Starting phenix.real_space_refine on Sun Mar 24 22:10:14 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oxp_17267/03_2024/8oxp_17267_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oxp_17267/03_2024/8oxp_17267.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oxp_17267/03_2024/8oxp_17267.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oxp_17267/03_2024/8oxp_17267.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oxp_17267/03_2024/8oxp_17267_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oxp_17267/03_2024/8oxp_17267_updated.pdb" } resolution = 2.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= 0.001 sd= 0.015 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: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 6 5.49 5 Mg 2 5.21 5 S 306 5.16 5 C 28406 2.51 5 N 7556 2.21 5 O 8182 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 1248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1415": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1424": "OE1" <-> "OE2" Residue "A TYR 1475": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1508": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1530": "OE1" <-> "OE2" Residue "A ASP 1573": "OD1" <-> "OD2" Residue "A GLU 2154": "OE1" <-> "OE2" Residue "A ASP 2320": "OD1" <-> "OD2" Residue "A GLU 2409": "OE1" <-> "OE2" Residue "A TYR 2969": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 3002": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1415": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1442": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1571": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 2154": "OE1" <-> "OE2" Residue "B GLU 2157": "OE1" <-> "OE2" Residue "B GLU 2950": "OE1" <-> "OE2" Residue "B PHE 3002": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 3041": "OD1" <-> "OD2" Time to flip residues: 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 44460 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 22197 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2772, 22197 Classifications: {'peptide': 2772} Incomplete info: {'truncation_to_alanine': 51} Link IDs: {'PTRANS': 88, 'TRANS': 2683} Chain breaks: 18 Unresolved non-hydrogen bonds: 174 Unresolved non-hydrogen angles: 214 Unresolved non-hydrogen dihedrals: 136 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 7, 'ASN:plan1': 3, 'HIS:plan': 1, 'GLU:plan': 10, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 112 Chain: "B" Number of atoms: 22197 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2772, 22197 Classifications: {'peptide': 2772} Incomplete info: {'truncation_to_alanine': 51} Link IDs: {'PTRANS': 88, 'TRANS': 2683} Chain breaks: 18 Unresolved non-hydrogen bonds: 174 Unresolved non-hydrogen angles: 214 Unresolved non-hydrogen dihedrals: 136 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 7, 'ASN:plan1': 3, 'HIS:plan': 1, 'GLU:plan': 10, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 112 Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, ' ZN': 1, 'ANP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, ' ZN': 1, 'ANP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 13455 SG CYS A1899 81.657 49.513 122.467 1.00269.33 S ATOM 13461 SG CYS A1900 79.712 51.597 121.450 1.00264.27 S ATOM 35652 SG CYS B1899 98.346 134.009 122.480 1.00269.62 S ATOM 35658 SG CYS B1900 100.286 131.926 121.447 1.00260.90 S Time building chain proxies: 22.19, per 1000 atoms: 0.50 Number of scatterers: 44460 At special positions: 0 Unit cell: (180.894, 184.198, 210.63, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 306 16.00 P 6 15.00 Mg 2 11.99 O 8182 8.00 N 7556 7.00 C 28406 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: 16.65 Conformation dependent library (CDL) restraints added in 7.6 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A3103 " pdb="ZN ZN A3103 " - pdb=" SG CYS A1899 " pdb="ZN ZN A3103 " - pdb=" SG CYS A1900 " pdb="ZN ZN A3103 " - pdb=" ND1 HIS A1876 " pdb=" ZN B3103 " pdb="ZN ZN B3103 " - pdb=" SG CYS B1899 " pdb="ZN ZN B3103 " - pdb=" SG CYS B1900 " pdb="ZN ZN B3103 " - pdb=" ND1 HIS B1876 " 10936 Ramachandran restraints generated. 5468 Oldfield, 0 Emsley, 5468 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10664 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 291 helices and 6 sheets defined 67.9% alpha, 1.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 18.89 Creating SS restraints... Processing helix chain 'A' and resid 6 through 17 Processing helix chain 'A' and resid 20 through 33 removed outlier: 4.188A pdb=" N LYS A 25 " --> pdb=" O THR A 21 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N GLU A 28 " --> pdb=" O LYS A 24 " (cutoff:3.500A) Processing helix chain 'A' and resid 36 through 42 Processing helix chain 'A' and resid 57 through 73 removed outlier: 3.749A pdb=" N GLU A 73 " --> pdb=" O GLN A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 108 removed outlier: 4.196A pdb=" N MET A 94 " --> pdb=" O GLN A 91 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ILE A 97 " --> pdb=" O MET A 94 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N VAL A 101 " --> pdb=" O SER A 98 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ILE A 105 " --> pdb=" O LYS A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 129 removed outlier: 3.718A pdb=" N VAL A 128 " --> pdb=" O ILE A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 135 through 148 Processing helix chain 'A' and resid 153 through 158 Processing helix chain 'A' and resid 161 through 176 removed outlier: 3.686A pdb=" N TYR A 171 " --> pdb=" O LEU A 167 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 201 removed outlier: 3.555A pdb=" N VAL A 185 " --> pdb=" O VAL A 182 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N GLN A 201 " --> pdb=" O CYS A 198 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 222 removed outlier: 4.094A pdb=" N ASP A 211 " --> pdb=" O LYS A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 244 Processing helix chain 'A' and resid 248 through 268 Proline residue: A 260 - end of helix Processing helix chain 'A' and resid 273 through 290 Processing helix chain 'A' and resid 298 through 300 No H-bonds generated for 'chain 'A' and resid 298 through 300' Processing helix chain 'A' and resid 306 through 323 Processing helix chain 'A' and resid 343 through 356 Processing helix chain 'A' and resid 393 through 402 Processing helix chain 'A' and resid 406 through 422 Proline residue: A 411 - end of helix Processing helix chain 'A' and resid 424 through 426 No H-bonds generated for 'chain 'A' and resid 424 through 426' Processing helix chain 'A' and resid 430 through 443 Proline residue: A 434 - end of helix Processing helix chain 'A' and resid 452 through 468 Processing helix chain 'A' and resid 474 through 492 Processing helix chain 'A' and resid 501 through 513 Processing helix chain 'A' and resid 521 through 525 removed outlier: 3.788A pdb=" N LYS A 525 " --> pdb=" O ARG A 521 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 521 through 525' Processing helix chain 'A' and resid 536 through 547 removed outlier: 3.504A pdb=" N LEU A 544 " --> pdb=" O CYS A 540 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 580 Processing helix chain 'A' and resid 597 through 600 No H-bonds generated for 'chain 'A' and resid 597 through 600' Processing helix chain 'A' and resid 608 through 616 Processing helix chain 'A' and resid 620 through 628 Processing helix chain 'A' and resid 646 through 656 Processing helix chain 'A' and resid 684 through 704 Processing helix chain 'A' and resid 713 through 731 Processing helix chain 'A' and resid 737 through 742 removed outlier: 3.681A pdb=" N LYS A 742 " --> pdb=" O GLU A 738 " (cutoff:3.500A) Processing helix chain 'A' and resid 744 through 765 removed outlier: 3.583A pdb=" N SER A 751 " --> pdb=" O GLN A 747 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N GLU A 758 " --> pdb=" O GLN A 754 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N SER A 759 " --> pdb=" O CYS A 755 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N ILE A 760 " --> pdb=" O ALA A 756 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ASN A 765 " --> pdb=" O THR A 761 " (cutoff:3.500A) Processing helix chain 'A' and resid 771 through 786 removed outlier: 4.143A pdb=" N SER A 775 " --> pdb=" O PHE A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 795 through 806 Processing helix chain 'A' and resid 809 through 824 removed outlier: 3.616A pdb=" N ASN A 813 " --> pdb=" O SER A 809 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N SER A 824 " --> pdb=" O LYS A 820 " (cutoff:3.500A) Processing helix chain 'A' and resid 887 through 889 No H-bonds generated for 'chain 'A' and resid 887 through 889' Processing helix chain 'A' and resid 892 through 913 removed outlier: 4.367A pdb=" N GLN A 912 " --> pdb=" O VAL A 908 " (cutoff:3.500A) removed outlier: 5.381A pdb=" N THR A 913 " --> pdb=" O THR A 909 " (cutoff:3.500A) Processing helix chain 'A' and resid 920 through 931 removed outlier: 3.897A pdb=" N ILE A 931 " --> pdb=" O LEU A 927 " (cutoff:3.500A) Processing helix chain 'A' and resid 941 through 953 removed outlier: 3.530A pdb=" N TYR A 947 " --> pdb=" O HIS A 943 " (cutoff:3.500A) Processing helix chain 'A' and resid 963 through 979 removed outlier: 3.717A pdb=" N LEU A 967 " --> pdb=" O MET A 963 " (cutoff:3.500A) Proline residue: A 972 - end of helix removed outlier: 4.706A pdb=" N ASN A 975 " --> pdb=" O LYS A 971 " (cutoff:3.500A) Processing helix chain 'A' and resid 984 through 1001 removed outlier: 3.536A pdb=" N LEU A 995 " --> pdb=" O LEU A 991 " (cutoff:3.500A) removed outlier: 5.143A pdb=" N HIS A 996 " --> pdb=" O ASN A 992 " (cutoff:3.500A) removed outlier: 4.902A pdb=" N VAL A 997 " --> pdb=" O HIS A 993 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N VAL A 998 " --> pdb=" O VAL A 994 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N LYS A 999 " --> pdb=" O LEU A 995 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N ASN A1000 " --> pdb=" O HIS A 996 " (cutoff:3.500A) Processing helix chain 'A' and resid 1009 through 1030 removed outlier: 3.683A pdb=" N VAL A1021 " --> pdb=" O GLN A1017 " (cutoff:3.500A) Processing helix chain 'A' and resid 1036 through 1052 Processing helix chain 'A' and resid 1070 through 1079 removed outlier: 3.653A pdb=" N THR A1075 " --> pdb=" O ASN A1071 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N GLN A1076 " --> pdb=" O GLU A1072 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N PHE A1077 " --> pdb=" O VAL A1073 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N LEU A1078 " --> pdb=" O PHE A1074 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N ALA A1079 " --> pdb=" O THR A1075 " (cutoff:3.500A) Processing helix chain 'A' and resid 1083 through 1096 removed outlier: 3.659A pdb=" N MET A1087 " --> pdb=" O HIS A1083 " (cutoff:3.500A) removed outlier: 4.993A pdb=" N ASN A1094 " --> pdb=" O ALA A1090 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N ARG A1095 " --> pdb=" O GLU A1091 " (cutoff:3.500A) removed outlier: 5.098A pdb=" N LEU A1096 " --> pdb=" O SER A1092 " (cutoff:3.500A) Processing helix chain 'A' and resid 1113 through 1132 Processing helix chain 'A' and resid 1144 through 1164 Processing helix chain 'A' and resid 1169 through 1181 removed outlier: 4.050A pdb=" N LYS A1181 " --> pdb=" O CYS A1177 " (cutoff:3.500A) Processing helix chain 'A' and resid 1187 through 1201 Processing helix chain 'A' and resid 1206 through 1212 Processing helix chain 'A' and resid 1214 through 1224 removed outlier: 3.617A pdb=" N LEU A1224 " --> pdb=" O GLU A1220 " (cutoff:3.500A) Processing helix chain 'A' and resid 1236 through 1238 No H-bonds generated for 'chain 'A' and resid 1236 through 1238' Processing helix chain 'A' and resid 1244 through 1261 removed outlier: 6.090A pdb=" N LYS A1253 " --> pdb=" O ARG A1249 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N VAL A1254 " --> pdb=" O SER A1250 " (cutoff:3.500A) Proline residue: A1257 - end of helix Processing helix chain 'A' and resid 1265 through 1275 removed outlier: 3.551A pdb=" N GLN A1274 " --> pdb=" O SER A1270 " (cutoff:3.500A) Processing helix chain 'A' and resid 1279 through 1285 Processing helix chain 'A' and resid 1287 through 1298 removed outlier: 3.896A pdb=" N ASN A1293 " --> pdb=" O LYS A1289 " (cutoff:3.500A) Proline residue: A1296 - end of helix Processing helix chain 'A' and resid 1306 through 1323 removed outlier: 3.784A pdb=" N GLN A1310 " --> pdb=" O SER A1306 " (cutoff:3.500A) removed outlier: 4.778A pdb=" N GLN A1311 " --> pdb=" O GLY A1307 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ARG A1312 " --> pdb=" O MET A1308 " (cutoff:3.500A) Processing helix chain 'A' and resid 1328 through 1330 No H-bonds generated for 'chain 'A' and resid 1328 through 1330' Processing helix chain 'A' and resid 1332 through 1338 Processing helix chain 'A' and resid 1340 through 1349 Processing helix chain 'A' and resid 1383 through 1396 Processing helix chain 'A' and resid 1404 through 1408 Processing helix chain 'A' and resid 1414 through 1428 Processing helix chain 'A' and resid 1432 through 1452 removed outlier: 3.789A pdb=" N ASP A1452 " --> pdb=" O LEU A1448 " (cutoff:3.500A) Processing helix chain 'A' and resid 1461 through 1477 Processing helix chain 'A' and resid 1485 through 1508 Processing helix chain 'A' and resid 1510 through 1515 removed outlier: 4.447A pdb=" N LEU A1513 " --> pdb=" O LYS A1510 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N GLU A1514 " --> pdb=" O ASP A1511 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N ASN A1515 " --> pdb=" O ALA A1512 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1510 through 1515' Processing helix chain 'A' and resid 1517 through 1528 Proline residue: A1526 - end of helix Processing helix chain 'A' and resid 1532 through 1546 removed outlier: 3.639A pdb=" N GLN A1537 " --> pdb=" O GLU A1533 " (cutoff:3.500A) Processing helix chain 'A' and resid 1556 through 1560 removed outlier: 3.545A pdb=" N LYS A1560 " --> pdb=" O TYR A1556 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1556 through 1560' Processing helix chain 'A' and resid 1572 through 1582 Processing helix chain 'A' and resid 1590 through 1601 removed outlier: 3.514A pdb=" N VAL A1600 " --> pdb=" O HIS A1596 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N SER A1601 " --> pdb=" O PHE A1597 " (cutoff:3.500A) Processing helix chain 'A' and resid 1607 through 1623 removed outlier: 4.510A pdb=" N GLU A1612 " --> pdb=" O THR A1609 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU A1623 " --> pdb=" O GLN A1620 " (cutoff:3.500A) Processing helix chain 'A' and resid 1625 through 1634 removed outlier: 4.013A pdb=" N VAL A1629 " --> pdb=" O LYS A1625 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N ASP A1630 " --> pdb=" O ASP A1626 " (cutoff:3.500A) Processing helix chain 'A' and resid 1639 through 1641 No H-bonds generated for 'chain 'A' and resid 1639 through 1641' Processing helix chain 'A' and resid 1643 through 1658 Processing helix chain 'A' and resid 1664 through 1677 Processing helix chain 'A' and resid 1694 through 1702 Processing helix chain 'A' and resid 1706 through 1723 removed outlier: 4.653A pdb=" N VAL A1723 " --> pdb=" O ASN A1719 " (cutoff:3.500A) Processing helix chain 'A' and resid 1727 through 1742 Processing helix chain 'A' and resid 1744 through 1753 removed outlier: 3.531A pdb=" N GLU A1751 " --> pdb=" O HIS A1747 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ILE A1752 " --> pdb=" O SER A1748 " (cutoff:3.500A) Processing helix chain 'A' and resid 1759 through 1763 Processing helix chain 'A' and resid 1792 through 1795 No H-bonds generated for 'chain 'A' and resid 1792 through 1795' Processing helix chain 'A' and resid 1802 through 1815 Processing helix chain 'A' and resid 1822 through 1833 removed outlier: 3.770A pdb=" N LEU A1826 " --> pdb=" O GLU A1822 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N LEU A1827 " --> pdb=" O ILE A1823 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N LYS A1828 " --> pdb=" O LEU A1824 " (cutoff:3.500A) Proline residue: A1829 - end of helix removed outlier: 3.917A pdb=" N VAL A1833 " --> pdb=" O PRO A1829 " (cutoff:3.500A) Processing helix chain 'A' and resid 1835 through 1851 Proline residue: A1843 - end of helix Processing helix chain 'A' and resid 1857 through 1874 Processing helix chain 'A' and resid 1903 through 1918 removed outlier: 3.871A pdb=" N ARG A1918 " --> pdb=" O ASP A1914 " (cutoff:3.500A) Processing helix chain 'A' and resid 1927 through 1932 removed outlier: 3.943A pdb=" N PHE A1932 " --> pdb=" O PHE A1928 " (cutoff:3.500A) Processing helix chain 'A' and resid 1938 through 1947 Processing helix chain 'A' and resid 1951 through 1973 Processing helix chain 'A' and resid 1986 through 1997 Processing helix chain 'A' and resid 2001 through 2012 removed outlier: 3.603A pdb=" N LEU A2006 " --> pdb=" O GLN A2002 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N GLU A2007 " --> pdb=" O ASP A2003 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ILE A2008 " --> pdb=" O LEU A2004 " (cutoff:3.500A) Processing helix chain 'A' and resid 2015 through 2019 removed outlier: 3.587A pdb=" N LEU A2018 " --> pdb=" O PRO A2015 " (cutoff:3.500A) Processing helix chain 'A' and resid 2029 through 2038 Processing helix chain 'A' and resid 2042 through 2051 Processing helix chain 'A' and resid 2057 through 2071 removed outlier: 3.790A pdb=" N ALA A2062 " --> pdb=" O SER A2058 " (cutoff:3.500A) Processing helix chain 'A' and resid 2074 through 2087 Processing helix chain 'A' and resid 2093 through 2105 Processing helix chain 'A' and resid 2124 through 2136 Processing helix chain 'A' and resid 2140 through 2160 removed outlier: 3.527A pdb=" N VAL A2155 " --> pdb=" O ARG A2151 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLU A2157 " --> pdb=" O LYS A2153 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N MET A2158 " --> pdb=" O GLU A2154 " (cutoff:3.500A) Processing helix chain 'A' and resid 2166 through 2190 Proline residue: A2171 - end of helix removed outlier: 3.677A pdb=" N SER A2174 " --> pdb=" O PRO A2171 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ILE A2185 " --> pdb=" O LEU A2182 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLU A2187 " --> pdb=" O SER A2184 " (cutoff:3.500A) Processing helix chain 'A' and resid 2195 through 2212 removed outlier: 3.646A pdb=" N LEU A2211 " --> pdb=" O LYS A2207 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU A2212 " --> pdb=" O HIS A2208 " (cutoff:3.500A) Processing helix chain 'A' and resid 2217 through 2236 Proline residue: A2222 - end of helix Processing helix chain 'A' and resid 2245 through 2264 Processing helix chain 'A' and resid 2269 through 2281 removed outlier: 3.721A pdb=" N TYR A2281 " --> pdb=" O GLN A2277 " (cutoff:3.500A) Processing helix chain 'A' and resid 2290 through 2301 Processing helix chain 'A' and resid 2305 through 2322 Processing helix chain 'A' and resid 2328 through 2348 removed outlier: 4.015A pdb=" N LEU A2332 " --> pdb=" O PRO A2328 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N THR A2333 " --> pdb=" O SER A2329 " (cutoff:3.500A) Processing helix chain 'A' and resid 2353 through 2359 Processing helix chain 'A' and resid 2361 through 2370 Processing helix chain 'A' and resid 2378 through 2406 Processing helix chain 'A' and resid 2408 through 2421 removed outlier: 3.507A pdb=" N LEU A2417 " --> pdb=" O LYS A2413 " (cutoff:3.500A) Processing helix chain 'A' and resid 2437 through 2475 removed outlier: 4.130A pdb=" N GLU A2449 " --> pdb=" O LEU A2445 " (cutoff:3.500A) Processing helix chain 'A' and resid 2481 through 2493 removed outlier: 3.521A pdb=" N LEU A2490 " --> pdb=" O LEU A2487 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LEU A2492 " --> pdb=" O SER A2489 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLU A2493 " --> pdb=" O LEU A2490 " (cutoff:3.500A) Processing helix chain 'A' and resid 2498 through 2506 Processing helix chain 'A' and resid 2508 through 2510 No H-bonds generated for 'chain 'A' and resid 2508 through 2510' Processing helix chain 'A' and resid 2513 through 2516 Processing helix chain 'A' and resid 2520 through 2526 removed outlier: 3.520A pdb=" N ARG A2526 " --> pdb=" O GLN A2522 " (cutoff:3.500A) Processing helix chain 'A' and resid 2537 through 2551 Processing helix chain 'A' and resid 2553 through 2564 removed outlier: 5.570A pdb=" N PHE A2558 " --> pdb=" O HIS A2554 " (cutoff:3.500A) removed outlier: 5.179A pdb=" N ILE A2559 " --> pdb=" O HIS A2555 " (cutoff:3.500A) Processing helix chain 'A' and resid 2568 through 2572 Processing helix chain 'A' and resid 2593 through 2612 removed outlier: 4.271A pdb=" N ARG A2612 " --> pdb=" O THR A2608 " (cutoff:3.500A) Processing helix chain 'A' and resid 2614 through 2632 Processing helix chain 'A' and resid 2637 through 2640 removed outlier: 4.573A pdb=" N THR A2640 " --> pdb=" O GLN A2637 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2637 through 2640' Processing helix chain 'A' and resid 2723 through 2741 removed outlier: 3.532A pdb=" N VAL A2731 " --> pdb=" O VAL A2727 " (cutoff:3.500A) Processing helix chain 'A' and resid 2743 through 2748 removed outlier: 3.956A pdb=" N ARG A2748 " --> pdb=" O GLU A2744 " (cutoff:3.500A) Processing helix chain 'A' and resid 2776 through 2780 Processing helix chain 'A' and resid 2787 through 2791 Processing helix chain 'A' and resid 2798 through 2807 Processing helix chain 'A' and resid 2813 through 2825 Processing helix chain 'A' and resid 2831 through 2838 removed outlier: 3.913A pdb=" N CYS A2835 " --> pdb=" O ARG A2832 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N GLU A2837 " --> pdb=" O PHE A2834 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LYS A2838 " --> pdb=" O CYS A2835 " (cutoff:3.500A) Processing helix chain 'A' and resid 2842 through 2865 Processing helix chain 'A' and resid 2873 through 2875 No H-bonds generated for 'chain 'A' and resid 2873 through 2875' Processing helix chain 'A' and resid 2912 through 2918 removed outlier: 3.719A pdb=" N MET A2918 " --> pdb=" O ILE A2914 " (cutoff:3.500A) Processing helix chain 'A' and resid 2926 through 2940 Processing helix chain 'A' and resid 2942 through 2953 Processing helix chain 'A' and resid 2964 through 2970 Processing helix chain 'A' and resid 3002 through 3017 Processing helix chain 'A' and resid 3028 through 3040 Processing helix chain 'A' and resid 3042 through 3047 removed outlier: 3.624A pdb=" N ARG A3047 " --> pdb=" O LYS A3043 " (cutoff:3.500A) Processing helix chain 'A' and resid 3050 through 3052 No H-bonds generated for 'chain 'A' and resid 3050 through 3052' Processing helix chain 'B' and resid 6 through 17 Processing helix chain 'B' and resid 20 through 33 removed outlier: 4.189A pdb=" N LYS B 25 " --> pdb=" O THR B 21 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N GLU B 28 " --> pdb=" O LYS B 24 " (cutoff:3.500A) Processing helix chain 'B' and resid 36 through 42 Processing helix chain 'B' and resid 57 through 73 removed outlier: 3.750A pdb=" N GLU B 73 " --> pdb=" O GLN B 69 " (cutoff:3.500A) Processing helix chain 'B' and resid 88 through 108 removed outlier: 4.195A pdb=" N MET B 94 " --> pdb=" O GLN B 91 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ILE B 97 " --> pdb=" O MET B 94 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N VAL B 101 " --> pdb=" O SER B 98 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ILE B 105 " --> pdb=" O LYS B 102 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 129 removed outlier: 3.706A pdb=" N VAL B 128 " --> pdb=" O ILE B 124 " (cutoff:3.500A) Processing helix chain 'B' and resid 135 through 148 Processing helix chain 'B' and resid 153 through 158 Processing helix chain 'B' and resid 161 through 176 removed outlier: 3.697A pdb=" N TYR B 171 " --> pdb=" O LEU B 167 " (cutoff:3.500A) Processing helix chain 'B' and resid 182 through 201 removed outlier: 3.556A pdb=" N VAL B 185 " --> pdb=" O VAL B 182 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N GLN B 201 " --> pdb=" O CYS B 198 " (cutoff:3.500A) Processing helix chain 'B' and resid 207 through 222 removed outlier: 4.094A pdb=" N ASP B 211 " --> pdb=" O LYS B 208 " (cutoff:3.500A) Processing helix chain 'B' and resid 229 through 244 Processing helix chain 'B' and resid 248 through 268 Proline residue: B 260 - end of helix Processing helix chain 'B' and resid 273 through 290 Processing helix chain 'B' and resid 298 through 300 No H-bonds generated for 'chain 'B' and resid 298 through 300' Processing helix chain 'B' and resid 306 through 323 Processing helix chain 'B' and resid 343 through 356 Processing helix chain 'B' and resid 393 through 402 Processing helix chain 'B' and resid 406 through 422 Proline residue: B 411 - end of helix Processing helix chain 'B' and resid 424 through 426 No H-bonds generated for 'chain 'B' and resid 424 through 426' Processing helix chain 'B' and resid 430 through 443 Proline residue: B 434 - end of helix Processing helix chain 'B' and resid 452 through 468 Processing helix chain 'B' and resid 474 through 492 Processing helix chain 'B' and resid 501 through 513 Processing helix chain 'B' and resid 521 through 527 removed outlier: 3.645A pdb=" N LYS B 525 " --> pdb=" O ARG B 521 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LEU B 526 " --> pdb=" O GLU B 522 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N PHE B 527 " --> pdb=" O PHE B 523 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 521 through 527' Processing helix chain 'B' and resid 536 through 548 removed outlier: 3.544A pdb=" N LEU B 544 " --> pdb=" O CYS B 540 " (cutoff:3.500A) Processing helix chain 'B' and resid 572 through 580 Processing helix chain 'B' and resid 597 through 600 No H-bonds generated for 'chain 'B' and resid 597 through 600' Processing helix chain 'B' and resid 608 through 616 Processing helix chain 'B' and resid 620 through 629 Processing helix chain 'B' and resid 646 through 655 Processing helix chain 'B' and resid 684 through 704 Processing helix chain 'B' and resid 713 through 731 Processing helix chain 'B' and resid 737 through 742 removed outlier: 3.680A pdb=" N LYS B 742 " --> pdb=" O GLU B 738 " (cutoff:3.500A) Processing helix chain 'B' and resid 744 through 765 removed outlier: 3.584A pdb=" N SER B 751 " --> pdb=" O GLN B 747 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLU B 758 " --> pdb=" O GLN B 754 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N SER B 759 " --> pdb=" O CYS B 755 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N ILE B 760 " --> pdb=" O ALA B 756 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ASN B 765 " --> pdb=" O THR B 761 " (cutoff:3.500A) Processing helix chain 'B' and resid 771 through 786 removed outlier: 4.102A pdb=" N SER B 775 " --> pdb=" O PHE B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 795 through 806 Processing helix chain 'B' and resid 809 through 824 removed outlier: 3.616A pdb=" N ASN B 813 " --> pdb=" O SER B 809 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N SER B 824 " --> pdb=" O LYS B 820 " (cutoff:3.500A) Processing helix chain 'B' and resid 887 through 889 No H-bonds generated for 'chain 'B' and resid 887 through 889' Processing helix chain 'B' and resid 892 through 913 removed outlier: 4.363A pdb=" N GLN B 912 " --> pdb=" O VAL B 908 " (cutoff:3.500A) removed outlier: 5.372A pdb=" N THR B 913 " --> pdb=" O THR B 909 " (cutoff:3.500A) Processing helix chain 'B' and resid 920 through 931 removed outlier: 3.879A pdb=" N ILE B 931 " --> pdb=" O LEU B 927 " (cutoff:3.500A) Processing helix chain 'B' and resid 941 through 953 Processing helix chain 'B' and resid 963 through 979 removed outlier: 3.723A pdb=" N LEU B 967 " --> pdb=" O MET B 963 " (cutoff:3.500A) Proline residue: B 972 - end of helix removed outlier: 4.697A pdb=" N ASN B 975 " --> pdb=" O LYS B 971 " (cutoff:3.500A) Processing helix chain 'B' and resid 984 through 1001 removed outlier: 3.538A pdb=" N LEU B 995 " --> pdb=" O LEU B 991 " (cutoff:3.500A) removed outlier: 5.143A pdb=" N HIS B 996 " --> pdb=" O ASN B 992 " (cutoff:3.500A) removed outlier: 4.900A pdb=" N VAL B 997 " --> pdb=" O HIS B 993 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N VAL B 998 " --> pdb=" O VAL B 994 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N LYS B 999 " --> pdb=" O LEU B 995 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N ASN B1000 " --> pdb=" O HIS B 996 " (cutoff:3.500A) Processing helix chain 'B' and resid 1009 through 1030 removed outlier: 3.685A pdb=" N VAL B1021 " --> pdb=" O GLN B1017 " (cutoff:3.500A) Processing helix chain 'B' and resid 1036 through 1052 Processing helix chain 'B' and resid 1070 through 1079 removed outlier: 3.655A pdb=" N THR B1075 " --> pdb=" O ASN B1071 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N GLN B1076 " --> pdb=" O GLU B1072 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N PHE B1077 " --> pdb=" O VAL B1073 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N LEU B1078 " --> pdb=" O PHE B1074 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N ALA B1079 " --> pdb=" O THR B1075 " (cutoff:3.500A) Processing helix chain 'B' and resid 1083 through 1096 removed outlier: 4.990A pdb=" N ASN B1094 " --> pdb=" O ALA B1090 " (cutoff:3.500A) removed outlier: 6.011A pdb=" N ARG B1095 " --> pdb=" O GLU B1091 " (cutoff:3.500A) removed outlier: 5.102A pdb=" N LEU B1096 " --> pdb=" O SER B1092 " (cutoff:3.500A) Processing helix chain 'B' and resid 1113 through 1132 Processing helix chain 'B' and resid 1144 through 1164 Processing helix chain 'B' and resid 1169 through 1181 removed outlier: 4.050A pdb=" N LYS B1181 " --> pdb=" O CYS B1177 " (cutoff:3.500A) Processing helix chain 'B' and resid 1187 through 1201 Processing helix chain 'B' and resid 1206 through 1212 Processing helix chain 'B' and resid 1214 through 1224 removed outlier: 3.616A pdb=" N LEU B1224 " --> pdb=" O GLU B1220 " (cutoff:3.500A) Processing helix chain 'B' and resid 1244 through 1261 removed outlier: 6.081A pdb=" N LYS B1253 " --> pdb=" O ARG B1249 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N VAL B1254 " --> pdb=" O SER B1250 " (cutoff:3.500A) Proline residue: B1257 - end of helix Processing helix chain 'B' and resid 1265 through 1275 Processing helix chain 'B' and resid 1279 through 1285 Processing helix chain 'B' and resid 1287 through 1298 removed outlier: 3.906A pdb=" N ASN B1293 " --> pdb=" O LYS B1289 " (cutoff:3.500A) Proline residue: B1296 - end of helix Processing helix chain 'B' and resid 1306 through 1323 removed outlier: 3.784A pdb=" N GLN B1310 " --> pdb=" O SER B1306 " (cutoff:3.500A) removed outlier: 4.778A pdb=" N GLN B1311 " --> pdb=" O GLY B1307 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ARG B1312 " --> pdb=" O MET B1308 " (cutoff:3.500A) Processing helix chain 'B' and resid 1328 through 1330 No H-bonds generated for 'chain 'B' and resid 1328 through 1330' Processing helix chain 'B' and resid 1332 through 1338 Processing helix chain 'B' and resid 1340 through 1350 removed outlier: 3.556A pdb=" N THR B1350 " --> pdb=" O GLU B1346 " (cutoff:3.500A) Processing helix chain 'B' and resid 1383 through 1396 Processing helix chain 'B' and resid 1404 through 1408 Processing helix chain 'B' and resid 1414 through 1428 Processing helix chain 'B' and resid 1432 through 1452 removed outlier: 3.698A pdb=" N ASP B1452 " --> pdb=" O LEU B1448 " (cutoff:3.500A) Processing helix chain 'B' and resid 1461 through 1477 Processing helix chain 'B' and resid 1485 through 1508 Processing helix chain 'B' and resid 1513 through 1515 No H-bonds generated for 'chain 'B' and resid 1513 through 1515' Processing helix chain 'B' and resid 1517 through 1528 Proline residue: B1526 - end of helix Processing helix chain 'B' and resid 1532 through 1546 removed outlier: 3.646A pdb=" N GLN B1537 " --> pdb=" O GLU B1533 " (cutoff:3.500A) Processing helix chain 'B' and resid 1556 through 1561 removed outlier: 3.566A pdb=" N LYS B1560 " --> pdb=" O TYR B1556 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LEU B1561 " --> pdb=" O ILE B1557 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1556 through 1561' Processing helix chain 'B' and resid 1572 through 1582 Processing helix chain 'B' and resid 1590 through 1601 removed outlier: 3.528A pdb=" N VAL B1600 " --> pdb=" O HIS B1596 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N SER B1601 " --> pdb=" O PHE B1597 " (cutoff:3.500A) Processing helix chain 'B' and resid 1607 through 1623 removed outlier: 4.730A pdb=" N GLU B1612 " --> pdb=" O THR B1609 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU B1623 " --> pdb=" O GLN B1620 " (cutoff:3.500A) Processing helix chain 'B' and resid 1625 through 1634 removed outlier: 4.084A pdb=" N VAL B1629 " --> pdb=" O LYS B1625 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N ASP B1630 " --> pdb=" O ASP B1626 " (cutoff:3.500A) Processing helix chain 'B' and resid 1639 through 1641 No H-bonds generated for 'chain 'B' and resid 1639 through 1641' Processing helix chain 'B' and resid 1643 through 1658 Processing helix chain 'B' and resid 1664 through 1677 Processing helix chain 'B' and resid 1694 through 1702 removed outlier: 3.530A pdb=" N LEU B1702 " --> pdb=" O LYS B1698 " (cutoff:3.500A) Processing helix chain 'B' and resid 1706 through 1722 removed outlier: 3.668A pdb=" N LEU B1722 " --> pdb=" O LEU B1718 " (cutoff:3.500A) Processing helix chain 'B' and resid 1727 through 1742 Processing helix chain 'B' and resid 1744 through 1753 removed outlier: 3.555A pdb=" N GLU B1751 " --> pdb=" O HIS B1747 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ILE B1752 " --> pdb=" O SER B1748 " (cutoff:3.500A) Processing helix chain 'B' and resid 1759 through 1763 Processing helix chain 'B' and resid 1792 through 1795 No H-bonds generated for 'chain 'B' and resid 1792 through 1795' Processing helix chain 'B' and resid 1802 through 1815 Processing helix chain 'B' and resid 1822 through 1831 removed outlier: 3.777A pdb=" N LEU B1826 " --> pdb=" O GLU B1822 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LEU B1827 " --> pdb=" O ILE B1823 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N LYS B1828 " --> pdb=" O LEU B1824 " (cutoff:3.500A) Proline residue: B1829 - end of helix No H-bonds generated for 'chain 'B' and resid 1822 through 1831' Processing helix chain 'B' and resid 1835 through 1851 Proline residue: B1843 - end of helix Processing helix chain 'B' and resid 1857 through 1874 Processing helix chain 'B' and resid 1903 through 1918 removed outlier: 3.696A pdb=" N ARG B1918 " --> pdb=" O ASP B1914 " (cutoff:3.500A) Processing helix chain 'B' and resid 1927 through 1932 removed outlier: 4.008A pdb=" N PHE B1932 " --> pdb=" O PHE B1928 " (cutoff:3.500A) Processing helix chain 'B' and resid 1938 through 1947 Processing helix chain 'B' and resid 1951 through 1973 Processing helix chain 'B' and resid 1986 through 1997 Processing helix chain 'B' and resid 2001 through 2012 removed outlier: 3.500A pdb=" N LEU B2006 " --> pdb=" O GLN B2002 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N GLU B2007 " --> pdb=" O ASP B2003 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ILE B2008 " --> pdb=" O LEU B2004 " (cutoff:3.500A) Processing helix chain 'B' and resid 2016 through 2019 Processing helix chain 'B' and resid 2029 through 2038 Processing helix chain 'B' and resid 2042 through 2051 Processing helix chain 'B' and resid 2057 through 2071 removed outlier: 3.727A pdb=" N ALA B2062 " --> pdb=" O SER B2058 " (cutoff:3.500A) Processing helix chain 'B' and resid 2074 through 2087 Processing helix chain 'B' and resid 2093 through 2105 removed outlier: 3.613A pdb=" N LEU B2098 " --> pdb=" O GLU B2094 " (cutoff:3.500A) Processing helix chain 'B' and resid 2124 through 2136 Processing helix chain 'B' and resid 2140 through 2159 removed outlier: 3.505A pdb=" N VAL B2155 " --> pdb=" O ARG B2151 " (cutoff:3.500A) Processing helix chain 'B' and resid 2166 through 2190 removed outlier: 3.596A pdb=" N TYR B2170 " --> pdb=" O TYR B2167 " (cutoff:3.500A) Proline residue: B2171 - end of helix removed outlier: 3.711A pdb=" N SER B2174 " --> pdb=" O PRO B2171 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLU B2187 " --> pdb=" O SER B2184 " (cutoff:3.500A) Processing helix chain 'B' and resid 2195 through 2212 removed outlier: 3.738A pdb=" N LEU B2211 " --> pdb=" O LYS B2207 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU B2212 " --> pdb=" O HIS B2208 " (cutoff:3.500A) Processing helix chain 'B' and resid 2217 through 2236 Proline residue: B2222 - end of helix Processing helix chain 'B' and resid 2245 through 2264 Processing helix chain 'B' and resid 2269 through 2281 removed outlier: 3.710A pdb=" N TYR B2281 " --> pdb=" O GLN B2277 " (cutoff:3.500A) Processing helix chain 'B' and resid 2290 through 2301 Processing helix chain 'B' and resid 2305 through 2322 Processing helix chain 'B' and resid 2328 through 2348 removed outlier: 4.023A pdb=" N LEU B2332 " --> pdb=" O PRO B2328 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N THR B2333 " --> pdb=" O SER B2329 " (cutoff:3.500A) Processing helix chain 'B' and resid 2353 through 2359 Processing helix chain 'B' and resid 2361 through 2370 Processing helix chain 'B' and resid 2377 through 2406 Processing helix chain 'B' and resid 2408 through 2421 Processing helix chain 'B' and resid 2437 through 2475 removed outlier: 4.140A pdb=" N GLU B2449 " --> pdb=" O LEU B2445 " (cutoff:3.500A) Processing helix chain 'B' and resid 2481 through 2493 removed outlier: 3.518A pdb=" N LEU B2490 " --> pdb=" O LEU B2487 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LEU B2492 " --> pdb=" O SER B2489 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N GLU B2493 " --> pdb=" O LEU B2490 " (cutoff:3.500A) Processing helix chain 'B' and resid 2498 through 2506 removed outlier: 3.629A pdb=" N GLY B2502 " --> pdb=" O SER B2498 " (cutoff:3.500A) Processing helix chain 'B' and resid 2508 through 2510 No H-bonds generated for 'chain 'B' and resid 2508 through 2510' Processing helix chain 'B' and resid 2513 through 2516 Processing helix chain 'B' and resid 2520 through 2526 Processing helix chain 'B' and resid 2537 through 2551 Processing helix chain 'B' and resid 2553 through 2564 removed outlier: 5.526A pdb=" N PHE B2558 " --> pdb=" O HIS B2554 " (cutoff:3.500A) removed outlier: 4.966A pdb=" N ILE B2559 " --> pdb=" O HIS B2555 " (cutoff:3.500A) Processing helix chain 'B' and resid 2568 through 2572 Processing helix chain 'B' and resid 2593 through 2612 removed outlier: 4.248A pdb=" N ARG B2612 " --> pdb=" O THR B2608 " (cutoff:3.500A) Processing helix chain 'B' and resid 2614 through 2632 Processing helix chain 'B' and resid 2637 through 2640 removed outlier: 4.572A pdb=" N THR B2640 " --> pdb=" O GLN B2637 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 2637 through 2640' Processing helix chain 'B' and resid 2652 through 2655 No H-bonds generated for 'chain 'B' and resid 2652 through 2655' Processing helix chain 'B' and resid 2723 through 2741 Processing helix chain 'B' and resid 2743 through 2747 Processing helix chain 'B' and resid 2776 through 2780 Processing helix chain 'B' and resid 2787 through 2791 Processing helix chain 'B' and resid 2798 through 2807 Processing helix chain 'B' and resid 2813 through 2825 Processing helix chain 'B' and resid 2831 through 2838 removed outlier: 3.912A pdb=" N CYS B2835 " --> pdb=" O ARG B2832 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N GLU B2837 " --> pdb=" O PHE B2834 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LYS B2838 " --> pdb=" O CYS B2835 " (cutoff:3.500A) Processing helix chain 'B' and resid 2842 through 2865 Processing helix chain 'B' and resid 2873 through 2875 No H-bonds generated for 'chain 'B' and resid 2873 through 2875' Processing helix chain 'B' and resid 2896 through 2899 Processing helix chain 'B' and resid 2912 through 2918 removed outlier: 3.773A pdb=" N MET B2918 " --> pdb=" O ILE B2914 " (cutoff:3.500A) Processing helix chain 'B' and resid 2926 through 2940 Processing helix chain 'B' and resid 2942 through 2953 Processing helix chain 'B' and resid 2964 through 2970 Processing helix chain 'B' and resid 3002 through 3017 Processing helix chain 'B' and resid 3028 through 3039 Processing helix chain 'B' and resid 3042 through 3046 Processing helix chain 'B' and resid 3050 through 3052 No H-bonds generated for 'chain 'B' and resid 3050 through 3052' Processing sheet with id= A, first strand: chain 'A' and resid 1060 through 1063 Processing sheet with id= B, first strand: chain 'A' and resid 2757 through 2759 Processing sheet with id= C, first strand: chain 'A' and resid 2773 through 2775 Processing sheet with id= D, first strand: chain 'B' and resid 1060 through 1063 Processing sheet with id= E, first strand: chain 'B' and resid 2757 through 2759 Processing sheet with id= F, first strand: chain 'B' and resid 2773 through 2775 2412 hydrogen bonds defined for protein. 6735 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: 22.81 Time building geometry restraints manager: 18.09 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 14340 1.34 - 1.46: 8342 1.46 - 1.58: 22146 1.58 - 1.70: 10 1.70 - 1.82: 450 Bond restraints: 45288 Sorted by residual: bond pdb=" O3A ANP A3101 " pdb=" PB ANP A3101 " ideal model delta sigma weight residual 1.700 1.558 0.142 2.00e-02 2.50e+03 5.06e+01 bond pdb=" O3A ANP B3101 " pdb=" PB ANP B3101 " ideal model delta sigma weight residual 1.700 1.558 0.142 2.00e-02 2.50e+03 5.03e+01 bond pdb=" N3B ANP B3101 " pdb=" PG ANP B3101 " ideal model delta sigma weight residual 1.795 1.692 0.103 2.00e-02 2.50e+03 2.65e+01 bond pdb=" N3B ANP A3101 " pdb=" PG ANP A3101 " ideal model delta sigma weight residual 1.795 1.693 0.102 2.00e-02 2.50e+03 2.59e+01 bond pdb=" O5' ANP B3101 " pdb=" PA ANP B3101 " ideal model delta sigma weight residual 1.655 1.581 0.074 2.00e-02 2.50e+03 1.35e+01 ... (remaining 45283 not shown) Histogram of bond angle deviations from ideal: 97.62 - 104.92: 642 104.92 - 112.21: 23229 112.21 - 119.51: 15060 119.51 - 126.81: 21712 126.81 - 134.11: 557 Bond angle restraints: 61200 Sorted by residual: angle pdb=" PB ANP B3101 " pdb=" N3B ANP B3101 " pdb=" PG ANP B3101 " ideal model delta sigma weight residual 126.95 109.74 17.21 3.00e+00 1.11e-01 3.29e+01 angle pdb=" PB ANP A3101 " pdb=" N3B ANP A3101 " pdb=" PG ANP A3101 " ideal model delta sigma weight residual 126.95 109.77 17.18 3.00e+00 1.11e-01 3.28e+01 angle pdb=" O1B ANP A3101 " pdb=" PB ANP A3101 " pdb=" O2B ANP A3101 " ideal model delta sigma weight residual 120.08 109.64 10.44 3.00e+00 1.11e-01 1.21e+01 angle pdb=" O1B ANP B3101 " pdb=" PB ANP B3101 " pdb=" O2B ANP B3101 " ideal model delta sigma weight residual 120.08 109.66 10.42 3.00e+00 1.11e-01 1.21e+01 angle pdb=" N PRO B1378 " pdb=" CA PRO B1378 " pdb=" C PRO B1378 " ideal model delta sigma weight residual 110.70 114.78 -4.08 1.22e+00 6.72e-01 1.12e+01 ... (remaining 61195 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.73: 25141 17.73 - 35.46: 2156 35.46 - 53.18: 245 53.18 - 70.91: 62 70.91 - 88.64: 50 Dihedral angle restraints: 27654 sinusoidal: 11302 harmonic: 16352 Sorted by residual: dihedral pdb=" CA ASN B1377 " pdb=" C ASN B1377 " pdb=" N PRO B1378 " pdb=" CA PRO B1378 " ideal model delta harmonic sigma weight residual 180.00 -153.03 -26.97 0 5.00e+00 4.00e-02 2.91e+01 dihedral pdb=" CA MET A2026 " pdb=" C MET A2026 " pdb=" N LEU A2027 " pdb=" CA LEU A2027 " ideal model delta harmonic sigma weight residual 180.00 -161.78 -18.22 0 5.00e+00 4.00e-02 1.33e+01 dihedral pdb=" CA PRO B 962 " pdb=" C PRO B 962 " pdb=" N MET B 963 " pdb=" CA MET B 963 " ideal model delta harmonic sigma weight residual -180.00 -163.25 -16.75 0 5.00e+00 4.00e-02 1.12e+01 ... (remaining 27651 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 6177 0.055 - 0.110: 800 0.110 - 0.165: 41 0.165 - 0.220: 0 0.220 - 0.274: 2 Chirality restraints: 7020 Sorted by residual: chirality pdb=" C3' ANP B3101 " pdb=" C2' ANP B3101 " pdb=" C4' ANP B3101 " pdb=" O3' ANP B3101 " both_signs ideal model delta sigma weight residual False -2.36 -2.63 0.27 2.00e-01 2.50e+01 1.88e+00 chirality pdb=" C3' ANP A3101 " pdb=" C2' ANP A3101 " pdb=" C4' ANP A3101 " pdb=" O3' ANP A3101 " both_signs ideal model delta sigma weight residual False -2.36 -2.63 0.27 2.00e-01 2.50e+01 1.88e+00 chirality pdb=" CA ILE A2055 " pdb=" N ILE A2055 " pdb=" C ILE A2055 " pdb=" CB ILE A2055 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.28e-01 ... (remaining 7017 not shown) Planarity restraints: 7702 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE A2055 " 0.030 5.00e-02 4.00e+02 4.62e-02 3.41e+00 pdb=" N PRO A2056 " -0.080 5.00e-02 4.00e+02 pdb=" CA PRO A2056 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO A2056 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE B2055 " -0.030 5.00e-02 4.00e+02 4.56e-02 3.33e+00 pdb=" N PRO B2056 " 0.079 5.00e-02 4.00e+02 pdb=" CA PRO B2056 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO B2056 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 595 " 0.030 5.00e-02 4.00e+02 4.50e-02 3.24e+00 pdb=" N PRO A 596 " -0.078 5.00e-02 4.00e+02 pdb=" CA PRO A 596 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 596 " 0.025 5.00e-02 4.00e+02 ... (remaining 7699 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 456 2.67 - 3.23: 43617 3.23 - 3.78: 69898 3.78 - 4.34: 94886 4.34 - 4.90: 152437 Nonbonded interactions: 361294 Sorted by model distance: nonbonded pdb=" OD1 ASN A2875 " pdb="MG MG A3102 " model vdw 2.109 2.170 nonbonded pdb=" OD1 ASN B2875 " pdb="MG MG B3102 " model vdw 2.113 2.170 nonbonded pdb=" O SER B 941 " pdb=" ND1 HIS B 945 " model vdw 2.221 2.520 nonbonded pdb=" O HIS B 399 " pdb=" OG SER B 403 " model vdw 2.222 2.440 nonbonded pdb=" O HIS A 399 " pdb=" OG SER A 403 " model vdw 2.222 2.440 ... (remaining 361289 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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: 3.830 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.040 Extract box with map and model: 15.630 Check model and map are aligned: 0.590 Set scattering table: 0.350 Process input model: 122.580 Find NCS groups from input model: 2.510 Set up NCS constraints: 0.280 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 159.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 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 : 0.002 0.142 45288 Z= 0.152 Angle : 0.498 17.215 61200 Z= 0.242 Chirality : 0.035 0.274 7020 Planarity : 0.003 0.046 7702 Dihedral : 13.270 88.641 16990 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 0.00 % Allowed : 0.16 % Favored : 99.84 % 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: 1.84 (0.11), residues: 5468 helix: 1.70 (0.08), residues: 3838 sheet: 1.59 (0.63), residues: 66 loop : 0.13 (0.16), residues: 1564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP B2091 HIS 0.006 0.001 HIS A1083 PHE 0.019 0.001 PHE B 652 TYR 0.013 0.001 TYR B1442 ARG 0.009 0.000 ARG A2443 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10936 Ramachandran restraints generated. 5468 Oldfield, 0 Emsley, 5468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10936 Ramachandran restraints generated. 5468 Oldfield, 0 Emsley, 5468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 401 residues out of total 5036 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 401 time to evaluate : 4.772 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 577 MET cc_start: 0.8329 (tmm) cc_final: 0.7214 (ptm) REVERT: A 578 LYS cc_start: 0.9456 (mmpt) cc_final: 0.9100 (mmtt) REVERT: A 624 MET cc_start: 0.7710 (mmt) cc_final: 0.7405 (mmt) REVERT: A 652 PHE cc_start: 0.8027 (m-80) cc_final: 0.7722 (m-10) REVERT: A 929 MET cc_start: 0.8652 (mpp) cc_final: 0.8363 (ppp) REVERT: A 996 HIS cc_start: 0.8485 (m-70) cc_final: 0.8276 (m-70) REVERT: A 1064 MET cc_start: 0.5098 (pmm) cc_final: 0.4494 (pmm) REVERT: A 1204 ARG cc_start: 0.8223 (mpp-170) cc_final: 0.7909 (mtm-85) REVERT: A 1210 MET cc_start: 0.9249 (mmp) cc_final: 0.8953 (mmm) REVERT: A 1308 MET cc_start: 0.7351 (tmm) cc_final: 0.7063 (tmm) REVERT: A 1342 GLU cc_start: 0.9263 (mp0) cc_final: 0.9047 (pm20) REVERT: A 1343 ILE cc_start: 0.9070 (pt) cc_final: 0.8852 (pp) REVERT: A 1349 MET cc_start: 0.8349 (tmm) cc_final: 0.7990 (tmm) REVERT: A 1425 GLN cc_start: 0.9275 (mm-40) cc_final: 0.9037 (mm-40) REVERT: A 1434 LYS cc_start: 0.9382 (tptt) cc_final: 0.8853 (tppt) REVERT: A 1693 ASP cc_start: 0.8352 (t0) cc_final: 0.8097 (t70) REVERT: A 1836 ASP cc_start: 0.8885 (t70) cc_final: 0.8580 (t0) REVERT: A 2157 GLU cc_start: 0.8132 (mp0) cc_final: 0.7874 (mp0) REVERT: A 2314 GLN cc_start: 0.8771 (tp-100) cc_final: 0.7836 (tp-100) REVERT: A 2479 GLU cc_start: 0.8439 (tp30) cc_final: 0.8153 (tp30) REVERT: A 2728 MET cc_start: 0.9067 (mmm) cc_final: 0.8836 (mmm) REVERT: B 624 MET cc_start: 0.7849 (mmt) cc_final: 0.7626 (mmt) REVERT: B 652 PHE cc_start: 0.8045 (m-80) cc_final: 0.7768 (m-10) REVERT: B 996 HIS cc_start: 0.8506 (m-70) cc_final: 0.8296 (m-70) REVERT: B 1204 ARG cc_start: 0.8154 (mpp-170) cc_final: 0.7874 (mtm-85) REVERT: B 1210 MET cc_start: 0.9278 (mmp) cc_final: 0.8970 (mmm) REVERT: B 1308 MET cc_start: 0.7369 (tmm) cc_final: 0.7085 (tmm) REVERT: B 1343 ILE cc_start: 0.9091 (pt) cc_final: 0.8799 (pp) REVERT: B 1425 GLN cc_start: 0.8755 (mp10) cc_final: 0.8499 (mp10) REVERT: B 1434 LYS cc_start: 0.9418 (tptt) cc_final: 0.8992 (tppt) REVERT: B 1760 MET cc_start: 0.8438 (ttp) cc_final: 0.8082 (ttp) REVERT: B 1773 LYS cc_start: 0.9328 (tptp) cc_final: 0.9101 (tptt) REVERT: B 2314 GLN cc_start: 0.8791 (tp-100) cc_final: 0.8182 (tp-100) outliers start: 0 outliers final: 0 residues processed: 401 average time/residue: 1.6686 time to fit residues: 824.2287 Evaluate side-chains 291 residues out of total 5036 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 291 time to evaluate : 5.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 554 random chunks: chunk 467 optimal weight: 0.9980 chunk 419 optimal weight: 1.9990 chunk 232 optimal weight: 0.7980 chunk 143 optimal weight: 6.9990 chunk 283 optimal weight: 10.0000 chunk 224 optimal weight: 0.9980 chunk 434 optimal weight: 5.9990 chunk 168 optimal weight: 0.9990 chunk 264 optimal weight: 0.6980 chunk 323 optimal weight: 50.0000 chunk 503 optimal weight: 7.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 700 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 945 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 975 ASN ** A1310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1719 ASN ** A2066 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2327 ASN A3014 GLN ** B 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 700 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 975 ASN ** B1310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2066 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2327 ASN B2730 GLN B3014 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.1169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 45288 Z= 0.164 Angle : 0.515 9.274 61200 Z= 0.255 Chirality : 0.036 0.157 7020 Planarity : 0.004 0.047 7702 Dihedral : 4.110 85.292 6014 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 0.97 % Allowed : 5.98 % Favored : 93.05 % 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: 2.28 (0.12), residues: 5468 helix: 2.05 (0.08), residues: 3868 sheet: 1.22 (0.66), residues: 62 loop : 0.21 (0.16), residues: 1538 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B2091 HIS 0.005 0.001 HIS B 290 PHE 0.025 0.001 PHE B 652 TYR 0.018 0.001 TYR A2437 ARG 0.007 0.000 ARG A2161 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10936 Ramachandran restraints generated. 5468 Oldfield, 0 Emsley, 5468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10936 Ramachandran restraints generated. 5468 Oldfield, 0 Emsley, 5468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 381 residues out of total 5036 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 333 time to evaluate : 5.078 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 577 MET cc_start: 0.8282 (tmm) cc_final: 0.7482 (ptm) REVERT: A 578 LYS cc_start: 0.9419 (mmpt) cc_final: 0.9211 (mmpt) REVERT: A 617 MET cc_start: 0.5871 (ppp) cc_final: 0.5484 (ppp) REVERT: A 624 MET cc_start: 0.7337 (mmt) cc_final: 0.7024 (mmt) REVERT: A 652 PHE cc_start: 0.7977 (m-80) cc_final: 0.7744 (m-10) REVERT: A 1064 MET cc_start: 0.4753 (pmm) cc_final: 0.4452 (pmm) REVERT: A 1087 MET cc_start: 0.8598 (OUTLIER) cc_final: 0.8248 (mtt) REVERT: A 1095 ARG cc_start: 0.8154 (mpt180) cc_final: 0.7585 (tpp80) REVERT: A 1134 MET cc_start: 0.6972 (mtm) cc_final: 0.6375 (mmt) REVERT: A 1204 ARG cc_start: 0.8192 (mpp-170) cc_final: 0.7826 (mtm-85) REVERT: A 1210 MET cc_start: 0.9229 (mmp) cc_final: 0.8981 (mmm) REVERT: A 1308 MET cc_start: 0.7335 (tmm) cc_final: 0.7069 (tmm) REVERT: A 1321 MET cc_start: 0.7150 (pp-130) cc_final: 0.6724 (pp-130) REVERT: A 1349 MET cc_start: 0.8430 (tmm) cc_final: 0.8132 (tmm) REVERT: A 1425 GLN cc_start: 0.9407 (mm-40) cc_final: 0.9174 (mm-40) REVERT: A 1693 ASP cc_start: 0.8537 (t0) cc_final: 0.8249 (t70) REVERT: A 1836 ASP cc_start: 0.8835 (t70) cc_final: 0.8446 (t0) REVERT: A 1992 LYS cc_start: 0.8577 (mptt) cc_final: 0.8264 (mptt) REVERT: A 2157 GLU cc_start: 0.8297 (mp0) cc_final: 0.8075 (mp0) REVERT: A 2314 GLN cc_start: 0.8603 (tp-100) cc_final: 0.7913 (tp-100) REVERT: A 2479 GLU cc_start: 0.8447 (tp30) cc_final: 0.8156 (tp30) REVERT: B 578 LYS cc_start: 0.9091 (mmpt) cc_final: 0.8883 (mmtt) REVERT: B 624 MET cc_start: 0.7577 (mmt) cc_final: 0.7304 (mmt) REVERT: B 652 PHE cc_start: 0.7931 (m-80) cc_final: 0.7634 (m-10) REVERT: B 1064 MET cc_start: 0.4723 (pmm) cc_final: 0.4421 (pmm) REVERT: B 1204 ARG cc_start: 0.8141 (mpp-170) cc_final: 0.7803 (mtm-85) REVERT: B 1210 MET cc_start: 0.9272 (mmp) cc_final: 0.9012 (mmm) REVERT: B 1308 MET cc_start: 0.7346 (tmm) cc_final: 0.7086 (tmm) REVERT: B 1321 MET cc_start: 0.7134 (pp-130) cc_final: 0.6702 (pp-130) REVERT: B 1425 GLN cc_start: 0.8988 (mp10) cc_final: 0.8695 (mm-40) REVERT: B 1434 LYS cc_start: 0.9438 (tptt) cc_final: 0.8966 (tppt) REVERT: B 1773 LYS cc_start: 0.9322 (tptp) cc_final: 0.9095 (tptt) REVERT: B 1836 ASP cc_start: 0.8894 (t70) cc_final: 0.8558 (t0) REVERT: B 2157 GLU cc_start: 0.8343 (mt-10) cc_final: 0.7922 (mm-30) REVERT: B 2280 GLN cc_start: 0.8866 (mm110) cc_final: 0.8664 (mm110) REVERT: B 2314 GLN cc_start: 0.8825 (tp-100) cc_final: 0.8157 (tp-100) outliers start: 48 outliers final: 17 residues processed: 361 average time/residue: 1.5392 time to fit residues: 693.1292 Evaluate side-chains 296 residues out of total 5036 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 278 time to evaluate : 4.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 290 HIS Chi-restraints excluded: chain A residue 1027 HIS Chi-restraints excluded: chain A residue 1087 MET Chi-restraints excluded: chain A residue 1351 LEU Chi-restraints excluded: chain A residue 1662 THR Chi-restraints excluded: chain A residue 2006 LEU Chi-restraints excluded: chain A residue 2841 ASP Chi-restraints excluded: chain A residue 2946 LEU Chi-restraints excluded: chain A residue 3024 THR Chi-restraints excluded: chain B residue 1027 HIS Chi-restraints excluded: chain B residue 1452 ASP Chi-restraints excluded: chain B residue 1662 THR Chi-restraints excluded: chain B residue 2096 GLU Chi-restraints excluded: chain B residue 2550 MET Chi-restraints excluded: chain B residue 2557 LEU Chi-restraints excluded: chain B residue 2667 MET Chi-restraints excluded: chain B residue 2841 ASP Chi-restraints excluded: chain B residue 2946 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 554 random chunks: chunk 279 optimal weight: 9.9990 chunk 156 optimal weight: 0.8980 chunk 418 optimal weight: 0.0270 chunk 342 optimal weight: 0.8980 chunk 138 optimal weight: 8.9990 chunk 503 optimal weight: 0.5980 chunk 544 optimal weight: 3.9990 chunk 448 optimal weight: 5.9990 chunk 499 optimal weight: 0.9980 chunk 171 optimal weight: 3.9990 chunk 404 optimal weight: 1.9990 overall best weight: 0.6838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 700 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 945 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1334 HIS A1431 ASN A1443 HIS ** A2066 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3014 GLN ** B 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 700 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 945 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1334 HIS ** B2066 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2305 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.1500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 45288 Z= 0.140 Angle : 0.485 10.126 61200 Z= 0.238 Chirality : 0.036 0.150 7020 Planarity : 0.003 0.047 7702 Dihedral : 4.071 88.456 6014 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 1.11 % Allowed : 7.76 % Favored : 91.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.38 (0.12), residues: 5468 helix: 2.14 (0.08), residues: 3856 sheet: 1.10 (0.66), residues: 62 loop : 0.22 (0.16), residues: 1550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B2091 HIS 0.006 0.001 HIS B1334 PHE 0.015 0.001 PHE B 652 TYR 0.022 0.001 TYR A1319 ARG 0.007 0.000 ARG B2161 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10936 Ramachandran restraints generated. 5468 Oldfield, 0 Emsley, 5468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10936 Ramachandran restraints generated. 5468 Oldfield, 0 Emsley, 5468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 5036 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 292 time to evaluate : 5.293 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 577 MET cc_start: 0.8219 (tmm) cc_final: 0.7306 (ptm) REVERT: A 578 LYS cc_start: 0.9423 (mmpt) cc_final: 0.9181 (mmpt) REVERT: A 617 MET cc_start: 0.5831 (ppp) cc_final: 0.5389 (ppp) REVERT: A 624 MET cc_start: 0.7353 (mmt) cc_final: 0.7052 (mmt) REVERT: A 652 PHE cc_start: 0.7994 (m-80) cc_final: 0.7756 (m-10) REVERT: A 1064 MET cc_start: 0.4690 (pmm) cc_final: 0.4332 (pmm) REVERT: A 1087 MET cc_start: 0.8686 (OUTLIER) cc_final: 0.8239 (mtp) REVERT: A 1095 ARG cc_start: 0.8153 (mpt180) cc_final: 0.7821 (mtt90) REVERT: A 1134 MET cc_start: 0.7127 (mtm) cc_final: 0.6512 (mmt) REVERT: A 1204 ARG cc_start: 0.8113 (mpp-170) cc_final: 0.7792 (mtm-85) REVERT: A 1210 MET cc_start: 0.9251 (mmp) cc_final: 0.8992 (mmm) REVERT: A 1308 MET cc_start: 0.7285 (tmm) cc_final: 0.7036 (tmm) REVERT: A 1321 MET cc_start: 0.6952 (pp-130) cc_final: 0.6631 (pp-130) REVERT: A 1349 MET cc_start: 0.8549 (tmm) cc_final: 0.8230 (tmm) REVERT: A 1425 GLN cc_start: 0.9435 (mm-40) cc_final: 0.9210 (mm-40) REVERT: A 1693 ASP cc_start: 0.8506 (t0) cc_final: 0.8212 (t70) REVERT: A 1836 ASP cc_start: 0.8823 (t70) cc_final: 0.8440 (t0) REVERT: A 2479 GLU cc_start: 0.8463 (tp30) cc_final: 0.8148 (tp30) REVERT: A 2667 MET cc_start: 0.8358 (mtp) cc_final: 0.8054 (mtp) REVERT: A 2668 GLU cc_start: 0.8654 (mm-30) cc_final: 0.8335 (pp20) REVERT: A 2935 MET cc_start: 0.9298 (OUTLIER) cc_final: 0.9079 (mmm) REVERT: B 617 MET cc_start: 0.4894 (OUTLIER) cc_final: 0.4409 (ppp) REVERT: B 624 MET cc_start: 0.7544 (mmt) cc_final: 0.7225 (mmt) REVERT: B 652 PHE cc_start: 0.7905 (m-80) cc_final: 0.7599 (m-10) REVERT: B 1064 MET cc_start: 0.4885 (pmm) cc_final: 0.4535 (pmm) REVERT: B 1134 MET cc_start: 0.7100 (mtm) cc_final: 0.6499 (mmt) REVERT: B 1204 ARG cc_start: 0.8068 (mpp-170) cc_final: 0.7765 (mtm-85) REVERT: B 1210 MET cc_start: 0.9279 (mmp) cc_final: 0.9012 (mmm) REVERT: B 1308 MET cc_start: 0.7323 (tmm) cc_final: 0.7076 (tmm) REVERT: B 1321 MET cc_start: 0.6984 (pp-130) cc_final: 0.6658 (pp-130) REVERT: B 1424 GLU cc_start: 0.9220 (mt-10) cc_final: 0.8753 (mm-30) REVERT: B 1434 LYS cc_start: 0.9459 (tptt) cc_final: 0.8978 (tppt) REVERT: B 1773 LYS cc_start: 0.9324 (tptp) cc_final: 0.9094 (tptt) REVERT: B 1836 ASP cc_start: 0.8876 (t70) cc_final: 0.8511 (t0) REVERT: B 2091 TRP cc_start: 0.7117 (t-100) cc_final: 0.6044 (t-100) REVERT: B 2096 GLU cc_start: 0.8673 (mm-30) cc_final: 0.8242 (mm-30) REVERT: B 2157 GLU cc_start: 0.8356 (mt-10) cc_final: 0.7901 (mm-30) REVERT: B 2280 GLN cc_start: 0.8815 (mm110) cc_final: 0.8586 (mm110) REVERT: B 2314 GLN cc_start: 0.8826 (tp-100) cc_final: 0.8152 (tp-100) REVERT: B 2479 GLU cc_start: 0.8262 (tp30) cc_final: 0.8049 (tp30) REVERT: B 2561 LEU cc_start: 0.9571 (OUTLIER) cc_final: 0.9317 (mm) outliers start: 55 outliers final: 22 residues processed: 325 average time/residue: 1.5612 time to fit residues: 633.0476 Evaluate side-chains 300 residues out of total 5036 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 274 time to evaluate : 4.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 290 HIS Chi-restraints excluded: chain A residue 1040 MET Chi-restraints excluded: chain A residue 1087 MET Chi-restraints excluded: chain A residue 1334 HIS Chi-restraints excluded: chain A residue 1351 LEU Chi-restraints excluded: chain A residue 1452 ASP Chi-restraints excluded: chain A residue 1678 VAL Chi-restraints excluded: chain A residue 2006 LEU Chi-restraints excluded: chain A residue 2405 MET Chi-restraints excluded: chain A residue 2935 MET Chi-restraints excluded: chain A residue 2946 LEU Chi-restraints excluded: chain A residue 3024 THR Chi-restraints excluded: chain B residue 290 HIS Chi-restraints excluded: chain B residue 617 MET Chi-restraints excluded: chain B residue 1040 MET Chi-restraints excluded: chain B residue 1334 HIS Chi-restraints excluded: chain B residue 1452 ASP Chi-restraints excluded: chain B residue 1668 LEU Chi-restraints excluded: chain B residue 1678 VAL Chi-restraints excluded: chain B residue 2163 LEU Chi-restraints excluded: chain B residue 2417 LEU Chi-restraints excluded: chain B residue 2535 LEU Chi-restraints excluded: chain B residue 2550 MET Chi-restraints excluded: chain B residue 2561 LEU Chi-restraints excluded: chain B residue 2667 MET Chi-restraints excluded: chain B residue 2946 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 554 random chunks: chunk 497 optimal weight: 6.9990 chunk 378 optimal weight: 20.0000 chunk 261 optimal weight: 0.0570 chunk 55 optimal weight: 2.9990 chunk 240 optimal weight: 6.9990 chunk 338 optimal weight: 20.0000 chunk 505 optimal weight: 3.9990 chunk 535 optimal weight: 0.9980 chunk 264 optimal weight: 0.6980 chunk 479 optimal weight: 0.7980 chunk 144 optimal weight: 0.9980 overall best weight: 0.7098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 700 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 945 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 996 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2066 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3014 GLN ** B 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 700 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 945 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 996 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1443 HIS ** B2066 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.1768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 45288 Z= 0.138 Angle : 0.488 13.362 61200 Z= 0.237 Chirality : 0.036 0.160 7020 Planarity : 0.003 0.048 7702 Dihedral : 4.048 89.419 6014 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 1.03 % Allowed : 8.88 % Favored : 90.09 % 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: 2.42 (0.12), residues: 5468 helix: 2.19 (0.08), residues: 3860 sheet: 1.03 (0.66), residues: 62 loop : 0.20 (0.16), residues: 1546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B2104 HIS 0.011 0.001 HIS B1334 PHE 0.021 0.001 PHE B1336 TYR 0.014 0.001 TYR A2437 ARG 0.006 0.000 ARG B1973 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10936 Ramachandran restraints generated. 5468 Oldfield, 0 Emsley, 5468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10936 Ramachandran restraints generated. 5468 Oldfield, 0 Emsley, 5468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 5036 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 292 time to evaluate : 5.184 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 617 MET cc_start: 0.5825 (ppp) cc_final: 0.5337 (ppp) REVERT: A 624 MET cc_start: 0.7325 (mmt) cc_final: 0.7007 (mmt) REVERT: A 652 PHE cc_start: 0.7965 (m-80) cc_final: 0.7744 (m-10) REVERT: A 1064 MET cc_start: 0.4782 (pmm) cc_final: 0.4397 (pmm) REVERT: A 1087 MET cc_start: 0.8661 (OUTLIER) cc_final: 0.8143 (mtp) REVERT: A 1095 ARG cc_start: 0.8196 (mpt180) cc_final: 0.7880 (mtt90) REVERT: A 1134 MET cc_start: 0.7157 (mtm) cc_final: 0.6574 (mmt) REVERT: A 1204 ARG cc_start: 0.8160 (mpp-170) cc_final: 0.7846 (mtm-85) REVERT: A 1210 MET cc_start: 0.9268 (mmp) cc_final: 0.9012 (mmm) REVERT: A 1308 MET cc_start: 0.7302 (tmm) cc_final: 0.7079 (tmm) REVERT: A 1321 MET cc_start: 0.6967 (pp-130) cc_final: 0.6671 (pp-130) REVERT: A 1349 MET cc_start: 0.8591 (tmm) cc_final: 0.8272 (tmm) REVERT: A 1425 GLN cc_start: 0.9444 (mm-40) cc_final: 0.9162 (mm-40) REVERT: A 1655 SER cc_start: 0.9316 (m) cc_final: 0.9112 (p) REVERT: A 1693 ASP cc_start: 0.8505 (t0) cc_final: 0.8179 (t70) REVERT: A 1836 ASP cc_start: 0.8799 (t70) cc_final: 0.8412 (t0) REVERT: A 2479 GLU cc_start: 0.8512 (tp30) cc_final: 0.8163 (tp30) REVERT: A 2668 GLU cc_start: 0.8652 (mm-30) cc_final: 0.8365 (pp20) REVERT: A 2935 MET cc_start: 0.9326 (OUTLIER) cc_final: 0.9117 (mmm) REVERT: B 617 MET cc_start: 0.5116 (OUTLIER) cc_final: 0.4708 (ppp) REVERT: B 624 MET cc_start: 0.7485 (mmt) cc_final: 0.7193 (mmt) REVERT: B 652 PHE cc_start: 0.7873 (m-80) cc_final: 0.7570 (m-10) REVERT: B 1064 MET cc_start: 0.4945 (OUTLIER) cc_final: 0.4545 (pmm) REVERT: B 1134 MET cc_start: 0.7165 (mtm) cc_final: 0.6586 (mmt) REVERT: B 1204 ARG cc_start: 0.8128 (mpp-170) cc_final: 0.7832 (mtm-85) REVERT: B 1210 MET cc_start: 0.9293 (mmp) cc_final: 0.9028 (mmm) REVERT: B 1308 MET cc_start: 0.7292 (tmm) cc_final: 0.7068 (tmm) REVERT: B 1321 MET cc_start: 0.7017 (pp-130) cc_final: 0.6702 (pp-130) REVERT: B 1434 LYS cc_start: 0.9493 (tptt) cc_final: 0.9053 (tppt) REVERT: B 1773 LYS cc_start: 0.9323 (tptp) cc_final: 0.9096 (tptt) REVERT: B 1836 ASP cc_start: 0.8851 (t70) cc_final: 0.8482 (t0) REVERT: B 2025 LYS cc_start: 0.8719 (mmpt) cc_final: 0.8518 (mmtm) REVERT: B 2091 TRP cc_start: 0.7261 (t-100) cc_final: 0.6983 (t-100) REVERT: B 2157 GLU cc_start: 0.8377 (mt-10) cc_final: 0.7907 (mm-30) REVERT: B 2239 MET cc_start: 0.5495 (mpp) cc_final: 0.5126 (mpp) REVERT: B 2280 GLN cc_start: 0.8826 (mm110) cc_final: 0.8543 (mm110) REVERT: B 2479 GLU cc_start: 0.8341 (tp30) cc_final: 0.8054 (tp30) REVERT: B 2561 LEU cc_start: 0.9587 (OUTLIER) cc_final: 0.9276 (mm) outliers start: 51 outliers final: 17 residues processed: 318 average time/residue: 1.5093 time to fit residues: 601.6927 Evaluate side-chains 296 residues out of total 5036 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 274 time to evaluate : 4.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 290 HIS Chi-restraints excluded: chain A residue 1087 MET Chi-restraints excluded: chain A residue 1351 LEU Chi-restraints excluded: chain A residue 1555 LEU Chi-restraints excluded: chain A residue 1678 VAL Chi-restraints excluded: chain A residue 2006 LEU Chi-restraints excluded: chain A residue 2235 MET Chi-restraints excluded: chain A residue 2405 MET Chi-restraints excluded: chain A residue 2935 MET Chi-restraints excluded: chain A residue 2946 LEU Chi-restraints excluded: chain A residue 3024 THR Chi-restraints excluded: chain B residue 290 HIS Chi-restraints excluded: chain B residue 617 MET Chi-restraints excluded: chain B residue 1064 MET Chi-restraints excluded: chain B residue 1662 THR Chi-restraints excluded: chain B residue 1668 LEU Chi-restraints excluded: chain B residue 1678 VAL Chi-restraints excluded: chain B residue 2535 LEU Chi-restraints excluded: chain B residue 2550 MET Chi-restraints excluded: chain B residue 2561 LEU Chi-restraints excluded: chain B residue 2667 MET Chi-restraints excluded: chain B residue 2946 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 554 random chunks: chunk 445 optimal weight: 0.0770 chunk 303 optimal weight: 40.0000 chunk 7 optimal weight: 5.9990 chunk 398 optimal weight: 8.9990 chunk 220 optimal weight: 7.9990 chunk 456 optimal weight: 0.0470 chunk 370 optimal weight: 8.9990 chunk 0 optimal weight: 60.0000 chunk 273 optimal weight: 6.9990 chunk 480 optimal weight: 0.5980 chunk 135 optimal weight: 0.0470 overall best weight: 1.3536 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 700 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 945 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 996 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2066 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2305 GLN ** B 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 700 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 945 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 996 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2066 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2210 GLN B2730 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.2245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 45288 Z= 0.183 Angle : 0.503 13.539 61200 Z= 0.245 Chirality : 0.036 0.175 7020 Planarity : 0.003 0.048 7702 Dihedral : 4.068 89.407 6014 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 1.18 % Allowed : 9.55 % Favored : 89.28 % 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: 2.42 (0.12), residues: 5468 helix: 2.20 (0.09), residues: 3870 sheet: 0.97 (0.65), residues: 62 loop : 0.15 (0.16), residues: 1536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B2104 HIS 0.005 0.001 HIS B 943 PHE 0.013 0.001 PHE A2143 TYR 0.013 0.001 TYR B1319 ARG 0.006 0.000 ARG B1973 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10936 Ramachandran restraints generated. 5468 Oldfield, 0 Emsley, 5468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10936 Ramachandran restraints generated. 5468 Oldfield, 0 Emsley, 5468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 5036 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 288 time to evaluate : 4.903 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 577 MET cc_start: 0.8440 (tmt) cc_final: 0.7057 (ptm) REVERT: A 578 LYS cc_start: 0.9193 (mmtt) cc_final: 0.8891 (mmtt) REVERT: A 617 MET cc_start: 0.5967 (ppp) cc_final: 0.5452 (ppp) REVERT: A 624 MET cc_start: 0.7349 (mmt) cc_final: 0.7034 (mmt) REVERT: A 652 PHE cc_start: 0.7908 (m-80) cc_final: 0.7704 (m-10) REVERT: A 900 MET cc_start: 0.5900 (OUTLIER) cc_final: 0.5622 (pmt) REVERT: A 1064 MET cc_start: 0.4814 (pmm) cc_final: 0.4410 (pmm) REVERT: A 1087 MET cc_start: 0.8719 (OUTLIER) cc_final: 0.8113 (mtp) REVERT: A 1134 MET cc_start: 0.7156 (mtm) cc_final: 0.6560 (mmt) REVERT: A 1204 ARG cc_start: 0.8185 (mpp-170) cc_final: 0.7876 (mtm-85) REVERT: A 1321 MET cc_start: 0.6975 (pp-130) cc_final: 0.6690 (pp-130) REVERT: A 1349 MET cc_start: 0.8645 (tmm) cc_final: 0.8360 (tmm) REVERT: A 1425 GLN cc_start: 0.9473 (mm-40) cc_final: 0.9180 (mm-40) REVERT: A 1655 SER cc_start: 0.9362 (m) cc_final: 0.9133 (p) REVERT: A 1693 ASP cc_start: 0.8497 (t0) cc_final: 0.8151 (t70) REVERT: A 1836 ASP cc_start: 0.8817 (t70) cc_final: 0.8383 (t0) REVERT: A 2239 MET cc_start: 0.6212 (mpp) cc_final: 0.5117 (mpp) REVERT: A 2479 GLU cc_start: 0.8556 (tp30) cc_final: 0.8200 (tp30) REVERT: B 437 MET cc_start: 0.7831 (mpt) cc_final: 0.7303 (pp-130) REVERT: B 617 MET cc_start: 0.5455 (OUTLIER) cc_final: 0.5044 (ppp) REVERT: B 624 MET cc_start: 0.7425 (mmt) cc_final: 0.7124 (mmt) REVERT: B 652 PHE cc_start: 0.7875 (m-80) cc_final: 0.7580 (m-10) REVERT: B 946 MET cc_start: 0.7927 (ptt) cc_final: 0.7258 (ttt) REVERT: B 1064 MET cc_start: 0.4994 (OUTLIER) cc_final: 0.4590 (pmm) REVERT: B 1134 MET cc_start: 0.7207 (mtm) cc_final: 0.6627 (mmt) REVERT: B 1204 ARG cc_start: 0.8155 (mpp-170) cc_final: 0.7859 (mtm-85) REVERT: B 1321 MET cc_start: 0.7035 (pp-130) cc_final: 0.6746 (pp-130) REVERT: B 1434 LYS cc_start: 0.9515 (tptt) cc_final: 0.9124 (tppt) REVERT: B 1657 MET cc_start: 0.8703 (OUTLIER) cc_final: 0.8497 (mtt) REVERT: B 1773 LYS cc_start: 0.9308 (tptp) cc_final: 0.9088 (tptt) REVERT: B 1836 ASP cc_start: 0.8841 (t70) cc_final: 0.8421 (t0) REVERT: B 2025 LYS cc_start: 0.8736 (mmpt) cc_final: 0.8532 (mmtm) REVERT: B 2086 TYR cc_start: 0.8622 (t80) cc_final: 0.8322 (t80) REVERT: B 2091 TRP cc_start: 0.7161 (t-100) cc_final: 0.6887 (t-100) REVERT: B 2157 GLU cc_start: 0.8509 (mt-10) cc_final: 0.8054 (mm-30) REVERT: B 2239 MET cc_start: 0.5942 (mpp) cc_final: 0.5420 (mpp) REVERT: B 2280 GLN cc_start: 0.8836 (mm110) cc_final: 0.8507 (mm110) REVERT: B 2479 GLU cc_start: 0.8393 (tp30) cc_final: 0.8044 (tp30) REVERT: B 2561 LEU cc_start: 0.9635 (OUTLIER) cc_final: 0.9282 (mm) outliers start: 58 outliers final: 23 residues processed: 322 average time/residue: 1.5624 time to fit residues: 626.3788 Evaluate side-chains 294 residues out of total 5036 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 265 time to evaluate : 4.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 1087 MET Chi-restraints excluded: chain A residue 1351 LEU Chi-restraints excluded: chain A residue 1399 THR Chi-restraints excluded: chain A residue 1452 ASP Chi-restraints excluded: chain A residue 1555 LEU Chi-restraints excluded: chain A residue 1678 VAL Chi-restraints excluded: chain A residue 1724 GLU Chi-restraints excluded: chain A residue 1792 ILE Chi-restraints excluded: chain A residue 2006 LEU Chi-restraints excluded: chain A residue 2235 MET Chi-restraints excluded: chain A residue 2935 MET Chi-restraints excluded: chain A residue 2946 LEU Chi-restraints excluded: chain A residue 3024 THR Chi-restraints excluded: chain B residue 290 HIS Chi-restraints excluded: chain B residue 617 MET Chi-restraints excluded: chain B residue 1064 MET Chi-restraints excluded: chain B residue 1399 THR Chi-restraints excluded: chain B residue 1657 MET Chi-restraints excluded: chain B residue 1668 LEU Chi-restraints excluded: chain B residue 1678 VAL Chi-restraints excluded: chain B residue 2006 LEU Chi-restraints excluded: chain B residue 2405 MET Chi-restraints excluded: chain B residue 2417 LEU Chi-restraints excluded: chain B residue 2535 LEU Chi-restraints excluded: chain B residue 2550 MET Chi-restraints excluded: chain B residue 2561 LEU Chi-restraints excluded: chain B residue 2935 MET Chi-restraints excluded: chain B residue 2946 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 554 random chunks: chunk 180 optimal weight: 0.0980 chunk 482 optimal weight: 2.9990 chunk 105 optimal weight: 5.9990 chunk 314 optimal weight: 20.0000 chunk 132 optimal weight: 2.9990 chunk 536 optimal weight: 2.9990 chunk 444 optimal weight: 0.5980 chunk 248 optimal weight: 0.9980 chunk 44 optimal weight: 8.9990 chunk 177 optimal weight: 8.9990 chunk 281 optimal weight: 40.0000 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 605 HIS ** A 700 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 996 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2066 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 605 HIS ** B 700 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 945 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 996 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2066 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2942 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8478 moved from start: 0.2631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 45288 Z= 0.192 Angle : 0.522 14.597 61200 Z= 0.253 Chirality : 0.036 0.215 7020 Planarity : 0.003 0.049 7702 Dihedral : 4.080 87.651 6014 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 1.20 % Allowed : 10.30 % Favored : 88.51 % 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: 2.46 (0.12), residues: 5468 helix: 2.23 (0.09), residues: 3854 sheet: 0.99 (0.65), residues: 62 loop : 0.17 (0.16), residues: 1552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A2104 HIS 0.005 0.001 HIS A2538 PHE 0.021 0.001 PHE B1336 TYR 0.015 0.001 TYR A1556 ARG 0.005 0.000 ARG B1973 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10936 Ramachandran restraints generated. 5468 Oldfield, 0 Emsley, 5468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10936 Ramachandran restraints generated. 5468 Oldfield, 0 Emsley, 5468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 5036 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 287 time to evaluate : 5.474 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 577 MET cc_start: 0.8377 (tmt) cc_final: 0.6928 (ptm) REVERT: A 578 LYS cc_start: 0.9140 (mmtt) cc_final: 0.8899 (mmtt) REVERT: A 617 MET cc_start: 0.6197 (ppp) cc_final: 0.5706 (ppp) REVERT: A 624 MET cc_start: 0.7308 (mmt) cc_final: 0.6984 (mmt) REVERT: A 652 PHE cc_start: 0.7864 (m-80) cc_final: 0.7627 (m-10) REVERT: A 946 MET cc_start: 0.7984 (ptt) cc_final: 0.7602 (ppp) REVERT: A 1064 MET cc_start: 0.4864 (pmm) cc_final: 0.4433 (pmm) REVERT: A 1087 MET cc_start: 0.8726 (OUTLIER) cc_final: 0.8063 (mtp) REVERT: A 1134 MET cc_start: 0.7196 (mtm) cc_final: 0.6585 (mmt) REVERT: A 1204 ARG cc_start: 0.8200 (mpp-170) cc_final: 0.7866 (mtm-85) REVERT: A 1210 MET cc_start: 0.9086 (mmm) cc_final: 0.8776 (mmm) REVERT: A 1214 LEU cc_start: 0.8790 (pt) cc_final: 0.8481 (tm) REVERT: A 1321 MET cc_start: 0.7006 (pp-130) cc_final: 0.6717 (pp-130) REVERT: A 1349 MET cc_start: 0.8750 (tmm) cc_final: 0.8499 (tmm) REVERT: A 1425 GLN cc_start: 0.9489 (mm-40) cc_final: 0.9209 (mm-40) REVERT: A 1655 SER cc_start: 0.9388 (m) cc_final: 0.9148 (p) REVERT: A 1693 ASP cc_start: 0.8500 (t0) cc_final: 0.8170 (t70) REVERT: A 1836 ASP cc_start: 0.8832 (t70) cc_final: 0.8384 (t0) REVERT: A 2025 LYS cc_start: 0.8751 (mmpt) cc_final: 0.8494 (mmtm) REVERT: A 2302 LYS cc_start: 0.9102 (OUTLIER) cc_final: 0.8788 (mtpp) REVERT: A 2479 GLU cc_start: 0.8586 (tp30) cc_final: 0.8179 (tp30) REVERT: B 437 MET cc_start: 0.7838 (mpt) cc_final: 0.7262 (pp-130) REVERT: B 617 MET cc_start: 0.5589 (OUTLIER) cc_final: 0.5148 (ppp) REVERT: B 624 MET cc_start: 0.7414 (mmt) cc_final: 0.7098 (mmt) REVERT: B 652 PHE cc_start: 0.7866 (m-80) cc_final: 0.7569 (m-10) REVERT: B 1064 MET cc_start: 0.5013 (OUTLIER) cc_final: 0.4591 (pmm) REVERT: B 1134 MET cc_start: 0.7205 (mtm) cc_final: 0.6614 (mmt) REVERT: B 1204 ARG cc_start: 0.8178 (mpp-170) cc_final: 0.7855 (mtm-85) REVERT: B 1210 MET cc_start: 0.9110 (mmm) cc_final: 0.8793 (mmm) REVERT: B 1214 LEU cc_start: 0.8857 (pt) cc_final: 0.8556 (tm) REVERT: B 1321 MET cc_start: 0.6998 (pp-130) cc_final: 0.6714 (pp-130) REVERT: B 1434 LYS cc_start: 0.9577 (tptt) cc_final: 0.9207 (tppt) REVERT: B 1668 LEU cc_start: 0.9433 (OUTLIER) cc_final: 0.9185 (mp) REVERT: B 1836 ASP cc_start: 0.8821 (t70) cc_final: 0.8389 (t0) REVERT: B 2086 TYR cc_start: 0.8676 (t80) cc_final: 0.8356 (t80) REVERT: B 2091 TRP cc_start: 0.7216 (t-100) cc_final: 0.6911 (t-100) REVERT: B 2157 GLU cc_start: 0.8608 (mt-10) cc_final: 0.8179 (mm-30) REVERT: B 2239 MET cc_start: 0.6379 (mpp) cc_final: 0.5988 (mpp) REVERT: B 2479 GLU cc_start: 0.8416 (tp30) cc_final: 0.8024 (tp30) REVERT: B 2531 MET cc_start: 0.7876 (tmm) cc_final: 0.6449 (ptp) REVERT: B 2561 LEU cc_start: 0.9660 (OUTLIER) cc_final: 0.9332 (mm) outliers start: 59 outliers final: 23 residues processed: 319 average time/residue: 1.4973 time to fit residues: 602.5929 Evaluate side-chains 292 residues out of total 5036 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 263 time to evaluate : 5.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1027 HIS Chi-restraints excluded: chain A residue 1087 MET Chi-restraints excluded: chain A residue 1351 LEU Chi-restraints excluded: chain A residue 1399 THR Chi-restraints excluded: chain A residue 1452 ASP Chi-restraints excluded: chain A residue 1555 LEU Chi-restraints excluded: chain A residue 1678 VAL Chi-restraints excluded: chain A residue 1724 GLU Chi-restraints excluded: chain A residue 1792 ILE Chi-restraints excluded: chain A residue 2006 LEU Chi-restraints excluded: chain A residue 2235 MET Chi-restraints excluded: chain A residue 2302 LYS Chi-restraints excluded: chain A residue 2935 MET Chi-restraints excluded: chain A residue 2946 LEU Chi-restraints excluded: chain A residue 3024 THR Chi-restraints excluded: chain B residue 617 MET Chi-restraints excluded: chain B residue 1027 HIS Chi-restraints excluded: chain B residue 1064 MET Chi-restraints excluded: chain B residue 1399 THR Chi-restraints excluded: chain B residue 1570 VAL Chi-restraints excluded: chain B residue 1609 THR Chi-restraints excluded: chain B residue 1668 LEU Chi-restraints excluded: chain B residue 1678 VAL Chi-restraints excluded: chain B residue 2006 LEU Chi-restraints excluded: chain B residue 2405 MET Chi-restraints excluded: chain B residue 2535 LEU Chi-restraints excluded: chain B residue 2561 LEU Chi-restraints excluded: chain B residue 2935 MET Chi-restraints excluded: chain B residue 2946 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 554 random chunks: chunk 516 optimal weight: 6.9990 chunk 60 optimal weight: 50.0000 chunk 305 optimal weight: 8.9990 chunk 391 optimal weight: 5.9990 chunk 303 optimal weight: 20.0000 chunk 451 optimal weight: 0.7980 chunk 299 optimal weight: 8.9990 chunk 533 optimal weight: 0.9990 chunk 334 optimal weight: 30.0000 chunk 325 optimal weight: 30.0000 chunk 246 optimal weight: 0.8980 overall best weight: 3.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 700 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 754 GLN A1188 HIS ** A1310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2066 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2241 ASN ** B 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 700 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 754 GLN ** B 945 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1188 HIS ** B1310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1380 HIS B1689 GLN ** B2066 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2070 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2197 GLN B2241 ASN B2802 GLN ** B2942 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8563 moved from start: 0.3374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.078 45288 Z= 0.328 Angle : 0.591 12.273 61200 Z= 0.290 Chirality : 0.039 0.188 7020 Planarity : 0.004 0.050 7702 Dihedral : 4.265 85.777 6014 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 1.30 % Allowed : 10.66 % Favored : 88.04 % 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: 2.27 (0.12), residues: 5468 helix: 2.09 (0.08), residues: 3860 sheet: 0.78 (0.65), residues: 62 loop : 0.09 (0.16), residues: 1546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B2491 HIS 0.007 0.001 HIS A1847 PHE 0.024 0.001 PHE A1336 TYR 0.016 0.001 TYR A1844 ARG 0.007 0.000 ARG A 717 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10936 Ramachandran restraints generated. 5468 Oldfield, 0 Emsley, 5468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10936 Ramachandran restraints generated. 5468 Oldfield, 0 Emsley, 5468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 5036 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 277 time to evaluate : 5.193 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 577 MET cc_start: 0.8378 (tmt) cc_final: 0.6976 (ptm) REVERT: A 578 LYS cc_start: 0.9138 (mmtt) cc_final: 0.8855 (mmtt) REVERT: A 617 MET cc_start: 0.6470 (ppp) cc_final: 0.5954 (ppp) REVERT: A 624 MET cc_start: 0.7329 (mmt) cc_final: 0.7031 (mmt) REVERT: A 652 PHE cc_start: 0.7817 (m-80) cc_final: 0.7604 (m-10) REVERT: A 900 MET cc_start: 0.5807 (OUTLIER) cc_final: 0.5555 (pmt) REVERT: A 946 MET cc_start: 0.7822 (ptt) cc_final: 0.7597 (ptt) REVERT: A 1064 MET cc_start: 0.4971 (pmm) cc_final: 0.4698 (pmm) REVERT: A 1087 MET cc_start: 0.8763 (OUTLIER) cc_final: 0.8045 (mtp) REVERT: A 1204 ARG cc_start: 0.8224 (mpp-170) cc_final: 0.7917 (mtm-85) REVERT: A 1308 MET cc_start: 0.7433 (tmm) cc_final: 0.7221 (pp-130) REVERT: A 1321 MET cc_start: 0.7184 (pp-130) cc_final: 0.6887 (pp-130) REVERT: A 1349 MET cc_start: 0.8882 (tmm) cc_final: 0.8638 (tmm) REVERT: A 1655 SER cc_start: 0.9470 (m) cc_final: 0.9140 (p) REVERT: A 1693 ASP cc_start: 0.8499 (t0) cc_final: 0.8152 (t70) REVERT: A 1836 ASP cc_start: 0.8934 (t70) cc_final: 0.8475 (t0) REVERT: A 2479 GLU cc_start: 0.8665 (tp30) cc_final: 0.8198 (tp30) REVERT: A 2531 MET cc_start: 0.7466 (ppp) cc_final: 0.6854 (ttp) REVERT: A 2532 MET cc_start: 0.7572 (OUTLIER) cc_final: 0.7257 (mmm) REVERT: B 617 MET cc_start: 0.5775 (OUTLIER) cc_final: 0.5299 (ppp) REVERT: B 624 MET cc_start: 0.7409 (mmt) cc_final: 0.7111 (mmt) REVERT: B 652 PHE cc_start: 0.7779 (m-80) cc_final: 0.7465 (m-10) REVERT: B 946 MET cc_start: 0.7782 (ptt) cc_final: 0.7114 (ptt) REVERT: B 1064 MET cc_start: 0.5054 (OUTLIER) cc_final: 0.4633 (pmm) REVERT: B 1134 MET cc_start: 0.7215 (mtm) cc_final: 0.6629 (mmt) REVERT: B 1204 ARG cc_start: 0.8209 (mpp-170) cc_final: 0.7910 (mtm-85) REVERT: B 1308 MET cc_start: 0.7458 (tmm) cc_final: 0.7249 (pp-130) REVERT: B 1321 MET cc_start: 0.7192 (pp-130) cc_final: 0.6906 (pp-130) REVERT: B 1668 LEU cc_start: 0.9487 (OUTLIER) cc_final: 0.9261 (mp) REVERT: B 1836 ASP cc_start: 0.8913 (t70) cc_final: 0.8470 (t0) REVERT: B 2086 TYR cc_start: 0.8775 (t80) cc_final: 0.8389 (t80) REVERT: B 2091 TRP cc_start: 0.7267 (t-100) cc_final: 0.6960 (t-100) REVERT: B 2157 GLU cc_start: 0.8678 (mt-10) cc_final: 0.8390 (mm-30) REVERT: B 2239 MET cc_start: 0.6884 (mpp) cc_final: 0.6016 (mpp) REVERT: B 2479 GLU cc_start: 0.8471 (tp30) cc_final: 0.8019 (tp30) REVERT: B 2561 LEU cc_start: 0.9714 (OUTLIER) cc_final: 0.9435 (mm) REVERT: B 2612 ARG cc_start: 0.8711 (OUTLIER) cc_final: 0.8411 (ptm160) outliers start: 64 outliers final: 21 residues processed: 315 average time/residue: 1.4406 time to fit residues: 569.2417 Evaluate side-chains 280 residues out of total 5036 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 251 time to evaluate : 5.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 1027 HIS Chi-restraints excluded: chain A residue 1087 MET Chi-restraints excluded: chain A residue 1351 LEU Chi-restraints excluded: chain A residue 1399 THR Chi-restraints excluded: chain A residue 1517 LEU Chi-restraints excluded: chain A residue 1555 LEU Chi-restraints excluded: chain A residue 1570 VAL Chi-restraints excluded: chain A residue 1678 VAL Chi-restraints excluded: chain A residue 1724 GLU Chi-restraints excluded: chain A residue 2006 LEU Chi-restraints excluded: chain A residue 2532 MET Chi-restraints excluded: chain A residue 2935 MET Chi-restraints excluded: chain A residue 2946 LEU Chi-restraints excluded: chain A residue 3024 THR Chi-restraints excluded: chain B residue 617 MET Chi-restraints excluded: chain B residue 1027 HIS Chi-restraints excluded: chain B residue 1064 MET Chi-restraints excluded: chain B residue 1399 THR Chi-restraints excluded: chain B residue 1452 ASP Chi-restraints excluded: chain B residue 1570 VAL Chi-restraints excluded: chain B residue 1668 LEU Chi-restraints excluded: chain B residue 1678 VAL Chi-restraints excluded: chain B residue 1693 ASP Chi-restraints excluded: chain B residue 2535 LEU Chi-restraints excluded: chain B residue 2561 LEU Chi-restraints excluded: chain B residue 2612 ARG Chi-restraints excluded: chain B residue 2935 MET Chi-restraints excluded: chain B residue 2946 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 554 random chunks: chunk 330 optimal weight: 10.0000 chunk 213 optimal weight: 2.9990 chunk 318 optimal weight: 6.9990 chunk 160 optimal weight: 0.0050 chunk 104 optimal weight: 7.9990 chunk 103 optimal weight: 5.9990 chunk 339 optimal weight: 10.0000 chunk 363 optimal weight: 20.0000 chunk 263 optimal weight: 0.8980 chunk 49 optimal weight: 40.0000 chunk 419 optimal weight: 0.8980 overall best weight: 2.1598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 700 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1188 HIS ** A1310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2066 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 133 ASN ** B 700 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 945 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1188 HIS ** B1310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2066 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8549 moved from start: 0.3527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 45288 Z= 0.239 Angle : 0.561 12.957 61200 Z= 0.271 Chirality : 0.038 0.249 7020 Planarity : 0.003 0.050 7702 Dihedral : 4.229 85.440 6014 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 0.87 % Allowed : 11.65 % Favored : 87.47 % 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: 2.32 (0.12), residues: 5468 helix: 2.13 (0.08), residues: 3870 sheet: 0.58 (0.64), residues: 62 loop : 0.11 (0.16), residues: 1536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A2104 HIS 0.004 0.001 HIS B2538 PHE 0.025 0.001 PHE B1336 TYR 0.012 0.001 TYR A 731 ARG 0.004 0.000 ARG B2613 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10936 Ramachandran restraints generated. 5468 Oldfield, 0 Emsley, 5468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10936 Ramachandran restraints generated. 5468 Oldfield, 0 Emsley, 5468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 5036 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 262 time to evaluate : 4.934 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 577 MET cc_start: 0.8422 (tmt) cc_final: 0.6973 (ptm) REVERT: A 578 LYS cc_start: 0.9126 (mmtt) cc_final: 0.8836 (mmtt) REVERT: A 617 MET cc_start: 0.6458 (ppp) cc_final: 0.5987 (ppp) REVERT: A 624 MET cc_start: 0.7320 (mmt) cc_final: 0.7030 (mmt) REVERT: A 652 PHE cc_start: 0.7794 (m-80) cc_final: 0.7584 (m-10) REVERT: A 900 MET cc_start: 0.5774 (OUTLIER) cc_final: 0.5543 (pmt) REVERT: A 1064 MET cc_start: 0.5018 (pmm) cc_final: 0.4746 (pmm) REVERT: A 1087 MET cc_start: 0.8779 (OUTLIER) cc_final: 0.8044 (mtp) REVERT: A 1204 ARG cc_start: 0.8179 (mpp-170) cc_final: 0.7839 (mtm-85) REVERT: A 1214 LEU cc_start: 0.8901 (pt) cc_final: 0.8602 (tm) REVERT: A 1308 MET cc_start: 0.7437 (tmm) cc_final: 0.7203 (pp-130) REVERT: A 1321 MET cc_start: 0.7189 (pp-130) cc_final: 0.6890 (pp-130) REVERT: A 1349 MET cc_start: 0.8902 (tmm) cc_final: 0.8612 (tmm) REVERT: A 1655 SER cc_start: 0.9427 (m) cc_final: 0.9142 (p) REVERT: A 1693 ASP cc_start: 0.8514 (t0) cc_final: 0.8172 (t70) REVERT: A 1836 ASP cc_start: 0.8861 (t70) cc_final: 0.8406 (t0) REVERT: A 2025 LYS cc_start: 0.8722 (mmpt) cc_final: 0.8199 (mmtp) REVERT: A 2479 GLU cc_start: 0.8680 (tp30) cc_final: 0.8219 (tp30) REVERT: A 2531 MET cc_start: 0.7491 (ppp) cc_final: 0.6843 (ttp) REVERT: A 2532 MET cc_start: 0.7970 (OUTLIER) cc_final: 0.7507 (mmm) REVERT: B 617 MET cc_start: 0.5911 (OUTLIER) cc_final: 0.5442 (ppp) REVERT: B 624 MET cc_start: 0.7415 (mmt) cc_final: 0.7104 (mmt) REVERT: B 652 PHE cc_start: 0.7760 (m-80) cc_final: 0.7502 (m-10) REVERT: B 946 MET cc_start: 0.7791 (ptt) cc_final: 0.7142 (ptt) REVERT: B 1064 MET cc_start: 0.5237 (OUTLIER) cc_final: 0.4811 (pmm) REVERT: B 1134 MET cc_start: 0.7199 (mtm) cc_final: 0.6564 (mmt) REVERT: B 1204 ARG cc_start: 0.8185 (mpp-170) cc_final: 0.7856 (mtm-85) REVERT: B 1214 LEU cc_start: 0.8967 (pt) cc_final: 0.8655 (tm) REVERT: B 1308 MET cc_start: 0.7461 (tmm) cc_final: 0.7232 (pp-130) REVERT: B 1321 MET cc_start: 0.7180 (pp-130) cc_final: 0.6789 (pp-130) REVERT: B 1836 ASP cc_start: 0.8876 (t70) cc_final: 0.8459 (t0) REVERT: B 2006 LEU cc_start: 0.9202 (tp) cc_final: 0.8994 (tm) REVERT: B 2025 LYS cc_start: 0.8864 (mmpt) cc_final: 0.8385 (mmtp) REVERT: B 2157 GLU cc_start: 0.8695 (mt-10) cc_final: 0.8486 (mm-30) REVERT: B 2479 GLU cc_start: 0.8461 (tp30) cc_final: 0.8003 (tp30) REVERT: B 2531 MET cc_start: 0.7686 (ppp) cc_final: 0.6780 (ptp) REVERT: B 2561 LEU cc_start: 0.9716 (OUTLIER) cc_final: 0.9393 (mm) REVERT: B 2612 ARG cc_start: 0.8642 (OUTLIER) cc_final: 0.8391 (ptm160) outliers start: 43 outliers final: 20 residues processed: 288 average time/residue: 1.4889 time to fit residues: 541.4400 Evaluate side-chains 280 residues out of total 5036 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 253 time to evaluate : 4.914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 1027 HIS Chi-restraints excluded: chain A residue 1087 MET Chi-restraints excluded: chain A residue 1351 LEU Chi-restraints excluded: chain A residue 1399 THR Chi-restraints excluded: chain A residue 1449 LEU Chi-restraints excluded: chain A residue 1452 ASP Chi-restraints excluded: chain A residue 1517 LEU Chi-restraints excluded: chain A residue 1555 LEU Chi-restraints excluded: chain A residue 1570 VAL Chi-restraints excluded: chain A residue 1678 VAL Chi-restraints excluded: chain A residue 1724 GLU Chi-restraints excluded: chain A residue 2006 LEU Chi-restraints excluded: chain A residue 2532 MET Chi-restraints excluded: chain A residue 2946 LEU Chi-restraints excluded: chain A residue 3024 THR Chi-restraints excluded: chain B residue 617 MET Chi-restraints excluded: chain B residue 1027 HIS Chi-restraints excluded: chain B residue 1064 MET Chi-restraints excluded: chain B residue 1399 THR Chi-restraints excluded: chain B residue 1570 VAL Chi-restraints excluded: chain B residue 1678 VAL Chi-restraints excluded: chain B residue 2535 LEU Chi-restraints excluded: chain B residue 2561 LEU Chi-restraints excluded: chain B residue 2612 ARG Chi-restraints excluded: chain B residue 2656 LEU Chi-restraints excluded: chain B residue 2946 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 554 random chunks: chunk 485 optimal weight: 0.6980 chunk 511 optimal weight: 2.9990 chunk 466 optimal weight: 7.9990 chunk 497 optimal weight: 0.8980 chunk 299 optimal weight: 9.9990 chunk 216 optimal weight: 0.8980 chunk 390 optimal weight: 6.9990 chunk 152 optimal weight: 0.6980 chunk 449 optimal weight: 0.8980 chunk 470 optimal weight: 0.0870 chunk 495 optimal weight: 4.9990 overall best weight: 0.6558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 133 ASN ** A 700 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 996 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1188 HIS ** A1310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2066 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2305 GLN ** B 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 133 ASN ** B 700 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 945 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1188 HIS ** B1310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1518 HIS ** B2066 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8520 moved from start: 0.3554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 45288 Z= 0.149 Angle : 0.548 15.750 61200 Z= 0.261 Chirality : 0.036 0.258 7020 Planarity : 0.003 0.050 7702 Dihedral : 4.167 82.707 6014 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 0.69 % Allowed : 11.98 % Favored : 87.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.38 (0.12), residues: 5468 helix: 2.18 (0.09), residues: 3866 sheet: 0.73 (0.66), residues: 62 loop : 0.12 (0.16), residues: 1540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A2104 HIS 0.004 0.001 HIS B1847 PHE 0.024 0.001 PHE A1336 TYR 0.017 0.001 TYR B 731 ARG 0.003 0.000 ARG B2136 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10936 Ramachandran restraints generated. 5468 Oldfield, 0 Emsley, 5468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10936 Ramachandran restraints generated. 5468 Oldfield, 0 Emsley, 5468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 5036 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 271 time to evaluate : 5.111 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 577 MET cc_start: 0.8414 (tmt) cc_final: 0.6960 (ptm) REVERT: A 578 LYS cc_start: 0.9134 (mmtt) cc_final: 0.8842 (mmtt) REVERT: A 617 MET cc_start: 0.6441 (ppp) cc_final: 0.5972 (ppp) REVERT: A 624 MET cc_start: 0.7338 (mmt) cc_final: 0.7057 (mmt) REVERT: A 652 PHE cc_start: 0.7779 (m-80) cc_final: 0.7562 (m-10) REVERT: A 900 MET cc_start: 0.5868 (OUTLIER) cc_final: 0.5604 (pmt) REVERT: A 1064 MET cc_start: 0.5013 (pmm) cc_final: 0.4794 (pmm) REVERT: A 1087 MET cc_start: 0.8760 (OUTLIER) cc_final: 0.8025 (mtp) REVERT: A 1204 ARG cc_start: 0.8196 (mpp-170) cc_final: 0.7836 (mtm-85) REVERT: A 1214 LEU cc_start: 0.8871 (pt) cc_final: 0.8579 (tm) REVERT: A 1308 MET cc_start: 0.7419 (tmm) cc_final: 0.7186 (pp-130) REVERT: A 1321 MET cc_start: 0.7139 (pp-130) cc_final: 0.6739 (pp-130) REVERT: A 1349 MET cc_start: 0.8898 (tmm) cc_final: 0.8617 (tmm) REVERT: A 1655 SER cc_start: 0.9412 (m) cc_final: 0.9161 (p) REVERT: A 1693 ASP cc_start: 0.8508 (t0) cc_final: 0.8175 (t70) REVERT: A 1724 GLU cc_start: 0.8172 (OUTLIER) cc_final: 0.7906 (mp0) REVERT: A 1836 ASP cc_start: 0.8783 (t70) cc_final: 0.8354 (t0) REVERT: A 2479 GLU cc_start: 0.8653 (tp30) cc_final: 0.8198 (tp30) REVERT: A 2532 MET cc_start: 0.7821 (OUTLIER) cc_final: 0.7483 (mmm) REVERT: B 437 MET cc_start: 0.7798 (mpp) cc_final: 0.7242 (pp-130) REVERT: B 617 MET cc_start: 0.5894 (OUTLIER) cc_final: 0.5441 (ppp) REVERT: B 624 MET cc_start: 0.7392 (mmt) cc_final: 0.7116 (mmt) REVERT: B 652 PHE cc_start: 0.7790 (m-80) cc_final: 0.7467 (m-10) REVERT: B 1064 MET cc_start: 0.5209 (OUTLIER) cc_final: 0.4777 (pmm) REVERT: B 1204 ARG cc_start: 0.8171 (mpp-170) cc_final: 0.7818 (mtm-85) REVERT: B 1214 LEU cc_start: 0.8969 (pt) cc_final: 0.8673 (tm) REVERT: B 1308 MET cc_start: 0.7422 (tmm) cc_final: 0.7190 (pp-130) REVERT: B 1321 MET cc_start: 0.7135 (pp-130) cc_final: 0.6745 (pp-130) REVERT: B 1655 SER cc_start: 0.9505 (m) cc_final: 0.9136 (p) REVERT: B 1836 ASP cc_start: 0.8811 (t70) cc_final: 0.8416 (t0) REVERT: B 2025 LYS cc_start: 0.8850 (mmpt) cc_final: 0.8361 (mmtp) REVERT: B 2239 MET cc_start: 0.6066 (mpp) cc_final: 0.5836 (mpp) REVERT: B 2479 GLU cc_start: 0.8463 (tp30) cc_final: 0.7999 (tp30) REVERT: B 2532 MET cc_start: 0.7680 (OUTLIER) cc_final: 0.7218 (mmm) REVERT: B 2561 LEU cc_start: 0.9708 (OUTLIER) cc_final: 0.9423 (mm) REVERT: B 2612 ARG cc_start: 0.8579 (OUTLIER) cc_final: 0.8322 (ptm160) outliers start: 34 outliers final: 15 residues processed: 288 average time/residue: 1.5238 time to fit residues: 557.0381 Evaluate side-chains 279 residues out of total 5036 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 255 time to evaluate : 5.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 1027 HIS Chi-restraints excluded: chain A residue 1087 MET Chi-restraints excluded: chain A residue 1351 LEU Chi-restraints excluded: chain A residue 1517 LEU Chi-restraints excluded: chain A residue 1555 LEU Chi-restraints excluded: chain A residue 1678 VAL Chi-restraints excluded: chain A residue 1702 LEU Chi-restraints excluded: chain A residue 1724 GLU Chi-restraints excluded: chain A residue 2532 MET Chi-restraints excluded: chain A residue 2946 LEU Chi-restraints excluded: chain A residue 3024 THR Chi-restraints excluded: chain B residue 617 MET Chi-restraints excluded: chain B residue 1027 HIS Chi-restraints excluded: chain B residue 1064 MET Chi-restraints excluded: chain B residue 1448 LEU Chi-restraints excluded: chain B residue 1449 LEU Chi-restraints excluded: chain B residue 1678 VAL Chi-restraints excluded: chain B residue 2532 MET Chi-restraints excluded: chain B residue 2535 LEU Chi-restraints excluded: chain B residue 2561 LEU Chi-restraints excluded: chain B residue 2612 ARG Chi-restraints excluded: chain B residue 2656 LEU Chi-restraints excluded: chain B residue 2946 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 554 random chunks: chunk 326 optimal weight: 9.9990 chunk 526 optimal weight: 0.8980 chunk 321 optimal weight: 20.0000 chunk 249 optimal weight: 2.9990 chunk 365 optimal weight: 6.9990 chunk 551 optimal weight: 1.9990 chunk 507 optimal weight: 0.9990 chunk 439 optimal weight: 0.7980 chunk 45 optimal weight: 8.9990 chunk 339 optimal weight: 0.1980 chunk 269 optimal weight: 0.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 133 ASN ** A 700 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 996 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1188 HIS ** A1310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2066 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2269 GLN ** B 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 133 ASN ** B 700 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 945 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1188 HIS ** B1310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2066 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2730 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8514 moved from start: 0.3627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 45288 Z= 0.148 Angle : 0.555 13.162 61200 Z= 0.262 Chirality : 0.036 0.262 7020 Planarity : 0.003 0.050 7702 Dihedral : 4.116 85.436 6014 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 0.53 % Allowed : 12.59 % Favored : 86.89 % 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: 2.41 (0.12), residues: 5468 helix: 2.18 (0.09), residues: 3872 sheet: 0.84 (0.67), residues: 62 loop : 0.19 (0.16), residues: 1534 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP B2091 HIS 0.004 0.001 HIS B2538 PHE 0.015 0.001 PHE A1336 TYR 0.019 0.001 TYR A 731 ARG 0.002 0.000 ARG B2136 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10936 Ramachandran restraints generated. 5468 Oldfield, 0 Emsley, 5468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10936 Ramachandran restraints generated. 5468 Oldfield, 0 Emsley, 5468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 5036 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 269 time to evaluate : 5.094 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 577 MET cc_start: 0.8394 (tmt) cc_final: 0.6951 (ptm) REVERT: A 578 LYS cc_start: 0.9132 (mmtt) cc_final: 0.8823 (mmtt) REVERT: A 617 MET cc_start: 0.6453 (ppp) cc_final: 0.6075 (ppp) REVERT: A 624 MET cc_start: 0.7357 (mmt) cc_final: 0.7099 (mmt) REVERT: A 652 PHE cc_start: 0.7791 (m-80) cc_final: 0.7579 (m-10) REVERT: A 1064 MET cc_start: 0.5056 (pmm) cc_final: 0.4840 (pmm) REVERT: A 1087 MET cc_start: 0.8770 (OUTLIER) cc_final: 0.8018 (mtp) REVERT: A 1204 ARG cc_start: 0.8187 (mpp-170) cc_final: 0.7820 (mtm-85) REVERT: A 1214 LEU cc_start: 0.8874 (pt) cc_final: 0.8580 (tm) REVERT: A 1308 MET cc_start: 0.7390 (tmm) cc_final: 0.7149 (pp-130) REVERT: A 1321 MET cc_start: 0.7118 (pp-130) cc_final: 0.6724 (pp-130) REVERT: A 1349 MET cc_start: 0.8969 (tmm) cc_final: 0.8693 (tmm) REVERT: A 1655 SER cc_start: 0.9409 (m) cc_final: 0.9167 (p) REVERT: A 1693 ASP cc_start: 0.8487 (t0) cc_final: 0.8150 (t70) REVERT: A 1836 ASP cc_start: 0.8744 (t70) cc_final: 0.8355 (t0) REVERT: A 2025 LYS cc_start: 0.8767 (mmpt) cc_final: 0.8508 (mmtm) REVERT: A 2479 GLU cc_start: 0.8636 (tp30) cc_final: 0.8201 (tp30) REVERT: A 2532 MET cc_start: 0.7822 (tpt) cc_final: 0.7418 (mmm) REVERT: B 437 MET cc_start: 0.7741 (mpp) cc_final: 0.7162 (pp-130) REVERT: B 617 MET cc_start: 0.5963 (OUTLIER) cc_final: 0.5520 (ppp) REVERT: B 624 MET cc_start: 0.7450 (mmt) cc_final: 0.7176 (mmt) REVERT: B 1064 MET cc_start: 0.5214 (OUTLIER) cc_final: 0.4776 (pmm) REVERT: B 1134 MET cc_start: 0.7128 (mtm) cc_final: 0.6535 (mmt) REVERT: B 1204 ARG cc_start: 0.8184 (mpp-170) cc_final: 0.7821 (mtm-85) REVERT: B 1214 LEU cc_start: 0.8983 (pt) cc_final: 0.8692 (tm) REVERT: B 1308 MET cc_start: 0.7415 (tmm) cc_final: 0.7178 (pp-130) REVERT: B 1321 MET cc_start: 0.7108 (pp-130) cc_final: 0.6723 (pp-130) REVERT: B 1655 SER cc_start: 0.9509 (m) cc_final: 0.9127 (p) REVERT: B 1836 ASP cc_start: 0.8761 (t70) cc_final: 0.8396 (t0) REVERT: B 2239 MET cc_start: 0.6103 (mpp) cc_final: 0.5892 (mpp) REVERT: B 2479 GLU cc_start: 0.8478 (tp30) cc_final: 0.7995 (tp30) REVERT: B 2532 MET cc_start: 0.7796 (OUTLIER) cc_final: 0.7307 (mmm) REVERT: B 2561 LEU cc_start: 0.9701 (OUTLIER) cc_final: 0.9392 (mm) outliers start: 26 outliers final: 16 residues processed: 284 average time/residue: 1.5208 time to fit residues: 545.3824 Evaluate side-chains 278 residues out of total 5036 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 257 time to evaluate : 5.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1027 HIS Chi-restraints excluded: chain A residue 1087 MET Chi-restraints excluded: chain A residue 1351 LEU Chi-restraints excluded: chain A residue 1517 LEU Chi-restraints excluded: chain A residue 1555 LEU Chi-restraints excluded: chain A residue 1678 VAL Chi-restraints excluded: chain A residue 1702 LEU Chi-restraints excluded: chain A residue 1724 GLU Chi-restraints excluded: chain A residue 2946 LEU Chi-restraints excluded: chain A residue 3024 THR Chi-restraints excluded: chain B residue 617 MET Chi-restraints excluded: chain B residue 1027 HIS Chi-restraints excluded: chain B residue 1064 MET Chi-restraints excluded: chain B residue 1449 LEU Chi-restraints excluded: chain B residue 1678 VAL Chi-restraints excluded: chain B residue 1693 ASP Chi-restraints excluded: chain B residue 2006 LEU Chi-restraints excluded: chain B residue 2532 MET Chi-restraints excluded: chain B residue 2535 LEU Chi-restraints excluded: chain B residue 2561 LEU Chi-restraints excluded: chain B residue 2946 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 554 random chunks: chunk 349 optimal weight: 40.0000 chunk 468 optimal weight: 1.9990 chunk 134 optimal weight: 2.9990 chunk 405 optimal weight: 5.9990 chunk 64 optimal weight: 6.9990 chunk 122 optimal weight: 0.9980 chunk 440 optimal weight: 0.9990 chunk 184 optimal weight: 0.6980 chunk 452 optimal weight: 0.0980 chunk 55 optimal weight: 3.9990 chunk 81 optimal weight: 4.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 700 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 996 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1188 HIS ** A1310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2066 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 133 ASN ** B 700 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 945 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 996 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1188 HIS ** B1310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2066 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2241 ASN B2412 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4413 r_free = 0.4413 target = 0.136224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.076034 restraints weight = 119225.525| |-----------------------------------------------------------------------------| r_work (start): 0.3225 rms_B_bonded: 3.27 r_work: 0.3039 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8551 moved from start: 0.3672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 45288 Z= 0.160 Angle : 0.561 13.489 61200 Z= 0.265 Chirality : 0.036 0.272 7020 Planarity : 0.003 0.050 7702 Dihedral : 4.110 86.178 6014 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 0.61 % Allowed : 12.67 % Favored : 86.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.40 (0.12), residues: 5468 helix: 2.17 (0.09), residues: 3872 sheet: 0.81 (0.67), residues: 62 loop : 0.18 (0.16), residues: 1534 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP B2091 HIS 0.006 0.001 HIS B 943 PHE 0.014 0.001 PHE B 897 TYR 0.016 0.001 TYR A 731 ARG 0.004 0.000 ARG B2613 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15539.92 seconds wall clock time: 278 minutes 9.97 seconds (16689.97 seconds total)