************************************************************************
********** REPORT OF PROTEIN ANALYSIS  by the WHAT IF program **********
************************************************************************

Date : 2023-12-07
This report was created by WHAT IF version WHATCHECK15.0

This document is a WHAT_CHECK 14.0 report for a PDB-file. Each reported
fact has an assigned severity, one of:

error  : 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 circumvents ambiguities in the
   many old PDB files in which DNA and RNA were both called A, C, G, and T.



=========================================
==== Compound code /zata/tempdir/6koo/wctemf/6koo_final.pdb         ====
=========================================
 
# 1 # Note: Introduction
WHAT CHECK needs to read a PDB file before it can check it. It does a
series of checks upon reading the file. The results of these checks are
reported in this section (section 2.1). The rest of the report will be more
systematic in that section 2.2 reports on administrative problems. Section
2.3 gives descriptive output that is not directly validating things but
more telling you how WHAT CHECK interpreted the input file. Section 2.4
looks at B-factors, occupancies, and the presence/absence of (spurious)
atoms. Section 2.5 deals with nomenclature problems. Section 2.6 deals with
geometric problems like bond lengths and bond angles. Section 2.7 deals with
torsion angle issues. Section 2.8 looks at atomic clashes. Section 2.9 deals
with packing, accessibility, etc, issues. Section 2.10 deals with hydrogen
bonds, ion packing, and other things that can be summarized under the common
name charge-charge interactions. Section 2.11 gives a summary of whole report
and tells you (if applicable) which symmetry matrices were used. Section 2.12
tells the crystallographer which are the things most in need of manual
correction. And the last section, section 2.13, lists all residues sorted
by their need for visual inspection in light of the electron density.
WARNING. Date error on HEADER card:
HEADER                                                        6KOO
 
# 2 # Note: Header records from PDB file
Header records from PDB file.
 
HEADER                                                        6KOO
 
# 3 # Error: Missing unit cell information
No SCALE matrix is given in the PDB file.
 
# 4 # Note: Proposal for corrected SCALE matrix
A corrected SCALE matrix has been derived.
 
Proposed scale matrix
  0.007998  0.000000  0.004080
  0.000000  0.006161  0.000000
  0.000000  0.000000  0.008738
 
# 5 # Warning: Problem detected upon counting molecules and matrices
The parameter Z as given on the CRYST card represents the molecular
multiplicity in the crystallographic cell. Normally, Z equals the number of
matrices of the space group multiplied by the number of NCS relations. The
value of Z is multiplied by the integrated molecular weight of the molecules
in the file to determine the Matthews coefficient. This relation is being
validated in this option. Be aware that the validation can get confused if
both multiple copies of the molecule are present in the ATOM records and
MTRIX records are present in the header of the PDB file.
 
 Space group as read from CRYST card: P 1 21 1
 Number of matrices in space group: 2
 Highest polymer chain multiplicity in structure: 1
 Highest polymer chain multiplicity according to SEQRES: 1
 No explicit MTRIX NCS matrices found in the input file
 Value of Z as found on the CRYST1 card: 0
 Z, symmetry, and molecular multiplicity disagree
 Could it be that Z must be: 2
 
# 6 # Warning: Matthews Coefficient (Vm) high
 
The Matthews coefficient [REF] is defined as the density of the protein
structure in cubic Angstroms per Dalton. Normal values are between 1.5
(tightly packed, little room for solvent) and 4.0 (loosely packed, much
space for solvent). Some very loosely packed structures can get values a bit
higher than that.
 
Very high numbers are most often caused by giving the wrong value for Z on
the CRYST1 card (or not giving this number at all), but can also result from
large fractions missing out of the molecular weight (e.g. a lot of UNK
residues, or DNA/RNA missing from virus structures).
 
 Molecular weight of all polymer chains: 359072.219
 Volume of the Unit Cell V= 2322671.2
 Space group multiplicity: 2
 No NCS symmetry matrices (MTRIX records) found in PDB file
 Matthews coefficient for observed atoms and Z is high: Vm= 6.469
 No Matthews coefficient given in REMARK 280
 Could it be that Z must be: 2
 This number is the multiplication of the spacegroup and NCS symmetry count
 Matthews coefficient for observed atoms and corrected Z: Vm= 3.234
 
# 7 # Note: All atoms are sufficiently far away from symmetry axes
None of the atoms in the structure is closer than 0.77 Angstrom to a proper
symmetry axis.
 
# 8 # Note: Chain identifiers OK
WHAT CHECK has not detected any serious chain identifier problems. But be
aware that WHAT CHECK doesn't care about the chain identifiers of waters.
 
# 9 # Note: No strange inter-chain connections detected
No covalent bonds have been detected between molecules with non-identical
chain identifiers.
 
# 10 # Note: No duplicate atom names in ligands
All atom names in ligands (if any) seem adequately unique.
 
# 11 # Note: In all cases the primary alternate atom was used
WHAT CHECK saw no need to make any alternate atom corrections (which means
they either are all correct, or there are none).
 
# 12 # 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).
 
# 13 # Note: No attached groups interfere with hydrogen bond calculations
It seems there are no sugars, lipids, etc., bound (or very close) to atoms
that otherwise could form hydrogen bonds.
 
# 14 # Note: No probable side chain atoms with zero occupancy detected.
Either there are no side chain atoms with zero occupancy, or the side chain
atoms with zero occupancy were not present in the input PDB file (in which
case they are listed as missing atoms), or their positions are sufficiently
improbable to warrant a zero occupancy.
 
# 15 # Note: No probable backbone atoms with zero occupancy detected.
Either there are no backbone atoms with zero occupancy, or the backbone
atoms with zero occupancy were left out of the input PDB file (in
which case they are listed as missing atoms), or their positions are
sufficiently improbable to warrant a zero occupancy.
 
# 16 # Note: All residues have a complete backbone.
No residues have missing backbone atoms.
 
# 17 # Note: No C-alpha only residues
There are no residues that consist of only an alpha carbon atom.
 
# 18 # Note: Content of the PDB file as interpreted by WHAT CHECK
Content of the PDB file as interpreted by WHAT CHECK.
WHAT CHECK 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 CHECK output formats can be found at
swift.cmbi.ru.nl. Look under output formats. A course on reading this
'Molecules' table is part of the WHAT CHECK website.
 
     1     1 (    4)   217 (  223) A Protein             /zata/tempdir/6ko...
     2   218 (    1)   447 (  236) B Protein             /zata/tempdir/6ko...
     3   448 (   21)  1582 ( 1158) C Protein             /zata/tempdir/6ko...
     4  1583 (    2)  2840 ( 1281) D Protein             /zata/tempdir/6ko...
     5  2841 (   25)  2915 (  107) E Protein             /zata/tempdir/6ko...
     6  2916 (   21)  3097 (  202) F Protein             /zata/tempdir/6ko...
     7  3098 (    4)  3104 (   10) I DNA/RNA             /zata/tempdir/6ko...
     8  3105 (    1)  3127 (   23) G DNA/RNA             /zata/tempdir/6ko...
     9  3128 (    1)  3147 (   20) H DNA/RNA             /zata/tempdir/6ko...
    10  3148 ( 2001)  3148 ( 2001) D  ZN                 /zata/tempdir/6ko...
    11  3149 ( 2002)  3149 ( 2002) D  ZN                 /zata/tempdir/6ko...
    12  3150 ( 2003)  3150 ( 2003) D  MG                 /zata/tempdir/6ko...
    13  3151 ( HOH )  3151 ( HOH ) C water   (    8)     /zata/tempdir/6ko...
    14  3152 ( HOH )  3152 ( HOH ) D water   (   11)     /zata/tempdir/6ko...
    15  3153 ( HOH )  3153 ( HOH ) F water   (    4)     /zata/tempdir/6ko...
    16  3154 ( HOH )  3154 ( HOH ) H water   (    3)     /zata/tempdir/6ko...
    17  3155 ( HOH )  3155 ( HOH ) I water   (    1)     /zata/tempdir/6ko...
MODELs skipped upon reading PDB file: 0
X-ray structure. No MODELs found
The total number of amino acids found is 3097
of which 1247 have poor or (essentially) missing atoms
The total number of nucleic acids found is 50
of which 33 have poor or (essentially) missing atoms
No sugars recognized in input file
Number of water molecules: 27
Residue numbers increase monotonously OK
 
# 19 # Note: Chain identifiers seem OK
All ions seem to have a logical chain identifier, or there are no ions
present in the input file.
ERROR. File not found:
TAPEOUT.DAT
ERROR. File not found:
TAPEOUT.DAT
ERROR. File not found:
TAPEOUT.DAT
ERROR. File not found:
TAPEOUT.DAT
ERROR. File not found:
TAPEOUT.DAT
ERROR. File not found:
TAPEOUT.DAT
 
# 20 # 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. Preferred 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
 
# 21 # Note: Ramachandran plot
 
 
In the TeX file, a plot has been inserted here
 
Chain identifier: B
 
# 22 # Note: Ramachandran plot
 
 
In the TeX file, a plot has been inserted here
 
Chain identifier: C
 
# 23 # Note: Ramachandran plot
 
 
In the TeX file, a plot has been inserted here
 
Chain identifier: D
 
# 24 # Note: Ramachandran plot
 
 
In the TeX file, a plot has been inserted here
 
Chain identifier: E
 
# 25 # Note: Ramachandran plot
 
 
In the TeX file, a plot has been inserted here
 
Chain identifier: F
 
# 26 # 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 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 SQRPTLSEDVLTDNRSQFVIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSIRIDGVLHEF
(   4)-(  63)
                     70        80        90       100       110       120
                      |         |         |         |         |         |
   61 -  120 TTVPGVKEDVTEIILNLKSLVVSSEEDEPVTMYLRKQGPGEVTAGDIVPPAGVTVHNPGM
(  64)-( 123)
                    130       140       150       160       170       180
                      |         |         |         |         |         |
  121 -  180 HIATLNDKGKLEVELVVERGRGYVPAVQNRASGAEIGRIPVDSIYSPVLKVTYKVDATRR
( 124)-( 186)
                    190       200       210
                      |         |         |
  181 -  217 TDFDKLILDVETKNSISPRDALASAGKTLVELFGLAR
( 187)-( 223)
             220       230       240       250       260       270
               |         |         |         |         |         |
  218 -  277 MLISQRPTLSEDVLTDNRSQFVIEPLEPGFGYTLGNSLRRTLLSSIPGAAVTSIRIDGVL
(   1)-(  60)
             280       290       300       310       320       330
               |         |         |         |         |         |
  278 -  337 HEFTTVPGVKEDVTEIILNLKSLVVSSEEDEPVTMYLRKQGPGEVTAGDIVPPAGVTVHN
(  61)-( 120)
             340       350       360       370       380       390
               |         |         |         |         |         |
  338 -  397 PGMHIATLNDKGKLEVELVVERGRGYVPAVQGAEIGRIPVDSIYSPVLKVTYKVDATRVR
( 121)-( 186)
             400       410       420       430       440
               |         |         |         |         |
  398 -  447 TDFDKLILDVETKNSISPRDALASAGKTLVELFGLARELNVEAEGIEIGP
( 187)-( 236)
             450       460       470       480       490       500
               |         |         |         |         |         |
  448 -  507 SSNNSVPGAPNRVSFAKLREPLEVPGLLDVQTDSFEWLIGSPRWRESAAERNPVGGLEEV
(  21)-(  83)
             510       520       530       540       550       560
               |         |         |         |         |         |
  508 -  567 LYELSPIEDFSGSMSLSFSDPRFDDVKAPVDECKDKDMTYAAPLFVTAEFINNNTGEIKS
(  84)-( 143)
             570       580       590       600       610       620
               |         |         |         |         |         |
  568 -  627 QTVFMGDFPMMTEKGTFIINGTERVVVSQLVRSPGVYFDETIDKSTDKTLHSVKVIPSRG
( 144)-( 203)
             630       640       650       660       670       680
               |         |         |         |         |         |
  628 -  687 AWLEFDVDKRDTVGVRIDRKRRQPVTVLLKALGWTSEQIVERFGFSEIMRSTLEKDNTVG
( 204)-( 263)
             690       700       710       720       730       740
               |         |         |         |         |         |
  688 -  747 TDEALLDIYRKLRPGEPPTKESAQTLLENLFFKEKRYDLARVGRYKVNKKLGLHVGEPIT
( 264)-( 323)
             750       760       770       780       790       800
               |         |         |         |         |         |
  748 -  807 SSTLTEEDVVATIEYLVRLHEGQTTMTVPGGVEVPVETDDIDHFGNRRLRTVGELIQNQI
( 324)-( 383)
             810       820       830       840       850       860
               |         |         |         |         |         |
  808 -  867 RVGMSRMERVVRERMTTQDVEAITPQTLINIRPVVAAIKEFFGTSQLSQFMDQNNPLSGL
( 384)-( 443)
             870       880       890       900       910       920
               |         |         |         |         |         |
  868 -  927 THKRRLSALGPGGLSRERAGLEVRDVHPSHYGRMCPIETPEGPNIGLIGSLSVYARVNPF
( 444)-( 503)
             930       940       950       960       970       980
               |         |         |         |         |         |
  928 -  987 GFIETPYRKVVDGVVSDEIVYLTADEEDRHVVAQANSPIDADGRFVEPRVLVRRKAGEVE
( 504)-( 563)
             990      1000      1010      1020      1030      1040
               |         |         |         |         |         |
  988 - 1047 YVPSSEVDYMDVSPRQMVSVATAMIPFLEHDDANRALMGANMQRQAVPLVRSEAPLVGTG
( 564)-( 623)
            1050      1060      1070      1080      1090      1100
               |         |         |         |         |         |
 1048 - 1107 MELRAAIDAGDVVVAEESGVIEEVSADYITVMHDNGTRRTYRMRKFARSNHGTCANQCPI
( 624)-( 683)
            1110      1120      1130      1140      1150      1160
               |         |         |         |         |         |
 1108 - 1167 VDAGDRVEAGQVIADGPCTDDGEMALGKNLLVAIMPWEGHNYEDAIILSNRLVEEDVLTS
( 684)-( 743)
            1170      1180      1190      1200      1210      1220
               |         |         |         |         |         |
 1168 - 1227 IHIEEHEIDARDTKLGAEEITRDIPNISDEVLADLDERGIVRIGAEVRDGDILVGKVTPK
( 744)-( 803)
            1230      1240      1250      1260      1270      1280
               |         |         |         |         |         |
 1228 - 1287 GETELTPEERLLRAIFGEKAREVRDTSLKVPHGESGKVIGIRVFSREDEDELPAGVNELV
( 804)-( 863)
            1290      1300      1310      1320      1330      1340
               |         |         |         |         |         |
 1288 - 1347 RVYVAQKRKISDGDKLAGRHGNKGVIGKILPVEDMPFLADGTPVDIILNTHGVPRRMNIG
( 864)-( 923)
            1350      1360      1370      1380      1390      1400
               |         |         |         |         |         |
 1348 - 1407 QILETHLGWCAHSGWKVDAAKGVPDWAARLPDELLEAQPNAIVSTPVFDGAQEAELQGLL
( 924)-( 983)
            1410      1420      1430      1440      1450      1460
               |         |         |         |         |         |
 1408 - 1467 SCTLPNRDGDVLVDADGKAMLFDGRSGEPFPYPVTVGYMYIMKLHHLVDDKIHARSTGPY
( 984)-(1043)
            1470      1480      1490      1500      1510      1520
               |         |         |         |         |         |
 1468 - 1527 SMITQQPLGGKAQFGGQRFGEMECWAMQAYGAAYTLQELLTIKSDDTVGRVKVYEAIVKG
(1044)-(1103)
            1530      1540      1550      1560      1570      1580
               |         |         |         |         |         |
 1528 - 1582 ENIPEPGIPESFKVLLKELQSLCLNVEVLSSDGAAIELREGEDEDLERAAANLGI
(1104)-(1158)
                 1590      1600      1610      1620      1630      1640
                    |         |         |         |         |         |
 1583 - 1642 LDVNFFDELRIGLATAEDIRQWSYGEVKKPETINYRTLKPEKDGLFCEKIFGPTRDWECY
(   2)-(  61)
                 1650      1660      1670      1680      1690      1700
                    |         |         |         |         |         |
 1643 - 1702 CGKYKRVRFKGIICERCGVEVTRAKVRRERMGHIELAAPVTHIWYFKGVPSRLGYLLDLA
(  62)-( 121)
                 1710      1720      1730      1740      1750      1760
                    |         |         |         |         |         |
 1703 - 1762 PKDLEKIIYFAAYVITSVDEEMRHNELSTLEAEMAVERKAVEDQRDGELEARAQKLEADL
( 122)-( 181)
                 1770      1780      1790      1800      1810      1820
                    |         |         |         |         |         |
 1763 - 1822 AELEAEGAKADARRKVRDGGEREMRQIRDRAQRELDRLEDIWSTFTKLAPKQLIVDENLY
( 182)-( 241)
                 1830      1840      1850      1860      1870      1880
                    |         |         |         |         |         |
 1823 - 1882 RELVDRYGEYFTGAMGAESIQKLIENFDIDAEAESLRDVIRNGKGQKKLRALKRLKVVAA
( 242)-( 301)
                 1890      1900      1910      1920      1930      1940
                    |         |         |         |         |         |
 1883 - 1942 FQQSGNSPMGMVLDAVPVIPPELRPMVQLDGGRFATSDLNDLYRRVINRNNRLKRLIDLG
( 302)-( 361)
                 1950      1960      1970      1980      1990      2000
                    |         |         |         |         |         |
 1943 - 2002 APEIIVNNEKRMLQESVDALFDNGRRGRPVTGPGNRPLKSLSDLLKGKQGRFRQNLLGKR
( 362)-( 421)
                 2010      2020      2030      2040      2050      2060
                    |         |         |         |         |         |
 2003 - 2062 VDYSGRSVIVVGPQLKLHQCGLPKLMALELFKPFVMKRLVDLNHAQNIKSAKRMVERQRP
( 422)-( 481)
                 2070      2080      2090      2100      2110      2120
                    |         |         |         |         |         |
 2063 - 2122 QVWDVLEEVIAEHPVLLNRAPTLHRLGIQAFEPMLVEGKAIQLHPLVCEAFNADFDGDQM
( 482)-( 541)
                 2130      2140      2150      2160      2170      2180
                    |         |         |         |         |         |
 2123 - 2182 AVHLPLSAEAQAEARILMLSSNNILSPASGRPLAMPRLDMVTGLYYLTTEVPGDTGEYQP
( 542)-( 601)
                 2190      2200      2210      2220      2230      2240
                    |         |         |         |         |         |
 2183 - 2242 ASGDHPETGVYSSPAEAIMAADRGVLSVRAKIKVRLTQLRPPVEIEAELFGHSGWQPGDA
( 602)-( 661)
                 2250      2260      2270      2280      2290      2300
                    |         |         |         |         |         |
 2243 - 2302 WMAETTLGRVMFNELLPLGYPFVNKQMHKKVQAAIINDLAERYPMIVVAQTVDKLKDAGF
( 662)-( 721)
                 2310      2320      2330      2340      2350      2360
                    |         |         |         |         |         |
 2303 - 2362 YWATRSGVTVSMADVLVPPRKKEILDHYEERADKVEKQFQRGALNHDERNEALVEIWKEA
( 722)-( 781)
                 2370      2380      2390      2400      2410      2420
                    |         |         |         |         |         |
 2363 - 2422 TDEVGQALREHYPDDNPIITIVDSGATGNFTQTRTLAGMKGLVTNPKGEFIPRPVKSSFR
( 782)-( 841)
                 2430      2440      2450      2460      2470      2480
                    |         |         |         |         |         |
 2423 - 2482 EGLTVLEYFINTHGARKGLADTALRTADSGYLTRRLVDVSQDVIVREHDCQTERGIVVEL
( 842)-( 901)
                 2490      2500      2510      2520      2530      2540
                    |         |         |         |         |         |
 2483 - 2542 ADGTLIRDPYIETSAYARTLGTDAVDEAGNVIVERGQDLGDPEIDALLAAGITQVKVRSV
( 902)-( 965)
                 2550      2560      2570      2580      2590      2600
                    |         |         |         |         |         |
 2543 - 2602 LTCATSTGVCATCYGRSMATGKLVDIGEAVGIVAAQSIGEPGTQLTMTGGLPRVQELFEA
( 966)-(1037)
                 2610      2620      2630      2640      2650      2660
                    |         |         |         |         |         |
 2603 - 2662 RVPRGKAPIADVTGRVRLEDGERFYKITIVPDDGGEEVVYDKISKRQRLRVFKHEDGSER
(1038)-(1097)
                 2670      2680      2690      2700      2710      2720
                    |         |         |         |         |         |
 2663 - 2722 VLSDGDHVEVGQQLMEGSADPHEVLRVQGPREVQIHLVREVQEVYRAQGVSIHDKHIEVI
(1098)-(1157)
                 2730      2740      2750      2760      2770      2780
                    |         |         |         |         |         |
 2723 - 2782 VRQMLRRVTIIDSGSTEFLPGSLIDRAEFEAENRRVVAAGRPVLMGITKASLATDSWLSA
(1158)-(1223)
                 2790      2800      2810      2820      2830      2840
                    |         |         |         |         |         |
 2783 - 2840 ASFQETTRVLTDAAINCRSDKLNGLKENVIIGKLIPAGTGINRYRNIAVQPTEEARAA
(1224)-(1281)
                   2850      2860      2870      2880      2890      2900
                      |         |         |         |         |         |
 2841 - 2900 SGGYDTPLGITNPPIDELLDRVSSKYALVIYAAKRARQINDYYNYVGPLVEPGLQEKPLS
(  25)-(  92)
                   2910
                      |
 2901 - 2915 IALREIHADLLEHTE
(  93)-( 107)
              2920      2930      2940      2950      2960      2970
                 |         |         |         |         |         |
 2916 - 2975 TDEELTARFERDAIPLLDQLYGGALRMTRNPADAEDLLQETMVKAYAGFRSFRHGTNLKA
(  21)-(  80)
              2980      2990      3000      3010      3020      3030
                 |         |         |         |         |         |
 2976 - 3035 WLYRILTNTYINSYRKKQRQPAEYPTEQITDWQLASNAEHSSTGLRSAEVEALEALPDTE
(  81)-( 140)
              3040      3050      3060      3070      3080      3090
                 |         |         |         |         |         |
 3036 - 3097 IKEALQALPEEFRMAVYYADVEGFPYKEIAEIMDTPIGTVMSRLHRGRRQLRGLLADVARDR
( 141)-( 202)
 
 
 3096 - 3097 DR
( 201)-( 202)
 
 
 
 
# 27 # Note: No rounded coordinates detected
No significant rounding of atom coordinates has been detected.
 
# 28 # Note: No artificial side chains detected
No artificial side-chain positions characterized by chi-1=0.0 or chi-1=180.0
have been detected.
 
# 29 # 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 elementary building
blocks (amino acids, nucleotides). Even the C-terminal oxygens are treated
separately.
 
# 30 # Warning: B-factors outside the range 0.0 - 100.0
In principle, B-factors can have a very wide range of values, but in
practice, B-factors should not be zero while B-factors above 100.0
are a good indicator that the location of that atom is meaningless. Be
aware that the cutoff at 100.0 is arbitrary. 'High' indicates that atoms
with a B-factor > 100.0 were observed; 'Zero' indicates that atoms with
a B-factor of zero were observed.
 
    1 SER  (   4-) A  -   High
    2 GLN  (   5-) A  -   High
    3 ARG  (   6-) A  -   High
    4 PRO  (   7-) A  -   High
    7 SER  (  10-) A  -   High
    8 GLU  (  11-) A  -   High
    9 ASP  (  12-) A  -   High
   13 ASP  (  16-) A  -   High
   14 ASN  (  17-) A  -   High
   21 GLU  (  24-) A  -   High
   22 PRO  (  25-) A  -   High
   24 GLU  (  27-) A  -   High
   25 PRO  (  28-) A  -   High
   26 GLY  (  29-) A  -   High
   27 PHE  (  30-) A  -   High
And so on for a total of  1278 lines.
 
# 31 # Note: C-terminus capping
The residues listed in the table below are either C-terminal or pseudo
C-terminal (i.e. last residue before a missing residue).
In X-ray the coordinates must be located in density. Mobility or disorder
sometimes cause this density to be so poor that the positions of the atoms
cannot be determined. Crystallographers tend to leave out the atoms in such
cases. In many cases the N- or C-terminal residues are too disordered to see.
In case of the N-terminus, you can often see from the residue numbers if
there are missing residues; at the C-terminus this is impossible. Therefore,
often the position of the backbone nitrogen of the first residue missing
at the C-terminal end is calculated and added to indicate that there
are missing residues. As a single N causes validation trouble, we remove
these single-N-residues before doing the validation. If this happened,
the label -N is added to the pseudo C-terminus. Other labels can be +X
in case something weird is bound to the backbone C, or +OXT if a spurious
OXT atom is found. -OXT indicates that an expected OXT is missing. 'Swap'
means that the O' and O'' (O and OXT in PDB files) have been swapped in
terms of nomenclature. 'Bad' means that something bad happened that WHAT IF
does not understand. In such cases you might get three residue numbers in
square brackets; one of those might be what WHAT IF had expected to find,
but then it also might not). In case of chain breaks the number of missing
residues is listen in round brackets. OK means what it suggests...
 
Be aware that we cannot easily see the difference between these errors and
errors in the chain and residue numbering schemes. So do not blindly trust
the table below. If you get weird errors at, or near, the left-over
incomplete C-terminal residue, please check by hand if a missing Oxt or
a removed single N is the cause. Also, many peptidic ligands get the same
chain identifier as the larger protein they are bound to. In such cases there
are more than one C-termini and OXTs with the same ID. WHAT IF gives some
random warnings about these cases. So, don't take everything at face value,
but think for yourself.
 
  179 ARG  ( 182-) A  -        OK (3)
  217 ARG  ( 223-) A  -        OK
  368 GLN  ( 151-) B  -        OK (4)
  396 VAL  ( 183-) B  -        OK (2)
  447 PRO  ( 236-) B  -        OK
  498 ARG  (  71-) C  -        OK (3)
  824 THR  ( 400-) C  -        OK
  882 SER  ( 458-) C  -        OK
  884 GLU  ( 460-) C  -        OK
 1302 LYS  ( 878-) C  -        OK
 1582 ILE  (1158-) C  -        OK
 1967 ARG  ( 386-) D  -        OK
 1968 ARG  ( 387-) D  -        OK
 2483 ALA  ( 902-) D  -        OK (4)
 2589 MET  (1012-) D  -        OK (12)
 2759 VAL  (1194-) D  -        OK (6)
 2840 ALA  (1281-) D  -        OK
 2884 ASN  (  68-) E  -        OK (8)
 2915 GLU  ( 107-) E  -        OK
 3097 ARG  ( 202-) F  -        OK
 
# 32 # Note: Weights administratively correct
All atomic occupancy factors ('weights') fall in the 0.0--1.0 range, which
makes them administratively correct.
 
# 33 # 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 CHECK'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.
 
# 34 # Warning: Occupancy atoms do not add up to 1.0.
In principle, the occupancy of all alternates of one atom should add up till
1.0. A valid exception is the missing atom (i.e. an atom not seen in the
electron density) that is allowed to have a 0.0 occupancy. Sometimes this
even happens when there are no alternate atoms given...
 
Atoms want to move. That is the direct result of the second law of
thermodynamics, in a somewhat weird way of thinking. Any way, many atoms
seem to have more than one position where they like to sit, and they jump
between them. The population difference between those sites (which is related
to their energy differences) is seen in the occupancy factors. As also for
atoms it is 'to be or not to be', these occupancies should add up to 1.0.
Obviously, it is possible that they add up to a number less than 1.0, in
cases where there are yet more, but undetected' rotamers/positions in play,
but also in those cases a warning is in place as the information shown
in the PDB file is less certain than it could have been. The residues
listed below contain atoms that have an occupancy greater than zero, but
their alternates do not add up to one. 'Strange' is added as a comment when
we believe that the structure shows no obvious reasons why this residue
should have a reduced occupancy.
 
WARNING. Presently WHAT CHECK only deals with a maximum of two alternate
positions. A small number of atoms in the PDB has three alternates. In
those cases the warning given here should obviously be neglected!
In a next release we will try to fix this.
 
 3005 THR  ( 110-) F  -   0.77
 3007 TRP  ( 112-) F  -   0.74
 3008 GLN  ( 113-) F  -   0.95
 3009 LEU  ( 114-) F  -   0.61
 3010 ALA  ( 115-) F  -   0.86
 3011 SER  ( 116-) F  -   0.73
 3012 ASN  ( 117-) F  -   0.64
 3013 ALA  ( 118-) F  -   0.75
 3014 GLU  ( 119-) F  -   0.78
 3015 HIS  ( 120-) F  -   0.71
 3016 SER  ( 121-) F  -   0.87
 3017 SER  ( 122-) F  -   0.75
 3019 GLY  ( 124-) F  -   0.65
 3107 DGUA (   3-) G  -   0.41
 3109 DGUA (   5-) G  -   0.89
 3115 DTHY (  11-) G  -   0.87
 3138 DADE (  11-) H  -   0.79
 3147 DTHY (  20-) H  -   0.92
 
# 35 # Warning: What type of B-factor?
WHAT CHECK does not yet know well how to cope with B-factors in case TLS has
been used. It simply assumes that the B-factor listed on the ATOM and HETATM
cards are the total B-factors. When TLS refinement is used that assumption
sometimes is not correct. The header of the PDB file states that TLS groups
were used. So, if WHAT CHECK complains about your  B-factors, while you think
that they are OK, then check for TLS related B-factor problems first.
 
Number of TLS groups mentione in PDB file header: 0
 
Temperature not mentioned in PDB file. This most likely means
that the temperature record is absent.
Room temperature assumed
 
# 36 # Note: Number of buried atoms with low B-factor is OK
For protein structures determined at room temperature, no more than about 1
percent of the B factors of buried atoms is below 5.0. In liquid
nitrogen this percentage is allowed to be higher, of course.
 
Percentage of buried atoms with B less than 5 :   0.00
 
# 37 # Note: B-factor distribution normal
The distribution of B-factors within residues is within expected ranges.
A value over 1.5 here would mean that the B-factors show signs of
over-refinement.
 
RMS Z-score :  0.716 over   14487 bonds
Average difference in B over a bond :    2.78
RMS difference in B over a bond :    3.65
ERROR. File not found:
TAPEOUT.DAT
ERROR. File not found:
TAPEOUT.DAT
ERROR. File not found:
TAPEOUT.DAT
ERROR. File not found:
TAPEOUT.DAT
ERROR. File not found:
TAPEOUT.DAT
ERROR. File not found:
TAPEOUT.DAT
ERROR. File not found:
TAPEOUT.DAT
ERROR. File not found:
TAPEOUT.DAT
ERROR. File not found:
TAPEOUT.DAT
ERROR. File not found:
TAPEOUT.DAT
ERROR. File not found:
TAPEOUT.DAT
ERROR. File not found:
TAPEOUT.DAT
ERROR. File not found:
TAPEOUT.DAT
ERROR. File not found:
TAPEOUT.DAT
ERROR. File not found:
TAPEOUT.DAT
ERROR. File not found:
TAPEOUT.DAT
ERROR. File not found:
TAPEOUT.DAT
ERROR. File not found:
TAPEOUT.DAT
 
# 38 # Note: B-factor plot
The average atomic B-factor per residue is plotted as function of the residue
number.
 
In the TeX file, a plot has been inserted here
 
Chain identifier: A
 
# 39 # Note: B-factor plot
 
 
In the TeX file, a plot has been inserted here
 
Chain identifier: B
 
# 40 # Note: B-factor plot
 
 
In the TeX file, a plot has been inserted here
 
Chain identifier: C
 
# 41 # Note: B-factor plot
 
 
In the TeX file, a plot has been inserted here
 
Chain identifier: D
 
# 42 # Note: B-factor plot
 
 
In the TeX file, a plot has been inserted here
 
Chain identifier: E
 
# 43 # Note: B-factor plot
 
 
In the TeX file, a plot has been inserted here
 
Chain identifier: F
 
# 44 # 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 delta2 and delta1 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 delta1 and delta2 and the
other uses C delta2 and delta1, 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.
 
# 45 # Note: Valine nomenclature OK
No errors were detected in valine nomenclature.
 
# 46 # Note: Threonine nomenclature OK
No errors were detected in threonine nomenclature.
 
# 47 # Note: Isoleucine nomenclature OK
No errors were detected in isoleucine nomenclature.
 
# 48 # Note: Leucine nomenclature OK
No errors were detected in leucine nomenclature.
 
# 49 # Note: Arginine nomenclature OK
No errors were detected in arginine nomenclature.
 
# 50 # Note: Tyrosine torsion conventions OK
No errors were detected in tyrosine torsion angle conventions.
 
# 51 # Note: Phenylalanine torsion conventions OK
No errors were detected in phenylalanine torsion angle conventions.
 
# 52 # Note: Aspartic acid torsion conventions OK
No errors were detected in aspartic acid torsion angle conventions.
 
# 53 # Note: Glutamic acid torsion conventions OK
No errors were detected in glutamic acid torsion angle conventions.
 
# 54 # Note: Phosphate group names OK in DNA/RNA
No errors were detected in nucleic acid phosphate group naming conventions
(or this structure contains no nucleic acids).
 
# 55 # 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.
 
# 56 # Note: No decreasing residue numbers
All residue numbers are strictly increasing within each chain.
 
# 57 # Warning: Unusual bond lengths
The bond lengths listed in the table below were found to deviate more than 4
sigma from standard bond lengths (both standard values and sigmas for amino
acid residues have been taken from Engh and Huber [REF], for DNA they were
taken from Parkinson et al [REF]). In the table below for each unusual bond
the bond length and the number of standard deviations it differs from the
normal value is given.
 
Atom names starting with "-" belong to the previous residue in the chain. If
the second atom name is "-SG*", the disulphide bridge has a deviating length.
 
  159 ILE  ( 162-) A  -    CG1  CD1   1.69    4.6
  271 ILE  (  54-) B  -    CG1  CD1   1.20   -8.1
  586 ILE  ( 162-) C  -    CG1  CD1   1.35   -4.1
  629 TRP  ( 205-) C  -    CA   CB    1.70    8.3
  630 LEU  ( 206-) C  -    CA   CB    1.63    5.2
  630 LEU  ( 206-) C  -    CB   CG    1.69    7.8
  631 GLU  ( 207-) C  -    N   -C     1.43    5.1
  632 PHE  ( 208-) C  -    CA   CB    1.62    4.4
  666 ILE  ( 242-) C  -    CG1  CD1   1.33   -4.7
  788 ILE  ( 364-) C  -    CA   CB    1.62    4.3
  788 ILE  ( 364-) C  -    CG1  CD1   1.76    6.4
  807 ILE  ( 383-) C  -    CG1  CD1   1.33   -4.8
  824 THR  ( 400-) C  -    CA   CB    1.63    4.8
  845 ILE  ( 421-) C  -    CG1  CD1   1.35   -4.1
  884 GLU  ( 460-) C  -    CA   CB    1.71    8.8
And so on for a total of    44 lines.
 
# 58 # 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: 0.568
 RMS-deviation in bond distances: 0.014
 
# 59 # Note: No bond length directionality
Comparison of bond distances with Engh and Huber [REF] standard values for
protein residues and Parkinson et al [REF] values for DNA/RNA does not show
significant systematic deviations.
 
# 60 # 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.
 
   59 GLU  (  62-) A  -    N    CA   CB  103.58   -4.1
   69 ASP  (  72-) A  -    CA   CB   CG  119.81    7.2
   87 ASP  (  90-) A  -    CA   CB   CG  118.02    5.4
  184 ASP  ( 190-) A  -    CA   CB   CG  118.06    5.5
  189 ASP  ( 195-) A  -    CA   CB   CG  117.42    4.8
  289 ASP  (  72-) B  -    CA   CB   CG  119.65    7.0
  293 ILE  (  76-) B  -    N    CA   CB  122.52    7.1
  304 SER  (  87-) B  -    N    CA   CB  117.74    4.3
  304 SER  (  87-) B  -    C    CA   CB  100.17   -5.2
  307 ASP  (  90-) B  -    CA   CB   CG  117.66    5.1
  326 ASP  ( 109-) B  -    CA   CB   CG  117.56    5.0
  346 ASN  ( 129-) B  -    CA   CB   CG  117.46    4.9
  406 ASP  ( 195-) B  -    CA   CB   CG  117.44    4.8
  437 ASN  ( 226-) B  -    CA   CB   CG  116.80    4.2
  628 ALA  ( 204-) C  -    N    CA   C   123.09    4.2
And so on for a total of   191 lines.
 
# 61 # 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 near 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: 0.893
 RMS-deviation in bond angles: 1.683
 
# 62 # Note: Residue hand check OK
No atoms are observed that have the wrong handedness. Be aware, though, that
WHAT CHECK might have corrected the handedness of some atoms already. The
handedness has not been corrected for any case where the problem is worse
than just an administrative discomfort.
 
# 63 # Warning: Chirality deviations detected
The atoms listed in the table below have an improper dihedral value
that is deviating from expected values. As the improper dihedral values
are all getting very close to ideal values in recent X-ray structures,
and as we actually do not know how big the spread around these values
should be, this check only warns for 6 sigma deviations.
 
Improper dihedrals are a measure of the chirality/planarity of the structure
at a specific atom. Values around -35 or +35 are expected for chiral atoms,
and values around 0 for planar atoms. Planar side chains are left out of the
calculations, these are better handled by the planarity checks.
 
Three numbers are given for each atom in the table. The first is the Z-score
for the improper dihedral. The second number is the measured improper
dihedral. The third number is the expected value for this atom type. A final
column contains an extra warning if the chirality for an atom is opposite
to the expected value.
 
  293 ILE  (  76-) B  -    CA   -35.1   -21.24    33.22 Wrong hand
  304 SER  (  87-) B  -    CA   -38.9   -33.75    34.26 Wrong hand
  630 LEU  ( 206-) C  -    CA     7.9    45.54    34.17
  789 ASP  ( 365-) C  -    CA   -29.1   -17.16    33.79 Wrong hand
  792 GLY  ( 368-) C  -    C      6.3     7.90     0.11
  883 ARG  ( 459-) C  -    C     -8.5   -13.06     0.16
  886 ALA  ( 462-) C  -    CA    -7.1    25.84    34.06
  887 GLY  ( 463-) C  -    C     -7.4    -8.97     0.11
  888 LEU  ( 464-) C  -    CA   -46.0   -32.09    34.17 Wrong hand
  911 ASN  ( 487-) C  -    C     -9.1   -14.20     0.23
  912 ILE  ( 488-) C  -    CA     9.0    47.19    33.22
  993 GLU  ( 569-) C  -    CA   -35.2   -20.34    33.90 Wrong hand
 1034 VAL  ( 610-) C  -    CA    10.8    48.47    33.31
 1035 PRO  ( 611-) C  -    N     -7.6   -30.29    -2.64
 1035 PRO  ( 611-) C  -    CA    12.2    54.14    38.15
 1036 LEU  ( 612-) C  -    CA    14.8    55.55    34.17
 1037 VAL  ( 613-) C  -    C     -9.0   -11.26     0.11
 1567 GLU  (1143-) C  -    CA   -40.9   -29.04    33.90 Wrong hand
 1691 VAL  ( 110-) D  -    CA   -48.7   -34.86    33.31 Wrong hand
 1694 ARG  ( 113-) D  -    CA    10.1    49.80    33.93
The average deviation= 0.848
 
# 64 # 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 : 0.813
 
# 65 # Error: Tau angle problems
The side chains of the residues listed in the table below contain a tau
angle (N-C-alpha-C) that was found to deviate from te expected value by
more than 4.0 times the expected standard deviation. The number in the
table is the number of standard deviations this value deviates from
the expected value.
 
 1034 VAL  ( 610-) C  -  15.50
 1036 LEU  ( 612-) C  -  12.93
  888 LEU  ( 464-) C  -  12.79
 1035 PRO  ( 611-) C  -   9.91
  887 GLY  ( 463-) C  -   8.63
 1037 VAL  ( 613-) C  -   8.05
  886 ALA  ( 462-) C  -   6.92
 1694 ARG  ( 113-) D  -   6.91
  912 ILE  ( 488-) C  -   5.70
 2943 THR  (  48-) F  -   5.37
  791 PHE  ( 367-) C  -   4.99
  826 ASP  ( 402-) C  -   4.90
  628 ALA  ( 204-) C  -   4.85
 1691 VAL  ( 110-) D  -   4.74
 2946 PRO  (  51-) F  -   4.69
  737 LYS  ( 313-) C  -   4.53
  485 LEU  (  58-) C  -   4.43
  633 ASP  ( 209-) C  -   4.42
  913 GLY  ( 489-) C  -   4.37
 1303 LEU  ( 879-) C  -   4.25
 1301 ASP  ( 877-) C  -   4.19
 
# 66 # Note: Normal tau angle deviations
The RMS Z-score for the tau angles (N-C-alpha-C) in the structure falls
within the normal range 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 : 1.104
 
# 67 # Error: Side chain planarity problems
The side chains of the residues listed in the table below contain a planar
group that was found to deviate from planarity by more than 4.0 times the
expected value. For an amino acid residue that has a side chain with a
planar group, the RMS deviation of the atoms to a least squares plane was
determined. The number in the table is the number of standard deviations
this RMS value deviates from the expected value. Not knowing better yet, we
assume that planarity of the groups analyzed should be perfect.
 
 3048 ARG  ( 153-) F  -   5.63
  599 ARG  ( 175-) C  -   5.27
    3 ARG  (   6-) A  -   4.96
 1343 ARG  ( 919-) C  -   4.86
 2307 ARG  ( 726-) D  -   4.65
 1968 ARG  ( 387-) D  -   4.24
 2087 ARG  ( 506-) D  -   4.01
 
# 68 # 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.
 
# 69 # Note: Uncalibrated side chain planarity OK
All of the side chains of DNA/RNA residues (and groups in proteins that
contain a proton and are supposed to be planar) are planar within 0.10
Angstrom RMS (or no intact DNA/RNA was found...). Please be aware that
this check cannot be callibrated and that the cutoff of 0.10 Angstrom thus
is a wild guess.
 
# 70 # Error: Ramachandran Z-score very low
The score expressing how well the backbone conformations of all residues
correspond to the known allowed areas in the Ramachandran plot is very low.
 
 Ramachandran Z-score : -4.354
 
# 71 # Note: Ramachandran check
The list contains per-residue Z-scores describing how well each residue
fits into the allowed areas of the Ramachandran plot will not be printed
because WHAT CHECK found no reason to cry.
 
# 72 # 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 CHECK 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.
 
  281 THR  (  64-) B  -   -3.5
  653 THR  ( 229-) C  -   -3.3
   61 THR  (  64-) A  -   -3.2
  878 PRO  ( 454-) C  -   -3.1
 1035 PRO  ( 611-) C  -   -3.1
  788 ILE  ( 364-) C  -   -3.0
  976 ARG  ( 552-) C  -   -3.0
  975 PRO  ( 551-) C  -   -3.0
  372 ILE  ( 159-) B  -   -2.9
 1481 PHE  (1057-) C  -   -2.9
  888 LEU  ( 464-) C  -   -2.9
 2626 PHE  (1061-) D  -   -2.9
 2871 TYR  (  55-) E  -   -2.9
 3034 THR  ( 139-) F  -   -2.8
  413 ILE  ( 202-) B  -   -2.8
And so on for a total of   164 lines.
 
# 73 # 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 ARG  (   6-) A  - Omega to (next) Pro poor
   21 GLU  (  24-) A  - Omega to (next) Pro poor
   24 GLU  (  27-) A  - Omega to (next) Pro poor
   26 GLY  (  29-) A  - Poor phi/psi
   41 SER  (  44-) A  - omega poor
   43 ILE  (  46-) A  - Omega to (next) Pro poor
   53 ILE  (  56-) A  - omega poor
   55 GLY  (  58-) A  - omega poor
   59 GLU  (  62-) A  - omega poor
   62 THR  (  65-) A  - omega poor
   63 VAL  (  66-) A  - Omega to (next) Pro poor
   65 GLY  (  68-) A  - Poor phi/psi
   85 GLU  (  88-) A  - omega poor
   87 ASP  (  90-) A  - Poor phi/psi, omega poor
   88 GLU  (  91-) A  - Omega to (next) Pro poor
And so on for a total of   565 lines.
 
# 74 # Error: Chi-1/chi-2 rotamer problems
List of residues with a poor chi-1/chi-2 combination. Be aware that for this
validation option the individual scores are far less important than the
overall score that is given below the table.
 
    6 LEU  (   9-) A  -    -1.32
   11 LEU  (  14-) A  -    -1.31
   57 LEU  (  60-) A  -    -1.30
   94 LEU  (  97-) A  -    -1.32
  135 LEU  ( 138-) A  -    -1.31
  188 LEU  ( 194-) A  -    -1.32
  202 LEU  ( 208-) A  -    -1.32
  212 LEU  ( 218-) A  -    -1.32
  219 LEU  (   2-) B  -    -1.31
  226 LEU  (   9-) B  -    -1.32
  231 LEU  (  14-) B  -    -1.31
  251 LEU  (  34-) B  -    -1.31
  260 LEU  (  43-) B  -    -1.32
  277 LEU  (  60-) B  -    -1.32
  295 LEU  (  78-) B  -    -1.31
And so on for a total of  1609 lines.
 
# 75 # Error: chi-1/chi-2 angle correlation Z-score very low
The score expressing how well the chi-1/chi-2 angles of all residues
correspond to the populated areas in the database is
very low.
 
 chi-1/chi-2 correlation Z-score : -5.789
 
# 76 # 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.
 
 1105 CYS  ( 681-) C  -   0.35
 2008 ARG  ( 427-) D  -   0.35
 2781 SER  (1222-) D  -   0.35
 3077 SER  ( 182-) F  -   0.35
  173 TYR  ( 176-) A  -   0.35
  204 SER  ( 210-) A  -   0.36
 2451 SER  ( 870-) D  -   0.36
 2744 SER  (1179-) D  -   0.37
   34 SER  (  37-) A  -   0.38
  421 SER  ( 210-) B  -   0.38
  481 SER  (  54-) C  -   0.38
 1070 GLU  ( 646-) C  -   0.38
 1204 GLU  ( 780-) C  -   0.38
 1167 SER  ( 743-) C  -   0.39
 1730 SER  ( 149-) D  -   0.39
 2773 SER  (1214-) D  -   0.39
 
# 77 # 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,
especially if a regular DSSP secondary structure (H or S for helix or strand,
respectively) is indicated!
 
   21 GLU  (  24-) A  -       0
   86 GLU  (  89-) A  -       0
   97 GLN  ( 100-) A  -       0
  193 LYS  ( 199-) A  -       0
  194 ASN  ( 200-) A  -       0
  224 PRO  (   7-) B  -       0
  241 GLU  (  24-) B  -       0
  293 ILE  (  76-) B  -       0
  304 SER  (  87-) B  -       0
  307 ASP  (  90-) B  -       0
  372 ILE  ( 159-) B  -       0
  432 LEU  ( 221-) B  -       0
  433 ALA  ( 222-) B  -       0
  437 ASN  ( 226-) B  -       0
  439 GLU  ( 228-) B  -       0
And so on for a total of   194 lines.
 
# 78 # 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 : -0.867
 
# 79 # Warning: Omega angle restraints not strong enough
The omega angles for trans-peptide bonds in a structure is expected to give
a gaussian distribution with the average around +178 degrees, and a standard
deviation around 5.5. In the current structure the standard deviation of
this distribution is above 7.0, which indicates that the omega values have
been under-restrained.
 
Omega average and std. deviation= 178.940 9.098
 
# 80 # Warning: Unusual PRO puckering amplitudes
The proline residues listed in the table below have a puckering amplitude
that is outside of normal ranges. Puckering parameters were calculated by
the method of Cremer and Pople [REF]. Normal PRO rings have a puckering
amplitude Q between 0.20 and 0.45 Angstrom. If Q is lower than 0.20 Angstrom
for a PRO residue, this could indicate disorder between the two different
normal ring forms (with C-gamma below and above the ring, respectively). If
Q is higher than 0.45 Angstrom something could have gone wrong during the
refinement. 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]
 
 1035 PRO  ( 611-) C  -   0.65 HIGH
 
# 81 # 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].
 
  167 PRO  ( 170-) A  -  -63.4 envelop C-beta (-72 degrees)
  198 PRO  ( 204-) A  -  100.2 envelop C-beta (108 degrees)
  468 PRO  (  41-) C  -  -61.8 half-chair C-beta/C-alpha (-54 degrees)
  624 PRO  ( 200-) C  -  -62.5 half-chair C-beta/C-alpha (-54 degrees)
  895 PRO  ( 471-) C  -   99.3 envelop C-beta (108 degrees)
  910 PRO  ( 486-) C  -   39.8 envelop C-delta (36 degrees)
 1035 PRO  ( 611-) C  -   -5.7 envelop N (0 degrees)
 1692 PRO  ( 111-) D  -   30.1 envelop C-delta (36 degrees)
 
# 82 # 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 CHECK database with superposable C-alpha
coordinates, and some restraints 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!
 
  887 GLY  ( 463-) C  -  3.54   27
 1887 GLY  ( 306-) D  -  3.24   45
  702 GLY  ( 278-) C  -  2.81   43
 2607 GLY  (1042-) D  -  1.78   11
 2762 GLY  (1203-) D  -  1.68   44
 1045 GLY  ( 621-) C  -  1.66   16
 1510 LYS  (1086-) C  -  1.63   39
 2424 GLY  ( 843-) D  -  1.61   43
  612 SER  ( 188-) C  -  1.53   14
 1644 GLY  (  63-) D  -  1.52   80
 
# 83 # Warning: Possible peptide flips
For the residues listed in the table below, the backbone formed by the
residue mentioned and the one N-terminal of it show systematic deviations
from normality that are consistent with a peptide flip. This can either
be a 180 degree flip of the entire peptide plane or a trans to cis flip.
(Cis to trans flips cannot be detected yet). The type can be TT+, TC-,
or TC+:
TT+ indicates a 180 degree flip of the entire peptide plane.
TC- indicates a trans to cis conversion that requires a flip of the N atom.
TC+ indicates a trans to cis conversion that requires a flip of the O atom.
Note that the method will only work correctly for PDB files with full
isotropic B-factors.
 
   55 GLY  (  58-) A  - TT+   Highly likely
  194 ASN  ( 200-) A  - TT+   Highly likely
 1243 PHE  ( 819-) C  - TT+   Highly likely
 1829 TYR  ( 248-) D  - TT+   Highly likely
 2135 GLU  ( 554-) D  - TT+   Highly likely
 2499 ALA  ( 922-) D  - TT+   Highly likely
   14 ASN  (  17-) A  - TT+   Likely
   42 SER  (  45-) A  - TT+   Likely
   60 PHE  (  63-) A  - TT+   Likely
   87 ASP  (  90-) A  - TT+   Likely
  117 ASN  ( 120-) A  - TT+   Likely
  128 LYS  ( 131-) A  - TT+   Likely
  157 GLY  ( 160-) A  - TT+   Likely
  234 ASN  (  17-) B  - TT+   Likely
  251 LEU  (  34-) B  - TT+   Likely
And so on for a total of    92 lines.
 
# 84 # Error: Abnormally short interatomic distances
The pairs of atoms listed in the table below have an unusually short
distance; each bump is listed in only one direction,
 
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.
 
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
are not 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.
 
It seems likely that at least some of the reported bumps are caused by
administrative errors in the chain names. I.e. covalently bound atoms with
different non-blank chain-names are reported as bumps. In rare cases this is
not an error.
 
Bumps between atoms for which the sum of their occupancies is lower than one
are not reported. If the MODEL number does not exist (as is the case in most
X-ray files), a minus sign is printed instead.
 
  883 ARG  ( 459-) C  -    CG   <-->    884 GLU  ( 460-) C  -    CB   1.96    1.14  INTRA BF
  883 ARG  ( 459-) C  -    CG   <-->    884 GLU  ( 460-) C  -    CG   1.79    1.41  INTRA BF
 2941 ARG  (  46-) F  -    NH1  <-->   2943 THR  (  48-) F  -    CB   1.54    1.56  INTRA BF
 2941 ARG  (  46-) F  -    NH1  <-->   2943 THR  (  48-) F  -    CA   1.47    1.63  INTRA BF
  204 SER  ( 210-) A  -    O    <-->    441 GLU  ( 230-) B  -    CD   1.42    1.38  INTRA BF
  824 THR  ( 400-) C  -    C    <-->   3108 DTHY (   4-) G  -    C6   1.42    1.78  INTRA BF
  823 THR  ( 399-) C  -    O    <-->   3108 DTHY (   4-) G  -    C2   1.39    1.41  INTRA BF
  790 HIS  ( 366-) C  -    NE2  <-->    888 LEU  ( 464-) C  -    CG   1.37    1.73  INTRA BF
  517 PHE  (  93-) C  -    CD2  <-->    824 THR  ( 400-) C  -    N    1.35    1.75  INTRA BF
  823 THR  ( 399-) C  -    O    <-->   3108 DTHY (   4-) G  -    O2   1.35    0.90  INTRA BF
  884 GLU  ( 460-) C  -    C    <-->   3101 OURA (   7-) I  -    P    1.34    2.06  INTRA BF
  883 ARG  ( 459-) C  -    CB   <-->    884 GLU  ( 460-) C  -    CB   1.28    1.72  INTRA BF
  883 ARG  ( 459-) C  -    CB   <-->    884 GLU  ( 460-) C  -    CG   1.23    1.87  INTRA BF
  884 GLU  ( 460-) C  -    C    <-->   3101 OURA (   7-) I  -    C5'  1.23    1.97  INTRA BF
  883 ARG  ( 459-) C  -    CD   <-->    884 GLU  ( 460-) C  -    CD   1.22    1.98  INTRA BF
And so on for a total of  1126 lines.
 
# 85 # Note: Some notes regarding these bumps
The bumps have been binned in 5 categories ranging from 'please look at'
till 'must fix'. Additionally, the integrated sum of all bumps, the squared
sum of all bumps, and these latter two values normalized by the number of
contacts are listed too for comparison purposes between, for example, small
and large proteins.
 
Total bump value: 242.813
Total bump value per residue: 0.358
Total number of bumps: 1126
Total squared bump value: 125.526
Total number of bumps in the mildest bin: 818
Total number of bumps in the second bin: 185
Total number of bumps in the middle bin: 65
Total number of bumps in the fourth bin: 33
Total number of bumps in the worst bin: 25
 
# 86 # Note: Inside/outside distribution check
The following list contains per-residue Z-scores describing how well the
residue's observed accessibility fits the expected one. A positive Z-score
indicates "more exposure than usual", whereas a negative Z-score means
"more buried than usual". The absolute value of the Z-score must be used to
judge the quality. Today WHAT CHECK saw no reason to complain.
 
# 87 # 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 : 1.029
 
# 88 # 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
 
# 89 # Note: Inside/Outside RMS Z-score plot
 
 
In the TeX file, a plot has been inserted here
 
Chain identifier: B
 
# 90 # Note: Inside/Outside RMS Z-score plot
 
 
In the TeX file, a plot has been inserted here
 
Chain identifier: C
 
# 91 # Note: Inside/Outside RMS Z-score plot
 
 
In the TeX file, a plot has been inserted here
 
Chain identifier: D
 
# 92 # Note: Inside/Outside RMS Z-score plot
 
 
In the TeX file, a plot has been inserted here
 
Chain identifier: E
 
# 93 # Note: Inside/Outside RMS Z-score plot
 
 
In the TeX file, a plot has been inserted here
 
Chain identifier: F
 
# 94 # 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.
 
  466 ARG  (  39-) C  -  -7.88
 1376 ARG  ( 952-) C  -  -7.53
 1414 ARG  ( 990-) C  -  -7.45
 1658 ARG  (  77-) D  -  -7.36
 1566 ARG  (1142-) C  -  -7.32
 2476 ARG  ( 895-) D  -  -7.27
 2606 ARG  (1041-) D  -  -7.25
 2941 ARG  (  46-) F  -  -7.16
 2603 ARG  (1038-) D  -  -7.14
    2 GLN  (   5-) A  -  -7.13
  395 ARG  ( 182-) B  -  -7.11
  223 ARG  (   6-) B  -  -6.87
 1970 ARG  ( 389-) D  -  -6.66
 1038 ARG  ( 614-) C  -  -6.62
 2234 HIS  ( 653-) D  -  -6.61
And so on for a total of    86 lines.
 
# 95 # 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.
 
  444 GLU  ( 233-) B  -      446 --- GLY   235- (B ) -       -4.29
  788 ILE  ( 364-) C  -      791 --- PHE   367- (C ) -       -4.41
 1565 LEU  (1141-) C  -     1567 --- GLU  1143- (C ) -       -5.77
 2655 LYS  (1090-) D  -     2657 --- GLU  1092- (D ) -       -4.91
 2889 LEU  (  81-) E  -     2891 --- GLU    83- (E ) -       -5.09
 
# 96 # Note: Structural average packing environment OK
The structural average packing score is within normal ranges.
 
 
Average for range     1 - 3147 :  -0.668
 
# 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
 
# 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: B
 
# 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: C
 
# 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: D
 
# 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: E
 
# 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: F
 
# 103 # 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 packing 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.
 
 2082 ALA  ( 501-) D  -  -3.33
 2941 ARG  (  46-) F  -  -3.03
 1691 VAL  ( 110-) D  -  -2.90
  608 THR  ( 184-) C  -  -2.89
 1489 MET  (1065-) C  -  -2.88
 1680 ALA  (  99-) D  -  -2.87
  912 ILE  ( 488-) C  -  -2.83
 2940 LEU  (  45-) F  -  -2.75
 2083 PRO  ( 502-) D  -  -2.68
  623 ILE  ( 199-) C  -  -2.66
  887 GLY  ( 463-) C  -  -2.57
  888 LEU  ( 464-) C  -  -2.55
 1685 ILE  ( 104-) D  -  -2.51
 
# 104 # Warning: Abnormal packing Z-score for sequential residues
A stretch of at least four sequential residues with a 2nd generation packing
Z-score below -1.75 was found. This could indicate that these residues are
part of a strange loop or that the residues in this range are incomplete,
but it might also be an indication of misthreading.
 
The table below lists the first and last residue in each stretch found,
as well as the average residue Z-score of the series.
 
  885 ARG  ( 461-) C  -   ---   888 LEU  ( 464-) C  -      -1.88
 1340 VAL  ( 916-) C  -   ---  1343 ARG  ( 919-) C  -      -1.89
 1452 HIS  (1028-) C  -   ---  1455 VAL  (1031-) C  -      -1.95
 1477 GLY  (1053-) C  -   ---  1480 GLN  (1056-) C  -      -1.78
 2939 ALA  (  44-) F  -   ---  2942 MET  (  47-) F  -      -2.06
ERROR. File not found:
TAPEOUT.DAT
ERROR. File not found:
TAPEOUT.DAT
ERROR. File not found:
TAPEOUT.DAT
ERROR. File not found:
TAPEOUT.DAT
ERROR. File not found:
TAPEOUT.DAT
ERROR. File not found:
TAPEOUT.DAT
ERROR. File not found:
TAPEOUT.DAT
ERROR. File not found:
TAPEOUT.DAT
ERROR. File not found:
TAPEOUT.DAT
ERROR. File not found:
TAPEOUT.DAT
ERROR. File not found:
TAPEOUT.DAT
ERROR. File not found:
TAPEOUT.DAT
ERROR. File not found:
TAPEOUT.DAT
ERROR. File not found:
TAPEOUT.DAT
ERROR. File not found:
TAPEOUT.DAT
ERROR. File not found:
TAPEOUT.DAT
ERROR. File not found:
TAPEOUT.DAT
ERROR. File not found:
TAPEOUT.DAT
 
# 105 # 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
 
# 106 # Note: Second generation quality Z-score plot
 
 
In the TeX file, a plot has been inserted here
 
Chain identifier: B
 
# 107 # Note: Second generation quality Z-score plot
 
 
In the TeX file, a plot has been inserted here
 
Chain identifier: C
 
# 108 # Note: Second generation quality Z-score plot
 
 
In the TeX file, a plot has been inserted here
 
Chain identifier: D
 
# 109 # Note: Second generation quality Z-score plot
 
 
In the TeX file, a plot has been inserted here
 
Chain identifier: E
 
# 110 # Note: Second generation quality Z-score plot
 
 
In the TeX file, a plot has been inserted here
 
Chain identifier: F
 
# 111 # 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.
 
# 112 # Error: Water clusters without contacts with non-water atoms
The water molecules listed in the table below are part of water molecule
clusters that do not make contacts with non-waters. These water molecules are
part of clusters that have a distance at least 1 Angstrom larger than the
sum of the Van der Waals radii to the nearest non-solvent atom. Because
these kinds of water clusters usually are not observed with X-ray diffraction
their presence could indicate a refinement artifact. The number in brackets
is the identifier of the water molecule in the input file.
 
 3152 HOH  (2111 ) D  -    O
 3154 HOH  ( 103 ) H  -    O
 
# 113 # Note: No waters need moving
All water molecules are sufficiently close to the asymmetric unit given in
the input file.
 
# 114 # Error: Water molecules without hydrogen bonds
The water molecules listed in the table below do not form any hydrogen bonds,
neither with the protein or DNA/RNA, nor with other water molecules. This is
a strong indication of a refinement problem.
 
 3151 HOH  (1207 ) C  -    O
 3151 HOH  (1208 ) C  -    O
 3152 HOH  (2111 ) D  -    O
 3152 HOH  (2112 ) D  -    O
 3154 HOH  ( 103 ) H  -    O
 
# 115 # 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.
 
  222 GLN  (   5-) B  -
  341 HIS  ( 124-) B  -
  450 ASN  (  23-) C  -
  618 HIS  ( 194-) C  -
  790 HIS  ( 366-) C  -
  861 ASN  ( 437-) C  -
  911 ASN  ( 487-) C  -
 1017 HIS  ( 593-) C  -
 1157 ASN  ( 733-) C  -
 1307 HIS  ( 883-) C  -
 1338 HIS  ( 914-) C  -
 1348 GLN  ( 924-) C  -
 1353 HIS  ( 929-) C  -
 1453 HIS  (1029-) C  -
 1460 HIS  (1036-) C  -
And so on for a total of    31 lines.
 
# 116 # 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, and if
enough (high resolution) data is available.
 
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.
 
   58 HIS  (  61-) A  -   HIS-E   0.47
  116 HIS  ( 119-) A  -   HIS-H   0.40 HIS-E   0.57
  121 HIS  ( 124-) A  -   HIS-E   0.65
  278 HIS  (  61-) B  -   HIS-E   0.45
  336 HIS  ( 119-) B  -   HIS-E   0.43
  341 HIS  ( 124-) B  -   HIS-E   0.40
  618 HIS  ( 194-) C  -   HIS-E   0.55
  741 HIS  ( 317-) C  -   HIS-E   0.54
  767 HIS  ( 343-) C  -   HIS-E   0.45
  790 HIS  ( 366-) C  -   HIS-H   1.79 HIS-E   1.95
  869 HIS  ( 445-) C  -   HIS-E   0.65
  894 HIS  ( 470-) C  -   HIS-E   0.66
  897 HIS  ( 473-) C  -   HIS-D   0.58 HIS-E   0.66
  957 HIS  ( 533-) C  -   HIS-E   0.58 HIS-D   0.84
 1017 HIS  ( 593-) C  -   HIS-H   0.48 HIS-D   0.65
And so on for a total of    56 lines.
 
# 117 # 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.
 
   29 TYR  (  32-) A  -    N
   30 THR  (  33-) A  -    OG1
   36 ARG  (  39-) A  -    NH1
   43 ILE  (  46-) A  -    N
   53 ILE  (  56-) A  -    N
   58 HIS  (  61-) A  -    N
   63 VAL  (  66-) A  -    N
   80 LEU  (  83-) A  -    N
   88 GLU  (  91-) A  -    N
  116 HIS  ( 119-) A  -    NE2
  126 ASN  ( 129-) A  -    ND2
  142 GLY  ( 145-) A  -    N
  151 ALA  ( 154-) A  -    N
  194 ASN  ( 200-) A  -    N
  195 SER  ( 201-) A  -    N
And so on for a total of   352 lines.
 
# 118 # 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 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.
 
   33 ASN  (  36-) A  -    OD1
  306 GLU  (  89-) B  -    OE1
  441 GLU  ( 230-) B  -    OE2
  478 GLN  (  51-) C  -    OE1
  516 ASP  (  92-) C  -    OD2
  618 HIS  ( 194-) C  -    ND1
  650 GLN  ( 226-) C  -    OE1
  815 GLU  ( 391-) C  -    OE1
  961 GLN  ( 537-) C  -    OE1
 1028 ASN  ( 604-) C  -    OD1
 1147 HIS  ( 723-) C  -    ND1
 1173 HIS  ( 749-) C  -    ND1
 1284 ASN  ( 860-) C  -    OD1
 1301 ASP  ( 877-) C  -    OD2
 1512 ASP  (1088-) C  -    OD1
 1545 GLU  (1121-) C  -    OE1
 1571 GLU  (1147-) C  -    OE1
 1586 ASN  (   5-) D  -    OD1
 1888 ASN  ( 307-) D  -    OD1
 2228 GLU  ( 647-) D  -    OE2
 2570 GLU  ( 993-) D  -    OE1
 2657 GLU  (1092-) D  -    OE2
 2704 GLN  (1139-) D  -    OE1
 2718 HIS  (1153-) D  -    ND1
 2725 GLN  (1160-) D  -    OE1
 2786 GLN  (1227-) D  -    OE1
 2856 ASP  (  40-) E  -    OD2
 3055 ASP  ( 160-) F  -    OD1
 
# 119 # Note: Some notes regarding these donors and acceptors
The donors and acceptors have been counted, also as function of their
accessibility. The buried donors and acceptors have been binned in five
categories ranging from not forming any hydrogen bond till forming a poor
till perfect hydrogen bond. Obviously, the buried donors and acceptors
with no or just a poor hydrogen bond should be a topic of concern. As every
protein contains more acceptors than donors, unsatisfied donors are more in
need of attention than unsatisfied acceptors.
 
Total number of donors: 4535
- of which buried: 2307
Total number of acceptors: 5163
- of which buried: 1915
Total number of donor+acceptors: 419
  (e.g. the Ser Ogamma that can donate and accept)
- of which buried: 111
Buried donors: 2307
- without H-bond: 327
- essentially without H-bond: 1
- with only a very poor H-bond: 25
- with a poor H-bond: 40
- with a H-bond: 1914
Buried acceptors: 1915
- without H-bond: 395
- essentially without H-bond: 3
- with only a very poor H-bond: 113
- with a poor H-bond: 865
- with a H-bond: 539
 
# 120 # Note: Content of the PDB file as interpreted by WHAT CHECK
Content of the PDB file as interpreted by WHAT CHECK.
WHAT CHECK 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 CHECK output formats can be found at
swift.cmbi.ru.nl. Look under output formats. A course on reading this
'Molecules' table is part of the WHAT CHECK website.
 
     1     1 (    4)   179 (  182) A Protein             /zata/tempdir/6ko...
     2   180 (  186)   217 (  223) A Protein             /zata/tempdir/6ko...
     3   218 (    1)   368 (  151) B Protein             /zata/tempdir/6ko...
     4   369 (  156)   396 (  183) B Protein             /zata/tempdir/6ko...
     5   397 (  186)   447 (  236) B Protein             /zata/tempdir/6ko...
     6   448 (   21)   498 (   71) C Protein             /zata/tempdir/6ko...
     7   499 (   75)   824 (  400) C Protein             /zata/tempdir/6ko...
     8   825 (  401)   882 (  458) C Protein             /zata/tempdir/6ko...
     9   883 (  459)   884 (  460) C Protein             /zata/tempdir/6ko...
    10   885 (  461)  1302 (  878) C Protein             /zata/tempdir/6ko...
    11  1303 (  879)  1582 ( 1158) C Protein             /zata/tempdir/6ko...
    12  1583 (    2)  1967 (  386) D Protein             /zata/tempdir/6ko...
    13  1968 (  387)  1968 (  387) D Protein             /zata/tempdir/6ko...
    14  1969 (  388)  2483 (  902) D Protein             /zata/tempdir/6ko...
    15  2484 (  907)  2589 ( 1012) D Protein             /zata/tempdir/6ko...
And so on for a total of    31 lines.
 
# 121 # Note: Summary report
This is an overall summary of the quality of the structure as compared with
current reliable structures. Numbers in brackets are the average and standard
deviation observed for a large number of files determined with a similar
resolution.
 
The second table mostly gives an impression of how well the model conforms
to common refinement restraint values. These numbers are less than 1.0 if the
spread in data is too little, and larger than 1.0 when the spread is too
large. The former does not need to be a problem, the latter always is bad.
 
 Structure Z-scores, positive is better than average:
  Resolution read from PDB file  :   2.790
  1st generation packing quality :  -0.419 (          (  -0.8,  2.5))
  2nd generation packing quality :  -1.748 (          (  -1.7,  1.3))
  Ramachandran plot appearance   :  -4.354 (bad       (  -3.4,  1.7))
  chi-1/chi-2 rotamer normality  :  -5.789 (bad       (  -5.0,  1.9))
  Backbone conformation          :  -0.867 (          (  -1.0,  3.7))
  Inside/Outside distribution    :   1.029
 
 RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.568 (tight)
  Bond angles                    :   0.893
  Omega angle restraints         :   1.654 (loose)
  Side chain planarity           :   0.940
  Improper dihedral distribution :   0.813
  B-factor distribution          :   0.716
 
# 122 # Note: Introduction to refinement recommendations
First, be aware that the recommendations for crystallographers listed below
are produced by a computer program that was written by a guy who got his
PhD in NMR...
 
We have tried to convert the messages written in this report into a small
set of things you can do with your refinement software to get a better
structure. The things you should do first are listed first. And in some
cases you should first fix that problem, then refine a bit further, and
then run WHAT CHECK again before looking at other problems. If, for example,
WHAT CHECK has found a problem with the SCALE and CRYST cards, then you must
first fix that problem, refine the structure a bit further, and run WHAT
CHECK again because errors in the SCALE and or CRYST card can lead to many
problems elsewhere in the validation process.
 
It is also important to keep in mind that WHAT CHECK is software and that it
occasionally totally misunderstands what is the cause of a problem. But, if
WHAT CHECK lists a problem there normally is a problem albeit that it not
always is the actual problem that gets listed.
 
# 123 # Note: Matthews coefficient problem
WHAT CHECK detected a Matthews coefficient problem. Most times this is an
administrative problem caused by typing the wrong cell multiplicity number
on the CRYST card (or not typing it at all). Occasionally it is caused by
typing the wrong space group on the CRYST card. You better fix this problem,
but normally this problem does not cause WHAT CHECK to give any erroneous
error messages further down in the report.
 
# 124 # Note: Hand problems
Your structure contains many residues with a reported hand problem (a
hand problem means that an atom was found with inverted chirality).
Obviously, things like D-amino acids exist, and if you know that your
molecule has groups with an inverted chirality, you can neglect this
message. If, however, this message comes as a surprise to you, then
you should correct the problems and do a considerable amount of
additional refinement before you run WHAT CHECK again.
 
# 125 # Error: Bumps in your structure
Upon analysing the bumps in your structure, WHAT CHECK got very, very
worried. Sometimes this means that you have forgotten to lower the
occupancy of overlapping ligands, residues, or water molecules. But,
whatever is the origin of this problem, you have to analyse it and
fix it.
 
# 126 # Note: Bond angle variabilty Z-score high
With a resolution of 2.5-3.0 Angstrom, you dont have enough data to warrant
the bond angle variability that we observed (almost 1.0). So, you better
tighten
the screws on the bond angle target values a bit.
 
# 127 # Note: Omega angles insufficiently restraint
Omega angles tend to fall around 178 degrees with a standard deviation of 5.5
degrees. With a resolution of 2.5-3.0 Angstrom, you dont have enough data to
warrant the omega angle variability that we observed. The variability is
larger than 7.0 degrees. So, tighten the screws on the omega angle target
values a bit.
 
# 128 # Note: His, Asn, Gln side chain flips.
His, Asn, and Gln have an asymmetry in their side chain that is hard to
detect unless you have data at much better than 1.0 Angstrom resolution.
WHAT CHECK thinks that your structure contains His, Asn, or Gln residues that
will make better hydrogen bonds when flipped around their chi-2, chi-2, or
chi-3 side chain torsion angle, respectively. You better
check these Asn, His, and Gln residues, and if you use a refinement program
that includes molecular dynamics, then you must (after the
flips were made) refine a bit further before running WHAT CHECK again.
 
# 129 # Note: Weird omega angles
WHAT CHECK has found multiple omega angles that are very wrong. You must
inspect this situation.
 
# 130 # Note: Free floating waters
Your structure contains a few water molecules that make no hydrogen bonds at
all. These waters must be removed, and you must then refine a bit further
before running WHAT CHECK again.
 
# 131 # Warning: Troublesome residues
The residues listed in the table below need to be inspected
 
This table is a very rough attempt to sort the residues according to how
badly they need your attention. The idea is that when you sit in  in front
of the graphics screen and study the residues with the electron density
present that you improve the structure most by dealing with the top residues
in this list first.
 
 1034 VAL  ( 610-) C  -     76.47
  883 ARG  ( 459-) C  -     67.53
 1035 PRO  ( 611-) C  -     66.41
 1037 VAL  ( 613-) C  -     56.12
 1036 LEU  ( 612-) C  -     55.86
 1301 ASP  ( 877-) C  -     49.63
  888 LEU  ( 464-) C  -     48.82
  884 GLU  ( 460-) C  -     40.56
 1303 LEU  ( 879-) C  -     38.27
 1694 ARG  ( 113-) D  -     36.44
  630 LEU  ( 206-) C  -     35.82
 1485 ARG  (1061-) C  -     33.60
  912 ILE  ( 488-) C  -     31.30
  629 TRP  ( 205-) C  -     30.63
  824 THR  ( 400-) C  -     30.49
And so on for a total of   618 lines.
==============
 
 
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
    information)
 
PDB facilities
    Touw WG, Baakman C, Black J, te Beek TA, Krieger E, Joosten RP, Vriend G.
      A series of PDB-related databanks for everyday needs.
    Nucleic Acids Research D364-368 Database issue (2015).
 
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) and
    R.Engh and R.Huber,
    International Tables for Crystallography (2001)
 
 
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).
 
Peptide flips
    Touw WG, Joosten RP, Vriend G.
      Detection of trans-cis flips and peptide-plane flips in protein
      structures.
    Acta Crystallogr D Biological Crystallograhy 71, 1604-1614 (2015).
 
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).
    R.W.W. Hooft, C.Sander and G.Vriend,
      Objectively judging the quality of a protein structure from a
      Ramachandran plot
    CABIOS (1997), 13, 425--430.
 
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).
 
Tau angle
    W.G.Touw and G.Vriend
      On the complexity of Engh and Huber refinement restraints: the angle
      tau as example.
    Acta Crystallogr D 66, 1341--1350 (2010).
 
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.
==============
 
 
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
    information)
 
PDB facilities
    Touw WG, Baakman C, Black J, te Beek TA, Krieger E, Joosten RP, Vriend G.
      A series of PDB-related databanks for everyday needs.
    Nucleic Acids Research D364-368 Database issue (2015).
 
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) and
    R.Engh and R.Huber,
    International Tables for Crystallography (2001)
 
 
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).
 
Peptide flips
    Touw WG, Joosten RP, Vriend G.
      Detection of trans-cis flips and peptide-plane flips in protein
      structures.
    Acta Crystallogr D Biological Crystallograhy 71, 1604-1614 (2015).
 
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).
    R.W.W. Hooft, C.Sander and G.Vriend,
      Objectively judging the quality of a protein structure from a
      Ramachandran plot
    CABIOS (1997), 13, 425--430.
 
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).
 
Tau angle
    W.G.Touw and G.Vriend
      On the complexity of Engh and Huber refinement restraints: the angle
      tau as example.
    Acta Crystallogr D 66, 1341--1350 (2010).
 
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.
