Starting phenix.real_space_refine on Sat Jul 20 22:56:07 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ask_11895/07_2024/7ask_11895_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ask_11895/07_2024/7ask_11895.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ask_11895/07_2024/7ask_11895.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ask_11895/07_2024/7ask_11895.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ask_11895/07_2024/7ask_11895_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ask_11895/07_2024/7ask_11895_neut.cif" } resolution = 4.3 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= 0.011 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 2 5.49 5 Mg 1 5.21 5 S 66 5.16 5 C 7744 2.51 5 N 2170 2.21 5 O 2302 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "F ASP 154": "OD1" <-> "OD2" Residue "F ASP 167": "OD1" <-> "OD2" Residue "F ARG 190": "NH1" <-> "NH2" Residue "F ARG 193": "NH1" <-> "NH2" Residue "F PHE 214": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 277": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 301": "OE1" <-> "OE2" Residue "F TYR 305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 805": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 880": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 945": "OE1" <-> "OE2" Residue "F ARG 1011": "NH1" <-> "NH2" Residue "F GLU 1016": "OE1" <-> "OE2" Residue "F ARG 1030": "NH1" <-> "NH2" Residue "F ARG 1039": "NH1" <-> "NH2" Residue "F PHE 1054": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 1057": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 1065": "NH1" <-> "NH2" Residue "F ARG 1066": "NH1" <-> "NH2" Residue "F TYR 1074": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 1079": "NH1" <-> "NH2" Residue "F ARG 1092": "NH1" <-> "NH2" Residue "F ARG 1103": "NH1" <-> "NH2" Residue "F GLU 1132": "OE1" <-> "OE2" Residue "F TYR 1149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 1169": "NH1" <-> "NH2" Residue "F PHE 1178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 1215": "OD1" <-> "OD2" Residue "F PHE 1216": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 1239": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 1289": "OE1" <-> "OE2" Residue "F PHE 1301": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 1331": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 1341": "NH1" <-> "NH2" Residue "F ARG 1343": "NH1" <-> "NH2" Residue "F GLU 1348": "OE1" <-> "OE2" Residue "F ARG 1391": "NH1" <-> "NH2" Residue "F GLU 1449": "OE1" <-> "OE2" Residue "F ARG 1476": "NH1" <-> "NH2" Residue "F ARG 1484": "NH1" <-> "NH2" Residue "F ARG 1489": "NH1" <-> "NH2" Residue "F ASP 1580": "OD1" <-> "OD2" Residue "F PHE 1583": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 1623": "NH1" <-> "NH2" Residue "F ARG 1627": "NH1" <-> "NH2" Residue "F ARG 1646": "NH1" <-> "NH2" Residue "F ARG 1649": "NH1" <-> "NH2" Residue "F ARG 1651": "NH1" <-> "NH2" Residue "F PHE 1657": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 1671": "NH1" <-> "NH2" Residue "F ARG 1688": "NH1" <-> "NH2" Residue "F ARG 1697": "NH1" <-> "NH2" Residue "F PHE 1707": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 1739": "NH1" <-> "NH2" Residue "F ASP 1745": "OD1" <-> "OD2" Residue "F ARG 1750": "NH1" <-> "NH2" Residue "F ARG 1768": "NH1" <-> "NH2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 12285 Number of models: 1 Model: "" Number of chains: 2 Chain: "F" Number of atoms: 12257 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1523, 12257 Classifications: {'peptide': 1523} Link IDs: {'CIS': 45, 'PCIS': 3, 'PTRANS': 50, 'TRANS': 1424} Chain breaks: 15 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 6.69, per 1000 atoms: 0.54 Number of scatterers: 12285 At special positions: 0 Unit cell: (156.96, 114.45, 160.23, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 66 16.00 P 2 15.00 Mg 1 11.99 O 2302 8.00 N 2170 7.00 C 7744 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: 4.04 Conformation dependent library (CDL) restraints added in 1.9 seconds 2978 Ramachandran restraints generated. 1489 Oldfield, 0 Emsley, 1489 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input volumes are d-peptide like pdb=" CB TYR F 296 " pdb=" CB TYR F 305 " pdb=" CB ILE F1155 " pdb=" CB ARG F1697 " Number of C-beta restraints generated: 2870 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 3 sheets defined 47.4% alpha, 3.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.24 Creating SS restraints... Processing helix chain 'F' and resid 1 through 16 removed outlier: 4.871A pdb=" N ILE F 9 " --> pdb=" O TYR F 5 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N ALA F 10 " --> pdb=" O ARG F 6 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N GLU F 14 " --> pdb=" O ALA F 10 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N PHE F 15 " --> pdb=" O ILE F 11 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N LEU F 16 " --> pdb=" O PHE F 12 " (cutoff:3.500A) Processing helix chain 'F' and resid 31 through 38 removed outlier: 3.631A pdb=" N THR F 35 " --> pdb=" O GLY F 31 " (cutoff:3.500A) Processing helix chain 'F' and resid 59 through 75 removed outlier: 3.947A pdb=" N ASP F 64 " --> pdb=" O ALA F 60 " (cutoff:3.500A) removed outlier: 5.021A pdb=" N ALA F 65 " --> pdb=" O ARG F 61 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ASN F 71 " --> pdb=" O ARG F 67 " (cutoff:3.500A) Processing helix chain 'F' and resid 92 through 109 removed outlier: 3.923A pdb=" N LEU F 96 " --> pdb=" O GLU F 92 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLY F 103 " --> pdb=" O LYS F 99 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N ALA F 104 " --> pdb=" O PHE F 100 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ALA F 106 " --> pdb=" O ILE F 102 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N ALA F 107 " --> pdb=" O GLY F 103 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N LYS F 108 " --> pdb=" O ALA F 104 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ASN F 109 " --> pdb=" O LEU F 105 " (cutoff:3.500A) Processing helix chain 'F' and resid 111 through 130 removed outlier: 3.822A pdb=" N VAL F 115 " --> pdb=" O GLU F 111 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N GLU F 119 " --> pdb=" O VAL F 115 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N VAL F 125 " --> pdb=" O LEU F 121 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N TYR F 129 " --> pdb=" O VAL F 125 " (cutoff:3.500A) Processing helix chain 'F' and resid 140 through 144 removed outlier: 3.584A pdb=" N LEU F 143 " --> pdb=" O PHE F 140 " (cutoff:3.500A) Processing helix chain 'F' and resid 153 through 161 Processing helix chain 'F' and resid 177 through 188 removed outlier: 3.783A pdb=" N GLN F 181 " --> pdb=" O ILE F 177 " (cutoff:3.500A) Processing helix chain 'F' and resid 215 through 228 removed outlier: 4.210A pdb=" N GLU F 228 " --> pdb=" O MET F 224 " (cutoff:3.500A) Processing helix chain 'F' and resid 249 through 256 removed outlier: 4.032A pdb=" N TRP F 255 " --> pdb=" O TYR F 251 " (cutoff:3.500A) Processing helix chain 'F' and resid 271 through 287 removed outlier: 3.579A pdb=" N GLN F 275 " --> pdb=" O LEU F 271 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ALA F 276 " --> pdb=" O ASN F 272 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N PHE F 277 " --> pdb=" O PRO F 273 " (cutoff:3.500A) Proline residue: F 281 - end of helix Processing helix chain 'F' and resid 671 through 675 Processing helix chain 'F' and resid 686 through 695 removed outlier: 3.842A pdb=" N HIS F 691 " --> pdb=" O VAL F 687 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N ALA F 692 " --> pdb=" O ASN F 688 " (cutoff:3.500A) Processing helix chain 'F' and resid 738 through 764 removed outlier: 4.540A pdb=" N ASP F 744 " --> pdb=" O THR F 740 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ILE F 749 " --> pdb=" O ARG F 745 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ILE F 752 " --> pdb=" O SER F 748 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLN F 761 " --> pdb=" O LYS F 757 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N GLU F 762 " --> pdb=" O ARG F 758 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N PHE F 764 " --> pdb=" O SER F 760 " (cutoff:3.500A) Processing helix chain 'F' and resid 776 through 779 Processing helix chain 'F' and resid 780 through 792 removed outlier: 3.798A pdb=" N LEU F 784 " --> pdb=" O THR F 780 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLU F 787 " --> pdb=" O PRO F 783 " (cutoff:3.500A) Processing helix chain 'F' and resid 810 through 815 Processing helix chain 'F' and resid 816 through 823 removed outlier: 3.782A pdb=" N LYS F 820 " --> pdb=" O LYS F 816 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ASP F 823 " --> pdb=" O SER F 819 " (cutoff:3.500A) Processing helix chain 'F' and resid 836 through 845 removed outlier: 3.680A pdb=" N PHE F 840 " --> pdb=" O VAL F 836 " (cutoff:3.500A) Processing helix chain 'F' and resid 853 through 860 removed outlier: 3.587A pdb=" N ARG F 858 " --> pdb=" O LEU F 854 " (cutoff:3.500A) Processing helix chain 'F' and resid 866 through 901 removed outlier: 3.909A pdb=" N LEU F 873 " --> pdb=" O ALA F 869 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LEU F 878 " --> pdb=" O ARG F 874 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N PHE F 880 " --> pdb=" O VAL F 876 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N HIS F 884 " --> pdb=" O PHE F 880 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LEU F 889 " --> pdb=" O ILE F 885 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N VAL F 893 " --> pdb=" O LEU F 889 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N LEU F 896 " --> pdb=" O ARG F 892 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N LEU F 898 " --> pdb=" O VAL F 894 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N GLU F 899 " --> pdb=" O LYS F 895 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ASN F 900 " --> pdb=" O LEU F 896 " (cutoff:3.500A) Processing helix chain 'F' and resid 901 through 907 removed outlier: 3.866A pdb=" N ARG F 905 " --> pdb=" O TRP F 901 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLU F 906 " --> pdb=" O ARG F 902 " (cutoff:3.500A) Processing helix chain 'F' and resid 921 through 932 Processing helix chain 'F' and resid 946 through 955 Processing helix chain 'F' and resid 962 through 976 removed outlier: 3.536A pdb=" N LYS F 966 " --> pdb=" O SER F 962 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ASP F 968 " --> pdb=" O TYR F 964 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N GLN F 969 " --> pdb=" O ASN F 965 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N CYS F 970 " --> pdb=" O LYS F 966 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N ARG F 973 " --> pdb=" O GLN F 969 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N TRP F 974 " --> pdb=" O CYS F 970 " (cutoff:3.500A) Processing helix chain 'F' and resid 1001 through 1007 removed outlier: 3.855A pdb=" N MET F1005 " --> pdb=" O GLN F1001 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N HIS F1007 " --> pdb=" O ILE F1003 " (cutoff:3.500A) Processing helix chain 'F' and resid 1028 through 1037 removed outlier: 4.968A pdb=" N ASP F1034 " --> pdb=" O ARG F1030 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ILE F1035 " --> pdb=" O GLU F1031 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N VAL F1036 " --> pdb=" O LEU F1032 " (cutoff:3.500A) Processing helix chain 'F' and resid 1053 through 1055 No H-bonds generated for 'chain 'F' and resid 1053 through 1055' Processing helix chain 'F' and resid 1056 through 1057 No H-bonds generated for 'chain 'F' and resid 1056 through 1057' Processing helix chain 'F' and resid 1059 through 1066 removed outlier: 3.836A pdb=" N ARG F1066 " --> pdb=" O LYS F1062 " (cutoff:3.500A) Processing helix chain 'F' and resid 1082 through 1092 removed outlier: 4.597A pdb=" N VAL F1086 " --> pdb=" O ILE F1082 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ARG F1092 " --> pdb=" O ASP F1088 " (cutoff:3.500A) Processing helix chain 'F' and resid 1127 through 1137 Processing helix chain 'F' and resid 1140 through 1145 removed outlier: 3.715A pdb=" N VAL F1144 " --> pdb=" O TYR F1140 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLU F1145 " --> pdb=" O THR F1141 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 1140 through 1145' Processing helix chain 'F' and resid 1155 through 1162 removed outlier: 3.714A pdb=" N ASN F1161 " --> pdb=" O SER F1157 " (cutoff:3.500A) Processing helix chain 'F' and resid 1166 through 1171 removed outlier: 3.613A pdb=" N ILE F1170 " --> pdb=" O VAL F1166 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU F1171 " --> pdb=" O TRP F1167 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 1166 through 1171' Processing helix chain 'F' and resid 1188 through 1206 removed outlier: 3.509A pdb=" N TRP F1194 " --> pdb=" O GLN F1190 " (cutoff:3.500A) Processing helix chain 'F' and resid 1271 through 1278 removed outlier: 3.947A pdb=" N GLN F1276 " --> pdb=" O ALA F1272 " (cutoff:3.500A) Processing helix chain 'F' and resid 1290 through 1298 removed outlier: 4.087A pdb=" N GLU F1295 " --> pdb=" O VAL F1291 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LYS F1296 " --> pdb=" O SER F1292 " (cutoff:3.500A) Processing helix chain 'F' and resid 1313 through 1331 removed outlier: 4.969A pdb=" N GLN F1321 " --> pdb=" O THR F1317 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N MET F1323 " --> pdb=" O ARG F1319 " (cutoff:3.500A) removed outlier: 5.218A pdb=" N LEU F1324 " --> pdb=" O ALA F1320 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N GLU F1326 " --> pdb=" O LEU F1322 " (cutoff:3.500A) Proline residue: F1327 - end of helix removed outlier: 3.568A pdb=" N TYR F1330 " --> pdb=" O GLU F1326 " (cutoff:3.500A) Processing helix chain 'F' and resid 1342 through 1349 removed outlier: 4.151A pdb=" N GLU F1346 " --> pdb=" O ALA F1342 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ALA F1347 " --> pdb=" O ARG F1343 " (cutoff:3.500A) Processing helix chain 'F' and resid 1349 through 1358 removed outlier: 4.082A pdb=" N TYR F1355 " --> pdb=" O ASN F1351 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N TRP F1356 " --> pdb=" O ALA F1352 " (cutoff:3.500A) Processing helix chain 'F' and resid 1381 through 1401 removed outlier: 3.804A pdb=" N ARG F1391 " --> pdb=" O GLU F1387 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N THR F1392 " --> pdb=" O SER F1388 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ALA F1394 " --> pdb=" O LEU F1390 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLN F1395 " --> pdb=" O ARG F1391 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N LYS F1396 " --> pdb=" O THR F1392 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ASN F1398 " --> pdb=" O ALA F1394 " (cutoff:3.500A) removed outlier: 5.345A pdb=" N GLU F1399 " --> pdb=" O GLN F1395 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N ASP F1400 " --> pdb=" O LYS F1396 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N GLU F1401 " --> pdb=" O LEU F1397 " (cutoff:3.500A) Processing helix chain 'F' and resid 1403 through 1420 removed outlier: 3.682A pdb=" N ALA F1408 " --> pdb=" O LEU F1404 " (cutoff:3.500A) removed outlier: 4.899A pdb=" N ALA F1409 " --> pdb=" O GLU F1405 " (cutoff:3.500A) Processing helix chain 'F' and resid 1420 through 1436 removed outlier: 3.849A pdb=" N HIS F1424 " --> pdb=" O LEU F1420 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LEU F1428 " --> pdb=" O HIS F1424 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N GLN F1429 " --> pdb=" O LEU F1425 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N GLU F1432 " --> pdb=" O LEU F1428 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ASN F1435 " --> pdb=" O GLN F1431 " (cutoff:3.500A) Processing helix chain 'F' and resid 1475 through 1488 removed outlier: 3.569A pdb=" N ILE F1479 " --> pdb=" O ILE F1475 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N LEU F1480 " --> pdb=" O ARG F1476 " (cutoff:3.500A) removed outlier: 4.999A pdb=" N ASN F1481 " --> pdb=" O GLU F1477 " (cutoff:3.500A) Processing helix chain 'F' and resid 1503 through 1521 Processing helix chain 'F' and resid 1527 through 1553 removed outlier: 3.692A pdb=" N ARG F1534 " --> pdb=" O LEU F1530 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ILE F1535 " --> pdb=" O TYR F1531 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ALA F1539 " --> pdb=" O ILE F1535 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N LYS F1547 " --> pdb=" O GLU F1543 " (cutoff:3.500A) Processing helix chain 'F' and resid 1588 through 1592 removed outlier: 3.779A pdb=" N GLU F1591 " --> pdb=" O VAL F1588 " (cutoff:3.500A) Processing helix chain 'F' and resid 1602 through 1617 removed outlier: 4.207A pdb=" N VAL F1606 " --> pdb=" O GLU F1602 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LYS F1615 " --> pdb=" O GLU F1611 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N GLU F1616 " --> pdb=" O ASP F1612 " (cutoff:3.500A) Processing helix chain 'F' and resid 1620 through 1627 removed outlier: 4.045A pdb=" N GLN F1626 " --> pdb=" O LEU F1622 " (cutoff:3.500A) Processing helix chain 'F' and resid 1637 through 1650 removed outlier: 3.615A pdb=" N ARG F1646 " --> pdb=" O ALA F1642 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N LEU F1647 " --> pdb=" O HIS F1643 " (cutoff:3.500A) Processing helix chain 'F' and resid 1660 through 1664 Processing helix chain 'F' and resid 1683 through 1692 removed outlier: 4.009A pdb=" N GLN F1689 " --> pdb=" O THR F1685 " (cutoff:3.500A) removed outlier: 4.892A pdb=" N MET F1690 " --> pdb=" O GLN F1686 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N GLY F1692 " --> pdb=" O ARG F1688 " (cutoff:3.500A) Processing helix chain 'F' and resid 1713 through 1720 removed outlier: 4.017A pdb=" N ARG F1717 " --> pdb=" O ARG F1713 " (cutoff:3.500A) Processing helix chain 'F' and resid 1733 through 1749 removed outlier: 3.799A pdb=" N ASN F1737 " --> pdb=" O ASP F1733 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N ASN F1747 " --> pdb=" O LEU F1743 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N THR F1748 " --> pdb=" O TYR F1744 " (cutoff:3.500A) Processing helix chain 'F' and resid 1754 through 1769 Processing helix chain 'F' and resid 1775 through 1780 Processing helix chain 'F' and resid 1791 through 1800 removed outlier: 4.410A pdb=" N MET F1797 " --> pdb=" O GLU F1793 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLY F1800 " --> pdb=" O GLN F1796 " (cutoff:3.500A) Processing helix chain 'F' and resid 1821 through 1825 removed outlier: 3.696A pdb=" N MET F1824 " --> pdb=" O GLN F1821 " (cutoff:3.500A) Processing helix chain 'F' and resid 1827 through 1831 Processing helix chain 'F' and resid 1841 through 1847 Processing helix chain 'F' and resid 1848 through 1850 No H-bonds generated for 'chain 'F' and resid 1848 through 1850' Processing helix chain 'F' and resid 1857 through 1867 removed outlier: 3.566A pdb=" N VAL F1865 " --> pdb=" O LEU F1861 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ASP F1867 " --> pdb=" O SER F1863 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'F' and resid 135 through 136 removed outlier: 3.669A pdb=" N TYR F 305 " --> pdb=" O GLU F 135 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ARG F 306 " --> pdb=" O LYS F 293 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LYS F 293 " --> pdb=" O ARG F 306 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N ILE F 260 " --> pdb=" O ALA F 294 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ASP F 152 " --> pdb=" O LEU F 261 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N PHE F 149 " --> pdb=" O VAL F 196 " (cutoff:3.500A) removed outlier: 8.106A pdb=" N PHE F 198 " --> pdb=" O PHE F 149 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N ILE F 151 " --> pdb=" O PHE F 198 " (cutoff:3.500A) removed outlier: 7.892A pdb=" N SER F 238 " --> pdb=" O HIS F 195 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N VAL F 197 " --> pdb=" O SER F 238 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'F' and resid 1105 through 1107 removed outlier: 6.757A pdb=" N VAL F1072 " --> pdb=" O LEU F1124 " (cutoff:3.500A) removed outlier: 8.582A pdb=" N THR F1126 " --> pdb=" O VAL F1072 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N TYR F1074 " --> pdb=" O THR F1126 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N VAL F1179 " --> pdb=" O VAL F1150 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N LEU F1152 " --> pdb=" O VAL F1179 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N LEU F1181 " --> pdb=" O LEU F1152 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N SER F1041 " --> pdb=" O VAL F1218 " (cutoff:3.500A) removed outlier: 7.718A pdb=" N LEU F1220 " --> pdb=" O SER F1041 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N VAL F1043 " --> pdb=" O LEU F1220 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'F' and resid 1233 through 1236 removed outlier: 7.121A pdb=" N THR F1494 " --> pdb=" O ILE F1656 " (cutoff:3.500A) removed outlier: 8.468A pdb=" N SER F1658 " --> pdb=" O THR F1494 " (cutoff:3.500A) removed outlier: 5.808A pdb=" N VAL F1496 " --> pdb=" O SER F1658 " (cutoff:3.500A) 371 hydrogen bonds defined for protein. 1071 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: 3.56 Time building geometry restraints manager: 4.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.03 - 1.42: 5288 1.42 - 1.81: 7130 1.81 - 2.20: 106 2.20 - 2.59: 0 2.59 - 2.98: 1 Bond restraints: 12525 Sorted by residual: bond pdb=" C ARG F1521 " pdb=" N TYR F1522 " ideal model delta sigma weight residual 1.335 2.980 -1.645 1.36e-02 5.41e+03 1.46e+04 bond pdb=" C TYR F1149 " pdb=" N VAL F1150 " ideal model delta sigma weight residual 1.331 1.724 -0.393 1.29e-02 6.01e+03 9.30e+02 bond pdb=" CA PRO F 304 " pdb=" C PRO F 304 " ideal model delta sigma weight residual 1.522 1.191 0.331 1.16e-02 7.43e+03 8.14e+02 bond pdb=" CA TYR F 305 " pdb=" C TYR F 305 " ideal model delta sigma weight residual 1.523 1.202 0.321 1.34e-02 5.57e+03 5.75e+02 bond pdb=" CA PHE F 259 " pdb=" C PHE F 259 " ideal model delta sigma weight residual 1.522 1.813 -0.291 1.24e-02 6.50e+03 5.51e+02 ... (remaining 12520 not shown) Histogram of bond angle deviations from ideal: 84.59 - 99.75: 81 99.75 - 114.90: 7343 114.90 - 130.05: 9303 130.05 - 145.20: 150 145.20 - 160.35: 10 Bond angle restraints: 16887 Sorted by residual: angle pdb=" O GLY F1051 " pdb=" C GLY F1051 " pdb=" N LYS F1052 " ideal model delta sigma weight residual 122.42 84.72 37.70 1.31e+00 5.83e-01 8.28e+02 angle pdb=" CA ASN F 303 " pdb=" C ASN F 303 " pdb=" N PRO F 304 " ideal model delta sigma weight residual 117.68 97.94 19.74 7.10e-01 1.98e+00 7.73e+02 angle pdb=" O ARG F1521 " pdb=" C ARG F1521 " pdb=" N TYR F1522 " ideal model delta sigma weight residual 122.22 90.29 31.93 1.17e+00 7.31e-01 7.45e+02 angle pdb=" O LEU F1136 " pdb=" C LEU F1136 " pdb=" N SER F1137 " ideal model delta sigma weight residual 122.08 148.00 -25.92 1.07e+00 8.73e-01 5.87e+02 angle pdb=" N ILE F1155 " pdb=" CA ILE F1155 " pdb=" CB ILE F1155 " ideal model delta sigma weight residual 111.50 150.54 -39.04 1.70e+00 3.46e-01 5.27e+02 ... (remaining 16882 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.31: 7025 25.31 - 50.63: 391 50.63 - 75.94: 147 75.94 - 101.26: 15 101.26 - 126.57: 12 Dihedral angle restraints: 7590 sinusoidal: 3163 harmonic: 4427 Sorted by residual: dihedral pdb=" CA GLY F1784 " pdb=" C GLY F1784 " pdb=" N GLY F1785 " pdb=" CA GLY F1785 " ideal model delta harmonic sigma weight residual -180.00 -53.43 -126.57 0 5.00e+00 4.00e-02 6.41e+02 dihedral pdb=" CA ARG F1214 " pdb=" C ARG F1214 " pdb=" N ASP F1215 " pdb=" CA ASP F1215 " ideal model delta harmonic sigma weight residual 180.00 53.77 126.23 0 5.00e+00 4.00e-02 6.37e+02 dihedral pdb=" CA SER F 144 " pdb=" C SER F 144 " pdb=" N ALA F 145 " pdb=" CA ALA F 145 " ideal model delta harmonic sigma weight residual 180.00 56.28 123.72 0 5.00e+00 4.00e-02 6.12e+02 ... (remaining 7587 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.858: 1817 0.858 - 1.717: 8 1.717 - 2.575: 0 2.575 - 3.434: 3 3.434 - 4.292: 1 Chirality restraints: 1829 Sorted by residual: chirality pdb=" CA ARG F1697 " pdb=" N ARG F1697 " pdb=" C ARG F1697 " pdb=" CB ARG F1697 " both_signs ideal model delta sigma weight residual False 2.51 -1.78 4.29 2.00e-01 2.50e+01 4.61e+02 chirality pdb=" CA ILE F1155 " pdb=" N ILE F1155 " pdb=" C ILE F1155 " pdb=" CB ILE F1155 " both_signs ideal model delta sigma weight residual False 2.43 -0.52 2.95 2.00e-01 2.50e+01 2.18e+02 chirality pdb=" CA TYR F 305 " pdb=" N TYR F 305 " pdb=" C TYR F 305 " pdb=" CB TYR F 305 " both_signs ideal model delta sigma weight residual False 2.51 -0.40 2.91 2.00e-01 2.50e+01 2.12e+02 ... (remaining 1826 not shown) Planarity restraints: 2193 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG F1521 " -0.179 2.00e-02 2.50e+03 2.65e-01 7.02e+02 pdb=" C ARG F1521 " 0.443 2.00e-02 2.50e+03 pdb=" O ARG F1521 " -0.227 2.00e-02 2.50e+03 pdb=" N TYR F1522 " -0.038 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR F1744 " -0.305 2.00e-02 2.50e+03 1.57e-01 4.90e+02 pdb=" CG TYR F1744 " 0.117 2.00e-02 2.50e+03 pdb=" CD1 TYR F1744 " 0.156 2.00e-02 2.50e+03 pdb=" CD2 TYR F1744 " 0.135 2.00e-02 2.50e+03 pdb=" CE1 TYR F1744 " 0.046 2.00e-02 2.50e+03 pdb=" CE2 TYR F1744 " 0.064 2.00e-02 2.50e+03 pdb=" CZ TYR F1744 " -0.013 2.00e-02 2.50e+03 pdb=" OH TYR F1744 " -0.201 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER F 146 " -0.111 2.00e-02 2.50e+03 1.89e-01 3.56e+02 pdb=" C SER F 146 " 0.326 2.00e-02 2.50e+03 pdb=" O SER F 146 " -0.120 2.00e-02 2.50e+03 pdb=" N GLU F 147 " -0.095 2.00e-02 2.50e+03 ... (remaining 2190 not shown) Histogram of nonbonded interaction distances: 0.77 - 1.59: 4 1.59 - 2.42: 65 2.42 - 3.25: 12024 3.25 - 4.07: 29186 4.07 - 4.90: 49247 Warning: very small nonbonded interaction distances. Nonbonded interactions: 90526 Sorted by model distance: nonbonded pdb=" CG ASP F 152 " pdb=" OD2 ASP F 200 " model vdw 0.766 3.270 nonbonded pdb=" OD2 ASP F 152 " pdb=" OD2 ASP F 200 " model vdw 1.024 3.040 nonbonded pdb=" OD1 ASP F 152 " pdb=" OD2 ASP F 200 " model vdw 1.257 3.040 nonbonded pdb=" CD2 LEU F 261 " pdb=" ND2 ASN F 295 " model vdw 1.407 3.540 nonbonded pdb=" CZ PHE F 149 " pdb=" CD1 LEU F 261 " model vdw 1.638 3.760 ... (remaining 90521 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.480 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.410 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 31.410 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5181 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 : 0.028 1.645 12525 Z= 1.721 Angle : 2.987 43.340 16887 Z= 1.949 Chirality : 0.219 4.292 1829 Planarity : 0.023 0.265 2193 Dihedral : 18.830 126.570 4720 Min Nonbonded Distance : 0.766 Molprobity Statistics. All-atom Clashscore : 14.21 Ramachandran Plot: Outliers : 9.67 % Allowed : 16.79 % Favored : 73.54 % Rotamer: Outliers : 2.58 % Allowed : 5.69 % Favored : 91.73 % Cbeta Deviations : 3.27 % Peptide Plane: Cis-proline : 5.66 % Cis-general : 2.75 % Twisted Proline : 13.21 % Twisted General : 9.98 % 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: -6.06 (0.15), residues: 1489 helix: -4.31 (0.12), residues: 570 sheet: -2.84 (0.47), residues: 75 loop : -4.10 (0.17), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.106 0.018 TRP F 851 HIS 0.005 0.001 HIS F1852 PHE 0.089 0.013 PHE F1648 TYR 0.305 0.023 TYR F1744 ARG 0.007 0.001 ARG F 292 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2978 Ramachandran restraints generated. 1489 Oldfield, 0 Emsley, 1489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2978 Ramachandran restraints generated. 1489 Oldfield, 0 Emsley, 1489 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 423 residues out of total 1318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 389 time to evaluate : 1.236 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 1 MET cc_start: 0.4478 (mtp) cc_final: 0.1993 (ttt) REVERT: F 308 ARG cc_start: 0.6867 (OUTLIER) cc_final: 0.5391 (tmm160) REVERT: F 864 MET cc_start: 0.5894 (ttm) cc_final: 0.5249 (ttt) REVERT: F 977 MET cc_start: 0.6275 (ttp) cc_final: 0.5544 (ttt) REVERT: F 1097 LYS cc_start: 0.7817 (mttp) cc_final: 0.7436 (ttpt) REVERT: F 1155 ILE cc_start: 0.4104 (mt) cc_final: 0.3548 (mt) REVERT: F 1209 MET cc_start: 0.3159 (ttt) cc_final: 0.1444 (mpp) REVERT: F 1298 HIS cc_start: 0.6478 (t-90) cc_final: 0.5355 (t-90) REVERT: F 1358 TYR cc_start: 0.5015 (m-80) cc_final: 0.4766 (m-80) REVERT: F 1386 VAL cc_start: 0.2922 (OUTLIER) cc_final: 0.1570 (t) REVERT: F 1396 LYS cc_start: 0.6061 (pttp) cc_final: 0.5536 (ttpt) REVERT: F 1515 LEU cc_start: 0.8172 (mp) cc_final: 0.7851 (mm) REVERT: F 1558 LEU cc_start: 0.5742 (OUTLIER) cc_final: 0.5509 (pp) REVERT: F 1633 HIS cc_start: 0.7703 (p90) cc_final: 0.7335 (p90) REVERT: F 1688 ARG cc_start: 0.6523 (mtm180) cc_final: 0.5690 (mtp180) REVERT: F 1847 VAL cc_start: 0.6863 (t) cc_final: 0.6626 (t) outliers start: 34 outliers final: 9 residues processed: 417 average time/residue: 0.3260 time to fit residues: 181.9341 Evaluate side-chains 245 residues out of total 1318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 233 time to evaluate : 1.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 128 optimal weight: 5.9990 chunk 115 optimal weight: 5.9990 chunk 63 optimal weight: 5.9990 chunk 39 optimal weight: 1.9990 chunk 77 optimal weight: 30.0000 chunk 61 optimal weight: 7.9990 chunk 119 optimal weight: 6.9990 chunk 46 optimal weight: 3.9990 chunk 72 optimal weight: 1.9990 chunk 88 optimal weight: 7.9990 chunk 138 optimal weight: 7.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 285 ASN ** F 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 679 ASN F 725 GLN F 989 GLN F1001 GLN F1007 HIS F1083 ASN ** F1156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F1163 ASN ** F1205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F1232 ASN ** F1308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F1369 ASN ** F1473 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F1632 HIS ** F1643 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1683 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1729 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1808 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5324 moved from start: 0.4761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 12525 Z= 0.298 Angle : 1.221 13.350 16887 Z= 0.637 Chirality : 0.090 2.388 1829 Planarity : 0.008 0.093 2193 Dihedral : 13.233 84.223 1674 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 17.52 Ramachandran Plot: Outliers : 2.95 % Allowed : 17.04 % Favored : 80.01 % Rotamer: Outliers : 0.38 % Allowed : 5.31 % Favored : 94.31 % Cbeta Deviations : 0.28 % Peptide Plane: Cis-proline : 5.66 % Cis-general : 3.03 % Twisted Proline : 9.43 % Twisted General : 4.40 % 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: -4.73 (0.18), residues: 1491 helix: -2.12 (0.18), residues: 589 sheet: -2.00 (0.62), residues: 45 loop : -4.20 (0.17), residues: 857 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP F 851 HIS 0.015 0.002 HIS F1118 PHE 0.036 0.003 PHE F 140 TYR 0.025 0.003 TYR F1149 ARG 0.012 0.001 ARG F 193 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2982 Ramachandran restraints generated. 1491 Oldfield, 0 Emsley, 1491 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2982 Ramachandran restraints generated. 1491 Oldfield, 0 Emsley, 1491 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 1318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 298 time to evaluate : 1.469 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 1 MET cc_start: 0.3679 (mtp) cc_final: 0.2591 (ttt) REVERT: F 96 LEU cc_start: 0.6735 (tp) cc_final: 0.6464 (tp) REVERT: F 193 ARG cc_start: 0.4888 (mpp-170) cc_final: 0.4165 (mpt-90) REVERT: F 726 MET cc_start: 0.2688 (ttp) cc_final: 0.2283 (mtp) REVERT: F 864 MET cc_start: 0.6439 (ttm) cc_final: 0.6179 (ttm) REVERT: F 886 GLN cc_start: 0.7928 (pt0) cc_final: 0.7632 (pt0) REVERT: F 1157 SER cc_start: 0.7598 (p) cc_final: 0.6583 (t) REVERT: F 1209 MET cc_start: 0.2807 (ttt) cc_final: 0.1897 (mpp) REVERT: F 1298 HIS cc_start: 0.6381 (t-90) cc_final: 0.5778 (t70) REVERT: F 1443 MET cc_start: 0.0721 (ppp) cc_final: 0.0420 (ptm) REVERT: F 1468 PHE cc_start: 0.5887 (OUTLIER) cc_final: 0.5389 (t80) REVERT: F 1471 SER cc_start: 0.7327 (p) cc_final: 0.6726 (p) REVERT: F 1491 MET cc_start: 0.4163 (OUTLIER) cc_final: 0.3495 (mmp) REVERT: F 1510 TYR cc_start: 0.6988 (t80) cc_final: 0.6736 (t80) REVERT: F 1588 VAL cc_start: 0.5770 (p) cc_final: 0.5450 (p) REVERT: F 1704 HIS cc_start: 0.7386 (m90) cc_final: 0.6876 (m90) REVERT: F 1847 VAL cc_start: 0.7739 (t) cc_final: 0.7334 (p) outliers start: 5 outliers final: 0 residues processed: 299 average time/residue: 0.2997 time to fit residues: 122.1817 Evaluate side-chains 204 residues out of total 1318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 202 time to evaluate : 1.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 76 optimal weight: 2.9990 chunk 42 optimal weight: 7.9990 chunk 114 optimal weight: 6.9990 chunk 93 optimal weight: 7.9990 chunk 38 optimal weight: 6.9990 chunk 138 optimal weight: 0.4980 chunk 149 optimal weight: 6.9990 chunk 123 optimal weight: 30.0000 chunk 137 optimal weight: 8.9990 chunk 47 optimal weight: 9.9990 chunk 110 optimal weight: 10.0000 overall best weight: 4.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 675 ASN F 678 ASN F 725 GLN ** F 838 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 839 GLN F1001 GLN F1118 HIS F1122 GLN ** F1205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F1219 HIS ** F1308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1369 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1431 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1473 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F1626 GLN ** F1683 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F1729 ASN F1751 HIS F1754 ASN F1780 ASN ** F1808 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5436 moved from start: 0.5979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 12525 Z= 0.283 Angle : 1.094 13.489 16887 Z= 0.567 Chirality : 0.062 1.047 1829 Planarity : 0.007 0.097 2193 Dihedral : 11.338 72.690 1674 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 18.71 Ramachandran Plot: Outliers : 2.55 % Allowed : 17.64 % Favored : 79.81 % Rotamer: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Cbeta Deviations : 0.21 % Peptide Plane: Cis-proline : 5.66 % Cis-general : 3.03 % Twisted Proline : 9.43 % Twisted General : 2.96 % 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: -4.02 (0.19), residues: 1491 helix: -1.15 (0.20), residues: 593 sheet: -1.66 (0.60), residues: 71 loop : -4.18 (0.17), residues: 827 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP F 851 HIS 0.007 0.002 HIS F1652 PHE 0.037 0.003 PHE F1013 TYR 0.034 0.003 TYR F 828 ARG 0.019 0.001 ARG F 193 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2982 Ramachandran restraints generated. 1491 Oldfield, 0 Emsley, 1491 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2982 Ramachandran restraints generated. 1491 Oldfield, 0 Emsley, 1491 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 1318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 262 time to evaluate : 1.210 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: F 1 MET cc_start: 0.3431 (mtp) cc_final: 0.2750 (ttt) REVERT: F 724 LYS cc_start: 0.8268 (ptpt) cc_final: 0.7698 (pttt) REVERT: F 726 MET cc_start: 0.2953 (ttp) cc_final: 0.2731 (mtp) REVERT: F 729 LEU cc_start: 0.4958 (tp) cc_final: 0.4660 (tp) REVERT: F 866 ILE cc_start: 0.7243 (mp) cc_final: 0.7007 (mp) REVERT: F 1157 SER cc_start: 0.7556 (p) cc_final: 0.6930 (t) REVERT: F 1209 MET cc_start: 0.2495 (ttt) cc_final: 0.1900 (mpp) REVERT: F 1412 MET cc_start: 0.7349 (tpp) cc_final: 0.7052 (ttp) REVERT: F 1510 TYR cc_start: 0.7196 (t80) cc_final: 0.6728 (t80) REVERT: F 1643 HIS cc_start: 0.6806 (m170) cc_final: 0.6523 (m-70) outliers start: 0 outliers final: 0 residues processed: 262 average time/residue: 0.2730 time to fit residues: 98.5171 Evaluate side-chains 196 residues out of total 1318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 196 time to evaluate : 1.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 136 optimal weight: 10.0000 chunk 103 optimal weight: 20.0000 chunk 71 optimal weight: 6.9990 chunk 15 optimal weight: 7.9990 chunk 65 optimal weight: 4.9990 chunk 92 optimal weight: 20.0000 chunk 138 optimal weight: 0.2980 chunk 146 optimal weight: 6.9990 chunk 72 optimal weight: 7.9990 chunk 131 optimal weight: 7.9990 chunk 39 optimal weight: 2.9990 overall best weight: 4.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 678 ASN F 725 GLN F1001 GLN F1024 ASN F1163 ASN ** F1205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1548 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1683 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F1704 HIS ** F1808 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5463 moved from start: 0.6619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 12525 Z= 0.255 Angle : 1.025 12.364 16887 Z= 0.532 Chirality : 0.056 0.882 1829 Planarity : 0.006 0.091 2193 Dihedral : 10.541 68.125 1674 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 18.59 Ramachandran Plot: Outliers : 2.28 % Allowed : 17.57 % Favored : 80.15 % Rotamer: Outliers : 0.08 % Allowed : 3.34 % Favored : 96.59 % Cbeta Deviations : 0.14 % Peptide Plane: Cis-proline : 5.66 % Cis-general : 3.09 % Twisted Proline : 9.43 % Twisted General : 2.06 % 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: -3.74 (0.20), residues: 1491 helix: -0.80 (0.20), residues: 614 sheet: -1.37 (0.59), residues: 76 loop : -4.22 (0.18), residues: 801 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP F 851 HIS 0.013 0.002 HIS F1156 PHE 0.022 0.002 PHE F 150 TYR 0.028 0.002 TYR F 828 ARG 0.013 0.001 ARG F1201 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2982 Ramachandran restraints generated. 1491 Oldfield, 0 Emsley, 1491 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2982 Ramachandran restraints generated. 1491 Oldfield, 0 Emsley, 1491 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 248 time to evaluate : 1.370 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 1 MET cc_start: 0.5604 (mtp) cc_final: 0.4186 (ttt) REVERT: F 189 CYS cc_start: 0.1416 (t) cc_final: 0.1199 (t) REVERT: F 724 LYS cc_start: 0.8119 (ptpt) cc_final: 0.7627 (pttt) REVERT: F 726 MET cc_start: 0.2643 (ttp) cc_final: 0.2325 (mtp) REVERT: F 1157 SER cc_start: 0.6859 (p) cc_final: 0.6121 (t) REVERT: F 1412 MET cc_start: 0.7162 (tpp) cc_final: 0.6898 (ttp) REVERT: F 1614 GLU cc_start: 0.7406 (tt0) cc_final: 0.7129 (tt0) REVERT: F 1708 LEU cc_start: 0.5759 (tp) cc_final: 0.5315 (mp) outliers start: 1 outliers final: 0 residues processed: 248 average time/residue: 0.2908 time to fit residues: 100.3490 Evaluate side-chains 187 residues out of total 1318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 187 time to evaluate : 1.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 122 optimal weight: 10.0000 chunk 83 optimal weight: 5.9990 chunk 2 optimal weight: 6.9990 chunk 109 optimal weight: 10.0000 chunk 60 optimal weight: 20.0000 chunk 125 optimal weight: 4.9990 chunk 101 optimal weight: 10.0000 chunk 0 optimal weight: 20.0000 chunk 75 optimal weight: 10.0000 chunk 131 optimal weight: 10.0000 chunk 37 optimal weight: 0.9980 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 78 HIS F 288 HIS F 303 ASN ** F 694 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 725 GLN ** F 839 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 965 ASN ** F1001 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F1115 HIS ** F1205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F1351 ASN ** F1383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1548 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1683 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F1772 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5568 moved from start: 0.7162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 12525 Z= 0.287 Angle : 1.038 12.545 16887 Z= 0.535 Chirality : 0.055 0.914 1829 Planarity : 0.007 0.155 2193 Dihedral : 10.136 64.817 1674 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 21.38 Ramachandran Plot: Outliers : 2.21 % Allowed : 17.97 % Favored : 79.81 % Rotamer: Outliers : 0.08 % Allowed : 4.63 % Favored : 95.30 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 5.66 % Cis-general : 3.09 % Twisted Proline : 9.43 % Twisted General : 1.93 % 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: -3.69 (0.20), residues: 1491 helix: -0.71 (0.20), residues: 607 sheet: -1.06 (0.65), residues: 68 loop : -4.21 (0.18), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP F 851 HIS 0.009 0.002 HIS F1633 PHE 0.027 0.003 PHE F1131 TYR 0.026 0.002 TYR F 828 ARG 0.012 0.001 ARG F 193 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2982 Ramachandran restraints generated. 1491 Oldfield, 0 Emsley, 1491 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2982 Ramachandran restraints generated. 1491 Oldfield, 0 Emsley, 1491 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 250 time to evaluate : 1.555 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 1 MET cc_start: 0.5717 (mtp) cc_final: 0.4275 (ttt) REVERT: F 726 MET cc_start: 0.2638 (ttp) cc_final: 0.2397 (mtp) REVERT: F 859 LYS cc_start: 0.7940 (mttt) cc_final: 0.7738 (mttt) REVERT: F 942 MET cc_start: 0.4431 (ttp) cc_final: 0.4141 (ttp) REVERT: F 1115 HIS cc_start: 0.3425 (OUTLIER) cc_final: 0.2911 (m170) REVERT: F 1157 SER cc_start: 0.6766 (p) cc_final: 0.6352 (t) REVERT: F 1297 MET cc_start: 0.2102 (ttm) cc_final: 0.1844 (ttm) REVERT: F 1486 LEU cc_start: 0.6909 (pp) cc_final: 0.6678 (pp) outliers start: 1 outliers final: 0 residues processed: 251 average time/residue: 0.2841 time to fit residues: 99.0931 Evaluate side-chains 193 residues out of total 1318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 192 time to evaluate : 1.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 49 optimal weight: 7.9990 chunk 132 optimal weight: 0.6980 chunk 29 optimal weight: 9.9990 chunk 86 optimal weight: 30.0000 chunk 36 optimal weight: 5.9990 chunk 147 optimal weight: 0.8980 chunk 122 optimal weight: 10.0000 chunk 68 optimal weight: 9.9990 chunk 12 optimal weight: 9.9990 chunk 48 optimal weight: 0.5980 chunk 77 optimal weight: 0.0070 overall best weight: 1.6400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 286 ASN ** F 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 725 GLN F 956 HIS F1001 GLN ** F1205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F1383 ASN F1433 GLN F1548 GLN F1683 ASN F1704 HIS ** F1808 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5382 moved from start: 0.7579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 12525 Z= 0.203 Angle : 0.961 12.771 16887 Z= 0.494 Chirality : 0.051 0.767 1829 Planarity : 0.006 0.093 2193 Dihedral : 9.305 59.910 1674 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 16.41 Ramachandran Plot: Outliers : 2.01 % Allowed : 16.43 % Favored : 81.56 % Rotamer: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 5.66 % Cis-general : 3.09 % Twisted Proline : 9.43 % Twisted General : 1.44 % 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: -3.27 (0.21), residues: 1491 helix: -0.21 (0.21), residues: 603 sheet: -0.75 (0.61), residues: 76 loop : -4.14 (0.19), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP F 851 HIS 0.006 0.001 HIS F1808 PHE 0.020 0.002 PHE F 198 TYR 0.019 0.002 TYR F 828 ARG 0.009 0.001 ARG F 193 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2982 Ramachandran restraints generated. 1491 Oldfield, 0 Emsley, 1491 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2982 Ramachandran restraints generated. 1491 Oldfield, 0 Emsley, 1491 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 243 time to evaluate : 1.397 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 1 MET cc_start: 0.5737 (mtp) cc_final: 0.4282 (ttt) REVERT: F 724 LYS cc_start: 0.8072 (ptpt) cc_final: 0.7854 (pptt) REVERT: F 864 MET cc_start: 0.6595 (ttm) cc_final: 0.5938 (ttt) REVERT: F 937 ASP cc_start: 0.6617 (t70) cc_final: 0.6392 (t70) REVERT: F 1157 SER cc_start: 0.6162 (p) cc_final: 0.5778 (t) REVERT: F 1293 LEU cc_start: 0.4780 (tt) cc_final: 0.4519 (tp) REVERT: F 1735 ILE cc_start: 0.7148 (pt) cc_final: 0.6926 (pt) outliers start: 0 outliers final: 0 residues processed: 243 average time/residue: 0.2748 time to fit residues: 92.9488 Evaluate side-chains 185 residues out of total 1318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 185 time to evaluate : 1.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 141 optimal weight: 10.0000 chunk 16 optimal weight: 1.9990 chunk 83 optimal weight: 6.9990 chunk 107 optimal weight: 10.0000 chunk 123 optimal weight: 0.0050 chunk 82 optimal weight: 0.0980 chunk 146 optimal weight: 10.0000 chunk 91 optimal weight: 9.9990 chunk 89 optimal weight: 6.9990 chunk 67 optimal weight: 1.9990 chunk 90 optimal weight: 7.9990 overall best weight: 2.2200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 288 HIS F 725 GLN F1001 GLN ** F1017 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1473 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F1478 HIS ** F1808 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1852 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5403 moved from start: 0.7852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 12525 Z= 0.199 Angle : 0.943 12.500 16887 Z= 0.483 Chirality : 0.051 0.810 1829 Planarity : 0.005 0.089 2193 Dihedral : 9.002 56.890 1674 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 16.78 Ramachandran Plot: Outliers : 1.68 % Allowed : 17.51 % Favored : 80.82 % Rotamer: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 5.66 % Cis-general : 3.09 % Twisted Proline : 9.43 % Twisted General : 1.31 % 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: -3.19 (0.21), residues: 1491 helix: -0.12 (0.21), residues: 616 sheet: -0.87 (0.62), residues: 76 loop : -4.16 (0.18), residues: 799 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP F 851 HIS 0.006 0.001 HIS F1808 PHE 0.024 0.002 PHE F 278 TYR 0.019 0.002 TYR F 244 ARG 0.009 0.001 ARG F1201 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2982 Ramachandran restraints generated. 1491 Oldfield, 0 Emsley, 1491 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2982 Ramachandran restraints generated. 1491 Oldfield, 0 Emsley, 1491 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 242 time to evaluate : 1.298 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 1 MET cc_start: 0.5699 (mtp) cc_final: 0.4958 (ttt) REVERT: F 291 ARG cc_start: 0.6009 (tpt90) cc_final: 0.5329 (tpt90) REVERT: F 1157 SER cc_start: 0.6418 (p) cc_final: 0.5893 (t) REVERT: F 1609 LEU cc_start: 0.6073 (mt) cc_final: 0.5521 (mt) REVERT: F 1735 ILE cc_start: 0.7009 (pt) cc_final: 0.6752 (pt) outliers start: 0 outliers final: 0 residues processed: 242 average time/residue: 0.2727 time to fit residues: 92.2921 Evaluate side-chains 189 residues out of total 1318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 189 time to evaluate : 1.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 58 optimal weight: 9.9990 chunk 87 optimal weight: 10.0000 chunk 44 optimal weight: 2.9990 chunk 28 optimal weight: 9.9990 chunk 93 optimal weight: 6.9990 chunk 99 optimal weight: 6.9990 chunk 72 optimal weight: 6.9990 chunk 13 optimal weight: 8.9990 chunk 115 optimal weight: 0.3980 chunk 133 optimal weight: 10.0000 chunk 140 optimal weight: 5.9990 overall best weight: 4.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 725 GLN ** F1001 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F1017 HIS ** F1205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F1339 GLN F1431 GLN ** F1473 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1852 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5495 moved from start: 0.8090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 12525 Z= 0.245 Angle : 0.977 12.203 16887 Z= 0.501 Chirality : 0.053 0.833 1829 Planarity : 0.006 0.090 2193 Dihedral : 8.971 56.064 1674 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 20.19 Ramachandran Plot: Outliers : 1.61 % Allowed : 18.58 % Favored : 79.81 % Rotamer: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 5.66 % Cis-general : 3.09 % Twisted Proline : 9.43 % Twisted General : 1.03 % 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: -3.26 (0.21), residues: 1491 helix: -0.15 (0.21), residues: 607 sheet: -1.04 (0.64), residues: 77 loop : -4.17 (0.18), residues: 807 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP F 206 HIS 0.007 0.001 HIS F1643 PHE 0.029 0.002 PHE F 150 TYR 0.032 0.002 TYR F 305 ARG 0.011 0.001 ARG F1201 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2982 Ramachandran restraints generated. 1491 Oldfield, 0 Emsley, 1491 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2982 Ramachandran restraints generated. 1491 Oldfield, 0 Emsley, 1491 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 227 time to evaluate : 1.456 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: F 1 MET cc_start: 0.5810 (mtp) cc_final: 0.5044 (ttt) REVERT: F 224 MET cc_start: 0.3273 (mpp) cc_final: 0.2749 (mmp) REVERT: F 291 ARG cc_start: 0.6113 (tpt90) cc_final: 0.5432 (tpt90) REVERT: F 1024 ASN cc_start: 0.7480 (t0) cc_final: 0.7201 (t0) REVERT: F 1062 LYS cc_start: 0.7219 (mppt) cc_final: 0.6132 (mtpt) REVERT: F 1149 TYR cc_start: 0.5843 (t80) cc_final: 0.5567 (t80) REVERT: F 1157 SER cc_start: 0.6459 (p) cc_final: 0.5999 (t) REVERT: F 1723 MET cc_start: 0.6655 (mmt) cc_final: 0.6175 (mmt) outliers start: 0 outliers final: 0 residues processed: 227 average time/residue: 0.2902 time to fit residues: 92.8716 Evaluate side-chains 187 residues out of total 1318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 187 time to evaluate : 1.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 128 optimal weight: 0.9990 chunk 136 optimal weight: 9.9990 chunk 140 optimal weight: 0.6980 chunk 82 optimal weight: 20.0000 chunk 59 optimal weight: 20.0000 chunk 107 optimal weight: 6.9990 chunk 41 optimal weight: 5.9990 chunk 123 optimal weight: 0.2980 chunk 129 optimal weight: 7.9990 chunk 89 optimal weight: 0.3980 chunk 144 optimal weight: 20.0000 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F1001 GLN F1118 HIS ** F1205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1473 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1808 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1852 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5388 moved from start: 0.8334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 12525 Z= 0.197 Angle : 0.937 13.147 16887 Z= 0.477 Chirality : 0.050 0.771 1829 Planarity : 0.005 0.090 2193 Dihedral : 8.584 56.191 1674 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 16.53 Ramachandran Plot: Outliers : 1.61 % Allowed : 17.71 % Favored : 80.68 % Rotamer: Outliers : 0.00 % Allowed : 0.46 % Favored : 99.54 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 5.66 % Cis-general : 3.09 % Twisted Proline : 9.43 % Twisted General : 0.89 % 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: -3.05 (0.21), residues: 1491 helix: 0.14 (0.21), residues: 595 sheet: -1.03 (0.62), residues: 76 loop : -4.08 (0.18), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP F 851 HIS 0.006 0.001 HIS F1643 PHE 0.032 0.002 PHE F1294 TYR 0.017 0.002 TYR F 244 ARG 0.008 0.001 ARG F 790 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2982 Ramachandran restraints generated. 1491 Oldfield, 0 Emsley, 1491 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2982 Ramachandran restraints generated. 1491 Oldfield, 0 Emsley, 1491 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 227 time to evaluate : 1.430 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 1 MET cc_start: 0.5747 (mtp) cc_final: 0.5019 (ttt) REVERT: F 224 MET cc_start: 0.3273 (mpp) cc_final: 0.2903 (mmp) REVERT: F 291 ARG cc_start: 0.5844 (tpt90) cc_final: 0.5173 (tpt90) REVERT: F 1114 TYR cc_start: 0.2872 (t80) cc_final: 0.2537 (t80) REVERT: F 1412 MET cc_start: 0.6493 (tpp) cc_final: 0.6122 (ttp) REVERT: F 1735 ILE cc_start: 0.7051 (pt) cc_final: 0.6828 (pt) outliers start: 0 outliers final: 0 residues processed: 227 average time/residue: 0.2771 time to fit residues: 87.9196 Evaluate side-chains 181 residues out of total 1318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 181 time to evaluate : 1.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 88 optimal weight: 0.0670 chunk 68 optimal weight: 9.9990 chunk 100 optimal weight: 20.0000 chunk 151 optimal weight: 5.9990 chunk 139 optimal weight: 5.9990 chunk 120 optimal weight: 3.9990 chunk 12 optimal weight: 10.0000 chunk 93 optimal weight: 7.9990 chunk 73 optimal weight: 0.0980 chunk 95 optimal weight: 30.0000 chunk 128 optimal weight: 10.0000 overall best weight: 3.2324 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 725 GLN F1001 GLN ** F1118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1473 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1852 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5445 moved from start: 0.8484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 12525 Z= 0.210 Angle : 0.935 13.044 16887 Z= 0.476 Chirality : 0.051 0.787 1829 Planarity : 0.005 0.090 2193 Dihedral : 8.472 54.981 1674 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 17.11 Ramachandran Plot: Outliers : 1.68 % Allowed : 18.71 % Favored : 79.61 % Rotamer: Outliers : 0.00 % Allowed : 0.61 % Favored : 99.39 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 5.66 % Cis-general : 3.09 % Twisted Proline : 9.43 % Twisted General : 0.83 % 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: -3.14 (0.21), residues: 1491 helix: 0.03 (0.21), residues: 610 sheet: -1.09 (0.62), residues: 76 loop : -4.17 (0.18), residues: 805 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP F 851 HIS 0.006 0.001 HIS F1808 PHE 0.026 0.002 PHE F1294 TYR 0.017 0.002 TYR F 244 ARG 0.007 0.001 ARG F1651 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2982 Ramachandran restraints generated. 1491 Oldfield, 0 Emsley, 1491 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2982 Ramachandran restraints generated. 1491 Oldfield, 0 Emsley, 1491 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 222 time to evaluate : 1.467 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 1 MET cc_start: 0.5773 (mtp) cc_final: 0.5038 (ttt) REVERT: F 32 GLU cc_start: 0.7377 (tp30) cc_final: 0.7028 (tp30) REVERT: F 291 ARG cc_start: 0.5800 (tpt90) cc_final: 0.5294 (tpt90) REVERT: F 864 MET cc_start: 0.6963 (ttm) cc_final: 0.6290 (ttm) REVERT: F 1517 GLU cc_start: 0.6492 (tt0) cc_final: 0.6275 (tm-30) REVERT: F 1723 MET cc_start: 0.6641 (mmt) cc_final: 0.6359 (mmt) REVERT: F 1735 ILE cc_start: 0.7117 (pt) cc_final: 0.6884 (pt) outliers start: 0 outliers final: 0 residues processed: 222 average time/residue: 0.2557 time to fit residues: 80.7408 Evaluate side-chains 184 residues out of total 1318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 184 time to evaluate : 1.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 36 optimal weight: 10.0000 chunk 111 optimal weight: 8.9990 chunk 17 optimal weight: 0.3980 chunk 33 optimal weight: 10.0000 chunk 120 optimal weight: 10.0000 chunk 50 optimal weight: 20.0000 chunk 124 optimal weight: 0.0000 chunk 15 optimal weight: 9.9990 chunk 22 optimal weight: 5.9990 chunk 106 optimal weight: 1.9990 chunk 6 optimal weight: 9.9990 overall best weight: 3.4790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 725 GLN ** F 839 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F1001 GLN F1118 HIS ** F1205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1473 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1852 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4425 r_free = 0.4425 target = 0.168864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4273 r_free = 0.4273 target = 0.156796 restraints weight = 47733.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.4293 r_free = 0.4293 target = 0.158270 restraints weight = 34831.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 61)----------------| | r_work = 0.4307 r_free = 0.4307 target = 0.159453 restraints weight = 27243.950| |-----------------------------------------------------------------------------| r_work (final): 0.4276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6203 moved from start: 0.8613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 12525 Z= 0.216 Angle : 0.939 13.224 16887 Z= 0.479 Chirality : 0.051 0.784 1829 Planarity : 0.006 0.090 2193 Dihedral : 8.354 53.782 1674 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 17.44 Ramachandran Plot: Outliers : 1.54 % Allowed : 18.98 % Favored : 79.48 % Rotamer: Outliers : 0.00 % Allowed : 0.23 % Favored : 99.77 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 5.66 % Cis-general : 3.09 % Twisted Proline : 7.55 % Twisted General : 0.76 % 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: -3.08 (0.21), residues: 1491 helix: 0.10 (0.21), residues: 606 sheet: -1.07 (0.63), residues: 75 loop : -4.13 (0.18), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP F 851 HIS 0.006 0.001 HIS F1808 PHE 0.027 0.002 PHE F1294 TYR 0.019 0.002 TYR F 305 ARG 0.024 0.001 ARG F 63 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2745.79 seconds wall clock time: 49 minutes 40.01 seconds (2980.01 seconds total)