Starting phenix.real_space_refine (version: 1.21rc1) on Wed Aug 16 05:20:20 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u5u_26359/08_2023/7u5u_26359.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u5u_26359/08_2023/7u5u_26359.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.16 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u5u_26359/08_2023/7u5u_26359.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u5u_26359/08_2023/7u5u_26359.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u5u_26359/08_2023/7u5u_26359.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u5u_26359/08_2023/7u5u_26359.pdb" } resolution = 3.16 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= -0.000 sd= 0.036 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 10000 atoms to isotropic. 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: 4 Type Number sf(0) Gaussians S 27 5.16 5 C 6411 2.51 5 N 1697 2.21 5 O 1900 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 897": "OD1" <-> "OD2" Residue "A PHE 937": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 941": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 953": "OE1" <-> "OE2" Residue "A ASP 954": "OD1" <-> "OD2" Residue "A GLU 1004": "OE1" <-> "OE2" Residue "A GLU 1009": "OE1" <-> "OE2" Residue "A PHE 1026": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1062": "OD1" <-> "OD2" Residue "A ASP 1078": "OD1" <-> "OD2" Residue "A ASP 1107": "OD1" <-> "OD2" Residue "A ASP 1125": "OD1" <-> "OD2" Residue "A GLU 1130": "OE1" <-> "OE2" Residue "A ASP 1147": "OD1" <-> "OD2" Residue "A ASP 1213": "OD1" <-> "OD2" Residue "A GLU 1261": "OE1" <-> "OE2" Residue "A PHE 1283": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1312": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1321": "OD1" <-> "OD2" Residue "A ASP 1355": "OD1" <-> "OD2" Residue "A GLU 1358": "OE1" <-> "OE2" Residue "A GLU 1370": "OE1" <-> "OE2" Residue "A ASP 1476": "OD1" <-> "OD2" Residue "A ARG 1509": "NH1" <-> "NH2" Residue "A GLU 1518": "OE1" <-> "OE2" Residue "A GLU 1551": "OE1" <-> "OE2" Residue "A GLU 1559": "OE1" <-> "OE2" Residue "B TYR 892": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 917": "OE1" <-> "OE2" Residue "B GLU 944": "OE1" <-> "OE2" Residue "B GLU 1000": "OE1" <-> "OE2" Residue "B GLU 1016": "OE1" <-> "OE2" Residue "B GLU 1035": "OE1" <-> "OE2" Residue "B ASP 1053": "OD1" <-> "OD2" Residue "B GLU 1056": "OE1" <-> "OE2" Residue "B GLU 1062": "OE1" <-> "OE2" Residue "B ASP 1080": "OD1" <-> "OD2" Residue "B GLU 1117": "OE1" <-> "OE2" Residue "B GLU 1121": "OE1" <-> "OE2" Residue "B ASP 1166": "OD1" <-> "OD2" Residue "B GLU 1170": "OE1" <-> "OE2" Residue "B GLU 1209": "OE1" <-> "OE2" Residue "B GLU 1252": "OE1" <-> "OE2" Residue "B PHE 1274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1307": "OE1" <-> "OE2" Residue "B ASP 1310": "OD1" <-> "OD2" Residue "B ASP 1312": "OD1" <-> "OD2" Residue "B ASP 1346": "OD1" <-> "OD2" Residue "B GLU 1349": "OE1" <-> "OE2" Residue "B GLU 1426": "OE1" <-> "OE2" Residue "B GLU 1439": "OE1" <-> "OE2" Residue "B GLU 1444": "OE1" <-> "OE2" Residue "B ASP 1467": "OD1" <-> "OD2" Residue "B GLU 1475": "OE1" <-> "OE2" Residue "B GLU 1509": "OE1" <-> "OE2" Residue "B GLU 1550": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/modules/chem_data/mon_lib" Total number of atoms: 10035 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4983 Number of conformers: 1 Conformer: "" Number of residues, atoms: 638, 4983 Classifications: {'peptide': 638} Link IDs: {'PTRANS': 25, 'TRANS': 612} Chain breaks: 3 Chain: "B" Number of atoms: 5052 Number of conformers: 1 Conformer: "" Number of residues, atoms: 645, 5052 Classifications: {'peptide': 645} Link IDs: {'PTRANS': 25, 'TRANS': 619} Chain breaks: 3 Time building chain proxies: 5.28, per 1000 atoms: 0.53 Number of scatterers: 10035 At special positions: 0 Unit cell: (88.7145, 128.699, 124.95, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 27 16.00 O 1900 8.00 N 1697 7.00 C 6411 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: 3.73 Conformation dependent library (CDL) restraints added in 1.4 seconds 2534 Ramachandran restraints generated. 1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2366 Finding SS restraints... Secondary structure from input PDB file: 59 helices and 11 sheets defined 41.5% alpha, 13.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.13 Creating SS restraints... Processing helix chain 'A' and resid 883 through 892 Processing helix chain 'A' and resid 924 through 930 removed outlier: 3.853A pdb=" N ILE A 928 " --> pdb=" O GLN A 924 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N VAL A 929 " --> pdb=" O GLU A 925 " (cutoff:3.500A) Processing helix chain 'A' and resid 931 through 935 Processing helix chain 'A' and resid 948 through 952 removed outlier: 3.961A pdb=" N GLY A 952 " --> pdb=" O ILE A 949 " (cutoff:3.500A) Processing helix chain 'A' and resid 953 through 966 removed outlier: 3.613A pdb=" N GLN A 957 " --> pdb=" O GLU A 953 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N LEU A 959 " --> pdb=" O ALA A 955 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N TYR A 962 " --> pdb=" O GLN A 958 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ALA A 963 " --> pdb=" O LEU A 959 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N ASP A 964 " --> pdb=" O LYS A 960 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ASN A 965 " --> pdb=" O SER A 961 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N GLY A 966 " --> pdb=" O TYR A 962 " (cutoff:3.500A) Processing helix chain 'A' and resid 1003 through 1008 Processing helix chain 'A' and resid 1022 through 1033 removed outlier: 3.617A pdb=" N LEU A1029 " --> pdb=" O GLU A1025 " (cutoff:3.500A) Processing helix chain 'A' and resid 1033 through 1041 removed outlier: 3.561A pdb=" N THR A1041 " --> pdb=" O ILE A1037 " (cutoff:3.500A) Processing helix chain 'A' and resid 1069 through 1074 Processing helix chain 'A' and resid 1091 through 1099 removed outlier: 3.514A pdb=" N ALA A1096 " --> pdb=" O ALA A1092 " (cutoff:3.500A) Processing helix chain 'A' and resid 1116 through 1120 removed outlier: 3.604A pdb=" N GLY A1120 " --> pdb=" O VAL A1117 " (cutoff:3.500A) Processing helix chain 'A' and resid 1128 through 1141 removed outlier: 3.593A pdb=" N LEU A1137 " --> pdb=" O SER A1133 " (cutoff:3.500A) Processing helix chain 'A' and resid 1153 through 1158 Processing helix chain 'A' and resid 1184 through 1197 removed outlier: 4.042A pdb=" N LYS A1188 " --> pdb=" O ASN A1184 " (cutoff:3.500A) Processing helix chain 'A' and resid 1211 through 1216 removed outlier: 3.914A pdb=" N LEU A1215 " --> pdb=" O ILE A1211 " (cutoff:3.500A) Processing helix chain 'A' and resid 1238 through 1244 Processing helix chain 'A' and resid 1264 through 1275 removed outlier: 3.522A pdb=" N ASN A1269 " --> pdb=" O ILE A1265 " (cutoff:3.500A) Processing helix chain 'A' and resid 1294 through 1307 removed outlier: 3.727A pdb=" N LEU A1298 " --> pdb=" O ARG A1294 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLY A1302 " --> pdb=" O LEU A1298 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ALA A1305 " --> pdb=" O ALA A1301 " (cutoff:3.500A) Processing helix chain 'A' and resid 1320 through 1325 Processing helix chain 'A' and resid 1340 through 1343 removed outlier: 3.544A pdb=" N LYS A1343 " --> pdb=" O MET A1340 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1340 through 1343' Processing helix chain 'A' and resid 1344 through 1349 removed outlier: 3.610A pdb=" N MET A1347 " --> pdb=" O LEU A1344 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LYS A1348 " --> pdb=" O ASP A1345 " (cutoff:3.500A) Processing helix chain 'A' and resid 1354 through 1361 Processing helix chain 'A' and resid 1379 through 1389 removed outlier: 3.817A pdb=" N PHE A1387 " --> pdb=" O ILE A1383 " (cutoff:3.500A) Processing helix chain 'A' and resid 1408 through 1418 removed outlier: 3.552A pdb=" N GLN A1418 " --> pdb=" O TYR A1414 " (cutoff:3.500A) Processing helix chain 'A' and resid 1435 through 1440 removed outlier: 3.758A pdb=" N LYS A1439 " --> pdb=" O GLU A1435 " (cutoff:3.500A) Processing helix chain 'A' and resid 1454 through 1459 removed outlier: 3.929A pdb=" N LYS A1458 " --> pdb=" O GLN A1454 " (cutoff:3.500A) Processing helix chain 'A' and resid 1476 through 1485 removed outlier: 3.894A pdb=" N LYS A1481 " --> pdb=" O GLY A1477 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ARG A1485 " --> pdb=" O LYS A1481 " (cutoff:3.500A) Processing helix chain 'A' and resid 1511 through 1519 Processing helix chain 'A' and resid 1528 through 1545 removed outlier: 3.717A pdb=" N ARG A1538 " --> pdb=" O ASN A1534 " (cutoff:3.500A) Processing helix chain 'A' and resid 1549 through 1555 Processing helix chain 'B' and resid 874 through 880 Processing helix chain 'B' and resid 919 through 924 removed outlier: 4.585A pdb=" N GLU B 923 " --> pdb=" O ILE B 919 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N CYS B 924 " --> pdb=" O VAL B 920 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 919 through 924' Processing helix chain 'B' and resid 943 through 956 removed outlier: 4.162A pdb=" N ARG B 947 " --> pdb=" O GLY B 943 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N GLN B 948 " --> pdb=" O GLU B 944 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N GLN B 949 " --> pdb=" O ASP B 945 " (cutoff:3.500A) Processing helix chain 'B' and resid 991 through 1002 removed outlier: 3.704A pdb=" N GLU B 995 " --> pdb=" O TRP B 991 " (cutoff:3.500A) removed outlier: 5.449A pdb=" N LYS B 996 " --> pdb=" O LEU B 992 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N TRP B 997 " --> pdb=" O ARG B 993 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N GLU B1000 " --> pdb=" O LYS B 996 " (cutoff:3.500A) Processing helix chain 'B' and resid 1013 through 1023 removed outlier: 3.826A pdb=" N ARG B1021 " --> pdb=" O PHE B1017 " (cutoff:3.500A) Processing helix chain 'B' and resid 1024 through 1032 removed outlier: 3.502A pdb=" N LEU B1030 " --> pdb=" O ASN B1026 " (cutoff:3.500A) Processing helix chain 'B' and resid 1060 through 1065 Processing helix chain 'B' and resid 1076 through 1078 No H-bonds generated for 'chain 'B' and resid 1076 through 1078' Processing helix chain 'B' and resid 1084 through 1091 removed outlier: 3.857A pdb=" N ALA B1091 " --> pdb=" O ALA B1087 " (cutoff:3.500A) Processing helix chain 'B' and resid 1091 through 1096 Processing helix chain 'B' and resid 1107 through 1111 removed outlier: 3.734A pdb=" N GLY B1111 " --> pdb=" O VAL B1108 " (cutoff:3.500A) Processing helix chain 'B' and resid 1119 through 1132 removed outlier: 3.537A pdb=" N ARG B1131 " --> pdb=" O LEU B1127 " (cutoff:3.500A) Processing helix chain 'B' and resid 1144 through 1152 removed outlier: 4.097A pdb=" N GLU B1150 " --> pdb=" O GLU B1146 " (cutoff:3.500A) Processing helix chain 'B' and resid 1176 through 1188 Processing helix chain 'B' and resid 1202 through 1215 removed outlier: 3.632A pdb=" N LEU B1206 " --> pdb=" O ILE B1202 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ASN B1210 " --> pdb=" O LEU B1206 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N LYS B1213 " --> pdb=" O GLU B1209 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLN B1214 " --> pdb=" O ASN B1210 " (cutoff:3.500A) Processing helix chain 'B' and resid 1229 through 1235 removed outlier: 3.599A pdb=" N GLN B1233 " --> pdb=" O GLY B1229 " (cutoff:3.500A) Processing helix chain 'B' and resid 1255 through 1266 removed outlier: 3.539A pdb=" N ASN B1260 " --> pdb=" O ILE B1256 " (cutoff:3.500A) Processing helix chain 'B' and resid 1285 through 1297 removed outlier: 3.645A pdb=" N ASN B1291 " --> pdb=" O PRO B1287 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ALA B1292 " --> pdb=" O ASN B1288 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ALA B1296 " --> pdb=" O ALA B1292 " (cutoff:3.500A) Processing helix chain 'B' and resid 1312 through 1317 removed outlier: 3.776A pdb=" N ASP B1316 " --> pdb=" O ASP B1312 " (cutoff:3.500A) Processing helix chain 'B' and resid 1332 through 1337 removed outlier: 3.985A pdb=" N ASP B1336 " --> pdb=" O PRO B1332 " (cutoff:3.500A) Processing helix chain 'B' and resid 1345 through 1352 removed outlier: 3.540A pdb=" N GLU B1349 " --> pdb=" O SER B1345 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N THR B1350 " --> pdb=" O ASP B1346 " (cutoff:3.500A) Processing helix chain 'B' and resid 1369 through 1380 removed outlier: 4.203A pdb=" N SER B1377 " --> pdb=" O GLY B1373 " (cutoff:3.500A) Processing helix chain 'B' and resid 1400 through 1410 removed outlier: 3.702A pdb=" N TYR B1405 " --> pdb=" O ARG B1401 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLN B1409 " --> pdb=" O TYR B1405 " (cutoff:3.500A) Processing helix chain 'B' and resid 1426 through 1431 removed outlier: 3.530A pdb=" N SER B1431 " --> pdb=" O GLU B1427 " (cutoff:3.500A) Processing helix chain 'B' and resid 1443 through 1449 removed outlier: 3.734A pdb=" N ALA B1447 " --> pdb=" O THR B1443 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ASP B1448 " --> pdb=" O GLU B1444 " (cutoff:3.500A) Processing helix chain 'B' and resid 1470 through 1478 removed outlier: 3.879A pdb=" N ILE B1474 " --> pdb=" O VAL B1470 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ARG B1476 " --> pdb=" O LYS B1472 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU B1478 " --> pdb=" O ILE B1474 " (cutoff:3.500A) Processing helix chain 'B' and resid 1502 through 1510 removed outlier: 3.545A pdb=" N LYS B1506 " --> pdb=" O THR B1502 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LEU B1507 " --> pdb=" O PRO B1503 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N GLU B1510 " --> pdb=" O LYS B1506 " (cutoff:3.500A) Processing helix chain 'B' and resid 1519 through 1535 removed outlier: 3.686A pdb=" N ASN B1525 " --> pdb=" O GLU B1521 " (cutoff:3.500A) Processing helix chain 'B' and resid 1540 through 1548 removed outlier: 3.865A pdb=" N ARG B1546 " --> pdb=" O GLU B1542 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 872 through 874 Processing sheet with id=AA2, first strand: chain 'A' and resid 894 through 897 removed outlier: 6.976A pdb=" N LYS A 894 " --> pdb=" O VAL A 942 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N SER A 944 " --> pdb=" O LYS A 894 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N LEU A 896 " --> pdb=" O SER A 944 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 1229 through 1232 removed outlier: 6.793A pdb=" N VAL A1202 " --> pdb=" O ILE A1230 " (cutoff:3.500A) removed outlier: 8.173A pdb=" N PHE A1232 " --> pdb=" O VAL A1202 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N LEU A1204 " --> pdb=" O PHE A1232 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N VAL A1169 " --> pdb=" O ILE A1201 " (cutoff:3.500A) removed outlier: 7.417A pdb=" N ARG A1203 " --> pdb=" O VAL A1169 " (cutoff:3.500A) removed outlier: 5.853A pdb=" N GLY A1171 " --> pdb=" O ARG A1203 " (cutoff:3.500A) removed outlier: 7.410A pdb=" N VAL A1205 " --> pdb=" O GLY A1171 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N TYR A1173 " --> pdb=" O VAL A1205 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N VAL A1080 " --> pdb=" O ILE A1111 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N THR A1113 " --> pdb=" O VAL A1080 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N LEU A1082 " --> pdb=" O THR A1113 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N ALA A1054 " --> pdb=" O ALA A1079 " (cutoff:3.500A) removed outlier: 7.517A pdb=" N GLU A1081 " --> pdb=" O ALA A1054 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N VAL A1056 " --> pdb=" O GLU A1081 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N ARG A1083 " --> pdb=" O VAL A1056 " (cutoff:3.500A) removed outlier: 7.585A pdb=" N LEU A1058 " --> pdb=" O ARG A1083 " (cutoff:3.500A) removed outlier: 5.922A pdb=" N ALA A1055 " --> pdb=" O ILE A1251 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1311 through 1316 removed outlier: 3.678A pdb=" N GLY A1287 " --> pdb=" O PHE A1315 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N LYS A1282 " --> pdb=" O GLY A1334 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N LEU A1336 " --> pdb=" O LYS A1282 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N TRP A1284 " --> pdb=" O LEU A1336 " (cutoff:3.500A) removed outlier: 5.594A pdb=" N ILE A1338 " --> pdb=" O TRP A1284 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N ILE A1286 " --> pdb=" O ILE A1338 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 1352 through 1353 removed outlier: 6.603A pdb=" N LYS A1352 " --> pdb=" O GLY A1375 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N GLY A1372 " --> pdb=" O ILE A1369 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 1447 through 1449 removed outlier: 6.356A pdb=" N ILE A1424 " --> pdb=" O GLU A1448 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N GLY A1400 " --> pdb=" O TYR A1425 " (cutoff:3.500A) removed outlier: 7.952A pdb=" N VAL A1427 " --> pdb=" O GLY A1400 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N VAL A1402 " --> pdb=" O VAL A1427 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N ASN A1399 " --> pdb=" O VAL A1462 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N LEU A1401 " --> pdb=" O LEU A1464 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N SER A1463 " --> pdb=" O THR A1500 " (cutoff:3.500A) removed outlier: 8.241A pdb=" N LEU A1502 " --> pdb=" O SER A1463 " (cutoff:3.500A) removed outlier: 7.486A pdb=" N ALA A1465 " --> pdb=" O LEU A1502 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 861 through 864 removed outlier: 6.438A pdb=" N ILE B 862 " --> pdb=" O LEU B 961 " (cutoff:3.500A) removed outlier: 7.659A pdb=" N LEU B 963 " --> pdb=" O ILE B 862 " (cutoff:3.500A) removed outlier: 7.429A pdb=" N ILE B 864 " --> pdb=" O LEU B 963 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 885 through 886 removed outlier: 6.909A pdb=" N LYS B 885 " --> pdb=" O VAL B 933 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'B' and resid 1220 through 1225 removed outlier: 6.222A pdb=" N VAL B1160 " --> pdb=" O ILE B1192 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N ARG B1194 " --> pdb=" O VAL B1160 " (cutoff:3.500A) removed outlier: 5.840A pdb=" N GLY B1162 " --> pdb=" O ARG B1194 " (cutoff:3.500A) removed outlier: 7.439A pdb=" N VAL B1196 " --> pdb=" O GLY B1162 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N TYR B1164 " --> pdb=" O VAL B1196 " (cutoff:3.500A) removed outlier: 8.407A pdb=" N LYS B1198 " --> pdb=" O TYR B1164 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N VAL B1137 " --> pdb=" O ILE B1161 " (cutoff:3.500A) removed outlier: 7.649A pdb=" N THR B1163 " --> pdb=" O VAL B1137 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N LEU B1139 " --> pdb=" O THR B1163 " (cutoff:3.500A) removed outlier: 8.643A pdb=" N GLN B1165 " --> pdb=" O LEU B1139 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N VAL B1071 " --> pdb=" O ILE B1102 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N THR B1104 " --> pdb=" O VAL B1071 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N LEU B1073 " --> pdb=" O THR B1104 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N ALA B1045 " --> pdb=" O ALA B1070 " (cutoff:3.500A) removed outlier: 7.782A pdb=" N GLU B1072 " --> pdb=" O ALA B1045 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N VAL B1047 " --> pdb=" O GLU B1072 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N ARG B1074 " --> pdb=" O VAL B1047 " (cutoff:3.500A) removed outlier: 7.513A pdb=" N LEU B1049 " --> pdb=" O ARG B1074 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 1302 through 1307 removed outlier: 3.729A pdb=" N GLY B1278 " --> pdb=" O PHE B1306 " (cutoff:3.500A) removed outlier: 5.518A pdb=" N LYS B1273 " --> pdb=" O PHE B1324 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N GLY B1326 " --> pdb=" O LYS B1273 " (cutoff:3.500A) removed outlier: 7.927A pdb=" N GLY B1325 " --> pdb=" O PRO B1359 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLY B1363 " --> pdb=" O ILE B1360 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N LYS B1343 " --> pdb=" O GLY B1366 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 1438 through 1440 removed outlier: 6.089A pdb=" N ILE B1415 " --> pdb=" O GLU B1439 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N TYR B1416 " --> pdb=" O GLY B1391 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N ASN B1390 " --> pdb=" O VAL B1453 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N LEU B1455 " --> pdb=" O ASN B1390 " (cutoff:3.500A) 295 hydrogen bonds defined for protein. 852 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: 3.01 Time building geometry restraints manager: 4.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3251 1.34 - 1.46: 1880 1.46 - 1.57: 5058 1.57 - 1.69: 0 1.69 - 1.81: 44 Bond restraints: 10233 Sorted by residual: bond pdb=" C ILE B1329 " pdb=" N THR B1330 " ideal model delta sigma weight residual 1.333 1.363 -0.030 1.30e-02 5.92e+03 5.27e+00 bond pdb=" N ARG A1002 " pdb=" CA ARG A1002 " ideal model delta sigma weight residual 1.457 1.485 -0.029 1.33e-02 5.65e+03 4.62e+00 bond pdb=" CB VAL B1524 " pdb=" CG2 VAL B1524 " ideal model delta sigma weight residual 1.521 1.455 0.066 3.30e-02 9.18e+02 3.96e+00 bond pdb=" CG1 ILE A1102 " pdb=" CD1 ILE A1102 " ideal model delta sigma weight residual 1.513 1.436 0.077 3.90e-02 6.57e+02 3.94e+00 bond pdb=" CB LEU A1217 " pdb=" CG LEU A1217 " ideal model delta sigma weight residual 1.530 1.501 0.029 2.00e-02 2.50e+03 2.12e+00 ... (remaining 10228 not shown) Histogram of bond angle deviations from ideal: 99.24 - 106.42: 262 106.42 - 113.61: 5621 113.61 - 120.79: 4662 120.79 - 127.98: 3223 127.98 - 135.16: 79 Bond angle restraints: 13847 Sorted by residual: angle pdb=" N VAL A1067 " pdb=" CA VAL A1067 " pdb=" C VAL A1067 " ideal model delta sigma weight residual 113.53 109.04 4.49 9.80e-01 1.04e+00 2.10e+01 angle pdb=" C PHE A1497 " pdb=" N LYS A1498 " pdb=" CA LYS A1498 " ideal model delta sigma weight residual 120.94 129.12 -8.18 1.90e+00 2.77e-01 1.85e+01 angle pdb=" C GLU A1260 " pdb=" N GLU A1261 " pdb=" CA GLU A1261 " ideal model delta sigma weight residual 122.82 128.48 -5.66 1.42e+00 4.96e-01 1.59e+01 angle pdb=" C VAL A1047 " pdb=" N VAL A1048 " pdb=" CA VAL A1048 " ideal model delta sigma weight residual 122.13 128.28 -6.15 1.85e+00 2.92e-01 1.10e+01 angle pdb=" N GLY A1068 " pdb=" CA GLY A1068 " pdb=" C GLY A1068 " ideal model delta sigma weight residual 115.66 110.55 5.11 1.56e+00 4.11e-01 1.07e+01 ... (remaining 13842 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.07: 5367 17.07 - 34.13: 609 34.13 - 51.20: 120 51.20 - 68.26: 27 68.26 - 85.33: 11 Dihedral angle restraints: 6134 sinusoidal: 2450 harmonic: 3684 Sorted by residual: dihedral pdb=" CA MET B1331 " pdb=" C MET B1331 " pdb=" N PRO B1332 " pdb=" CA PRO B1332 " ideal model delta harmonic sigma weight residual 180.00 150.01 29.99 0 5.00e+00 4.00e-02 3.60e+01 dihedral pdb=" CA VAL A1047 " pdb=" C VAL A1047 " pdb=" N VAL A1048 " pdb=" CA VAL A1048 " ideal model delta harmonic sigma weight residual 180.00 153.51 26.49 0 5.00e+00 4.00e-02 2.81e+01 dihedral pdb=" CA VAL A1048 " pdb=" C VAL A1048 " pdb=" N PRO A1049 " pdb=" CA PRO A1049 " ideal model delta harmonic sigma weight residual 180.00 -154.10 -25.90 0 5.00e+00 4.00e-02 2.68e+01 ... (remaining 6131 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 964 0.048 - 0.096: 481 0.096 - 0.144: 92 0.144 - 0.192: 20 0.192 - 0.240: 6 Chirality restraints: 1563 Sorted by residual: chirality pdb=" CB VAL B1137 " pdb=" CA VAL B1137 " pdb=" CG1 VAL B1137 " pdb=" CG2 VAL B1137 " both_signs ideal model delta sigma weight residual False -2.63 -2.39 -0.24 2.00e-01 2.50e+01 1.44e+00 chirality pdb=" CB VAL A1381 " pdb=" CA VAL A1381 " pdb=" CG1 VAL A1381 " pdb=" CG2 VAL A1381 " both_signs ideal model delta sigma weight residual False -2.63 -2.42 -0.21 2.00e-01 2.50e+01 1.13e+00 chirality pdb=" CA SER B1279 " pdb=" N SER B1279 " pdb=" C SER B1279 " pdb=" CB SER B1279 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.13e+00 ... (remaining 1560 not shown) Planarity restraints: 1780 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C MET B1331 " 0.062 5.00e-02 4.00e+02 9.50e-02 1.44e+01 pdb=" N PRO B1332 " -0.164 5.00e-02 4.00e+02 pdb=" CA PRO B1332 " 0.051 5.00e-02 4.00e+02 pdb=" CD PRO B1332 " 0.051 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR B1502 " -0.046 5.00e-02 4.00e+02 6.97e-02 7.77e+00 pdb=" N PRO B1503 " 0.121 5.00e-02 4.00e+02 pdb=" CA PRO B1503 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO B1503 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS B1218 " -0.043 5.00e-02 4.00e+02 6.52e-02 6.81e+00 pdb=" N PRO B1219 " 0.113 5.00e-02 4.00e+02 pdb=" CA PRO B1219 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO B1219 " -0.036 5.00e-02 4.00e+02 ... (remaining 1777 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 2936 2.80 - 3.33: 8603 3.33 - 3.85: 16690 3.85 - 4.38: 20307 4.38 - 4.90: 33899 Nonbonded interactions: 82435 Sorted by model distance: nonbonded pdb=" OE2 GLU A1081 " pdb=" OG1 THR A1113 " model vdw 2.279 2.440 nonbonded pdb=" OG SER A 869 " pdb=" O SER A 938 " model vdw 2.291 2.440 nonbonded pdb=" OG1 THR B1050 " pdb=" O PRO B1248 " model vdw 2.296 2.440 nonbonded pdb=" O GLY B 938 " pdb=" OH TYR B 998 " model vdw 2.310 2.440 nonbonded pdb=" O ILE A1037 " pdb=" OG1 THR A1041 " model vdw 2.324 2.440 ... (remaining 82430 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 866 through 874 or resid 882 through 1559)) selection = (chain 'B' and (resid 857 through 889 or resid 914 through 964 or resid 992 thro \ ugh 1550)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.010 Normalize map: mean=0, sd=1: 4.300 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.100 Construct map_model_manager: 0.010 Extract box with map and model: 14.260 Check model and map are aligned: 0.140 Set scattering table: 0.090 Process input model: 28.370 Find NCS groups from input model: 0.670 Set up NCS constraints: 0.060 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:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7404 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 : 0.007 0.077 10233 Z= 0.485 Angle : 0.883 10.161 13847 Z= 0.475 Chirality : 0.056 0.240 1563 Planarity : 0.007 0.095 1780 Dihedral : 15.343 85.329 3768 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.67 (0.17), residues: 1267 helix: -4.79 (0.07), residues: 529 sheet: -2.74 (0.28), residues: 269 loop : -2.70 (0.24), residues: 469 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2534 Ramachandran restraints generated. 1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2534 Ramachandran restraints generated. 1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1091 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 220 time to evaluate : 1.222 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 220 average time/residue: 0.2731 time to fit residues: 80.0872 Evaluate side-chains 118 residues out of total 1091 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 118 time to evaluate : 1.157 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.6612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 107 optimal weight: 0.6980 chunk 96 optimal weight: 0.9980 chunk 53 optimal weight: 5.9990 chunk 32 optimal weight: 1.9990 chunk 64 optimal weight: 0.9990 chunk 51 optimal weight: 5.9990 chunk 99 optimal weight: 0.6980 chunk 38 optimal weight: 0.5980 chunk 60 optimal weight: 0.6980 chunk 74 optimal weight: 0.9980 chunk 115 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1198 ASN A1209 ASN B1214 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7438 moved from start: 0.2108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.045 10233 Z= 0.217 Angle : 0.572 7.726 13847 Z= 0.299 Chirality : 0.044 0.205 1563 Planarity : 0.005 0.090 1780 Dihedral : 5.229 22.139 1366 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer Outliers : 2.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.14 (0.20), residues: 1267 helix: -3.28 (0.15), residues: 529 sheet: -2.09 (0.34), residues: 215 loop : -2.20 (0.24), residues: 523 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2534 Ramachandran restraints generated. 1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2534 Ramachandran restraints generated. 1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1091 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 129 time to evaluate : 1.164 Fit side-chains revert: symmetry clash outliers start: 22 outliers final: 14 residues processed: 145 average time/residue: 0.2361 time to fit residues: 48.2613 Evaluate side-chains 115 residues out of total 1091 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 101 time to evaluate : 1.059 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.0963 time to fit residues: 4.0971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 64 optimal weight: 0.0050 chunk 35 optimal weight: 2.9990 chunk 95 optimal weight: 1.9990 chunk 78 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 chunk 115 optimal weight: 3.9990 chunk 124 optimal weight: 0.3980 chunk 102 optimal weight: 0.9990 chunk 114 optimal weight: 0.6980 chunk 39 optimal weight: 0.9990 chunk 92 optimal weight: 3.9990 overall best weight: 0.6196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1535 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1189 ASN B1511 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7448 moved from start: 0.2560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.046 10233 Z= 0.181 Angle : 0.520 7.606 13847 Z= 0.268 Chirality : 0.042 0.190 1563 Planarity : 0.004 0.091 1780 Dihedral : 4.802 22.079 1366 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer Outliers : 1.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.03 (0.22), residues: 1267 helix: -2.11 (0.19), residues: 523 sheet: -1.90 (0.34), residues: 228 loop : -1.69 (0.26), residues: 516 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2534 Ramachandran restraints generated. 1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2534 Ramachandran restraints generated. 1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1091 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 111 time to evaluate : 1.262 Fit side-chains outliers start: 14 outliers final: 6 residues processed: 121 average time/residue: 0.2235 time to fit residues: 39.2028 Evaluate side-chains 105 residues out of total 1091 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 99 time to evaluate : 1.196 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1021 time to fit residues: 2.7004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/modules/cctbx_project/iotbx/cli_parser.py", line 881, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/modules/phenix/phenix/programs/real_space_refine.py", line 192, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 673, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 737, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 67.9321 > 50: distance: 41 - 48: 19.535 distance: 48 - 49: 19.557 distance: 49 - 50: 9.530 distance: 49 - 52: 17.919 distance: 50 - 51: 12.536 distance: 50 - 53: 19.339 distance: 53 - 54: 9.221 distance: 54 - 55: 12.500 distance: 54 - 57: 10.979 distance: 55 - 56: 18.246 distance: 55 - 59: 40.950 distance: 57 - 58: 32.578 distance: 59 - 60: 27.264 distance: 60 - 61: 33.714 distance: 60 - 63: 26.192 distance: 61 - 62: 39.627 distance: 61 - 71: 16.623 distance: 64 - 65: 35.154 distance: 65 - 67: 7.136 distance: 66 - 68: 6.719 distance: 67 - 69: 12.018 distance: 68 - 69: 31.270 distance: 69 - 70: 46.224 distance: 71 - 72: 26.077 distance: 72 - 73: 14.207 distance: 72 - 75: 40.185 distance: 73 - 74: 46.484 distance: 73 - 80: 28.344 distance: 75 - 76: 21.414 distance: 76 - 77: 23.446 distance: 77 - 78: 29.354 distance: 78 - 79: 23.718 distance: 80 - 81: 37.172 distance: 80 - 86: 27.432 distance: 81 - 82: 19.731 distance: 81 - 84: 33.074 distance: 82 - 83: 27.707 distance: 82 - 87: 44.638 distance: 84 - 85: 20.149 distance: 85 - 86: 42.992 distance: 87 - 88: 9.419 distance: 88 - 89: 39.687 distance: 88 - 91: 22.441 distance: 89 - 90: 6.520 distance: 89 - 98: 35.340 distance: 91 - 92: 39.253 distance: 92 - 93: 13.077 distance: 93 - 94: 23.822 distance: 95 - 96: 33.232 distance: 95 - 97: 28.677 distance: 98 - 99: 50.343 distance: 99 - 100: 27.534 distance: 99 - 102: 25.582 distance: 100 - 101: 23.128 distance: 100 - 105: 39.861 distance: 102 - 103: 37.663 distance: 102 - 104: 34.304 distance: 105 - 106: 49.475 distance: 106 - 107: 33.596 distance: 107 - 108: 36.998 distance: 107 - 112: 14.847 distance: 109 - 110: 34.031 distance: 109 - 111: 48.840 distance: 112 - 113: 9.811 distance: 112 - 118: 22.273 distance: 113 - 114: 46.610 distance: 113 - 116: 5.151 distance: 114 - 115: 12.671 distance: 114 - 119: 30.558 distance: 116 - 117: 50.155 distance: 117 - 118: 27.758 distance: 119 - 120: 16.988 distance: 120 - 121: 15.585 distance: 120 - 123: 10.017 distance: 121 - 122: 27.226 distance: 121 - 127: 23.428 distance: 122 - 151: 17.497 distance: 123 - 124: 31.817 distance: 123 - 125: 35.751 distance: 124 - 126: 40.622