/usr/lib/python2.7/dist-packages/csb/test/data/pdbout.txt is in python-csb 1.2.3+dfsg-3.
This file is owned by root:root, with mode 0o644.
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********** REPORT OF PROTEIN ANALYSIS by the WHAT IF program **********
************************************************************************
Date : 2011-01-31
This report was created by WHAT IF version WHATCHECK 8.0
WHAT_CHECK is the name of the validation option in WHAT IF. It
doesn't matter whether you use the WHAT_CHECK program or the
WHAT_CHECK program for validation. Both produce exactly the same
WHAT_CHECK-report.
This document is a WHAT_CHECK-report that holds the findings of
the WHAT IF program
during the analysis of a PDB-file. Each reported fact has
an assigned severity, one of:
error : severe errors encountered during the analyses. Items marked as errors
are considered severe problems requiring immediate attention.
warning: Either less severe problems or uncommon structural features. These
still need special attention.
note : Statistical values, plots, or other verbose results of tests and
analyses that have been performed.
If alternate conformations are present, only the first is evaluated. Hydrogen
atoms are only included if explicitly requested, and even then they are not
used in all checks. The software functions less well for non-canonical amino
acids and exotic ligands than for the 20 canonical residues and canonical
nucleic acids.
Some remarks regarding the output:
Residues/atoms in tables are normally given in a few parts:
A number. This is the internal sequence number of the residue used
by WHAT IF. The first residues in the file get number 1, 2, etc.
The residue type. Normally this is a three letter amino acid type.
The sequence number, between brackets. This is the residue number
as it was given in the input file. It can be followed by the insertion
code.
The chain identifier. A single character. If no chain identifier
was given in the input file, this will be a minus sign or a blank.
A model number. If no model number exists, like in most X-ray files,
this will be a blank or occasionally a minus sign.
In case an atom is part of the output, the atom will be listed using
the PDB nomenclature for type and identifier.
To indicate the normality of a score, the score
may be expressed as a Z-value or Z-score. This is just the number
of standard deviations that the score deviates from the expected
value. A property of Z-values is that the root-mean-square of a
group of Z-values (the RMS Z-value) is expected to be 1.0. Z-values
above 4.0 and below $-4.0$ are very uncommon. If a Z-score is used
in WHAT IF, the accompanying text will explain how the expected
value and standard deviation were obtained.
The names of nucleic acids are DGUA, DTHY, OCYT, OADE, etc. The first
character is a D or O for DNA or RNA respectively.
This is done to circumvent ambiguities in the many old PDB files in which
DNA and RNA were both called A, C, G, and T.
Command line args 2JZC.pdb
========================================================================
==== Compound code 2JZC.pdb ====
========================================================================
# 1 # Note: Cell is 1 Angstrom cube
The unit cell in the CRYST1 card of the PDB file is given as a cube
with vertices of 1 Angstrom. This is the convention for structures
obtained using a method other than crystallography.
The scale matrix found in the PDB file is the unit matrix
DBG> Lines in first NMR model .... : 2215
DBG> Atoms in first NMR model .... : 1584
1 - 10 GLY ILE ILE GLU GLU LYS ALA LEU PHE VAL
11 - 20 THR CYS GLY ALA THR VAL PRO PHE PRO LYS
21 - 30 LEU VAL SER CYS VAL LEU SER ASP GLU PHE
31 - 40 CYS GLN GLU LEU ILE GLN TYR GLY PHE VAL
41 - 50 ARG LEU ILE ILE GLN PHE GLY ARG ASN TYR
51 - 60 SER SER GLU PHE GLU HIS LEU VAL GLN GLU
61 - 70 ARG GLY GLY GLN ARG GLU SER GLN LYS ILE
71 - 80 PRO ILE ASP GLN PHE GLY CYS GLY ASP THR
81 - 90 ALA ARG GLN TYR VAL LEU MET ASN GLY LYS
91 - 100 LEU LYS VAL ILE GLY PHE ASP PHE SER THR
101 - 110 LYS MET GLN SER ILE ILE ARG ASP TYR SER
111 - 120 ASP LEU VAL ILE SER HIS ALA GLY THR GLY
121 - 130 SER ILE LEU ASP SER LEU ARG LEU ASN LYS
131 - 140 PRO LEU ILE VAL CYS VAL ASN ASP SER LEU
141 - 150 MET ASP ASN HIS GLN GLN GLN ILE ALA ASP
151 - 160 LYS PHE VAL GLU LEU GLY TYR VAL TRP SER
161 - 170 CYS ALA PRO THR GLU THR GLY LEU ILE ALA
171 - 180 GLY LEU ARG ALA SER GLN THR GLU LYS LEU
181 - 190 LYS PRO PHE PRO VAL SER HIS ASN PRO SER
191 - 200 PHE GLU ARG LEU LEU VAL GLU THR ILE TYR
201 - 210 SER GLY ILE ILE GLU GLU LYS ALA LEU PHE
211 - 220 VAL THR CYS GLY ALA THR VAL PRO PHE PRO
221 - 230 LYS LEU VAL SER CYS VAL LEU SER ASP GLU
231 - 240 PHE CYS GLN GLU LEU ILE GLN TYR GLY PHE
241 - 250 VAL ARG LEU ILE ILE GLN PHE GLY ARG ASN
251 - 260 TYR SER SER GLU PHE GLU HIS LEU VAL GLN
261 - 270 GLU ARG GLY GLY GLN ARG GLU SER GLN LYS
271 - 280 ILE PRO ILE ASP GLN PHE GLY CYS GLY ASP
281 - 290 THR ALA ARG GLN TYR VAL LEU MET ASN GLY
291 - 300 LYS LEU LYS VAL ILE GLY PHE ASP PHE SER
301 - 310 THR LYS MET GLN SER ILE ILE ARG ASP TYR
311 - 320 SER ASP LEU VAL ILE SER HIS ALA GLY THR
321 - 330 GLY SER ILE LEU ASP SER LEU ARG LEU ASN
331 - 340 LYS PRO LEU ILE VAL CYS VAL ASN ASP SER
341 - 350 LEU MET ASP ASN HIS GLN GLN GLN ILE ALA
351 - 360 ASP LYS PHE VAL GLU LEU GLY TYR VAL TRP
361 - 370 SER CYS ALA PRO THR GLU THR GLY LEU ILE
371 - 380 ALA GLY LEU ARG ALA SER GLN THR GLU LYS
381 - 390 LEU LYS PRO PHE PRO VAL SER HIS ASN PRO
391 - 400 SER PHE GLU ARG LEU LEU VAL GLU THR ILE
401 - 410 TYR SER GLY ILE ILE GLU GLU LYS ALA LEU
411 - 420 PHE VAL THR CYS GLY ALA THR VAL PRO PHE
421 - 430 PRO LYS LEU VAL SER CYS VAL LEU SER ASP
431 - 440 GLU PHE CYS GLN GLU LEU ILE GLN TYR GLY
441 - 450 PHE VAL ARG LEU ILE ILE GLN PHE GLY ARG
451 - 460 ASN TYR SER SER GLU PHE GLU HIS LEU VAL
461 - 470 GLN GLU ARG GLY GLY GLN ARG GLU SER GLN
471 - 480 LYS ILE PRO ILE ASP GLN PHE GLY CYS GLY
481 - 490 ASP THR ALA ARG GLN TYR VAL LEU MET ASN
491 - 500 GLY LYS LEU LYS VAL ILE GLY PHE ASP PHE
501 - 510 SER THR LYS MET GLN SER ILE ILE ARG ASP
511 - 520 TYR SER ASP LEU VAL ILE SER HIS ALA GLY
521 - 530 THR GLY SER ILE LEU ASP SER LEU ARG LEU
531 - 540 ASN LYS PRO LEU ILE VAL CYS VAL ASN ASP
541 - 550 SER LEU MET ASP ASN HIS GLN GLN GLN ILE
551 - 560 ALA ASP LYS PHE VAL GLU LEU GLY TYR VAL
561 - 570 TRP SER CYS ALA PRO THR GLU THR GLY LEU
571 - 580 ILE ALA GLY LEU ARG ALA SER GLN THR GLU
581 - 590 LYS LEU LYS PRO PHE PRO VAL SER HIS ASN
591 - 600 PRO SER PHE GLU ARG LEU LEU VAL GLU THR
601 - 610 ILE TYR SER GLY ILE ILE GLU GLU LYS ALA
611 - 620 LEU PHE VAL THR CYS GLY ALA THR VAL PRO
621 - 630 PHE PRO LYS LEU VAL SER CYS VAL LEU SER
631 - 640 ASP GLU PHE CYS GLN GLU LEU ILE GLN TYR
641 - 650 GLY PHE VAL ARG LEU ILE ILE GLN PHE GLY
651 - 660 ARG ASN TYR SER SER GLU PHE GLU HIS LEU
661 - 670 VAL GLN GLU ARG GLY GLY GLN ARG GLU SER
671 - 680 GLN LYS ILE PRO ILE ASP GLN PHE GLY CYS
681 - 690 GLY ASP THR ALA ARG GLN TYR VAL LEU MET
691 - 700 ASN GLY LYS LEU LYS VAL ILE GLY PHE ASP
701 - 710 PHE SER THR LYS MET GLN SER ILE ILE ARG
711 - 720 ASP TYR SER ASP LEU VAL ILE SER HIS ALA
721 - 730 GLY THR GLY SER ILE LEU ASP SER LEU ARG
731 - 740 LEU ASN LYS PRO LEU ILE VAL CYS VAL ASN
741 - 750 ASP SER LEU MET ASP ASN HIS GLN GLN GLN
751 - 760 ILE ALA ASP LYS PHE VAL GLU LEU GLY TYR
761 - 770 VAL TRP SER CYS ALA PRO THR GLU THR GLY
771 - 780 LEU ILE ALA GLY LEU ARG ALA SER GLN THR
781 - 790 GLU LYS LEU LYS PRO PHE PRO VAL SER HIS
791 - 800 ASN PRO SER PHE GLU ARG LEU LEU VAL GLU
801 - 810 THR ILE TYR SER GLY ILE ILE GLU GLU LYS
811 - 820 ALA LEU PHE VAL THR CYS GLY ALA THR VAL
821 - 830 PRO PHE PRO LYS LEU VAL SER CYS VAL LEU
831 - 840 SER ASP GLU PHE CYS GLN GLU LEU ILE GLN
841 - 850 TYR GLY PHE VAL ARG LEU ILE ILE GLN PHE
851 - 860 GLY ARG ASN TYR SER SER GLU PHE GLU HIS
861 - 870 LEU VAL GLN GLU ARG GLY GLY GLN ARG GLU
871 - 880 SER GLN LYS ILE PRO ILE ASP GLN PHE GLY
881 - 890 CYS GLY ASP THR ALA ARG GLN TYR VAL LEU
891 - 900 MET ASN GLY LYS LEU LYS VAL ILE GLY PHE
901 - 910 ASP PHE SER THR LYS MET GLN SER ILE ILE
911 - 920 ARG ASP TYR SER ASP LEU VAL ILE SER HIS
921 - 930 ALA GLY THR GLY SER ILE LEU ASP SER LEU
931 - 940 ARG LEU ASN LYS PRO LEU ILE VAL CYS VAL
941 - 950 ASN ASP SER LEU MET ASP ASN HIS GLN GLN
951 - 960 GLN ILE ALA ASP LYS PHE VAL GLU LEU GLY
961 - 970 TYR VAL TRP SER CYS ALA PRO THR GLU THR
971 - 980 GLY LEU ILE ALA GLY LEU ARG ALA SER GLN
981 - 990 THR GLU LYS LEU LYS PRO PHE PRO VAL SER
991 - 1000 HIS ASN PRO SER PHE GLU ARG LEU LEU VAL
1001 - 1010 GLU THR ILE TYR SER GLY ILE ILE GLU GLU
1011 - 1020 LYS ALA LEU PHE VAL THR CYS GLY ALA THR
1021 - 1030 VAL PRO PHE PRO LYS LEU VAL SER CYS VAL
1031 - 1040 LEU SER ASP GLU PHE CYS GLN GLU LEU ILE
1041 - 1050 GLN TYR GLY PHE VAL ARG LEU ILE ILE GLN
1051 - 1060 PHE GLY ARG ASN TYR SER SER GLU PHE GLU
1061 - 1070 HIS LEU VAL GLN GLU ARG GLY GLY GLN ARG
1071 - 1080 GLU SER GLN LYS ILE PRO ILE ASP GLN PHE
1081 - 1090 GLY CYS GLY ASP THR ALA ARG GLN TYR VAL
1091 - 1100 LEU MET ASN GLY LYS LEU LYS VAL ILE GLY
1101 - 1110 PHE ASP PHE SER THR LYS MET GLN SER ILE
1111 - 1120 ILE ARG ASP TYR SER ASP LEU VAL ILE SER
1121 - 1130 HIS ALA GLY THR GLY SER ILE LEU ASP SER
1131 - 1140 LEU ARG LEU ASN LYS PRO LEU ILE VAL CYS
1141 - 1150 VAL ASN ASP SER LEU MET ASP ASN HIS GLN
1151 - 1160 GLN GLN ILE ALA ASP LYS PHE VAL GLU LEU
1161 - 1170 GLY TYR VAL TRP SER CYS ALA PRO THR GLU
1171 - 1180 THR GLY LEU ILE ALA GLY LEU ARG ALA SER
1181 - 1190 GLN THR GLU LYS LEU LYS PRO PHE PRO VAL
1191 - 1200 SER HIS ASN PRO SER PHE GLU ARG LEU LEU
1201 - 1210 VAL GLU THR ILE TYR SER GLY ILE ILE GLU
1211 - 1220 GLU LYS ALA LEU PHE VAL THR CYS GLY ALA
1221 - 1230 THR VAL PRO PHE PRO LYS LEU VAL SER CYS
1231 - 1240 VAL LEU SER ASP GLU PHE CYS GLN GLU LEU
1241 - 1250 ILE GLN TYR GLY PHE VAL ARG LEU ILE ILE
1251 - 1260 GLN PHE GLY ARG ASN TYR SER SER GLU PHE
1261 - 1270 GLU HIS LEU VAL GLN GLU ARG GLY GLY GLN
1271 - 1280 ARG GLU SER GLN LYS ILE PRO ILE ASP GLN
1281 - 1290 PHE GLY CYS GLY ASP THR ALA ARG GLN TYR
1291 - 1300 VAL LEU MET ASN GLY LYS LEU LYS VAL ILE
1301 - 1310 GLY PHE ASP PHE SER THR LYS MET GLN SER
1311 - 1320 ILE ILE ARG ASP TYR SER ASP LEU VAL ILE
1321 - 1330 SER HIS ALA GLY THR GLY SER ILE LEU ASP
1331 - 1340 SER LEU ARG LEU ASN LYS PRO LEU ILE VAL
1341 - 1350 CYS VAL ASN ASP SER LEU MET ASP ASN HIS
1351 - 1360 GLN GLN GLN ILE ALA ASP LYS PHE VAL GLU
1361 - 1370 LEU GLY TYR VAL TRP SER CYS ALA PRO THR
1371 - 1380 GLU THR GLY LEU ILE ALA GLY LEU ARG ALA
1381 - 1390 SER GLN THR GLU LYS LEU LYS PRO PHE PRO
1391 - 1400 VAL SER HIS ASN PRO SER PHE GLU ARG LEU
1401 - 1410 LEU VAL GLU THR ILE TYR SER GLY ILE ILE
1411 - 1420 GLU GLU LYS ALA LEU PHE VAL THR CYS GLY
1421 - 1430 ALA THR VAL PRO PHE PRO LYS LEU VAL SER
1431 - 1440 CYS VAL LEU SER ASP GLU PHE CYS GLN GLU
1441 - 1450 LEU ILE GLN TYR GLY PHE VAL ARG LEU ILE
1451 - 1460 ILE GLN PHE GLY ARG ASN TYR SER SER GLU
1461 - 1470 PHE GLU HIS LEU VAL GLN GLU ARG GLY GLY
1471 - 1480 GLN ARG GLU SER GLN LYS ILE PRO ILE ASP
1481 - 1490 GLN PHE GLY CYS GLY ASP THR ALA ARG GLN
1491 - 1500 TYR VAL LEU MET ASN GLY LYS LEU LYS VAL
1501 - 1510 ILE GLY PHE ASP PHE SER THR LYS MET GLN
1511 - 1520 SER ILE ILE ARG ASP TYR SER ASP LEU VAL
1521 - 1530 ILE SER HIS ALA GLY THR GLY SER ILE LEU
1531 - 1540 ASP SER LEU ARG LEU ASN LYS PRO LEU ILE
1541 - 1550 VAL CYS VAL ASN ASP SER LEU MET ASP ASN
1551 - 1560 HIS GLN GLN GLN ILE ALA ASP LYS PHE VAL
1561 - 1570 GLU LEU GLY TYR VAL TRP SER CYS ALA PRO
1571 - 1580 THR GLU THR GLY LEU ILE ALA GLY LEU ARG
1581 - 1590 ALA SER GLN THR GLU LYS LEU LYS PRO PHE
1591 - 1600 PRO VAL SER HIS ASN PRO SER PHE GLU ARG
1601 - 1610 LEU LEU VAL GLU THR ILE TYR SER GLY ILE
1611 - 1620 ILE GLU GLU LYS ALA LEU PHE VAL THR CYS
1621 - 1630 GLY ALA THR VAL PRO PHE PRO LYS LEU VAL
1631 - 1640 SER CYS VAL LEU SER ASP GLU PHE CYS GLN
1641 - 1650 GLU LEU ILE GLN TYR GLY PHE VAL ARG LEU
1651 - 1660 ILE ILE GLN PHE GLY ARG ASN TYR SER SER
1661 - 1670 GLU PHE GLU HIS LEU VAL GLN GLU ARG GLY
1671 - 1680 GLY GLN ARG GLU SER GLN LYS ILE PRO ILE
1681 - 1690 ASP GLN PHE GLY CYS GLY ASP THR ALA ARG
1691 - 1700 GLN TYR VAL LEU MET ASN GLY LYS LEU LYS
1701 - 1710 VAL ILE GLY PHE ASP PHE SER THR LYS MET
1711 - 1720 GLN SER ILE ILE ARG ASP TYR SER ASP LEU
1721 - 1730 VAL ILE SER HIS ALA GLY THR GLY SER ILE
1731 - 1740 LEU ASP SER LEU ARG LEU ASN LYS PRO LEU
1741 - 1750 ILE VAL CYS VAL ASN ASP SER LEU MET ASP
1751 - 1760 ASN HIS GLN GLN GLN ILE ALA ASP LYS PHE
1761 - 1770 VAL GLU LEU GLY TYR VAL TRP SER CYS ALA
1771 - 1780 PRO THR GLU THR GLY LEU ILE ALA GLY LEU
1781 - 1790 ARG ALA SER GLN THR GLU LYS LEU LYS PRO
1791 - 1800 PHE PRO VAL SER HIS ASN PRO SER PHE GLU
1801 - 1810 ARG LEU LEU VAL GLU THR ILE TYR SER GLY
1811 - 1820 ILE ILE GLU GLU LYS ALA LEU PHE VAL THR
1821 - 1830 CYS GLY ALA THR VAL PRO PHE PRO LYS LEU
1831 - 1840 VAL SER CYS VAL LEU SER ASP GLU PHE CYS
1841 - 1850 GLN GLU LEU ILE GLN TYR GLY PHE VAL ARG
1851 - 1860 LEU ILE ILE GLN PHE GLY ARG ASN TYR SER
1861 - 1870 SER GLU PHE GLU HIS LEU VAL GLN GLU ARG
1871 - 1880 GLY GLY GLN ARG GLU SER GLN LYS ILE PRO
1881 - 1890 ILE ASP GLN PHE GLY CYS GLY ASP THR ALA
1891 - 1900 ARG GLN TYR VAL LEU MET ASN GLY LYS LEU
1901 - 1910 LYS VAL ILE GLY PHE ASP PHE SER THR LYS
1911 - 1920 MET GLN SER ILE ILE ARG ASP TYR SER ASP
1921 - 1930 LEU VAL ILE SER HIS ALA GLY THR GLY SER
1931 - 1940 ILE LEU ASP SER LEU ARG LEU ASN LYS PRO
1941 - 1950 LEU ILE VAL CYS VAL ASN ASP SER LEU MET
1951 - 1960 ASP ASN HIS GLN GLN GLN ILE ALA ASP LYS
1961 - 1970 PHE VAL GLU LEU GLY TYR VAL TRP SER CYS
1971 - 1980 ALA PRO THR GLU THR GLY LEU ILE ALA GLY
1981 - 1990 LEU ARG ALA SER GLN THR GLU LYS LEU LYS
1991 - 2000 PRO PHE PRO VAL SER HIS ASN PRO SER PHE
2001 - 2010 GLU ARG LEU LEU VAL GLU THR ILE TYR SER
Content of the SOUP. See the writeup for an explanation.
Protein .................... : 10
Drug, ligand or co-factor .. : 0
DNA or RNA ................. : 0
Single atom entity ......... : 10
(Groups of) water .......... : 0
Drug with known topology ... : 0
Sugar or sugar-like ........ : 0
Residues with alternate atom : 0
Molecule Range Type Set name
1 1 ( 24) 201 ( 224)A Protein Mod 1 2JZC.pdb 1
2 202 ( 24) 402 ( 224)A Protein Mod 2 2JZC.pdb 1
3 403 ( 24) 603 ( 224)A Protein Mod 3 2JZC.pdb 1
4 604 ( 24) 804 ( 224)A Protein Mod 4 2JZC.pdb 1
5 805 ( 24) 1005 ( 224)A Protein Mod 5 2JZC.pdb 1
6 1006 ( 24) 1206 ( 224)A Protein Mod 6 2JZC.pdb 1
7 1207 ( 24) 1407 ( 224)A Protein Mod 7 2JZC.pdb 1
8 1408 ( 24) 1608 ( 224)A Protein Mod 8 2JZC.pdb 1
9 1609 ( 24) 1809 ( 224)A Protein Mod 9 2JZC.pdb 1
10 1810 ( 24) 2010 ( 224)A Protein Mod 10 2JZC.pdb 1
11 2011 ( 224) 2011 ( 224)A S O2 <- 201 1 2JZC.pdb 4
12 2012 ( 224) 2012 ( 224)A S O2 <- 402 2 2JZC.pdb 4
13 2013 ( 224) 2013 ( 224)A S O2 <- 603 3 2JZC.pdb 4
14 2014 ( 224) 2014 ( 224)A S O2 <- 804 4 2JZC.pdb 4
15 2015 ( 224) 2015 ( 224)A S O2 <- 1005 5 2JZC.pdb 4
16 2016 ( 224) 2016 ( 224)A S O2 <- 1206 6 2JZC.pdb 4
17 2017 ( 224) 2017 ( 224)A S O2 <- 1407 7 2JZC.pdb 4
18 2018 ( 224) 2018 ( 224)A S O2 <- 1608 8 2JZC.pdb 4
19 2019 ( 224) 2019 ( 224)A S O2 <- 1809 9 2JZC.pdb 4
20 2020 ( 224) 2020 ( 224)A S O2 <- 2010 10 2JZC.pdb 4
Note: Since neither a valid SCALE matrix, nor a valid CRYST1 card were
found, SYMMETRY will be unavailable for this molecule.
# 2 # Note: Ligand topologies OK
The topology could be determined for all ligands (or there are no ligands
for which a topology is needed, in which case there is absolutely no
problem, of course). That is good because it means that all ligands can
be included in the hydrogen bond optimization and related options.
# 3 # Note: No strange inter-chain connections detected
No covalent bonds have been detected between molecules with
non-identical chain identifiers.
# 4 # Note: No duplicate atom names in ligands
All atom names in ligands seem adequately unique.
# 5 # Note: No alternate atoms detected in NMR file
This PDB file does not contain alternate atoms. That is good, because
it should not contain alternate atoms.
# 6 # Note: No mixed usage of alternate atom problems detected
Either this structure does not contain alternate atoms, or they have not
been mixed up, or the errors have remained unnoticed.
# 7 # Note: In all cases the primary alternate atom was used
WHAT IF saw no need to make any alternate atom corrections (which means they
are all correct, or there aren't any).
# 8 # Note: No residues detected inside ligands
Either this structure does not contain ligands with amino acid groups
inside it, or their naming is proper (enough).
# 9 # Note: No attached groups interfere with hydrogen bond calculations
It seems there are no sugars, lipids, etc., bound (very close) to
atoms that otherwise could form hydrogen bonds.
# 10 # Note: No probable side chain atoms with zero occupancy detected.
Either there are no atoms with zero occupancy, or they are not present in
the file, or their positions are sufficiently improbable to warrant a
zero occupancy.
# 11 # Note: No probable backbone atoms with zero occupancy detected.
Either there are no backbone atoms with zero occupancy, or they are not
present in the file, or their positions are sufficiently improbable to
warrant a zero occupancy.
# 12 # Note: All residues have a complete backbone.
No residues have missing backbone atoms.
# 13 # Note: No C-alpha only residues
There are no residues that consist of only an alpha carbon atom.
# 14 # Note: Non-canonicals
WHAT IF has not detected any non-canonical residue that it doesn't
understand, or there are no non-canonical residues in the PDB file.
# 15 # Note: Content of the PDB file as interpreted by WHAT IF
Content of the PDB file as interpreted by WHAT IF.
WHAT IF has read your PDB file, and stored it internally in
what is called 'the soup'. The content of this soup is listed here.
An extensive explanation of all frequently used WHAT IF output formats
can be found at http://swift.cmbi.ru.nl/. Look under output formats.
A course on reading this 'Molecules' table is part of the WHAT\_CHECK
web pages [REF].
1 1 ( 24) 201 ( 224) A Protein Mod 1 2JZC.pdb
2 202 ( 24) 402 ( 224) A Protein Mod 2 2JZC.pdb
3 403 ( 24) 603 ( 224) A Protein Mod 3 2JZC.pdb
4 604 ( 24) 804 ( 224) A Protein Mod 4 2JZC.pdb
5 805 ( 24) 1005 ( 224) A Protein Mod 5 2JZC.pdb
6 1006 ( 24) 1206 ( 224) A Protein Mod 6 2JZC.pdb
7 1207 ( 24) 1407 ( 224) A Protein Mod 7 2JZC.pdb
8 1408 ( 24) 1608 ( 224) A Protein Mod 8 2JZC.pdb
9 1609 ( 24) 1809 ( 224) A Protein Mod 9 2JZC.pdb
10 1810 ( 24) 2010 ( 224) A Protein Mod 10 2JZC.pdb
11 2011 ( 224) 2011 ( 224) A S O2 <- 201 1 2JZC.pdb
12 2012 ( 224) 2012 ( 224) A S O2 <- 402 2 2JZC.pdb
13 2013 ( 224) 2013 ( 224) A S O2 <- 603 3 2JZC.pdb
14 2014 ( 224) 2014 ( 224) A S O2 <- 804 4 2JZC.pdb
15 2015 ( 224) 2015 ( 224) A S O2 <- 1005 5 2JZC.pdb
16 2016 ( 224) 2016 ( 224) A S O2 <- 1206 6 2JZC.pdb
17 2017 ( 224) 2017 ( 224) A S O2 <- 1407 7 2JZC.pdb
18 2018 ( 224) 2018 ( 224) A S O2 <- 1608 8 2JZC.pdb
19 2019 ( 224) 2019 ( 224) A S O2 <- 1809 9 2JZC.pdb
20 2020 ( 224) 2020 ( 224) A S O2 <- 2010 10 2JZC.pdb
# 16 # Note: Some notes regarding the PDB file contents
The numbers and remarks listed below have no explicit validation
purpose, they are merely meant for the crystallographer or NMR
spectroscopists to perhaps pinpoint something unexpected. See the
WHAT\_CHECK course [REF] for an explanation of terms like 'poor',
'missing', etcetera (in case those words pop up in the lines underneath
this message).
Number of amino acids 2010
# 17 # Note: Ramachandran plot
In this Ramachandran plot x-signs represent glycines, squares represent
prolines, and plus-signs represent the other residues. If too many
plus-signs fall outside the contoured areas then the molecule is poorly
refined (or worse). Proline can only occur in the narrow region around
phi=60 that also falls within the other contour islands.
In a colour picture, the residues that are part of a helix are
shown in blue, strand residues in red. "Allowed" regions for
helical residues are drawn in blue, for strand residues in red, and
for all other residues in green.
A full explanation of the Ramachandran plot together with a series of
examples can be found at the WHAT\_CHECK website [REF].
In the TeX file, a plot has been inserted here
Chain identifier: A; Model number 1
# 18 # Note: Ramachandran plot
In the TeX file, a plot has been inserted here
Chain identifier: A; Model number 2
# 19 # Note: Ramachandran plot
In the TeX file, a plot has been inserted here
Chain identifier: A; Model number 3
# 20 # Note: Ramachandran plot
In the TeX file, a plot has been inserted here
Chain identifier: A; Model number 4
# 21 # Note: Ramachandran plot
In the TeX file, a plot has been inserted here
Chain identifier: A; Model number 5
# 22 # Note: Ramachandran plot
In the TeX file, a plot has been inserted here
Chain identifier: A; Model number 6
# 23 # Note: Ramachandran plot
In the TeX file, a plot has been inserted here
Chain identifier: A; Model number 7
# 24 # Note: Ramachandran plot
In the TeX file, a plot has been inserted here
Chain identifier: A; Model number 8
# 25 # Note: Ramachandran plot
In the TeX file, a plot has been inserted here
Chain identifier: A; Model number 9
# 26 # Note: Ramachandran plot
In the TeX file, a plot has been inserted here
Chain identifier: A; Model number 10
# 27 # Note: Secondary structure
This is the secondary structure according to DSSP. Only helix (H),
overwound or 3/10-helix (3), strand (S), turn (T) and coil (blank)
are shown [REF]. All DSSP related information can be found at
http://swift.cmbi.ru.nl/gv/dssp/.
This is not really a structure validation option, but a very scattered
secondary structure (i.e. many strands of only a few residues length,
many Ts inside helices, etc) tends to indicate a poor structure. A full
explanation of the DSSP secondary structure determination program
together with a series of examples can be found at the WHAT\_CHECK
website [REF].
Secondary structure assignment
10 20 30 40 50 60
| | | | | |
1 - 60 GIIEEKALFVTCGATVPFPKLVSCVLSDEFCQELIQYGFVRLIIQFGRNYSSEFEHLVQE
( 24)-( 83) T SSSS T T HHHHHHHTTHHHHHHHHTTT SSS TTT THHHH
70 80 90 100 110 120
| | | | | |
61 - 120 RGGQRESQKIPIDQFGCGDTARQYVLMNGKLKVIGFDFSTKMQSIIRDYSDLVISHAGTG
( 84)-( 143)HT SS T TT TT TT T SSSSTTTTTTSSSS TTTTHHHHHHHH T SSSTT HH
130 140 150 160 170 180
| | | | | |
121 - 180 SILDSLRLNKPLIVCVNDSLMDNHQQQIADKFVELGYVWSCAPTETGLIAGLRASQTEKL
( 144)-( 203)HHHHHHHTT SS TT HHHHHHHHHHHHT SS T TTTHHHHHHHHTT
190 200
| |
181 - 201 KPFPVSHNPSFERLLVETIYS
( 204)-( 224) T TTT THHHHHHHH
210 220 230 240 250 260
| | | | | |
202 - 261 GIIEEKALFVTCGATVPFPKLVSCVLSDEFCQELIQYGFVRLIIQFGRNYSSEFEHLVQE
( 24)-( 83) T SSSS TT T HHHHHHHHTHHHHHHHHHTT SSS T333 THHHH
270 280 290 300 310 320
| | | | | |
262 - 321 RGGQRESQKIPIDQFGCGDTARQYVLMNGKLKVIGFDFSTKMQSIIRDYSDLVISHAGTG
( 84)-( 143)TT SS TT T TTTT SSSS TTTT SSS TTTTHHHH333T TSSSSTT HH
330 340 350 360 370 380
| | | | | |
322 - 381 SILDSLRLNKPLIVCVNDSLMDNHQQQIADKFVELGYVWSCAPTETGLIAGLRASQTEKL
( 144)-( 203)HHHHHHHTT SSS TTTHHHHHHHHHHHHTT T SS TTHHHHHHHHHHHHH
390 400
| |
382 - 402 KPFPVSHNPSFERLLVETIYS
( 204)-( 224) T T HHHHHHHHHT
410 420 430 440 450 460
| | | | | |
403 - 462 GIIEEKALFVTCGATVPFPKLVSCVLSDEFCQELIQYGFVRLIIQFGRNYSSEFEHLVQE
( 24)-( 83) T SSSS T T THHHHHHTTHHHHHHHHHHT SSSS TTT TTTHHHHHH
470 480 490 500 510 520
| | | | | |
463 - 522 RGGQRESQKIPIDQFGCGDTARQYVLMNGKLKVIGFDFSTKMQSIIRDYSDLVISHAGTG
( 84)-( 143)HT TT TTTTT TTT SSSTTTTSSSS TT HHHHHHHH TSSS TT HH
530 540 550 560 570 580
| | | | | |
523 - 582 SILDSLRLNKPLIVCVNDSLMDNHQQQIADKFVELGYVWSCAPTETGLIAGLRASQTEKL
( 144)-( 203)HHHHHHHTT SS TTTTTTTHHHHHHHHHHHTT TTHHHHHHHHHHHTT
590 600
| |
583 - 603 KPFPVSHNPSFERLLVETIYS
( 204)-( 224) T TT HHHHHHHHHT
610 620 630 640 650 660
| | | | | |
604 - 663 GIIEEKALFVTCGATVPFPKLVSCVLSDEFCQELIQYGFVRLIIQFGRNYSSEFEHLVQE
( 24)-( 83) TT SSSS TTT T HHHHHHHTTHHHHHHHHTTT SSS TTT T THHHH
670 680 690 700 710 720
| | | | | |
664 - 723 RGGQRESQKIPIDQFGCGDTARQYVLMNGKLKVIGFDFSTKMQSIIRDYSDLVISHAGTG
( 84)-( 143)HT SSTTT TT TTTT SSSSTTTTSSSS TTTHHHHHHHH TSSSSTT TH
730 740 750 760 770 780
| | | | | |
724 - 783 SILDSLRLNKPLIVCVNDSLMDNHQQQIADKFVELGYVWSCAPTETGLIAGLRASQTEKL
( 144)-( 203)HHHHHHHTT SS T TT THHHHHHHHHHHHT SS T HHHHHHHHHHHTT
790 800
| |
784 - 804 KPFPVSHNPSFERLLVETIYS
( 204)-( 224) TT THHHHHHHHH
810 820 830 840 850 860
| | | | | |
805 - 864 GIIEEKALFVTCGATVPFPKLVSCVLSDEFCQELIQYGFVRLIIQFGRNYSSEFEHLVQE
( 24)-( 83) TTT SSSSS T HHHH3333THHHHHHHHHH TSSSSS TT THHHH
870 880 890 900 910 920
| | | | | |
865 - 924 RGGQRESQKIPIDQFGCGDTARQYVLMNGKLKVIGFDFSTKMQSIIRDYSDLVISHAGTG
( 84)-( 143)TT SS TTT T T TTTTT SS TTTTT TTT HHHHHHHH T SS TT TT
930 940 950 960 970 980
| | | | | |
925 - 984 SILDSLRLNKPLIVCVNDSLMDNHQQQIADKFVELGYVWSCAPTETGLIAGLRASQTEKL
( 144)-( 203)HHHHHHHTT SSSS TTT HHHHHHHHHHHHHT TSSS TTHHHHHHHHHHHHH
990 1000
| |
985 - 1005 KPFPVSHNPSFERLLVETIYS
( 204)-( 224) T TTTTHHHHHHHHT
1010 1020 1030 1040 1050 1060
| | | | | |
1006 - 1065 GIIEEKALFVTCGATVPFPKLVSCVLSDEFCQELIQYGFVRLIIQFGRNYSSEFEHLVQE
( 24)-( 83) T SSSS TT HHHH3333THHHHHHHHHHT SSS TT TTHHHH
1070 1080 1090 1100 1110 1120
| | | | | |
1066 - 1125 RGGQRESQKIPIDQFGCGDTARQYVLMNGKLKVIGFDFSTKMQSIIRDYSDLVISHAGTG
( 84)-( 143)HT SS TTTT TT TTT SSSS333TSSSS TTTHHHHHHHH SSSSTT TT
1130 1140 1150 1160 1170 1180
| | | | | |
1126 - 1185 SILDSLRLNKPLIVCVNDSLMDNHQQQIADKFVELGYVWSCAPTETGLIAGLRASQTEKL
( 144)-( 203)THHHHHHTT SSS TTT TTTHHHHHHHHH333T SSS TTHHHHHHHHHHHTT
1190 1200
| |
1186 - 1206 KPFPVSHNPSFERLLVETIYS
( 204)-( 224) TTHHHHHHHTT
1210 1220 1230 1240 1250 1260
| | | | | |
1207 - 1266 GIIEEKALFVTCGATVPFPKLVSCVLSDEFCQELIQYGFVRLIIQFGRNYSSEFEHLVQE
( 24)-( 83) T SSSSS TT T HHHHHHHTTHHHHHHHHTTT SSSSS TTT T TTHHHH
1270 1280 1290 1300 1310 1320
| | | | | |
1267 - 1326 RGGQRESQKIPIDQFGCGDTARQYVLMNGKLKVIGFDFSTKMQSIIRDYSDLVISHAGTG
( 84)-( 143)HT SS TTT TT TT TTT SSSTTTTSSSSS TT HHHHHHHT SSSSTT TT
1330 1340 1350 1360 1370 1380
| | | | | |
1327 - 1386 SILDSLRLNKPLIVCVNDSLMDNHQQQIADKFVELGYVWSCAPTETGLIAGLRASQTEKL
( 144)-( 203)HHHHHHHTT SS T TT HHHHHHHHHHTTT SS TTHHHHHHHHHHHTT
1390 1400
| |
1387 - 1407 KPFPVSHNPSFERLLVETIYS
( 204)-( 224) TTTTHHHHHHHHT
1410 1420 1430 1440 1450 1460
| | | | | |
1408 - 1467 GIIEEKALFVTCGATVPFPKLVSCVLSDEFCQELIQYGFVRLIIQFGRNYSSEFEHLVQE
( 24)-( 83) TTT SSS TTT T HHHHHHTTTHHHHHHHHHHT SSS TT THHHH
1470 1480 1490 1500 1510 1520
| | | | | |
1468 - 1527 RGGQRESQKIPIDQFGCGDTARQYVLMNGKLKVIGFDFSTKMQSIIRDYSDLVISHAGTG
( 84)-( 143)HT T TTTTTT TTSSSS TTTT SSSS TT HHHHHHHH T SS T TH
1530 1540 1550 1560 1570 1580
| | | | | |
1528 - 1587 SILDSLRLNKPLIVCVNDSLMDNHQQQIADKFVELGYVWSCAPTETGLIAGLRASQTEKL
( 144)-( 203)HHHHHHHTT SSSS T TT THHHHHHHHHHHHT SS TTHHHHHHHHHHHTT
1590 1600
| |
1588 - 1608 KPFPVSHNPSFERLLVETIYS
( 204)-( 224) T HHHHHHHHHH
1610 1620 1630 1640 1650 1660
| | | | | |
1609 - 1668 GIIEEKALFVTCGATVPFPKLVSCVLSDEFCQELIQYGFVRLIIQFGRNYSSEFEHLVQE
( 24)-( 83) T T SSSS T T HHHHHHHHTHHHHHHHHHHTT SSSS TTTT HHHH
1670 1680 1690 1700 1710 1720
| | | | | |
1669 - 1728 RGGQRESQKIPIDQFGCGDTARQYVLMNGKLKVIGFDFSTKMQSIIRDYSDLVISHAGTG
( 84)-( 143)HTSSS TT HHHHTTT SSSSTTTT SSST TTTTHHHHHHHH TSSSSTT TH
1730 1740 1750 1760 1770 1780
| | | | | |
1729 - 1788 SILDSLRLNKPLIVCVNDSLMDNHQQQIADKFVELGYVWSCAPTETGLIAGLRASQTEKL
( 144)-( 203)HHHHHHHTT SSS T TTTTHHHHHHHHHHHHHTTTSS T HHHHHHHHHHHTT
1790 1800
| |
1789 - 1809 KPFPVSHNPSFERLLVETIYS
( 204)-( 224) TT T T HHHHHHHHHH
1810 1820 1830 1840 1850 1860
| | | | | |
1810 - 1869 GIIEEKALFVTCGATVPFPKLVSCVLSDEFCQELIQYGFVRLIIQFGRNYSSEFEHLVQE
( 24)-( 83) T SSSS TT TTHHHHHHHHTHHHHHHHHHHTT SSSS TT THHHH
1870 1880 1890 1900 1910 1920
| | | | | |
1870 - 1929 RGGQRESQKIPIDQFGCGDTARQYVLMNGKLKVIGFDFSTKMQSIIRDYSDLVISHAGTG
( 84)-( 143)TT SS TT TTTT SSTTSS SS TTTT SS T TTTHHHHHHHH SSS T TH
1930 1940 1950 1960 1970 1980
| | | | | |
1930 - 1989 SILDSLRLNKPLIVCVNDSLMDNHQQQIADKFVELGYVWSCAPTETGLIAGLRASQTEKL
( 144)-( 203)HHHHHHHTT SSS TT HHHHHHHHHHHTT SS TTHHHHHHHHHHHTT
1990 2000 2010
| | |
1990 - 2010 KPFPVSHNPSFERLLVETIYS
( 204)-( 224) TT TTHHHHHHHHT
# 28 # Note: No rounded coordinates detected
No significant rounding of atom coordinates has been detected.
# 29 # Note: No artificial side chains detected
No artificial side-chain positions characterized by chi-1=0.00 or
chi-1=180.00 have been detected.
# 30 # Note: No missing atoms detected in residues
All expected atoms are present in residues. This validation option has
not looked at 'things' that can or should be attached to the elemantary
building blocks (amino acids, nucleotides). Even the C-terminal oxygens
are treated separately.
# 31 # Note: No C-terminal nitrogen detected
The PDB indicates that a residue is not the true C-terminus
by including only the backbone N of the next residue. This has not been
observed in this PDB file.
# 32 # Note: Test capping of (pseudo) C-termini
No extra capping groups were found on pseudo C-termini. This can imply
that no pseudo C-termini are present.
# 33 # Note: Proper C-terminal capping groups found
All (presumably) real C-termini either contain a proper capping group (OXT,
or something else), or they are followed by a single Nitrogen, indicating
that the rest of the chain is invisible.
# 34 # Note: No OXT found in the middle of chains
No OXT groups were found in the middle of protein chains.
# 35 # Note: Weights checked OK
All atomic occupancy factors ('weights') fall in the 0.0--1.0 range.
# 36 # Note: Normal distribution of occupancy values
The distribution of the occupancy values in this file seems 'normal'.
Be aware that this evaluation is merely the result of comparing this
file with about 500 well-refined high-resolution files in the PDB. If
this file has much higher or much lower resolution than the PDB files
used in WHAT IF's training set, non-normal values might very well be
perfectly fine, or normal values might actually be not so normal.
So, this check is actually more an indicator and certainly not a check
in which I have great confidence.
# 37 # Note: All occupancies seem to add up to 0.0 - 1.0.
In principle, the occupancy of all alternates of one atom should add up
till 0.0 - 1.0. 0.0 is used for the missing atom (i.e. an atom not
seen in the electron density).
Obviously, there is nothing terribly wrong when a few occupancies
add up to a bit more than 1.0, because the mathematics of refinement
allow for that. However, if it happens often, it seems worth evaluating
this in light of the refinement protocol used.
# 38 # Note: Introduction to the nomenclature section.
Nomenclature problems seem, at first, rather unimportant. After all who
cares if we call the delta atoms in leucine delta 2 and delta 1 rather than
the other way around. Chemically speaking that is correct. But structures
have not been solved and deposited just for chemists to look at them. Most
times a structure is used, it is by software in a bioinformatics lab. And
if they compare structures in which the one used C delta 1 and 2 and the
other uses C delta 2 and 1, then that comparison will fail. Also, we
recalculate all structures every so many years to make sure that everybody
always can get access to the best coordinates that can be obtained from
the (your?) experimental data. These recalculations will be troublesome if
there are nomenclature problems.
Several Nomenclature problems actually are worse than that. At the
WHAT\_CHECK website [REF] you can get an overview of the importance of all
nomenclature problems that we list.
# 39 # Note: Valine nomenclature OK
No errors were detected in valine nomenclature.
# 40 # Note: Threonine nomenclature OK
No errors were detected in threonine nomenclature.
# 41 # Note: Isoleucine nomenclature OK
No errors were detected in isoleucine nomenclature.
# 42 # Note: Leucine nomenclature OK
No errors were detected in leucine nomenclature.
# 43 # Note: Arginine nomenclature OK
No errors were detected in arginine nomenclature.
# 44 # Note: Tyrosine torsion conventions OK
No errors were detected in tyrosine torsion angle conventions.
# 45 # Note: Phenylalanine torsion conventions OK
No errors were detected in phenylalanine torsion angle conventions.
# 46 # Note: Aspartic acid torsion conventions OK
No errors were detected in aspartic acid torsion angle conventions.
# 47 # Note: Glutamic acid torsion conventions OK
No errors were detected in glutamic acid torsion angle conventions.
# 48 # Note: Phosphate group names OK
No errors were detected in phosphate group naming conventions.
# 49 # Note: Heavy atom naming OK
No errors were detected in the atom names for non-hydrogen atoms. Please
be aware that the PDB wants us to deliberately make some nomenclature errors;
especially in non-canonical amino acids.
# 50 # Note: Chain names are OK
All chain names assigned to polymer molecules are unique, and all
residue numbers are strictly increasing within each chain.
# 51 # Note: All bond lengths OK
All bond lengths are in agreement with standard bond lengths using
a tolerance of 4 sigma (both standard values and sigma for amino
acid residues have been taken from Engh and Huber [REF], for
DNA/RNA from Parkinson et al [REF])
# 52 # Note: Normal bond length variability
Bond lengths were found to deviate normally from the standard bond
lengths (values for Protein residues were taken from Engh and Huber
[REF], for DNA/RNA from Parkinson et al [REF]).
RMS Z-score for bond lengths: 0.742
RMS-deviation in bond distances: 0.017
# 53 # Note: Per-model averages for bond-length check
The table below gives the per-model bond-length RMS Z-scores.
Model 1 : 0.742
Model 2 : 0.729
Model 3 : 0.755
Model 4 : 0.701
Model 5 : 0.797
Model 6 : 0.748
Model 7 : 0.713
Model 8 : 0.746
Model 9 : 0.738
Model 10 : 0.752
# 54 # Warning: Directionality in bond lengths
Comparison of bond distances with Engh and Huber [REF] standard
values for protein residues and Parkinson et al [REF] standard values
for DNA/RNA shows a significant systematic deviation.
Since this is not an XRAY structure this effect is hard to explain.
# 55 # Warning: Unusual bond angles
The bond angles listed in the table below were found to deviate
more than 4 sigma from standard bond angles (both standard values
and sigma for protein residues have been taken from Engh and Huber
[REF], for DNA/RNA from Parkinson et al [REF]). In the table below
for each strange angle the bond angle and the number of standard
deviations it differs from the standard values is given. Please
note that disulphide bridges are neglected. Atoms starting with "-"
belong to the previous residue in the sequence.
18 PHE ( 41-) A 1 CA CB CG 108.91 -4.9
98 PHE ( 121-) A 1 CA CB CG 109.36 -4.4
144 HIS ( 167-) A 1 CA CB CG 109.60 -4.2
183 PHE ( 206-) A 1 CA CB CG 109.56 -4.2
210 PHE ( 32-) A 2 CA CB CG 109.52 -4.3
219 PHE ( 41-) A 2 CA CB CG 109.40 -4.4
276 PHE ( 98-) A 2 CA CB CG 109.76 -4.0
317 HIS ( 139-) A 2 CA CB CG 109.52 -4.3
388 HIS ( 210-) A 2 CA CB CG 109.55 -4.3
392 PHE ( 214-) A 2 CA CB CG 109.56 -4.2
441 PHE ( 62-) A 3 CA CB CG 108.34 -5.5
477 PHE ( 98-) A 3 CA CB CG 109.75 -4.0
546 HIS ( 167-) A 3 CA CB CG 109.67 -4.1
585 PHE ( 206-) A 3 CA CB CG 109.11 -4.7
593 PHE ( 214-) A 3 CA CB CG 109.61 -4.2
659 HIS ( 79-) A 4 CA CB CG 109.54 -4.3
678 PHE ( 98-) A 4 CA CB CG 109.13 -4.7
701 PHE ( 121-) A 4 CA CB CG 109.75 -4.0
786 PHE ( 206-) A 4 CA CB CG 109.40 -4.4
790 HIS ( 210-) A 4 CA CB CG 109.36 -4.4
850 PHE ( 69-) A 5 CA CB CG 109.43 -4.4
900 PHE ( 119-) A 5 CA CB CG 109.64 -4.2
902 PHE ( 121-) A 5 CA CB CG 109.32 -4.5
948 HIS ( 167-) A 5 CA CB CG 109.70 -4.1
991 HIS ( 210-) A 5 CA CB CG 109.62 -4.2
1023 PHE ( 41-) A 6 CA CB CG 109.38 -4.4
1080 PHE ( 98-) A 6 CA CB CG 109.73 -4.1
1121 HIS ( 139-) A 6 CA CB CG 109.64 -4.2
1188 PHE ( 206-) A 6 CA CB CG 109.41 -4.4
1215 PHE ( 32-) A 7 CA CB CG 109.78 -4.0
1224 PHE ( 41-) A 7 CA CB CG 109.06 -4.7
1252 PHE ( 69-) A 7 CA CB CG 109.38 -4.4
1262 HIS ( 79-) A 7 CA CB CG 109.57 -4.2
1304 PHE ( 121-) A 7 CA CB CG 109.56 -4.2
1350 HIS ( 167-) A 7 CA CB CG 109.58 -4.2
1389 PHE ( 206-) A 7 CA CB CG 109.68 -4.1
1503 PHE ( 119-) A 8 CA CB CG 109.71 -4.1
1505 PHE ( 121-) A 8 CA CB CG 109.71 -4.1
1523 HIS ( 139-) A 8 CA CB CG 109.31 -4.5
1617 PHE ( 32-) A 9 CA CB CG 109.33 -4.5
1626 PHE ( 41-) A 9 CA CB CG 109.21 -4.6
1647 PHE ( 62-) A 9 CA CB CG 109.74 -4.1
1654 PHE ( 69-) A 9 CA CB CG 109.32 -4.5
1683 PHE ( 98-) A 9 CA CB CG 109.58 -4.2
1724 HIS ( 139-) A 9 CA CB CG 109.44 -4.4
1799 PHE ( 214-) A 9 CA CB CG 109.76 -4.0
1827 PHE ( 41-) A 10 CA CB CG 109.65 -4.2
1865 HIS ( 79-) A 10 CA CB CG 109.57 -4.2
1961 PHE ( 175-) A 10 CA CB CG 109.65 -4.1
1992 PHE ( 206-) A 10 CA CB CG 109.61 -4.2
# 56 # Note: Normal bond angle variability
Bond angles were found to deviate normally from the mean standard
bond angles (normal values for protein residues were taken from
Engh and Huber [REF], for DNA/RNA from Parkinson et al [REF]). The
RMS Z-score given below is expected to be around 1.0 for a normally
restrained data set, and this is indeed observed for very high
resolution X-ray structures.
RMS Z-score for bond angles: 0.780
RMS-deviation in bond angles: 1.350
# 57 # Note: Per-model averages for bond-angle check
The table below gives the per-model bond-angle RMS Z-scores.
Model 1 : 0.793
Model 2 : 0.776
Model 3 : 0.790
Model 4 : 0.781
Model 5 : 0.781
Model 6 : 0.770
Model 7 : 0.785
Model 8 : 0.773
Model 9 : 0.779
Model 10 : 0.776
# 58 # Note: Residue hand error(s)
You are asking for a hand-check. WHAT IF has over the course of this
session perhaps corrected the handedness of atoms in several residues.
These residues are listed here. You better check these by hand.
# 59 # Note: Chirality OK
All protein atoms have proper chirality.
The average deviation= 0.805
# 60 # Note: Improper dihedral angle distribution OK
The RMS Z-score for all improper dihedrals in the structure is within
normal ranges.
Improper dihedral RMS Z-score : 0.675
# 61 # Note: Per-model averages for chirality check
The table below gives the per-model improper dihedral RMS Z-scores.
Model 1 : 0.703
Model 2 : 0.674
Model 3 : 0.683
Model 4 : 0.690
Model 5 : 0.652
Model 6 : 0.650
Model 7 : 0.699
Model 8 : 0.661
Model 9 : 0.685
Model 10 : 0.653
10 20 30 40 50 60
| | | | | |
1 - 60 GIIEEKALFVTCGATVPFPKLVSCVLSDEFCQELIQYGFVRLIIQFGRNYSSEFEHLVQE
( 24)-( 83) T SSSS T T HHHHHHHTTHHHHHHHHTTT SSS TTT THHHH
70 80 90 100 110 120
| | | | | |
61 - 120 RGGQRESQKIPIDQFGCGDTARQYVLMNGKLKVIGFDFSTKMQSIIRDYSDLVISHAGTG
( 84)-( 143)HT SS T TT TT TT T SSSSTTTTTTSSSS TTTTHHHHHHHH T SSSTT HH
130 140 150 160 170 180
| | | | | |
121 - 180 SILDSLRLNKPLIVCVNDSLMDNHQQQIADKFVELGYVWSCAPTETGLIAGLRASQTEKL
( 144)-( 203)HHHHHHHTT SS TT HHHHHHHHHHHHT SS T TTTHHHHHHHHTT
190 200
| |
181 - 201 KPFPVSHNPSFERLLVETIYS
( 204)-( 224) T TTT THHHHHHHH
210 220 230 240 250 260
| | | | | |
202 - 261 GIIEEKALFVTCGATVPFPKLVSCVLSDEFCQELIQYGFVRLIIQFGRNYSSEFEHLVQE
( 24)-( 83) T SSSS TT T HHHHHHHHTHHHHHHHHHTT SSS T333 THHHH
270 280 290 300 310 320
| | | | | |
262 - 321 RGGQRESQKIPIDQFGCGDTARQYVLMNGKLKVIGFDFSTKMQSIIRDYSDLVISHAGTG
( 84)-( 143)TT SS TT T TTTT SSSS TTTT SSS TTTTHHHH333T TSSSSTT HH
330 340 350 360 370 380
| | | | | |
322 - 381 SILDSLRLNKPLIVCVNDSLMDNHQQQIADKFVELGYVWSCAPTETGLIAGLRASQTEKL
( 144)-( 203)HHHHHHHTT SSS TTTHHHHHHHHHHHHTT T SS TTHHHHHHHHHHHHH
390 400
| |
382 - 402 KPFPVSHNPSFERLLVETIYS
( 204)-( 224) T T HHHHHHHHHT
410 420 430 440 450 460
| | | | | |
403 - 462 GIIEEKALFVTCGATVPFPKLVSCVLSDEFCQELIQYGFVRLIIQFGRNYSSEFEHLVQE
( 24)-( 83) T SSSS T T THHHHHHTTHHHHHHHHHHT SSSS TTT TTTHHHHHH
470 480 490 500 510 520
| | | | | |
463 - 522 RGGQRESQKIPIDQFGCGDTARQYVLMNGKLKVIGFDFSTKMQSIIRDYSDLVISHAGTG
( 84)-( 143)HT TT TTTTT TTT SSSTTTTSSSS TT HHHHHHHH TSSS TT HH
530 540 550 560 570 580
| | | | | |
523 - 582 SILDSLRLNKPLIVCVNDSLMDNHQQQIADKFVELGYVWSCAPTETGLIAGLRASQTEKL
( 144)-( 203)HHHHHHHTT SS TTTTTTTHHHHHHHHHHHTT TTHHHHHHHHHHHTT
590 600
| |
583 - 603 KPFPVSHNPSFERLLVETIYS
( 204)-( 224) T TT HHHHHHHHHT
610 620 630 640 650 660
| | | | | |
604 - 663 GIIEEKALFVTCGATVPFPKLVSCVLSDEFCQELIQYGFVRLIIQFGRNYSSEFEHLVQE
( 24)-( 83) TT SSSS TTT T HHHHHHHTTHHHHHHHHTTT SSS TTT T THHHH
670 680 690 700 710 720
| | | | | |
664 - 723 RGGQRESQKIPIDQFGCGDTARQYVLMNGKLKVIGFDFSTKMQSIIRDYSDLVISHAGTG
( 84)-( 143)HT SSTTT TT TTTT SSSSTTTTSSSS TTTHHHHHHHH TSSSSTT TH
730 740 750 760 770 780
| | | | | |
724 - 783 SILDSLRLNKPLIVCVNDSLMDNHQQQIADKFVELGYVWSCAPTETGLIAGLRASQTEKL
( 144)-( 203)HHHHHHHTT SS T TT THHHHHHHHHHHHT SS T HHHHHHHHHHHTT
790 800
| |
784 - 804 KPFPVSHNPSFERLLVETIYS
( 204)-( 224) TT THHHHHHHHH
810 820 830 840 850 860
| | | | | |
805 - 864 GIIEEKALFVTCGATVPFPKLVSCVLSDEFCQELIQYGFVRLIIQFGRNYSSEFEHLVQE
( 24)-( 83) TTT SSSSS T HHHH3333THHHHHHHHHH TSSSSS TT THHHH
870 880 890 900 910 920
| | | | | |
865 - 924 RGGQRESQKIPIDQFGCGDTARQYVLMNGKLKVIGFDFSTKMQSIIRDYSDLVISHAGTG
( 84)-( 143)TT SS TTT T T TTTTT SS TTTTT TTT HHHHHHHH T SS TT TT
930 940 950 960 970 980
| | | | | |
925 - 984 SILDSLRLNKPLIVCVNDSLMDNHQQQIADKFVELGYVWSCAPTETGLIAGLRASQTEKL
( 144)-( 203)HHHHHHHTT SSSS TTT HHHHHHHHHHHHHT TSSS TTHHHHHHHHHHHHH
990 1000
| |
985 - 1005 KPFPVSHNPSFERLLVETIYS
( 204)-( 224) T TTTTHHHHHHHHT
1010 1020 1030 1040 1050 1060
| | | | | |
1006 - 1065 GIIEEKALFVTCGATVPFPKLVSCVLSDEFCQELIQYGFVRLIIQFGRNYSSEFEHLVQE
( 24)-( 83) T SSSS TT HHHH3333THHHHHHHHHHT SSS TT TTHHHH
1070 1080 1090 1100 1110 1120
| | | | | |
1066 - 1125 RGGQRESQKIPIDQFGCGDTARQYVLMNGKLKVIGFDFSTKMQSIIRDYSDLVISHAGTG
( 84)-( 143)HT SS TTTT TT TTT SSSS333TSSSS TTTHHHHHHHH SSSSTT TT
1130 1140 1150 1160 1170 1180
| | | | | |
1126 - 1185 SILDSLRLNKPLIVCVNDSLMDNHQQQIADKFVELGYVWSCAPTETGLIAGLRASQTEKL
( 144)-( 203)THHHHHHTT SSS TTT TTTHHHHHHHHH333T SSS TTHHHHHHHHHHHTT
1190 1200
| |
1186 - 1206 KPFPVSHNPSFERLLVETIYS
( 204)-( 224) TTHHHHHHHTT
1210 1220 1230 1240 1250 1260
| | | | | |
1207 - 1266 GIIEEKALFVTCGATVPFPKLVSCVLSDEFCQELIQYGFVRLIIQFGRNYSSEFEHLVQE
( 24)-( 83) T SSSSS TT T HHHHHHHTTHHHHHHHHTTT SSSSS TTT T TTHHHH
1270 1280 1290 1300 1310 1320
| | | | | |
1267 - 1326 RGGQRESQKIPIDQFGCGDTARQYVLMNGKLKVIGFDFSTKMQSIIRDYSDLVISHAGTG
( 84)-( 143)HT SS TTT TT TT TTT SSSTTTTSSSSS TT HHHHHHHT SSSSTT TT
1330 1340 1350 1360 1370 1380
| | | | | |
1327 - 1386 SILDSLRLNKPLIVCVNDSLMDNHQQQIADKFVELGYVWSCAPTETGLIAGLRASQTEKL
( 144)-( 203)HHHHHHHTT SS T TT HHHHHHHHHHTTT SS TTHHHHHHHHHHHTT
1390 1400
| |
1387 - 1407 KPFPVSHNPSFERLLVETIYS
( 204)-( 224) TTTTHHHHHHHHT
1410 1420 1430 1440 1450 1460
| | | | | |
1408 - 1467 GIIEEKALFVTCGATVPFPKLVSCVLSDEFCQELIQYGFVRLIIQFGRNYSSEFEHLVQE
( 24)-( 83) TTT SSS TTT T HHHHHHTTTHHHHHHHHHHT SSS TT THHHH
1470 1480 1490 1500 1510 1520
| | | | | |
1468 - 1527 RGGQRESQKIPIDQFGCGDTARQYVLMNGKLKVIGFDFSTKMQSIIRDYSDLVISHAGTG
( 84)-( 143)HT T TTTTTT TTSSSS TTTT SSSS TT HHHHHHHH T SS T TH
1530 1540 1550 1560 1570 1580
| | | | | |
1528 - 1587 SILDSLRLNKPLIVCVNDSLMDNHQQQIADKFVELGYVWSCAPTETGLIAGLRASQTEKL
( 144)-( 203)HHHHHHHTT SSSS T TT THHHHHHHHHHHHT SS TTHHHHHHHHHHHTT
1590 1600
| |
1588 - 1608 KPFPVSHNPSFERLLVETIYS
( 204)-( 224) T HHHHHHHHHH
1610 1620 1630 1640 1650 1660
| | | | | |
1609 - 1668 GIIEEKALFVTCGATVPFPKLVSCVLSDEFCQELIQYGFVRLIIQFGRNYSSEFEHLVQE
( 24)-( 83) T T SSSS T T HHHHHHHHTHHHHHHHHHHTT SSSS TTTT HHHH
1670 1680 1690 1700 1710 1720
| | | | | |
1669 - 1728 RGGQRESQKIPIDQFGCGDTARQYVLMNGKLKVIGFDFSTKMQSIIRDYSDLVISHAGTG
( 84)-( 143)HTSSS TT HHHHTTT SSSSTTTT SSST TTTTHHHHHHHH TSSSSTT TH
1730 1740 1750 1760 1770 1780
| | | | | |
1729 - 1788 SILDSLRLNKPLIVCVNDSLMDNHQQQIADKFVELGYVWSCAPTETGLIAGLRASQTEKL
( 144)-( 203)HHHHHHHTT SSS T TTTTHHHHHHHHHHHHHTTTSS T HHHHHHHHHHHTT
1790 1800
| |
1789 - 1809 KPFPVSHNPSFERLLVETIYS
( 204)-( 224) TT T T HHHHHHHHHH
1810 1820 1830 1840 1850 1860
| | | | | |
1810 - 1869 GIIEEKALFVTCGATVPFPKLVSCVLSDEFCQELIQYGFVRLIIQFGRNYSSEFEHLVQE
( 24)-( 83) T SSSS TT TTHHHHHHHHTHHHHHHHHHHTT SSSS TT THHHH
1870 1880 1890 1900 1910 1920
| | | | | |
1870 - 1929 RGGQRESQKIPIDQFGCGDTARQYVLMNGKLKVIGFDFSTKMQSIIRDYSDLVISHAGTG
( 84)-( 143)TT SS TT TTTT SSTTSS SS TTTT SS T TTTHHHHHHHH SSS T TH
1930 1940 1950 1960 1970 1980
| | | | | |
1930 - 1989 SILDSLRLNKPLIVCVNDSLMDNHQQQIADKFVELGYVWSCAPTETGLIAGLRASQTEKL
( 144)-( 203)HHHHHHHTT SSS TT HHHHHHHHHHHTT SS TTHHHHHHHHHHHTT
1990 2000 2010
| | |
1990 - 2010 KPFPVSHNPSFERLLVETIYS
( 204)-( 224) TT TTHHHHHHHHT
# 62 # Note: Tau angles OK
All of the tau angles of amino acids that actually have a tau angle
fall within expected RMS deviations.
# 63 # Note: Normal tau angle deviations
The RMS Z-score for the tau angles in the structure falls within the
normal rannge that we guess to be 0.5 - 1.5.
Be aware, we determined the tau normal distributions from 500
high-resolution X-ray structures, rather than from CSD data, so we cannot
be 100 percent certain about these numbers.
Tau angle RMS Z-score : 0.614
# 64 # Note: Side chain planarity OK
All of the side chains of residues that have a planar group are
planar within expected RMS deviations.
# 65 # Note: Atoms connected to aromatic rings OK
All of the atoms that are connected to planar aromatic rings in side
chains of amino-acid residues are in the plane within expected RMS
deviations.
Since there is no DNA and no protein with hydrogens, no uncalibrated
planarity check was performed.
# 66 # Note: PRO puckering amplitude OK
Puckering amplitudes for all PRO residues are within normal ranges.
# 67 # Warning: Unusual PRO puckering phases
The proline residues listed in the table below have a puckering phase
that is not expected to occur in protein structures. Puckering
parameters were calculated by the method of Cremer and Pople
[REF]. Normal PRO rings approximately show a so-called envelope
conformation with the C-gamma atom above the plane of the ring
(phi=+72 degrees), or a half-chair conformation with C-gamma below
and C-beta above the plane of the ring (phi=-90 degrees). If phi
deviates strongly from these values, this is indicative of a very
strange conformation for a PRO residue, and definitely requires a
manual check of the data. Be aware that this is a warning with a low
confidence level.
See: Who checks the checkers? Four validation tools applied to eight
atomic resolution structures [REF].
182 PRO ( 205-) A 1 99.8 envelop C-beta (108 degrees)
184 PRO ( 207-) A 1 -59.5 half-chair C-beta/C-alpha (-54 degrees)
218 PRO ( 40-) A 2 100.4 envelop C-beta (108 degrees)
220 PRO ( 42-) A 2 100.6 envelop C-beta (108 degrees)
533 PRO ( 154-) A 3 99.1 envelop C-beta (108 degrees)
1277 PRO ( 94-) A 7 -62.7 half-chair C-beta/C-alpha (-54 degrees)
1337 PRO ( 154-) A 7 107.9 envelop C-beta (108 degrees)
1478 PRO ( 94-) A 8 121.6 half-chair C-beta/C-alpha (126 degrees)
1538 PRO ( 154-) A 8 104.0 envelop C-beta (108 degrees)
1589 PRO ( 205-) A 8 114.8 envelop C-beta (108 degrees)
1596 PRO ( 212-) A 8 -58.8 half-chair C-beta/C-alpha (-54 degrees)
1625 PRO ( 40-) A 9 -55.6 half-chair C-beta/C-alpha (-54 degrees)
1679 PRO ( 94-) A 9 107.5 envelop C-beta (108 degrees)
1739 PRO ( 154-) A 9 109.9 envelop C-beta (108 degrees)
1792 PRO ( 207-) A 9 -54.0 half-chair C-beta/C-alpha (-54 degrees)
1880 PRO ( 94-) A 10 -57.4 half-chair C-beta/C-alpha (-54 degrees)
# 68 # Warning: Torsion angle evaluation shows unusual residues
The residues listed in the table below contain bad or abnormal
torsion angles.
These scores give an impression of how `normal' the torsion
angles in protein residues are. All torsion angles except omega are
used for calculating a `normality' score. Average values and
standard deviations were obtained from the residues in the WHAT IF
database. These are used to calculate Z-scores. A residue with a
Z-score of below -2.0 is poor, and a score of less than -3.0 is
worrying. For such residues more than one torsion angle is in a
highly unlikely position.
923 THR ( 142-) A 5 -3.6
1286 THR ( 103-) A 7 -3.3
1727 THR ( 142-) A 9 -3.3
1662 PHE ( 77-) A 9 -3.3
1664 HIS ( 79-) A 9 -3.0
1085 THR ( 103-) A 6 -2.9
100 THR ( 123-) A 1 -2.9
1589 PRO ( 205-) A 8 -2.8
881 CYS ( 100-) A 5 -2.7
1835 LEU ( 49-) A 10 -2.7
1124 THR ( 142-) A 6 -2.7
240 PHE ( 62-) A 2 -2.7
904 THR ( 123-) A 5 -2.7
1879 ILE ( 93-) A 10 -2.7
820 VAL ( 39-) A 5 -2.6
469 SER ( 90-) A 3 -2.6
1031 LEU ( 49-) A 6 -2.6
936 LEU ( 155-) A 5 -2.5
860 HIS ( 79-) A 5 -2.5
26 LEU ( 49-) A 1 -2.5
1595 ASN ( 211-) A 8 -2.5
1059 PHE ( 77-) A 6 -2.5
1506 SER ( 122-) A 8 -2.5
1848 PHE ( 62-) A 10 -2.5
428 LEU ( 49-) A 3 -2.5
And so on for a total of 135 lines.
# 69 # Warning: Backbone evaluation reveals unusual conformations
The residues listed in the table below have abnormal backbone torsion
angles.
Residues with `forbidden' phi-psi combinations are listed, as
well as residues with unusual omega angles (deviating by more than
3 sigma from the normal value). Please note that it is normal if
about 5 percent of the residues is listed here as having unusual
phi-psi combinations.
3 ILE ( 26-) A 1 Poor phi/psi
5 GLU ( 28-) A 1 Poor phi/psi
27 SER ( 50-) A 1 Poor phi/psi
39 PHE ( 62-) A 1 Poor phi/psi
51 SER ( 74-) A 1 Poor phi/psi
52 SER ( 75-) A 1 Poor phi/psi
54 PHE ( 77-) A 1 Poor phi/psi
55 GLU ( 78-) A 1 Poor phi/psi
66 GLU ( 89-) A 1 Poor phi/psi
71 PRO ( 94-) A 1 Poor phi/psi
73 ASP ( 96-) A 1 Poor phi/psi
74 GLN ( 97-) A 1 Poor phi/psi
87 MET ( 110-) A 1 Poor phi/psi
90 LYS ( 113-) A 1 Poor phi/psi
101 LYS ( 124-) A 1 Poor phi/psi
110 SER ( 133-) A 1 Poor phi/psi
117 ALA ( 140-) A 1 Poor phi/psi
141 MET ( 164-) A 1 Poor phi/psi
177 THR ( 200-) A 1 Poor phi/psi
184 PRO ( 207-) A 1 Poor PRO-phi
186 SER ( 209-) A 1 Poor phi/psi
187 HIS ( 210-) A 1 Poor phi/psi
199 ILE ( 222-) A 1 Poor phi/psi
204 ILE ( 26-) A 2 Poor phi/psi
215 ALA ( 37-) A 2 Poor phi/psi
And so on for a total of 253 lines.
Ramachandran Z-score : -4.617
# 70 # Error: Ramachandran Z-score very low
The score expressing how well the backbone conformations of all residues
are corresponding to the known allowed areas in the Ramachandran plot is
very low.
Ramachandran Z-score : -4.617
# 71 # Note: Per-model averages for Ramachandran check
The table below gives the per-model Ramachandran Z-scores.
Model 1 : -4.606
Model 2 : -4.266
Model 3 : -4.349
Model 4 : -4.547
Model 5 : -4.253
Model 6 : -5.454
Model 7 : -4.406
Model 8 : -4.667
Model 9 : -4.719
Model 10 : -4.906
Omega average and std. deviation= 180.142 0.969
Significant deviations from expected 5.5!!!
# 72 # Warning: Omega angles too tightly restrained
The omega angles for trans-peptide bonds in a structure are
expected to give a gaussian distribution with the average around
+178 degrees and a standard deviation around 5.5 degrees. These
expected values were obtained from very accurately determined
structures. Many protein structures are too tightly restrained.
This seems to be the case with the current structure too, as the
observed standard deviation is below 4.0 degrees.
Standard deviation of omega values : 0.969
# 73 # Note: Per-model averages for omega angle check
The table below gives the per-model omega angle standard deviations.
Model 1 : 0.976
Model 2 : 0.909
Model 3 : 0.922
Model 4 : 1.067
Model 5 : 1.154
Model 6 : 1.061
Model 7 : 0.991
Model 8 : 0.830
Model 9 : 0.821
Model 10 : 0.931
chi-1/chi-2 correlation Z-score : -2.103
# 74 # Note: chi-1/chi-2 angle correlation Z-score OK
The score expressing how well the chi-1/chi-2 angles of all residues
are corresponding to the populated areas in the database is
within expected ranges for well-refined structures.
chi-1/chi-2 correlation Z-score : -2.103
# 75 # Note: Per-model averages for chi-1/chi-2 angle check
The table below gives the per-model chi-1/chi-2 correlation Z-scores.
Model 1 : -1.557
Model 2 : -1.957
Model 3 : -2.013
Model 4 : -2.135
Model 5 : -2.691
Model 6 : -2.975
Model 7 : -1.026
Model 8 : -1.565
Model 9 : -2.399
Model 10 : -2.711
# 76 # Warning: Backbone oxygen evaluation
The residues listed in the table below have an unusual backbone
oxygen position.
For each of the residues in the structure, a search was performed
to find 5-residue stretches in the WHAT IF database with
superposable C-alpha coordinates, and some restraining on the
neighbouring backbone oxygens.
In the following table the RMS distance between the backbone oxygen
positions of these matching structures in the database and the
position of the backbone oxygen atom in the current residue is
given. If this number is larger than 1.5 a significant number of
structures in the database show an alternative position for the
backbone oxygen. If the number is larger than 2.0 most matching
backbone fragments in the database have the peptide plane
flipped. A manual check needs to be performed to assess whether the
experimental data can support that alternative as well. The number
in the last column is the number of database hits (maximum 80) used
in the calculation. It is "normal" that some glycine residues show
up in this list, but they are still worth checking!
1525 GLY ( 141-) A 8 2.14 11
357 GLY ( 179-) A 2 2.02 50
1485 GLY ( 101-) A 8 1.72 25
1253 GLY ( 70-) A 7 1.53 24
# 77 # Warning: Unusual rotamers
The residues listed in the table below have a rotamer that is not
seen very often in the database of solved protein structures. This
option determines for every residue the position specific chi-1
rotamer distribution. Thereafter it verified whether the actual
residue in the molecule has the most preferred rotamer or not. If
the actual rotamer is the preferred one, the score is 1.0. If the
actual rotamer is unique, the score is 0.0. If there are two
preferred rotamers, with a population distribution of 3:2 and your
rotamer sits in the lesser populated rotamer, the score will be
0.667. No value will be given if insufficient hits are found in the
database.
It is not necessarily an error if a few residues have rotamer
values below 0.3, but careful inspection of all residues with these
low values could be worth it.
625 VAL ( 45-) A 4 0.36
1913 SER ( 127-) A 10 0.36
979 SER ( 198-) A 5 0.36
1528 SER ( 144-) A 8 0.37
1582 SER ( 198-) A 8 0.38
1130 SER ( 148-) A 6 0.38
322 SER ( 144-) A 2 0.39
778 SER ( 198-) A 4 0.39
121 SER ( 144-) A 1 0.39
# 78 # Warning: Unusual backbone conformations
For the residues listed in the table below, the backbone formed by
itself and two neighbouring residues on either side is in a
conformation that is not seen very often in the database of solved
protein structures. The number given in the table is the number of
similar backbone conformations in the database with the same amino
acid in the centre.
For this check, backbone conformations are compared with database
structures using C-alpha superpositions with some restraints on the
backbone oxygen positions.
A residue mentioned in the table can be part of a strange loop, or
there might be something wrong with it or its directly surrounding
residues. There are a few of these in every protein, but in any
case it is worth looking at!
3 ILE ( 26-) A 1 0
4 GLU ( 27-) A 1 0
5 GLU ( 28-) A 1 0
12 CYS ( 35-) A 1 0
14 ALA ( 37-) A 1 0
17 PRO ( 40-) A 1 0
18 PHE ( 41-) A 1 0
26 LEU ( 49-) A 1 0
37 TYR ( 60-) A 1 0
39 PHE ( 62-) A 1 0
40 VAL ( 63-) A 1 0
45 GLN ( 68-) A 1 0
46 PHE ( 69-) A 1 0
48 ARG ( 71-) A 1 0
51 SER ( 74-) A 1 0
52 SER ( 75-) A 1 0
53 GLU ( 76-) A 1 0
54 PHE ( 77-) A 1 0
55 GLU ( 78-) A 1 0
66 GLU ( 89-) A 1 0
67 SER ( 90-) A 1 0
68 GLN ( 91-) A 1 0
71 PRO ( 94-) A 1 0
72 ILE ( 95-) A 1 0
73 ASP ( 96-) A 1 0
And so on for a total of 984 lines.
# 79 # Note: Backbone conformation Z-score OK
The backbone conformation analysis gives a score that is normal
for well refined protein structures.
Backbone conformation Z-score : -1.421
# 80 # Error: Abnormally short interatomic distances
The pairs of atoms listed in the table below have an unusually
short distance.
The contact distances of all atom pairs have been checked. Two
atoms are said to `bump' if they are closer than the sum of their
Van der Waals radii minus 0.40 Angstrom. For hydrogen bonded pairs
a tolerance of 0.55 Angstrom is used. The first number in the
table tells you how much shorter that specific contact is than the
acceptable limit. The second distance is the distance between the
centres of the two atoms. Although we believe that two water atoms
at 2.4 A distance are too close, we only report water pairs that are
closer than this rather short distance.
The last text-item on each line represents the status of the atom
pair. The text `INTRA' means that the bump is between atoms that
are explicitly listed in the PDB file. `INTER' means it is an
inter-symmetry bump. If the final column contains the text 'HB',
the bump criterion was relaxed because there could be a hydrogen
bond. Similarly relaxed criteria are used for 1--3 and 1--4
interactions (listed as 'B2' and 'B3', respectively). If the last
column is 'BF', the sum of the B-factors of the atoms is higher
than 80, which makes the appearance of the bump somewhat less
severe because the atoms probably aren't there anyway. BL, on the
other hand, indicates that the bumping atoms both have a low
B-factor, and that makes the bumps more worrisome.
Bumps between atoms for which the sum of their occupancies is lower
than one are not reported. In any case, each bump is listed in only
one direction. If the MODEL number doesn't exist (like in most X-ray
files), a minus sign is printed instead.
303 MET ( 125-) A 2 SD <--> 304 GLN ( 126-) A 2 NE2 0.45 2.85 INTRA BL
849 GLN ( 68-) A 5 NE2 <--> 906 MET ( 125-) A 5 SD 0.44 2.86 INTRA BL
1452 GLN ( 68-) A 8 NE2 <--> 1509 MET ( 125-) A 8 SD 0.41 2.89 INTRA BL
1132 ARG ( 150-) A 6 NH1 <--> 1192 HIS ( 210-) A 6 ND1 0.40 2.60 INTRA BL
1161 GLY ( 179-) A 6 O <--> 1163 VAL ( 181-) A 6 N 0.39 2.31 INTRA BL
31 CYS ( 54-) A 1 SG <--> 90 LYS ( 113-) A 1 NZ 0.39 2.91 INTRA BL
1961 PHE ( 175-) A 10 O <--> 1965 GLY ( 179-) A 10 N 0.37 2.33 INTRA BL
1420 GLY ( 36-) A 8 N <--> 1523 HIS ( 139-) A 8 NE2 0.37 2.63 INTRA BL
1563 GLY ( 179-) A 8 O <--> 1565 VAL ( 181-) A 8 N 0.36 2.34 INTRA BL
1237 CYS ( 54-) A 7 SG <--> 1296 LYS ( 113-) A 7 NZ 0.36 2.94 INTRA BL
1832 SER ( 46-) A 10 O <--> 1836 SER ( 50-) A 10 N 0.34 2.36 INTRA BL
362 CYS ( 184-) A 2 SG <--> 368 GLY ( 190-) A 2 C 0.34 3.06 INTRA BL
224 SER ( 46-) A 2 O <--> 228 SER ( 50-) A 2 N 0.33 2.37 INTRA BL
1683 PHE ( 98-) A 9 CE2 <--> 1690 ARG ( 105-) A 9 NE 0.33 2.77 INTRA BL
759 GLY ( 179-) A 4 O <--> 761 VAL ( 181-) A 4 N 0.33 2.37 INTRA BL
1631 SER ( 46-) A 9 O <--> 1635 SER ( 50-) A 9 N 0.33 2.37 INTRA BL
1452 GLN ( 68-) A 8 CD <--> 1509 MET ( 125-) A 8 SD 0.33 3.07 INTRA BL
1229 SER ( 46-) A 7 O <--> 1233 SER ( 50-) A 7 N 0.33 2.37 INTRA BL
558 GLY ( 179-) A 3 O <--> 560 VAL ( 181-) A 3 N 0.32 2.38 INTRA BL
1710 MET ( 125-) A 9 SD <--> 1711 GLN ( 126-) A 9 N 0.32 2.88 INTRA BL
491 GLY ( 112-) A 3 C <--> 494 LYS ( 115-) A 3 NZ 0.32 2.78 INTRA BL
411 PHE ( 32-) A 3 CE2 <--> 447 GLN ( 68-) A 3 NE2 0.32 2.78 INTRA BL
1138 ILE ( 156-) A 6 CG2 <--> 1166 CYS ( 184-) A 6 SG 0.32 3.08 INTRA BL
414 CYS ( 35-) A 3 SG <--> 448 PHE ( 69-) A 3 CE1 0.32 3.08 INTRA BL
1523 HIS ( 139-) A 8 CD2 <--> 1552 GLN ( 168-) A 8 NE2 0.32 2.78 INTRA BL
And so on for a total of 742 lines.
# 81 # Note: Inside/Outside residue distribution normal
The distribution of residue types over the inside and the outside of the
protein is normal.
inside/outside RMS Z-score : 1.127
# 82 # Note: Per-model averages for inside/outside residue distributi ...
The table below gives the per-model inside/outside residue distribution
RMS Z-scores.
Model 1 : 1.109
Model 2 : 1.176
Model 3 : 1.092
Model 4 : 1.138
Model 5 : 1.159
Model 6 : 1.117
Model 7 : 1.094
Model 8 : 1.122
Model 9 : 1.155
Model 10 : 1.102
# 83 # Note: Inside/Outside RMS Z-score plot
The Inside/Outside distribution normality RMS Z-score over a 15
residue window is plotted as function of the residue number. High
areas in the plot (above 1.5) indicate unusual inside/outside
patterns.
In the TeX file, a plot has been inserted here
Chain identifier: A; Model number 1
# 84 # Note: Inside/Outside RMS Z-score plot
In the TeX file, a plot has been inserted here
Chain identifier: A; Model number 2
# 85 # Note: Inside/Outside RMS Z-score plot
In the TeX file, a plot has been inserted here
Chain identifier: A; Model number 3
# 86 # Note: Inside/Outside RMS Z-score plot
In the TeX file, a plot has been inserted here
Chain identifier: A; Model number 4
# 87 # Note: Inside/Outside RMS Z-score plot
In the TeX file, a plot has been inserted here
Chain identifier: A; Model number 5
# 88 # Note: Inside/Outside RMS Z-score plot
In the TeX file, a plot has been inserted here
Chain identifier: A; Model number 6
# 89 # Note: Inside/Outside RMS Z-score plot
In the TeX file, a plot has been inserted here
Chain identifier: A; Model number 7
# 90 # Note: Inside/Outside RMS Z-score plot
In the TeX file, a plot has been inserted here
Chain identifier: A; Model number 8
# 91 # Note: Inside/Outside RMS Z-score plot
In the TeX file, a plot has been inserted here
Chain identifier: A; Model number 9
# 92 # Note: Inside/Outside RMS Z-score plot
In the TeX file, a plot has been inserted here
Chain identifier: A; Model number 10
# 93 # Warning: Abnormal packing environment for some residues
The residues listed in the table below have an unusual packing
environment.
The packing environment of the residues is compared with the
average packing environment for all residues of the same type in
good PDB files. A low packing score can indicate one of several
things: Poor packing, misthreading of the sequence through the
density, crystal contacts, contacts with a co-factor, or the
residue is part of the active site. It is not uncommon to see a few
of these, but in any case this requires further inspection of the
residue.
1406 TYR ( 223-) A 7 -8.72
602 TYR ( 223-) A 3 -8.43
401 TYR ( 223-) A 2 -7.93
2009 TYR ( 223-) A 10 -7.93
1205 TYR ( 223-) A 6 -7.88
200 TYR ( 223-) A 1 -7.82
803 TYR ( 223-) A 4 -7.77
1808 TYR ( 223-) A 9 -7.66
1607 TYR ( 223-) A 8 -7.60
467 ARG ( 88-) A 3 -7.26
1004 TYR ( 223-) A 5 -7.23
157 TYR ( 180-) A 1 -7.10
1146 MET ( 164-) A 6 -7.08
299 PHE ( 121-) A 2 -7.02
1304 PHE ( 121-) A 7 -6.96
872 GLN ( 91-) A 5 -6.83
470 GLN ( 91-) A 3 -6.61
1966 TYR ( 180-) A 10 -6.59
187 HIS ( 210-) A 1 -6.42
1706 PHE ( 121-) A 9 -6.39
873 LYS ( 92-) A 5 -6.39
1594 HIS ( 210-) A 8 -6.38
388 HIS ( 210-) A 2 -6.34
744 MET ( 164-) A 4 -6.33
902 PHE ( 121-) A 5 -6.33
And so on for a total of 112 lines.
# 94 # Warning: Abnormal packing environment for sequential residues
A stretch of at least three sequential residues with a questionable packing
environment was found. This could indicate that these residues are part
of a strange loop. It might also be an indication of misthreading in the
density. However, it can also indicate that one or more residues in this
stretch have other problems such as, for example, missing atoms, very
weird angles or bond lengths, etc.
The table below lists the first and last residue in each stretch found,
as well as the average residue score of the series.
269 GLN ( 91-) A 2 271 --- ILE 93- ( A) 2 -4.59
470 GLN ( 91-) A 3 472 --- ILE 93- ( A) 3 -5.67
500 PHE ( 121-) A 3 502 --- THR 123- ( A) 3 -4.53
604 GLY ( 24-) A 4 607 --- GLU 27- ( A) 4 -4.22
671 GLN ( 91-) A 4 673 --- ILE 93- ( A) 4 -5.16
782 LYS ( 202-) A 4 784 --- LYS 204- ( A) 4 -4.74
872 GLN ( 91-) A 5 874 --- ILE 93- ( A) 5 -6.10
1006 GLY ( 24-) A 6 1009 --- GLU 27- ( A) 6 -4.62
1409 ILE ( 25-) A 8 1412 --- GLU 28- ( A) 8 -4.46
1475 GLN ( 91-) A 8 1477 --- ILE 93- ( A) 8 -5.29
1680 ILE ( 95-) A 9 1683 --- PHE 98- ( A) 9 -4.64
1807 ILE ( 222-) A 9 1809 --- SER 224- ( A) 9 -5.60
# 95 # Warning: Structural average packing environment a bit worrysome
The structural average quality control value is a bit low.
The protein is probably threaded correctly, but either poorly
refined, or it is just a protein with an unusual (but correct)
structure. The average quality of 200 highly refined Xray
structures was -0.5+/-0.4 [REF].
Average for range 1 - 2010 : -1.874
# 96 # Note: Quality value plot
The quality value smoothed over a 10 residue window is plotted as
function of the residue number. Low areas in the plot (below
-2.0) indicate "unusual" packing.
In the TeX file, a plot has been inserted here
Chain identifier: A; Model number 1
# 97 # Note: Quality value plot
The quality value smoothed over a 10 residue window is plotted as
function of the residue number. Low areas in the plot (below
-2.0) indicate "unusual" packing.
In the TeX file, a plot has been inserted here
Chain identifier: A; Model number 2
# 98 # Note: Quality value plot
The quality value smoothed over a 10 residue window is plotted as
function of the residue number. Low areas in the plot (below
-2.0) indicate "unusual" packing.
In the TeX file, a plot has been inserted here
Chain identifier: A; Model number 3
# 99 # Note: Quality value plot
The quality value smoothed over a 10 residue window is plotted as
function of the residue number. Low areas in the plot (below
-2.0) indicate "unusual" packing.
In the TeX file, a plot has been inserted here
Chain identifier: A; Model number 4
# 100 # Note: Quality value plot
The quality value smoothed over a 10 residue window is plotted as
function of the residue number. Low areas in the plot (below
-2.0) indicate "unusual" packing.
In the TeX file, a plot has been inserted here
Chain identifier: A; Model number 5
# 101 # Note: Quality value plot
The quality value smoothed over a 10 residue window is plotted as
function of the residue number. Low areas in the plot (below
-2.0) indicate "unusual" packing.
In the TeX file, a plot has been inserted here
Chain identifier: A; Model number 6
# 102 # Note: Quality value plot
The quality value smoothed over a 10 residue window is plotted as
function of the residue number. Low areas in the plot (below
-2.0) indicate "unusual" packing.
In the TeX file, a plot has been inserted here
Chain identifier: A; Model number 7
# 103 # Note: Quality value plot
The quality value smoothed over a 10 residue window is plotted as
function of the residue number. Low areas in the plot (below
-2.0) indicate "unusual" packing.
In the TeX file, a plot has been inserted here
Chain identifier: A; Model number 8
# 104 # Note: Quality value plot
The quality value smoothed over a 10 residue window is plotted as
function of the residue number. Low areas in the plot (below
-2.0) indicate "unusual" packing.
In the TeX file, a plot has been inserted here
Chain identifier: A; Model number 9
# 105 # Note: Quality value plot
The quality value smoothed over a 10 residue window is plotted as
function of the residue number. Low areas in the plot (below
-2.0) indicate "unusual" packing.
In the TeX file, a plot has been inserted here
Chain identifier: A; Model number 10
----Residue------- State AllAll BB-BB BB-SC SC-BB SC-SC
---------------------------------------------------------------------------
============================================================
All contacts : Average = -0.764 Z-score = -4.27
BB-BB contacts : Average = -0.521 Z-score = -3.21
BB-SC contacts : Average = -0.514 Z-score = -3.62
SC-BB contacts : Average = -0.662 Z-score = -3.88
SC-SC contacts : Average = -0.588 Z-score = -3.71
============================================================
# 106 # Warning: Low packing Z-score for some residues
The residues listed in the table below have an unusual packing
environment according to the 2nd generation quality check. The score
listed in the table is a packing normality Z-score: positive means
better than average, negative means worse than average. Only residues
scoring less than -2.50 are listed here. These are the "unusual"
residues in the structure, so it will be interesting to take a
special look at them.
1455 ARG ( 71-) A 8 -2.72
1091 LEU ( 109-) A 6 -2.64
1918 TYR ( 132-) A 10 -2.63
331 LYS ( 153-) A 2 -2.59
# 107 # Note: No series of residues with abnormal new packing environment
There are no stretches of four or more residues each having a quality
control Z-score worse than -1.75.
# 108 # Error: Abnormal structural average packing Z-score
The quality control Z-score for the structure is very low.
A molecule is certain to be incorrect if the Z-score is below -5.0.
Poorly refined molecules, very well energy minimized misthreaded
molecules and low homology models give values between -2.0 and
-5.0. The average quality of properly refined Xray structures is
0.0+/-1.0.
All contacts : Average = -0.764 Z-score = -4.27
BB-BB contacts : Average = -0.521 Z-score = -3.21
BB-SC contacts : Average = -0.514 Z-score = -3.62
SC-BB contacts : Average = -0.662 Z-score = -3.88
SC-SC contacts : Average = -0.588 Z-score = -3.71
# 109 # Note: Per-model averages for NQA
The table below gives the per-model NQA averages and Z-scores. These are the
numbers for all contacts.
Model 1 : -0.856; -4.778
Model 2 : -0.720; -4.031
Model 3 : -0.722; -4.042
Model 4 : -0.727; -4.068
Model 5 : -0.793; -4.432
Model 6 : -0.799; -4.463
Model 7 : -0.764; -4.270
Model 8 : -0.773; -4.322
Model 9 : -0.692; -3.876
Model 10 : -0.792; -4.424
# 110 # Note: Second generation quality Z-score plot
The second generation quality Z-score smoothed over a 10 residue window
is plotted as function of the residue number. Low areas in the plot (below
-1.3) indicate "unusual" packing.
In the TeX file, a plot has been inserted here
Chain identifier: A; Model number 1
# 111 # Note: Second generation quality Z-score plot
In the TeX file, a plot has been inserted here
Chain identifier: A; Model number 2
# 112 # Note: Second generation quality Z-score plot
In the TeX file, a plot has been inserted here
Chain identifier: A; Model number 3
# 113 # Note: Second generation quality Z-score plot
In the TeX file, a plot has been inserted here
Chain identifier: A; Model number 4
# 114 # Note: Second generation quality Z-score plot
In the TeX file, a plot has been inserted here
Chain identifier: A; Model number 5
# 115 # Note: Second generation quality Z-score plot
In the TeX file, a plot has been inserted here
Chain identifier: A; Model number 6
# 116 # Note: Second generation quality Z-score plot
In the TeX file, a plot has been inserted here
Chain identifier: A; Model number 7
# 117 # Note: Second generation quality Z-score plot
In the TeX file, a plot has been inserted here
Chain identifier: A; Model number 8
# 118 # Note: Second generation quality Z-score plot
In the TeX file, a plot has been inserted here
Chain identifier: A; Model number 9
# 119 # Note: Second generation quality Z-score plot
In the TeX file, a plot has been inserted here
Chain identifier: A; Model number 10
Since there are no waters, the water check has been skipped.
O2 located for residue 201
O2 located for residue 402
O2 located for residue 603
O2 located for residue 804
O2 located for residue 1005
O2 located for residue 1206
O2 located for residue 1407
O2 located for residue 1608
O2 located for residue 1809
O2 located for residue 2010
Number of donors: 3360
Number of H-atoms: 3950
Number of donor groups: 270
Symmetry related molecules will be taken into account
Calculating accessibilities and coordinates
56 HIS ( 79-) A 1 ND1 Acc, Acc-alt, Pen= 5.46 0.31 0.40
56 HIS ( 79-) A 1 NE2 Acc, Acc-alt, Pen= 5.30 9.35 0.40
The FLIP penalty for 56 HIS ( 79-) A 1 was set to 0.4
116 HIS ( 139-) A 1 ND1 Acc, Acc-alt, Pen= 0.00 1.56 0.60
116 HIS ( 139-) A 1 NE2 Acc, Acc-alt, Pen= 0.78 0.00 0.40
The FLIP penalty for 116 HIS ( 139-) A 1 was set to 0.4
144 HIS ( 167-) A 1 ND1 Acc, Acc-alt, Pen= 6.70 6.86 0.40
144 HIS ( 167-) A 1 NE2 Acc, Acc-alt, Pen= 9.20 8.57 0.40
The FLIP penalty for 144 HIS ( 167-) A 1 was set to 0.4
187 HIS ( 210-) A 1 ND1 Acc, Acc-alt, Pen= 8.26 4.52 0.40
187 HIS ( 210-) A 1 NE2 Acc, Acc-alt, Pen= 10.13 10.44 0.40
The FLIP penalty for 187 HIS ( 210-) A 1 was set to 0.4
257 HIS ( 79-) A 2 ND1 Acc, Acc-alt, Pen= 6.70 0.16 0.40
257 HIS ( 79-) A 2 NE2 Acc, Acc-alt, Pen= 8.88 9.66 0.40
The FLIP penalty for 257 HIS ( 79-) A 2 was set to 0.4
317 HIS ( 139-) A 2 ND1 Acc, Acc-alt, Pen= 0.00 0.16 0.60
317 HIS ( 139-) A 2 NE2 Acc, Acc-alt, Pen= 3.90 1.40 0.60
The FLIP penalty for 317 HIS ( 139-) A 2 was set to 0.6
345 HIS ( 167-) A 2 ND1 Acc, Acc-alt, Pen= 3.58 3.90 0.40
345 HIS ( 167-) A 2 NE2 Acc, Acc-alt, Pen= 9.66 8.88 0.40
The FLIP penalty for 345 HIS ( 167-) A 2 was set to 0.4
388 HIS ( 210-) A 2 ND1 Acc, Acc-alt, Pen= 6.08 5.46 0.40
388 HIS ( 210-) A 2 NE2 Acc, Acc-alt, Pen= 7.64 5.30 0.40
The FLIP penalty for 388 HIS ( 210-) A 2 was set to 0.4
458 HIS ( 79-) A 3 ND1 Acc, Acc-alt, Pen= 5.14 2.81 0.40
458 HIS ( 79-) A 3 NE2 Acc, Acc-alt, Pen= 0.62 2.65 0.40
The FLIP penalty for 458 HIS ( 79-) A 3 was set to 0.4
518 HIS ( 139-) A 3 ND1 Acc, Acc-alt, Pen= 0.16 0.16 0.40
518 HIS ( 139-) A 3 NE2 Acc, Acc-alt, Pen= 2.18 4.52 0.40
The FLIP penalty for 518 HIS ( 139-) A 3 was set to 0.4
546 HIS ( 167-) A 3 ND1 Acc, Acc-alt, Pen= 5.14 5.61 0.40
546 HIS ( 167-) A 3 NE2 Acc, Acc-alt, Pen= 9.35 8.73 0.40
The FLIP penalty for 546 HIS ( 167-) A 3 was set to 0.4
589 HIS ( 210-) A 3 ND1 Acc, Acc-alt, Pen= 6.08 1.71 0.40
589 HIS ( 210-) A 3 NE2 Acc, Acc-alt, Pen= 4.52 7.01 0.40
The FLIP penalty for 589 HIS ( 210-) A 3 was set to 0.4
659 HIS ( 79-) A 4 ND1 Acc, Acc-alt, Pen= 7.95 0.00 0.20
659 HIS ( 79-) A 4 NE2 Acc, Acc-alt, Pen= 0.78 7.48 0.20
The FLIP penalty for 659 HIS ( 79-) A 4 was set to 0.2
719 HIS ( 139-) A 4 ND1 Acc, Acc-alt, Pen= 2.49 0.00 0.20
719 HIS ( 139-) A 4 NE2 Acc, Acc-alt, Pen= 0.62 0.16 0.20
The FLIP penalty for 719 HIS ( 139-) A 4 was set to 0.2
747 HIS ( 167-) A 4 ND1 Acc, Acc-alt, Pen= 1.87 0.00 0.20
747 HIS ( 167-) A 4 NE2 Acc, Acc-alt, Pen= 4.52 1.87 0.20
The FLIP penalty for 747 HIS ( 167-) A 4 was set to 0.2
790 HIS ( 210-) A 4 ND1 Acc, Acc-alt, Pen= 8.26 5.30 0.40
790 HIS ( 210-) A 4 NE2 Acc, Acc-alt, Pen= 8.26 10.13 0.40
The FLIP penalty for 790 HIS ( 210-) A 4 was set to 0.4
860 HIS ( 79-) A 5 ND1 Acc, Acc-alt, Pen= 0.31 5.92 0.40
860 HIS ( 79-) A 5 NE2 Acc, Acc-alt, Pen= 10.29 10.29 0.40
The FLIP penalty for 860 HIS ( 79-) A 5 was set to 0.4
920 HIS ( 139-) A 5 ND1 Acc, Acc-alt, Pen= 0.00 4.05 0.60
920 HIS ( 139-) A 5 NE2 Acc, Acc-alt, Pen= 1.09 2.65 0.60
The FLIP penalty for 920 HIS ( 139-) A 5 was set to 0.6
948 HIS ( 167-) A 5 ND1 Acc, Acc-alt, Pen= 4.21 3.43 0.40
948 HIS ( 167-) A 5 NE2 Acc, Acc-alt, Pen= 10.60 10.13 0.40
The FLIP penalty for 948 HIS ( 167-) A 5 was set to 0.4
991 HIS ( 210-) A 5 ND1 Acc, Acc-alt, Pen= 4.36 3.12 0.40
991 HIS ( 210-) A 5 NE2 Acc, Acc-alt, Pen= 8.26 4.05 0.40
The FLIP penalty for 991 HIS ( 210-) A 5 was set to 0.4
1061 HIS ( 79-) A 6 ND1 Acc, Acc-alt, Pen= 3.90 0.47 0.40
1061 HIS ( 79-) A 6 NE2 Acc, Acc-alt, Pen= 9.98 9.66 0.40
The FLIP penalty for 1061 HIS ( 79-) A 6 was set to 0.4
1121 HIS ( 139-) A 6 ND1 Acc, Acc-alt, Pen= 2.18 0.00 0.20
1121 HIS ( 139-) A 6 NE2 Acc, Acc-alt, Pen= 1.40 0.16 0.20
The FLIP penalty for 1121 HIS ( 139-) A 6 was set to 0.2
1149 HIS ( 167-) A 6 ND1 Acc, Acc-alt, Pen= 6.23 3.74 0.40
1149 HIS ( 167-) A 6 NE2 Acc, Acc-alt, Pen= 0.16 5.30 0.40
The FLIP penalty for 1149 HIS ( 167-) A 6 was set to 0.4
1192 HIS ( 210-) A 6 ND1 Acc, Acc-alt, Pen= 1.56 0.00 0.20
1192 HIS ( 210-) A 6 NE2 Acc, Acc-alt, Pen= 9.20 9.82 0.20
The FLIP penalty for 1192 HIS ( 210-) A 6 was set to 0.2
1262 HIS ( 79-) A 7 ND1 Acc, Acc-alt, Pen= 3.43 2.96 0.40
1262 HIS ( 79-) A 7 NE2 Acc, Acc-alt, Pen= 7.79 10.13 0.40
The FLIP penalty for 1262 HIS ( 79-) A 7 was set to 0.4
1322 HIS ( 139-) A 7 ND1 Acc, Acc-alt, Pen= 1.40 0.47 0.40
1322 HIS ( 139-) A 7 NE2 Acc, Acc-alt, Pen= 0.31 0.62 0.40
The FLIP penalty for 1322 HIS ( 139-) A 7 was set to 0.4
1350 HIS ( 167-) A 7 ND1 Acc, Acc-alt, Pen= 3.12 3.90 0.40
1350 HIS ( 167-) A 7 NE2 Acc, Acc-alt, Pen= 8.73 9.51 0.40
The FLIP penalty for 1350 HIS ( 167-) A 7 was set to 0.4
1393 HIS ( 210-) A 7 ND1 Acc, Acc-alt, Pen= 5.92 0.16 0.40
1393 HIS ( 210-) A 7 NE2 Acc, Acc-alt, Pen= 2.65 1.25 0.40
The FLIP penalty for 1393 HIS ( 210-) A 7 was set to 0.4
1463 HIS ( 79-) A 8 ND1 Acc, Acc-alt, Pen= 7.01 0.00 0.20
1463 HIS ( 79-) A 8 NE2 Acc, Acc-alt, Pen= 4.05 7.95 0.20
The FLIP penalty for 1463 HIS ( 79-) A 8 was set to 0.2
1523 HIS ( 139-) A 8 ND1 Acc, Acc-alt, Pen= 2.03 0.00 0.20
1523 HIS ( 139-) A 8 NE2 Acc, Acc-alt, Pen= 0.00 0.78 0.40
The FLIP penalty for 1523 HIS ( 139-) A 8 was set to 0.4
1551 HIS ( 167-) A 8 ND1 Acc, Acc-alt, Pen= 4.52 5.14 0.40
1551 HIS ( 167-) A 8 NE2 Acc, Acc-alt, Pen= 8.57 5.46 0.40
The FLIP penalty for 1551 HIS ( 167-) A 8 was set to 0.4
1594 HIS ( 210-) A 8 ND1 Acc, Acc-alt, Pen= 5.61 4.99 0.40
1594 HIS ( 210-) A 8 NE2 Acc, Acc-alt, Pen= 6.55 9.35 0.40
The FLIP penalty for 1594 HIS ( 210-) A 8 was set to 0.4
1664 HIS ( 79-) A 9 ND1 Acc, Acc-alt, Pen= 0.00 5.77 0.60
1664 HIS ( 79-) A 9 NE2 Acc, Acc-alt, Pen= 7.01 2.34 0.60
The FLIP penalty for 1664 HIS ( 79-) A 9 was set to 0.6
1724 HIS ( 139-) A 9 ND1 Acc, Acc-alt, Pen= 0.00 0.31 0.60
1724 HIS ( 139-) A 9 NE2 Acc, Acc-alt, Pen= 0.31 0.00 0.40
The FLIP penalty for 1724 HIS ( 139-) A 9 was set to 0.4
1752 HIS ( 167-) A 9 ND1 Acc, Acc-alt, Pen= 0.78 0.00 0.20
1752 HIS ( 167-) A 9 NE2 Acc, Acc-alt, Pen= 0.47 4.83 0.20
The FLIP penalty for 1752 HIS ( 167-) A 9 was set to 0.2
1795 HIS ( 210-) A 9 ND1 Acc, Acc-alt, Pen= 0.16 7.17 0.40
1795 HIS ( 210-) A 9 NE2 Acc, Acc-alt, Pen= 6.70 1.71 0.40
The FLIP penalty for 1795 HIS ( 210-) A 9 was set to 0.4
1865 HIS ( 79-) A 10 ND1 Acc, Acc-alt, Pen= 3.90 0.94 0.40
1865 HIS ( 79-) A 10 NE2 Acc, Acc-alt, Pen= 7.33 9.82 0.40
The FLIP penalty for 1865 HIS ( 79-) A 10 was set to 0.4
1925 HIS ( 139-) A 10 ND1 Acc, Acc-alt, Pen= 1.56 0.31 0.40
1925 HIS ( 139-) A 10 NE2 Acc, Acc-alt, Pen= 0.16 0.00 0.20
The FLIP penalty for 1925 HIS ( 139-) A 10 was set to 0.2
1953 HIS ( 167-) A 10 ND1 Acc, Acc-alt, Pen= 4.21 5.30 0.40
1953 HIS ( 167-) A 10 NE2 Acc, Acc-alt, Pen= 7.33 7.01 0.40
The FLIP penalty for 1953 HIS ( 167-) A 10 was set to 0.4
1996 HIS ( 210-) A 10 ND1 Acc, Acc-alt, Pen= 5.77 1.71 0.40
1996 HIS ( 210-) A 10 NE2 Acc, Acc-alt, Pen= 4.05 7.95 0.40
The FLIP penalty for 1996 HIS ( 210-) A 10 was set to 0.4
Number of positive ions : 0
Finding possible acceptors for all donors...
Total number of potential acceptors: 1816
Locating affected donors for all ambiguities...
Number of donors affected by ambiguities: 401
Initializing group penalty for all donors 3360
DBG> Total flip penalty: 0.000
Fraction of hydrogen network done : 0.000
Fraction of hydrogen network done : 0.002
Fraction of hydrogen network done : 0.002
Fraction of hydrogen network done : 0.003
Fraction of hydrogen network done : 0.005
Fraction of hydrogen network done : 0.005
Fraction of hydrogen network done : 0.006
Fraction of hydrogen network done : 0.009
Fraction of hydrogen network done : 0.009
Fraction of hydrogen network done : 0.010
Fraction of hydrogen network done : 0.011
Fraction of hydrogen network done : 0.013
Fraction of hydrogen network done : 0.014
Fraction of hydrogen network done : 0.020
Fraction of hydrogen network done : 0.022
Fraction of hydrogen network done : 0.024
Fraction of hydrogen network done : 0.025
Fraction of hydrogen network done : 0.026
Fraction of hydrogen network done : 0.032
Fraction of hydrogen network done : 0.033
Fraction of hydrogen network done : 0.034
Fraction of hydrogen network done : 0.037
Fraction of hydrogen network done : 0.037
Fraction of hydrogen network done : 0.039
Fraction of hydrogen network done : 0.039
Fraction of hydrogen network done : 0.041
Fraction of hydrogen network done : 0.042
Fraction of hydrogen network done : 0.042
Fraction of hydrogen network done : 0.046
Fraction of hydrogen network done : 0.047
Fraction of hydrogen network done : 0.050
Fraction of hydrogen network done : 0.052
Fraction of hydrogen network done : 0.056
Fraction of hydrogen network done : 0.057
Fraction of hydrogen network done : 0.057
Fraction of hydrogen network done : 0.059
Fraction of hydrogen network done : 0.060
Fraction of hydrogen network done : 0.060
Fraction of hydrogen network done : 0.063
Fraction of hydrogen network done : 0.066
Fraction of hydrogen network done : 0.066
Fraction of hydrogen network done : 0.068
Fraction of hydrogen network done : 0.068
Fraction of hydrogen network done : 0.072
Fraction of hydrogen network done : 0.072
Fraction of hydrogen network done : 0.073
Fraction of hydrogen network done : 0.074
Fraction of hydrogen network done : 0.075
Fraction of hydrogen network done : 0.076
Fraction of hydrogen network done : 0.077
Fraction of hydrogen network done : 0.078
Fraction of hydrogen network done : 0.079
Fraction of hydrogen network done : 0.079
Fraction of hydrogen network done : 0.080
Fraction of hydrogen network done : 0.082
Fraction of hydrogen network done : 0.083
Fraction of hydrogen network done : 0.084
Fraction of hydrogen network done : 0.085
Fraction of hydrogen network done : 0.087
Fraction of hydrogen network done : 0.093
Fraction of hydrogen network done : 0.095
Fraction of hydrogen network done : 0.095
Fraction of hydrogen network done : 0.097
Fraction of hydrogen network done : 0.097
Fraction of hydrogen network done : 0.099
Fraction of hydrogen network done : 0.100
Fraction of hydrogen network done : 0.101
Fraction of hydrogen network done : 0.103
Fraction of hydrogen network done : 0.104
Fraction of hydrogen network done : 0.105
Fraction of hydrogen network done : 0.106
Fraction of hydrogen network done : 0.106
Fraction of hydrogen network done : 0.108
Fraction of hydrogen network done : 0.109
Fraction of hydrogen network done : 0.109
Fraction of hydrogen network done : 0.111
Fraction of hydrogen network done : 0.112
Fraction of hydrogen network done : 0.112
Fraction of hydrogen network done : 0.117
Fraction of hydrogen network done : 0.117
Fraction of hydrogen network done : 0.118
Fraction of hydrogen network done : 0.120
Fraction of hydrogen network done : 0.123
Fraction of hydrogen network done : 0.123
Fraction of hydrogen network done : 0.124
Fraction of hydrogen network done : 0.124
Fraction of hydrogen network done : 0.125
Fraction of hydrogen network done : 0.126
Fraction of hydrogen network done : 0.129
Fraction of hydrogen network done : 0.130
Fraction of hydrogen network done : 0.130
Fraction of hydrogen network done : 0.132
Fraction of hydrogen network done : 0.132
Fraction of hydrogen network done : 0.135
Fraction of hydrogen network done : 0.140
Fraction of hydrogen network done : 0.140
Fraction of hydrogen network done : 0.141
Fraction of hydrogen network done : 0.142
Fraction of hydrogen network done : 0.145
Fraction of hydrogen network done : 0.148
Fraction of hydrogen network done : 0.152
Fraction of hydrogen network done : 0.153
Fraction of hydrogen network done : 0.154
Fraction of hydrogen network done : 0.158
Fraction of hydrogen network done : 0.161
Fraction of hydrogen network done : 0.162
Fraction of hydrogen network done : 0.163
Fraction of hydrogen network done : 0.164
Fraction of hydrogen network done : 0.165
Fraction of hydrogen network done : 0.168
Fraction of hydrogen network done : 0.170
Fraction of hydrogen network done : 0.172
Fraction of hydrogen network done : 0.173
Fraction of hydrogen network done : 0.176
Fraction of hydrogen network done : 0.179
Fraction of hydrogen network done : 0.182
Fraction of hydrogen network done : 0.183
Fraction of hydrogen network done : 0.185
Fraction of hydrogen network done : 0.188
Fraction of hydrogen network done : 0.189
Fraction of hydrogen network done : 0.192
Fraction of hydrogen network done : 0.195
Fraction of hydrogen network done : 0.198
Fraction of hydrogen network done : 0.201
Fraction of hydrogen network done : 0.204
Fraction of hydrogen network done : 0.205
Fraction of hydrogen network done : 0.206
Fraction of hydrogen network done : 0.207
Fraction of hydrogen network done : 0.208
Fraction of hydrogen network done : 0.210
Fraction of hydrogen network done : 0.212
Fraction of hydrogen network done : 0.213
Fraction of hydrogen network done : 0.216
Fraction of hydrogen network done : 0.219
Fraction of hydrogen network done : 0.222
Fraction of hydrogen network done : 0.223
Fraction of hydrogen network done : 0.224
Fraction of hydrogen network done : 0.227
Fraction of hydrogen network done : 0.229
Fraction of hydrogen network done : 0.230
Fraction of hydrogen network done : 0.231
Fraction of hydrogen network done : 0.236
Fraction of hydrogen network done : 0.239
Fraction of hydrogen network done : 0.242
Fraction of hydrogen network done : 0.243
Fraction of hydrogen network done : 0.244
Fraction of hydrogen network done : 0.247
Fraction of hydrogen network done : 0.250
Fraction of hydrogen network done : 0.251
Fraction of hydrogen network done : 0.252
Fraction of hydrogen network done : 0.253
Fraction of hydrogen network done : 0.255
Fraction of hydrogen network done : 0.257
Fraction of hydrogen network done : 0.259
Fraction of hydrogen network done : 0.262
Fraction of hydrogen network done : 0.263
Fraction of hydrogen network done : 0.264
Fraction of hydrogen network done : 0.267
Fraction of hydrogen network done : 0.268
Fraction of hydrogen network done : 0.271
Fraction of hydrogen network done : 0.274
Fraction of hydrogen network done : 0.275
Fraction of hydrogen network done : 0.277
Fraction of hydrogen network done : 0.280
Fraction of hydrogen network done : 0.281
Fraction of hydrogen network done : 0.282
Fraction of hydrogen network done : 0.285
Fraction of hydrogen network done : 0.288
Fraction of hydrogen network done : 0.289
Fraction of hydrogen network done : 0.292
Fraction of hydrogen network done : 0.294
Fraction of hydrogen network done : 0.295
Fraction of hydrogen network done : 0.297
Fraction of hydrogen network done : 0.300
Fraction of hydrogen network done : 0.301
Fraction of hydrogen network done : 0.302
Fraction of hydrogen network done : 0.305
Fraction of hydrogen network done : 0.306
Fraction of hydrogen network done : 0.307
Fraction of hydrogen network done : 0.313
Fraction of hydrogen network done : 0.317
Fraction of hydrogen network done : 0.319
Fraction of hydrogen network done : 0.323
Fraction of hydrogen network done : 0.325
Fraction of hydrogen network done : 0.328
Fraction of hydrogen network done : 0.329
Fraction of hydrogen network done : 0.330
Fraction of hydrogen network done : 0.331
Fraction of hydrogen network done : 0.332
Fraction of hydrogen network done : 0.333
Fraction of hydrogen network done : 0.337
Fraction of hydrogen network done : 0.340
Fraction of hydrogen network done : 0.341
Fraction of hydrogen network done : 0.347
Fraction of hydrogen network done : 0.349
Fraction of hydrogen network done : 0.350
Fraction of hydrogen network done : 0.351
Fraction of hydrogen network done : 0.353
Fraction of hydrogen network done : 0.354
Fraction of hydrogen network done : 0.356
Fraction of hydrogen network done : 0.357
Fraction of hydrogen network done : 0.360
Fraction of hydrogen network done : 0.361
Fraction of hydrogen network done : 0.362
Fraction of hydrogen network done : 0.368
Fraction of hydrogen network done : 0.371
Fraction of hydrogen network done : 0.373
Fraction of hydrogen network done : 0.376
Fraction of hydrogen network done : 0.377
Fraction of hydrogen network done : 0.379
Fraction of hydrogen network done : 0.380
Fraction of hydrogen network done : 0.383
Fraction of hydrogen network done : 0.384
Fraction of hydrogen network done : 0.387
Fraction of hydrogen network done : 0.388
Fraction of hydrogen network done : 0.392
Fraction of hydrogen network done : 0.395
Fraction of hydrogen network done : 0.397
Fraction of hydrogen network done : 0.401
Fraction of hydrogen network done : 0.404
Fraction of hydrogen network done : 0.407
Fraction of hydrogen network done : 0.408
Fraction of hydrogen network done : 0.409
Fraction of hydrogen network done : 0.410
Fraction of hydrogen network done : 0.413
Fraction of hydrogen network done : 0.416
Fraction of hydrogen network done : 0.417
Fraction of hydrogen network done : 0.418
Fraction of hydrogen network done : 0.419
Fraction of hydrogen network done : 0.423
Fraction of hydrogen network done : 0.424
Fraction of hydrogen network done : 0.426
Fraction of hydrogen network done : 0.428
Fraction of hydrogen network done : 0.431
Fraction of hydrogen network done : 0.432
Fraction of hydrogen network done : 0.440
Fraction of hydrogen network done : 0.441
Fraction of hydrogen network done : 0.444
Fraction of hydrogen network done : 0.447
Fraction of hydrogen network done : 0.450
Fraction of hydrogen network done : 0.451
Fraction of hydrogen network done : 0.454
Fraction of hydrogen network done : 0.456
Fraction of hydrogen network done : 0.458
Fraction of hydrogen network done : 0.459
Fraction of hydrogen network done : 0.460
Fraction of hydrogen network done : 0.461
Fraction of hydrogen network done : 0.463
Fraction of hydrogen network done : 0.465
Fraction of hydrogen network done : 0.468
Fraction of hydrogen network done : 0.469
Fraction of hydrogen network done : 0.472
Fraction of hydrogen network done : 0.475
Fraction of hydrogen network done : 0.476
Fraction of hydrogen network done : 0.479
Fraction of hydrogen network done : 0.481
Fraction of hydrogen network done : 0.482
Fraction of hydrogen network done : 0.483
Fraction of hydrogen network done : 0.486
Fraction of hydrogen network done : 0.487
Fraction of hydrogen network done : 0.488
Fraction of hydrogen network done : 0.491
Fraction of hydrogen network done : 0.494
Fraction of hydrogen network done : 0.497
Fraction of hydrogen network done : 0.498
Fraction of hydrogen network done : 0.499
Fraction of hydrogen network done : 0.500
Fraction of hydrogen network done : 0.503
Fraction of hydrogen network done : 0.505
Fraction of hydrogen network done : 0.508
Fraction of hydrogen network done : 0.509
Fraction of hydrogen network done : 0.510
Fraction of hydrogen network done : 0.511
Fraction of hydrogen network done : 0.512
Fraction of hydrogen network done : 0.513
Fraction of hydrogen network done : 0.515
Fraction of hydrogen network done : 0.517
Fraction of hydrogen network done : 0.520
Fraction of hydrogen network done : 0.522
Fraction of hydrogen network done : 0.523
Fraction of hydrogen network done : 0.526
Fraction of hydrogen network done : 0.529
Fraction of hydrogen network done : 0.530
Fraction of hydrogen network done : 0.532
Fraction of hydrogen network done : 0.533
Fraction of hydrogen network done : 0.536
Fraction of hydrogen network done : 0.539
Fraction of hydrogen network done : 0.542
Fraction of hydrogen network done : 0.543
Fraction of hydrogen network done : 0.546
Fraction of hydrogen network done : 0.547
Fraction of hydrogen network done : 0.549
Fraction of hydrogen network done : 0.550
Fraction of hydrogen network done : 0.551
Fraction of hydrogen network done : 0.552
Fraction of hydrogen network done : 0.554
Fraction of hydrogen network done : 0.555
Fraction of hydrogen network done : 0.556
Fraction of hydrogen network done : 0.559
Fraction of hydrogen network done : 0.561
Fraction of hydrogen network done : 0.562
Fraction of hydrogen network done : 0.563
Fraction of hydrogen network done : 0.566
Fraction of hydrogen network done : 0.567
Fraction of hydrogen network done : 0.568
Fraction of hydrogen network done : 0.571
Fraction of hydrogen network done : 0.572
Fraction of hydrogen network done : 0.573
Fraction of hydrogen network done : 0.582
Fraction of hydrogen network done : 0.584
Fraction of hydrogen network done : 0.587
Fraction of hydrogen network done : 0.590
Fraction of hydrogen network done : 0.591
Fraction of hydrogen network done : 0.592
Fraction of hydrogen network done : 0.593
Fraction of hydrogen network done : 0.596
Fraction of hydrogen network done : 0.599
Fraction of hydrogen network done : 0.600
Fraction of hydrogen network done : 0.601
Fraction of hydrogen network done : 0.602
Fraction of hydrogen network done : 0.605
Fraction of hydrogen network done : 0.606
Fraction of hydrogen network done : 0.607
Fraction of hydrogen network done : 0.608
Fraction of hydrogen network done : 0.610
Fraction of hydrogen network done : 0.614
Fraction of hydrogen network done : 0.615
Fraction of hydrogen network done : 0.618
Fraction of hydrogen network done : 0.619
Fraction of hydrogen network done : 0.622
Fraction of hydrogen network done : 0.625
Fraction of hydrogen network done : 0.626
Fraction of hydrogen network done : 0.627
Fraction of hydrogen network done : 0.628
Fraction of hydrogen network done : 0.629
Fraction of hydrogen network done : 0.632
Fraction of hydrogen network done : 0.635
Fraction of hydrogen network done : 0.638
Fraction of hydrogen network done : 0.639
Fraction of hydrogen network done : 0.641
Fraction of hydrogen network done : 0.642
Fraction of hydrogen network done : 0.645
Fraction of hydrogen network done : 0.648
Fraction of hydrogen network done : 0.649
Fraction of hydrogen network done : 0.652
Fraction of hydrogen network done : 0.655
Fraction of hydrogen network done : 0.659
Fraction of hydrogen network done : 0.660
Fraction of hydrogen network done : 0.662
Fraction of hydrogen network done : 0.665
Fraction of hydrogen network done : 0.666
Fraction of hydrogen network done : 0.667
Fraction of hydrogen network done : 0.668
Fraction of hydrogen network done : 0.674
Fraction of hydrogen network done : 0.677
Fraction of hydrogen network done : 0.678
Fraction of hydrogen network done : 0.679
Fraction of hydrogen network done : 0.680
Fraction of hydrogen network done : 0.681
Fraction of hydrogen network done : 0.684
Fraction of hydrogen network done : 0.685
Fraction of hydrogen network done : 0.688
Fraction of hydrogen network done : 0.689
Fraction of hydrogen network done : 0.691
Fraction of hydrogen network done : 0.693
Fraction of hydrogen network done : 0.696
Fraction of hydrogen network done : 0.697
Fraction of hydrogen network done : 0.700
Fraction of hydrogen network done : 0.703
Fraction of hydrogen network done : 0.704
Fraction of hydrogen network done : 0.709
Fraction of hydrogen network done : 0.712
Fraction of hydrogen network done : 0.715
Fraction of hydrogen network done : 0.716
Fraction of hydrogen network done : 0.717
Fraction of hydrogen network done : 0.718
Fraction of hydrogen network done : 0.719
Fraction of hydrogen network done : 0.725
Fraction of hydrogen network done : 0.727
Fraction of hydrogen network done : 0.728
Fraction of hydrogen network done : 0.731
Fraction of hydrogen network done : 0.734
Fraction of hydrogen network done : 0.737
Fraction of hydrogen network done : 0.738
Fraction of hydrogen network done : 0.741
Fraction of hydrogen network done : 0.742
Fraction of hydrogen network done : 0.743
Fraction of hydrogen network done : 0.745
Fraction of hydrogen network done : 0.746
Fraction of hydrogen network done : 0.748
Fraction of hydrogen network done : 0.750
Fraction of hydrogen network done : 0.753
Fraction of hydrogen network done : 0.756
Fraction of hydrogen network done : 0.757
Fraction of hydrogen network done : 0.758
Fraction of hydrogen network done : 0.759
Fraction of hydrogen network done : 0.762
Fraction of hydrogen network done : 0.765
Fraction of hydrogen network done : 0.766
Fraction of hydrogen network done : 0.767
Fraction of hydrogen network done : 0.768
Fraction of hydrogen network done : 0.769
Fraction of hydrogen network done : 0.770
Fraction of hydrogen network done : 0.771
Fraction of hydrogen network done : 0.774
Fraction of hydrogen network done : 0.777
Fraction of hydrogen network done : 0.778
Fraction of hydrogen network done : 0.780
Fraction of hydrogen network done : 0.781
Fraction of hydrogen network done : 0.784
Fraction of hydrogen network done : 0.787
Fraction of hydrogen network done : 0.788
Fraction of hydrogen network done : 0.794
Fraction of hydrogen network done : 0.796
Fraction of hydrogen network done : 0.800
Fraction of hydrogen network done : 0.803
Fraction of hydrogen network done : 0.805
Fraction of hydrogen network done : 0.806
Fraction of hydrogen network done : 0.809
Fraction of hydrogen network done : 0.810
Fraction of hydrogen network done : 0.811
Fraction of hydrogen network done : 0.812
Fraction of hydrogen network done : 0.813
Fraction of hydrogen network done : 0.816
Fraction of hydrogen network done : 0.817
Fraction of hydrogen network done : 0.820
Fraction of hydrogen network done : 0.822
Fraction of hydrogen network done : 0.825
Fraction of hydrogen network done : 0.826
Fraction of hydrogen network done : 0.827
Fraction of hydrogen network done : 0.828
Fraction of hydrogen network done : 0.829
Fraction of hydrogen network done : 0.832
Fraction of hydrogen network done : 0.833
Fraction of hydrogen network done : 0.834
Fraction of hydrogen network done : 0.837
Fraction of hydrogen network done : 0.840
Fraction of hydrogen network done : 0.842
Fraction of hydrogen network done : 0.845
Fraction of hydrogen network done : 0.846
Fraction of hydrogen network done : 0.847
Fraction of hydrogen network done : 0.848
Fraction of hydrogen network done : 0.851
Fraction of hydrogen network done : 0.854
Fraction of hydrogen network done : 0.855
Fraction of hydrogen network done : 0.856
Fraction of hydrogen network done : 0.857
Fraction of hydrogen network done : 0.858
Fraction of hydrogen network done : 0.859
Fraction of hydrogen network done : 0.862
Fraction of hydrogen network done : 0.863
Fraction of hydrogen network done : 0.866
Fraction of hydrogen network done : 0.869
Fraction of hydrogen network done : 0.871
Fraction of hydrogen network done : 0.873
Fraction of hydrogen network done : 0.877
Fraction of hydrogen network done : 0.878
Fraction of hydrogen network done : 0.881
Fraction of hydrogen network done : 0.884
Fraction of hydrogen network done : 0.887
Fraction of hydrogen network done : 0.888
Fraction of hydrogen network done : 0.890
Fraction of hydrogen network done : 0.891
Fraction of hydrogen network done : 0.894
Fraction of hydrogen network done : 0.895
Fraction of hydrogen network done : 0.896
Fraction of hydrogen network done : 0.897
Fraction of hydrogen network done : 0.898
Fraction of hydrogen network done : 0.900
Fraction of hydrogen network done : 0.902
Fraction of hydrogen network done : 0.905
Fraction of hydrogen network done : 0.906
Fraction of hydrogen network done : 0.908
Fraction of hydrogen network done : 0.909
Fraction of hydrogen network done : 0.910
Fraction of hydrogen network done : 0.911
Fraction of hydrogen network done : 0.914
Fraction of hydrogen network done : 0.916
Fraction of hydrogen network done : 0.917
Fraction of hydrogen network done : 0.923
Fraction of hydrogen network done : 0.928
Fraction of hydrogen network done : 0.932
Fraction of hydrogen network done : 0.933
Fraction of hydrogen network done : 0.934
Fraction of hydrogen network done : 0.937
Fraction of hydrogen network done : 0.940
Fraction of hydrogen network done : 0.941
Fraction of hydrogen network done : 0.942
Fraction of hydrogen network done : 0.943
Fraction of hydrogen network done : 0.944
Fraction of hydrogen network done : 0.947
Fraction of hydrogen network done : 0.950
Fraction of hydrogen network done : 0.955
Fraction of hydrogen network done : 0.960
Fraction of hydrogen network done : 0.961
Fraction of hydrogen network done : 0.964
Fraction of hydrogen network done : 0.966
Fraction of hydrogen network done : 0.967
Fraction of hydrogen network done : 0.970
Fraction of hydrogen network done : 0.971
Fraction of hydrogen network done : 0.972
Fraction of hydrogen network done : 0.973
Fraction of hydrogen network done : 0.976
Fraction of hydrogen network done : 0.977
Fraction of hydrogen network done : 0.980
Fraction of hydrogen network done : 0.983
Fraction of hydrogen network done : 0.984
Fraction of hydrogen network done : 0.986
Fraction of hydrogen network done : 0.989
Fraction of hydrogen network done : 0.990
Fraction of hydrogen network done : 0.992
Fraction of hydrogen network done : 0.993
Fraction of hydrogen network done : 0.994
Fraction of hydrogen network done : 0.997
Fraction of hydrogen network done : 1.000
Total log10 N solved by Cutting.....: 31.972
Total log10 N solved by Treshold Acc: 4.669
Total log10 N solved by Brute Force.: 526.764
Of these only TA is a heuristic method.
Total number of positions evaluated 47961
# 120 # Error: HIS, ASN, GLN side chain flips
Listed here are Histidine, Asparagine or Glutamine residues for
which the orientation determined from hydrogen bonding analysis are
different from the assignment given in the input. Either they could
form energetically more favourable hydrogen bonds if the terminal
group was rotated by 180 degrees, or there is no assignment in the
input file (atom type 'A') but an assignment could be made. Be aware,
though, that if the topology could not be determined for one or more
ligands, then this option will make errors.
116 HIS ( 139-) A 1
346 GLN ( 168-) A 2
348 GLN ( 170-) A 2
447 GLN ( 68-) A 3
476 GLN ( 97-) A 3
686 GLN ( 106-) A 4
691 ASN ( 111-) A 4
791 ASN ( 211-) A 4
853 ASN ( 72-) A 5
933 ASN ( 152-) A 5
941 ASN ( 160-) A 5
1108 GLN ( 126-) A 6
1193 ASN ( 211-) A 6
1280 GLN ( 97-) A 7
1745 ASN ( 160-) A 9
1845 GLN ( 59-) A 10
1873 GLN ( 87-) A 10
1892 GLN ( 106-) A 10
# 121 # Note: Histidine type assignments
For all complete HIS residues in the structure a tentative
assignment to HIS-D (protonated on ND1), HIS-E (protonated on NE2),
or HIS-H (protonated on both ND1 and NE2, positively charged) is
made based on the hydrogen bond network. A second assignment is
made based on which of the Engh and Huber [REF] histidine
geometries fits best to the structure.
In the table below all normal histidine residues are listed. The
assignment based on the geometry of the residue is listed first,
together with the RMS Z-score for the fit to the Engh and Huber
parameters. For all residues where the H-bond assignment is
different, the assignment is listed in the last columns, together
with its RMS Z-score to the Engh and Huber parameters.
As always, the RMS Z-scores should be close to 1.0 if the residues
were restrained to the Engh and Huber parameters during refinement.
Please note that because the differences between the geometries of
the different types are small it is possible that the geometric
assignment given here does not correspond to the type used in
refinement. This is especially true if the RMS Z-scores are much
higher than 1.0.
If the two assignments differ, or the `geometry' RMS Z-score is high,
it is advisable to verify the hydrogen bond assignment, check the
HIS type used during the refinement and possibly adjust it.
56 HIS ( 79-) A 1 HIS-D 0.98
116 HIS ( 139-) A 1 HIS-D 1.00 HIS-E 1.32
144 HIS ( 167-) A 1 HIS-D 1.00 HIS-E 1.33
187 HIS ( 210-) A 1 HIS-D 0.96
257 HIS ( 79-) A 2 HIS-D 1.02
317 HIS ( 139-) A 2 HIS-D 0.97 HIS-E 1.31
345 HIS ( 167-) A 2 HIS-D 0.95 HIS-E 1.28
388 HIS ( 210-) A 2 HIS-D 0.95 HIS-E 1.28
458 HIS ( 79-) A 3 HIS-D 0.98 HIS-E 1.30
518 HIS ( 139-) A 3 HIS-D 0.98 HIS-E 1.31
546 HIS ( 167-) A 3 HIS-D 1.02 HIS-E 1.32
589 HIS ( 210-) A 3 HIS-D 0.97 HIS-E 1.30
659 HIS ( 79-) A 4 HIS-D 1.02 HIS-E 1.32
719 HIS ( 139-) A 4 HIS-D 0.97 HIS-H 1.68
747 HIS ( 167-) A 4 HIS-D 0.97 HIS-E 1.28
790 HIS ( 210-) A 4 HIS-D 1.00 HIS-E 1.33
860 HIS ( 79-) A 5 HIS-D 0.95 HIS-E 1.33
920 HIS ( 139-) A 5 HIS-D 1.03 HIS-E 1.32
948 HIS ( 167-) A 5 HIS-D 1.00 HIS-E 1.31
991 HIS ( 210-) A 5 HIS-D 1.02 HIS-E 1.29
1061 HIS ( 79-) A 6 HIS-D 0.98 HIS-E 1.29
1121 HIS ( 139-) A 6 HIS-D 0.96
1149 HIS ( 167-) A 6 HIS-D 0.99 HIS-E 1.33
1192 HIS ( 210-) A 6 HIS-D 0.98 HIS-E 1.31
1262 HIS ( 79-) A 7 HIS-D 0.98 HIS-E 1.29
1322 HIS ( 139-) A 7 HIS-D 0.98 HIS-E 1.31
1350 HIS ( 167-) A 7 HIS-D 0.97 HIS-E 1.27
1393 HIS ( 210-) A 7 HIS-D 0.99 HIS-E 1.28
1463 HIS ( 79-) A 8 HIS-D 0.98 HIS-E 1.30
1523 HIS ( 139-) A 8 HIS-D 0.98 HIS-E 1.30
1551 HIS ( 167-) A 8 HIS-D 0.97 HIS-E 1.32
1594 HIS ( 210-) A 8 HIS-D 0.95 HIS-E 1.30
1664 HIS ( 79-) A 9 HIS-D 1.01 HIS-E 1.32
1724 HIS ( 139-) A 9 HIS-D 0.97
1752 HIS ( 167-) A 9 HIS-D 1.00 HIS-E 1.30
1795 HIS ( 210-) A 9 HIS-D 0.98 HIS-E 1.32
1865 HIS ( 79-) A 10 HIS-D 0.98
1925 HIS ( 139-) A 10 HIS-D 0.98
1953 HIS ( 167-) A 10 HIS-D 0.98 HIS-E 1.32
1996 HIS ( 210-) A 10 HIS-D 1.03 HIS-E 1.34
Unsatisfied donor : 6 LYS ( 29-) A 1 N
Unsatisfied donor : 12 CYS ( 35-) A 1 N
Unsatisfied donor : 18 PHE ( 41-) A 1 N
Unsatisfied donor : 27 SER ( 50-) A 1 N
Unsatisfied donor : 29 GLU ( 52-) A 1 N
Unsatisfied donor : 37 TYR ( 60-) A 1 OH
Unsatisfied donor : 46 PHE ( 69-) A 1 N
Unsatisfied donor : 51 SER ( 74-) A 1 N
Unsatisfied donor : 52 SER ( 75-) A 1 N
Unsatisfied donor : 52 SER ( 75-) A 1 OG
Unsatisfied donor : 53 GLU ( 76-) A 1 N
Unsatisfied donor : 55 GLU ( 78-) A 1 N
Unsatisfied donor : 59 GLN ( 82-) A 1 N
Unsatisfied donor : 72 ILE ( 95-) A 1 N
Unsatisfied donor : 73 ASP ( 96-) A 1 N
Unsatisfied donor : 75 PHE ( 98-) A 1 N
Unsatisfied donor : 82 ARG ( 105-) A 1 NH1
--Potential acceptor : 69 LYS ( 92-) A 1 O
Unsatisfied donor : 85 VAL ( 108-) A 1 N
Unsatisfied donor : 91 LEU ( 114-) A 1 N
Unsatisfied donor : 97 ASP ( 120-) A 1 N
Unsatisfied donor : 98 PHE ( 121-) A 1 N
Unsatisfied donor : 100 THR ( 123-) A 1 N
Unsatisfied donor : 113 VAL ( 136-) A 1 N
Unsatisfied donor : 115 SER ( 138-) A 1 N
--Potential acceptor : 115 SER ( 138-) A 1 OG
Unsatisfied donor : 118 GLY ( 141-) A 1 N
Unsatisfied donor : 133 ILE ( 156-) A 1 N
Unsatisfied donor : 137 ASN ( 160-) A 1 N
Unsatisfied donor : 140 LEU ( 163-) A 1 N
Unsatisfied donor : 145 GLN ( 168-) A 1 NE2
--Potential acceptor : 12 CYS ( 35-) A 1 O
--Potential acceptor : 116 HIS ( 139-) A 1 NE2
Unsatisfied donor : 169 ILE ( 192-) A 1 N
Unsatisfied donor : 191 PHE ( 214-) A 1 N
Unsatisfied donor : 205 GLU ( 27-) A 2 N
Unsatisfied donor : 207 LYS ( 29-) A 2 N
Unsatisfied donor : 215 ALA ( 37-) A 2 N
Unsatisfied donor : 217 VAL ( 39-) A 2 N
Unsatisfied donor : 219 PHE ( 41-) A 2 N
Unsatisfied donor : 221 LYS ( 43-) A 2 N
Unsatisfied donor : 228 SER ( 50-) A 2 N
--Potential acceptor : 228 SER ( 50-) A 2 OG
Unsatisfied donor : 245 ILE ( 67-) A 2 N
Unsatisfied donor : 247 PHE ( 69-) A 2 N
Unsatisfied donor : 255 PHE ( 77-) A 2 N
Unsatisfied donor : 256 GLU ( 78-) A 2 N
Unsatisfied donor : 257 HIS ( 79-) A 2 N
Unsatisfied donor : 258 LEU ( 80-) A 2 N
Unsatisfied donor : 259 VAL ( 81-) A 2 N
Unsatisfied donor : 260 GLN ( 82-) A 2 N
Unsatisfied donor : 266 ARG ( 88-) A 2 NE
Unsatisfied donor : 266 ARG ( 88-) A 2 NH1
Unsatisfied donor : 268 SER ( 90-) A 2 OG
--Potential acceptor : 267 GLU ( 89-) A 2 O
Unsatisfied donor : 277 GLY ( 99-) A 2 N
Unsatisfied donor : 279 GLY ( 101-) A 2 N
Unsatisfied donor : 281 THR ( 103-) A 2 N
Unsatisfied donor : 283 ARG ( 105-) A 2 NE
Unsatisfied donor : 284 GLN ( 106-) A 2 N
Unsatisfied donor : 293 LYS ( 115-) A 2 N
Unsatisfied donor : 295 ILE ( 117-) A 2 N
Unsatisfied donor : 297 PHE ( 119-) A 2 N
Unsatisfied donor : 312 ASP ( 134-) A 2 N
Unsatisfied donor : 313 LEU ( 135-) A 2 N
Unsatisfied donor : 314 VAL ( 136-) A 2 N
Unsatisfied donor : 317 HIS ( 139-) A 2 N
--Potential acceptor : 317 HIS ( 139-) A 2 ND1
Unsatisfied donor : 319 GLY ( 141-) A 2 N
Unsatisfied donor : 321 GLY ( 143-) A 2 N
Unsatisfied donor : 334 ILE ( 156-) A 2 N
Unsatisfied donor : 343 ASP ( 165-) A 2 N
Unsatisfied donor : 344 ASN ( 166-) A 2 N
Unsatisfied donor : 347 GLN ( 169-) A 2 NE2
--Potential acceptor : 317 HIS ( 139-) A 2 O
--Potential acceptor : 336 CYS ( 158-) A 2 O
Unsatisfied donor : 360 TRP ( 182-) A 2 N
Unsatisfied donor : 360 TRP ( 182-) A 2 NE1
Unsatisfied donor : 367 THR ( 189-) A 2 N
Unsatisfied donor : 370 ILE ( 192-) A 2 N
Unsatisfied donor : 386 VAL ( 208-) A 2 N
Unsatisfied donor : 387 SER ( 209-) A 2 N
Unsatisfied donor : 389 ASN ( 211-) A 2 N
Unsatisfied donor : 391 SER ( 213-) A 2 N
Unsatisfied donor : 394 ARG ( 216-) A 2 N
Unsatisfied donor : 405 ILE ( 26-) A 3 N
Unsatisfied donor : 407 GLU ( 28-) A 3 N
Unsatisfied donor : 408 LYS ( 29-) A 3 N
Unsatisfied donor : 413 THR ( 34-) A 3 N
Unsatisfied donor : 415 GLY ( 36-) A 3 N
Unsatisfied donor : 416 ALA ( 37-) A 3 N
Unsatisfied donor : 420 PHE ( 41-) A 3 N
Unsatisfied donor : 422 LYS ( 43-) A 3 N
Unsatisfied donor : 424 VAL ( 45-) A 3 N
Unsatisfied donor : 429 SER ( 50-) A 3 N
Unsatisfied donor : 447 GLN ( 68-) A 3 NE2
--Potential acceptor : 412 VAL ( 33-) A 3 O
--Potential acceptor : 445 ILE ( 66-) A 3 O
Unsatisfied donor : 450 ARG ( 71-) A 3 N
Unsatisfied donor : 451 ASN ( 72-) A 3 N
Unsatisfied donor : 453 SER ( 74-) A 3 N
Unsatisfied donor : 459 LEU ( 80-) A 3 N
Unsatisfied donor : 463 ARG ( 84-) A 3 NH1
Unsatisfied donor : 466 GLN ( 87-) A 3 N
Unsatisfied donor : 470 GLN ( 91-) A 3 N
Unsatisfied donor : 475 ASP ( 96-) A 3 N
Unsatisfied donor : 477 PHE ( 98-) A 3 N
Unsatisfied donor : 479 CYS ( 100-) A 3 N
Unsatisfied donor : 484 ARG ( 105-) A 3 N
Unsatisfied donor : 495 VAL ( 116-) A 3 N
Unsatisfied donor : 498 PHE ( 119-) A 3 N
Unsatisfied donor : 499 ASP ( 120-) A 3 N
Unsatisfied donor : 502 THR ( 123-) A 3 N
Unsatisfied donor : 504 MET ( 125-) A 3 N
Unsatisfied donor : 515 VAL ( 136-) A 3 N
Unsatisfied donor : 517 SER ( 138-) A 3 OG
Unsatisfied donor : 518 HIS ( 139-) A 3 N
Unsatisfied donor : 519 ALA ( 140-) A 3 N
Unsatisfied donor : 520 GLY ( 141-) A 3 N
Unsatisfied donor : 534 LEU ( 155-) A 3 N
--Potential acceptor : 577 SER ( 198-) A 3 OG
Unsatisfied donor : 537 CYS ( 158-) A 3 N
Unsatisfied donor : 538 VAL ( 159-) A 3 N
Unsatisfied donor : 540 ASP ( 161-) A 3 N
Unsatisfied donor : 542 LEU ( 163-) A 3 N
Unsatisfied donor : 546 HIS ( 167-) A 3 N
Unsatisfied donor : 547 GLN ( 168-) A 3 N
Unsatisfied donor : 548 GLN ( 169-) A 3 N
Unsatisfied donor : 567 GLU ( 188-) A 3 N
Unsatisfied donor : 577 SER ( 198-) A 3 OG
Unsatisfied donor : 583 LYS ( 204-) A 3 N
Unsatisfied donor : 585 PHE ( 206-) A 3 N
Unsatisfied donor : 588 SER ( 209-) A 3 N
Unsatisfied donor : 606 ILE ( 26-) A 4 N
Unsatisfied donor : 607 GLU ( 27-) A 4 N
Unsatisfied donor : 609 LYS ( 29-) A 4 N
Unsatisfied donor : 610 ALA ( 30-) A 4 N
Unsatisfied donor : 618 THR ( 38-) A 4 N
Unsatisfied donor : 632 GLU ( 52-) A 4 N
Unsatisfied donor : 643 VAL ( 63-) A 4 N
Unsatisfied donor : 644 ARG ( 64-) A 4 N
Unsatisfied donor : 644 ARG ( 64-) A 4 NE
Unsatisfied donor : 650 GLY ( 70-) A 4 N
Unsatisfied donor : 651 ARG ( 71-) A 4 N
Unsatisfied donor : 653 TYR ( 73-) A 4 N
Unsatisfied donor : 654 SER ( 74-) A 4 N
Unsatisfied donor : 657 PHE ( 77-) A 4 N
Unsatisfied donor : 661 VAL ( 81-) A 4 N
Unsatisfied donor : 662 GLN ( 82-) A 4 N
Unsatisfied donor : 668 ARG ( 88-) A 4 N
Unsatisfied donor : 670 SER ( 90-) A 4 N
Unsatisfied donor : 671 GLN ( 91-) A 4 N
Unsatisfied donor : 675 ILE ( 95-) A 4 N
Unsatisfied donor : 676 ASP ( 96-) A 4 N
Unsatisfied donor : 678 PHE ( 98-) A 4 N
Unsatisfied donor : 679 GLY ( 99-) A 4 N
Unsatisfied donor : 684 ALA ( 104-) A 4 N
Unsatisfied donor : 685 ARG ( 105-) A 4 N
Unsatisfied donor : 685 ARG ( 105-) A 4 NE
Unsatisfied donor : 685 ARG ( 105-) A 4 NH1
Unsatisfied donor : 685 ARG ( 105-) A 4 NH2
Unsatisfied donor : 695 LYS ( 115-) A 4 N
Unsatisfied donor : 706 GLN ( 126-) A 4 N
Unsatisfied donor : 715 LEU ( 135-) A 4 N
Unsatisfied donor : 716 VAL ( 136-) A 4 N
Unsatisfied donor : 718 SER ( 138-) A 4 N
Unsatisfied donor : 718 SER ( 138-) A 4 OG
Unsatisfied donor : 722 THR ( 142-) A 4 N
Unsatisfied donor : 723 GLY ( 143-) A 4 N
Unsatisfied donor : 724 SER ( 144-) A 4 N
Unsatisfied donor : 724 SER ( 144-) A 4 OG
Unsatisfied donor : 725 ILE ( 145-) A 4 N
Unsatisfied donor : 735 LEU ( 155-) A 4 N
Unsatisfied donor : 738 CYS ( 158-) A 4 N
Unsatisfied donor : 740 ASN ( 160-) A 4 N
Unsatisfied donor : 742 SER ( 162-) A 4 N
Unsatisfied donor : 744 MET ( 164-) A 4 N
Unsatisfied donor : 748 GLN ( 168-) A 4 N
Unsatisfied donor : 760 TYR ( 180-) A 4 N
Unsatisfied donor : 762 TRP ( 182-) A 4 N
Unsatisfied donor : 783 LEU ( 203-) A 4 N
Unsatisfied donor : 795 GLU ( 215-) A 4 N
Unsatisfied donor : 807 ILE ( 26-) A 5 N
Unsatisfied donor : 811 ALA ( 30-) A 5 N
Unsatisfied donor : 816 CYS ( 35-) A 5 N
Unsatisfied donor : 822 PHE ( 41-) A 5 N
Unsatisfied donor : 824 LYS ( 43-) A 5 N
Unsatisfied donor : 825 LEU ( 44-) A 5 N
Unsatisfied donor : 833 GLU ( 52-) A 5 N
Unsatisfied donor : 839 ILE ( 58-) A 5 N
Unsatisfied donor : 843 PHE ( 62-) A 5 N
Unsatisfied donor : 848 ILE ( 67-) A 5 N
Unsatisfied donor : 850 PHE ( 69-) A 5 N
Unsatisfied donor : 851 GLY ( 70-) A 5 N
Unsatisfied donor : 852 ARG ( 71-) A 5 N
Unsatisfied donor : 854 TYR ( 73-) A 5 N
Unsatisfied donor : 860 HIS ( 79-) A 5 N
Unsatisfied donor : 862 VAL ( 81-) A 5 N
Unsatisfied donor : 869 ARG ( 88-) A 5 NH1
Unsatisfied donor : 871 SER ( 90-) A 5 N
Unsatisfied donor : 877 ASP ( 96-) A 5 N
Unsatisfied donor : 882 GLY ( 101-) A 5 N
Unsatisfied donor : 883 ASP ( 102-) A 5 N
Unsatisfied donor : 884 THR ( 103-) A 5 N
Unsatisfied donor : 885 ALA ( 104-) A 5 N
Unsatisfied donor : 886 ARG ( 105-) A 5 N
Unsatisfied donor : 886 ARG ( 105-) A 5 NE
Unsatisfied donor : 886 ARG ( 105-) A 5 NH1
--Potential acceptor : 848 ILE ( 67-) A 5 O
Unsatisfied donor : 886 ARG ( 105-) A 5 NH2
Unsatisfied donor : 887 GLN ( 106-) A 5 N
Unsatisfied donor : 890 LEU ( 109-) A 5 N
Unsatisfied donor : 895 LEU ( 114-) A 5 N
Unsatisfied donor : 898 ILE ( 117-) A 5 N
Unsatisfied donor : 901 ASP ( 120-) A 5 N
Unsatisfied donor : 902 PHE ( 121-) A 5 N
Unsatisfied donor : 917 VAL ( 136-) A 5 N
Unsatisfied donor : 923 THR ( 142-) A 5 N
Unsatisfied donor : 926 ILE ( 145-) A 5 N
Unsatisfied donor : 936 LEU ( 155-) A 5 N
Unsatisfied donor : 937 ILE ( 156-) A 5 N
Unsatisfied donor : 948 HIS ( 167-) A 5 N
Unsatisfied donor : 961 TYR ( 180-) A 5 N
Unsatisfied donor : 961 TYR ( 180-) A 5 OH
Unsatisfied donor : 962 VAL ( 181-) A 5 N
Unsatisfied donor : 963 TRP ( 182-) A 5 N
Unsatisfied donor : 989 VAL ( 208-) A 5 N
Unsatisfied donor : 990 SER ( 209-) A 5 N
Unsatisfied donor : 997 ARG ( 216-) A 5 N
Unsatisfied donor : 1011 LYS ( 29-) A 6 N
Unsatisfied donor : 1025 LYS ( 43-) A 6 N
Unsatisfied donor : 1032 SER ( 50-) A 6 N
Unsatisfied donor : 1033 ASP ( 51-) A 6 N
Unsatisfied donor : 1034 GLU ( 52-) A 6 N
Unsatisfied donor : 1045 VAL ( 63-) A 6 N
Unsatisfied donor : 1052 GLY ( 70-) A 6 N
Unsatisfied donor : 1054 ASN ( 72-) A 6 N
Unsatisfied donor : 1059 PHE ( 77-) A 6 N
Unsatisfied donor : 1061 HIS ( 79-) A 6 N
Unsatisfied donor : 1063 VAL ( 81-) A 6 N
Unsatisfied donor : 1064 GLN ( 82-) A 6 N
Unsatisfied donor : 1074 LYS ( 92-) A 6 N
Unsatisfied donor : 1075 ILE ( 93-) A 6 N
Unsatisfied donor : 1079 GLN ( 97-) A 6 N
Unsatisfied donor : 1080 PHE ( 98-) A 6 N
Unsatisfied donor : 1085 THR ( 103-) A 6 N
Unsatisfied donor : 1085 THR ( 103-) A 6 OG1
Unsatisfied donor : 1087 ARG ( 105-) A 6 NH2
--Potential acceptor : 1080 PHE ( 98-) A 6 O
Unsatisfied donor : 1088 GLN ( 106-) A 6 N
Unsatisfied donor : 1099 ILE ( 117-) A 6 N
Unsatisfied donor : 1103 PHE ( 121-) A 6 N
Unsatisfied donor : 1114 TYR ( 132-) A 6 OH
Unsatisfied donor : 1116 ASP ( 134-) A 6 N
Unsatisfied donor : 1118 VAL ( 136-) A 6 N
Unsatisfied donor : 1120 SER ( 138-) A 6 N
Unsatisfied donor : 1124 THR ( 142-) A 6 N
Unsatisfied donor : 1125 GLY ( 143-) A 6 N
Unsatisfied donor : 1128 LEU ( 146-) A 6 N
Unsatisfied donor : 1137 LEU ( 155-) A 6 N
Unsatisfied donor : 1142 ASN ( 160-) A 6 N
Unsatisfied donor : 1149 HIS ( 167-) A 6 N
Unsatisfied donor : 1150 GLN ( 168-) A 6 NE2
Unsatisfied donor : 1151 GLN ( 169-) A 6 N
Unsatisfied donor : 1164 TRP ( 182-) A 6 N
Unsatisfied donor : 1185 LEU ( 203-) A 6 N
Unsatisfied donor : 1188 PHE ( 206-) A 6 N
Unsatisfied donor : 1191 SER ( 209-) A 6 N
Unsatisfied donor : 1193 ASN ( 211-) A 6 N
Unsatisfied donor : 1210 GLU ( 27-) A 7 N
Unsatisfied donor : 1213 ALA ( 30-) A 7 N
Unsatisfied donor : 1217 THR ( 34-) A 7 N
Unsatisfied donor : 1218 CYS ( 35-) A 7 N
Unsatisfied donor : 1222 VAL ( 39-) A 7 N
Unsatisfied donor : 1224 PHE ( 41-) A 7 N
Unsatisfied donor : 1233 SER ( 50-) A 7 N
Unsatisfied donor : 1236 PHE ( 53-) A 7 N
Unsatisfied donor : 1247 ARG ( 64-) A 7 N
Unsatisfied donor : 1252 PHE ( 69-) A 7 N
Unsatisfied donor : 1253 GLY ( 70-) A 7 N
Unsatisfied donor : 1254 ARG ( 71-) A 7 NE
Unsatisfied donor : 1256 TYR ( 73-) A 7 N
Unsatisfied donor : 1260 PHE ( 77-) A 7 N
Unsatisfied donor : 1262 HIS ( 79-) A 7 N
Unsatisfied donor : 1264 VAL ( 81-) A 7 N
Unsatisfied donor : 1265 GLN ( 82-) A 7 N
Unsatisfied donor : 1268 GLY ( 85-) A 7 N
Unsatisfied donor : 1271 ARG ( 88-) A 7 NH1
--Potential acceptor : 1279 ASP ( 96-) A 7 OD1
Unsatisfied donor : 1273 SER ( 90-) A 7 N
Unsatisfied donor : 1275 LYS ( 92-) A 7 N
Unsatisfied donor : 1278 ILE ( 95-) A 7 N
Unsatisfied donor : 1280 GLN ( 97-) A 7 N
Unsatisfied donor : 1286 THR ( 103-) A 7 N
Unsatisfied donor : 1288 ARG ( 105-) A 7 N
Unsatisfied donor : 1288 ARG ( 105-) A 7 NE
Unsatisfied donor : 1289 GLN ( 106-) A 7 N
Unsatisfied donor : 1289 GLN ( 106-) A 7 NE2
--Potential acceptor : 1290 TYR ( 107-) A 7 O
Unsatisfied donor : 1290 TYR ( 107-) A 7 N
--Potential acceptor : 1289 GLN ( 106-) A 7 OE1
Unsatisfied donor : 1295 GLY ( 112-) A 7 N
Unsatisfied donor : 1296 LYS ( 113-) A 7 NZ
--Potential acceptor : 1237 CYS ( 54-) A 7 O
--Potential acceptor : 1237 CYS ( 54-) A 7 SG
Unsatisfied donor : 1298 LYS ( 115-) A 7 N
Unsatisfied donor : 1299 VAL ( 116-) A 7 N
Unsatisfied donor : 1300 ILE ( 117-) A 7 N
Unsatisfied donor : 1303 ASP ( 120-) A 7 N
Unsatisfied donor : 1304 PHE ( 121-) A 7 N
Unsatisfied donor : 1308 MET ( 125-) A 7 N
Unsatisfied donor : 1313 ARG ( 130-) A 7 N
Unsatisfied donor : 1317 ASP ( 134-) A 7 N
Unsatisfied donor : 1321 SER ( 138-) A 7 N
--Potential acceptor : 1321 SER ( 138-) A 7 OG
Unsatisfied donor : 1339 ILE ( 156-) A 7 N
Unsatisfied donor : 1348 ASP ( 165-) A 7 N
Unsatisfied donor : 1350 HIS ( 167-) A 7 N
Unsatisfied donor : 1351 GLN ( 168-) A 7 N
Unsatisfied donor : 1360 GLU ( 177-) A 7 N
Unsatisfied donor : 1365 TRP ( 182-) A 7 N
Unsatisfied donor : 1376 ALA ( 193-) A 7 N
Unsatisfied donor : 1381 SER ( 198-) A 7 OG
--Potential acceptor : 1338 LEU ( 155-) A 7 O
Unsatisfied donor : 1391 VAL ( 208-) A 7 N
Unsatisfied donor : 1392 SER ( 209-) A 7 N
Unsatisfied donor : 1410 ILE ( 26-) A 8 N
Unsatisfied donor : 1411 GLU ( 27-) A 8 N
Unsatisfied donor : 1418 THR ( 34-) A 8 N
Unsatisfied donor : 1425 PHE ( 41-) A 8 N
Unsatisfied donor : 1427 LYS ( 43-) A 8 N
Unsatisfied donor : 1428 LEU ( 44-) A 8 N
Unsatisfied donor : 1429 VAL ( 45-) A 8 N
Unsatisfied donor : 1452 GLN ( 68-) A 8 NE2
Unsatisfied donor : 1454 GLY ( 70-) A 8 N
Unsatisfied donor : 1462 GLU ( 78-) A 8 N
Unsatisfied donor : 1465 VAL ( 81-) A 8 N
Unsatisfied donor : 1466 GLN ( 82-) A 8 N
Unsatisfied donor : 1468 ARG ( 84-) A 8 NE
Unsatisfied donor : 1471 GLN ( 87-) A 8 N
Unsatisfied donor : 1474 SER ( 90-) A 8 N
Unsatisfied donor : 1476 LYS ( 92-) A 8 N
Unsatisfied donor : 1480 ASP ( 96-) A 8 N
Unsatisfied donor : 1484 CYS ( 100-) A 8 N
Unsatisfied donor : 1485 GLY ( 101-) A 8 N
Unsatisfied donor : 1486 ASP ( 102-) A 8 N
Unsatisfied donor : 1489 ARG ( 105-) A 8 NE
Unsatisfied donor : 1489 ARG ( 105-) A 8 NH2
Unsatisfied donor : 1492 VAL ( 108-) A 8 N
Unsatisfied donor : 1498 LEU ( 114-) A 8 N
Unsatisfied donor : 1510 GLN ( 126-) A 8 N
Unsatisfied donor : 1522 SER ( 138-) A 8 N
Unsatisfied donor : 1522 SER ( 138-) A 8 OG
--Potential acceptor : 1528 SER ( 144-) A 8 OG
Unsatisfied donor : 1524 ALA ( 140-) A 8 N
Unsatisfied donor : 1528 SER ( 144-) A 8 N
Unsatisfied donor : 1539 LEU ( 155-) A 8 N
Unsatisfied donor : 1540 ILE ( 156-) A 8 N
Unsatisfied donor : 1542 CYS ( 158-) A 8 N
Unsatisfied donor : 1548 MET ( 164-) A 8 N
Unsatisfied donor : 1549 ASP ( 165-) A 8 N
Unsatisfied donor : 1552 GLN ( 168-) A 8 NE2
--Potential acceptor : 1523 HIS ( 139-) A 8 ND1
Unsatisfied donor : 1566 TRP ( 182-) A 8 N
Unsatisfied donor : 1566 TRP ( 182-) A 8 NE1
Unsatisfied donor : 1577 ALA ( 193-) A 8 N
Unsatisfied donor : 1590 PHE ( 206-) A 8 N
Unsatisfied donor : 1595 ASN ( 211-) A 8 N
Unsatisfied donor : 1600 ARG ( 216-) A 8 N
Unsatisfied donor : 1612 GLU ( 27-) A 9 N
Unsatisfied donor : 1614 LYS ( 29-) A 9 N
Unsatisfied donor : 1620 CYS ( 35-) A 9 N
Unsatisfied donor : 1626 PHE ( 41-) A 9 N
Unsatisfied donor : 1628 LYS ( 43-) A 9 N
Unsatisfied donor : 1648 VAL ( 63-) A 9 N
Unsatisfied donor : 1649 ARG ( 64-) A 9 N
Unsatisfied donor : 1650 LEU ( 65-) A 9 N
Unsatisfied donor : 1658 TYR ( 73-) A 9 N
Unsatisfied donor : 1659 SER ( 74-) A 9 N
--Potential acceptor : 1659 SER ( 74-) A 9 OG
Unsatisfied donor : 1662 PHE ( 77-) A 9 N
Unsatisfied donor : 1664 HIS ( 79-) A 9 N
Unsatisfied donor : 1665 LEU ( 80-) A 9 N
Unsatisfied donor : 1667 GLN ( 82-) A 9 N
Unsatisfied donor : 1673 ARG ( 88-) A 9 N
Unsatisfied donor : 1690 ARG ( 105-) A 9 N
Unsatisfied donor : 1690 ARG ( 105-) A 9 NE
Unsatisfied donor : 1690 ARG ( 105-) A 9 NH1
--Potential acceptor : 1683 PHE ( 98-) A 9 O
Unsatisfied donor : 1690 ARG ( 105-) A 9 NH2
Unsatisfied donor : 1695 MET ( 110-) A 9 N
Unsatisfied donor : 1699 LEU ( 114-) A 9 N
Unsatisfied donor : 1702 ILE ( 117-) A 9 N
Unsatisfied donor : 1704 PHE ( 119-) A 9 N
Unsatisfied donor : 1711 GLN ( 126-) A 9 N
Unsatisfied donor : 1721 VAL ( 136-) A 9 N
Unsatisfied donor : 1723 SER ( 138-) A 9 N
Unsatisfied donor : 1723 SER ( 138-) A 9 OG
Unsatisfied donor : 1725 ALA ( 140-) A 9 N
Unsatisfied donor : 1726 GLY ( 141-) A 9 N
--Potential acceptor : 1723 SER ( 138-) A 9 OG
Unsatisfied donor : 1727 THR ( 142-) A 9 N
Unsatisfied donor : 1729 SER ( 144-) A 9 N
Unsatisfied donor : 1730 ILE ( 145-) A 9 N
Unsatisfied donor : 1740 LEU ( 155-) A 9 N
Unsatisfied donor : 1741 ILE ( 156-) A 9 N
Unsatisfied donor : 1745 ASN ( 160-) A 9 N
--Potential acceptor : 1753 GLN ( 168-) A 9 OE1
Unsatisfied donor : 1751 ASN ( 166-) A 9 N
Unsatisfied donor : 1752 HIS ( 167-) A 9 N
Unsatisfied donor : 1753 GLN ( 168-) A 9 N
Unsatisfied donor : 1753 GLN ( 168-) A 9 NE2
--Potential acceptor : 1724 HIS ( 139-) A 9 O
--Potential acceptor : 1743 CYS ( 158-) A 9 O
Unsatisfied donor : 1766 VAL ( 181-) A 9 N
Unsatisfied donor : 1767 TRP ( 182-) A 9 N
Unsatisfied donor : 1774 THR ( 189-) A 9 N
Unsatisfied donor : 1787 LYS ( 202-) A 9 NZ
--Potential acceptor : 1783 SER ( 198-) A 9 O
Unsatisfied donor : 1793 VAL ( 208-) A 9 N
Unsatisfied donor : 1796 ASN ( 211-) A 9 N
Unsatisfied donor : 1798 SER ( 213-) A 9 N
Unsatisfied donor : 1799 PHE ( 214-) A 9 N
Unsatisfied donor : 1814 GLU ( 28-) A 10 N
Unsatisfied donor : 1822 GLY ( 36-) A 10 N
Unsatisfied donor : 1824 THR ( 38-) A 10 N
Unsatisfied donor : 1825 VAL ( 39-) A 10 N
--Potential acceptor : 1824 THR ( 38-) A 10 OG1
Unsatisfied donor : 1827 PHE ( 41-) A 10 N
Unsatisfied donor : 1829 LYS ( 43-) A 10 N
Unsatisfied donor : 1831 VAL ( 45-) A 10 N
Unsatisfied donor : 1836 SER ( 50-) A 10 N
Unsatisfied donor : 1851 LEU ( 65-) A 10 N
Unsatisfied donor : 1853 ILE ( 67-) A 10 N
Unsatisfied donor : 1855 PHE ( 69-) A 10 N
Unsatisfied donor : 1856 GLY ( 70-) A 10 N
Unsatisfied donor : 1859 TYR ( 73-) A 10 N
Unsatisfied donor : 1865 HIS ( 79-) A 10 N
Unsatisfied donor : 1866 LEU ( 80-) A 10 N
Unsatisfied donor : 1867 VAL ( 81-) A 10 N
Unsatisfied donor : 1868 GLN ( 82-) A 10 N
Unsatisfied donor : 1868 GLN ( 82-) A 10 NE2
Unsatisfied donor : 1874 ARG ( 88-) A 10 NE
Unsatisfied donor : 1881 ILE ( 95-) A 10 N
Unsatisfied donor : 1882 ASP ( 96-) A 10 N
Unsatisfied donor : 1884 PHE ( 98-) A 10 N
Unsatisfied donor : 1885 GLY ( 99-) A 10 N
Unsatisfied donor : 1886 CYS ( 100-) A 10 N
Unsatisfied donor : 1892 GLN ( 106-) A 10 N
Unsatisfied donor : 1896 MET ( 110-) A 10 N
Unsatisfied donor : 1903 ILE ( 117-) A 10 N
Unsatisfied donor : 1904 GLY ( 118-) A 10 N
Unsatisfied donor : 1918 TYR ( 132-) A 10 OH
Unsatisfied donor : 1925 HIS ( 139-) A 10 N
Unsatisfied donor : 1926 ALA ( 140-) A 10 N
Unsatisfied donor : 1927 GLY ( 141-) A 10 N
Unsatisfied donor : 1931 ILE ( 145-) A 10 N
Unsatisfied donor : 1941 LEU ( 155-) A 10 N
Unsatisfied donor : 1942 ILE ( 156-) A 10 N
Unsatisfied donor : 1946 ASN ( 160-) A 10 N
Unsatisfied donor : 1951 ASP ( 165-) A 10 N
Unsatisfied donor : 1952 ASN ( 166-) A 10 N
Unsatisfied donor : 1954 GLN ( 168-) A 10 N
Unsatisfied donor : 1967 VAL ( 181-) A 10 N
Unsatisfied donor : 1968 TRP ( 182-) A 10 N
Unsatisfied donor : 1976 GLY ( 190-) A 10 N
Unsatisfied donor : 1989 LEU ( 203-) A 10 N
Unsatisfied donor : 1994 VAL ( 208-) A 10 N
Unsatisfied donor : 1996 HIS ( 210-) A 10 N
Unsatisfied donor : 1997 ASN ( 211-) A 10 N
Unsatisfied donor : 2001 GLU ( 215-) A 10 N
# 122 # Warning: Buried unsatisfied hydrogen bond donors
The buried hydrogen bond donors listed in the table below have a
hydrogen atom that is not involved in a hydrogen bond in the
optimized hydrogen bond network.
Hydrogen bond donors that are buried inside the protein normally
use all of their hydrogens to form hydrogen bonds within the
protein. If there are any non hydrogen bonded buried hydrogen bond
donors in the structure they will be listed here. In very good
structures the number of listed atoms will tend to zero.
Waters are not listed by this option.
6 LYS ( 29-) A 1 N
12 CYS ( 35-) A 1 N
18 PHE ( 41-) A 1 N
27 SER ( 50-) A 1 N
29 GLU ( 52-) A 1 N
37 TYR ( 60-) A 1 OH
46 PHE ( 69-) A 1 N
51 SER ( 74-) A 1 N
52 SER ( 75-) A 1 N
52 SER ( 75-) A 1 OG
53 GLU ( 76-) A 1 N
55 GLU ( 78-) A 1 N
59 GLN ( 82-) A 1 N
72 ILE ( 95-) A 1 N
73 ASP ( 96-) A 1 N
75 PHE ( 98-) A 1 N
82 ARG ( 105-) A 1 NH1
85 VAL ( 108-) A 1 N
91 LEU ( 114-) A 1 N
97 ASP ( 120-) A 1 N
98 PHE ( 121-) A 1 N
100 THR ( 123-) A 1 N
113 VAL ( 136-) A 1 N
115 SER ( 138-) A 1 N
118 GLY ( 141-) A 1 N
And so on for a total of 440 lines.
Acceptor does not accept : 2 ILE ( 25-) A 1 O
Acceptor does not accept : 7 ALA ( 30-) A 1 O
Acceptor does not accept : 14 ALA ( 37-) A 1 O
Acceptor does not accept : 37 TYR ( 60-) A 1 OH
Acceptor does not accept : 44 ILE ( 67-) A 1 O
Acceptor does not accept : 45 GLN ( 68-) A 1 OE1
Acceptor does not accept : 46 PHE ( 69-) A 1 O
--Potential donor : 45 GLN ( 68-) A 1 NE2
Acceptor does not accept : 52 SER ( 75-) A 1 OG
Acceptor does not accept : 64 GLN ( 87-) A 1 O
Acceptor does not accept : 66 GLU ( 89-) A 1 O
Acceptor does not accept : 75 PHE ( 98-) A 1 O
Acceptor does not accept : 79 ASP ( 102-) A 1 O
Acceptor does not accept : 79 ASP ( 102-) A 1 OD2
Acceptor does not accept : 81 ALA ( 104-) A 1 O
Acceptor does not accept : 90 LYS ( 113-) A 1 O
Acceptor does not accept : 95 GLY ( 118-) A 1 O
Acceptor does not accept : 113 VAL ( 136-) A 1 O
Acceptor does not accept : 115 SER ( 138-) A 1 OG
--Potential donor : 115 SER ( 138-) A 1 N
Acceptor does not accept : 116 HIS ( 139-) A 1 O
Acceptor does not accept : 124 ASP ( 147-) A 1 OD2
--Potential donor : 190 SER ( 213-) A 1 OG
Acceptor does not accept : 125 SER ( 148-) A 1 OG
Acceptor does not accept : 129 ASN ( 152-) A 1 O
--Potential donor : 129 ASN ( 152-) A 1 ND2
Acceptor does not accept : 131 PRO ( 154-) A 1 O
Acceptor does not accept : 132 LEU ( 155-) A 1 O
--Potential donor : 175 SER ( 198-) A 1 OG
Acceptor does not accept : 133 ILE ( 156-) A 1 O
Acceptor does not accept : 135 CYS ( 158-) A 1 O
Acceptor does not accept : 148 ILE ( 171-) A 1 O
Acceptor does not accept : 175 SER ( 198-) A 1 OG
Acceptor does not accept : 178 GLU ( 201-) A 1 O
Acceptor does not accept : 185 VAL ( 208-) A 1 O
Acceptor does not accept : 188 ASN ( 211-) A 1 O
Acceptor does not accept : 208 ALA ( 30-) A 2 O
Acceptor does not accept : 212 THR ( 34-) A 2 O
--Potential donor : 317 HIS ( 139-) A 2 ND1
Acceptor does not accept : 215 ALA ( 37-) A 2 O
--Potential donor : 252 SER ( 74-) A 2 OG
Acceptor does not accept : 216 THR ( 38-) A 2 OG1
--Potential donor : 343 ASP ( 165-) A 2 OD1
--Potential donor : 343 ASP ( 165-) A 2 OD2
Acceptor does not accept : 222 LEU ( 44-) A 2 O
Acceptor does not accept : 225 CYS ( 47-) A 2 O
Acceptor does not accept : 239 GLY ( 61-) A 2 O
Acceptor does not accept : 242 ARG ( 64-) A 2 O
Acceptor does not accept : 243 LEU ( 65-) A 2 O
Acceptor does not accept : 247 PHE ( 69-) A 2 O
Acceptor does not accept : 252 SER ( 74-) A 2 OG
--Potential donor : 252 SER ( 74-) A 2 N
Acceptor does not accept : 276 PHE ( 98-) A 2 O
Acceptor does not accept : 285 TYR ( 107-) A 2 OH
Acceptor does not accept : 295 ILE ( 117-) A 2 O
Acceptor does not accept : 299 PHE ( 121-) A 2 O
Acceptor does not accept : 314 VAL ( 136-) A 2 O
Acceptor does not accept : 316 SER ( 138-) A 2 OG
Acceptor does not accept : 320 THR ( 142-) A 2 OG1
--Potential donor : 320 THR ( 142-) A 2 N
Acceptor does not accept : 332 PRO ( 154-) A 2 O
Acceptor does not accept : 333 LEU ( 155-) A 2 O
Acceptor does not accept : 339 ASP ( 161-) A 2 OD1
Acceptor does not accept : 339 ASP ( 161-) A 2 OD2
Acceptor does not accept : 341 LEU ( 163-) A 2 O
--Potential donor : 216 THR ( 38-) A 2 OG1
Acceptor does not accept : 358 TYR ( 180-) A 2 OH
Acceptor does not accept : 364 PRO ( 186-) A 2 O
Acceptor does not accept : 376 SER ( 198-) A 2 O
Acceptor does not accept : 376 SER ( 198-) A 2 OG
Acceptor does not accept : 379 GLU ( 201-) A 2 O
Acceptor does not accept : 387 SER ( 209-) A 2 O
Acceptor does not accept : 400 ILE ( 222-) A 2 O
Acceptor does not accept : 405 ILE ( 26-) A 3 O
Acceptor does not accept : 417 THR ( 38-) A 3 OG1
--Potential donor : 417 THR ( 38-) A 3 N
--Potential donor : 544 ASP ( 165-) A 3 OD2
Acceptor does not accept : 427 VAL ( 48-) A 3 O
Acceptor does not accept : 440 GLY ( 61-) A 3 O
Acceptor does not accept : 441 PHE ( 62-) A 3 O
Acceptor does not accept : 443 ARG ( 64-) A 3 O
Acceptor does not accept : 447 GLN ( 68-) A 3 OE1
Acceptor does not accept : 451 ASN ( 72-) A 3 OD1
Acceptor does not accept : 455 GLU ( 76-) A 3 O
Acceptor does not accept : 455 GLU ( 76-) A 3 OE2
Acceptor does not accept : 477 PHE ( 98-) A 3 O
Acceptor does not accept : 478 GLY ( 99-) A 3 O
Acceptor does not accept : 479 CYS ( 100-) A 3 O
Acceptor does not accept : 482 THR ( 103-) A 3 O
Acceptor does not accept : 486 TYR ( 107-) A 3 O
Acceptor does not accept : 490 ASN ( 111-) A 3 OD1
Acceptor does not accept : 497 GLY ( 118-) A 3 O
Acceptor does not accept : 499 ASP ( 120-) A 3 O
Acceptor does not accept : 499 ASP ( 120-) A 3 OD1
Acceptor does not accept : 516 ILE ( 137-) A 3 O
Acceptor does not accept : 517 SER ( 138-) A 3 OG
Acceptor does not accept : 522 GLY ( 143-) A 3 O
Acceptor does not accept : 532 LYS ( 153-) A 3 O
Acceptor does not accept : 533 PRO ( 154-) A 3 O
Acceptor does not accept : 534 LEU ( 155-) A 3 O
Acceptor does not accept : 540 ASP ( 161-) A 3 O
Acceptor does not accept : 541 SER ( 162-) A 3 OG
Acceptor does not accept : 543 MET ( 164-) A 3 SD
--Potential donor : 417 THR ( 38-) A 3 OG1
Acceptor does not accept : 548 GLN ( 169-) A 3 OE1
--Potential donor : 552 ASP ( 173-) A 3 OD1
--Potential donor : 552 ASP ( 173-) A 3 OD2
Acceptor does not accept : 560 VAL ( 181-) A 3 O
Acceptor does not accept : 563 CYS ( 184-) A 3 O
Acceptor does not accept : 563 CYS ( 184-) A 3 SG
Acceptor does not accept : 577 SER ( 198-) A 3 OG
--Potential donor : 534 LEU ( 155-) A 3 N
Acceptor does not accept : 599 GLU ( 220-) A 3 OE2
Acceptor does not accept : 609 LYS ( 29-) A 4 O
Acceptor does not accept : 610 ALA ( 30-) A 4 O
Acceptor does not accept : 619 VAL ( 39-) A 4 O
Acceptor does not accept : 628 VAL ( 48-) A 4 O
Acceptor does not accept : 636 GLU ( 56-) A 4 O
Acceptor does not accept : 647 ILE ( 67-) A 4 O
Acceptor does not accept : 648 GLN ( 68-) A 4 O
Acceptor does not accept : 655 SER ( 75-) A 4 O
Acceptor does not accept : 659 HIS ( 79-) A 4 ND1
Acceptor does not accept : 668 ARG ( 88-) A 4 O
Acceptor does not accept : 673 ILE ( 93-) A 4 O
Acceptor does not accept : 681 GLY ( 101-) A 4 O
Acceptor does not accept : 687 TYR ( 107-) A 4 OH
Acceptor does not accept : 693 LYS ( 113-) A 4 O
Acceptor does not accept : 698 GLY ( 118-) A 4 O
Acceptor does not accept : 718 SER ( 138-) A 4 O
Acceptor does not accept : 724 SER ( 144-) A 4 OG
Acceptor does not accept : 735 LEU ( 155-) A 4 O
Acceptor does not accept : 736 ILE ( 156-) A 4 O
Acceptor does not accept : 739 VAL ( 159-) A 4 O
Acceptor does not accept : 747 HIS ( 167-) A 4 ND1
Acceptor does not accept : 748 GLN ( 168-) A 4 OE1
Acceptor does not accept : 756 VAL ( 176-) A 4 O
Acceptor does not accept : 778 SER ( 198-) A 4 OG
--Potential donor : 779 GLN ( 199-) A 4 N
Acceptor does not accept : 810 LYS ( 29-) A 5 O
Acceptor does not accept : 811 ALA ( 30-) A 5 O
Acceptor does not accept : 820 VAL ( 39-) A 5 O
Acceptor does not accept : 846 LEU ( 65-) A 5 O
Acceptor does not accept : 849 GLN ( 68-) A 5 O
Acceptor does not accept : 849 GLN ( 68-) A 5 OE1
Acceptor does not accept : 857 GLU ( 76-) A 5 OE1
Acceptor does not accept : 870 GLU ( 89-) A 5 OE2
Acceptor does not accept : 883 ASP ( 102-) A 5 O
Acceptor does not accept : 895 LEU ( 114-) A 5 O
Acceptor does not accept : 906 MET ( 125-) A 5 SD
Acceptor does not accept : 917 VAL ( 136-) A 5 O
Acceptor does not accept : 920 HIS ( 139-) A 5 O
Acceptor does not accept : 921 ALA ( 140-) A 5 O
Acceptor does not accept : 928 ASP ( 147-) A 5 OD2
Acceptor does not accept : 929 SER ( 148-) A 5 OG
Acceptor does not accept : 935 PRO ( 154-) A 5 O
Acceptor does not accept : 936 LEU ( 155-) A 5 O
Acceptor does not accept : 939 CYS ( 158-) A 5 O
Acceptor does not accept : 941 ASN ( 160-) A 5 O
Acceptor does not accept : 961 TYR ( 180-) A 5 O
Acceptor does not accept : 961 TYR ( 180-) A 5 OH
Acceptor does not accept : 965 CYS ( 184-) A 5 SG
Acceptor does not accept : 979 SER ( 198-) A 5 O
Acceptor does not accept : 979 SER ( 198-) A 5 OG
--Potential donor : 979 SER ( 198-) A 5 N
Acceptor does not accept : 982 GLU ( 201-) A 5 O
Acceptor does not accept : 987 PHE ( 206-) A 5 O
Acceptor does not accept : 996 GLU ( 215-) A 5 OE1
Acceptor does not accept : 1011 LYS ( 29-) A 6 O
Acceptor does not accept : 1012 ALA ( 30-) A 6 O
Acceptor does not accept : 1017 CYS ( 35-) A 6 O
Acceptor does not accept : 1030 VAL ( 48-) A 6 O
Acceptor does not accept : 1038 GLU ( 56-) A 6 OE1
Acceptor does not accept : 1046 ARG ( 64-) A 6 O
Acceptor does not accept : 1047 LEU ( 65-) A 6 O
Acceptor does not accept : 1049 ILE ( 67-) A 6 O
Acceptor does not accept : 1051 PHE ( 69-) A 6 O
Acceptor does not accept : 1056 SER ( 74-) A 6 OG
--Potential donor : 1056 SER ( 74-) A 6 N
Acceptor does not accept : 1058 GLU ( 76-) A 6 O
Acceptor does not accept : 1058 GLU ( 76-) A 6 OE1
Acceptor does not accept : 1058 GLU ( 76-) A 6 OE2
Acceptor does not accept : 1085 THR ( 103-) A 6 OG1
Acceptor does not accept : 1086 ALA ( 104-) A 6 O
Acceptor does not accept : 1097 LYS ( 115-) A 6 O
Acceptor does not accept : 1114 TYR ( 132-) A 6 OH
Acceptor does not accept : 1115 SER ( 133-) A 6 OG
Acceptor does not accept : 1124 THR ( 142-) A 6 O
Acceptor does not accept : 1125 GLY ( 143-) A 6 O
Acceptor does not accept : 1129 ASP ( 147-) A 6 OD1
Acceptor does not accept : 1130 SER ( 148-) A 6 OG
--Potential donor : 1130 SER ( 148-) A 6 N
Acceptor does not accept : 1134 ASN ( 152-) A 6 O
Acceptor does not accept : 1135 LYS ( 153-) A 6 O
Acceptor does not accept : 1137 LEU ( 155-) A 6 O
Acceptor does not accept : 1138 ILE ( 156-) A 6 O
Acceptor does not accept : 1140 CYS ( 158-) A 6 O
Acceptor does not accept : 1141 VAL ( 159-) A 6 O
Acceptor does not accept : 1142 ASN ( 160-) A 6 O
Acceptor does not accept : 1143 ASP ( 161-) A 6 O
Acceptor does not accept : 1154 ALA ( 172-) A 6 O
Acceptor does not accept : 1162 TYR ( 180-) A 6 O
Acceptor does not accept : 1166 CYS ( 184-) A 6 SG
Acceptor does not accept : 1180 SER ( 198-) A 6 OG
--Potential donor : 1042 TYR ( 60-) A 6 OH
Acceptor does not accept : 1185 LEU ( 203-) A 6 O
Acceptor does not accept : 1186 LYS ( 204-) A 6 O
Acceptor does not accept : 1193 ASN ( 211-) A 6 OD1
Acceptor does not accept : 1230 CYS ( 47-) A 7 O
Acceptor does not accept : 1239 GLU ( 56-) A 7 O
Acceptor does not accept : 1248 LEU ( 65-) A 7 O
Acceptor does not accept : 1251 GLN ( 68-) A 7 O
Acceptor does not accept : 1251 GLN ( 68-) A 7 OE1
Acceptor does not accept : 1275 LYS ( 92-) A 7 O
Acceptor does not accept : 1281 PHE ( 98-) A 7 O
Acceptor does not accept : 1282 GLY ( 99-) A 7 O
Acceptor does not accept : 1287 ALA ( 104-) A 7 O
Acceptor does not accept : 1289 GLN ( 106-) A 7 OE1
--Potential donor : 1290 TYR ( 107-) A 7 N
Acceptor does not accept : 1299 VAL ( 116-) A 7 O
Acceptor does not accept : 1301 GLY ( 118-) A 7 O
Acceptor does not accept : 1302 PHE ( 119-) A 7 O
Acceptor does not accept : 1316 SER ( 133-) A 7 O
Acceptor does not accept : 1316 SER ( 133-) A 7 OG
Acceptor does not accept : 1319 VAL ( 136-) A 7 O
Acceptor does not accept : 1320 ILE ( 137-) A 7 O
Acceptor does not accept : 1321 SER ( 138-) A 7 OG
--Potential donor : 1321 SER ( 138-) A 7 N
Acceptor does not accept : 1338 LEU ( 155-) A 7 O
--Potential donor : 1381 SER ( 198-) A 7 OG
Acceptor does not accept : 1339 ILE ( 156-) A 7 O
Acceptor does not accept : 1343 ASN ( 160-) A 7 O
Acceptor does not accept : 1351 GLN ( 168-) A 7 OE1
Acceptor does not accept : 1364 VAL ( 181-) A 7 O
Acceptor does not accept : 1409 ILE ( 25-) A 8 O
Acceptor does not accept : 1414 ALA ( 30-) A 8 O
Acceptor does not accept : 1433 LEU ( 49-) A 8 O
Acceptor does not accept : 1438 CYS ( 54-) A 8 O
Acceptor does not accept : 1446 PHE ( 62-) A 8 O
Acceptor does not accept : 1452 GLN ( 68-) A 8 OE1
Acceptor does not accept : 1453 PHE ( 69-) A 8 O
Acceptor does not accept : 1458 SER ( 74-) A 8 O
Acceptor does not accept : 1459 SER ( 75-) A 8 O
Acceptor does not accept : 1463 HIS ( 79-) A 8 ND1
Acceptor does not accept : 1478 PRO ( 94-) A 8 O
Acceptor does not accept : 1480 ASP ( 96-) A 8 O
Acceptor does not accept : 1481 GLN ( 97-) A 8 O
Acceptor does not accept : 1484 CYS ( 100-) A 8 SG
Acceptor does not accept : 1485 GLY ( 101-) A 8 O
Acceptor does not accept : 1486 ASP ( 102-) A 8 O
Acceptor does not accept : 1486 ASP ( 102-) A 8 OD1
Acceptor does not accept : 1488 ALA ( 104-) A 8 O
--Potential donor : 1486 ASP ( 102-) A 8 OD1
Acceptor does not accept : 1499 LYS ( 115-) A 8 O
Acceptor does not accept : 1502 GLY ( 118-) A 8 O
Acceptor does not accept : 1503 PHE ( 119-) A 8 O
Acceptor does not accept : 1522 SER ( 138-) A 8 O
Acceptor does not accept : 1523 HIS ( 139-) A 8 O
Acceptor does not accept : 1524 ALA ( 140-) A 8 O
Acceptor does not accept : 1531 ASP ( 147-) A 8 OD1
Acceptor does not accept : 1532 SER ( 148-) A 8 OG
Acceptor does not accept : 1539 LEU ( 155-) A 8 O
Acceptor does not accept : 1540 ILE ( 156-) A 8 O
Acceptor does not accept : 1543 VAL ( 159-) A 8 O
Acceptor does not accept : 1549 ASP ( 165-) A 8 OD1
Acceptor does not accept : 1564 TYR ( 180-) A 8 O
Acceptor does not accept : 1565 VAL ( 181-) A 8 O
Acceptor does not accept : 1612 GLU ( 27-) A 9 OE2
Acceptor does not accept : 1614 LYS ( 29-) A 9 O
Acceptor does not accept : 1615 ALA ( 30-) A 9 O
Acceptor does not accept : 1622 ALA ( 37-) A 9 O
Acceptor does not accept : 1623 THR ( 38-) A 9 O
Acceptor does not accept : 1633 VAL ( 48-) A 9 O
Acceptor does not accept : 1639 CYS ( 54-) A 9 O
Acceptor does not accept : 1648 VAL ( 63-) A 9 O
Acceptor does not accept : 1650 LEU ( 65-) A 9 O
Acceptor does not accept : 1652 ILE ( 67-) A 9 O
Acceptor does not accept : 1653 GLN ( 68-) A 9 O
--Potential donor : 1619 THR ( 34-) A 9 OG1
Acceptor does not accept : 1657 ASN ( 72-) A 9 O
--Potential donor : 1660 SER ( 75-) A 9 OG
Acceptor does not accept : 1679 PRO ( 94-) A 9 O
Acceptor does not accept : 1698 LYS ( 113-) A 9 O
Acceptor does not accept : 1700 LYS ( 115-) A 9 O
Acceptor does not accept : 1704 PHE ( 119-) A 9 O
Acceptor does not accept : 1707 SER ( 122-) A 9 O
Acceptor does not accept : 1721 VAL ( 136-) A 9 O
Acceptor does not accept : 1723 SER ( 138-) A 9 OG
--Potential donor : 1726 GLY ( 141-) A 9 N
Acceptor does not accept : 1724 HIS ( 139-) A 9 NE2
Acceptor does not accept : 1732 ASP ( 147-) A 9 OD2
Acceptor does not accept : 1738 LYS ( 153-) A 9 O
Acceptor does not accept : 1741 ILE ( 156-) A 9 O
Acceptor does not accept : 1752 HIS ( 167-) A 9 ND1
Acceptor does not accept : 1753 GLN ( 168-) A 9 OE1
--Potential donor : 1745 ASN ( 160-) A 9 N
Acceptor does not accept : 1783 SER ( 198-) A 9 OG
Acceptor does not accept : 1786 GLU ( 201-) A 9 O
Acceptor does not accept : 1790 PRO ( 205-) A 9 O
Acceptor does not accept : 1816 ALA ( 30-) A 10 O
Acceptor does not accept : 1833 CYS ( 47-) A 10 O
Acceptor does not accept : 1834 VAL ( 48-) A 10 O
Acceptor does not accept : 1853 ILE ( 67-) A 10 O
Acceptor does not accept : 1854 GLN ( 68-) A 10 OE1
--Potential donor : 1906 ASP ( 120-) A 10 OD2
Acceptor does not accept : 1862 GLU ( 76-) A 10 OE1
Acceptor does not accept : 1862 GLU ( 76-) A 10 OE2
Acceptor does not accept : 1868 GLN ( 82-) A 10 OE1
Acceptor does not accept : 1875 GLU ( 89-) A 10 O
Acceptor does not accept : 1879 ILE ( 93-) A 10 O
Acceptor does not accept : 1885 GLY ( 99-) A 10 O
Acceptor does not accept : 1899 LYS ( 113-) A 10 O
Acceptor does not accept : 1901 LYS ( 115-) A 10 O
Acceptor does not accept : 1903 ILE ( 117-) A 10 O
Acceptor does not accept : 1904 GLY ( 118-) A 10 O
Acceptor does not accept : 1906 ASP ( 120-) A 10 O
Acceptor does not accept : 1907 PHE ( 121-) A 10 O
Acceptor does not accept : 1918 TYR ( 132-) A 10 OH
Acceptor does not accept : 1922 VAL ( 136-) A 10 O
Acceptor does not accept : 1923 ILE ( 137-) A 10 O
Acceptor does not accept : 1924 SER ( 138-) A 10 OG
--Potential donor : 1924 SER ( 138-) A 10 N
Acceptor does not accept : 1925 HIS ( 139-) A 10 NE2
--Potential donor : 1946 ASN ( 160-) A 10 ND2
Acceptor does not accept : 1926 ALA ( 140-) A 10 O
Acceptor does not accept : 1928 THR ( 142-) A 10 OG1
Acceptor does not accept : 1929 GLY ( 143-) A 10 O
Acceptor does not accept : 1938 ASN ( 152-) A 10 OD1
Acceptor does not accept : 1941 LEU ( 155-) A 10 O
Acceptor does not accept : 1944 CYS ( 158-) A 10 O
--Potential donor : 1946 ASN ( 160-) A 10 ND2
Acceptor does not accept : 1946 ASN ( 160-) A 10 OD1
Acceptor does not accept : 1952 ASN ( 166-) A 10 OD1
Acceptor does not accept : 1959 ASP ( 173-) A 10 OD1
--Potential donor : 1955 GLN ( 169-) A 10 NE2
--Potential donor : 1959 ASP ( 173-) A 10 N
Acceptor does not accept : 1967 VAL ( 181-) A 10 O
Acceptor does not accept : 1970 CYS ( 184-) A 10 SG
Acceptor does not accept : 1984 SER ( 198-) A 10 OG
Acceptor does not accept : 1987 GLU ( 201-) A 10 O
Acceptor does not accept : 1992 PHE ( 206-) A 10 O
Acceptor does not accept : 1994 VAL ( 208-) A 10 O
--Potential donor : 1997 ASN ( 211-) A 10 ND2
Acceptor does not accept : 1998 PRO ( 212-) A 10 O
# 123 # Warning: Buried unsatisfied hydrogen bond acceptors
The buried side-chain hydrogen bond acceptors listed in the table
below are not involved in a hydrogen bond in the optimized hydrogen
bond network.
Side-chain hydrogen bond acceptors that are buried inside the
protein normally form hydrogen bonds within the protein. If there
are any not hydrogen bonded in the optimized hydrogen bond network
they will be listed here.
Waters are not listed by this option.
45 GLN ( 68-) A 1 OE1
79 ASP ( 102-) A 1 OD2
124 ASP ( 147-) A 1 OD2
339 ASP ( 161-) A 2 OD1
339 ASP ( 161-) A 2 OD2
447 GLN ( 68-) A 3 OE1
451 ASN ( 72-) A 3 OD1
455 GLU ( 76-) A 3 OE2
490 ASN ( 111-) A 3 OD1
499 ASP ( 120-) A 3 OD1
548 GLN ( 169-) A 3 OE1
599 GLU ( 220-) A 3 OE2
659 HIS ( 79-) A 4 ND1
747 HIS ( 167-) A 4 ND1
748 GLN ( 168-) A 4 OE1
849 GLN ( 68-) A 5 OE1
857 GLU ( 76-) A 5 OE1
870 GLU ( 89-) A 5 OE2
928 ASP ( 147-) A 5 OD2
996 GLU ( 215-) A 5 OE1
1038 GLU ( 56-) A 6 OE1
1058 GLU ( 76-) A 6 OE1
1058 GLU ( 76-) A 6 OE2
1129 ASP ( 147-) A 6 OD1
1193 ASN ( 211-) A 6 OD1
1251 GLN ( 68-) A 7 OE1
1289 GLN ( 106-) A 7 OE1
1351 GLN ( 168-) A 7 OE1
1452 GLN ( 68-) A 8 OE1
1463 HIS ( 79-) A 8 ND1
1486 ASP ( 102-) A 8 OD1
1531 ASP ( 147-) A 8 OD1
1549 ASP ( 165-) A 8 OD1
1612 GLU ( 27-) A 9 OE2
1724 HIS ( 139-) A 9 NE2
1732 ASP ( 147-) A 9 OD2
1752 HIS ( 167-) A 9 ND1
1753 GLN ( 168-) A 9 OE1
1854 GLN ( 68-) A 10 OE1
1862 GLU ( 76-) A 10 OE1
1862 GLU ( 76-) A 10 OE2
1868 GLN ( 82-) A 10 OE1
1925 HIS ( 139-) A 10 NE2
1938 ASN ( 152-) A 10 OD1
1946 ASN ( 160-) A 10 OD1
1952 ASN ( 166-) A 10 OD1
1959 ASP ( 173-) A 10 OD1
# 124 # Note: Content of the PDB file as interpreted by WHAT IF
Content of the PDB file as interpreted by WHAT IF.
WHAT IF has read your PDB file, and stored it internally in
what is called 'the soup'. The content of this soup is listed here.
An extensive explanation of all frequently used WHAT IF output formats
can be found at http://swift.cmbi.ru.nl/. Look under output formats.
A course on reading this 'Molecules' table is part of the WHAT\_CHECK
web pages [REF].
1 1 ( 24) 201 ( 224) A Protein Mod 1 2JZC.pdb
2 202 ( 24) 402 ( 224) A Protein Mod 2 2JZC.pdb
3 403 ( 24) 603 ( 224) A Protein Mod 3 2JZC.pdb
4 604 ( 24) 804 ( 224) A Protein Mod 4 2JZC.pdb
5 805 ( 24) 1005 ( 224) A Protein Mod 5 2JZC.pdb
6 1006 ( 24) 1206 ( 224) A Protein Mod 6 2JZC.pdb
7 1207 ( 24) 1407 ( 224) A Protein Mod 7 2JZC.pdb
8 1408 ( 24) 1608 ( 224) A Protein Mod 8 2JZC.pdb
9 1609 ( 24) 1809 ( 224) A Protein Mod 9 2JZC.pdb
10 1810 ( 24) 2010 ( 224) A Protein Mod 10 2JZC.pdb
11 2011 ( 224) 2011 ( 224) A S O2 <- 201 1 2JZC.pdb
12 2012 ( 224) 2012 ( 224) A S O2 <- 402 2 2JZC.pdb
13 2013 ( 224) 2013 ( 224) A S O2 <- 603 3 2JZC.pdb
14 2014 ( 224) 2014 ( 224) A S O2 <- 804 4 2JZC.pdb
15 2015 ( 224) 2015 ( 224) A S O2 <- 1005 5 2JZC.pdb
16 2016 ( 224) 2016 ( 224) A S O2 <- 1206 6 2JZC.pdb
17 2017 ( 224) 2017 ( 224) A S O2 <- 1407 7 2JZC.pdb
18 2018 ( 224) 2018 ( 224) A S O2 <- 1608 8 2JZC.pdb
19 2019 ( 224) 2019 ( 224) A S O2 <- 1809 9 2JZC.pdb
20 2020 ( 224) 2020 ( 224) A S O2 <- 2010 10 2JZC.pdb
# 125 # Warning: No crystallisation information
No, or very inadequate, crystallisation information was observed upon
reading the PDB file header records. This information should be available
in the form of a series of REMARK 280 lines. Without this information a
few things, such as checking ions in the structure, cannot be performed
optimally.
# 126 # Note: No ions (of a type we can validate) in structure
Since there are no ions in the structure of a type we can validate, this
check will not be executed.
Since there are no waters, the water check has been skipped.
SOUP contains no water:
# 127 # Note: Summary report for users of a structure
This is an overall summary of the quality of the structure as
compared with current reliable structures. This summary is most
useful for biologists seeking a good structure to use for modelling
calculations.
The second part of the table mostly gives an impression of how well
the model conforms to common refinement restraint values. The
first part of the table shows a number of restraint-independent
quality indicators.
Structure Z-scores, positive is better than average:
1st generation packing quality : -3.436
2nd generation packing quality : -4.424 (bad)
Ramachandran plot appearance : -4.617 (bad)
chi-1/chi-2 rotamer normality : -2.103
Backbone conformation : -1.421
RMS Z-scores, should be close to 1.0:
Bond lengths : 0.742
Bond angles : 0.780
Omega angle restraints : 0.176 (tight)
Side chain planarity : 0.274 (tight)
Improper dihedral distribution : 0.675
Inside/Outside distribution : 1.127
==============
WHAT IF
G.Vriend,
WHAT IF: a molecular modelling and drug design program,
J. Mol. Graph. 8, 52--56 (1990).
WHAT_CHECK (verification routines from WHAT IF)
R.W.W.Hooft, G.Vriend, C.Sander and E.E.Abola,
Errors in protein structures
Nature 381, 272 (1996).
(see also http://swift.cmbi.ru.nl/gv/whatcheck for a course and extra inform
Bond lengths and angles, protein residues
R.Engh and R.Huber,
Accurate bond and angle parameters for X-ray protein structure
refinement,
Acta Crystallogr. A47, 392--400 (1991).
Bond lengths and angles, DNA/RNA
G.Parkinson, J.Voitechovsky, L.Clowney, A.T.Bruenger and H.Berman,
New parameters for the refinement of nucleic acid-containing structures
Acta Crystallogr. D52, 57--64 (1996).
DSSP
W.Kabsch and C.Sander,
Dictionary of protein secondary structure: pattern
recognition of hydrogen bond and geometrical features
Biopolymers 22, 2577--2637 (1983).
Hydrogen bond networks
R.W.W.Hooft, C.Sander and G.Vriend,
Positioning hydrogen atoms by optimizing hydrogen bond networks in
protein structures
PROTEINS, 26, 363--376 (1996).
Matthews' Coefficient
B.W.Matthews
Solvent content of Protein Crystals
J. Mol. Biol. 33, 491--497 (1968).
Protein side chain planarity
R.W.W. Hooft, C. Sander and G. Vriend,
Verification of protein structures: side-chain planarity
J. Appl. Cryst. 29, 714--716 (1996).
Puckering parameters
D.Cremer and J.A.Pople,
A general definition of ring puckering coordinates
J. Am. Chem. Soc. 97, 1354--1358 (1975).
Quality Control
G.Vriend and C.Sander,
Quality control of protein models: directional atomic
contact analysis,
J. Appl. Cryst. 26, 47--60 (1993).
Ramachandran plot
G.N.Ramachandran, C.Ramakrishnan and V.Sasisekharan,
Stereochemistry of Polypeptide Chain Conformations
J. Mol. Biol. 7, 95--99 (1963).
Symmetry Checks
R.W.W.Hooft, C.Sander and G.Vriend,
Reconstruction of symmetry related molecules from protein
data bank (PDB) files
J. Appl. Cryst. 27, 1006--1009 (1994).
Ion Checks
I.D.Brown and K.K.Wu,
Empirical Parameters for Calculating Cation-Oxygen Bond Valences
Acta Cryst. B32, 1957--1959 (1975).
M.Nayal and E.Di Cera,
Valence Screening of Water in Protein Crystals Reveals Potential Na+
Binding Sites
J.Mol.Biol. 256 228--234 (1996).
P.Mueller, S.Koepke and G.M.Sheldrick,
Is the bond-valence method able to identify metal atoms in protein
structures?
Acta Cryst. D 59 32--37 (2003).
Checking checks
K.Wilson, C.Sander, R.W.W.Hooft, G.Vriend, et al.
Who checks the checkers
J.Mol.Biol. (1998) 276,417-436.
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