WHAT IF Check report

This file was created 2017-01-25 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 /srv/data/pdb/flat/pdb4zvv.ent

Checks that need to be done early-on in validation

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.

Note: Header records from PDB file

Header records from PDB file.

HEADER    OXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR 18-MAY-15   4ZVV
LACTATE DEHYDROGENASE A IN COMPLEX WITH A TRISUBSTITUTED PIPERIDINE-2,
 4-DIONE INHIBITOR GNE-140
OXIDOREDUCTASE INHIBITOR COMPLEX, LDHA-G02792140, OXIDOREDUCTASE-
 OXIDOREDUCTASE INHIBITOR COMPLEX
JRNL        A.BOUDREAU,H.E.PURKEY,A.HITZ,K.ROBARGE,D.PETERSON,S.LABADIE,
JRNL        M.KWONG,R.HONG,M.GAO,C.DEL NAGRO,R.PUSAPATI,S.MA,L.SALPHATI,
JRNL        J.PANG,A.ZHOU,T.LAI,Y.LI,Z.CHEN,B.WEI,I.YEN,S.SIDERIS,
JRNL        M.MCCLELAND,R.FIRESTEIN,L.CORSON,A.VANDERBILT,S.WILLIAMS,
JRNL        A.DAEMEN,M.BELVIN,C.EIGENBROT,P.K.JACKSON,S.MALEK,
JRNL        G.HATZIVASSILIOU,D.SAMPATH,M.EVANGELISTA,T.O'BRIEN
JRNL        METABOLIC PLASTICITY UNDERPINS INNATE AND ACQUIRED
JRNL        RESISTANCE TO LDHA INHIBITION.
JRNL        REF    NAT.CHEM.BIOL.                V.  12   779 2016
JRNL        REFN                   ESSN 1552-4469
JRNL        PMID   27479743
JRNL        DOI    10.1038/NCHEMBIO.2143

Note: Non crystallographic symmetry RMS plot

The plot shows the RMS differences between two similar chains on a residue- by-residue basis. Individual "spikes" can be indicative of interesting or wrong residues. If all residues show a high RMS value, the structure could be incorrectly refined.

Chain identifiers of the two chains: A and B

All-atom RMS fit for the two chains : 0.961
CA-only RMS fit for the two chains : 0.530

Note: Non crystallographic symmetry backbone difference plot

The plot shows the differences in backbone torsion angles between two similar chains on a residue-by-residue basis. Individual "spikes" can be indicative of interesting or wrong residues. If all residues show high differences, the structure could be incorrectly refined.

Chain identifiers of the two chains: A and B

Note: Non crystallographic symmetry RMS plot

The plot shows the RMS differences between two similar chains on a residue- by-residue basis. Individual "spikes" can be indicative of interesting or wrong residues. If all residues show a high RMS value, the structure could be incorrectly refined.

Chain identifiers of the two chains: A and C

All-atom RMS fit for the two chains : 0.841
CA-only RMS fit for the two chains : 0.364

Note: Non crystallographic symmetry backbone difference plot

The plot shows the differences in backbone torsion angles between two similar chains on a residue-by-residue basis. Individual "spikes" can be indicative of interesting or wrong residues. If all residues show high differences, the structure could be incorrectly refined.

Chain identifiers of the two chains: A and C

Note: Non crystallographic symmetry RMS plot

The plot shows the RMS differences between two similar chains on a residue- by-residue basis. Individual "spikes" can be indicative of interesting or wrong residues. If all residues show a high RMS value, the structure could be incorrectly refined.

Chain identifiers of the two chains: A and D

All-atom RMS fit for the two chains : 1.681
CA-only RMS fit for the two chains : 1.357

Note: Non crystallographic symmetry backbone difference plot

The plot shows the differences in backbone torsion angles between two similar chains on a residue-by-residue basis. Individual "spikes" can be indicative of interesting or wrong residues. If all residues show high differences, the structure could be incorrectly refined.

Chain identifiers of the two chains: A and D

Note: Non crystallographic symmetry RMS plot

The plot shows the RMS differences between two similar chains on a residue- by-residue basis. Individual "spikes" can be indicative of interesting or wrong residues. If all residues show a high RMS value, the structure could be incorrectly refined.

Chain identifiers of the two chains: B and C

All-atom RMS fit for the two chains : 0.882
CA-only RMS fit for the two chains : 0.399

Note: Non crystallographic symmetry backbone difference plot

The plot shows the differences in backbone torsion angles between two similar chains on a residue-by-residue basis. Individual "spikes" can be indicative of interesting or wrong residues. If all residues show high differences, the structure could be incorrectly refined.

Chain identifiers of the two chains: B and C

Note: Non crystallographic symmetry RMS plot

The plot shows the RMS differences between two similar chains on a residue- by-residue basis. Individual "spikes" can be indicative of interesting or wrong residues. If all residues show a high RMS value, the structure could be incorrectly refined.

Chain identifiers of the two chains: B and D

All-atom RMS fit for the two chains : 1.613
CA-only RMS fit for the two chains : 1.156

Note: Non crystallographic symmetry backbone difference plot

The plot shows the differences in backbone torsion angles between two similar chains on a residue-by-residue basis. Individual "spikes" can be indicative of interesting or wrong residues. If all residues show high differences, the structure could be incorrectly refined.

Chain identifiers of the two chains: B and D

Note: NCS statistics suppressed

There are more pairs of NCS equivalent molecules, but the statistics will not be shown.

Warning: New symmetry found

Independent molecules in the asymmetric unit actually look like symmetry relatives. This fact needs manual checking.

Note: Counting molecules and matrices

The parameter Z as given on the CRYST card represents the molecular multiplicity in the crystallographic cell. Z equals the number of matrices of the space group multiplied by the number of NCS relations. These numbers seem to be consistent.

Space group as read from CRYST card: P 1 21 1
Number of matrices in space group: 2
Highest polymer chain multiplicity in structure: 4
Highest polymer chain multiplicity according to SEQRES: 4
No explicit MTRIX NCS matrices found in the input file
Value of Z as found on the CRYST1 card: 8
Z, spacegroup, and NCS seem to agree administratively

Note: Matthews coefficient OK

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.

Molecular weight of all polymer chains: 148126.906
Volume of the Unit Cell V= 652443.750
Space group multiplicity: 2
No NCS symmetry matrices (MTRIX records) found in PDB file
Matthews coefficient for observed atoms and Z: Vm= 2.202
A few residues have missing atoms that did not enter the Vm calculation
One BIOMT matrix observed in the PDB file, but that is the unitary one
Matthews coefficient read from REMARK 280 Vm= 2.230
Vm by authors and this calculated Vm agree remarkably well

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 CHECK has not detected any serious chain identifier problems. But be aware that WHAT CHECK 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 CHECK uses the CCP4 monomer library 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 the CCP4. 'Attached' means that the ligand is covalently attached to a macromolecule.

 1329 NAD  ( 401-) A  -          OK
 1332 GN0  ( 405-) A  -
 1334 NAD  ( 401-) B  -          OK
 1336 GN0  ( 404-) B  -
 1338 NAD  ( 401-) C  -          OK
 1339 GN0  ( 403-) C  -
 1341 NAD  ( 401-) D  -          OK
 1342 GN0  ( 403-) D  -

Note: Covalently bound ligands

No problems were detected that seem related to covalently bound ligands.

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 (if any) seem adequately unique.

Warning: Alternate atom problems

The residues listed in the table below have alternate atoms that do not follow normal logic (like the first of the atoms gets label A and has the highest occupancy). Residues listed here have at least one such problem. The Note Mixed means that the the best solution found by WHAT CHECK has mixed alternate atom labels. If the Note contains Occupancy, then at in at least one case does the not-used alternate atom have a higher occupancy then the one used. Corrected in the Note means that WHAT CHECK found a solution, but that does not mean it is guaranteed solved. If you find weird problems for this residue later-on in the report, especially when those are rotamer or bump related, please look at this residue in the PDB file itself, solve the problem by hand, and run WHAT CHECK again.

 1048 ASP  (  55-) D  - Corrected

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 (or 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 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.

Warning: Residues with missing backbone atoms.

Residues were detected with missing backbone atoms. This can be a normal result of poor or missing density, but it can also be an error.

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. This is not an error, albeit that we would prefer them to give it their best shot and provide coordinates with an occupancy of zero in cases where only a few atoms are involved. Anyway, several checks depend on the presence of the backbone atoms, so if you find errors in, or directly adjacent to, residues with missing backbone atoms, then please check by hand what is going on.

 1006 LYS  (  13-) D  -

Note: No C-alpha only residues

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

Note: Non-canonical residues

WHAT CHECK has not detected any non-canonical residue(s).

Non-validating, descriptive output paragraph

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 (    1)   331 (  331) A Protein             /srv/data/pdb/fla...
     2   332 (    1)   662 (  331) B Protein             /srv/data/pdb/fla...
     3   663 (    1)   993 (  331) C Protein             /srv/data/pdb/fla...
     4   994 (    1)  1324 (  331) D Protein             /srv/data/pdb/fla...
     5  1325 (  331)  1325 (  331) A F O2 <-   331       /srv/data/pdb/fla...
     6  1326 (  331)  1326 (  331) B F O2 <-   662       /srv/data/pdb/fla...
     7  1327 (  331)  1327 (  331) C F O2 <-   993       /srv/data/pdb/fla...
     8  1328 (  331)  1328 (  331) D F O2 <-  1324       /srv/data/pdb/fla...
     9  1329 (  401)  1329 (  401) A NAD                 /srv/data/pdb/fla...
    10  1330 (  402)  1330 (  402) A SO4                 /srv/data/pdb/fla...
    11  1331 (  403)  1331 (  403) A SO4                 /srv/data/pdb/fla...
    12  1332 (  405)  1332 (  405) A GN0                 /srv/data/pdb/fla...
    13  1333 (  404)  1333 (  404) A SO4                 /srv/data/pdb/fla...
    14  1334 (  401)  1334 (  401) B NAD                 /srv/data/pdb/fla...
    15  1335 (  402)  1335 (  402) B SO4                 /srv/data/pdb/fla...
    16  1336 (  404)  1336 (  404) B GN0                 /srv/data/pdb/fla...
    17  1337 (  403)  1337 (  403) B SO4                 /srv/data/pdb/fla...
    18  1338 (  401)  1338 (  401) C NAD                 /srv/data/pdb/fla...
    19  1339 (  403)  1339 (  403) C GN0                 /srv/data/pdb/fla...
    20  1340 (  402)  1340 (  402) C SO4                 /srv/data/pdb/fla...
    21  1341 (  401)  1341 (  401) D NAD                 /srv/data/pdb/fla...
    22  1342 (  403)  1342 (  403) D GN0                 /srv/data/pdb/fla...
    23  1343 (  402)  1343 (  402) D SO4                 /srv/data/pdb/fla...
    24  1344 ( HOH )  1344 ( HOH ) A water   (   72)     /srv/data/pdb/fla...
    25  1345 ( HOH )  1345 ( HOH ) B water   (   71)     /srv/data/pdb/fla...
    26  1346 ( HOH )  1346 ( HOH ) C water   (   82)     /srv/data/pdb/fla...
    27  1347 ( HOH )  1347 ( HOH ) D water   (   84)     /srv/data/pdb/fla...

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: 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 ATLKDQLIYNLLKEEQTPQNKITVVGVGAVGMACAISILMKDLADELALVDVIEDKLKGE
(   1)-(  60)  HHHHH             SSSSS   HHHHHHHHHHHHHT   SSSSS   HHHHHHH
                     70        80        90       100       110       120
                      |         |         |         |         |         |
   61 -  120 MMDLQHGSLFLRTPKIVSGKDYNVTANSKLVIITAGARQQEGESRLNLVQRNVNIFKFII
(  61)-( 120)HHHHHTTHHH    SSSS   HHHHTT  SSSS       TT  HHHHHHHHHHHHHHHH
                    130       140       150       160       170       180
                      |         |         |         |         |         |
  121 -  180 PNVVKYSPNCKLLIVSNPVDILTYVAWKISGFPKNRVIGSGCNLDSARFRYLMGERLGVH
( 121)-( 180)HHHHHH TT SSSS    HHHHHHHHHHHH   HHHSSS TTHHHHHHHHHHHHHHHT
                    190       200       210       220       230       240
                      |         |         |         |         |         |
  181 -  240 PLSCHGWVLGEHGDSSVPVWSGMNVAGVSLKTLHPDLGTDKDKEQWKEVHKQVVESAYEV
( 181)-( 240)HHH    SS    TT SS HHH SSTTSSHHHH TTTT TT TT TTHHHHHHHHHHHHH
                    250       260       270       280       290       300
                      |         |         |         |         |         |
  241 -  300 IKLKGYTSWAIGLSVADLAESIMKNLRRVHPVSTMIKGLYGIKDDVFLSVPCILGQNGIS
( 241)-( 300)HHHH    HHHHHHHHHHHHHHHTT  SSSSSSSS TT TT     SSSSSSSSSTTSSS
                    310       320       330
                      |         |         |
  301 -  331 DLVKVTLTSEEEARLKKSADTLWGIQKELQF
( 301)-( 331)SS      HHHHHHHHHHHHHHHHHHTT
 
                   340       350       360       370       380       390
                     |         |         |         |         |         |
  332 -  391 ATLKDQLIYNLLKEEQTPQNKITVVGVGAVGMACAISILMKDLADELALVDVIEDKLKGE
(   1)-(  60)  HHHHH             SSSSS   HHHHHHHHHHHHTT   SSSSS   HHHHHHH
                   400       410       420       430       440       450
                     |         |         |         |         |         |
  392 -  451 MMDLQHGSLFLRTPKIVSGKDYNVTANSKLVIITAGARQQEGESRLNLVQRNVNIFKFII
(  61)-( 120)HHHHHTTHHH     SSS   HHH TT  SSSS           HHHHHHHHHHHHHHHH
                   460       470       480       490       500       510
                     |         |         |         |         |         |
  452 -  511 PNVVKYSPNCKLLIVSNPVDILTYVAWKISGFPKNRVIGSGCNLDSARFRYLMGERLGVH
( 121)-( 180)HHHHHH TT SSSS    HHHHHHHHHHHH   HHHSSS TTHHHHHHHHHHHHHHHT
                   520       530       540       550       560       570
                     |         |         |         |         |         |
  512 -  571 PLSCHGWVLGEHGDSSVPVWSGMNVAGVSLKTLHPDLGTDKDKEQWKEVHKQVVESAYEV
( 181)-( 240)HHHSS  SSS   TTSSS HHH SSTTSSHHHH TTTT TT TT THHHHHHHHHHHHHH
                   580       590       600       610       620       630
                     |         |         |         |         |         |
  572 -  631 IKLKGYTSWAIGLSVADLAESIMKNLRRVHPVSTMIKGLYGIKDDVFLSVPCILGQNGIS
( 241)-( 300)HHHH    HHHHHHHHHHHHHHHHT  SSSSSSSS TT TT     SSSSSSSSSTTSSS
                   640       650       660
                     |         |         |
  632 -  662 DLVKVTLTSEEEARLKKSADTLWGIQKELQF
( 301)-( 331)SS      HHHHHHHHHHHHHHHHHHTT
 
                  670       680       690       700       710       720
                    |         |         |         |         |         |
  663 -  722 ATLKDQLIYNLLKEEQTPQNKITVVGVGAVGMACAISILMKDLADELALVDVIEDKLKGE
(   1)-(  60)  HHHHH             SSSSS   HHHHHHHHHHHHTT   SSSSS   HHHHHHH
                  730       740       750       760       770       780
                    |         |         |         |         |         |
  723 -  782 MMDLQHGSLFLRTPKIVSGKDYNVTANSKLVIITAGARQQEGESRLNLVQRNVNIFKFII
(  61)-( 120)HHHHHHTHHH     SSS   HHHHTTSSSSSS       TT  HHHHHHHHHHHHHHHH
                  790       800       810       820       830       840
                    |         |         |         |         |         |
  783 -  842 PNVVKYSPNCKLLIVSNPVDILTYVAWKISGFPKNRVIGSGCNLDSARFRYLMGERLGVH
( 121)-( 180)HHHHHH TT SSSS    HHHHHHHHHHHH   HHHSSS TTHHHHHHHHHHHHHHHT
                  850       860       870       880       890       900
                    |         |         |         |         |         |
  843 -  902 PLSCHGWVLGEHGDSSVPVWSGMNVAGVSLKTLHPDLGTDKDKEQWKEVHKQVVESAYEV
( 181)-( 240)HHHSS  SS    TT SS TTT SSTTSSHHHH TTTT TT TT THHHHHHHHHHHHHH
                  910       920       930       940       950       960
                    |         |         |         |         |         |
  903 -  962 IKLKGYTSWAIGLSVADLAESIMKNLRRVHPVSTMIKGLYGIKDDVFLSVPCILGQNGIS
( 241)-( 300)HHHH    HHHHHHHHHHHHHHHTT  SSSSSSSS TT TT     SSSSSSSSSTTSSS
                  970       980       990
                    |         |         |
  963 -  993 DLVKVTLTSEEEARLKKSADTLWGIQKELQF
( 301)-( 331)SS      HHHHHHHHHHHHHHHHHHTT
 
                1000      1010      1020      1030      1040      1050
                   |         |         |         |         |         |
  994 - 1053 ATLKDQLIYNLLKEEQTPQNKITVVGVGAVGMACAISILMKDLADELALVDVIEDKLKGE
(   1)-(  60)  HHHHH             SSSSS   HHHHHHHHHHHHTT   SSSSS   HHHHHHH
                1060      1070      1080      1090      1100      1110
                   |         |         |         |         |         |
 1054 - 1113 MMDLQHGSLFLRTPKIVSGKDYNVTANSKLVIITAGARQQEGESRLNLVQRNVNIFKFII
(  61)-( 120)HHHHHTTHHH    SSSS   HHHHTT  SSSS       TT     HHHHHHHHHHHHH
                1120      1130      1140      1150      1160      1170
                   |         |         |         |         |         |
 1114 - 1173 PNVVKYSPNCKLLIVSNPVDILTYVAWKISGFPKNRVIGSGCNLDSARFRYLMGERLGVH
( 121)-( 180)HHHHHH TT SSSS    HHHHHHHHHHHH   HHHSSS TTHHHHHHHHHHHHHHHT
                1180      1190      1200      1210      1220      1230
                   |         |         |         |         |         |
 1174 - 1233 PLSCHGWVLGEHGDSSVPVWSGMNVAGVSLKTLHPDLGTDKDKEQWKEVHKQVVESAYEV
( 181)-( 240)HHH SSSSS    TT SSSSSSSSSTTSSHHHH TTTT    TT TTHHHHHHHHHHHHH
                1240      1250      1260      1270      1280      1290
                   |         |         |         |         |         |
 1234 - 1293 IKLKGYTSWAIGLSVADLAESIMKNLRRVHPVSTMIKGLYGIKDDVFLSVPCILGQNGIS
( 241)-( 300)HHHH    HHHHHHHHHHHHHHHTT  SSSSSSSS TT TT     SSSSSSSSSTTSSS
                1300      1310      1320
                   |         |         |
 1294 - 1324 DLVKVTLTSEEEARLKKSADTLWGIQKELQF
( 301)-( 331)SS      HHHHHHHHHHHHHHHHHHTT
 
 
 

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'.

 1006 LYS  (  13-) D  -    O

Note: All B-factors fall in the range 0.0 - 100.0

All B-factors are larger than zero, and none are observed above 100.0.

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: Capping of (pseudo) C-termini OK

No extra capping groups were found on pseudo C-termini. This can imply that no pseudo C-termini are present.

Note: No OXT found in the middle of chains

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

Note: Weights administratively correct

All atomic occupancy factors ('weights') fall in the 0.0--1.0 range, which makes them administratively correct.

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.

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.

  344 LYS  (  13-) B  -   0.71
  676 GLU  (  14-) C  -   0.59
  677 GLU  (  15-) C  -   0.86
  678 GLN  (  16-) C  -   0.51
 1006 LYS  (  13-) D  -   0.10

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

Crystal temperature (K) :110.000

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. In liquid nitrogen this percentage is allowed to be higher, of course.

Percentage of buried atoms with B less than 5 : 0.00

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 : 0.354 over 9123 bonds
Average difference in B over a bond : 0.36
RMS difference in B over a bond : 0.87

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

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.

Warning: Arginine nomenclature problem

The arginine residues listed in the table below have their N-H-1 and N-H-2 swapped.

   98 ARG  (  98-) A  -
  105 ARG  ( 105-) A  -
  168 ARG  ( 168-) A  -
  268 ARG  ( 268-) A  -
  499 ARG  ( 168-) B  -
  501 ARG  ( 170-) B  -
  599 ARG  ( 268-) B  -
  767 ARG  ( 105-) C  -
  830 ARG  ( 168-) C  -
  832 ARG  ( 170-) C  -
 1091 ARG  (  98-) D  -
 1161 ARG  ( 168-) D  -
 1163 ARG  ( 170-) D  -
 1169 ARG  ( 176-) D  -
 1261 ARG  ( 268-) D  -
 1307 ARG  ( 314-) D  -

Note: Tyrosine torsion conventions OK

No errors were detected in tyrosine torsion angle conventions.

Warning: Phenylalanine convention problem

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

 1111 PHE  ( 118-) D  -

Note: Aspartic acid torsion conventions OK

No errors were detected in aspartic acid torsion angle conventions.

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.

   54 GLU  (  54-) A  -
  103 GLU  ( 103-) A  -
  191 GLU  ( 191-) A  -
  224 GLU  ( 224-) A  -
  228 GLU  ( 228-) A  -
  235 GLU  ( 235-) A  -
  328 GLU  ( 328-) A  -
  346 GLU  (  15-) B  -
  385 GLU  (  54-) B  -
  432 GLU  ( 101-) B  -
  434 GLU  ( 103-) B  -
  522 GLU  ( 191-) B  -
  559 GLU  ( 228-) B  -
  642 GLU  ( 311-) B  -
  763 GLU  ( 101-) C  -
  765 GLU  ( 103-) C  -
  837 GLU  ( 175-) C  -
  901 GLU  ( 239-) C  -
  973 GLU  ( 311-) C  -
 1007 GLU  (  14-) D  -
 1047 GLU  (  54-) D  -
 1184 GLU  ( 191-) D  -
 1304 GLU  ( 311-) D  -
 1305 GLU  ( 312-) D  -

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).

Warning: SO4/PO4 problem

There is something wrong with the SO4 and/or PO4 groups listed in the table. The message 'geometry' is listed if an SO4 or PO4 group is deformed in any way. 'Hand' is listed if two atoms have been swapped so that it is the nomenclature technical mirror image of a standard SO4/PO4. 'Incomplete' is listed if atoms are missing. This often happens if the group is located at a symmetry axis (a so-called special position); if that is the case 'Special position' is listed to indicate that the missing atoms might be genuinely missing. 'Bound' is listed if the SO4 is observed bound to something; this, of course, is not an error of any kind, but SO4 groups bound to something often are a cause of hard to detect problems...

 1330 SO4  ( 402-) A  - Hand
 1331 SO4  ( 403-) A  - Hand
 1333 SO4  ( 404-) A  - Hand
 1340 SO4  ( 402-) C  - Hand
 1343 SO4  ( 402-) D  - Hand

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: No decreasing residue numbers

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.

   80 LYS  (  80-) A  -    CE   NZ    1.65    5.3
   99 GLN  (  99-) A  -    CG   CD    1.65    5.2
   99 GLN  (  99-) A  -    CD   NE2   1.49    7.9
  101 GLU  ( 101-) A  -    CG   CD    1.36   -6.3
  101 GLU  ( 101-) A  -    CD   OE1   1.37    6.2
  105 ARG  ( 105-) A  -    CG   CD    1.69    5.7
  106 LEU  ( 106-) A  -    CG   CD1   1.73    6.5
  108 LEU  ( 108-) A  -    CG   CD2   1.33   -5.8
  154 LYS  ( 154-) A  -    CE   NZ    1.62    4.3
  223 LYS  ( 223-) A  -    CE   NZ    1.61    4.1
  231 LYS  ( 231-) A  -    CD   CE    1.66    4.6
  344 LYS  (  13-) B  -    CB   CG    1.22   -9.9
  677 GLU  (  15-) C  -    CB   CG    1.40   -4.1
  883 LYS  ( 221-) C  -    CE   NZ    1.63    4.6
  889 LYS  ( 227-) C  -    CE   NZ    1.62    4.3
  904 LYS  ( 242-) C  -    CD   CE    1.65    4.4
  904 LYS  ( 242-) C  -    CE   NZ    1.74    8.3
  945 LYS  ( 283-) C  -    CE   NZ    1.71    7.5
 1006 LYS  (  13-) D  -    CA   C     1.95   20.5
 1006 LYS  (  13-) D  -    CB   CG    1.23   -9.8
 1007 GLU  (  14-) D  -    N   -C     1.20   -6.4
 1091 ARG  (  98-) D  -    CZ   NH1   1.43    6.0
 1092 GLN  (  99-) D  -    CB   CG    1.65    4.4
 1096 GLU  ( 103-) D  -    CD   OE1   1.34    4.9
 1110 LYS  ( 117-) D  -    CE   NZ    1.65    5.3
 1204 LYS  ( 211-) D  -    CE   NZ    1.63    4.6
 1224 LYS  ( 231-) D  -    CD   CE    1.65    4.5

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: 0.539
RMS-deviation in bond distances: 0.014

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.

SCALE matrix obtained from PDB file

 |  0.012632  0.000000  0.001846|
 |  0.000000  0.012302  0.000000|
 |  0.000000  0.000000  0.009863|
Unit Cell deformation matrix

 |  0.996390  0.000077 -0.000039|
 |  0.000077  0.995841  0.000121|
 | -0.000039  0.000121  0.995857|
Proposed new scale matrix

 |  0.012678 -0.000001  0.001854|
 |  0.000000  0.012353 -0.000001|
 |  0.000000 -0.000001  0.009904|
With corresponding cell

    A    =  78.878  B   =  80.949  C    = 102.043
    Alpha=  90.000  Beta=  98.321  Gamma=  90.000

The CRYST1 cell dimensions

    A    =  79.164  B   =  81.288  C    = 102.470
    Alpha=  90.000  Beta=  98.310  Gamma=  90.000

Variance: 667.244
(Under-)estimated Z-score: 19.037

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.

  101 GLU  ( 101-) A  -    CB   CG   CD  125.01    7.3
  107 ASN  ( 107-) A  -    ND2  CG   OD1 128.00    5.4
  344 LYS  (  13-) B  -    CA   CB   CG  125.59    5.7
  677 GLU  (  15-) C  -    CA   CB   CG  123.24    4.6
  677 GLU  (  15-) C  -    CB   CG   CD  120.73    4.8
  904 LYS  ( 242-) C  -    CD   CE   NZ   98.93   -4.1
 1006 LYS  (  13-) D  -    C    CA   CB  136.18   13.7
 1006 LYS  (  13-) D  -    CA   CB   CG  100.66   -6.7
 1006 LYS  (  13-) D  -    CB   CG   CD  136.84   11.1
 1007 GLU  (  14-) D  -   -C    N    CA  111.65   -5.6

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: 0.526
RMS-deviation in bond angles: 1.083

Error: Nomenclature error(s)

Checking for a hand-check. WHAT CHECK 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.

   54 GLU  (  54-) A  -
   98 ARG  (  98-) A  -
  103 GLU  ( 103-) A  -
  105 ARG  ( 105-) A  -
  168 ARG  ( 168-) A  -
  191 GLU  ( 191-) A  -
  224 GLU  ( 224-) A  -
  228 GLU  ( 228-) A  -
  235 GLU  ( 235-) A  -
  268 ARG  ( 268-) A  -
  328 GLU  ( 328-) A  -
  346 GLU  (  15-) B  -
  385 GLU  (  54-) B  -
  432 GLU  ( 101-) B  -
  434 GLU  ( 103-) B  -
And so on for a total of 40 lines.

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.

 1006 LYS  (  13-) D  -    CA   -11.3    16.13    33.93
The average deviation= 0.531

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 : 0.514

Note: Tau angles OK

All of the tau angles (N-Calpha-C) of amino acids fall within expected RMS deviations.

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 : 0.818

Note: Side chain planarity OK

All of the side chains of residues that have an intact planar group are planar within expected RMS deviations.

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.

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 : -1.380

Note: Ramachandran check

The following list contains per-residue Z-scores describing how well each residue fits into the allowed areas of the Ramachandran plot. WHAT CHECK saw no reasons for crying.

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.

  942 TYR  ( 280-) C  -   -2.7
 1273 TYR  ( 280-) D  -   -2.6
  611 TYR  ( 280-) B  -   -2.5
  343 LEU  (  12-) B  -   -2.5
  938 ILE  ( 276-) C  -   -2.5
  276 ILE  ( 276-) A  -   -2.4
  302 LEU  ( 302-) A  -   -2.4
  602 PRO  ( 271-) B  -   -2.4
  246 TYR  ( 246-) A  -   -2.3
  290 VAL  ( 290-) A  -   -2.3
  964 LEU  ( 302-) C  -   -2.2
  556 GLN  ( 225-) B  -   -2.2
  280 TYR  ( 280-) A  -   -2.2
  941 LEU  ( 279-) C  -   -2.2
  936 THR  ( 274-) C  -   -2.2
  637 THR  ( 306-) B  -   -2.2
  910 SER  ( 248-) C  -   -2.2
 1295 LEU  ( 302-) D  -   -2.2
  734 ARG  (  72-) C  -   -2.1
 1091 ARG  (  98-) D  -   -2.1
  945 LYS  ( 283-) C  -   -2.1
   72 ARG  (  72-) A  -   -2.1
 1218 GLN  ( 225-) D  -   -2.1
 1020 VAL  (  27-) D  -   -2.1
  544 LEU  ( 213-) B  -   -2.1
 1197 ASN  ( 204-) D  -   -2.1
 1005 LEU  (  12-) D  -   -2.1
  358 VAL  (  27-) B  -   -2.0
 1269 ILE  ( 276-) D  -   -2.0
  793 LYS  ( 131-) C  -   -2.0

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.

   17 THR  (  17-) A  - Omega to (next) Pro poor
   26 GLY  (  26-) A  - Poor phi/psi
   42 ASP  (  42-) A  - Poor phi/psi
   73 THR  (  73-) A  - Omega to (next) Pro poor
   79 GLY  (  79-) A  - Poor phi/psi
   87 ASN  (  87-) A  - Poor phi/psi
  120 ILE  ( 120-) A  - Omega to (next) Pro poor
  127 SER  ( 127-) A  - Omega to (next) Pro poor
  137 ASN  ( 137-) A  - Omega to (next) Pro poor
  138 PRO  ( 138-) A  - omega poor
  151 GLY  ( 151-) A  - Poor phi/psi
  152 PHE  ( 152-) A  - Omega to (next) Pro poor
  161 GLY  ( 161-) A  - Poor phi/psi
  178 GLY  ( 178-) A  - Poor phi/psi
  180 HIS  ( 180-) A  - Omega to (next) Pro poor
And so on for a total of 122 lines.

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.

    3 LEU  (   3-) A  -    -1.44
  106 LEU  ( 106-) A  -    -1.44
  315 LEU  ( 315-) A  -    -1.44
  544 LEU  ( 213-) B  -    -1.42
  646 LEU  ( 315-) B  -    -1.44
  770 LEU  ( 108-) C  -    -1.42
 1175 LEU  ( 182-) D  -    -1.42
 1308 LEU  ( 315-) D  -    -1.44
   11 LEU  (  11-) A  -    -1.31
   12 LEU  (  12-) A  -    -1.31
  210 LEU  ( 210-) A  -    -1.38
  279 LEU  ( 279-) A  -    -1.32
  294 LEU  ( 294-) A  -    -1.33
  329 LEU  ( 329-) A  -    -1.32
  343 LEU  (  12-) B  -    -1.31
And so on for a total of 563 lines.

Warning: chi-1/chi-2 angle correlation Z-score low

The score expressing how well the chi-1/chi-2 angles of all residues correspond to the populated areas in the database is a bit low.

chi-1/chi-2 correlation Z-score : -3.392

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.

  368 SER  (  37-) B  -   0.35
 1059 HIS  (  66-) D  -   0.35
   66 HIS  (  66-) A  -   0.36
  592 SER  ( 261-) B  -   0.36
  261 SER  ( 261-) A  -   0.38
  497 SER  ( 166-) B  -   0.38
  828 SER  ( 166-) C  -   0.39
 1030 SER  (  37-) D  -   0.39
  323 TRP  ( 323-) A  -   0.39
  397 HIS  (  66-) B  -   0.39

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) is indicated!

  160 SER  ( 160-) A  -       0
  162 CYS  ( 162-) A  -       0
  189 LEU  ( 189-) A  - S     0
  491 SER  ( 160-) B  -       0
  493 CYS  ( 162-) B  -       0
  580 TRP  ( 249-) B  - H     0
  630 ILE  ( 299-) B  - S     0
  822 SER  ( 160-) C  -       0
  824 CYS  ( 162-) C  -       0
  961 ILE  ( 299-) C  - S     0
 1006 LYS  (  13-) D  -       0
 1153 SER  ( 160-) D  -       0
 1155 CYS  ( 162-) D  -       0
 1182 LEU  ( 189-) D  - S     0
 1184 GLU  ( 191-) D  -       0
And so on for a total of 35 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 : -0.987

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.

Omega average and std. deviation= 179.340 4.634

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].

  181 PRO  ( 181-) A  -  104.0 envelop C-beta (108 degrees)
  271 PRO  ( 271-) A  -  -53.0 half-chair C-beta/C-alpha (-54 degrees)
  602 PRO  ( 271-) B  -  -59.2 half-chair C-beta/C-alpha (-54 degrees)
  680 PRO  (  18-) C  - -114.7 envelop C-gamma (-108 degrees)
  843 PRO  ( 181-) C  - -126.1 half-chair C-delta/C-gamma (-126 degrees)
 1264 PRO  ( 271-) D  -   41.1 envelop C-delta (36 degrees)

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 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!

  186 GLY  ( 186-) A  -  1.62   80
  517 GLY  ( 186-) B  -  1.51   80
ERROR in internal write in routine SC6013. This could be a bug.

Note: Peptide bond conformations

There was no need to complain about the peptide bond of a single amino acid

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). 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. INTRA and INTER indicate whether the clashes are between atoms in the same asymmetric unit, or atoms in symmetry related asymmetric units, respectively.

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.

   99 GLN  (  99-) A  -    NE2 <-->   103 GLU  ( 103-) A  -    OE1    0.79    1.91  INTRA BF
  297 ASN  ( 297-) A  -    CG  <-->  1009 GLN  (  16-) D  -    NE2    0.40    2.70  INTRA BL
  559 GLU  ( 228-) B  -    O   <-->   563 GLN  ( 232-) B  -    N      0.31    2.39  INTRA BF
  297 ASN  ( 297-) A  -    OD1 <-->  1009 GLN  (  16-) D  -    NE2    0.30    2.40  INTRA BL
 1091 ARG  (  98-) D  -    CD  <-->  1096 GLU  ( 103-) D  -    OE1    0.28    2.52  INTRA BF
 1091 ARG  (  98-) D  -    NE  <-->  1096 GLU  ( 103-) D  -    OE1    0.28    2.42  INTRA BF
  297 ASN  ( 297-) A  -    ND2 <-->  1009 GLN  (  16-) D  -    NE2    0.27    2.58  INTRA
  168 ARG  ( 168-) A  -    NH1 <-->  1332 GN0  ( 405-) A  -    S21    0.24    3.06  INTRA BL
   99 GLN  (  99-) A  -    NE2 <-->   100 GLN  ( 100-) A  -    N      0.24    2.51  INTRA BF
  531 TRP  ( 200-) B  -    CE3 <-->   534 MET  ( 203-) B  -    SD     0.23    3.17  INTRA BL
  347 GLN  (  16-) B  -    OE1 <-->   959 ASN  ( 297-) C  -    ND2    0.23    2.47  INTRA BF
 1161 ARG  ( 168-) D  -    NH1 <-->  1342 GN0  ( 403-) D  -    S21    0.19    3.11  INTRA BL
  499 ARG  ( 168-) B  -    NH1 <-->  1336 GN0  ( 404-) B  -    S21    0.19    3.11  INTRA BL
  553 ASP  ( 222-) B  -    CB  <-->   558 LYS  ( 227-) B  -    NZ     0.17    2.93  INTRA BF
  465 ILE  ( 134-) B  -    CG2 <-->   490 GLY  ( 159-) B  -    CA     0.17    3.03  INTRA BL
And so on for a total of 72 lines.

Note: Some notes regarding these bumps

The bumps have been binned in 5 categories ranging from 'should deal with' 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: 7.642
Total bump value per residue: 0.054
Total number of bumps: 72
Total squared bump value: 1.833
Total number of bumps in the mildest bin: 65
Total number of bumps in the second bin: 6
Total number of bumps in the middle bin: 0
Total number of bumps in the fourth bin: 1
Total number of bumps in the worst bin: 0

Packing, accessibility and threading

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". |Z-score| must be used to judge the quality. WHAT CHECK saw no reason to complain.

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 : 0.951

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

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.

  403 ARG  (  72-) B  -  -6.46
 1323 GLN  ( 330-) D  -  -6.43
  330 GLN  ( 330-) A  -  -6.39
  347 GLN  (  16-) B  -  -6.15
  678 GLN  (  16-) C  -  -6.07
 1065 ARG  (  72-) D  -  -6.06
   16 GLN  (  16-) A  -  -6.06
  661 GLN  ( 330-) B  -  -6.03
  992 GLN  ( 330-) C  -  -5.96
 1009 GLN  (  16-) D  -  -5.93
  734 ARG  (  72-) C  -  -5.86
  675 LYS  (  13-) C  -  -5.61
  283 LYS  ( 283-) A  -  -5.56
  346 GLU  (  15-) B  -  -5.44
 1008 GLU  (  15-) D  -  -5.39
   72 ARG  (  72-) A  -  -5.33
  838 ARG  ( 176-) C  -  -5.32
 1091 ARG  (  98-) D  -  -5.30
 1289 GLN  ( 296-) D  -  -5.30
 1169 ARG  ( 176-) D  -  -5.27
  958 GLN  ( 296-) C  -  -5.25
  507 ARG  ( 176-) B  -  -5.25
  176 ARG  ( 176-) A  -  -5.19
  627 GLN  ( 296-) B  -  -5.13
 1098 ARG  ( 105-) D  -  -5.12
   99 GLN  (  99-) A  -  -5.08
 1094 GLU  ( 101-) D  -  -5.04
  296 GLN  ( 296-) A  -  -5.04

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.

   98 ARG  (  98-) A  -      101 --- GLU   101- (A ) -       -4.81
 1091 ARG  (  98-) D  -     1094 --- GLU   101- (D ) -       -4.85

Note: Structural average packing environment OK

The structural average packing score is within normal ranges.

Average for range 1 - 1324 : -0.424

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

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.

 1005 LEU  (  12-) D  -  -2.51

Note: No series of residues with abnormal new packing environment

There are no stretches of four or more residues each having a packing Z-score worse than -1.75.

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

Water, ion, and hydrogenbond related checks

Note: Crystallisation conditions from REMARK 280

Crystallisation conditions as found in the PDB file header.

CRYSTAL
SOLVENT CONTENT, VS   (%): 44.00
MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.23
CRYSTALLIZATION CONDITIONS: PEG3350, MALONATE PH 7.0, VAPOR
       DIFFUSION, SITTING DROP, TEMPERATURE 293K

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.

 1345 HOH  ( 570 ) B  -    O

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.

 1345 HOH  ( 570 ) B  -    O

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.

   16 GLN  (  16-) A  -
  100 GLN  ( 100-) A  -
  326 GLN  ( 326-) A  -
  350 GLN  (  19-) B  -
  772 GLN  ( 110-) C  -
  958 GLN  ( 296-) C  -
  988 GLN  ( 326-) C  -
 1009 GLN  (  16-) D  -
 1319 GLN  ( 326-) D  -

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.

   66 HIS  (  66-) A  -   HIS-E   0.56 HIS-D   0.82
  180 HIS  ( 180-) A  -   HIS-H   0.13 HIS-E   0.55
  185 HIS  ( 185-) A  -   HIS-H   0.29
  192 HIS  ( 192-) A  -   HIS-H   0.07 HIS-D   0.56
  214 HIS  ( 214-) A  -   HIS-H   0.16 HIS-E   0.55
  230 HIS  ( 230-) A  -   HIS-H   0.11 HIS-E   0.57
  270 HIS  ( 270-) A  -   HIS-H   0.06 HIS-D   0.55
  397 HIS  (  66-) B  -   HIS-E   0.56
  511 HIS  ( 180-) B  -   HIS-H   0.09 HIS-E   0.56
  516 HIS  ( 185-) B  -   HIS-H   0.04 HIS-E   0.57
  523 HIS  ( 192-) B  -   HIS-H   0.03 HIS-D   0.56
  545 HIS  ( 214-) B  -   HIS-H   0.13 HIS-E   0.56
  561 HIS  ( 230-) B  -   HIS-H   0.30 HIS-E   0.61
  601 HIS  ( 270-) B  -   HIS-H   0.06 HIS-D   0.55
  728 HIS  (  66-) C  -   HIS-H   0.50 HIS-E   0.54
  842 HIS  ( 180-) C  -   HIS-H   0.05 HIS-E   0.60
  847 HIS  ( 185-) C  -   HIS-H   0.05
  854 HIS  ( 192-) C  -   HIS-H   0.03 HIS-D   0.55
  876 HIS  ( 214-) C  -   HIS-H   0.18 HIS-E   0.58
  892 HIS  ( 230-) C  -   HIS-H   0.06 HIS-E   0.57
  932 HIS  ( 270-) C  -   HIS-H   0.04 HIS-D   0.54
 1059 HIS  (  66-) D  -   HIS-H   0.54 HIS-D   0.73
 1173 HIS  ( 180-) D  -   HIS-H   0.11 HIS-E   0.56
 1178 HIS  ( 185-) D  -   HIS-H   0.04
 1185 HIS  ( 192-) D  -   HIS-H   0.11 HIS-D   0.53
 1207 HIS  ( 214-) D  -   HIS-E   0.54
 1223 HIS  ( 230-) D  -   HIS-H   0.51 HIS-E   0.56
 1263 HIS  ( 270-) D  -   HIS-H   0.09 HIS-D   0.57

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.

   16 GLN  (  16-) A  -    N
   21 LYS  (  21-) A  -    N
   51 ASP  (  51-) A  -    N
   73 THR  (  73-) A  -    N
   95 ALA  (  95-) A  -    N
  110 GLN  ( 110-) A  -    NE2
  155 ASN  ( 155-) A  -    N
  161 GLY  ( 161-) A  -    N
  163 ASN  ( 163-) A  -    ND2
  168 ARG  ( 168-) A  -    NH1
  168 ARG  ( 168-) A  -    NH2
  186 GLY  ( 186-) A  -    N
  218 GLY  ( 218-) A  -    N
  227 LYS  ( 227-) A  -    N
  244 LYS  ( 244-) A  -    NZ
And so on for a total of 92 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.

  192 HIS  ( 192-) A  -    NE2
  296 GLN  ( 296-) A  -    OE1
  347 GLN  (  16-) B  -    OE1
  516 HIS  ( 185-) B  -    ND1
  523 HIS  ( 192-) B  -    NE2
  854 HIS  ( 192-) C  -    NE2
 1187 ASP  ( 194-) D  -    OD1

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: 1871
- of which buried: 1133
Total number of acceptors: 1980
- of which buried: 964
Total number of donor+acceptors: 184 (e.g. the Ser Ogamma that can donate and accept)
- of which buried: 68
Buried donors: 1133
- without H-bond: 73
- essentially without H-bond: 0
- with only a very poor H-bond: 7
- with a poor H-bond: 17
- with a H-bond: 1036
Buried acceptors: 964
- without H-bond: 131
- essentially without H-bond: 0
- with only a very poor H-bond: 10
- with a poor H-bond: 24
- with a H-bond: 799

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 (    1)   331 (  331) A Protein             /srv/data/pdb/fla...
     2   332 (    1)   662 (  331) B Protein             /srv/data/pdb/fla...
     3   663 (    1)   993 (  331) C Protein             /srv/data/pdb/fla...
     4   994 (    1)  1324 (  331) D Protein             /srv/data/pdb/fla...
     5  1325 (  331)  1325 (  331) A F O2 <-   331       /srv/data/pdb/fla...
     6  1326 (  331)  1326 (  331) B F O2 <-   662       /srv/data/pdb/fla...
     7  1327 (  331)  1327 (  331) C F O2 <-   993       /srv/data/pdb/fla...
     8  1328 (  331)  1328 (  331) D F O2 <-  1324       /srv/data/pdb/fla...
     9  1329 (  401)  1329 (  401) A NAD                 /srv/data/pdb/fla...
    10  1330 (  402)  1330 (  402) A SO4                 /srv/data/pdb/fla...
    11  1331 (  403)  1331 (  403) A SO4                 /srv/data/pdb/fla...
    12  1332 (  405)  1332 (  405) A GN0                 /srv/data/pdb/fla...
    13  1333 (  404)  1333 (  404) A SO4                 /srv/data/pdb/fla...
    14  1334 (  401)  1334 (  401) B NAD                 /srv/data/pdb/fla...
    15  1335 (  402)  1335 (  402) B SO4                 /srv/data/pdb/fla...
    16  1336 (  404)  1336 (  404) B GN0                 /srv/data/pdb/fla...
    17  1337 (  403)  1337 (  403) B SO4                 /srv/data/pdb/fla...
    18  1338 (  401)  1338 (  401) C NAD                 /srv/data/pdb/fla...
    19  1339 (  403)  1339 (  403) C GN0                 /srv/data/pdb/fla...
    20  1340 (  402)  1340 (  402) C SO4                 /srv/data/pdb/fla...
    21  1341 (  401)  1341 (  401) D NAD                 /srv/data/pdb/fla...
    22  1342 (  403)  1342 (  403) D GN0                 /srv/data/pdb/fla...
    23  1343 (  402)  1343 (  402) D SO4                 /srv/data/pdb/fla...
    24  1344 ( HOH )  1344 ( HOH ) A water   (   72)     /srv/data/pdb/fla...
    25  1345 ( HOH )  1345 ( HOH ) B water   (   71)     /srv/data/pdb/fla...
    26  1346 ( HOH )  1346 ( HOH ) C water   (   82)     /srv/data/pdb/fla...
    27  1347 ( HOH )  1347 ( HOH ) D water   (   84)     /srv/data/pdb/fla...

Final summary

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  :   2.200
  1st generation packing quality :   0.190 (          (  -0.3,  2.5))
  2nd generation packing quality :  -1.609 (          (  -1.1,  1.3))
  Ramachandran plot appearance   :  -1.380 (          (  -1.3,  1.2))
  chi-1/chi-2 rotamer normality  :  -3.392 (poor      (  -3.1,  1.5))
  Backbone conformation          :  -0.987 (          (  -0.6,  3.4))
  Inside/Outside distribution    :   0.951

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.539 (tight)
  Bond angles                    :   0.526 (tight)
  Omega angle restraints         :   0.843
  Side chain planarity           :   0.315 (tight)
  Improper dihedral distribution :   0.514
  B-factor distribution          :   0.354

Suggestions for the refinement process

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.

Note: No crippling problems detected

Some problems can be so crippling that they negatively influence the validity of other validation steps. If such a problem is detected, it must be solved and some further refinemnet must be done before you can continue working with a new WHAT CHECK report. In this file such problems were not detected. You can therefore try to fix as many problems in one go as you want.

Note: Cell parameter anomaly

WHAT CHECK has compared the observed bond lengths with the Engh and Huber parameters, and has done this as function of the direction of the bond relative to the cell axes. From this analysis it was concluded that the cell dimensions are probably not entirely perfect. The problem is not very big, so you do not need to fix this before you start dealing with the other suggestions, but you better fix this.

If this problem is caused by refining with another set of target values than the Engh and Huber values, then I cannot help you because systematic target value deviations can also cause this message to pop up.

Error: Bumps in your structure

Upon analysing the bumps in your structure, WHAT CHECK got very worried. Often 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.

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.

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.

Residues in need of attention

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.

 1006 LYS  (  13-) D  -     43.70
 1009 GLN  (  16-) D  -     26.22
   99 GLN  (  99-) A  -     17.61
   16 GLN  (  16-) A  -     15.13
  347 GLN  (  16-) B  -     14.49
 1091 ARG  (  98-) D  -     14.20
  403 ARG  (  72-) B  -     12.92
  993 PHE  ( 331-) C  -     12.91
 1323 GLN  ( 330-) D  -     12.86
  330 GLN  ( 330-) A  -     12.85
  958 GLN  ( 296-) C  -     12.50
  297 ASN  ( 297-) A  -     12.37
  678 GLN  (  16-) C  -     12.14
 1065 ARG  (  72-) D  -     12.13
  661 GLN  ( 330-) B  -     12.05
And so on for a total of 119 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)
 
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).
    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.