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 214 time to evaluate : 0.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 98 optimal weight: 4.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 0.5980 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 3.9990 chunk 149 optimal weight: 7.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 803 ASN E 910 GLN E1032 GLN E1599 ASN ** E1746 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.154932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.109458 restraints weight = 63657.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.113263 restraints weight = 46557.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.114665 restraints weight = 28793.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.115534 restraints weight = 22055.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.115936 restraints weight = 20504.372| |-----------------------------------------------------------------------------| r_work (final): 0.3445 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7178 moved from start: 0.2863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 14932 Z= 0.172 Angle : 0.630 9.375 20293 Z= 0.329 Chirality : 0.040 0.146 2337 Planarity : 0.005 0.040 2535 Dihedral : 9.839 69.864 2157 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 0.65 % Allowed : 9.98 % Favored : 89.37 % 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: 0.90 (0.20), residues: 1783 helix: 1.11 (0.16), residues: 1012 sheet: -1.05 (0.42), residues: 123 loop : 0.32 (0.27), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 113 TYR 0.014 0.002 TYR E1549 PHE 0.013 0.002 PHE E 813 TRP 0.019 0.002 TRP E1859 HIS 0.006 0.001 HIS E1746 Details of bonding type rmsd covalent geometry : bond 0.00408 (14932) covalent geometry : angle 0.63044 (20293) hydrogen bonds : bond 0.04771 ( 812) hydrogen bonds : angle 4.72815 ( 2310) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3566 Ramachandran restraints generated. 1783 Oldfield, 0 Emsley, 1783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3566 Ramachandran restraints generated. 1783 Oldfield, 0 Emsley, 1783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 507 is missing expected H atoms. Skipping. Evaluate side-chains 237 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 227 time to evaluate : 0.621 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 113 ARG cc_start: 0.7129 (ttm110) cc_final: 0.6783 (ttm110) REVERT: E 318 GLU cc_start: 0.7592 (tp30) cc_final: 0.7345 (mm-30) REVERT: E 323 ASP cc_start: 0.7178 (t70) cc_final: 0.6906 (t0) REVERT: E 439 MET cc_start: 0.6290 (ttm) cc_final: 0.6053 (mtp) REVERT: E 827 SER cc_start: 0.8597 (p) cc_final: 0.8270 (t) REVERT: E 886 LYS cc_start: 0.8650 (tmtt) cc_final: 0.8424 (tptp) REVERT: E 1136 MET cc_start: 0.8430 (tpp) cc_final: 0.8120 (tpp) REVERT: E 1347 PHE cc_start: 0.7487 (t80) cc_final: 0.7200 (t80) outliers start: 10 outliers final: 4 residues processed: 232 average time/residue: 0.2614 time to fit residues: 91.6605 Evaluate side-chains 206 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 202 time to evaluate : 0.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 139 THR Chi-restraints excluded: chain D residue 229 LEU Chi-restraints excluded: chain E residue 1525 VAL Chi-restraints excluded: chain E residue 1849 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 33 optimal weight: 10.0000 chunk 15 optimal weight: 7.9990 chunk 26 optimal weight: 4.9990 chunk 128 optimal weight: 1.9990 chunk 17 optimal weight: 0.7980 chunk 133 optimal weight: 7.9990 chunk 89 optimal weight: 0.0570 chunk 176 optimal weight: 10.0000 chunk 179 optimal weight: 2.9990 chunk 53 optimal weight: 0.9980 chunk 144 optimal weight: 1.9990 overall best weight: 1.1702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 803 ASN E1277 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.153534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.107002 restraints weight = 63544.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.111437 restraints weight = 44119.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.113174 restraints weight = 25756.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.113610 restraints weight = 19971.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.114189 restraints weight = 19450.065| |-----------------------------------------------------------------------------| r_work (final): 0.3421 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7417 moved from start: 0.4112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 14932 Z= 0.160 Angle : 0.586 6.192 20293 Z= 0.304 Chirality : 0.040 0.212 2337 Planarity : 0.004 0.045 2535 Dihedral : 9.726 71.422 2157 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 0.97 % Allowed : 10.76 % Favored : 88.27 % 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: 1.13 (0.20), residues: 1783 helix: 1.43 (0.16), residues: 1020 sheet: -1.03 (0.44), residues: 113 loop : 0.14 (0.26), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E 505 TYR 0.016 0.001 TYR E1155 PHE 0.017 0.001 PHE E1713 TRP 0.028 0.002 TRP E1859 HIS 0.007 0.001 HIS E 333 Details of bonding type rmsd covalent geometry : bond 0.00374 (14932) covalent geometry : angle 0.58649 (20293) hydrogen bonds : bond 0.04355 ( 812) hydrogen bonds : angle 4.46163 ( 2310) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3566 Ramachandran restraints generated. 1783 Oldfield, 0 Emsley, 1783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3566 Ramachandran restraints generated. 1783 Oldfield, 0 Emsley, 1783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 507 is missing expected H atoms. Skipping. Evaluate side-chains 225 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 210 time to evaluate : 0.759 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 96 ASP cc_start: 0.7849 (t0) cc_final: 0.7635 (t0) REVERT: E 318 GLU cc_start: 0.7830 (tp30) cc_final: 0.7537 (mm-30) REVERT: E 323 ASP cc_start: 0.8209 (t70) cc_final: 0.7920 (t0) REVERT: E 439 MET cc_start: 0.6324 (ttm) cc_final: 0.5969 (mtp) REVERT: E 627 MET cc_start: 0.7904 (tpp) cc_final: 0.7535 (tpt) REVERT: E 797 ILE cc_start: 0.8785 (mt) cc_final: 0.8565 (mt) REVERT: E 827 SER cc_start: 0.8667 (p) cc_final: 0.8371 (t) REVERT: E 1136 MET cc_start: 0.8379 (tpp) cc_final: 0.8095 (tpp) REVERT: E 1156 MET cc_start: 0.7174 (mmm) cc_final: 0.6933 (mmm) REVERT: E 1347 PHE cc_start: 0.7692 (t80) cc_final: 0.7444 (t80) REVERT: E 1522 HIS cc_start: 0.7430 (t-170) cc_final: 0.6734 (m170) REVERT: E 1866 LEU cc_start: 0.8525 (tp) cc_final: 0.8322 (tp) outliers start: 15 outliers final: 11 residues processed: 220 average time/residue: 0.2572 time to fit residues: 85.7247 Evaluate side-chains 189 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 178 time to evaluate : 0.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 127 THR Chi-restraints excluded: chain D residue 139 THR Chi-restraints excluded: chain D residue 197 PHE Chi-restraints excluded: chain E residue 337 MET Chi-restraints excluded: chain E residue 1167 VAL Chi-restraints excluded: chain E residue 1206 VAL Chi-restraints excluded: chain E residue 1334 CYS Chi-restraints excluded: chain E residue 1339 ASP Chi-restraints excluded: chain E residue 1641 LEU Chi-restraints excluded: chain E residue 1676 MET Chi-restraints excluded: chain E residue 1710 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 94 optimal weight: 0.7980 chunk 146 optimal weight: 3.9990 chunk 129 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 156 optimal weight: 10.0000 chunk 175 optimal weight: 0.9990 chunk 169 optimal weight: 9.9990 chunk 127 optimal weight: 3.9990 chunk 15 optimal weight: 5.9990 chunk 47 optimal weight: 2.9990 chunk 176 optimal weight: 9.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 159 GLN E 664 HIS E1277 GLN E1317 HIS E1466 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.150120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.103443 restraints weight = 63340.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.106983 restraints weight = 45638.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.108510 restraints weight = 28715.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.111045 restraints weight = 22410.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.111397 restraints weight = 19228.625| |-----------------------------------------------------------------------------| r_work (final): 0.3381 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7595 moved from start: 0.5259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 14932 Z= 0.193 Angle : 0.608 8.391 20293 Z= 0.318 Chirality : 0.041 0.161 2337 Planarity : 0.005 0.035 2535 Dihedral : 9.586 67.618 2157 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 1.62 % Allowed : 11.86 % Favored : 86.52 % 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: 1.08 (0.20), residues: 1783 helix: 1.45 (0.16), residues: 1023 sheet: -0.88 (0.44), residues: 117 loop : -0.03 (0.26), residues: 643 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 105 TYR 0.018 0.002 TYR E1155 PHE 0.023 0.002 PHE E 501 TRP 0.016 0.002 TRP E1859 HIS 0.008 0.001 HIS E 333 Details of bonding type rmsd covalent geometry : bond 0.00451 (14932) covalent geometry : angle 0.60794 (20293) hydrogen bonds : bond 0.04463 ( 812) hydrogen bonds : angle 4.47203 ( 2310) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3566 Ramachandran restraints generated. 1783 Oldfield, 0 Emsley, 1783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3566 Ramachandran restraints generated. 1783 Oldfield, 0 Emsley, 1783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 507 is missing expected H atoms. Skipping. Evaluate side-chains 230 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 205 time to evaluate : 0.823 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 83 GLN cc_start: 0.8449 (mm-40) cc_final: 0.8154 (mm-40) REVERT: E 140 LEU cc_start: 0.7547 (OUTLIER) cc_final: 0.7263 (tt) REVERT: E 439 MET cc_start: 0.6262 (ttm) cc_final: 0.5959 (mtp) REVERT: E 447 MET cc_start: 0.8750 (tpp) cc_final: 0.8523 (tpp) REVERT: E 627 MET cc_start: 0.8129 (tpp) cc_final: 0.7697 (tpp) REVERT: E 917 GLN cc_start: 0.8188 (mt0) cc_final: 0.7848 (mt0) REVERT: E 1136 MET cc_start: 0.8322 (tpp) cc_final: 0.8095 (tpp) REVERT: E 1347 PHE cc_start: 0.7916 (t80) cc_final: 0.7706 (t80) REVERT: E 1480 MET cc_start: 0.8505 (mtp) cc_final: 0.8233 (mtp) REVERT: E 1491 LEU cc_start: 0.8593 (mm) cc_final: 0.8379 (mm) REVERT: E 1522 HIS cc_start: 0.7408 (t-170) cc_final: 0.6803 (m-70) outliers start: 25 outliers final: 18 residues processed: 222 average time/residue: 0.2819 time to fit residues: 91.4398 Evaluate side-chains 189 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 170 time to evaluate : 0.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain D residue 127 THR Chi-restraints excluded: chain D residue 139 THR Chi-restraints excluded: chain D residue 178 SER Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain E residue 140 LEU Chi-restraints excluded: chain E residue 337 MET Chi-restraints excluded: chain E residue 438 ASN Chi-restraints excluded: chain E residue 850 PHE Chi-restraints excluded: chain E residue 955 SER Chi-restraints excluded: chain E residue 1124 THR Chi-restraints excluded: chain E residue 1148 SER Chi-restraints excluded: chain E residue 1167 VAL Chi-restraints excluded: chain E residue 1206 VAL Chi-restraints excluded: chain E residue 1334 CYS Chi-restraints excluded: chain E residue 1641 LEU Chi-restraints excluded: chain E residue 1710 VAL Chi-restraints excluded: chain E residue 1723 LEU Chi-restraints excluded: chain E residue 1849 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 146 optimal weight: 3.9990 chunk 127 optimal weight: 0.7980 chunk 152 optimal weight: 0.7980 chunk 23 optimal weight: 0.9980 chunk 9 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 86 optimal weight: 7.9990 chunk 177 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 80 optimal weight: 0.5980 chunk 54 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 240 GLN E1277 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.153958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.112249 restraints weight = 59992.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.115542 restraints weight = 54422.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.117127 restraints weight = 34255.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.117345 restraints weight = 24867.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.117518 restraints weight = 24373.911| |-----------------------------------------------------------------------------| r_work (final): 0.3399 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7681 moved from start: 0.5623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14932 Z= 0.118 Angle : 0.531 5.947 20293 Z= 0.273 Chirality : 0.038 0.156 2337 Planarity : 0.004 0.043 2535 Dihedral : 9.475 68.054 2157 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 1.23 % Allowed : 13.42 % Favored : 85.35 % 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: 1.44 (0.21), residues: 1783 helix: 1.77 (0.17), residues: 1023 sheet: -0.84 (0.46), residues: 113 loop : 0.07 (0.26), residues: 647 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 993 TYR 0.027 0.001 TYR E1300 PHE 0.021 0.001 PHE E 501 TRP 0.016 0.001 TRP E1859 HIS 0.006 0.001 HIS E 333 Details of bonding type rmsd covalent geometry : bond 0.00271 (14932) covalent geometry : angle 0.53061 (20293) hydrogen bonds : bond 0.03716 ( 812) hydrogen bonds : angle 4.20609 ( 2310) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3566 Ramachandran restraints generated. 1783 Oldfield, 0 Emsley, 1783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3566 Ramachandran restraints generated. 1783 Oldfield, 0 Emsley, 1783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 507 is missing expected H atoms. Skipping. Evaluate side-chains 198 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 179 time to evaluate : 0.762 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 439 MET cc_start: 0.6254 (ttm) cc_final: 0.6044 (mtp) REVERT: E 447 MET cc_start: 0.8549 (tpp) cc_final: 0.8335 (tpp) REVERT: E 627 MET cc_start: 0.7921 (tpp) cc_final: 0.7570 (tpp) REVERT: E 917 GLN cc_start: 0.8052 (mt0) cc_final: 0.7772 (mt0) REVERT: E 1049 GLU cc_start: 0.7749 (tp30) cc_final: 0.7501 (tp30) REVERT: E 1136 MET cc_start: 0.8232 (tpp) cc_final: 0.7757 (mmm) REVERT: E 1347 PHE cc_start: 0.8119 (t80) cc_final: 0.7905 (t80) REVERT: E 1522 HIS cc_start: 0.7381 (t-170) cc_final: 0.7133 (m-70) outliers start: 19 outliers final: 15 residues processed: 192 average time/residue: 0.2598 time to fit residues: 76.8164 Evaluate side-chains 183 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 168 time to evaluate : 0.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 127 THR Chi-restraints excluded: chain D residue 139 THR Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain D residue 197 PHE Chi-restraints excluded: chain D residue 240 GLN Chi-restraints excluded: chain E residue 337 MET Chi-restraints excluded: chain E residue 481 ASP Chi-restraints excluded: chain E residue 850 PHE Chi-restraints excluded: chain E residue 1148 SER Chi-restraints excluded: chain E residue 1167 VAL Chi-restraints excluded: chain E residue 1206 VAL Chi-restraints excluded: chain E residue 1334 CYS Chi-restraints excluded: chain E residue 1676 MET Chi-restraints excluded: chain E residue 1710 VAL Chi-restraints excluded: chain E residue 1723 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 59 optimal weight: 1.9990 chunk 67 optimal weight: 2.9990 chunk 119 optimal weight: 0.6980 chunk 138 optimal weight: 6.9990 chunk 91 optimal weight: 6.9990 chunk 80 optimal weight: 2.9990 chunk 144 optimal weight: 0.9990 chunk 95 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 129 optimal weight: 2.9990 chunk 68 optimal weight: 0.7980 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E1277 GLN E1511 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.152587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.110750 restraints weight = 59796.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.112779 restraints weight = 60095.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.114365 restraints weight = 40183.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.114728 restraints weight = 31706.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.114883 restraints weight = 29604.026| |-----------------------------------------------------------------------------| r_work (final): 0.3360 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7736 moved from start: 0.5895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14932 Z= 0.149 Angle : 0.541 8.336 20293 Z= 0.281 Chirality : 0.039 0.157 2337 Planarity : 0.004 0.041 2535 Dihedral : 9.446 66.138 2157 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 1.56 % Allowed : 13.74 % Favored : 84.71 % 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: 1.47 (0.21), residues: 1783 helix: 1.80 (0.17), residues: 1030 sheet: -0.84 (0.46), residues: 113 loop : 0.06 (0.26), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 993 TYR 0.026 0.001 TYR E1300 PHE 0.018 0.001 PHE E1713 TRP 0.015 0.001 TRP E1859 HIS 0.006 0.001 HIS E 333 Details of bonding type rmsd covalent geometry : bond 0.00348 (14932) covalent geometry : angle 0.54120 (20293) hydrogen bonds : bond 0.03778 ( 812) hydrogen bonds : angle 4.19863 ( 2310) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3566 Ramachandran restraints generated. 1783 Oldfield, 0 Emsley, 1783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3566 Ramachandran restraints generated. 1783 Oldfield, 0 Emsley, 1783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 507 is missing expected H atoms. Skipping. Evaluate side-chains 197 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 173 time to evaluate : 0.719 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 627 MET cc_start: 0.7919 (tpp) cc_final: 0.7604 (tpp) REVERT: E 917 GLN cc_start: 0.8048 (mt0) cc_final: 0.7757 (mt0) REVERT: E 1049 GLU cc_start: 0.7763 (tp30) cc_final: 0.7520 (tp30) REVERT: E 1347 PHE cc_start: 0.8155 (t80) cc_final: 0.7954 (t80) REVERT: E 1480 MET cc_start: 0.8528 (mtp) cc_final: 0.8303 (mtp) REVERT: E 1522 HIS cc_start: 0.7420 (t-170) cc_final: 0.7219 (m-70) outliers start: 24 outliers final: 17 residues processed: 188 average time/residue: 0.2506 time to fit residues: 73.5950 Evaluate side-chains 181 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 164 time to evaluate : 0.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 127 THR Chi-restraints excluded: chain D residue 139 THR Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain D residue 197 PHE Chi-restraints excluded: chain E residue 337 MET Chi-restraints excluded: chain E residue 438 ASN Chi-restraints excluded: chain E residue 481 ASP Chi-restraints excluded: chain E residue 850 PHE Chi-restraints excluded: chain E residue 1167 VAL Chi-restraints excluded: chain E residue 1206 VAL Chi-restraints excluded: chain E residue 1334 CYS Chi-restraints excluded: chain E residue 1429 TYR Chi-restraints excluded: chain E residue 1511 GLN Chi-restraints excluded: chain E residue 1641 LEU Chi-restraints excluded: chain E residue 1676 MET Chi-restraints excluded: chain E residue 1723 LEU Chi-restraints excluded: chain E residue 1793 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 38 optimal weight: 5.9990 chunk 53 optimal weight: 5.9990 chunk 147 optimal weight: 8.9990 chunk 112 optimal weight: 0.0670 chunk 96 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 146 optimal weight: 1.9990 chunk 48 optimal weight: 0.9990 chunk 94 optimal weight: 0.0970 chunk 80 optimal weight: 2.9990 overall best weight: 1.0322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E1277 GLN ** E1599 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 = 0.3893 r_free = 0.3893 target = 0.152728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.110550 restraints weight = 60020.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.113943 restraints weight = 59506.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.115664 restraints weight = 36361.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.115798 restraints weight = 27988.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.116176 restraints weight = 25124.600| |-----------------------------------------------------------------------------| r_work (final): 0.3360 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7712 moved from start: 0.6077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 14932 Z= 0.130 Angle : 0.532 7.654 20293 Z= 0.274 Chirality : 0.038 0.148 2337 Planarity : 0.004 0.040 2535 Dihedral : 9.405 65.630 2157 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 1.43 % Allowed : 13.61 % Favored : 84.96 % 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: 1.57 (0.21), residues: 1783 helix: 1.87 (0.17), residues: 1031 sheet: -0.82 (0.47), residues: 113 loop : 0.12 (0.26), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 993 TYR 0.025 0.001 TYR E1300 PHE 0.019 0.001 PHE E1713 TRP 0.016 0.001 TRP E1859 HIS 0.006 0.001 HIS E 333 Details of bonding type rmsd covalent geometry : bond 0.00302 (14932) covalent geometry : angle 0.53211 (20293) hydrogen bonds : bond 0.03610 ( 812) hydrogen bonds : angle 4.12548 ( 2310) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3566 Ramachandran restraints generated. 1783 Oldfield, 0 Emsley, 1783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3566 Ramachandran restraints generated. 1783 Oldfield, 0 Emsley, 1783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 507 is missing expected H atoms. Skipping. Evaluate side-chains 193 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 171 time to evaluate : 0.793 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 439 MET cc_start: 0.5988 (ttm) cc_final: 0.5708 (mtp) REVERT: E 627 MET cc_start: 0.7882 (tpp) cc_final: 0.7587 (tpp) REVERT: E 917 GLN cc_start: 0.8025 (mt0) cc_final: 0.7758 (mt0) REVERT: E 1049 GLU cc_start: 0.7691 (tp30) cc_final: 0.7458 (tp30) REVERT: E 1136 MET cc_start: 0.8203 (tpp) cc_final: 0.7833 (mmm) REVERT: E 1347 PHE cc_start: 0.8177 (t80) cc_final: 0.7976 (t80) REVERT: E 1480 MET cc_start: 0.8452 (mtp) cc_final: 0.8225 (mtp) REVERT: E 1522 HIS cc_start: 0.7453 (t-170) cc_final: 0.7243 (m-70) outliers start: 22 outliers final: 18 residues processed: 187 average time/residue: 0.2548 time to fit residues: 74.1957 Evaluate side-chains 183 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 165 time to evaluate : 0.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 127 THR Chi-restraints excluded: chain D residue 139 THR Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain D residue 197 PHE Chi-restraints excluded: chain E residue 337 MET Chi-restraints excluded: chain E residue 438 ASN Chi-restraints excluded: chain E residue 481 ASP Chi-restraints excluded: chain E residue 850 PHE Chi-restraints excluded: chain E residue 1167 VAL Chi-restraints excluded: chain E residue 1206 VAL Chi-restraints excluded: chain E residue 1269 ASP Chi-restraints excluded: chain E residue 1334 CYS Chi-restraints excluded: chain E residue 1423 GLU Chi-restraints excluded: chain E residue 1641 LEU Chi-restraints excluded: chain E residue 1676 MET Chi-restraints excluded: chain E residue 1723 LEU Chi-restraints excluded: chain E residue 1770 ASN Chi-restraints excluded: chain E residue 1793 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 72 optimal weight: 3.9990 chunk 14 optimal weight: 1.9990 chunk 98 optimal weight: 3.9990 chunk 115 optimal weight: 0.9980 chunk 139 optimal weight: 4.9990 chunk 130 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 113 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 chunk 178 optimal weight: 10.0000 chunk 117 optimal weight: 0.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E1277 GLN E1511 GLN ** E1599 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 = 0.3876 r_free = 0.3876 target = 0.151256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.110487 restraints weight = 60355.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.114073 restraints weight = 59812.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.115303 restraints weight = 36382.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.115516 restraints weight = 28728.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.115882 restraints weight = 26315.175| |-----------------------------------------------------------------------------| r_work (final): 0.3394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7738 moved from start: 0.6390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 14932 Z= 0.167 Angle : 0.550 5.830 20293 Z= 0.286 Chirality : 0.039 0.155 2337 Planarity : 0.004 0.042 2535 Dihedral : 9.404 64.194 2157 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 1.62 % Allowed : 13.48 % Favored : 84.90 % 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: 1.48 (0.21), residues: 1783 helix: 1.83 (0.17), residues: 1031 sheet: -0.91 (0.47), residues: 113 loop : 0.04 (0.26), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 993 TYR 0.026 0.001 TYR E1300 PHE 0.021 0.001 PHE E1713 TRP 0.017 0.001 TRP E1859 HIS 0.008 0.001 HIS E 333 Details of bonding type rmsd covalent geometry : bond 0.00395 (14932) covalent geometry : angle 0.54980 (20293) hydrogen bonds : bond 0.03857 ( 812) hydrogen bonds : angle 4.19770 ( 2310) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3566 Ramachandran restraints generated. 1783 Oldfield, 0 Emsley, 1783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3566 Ramachandran restraints generated. 1783 Oldfield, 0 Emsley, 1783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 507 is missing expected H atoms. Skipping. Evaluate side-chains 193 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 168 time to evaluate : 0.784 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 627 MET cc_start: 0.7866 (tpp) cc_final: 0.7618 (tpp) REVERT: E 735 MET cc_start: 0.9059 (tpt) cc_final: 0.8701 (tpt) REVERT: E 917 GLN cc_start: 0.8012 (mt0) cc_final: 0.7765 (mt0) REVERT: E 1136 MET cc_start: 0.8220 (tpp) cc_final: 0.7860 (mmm) REVERT: E 1480 MET cc_start: 0.8439 (mtp) cc_final: 0.8223 (mtp) outliers start: 25 outliers final: 19 residues processed: 185 average time/residue: 0.2602 time to fit residues: 74.0597 Evaluate side-chains 178 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 159 time to evaluate : 0.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain D residue 127 THR Chi-restraints excluded: chain D residue 139 THR Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain D residue 197 PHE Chi-restraints excluded: chain E residue 337 MET Chi-restraints excluded: chain E residue 481 ASP Chi-restraints excluded: chain E residue 850 PHE Chi-restraints excluded: chain E residue 1167 VAL Chi-restraints excluded: chain E residue 1206 VAL Chi-restraints excluded: chain E residue 1269 ASP Chi-restraints excluded: chain E residue 1334 CYS Chi-restraints excluded: chain E residue 1429 TYR Chi-restraints excluded: chain E residue 1511 GLN Chi-restraints excluded: chain E residue 1641 LEU Chi-restraints excluded: chain E residue 1676 MET Chi-restraints excluded: chain E residue 1723 LEU Chi-restraints excluded: chain E residue 1770 ASN Chi-restraints excluded: chain E residue 1793 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 29 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 chunk 177 optimal weight: 0.8980 chunk 113 optimal weight: 1.9990 chunk 72 optimal weight: 2.9990 chunk 70 optimal weight: 0.6980 chunk 116 optimal weight: 1.9990 chunk 82 optimal weight: 4.9990 chunk 64 optimal weight: 0.9980 chunk 28 optimal weight: 0.7980 chunk 69 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 240 GLN E1277 GLN ** E1599 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 = 0.3875 r_free = 0.3875 target = 0.149525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.104684 restraints weight = 61901.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.108407 restraints weight = 46095.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.109583 restraints weight = 29511.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.110313 restraints weight = 24021.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.110950 restraints weight = 22340.761| |-----------------------------------------------------------------------------| r_work (final): 0.3364 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7577 moved from start: 0.6548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 14932 Z= 0.120 Angle : 0.531 7.482 20293 Z= 0.273 Chirality : 0.038 0.149 2337 Planarity : 0.004 0.041 2535 Dihedral : 9.354 64.796 2157 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 1.04 % Allowed : 14.39 % Favored : 84.58 % 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: 1.66 (0.21), residues: 1783 helix: 1.98 (0.17), residues: 1034 sheet: -0.86 (0.47), residues: 113 loop : 0.08 (0.26), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 894 TYR 0.030 0.001 TYR E1300 PHE 0.021 0.001 PHE E1713 TRP 0.019 0.001 TRP E1859 HIS 0.006 0.001 HIS E 333 Details of bonding type rmsd covalent geometry : bond 0.00276 (14932) covalent geometry : angle 0.53077 (20293) hydrogen bonds : bond 0.03528 ( 812) hydrogen bonds : angle 4.05936 ( 2310) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3566 Ramachandran restraints generated. 1783 Oldfield, 0 Emsley, 1783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3566 Ramachandran restraints generated. 1783 Oldfield, 0 Emsley, 1783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 507 is missing expected H atoms. Skipping. Evaluate side-chains 180 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 164 time to evaluate : 0.784 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 627 MET cc_start: 0.8074 (tpp) cc_final: 0.7771 (tpp) REVERT: E 735 MET cc_start: 0.9151 (tpt) cc_final: 0.8771 (tpt) REVERT: E 917 GLN cc_start: 0.8028 (mt0) cc_final: 0.7731 (mt0) REVERT: E 1136 MET cc_start: 0.8274 (tpp) cc_final: 0.7874 (mmm) REVERT: E 1480 MET cc_start: 0.8341 (mtp) cc_final: 0.8039 (mtp) outliers start: 16 outliers final: 14 residues processed: 174 average time/residue: 0.2603 time to fit residues: 69.8636 Evaluate side-chains 173 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 159 time to evaluate : 0.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 127 THR Chi-restraints excluded: chain D residue 139 THR Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain D residue 197 PHE Chi-restraints excluded: chain E residue 337 MET Chi-restraints excluded: chain E residue 850 PHE Chi-restraints excluded: chain E residue 1167 VAL Chi-restraints excluded: chain E residue 1206 VAL Chi-restraints excluded: chain E residue 1269 ASP Chi-restraints excluded: chain E residue 1334 CYS Chi-restraints excluded: chain E residue 1429 TYR Chi-restraints excluded: chain E residue 1641 LEU Chi-restraints excluded: chain E residue 1723 LEU Chi-restraints excluded: chain E residue 1770 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 42 optimal weight: 1.9990 chunk 121 optimal weight: 0.9990 chunk 159 optimal weight: 10.0000 chunk 81 optimal weight: 1.9990 chunk 91 optimal weight: 0.9990 chunk 65 optimal weight: 0.9990 chunk 85 optimal weight: 1.9990 chunk 116 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 chunk 12 optimal weight: 0.9990 chunk 128 optimal weight: 2.9990 overall best weight: 1.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 240 GLN E1277 GLN E1511 GLN ** E1599 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 = 0.3866 r_free = 0.3866 target = 0.148788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.106453 restraints weight = 61238.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.109223 restraints weight = 54511.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.110412 restraints weight = 37011.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.110678 restraints weight = 29571.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.111093 restraints weight = 26505.373| |-----------------------------------------------------------------------------| r_work (final): 0.3368 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7633 moved from start: 0.6747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 14932 Z= 0.141 Angle : 0.536 5.805 20293 Z= 0.277 Chirality : 0.039 0.150 2337 Planarity : 0.004 0.041 2535 Dihedral : 9.350 66.247 2157 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 1.04 % Allowed : 14.32 % Favored : 84.64 % 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: 1.70 (0.21), residues: 1783 helix: 2.05 (0.17), residues: 1028 sheet: -0.79 (0.48), residues: 113 loop : 0.06 (0.26), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 894 TYR 0.030 0.001 TYR E1300 PHE 0.022 0.001 PHE E1713 TRP 0.019 0.001 TRP E1859 HIS 0.007 0.001 HIS E 333 Details of bonding type rmsd covalent geometry : bond 0.00331 (14932) covalent geometry : angle 0.53648 (20293) hydrogen bonds : bond 0.03606 ( 812) hydrogen bonds : angle 4.07901 ( 2310) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3566 Ramachandran restraints generated. 1783 Oldfield, 0 Emsley, 1783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3566 Ramachandran restraints generated. 1783 Oldfield, 0 Emsley, 1783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 507 is missing expected H atoms. Skipping. Evaluate side-chains 177 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 161 time to evaluate : 0.752 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 96 ASP cc_start: 0.8049 (t0) cc_final: 0.7829 (t0) REVERT: E 627 MET cc_start: 0.8033 (tpp) cc_final: 0.7739 (tpp) REVERT: E 735 MET cc_start: 0.9164 (tpt) cc_final: 0.8800 (tpt) REVERT: E 917 GLN cc_start: 0.8051 (mt0) cc_final: 0.7760 (mt0) REVERT: E 1136 MET cc_start: 0.8429 (tpp) cc_final: 0.8077 (mmm) REVERT: E 1480 MET cc_start: 0.8429 (mtp) cc_final: 0.8157 (mtp) REVERT: E 1522 HIS cc_start: 0.7156 (m170) cc_final: 0.6764 (m-70) outliers start: 16 outliers final: 15 residues processed: 171 average time/residue: 0.2658 time to fit residues: 69.1444 Evaluate side-chains 171 residues out of total 1544 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 156 time to evaluate : 0.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 127 THR Chi-restraints excluded: chain D residue 139 THR Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain D residue 197 PHE Chi-restraints excluded: chain E residue 337 MET Chi-restraints excluded: chain E residue 850 PHE Chi-restraints excluded: chain E residue 1167 VAL Chi-restraints excluded: chain E residue 1206 VAL Chi-restraints excluded: chain E residue 1269 ASP Chi-restraints excluded: chain E residue 1334 CYS Chi-restraints excluded: chain E residue 1429 TYR Chi-restraints excluded: chain E residue 1511 GLN Chi-restraints excluded: chain E residue 1641 LEU Chi-restraints excluded: chain E residue 1723 LEU Chi-restraints excluded: chain E residue 1770 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 175 optimal weight: 0.0270 chunk 61 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 155 optimal weight: 9.9990 chunk 176 optimal weight: 10.0000 chunk 127 optimal weight: 0.0020 chunk 53 optimal weight: 7.9990 chunk 156 optimal weight: 0.8980 chunk 2 optimal weight: 0.6980 chunk 122 optimal weight: 2.9990 overall best weight: 0.7248 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E1599 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 = 0.3867 r_free = 0.3867 target = 0.148957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.104746 restraints weight = 62084.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.106774 restraints weight = 46153.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.107671 restraints weight = 31726.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.108930 restraints weight = 27349.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.109383 restraints weight = 24013.617| |-----------------------------------------------------------------------------| r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7621 moved from start: 0.6749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.264 14932 Z= 0.202 Angle : 0.748 59.200 20293 Z= 0.430 Chirality : 0.038 0.149 2337 Planarity : 0.004 0.041 2535 Dihedral : 9.349 66.245 2157 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 0.91 % Allowed : 14.52 % Favored : 84.58 % 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: 1.69 (0.21), residues: 1783 helix: 2.04 (0.17), residues: 1028 sheet: -0.80 (0.48), residues: 113 loop : 0.06 (0.26), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 894 TYR 0.026 0.001 TYR E1300 PHE 0.020 0.001 PHE E1713 TRP 0.016 0.001 TRP E1859 HIS 0.006 0.001 HIS E 333 Details of bonding type rmsd covalent geometry : bond 0.00439 (14932) covalent geometry : angle 0.74800 (20293) hydrogen bonds : bond 0.03581 ( 812) hydrogen bonds : angle 4.07379 ( 2310) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4050.42 seconds wall clock time: 70 minutes 10.93 seconds (4210.93 seconds total)