Starting phenix.real_space_refine (version: dev) on Wed Feb 22 03:21:56 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7px3_13690/02_2023/7px3_13690.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7px3_13690/02_2023/7px3_13690.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.05 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7px3_13690/02_2023/7px3_13690.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7px3_13690/02_2023/7px3_13690.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7px3_13690/02_2023/7px3_13690.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7px3_13690/02_2023/7px3_13690.pdb" } resolution = 3.05 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 ------------------------------------------------------------------------------- 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= 0.008 sd= 0.069 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 Process input model Symmetric amino acids flipped Residue "B TYR 442": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 470": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 540": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 562": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 674": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 675": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 676": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 701": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 751": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 782": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 878": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 922": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 936": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 992": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1018": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1075": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1254": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1321": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1327": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1336": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1340": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1394": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1547": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1619": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1754": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1823": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 2021": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 2094": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 2104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 2122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 2235": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 2251": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 2256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 2270": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 2294": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 2314": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T PHE 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T PHE 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 16430 Number of models: 1 Model: "" Number of chains: 3 Chain: "B" Number of atoms: 13870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1725, 13870 Classifications: {'peptide': 1725} Link IDs: {'PTRANS': 79, 'TRANS': 1645} Chain: "J" Number of atoms: 2030 Number of conformers: 1 Conformer: "" Number of residues, atoms: 250, 2030 Classifications: {'peptide': 250} Link IDs: {'PTRANS': 20, 'TRANS': 229} Chain: "T" Number of atoms: 530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 530 Classifications: {'peptide': 66} Link IDs: {'PTRANS': 5, 'TRANS': 60} Chain breaks: 3 Time building chain proxies: 9.56, per 1000 atoms: 0.58 Number of scatterers: 16430 At special positions: 0 Unit cell: (105.12, 142.788, 149.796, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 84 16.00 O 3022 8.00 N 2826 7.00 C 10498 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 - 3.50 Amino acid : False - 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: 6.48 Conformation dependent library (CDL) restraints added in 2.4 seconds 4058 Ramachandran restraints generated. 2029 Oldfield, 0 Emsley, 2029 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3882 Finding SS restraints... Secondary structure from input PDB file: 91 helices and 15 sheets defined 48.2% alpha, 16.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.41 Creating SS restraints... Processing helix chain 'B' and resid 410 through 415 removed outlier: 3.620A pdb=" N LEU B 414 " --> pdb=" O ASP B 410 " (cutoff:3.500A) Processing helix chain 'B' and resid 418 through 422 Processing helix chain 'B' and resid 468 through 473 removed outlier: 4.108A pdb=" N ALA B 473 " --> pdb=" O LYS B 469 " (cutoff:3.500A) Processing helix chain 'B' and resid 482 through 488 Processing helix chain 'B' and resid 488 through 494 Processing helix chain 'B' and resid 508 through 523 removed outlier: 3.998A pdb=" N VAL B 512 " --> pdb=" O GLY B 508 " (cutoff:3.500A) Processing helix chain 'B' and resid 544 through 560 Processing helix chain 'B' and resid 561 through 563 No H-bonds generated for 'chain 'B' and resid 561 through 563' Processing helix chain 'B' and resid 578 through 583 Processing helix chain 'B' and resid 589 through 600 removed outlier: 3.947A pdb=" N GLY B 600 " --> pdb=" O ILE B 596 " (cutoff:3.500A) Processing helix chain 'B' and resid 601 through 606 removed outlier: 3.939A pdb=" N TYR B 605 " --> pdb=" O GLY B 601 " (cutoff:3.500A) Processing helix chain 'B' and resid 617 through 622 removed outlier: 3.603A pdb=" N LEU B 620 " --> pdb=" O ILE B 617 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N HIS B 621 " --> pdb=" O HIS B 618 " (cutoff:3.500A) Processing helix chain 'B' and resid 624 through 643 removed outlier: 3.656A pdb=" N LEU B 628 " --> pdb=" O ARG B 624 " (cutoff:3.500A) Processing helix chain 'B' and resid 657 through 665 Processing helix chain 'B' and resid 677 through 681 Processing helix chain 'B' and resid 696 through 716 removed outlier: 3.721A pdb=" N PHE B 701 " --> pdb=" O ALA B 697 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N GLN B 702 " --> pdb=" O ILE B 698 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N HIS B 715 " --> pdb=" O LYS B 711 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ALA B 716 " --> pdb=" O ILE B 712 " (cutoff:3.500A) Processing helix chain 'B' and resid 729 through 745 Processing helix chain 'B' and resid 749 through 753 removed outlier: 3.534A pdb=" N LEU B 752 " --> pdb=" O GLY B 749 " (cutoff:3.500A) Processing helix chain 'B' and resid 760 through 767 Processing helix chain 'B' and resid 773 through 778 removed outlier: 3.818A pdb=" N LEU B 777 " --> pdb=" O GLU B 773 " (cutoff:3.500A) Processing helix chain 'B' and resid 792 through 803 removed outlier: 3.778A pdb=" N ASP B 799 " --> pdb=" O THR B 795 " (cutoff:3.500A) Processing helix chain 'B' and resid 813 through 819 removed outlier: 3.891A pdb=" N TRP B 817 " --> pdb=" O ALA B 813 " (cutoff:3.500A) Processing helix chain 'B' and resid 845 through 854 Processing helix chain 'B' and resid 878 through 884 Processing helix chain 'B' and resid 896 through 908 Processing helix chain 'B' and resid 912 through 922 removed outlier: 3.504A pdb=" N GLY B 921 " --> pdb=" O VAL B 917 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N TYR B 922 " --> pdb=" O ASN B 918 " (cutoff:3.500A) Processing helix chain 'B' and resid 923 through 932 removed outlier: 3.677A pdb=" N ILE B 927 " --> pdb=" O ALA B 923 " (cutoff:3.500A) Processing helix chain 'B' and resid 939 through 946 Processing helix chain 'B' and resid 949 through 967 Processing helix chain 'B' and resid 982 through 992 Processing helix chain 'B' and resid 994 through 1005 Processing helix chain 'B' and resid 1010 through 1020 Processing helix chain 'B' and resid 1021 through 1025 removed outlier: 3.587A pdb=" N PHE B1024 " --> pdb=" O SER B1021 " (cutoff:3.500A) Processing helix chain 'B' and resid 1033 through 1043 removed outlier: 3.841A pdb=" N ARG B1043 " --> pdb=" O LYS B1039 " (cutoff:3.500A) Processing helix chain 'B' and resid 1054 through 1068 Processing helix chain 'B' and resid 1074 through 1103 removed outlier: 4.200A pdb=" N ARG B1090 " --> pdb=" O GLN B1086 " (cutoff:3.500A) Processing helix chain 'B' and resid 1105 through 1121 Processing helix chain 'B' and resid 1127 through 1132 Processing helix chain 'B' and resid 1136 through 1146 Processing helix chain 'B' and resid 1150 through 1155 Processing helix chain 'B' and resid 1157 through 1166 Processing helix chain 'B' and resid 1170 through 1181 removed outlier: 3.711A pdb=" N HIS B1179 " --> pdb=" O HIS B1175 " (cutoff:3.500A) Processing helix chain 'B' and resid 1308 through 1312 Processing helix chain 'B' and resid 1314 through 1322 removed outlier: 3.737A pdb=" N LEU B1320 " --> pdb=" O ALA B1316 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N TYR B1321 " --> pdb=" O PHE B1317 " (cutoff:3.500A) Processing helix chain 'B' and resid 1329 through 1341 removed outlier: 4.567A pdb=" N ASN B1337 " --> pdb=" O THR B1333 " (cutoff:3.500A) removed outlier: 5.045A pdb=" N THR B1338 " --> pdb=" O GLN B1334 " (cutoff:3.500A) Processing helix chain 'B' and resid 1355 through 1371 removed outlier: 3.932A pdb=" N CYS B1359 " --> pdb=" O GLY B1355 " (cutoff:3.500A) Processing helix chain 'B' and resid 1382 through 1398 removed outlier: 4.094A pdb=" N GLU B1395 " --> pdb=" O MET B1391 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LYS B1396 " --> pdb=" O ASP B1392 " (cutoff:3.500A) Processing helix chain 'B' and resid 1411 through 1422 Processing helix chain 'B' and resid 1428 through 1437 Processing helix chain 'B' and resid 1442 through 1447 removed outlier: 3.700A pdb=" N GLN B1446 " --> pdb=" O ARG B1442 " (cutoff:3.500A) Processing helix chain 'B' and resid 1456 through 1460 removed outlier: 3.501A pdb=" N GLY B1460 " --> pdb=" O HIS B1457 " (cutoff:3.500A) Processing helix chain 'B' and resid 1463 through 1482 removed outlier: 3.850A pdb=" N LEU B1467 " --> pdb=" O ASN B1463 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N GLU B1482 " --> pdb=" O SER B1478 " (cutoff:3.500A) Processing helix chain 'B' and resid 1496 through 1504 removed outlier: 3.636A pdb=" N VAL B1500 " --> pdb=" O ASN B1496 " (cutoff:3.500A) Processing helix chain 'B' and resid 1515 through 1519 removed outlier: 3.858A pdb=" N ARG B1519 " --> pdb=" O PRO B1516 " (cutoff:3.500A) Processing helix chain 'B' and resid 1534 through 1554 removed outlier: 4.620A pdb=" N LYS B1544 " --> pdb=" O LEU B1540 " (cutoff:3.500A) Proline residue: B1545 - end of helix Processing helix chain 'B' and resid 1565 through 1583 removed outlier: 3.650A pdb=" N ARG B1570 " --> pdb=" O ARG B1566 " (cutoff:3.500A) Processing helix chain 'B' and resid 1593 through 1604 Proline residue: B1599 - end of helix removed outlier: 3.907A pdb=" N LYS B1603 " --> pdb=" O PRO B1599 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LEU B1604 " --> pdb=" O TYR B1600 " (cutoff:3.500A) Processing helix chain 'B' and resid 1606 through 1615 removed outlier: 3.512A pdb=" N ASN B1615 " --> pdb=" O GLU B1611 " (cutoff:3.500A) Processing helix chain 'B' and resid 1625 through 1639 Processing helix chain 'B' and resid 1649 through 1651 No H-bonds generated for 'chain 'B' and resid 1649 through 1651' Processing helix chain 'B' and resid 1680 through 1690 removed outlier: 3.549A pdb=" N HIS B1690 " --> pdb=" O GLN B1686 " (cutoff:3.500A) Processing helix chain 'B' and resid 1710 through 1719 removed outlier: 4.195A pdb=" N TYR B1719 " --> pdb=" O LYS B1715 " (cutoff:3.500A) Processing helix chain 'B' and resid 1731 through 1742 removed outlier: 4.554A pdb=" N HIS B1735 " --> pdb=" O CYS B1731 " (cutoff:3.500A) Processing helix chain 'B' and resid 1747 through 1755 removed outlier: 3.544A pdb=" N VAL B1752 " --> pdb=" O LYS B1748 " (cutoff:3.500A) Processing helix chain 'B' and resid 1758 through 1767 removed outlier: 3.652A pdb=" N ARG B1762 " --> pdb=" O THR B1758 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N THR B1765 " --> pdb=" O TYR B1761 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N GLN B1766 " --> pdb=" O ARG B1762 " (cutoff:3.500A) Processing helix chain 'B' and resid 1768 through 1772 Processing helix chain 'B' and resid 1777 through 1799 Processing helix chain 'B' and resid 1813 through 1823 Processing helix chain 'B' and resid 1825 through 1836 Processing helix chain 'B' and resid 1841 through 1851 Processing helix chain 'B' and resid 1852 through 1858 removed outlier: 4.291A pdb=" N ASN B1857 " --> pdb=" O GLU B1854 " (cutoff:3.500A) Processing helix chain 'B' and resid 1863 through 1875 removed outlier: 4.124A pdb=" N LEU B1867 " --> pdb=" O HIS B1863 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N GLN B1873 " --> pdb=" O ARG B1869 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N LYS B1874 " --> pdb=" O GLN B1870 " (cutoff:3.500A) Processing helix chain 'B' and resid 1886 through 1900 Processing helix chain 'B' and resid 1905 through 1934 removed outlier: 3.827A pdb=" N LYS B1918 " --> pdb=" O GLU B1914 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N ILE B1920 " --> pdb=" O LEU B1916 " (cutoff:3.500A) removed outlier: 5.199A pdb=" N ARG B1921 " --> pdb=" O SER B1917 " (cutoff:3.500A) Processing helix chain 'B' and resid 1935 through 1952 removed outlier: 3.676A pdb=" N ALA B1939 " --> pdb=" O TRP B1935 " (cutoff:3.500A) Processing helix chain 'B' and resid 1958 through 1963 removed outlier: 3.559A pdb=" N GLN B1962 " --> pdb=" O TYR B1959 " (cutoff:3.500A) Processing helix chain 'B' and resid 1967 through 1978 Processing helix chain 'B' and resid 1981 through 1988 removed outlier: 3.946A pdb=" N ILE B1985 " --> pdb=" O SER B1981 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N MET B1986 " --> pdb=" O VAL B1982 " (cutoff:3.500A) Processing helix chain 'B' and resid 1989 through 1997 removed outlier: 3.685A pdb=" N LEU B1997 " --> pdb=" O ARG B1993 " (cutoff:3.500A) Processing helix chain 'B' and resid 2000 through 2014 Processing helix chain 'J' and resid 2072 through 2082 removed outlier: 4.107A pdb=" N ASN J2082 " --> pdb=" O ILE J2078 " (cutoff:3.500A) Processing helix chain 'J' and resid 2083 through 2088 removed outlier: 3.557A pdb=" N ARG J2086 " --> pdb=" O LEU J2083 " (cutoff:3.500A) Processing helix chain 'J' and resid 2108 through 2117 Processing helix chain 'J' and resid 2166 through 2170 Processing helix chain 'J' and resid 2189 through 2203 Processing helix chain 'J' and resid 2231 through 2241 removed outlier: 3.797A pdb=" N GLN J2240 " --> pdb=" O GLU J2236 " (cutoff:3.500A) Processing helix chain 'J' and resid 2252 through 2254 No H-bonds generated for 'chain 'J' and resid 2252 through 2254' Processing helix chain 'J' and resid 2284 through 2288 Processing helix chain 'J' and resid 2306 through 2309 Processing helix chain 'J' and resid 2310 through 2320 removed outlier: 3.907A pdb=" N PHE J2314 " --> pdb=" O ARG J2310 " (cutoff:3.500A) Processing helix chain 'T' and resid 154 through 158 Processing sheet with id=AA1, first strand: chain 'B' and resid 436 through 438 removed outlier: 6.969A pdb=" N THR B 688 " --> pdb=" O LEU B 869 " (cutoff:3.500A) removed outlier: 8.093A pdb=" N THR B 871 " --> pdb=" O THR B 688 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N VAL B 690 " --> pdb=" O THR B 871 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N LEU B 722 " --> pdb=" O ILE B 827 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N ALA B 783 " --> pdb=" O VAL B 810 " (cutoff:3.500A) removed outlier: 8.457A pdb=" N THR B 812 " --> pdb=" O ALA B 783 " (cutoff:3.500A) removed outlier: 7.528A pdb=" N HIS B 785 " --> pdb=" O THR B 812 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 566 through 568 removed outlier: 3.584A pdb=" N VAL B 587 " --> pdb=" O ALA B 567 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N LYS B 537 " --> pdb=" O VAL B 609 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N LEU B 611 " --> pdb=" O LYS B 537 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N ARG B 610 " --> pdb=" O ARG B 647 " (cutoff:3.500A) removed outlier: 8.180A pdb=" N ILE B 649 " --> pdb=" O ARG B 610 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N ILE B 612 " --> pdb=" O ILE B 649 " (cutoff:3.500A) removed outlier: 8.054A pdb=" N LEU B 651 " --> pdb=" O ILE B 612 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N LEU B 614 " --> pdb=" O LEU B 651 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N LEU B 499 " --> pdb=" O GLY B 650 " (cutoff:3.500A) removed outlier: 7.364A pdb=" N SER B 652 " --> pdb=" O LEU B 499 " (cutoff:3.500A) removed outlier: 5.901A pdb=" N LEU B 501 " --> pdb=" O SER B 652 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 832 through 835 removed outlier: 3.750A pdb=" N ARG B 840 " --> pdb=" O SER B 835 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 970 through 973 removed outlier: 3.586A pdb=" N ASP B 973 " --> pdb=" O ASN B 978 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ASN B 978 " --> pdb=" O ASP B 973 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 1184 through 1192 Processing sheet with id=AA6, first strand: chain 'B' and resid 1233 through 1242 removed outlier: 3.623A pdb=" N HIS B1235 " --> pdb=" O VAL B1225 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 1405 through 1407 removed outlier: 6.229A pdb=" N VAL B1377 " --> pdb=" O VAL B1452 " (cutoff:3.500A) removed outlier: 7.457A pdb=" N ASP B1454 " --> pdb=" O VAL B1377 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N ILE B1379 " --> pdb=" O ASP B1454 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N PHE B1451 " --> pdb=" O VAL B1488 " (cutoff:3.500A) removed outlier: 7.809A pdb=" N LEU B1490 " --> pdb=" O PHE B1451 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N VAL B1453 " --> pdb=" O LEU B1490 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 1523 through 1530 removed outlier: 6.350A pdb=" N VAL B1661 " --> pdb=" O VAL B1703 " (cutoff:3.500A) removed outlier: 7.546A pdb=" N MET B1705 " --> pdb=" O VAL B1661 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N ILE B1663 " --> pdb=" O MET B1705 " (cutoff:3.500A) removed outlier: 8.413A pdb=" N GLN B1707 " --> pdb=" O ILE B1663 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N VAL B1559 " --> pdb=" O VAL B1644 " (cutoff:3.500A) removed outlier: 7.704A pdb=" N ALA B1646 " --> pdb=" O VAL B1559 " (cutoff:3.500A) removed outlier: 5.968A pdb=" N VAL B1561 " --> pdb=" O ALA B1646 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 1667 through 1670 Processing sheet with id=AB1, first strand: chain 'B' and resid 1802 through 1805 Processing sheet with id=AB2, first strand: chain 'B' and resid 2017 through 2023 removed outlier: 3.654A pdb=" N GLU B2018 " --> pdb=" O GLU B2042 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLU B2042 " --> pdb=" O GLU B2018 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU B2041 " --> pdb=" O ALA B2088 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 2075 through 2082 removed outlier: 5.826A pdb=" N LEU B2076 " --> pdb=" O ASP B2070 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N ASP B2070 " --> pdb=" O LEU B2076 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'J' and resid 2256 through 2258 removed outlier: 9.477A pdb=" N ILE J2212 " --> pdb=" O GLU J2173 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N LEU J2175 " --> pdb=" O ILE J2212 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N ILE J2214 " --> pdb=" O LEU J2175 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N TRP J2177 " --> pdb=" O ILE J2214 " (cutoff:3.500A) removed outlier: 7.946A pdb=" N CYS J2216 " --> pdb=" O TRP J2177 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N HIS J2179 " --> pdb=" O CYS J2216 " (cutoff:3.500A) removed outlier: 7.770A pdb=" N PHE J2218 " --> pdb=" O HIS J2179 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N GLN J2181 " --> pdb=" O PHE J2218 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N LEU J2128 " --> pdb=" O LEU J2175 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N TRP J2177 " --> pdb=" O GLY J2126 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N GLY J2126 " --> pdb=" O TRP J2177 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N VAL J2131 " --> pdb=" O ILE J2142 " (cutoff:3.500A) removed outlier: 5.156A pdb=" N ILE J2142 " --> pdb=" O VAL J2131 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'J' and resid 2260 through 2264 removed outlier: 6.450A pdb=" N THR J2103 " --> pdb=" O LYS J2140 " (cutoff:3.500A) removed outlier: 7.530A pdb=" N ILE J2142 " --> pdb=" O THR J2103 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N ILE J2105 " --> pdb=" O ILE J2142 " (cutoff:3.500A) removed outlier: 7.974A pdb=" N CYS J2144 " --> pdb=" O ILE J2105 " (cutoff:3.500A) removed outlier: 12.051A pdb=" N VAL J2146 " --> pdb=" O PRO J2107 " (cutoff:3.500A) removed outlier: 5.156A pdb=" N ILE J2142 " --> pdb=" O VAL J2131 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N VAL J2131 " --> pdb=" O ILE J2142 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N GLY J2126 " --> pdb=" O TRP J2177 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N TRP J2177 " --> pdb=" O GLY J2126 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N LEU J2128 " --> pdb=" O LEU J2175 " (cutoff:3.500A) removed outlier: 9.477A pdb=" N ILE J2212 " --> pdb=" O GLU J2173 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N LEU J2175 " --> pdb=" O ILE J2212 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N ILE J2214 " --> pdb=" O LEU J2175 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N TRP J2177 " --> pdb=" O ILE J2214 " (cutoff:3.500A) removed outlier: 7.946A pdb=" N CYS J2216 " --> pdb=" O TRP J2177 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N HIS J2179 " --> pdb=" O CYS J2216 " (cutoff:3.500A) removed outlier: 7.770A pdb=" N PHE J2218 " --> pdb=" O HIS J2179 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N GLN J2181 " --> pdb=" O PHE J2218 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N TYR J2091 " --> pdb=" O LEU J2225 " (cutoff:3.500A) removed outlier: 8.683A pdb=" N ALA J2227 " --> pdb=" O TYR J2091 " (cutoff:3.500A) removed outlier: 8.180A pdb=" N SER J2093 " --> pdb=" O ALA J2227 " (cutoff:3.500A) removed outlier: 11.882A pdb=" N LYS J2229 " --> pdb=" O SER J2093 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'J' and resid 2151 through 2152 743 hydrogen bonds defined for protein. 2097 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.83 Time building geometry restraints manager: 6.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 5378 1.34 - 1.46: 3427 1.46 - 1.58: 7860 1.58 - 1.69: 0 1.69 - 1.81: 138 Bond restraints: 16803 Sorted by residual: bond pdb=" C ARG B 624 " pdb=" N GLY B 625 " ideal model delta sigma weight residual 1.340 1.331 0.009 6.60e-03 2.30e+04 2.04e+00 bond pdb=" CA VAL B1563 " pdb=" CB VAL B1563 " ideal model delta sigma weight residual 1.546 1.535 0.011 8.80e-03 1.29e+04 1.70e+00 bond pdb=" CA VAL J2148 " pdb=" CB VAL J2148 " ideal model delta sigma weight residual 1.546 1.536 0.010 8.80e-03 1.29e+04 1.32e+00 bond pdb=" CA THR B 606 " pdb=" C THR B 606 " ideal model delta sigma weight residual 1.523 1.503 0.020 1.80e-02 3.09e+03 1.23e+00 bond pdb=" CA VAL J2273 " pdb=" CB VAL J2273 " ideal model delta sigma weight residual 1.547 1.536 0.011 1.10e-02 8.26e+03 1.09e+00 ... (remaining 16798 not shown) Histogram of bond angle deviations from ideal: 100.12 - 106.89: 572 106.89 - 113.66: 9418 113.66 - 120.43: 6194 120.43 - 127.20: 6370 127.20 - 133.98: 220 Bond angle restraints: 22774 Sorted by residual: angle pdb=" C ARG T 312 " pdb=" N ASP T 313 " pdb=" CA ASP T 313 " ideal model delta sigma weight residual 121.54 128.34 -6.80 1.91e+00 2.74e-01 1.27e+01 angle pdb=" N ILE B1776 " pdb=" CA ILE B1776 " pdb=" C ILE B1776 " ideal model delta sigma weight residual 112.43 109.21 3.22 9.20e-01 1.18e+00 1.23e+01 angle pdb=" N ILE B 617 " pdb=" CA ILE B 617 " pdb=" C ILE B 617 " ideal model delta sigma weight residual 112.98 109.46 3.52 1.25e+00 6.40e-01 7.94e+00 angle pdb=" C LYS B 426 " pdb=" CA LYS B 426 " pdb=" CB LYS B 426 " ideal model delta sigma weight residual 110.42 115.99 -5.57 1.99e+00 2.53e-01 7.83e+00 angle pdb=" C GLY B 874 " pdb=" N GLU B 875 " pdb=" CA GLU B 875 " ideal model delta sigma weight residual 121.54 126.50 -4.96 1.91e+00 2.74e-01 6.73e+00 ... (remaining 22769 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 9599 17.96 - 35.92: 456 35.92 - 53.88: 120 53.88 - 71.84: 24 71.84 - 89.80: 4 Dihedral angle restraints: 10203 sinusoidal: 4210 harmonic: 5993 Sorted by residual: dihedral pdb=" CA ALA B 757 " pdb=" C ALA B 757 " pdb=" N SER B 758 " pdb=" CA SER B 758 " ideal model delta harmonic sigma weight residual 180.00 -162.24 -17.76 0 5.00e+00 4.00e-02 1.26e+01 dihedral pdb=" CA MET B1664 " pdb=" C MET B1664 " pdb=" N ASP B1665 " pdb=" CA ASP B1665 " ideal model delta harmonic sigma weight residual 180.00 163.33 16.67 0 5.00e+00 4.00e-02 1.11e+01 dihedral pdb=" CA LYS B1716 " pdb=" C LYS B1716 " pdb=" N PHE B1717 " pdb=" CA PHE B1717 " ideal model delta harmonic sigma weight residual -180.00 -163.49 -16.51 0 5.00e+00 4.00e-02 1.09e+01 ... (remaining 10200 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 1637 0.030 - 0.061: 609 0.061 - 0.091: 152 0.091 - 0.122: 143 0.122 - 0.152: 10 Chirality restraints: 2551 Sorted by residual: chirality pdb=" CG LEU B1999 " pdb=" CB LEU B1999 " pdb=" CD1 LEU B1999 " pdb=" CD2 LEU B1999 " both_signs ideal model delta sigma weight residual False -2.59 -2.44 -0.15 2.00e-01 2.50e+01 5.81e-01 chirality pdb=" CB VAL T 219 " pdb=" CA VAL T 219 " pdb=" CG1 VAL T 219 " pdb=" CG2 VAL T 219 " both_signs ideal model delta sigma weight residual False -2.63 -2.49 -0.14 2.00e-01 2.50e+01 4.81e-01 chirality pdb=" CA ILE J2213 " pdb=" N ILE J2213 " pdb=" C ILE J2213 " pdb=" CB ILE J2213 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.71e-01 ... (remaining 2548 not shown) Planarity restraints: 2919 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS B1515 " -0.031 5.00e-02 4.00e+02 4.67e-02 3.49e+00 pdb=" N PRO B1516 " 0.081 5.00e-02 4.00e+02 pdb=" CA PRO B1516 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO B1516 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY B 625 " -0.030 5.00e-02 4.00e+02 4.56e-02 3.33e+00 pdb=" N PRO B 626 " 0.079 5.00e-02 4.00e+02 pdb=" CA PRO B 626 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO B 626 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY B1464 " 0.029 5.00e-02 4.00e+02 4.42e-02 3.12e+00 pdb=" N PRO B1465 " -0.076 5.00e-02 4.00e+02 pdb=" CA PRO B1465 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO B1465 " 0.025 5.00e-02 4.00e+02 ... (remaining 2916 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 3194 2.77 - 3.30: 15962 3.30 - 3.84: 27067 3.84 - 4.37: 32432 4.37 - 4.90: 55880 Nonbonded interactions: 134535 Sorted by model distance: nonbonded pdb=" OG SER B1981 " pdb=" OD1 ASP B1984 " model vdw 2.241 2.440 nonbonded pdb=" O HIS J2084 " pdb=" OG1 THR J2087 " model vdw 2.246 2.440 nonbonded pdb=" NH1 ARG B 436 " pdb=" OE2 GLU B 443 " model vdw 2.255 2.520 nonbonded pdb=" OD2 ASP B 973 " pdb=" OG1 THR B 976 " model vdw 2.258 2.440 nonbonded pdb=" ND1 HIS B1515 " pdb=" OD1 ASN B1517 " model vdw 2.268 2.520 ... (remaining 134530 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 Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 84 5.16 5 C 10498 2.51 5 N 2826 2.21 5 O 3022 1.98 5 sf(0) = scattering factor at diffraction angle 0. 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: 1.490 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: 0.020 Extract box with map and model: 8.460 Check model and map are aligned: 0.230 Process input model: 46.810 Find NCS groups from input model: 0.470 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Set scattering table: 0.170 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:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 60.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8791 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 0.040 16803 Z= 0.174 Angle : 0.524 7.821 22774 Z= 0.300 Chirality : 0.040 0.152 2551 Planarity : 0.004 0.047 2919 Dihedral : 11.547 89.797 6321 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer Outliers : 5.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.05 (0.19), residues: 2029 helix: 1.44 (0.18), residues: 848 sheet: 0.97 (0.28), residues: 359 loop : -0.12 (0.22), residues: 822 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4058 Ramachandran restraints generated. 2029 Oldfield, 0 Emsley, 2029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4058 Ramachandran restraints generated. 2029 Oldfield, 0 Emsley, 2029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 1826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 265 time to evaluate : 1.977 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 95 outliers final: 27 residues processed: 348 average time/residue: 0.4095 time to fit residues: 195.7005 Evaluate side-chains 183 residues out of total 1826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 156 time to evaluate : 2.235 Switching outliers to nearest non-outliers outliers start: 27 outliers final: 0 residues processed: 27 average time/residue: 0.1633 time to fit residues: 10.9175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 171 optimal weight: 7.9990 chunk 153 optimal weight: 4.9990 chunk 85 optimal weight: 2.9990 chunk 52 optimal weight: 7.9990 chunk 103 optimal weight: 2.9990 chunk 82 optimal weight: 0.2980 chunk 159 optimal weight: 0.2980 chunk 61 optimal weight: 2.9990 chunk 96 optimal weight: 1.9990 chunk 118 optimal weight: 5.9990 chunk 184 optimal weight: 2.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 460 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1101 ASN B1209 GLN ** B1447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J2183 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8815 moved from start: 0.1893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.052 16803 Z= 0.284 Angle : 0.593 9.910 22774 Z= 0.303 Chirality : 0.044 0.176 2551 Planarity : 0.005 0.160 2919 Dihedral : 4.074 17.528 2216 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer Outliers : 2.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.88 (0.19), residues: 2029 helix: 1.25 (0.18), residues: 876 sheet: 0.73 (0.27), residues: 374 loop : -0.13 (0.22), residues: 779 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4058 Ramachandran restraints generated. 2029 Oldfield, 0 Emsley, 2029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4058 Ramachandran restraints generated. 2029 Oldfield, 0 Emsley, 2029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 166 time to evaluate : 2.052 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 40 outliers final: 20 residues processed: 199 average time/residue: 0.3711 time to fit residues: 105.7413 Evaluate side-chains 162 residues out of total 1826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 142 time to evaluate : 2.126 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 0 residues processed: 20 average time/residue: 0.1930 time to fit residues: 9.6332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 102 optimal weight: 0.9980 chunk 57 optimal weight: 5.9990 chunk 153 optimal weight: 2.9990 chunk 125 optimal weight: 0.8980 chunk 50 optimal weight: 1.9990 chunk 184 optimal weight: 1.9990 chunk 199 optimal weight: 0.9990 chunk 164 optimal weight: 10.0000 chunk 183 optimal weight: 0.7980 chunk 62 optimal weight: 0.8980 chunk 148 optimal weight: 5.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 460 GLN B1101 ASN ** B1447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1798 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8796 moved from start: 0.2182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 16803 Z= 0.194 Angle : 0.567 10.781 22774 Z= 0.282 Chirality : 0.043 0.197 2551 Planarity : 0.004 0.094 2919 Dihedral : 4.051 19.397 2216 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer Outliers : 1.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.19), residues: 2029 helix: 1.36 (0.18), residues: 869 sheet: 0.73 (0.27), residues: 368 loop : -0.15 (0.22), residues: 792 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4058 Ramachandran restraints generated. 2029 Oldfield, 0 Emsley, 2029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4058 Ramachandran restraints generated. 2029 Oldfield, 0 Emsley, 2029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 162 time to evaluate : 2.113 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 29 outliers final: 13 residues processed: 186 average time/residue: 0.3665 time to fit residues: 98.4458 Evaluate side-chains 159 residues out of total 1826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 146 time to evaluate : 2.098 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.1940 time to fit residues: 7.2804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 182 optimal weight: 0.0870 chunk 138 optimal weight: 0.9980 chunk 95 optimal weight: 2.9990 chunk 20 optimal weight: 5.9990 chunk 88 optimal weight: 0.7980 chunk 124 optimal weight: 2.9990 chunk 185 optimal weight: 4.9990 chunk 196 optimal weight: 0.9980 chunk 96 optimal weight: 0.8980 chunk 175 optimal weight: 2.9990 chunk 52 optimal weight: 4.9990 overall best weight: 0.7558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 460 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1749 GLN ** B1998 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2003 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2012 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8787 moved from start: 0.2390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 16803 Z= 0.171 Angle : 0.540 10.398 22774 Z= 0.270 Chirality : 0.042 0.230 2551 Planarity : 0.004 0.050 2919 Dihedral : 3.956 16.951 2216 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer Outliers : 1.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.99 (0.19), residues: 2029 helix: 1.42 (0.18), residues: 870 sheet: 0.63 (0.27), residues: 369 loop : -0.07 (0.22), residues: 790 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4058 Ramachandran restraints generated. 2029 Oldfield, 0 Emsley, 2029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4058 Ramachandran restraints generated. 2029 Oldfield, 0 Emsley, 2029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 151 time to evaluate : 2.154 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 22 outliers final: 5 residues processed: 171 average time/residue: 0.3533 time to fit residues: 89.0888 Evaluate side-chains 145 residues out of total 1826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 140 time to evaluate : 2.211 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1591 time to fit residues: 4.4246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 163 optimal weight: 0.0670 chunk 111 optimal weight: 1.9990 chunk 2 optimal weight: 7.9990 chunk 146 optimal weight: 2.9990 chunk 80 optimal weight: 4.9990 chunk 167 optimal weight: 6.9990 chunk 135 optimal weight: 0.0000 chunk 0 optimal weight: 20.0000 chunk 100 optimal weight: 1.9990 chunk 176 optimal weight: 0.8980 chunk 49 optimal weight: 0.5980 overall best weight: 0.7124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 460 GLN B1101 ASN ** B1447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1998 GLN B2003 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8782 moved from start: 0.2521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 16803 Z= 0.164 Angle : 0.540 11.284 22774 Z= 0.268 Chirality : 0.042 0.235 2551 Planarity : 0.004 0.050 2919 Dihedral : 3.894 17.145 2216 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.81 % Favored : 97.14 % Rotamer Outliers : 1.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.19), residues: 2029 helix: 1.47 (0.18), residues: 869 sheet: 0.68 (0.28), residues: 368 loop : -0.09 (0.22), residues: 792 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4058 Ramachandran restraints generated. 2029 Oldfield, 0 Emsley, 2029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4058 Ramachandran restraints generated. 2029 Oldfield, 0 Emsley, 2029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 152 time to evaluate : 2.032 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 28 outliers final: 8 residues processed: 176 average time/residue: 0.3256 time to fit residues: 86.1863 Evaluate side-chains 151 residues out of total 1826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 143 time to evaluate : 1.869 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1687 time to fit residues: 5.2511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 66 optimal weight: 0.4980 chunk 176 optimal weight: 0.7980 chunk 38 optimal weight: 6.9990 chunk 115 optimal weight: 0.5980 chunk 48 optimal weight: 0.8980 chunk 196 optimal weight: 0.5980 chunk 163 optimal weight: 7.9990 chunk 90 optimal weight: 2.9990 chunk 16 optimal weight: 10.0000 chunk 64 optimal weight: 0.6980 chunk 103 optimal weight: 2.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 705 ASN B1101 ASN ** B1447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1881 ASN ** B2003 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8777 moved from start: 0.2647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.036 16803 Z= 0.160 Angle : 0.545 11.657 22774 Z= 0.270 Chirality : 0.042 0.204 2551 Planarity : 0.004 0.050 2919 Dihedral : 3.859 16.869 2216 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.96 % Favored : 96.99 % Rotamer Outliers : 0.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.06 (0.19), residues: 2029 helix: 1.50 (0.18), residues: 877 sheet: 0.67 (0.28), residues: 368 loop : -0.08 (0.23), residues: 784 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4058 Ramachandran restraints generated. 2029 Oldfield, 0 Emsley, 2029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4058 Ramachandran restraints generated. 2029 Oldfield, 0 Emsley, 2029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 146 time to evaluate : 2.053 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 18 outliers final: 5 residues processed: 161 average time/residue: 0.3206 time to fit residues: 77.3965 Evaluate side-chains 145 residues out of total 1826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 140 time to evaluate : 1.927 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1553 time to fit residues: 4.0256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 189 optimal weight: 7.9990 chunk 22 optimal weight: 0.0010 chunk 111 optimal weight: 0.9990 chunk 143 optimal weight: 0.0870 chunk 165 optimal weight: 0.1980 chunk 109 optimal weight: 0.8980 chunk 195 optimal weight: 4.9990 chunk 122 optimal weight: 4.9990 chunk 119 optimal weight: 0.0030 chunk 90 optimal weight: 2.9990 chunk 121 optimal weight: 1.9990 overall best weight: 0.2374 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1101 ASN ** B1447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2003 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8753 moved from start: 0.2812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.037 16803 Z= 0.138 Angle : 0.544 11.851 22774 Z= 0.267 Chirality : 0.041 0.189 2551 Planarity : 0.004 0.051 2919 Dihedral : 3.775 16.021 2216 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.06 % Favored : 96.90 % Rotamer Outliers : 0.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.19), residues: 2029 helix: 1.60 (0.18), residues: 878 sheet: 0.72 (0.27), residues: 370 loop : -0.12 (0.23), residues: 781 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4058 Ramachandran restraints generated. 2029 Oldfield, 0 Emsley, 2029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4058 Ramachandran restraints generated. 2029 Oldfield, 0 Emsley, 2029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 148 time to evaluate : 2.101 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 5 residues processed: 157 average time/residue: 0.3443 time to fit residues: 80.9902 Evaluate side-chains 150 residues out of total 1826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 145 time to evaluate : 2.237 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1845 time to fit residues: 4.6605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 78 optimal weight: 3.9990 chunk 116 optimal weight: 1.9990 chunk 58 optimal weight: 0.6980 chunk 38 optimal weight: 20.0000 chunk 37 optimal weight: 2.9990 chunk 124 optimal weight: 3.9990 chunk 133 optimal weight: 5.9990 chunk 96 optimal weight: 1.9990 chunk 18 optimal weight: 4.9990 chunk 153 optimal weight: 1.9990 chunk 177 optimal weight: 0.9980 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1101 ASN ** B1447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8803 moved from start: 0.2786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.041 16803 Z= 0.252 Angle : 0.568 11.324 22774 Z= 0.281 Chirality : 0.043 0.193 2551 Planarity : 0.004 0.052 2919 Dihedral : 3.846 16.905 2216 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.10 % Favored : 96.85 % Rotamer Outliers : 0.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.08 (0.19), residues: 2029 helix: 1.54 (0.18), residues: 872 sheet: 0.72 (0.28), residues: 362 loop : -0.11 (0.22), residues: 795 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4058 Ramachandran restraints generated. 2029 Oldfield, 0 Emsley, 2029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4058 Ramachandran restraints generated. 2029 Oldfield, 0 Emsley, 2029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 142 time to evaluate : 2.182 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 4 residues processed: 147 average time/residue: 0.3415 time to fit residues: 74.8242 Evaluate side-chains 140 residues out of total 1826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 136 time to evaluate : 2.094 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1664 time to fit residues: 4.0528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 187 optimal weight: 1.9990 chunk 171 optimal weight: 7.9990 chunk 182 optimal weight: 3.9990 chunk 109 optimal weight: 0.9990 chunk 79 optimal weight: 2.9990 chunk 143 optimal weight: 0.0570 chunk 55 optimal weight: 8.9990 chunk 164 optimal weight: 7.9990 chunk 172 optimal weight: 0.9990 chunk 181 optimal weight: 0.8980 chunk 119 optimal weight: 0.0270 overall best weight: 0.5960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1101 ASN ** B1447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8771 moved from start: 0.2898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.040 16803 Z= 0.156 Angle : 0.555 12.115 22774 Z= 0.274 Chirality : 0.042 0.186 2551 Planarity : 0.004 0.054 2919 Dihedral : 3.780 16.368 2216 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.10 % Favored : 96.85 % Rotamer Outliers : 0.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.12 (0.19), residues: 2029 helix: 1.59 (0.18), residues: 876 sheet: 0.78 (0.28), residues: 362 loop : -0.16 (0.22), residues: 791 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4058 Ramachandran restraints generated. 2029 Oldfield, 0 Emsley, 2029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4058 Ramachandran restraints generated. 2029 Oldfield, 0 Emsley, 2029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 148 time to evaluate : 2.120 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 2 residues processed: 152 average time/residue: 0.3449 time to fit residues: 79.2036 Evaluate side-chains 138 residues out of total 1826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 136 time to evaluate : 2.041 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1748 time to fit residues: 3.3741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 192 optimal weight: 0.6980 chunk 117 optimal weight: 6.9990 chunk 91 optimal weight: 0.9980 chunk 134 optimal weight: 2.9990 chunk 202 optimal weight: 0.8980 chunk 186 optimal weight: 0.7980 chunk 161 optimal weight: 0.2980 chunk 16 optimal weight: 10.0000 chunk 124 optimal weight: 1.9990 chunk 98 optimal weight: 3.9990 chunk 127 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1101 ASN ** B1447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8775 moved from start: 0.2945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.045 16803 Z= 0.173 Angle : 0.578 12.661 22774 Z= 0.281 Chirality : 0.042 0.193 2551 Planarity : 0.004 0.059 2919 Dihedral : 3.754 16.519 2216 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.25 % Favored : 96.70 % Rotamer Outliers : 0.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.08 (0.19), residues: 2029 helix: 1.56 (0.18), residues: 877 sheet: 0.71 (0.28), residues: 359 loop : -0.14 (0.22), residues: 793 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4058 Ramachandran restraints generated. 2029 Oldfield, 0 Emsley, 2029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4058 Ramachandran restraints generated. 2029 Oldfield, 0 Emsley, 2029 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 140 time to evaluate : 2.097 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 141 average time/residue: 0.3236 time to fit residues: 69.3240 Evaluate side-chains 136 residues out of total 1826 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 136 time to evaluate : 2.004 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.8317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 171 optimal weight: 6.9990 chunk 49 optimal weight: 0.8980 chunk 148 optimal weight: 2.9990 chunk 23 optimal weight: 10.0000 chunk 44 optimal weight: 0.0030 chunk 161 optimal weight: 0.1980 chunk 67 optimal weight: 0.9980 chunk 165 optimal weight: 0.0170 chunk 20 optimal weight: 4.9990 chunk 29 optimal weight: 4.9990 chunk 141 optimal weight: 3.9990 overall best weight: 0.4228 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 618 HIS B1101 ASN ** B1447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.080120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.055228 restraints weight = 43570.740| |-----------------------------------------------------------------------------| r_work (start): 0.2918 rms_B_bonded: 3.02 r_work: 0.2770 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.2770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8864 moved from start: 0.3044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.037 16803 Z= 0.151 Angle : 0.576 12.187 22774 Z= 0.282 Chirality : 0.042 0.193 2551 Planarity : 0.004 0.059 2919 Dihedral : 3.711 16.730 2216 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.10 % Favored : 96.85 % Rotamer Outliers : 0.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.19), residues: 2029 helix: 1.59 (0.18), residues: 869 sheet: 0.72 (0.28), residues: 359 loop : -0.08 (0.22), residues: 801 =============================================================================== Job complete usr+sys time: 3531.60 seconds wall clock time: 64 minutes 49.13 seconds (3889.13 seconds total)