Starting phenix.real_space_refine on Sat Dec 9 20:48:00 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ask_11895/12_2023/7ask_11895_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ask_11895/12_2023/7ask_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_11895/12_2023/7ask_11895.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ask_11895/12_2023/7ask_11895.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ask_11895/12_2023/7ask_11895_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ask_11895/12_2023/7ask_11895_updated.pdb" } 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-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 12285 Number of models: 1 Model: "" Number of chains: 1 Chain: "F" Number of atoms: 12285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1525, 12285 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'peptide': 1523, 'undetermined': 2} Link IDs: {'CIS': 45, 'PCIS': 3, 'PTRANS': 50, 'TRANS': 1424, None: 2} Not linked: pdbres="ASP F1867 " pdbres=" MG F2201 " Not linked: pdbres=" MG F2201 " pdbres="ADP F2202 " Chain breaks: 15 Time building chain proxies: 6.52, per 1000 atoms: 0.53 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: 4.57 Conformation dependent library (CDL) restraints added in 2.3 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... running ksdssp... Secondary structure from input PDB file: 57 helices and 7 sheets defined 41.7% alpha, 3.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.79 Creating SS restraints... Processing helix chain 'F' and resid 2 through 15 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) Processing helix chain 'F' and resid 32 through 39 Processing helix chain 'F' and resid 60 through 74 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 93 through 108 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) Processing helix chain 'F' and resid 111 through 129 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 153 through 160 Processing helix chain 'F' and resid 178 through 187 Processing helix chain 'F' and resid 215 through 227 Processing helix chain 'F' and resid 249 through 255 removed outlier: 4.032A pdb=" N TRP F 255 " --> pdb=" O TYR F 251 " (cutoff:3.500A) Processing helix chain 'F' and resid 272 through 288 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 672 through 674 No H-bonds generated for 'chain 'F' and resid 672 through 674' Processing helix chain 'F' and resid 687 through 694 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 763 removed outlier: 5.673A pdb=" N ARG F 743 " --> pdb=" O THR F 740 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ARG F 745 " --> pdb=" O ASN F 742 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N GLU F 747 " --> pdb=" O ASP F 744 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N SER F 748 " --> pdb=" O ARG F 745 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N MET F 753 " --> pdb=" O ASN F 750 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ALA F 755 " --> pdb=" O ILE F 752 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ILE F 756 " --> pdb=" O MET F 753 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ARG F 758 " --> pdb=" O ALA F 755 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N LEU F 759 " --> pdb=" O ILE F 756 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N GLN F 761 " --> pdb=" O ARG F 758 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LYS F 763 " --> pdb=" O SER F 760 " (cutoff:3.500A) Processing helix chain 'F' and resid 777 through 791 removed outlier: 4.578A pdb=" N VAL F 782 " --> pdb=" O ASN F 779 " (cutoff:3.500A) Proline residue: F 783 - end of helix removed outlier: 3.925A pdb=" N LEU F 786 " --> pdb=" O PRO F 783 " (cutoff:3.500A) Processing helix chain 'F' and resid 809 through 814 removed outlier: 3.851A pdb=" N LEU F 812 " --> pdb=" O ASP F 809 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ASP F 814 " --> pdb=" O ALA F 811 " (cutoff:3.500A) Processing helix chain 'F' and resid 817 through 822 Processing helix chain 'F' and resid 837 through 844 Processing helix chain 'F' and resid 854 through 858 removed outlier: 3.587A pdb=" N ARG F 858 " --> pdb=" O LEU F 854 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 854 through 858' Processing helix chain 'F' and resid 867 through 876 removed outlier: 3.909A pdb=" N LEU F 873 " --> pdb=" O ALA F 869 " (cutoff:3.500A) Processing helix chain 'F' and resid 879 through 900 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 902 through 906 removed outlier: 3.607A pdb=" N GLU F 906 " --> pdb=" O ARG F 902 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 902 through 906' Processing helix chain 'F' and resid 921 through 933 removed outlier: 3.623A pdb=" N LEU F 925 " --> pdb=" O PRO F 922 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N HIS F 928 " --> pdb=" O LEU F 925 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N HIS F 930 " --> pdb=" O CYS F 927 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LEU F 932 " --> pdb=" O HIS F 929 " (cutoff:3.500A) Processing helix chain 'F' and resid 947 through 954 Processing helix chain 'F' and resid 965 through 975 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 1000 through 1006 removed outlier: 4.238A pdb=" N GLY F1006 " --> pdb=" O ILE F1003 " (cutoff:3.500A) Processing helix chain 'F' and resid 1028 through 1036 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 1054 through 1064 removed outlier: 3.834A pdb=" N ALA F1063 " --> pdb=" O MET F1060 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N LEU F1064 " --> pdb=" O TYR F1061 " (cutoff:3.500A) Processing helix chain 'F' and resid 1083 through 1092 removed outlier: 3.507A pdb=" N ARG F1092 " --> pdb=" O ASP F1088 " (cutoff:3.500A) Processing helix chain 'F' and resid 1128 through 1136 Processing helix chain 'F' and resid 1141 through 1146 removed outlier: 3.709A pdb=" N GLU F1145 " --> pdb=" O THR F1141 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N LEU F1146 " --> pdb=" O ASP F1142 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 1141 through 1146' Processing helix chain 'F' and resid 1156 through 1161 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 1189 through 1206 removed outlier: 3.509A pdb=" N TRP F1194 " --> pdb=" O GLN F1190 " (cutoff:3.500A) Processing helix chain 'F' and resid 1272 through 1277 removed outlier: 3.947A pdb=" N GLN F1276 " --> pdb=" O ALA F1272 " (cutoff:3.500A) Processing helix chain 'F' and resid 1291 through 1299 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) removed outlier: 3.986A pdb=" N SER F1299 " --> pdb=" O GLU F1295 " (cutoff:3.500A) Processing helix chain 'F' and resid 1314 through 1330 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 1357 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) removed outlier: 3.673A pdb=" N ASN F1351 " --> pdb=" O ALA F1347 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ALA F1352 " --> pdb=" O GLU F1348 " (cutoff:3.500A) 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 1382 through 1400 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) Processing helix chain 'F' and resid 1404 through 1435 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) removed outlier: 4.288A pdb=" N ARG F1421 " --> pdb=" O ARG F1417 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N GLN F1422 " --> pdb=" O MET F1418 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N GLN F1423 " --> pdb=" O LEU F1419 " (cutoff:3.500A) 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 1474 through 1489 removed outlier: 3.583A pdb=" N GLU F1477 " --> pdb=" O PHE F1474 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N LEU F1480 " --> pdb=" O GLU F1477 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N LEU F1483 " --> pdb=" O LEU F1480 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ARG F1484 " --> pdb=" O ASN F1481 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ILE F1487 " --> pdb=" O ARG F1484 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ALA F1488 " --> pdb=" O GLU F1485 " (cutoff:3.500A) Processing helix chain 'F' and resid 1502 through 1522 removed outlier: 3.654A pdb=" N LEU F1507 " --> pdb=" O CYS F1504 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LYS F1509 " --> pdb=" O ASP F1506 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLU F1513 " --> pdb=" O TYR F1510 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLU F1519 " --> pdb=" O GLU F1516 " (cutoff:3.500A) Processing helix chain 'F' and resid 1528 through 1552 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 1589 through 1591 No H-bonds generated for 'chain 'F' and resid 1589 through 1591' Processing helix chain 'F' and resid 1603 through 1615 removed outlier: 3.704A pdb=" N LYS F1615 " --> pdb=" O GLU F1611 " (cutoff:3.500A) Processing helix chain 'F' and resid 1621 through 1627 removed outlier: 4.045A pdb=" N GLN F1626 " --> pdb=" O LEU F1622 " (cutoff:3.500A) Processing helix chain 'F' and resid 1638 through 1649 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 1663 Processing helix chain 'F' and resid 1684 through 1691 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) Processing helix chain 'F' and resid 1714 through 1719 Processing helix chain 'F' and resid 1734 through 1748 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 1755 through 1768 Processing helix chain 'F' and resid 1776 through 1779 Processing helix chain 'F' and resid 1792 through 1801 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) removed outlier: 4.352A pdb=" N TYR F1801 " --> pdb=" O MET F1797 " (cutoff:3.500A) Processing helix chain 'F' and resid 1822 through 1824 No H-bonds generated for 'chain 'F' and resid 1822 through 1824' Processing helix chain 'F' and resid 1828 through 1830 No H-bonds generated for 'chain 'F' and resid 1828 through 1830' Processing helix chain 'F' and resid 1840 through 1846 removed outlier: 4.260A pdb=" N THR F1844 " --> pdb=" O ARG F1841 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N SER F1845 " --> pdb=" O MET F1842 " (cutoff:3.500A) Processing helix chain 'F' and resid 1857 through 1866 removed outlier: 3.566A pdb=" N VAL F1865 " --> pdb=" O LEU F1861 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'F' and resid 135 through 137 removed outlier: 3.669A pdb=" N TYR F 305 " --> pdb=" O GLU F 135 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'F' and resid 149 through 152 removed outlier: 3.616A pdb=" N PHE F 198 " --> pdb=" O ILE F 151 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N SER F 236 " --> pdb=" O VAL F 197 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'F' and resid 260 through 262 Processing sheet with id= D, first strand: chain 'F' and resid 1041 through 1044 Processing sheet with id= E, first strand: chain 'F' and resid 1178 through 1180 removed outlier: 6.511A pdb=" N VAL F1150 " --> pdb=" O VAL F1179 " (cutoff:3.500A) removed outlier: 5.796A pdb=" N VAL F1073 " --> pdb=" O ILE F1151 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N TYR F1074 " --> pdb=" O LEU F1124 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N THR F1126 " --> pdb=" O TYR F1074 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'F' and resid 1233 through 1236 Processing sheet with id= G, first strand: chain 'F' and resid 1629 through 1632 removed outlier: 6.920A pdb=" N VAL F1655 " --> pdb=" O GLY F1630 " (cutoff:3.500A) removed outlier: 8.421A pdb=" N HIS F1632 " --> pdb=" O VAL F1655 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N PHE F1657 " --> pdb=" O HIS F1632 " (cutoff:3.500A) No H-bonds generated for sheet with id= G 307 hydrogen bonds defined for protein. 735 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: 3.90 Time building geometry restraints manager: 4.94 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: 12072 3.25 - 4.07: 29261 4.07 - 4.90: 49382 Warning: very small nonbonded interaction distances. Nonbonded interactions: 90784 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 90779 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: 1.400 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: 6.440 Check model and map are aligned: 0.180 Set scattering table: 0.100 Process input model: 34.210 Find NCS groups from input model: 0.300 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: 0.010 Load rotamer database and sin/cos tables:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.360 ------------------------------------------------------------------------------- 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= 2.001 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 : 1.561 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 outliers start: 34 outliers final: 9 residues processed: 417 average time/residue: 0.3324 time to fit residues: 184.4487 Evaluate side-chains 237 residues out of total 1318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 228 time to evaluate : 1.279 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 1 residues processed: 9 average time/residue: 0.1671 time to fit residues: 4.1942 ------------------------------------------------------------------------------- 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: 6.9990 chunk 63 optimal weight: 10.0000 chunk 39 optimal weight: 1.9990 chunk 77 optimal weight: 0.0010 chunk 61 optimal weight: 20.0000 chunk 119 optimal weight: 6.9990 chunk 46 optimal weight: 0.9980 chunk 72 optimal weight: 5.9990 chunk 88 optimal weight: 7.9990 chunk 138 optimal weight: 4.9990 overall best weight: 2.7992 ------------------------------------------------------------------------------- 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** ** F1219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F1308 ASN F1369 ASN ** F1473 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1632 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5279 moved from start: 0.4641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 12525 Z= 0.287 Angle : 1.200 13.846 16887 Z= 0.628 Chirality : 0.086 2.384 1829 Planarity : 0.008 0.093 2193 Dihedral : 13.331 85.087 1674 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 16.12 Ramachandran Plot: Outliers : 2.95 % Allowed : 17.37 % Favored : 79.68 % Rotamer: Outliers : 0.46 % Allowed : 5.24 % Favored : 94.31 % Cbeta Deviations : 0.28 % Peptide Plane: Cis-proline : 5.66 % Cis-general : 3.03 % Twisted Proline : 9.43 % Twisted General : 4.61 % 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: -4.95 (0.17), residues: 1491 helix: -2.47 (0.17), residues: 602 sheet: -2.22 (0.63), residues: 50 loop : -4.20 (0.17), residues: 839 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.003 TRP F 255 HIS 0.015 0.002 HIS F1118 PHE 0.036 0.003 PHE F 140 TYR 0.027 0.002 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 301 residues out of total 1318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 295 time to evaluate : 1.890 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 outliers start: 6 outliers final: 2 residues processed: 298 average time/residue: 0.3059 time to fit residues: 124.3537 Evaluate side-chains 200 residues out of total 1318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 198 time to evaluate : 1.305 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.3455 time to fit residues: 2.7846 ------------------------------------------------------------------------------- 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: 6.9990 chunk 42 optimal weight: 2.9990 chunk 114 optimal weight: 0.0030 chunk 93 optimal weight: 2.9990 chunk 38 optimal weight: 8.9990 chunk 138 optimal weight: 40.0000 chunk 149 optimal weight: 4.9990 chunk 123 optimal weight: 10.0000 chunk 137 optimal weight: 7.9990 chunk 47 optimal weight: 8.9990 chunk 110 optimal weight: 10.0000 overall best weight: 3.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 288 HIS ** F 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 725 GLN ** F 838 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 839 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F1001 GLN F1118 HIS F1122 GLN F1196 ASN ** F1205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F1232 ASN ** F1308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F1339 GLN F1361 HIS ** F1369 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F1473 GLN F1626 GLN ** F1632 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1683 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F1704 HIS F1729 ASN F1780 ASN ** F1808 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5361 moved from start: 0.5821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 12525 Z= 0.263 Angle : 1.074 13.254 16887 Z= 0.558 Chirality : 0.061 1.191 1829 Planarity : 0.006 0.096 2193 Dihedral : 11.418 73.048 1674 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 17.19 Ramachandran Plot: Outliers : 2.55 % Allowed : 17.17 % Favored : 80.28 % Rotamer: Outliers : 0.15 % Allowed : 3.64 % Favored : 96.21 % Cbeta Deviations : 0.21 % Peptide Plane: Cis-proline : 5.66 % Cis-general : 3.09 % Twisted Proline : 9.43 % Twisted General : 2.89 % 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: -4.18 (0.19), residues: 1491 helix: -1.50 (0.19), residues: 590 sheet: -1.61 (0.60), residues: 69 loop : -4.07 (0.17), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP F 851 HIS 0.012 0.002 HIS F1219 PHE 0.034 0.002 PHE F1013 TYR 0.030 0.002 TYR F 828 ARG 0.008 0.001 ARG F1651 *********************** 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 267 residues out of total 1318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 265 time to evaluate : 1.476 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 outliers start: 2 outliers final: 0 residues processed: 265 average time/residue: 0.3059 time to fit residues: 112.1267 Evaluate side-chains 196 residues out of total 1318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 196 time to evaluate : 1.428 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.0598 ------------------------------------------------------------------------------- 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: 30.0000 chunk 103 optimal weight: 20.0000 chunk 71 optimal weight: 9.9990 chunk 15 optimal weight: 5.9990 chunk 65 optimal weight: 9.9990 chunk 92 optimal weight: 20.0000 chunk 138 optimal weight: 4.9990 chunk 146 optimal weight: 8.9990 chunk 72 optimal weight: 6.9990 chunk 131 optimal weight: 9.9990 chunk 39 optimal weight: 4.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 288 HIS ** F 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 678 ASN F 725 GLN ** F 839 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F1001 GLN F1115 HIS F1163 ASN F1196 ASN ** F1205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1308 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1548 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1632 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1683 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1704 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F1751 HIS F1754 ASN F1772 ASN ** F1808 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F1852 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5563 moved from start: 0.6670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 12525 Z= 0.303 Angle : 1.066 12.754 16887 Z= 0.553 Chirality : 0.055 0.696 1829 Planarity : 0.007 0.093 2193 Dihedral : 10.825 70.206 1674 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 21.17 Ramachandran Plot: Outliers : 2.35 % Allowed : 18.71 % Favored : 78.94 % Rotamer: Outliers : 0.08 % Allowed : 5.08 % Favored : 94.84 % Cbeta Deviations : 0.14 % Peptide Plane: Cis-proline : 5.66 % Cis-general : 3.09 % Twisted Proline : 9.43 % Twisted General : 2.13 % 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: -4.07 (0.19), residues: 1491 helix: -1.32 (0.20), residues: 591 sheet: -1.36 (0.58), residues: 72 loop : -4.13 (0.18), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP F 851 HIS 0.010 0.002 HIS F1652 PHE 0.023 0.003 PHE F1468 TYR 0.032 0.002 TYR F 926 ARG 0.024 0.001 ARG F1476 *********************** 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 250 residues out of total 1318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 249 time to evaluate : 1.521 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 outliers start: 1 outliers final: 0 residues processed: 250 average time/residue: 0.3009 time to fit residues: 103.8950 Evaluate side-chains 188 residues out of total 1318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 188 time to evaluate : 1.442 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.0948 ------------------------------------------------------------------------------- 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: 2.9990 chunk 83 optimal weight: 10.0000 chunk 2 optimal weight: 10.0000 chunk 109 optimal weight: 40.0000 chunk 60 optimal weight: 4.9990 chunk 125 optimal weight: 10.0000 chunk 101 optimal weight: 20.0000 chunk 0 optimal weight: 20.0000 chunk 75 optimal weight: 6.9990 chunk 131 optimal weight: 7.9990 chunk 37 optimal weight: 10.0000 overall best weight: 6.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 725 GLN F 839 GLN ** F 956 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F1001 GLN F1024 ASN F1196 ASN ** F1205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F1257 ASN F1351 ASN ** F1383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F1431 GLN ** F1548 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1632 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1683 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F1704 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5597 moved from start: 0.7220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 12525 Z= 0.298 Angle : 1.049 12.725 16887 Z= 0.542 Chirality : 0.056 0.669 1829 Planarity : 0.006 0.095 2193 Dihedral : 10.403 68.193 1674 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 20.35 Ramachandran Plot: Outliers : 1.95 % Allowed : 18.65 % Favored : 79.41 % Rotamer: Outliers : 0.15 % Allowed : 4.17 % Favored : 95.68 % Cbeta Deviations : 0.21 % Peptide Plane: Cis-proline : 5.66 % Cis-general : 3.09 % Twisted Proline : 9.43 % Twisted General : 1.79 % 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: -4.07 (0.19), residues: 1491 helix: -1.26 (0.20), residues: 586 sheet: -0.75 (0.72), residues: 53 loop : -4.16 (0.18), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP F 851 HIS 0.015 0.002 HIS F1219 PHE 0.023 0.003 PHE F1294 TYR 0.026 0.003 TYR F 296 ARG 0.011 0.001 ARG F1476 *********************** 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 244 residues out of total 1318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 242 time to evaluate : 1.355 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 244 average time/residue: 0.2855 time to fit residues: 96.0768 Evaluate side-chains 183 residues out of total 1318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 183 time to evaluate : 1.396 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.9174 ------------------------------------------------------------------------------- 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: 2.9990 chunk 132 optimal weight: 8.9990 chunk 29 optimal weight: 0.9990 chunk 86 optimal weight: 0.0770 chunk 36 optimal weight: 20.0000 chunk 147 optimal weight: 40.0000 chunk 122 optimal weight: 7.9990 chunk 68 optimal weight: 10.0000 chunk 12 optimal weight: 5.9990 chunk 48 optimal weight: 8.9990 chunk 77 optimal weight: 6.9990 overall best weight: 3.4146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 725 GLN ** F 956 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F1001 GLN ** F1118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F1383 ASN F1433 GLN ** F1548 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1632 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1683 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F1704 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5496 moved from start: 0.7523 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= 0.229 Angle : 0.973 13.094 16887 Z= 0.503 Chirality : 0.053 0.658 1829 Planarity : 0.006 0.092 2193 Dihedral : 9.648 63.630 1674 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 18.59 Ramachandran Plot: Outliers : 1.88 % Allowed : 18.04 % Favored : 80.08 % Rotamer: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Cbeta Deviations : 0.14 % Peptide Plane: Cis-proline : 5.66 % Cis-general : 3.09 % Twisted Proline : 9.43 % Twisted General : 1.24 % 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: -3.71 (0.20), residues: 1491 helix: -0.83 (0.20), residues: 585 sheet: -0.95 (0.61), residues: 72 loop : -4.09 (0.18), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP F 851 HIS 0.011 0.001 HIS F1643 PHE 0.024 0.002 PHE F1294 TYR 0.021 0.002 TYR F1744 ARG 0.007 0.001 ARG F1201 *********************** 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 244 residues out of total 1318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 244 time to evaluate : 1.413 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 outliers start: 0 outliers final: 0 residues processed: 244 average time/residue: 0.2925 time to fit residues: 98.9222 Evaluate side-chains 179 residues out of total 1318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 179 time to evaluate : 1.367 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.9679 ------------------------------------------------------------------------------- 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: 2.9990 chunk 83 optimal weight: 3.9990 chunk 107 optimal weight: 5.9990 chunk 123 optimal weight: 8.9990 chunk 82 optimal weight: 10.0000 chunk 146 optimal weight: 0.7980 chunk 91 optimal weight: 0.0670 chunk 89 optimal weight: 8.9990 chunk 67 optimal weight: 0.0010 chunk 90 optimal weight: 0.5980 overall best weight: 0.8926 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 218 ASN ** F 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 725 GLN ** F 839 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 930 HIS F 956 HIS F1001 GLN ** F1017 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F1190 GLN ** F1205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F1473 GLN ** F1632 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 0.5379 moved from start: 0.7829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 12525 Z= 0.196 Angle : 0.949 12.242 16887 Z= 0.486 Chirality : 0.051 0.627 1829 Planarity : 0.005 0.089 2193 Dihedral : 9.073 57.345 1674 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 17.23 Ramachandran Plot: Outliers : 1.54 % Allowed : 17.37 % Favored : 81.09 % Rotamer: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Cbeta Deviations : 0.14 % Peptide Plane: Cis-proline : 5.66 % Cis-general : 3.09 % Twisted Proline : 9.43 % Twisted General : 1.10 % 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: -3.48 (0.20), residues: 1491 helix: -0.60 (0.21), residues: 585 sheet: -0.70 (0.63), residues: 75 loop : -4.01 (0.18), residues: 831 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP F1028 HIS 0.010 0.001 HIS F1643 PHE 0.035 0.002 PHE F 12 TYR 0.020 0.002 TYR F 244 ARG 0.006 0.001 ARG F 790 *********************** 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 : 1.507 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 242 average time/residue: 0.3040 time to fit residues: 101.0815 Evaluate side-chains 185 residues out of total 1318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 185 time to evaluate : 1.379 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.9162 ------------------------------------------------------------------------------- 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: 3.9990 chunk 87 optimal weight: 7.9990 chunk 44 optimal weight: 7.9990 chunk 28 optimal weight: 5.9990 chunk 93 optimal weight: 10.0000 chunk 99 optimal weight: 0.3980 chunk 72 optimal weight: 7.9990 chunk 13 optimal weight: 7.9990 chunk 115 optimal weight: 6.9990 chunk 133 optimal weight: 20.0000 chunk 140 optimal weight: 6.9990 overall best weight: 4.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 286 ASN ** F 694 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 725 GLN ** F 839 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 850 HIS F1001 GLN F1017 HIS ** F1118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1548 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1632 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5512 moved from start: 0.8113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 12525 Z= 0.252 Angle : 0.974 12.221 16887 Z= 0.501 Chirality : 0.053 0.626 1829 Planarity : 0.006 0.090 2193 Dihedral : 9.147 56.177 1674 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 20.72 Ramachandran Plot: Outliers : 1.48 % Allowed : 18.85 % Favored : 79.68 % Rotamer: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Cbeta Deviations : 0.14 % 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: -3.52 (0.20), residues: 1491 helix: -0.57 (0.21), residues: 582 sheet: -0.96 (0.61), residues: 75 loop : -4.05 (0.18), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP F 206 HIS 0.007 0.002 HIS F1808 PHE 0.026 0.002 PHE F1294 TYR 0.032 0.002 TYR F1104 ARG 0.010 0.001 ARG F 291 *********************** 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 228 residues out of total 1318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 228 time to evaluate : 1.434 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 228 average time/residue: 0.2973 time to fit residues: 93.2883 Evaluate side-chains 173 residues out of total 1318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 173 time to evaluate : 1.320 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.9065 ------------------------------------------------------------------------------- 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: 20.0000 chunk 136 optimal weight: 9.9990 chunk 140 optimal weight: 20.0000 chunk 82 optimal weight: 0.0000 chunk 59 optimal weight: 0.9990 chunk 107 optimal weight: 6.9990 chunk 41 optimal weight: 10.0000 chunk 123 optimal weight: 0.0980 chunk 129 optimal weight: 8.9990 chunk 89 optimal weight: 40.0000 chunk 144 optimal weight: 0.0070 overall best weight: 1.6206 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 694 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 725 GLN ** F 839 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 850 HIS F1001 GLN ** F1118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F1339 GLN ** F1548 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1632 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5395 moved from start: 0.8350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 12525 Z= 0.201 Angle : 0.940 13.128 16887 Z= 0.481 Chirality : 0.051 0.593 1829 Planarity : 0.005 0.091 2193 Dihedral : 8.693 56.098 1674 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 17.68 Ramachandran Plot: Outliers : 1.48 % Allowed : 17.04 % Favored : 81.49 % Rotamer: Outliers : 0.00 % Allowed : 0.76 % Favored : 99.24 % Cbeta Deviations : 0.14 % Peptide Plane: Cis-proline : 5.66 % Cis-general : 3.09 % Twisted Proline : 9.43 % 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: -3.40 (0.20), residues: 1491 helix: -0.43 (0.21), residues: 576 sheet: -1.06 (0.67), residues: 65 loop : -3.94 (0.18), residues: 850 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP F1028 HIS 0.007 0.001 HIS F1643 PHE 0.027 0.002 PHE F1294 TYR 0.017 0.001 TYR F 244 ARG 0.016 0.001 ARG F1201 *********************** 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 221 residues out of total 1318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 221 time to evaluate : 1.420 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 221 average time/residue: 0.3119 time to fit residues: 94.3521 Evaluate side-chains 177 residues out of total 1318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 177 time to evaluate : 1.509 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.7839 ------------------------------------------------------------------------------- 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: 20.0000 chunk 68 optimal weight: 10.0000 chunk 100 optimal weight: 6.9990 chunk 151 optimal weight: 3.9990 chunk 139 optimal weight: 5.9990 chunk 120 optimal weight: 10.0000 chunk 12 optimal weight: 5.9990 chunk 93 optimal weight: 5.9990 chunk 73 optimal weight: 6.9990 chunk 95 optimal weight: 0.0770 chunk 128 optimal weight: 10.0000 overall best weight: 4.4146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 694 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 725 GLN ** F 839 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F1001 GLN ** F1118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F1431 GLN ** F1548 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1632 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F1754 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5510 moved from start: 0.8522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 12525 Z= 0.248 Angle : 0.963 12.964 16887 Z= 0.493 Chirality : 0.052 0.600 1829 Planarity : 0.006 0.091 2193 Dihedral : 8.778 54.495 1674 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 20.80 Ramachandran Plot: Outliers : 1.54 % Allowed : 18.85 % Favored : 79.61 % Rotamer: Outliers : 0.00 % Allowed : 0.61 % Favored : 99.39 % Cbeta Deviations : 0.14 % 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: -3.51 (0.20), residues: 1491 helix: -0.60 (0.21), residues: 577 sheet: -0.98 (0.66), residues: 69 loop : -3.97 (0.18), residues: 845 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP F 851 HIS 0.007 0.001 HIS F1808 PHE 0.031 0.002 PHE F1294 TYR 0.026 0.002 TYR F 926 ARG 0.012 0.001 ARG F1201 ********************** 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 215 residues out of total 1318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 215 time to evaluate : 1.274 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 215 average time/residue: 0.2995 time to fit residues: 89.3554 Evaluate side-chains 178 residues out of total 1318 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 178 time to evaluate : 1.426 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.0787 ------------------------------------------------------------------------------- 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: 20.0000 chunk 111 optimal weight: 0.1980 chunk 17 optimal weight: 8.9990 chunk 33 optimal weight: 6.9990 chunk 120 optimal weight: 9.9990 chunk 50 optimal weight: 5.9990 chunk 124 optimal weight: 3.9990 chunk 15 optimal weight: 9.9990 chunk 22 optimal weight: 5.9990 chunk 106 optimal weight: 20.0000 chunk 6 optimal weight: 4.9990 overall best weight: 4.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 694 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 725 GLN ** F 839 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F1001 GLN ** F1118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F1431 GLN ** F1548 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1632 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 = 0.4409 r_free = 0.4409 target = 0.167320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.4263 r_free = 0.4263 target = 0.155634 restraints weight = 46828.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.4283 r_free = 0.4283 target = 0.157163 restraints weight = 33792.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 69)----------------| | r_work = 0.4298 r_free = 0.4298 target = 0.158385 restraints weight = 26077.131| |-----------------------------------------------------------------------------| r_work (final): 0.4299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6179 moved from start: 0.8701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 12525 Z= 0.239 Angle : 0.951 12.972 16887 Z= 0.490 Chirality : 0.051 0.572 1829 Planarity : 0.006 0.091 2193 Dihedral : 8.695 54.433 1674 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 19.61 Ramachandran Plot: Outliers : 1.41 % Allowed : 18.71 % Favored : 79.88 % Rotamer: Outliers : 0.00 % Allowed : 0.53 % Favored : 99.47 % Cbeta Deviations : 0.14 % 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: -3.48 (0.20), residues: 1491 helix: -0.56 (0.21), residues: 569 sheet: -1.09 (0.68), residues: 70 loop : -3.92 (0.18), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP F 851 HIS 0.007 0.001 HIS F1808 PHE 0.028 0.002 PHE F1294 TYR 0.020 0.002 TYR F1104 ARG 0.010 0.001 ARG F1201 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2865.56 seconds wall clock time: 52 minutes 52.53 seconds (3172.53 seconds total)