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/pdb5fjr.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.

Warning: Class of conventional cell differs from CRYST1 cell

The crystal class of the conventional cell is different from the crystal class of the cell given on the CRYST1 card. If the new class is supported by the coordinates this is an indication of a wrong space group assignment.

The CRYST1 cell dimensions

    A    = 217.670  B   = 217.670  C    = 263.150
    Alpha=  90.000  Beta=  90.000  Gamma= 120.000

Dimensions of a reduced cell

    A    = 153.257  B   = 153.257  C    = 153.257
    Alpha=  90.494  Beta=  90.494  Gamma=  90.494

Dimensions of the conventional cell

    A    = 153.257  B   = 153.257  C    = 153.257
    Alpha=  90.494  Beta=  90.494  Gamma=  90.494

Transformation to conventional cell

 | -0.333333  0.333333  0.333333|
 | -0.333333 -0.666667  0.333333|
 |  0.666667  0.333333  0.333333|

Crystal class of the cell: HEXAGONAL

Crystal class of the conventional cell: CUBIC

Space group name: H 3 2

Bravais type of conventional cell is: P

Note: Header records from PDB file

Header records from PDB file.

HEADER    LYASE                                   12-OCT-15   5FJR
N-ACYL AMINO ACID RACEMASE FROM AMYCOLATOPSIS SP. TS-1-60:
 Q26A M50I G291D F323Y MUTANT IN COMPLEX WITH N-ACETYL
 NAPTHYLALANINE
LYASE, RACEMASE, N-ACYLAMINO ACID, ISOMERASE
JRNL        G.SANCHEZ-CARRON,D.CAMPOPIANO,G.GROGAN
JRNL        STRUCTURE OF N-ACYLAMINO ACID RACEMASE MUTANTS IN COMPLEX
JRNL        WITH SUBSTRATES
JRNL        REF    TO BE PUBLISHED
JRNL        REFN

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 : 0.371
CA-only RMS fit for the two chains : 0.236

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 : 0.368
CA-only RMS fit for the two chains : 0.203

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 : 0.389
CA-only RMS fit for the two chains : 0.218

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 : 0.302
CA-only RMS fit for the two chains : 0.172

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 : 0.341
CA-only RMS fit for the two chains : 0.211

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

In the conventional cell, independent molecules in the asymmetric unit seemingly become symmetry relatives. This fact needs manual checking.

Error: Value of Z incompatible with space group

The value of Z (given on the CRYST1 line) is not an integer multiple of the number of symmetry operations in the space group.

Number of operations in space group: 18

Z-value from CRYST1: 1

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: H 3 2
Number of matrices in space group: 18
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
but NCS matrices (but not the unitary matrix) are found labeled `dont use`: 3
SEQRES multiplicity agrees with number of MTRIX matrices labeled `dont use`
Value of Z as found on the CRYST1 card: 1
BIOMT matrices have been found but not enough to explain the difference

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: 157386.656
Volume of the Unit Cell V= 10797917.0
Space group multiplicity: 18
No NCS symmetry matrices (MTRIX records) found in PDB file
but the number of MTRIX matrices flagged as `do not use` = 3
which seems more or less consistent with the SEQRES multiplicity
because the unitary MTRIX record gets forgotten more often ...
Matthews coefficient for observed atoms and Z is high: Vm= 274.430
Be aware though that the number of residues with missing atoms is: 42
BIOMT matrices observed in the PDB file: 2
But accounting for these BIOMT matrices does not make Vm reasonable yet
Matthews coefficient read from REMARK 280 Vm= 3.800
Vm by authors and this calculated Vm do not agree very 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: Ligands for which a topology was generated automatically

The topology for the ligands in the table below were determined automatically. WHAT CHECK uses a local copy of CCP4 monomer library to generate topology information for ligands. Be aware that automatic topology generation is a complicated task. So, if you get messages that you fail to understand or that you believe are wrong, and one of these ligands is involved, then check the ligand topology entry in the monomers library first.

 1471 NPQ  (1369-) A  -
 1473 NPQ  (1368-) B  -
 1475 NPQ  (1368-) C  -
 1477 NPQ  (1368-) 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.

Note: In all cases the primary alternate atom was used

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

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.

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-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)   368 (  368) A Protein             /srv/data/pdb/fla...
     2   369 (    1)   735 (  367) B Protein             /srv/data/pdb/fla...
     3   736 (    1)  1102 (  367) C Protein             /srv/data/pdb/fla...
     4  1103 (    1)  1469 (  367) D Protein             /srv/data/pdb/fla...
     5  1470 ( 1370)  1470 ( 1370) A  MG                 /srv/data/pdb/fla...
     6  1471 ( 1369)  1471 ( 1369) A NPQ                 /srv/data/pdb/fla...
     7  1472 ( 1369)  1472 ( 1369) B  MG                 /srv/data/pdb/fla...
     8  1473 ( 1368)  1473 ( 1368) B NPQ                 /srv/data/pdb/fla...
     9  1474 ( 1369)  1474 ( 1369) C  MG                 /srv/data/pdb/fla...
    10  1475 ( 1368)  1475 ( 1368) C NPQ                 /srv/data/pdb/fla...
    11  1476 ( 1369)  1476 ( 1369) D  MG                 /srv/data/pdb/fla...
    12  1477 ( 1368)  1477 ( 1368) D NPQ                 /srv/data/pdb/fla...
    13  1478 ( HOH )  1478 ( HOH ) A water   (  246)     /srv/data/pdb/fla...
    14  1479 ( HOH )  1479 ( HOH ) B water   (  145)     /srv/data/pdb/fla...
    15  1480 ( HOH )  1480 ( HOH ) C water   (  118)     /srv/data/pdb/fla...
    16  1481 ( HOH )  1481 ( HOH ) D water   (  108)     /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 MKLSGVELRRVQMPLVAPFRTSFGTASVRELLLLRAVTPAGEGWGECVTIAGPLYSSEYN
(   1)-(  60)    SSSSSSSSSSSSSSSSSTTSSSSSSSSSSSSSSSTTSSSSSSS     TT     H
                     70        80        90       100       110       120
                      |         |         |         |         |         |
   61 -  120 DGAEHVLRHYLIPALLAAEDITAAKVTPLLAKFKGHRMAKGALEMAVLDAELRAHERSFA
(  61)-( 120)HHHHHHHHHHHHHHHHT     HHHHHHHHTT    HHHHHHHHHHHHHHHHHHTT  HH
                    130       140       150       160       170       180
                      |         |         |         |         |         |
  121 -  180 AELGSVRDSVPCGVSVGIMDTIPQLLDVVGGYLDEGYVRIKLKIEPGWDVEPVRAVRERF
( 121)-( 180)HHHT    SSS  SSS     HHHHHHHHHHHHHTT   SSSS  TT  HHHHHHHHHHH
                    190       200       210       220       230       240
                      |         |         |         |         |         |
  181 -  240 GDDVLLQVDANTAYTLGDAPQLARLDPFGLLLIEQPLEEEDVLGHAELARRIQTPICLDE
( 181)-( 240)     SSSS TT   HHHHHHHHTTHHH    SS    TT HHHHHHHHHH    SSS T
                    250       260       270       280       290       300
                      |         |         |         |         |         |
  241 -  300 SIVSARAAADAIKLGAVQIVNIKPGRVGGYLEARRVHDVCAAHGIPVWCGDMIETGLGRA
( 241)-( 300)T   HHHHHHHHHTT   SSSS TTTTT HHHHHHHHHHHHHTT  SSS      HHHHH
                    310       320       330       340       350       360
                      |         |         |         |         |         |
  301 -  360 ANVALASLPNFTLPGDTSASDRYYKTDITEPFVLSGGHLPVPTGPGLGVAPIPELLDEVT
( 301)-( 360)HHHHHTT TT         HHHT            TTSSS      T     HHHHHHHS
 
 
  361 -  368 TAKVWIGS
( 361)-( 368)SSSSSSS
 
            370       380       390       400       410       420
              |         |         |         |         |         |
  369 -  428 MKLSGVELRRVQMPLVAPFRTSFGTASVRELLLLRAVTPAGEGWGECVTIAGPLYSSEYN
(   1)-(  60)    SSSSSSSSSSSSSSSSSTTSSSSSSSSSSSSSS    SSSSS      TT     H
            430       440       450       460       470       480
              |         |         |         |         |         |
  429 -  488 DGAEHVLRHYLIPALLAAEDITAAKVTPLLAKFKGHRMAKGALEMAVLDAELRAHERSFA
(  61)-( 120)HHHHHHHHHHHHHHHHT     HHHHHHH TT    HHHHHHHHHHHHHHHHHHTT  HH
            490       500       510       520       530       540
              |         |         |         |         |         |
  489 -  548 AELGSVRDSVPCGVSVGIMDTIPQLLDVVGGYLDEGYVRIKLKIEPGWDVEPVRAVRERF
( 121)-( 180)HHHT    SSS  SSS     HHHHHHHHHHHHHTT  SSSSS  TT  HHHHHHHHHHH
            550       560       570       580       590       600
              |         |         |         |         |         |
  549 -  608 GDDVLLQVDANTAYTLGDAPQLARLDPFGLLLIEQPLEEEDVLGHAELARRIQTPICLDE
( 181)-( 240)    SSSSS TT   HHHHHHHHTTHHH    SS    TT HHHHHHHHHH    SSS T
            610       620       630       640       650       660
              |         |         |         |         |         |
  609 -  668 SIVSARAAADAIKLGAVQIVNIKPGRVGGYLEARRVHDVCAAHGIPVWCGDMIETGLGRA
( 241)-( 300)T   HHHHHHHHHTT   SSSS TTTTT HHHHHHHHHHHHHTT  SSS      HHHHH
            670       680       690       700       710       720
              |         |         |         |         |         |
  669 -  728 ANVALASLPNFTLPGDTSASDRYYKTDITEPFVLSGGHLPVPTGPGLGVAPIPELLDEVT
( 301)-( 360)HHHHHTT TT         HHHT            TTSSS      T     HHHHHHTS
            730
              |
  729 -  735 TAKVWIG
( 361)-( 367)SSSSSS
 
               740       750       760       770       780       790
                 |         |         |         |         |         |
  736 -  795 MKLSGVELRRVQMPLVAPFRTSFGTASVRELLLLRAVTPAGEGWGECVTIAGPLYSSEYN
(   1)-(  60)    SSSSSSSSSSSSSSSSSTTSSSSSSSSSSSSSSSTTSSSSSS      TT     H
               800       810       820       830       840       850
                 |         |         |         |         |         |
  796 -  855 DGAEHVLRHYLIPALLAAEDITAAKVTPLLAKFKGHRMAKGALEMAVLDAELRAHERSFA
(  61)-( 120)HHHHHHHHHHHHHHHHT     HHHHHHHHTT    HHHHHHHHHHHHHHHHHTTT  HH
               860       870       880       890       900       910
                 |         |         |         |         |         |
  856 -  915 AELGSVRDSVPCGVSVGIMDTIPQLLDVVGGYLDEGYVRIKLKIEPGWDVEPVRAVRERF
( 121)-( 180)HHHT    SSS  SSS     HHHHHHHHHHHHHTT  SSSSS  TT  HHHHHHHHHHH
               920       930       940       950       960       970
                 |         |         |         |         |         |
  916 -  975 GDDVLLQVDANTAYTLGDAPQLARLDPFGLLLIEQPLEEEDVLGHAELARRIQTPICLDE
( 181)-( 240) TT SSSSS TT   HHHHHHHHTTHHH    SS    TT HHHHHHHHTT    SSS T
               980       990      1000      1010      1020      1030
                 |         |         |         |         |         |
  976 - 1035 SIVSARAAADAIKLGAVQIVNIKPGRVGGYLEARRVHDVCAAHGIPVWCGDMIETGLGRA
( 241)-( 300)T   HHHHHHHHHTT   SSSS TTTTT HHHHHHHHHHHHHTT  SSS      HHHHH
              1040      1050      1060      1070      1080      1090
                 |         |         |         |         |         |
 1036 - 1095 ANVALASLPNFTLPGDTSASDRYYKTDITEPFVLSGGHLPVPTGPGLGVAPIPELLDEVT
( 301)-( 360)HHHHHTT TT         HHHT              SSS      T     HHHHHHHS
              1100
                 |
 1096 - 1102 TAKVWIG
( 361)-( 367)SSSSSS
 
                 1110      1120      1130      1140      1150      1160
                    |         |         |         |         |         |
 1103 - 1162 MKLSGVELRRVQMPLVAPFRTSFGTASVRELLLLRAVTPAGEGWGECVTIAGPLYSSEYN
(   1)-(  60)    SSSSSSSSSSSSSSSSSTTSSSSSSSSSSSSSSSTTSSSSSS      TT     H
                 1170      1180      1190      1200      1210      1220
                    |         |         |         |         |         |
 1163 - 1222 DGAEHVLRHYLIPALLAAEDITAAKVTPLLAKFKGHRMAKGALEMAVLDAELRAHERSFA
(  61)-( 120)HHHHHHHHHHHHHHHHT     HHHHHHHTTT    HHHHHHHHHHHHHHHHHTTT  HH
                 1230      1240      1250      1260      1270      1280
                    |         |         |         |         |         |
 1223 - 1282 AELGSVRDSVPCGVSVGIMDTIPQLLDVVGGYLDEGYVRIKLKIEPGWDVEPVRAVRERF
( 121)-( 180)HHHT    SSS  SSS     HHHHHHHHHHHHHTT  SSSSS  TT  HHHHHHHHHHH
                 1290      1300      1310      1320      1330      1340
                    |         |         |         |         |         |
 1283 - 1342 GDDVLLQVDANTAYTLGDAPQLARLDPFGLLLIEQPLEEEDVLGHAELARRIQTPICLDE
( 181)-( 240)    SSSSS TT   HHHHHHHHHHHHH    SS    TT HHHHHHHHHH    SSS T
                 1350      1360      1370      1380      1390      1400
                    |         |         |         |         |         |
 1343 - 1402 SIVSARAAADAIKLGAVQIVNIKPGRVGGYLEARRVHDVCAAHGIPVWCGDMIETGLGRA
( 241)-( 300)T   HHHHHHHHHHT   SSSS TTTTT HHHHHHHHHHHHHTT  SSS      HHHHH
                 1410      1420      1430      1440      1450      1460
                    |         |         |         |         |         |
 1403 - 1462 ANVALASLPNFTLPGDTSASDRYYKTDITEPFVLSGGHLPVPTGPGLGVAPIPELLDEVT
( 301)-( 360)HHHHHTT TT         HHHH            TTSSS      T     HHHHHHTS
 
 
 1463 - 1469 TAKVWIG
( 361)-( 367)SSSSSS
 
 
 

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'.

   79 GLU  (  79-) A  -    CG
   79 GLU  (  79-) A  -    CD
   79 GLU  (  79-) A  -    OE1
   79 GLU  (  79-) A  -    OE2
  178 GLU  ( 178-) A  -    CG
  178 GLU  ( 178-) A  -    CD
  178 GLU  ( 178-) A  -    OE1
  178 GLU  ( 178-) A  -    OE2
  369 MET  (   1-) B  -    CG
  369 MET  (   1-) B  -    SD
  369 MET  (   1-) B  -    CE
  447 GLU  (  79-) B  -    CG
  447 GLU  (  79-) B  -    CD
  447 GLU  (  79-) B  -    OE1
  447 GLU  (  79-) B  -    OE2
And so on for a total of 158 lines.

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.

  370 LYS  (   2-) B  -   High
  378 ARG  (  10-) B  -   High
  408 ALA  (  40-) B  -   High
  447 GLU  (  79-) B  -   High
  448 ASP  (  80-) B  -   High
  484 GLU  ( 116-) B  -   High
  508 ASP  ( 140-) B  -   High
  522 ASP  ( 154-) B  -   High
  725 ASP  ( 357-) B  -   High
  745 ARG  (  10-) C  -   High
  774 PRO  (  39-) C  -   High
  775 ALA  (  40-) C  -   High
  776 GLY  (  41-) C  -   High
  814 GLU  (  79-) C  -   High
  815 ASP  (  80-) C  -   High
  863 ASP  ( 128-) C  -   High
  906 GLU  ( 171-) C  -   High
  914 ARG  ( 179-) C  -   High
  918 ASP  ( 183-) C  -   High
  939 ARG  ( 204-) C  -   High
 1104 LYS  (   2-) D  -   High
 1112 ARG  (  10-) D  -   High
 1141 PRO  (  39-) D  -   High
 1143 GLY  (  41-) D  -   High
 1146 TRP  (  44-) D  -   High
 1182 ASP  (  80-) D  -   High
 1242 ASP  ( 140-) D  -   High
 1249 ASP  ( 147-) D  -   High
 1432 GLU  ( 330-) D  -   High
 1459 ASP  ( 357-) D  -   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.

  368 SER  ( 368-) A  -        : REAL Oxt missing
  735 GLY  ( 367-) B  -        : PSEUDO OK
 1102 GLY  ( 367-) C  -        : PSEUDO OK
 1469 GLY  ( 367-) D  -        : PSEUDO OK

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.

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 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) :120.000

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 : 1.250 over 9595 bonds
Average difference in B over a bond : 4.42
RMS difference in B over a bond : 5.87

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.

Note: Arginine nomenclature OK

No errors were detected in arginine nomenclature.

Note: Tyrosine torsion conventions OK

No errors were detected in tyrosine torsion angle conventions.

Note: Phenylalanine torsion conventions OK

No errors were detected in phenylalanine torsion angle conventions.

Note: Aspartic acid torsion conventions OK

No errors were detected in aspartic acid torsion angle conventions.

Note: Glutamic acid torsion conventions OK

No errors were detected in glutamic acid torsion angle conventions.

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).

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.

   21 THR  (  21-) A  -    CB   CG2   1.39   -4.1
  141 THR  ( 141-) A  -    CB   CG2   1.65    4.1
  221 ASP  ( 221-) A  -    CG   OD1   1.34    4.6
  250 ASP  ( 250-) A  -    CB   CG    1.62    4.3
  344 GLY  ( 344-) A  -    N    CA    1.52    4.3
  505 GLY  ( 137-) B  -    N    CA    1.52    4.1
 1154 GLY  (  52-) D  -    N    CA    1.52    4.1
 1341 ASP  ( 239-) D  -    CB   CG    1.62    4.3
 1458 LEU  ( 356-) D  -    CA   CB    1.63    5.2
 1458 LEU  ( 356-) D  -    CB   CG    1.62    4.3
 1463 THR  ( 361-) D  -    CB   CG2   1.69    5.2

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: 0.957
RMS-deviation in bond distances: 0.020

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

 |  0.004594  0.002652  0.000000|
 |  0.000000  0.005305  0.000000|
 |  0.000000  0.000000  0.003800|
Unit Cell deformation matrix

 |  0.995241 -0.000635 -0.000424|
 | -0.000635  0.995687  0.000012|
 | -0.000424  0.000012  0.994623|
Proposed new scale matrix

 |  0.004618  0.002666  0.000002|
 |  0.000003  0.005328  0.000000|
 |  0.000002  0.000000  0.003821|
With corresponding cell

    A    = 216.639  B   = 216.812  C    = 261.743
    Alpha=  90.000  Beta=  90.000  Gamma= 120.000

The CRYST1 cell dimensions

    A    = 217.670  B   = 217.670  C    = 263.150
    Alpha=  90.000  Beta=  90.000  Gamma= 120.000

Variance: 1074.670
(Under-)estimated Z-score: 24.160

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.

   21 THR  (  21-) A  -    N    CA   CB  101.94   -5.0
   42 GLU  (  42-) A  -    C    CA   CB  101.30   -4.6
  113 ARG  ( 113-) A  -    CG   CD   NE   96.76   -8.1
  113 ARG  ( 113-) A  -    CD   NE   CZ  131.96    5.7
  113 ARG  ( 113-) A  -    NE   CZ   NH2 111.38   -4.5
  117 ARG  ( 117-) A  -    CB   CG   CD  105.64   -4.2
  128 ASP  ( 128-) A  -    C    CA   CB  101.84   -4.3
  159 ARG  ( 159-) A  -    CG   CD   NE  101.19   -5.5
  225 HIS  ( 225-) A  -    CG   ND1  CE1 109.79    4.2
  231 ARG  ( 231-) A  -    CG   CD   NE   98.41   -7.1
  338 HIS  ( 338-) A  -    CG   ND1  CE1 109.69    4.1
  344 GLY  ( 344-) A  -   -C    N    CA  108.56   -7.1
  359 VAL  ( 359-) A  -    N    CA   CB  101.00   -5.6
  359 VAL  ( 359-) A  -    C    CA   CB  121.28    5.9
  359 VAL  ( 359-) A  -    CG1  CB   CG2 121.28    4.8
And so on for a total of 58 lines.

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: 1.074
RMS-deviation in bond angles: 2.239

Note: Residue hand check OK

No atoms are observed that have the wrong handedness. Be aware, though, that WHAT CHECK might have corrected the handedness of some atoms already. The handedness has not been corrected for any case where the problem is worse than just an administrative discomfort.

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.

  359 VAL  ( 359-) A  -    CB     9.8   -21.02   -32.96
  726 GLU  ( 358-) B  -    CA    -7.3    22.71    33.90
The average deviation= 1.529

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 : 1.275

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.

  370 LYS  (   2-) B  -   7.88
 1104 LYS  (   2-) D  -   5.63
  599 ARG  ( 231-) B  -   5.31
  737 LYS  (   2-) C  -   4.99
  429 ASP  (  61-) B  -   4.97
  378 ARG  (  10-) B  -   4.87
  245 ALA  ( 245-) A  -   4.60
 1333 ARG  ( 231-) D  -   4.49
 1098 LYS  ( 363-) C  -   4.27
  837 ALA  ( 102-) C  -   4.22
 1201 ALA  (  99-) D  -   4.21
 1282 PHE  ( 180-) D  -   4.20
  690 ARG  ( 322-) B  -   4.10
 1137 ARG  (  35-) D  -   4.09
  231 ARG  ( 231-) A  -   4.05
  696 ILE  ( 328-) B  -   4.03

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 : 1.454

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.

  996 ASN  ( 261-) C  -   4.21

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 : -2.515

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.

 1294 THR  ( 192-) D  -   -3.0
  927 THR  ( 192-) C  -   -2.9
 1395 ILE  ( 293-) D  -   -2.8
  560 THR  ( 192-) B  -   -2.8
   31 LEU  (  31-) A  -   -2.7
  580 LEU  ( 212-) B  -   -2.7
  766 LEU  (  31-) C  -   -2.6
 1133 LEU  (  31-) D  -   -2.6
  116 GLU  ( 116-) A  -   -2.6
 1314 LEU  ( 212-) D  -   -2.6
  399 LEU  (  31-) B  -   -2.6
  484 GLU  ( 116-) B  -   -2.6
  851 GLU  ( 116-) C  -   -2.6
  212 LEU  ( 212-) A  -   -2.6
  947 LEU  ( 212-) C  -   -2.5
And so on for a total of 56 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.

    5 GLY  (   5-) A  - Poor phi/psi
    9 ARG  (   9-) A  - omega poor
   13 MET  (  13-) A  - Omega to (next) Pro poor
   17 ALA  (  17-) A  - Omega to (next) Pro poor
   24 GLY  (  24-) A  - Poor phi/psi
   38 THR  (  38-) A  - Omega to (next) Pro poor
   41 GLY  (  41-) A  - Poor phi/psi
   52 GLY  (  52-) A  - Omega to (next) Pro poor
   53 PRO  (  53-) A  - Poor phi/psi
   59 TYR  (  59-) A  - omega poor
   70 TYR  (  70-) A  - omega poor
   72 ILE  (  72-) A  - Omega to (next) Pro poor
   81 ILE  (  81-) A  - omega poor
   87 THR  (  87-) A  - Omega to (next) Pro poor
   95 GLY  (  95-) A  - Poor phi/psi
And so on for a total of 217 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.

  297 LEU  ( 297-) A  -    -1.44
  356 LEU  ( 356-) A  -    -1.44
  513 LEU  ( 145-) B  -    -1.40
  514 LEU  ( 146-) B  -    -1.44
  521 LEU  ( 153-) B  -    -1.44
  723 LEU  ( 355-) B  -    -1.44
 1032 LEU  ( 297-) C  -    -1.42
 1090 LEU  ( 355-) C  -    -1.42
 1247 LEU  ( 145-) D  -    -1.43
    3 LEU  (   3-) A  -    -1.30
    8 LEU  (   8-) A  -    -1.35
   31 LEU  (  31-) A  -    -1.35
   75 LEU  (  75-) A  -    -1.40
  212 LEU  ( 212-) A  -    -1.31
  305 LEU  ( 305-) A  -    -1.31
And so on for a total of 566 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 : -4.607

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.

 1106 SER  (   4-) D  -   0.35
  748 MET  (  13-) C  -   0.38
 1063 ILE  ( 328-) 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, especially if a regular DSSP secondary structure (H or S for helix or strand) is indicated!

  125 SER  ( 125-) A  -       0
  293 ILE  ( 293-) A  -       0
  329 THR  ( 329-) A  -       0
  347 LEU  ( 347-) A  -       0
  464 HIS  (  96-) B  -       0
  560 THR  ( 192-) B  -       0
  661 ILE  ( 293-) B  -       0
  715 LEU  ( 347-) B  -       0
 1028 ILE  ( 293-) C  -       0
 1064 THR  ( 329-) C  -       0
 1082 LEU  ( 347-) C  -       0
 1198 HIS  (  96-) D  -       0
 1294 THR  ( 192-) D  -       0
 1395 ILE  ( 293-) D  -       0
 1449 LEU  ( 347-) D  -       0
And so on for a total of 41 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 : -0.799

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= 179.050 6.793

Warning: Unusual PRO puckering amplitudes

The proline residues listed in the table below have a puckering amplitude that is outside of normal ranges. Puckering parameters were calculated by the method of Cremer and Pople [REF]. Normal PRO rings have a puckering amplitude Q between 0.20 and 0.45 Angstrom. If Q is lower than 0.20 Angstrom for a PRO residue, this could indicate disorder between the two different normal ring forms (with C-gamma below and above the ring, respectively). If Q is higher than 0.45 Angstrom something could have gone wrong during the refinement. Be aware that this is a warning with a low confidence level. See: Who checks the checkers? Four validation tools applied to eight atomic resolution structures [REF]

  207 PRO  ( 207-) A  -   0.19 LOW
  351 PRO  ( 351-) A  -   0.48 HIGH
  584 PRO  ( 216-) B  -   0.12 LOW
  677 PRO  ( 309-) B  -   0.08 LOW
  753 PRO  (  18-) C  -   0.12 LOW
  907 PRO  ( 172-) C  -   0.16 LOW
  951 PRO  ( 216-) C  -   0.14 LOW
 1021 PRO  ( 286-) C  -   0.19 LOW
 1044 PRO  ( 309-) C  -   0.17 LOW
 1049 PRO  ( 314-) C  -   0.15 LOW
 1274 PRO  ( 172-) D  -   0.15 LOW
 1411 PRO  ( 309-) D  -   0.19 LOW

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].

   53 PRO  (  53-) A  -  -61.2 half-chair C-beta/C-alpha (-54 degrees)
   73 PRO  (  73-) A  -  105.4 envelop C-beta (108 degrees)
   88 PRO  (  88-) A  - -138.4 envelop C-delta (-144 degrees)
  216 PRO  ( 216-) A  - -115.5 envelop C-gamma (-108 degrees)
  345 PRO  ( 345-) A  - -126.0 half-chair C-delta/C-gamma (-126 degrees)
  382 PRO  (  14-) B  - -115.2 envelop C-gamma (-108 degrees)
  441 PRO  (  73-) B  -  144.1 envelop C-alpha (144 degrees)
  456 PRO  (  88-) B  - -123.8 half-chair C-delta/C-gamma (-126 degrees)
  540 PRO  ( 172-) B  -  111.2 envelop C-beta (108 degrees)
  575 PRO  ( 207-) B  -   44.6 envelop C-delta (36 degrees)
  632 PRO  ( 264-) B  -  105.8 envelop C-beta (108 degrees)
  713 PRO  ( 345-) B  -  107.4 envelop C-beta (108 degrees)
  721 PRO  ( 353-) B  -   34.2 envelop C-delta (36 degrees)
  774 PRO  (  39-) C  -  102.0 envelop C-beta (108 degrees)
  823 PRO  (  88-) C  - -127.0 half-chair C-delta/C-gamma (-126 degrees)
  866 PRO  ( 131-) C  -  -46.5 half-chair C-beta/C-alpha (-54 degrees)
  999 PRO  ( 264-) C  -  103.6 envelop C-beta (108 degrees)
 1086 PRO  ( 351-) C  -   50.0 half-chair C-delta/C-gamma (54 degrees)
 1141 PRO  (  39-) D  -  102.9 envelop C-beta (108 degrees)
 1175 PRO  (  73-) D  -  102.0 envelop C-beta (108 degrees)
 1190 PRO  (  88-) D  - -118.7 half-chair C-delta/C-gamma (-126 degrees)
 1309 PRO  ( 207-) D  -   21.6 half-chair N/C-delta (18 degrees)
 1318 PRO  ( 216-) D  - -116.3 envelop C-gamma (-108 degrees)
 1366 PRO  ( 264-) D  -  100.9 envelop C-beta (108 degrees)
 1442 PRO  ( 340-) D  -  -22.8 half-chair C-alpha/N (-18 degrees)
 1444 PRO  ( 342-) D  -  166.3 half-chair C-alpha/N (162 degrees)
 1447 PRO  ( 345-) D  - -114.3 envelop C-gamma (-108 degrees)
 1453 PRO  ( 351-) D  -   46.5 half-chair C-delta/C-gamma (54 degrees)
 1455 PRO  ( 353-) D  -   27.1 envelop C-delta (36 degrees)

Note: Backbone oxygen evaluation OK

All residues for which similar local backbone conformations could be found in the WHAT CHECK database have a backbone oxygen position that has been observed at least a few times in that database.

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.

  894 ARG  ( 159-) C  -    NH2 <-->  1051 ASP  ( 316-) C  -    OD1    0.42    2.28  INTRA BF
  527 ARG  ( 159-) B  -    NH2 <-->   684 ASP  ( 316-) B  -    OD1    0.41    2.29  INTRA BF
 1261 ARG  ( 159-) D  -    NH2 <-->  1418 ASP  ( 316-) D  -    OD1    0.41    2.29  INTRA BL
  742 GLU  (   7-) C  -    OE1 <-->   770 ARG  (  35-) C  -    NH1    0.34    2.36  INTRA BF
  159 ARG  ( 159-) A  -    NH2 <-->   316 ASP  ( 316-) A  -    OD1    0.28    2.42  INTRA BL
  277 HIS  ( 277-) A  -    NE2 <-->   310 ASN  ( 310-) A  -    N      0.28    2.72  INTRA BL
    7 GLU  (   7-) A  -    CD  <-->    35 ARG  (  35-) A  -    NH1    0.27    2.83  INTRA BF
   35 ARG  (  35-) A  -    NE  <-->    42 GLU  (  42-) A  -    OE2    0.26    2.44  INTRA BF
 1131 ARG  (  29-) D  -    NH2 <-->  1394 MET  ( 292-) D  -    O      0.25    2.45  INTRA BF
  667 ARG  ( 299-) B  -    NH1 <-->   686 SER  ( 318-) B  -    O      0.20    2.50  INTRA BL
  397 ARG  (  29-) B  -    NH2 <-->   660 MET  ( 292-) B  -    O      0.19    2.51  INTRA BL
  477 ASP  ( 109-) B  -    OD2 <-->   481 ARG  ( 113-) B  -    NH1    0.19    2.51  INTRA BF
   29 ARG  (  29-) A  -    NH2 <-->   292 MET  ( 292-) A  -    O      0.19    2.51  INTRA BL
  389 THR  (  21-) B  -    CG2 <-->   391 PHE  (  23-) B  -    CD2    0.19    3.01  INTRA BF
  998 LYS  ( 263-) C  -    NZ  <-->  1475 NPQ  (1368-) C  -    C      0.18    2.92  INTRA BF
And so on for a total of 120 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: 11.031
Total bump value per residue: 0.082
Total number of bumps: 120
Total squared bump value: 1.889
Total number of bumps in the mildest bin: 111
Total number of bumps in the second bin: 9
Total number of bumps in the middle bin: 0
Total number of bumps in the fourth bin: 0
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 : 1.015

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.

  601 GLN  ( 233-) B  -  -6.34
  233 GLN  ( 233-) A  -  -6.32
  804 HIS  (  69-) C  -  -6.24
  437 HIS  (  69-) B  -  -6.23
  968 GLN  ( 233-) C  -  -6.13
 1171 HIS  (  69-) D  -  -5.99
   69 HIS  (  69-) A  -  -5.82
  179 ARG  ( 179-) A  -  -5.64
  575 PRO  ( 207-) B  -  -5.58
  231 ARG  ( 231-) A  -  -5.55
 1309 PRO  ( 207-) D  -  -5.55
  599 ARG  ( 231-) B  -  -5.55
 1333 ARG  ( 231-) D  -  -5.53
  207 PRO  ( 207-) A  -  -5.52
  942 PRO  ( 207-) C  -  -5.42
 1157 TYR  (  55-) D  -  -5.39
  914 ARG  ( 179-) C  -  -5.35
  790 TYR  (  55-) C  -  -5.26
  874 MET  ( 139-) C  -  -5.19
   55 TYR  (  55-) A  -  -5.18
  423 TYR  (  55-) B  -  -5.18
  690 ARG  ( 322-) B  -  -5.12
  322 ARG  ( 322-) A  -  -5.11
 1424 ARG  ( 322-) D  -  -5.04
 1057 ARG  ( 322-) C  -  -5.02

Note: No series of residues with bad packing environment

There are no stretches of three or more residues each having a packing score worse than -4.0.

Note: Structural average packing environment OK

The structural average packing score is within normal ranges.

Average for range 1 - 1469 : -0.781

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.

   17 ALA  (  17-) A  -  -3.14
  752 ALA  (  17-) C  -  -2.70
 1119 ALA  (  17-) D  -  -2.70
  385 ALA  (  17-) B  -  -2.63
 1065 GLU  ( 330-) C  -  -2.53
  698 GLU  ( 330-) B  -  -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   (%): 67.7
MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.8
CRYSTALLIZATION CONDITIONS: 100 MM TRIS HCL PH 8.0; 15%
       (W/V) PEG 4K; 800 MM SODIUM FORMATE; PROTEIN AT 8 MG PER
       ML

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.

 1478 HOH  (2218 ) A  -    O
 1479 HOH  (2049 ) B  -    O
 1479 HOH  (2074 ) 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.

 1478 HOH  (2036 ) A  -    O
 1478 HOH  (2218 ) A  -    O
 1479 HOH  (2049 ) B  -    O
 1479 HOH  (2074 ) B  -    O
 1479 HOH  (2090 ) B  -    O
 1480 HOH  (2002 ) C  -    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.

  626 GLN  ( 258-) B  -
 1440 HIS  ( 338-) 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.

   65 HIS  (  65-) A  -   HIS-H   0.61 HIS-E   0.67
   69 HIS  (  69-) A  -   HIS-H   0.21 HIS-D   0.48
   96 HIS  (  96-) A  -   HIS-H   0.35
  115 HIS  ( 115-) A  -   HIS-H   0.44 HIS-D   0.65
  225 HIS  ( 225-) A  -   HIS-E   0.59 HIS-D   0.65
  277 HIS  ( 277-) A  -   HIS-D   0.70
  283 HIS  ( 283-) A  -   HIS-D   0.60 HIS-E   0.77
  338 HIS  ( 338-) A  -   HIS-H   0.42 HIS-D   0.47
  433 HIS  (  65-) B  -   HIS-D   0.53 HIS-E   0.75
  437 HIS  (  69-) B  -   HIS-H   0.28 HIS-E   0.55
  464 HIS  (  96-) B  -   HIS-H   0.65 HIS-E   0.70
  483 HIS  ( 115-) B  -   HIS-H   0.33 HIS-D   0.58
  593 HIS  ( 225-) B  -   HIS-H   0.39 HIS-D   0.60
  645 HIS  ( 277-) B  -   HIS-D   0.48
  651 HIS  ( 283-) B  -   HIS-H   0.39 HIS-D   0.69
And so on for a total of 32 lines.

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.

    1 MET  (   1-) A  -    N
   17 ALA  (  17-) A  -    N
   23 PHE  (  23-) A  -    N
   82 THR  (  82-) A  -    N
  139 MET  ( 139-) A  -    N
  141 THR  ( 141-) A  -    N
  159 ARG  ( 159-) A  -    N
  159 ARG  ( 159-) A  -    NE
  183 ASP  ( 183-) A  -    N
  187 GLN  ( 187-) A  -    NE2
  212 LEU  ( 212-) A  -    N
  230 ARG  ( 230-) A  -    NH1
  244 SER  ( 244-) A  -    N
  257 VAL  ( 257-) A  -    N
  263 LYS  ( 263-) A  -    N
And so on for a total of 78 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.

 1018 HIS  ( 283-) C  -    NE2
 1026 ASP  ( 291-) C  -    OD1
 1385 HIS  ( 283-) D  -    NE2

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: 1933
- of which buried: 1162
Total number of acceptors: 2091
- of which buried: 941
Total number of donor+acceptors: 169 (e.g. the Ser Ogamma that can donate and accept)
- of which buried: 61
Buried donors: 1162
- without H-bond: 61
- essentially without H-bond: 1
- with only a very poor H-bond: 4
- with a poor H-bond: 20
- with a H-bond: 1076
Buried acceptors: 941
- without H-bond: 96
- essentially without H-bond: 0
- with only a very poor H-bond: 31
- with a poor H-bond: 371
- with a H-bond: 443

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)   368 (  368) A Protein             /srv/data/pdb/fla...
     2   369 (    1)   735 (  367) B Protein             /srv/data/pdb/fla...
     3   736 (    1)  1102 (  367) C Protein             /srv/data/pdb/fla...
     4  1103 (    1)  1469 (  367) D Protein             /srv/data/pdb/fla...
     5  1470 ( 1370)  1470 ( 1370) A  MG                 /srv/data/pdb/fla...
     6  1471 ( 1369)  1471 ( 1369) A NPQ                 /srv/data/pdb/fla...
     7  1472 ( 1369)  1472 ( 1369) B  MG                 /srv/data/pdb/fla...
     8  1473 ( 1368)  1473 ( 1368) B NPQ                 /srv/data/pdb/fla...
     9  1474 ( 1369)  1474 ( 1369) C  MG                 /srv/data/pdb/fla...
    10  1475 ( 1368)  1475 ( 1368) C NPQ                 /srv/data/pdb/fla...
    11  1476 ( 1369)  1476 ( 1369) D  MG                 /srv/data/pdb/fla...
    12  1477 ( 1368)  1477 ( 1368) D NPQ                 /srv/data/pdb/fla...
    13  1478 ( HOH )  1478 ( HOH ) A water   (  246)     /srv/data/pdb/fla...
    14  1479 ( HOH )  1479 ( HOH ) B water   (  145)     /srv/data/pdb/fla...
    15  1480 ( HOH )  1480 ( HOH ) C water   (  118)     /srv/data/pdb/fla...
    16  1481 ( HOH )  1481 ( HOH ) D water   (  108)     /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  :   2.440
  1st generation packing quality :  -0.703 (          (  -0.3,  2.5))
  2nd generation packing quality :  -1.981 (          (  -1.4,  1.2))
  Ramachandran plot appearance   :  -2.515 (          (  -2.4,  1.5))
  chi-1/chi-2 rotamer normality  :  -4.607 (bad       (  -4.2,  1.7))
  Backbone conformation          :  -0.799 (          (  -0.7,  3.6))
  Inside/Outside distribution    :   1.015

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.957
  Bond angles                    :   1.074
  Omega angle restraints         :   1.235
  Side chain planarity           :   0.956
  Improper dihedral distribution :   1.275
  B-factor distribution          :   1.250

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: Matthews coefficient problem

WHAT CHECK detected a Matthews coefficient problem. Most times this is an administrative problem caused by typing the wrong cell multiplicity number on the CRYST card (or not typing it at all). Occasionally it is caused by typing the wrong space group on the CRYST card. You better fix this problem, but normally this problem does not cause WHAT CHECK to give any erroneous error messages further down in the report.

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 a bit 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: Bond angle variabilty Z-score high

With a resolution of 1.5-2.5 Angstrom, you dont have enough data to warant the bond angle variability that we observed (more than 1.0). So, you better tighten the screws on the bond angle target values a bit.

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.

  231 ARG  ( 231-) A  -     17.45
  599 ARG  ( 231-) B  -     15.64
 1057 ARG  ( 322-) C  -     14.32
  359 VAL  ( 359-) A  -     13.81
  113 ARG  ( 113-) A  -     13.74
  601 GLN  ( 233-) B  -     12.68
  233 GLN  ( 233-) A  -     12.65
  804 HIS  (  69-) C  -     12.49
  437 HIS  (  69-) B  -     12.47
  968 GLN  ( 233-) C  -     12.26
 1333 ARG  ( 231-) D  -     12.19
 1171 HIS  (  69-) D  -     11.99
  159 ARG  ( 159-) A  -     11.65
   69 HIS  (  69-) A  -     11.64
 1309 PRO  ( 207-) D  -     11.52
And so on for a total of 160 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.