WHAT IF Check report

This file was created 2014-10-30 from WHAT_CHECK output by a conversion script. If you are new to WHAT_CHECK, please study the pdbreport pages. There also exists a legend to the output.

Verification log for pdb1sqp.ent

Checks that need to be done early-on in validation

Note: Symmetry information inconsistent

The SCALE and CRYST1 information disagree.

Possible cause: The CRYST1 dimensions were rounded.

The CRYST1 cell dimensions

    A    = 153.700  B   = 153.700  C    = 596.534
    Alpha=  90.000  Beta=  90.000  Gamma=  90.000

Cell as derived from the SCALE matrix

    A    = 153.704  B   = 153.704  C    = 596.659
    Alpha=  90.000  Beta=  90.000  Gamma=  90.000

Note: Bump analysis can not decide between SCALE and CRYST1 cells

No significant difference exists between the inter-molecular contacts found when using the CRYST1 or SCALE cells.

Note: No crystallographic symmetry between molecules

No extra crystallographic symmetry was observed between the independent molecules.

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: I 41 2 2
Number of matrices in space group: 16
Highest polymer chain multiplicity in structure: 1
Highest polymer chain multiplicity according to SEQRES: 2
Such multiplicity differences are not by definition worrisome as it is very
well possible that this merely indicates that it is difficult to superpose
chains due to crystal induced differences
No explicit MTRIX NCS matrices found in the input file
Value of Z as found on the CRYST1 card: 16
Polymer chain multiplicity and SEQRES multiplicity disagree 1 2
Z and NCS seem to support the 3D multiplicity
There is strong evidence, though, for multiplicity and Z: 1 16

Error: Matthews Coefficient (Vm) very 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.

Numbers this high are almost always caused by giving the wrong value for Z on the CRYST1 card (or not giving this number at all).

Molecular weight of all polymer chains: 240196.625
Volume of the Unit Cell V= 14096064.0
Space group multiplicity: 16
No NCS symmetry matrices (MTRIX records) found in PDB file
Matthews coefficient for observed atoms and Z high: Vm= 7.336
Vm by authors and this calculated Vm do not agree very well
Matthews coefficient read from REMARK 280 Vm= 3.570 SEQRES and ATOM multiplicities disagree. Error-reasoning thus is difficult.
(and the absence of MTRIX records doesn't help)
There is strong evidence, though, for multiplicity and Z: 1 16
which would result in the much more normal Vm= 3.668
and which also agrees with the number of NCS matrices (labeled `don't use')
that the user provided in the MTRIX records 1

Note: No atoms with high occupancy detected at special positions

Either there were no atoms at special positions, or all atoms at special positions have adequately reduced occupancies. An atom is considered to be located at a special position if it is within 0.3 Angstrom from one of its own symmetry copies. See also the next check...

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.

Note: Chain identifiers OK

WHAT IF has not detected any serious chain identifier problems. But be aware that WHAT IF doesn't care about the chain identifiers of waters.

Warning: Topology could not be determined for some ligands

Some ligands in the table below are too complicated for the automatic topology determination. WHAT IF uses a local copy of Daan van Aalten's Dundee PRODRG server to automatically generate topology information for ligands. Some molecules are too complicated for this software. If that happens, WHAT IF / WHAT-CHECK continue with a simplified topology that lacks certain information. Ligands with a simplified topology can, for example, not form hydrogen bonds, and that reduces the accuracy of all hydrogen bond related checking facilities.

The reason for topology generation failure is indicated. 'Atom types' indicates that the ligand contains atom types not known to PRODRUG. 'Attached' means that the ligand is covalently attached to a macromolecule. 'Size' indicates that the ligand has either too many atoms (or two or less which PRODRUG also cannot cope with), or too many bonds, angles, or torsion angles. 'Fragmented' is written when the ligand is not one fully covalently connected molecule but consists of multiple fragments. 'N/O only' is given when the ligand contains only N and/or O atoms. 'OK' indicates that the automatic topology generation succeeded.

2110 CDL   ( 447-)  A  -         Fragmented
2111 PEE   ( 448-)  A  -         OK
2112 PEE   ( 380-)  C  -         OK
2114 CDL   ( 242-)  G  -         Fragmented
2117 CDL   (  82-)  G  -         Fragmented
2119 PLX   (  63-)  E  -         OK
2120 PEE   ( 197-)  E  -         OK
2121 MYX   ( 383-)  C  -         OK

Administrative problems that can generate validation failures

Note: No strange inter-chain connections detected

No covalent bonds have been detected between molecules with non-identical chain identifiers.

Note: No duplicate atom names in ligands

All atom names in ligands seem adequately unique.

Note: No mixed usage of alternate atom problems detected

Either this structure does not contain alternate atoms, or they have not been mixed up, or the errors have remained unnoticed.

Note: In all cases the primary alternate atom was used

WHAT IF saw no need to make any alternate atom corrections (which means they are all correct, or there are none).

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).

Note: No attached groups interfere with hydrogen bond calculations

It seems there are no sugars, lipids, etc., bound (very close) to atoms that otherwise could form hydrogen bonds.

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.

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 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.

Note: All residues have a complete backbone.

No residues have missing backbone atoms.

Note: No C-alpha only residues

There are no residues that consist of only an alpha carbon atom.

Note: Non-canonicals

WHAT IF has not detected any non-canonical residue that it does not understand (or there are no non-canonical residues in the PDB file).

Non-validating, descriptive output paragraph

Note: Content of the PDB file as interpreted by WHAT IF

Content of the PDB file as interpreted by WHAT IF. WHAT IF has read your PDB file, and stored it internally in what is called 'the soup'. The content of this soup is listed here. An extensive explanation of all frequently used WHAT IF output formats can be found at swift.cmbi.ru.nl. Look under output formats. A course on reading this 'Molecules' table is part of the WHAT CHECK web pages.

     1     1 (    1)   446 (  446) A Protein             pdb1sqp.ent
     2   447 (   17)   869 (  439) B Protein             pdb1sqp.ent
     3   870 (    2)  1247 (  379) C Protein             pdb1sqp.ent
     4  1248 (    1)  1488 (  241) D Protein             pdb1sqp.ent
     5  1489 (    1)  1684 (  196) E Protein             pdb1sqp.ent
     6  1685 (    6)  1789 (  110) F Protein             pdb1sqp.ent
     7  1790 (    1)  1864 (   75) G Protein             pdb1sqp.ent
     8  1865 (   12)  1931 (   78) H Protein             pdb1sqp.ent
     9  1932 (    1)  1988 (   57) I Protein             pdb1sqp.ent
    10  1989 (    1)  2049 (   61) J Protein             pdb1sqp.ent
    11  2050 (    1)  2102 (   53) K Protein             pdb1sqp.ent
    12  2103 (  446)  2103 (  446) A F O2 <-   446       pdb1sqp.ent
    13  2104 (  439)  2104 (  439) B L O2 <-   869       pdb1sqp.ent
    14  2105 (  379)  2105 (  379) C W O2 <-  1247       pdb1sqp.ent
    15  2106 (  241)  2106 (  241) D K O2 <-  1488       pdb1sqp.ent
    16  2107 (  196)  2107 (  196) E G O2 <-  1684       pdb1sqp.ent
    17  2108 (  110)  2108 (  110) F K O2 <-  1789       pdb1sqp.ent
    18  2109 (   78)  2109 (   78) H K O2 <-  1931       pdb1sqp.ent
    19  2110 (  447)  2110 (  447) A CDL                 pdb1sqp.ent
    20  2111 (  448)  2111 (  448) A PEE                 pdb1sqp.ent
    21  2112 (  380)  2112 (  380) C PEE                 pdb1sqp.ent
    22  2113 (  381)  2113 (  381) C HEM                 pdb1sqp.ent
    23  2114 (  242)  2114 (  242) G CDL                 pdb1sqp.ent
    24  2115 (  382)  2115 (  382) C HEM                 pdb1sqp.ent
    25  2116 (  243)  2116 (  243) D HEM  <=             pdb1sqp.ent
    26  2117 (   82)  2117 (   82) G CDL                 pdb1sqp.ent
    27  2118 (  198)  2118 (  198) E FES                 pdb1sqp.ent
    28  2119 (   63)  2119 (   63) E PLX                 pdb1sqp.ent
    29  2120 (  197)  2120 (  197) E PEE                 pdb1sqp.ent
    30  2121 (  383)  2121 (  383) C MYX                 pdb1sqp.ent
    31  2122 ( HOH )  2122 ( HOH ) A water   (   51)     pdb1sqp.ent
    32  2123 ( HOH )  2123 ( HOH ) B water   (   84)     pdb1sqp.ent
    33  2124 ( HOH )  2124 ( HOH ) C water   (   36)     pdb1sqp.ent
    34  2125 ( HOH )  2125 ( HOH ) D water   (   11)     pdb1sqp.ent
    35  2126 ( HOH )  2126 ( HOH ) E water   (    2)     pdb1sqp.ent
    36  2127 ( HOH )  2127 ( HOH ) F water   (   15)     pdb1sqp.ent
    37  2128 ( HOH )  2128 ( HOH ) G water   (   11)     pdb1sqp.ent
    38  2129 ( HOH )  2129 ( HOH ) I water   (    2)     pdb1sqp.ent
    39  2130 ( HOH )  2130 ( HOH ) K water   (    3)     pdb1sqp.ent

Note: Some notes regarding the PDB file contents

The numbers and remarks listed below have no explicit validation purpose, they are merely meant for the crystallographer or NMR spectroscopists to perhaps pinpoint something unexpected. See the WHAT_CHECK course for an explanation of terms like 'poor', 'missing', etcetera (in case those words pop up in the lines underneath this message).

The total number of amino acids found is 2102.
of which 17 have poor or missing atoms.
Number of water molecules 215

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.

Chain identifier: A

Note: Ramachandran plot

Chain identifier: B

Note: Ramachandran plot

Chain identifier: C

Note: Ramachandran plot

Chain identifier: D

Note: Ramachandran plot

Chain identifier: E

Note: Ramachandran plot

Chain identifier: F

Note: Ramachandran plot

Chain identifier: G

Note: Ramachandran plot

Chain identifier: H

Note: Ramachandran plot

Chain identifier: I

Note: Ramachandran plot

Chain identifier: J

Note: Ramachandran plot

Chain identifier: K

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 the DSSP page 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.
                     10        20        30        40        50        60
                      |         |         |         |         |         |
    1 -   60 TATYAQALQSVPETQVSQLDNGLRVASEQSSQPTCTVGVWIDAGSRYESEKNNGAGYFVE
(   1)-(  60)   HHHHHHHT   SSSS TTT SSSSSS T TSSSSSSSST TTTT  TTTTTHHHHHH
                     70        80        90       100       110       120
                      |         |         |         |         |         |
   61 -  120 HLAFKGTKNRPGNALEKEVESMGAHLNAYSTREHTAYYIKALSKDLPKAVELLADIVQNC
(  61)-( 120)HHTTT  TTT TTHHHHHHHHHT SSSSSS TT SSSSSSSS333HHHHHHHHHHHHH
                    130       140       150       160       170       180
                      |         |         |         |         |         |
  121 -  180 SLEDSQIEKERDVILQELQENDTSMRDVVFNYLHATAFQGTPLAQSVEGPSENVRKLSRA
( 121)-( 180)   HHHHHHHHHHHHHHHHHHTT HHHHHHHHHHHHHTTTT333T TT  HHHHHH  HH
                    190       200       210       220       230       240
                      |         |         |         |         |         |
  181 -  240 DLTEYLSRHYKAPRMVLAAAGGLEHRQLLDLAQKHFSGLSGTYDEDAVPTLSPCRFTGSQ
( 181)-( 240)HHHHHHHHHT 333SSSSSSST  HHHHHHHHHHHT  T TT TTT             S
                    250       260       270       280       290       300
                      |         |         |         |         |         |
  241 -  300 ICHREDGLPLAHVAIAVEGPGWAHPDNVALQVANAIIGHYDCTYGGGAHLSSPLASIAAT
( 241)-( 300)SSSS TTTTTSSSSSSSSS  TT TTHHHHHHHHHHH SSSTT T 333 TTHHHHHHHH
                    310       320       330       340       350       360
                      |         |         |         |         |         |
  301 -  360 NKLCQSFQTFNICYADTGLLGAHFVCDHMSIDDMMFVLQGQWMRLCTSATESEVLRGKNL
( 301)-( 360)TT  TSSSSSSSSSTTSSSSSSSSSS 333HHHHHHHHHHHHHHHHHH  HHHHHHHHHH
                    370       380       390       400       410       420
                      |         |         |         |         |         |
  361 -  420 LRNALVSHLDGTTPVCEDIGRSLLTYGRRIPLAEWESRIAEVDARVVREVCSKYFYDQCP
( 361)-( 420)HHHHHHHHT THHHHHHHHHHHHHHTTT   HHHHHHHHHT  HHHHHHHHHHHTTT
                    430       440
                      |         |
  421 -  446 AVAGFGPIEQLPDYNRIRSGMFWLRF
( 421)-( 446)SSSSSST TTT  HHHHHHTTT T
 
              450       460       470       480       490       500
                |         |         |         |         |         |
  447 -  506 VPPHPQDLEFTRLPNGLVIASLENYAPASRIGLFIKAGSRYENSNNLGTSHLLRLASSLT
(  17)-(  76)        SSSS TTT SSSSS    TSSSSSSSST T333  TTTTTHHHHHHHTTTT
              510       520       530       540       550       560
                |         |         |         |         |         |
  507 -  566 TKGASSFKITRGIEAVGGKLSVTSTRENMAYTVECLRDDVDILMEFLLNVTTAPEFRRWE
(  77)-( 136) TT  HHHHHHHHHHHT SSSSSS TT SSSSSSSS333HHHHHHHHHHHHHT    HHH
              570       580       590       600       610       620
                |         |         |         |         |         |
  567 -  626 VAALQPQLRIDKAVALQNPQAHVIENLHAAAYRNALANSLYCPDYRIGKVTPVELHDYVQ
( 137)-( 196)HHHHHHHHHHHHHHHHTTHHHHHHHHHHHHH TTTTTT TT  333TTT  HHHHHHHHH
              630       640       650       660       670       680
                |         |         |         |         |         |
  627 -  686 NHFTSARMALIGLGVSHPVLKQVAEQFLNIRGGLGLSGAKAKYHGGEIREQNGDSLVHAA
( 197)-( 256)HHTT333SSSSSSTT HHHHHHHHHHH     T   T T      SSSSSS   TSSSSS
              690       700       710       720       730       740
                |         |         |         |         |         |
  687 -  746 LVAESAAIGSAEANAFSVLQHVLGAGPHVKRGSNATSSLYQAVAKGVHQPFDVSAFNASY
( 257)-( 316)SSSS   TTTHHHHHHHHHHHHH  T TTTT   TT HHHHHHHTT  TTSSSSSSSSS
              750       760       770       780       790       800
                |         |         |         |         |         |
  747 -  806 SDSGLFGFYTISQAASAGDVIKAAYNQVKTIAQGNLSNPDVQAAKNKLKAGYLMSVESSE
( 317)-( 376)TT SSSSSSSSSS333HHHHHHHHHHHHHHHHTT   HHHHHHHHHHHHHHHHHHTTTHH
              810       820       830       840       850       860
                |         |         |         |         |         |
  807 -  869 GFLDEVGSQALAAGSYTPPSTVLQQIDAVADADVINAAKKFVSGRKSMAASGNLGHTPFIDEL
( 377)-( 439)HHHHHHHHHHHHTTT   HHHHHHHHHH  HHHHHHHHHHHHTT SSSSSSS  TT   TTT
 
           870       880       890       900       910       920
             |         |         |         |         |         |
  870 -  929 TNIRKSHPLMKIVNNAFIDLPAPSNISSWWNFGSLLGICLILQILTGLFLAMHYTSDTTT
(   2)-(  61)  HHHHTTTHHHHHHHHTT SSSTT  333THHHHHHHHHHHHHHHHHHHHTT   THHH
           930       940       950       960       970       980
             |         |         |         |         |         |
  930 -  989 AFSSVTHICRDVNYGWIIRYMHANGASMFFICLYMHVGRGLYYGSYTFLETWNIGVILLL
(  62)-( 121)HHHHHHHHHHHTTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT333THHHHHHHHHHHH
           990      1000      1010      1020      1030      1040
             |         |         |         |         |         |
  990 - 1049 TVMATAFMGYVLPWGQMSFWGATVITNLLSAIPYIGTNLVEWIWGGFSVDKATLTRFFAF
( 122)-( 181)HHHHHHHHHHHTT  HHHHHHHHHHHH3333TTTTHHHHHHHHHTTTTT HHHHHHHHHH
          1050      1060      1070      1080      1090      1100
             |         |         |         |         |         |
 1050 - 1109 HFILPFIIMAIAMVHLLFLHETGSNNPTGISSDVDKIPFHPYYTIKDILGALLLILALML
( 182)-( 241)HHHHHHHHHHHHHHHHHHHHTT    TT T  TTTSSSHHHHHHHHHHHHHHHHHHHHHH
          1110      1120      1130      1140      1150      1160
             |         |         |         |         |         |
 1110 - 1169 LVLFAPDLLGDPDNYTPANPLNTPPHIKPEWYFLFAYAILRSIPNKLGGVLALAFSILIL
( 242)-( 301)HHHT TTTTT 3333T   TTT  T     HHHHHHHHHHHHT THHHHHHHHHHHHH33
          1170      1180      1190      1200      1210      1220
             |         |         |         |         |         |
 1170 - 1229 ALIPLLHTSKQRSMMFRPLSQCLFWALVADLLTLTWIGGQPVEHPYITIGQLASVLYFLL
( 302)-( 361)3T3333   TTTTTTT HHHHHHHHHHHHHHHHHHHHHTT TTHHHHHHHHHHHHHHHHH
          1230      1240
             |         |
 1230 - 1247 ILVLMPTAGTIENKLLKW
( 362)-( 379)HHTHHHHHHHHHHHHTT
 
            1250      1260      1270      1280      1290      1300
               |         |         |         |         |         |
 1248 - 1307 SDLELHPPSYPWSHRGLLSSLDHTSIRRGFQVYKQVCSSCHSMDYVAYRHLVGVCYTEDE
(   1)-(  60)            TTTTTT    HHHHHHHHHHHHTT333T   TT  T333 TTT  HHH
            1310      1320      1330      1340      1350      1360
               |         |         |         |         |         |
 1308 - 1367 AKALAEEVEVQDGPNEDGEMFMRPGKLSDYFPKPYPNPEAARAANNGALPPDLSYIVRAR
(  61)-( 120)HHHHHTTTSSSS   TTTT SSSS  TT     TTTTHHHHHHTTTTT    TTT TTTT
            1370      1380      1390      1400      1410      1420
               |         |         |         |         |         |
 1368 - 1427 HGGEDYVFSLLTGYCEPPTGVSLREGLYFNPYFPGQAIGMAPPIYNEVLEFDDGTPATMS
( 121)-( 180)TTTHHHHHHHHH      TT    TTT   TTTTTT  T     TT TT  TTT    HH
            1430      1440      1450      1460      1470      1480
               |         |         |         |         |         |
 1428 - 1488 QVAKDVCTFLRWAAEPEHDHRKRMGLKMLLMMGLLLPLVYAMKRHKWSVLKSRKLAYRPPK
( 181)-( 241)HHHHHHHHHHTTTT TTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT
 
           1490      1500      1510      1520      1530      1540
              |         |         |         |         |         |
 1489 - 1548 SHTDIKVPDFSDYRRPEVLDSTKSSKESSEARKGFSYLVTATTTVGVAYAAKNVVSQFVS
(   1)-(  60) 333      TTT  333  TTT THHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
           1550      1560      1570      1580      1590      1600
              |         |         |         |         |         |
 1549 - 1608 SMSASADVLAMSKIEIKLSDIPEGKNMAFKWRGKPLFVRHRTKKEIDQEAAVEVSQLRDP
(  61)-( 120)HHH  HHHHTTTT    TTTT TT      TTTT SSSSS  TTTHHHHHTT TTTTTT
           1610      1620      1630      1640      1650      1660
              |         |         |         |         |         |
 1609 - 1668 QHDLERVKKPEWVILIGVCTHLGCVPIANAGDFGGYYCPCHGSHYDASGRIRKGPAPLNL
( 121)-( 180)  T333 TTTTSSSSST  TTT    SST TTTTTSSSTTTTSSS TT  SSSTT TT T
           1670      1680
              |         |
 1669 - 1684 EVPSYEFTSDDMVIVG
( 181)-( 196)    SSSTTTT SSS
 
               1690      1700      1710      1720      1730      1740
                  |         |         |         |         |         |
 1685 - 1744 VSASSRWLEKIRKWYYNAAGFNKLGLMRDDTIHENDDVKEAIRRLPENLYDDRVFRIKRA
(   6)-(  65)  TTTTTHHHHHHHHHHHH T333T  333TT   HHHHHHHHHT HHHHHHHHHHHHHH
               1750      1760      1770      1780
                  |         |         |         |
 1745 - 1789 LDLSMRQQILPKEQWTKYEEDKSYLEPYLKEVIRERKEREEWAKK
(  66)-( 110)HHHHHHT    333T  TTT   TTHHHHHHHHHHHHHHHHHTT
 
          1790      1800      1810      1820      1830      1840
             |         |         |         |         |         |
 1790 - 1849 GRQFGHLTRVRHVITYSLSPFEQRAFPHYFSKGIPNVLRRTRACILRVAPPFVAFYLVYT
(   1)-(  60)   TTTT    T       TTTT TTTTTTTTHHHHHHHHHHHHHHHHHHHHHHHHHHHH
          1850      1860
             |         |
 1850 - 1864 WGTQEFEKSKRKNPA
(  61)-(  75)HHHHHHHHHHT T
 
               1870      1880      1890      1900      1910      1920
                  |         |         |         |         |         |
 1865 - 1924 ELVDPLTTVREQCEQLEKCVKARERLELCDERVSSRSQTEEDCTEELLDFLHARDHCVAH
(  12)-(  71)    HHHHHHHHHHTTHHHHHHHHHHHHHHHHHTTTTT    THHHHHHHHHHHHHHHHH
               1930
                  |
 1925 - 1931 KLFNSLK
(  72)-(  78)HTTTT
 
                  1940      1950      1960      1970      1980
                     |         |         |         |         |
 1932 - 1988 MLSVAARSGPFAPVLSATSRGVAGALRPLVQAAVPATSESPVLDLKRSVLCRESLRG
(   1)-(  57)   TTTTT T  SS  TTT  SS   TT TTTTTTT       TT   TT
 
           1990      2000      2010      2020      2030      2040
              |         |         |         |         |         |
 1989 - 2049 VAPTLTARLYSLLFRRTSTFALTIVVGALFFERAFDQGADAIYEHINEGKLWKHIKHKYEN
(   1)-(  61)  T HHHHHHHHTTTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTTTTHHHH333T
 
          2050      2060      2070      2080      2090      2100
             |         |         |         |         |         |
 2050 - 2102 MLTRFLGPRYRQLARNWVPTAGLWGAVGAVGLVWATDWRLILDWVPYINGKFK
(   1)-(  53)  333 THHHHHHHHHHHHHHHHHHHHHHHHHHHHHT HHHHTTTTT  TT
 
 
 

Coordinate problems, unexpected atoms, B-factor and occupancy checks

Note: No rounded coordinates detected

No significant rounding of atom coordinates has been detected.

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.

Warning: Missing atoms

The atoms listed in the table below are missing from the entry. If many atoms are missing, the other checks can become less sensitive. Be aware that it often happens that groups at the termini of DNA or RNA are really missing, so that the absence of these atoms normally is neither an error nor the result of poor electron density. Some of the atoms listed here might also be listed by other checks, most noticeably by the options in the previous section that list missing atoms in several categories. The plausible atoms with zero occupancy are not listed here, as they already got assigned a non-zero occupancy, and thus are no longer 'missing'.

1694 LYS   (  15-)  F      CB
1694 LYS   (  15-)  F      CG
1694 LYS   (  15-)  F      CD
1694 LYS   (  15-)  F      CE
1694 LYS   (  15-)  F      NZ

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.

1968 THR   (  37-)  I    High
1969 SER   (  38-)  I    High
1970 GLU   (  39-)  I    High
1971 SER   (  40-)  I    High
1972 PRO   (  41-)  I    High
1978 ARG   (  47-)  I    High
1979 SER   (  48-)  I    High
1980 VAL   (  49-)  I    High
1981 LEU   (  50-)  I    High
1982 CYS   (  51-)  I    High
1983 ARG   (  52-)  I    High
1984 GLU   (  53-)  I    High
1985 SER   (  54-)  I    High
1986 LEU   (  55-)  I    High
1987 ARG   (  56-)  I    High
1988 GLY   (  57-)  I    High

Note: No C-terminal nitrogen detected

The PDB indicates that a residue is not the true C-terminus by including only the backbone N of the next residue. This has not been observed in this PDB file.

Note: C-terminus capping

The residues listed in the table below either are pseudo C-terminal residues, or have two groups attached of which neither is the normal C-terminal O. In this table REAL means that the C-terminal residue is likely to be the real C-terminus of its chain; OX means that an incorrect second oxygen (OXT) was detected that should not be there; -O indicates that the 'normal' oxygen (i.e. not the OXT) is missing; OT indicates the detection of any other capping group. C-terminal nitrogen atoms, if any, have already been dealt with in a previous check and are indicated here by -N. PSEUDO means that this is the last visible residue in the chain, but not the real C-terminus, i.e. all residues after this one are missing in this chain. BREAK means that this is the last residue before a chain-break, i.e. the chain continues but after this residue a number of residues is missing. In case a break is observed the number of residues that seems to be missing is shown in brackets. OK means that given the status (REAL, PSEUDO, BREAK), no problems were found.

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.

1864 ALA   (  75-)  G          : PSEUDO OK
1988 GLY   (  57-)  I          : PSEUDO OK
2049 ASN   (  61-)  J          : PSEUDO OK
2102 LYS   (  53-)  K          : PSEUDO OK

Note: No OXT found in the middle of chains

No OXT groups were found in the middle of protein chains.

Note: Weights checked OK

All atomic occupancy factors ('weights') fall in the 0.0-1.0 range.

Note: Normal distribution of occupancy values

The distribution of the occupancy values in this file seems 'normal'.

Be aware that this evaluation is merely the result of comparing this file with about 500 well-refined high-resolution files in the PDB. If this file has much higher or much lower resolution than the PDB files used in WHAT IF's training set, non-normal values might very well be perfectly fine, or normal values might actually be not so normal. So, this check is actually more an indicator and certainly not a check in which I have great confidence.

Note: All occupancies seem to add up to 0.0 - 1.0.

In principle, the occupancy of all alternates of one atom should add up till 0.0 - 1.0. 0.0 is used for the missing atom (i.e. an atom not seen in the electron density). Obviously, there is nothing terribly wrong when a few occupancies add up to a bit more than 1.0, because the mathematics of refinement allow for that. However, if it happens often, it seems worth evaluating this in light of the refinement protocol used.

Warning: What type of B-factor?

WHAT IF 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 IF complains about your B-factors, while you think that they are OK, then check for TLS related B-factor problems first.

Obviously, the temperature at which the X-ray data was collected has some importance too:


Number of TLS groups mentione in PDB file header: 18

Crystal temperature (K) :100.000

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.

Percentage of buried atoms with B less than 5 : 0.30

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 : 0.631 over 14704 bonds
Average difference in B over a bond : 1.08
RMS difference in B over a bond : 1.72

Note: B-factor plot

The average atomic B-factor per residue is plotted as function of the residue number.

Chain identifier: A

Note: B-factor plot

Chain identifier: B

Note: B-factor plot

Chain identifier: C

Note: B-factor plot

Chain identifier: D

Note: B-factor plot

Chain identifier: E

Note: B-factor plot

Chain identifier: F

Note: B-factor plot

Chain identifier: G

Note: B-factor plot

Chain identifier: H

Note: B-factor plot

Chain identifier: I

Note: B-factor plot

Chain identifier: J

Note: B-factor plot

Chain identifier: K

Nomenclature related problems

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 you can get an overview of the importance of all nomenclature problems that we list.

Note: Valine nomenclature OK

No errors were detected in valine nomenclature.

Note: Threonine nomenclature OK

No errors were detected in threonine nomenclature.

Note: Isoleucine nomenclature OK

No errors were detected in isoleucine nomenclature.

Note: Leucine nomenclature OK

No errors were detected in leucine nomenclature.

Note: Arginine nomenclature OK

No errors were detected in arginine nomenclature.

Warning: Tyrosine convention problem

The tyrosine residues listed in the table below have their chi-2 not between -90.0 and 90.0

  47 TYR   (  47-)  A
  89 TYR   (  89-)  A
 669 TYR   ( 239-)  B

Warning: Phenylalanine convention problem

The phenylalanine residues listed in the table below have their chi-2 not between -90.0 and 90.0.

 752 PHE   ( 322-)  B
 931 PHE   (  63-)  C
1008 PHE   ( 140-)  C
1088 PHE   ( 220-)  C
1577 PHE   (  89-)  E
1641 PHE   ( 153-)  E

Warning: Aspartic acid convention problem

The aspartic acid residues listed in the table below have their chi-2 not between -90.0 and 90.0, or their proton on OD1 instead of OD2.

  20 ASP   (  20-)  A
 316 ASP   ( 316-)  A
 403 ASP   ( 403-)  A
1419 ASP   ( 172-)  D
1555 ASP   (  67-)  E
1640 ASP   ( 152-)  E
2086 ASP   (  37-)  K

Warning: Glutamic acid convention problem

The glutamic acid residues listed in the table below have their chi-3 outside the -90.0 to 90.0 range, or their proton on OE1 instead of OE2.

 204 GLU   ( 204-)  A
 225 GLU   ( 225-)  A
 394 GLU   ( 394-)  A
 533 GLU   ( 103-)  B
1251 GLU   (   4-)  D
1392 GLU   ( 145-)  D
1414 GLU   ( 167-)  D
1601 GLU   ( 113-)  E
1613 GLU   ( 125-)  E
1619 GLU   ( 131-)  E
1669 GLU   ( 181-)  E
1764 GLU   (  85-)  F
1785 GLU   ( 106-)  F
1856 GLU   (  67-)  G
1865 GLU   (  12-)  H
1881 GLU   (  28-)  H
1904 GLU   (  51-)  H
1909 GLU   (  56-)  H
1970 GLU   (  39-)  I
2036 GLU   (  48-)  J

Note: Phosphate group names OK

No errors were detected in phosphate group naming conventions.

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.

Note: Chain names are OK

All chain names assigned to polymer molecules are unique, and all residue numbers are strictly increasing within each chain.

Geometric checks

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.

 127 ILE   ( 127-)  A      CA   CB    1.63    4.8
 228 VAL   ( 228-)  A      CA   CB    1.61    4.0
 447 VAL   (  17-)  B      CA   CB    1.63    5.0
 619 VAL   ( 189-)  B      CA   CB    1.63    4.9
 947 ILE   (  79-)  C      CA   CB    1.62    4.5
 960 ILE   (  92-)  C      CA   CB    1.65    5.9
1024 ILE   ( 156-)  C      CA   CB    1.62    4.3
1211 VAL   ( 343-)  C      CA   CB    1.62    4.4
1216 ILE   ( 348-)  C      CA   CB    1.63    4.9
1218 ILE   ( 350-)  C      CA   CB    1.61    4.2
1224 VAL   ( 356-)  C      CA   CB    1.62    4.5
1232 VAL   ( 364-)  C      CA   CB    1.62    4.7
1273 ILE   (  26-)  D      CA   CB    1.62    4.5
1405 ILE   ( 158-)  D      CA   CB    1.64    5.3
1543 VAL   (  55-)  E      CA   CB    1.62    4.7
1562 ILE   (  74-)  E      CA   CB    1.61    4.1
1594 ILE   ( 106-)  E      CA   CB    1.61    4.2
1602 VAL   ( 114-)  E      CA   CB    1.61    4.0
1659 ILE   ( 171-)  E      CA   CB    1.63    4.9
1842 VAL   (  53-)  G      CA   CB    1.61    4.1
1873 VAL   (  20-)  H      CA   CB    1.62    4.4
1922 VAL   (  69-)  H      CA   CB    1.63    4.9
1948 ALA   (  17-)  I      CA   C     1.62    4.4
1957 LEU   (  26-)  I      CA   C     1.62    4.5
1961 VAL   (  30-)  I      CA   CB    1.63    4.9
1968 THR   (  37-)  I      CA   CB    1.64    5.3
1973 VAL   (  42-)  I      CA   CB    1.61    4.2
1980 VAL   (  49-)  I      CA   CB    1.63    4.8
1989 VAL   (   1-)  J      CA   CB    1.62    4.3

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: 0.919
RMS-deviation in bond distances: 0.021

Warning: Possible cell scaling problem

Comparison of bond distances with Engh and Huber [REF] standard values for protein residues and Parkinson et al [REF] values for DNA/RNA shows a significant systematic deviation. It could be that the unit cell used in refinement was not accurate enough. The deformation matrix given below gives the deviations found: the three numbers on the diagonal represent the relative corrections needed along the A, B and C cell axis. These values are 1.000 in a normal case, but have significant deviations here (significant at the 99.99 percent confidence level)

There are a number of different possible causes for the discrepancy. First the cell used in refinement can be different from the best cell calculated. Second, the value of the wavelength used for a synchrotron data set can be miscalibrated. Finally, the discrepancy can be caused by a dataset that has not been corrected for significant anisotropic thermal motion.

Please note that the proposed scale matrix has NOT been restrained to obey the space group symmetry. This is done on purpose. The distortions can give you an indication of the accuracy of the determination.

If you intend to use the result of this check to change the cell dimension of your crystal, please read the extensive literature on this topic first. This check depends on the wavelength, the cell dimensions, and on the standard bond lengths and bond angles used by your refinement software.

Unit Cell deformation matrix

 |  0.992682 -0.000144 -0.000391|
 | -0.000144  0.992478  0.000052|
 | -0.000391  0.000052  0.994220|
Proposed new scale matrix

 |  0.006554  0.000000  0.000003|
 |  0.000000  0.006555  0.000000|
 |  0.000000  0.000000  0.001686|
With corresponding cell

    A    = 152.579  B   = 152.548  C    = 593.210
    Alpha=  90.004  Beta=  90.026  Gamma=  90.002

The CRYST1 cell dimensions

    A    = 153.704  B   = 153.704  C    = 596.659
    Alpha=  90.000  Beta=  90.000  Gamma=  90.000

Variance: 3302.977
(Under-)estimated Z-score: 42.356

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.

 243 HIS   ( 243-)  A      CG   ND1  CE1 109.71    4.1
 538 THR   ( 108-)  B      CG2  CB   OG1 101.08   -4.1
 575 ARG   ( 145-)  B      CG   CD   NE  117.98    4.4
 990 THR   ( 122-)  C      CG2  CB   OG1 101.03   -4.1
1213 HIS   ( 345-)  C      N    CA   C   124.00    4.6
1282 GLN   (  35-)  D      CG   CD   NE2 125.38    6.0
1282 GLN   (  35-)  D      NE2  CD   OE1 113.01   -9.6
1406 GLY   ( 159-)  D      N    CA   C   124.11    4.0
1958 ARG   (  27-)  I     -C    N    CA  129.26    4.2
1958 ARG   (  27-)  I      N    CA   C   122.77    4.1
1960 LEU   (  29-)  I     -C    N    CA  129.23    4.2
2086 ASP   (  37-)  K      CA   CB   CG  116.79    4.2

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: 0.828
RMS-deviation in bond angles: 1.693

Error: Nomenclature error(s)

Checking for a hand-check. WHAT IF has over the course of this session already corrected the handedness of atoms in several residues. These were administrative corrections. These residues are listed here.

  20 ASP   (  20-)  A
 204 GLU   ( 204-)  A
 225 GLU   ( 225-)  A
 316 ASP   ( 316-)  A
 394 GLU   ( 394-)  A
 403 ASP   ( 403-)  A
 533 GLU   ( 103-)  B
1251 GLU   (   4-)  D
1392 GLU   ( 145-)  D
1414 GLU   ( 167-)  D
1419 ASP   ( 172-)  D
1555 ASP   (  67-)  E
1601 GLU   ( 113-)  E
1613 GLU   ( 125-)  E
1619 GLU   ( 131-)  E
1640 ASP   ( 152-)  E
1669 GLU   ( 181-)  E
1764 GLU   (  85-)  F
1785 GLU   ( 106-)  F
1856 GLU   (  67-)  G
1865 GLU   (  12-)  H
1881 GLU   (  28-)  H
1904 GLU   (  51-)  H
1909 GLU   (  56-)  H
1970 GLU   (  39-)  I
2036 GLU   (  48-)  J
2086 ASP   (  37-)  K

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.

Please also see the previous table that lists a series of administrative chirality problems that were corrected automatically upon reading-in the PDB file.

 238 GLY   ( 238-)  A      C     -7.0    -9.14     0.06
 508 LYS   (  78-)  B      C     -6.8   -10.15     0.11
 528 VAL   (  98-)  B      CA    -6.7    23.54    33.23
 539 VAL   ( 109-)  B      C     -6.0    -8.10     0.15
 584 ASN   ( 154-)  B      C     -6.2    -9.45     0.27
 599 ARG   ( 169-)  B      C      7.4    11.35     0.13
 666 LYS   ( 236-)  B      CA    -6.5    23.13    33.92
1405 ILE   ( 158-)  D      C     -6.9    -9.00     0.03
1778 ARG   (  99-)  F      C      7.6    11.63     0.13
1958 ARG   (  27-)  I      CA    -7.8    21.04    33.91
1959 PRO   (  28-)  I      C      6.3    10.45     0.42
2067 VAL   (  18-)  K      CA    -9.8    19.06    33.23
The average deviation= 1.934

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 : 1.658

Error: Tau angle problems

The side chains of the residues listed in the table below contain a tau angle (N-Calpha-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 RMS value deviates from the expected value.

 192 ALA   ( 192-)  A    6.43
1213 HIS   ( 345-)  C    6.28
2067 VAL   (  18-)  K    5.99
1025 GLY   ( 157-)  C    5.52
  74 ALA   (  74-)  A    4.92
1838 ALA   (  49-)  G    4.74
2044 LYS   (  56-)  J    4.65
2091 LEU   (  42-)  K    4.53
1281 LYS   (  34-)  D    4.40
 875 SER   (   7-)  C    4.40
 351 GLU   ( 351-)  A    4.40
1833 CYS   (  44-)  G    4.39
 582 LEU   ( 152-)  B    4.32
1958 ARG   (  27-)  I    4.29
1974 LEU   (  43-)  I    4.27
1053 LEU   ( 185-)  C    4.26

Note: Normal tau angle deviations

The RMS Z-score for the tau angles (N-Calpha-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 : 1.271

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.

 281 ASP   ( 281-)  A    9.17
1472 HIS   ( 225-)  D    5.98
 953 ASN   (  85-)  C    5.68
 534 ASN   ( 104-)  B    5.48
 670 HIS   ( 240-)  B    5.24
 707 HIS   ( 277-)  B    4.96
 678 ASN   ( 248-)  B    4.78
 555 ASN   ( 125-)  B    4.77
 600 ASN   ( 170-)  B    4.74
 594 HIS   ( 164-)  B    4.71
1721 ASP   (  42-)  F    4.66
 266 ASP   ( 266-)  A    4.42
 781 ASN   ( 351-)  B    4.40
 680 ASP   ( 250-)  B    4.27

Error: Connections to aromatic rings out of plane

The atoms listed in the table below are connected to a planar aromatic group in the sidechain of a protein residue but were found to deviate from the least squares plane.

For all atoms that are connected to an aromatic side chain in a protein residue the distance of the atom to the least squares plane through the aromatic system was determined. This value was divided by the standard deviation from a distribution of similar values from a database of small molecule structures.

 965 HIS   (  97-)  C      CB   4.42
Since there is no DNA and no protein with hydrogens, no uncalibrated
planarity check was performed.
 Ramachandran Z-score : -2.157

Torsion-related checks

Note: Ramachandran Z-score OK

The score expressing how well the backbone conformations of all residues correspond to the known allowed areas in the Ramachandran plot is within expected ranges for well-refined structures.

Ramachandran Z-score : -2.157

Warning: Torsion angle evaluation shows unusual residues

The residues listed in the table below contain bad or abnormal torsion angles.

These scores give an impression of how `normal' the torsion angles in protein residues are. All torsion angles except omega are used for calculating a `normality' score. Average values and standard deviations were obtained from the residues in the WHAT IF database. These are used to calculate Z-scores. A residue with a Z-score of below -2.0 is poor, and a score of less than -3.0 is worrying. For such residues more than one torsion angle is in a highly unlikely position.

1968 THR   (  37-)  I    -3.5
1022 PRO   ( 154-)  C    -3.1
1410 PRO   ( 163-)  D    -3.0
1991 PRO   (   3-)  J    -3.0
1863 PRO   (  74-)  G    -3.0
 448 PRO   (  18-)  B    -3.0
1663 PRO   ( 175-)  E    -2.9
 229 PRO   ( 229-)  A    -2.9
1958 ARG   (  27-)  I    -2.9
2044 LYS   (  56-)  J    -2.8
1409 PRO   ( 162-)  D    -2.8
1605 LEU   ( 117-)  E    -2.8
1003 TRP   ( 135-)  C    -2.8
 302 LYS   ( 302-)  A    -2.7
1992 THR   (   4-)  J    -2.7
1866 LEU   (  13-)  H    -2.7
1265 LEU   (  18-)  D    -2.6
1256 SER   (   9-)  D    -2.6
1024 ILE   ( 156-)  C    -2.6
1957 LEU   (  26-)  I    -2.6
1801 HIS   (  12-)  G    -2.6
1974 LEU   (  43-)  I    -2.5
1861 LYS   (  72-)  G    -2.5
1976 LEU   (  45-)  I    -2.5
1262 ARG   (  15-)  D    -2.5
And so on for a total of 130 lines.

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.

  42 ASP   (  42-)  A  Poor phi/psi
  48 GLU   (  48-)  A  omega poor
  49 SER   (  49-)  A  omega poor
  50 GLU   (  50-)  A  Poor phi/psi
 122 LEU   ( 122-)  A  Poor phi/psi
 159 GLN   ( 159-)  A  Poor phi/psi
 190 TYR   ( 190-)  A  Poor phi/psi
 203 LEU   ( 203-)  A  omega poor
 218 GLY   ( 218-)  A  Poor phi/psi
 220 SER   ( 220-)  A  Poor phi/psi
 224 ASP   ( 224-)  A  Poor phi/psi
 303 LEU   ( 303-)  A  omega poor
 304 CYS   ( 304-)  A  Poor phi/psi
 306 SER   ( 306-)  A  Poor phi/psi
 316 ASP   ( 316-)  A  Poor phi/psi
 369 LEU   ( 369-)  A  Poor phi/psi
 417 ASP   ( 417-)  A  Poor phi/psi
 420 PRO   ( 420-)  A  omega poor
 457 THR   (  27-)  B  omega poor
 471 TYR   (  41-)  B  Poor phi/psi
 534 ASN   ( 104-)  B  omega poor
 541 CYS   ( 111-)  B  Poor phi/psi
 583 GLN   ( 153-)  B  omega poor
 590 ILE   ( 160-)  B  omega poor
 599 ARG   ( 169-)  B  omega poor
And so on for a total of 106 lines.

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 : -5.660

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.

1007 SER   ( 139-)  C    0.36
 956 SER   (  88-)  C    0.38

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!

  11 VAL   (  11-)  A      0
  19 LEU   (  19-)  A      0
  21 ASN   (  21-)  A      0
  31 SER   (  31-)  A      0
  34 THR   (  34-)  A      0
  42 ASP   (  42-)  A      0
  43 ALA   (  43-)  A      0
  45 SER   (  45-)  A      0
  49 SER   (  49-)  A      0
  50 GLU   (  50-)  A      0
  53 ASN   (  53-)  A      0
  65 LYS   (  65-)  A      0
  70 ARG   (  70-)  A      0
  71 PRO   (  71-)  A      0
  82 MET   (  82-)  A      0
 102 LEU   ( 102-)  A      0
 119 ASN   ( 119-)  A      0
 121 SER   ( 121-)  A      0
 123 GLU   ( 123-)  A      0
 145 MET   ( 145-)  A      0
 159 GLN   ( 159-)  A      0
 168 GLU   ( 168-)  A      0
 189 HIS   ( 189-)  A      0
 190 TYR   ( 190-)  A      0
 195 MET   ( 195-)  A      0
And so on for a total of 719 lines.

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 : -0.629

Note: Omega angle restraint OK

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 agrees with this expectation.

Standard deviation of omega values : 5.661

Warning: Backbone oxygen evaluation

The residues listed in the table below have an unusual backbone oxygen position.

For each of the residues in the structure, a search was performed to find 5-residue stretches in the WHAT IF database with superposable C-alpha coordinates, and some restraining on the neighbouring backbone oxygens.

In the following table the RMS distance between the backbone oxygen positions of these matching structures in the database and the position of the backbone oxygen atom in the current residue is given. If this number is larger than 1.5 a significant number of structures in the database show an alternative position for the backbone oxygen. If the number is larger than 2.0 most matching backbone fragments in the database have the peptide plane flipped. A manual check needs to be performed to assess whether the experimental data can support that alternative as well. The number in the last column is the number of database hits (maximum 80) used in the calculation. It is "normal" that some glycine residues show up in this list, but they are still worth checking!

1895 GLU   (  42-)  H   1.77   13
1650 GLY   ( 162-)  E   1.74   17
1572 GLY   (  84-)  E   1.52   39

Note: Peptide bond conformations

We could not find any peptide bonds that are likely to actually be a cis bond. This check has not yet fully matured...

Note: PRO puckering amplitude OK

Puckering amplitudes for all PRO residues are within normal ranges.

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].

  33 PRO   (  33-)  A    50.1 half-chair C-delta/C-gamma (54 degrees)
 107 PRO   ( 107-)  A  -122.4 half-chair C-delta/C-gamma (-126 degrees)
 229 PRO   ( 229-)  A   -16.7 half-chair C-alpha/N (-18 degrees)
 249 PRO   ( 249-)  A    21.9 half-chair N/C-delta (18 degrees)
 427 PRO   ( 427-)  A    43.1 envelop C-delta (36 degrees)
 448 PRO   (  18-)  B    25.2 half-chair N/C-delta (18 degrees)
 460 PRO   (  30-)  B  -154.7 half-chair N/C-delta (-162 degrees)
 560 PRO   ( 130-)  B   -59.2 half-chair C-beta/C-alpha (-54 degrees)
 585 PRO   ( 155-)  B  -145.5 envelop C-delta (-144 degrees)
 609 PRO   ( 179-)  B  -133.9 half-chair C-delta/C-gamma (-126 degrees)
 618 PRO   ( 188-)  B  -132.4 half-chair C-delta/C-gamma (-126 degrees)
 713 PRO   ( 283-)  B   -40.6 envelop C-alpha (-36 degrees)
 736 PRO   ( 306-)  B   106.3 envelop C-beta (108 degrees)
 825 PRO   ( 395-)  B  -125.7 half-chair C-delta/C-gamma (-126 degrees)
1002 PRO   ( 134-)  C   111.0 envelop C-beta (108 degrees)
1022 PRO   ( 154-)  C   137.0 envelop C-alpha (144 degrees)
1076 PRO   ( 208-)  C   101.8 envelop C-beta (108 degrees)
1090 PRO   ( 222-)  C    -6.5 envelop N (0 degrees)
1173 PRO   ( 305-)  C  -130.4 half-chair C-delta/C-gamma (-126 degrees)
1254 PRO   (   7-)  D  -122.6 half-chair C-delta/C-gamma (-126 degrees)
1258 PRO   (  11-)  D   -56.8 half-chair C-beta/C-alpha (-54 degrees)
1358 PRO   ( 111-)  D    49.9 half-chair C-delta/C-gamma (54 degrees)
1385 PRO   ( 138-)  D   -53.7 half-chair C-beta/C-alpha (-54 degrees)
1401 PRO   ( 154-)  D  -121.0 half-chair C-delta/C-gamma (-126 degrees)
1409 PRO   ( 162-)  D   -22.2 half-chair C-alpha/N (-18 degrees)
1410 PRO   ( 163-)  D    36.1 envelop C-delta (36 degrees)
1487 PRO   ( 240-)  D   -58.2 half-chair C-beta/C-alpha (-54 degrees)
1496 PRO   (   8-)  E    99.8 envelop C-beta (108 degrees)
1647 PRO   ( 159-)  E   -35.0 envelop C-alpha (-36 degrees)
1663 PRO   ( 175-)  E    -6.1 envelop N (0 degrees)
1755 PRO   (  76-)  F   145.7 envelop C-alpha (144 degrees)
1809 PRO   (  20-)  G    44.1 envelop C-delta (36 degrees)
1816 PRO   (  27-)  G  -120.7 half-chair C-delta/C-gamma (-126 degrees)
1824 PRO   (  35-)  G   116.8 envelop C-beta (108 degrees)
1863 PRO   (  74-)  G   -46.4 half-chair C-beta/C-alpha (-54 degrees)
1941 PRO   (  10-)  I     2.9 envelop N (0 degrees)
1959 PRO   (  28-)  I   125.3 half-chair C-beta/C-alpha (126 degrees)
1972 PRO   (  41-)  I   104.0 envelop C-beta (108 degrees)
1991 PRO   (   3-)  J   -10.1 half-chair C-alpha/N (-18 degrees)
2057 PRO   (   8-)  K  -115.3 envelop C-gamma (-108 degrees)
2068 PRO   (  19-)  K   113.8 envelop C-beta (108 degrees)

Bump checks

Error: Abnormally short interatomic distances

The pairs of atoms listed in the table below have an unusually short interactomic 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. Although we believe that two water atoms at 2.4 A distance are too close, we only report water pairs that are closer than this rather short distance.

The last text-item on each line represents the status of the atom pair. 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). BL indicates that the B-factors of the clashing atoms have a low B-factor thereby making this clash even more worrisome. INTRA and INTER indicate whether the clashes are between atoms in the same asymmetric unit, or atoms in symmetry related asymmetric units, respectively.

2087 TRP   (  38-)  K      CE3 <-> 2090 ILE   (  41-)  K      CD1    1.16    2.04  INTRA
1407 MET   ( 160-)  D      SD  <-> 2116 HEM   ( 243-)  D      NA     0.58    2.72  INTRA BF
1407 MET   ( 160-)  D      SD  <-> 2116 HEM   ( 243-)  D      ND     0.46    2.84  INTRA BF
 419 CYS   ( 419-)  A      SG  <->  438 ARG   ( 438-)  A      NH1    0.41    2.89  INTRA
 600 ASN   ( 170-)  B      ND2 <->  666 LYS   ( 236-)  B      O      0.32    2.38  INTRA
 675 ARG   ( 245-)  B      NH2 <->  863 THR   ( 433-)  B      O      0.30    2.40  INTRA BL
2087 TRP   (  38-)  K      CZ3 <-> 2090 ILE   (  41-)  K      CD1    0.29    2.91  INTRA
1279 VAL   (  32-)  D      O   <-> 1284 CYS   (  37-)  D      SG     0.26    2.74  INTRA
1407 MET   ( 160-)  D      SD  <-> 2116 HEM   ( 243-)  D      C1A    0.26    3.14  INTRA BF
 131 ARG   ( 131-)  A      NH2 <->  177 LEU   ( 177-)  A      O      0.25    2.45  INTRA BL
 154 HIS   ( 154-)  A      NE2 <->  314 TYR   ( 314-)  A      OH     0.25    2.45  INTRA BL
 534 ASN   ( 104-)  B      ND2 <-> 2123 HOH   ( 573 )  B      O      0.24    2.46  INTRA
 564 ARG   ( 134-)  B      NH1 <-> 2123 HOH   ( 580 )  B      O      0.24    2.46  INTRA BF
1627 CYS   ( 139-)  E      SG  <-> 1653 TYR   ( 165-)  E      OH     0.22    2.78  INTRA
 578 LYS   ( 148-)  B      NZ  <->  610 ASP   ( 180-)  B      OD1    0.22    2.48  INTRA
1731 GLU   (  52-)  F      OE2 <-> 1800 ARG   (  11-)  G      NH1    0.21    2.49  INTRA BL
  60 GLU   (  60-)  A      OE1 <->  717 ARG   ( 287-)  B      NH2    0.21    2.49  INTRA
 339 GLN   ( 339-)  A      NE2 <->  441 MET   ( 441-)  A      SD     0.21    3.09  INTRA BL
 150 PHE   ( 150-)  A      O   <->  154 HIS   ( 154-)  A      ND1    0.20    2.50  INTRA BL
1470 LYS   ( 223-)  D      NZ  <-> 2114 CDL   ( 242-)  G      OA4    0.19    2.51  INTRA
2087 TRP   (  38-)  K      CD2 <-> 2090 ILE   (  41-)  K      CD1    0.19    3.01  INTRA
 683 VAL   ( 253-)  B      N   <->  758 SER   ( 328-)  B      O      0.19    2.51  INTRA BL
 815 GLN   ( 385-)  B      OE1 <->  823 THR   ( 393-)  B      N      0.19    2.51  INTRA BL
1288 HIS   (  41-)  D      NE2 <-> 2116 HEM   ( 243-)  D      ND     0.18    2.82  INTRA BF
 489 ASN   (  59-)  B      OD1 <->  491 ASN   (  61-)  B      N      0.18    2.52  INTRA
And so on for a total of 149 lines.

Packing, accessibility and threading

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 : 1.110

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.

Chain identifier: A

Note: Inside/Outside RMS Z-score plot

Chain identifier: B

Note: Inside/Outside RMS Z-score plot

Chain identifier: C

Note: Inside/Outside RMS Z-score plot

Chain identifier: D

Note: Inside/Outside RMS Z-score plot

Chain identifier: E

Note: Inside/Outside RMS Z-score plot

Chain identifier: F

Note: Inside/Outside RMS Z-score plot

Chain identifier: G

Note: Inside/Outside RMS Z-score plot

Chain identifier: H

Note: Inside/Outside RMS Z-score plot

Chain identifier: I

Note: Inside/Outside RMS Z-score plot

Chain identifier: J

Note: Inside/Outside RMS Z-score plot

Chain identifier: K

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.

1023 TYR   ( 155-)  C      -8.24
1606 ARG   ( 118-)  E      -7.45
1987 ARG   (  56-)  I      -7.43
 657 ARG   ( 227-)  B      -6.77
1791 ARG   (   2-)  G      -6.76
1264 LEU   (  17-)  D      -6.72
2101 PHE   (  52-)  K      -6.70
1368 HIS   ( 121-)  D      -6.68
1407 MET   ( 160-)  D      -6.64
 851 ARG   ( 421-)  B      -6.61
1861 LYS   (  72-)  G      -6.54
1983 ARG   (  52-)  I      -6.39
 450 HIS   (  20-)  B      -6.37
1253 HIS   (   6-)  D      -6.32
 599 ARG   ( 169-)  B      -6.31
1036 PHE   ( 168-)  C      -6.31
1604 GLN   ( 116-)  E      -6.28
1356 LEU   ( 109-)  D      -6.27
1924 HIS   (  71-)  H      -6.26
 471 TYR   (  41-)  B      -6.22
1485 ARG   ( 238-)  D      -6.21
1117 LEU   ( 249-)  C      -6.09
 662 LEU   ( 232-)  B      -6.08
 734 HIS   ( 304-)  B      -6.07
1616 LYS   ( 128-)  E      -6.05
And so on for a total of 70 lines.

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.

  68 LYS   (  68-)  A        70 - ARG     70- ( A)         -4.30
 225 GLU   ( 225-)  A       227 - ALA    227- ( A)         -4.21
1250 LEU   (   3-)  D      1253 - HIS      6- ( D)         -5.08
1381 TYR   ( 134-)  D      1383 - GLU    136- ( D)         -4.64
1750 ARG   (  71-)  F      1752 - GLN     73- ( F)         -4.52
1860 ARG   (  71-)  G      1862 - ASN     73- ( G)         -5.84

Note: Structural average packing environment OK

The structural average packing score is within normal ranges.

Average for range 1 - 2102 : -1.080

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.

Chain identifier: A

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.

Chain identifier: B

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.

Chain identifier: C

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.

Chain identifier: D

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.

Chain identifier: E

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.

Chain identifier: F

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.

Chain identifier: G

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.

Chain identifier: H

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.

Chain identifier: I

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.

Chain identifier: J

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.

Chain identifier: K

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.

 444 LEU   ( 444-)  A   -2.95
 601 ALA   ( 171-)  B   -2.76
 860 LEU   ( 430-)  B   -2.67
1020 ALA   ( 152-)  C   -2.62
1694 LYS   (  15-)  F   -2.59
1283 VAL   (  36-)  D   -2.55

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.

1964 ALA   (  33-)  I     - 1967 ALA   (  36-)  I        -1.47

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.

Chain identifier: A

Note: Second generation quality Z-score plot

Chain identifier: B

Note: Second generation quality Z-score plot

Chain identifier: C

Note: Second generation quality Z-score plot

Chain identifier: D

Note: Second generation quality Z-score plot

Chain identifier: E

Note: Second generation quality Z-score plot

Chain identifier: F

Note: Second generation quality Z-score plot

Chain identifier: G

Note: Second generation quality Z-score plot

Chain identifier: H

Note: Second generation quality Z-score plot

Chain identifier: I

Note: Second generation quality Z-score plot

Chain identifier: J

Note: Second generation quality Z-score plot

Chain identifier: K

Water, ion, and hydrogenbond related checks

Note: Water contacts OK

All water clusters make at least one contact with a non-water atom.

Note: No waters need moving

All water molecules are sufficiently close to the asymmetric unit given in the input file.

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. The last number on each line is the identifier of the water molecule in the input file.

2122 HOH   ( 509 )  A      O
2123 HOH   ( 622 )  B      O
2124 HOH   ( 638 )  C      O
2124 HOH   ( 640 )  C      O
2124 HOH   ( 660 )  C      O
2124 HOH   ( 691 )  C      O
Metal-coordinating Histidine residue 965 fixed to   1
Metal-coordinating Histidine residue1064 fixed to   1
Metal-coordinating Histidine residue 951 fixed to   1
Metal-coordinating Histidine residue1050 fixed to   1
Metal-coordinating Histidine residue1288 fixed to   1
Metal-coordinating Histidine residue1649 fixed to   1

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.

  18 GLN   (  18-)  A
  53 ASN   (  53-)  A
 119 ASN   ( 119-)  A
 308 GLN   ( 308-)  A
 604 ASN   ( 174-)  B
 678 ASN   ( 248-)  B
 792 ASN   ( 362-)  B
 922 HIS   (  54-)  C
 942 ASN   (  74-)  C
1154 ASN   ( 286-)  C
1261 HIS   (  14-)  D
1278 GLN   (  31-)  D
1588 HIS   ( 100-)  E
1928 ASN   (  75-)  H
1962 GLN   (  31-)  I
2025 GLN   (  37-)  J
2061 GLN   (  12-)  K
2098 ASN   (  49-)  K

Note: Histidine type assignments

For all complete HIS residues in the structure a tentative assignment to HIS-D (protonated on ND1), HIS-E (protonated on NE2), or HIS-H (protonated on both ND1 and NE2, positively charged) is made based on the hydrogen bond network. A second assignment is made based on which of the Engh and Huber [REF] histidine geometries fits best to the structure.

In the table below all normal histidine residues are listed. The assignment based on the geometry of the residue is listed first, together with the RMS Z-score for the fit to the Engh and Huber parameters. For all residues where the H-bond assignment is different, the assignment is listed in the last columns, together with its RMS Z-score to the Engh and Huber parameters.

As always, the RMS Z-scores should be close to 1.0 if the residues were restrained to the Engh and Huber parameters during refinement.

Please note that because the differences between the geometries of the different types are small it is possible that the geometric assignment given here does not correspond to the type used in refinement. This is especially true if the RMS Z-scores are much higher than 1.0.

If the two assignments differ, or the `geometry' RMS Z-score is high, it is advisable to verify the hydrogen bond assignment, check the HIS type used during the refinement and possibly adjust it.

  61 HIS   (  61-)  A     HIS-H   0.32 HIS-D   0.70
  85 HIS   (  85-)  A     HIS-H   0.37 HIS-D   0.54
  94 HIS   (  94-)  A     HIS-H   0.23 HIS-E   0.53
 154 HIS   ( 154-)  A     HIS-H   0.33 HIS-D   0.69
 189 HIS   ( 189-)  A     HIS-H   0.16 HIS-E   0.61
 205 HIS   ( 205-)  A     HIS-H   0.10 HIS-D   0.54
 215 HIS   ( 215-)  A     HIS-H   0.07 HIS-E   0.57
 243 HIS   ( 243-)  A     HIS-H   0.26 HIS-E   0.60
 252 HIS   ( 252-)  A     HIS-H   0.19 HIS-E   0.64
 264 HIS   ( 264-)  A     HIS-H   0.24 HIS-E   0.62
 279 HIS   ( 279-)  A     HIS-H   0.22 HIS-D   0.57
 289 HIS   ( 289-)  A     HIS-H   0.21 HIS-D   0.57
 323 HIS   ( 323-)  A     HIS-H   0.35 HIS-E   0.64
 328 HIS   ( 328-)  A     HIS-H   0.19 HIS-D   0.60
 368 HIS   ( 368-)  A     HIS-H   0.16 HIS-E   0.57
 450 HIS   (  20-)  B     HIS-H   0.42 HIS-E   0.60
 497 HIS   (  67-)  B     HIS-H   0.41 HIS-E   0.63
 588 HIS   ( 158-)  B     HIS-H   0.60 HIS-D   0.78
 594 HIS   ( 164-)  B     HIS-H   0.28 HIS-D   0.47
 622 HIS   ( 192-)  B     HIS-E   0.79
 628 HIS   ( 198-)  B     HIS-H   0.29 HIS-D   0.63
 643 HIS   ( 213-)  B     HIS-H   0.38 HIS-D   0.63
 670 HIS   ( 240-)  B     HIS-H   0.15 HIS-E   0.56
 684 HIS   ( 254-)  B     HIS-H   0.20 HIS-E   0.59
 707 HIS   ( 277-)  B     HIS-H   0.17 HIS-D   0.62
 714 HIS   ( 284-)  B     HIS-H   0.20 HIS-D   0.62
 734 HIS   ( 304-)  B     HIS-H   0.14 HIS-E   0.59
 862 HIS   ( 432-)  B     HIS-H   0.08 HIS-E   0.59
 876 HIS   (   8-)  C     HIS-H   0.05 HIS-E   0.59
 922 HIS   (  54-)  C     HIS-H   0.25 HIS-D   0.64
 936 HIS   (  68-)  C     HIS-H   0.17 HIS-E   0.57
 951 HIS   (  83-)  C     HIS-H   0.45 HIS-D   0.72
 965 HIS   (  97-)  C     HIS-H   0.39 HIS-D   0.64
1050 HIS   ( 182-)  C     HIS-H   0.39 HIS-D   0.69
1064 HIS   ( 196-)  C     HIS-H   0.50 HIS-D   0.72
1069 HIS   ( 201-)  C     HIS-H   0.48 HIS-E   0.63
1089 HIS   ( 221-)  C     HIS-H   0.10 HIS-D   0.53
1135 HIS   ( 267-)  C     HIS-H   0.29 HIS-E   0.58
1176 HIS   ( 308-)  C     HIS-H   0.27 HIS-E   0.62
1213 HIS   ( 345-)  C     HIS-H   0.15 HIS-E   0.55
1253 HIS   (   6-)  D     HIS-H   0.04 HIS-E   0.59
1261 HIS   (  14-)  D     HIS-H   0.21 HIS-E   0.59
1270 HIS   (  23-)  D     HIS-H   0.18 HIS-D   0.60
1288 HIS   (  41-)  D     HIS-H   0.24 HIS-D   0.66
1297 HIS   (  50-)  D     HIS-H   0.09 HIS-E   0.58
1368 HIS   ( 121-)  D     HIS-H   0.08 HIS-E   0.56
1445 HIS   ( 198-)  D     HIS-H   0.15 HIS-E   0.56
1447 HIS   ( 200-)  D     HIS-H   0.18 HIS-D   0.57
1472 HIS   ( 225-)  D     HIS-H   0.14 HIS-D   0.51
1490 HIS   (   2-)  E     HIS-H   0.09 HIS-D   0.60
1588 HIS   ( 100-)  E     HIS-H   0.20 HIS-E   0.62
1610 HIS   ( 122-)  E     HIS-H   0.17 HIS-E   0.62
1629 HIS   ( 141-)  E     HIS-H   0.05 HIS-E   0.57
1649 HIS   ( 161-)  E     HIS-H   0.11 HIS-E   0.60
1652 HIS   ( 164-)  E     HIS-H   0.07 HIS-E   0.57
1717 HIS   (  38-)  F     HIS-H   0.29 HIS-E   0.56
1795 HIS   (   6-)  G     HIS-H   0.28 HIS-E   0.59
1801 HIS   (  12-)  G     HIS-H   0.15 HIS-E   0.63
1817 HIS   (  28-)  G     HIS-H   0.11 HIS-D   0.53
1916 HIS   (  63-)  H     HIS-H   0.24 HIS-E   0.61
1920 HIS   (  67-)  H     HIS-H   0.24 HIS-E   0.67
1924 HIS   (  71-)  H     HIS-H   0.18 HIS-E   0.58
2033 HIS   (  45-)  J     HIS-H   0.06 HIS-E   0.57
2042 HIS   (  54-)  J     HIS-H   0.13 HIS-E   0.59
2045 HIS   (  57-)  J     HIS-H   0.18 HIS-E   0.59

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.

  23 LEU   (  23-)  A      N
  44 GLY   (  44-)  A      N
  45 SER   (  45-)  A      N
  47 TYR   (  47-)  A      N
  51 LYS   (  51-)  A      N
  52 ASN   (  52-)  A      N
  53 ASN   (  53-)  A      N
  54 GLY   (  54-)  A      N
  75 LEU   (  75-)  A      N
  88 ALA   (  88-)  A      N
  97 TYR   (  97-)  A      OH
 131 ARG   ( 131-)  A      NH1
 145 MET   ( 145-)  A      N
 159 GLN   ( 159-)  A      N
 159 GLN   ( 159-)  A      NE2
 168 GLU   ( 168-)  A      N
 192 ALA   ( 192-)  A      N
 204 GLU   ( 204-)  A      N
 206 ARG   ( 206-)  A      N
 219 LEU   ( 219-)  A      N
 250 LEU   ( 250-)  A      N
 252 HIS   ( 252-)  A      NE2
 281 ASP   ( 281-)  A      N
 292 SER   ( 292-)  A      N
 328 HIS   ( 328-)  A      N
And so on for a total of 262 lines.

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.

  48 GLU   (  48-)  A      OE1
  61 HIS   (  61-)  A      NE2
 205 HIS   ( 205-)  A      NE2
 240 GLN   ( 240-)  A      OE1
 394 GLU   ( 394-)  A      OE1
 586 GLN   ( 156-)  B      OE1
 670 HIS   ( 240-)  B      ND1
 706 GLN   ( 276-)  B      OE1
 811 GLU   ( 381-)  B      OE1
 912 GLN   (  44-)  C      OE1
1180 GLN   ( 312-)  C      OE1
1199 ASP   ( 331-)  C      OD2
1213 HIS   ( 345-)  C      ND1
1352 ASN   ( 105-)  D      OD1
1371 GLU   ( 124-)  D      OE2
1629 HIS   ( 141-)  E      ND1
1667 ASN   ( 179-)  E      OD1
1811 GLU   (  22-)  G      OE1
2042 HIS   (  54-)  J      ND1
2065 ASN   (  16-)  K      OD1

Note: Crystallisation conditions from REMARK 280

Crystallisation conditions as found in the PDB file header.

CRYSTAL
SOLVENT CONTENT, VS   (%): 65.56
MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.57
CRYSTALLIZATION CONDITIONS: 20MM AMMONIUM ACETATE, 20% GLYCEROL,
       12% PEG4000, 0.5M KCL, 0.1% DIHEPTANOYL-PHOSPHATIDYLCHOLINE, PH
       7.2, VAPOR DIFFUSION, TEMPERATURE 277K

Note: No ions (of a type we can validate) in structure

Since there are no ions in the structure of a type we can validate, this check will not be executed.

Note: Water packing OK

All waters seem properly packed, or at least not packed like an ion. This method is experimental. See: swift.cmbi.ru.nl/teach/theory/

Warning: Possible wrong residue type

The residues listed in the table below have a weird environment that cannot be improved by rotamer flips. This can mean one of three things, non of which WHAT CHECK really can do much about. 1) The side chain has actually another rotamer than is present in the PDB file; 2) A counter ion is present in the structure but is not given in the PDB file; 3) The residue actually is another amino acid type. The annotation 'Alt-rotamer' indicates that WHAT CHECK thinks you might want to find an alternate rotamer for this residue. The annotation 'Sym-induced' indicates that WHAT CHECK believes that symmetry contacts might have something to do with the difficulties of this residue's side chain. Determination of these two annotations is difficult, so their absence is less meaningful than their presence. The annotation Ligand-bound indicates that a ligand seems involved with this residue. In nine of ten of these cases this indicates that the ligand is causing the weird situation rather than the residue.

  48 GLU   (  48-)  A   H-bonding suggests Gln; but Alt-Rotamer
 142 ASP   ( 142-)  A   H-bonding suggests Asn
 204 GLU   ( 204-)  A   H-bonding suggests Gln
 673 GLU   ( 243-)  B   H-bonding suggests Gln; but Alt-Rotamer
1139 GLU   ( 271-)  C   H-bonding suggests Gln
1313 GLU   (  66-)  D   H-bonding suggests Gln
1492 ASP   (   4-)  E   H-bonding suggests Asn; but Alt-Rotamer
1654 ASP   ( 166-)  E   H-bonding suggests Asn; but Alt-Rotamer
1713 ASP   (  34-)  F   H-bonding suggests Asn; but Alt-Rotamer
1736 ASP   (  57-)  F   H-bonding suggests Asn
1875 GLU   (  22-)  H   H-bonding suggests Gln
1878 GLU   (  25-)  H   H-bonding suggests Gln
1894 ASP   (  41-)  H   H-bonding suggests Asn
1913 ASP   (  60-)  H   H-bonding suggests Asn; but Alt-Rotamer
1975 ASP   (  44-)  I   H-bonding suggests Asn
2024 ASP   (  36-)  J   H-bonding suggests Asn; Ligand-contact
2032 GLU   (  44-)  J   H-bonding suggests Gln; but Alt-Rotamer

Note: Content of the PDB file as interpreted by WHAT IF

Content of the PDB file as interpreted by WHAT IF. WHAT IF has read your PDB file, and stored it internally in what is called 'the soup'. The content of this soup is listed here. An extensive explanation of all frequently used WHAT IF output formats can be found at swift.cmbi.ru.nl. Look under output formats. A course on reading this 'Molecules' table is part of the WHAT CHECK web pages.

     1     1 (    1)   446 (  446) A Protein             pdb1sqp.ent
     2   447 (   17)   869 (  439) B Protein             pdb1sqp.ent
     3   870 (    2)  1247 (  379) C Protein             pdb1sqp.ent
     4  1248 (    1)  1488 (  241) D Protein             pdb1sqp.ent
     5  1489 (    1)  1684 (  196) E Protein             pdb1sqp.ent
     6  1685 (    6)  1789 (  110) F Protein             pdb1sqp.ent
     7  1790 (    1)  1864 (   75) G Protein             pdb1sqp.ent
     8  1865 (   12)  1931 (   78) H Protein             pdb1sqp.ent
     9  1932 (    1)  1988 (   57) I Protein             pdb1sqp.ent
    10  1989 (    1)  2049 (   61) J Protein             pdb1sqp.ent
    11  2050 (    1)  2102 (   53) K Protein             pdb1sqp.ent
    12  2103 (  446)  2103 (  446) A F O2 <-   446       pdb1sqp.ent
    13  2104 (  439)  2104 (  439) B L O2 <-   869       pdb1sqp.ent
    14  2105 (  379)  2105 (  379) C W O2 <-  1247       pdb1sqp.ent
    15  2106 (  241)  2106 (  241) D K O2 <-  1488       pdb1sqp.ent
    16  2107 (  196)  2107 (  196) E G O2 <-  1684       pdb1sqp.ent
    17  2108 (  110)  2108 (  110) F K O2 <-  1789       pdb1sqp.ent
    18  2109 (   78)  2109 (   78) H K O2 <-  1931       pdb1sqp.ent
    19  2110 (  447)  2110 (  447) A CDL                 pdb1sqp.ent
    20  2111 (  448)  2111 (  448) A PEE                 pdb1sqp.ent
    21  2112 (  380)  2112 (  380) C PEE                 pdb1sqp.ent
    22  2113 (  381)  2113 (  381) C HEM                 pdb1sqp.ent
    23  2114 (  242)  2114 (  242) G CDL                 pdb1sqp.ent
    24  2115 (  382)  2115 (  382) C HEM                 pdb1sqp.ent
    25  2116 (  243)  2116 (  243) D HEM  <=             pdb1sqp.ent
    26  2117 (   82)  2117 (   82) G CDL                 pdb1sqp.ent
    27  2118 (  198)  2118 (  198) E FES                 pdb1sqp.ent
    28  2119 (   63)  2119 (   63) E PLX                 pdb1sqp.ent
    29  2120 (  197)  2120 (  197) E PEE                 pdb1sqp.ent
    30  2121 (  383)  2121 (  383) C MYX                 pdb1sqp.ent
    31  2122 ( HOH )  2122 ( HOH ) A water   (   51)     pdb1sqp.ent
    32  2123 ( HOH )  2123 ( HOH ) B water   (   84)     pdb1sqp.ent
    33  2124 ( HOH )  2124 ( HOH ) C water   (   36)     pdb1sqp.ent
    34  2125 ( HOH )  2125 ( HOH ) D water   (   11)     pdb1sqp.ent
    35  2126 ( HOH )  2126 ( HOH ) E water   (    2)     pdb1sqp.ent
    36  2127 ( HOH )  2127 ( HOH ) F water   (   15)     pdb1sqp.ent
    37  2128 ( HOH )  2128 ( HOH ) G water   (   11)     pdb1sqp.ent
    38  2129 ( HOH )  2129 ( HOH ) I water   (    2)     pdb1sqp.ent
    39  2130 ( HOH )  2130 ( HOH ) K water   (    3)     pdb1sqp.ent

Final summary

Note: Summary report for users of a structure

This is an overall summary of the quality of the structure as compared with current reliable structures. This summary is most useful for biologists seeking a good structure to use for modelling calculations.

The second part of the table mostly gives an impression of how well the model conforms to common refinement restraint values. The first part of the table shows a number of global quality indicators.


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -1.449
  2nd generation packing quality :  -2.031
  Ramachandran plot appearance   :  -2.157
  chi-1/chi-2 rotamer normality  :  -5.660 (bad)
  Backbone conformation          :  -0.629

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.919
  Bond angles                    :   0.828
  Omega angle restraints         :   1.029
  Side chain planarity           :   1.554
  Improper dihedral distribution :   1.658 (loose)
  B-factor distribution          :   0.631
  Inside/Outside distribution    :   1.110

Note: Summary report for depositors of a structure

This is an overall summary of the quality of the X-ray structure as compared with structures solved at similar resolutions. This summary can be useful for a crystallographer to see if the structure makes the best possible use of the data. Warning. This table works well for structures solved in the resolution range of the structures in the WHAT IF database, which is presently (summer 2008) mainly 1.1 - 1.3 Angstrom. The further the resolution of your file deviates from this range the more meaningless this table becomes.

The second part of the table mostly gives an impression of how well the model conforms to common refinement restraint values. The first part of the table shows a number of global quality indicators, which have been calibrated against structures of similar resolution.

Resolution found in PDB file : 2.70


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -0.5
  2nd generation packing quality :  -0.4
  Ramachandran plot appearance   :   0.4
  chi-1/chi-2 rotamer normality  :  -3.1 (poor)
  Backbone conformation          :  -0.0

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.919
  Bond angles                    :   0.828
  Omega angle restraints         :   1.029
  Side chain planarity           :   1.554
  Improper dihedral distribution :   1.658 (loose)
  B-factor distribution          :   0.631
  Inside/Outside distribution    :   1.110
==============

WHAT IF
    G.Vriend,
      WHAT IF: a molecular modelling and drug design program,
    J. Mol. Graph. 8, 52--56 (1990).

WHAT_CHECK (verification routines from WHAT IF)
    R.W.W.Hooft, G.Vriend, C.Sander and E.E.Abola,
      Errors in protein structures
    Nature 381, 272 (1996).
    (see also http://swift.cmbi.ru.nl/gv/whatcheck for a course and extra inform

Bond lengths and angles, protein residues
    R.Engh and R.Huber,
      Accurate bond and angle parameters for X-ray protein structure
      refinement,
    Acta Crystallogr. A47, 392--400 (1991).

Bond lengths and angles, DNA/RNA
    G.Parkinson, J.Voitechovsky, L.Clowney, A.T.Bruenger and H.Berman,
      New parameters for the refinement of nucleic acid-containing structures
    Acta Crystallogr. D52, 57--64 (1996).

DSSP
    W.Kabsch and C.Sander,
      Dictionary of protein secondary structure: pattern
      recognition of hydrogen bond and geometrical features
    Biopolymers 22, 2577--2637 (1983).

Hydrogen bond networks
    R.W.W.Hooft, C.Sander and G.Vriend,
      Positioning hydrogen atoms by optimizing hydrogen bond networks in
      protein structures
    PROTEINS, 26, 363--376 (1996).

Matthews' Coefficient
    B.W.Matthews
      Solvent content of Protein Crystals
    J. Mol. Biol. 33, 491--497 (1968).

Protein side chain planarity
    R.W.W. Hooft, C. Sander and G. Vriend,
      Verification of protein structures: side-chain planarity
    J. Appl. Cryst. 29, 714--716 (1996).

Puckering parameters
    D.Cremer and J.A.Pople,
      A general definition of ring puckering coordinates
    J. Am. Chem. Soc. 97, 1354--1358 (1975).

Quality Control
    G.Vriend and C.Sander,
      Quality control of protein models: directional atomic
      contact analysis,
    J. Appl. Cryst. 26, 47--60 (1993).

Ramachandran plot
    G.N.Ramachandran, C.Ramakrishnan and V.Sasisekharan,
      Stereochemistry of Polypeptide Chain Conformations
    J. Mol. Biol. 7, 95--99 (1963).

Symmetry Checks
    R.W.W.Hooft, C.Sander and G.Vriend,
      Reconstruction of symmetry related molecules from protein
      data bank (PDB) files
    J. Appl. Cryst. 27, 1006--1009 (1994).

Ion Checks
    I.D.Brown and K.K.Wu,
      Empirical Parameters for Calculating Cation-Oxygen Bond Valences
    Acta Cryst. B32, 1957--1959 (1975).

    M.Nayal and E.Di Cera,
      Valence Screening of Water in Protein Crystals Reveals Potential Na+
      Binding Sites
    J.Mol.Biol. 256 228--234 (1996).

    P.Mueller, S.Koepke and G.M.Sheldrick,
      Is the bond-valence method able to identify metal atoms in protein
      structures?
    Acta Cryst. D 59 32--37 (2003).

Checking checks
    K.Wilson, C.Sander, R.W.W.Hooft, G.Vriend, et al.
      Who checks the checkers
    J.Mol.Biol. (1998) 276,417-436.