Starting phenix.real_space_refine on Wed Jan 14 21:33:05 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7pog_13574/01_2026/7pog_13574.cif Found real_map, /net/cci-nas-00/data/ceres_data/7pog_13574/01_2026/7pog_13574.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.83 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7pog_13574/01_2026/7pog_13574.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7pog_13574/01_2026/7pog_13574.map" model { file = "/net/cci-nas-00/data/ceres_data/7pog_13574/01_2026/7pog_13574.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7pog_13574/01_2026/7pog_13574.cif" } resolution = 2.83 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 1 6.06 5 S 32 5.16 5 C 12290 2.51 5 N 3103 2.21 5 O 3773 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 25 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5927/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 19199 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 19198 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2382, 19198 Classifications: {'peptide': 2382} Link IDs: {'PTRANS': 55, 'TRANS': 2326} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 5686 SG CYS A 700 41.109 54.964 37.131 1.00 61.61 S Time building chain proxies: 4.01, per 1000 atoms: 0.21 Number of scatterers: 19199 At special positions: 0 Unit cell: (95.36, 142.08, 223.36, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 1 29.99 S 32 16.00 O 3773 8.00 N 3103 7.00 C 12290 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.59 Conformation dependent library (CDL) restraints added in 991.4 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A3001 " pdb="ZN ZN A3001 " - pdb=" NE2 HIS A 759 " pdb="ZN ZN A3001 " - pdb=" ND1 HIS A 655 " pdb="ZN ZN A3001 " - pdb=" SG CYS A 700 " 4760 Ramachandran restraints generated. 2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4514 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 41 sheets defined 31.7% alpha, 19.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.09 Creating SS restraints... Processing helix chain 'A' and resid 20 through 35 Processing helix chain 'A' and resid 40 through 62 removed outlier: 3.816A pdb=" N LEU A 48 " --> pdb=" O LYS A 44 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N GLU A 53 " --> pdb=" O LYS A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 67 through 82 Processing helix chain 'A' and resid 107 through 121 removed outlier: 3.588A pdb=" N GLN A 116 " --> pdb=" O GLU A 112 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N TRP A 117 " --> pdb=" O TYR A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 156 Processing helix chain 'A' and resid 156 through 161 removed outlier: 3.819A pdb=" N GLN A 161 " --> pdb=" O GLU A 157 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 194 removed outlier: 4.110A pdb=" N PHE A 170 " --> pdb=" O ASP A 166 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ASN A 194 " --> pdb=" O LYS A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 200 through 214 removed outlier: 3.887A pdb=" N ASN A 214 " --> pdb=" O VAL A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 216 through 234 Processing helix chain 'A' and resid 247 through 259 removed outlier: 3.775A pdb=" N GLU A 257 " --> pdb=" O ILE A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 279 removed outlier: 3.817A pdb=" N LEU A 273 " --> pdb=" O ASP A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 323 Processing helix chain 'A' and resid 338 through 351 Processing helix chain 'A' and resid 354 through 359 removed outlier: 3.564A pdb=" N PHE A 359 " --> pdb=" O LYS A 355 " (cutoff:3.500A) Processing helix chain 'A' and resid 392 through 419 Proline residue: A 415 - end of helix removed outlier: 3.929A pdb=" N SER A 419 " --> pdb=" O PRO A 415 " (cutoff:3.500A) Processing helix chain 'A' and resid 422 through 437 Processing helix chain 'A' and resid 442 through 450 Processing helix chain 'A' and resid 451 through 455 Processing helix chain 'A' and resid 463 through 468 Processing helix chain 'A' and resid 469 through 483 removed outlier: 3.561A pdb=" N TYR A 473 " --> pdb=" O GLY A 469 " (cutoff:3.500A) Processing helix chain 'A' and resid 493 through 498 removed outlier: 3.511A pdb=" N ILE A 498 " --> pdb=" O ALA A 494 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 501 No H-bonds generated for 'chain 'A' and resid 499 through 501' Processing helix chain 'A' and resid 503 through 505 No H-bonds generated for 'chain 'A' and resid 503 through 505' Processing helix chain 'A' and resid 511 through 518 Processing helix chain 'A' and resid 522 through 537 removed outlier: 3.603A pdb=" N TYR A 528 " --> pdb=" O ALA A 524 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 547 Processing helix chain 'A' and resid 557 through 564 Processing helix chain 'A' and resid 589 through 603 removed outlier: 3.664A pdb=" N ALA A 595 " --> pdb=" O ILE A 591 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N ASN A 603 " --> pdb=" O LEU A 599 " (cutoff:3.500A) Processing helix chain 'A' and resid 614 through 618 removed outlier: 3.922A pdb=" N SER A 617 " --> pdb=" O MET A 614 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N ALA A 618 " --> pdb=" O ASN A 615 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 614 through 618' Processing helix chain 'A' and resid 670 through 685 Processing helix chain 'A' and resid 708 through 711 Processing helix chain 'A' and resid 712 through 721 Processing helix chain 'A' and resid 722 through 729 Processing helix chain 'A' and resid 733 through 736 Processing helix chain 'A' and resid 766 through 776 Processing helix chain 'A' and resid 795 through 812 Processing helix chain 'A' and resid 816 through 840 removed outlier: 3.692A pdb=" N ILE A 838 " --> pdb=" O ILE A 834 " (cutoff:3.500A) Processing helix chain 'A' and resid 848 through 877 removed outlier: 3.503A pdb=" N ILE A 854 " --> pdb=" O ILE A 850 " (cutoff:3.500A) Processing helix chain 'A' and resid 918 through 937 Processing helix chain 'A' and resid 953 through 972 Processing helix chain 'A' and resid 977 through 982 Processing helix chain 'A' and resid 982 through 997 Processing helix chain 'A' and resid 999 through 1003 removed outlier: 3.748A pdb=" N ILE A1003 " --> pdb=" O LEU A1000 " (cutoff:3.500A) Processing helix chain 'A' and resid 1005 through 1019 removed outlier: 3.937A pdb=" N ASN A1011 " --> pdb=" O ILE A1007 " (cutoff:3.500A) Processing helix chain 'A' and resid 1043 through 1054 Processing helix chain 'A' and resid 1055 through 1065 Processing helix chain 'A' and resid 1074 through 1093 Processing helix chain 'A' and resid 1118 through 1129 Processing helix chain 'A' and resid 1130 through 1134 removed outlier: 3.627A pdb=" N LYS A1133 " --> pdb=" O SER A1130 " (cutoff:3.500A) Processing helix chain 'A' and resid 1247 through 1260 Processing helix chain 'A' and resid 1306 through 1311 Processing helix chain 'A' and resid 1349 through 1353 Processing helix chain 'A' and resid 1433 through 1440 Processing helix chain 'A' and resid 1440 through 1452 Processing helix chain 'A' and resid 1531 through 1533 No H-bonds generated for 'chain 'A' and resid 1531 through 1533' Processing helix chain 'A' and resid 1558 through 1572 Processing helix chain 'A' and resid 1578 through 1590 removed outlier: 4.116A pdb=" N MET A1582 " --> pdb=" O THR A1578 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ASN A1583 " --> pdb=" O SER A1579 " (cutoff:3.500A) Processing helix chain 'A' and resid 1591 through 1595 Processing helix chain 'A' and resid 1680 through 1684 removed outlier: 4.058A pdb=" N ARG A1683 " --> pdb=" O GLY A1680 " (cutoff:3.500A) Processing helix chain 'A' and resid 1771 through 1776 Processing helix chain 'A' and resid 1790 through 1797 Processing helix chain 'A' and resid 1804 through 1808 Processing helix chain 'A' and resid 2216 through 2220 Processing sheet with id=AA1, first strand: chain 'A' and resid 236 through 238 removed outlier: 6.313A pdb=" N ILE A 237 " --> pdb=" O ILE A 126 " (cutoff:3.500A) removed outlier: 5.762A pdb=" N LEU A 128 " --> pdb=" O ILE A 237 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N LEU A 97 " --> pdb=" O LYS A 127 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N TRP A 129 " --> pdb=" O LEU A 97 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N PHE A 99 " --> pdb=" O TRP A 129 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N VAL A 100 " --> pdb=" O LEU A 284 " (cutoff:3.500A) removed outlier: 7.305A pdb=" N GLN A 384 " --> pdb=" O LYS A 373 " (cutoff:3.500A) removed outlier: 10.764A pdb=" N LYS A 373 " --> pdb=" O GLN A 384 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 289 through 290 removed outlier: 4.116A pdb=" N LEU A 289 " --> pdb=" O SER A 508 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 582 through 583 Processing sheet with id=AA4, first strand: chain 'A' and resid 621 through 623 Processing sheet with id=AA5, first strand: chain 'A' and resid 647 through 650 removed outlier: 5.855A pdb=" N VAL A 648 " --> pdb=" O GLU A 694 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N ASN A 696 " --> pdb=" O VAL A 648 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N VAL A 650 " --> pdb=" O ASN A 696 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N LEU A 698 " --> pdb=" O VAL A 650 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 664 through 665 Processing sheet with id=AA7, first strand: chain 'A' and resid 746 through 748 Processing sheet with id=AA8, first strand: chain 'A' and resid 886 through 892 removed outlier: 9.731A pdb=" N PHE A 888 " --> pdb=" O ILE A 903 " (cutoff:3.500A) removed outlier: 11.201A pdb=" N ILE A 903 " --> pdb=" O PHE A 888 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N ASP A 890 " --> pdb=" O ARG A 901 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N ARG A 901 " --> pdb=" O ASP A 890 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 1037 through 1038 Processing sheet with id=AB1, first strand: chain 'A' and resid 1068 through 1070 removed outlier: 5.753A pdb=" N ASP A1512 " --> pdb=" O LYS A1527 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N LYS A1527 " --> pdb=" O ASP A1512 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N ASN A1522 " --> pdb=" O LEU A1544 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N LEU A1544 " --> pdb=" O ASN A1522 " (cutoff:3.500A) removed outlier: 7.905A pdb=" N SER A1537 " --> pdb=" O LEU A1557 " (cutoff:3.500A) removed outlier: 5.285A pdb=" N LEU A1557 " --> pdb=" O SER A1537 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N ASP A1539 " --> pdb=" O LEU A1555 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N LEU A1555 " --> pdb=" O ASP A1539 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N SER A1541 " --> pdb=" O ASN A1553 " (cutoff:3.500A) removed outlier: 9.853A pdb=" N GLN A1549 " --> pdb=" O VAL A1603 " (cutoff:3.500A) removed outlier: 11.383A pdb=" N ASP A1605 " --> pdb=" O GLN A1549 " (cutoff:3.500A) removed outlier: 10.200A pdb=" N LYS A1551 " --> pdb=" O ASP A1605 " (cutoff:3.500A) removed outlier: 9.942A pdb=" N TYR A1607 " --> pdb=" O LYS A1551 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N ASN A1553 " --> pdb=" O TYR A1607 " (cutoff:3.500A) removed outlier: 5.046A pdb=" N PHE A1608 " --> pdb=" O CYS A1623 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N TYR A1618 " --> pdb=" O GLY A1634 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N GLY A1634 " --> pdb=" O TYR A1618 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N GLU A1620 " --> pdb=" O TYR A1632 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N VAL A1688 " --> pdb=" O ILE A1715 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 1107 through 1109 Processing sheet with id=AB3, first strand: chain 'A' and resid 1138 through 1141 removed outlier: 6.938A pdb=" N LEU A1146 " --> pdb=" O MET A1223 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N ARG A1297 " --> pdb=" O SER A1325 " (cutoff:3.500A) removed outlier: 8.405A pdb=" N LEU A1327 " --> pdb=" O ARG A1297 " (cutoff:3.500A) removed outlier: 7.355A pdb=" N PHE A1299 " --> pdb=" O LEU A1327 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N SER A1414 " --> pdb=" O SER A1431 " (cutoff:3.500A) removed outlier: 9.881A pdb=" N TYR A1426 " --> pdb=" O ASN A1457 " (cutoff:3.500A) removed outlier: 9.608A pdb=" N ALA A1459 " --> pdb=" O TYR A1426 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N LEU A1428 " --> pdb=" O ALA A1459 " (cutoff:3.500A) removed outlier: 7.824A pdb=" N ASN A1461 " --> pdb=" O LEU A1428 " (cutoff:3.500A) removed outlier: 7.875A pdb=" N LEU A1430 " --> pdb=" O ASN A1461 " (cutoff:3.500A) removed outlier: 8.512A pdb=" N THR A1463 " --> pdb=" O LEU A1430 " (cutoff:3.500A) removed outlier: 5.303A pdb=" N LYS A1469 " --> pdb=" O LYS A1486 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N LYS A1486 " --> pdb=" O LYS A1469 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N LYS A1480 " --> pdb=" O SER A1475 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N LEU A1493 " --> pdb=" O ASN A1504 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N ASN A1504 " --> pdb=" O LEU A1493 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N PHE A1495 " --> pdb=" O GLU A1502 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 1163 through 1166 removed outlier: 6.649A pdb=" N SER A1155 " --> pdb=" O LYS A1289 " (cutoff:3.500A) removed outlier: 7.766A pdb=" N LYS A1291 " --> pdb=" O SER A1155 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N ILE A1157 " --> pdb=" O LYS A1291 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N LEU A1313 " --> pdb=" O SER A1334 " (cutoff:3.500A) removed outlier: 8.618A pdb=" N ASN A1336 " --> pdb=" O LEU A1313 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N TYR A1315 " --> pdb=" O ASN A1336 " (cutoff:3.500A) removed outlier: 7.524A pdb=" N ASN A1338 " --> pdb=" O TYR A1315 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N PHE A1317 " --> pdb=" O ASN A1338 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N MET A1335 " --> pdb=" O THR A1389 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 1181 through 1183 removed outlier: 7.548A pdb=" N ASP A1187 " --> pdb=" O TYR A1269 " (cutoff:3.500A) removed outlier: 5.354A pdb=" N ILE A1276 " --> pdb=" O GLY A1237 " (cutoff:3.500A) removed outlier: 5.353A pdb=" N GLY A1237 " --> pdb=" O ILE A1276 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N SER A1229 " --> pdb=" O GLU A1284 " (cutoff:3.500A) removed outlier: 7.767A pdb=" N ASN A1170 " --> pdb=" O PHE A1232 " (cutoff:3.500A) removed outlier: 8.250A pdb=" N TRP A1234 " --> pdb=" O ASN A1170 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 1173 through 1175 removed outlier: 4.067A pdb=" N ALA A1173 " --> pdb=" O SER A1196 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLU A1175 " --> pdb=" O TYR A1194 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N TYR A1194 " --> pdb=" O GLU A1175 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 1354 through 1359 removed outlier: 4.645A pdb=" N ASN A1367 " --> pdb=" O GLU A1355 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N SER A1357 " --> pdb=" O LYS A1365 " (cutoff:3.500A) removed outlier: 5.502A pdb=" N LYS A1365 " --> pdb=" O SER A1357 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N GLU A1359 " --> pdb=" O ILE A1363 " (cutoff:3.500A) removed outlier: 4.985A pdb=" N ILE A1363 " --> pdb=" O GLU A1359 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 1670 through 1674 removed outlier: 6.614A pdb=" N LEU A1671 " --> pdb=" O ASN A1700 " (cutoff:3.500A) removed outlier: 7.797A pdb=" N ASN A1702 " --> pdb=" O LEU A1671 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N PHE A1673 " --> pdb=" O ASN A1702 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 1813 through 1814 Processing sheet with id=AC1, first strand: chain 'A' and resid 1832 through 1836 Processing sheet with id=AC2, first strand: chain 'A' and resid 1853 through 1857 Processing sheet with id=AC3, first strand: chain 'A' and resid 1876 through 1878 Processing sheet with id=AC4, first strand: chain 'A' and resid 1894 through 1898 removed outlier: 4.047A pdb=" N GLN A1918 " --> pdb=" O ALA A1906 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'A' and resid 1894 through 1898 removed outlier: 4.526A pdb=" N PHE A1902 " --> pdb=" O ALA A1942 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'A' and resid 1926 through 1929 Processing sheet with id=AC7, first strand: chain 'A' and resid 1946 through 1948 Processing sheet with id=AC8, first strand: chain 'A' and resid 1966 through 1970 Processing sheet with id=AC9, first strand: chain 'A' and resid 1987 through 1991 Processing sheet with id=AD1, first strand: chain 'A' and resid 2008 through 2012 Processing sheet with id=AD2, first strand: chain 'A' and resid 2038 through 2040 removed outlier: 4.080A pdb=" N TYR A2038 " --> pdb=" O ILE A2054 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N GLN A2052 " --> pdb=" O ALA A2040 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'A' and resid 2079 through 2080 Processing sheet with id=AD4, first strand: chain 'A' and resid 2100 through 2102 Processing sheet with id=AD5, first strand: chain 'A' and resid 2122 through 2125 Processing sheet with id=AD6, first strand: chain 'A' and resid 2144 through 2146 Processing sheet with id=AD7, first strand: chain 'A' and resid 2163 through 2166 Processing sheet with id=AD8, first strand: chain 'A' and resid 2193 through 2196 Processing sheet with id=AD9, first strand: chain 'A' and resid 2213 through 2215 Processing sheet with id=AE1, first strand: chain 'A' and resid 2235 through 2236 Processing sheet with id=AE2, first strand: chain 'A' and resid 2254 through 2258 Processing sheet with id=AE3, first strand: chain 'A' and resid 2277 through 2278 removed outlier: 3.641A pdb=" N PHE A2278 " --> pdb=" O GLU A2285 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'A' and resid 2308 through 2309 removed outlier: 3.608A pdb=" N LEU A2309 " --> pdb=" O TYR A2316 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'A' and resid 2329 through 2330 777 hydrogen bonds defined for protein. 2109 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.84 Time building geometry restraints manager: 2.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4623 1.33 - 1.45: 4075 1.45 - 1.57: 10844 1.57 - 1.69: 0 1.69 - 1.81: 57 Bond restraints: 19599 Sorted by residual: bond pdb=" N VAL A2325 " pdb=" CA VAL A2325 " ideal model delta sigma weight residual 1.456 1.494 -0.038 1.14e-02 7.69e+03 1.08e+01 bond pdb=" N ASP A 131 " pdb=" CA ASP A 131 " ideal model delta sigma weight residual 1.454 1.490 -0.036 1.23e-02 6.61e+03 8.64e+00 bond pdb=" N MET A1223 " pdb=" CA MET A1223 " ideal model delta sigma weight residual 1.455 1.488 -0.033 1.21e-02 6.83e+03 7.45e+00 bond pdb=" N ASN A1226 " pdb=" CA ASN A1226 " ideal model delta sigma weight residual 1.457 1.488 -0.031 1.16e-02 7.43e+03 7.20e+00 bond pdb=" N LEU A1224 " pdb=" CA LEU A1224 " ideal model delta sigma weight residual 1.452 1.489 -0.037 1.41e-02 5.03e+03 7.02e+00 ... (remaining 19594 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.72: 26017 1.72 - 3.43: 453 3.43 - 5.15: 53 5.15 - 6.87: 11 6.87 - 8.59: 6 Bond angle restraints: 26540 Sorted by residual: angle pdb=" N CYS A1169 " pdb=" CA CYS A1169 " pdb=" C CYS A1169 " ideal model delta sigma weight residual 110.70 103.63 7.07 1.55e+00 4.16e-01 2.08e+01 angle pdb=" N GLU A 870 " pdb=" CA GLU A 870 " pdb=" CB GLU A 870 " ideal model delta sigma weight residual 110.39 116.51 -6.12 1.66e+00 3.63e-01 1.36e+01 angle pdb=" CA ASP A1488 " pdb=" C ASP A1488 " pdb=" O ASP A1488 " ideal model delta sigma weight residual 122.03 117.76 4.27 1.25e+00 6.40e-01 1.17e+01 angle pdb=" C ASP A 869 " pdb=" N GLU A 870 " pdb=" CA GLU A 870 " ideal model delta sigma weight residual 120.72 115.33 5.39 1.67e+00 3.59e-01 1.04e+01 angle pdb=" C LEU A1038 " pdb=" N ASP A1039 " pdb=" CA ASP A1039 " ideal model delta sigma weight residual 121.54 127.28 -5.74 1.91e+00 2.74e-01 9.04e+00 ... (remaining 26535 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.85: 10486 17.85 - 35.70: 997 35.70 - 53.56: 168 53.56 - 71.41: 29 71.41 - 89.26: 13 Dihedral angle restraints: 11693 sinusoidal: 4654 harmonic: 7039 Sorted by residual: dihedral pdb=" CA GLU A2270 " pdb=" C GLU A2270 " pdb=" N SER A2271 " pdb=" CA SER A2271 " ideal model delta harmonic sigma weight residual 180.00 156.64 23.36 0 5.00e+00 4.00e-02 2.18e+01 dihedral pdb=" CA ASN A2114 " pdb=" C ASN A2114 " pdb=" N THR A2115 " pdb=" CA THR A2115 " ideal model delta harmonic sigma weight residual 180.00 156.92 23.08 0 5.00e+00 4.00e-02 2.13e+01 dihedral pdb=" CA THR A2363 " pdb=" C THR A2363 " pdb=" N ALA A2364 " pdb=" CA ALA A2364 " ideal model delta harmonic sigma weight residual 180.00 -159.34 -20.66 0 5.00e+00 4.00e-02 1.71e+01 ... (remaining 11690 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 2227 0.046 - 0.092: 526 0.092 - 0.138: 172 0.138 - 0.184: 12 0.184 - 0.230: 4 Chirality restraints: 2941 Sorted by residual: chirality pdb=" CA CYS A1169 " pdb=" N CYS A1169 " pdb=" C CYS A1169 " pdb=" CB CYS A1169 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.33e+00 chirality pdb=" CB THR A 897 " pdb=" CA THR A 897 " pdb=" OG1 THR A 897 " pdb=" CG2 THR A 897 " both_signs ideal model delta sigma weight residual False 2.55 2.34 0.22 2.00e-01 2.50e+01 1.17e+00 chirality pdb=" CB ILE A 610 " pdb=" CA ILE A 610 " pdb=" CG1 ILE A 610 " pdb=" CG2 ILE A 610 " both_signs ideal model delta sigma weight residual False 2.64 2.85 -0.20 2.00e-01 2.50e+01 1.03e+00 ... (remaining 2938 not shown) Planarity restraints: 3409 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU A1057 " 0.009 2.00e-02 2.50e+03 1.71e-02 2.92e+00 pdb=" C LEU A1057 " -0.030 2.00e-02 2.50e+03 pdb=" O LEU A1057 " 0.011 2.00e-02 2.50e+03 pdb=" N LEU A1058 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN A 578 " 0.008 2.00e-02 2.50e+03 1.56e-02 2.44e+00 pdb=" C ASN A 578 " -0.027 2.00e-02 2.50e+03 pdb=" O ASN A 578 " 0.010 2.00e-02 2.50e+03 pdb=" N TYR A 579 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA A2174 " -0.023 5.00e-02 4.00e+02 3.51e-02 1.97e+00 pdb=" N PRO A2175 " 0.061 5.00e-02 4.00e+02 pdb=" CA PRO A2175 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO A2175 " -0.019 5.00e-02 4.00e+02 ... (remaining 3406 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.70: 596 2.70 - 3.25: 19949 3.25 - 3.80: 31532 3.80 - 4.35: 41942 4.35 - 4.90: 69499 Nonbonded interactions: 163518 Sorted by model distance: nonbonded pdb=" OD1 ASP A 545 " pdb="ZN ZN A3001 " model vdw 2.155 2.230 nonbonded pdb=" O ASP A1573 " pdb=" OH TYR A1842 " model vdw 2.200 3.040 nonbonded pdb=" OH TYR A1426 " pdb=" OD1 ASP A1454 " model vdw 2.201 3.040 nonbonded pdb=" OH TYR A 636 " pdb=" OE2 GLU A 676 " model vdw 2.212 3.040 nonbonded pdb=" OG SER A1035 " pdb=" OG1 THR A1609 " model vdw 2.217 3.040 ... (remaining 163513 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 27.470 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: 0.000 Extract box with map and model: 0.550 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 22.910 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:9.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 60.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7645 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 19602 Z= 0.162 Angle : 0.567 8.586 26540 Z= 0.318 Chirality : 0.045 0.230 2941 Planarity : 0.003 0.050 3409 Dihedral : 14.165 89.259 7179 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 12.59 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.56 % Favored : 92.35 % Rotamer: Outliers : 0.28 % Allowed : 0.51 % Favored : 99.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.06 (0.17), residues: 2380 helix: 1.05 (0.21), residues: 662 sheet: -1.34 (0.23), residues: 496 loop : -1.42 (0.17), residues: 1222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1230 TYR 0.016 0.001 TYR A 973 PHE 0.023 0.001 PHE A 966 TRP 0.008 0.001 TRP A1636 HIS 0.004 0.001 HIS A1128 Details of bonding type rmsd covalent geometry : bond 0.00308 (19599) covalent geometry : angle 0.56746 (26540) hydrogen bonds : bond 0.14632 ( 771) hydrogen bonds : angle 6.62519 ( 2109) metal coordination : bond 0.00044 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4760 Ramachandran restraints generated. 2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4760 Ramachandran restraints generated. 2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 2151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 194 time to evaluate : 0.811 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: A 2075 LYS cc_start: 0.8092 (ttpt) cc_final: 0.7677 (mptt) outliers start: 6 outliers final: 5 residues processed: 198 average time/residue: 0.5568 time to fit residues: 126.3582 Evaluate side-chains 91 residues out of total 2151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 86 time to evaluate : 0.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1216 ASP Chi-restraints excluded: chain A residue 1659 TYR Chi-restraints excluded: chain A residue 2012 ILE Chi-restraints excluded: chain A residue 2105 ASP Chi-restraints excluded: chain A residue 2266 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 216 optimal weight: 2.9990 chunk 98 optimal weight: 4.9990 chunk 194 optimal weight: 0.0370 chunk 227 optimal weight: 1.9990 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 0.0970 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 0.6980 chunk 235 optimal weight: 0.2980 overall best weight: 0.4258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 765 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1553 ASN A1892 GLN A2034 ASN A2057 GLN A2123 GLN ** A2182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.066923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.054536 restraints weight = 84231.075| |-----------------------------------------------------------------------------| r_work (start): 0.3362 rms_B_bonded: 3.95 r_work: 0.3238 rms_B_bonded: 4.55 restraints_weight: 0.5000 r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.1357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 19602 Z= 0.123 Angle : 0.559 8.696 26540 Z= 0.301 Chirality : 0.044 0.152 2941 Planarity : 0.003 0.039 3409 Dihedral : 5.279 93.020 2577 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 11.70 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.97 % Favored : 92.98 % Rotamer: Outliers : 1.30 % Allowed : 7.95 % Favored : 90.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.00 (0.17), residues: 2380 helix: 1.13 (0.21), residues: 673 sheet: -1.25 (0.23), residues: 496 loop : -1.45 (0.18), residues: 1211 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 224 TYR 0.026 0.001 TYR A2009 PHE 0.016 0.001 PHE A2030 TRP 0.008 0.001 TRP A2080 HIS 0.005 0.001 HIS A 412 Details of bonding type rmsd covalent geometry : bond 0.00266 (19599) covalent geometry : angle 0.55910 (26540) hydrogen bonds : bond 0.03653 ( 771) hydrogen bonds : angle 5.32277 ( 2109) metal coordination : bond 0.00154 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4760 Ramachandran restraints generated. 2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4760 Ramachandran restraints generated. 2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 2151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 110 time to evaluate : 0.880 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 ARG cc_start: 0.8430 (OUTLIER) cc_final: 0.8130 (mpp-170) REVERT: A 215 ARG cc_start: 0.8462 (mmm160) cc_final: 0.8200 (mmm160) REVERT: A 288 MET cc_start: 0.8427 (mmm) cc_final: 0.8220 (mmt) REVERT: A 320 MET cc_start: 0.8663 (mtt) cc_final: 0.8343 (mtt) REVERT: A 722 MET cc_start: 0.8069 (mtm) cc_final: 0.7787 (mtm) REVERT: A 790 LYS cc_start: 0.7093 (OUTLIER) cc_final: 0.6819 (mptt) REVERT: A 905 LYS cc_start: 0.9419 (mttt) cc_final: 0.8946 (pmtt) REVERT: A 980 LEU cc_start: 0.8717 (tt) cc_final: 0.8071 (tt) REVERT: A 1143 ASP cc_start: 0.8699 (t0) cc_final: 0.8464 (t0) REVERT: A 1223 MET cc_start: 0.7799 (OUTLIER) cc_final: 0.7410 (ttt) REVERT: A 1535 ASP cc_start: 0.9045 (m-30) cc_final: 0.8806 (p0) REVERT: A 1778 MET cc_start: 0.9627 (mmt) cc_final: 0.9310 (mmt) REVERT: A 2026 LYS cc_start: 0.8967 (mmmt) cc_final: 0.8672 (tptp) REVERT: A 2075 LYS cc_start: 0.8175 (ttpt) cc_final: 0.7621 (mptt) outliers start: 28 outliers final: 7 residues processed: 126 average time/residue: 0.5138 time to fit residues: 75.6653 Evaluate side-chains 95 residues out of total 2151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 85 time to evaluate : 0.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ARG Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 374 ILE Chi-restraints excluded: chain A residue 790 LYS Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 1192 SER Chi-restraints excluded: chain A residue 1223 MET Chi-restraints excluded: chain A residue 1949 ILE Chi-restraints excluded: chain A residue 2235 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 196 optimal weight: 6.9990 chunk 228 optimal weight: 0.8980 chunk 11 optimal weight: 0.4980 chunk 21 optimal weight: 3.9990 chunk 159 optimal weight: 0.9990 chunk 181 optimal weight: 5.9990 chunk 120 optimal weight: 3.9990 chunk 59 optimal weight: 5.9990 chunk 101 optimal weight: 2.9990 chunk 93 optimal weight: 0.4980 chunk 71 optimal weight: 3.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 138 ASN ** A1652 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2034 ASN A2057 GLN ** A2182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2329 GLN ** 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 = 0.3657 r_free = 0.3657 target = 0.064919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.052401 restraints weight = 85138.621| |-----------------------------------------------------------------------------| r_work (start): 0.3312 rms_B_bonded: 3.93 r_work: 0.3184 rms_B_bonded: 4.51 restraints_weight: 0.5000 r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.1667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 19602 Z= 0.169 Angle : 0.544 9.034 26540 Z= 0.293 Chirality : 0.044 0.180 2941 Planarity : 0.003 0.040 3409 Dihedral : 4.528 22.757 2567 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 12.59 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.18 % Favored : 92.77 % Rotamer: Outliers : 1.44 % Allowed : 10.88 % Favored : 87.68 % 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: -0.88 (0.18), residues: 2380 helix: 1.25 (0.20), residues: 678 sheet: -1.10 (0.24), residues: 495 loop : -1.43 (0.18), residues: 1207 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 224 TYR 0.029 0.001 TYR A2009 PHE 0.014 0.001 PHE A2006 TRP 0.012 0.001 TRP A2080 HIS 0.004 0.001 HIS A 581 Details of bonding type rmsd covalent geometry : bond 0.00374 (19599) covalent geometry : angle 0.54427 (26540) hydrogen bonds : bond 0.03480 ( 771) hydrogen bonds : angle 5.08825 ( 2109) metal coordination : bond 0.00372 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4760 Ramachandran restraints generated. 2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4760 Ramachandran restraints generated. 2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 2151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 94 time to evaluate : 0.946 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 ARG cc_start: 0.8419 (OUTLIER) cc_final: 0.8100 (mpp-170) REVERT: A 215 ARG cc_start: 0.8498 (mmm160) cc_final: 0.8233 (mmm160) REVERT: A 320 MET cc_start: 0.8662 (mtt) cc_final: 0.8386 (mtt) REVERT: A 489 GLU cc_start: 0.8611 (mm-30) cc_final: 0.7643 (mm-30) REVERT: A 905 LYS cc_start: 0.9420 (mttt) cc_final: 0.8942 (pmtt) REVERT: A 1013 ILE cc_start: 0.9574 (OUTLIER) cc_final: 0.9229 (pp) REVERT: A 1143 ASP cc_start: 0.8730 (t0) cc_final: 0.8473 (t0) REVERT: A 1174 MET cc_start: 0.8677 (OUTLIER) cc_final: 0.7259 (mmm) REVERT: A 1223 MET cc_start: 0.7926 (OUTLIER) cc_final: 0.7659 (ttm) REVERT: A 1294 LYS cc_start: 0.8789 (tptt) cc_final: 0.8554 (tppt) REVERT: A 1535 ASP cc_start: 0.9056 (m-30) cc_final: 0.8824 (p0) REVERT: A 2075 LYS cc_start: 0.8341 (ttpt) cc_final: 0.7785 (mptt) outliers start: 31 outliers final: 10 residues processed: 112 average time/residue: 0.5834 time to fit residues: 75.3552 Evaluate side-chains 96 residues out of total 2151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 82 time to evaluate : 0.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ARG Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 374 ILE Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 1013 ILE Chi-restraints excluded: chain A residue 1061 GLU Chi-restraints excluded: chain A residue 1174 MET Chi-restraints excluded: chain A residue 1192 SER Chi-restraints excluded: chain A residue 1223 MET Chi-restraints excluded: chain A residue 1949 ILE Chi-restraints excluded: chain A residue 2023 CYS Chi-restraints excluded: chain A residue 2057 GLN Chi-restraints excluded: chain A residue 2235 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 156 optimal weight: 0.5980 chunk 64 optimal weight: 0.7980 chunk 39 optimal weight: 1.9990 chunk 91 optimal weight: 4.9990 chunk 12 optimal weight: 0.7980 chunk 172 optimal weight: 0.7980 chunk 231 optimal weight: 8.9990 chunk 102 optimal weight: 3.9990 chunk 80 optimal weight: 1.9990 chunk 140 optimal weight: 0.8980 chunk 73 optimal weight: 6.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2034 ASN ** A2182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.064895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.052497 restraints weight = 84617.571| |-----------------------------------------------------------------------------| r_work (start): 0.3319 rms_B_bonded: 3.85 r_work: 0.3195 rms_B_bonded: 4.44 restraints_weight: 0.5000 r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.1849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 19602 Z= 0.131 Angle : 0.523 9.298 26540 Z= 0.281 Chirality : 0.043 0.160 2941 Planarity : 0.003 0.040 3409 Dihedral : 4.442 23.038 2567 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 11.57 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.10 % Favored : 92.86 % Rotamer: Outliers : 1.67 % Allowed : 12.32 % Favored : 86.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.82 (0.18), residues: 2380 helix: 1.28 (0.20), residues: 683 sheet: -1.06 (0.24), residues: 473 loop : -1.39 (0.18), residues: 1224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 224 TYR 0.032 0.001 TYR A2009 PHE 0.012 0.001 PHE A2006 TRP 0.009 0.001 TRP A2080 HIS 0.003 0.001 HIS A 412 Details of bonding type rmsd covalent geometry : bond 0.00289 (19599) covalent geometry : angle 0.52348 (26540) hydrogen bonds : bond 0.03190 ( 771) hydrogen bonds : angle 4.95808 ( 2109) metal coordination : bond 0.00260 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4760 Ramachandran restraints generated. 2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4760 Ramachandran restraints generated. 2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 2151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 92 time to evaluate : 0.716 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 ARG cc_start: 0.8394 (OUTLIER) cc_final: 0.8084 (mpp-170) REVERT: A 215 ARG cc_start: 0.8514 (mmm160) cc_final: 0.8250 (mmm160) REVERT: A 320 MET cc_start: 0.8643 (mtt) cc_final: 0.8305 (mtt) REVERT: A 489 GLU cc_start: 0.8614 (mm-30) cc_final: 0.7675 (mt-10) REVERT: A 734 LYS cc_start: 0.8468 (OUTLIER) cc_final: 0.8137 (tppp) REVERT: A 905 LYS cc_start: 0.9417 (mttt) cc_final: 0.8929 (pmtt) REVERT: A 1013 ILE cc_start: 0.9576 (OUTLIER) cc_final: 0.9219 (pp) REVERT: A 1143 ASP cc_start: 0.8730 (t0) cc_final: 0.8443 (t0) REVERT: A 1174 MET cc_start: 0.8698 (OUTLIER) cc_final: 0.7222 (mmm) REVERT: A 1294 LYS cc_start: 0.8807 (tptt) cc_final: 0.8558 (tppt) REVERT: A 2075 LYS cc_start: 0.8283 (ttpt) cc_final: 0.7728 (mptt) outliers start: 36 outliers final: 11 residues processed: 118 average time/residue: 0.5161 time to fit residues: 70.3984 Evaluate side-chains 94 residues out of total 2151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 79 time to evaluate : 0.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ARG Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 374 ILE Chi-restraints excluded: chain A residue 734 LYS Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 1013 ILE Chi-restraints excluded: chain A residue 1061 GLU Chi-restraints excluded: chain A residue 1174 MET Chi-restraints excluded: chain A residue 1192 SER Chi-restraints excluded: chain A residue 1949 ILE Chi-restraints excluded: chain A residue 1969 VAL Chi-restraints excluded: chain A residue 2023 CYS Chi-restraints excluded: chain A residue 2235 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 33 optimal weight: 0.6980 chunk 194 optimal weight: 6.9990 chunk 89 optimal weight: 1.9990 chunk 120 optimal weight: 4.9990 chunk 218 optimal weight: 7.9990 chunk 234 optimal weight: 10.0000 chunk 175 optimal weight: 0.9980 chunk 100 optimal weight: 0.0770 chunk 184 optimal weight: 1.9990 chunk 52 optimal weight: 4.9990 chunk 200 optimal weight: 7.9990 overall best weight: 1.1542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1652 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1892 GLN A2034 ASN A2057 GLN ** A2182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2329 GLN ** 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 = 0.3638 r_free = 0.3638 target = 0.063944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.051534 restraints weight = 84821.951| |-----------------------------------------------------------------------------| r_work (start): 0.3295 rms_B_bonded: 3.84 r_work: 0.3172 rms_B_bonded: 4.43 restraints_weight: 0.5000 r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.2021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 19602 Z= 0.163 Angle : 0.539 9.261 26540 Z= 0.288 Chirality : 0.044 0.199 2941 Planarity : 0.003 0.039 3409 Dihedral : 4.487 23.241 2567 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 12.15 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.56 % Favored : 92.39 % Rotamer: Outliers : 1.67 % Allowed : 13.58 % Favored : 84.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.85 (0.18), residues: 2380 helix: 1.29 (0.20), residues: 686 sheet: -1.15 (0.23), residues: 495 loop : -1.41 (0.18), residues: 1199 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 224 TYR 0.034 0.001 TYR A2009 PHE 0.016 0.001 PHE A 821 TRP 0.011 0.001 TRP A2080 HIS 0.004 0.001 HIS A 581 Details of bonding type rmsd covalent geometry : bond 0.00360 (19599) covalent geometry : angle 0.53917 (26540) hydrogen bonds : bond 0.03243 ( 771) hydrogen bonds : angle 4.95926 ( 2109) metal coordination : bond 0.00354 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4760 Ramachandran restraints generated. 2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4760 Ramachandran restraints generated. 2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 2151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 84 time to evaluate : 0.625 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 ARG cc_start: 0.8398 (OUTLIER) cc_final: 0.8190 (mpp80) REVERT: A 215 ARG cc_start: 0.8522 (mmm160) cc_final: 0.8251 (mmm160) REVERT: A 320 MET cc_start: 0.8650 (mtt) cc_final: 0.8260 (mtt) REVERT: A 489 GLU cc_start: 0.8663 (mm-30) cc_final: 0.7842 (mm-30) REVERT: A 905 LYS cc_start: 0.9406 (mttt) cc_final: 0.8938 (pmtt) REVERT: A 1013 ILE cc_start: 0.9582 (OUTLIER) cc_final: 0.9233 (pp) REVERT: A 1143 ASP cc_start: 0.8773 (t0) cc_final: 0.8453 (t0) REVERT: A 1174 MET cc_start: 0.8722 (OUTLIER) cc_final: 0.7285 (mmm) REVERT: A 1223 MET cc_start: 0.7930 (OUTLIER) cc_final: 0.7715 (ttm) REVERT: A 1294 LYS cc_start: 0.8800 (tptt) cc_final: 0.8551 (tppt) REVERT: A 2057 GLN cc_start: 0.9129 (OUTLIER) cc_final: 0.8725 (mm-40) REVERT: A 2075 LYS cc_start: 0.8322 (ttpt) cc_final: 0.7774 (mptt) REVERT: A 2159 MET cc_start: 0.8209 (tmm) cc_final: 0.7870 (ttt) outliers start: 36 outliers final: 16 residues processed: 108 average time/residue: 0.5125 time to fit residues: 64.2741 Evaluate side-chains 100 residues out of total 2151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 79 time to evaluate : 0.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ARG Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 288 MET Chi-restraints excluded: chain A residue 374 ILE Chi-restraints excluded: chain A residue 458 MET Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 965 PHE Chi-restraints excluded: chain A residue 1013 ILE Chi-restraints excluded: chain A residue 1061 GLU Chi-restraints excluded: chain A residue 1098 ILE Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1174 MET Chi-restraints excluded: chain A residue 1192 SER Chi-restraints excluded: chain A residue 1223 MET Chi-restraints excluded: chain A residue 1949 ILE Chi-restraints excluded: chain A residue 1969 VAL Chi-restraints excluded: chain A residue 2023 CYS Chi-restraints excluded: chain A residue 2057 GLN Chi-restraints excluded: chain A residue 2235 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 99 optimal weight: 5.9990 chunk 131 optimal weight: 2.9990 chunk 44 optimal weight: 3.9990 chunk 233 optimal weight: 6.9990 chunk 180 optimal weight: 0.2980 chunk 95 optimal weight: 0.0030 chunk 39 optimal weight: 0.7980 chunk 206 optimal weight: 0.9980 chunk 50 optimal weight: 0.7980 chunk 71 optimal weight: 2.9990 chunk 203 optimal weight: 5.9990 overall best weight: 0.5790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 ASN A 454 GLN A 825 ASN ** A1652 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1892 GLN A2034 ASN ** A2182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2262 ASN ** A2329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.064816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.052487 restraints weight = 84830.262| |-----------------------------------------------------------------------------| r_work (start): 0.3324 rms_B_bonded: 3.85 r_work: 0.3200 rms_B_bonded: 4.46 restraints_weight: 0.5000 r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.2149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 19602 Z= 0.115 Angle : 0.515 9.729 26540 Z= 0.275 Chirality : 0.043 0.174 2941 Planarity : 0.003 0.040 3409 Dihedral : 4.376 23.309 2567 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.72 % Favored : 93.24 % Rotamer: Outliers : 1.67 % Allowed : 14.37 % Favored : 83.96 % 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: -0.77 (0.18), residues: 2380 helix: 1.37 (0.20), residues: 685 sheet: -1.14 (0.24), residues: 497 loop : -1.36 (0.18), residues: 1198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 224 TYR 0.034 0.001 TYR A2009 PHE 0.012 0.001 PHE A 821 TRP 0.008 0.001 TRP A1234 HIS 0.003 0.001 HIS A1128 Details of bonding type rmsd covalent geometry : bond 0.00253 (19599) covalent geometry : angle 0.51454 (26540) hydrogen bonds : bond 0.03028 ( 771) hydrogen bonds : angle 4.83130 ( 2109) metal coordination : bond 0.00171 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4760 Ramachandran restraints generated. 2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4760 Ramachandran restraints generated. 2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 2151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 90 time to evaluate : 0.574 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 215 ARG cc_start: 0.8524 (mmm160) cc_final: 0.8150 (mmm160) REVERT: A 320 MET cc_start: 0.8565 (OUTLIER) cc_final: 0.8169 (mtt) REVERT: A 489 GLU cc_start: 0.8422 (mm-30) cc_final: 0.7679 (mt-10) REVERT: A 734 LYS cc_start: 0.8117 (OUTLIER) cc_final: 0.7745 (tppt) REVERT: A 766 LYS cc_start: 0.8413 (mmpt) cc_final: 0.7840 (mmtt) REVERT: A 905 LYS cc_start: 0.9403 (mttt) cc_final: 0.8921 (pmtt) REVERT: A 1013 ILE cc_start: 0.9570 (OUTLIER) cc_final: 0.9217 (pp) REVERT: A 1143 ASP cc_start: 0.8743 (t0) cc_final: 0.8394 (t0) REVERT: A 1174 MET cc_start: 0.8707 (OUTLIER) cc_final: 0.7285 (mmm) REVERT: A 2057 GLN cc_start: 0.9025 (mm110) cc_final: 0.8726 (mm-40) REVERT: A 2075 LYS cc_start: 0.8262 (ttpt) cc_final: 0.7690 (mptt) outliers start: 36 outliers final: 15 residues processed: 117 average time/residue: 0.4861 time to fit residues: 66.3174 Evaluate side-chains 97 residues out of total 2151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 78 time to evaluate : 0.832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 175 MET Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 320 MET Chi-restraints excluded: chain A residue 374 ILE Chi-restraints excluded: chain A residue 734 LYS Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 965 PHE Chi-restraints excluded: chain A residue 1013 ILE Chi-restraints excluded: chain A residue 1061 GLU Chi-restraints excluded: chain A residue 1098 ILE Chi-restraints excluded: chain A residue 1174 MET Chi-restraints excluded: chain A residue 1192 SER Chi-restraints excluded: chain A residue 1969 VAL Chi-restraints excluded: chain A residue 2009 TYR Chi-restraints excluded: chain A residue 2011 THR Chi-restraints excluded: chain A residue 2023 CYS Chi-restraints excluded: chain A residue 2235 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 181 optimal weight: 3.9990 chunk 124 optimal weight: 3.9990 chunk 234 optimal weight: 9.9990 chunk 64 optimal weight: 3.9990 chunk 208 optimal weight: 4.9990 chunk 164 optimal weight: 0.0040 chunk 44 optimal weight: 1.9990 chunk 65 optimal weight: 0.9980 chunk 15 optimal weight: 0.9990 chunk 161 optimal weight: 0.4980 chunk 153 optimal weight: 3.9990 overall best weight: 0.8996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1652 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2034 ASN ** A2182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.064251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.051901 restraints weight = 85843.247| |-----------------------------------------------------------------------------| r_work (start): 0.3309 rms_B_bonded: 3.87 r_work: 0.3185 rms_B_bonded: 4.46 restraints_weight: 0.5000 r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.2239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 19602 Z= 0.139 Angle : 0.527 9.651 26540 Z= 0.281 Chirality : 0.043 0.157 2941 Planarity : 0.003 0.038 3409 Dihedral : 4.401 25.634 2567 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 11.41 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.31 % Favored : 92.65 % Rotamer: Outliers : 1.58 % Allowed : 15.48 % Favored : 82.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.76 (0.18), residues: 2380 helix: 1.40 (0.20), residues: 685 sheet: -1.14 (0.24), residues: 497 loop : -1.35 (0.18), residues: 1198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 224 TYR 0.034 0.001 TYR A2009 PHE 0.035 0.001 PHE A1272 TRP 0.009 0.001 TRP A2080 HIS 0.004 0.001 HIS A 581 Details of bonding type rmsd covalent geometry : bond 0.00310 (19599) covalent geometry : angle 0.52729 (26540) hydrogen bonds : bond 0.03064 ( 771) hydrogen bonds : angle 4.80300 ( 2109) metal coordination : bond 0.00253 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4760 Ramachandran restraints generated. 2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4760 Ramachandran restraints generated. 2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 2151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 84 time to evaluate : 0.708 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 215 ARG cc_start: 0.8510 (mmm160) cc_final: 0.8132 (mmm160) REVERT: A 257 GLU cc_start: 0.8470 (mp0) cc_final: 0.8252 (mp0) REVERT: A 320 MET cc_start: 0.8565 (OUTLIER) cc_final: 0.8265 (mtt) REVERT: A 489 GLU cc_start: 0.8580 (mm-30) cc_final: 0.7651 (mt-10) REVERT: A 542 LEU cc_start: 0.8235 (mt) cc_final: 0.8024 (mp) REVERT: A 905 LYS cc_start: 0.9402 (mttt) cc_final: 0.8933 (pmtt) REVERT: A 1013 ILE cc_start: 0.9568 (OUTLIER) cc_final: 0.9218 (pp) REVERT: A 1174 MET cc_start: 0.8698 (OUTLIER) cc_final: 0.7251 (mmm) REVERT: A 2057 GLN cc_start: 0.9066 (mm110) cc_final: 0.8755 (mm-40) REVERT: A 2075 LYS cc_start: 0.8274 (ttpt) cc_final: 0.7709 (mptt) REVERT: A 2308 PHE cc_start: 0.8125 (m-80) cc_final: 0.7659 (m-80) outliers start: 34 outliers final: 15 residues processed: 110 average time/residue: 0.4782 time to fit residues: 61.6206 Evaluate side-chains 94 residues out of total 2151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 76 time to evaluate : 0.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 320 MET Chi-restraints excluded: chain A residue 374 ILE Chi-restraints excluded: chain A residue 580 VAL Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 965 PHE Chi-restraints excluded: chain A residue 1013 ILE Chi-restraints excluded: chain A residue 1061 GLU Chi-restraints excluded: chain A residue 1098 ILE Chi-restraints excluded: chain A residue 1174 MET Chi-restraints excluded: chain A residue 1192 SER Chi-restraints excluded: chain A residue 1949 ILE Chi-restraints excluded: chain A residue 1969 VAL Chi-restraints excluded: chain A residue 2009 TYR Chi-restraints excluded: chain A residue 2011 THR Chi-restraints excluded: chain A residue 2023 CYS Chi-restraints excluded: chain A residue 2235 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 18 optimal weight: 0.8980 chunk 57 optimal weight: 4.9990 chunk 174 optimal weight: 0.7980 chunk 176 optimal weight: 0.9980 chunk 55 optimal weight: 7.9990 chunk 14 optimal weight: 0.8980 chunk 113 optimal weight: 0.7980 chunk 221 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 chunk 204 optimal weight: 0.9990 chunk 28 optimal weight: 0.3980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 611 GLN ** A1652 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2034 ASN ** A2182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2329 GLN ** 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 = 0.3655 r_free = 0.3655 target = 0.064517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.052187 restraints weight = 85405.212| |-----------------------------------------------------------------------------| r_work (start): 0.3318 rms_B_bonded: 3.86 r_work: 0.3194 rms_B_bonded: 4.47 restraints_weight: 0.5000 r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 moved from start: 0.2325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 19602 Z= 0.130 Angle : 0.534 11.661 26540 Z= 0.285 Chirality : 0.043 0.168 2941 Planarity : 0.003 0.038 3409 Dihedral : 4.389 24.062 2567 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 11.20 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.89 % Favored : 93.07 % Rotamer: Outliers : 1.12 % Allowed : 16.32 % Favored : 82.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.72 (0.18), residues: 2380 helix: 1.46 (0.20), residues: 683 sheet: -1.13 (0.24), residues: 497 loop : -1.34 (0.18), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 224 TYR 0.034 0.001 TYR A2009 PHE 0.031 0.001 PHE A1272 TRP 0.009 0.001 TRP A2080 HIS 0.004 0.001 HIS A 581 Details of bonding type rmsd covalent geometry : bond 0.00294 (19599) covalent geometry : angle 0.53368 (26540) hydrogen bonds : bond 0.03019 ( 771) hydrogen bonds : angle 4.79842 ( 2109) metal coordination : bond 0.00197 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4760 Ramachandran restraints generated. 2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4760 Ramachandran restraints generated. 2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 2151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 84 time to evaluate : 0.734 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: A 116 GLN cc_start: 0.7817 (mm-40) cc_final: 0.7485 (mp10) REVERT: A 215 ARG cc_start: 0.8509 (mmm160) cc_final: 0.8133 (mmm160) REVERT: A 320 MET cc_start: 0.8561 (OUTLIER) cc_final: 0.8173 (mtt) REVERT: A 593 TYR cc_start: 0.8306 (t80) cc_final: 0.8105 (t80) REVERT: A 722 MET cc_start: 0.8001 (mtm) cc_final: 0.7767 (mtm) REVERT: A 905 LYS cc_start: 0.9401 (mttt) cc_final: 0.8926 (pmtt) REVERT: A 1013 ILE cc_start: 0.9570 (OUTLIER) cc_final: 0.9219 (pp) REVERT: A 1174 MET cc_start: 0.8703 (OUTLIER) cc_final: 0.7250 (mmm) REVERT: A 2057 GLN cc_start: 0.9050 (mm110) cc_final: 0.8757 (mm-40) REVERT: A 2075 LYS cc_start: 0.8263 (ttpt) cc_final: 0.7695 (mptt) outliers start: 24 outliers final: 15 residues processed: 102 average time/residue: 0.4978 time to fit residues: 59.1899 Evaluate side-chains 94 residues out of total 2151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 76 time to evaluate : 0.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 320 MET Chi-restraints excluded: chain A residue 374 ILE Chi-restraints excluded: chain A residue 580 VAL Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 965 PHE Chi-restraints excluded: chain A residue 1013 ILE Chi-restraints excluded: chain A residue 1061 GLU Chi-restraints excluded: chain A residue 1098 ILE Chi-restraints excluded: chain A residue 1141 GLU Chi-restraints excluded: chain A residue 1174 MET Chi-restraints excluded: chain A residue 1192 SER Chi-restraints excluded: chain A residue 1969 VAL Chi-restraints excluded: chain A residue 2009 TYR Chi-restraints excluded: chain A residue 2011 THR Chi-restraints excluded: chain A residue 2023 CYS Chi-restraints excluded: chain A residue 2235 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 35 optimal weight: 4.9990 chunk 68 optimal weight: 0.0870 chunk 69 optimal weight: 1.9990 chunk 122 optimal weight: 0.9980 chunk 73 optimal weight: 2.9990 chunk 11 optimal weight: 3.9990 chunk 137 optimal weight: 5.9990 chunk 38 optimal weight: 2.9990 chunk 43 optimal weight: 5.9990 chunk 174 optimal weight: 0.9990 chunk 128 optimal weight: 1.9990 overall best weight: 1.2164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2034 ASN ** A2182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.063087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.050758 restraints weight = 85217.768| |-----------------------------------------------------------------------------| r_work (start): 0.3278 rms_B_bonded: 3.86 r_work: 0.3157 rms_B_bonded: 4.43 restraints_weight: 0.5000 r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 moved from start: 0.2392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 19602 Z= 0.170 Angle : 0.562 12.340 26540 Z= 0.298 Chirality : 0.044 0.159 2941 Planarity : 0.003 0.039 3409 Dihedral : 4.476 22.647 2567 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 12.23 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.69 % Favored : 92.27 % Rotamer: Outliers : 1.35 % Allowed : 16.27 % Favored : 82.38 % 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: -0.75 (0.18), residues: 2380 helix: 1.40 (0.20), residues: 683 sheet: -1.12 (0.24), residues: 501 loop : -1.34 (0.18), residues: 1196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 224 TYR 0.035 0.001 TYR A2009 PHE 0.028 0.001 PHE A1272 TRP 0.011 0.001 TRP A2080 HIS 0.004 0.001 HIS A 581 Details of bonding type rmsd covalent geometry : bond 0.00380 (19599) covalent geometry : angle 0.56154 (26540) hydrogen bonds : bond 0.03155 ( 771) hydrogen bonds : angle 4.87763 ( 2109) metal coordination : bond 0.00336 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4760 Ramachandran restraints generated. 2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4760 Ramachandran restraints generated. 2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 2151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 76 time to evaluate : 0.727 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 215 ARG cc_start: 0.8525 (mmm160) cc_final: 0.8132 (mmm160) REVERT: A 320 MET cc_start: 0.8562 (OUTLIER) cc_final: 0.8255 (mtt) REVERT: A 489 GLU cc_start: 0.8444 (mm-30) cc_final: 0.8170 (mm-30) REVERT: A 766 LYS cc_start: 0.8484 (mmpt) cc_final: 0.7880 (mmtp) REVERT: A 905 LYS cc_start: 0.9397 (mttt) cc_final: 0.8927 (pmtt) REVERT: A 1013 ILE cc_start: 0.9566 (OUTLIER) cc_final: 0.9213 (pp) REVERT: A 1141 GLU cc_start: 0.7758 (OUTLIER) cc_final: 0.7552 (mp0) REVERT: A 1174 MET cc_start: 0.8741 (OUTLIER) cc_final: 0.7294 (mmm) REVERT: A 2075 LYS cc_start: 0.8285 (ttpt) cc_final: 0.7747 (mptt) outliers start: 29 outliers final: 15 residues processed: 97 average time/residue: 0.5125 time to fit residues: 58.1752 Evaluate side-chains 91 residues out of total 2151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 72 time to evaluate : 0.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 320 MET Chi-restraints excluded: chain A residue 374 ILE Chi-restraints excluded: chain A residue 580 VAL Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 965 PHE Chi-restraints excluded: chain A residue 1013 ILE Chi-restraints excluded: chain A residue 1061 GLU Chi-restraints excluded: chain A residue 1098 ILE Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1141 GLU Chi-restraints excluded: chain A residue 1174 MET Chi-restraints excluded: chain A residue 1192 SER Chi-restraints excluded: chain A residue 1969 VAL Chi-restraints excluded: chain A residue 2009 TYR Chi-restraints excluded: chain A residue 2011 THR Chi-restraints excluded: chain A residue 2023 CYS Chi-restraints excluded: chain A residue 2235 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 92 optimal weight: 3.9990 chunk 161 optimal weight: 0.0570 chunk 119 optimal weight: 0.0170 chunk 99 optimal weight: 5.9990 chunk 152 optimal weight: 3.9990 chunk 91 optimal weight: 3.9990 chunk 137 optimal weight: 4.9990 chunk 124 optimal weight: 2.9990 chunk 168 optimal weight: 0.9990 chunk 179 optimal weight: 3.9990 chunk 46 optimal weight: 3.9990 overall best weight: 1.6142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 ASN A 138 ASN A 454 GLN A 598 ASN A 825 ASN A2034 ASN A2181 ASN ** A2182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.062136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.049787 restraints weight = 85986.649| |-----------------------------------------------------------------------------| r_work (start): 0.3252 rms_B_bonded: 3.86 r_work: 0.3131 rms_B_bonded: 4.41 restraints_weight: 0.5000 r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.2489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 19602 Z= 0.209 Angle : 0.593 12.410 26540 Z= 0.315 Chirality : 0.044 0.168 2941 Planarity : 0.003 0.039 3409 Dihedral : 4.667 27.708 2567 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 13.38 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.98 % Favored : 91.97 % Rotamer: Outliers : 1.02 % Allowed : 16.64 % Favored : 82.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.81 (0.18), residues: 2380 helix: 1.30 (0.20), residues: 683 sheet: -1.21 (0.24), residues: 477 loop : -1.33 (0.18), residues: 1220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1947 TYR 0.035 0.001 TYR A2009 PHE 0.026 0.002 PHE A1272 TRP 0.012 0.001 TRP A2080 HIS 0.005 0.001 HIS A 581 Details of bonding type rmsd covalent geometry : bond 0.00468 (19599) covalent geometry : angle 0.59335 (26540) hydrogen bonds : bond 0.03376 ( 771) hydrogen bonds : angle 5.01414 ( 2109) metal coordination : bond 0.00419 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4760 Ramachandran restraints generated. 2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4760 Ramachandran restraints generated. 2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 2151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 69 time to evaluate : 0.649 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 161 GLN cc_start: 0.8722 (mt0) cc_final: 0.8379 (pm20) REVERT: A 215 ARG cc_start: 0.8476 (mmm160) cc_final: 0.8171 (mmm160) REVERT: A 320 MET cc_start: 0.8603 (OUTLIER) cc_final: 0.8315 (mtt) REVERT: A 489 GLU cc_start: 0.8503 (mm-30) cc_final: 0.8214 (mm-30) REVERT: A 1013 ILE cc_start: 0.9572 (OUTLIER) cc_final: 0.9228 (pp) REVERT: A 1141 GLU cc_start: 0.7757 (OUTLIER) cc_final: 0.7507 (mp0) REVERT: A 1174 MET cc_start: 0.8792 (OUTLIER) cc_final: 0.7345 (mmm) REVERT: A 1202 LEU cc_start: 0.8361 (mt) cc_final: 0.8114 (mp) REVERT: A 2075 LYS cc_start: 0.8383 (ttpt) cc_final: 0.7980 (mptt) outliers start: 22 outliers final: 16 residues processed: 84 average time/residue: 0.5246 time to fit residues: 51.6566 Evaluate side-chains 87 residues out of total 2151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 67 time to evaluate : 0.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 320 MET Chi-restraints excluded: chain A residue 374 ILE Chi-restraints excluded: chain A residue 580 VAL Chi-restraints excluded: chain A residue 702 MET Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 965 PHE Chi-restraints excluded: chain A residue 1013 ILE Chi-restraints excluded: chain A residue 1061 GLU Chi-restraints excluded: chain A residue 1098 ILE Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1141 GLU Chi-restraints excluded: chain A residue 1174 MET Chi-restraints excluded: chain A residue 1390 ILE Chi-restraints excluded: chain A residue 1969 VAL Chi-restraints excluded: chain A residue 2009 TYR Chi-restraints excluded: chain A residue 2011 THR Chi-restraints excluded: chain A residue 2023 CYS Chi-restraints excluded: chain A residue 2235 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 3 optimal weight: 5.9990 chunk 68 optimal weight: 0.0370 chunk 176 optimal weight: 1.9990 chunk 130 optimal weight: 0.3980 chunk 2 optimal weight: 0.9980 chunk 221 optimal weight: 2.9990 chunk 194 optimal weight: 3.9990 chunk 53 optimal weight: 0.6980 chunk 214 optimal weight: 0.0370 chunk 78 optimal weight: 0.5980 chunk 184 optimal weight: 0.8980 overall best weight: 0.3536 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 ASN A 454 GLN A 825 ASN A1338 ASN A2034 ASN ** A2182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.064388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.052137 restraints weight = 85266.981| |-----------------------------------------------------------------------------| r_work (start): 0.3320 rms_B_bonded: 3.89 r_work: 0.3200 rms_B_bonded: 4.48 restraints_weight: 0.5000 r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.2539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 19602 Z= 0.108 Angle : 0.544 12.927 26540 Z= 0.288 Chirality : 0.043 0.165 2941 Planarity : 0.003 0.039 3409 Dihedral : 4.415 22.862 2567 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 10.83 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.76 % Favored : 93.19 % Rotamer: Outliers : 0.88 % Allowed : 16.78 % Favored : 82.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.71 (0.18), residues: 2380 helix: 1.43 (0.20), residues: 683 sheet: -1.15 (0.24), residues: 496 loop : -1.29 (0.18), residues: 1201 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 224 TYR 0.035 0.001 TYR A2009 PHE 0.028 0.001 PHE A1272 TRP 0.012 0.001 TRP A2122 HIS 0.003 0.001 HIS A1128 Details of bonding type rmsd covalent geometry : bond 0.00236 (19599) covalent geometry : angle 0.54375 (26540) hydrogen bonds : bond 0.02977 ( 771) hydrogen bonds : angle 4.76186 ( 2109) metal coordination : bond 0.00082 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6609.70 seconds wall clock time: 113 minutes 55.20 seconds (6835.20 seconds total)