WHAT IF Check report

This file was created 2015-09-12 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 pdb2d6b.ent

Checks that need to be done early-on in validation

Note: Low non-crystallographic symmetry RMS

All comparable residues in the two chains mentioned below have comparable locations.

Chain identifiers of the two chains: A and A

All-atom RMS fit for the two chains : 0.052
CA-only RMS fit for the two chains : 0.019

Note: Low non-crystallographic symmetry phi and psi differences

All comparable residues in the two chains mentioned below have comparable backbone torsion angles

Chain identifiers of the two chains: A and A

Note: Low non-crystallographic symmetry RMS

All comparable residues in the two chains mentioned below have comparable locations.

Chain identifiers of the two chains: A and A

All-atom RMS fit for the two chains : 0.061
CA-only RMS fit for the two chains : 0.023

Note: Low non-crystallographic symmetry phi and psi differences

All comparable residues in the two chains mentioned below have comparable backbone torsion angles

Chain identifiers of the two chains: A and A

Note: Low non-crystallographic symmetry RMS

All comparable residues in the two chains mentioned below have comparable locations.

Chain identifiers of the two chains: A and A

All-atom RMS fit for the two chains : 0.058
CA-only RMS fit for the two chains : 0.021

Note: Low non-crystallographic symmetry phi and psi differences

All comparable residues in the two chains mentioned below have comparable backbone torsion angles

Chain identifiers of the two chains: A and A

Note: Low non-crystallographic symmetry RMS

All comparable residues in the two chains mentioned below have comparable locations.

Chain identifiers of the two chains: A and A

All-atom RMS fit for the two chains : 0.060
CA-only RMS fit for the two chains : 0.022

Note: Low non-crystallographic symmetry phi and psi differences

All comparable residues in the two chains mentioned below have comparable backbone torsion angles

Chain identifiers of the two chains: A and A

Note: Low non-crystallographic symmetry RMS

All comparable residues in the two chains mentioned below have comparable locations.

Chain identifiers of the two chains: A and A

All-atom RMS fit for the two chains : 0.087
CA-only RMS fit for the two chains : 0.022

Note: Low non-crystallographic symmetry phi and psi differences

All comparable residues in the two chains mentioned below have comparable backbone torsion angles

Chain identifiers of the two chains: A and A

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.

Warning: Problem detected upon counting molecules and matrices

The parameter Z as given on the CRYST card represents the molecular multiplicity in the crystallographic cell. Normally, Z equals the number of matrices of the space group multiplied by the number of NCS relations. The value of Z is multiplied by the integrated molecular weight of the molecules in the file to determine the Matthews coefficient. This relation is being validated in this option. Be aware that the validation can get confused if both multiple copies of the molecule are present in the ATOM records and MTRIX records are present in the header of the PDB file.

Space group as read from CRYST card: P 43 21 2
Number of matrices in space group: 8
Highest polymer chain multiplicity in structure: 10
Highest polymer chain multiplicity according to SEQRES: 1
No explicit MTRIX NCS matrices found in the input file
Value of Z as found on the CRYST1 card: 8
Polymer chain multiplicity and SEQRES multiplicity disagree 10 1
Z and NCS seem to support the SEQRES multiplicity (so the matrix counting
problems seem not overly severe)

Error: Matthews Coefficient (Vm) too low

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.

The fact that it is lower than 1.5 in this structure might be caused by a miscalculated value of Z on the CRYST1 card.

Molecular weight of all polymer chains: 153801.891
Volume of the Unit Cell V= 227661.891
Space group multiplicity: 8
No NCS symmetry matrices (MTRIX records) found in PDB file
Matthews coefficient for observed atoms and Z low: Vm= 0.185
Vm by authors and this calculated Vm do not agree very well
Matthews coefficient read from REMARK 280 Vm= 1.950

Note: No atoms with high occupancy detected at special positions

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

Note: All atoms are sufficiently far away from symmetry axes

None of the atoms in the structure is closer than 0.77 Angstrom to a proper symmetry axis.

Note: Chain identifiers OK

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

Warning: Ligands for which topology could not be determined

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

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

1295 202   ( 131-)  A  1
1296 202   ( 132-)  A  1         Fragmented
1297 202   ( 133-)  A  1         Fragmented
1298 A10   ( 134-)  A  1         Fragmented
1299 A11   ( 135-)  A  1         Size
1300 A12   ( 136-)  A  1         Fragmented
1301 A13   ( 137-)  A  1         Size
1302 A14   ( 138-)  A  1         Size
1303 A15   ( 139-)  A  1         Size
1308 202   ( 131-)  A  2
1309 202   ( 132-)  A  2         Fragmented
1310 202   ( 133-)  A  2         Fragmented
1311 A16   ( 134-)  A  2         Fragmented
1312 A17   ( 135-)  A  2         Size
1313 A18   ( 136-)  A  2         Fragmented
1314 A19   ( 137-)  A  2         Size
1315 A20   ( 138-)  A  2         Size
1316 A21   ( 139-)  A  2         Size
1321 202   ( 131-)  A  3         Fragmented
1322 202   ( 132-)  A  3         Fragmented
1323 202   ( 133-)  A  3         Fragmented
1324 A22   ( 134-)  A  3         Fragmented
1325 A23   ( 135-)  A  3         Size
1326 A24   ( 136-)  A  3         Fragmented
1327 A25   ( 137-)  A  3         Size
And so on for a total of 90 lines.

Administrative problems that can generate validation failures

Note: No strange inter-chain connections detected

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

Note: No duplicate atom names in ligands

All atom names in ligands seem adequately unique.

Note: No alternate atoms detected in NMR file

This PDB file does not contain alternate atoms. That is good, because it should not contain alternate atoms.

Warning: Alternate atom problems encountered

The residues listed in the table below have alternate atoms. One of two problems might have been encountered: 1) The software did not properly deal with the alternate atoms; 2) The alternate atom indicators are too wrong to sort out.

Alternate atom indicators in PDB files are known to often be erroneous. It has been observed that alternate atom indicators are missing, or that there are too many of them. It is common to see that the distance between two atoms that should be covalently bound is far too big, but the distance between the alternate A of one of them and alternate B of the other is proper for a covalent bond. We have discovered many, many ways in which alternate atoms can be abused. The software tries to deal with most cases, but we know for sure that it cannot deal with all cases. If an alternate atom indicator problem is not properly solved, subsequent checks will list errors that are based on wrong coordinate combinations. So, any problem listed in this table should be solved before error messages further down in this report can be trusted.

   1 LYS   (   1-)  A  1
  86 SER   (  86-)  A  1
 215 SER   (  86-)  A  2
 259 LYS   (   1-)  A  3
 344 SER   (  86-)  A  3
 473 SER   (  86-)  A  4
 602 SER   (  86-)  A  5
 646 LYS   (   1-)  A  6
 724 PRO   (  79-)  A  6
 731 SER   (  86-)  A  6
 775 LYS   (   1-)  A  7
 860 SER   (  86-)  A  7
 904 LYS   (   1-)  A  8
 989 SER   (  86-)  A  8
1118 SER   (  86-)  A  9
1247 SER   (  86-)  A 10

Warning: Alternate atom problems quasi solved

The residues listed in the table below have alternate atoms that WHAT IF decided to correct (e.g. take alternate atom B instead of A for one or more of the atoms). Residues for which the use of alternate atoms is non-standard, but WHAT IF left it that way because he liked the non-standard situation better than other solutions, are listed too in this table.

In case any of these residues shows up as poor or bad in checks further down this report, please check the consistency of the alternate atoms in this residue first, correct it yourself if needed, and run the validation again.

   1 LYS   (   1-)  A  1
  86 SER   (  86-)  A  1
 215 SER   (  86-)  A  2
 259 LYS   (   1-)  A  3
 344 SER   (  86-)  A  3
 473 SER   (  86-)  A  4
 602 SER   (  86-)  A  5
 646 LYS   (   1-)  A  6
 724 PRO   (  79-)  A  6
 731 SER   (  86-)  A  6
 775 LYS   (   1-)  A  7
 860 SER   (  86-)  A  7
 904 LYS   (   1-)  A  8
 989 SER   (  86-)  A  8
1118 SER   (  86-)  A  9
1247 SER   (  86-)  A 10

Note: No residues detected inside ligands

Either this structure does not contain ligands with amino acid groups inside it, or their naming is proper (enough).

Note: No attached groups interfere with hydrogen bond calculations

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

Note: No probable side chain atoms with zero occupancy detected.

Either there are no side chain atoms with zero occupancy, or the side chain atoms with zero occupancy were not present in the input PDB file (in which case they are listed as missing atoms), or their positions are sufficiently improbable to warrant a zero occupancy.

Note: No probable backbone atoms with zero occupancy detected.

Either there are no backbone atoms with zero occupancy, or the backbone atoms with zero occupancy were not present in the input PDB file (in which case they are listed as missing atoms), or their positions are sufficiently improbable to warrant a zero occupancy.

Note: All residues have a complete backbone.

No residues have missing backbone atoms.

Note: No C-alpha only residues

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

Note: Non-canonicals

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

Non-validating, descriptive output paragraph

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

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

     1     1 (    1)   129 (  129) A Protein   Mod  1    pdb2d6b.ent
     2   130 (    1)   258 (  129) A Protein   Mod  2    pdb2d6b.ent
     3   259 (    1)   387 (  129) A Protein   Mod  3    pdb2d6b.ent
     4   388 (    1)   516 (  129) A Protein   Mod  4    pdb2d6b.ent
     5   517 (    1)   645 (  129) A Protein   Mod  5    pdb2d6b.ent
     6   646 (    1)   774 (  129) A Protein   Mod  6    pdb2d6b.ent
     7   775 (    1)   903 (  129) A Protein   Mod  7    pdb2d6b.ent
     8   904 (    1)  1032 (  129) A Protein   Mod  8    pdb2d6b.ent
     9  1033 (    1)  1161 (  129) A Protein   Mod  9    pdb2d6b.ent
    10  1162 (    1)  1290 (  129) A Protein   Mod 10    pdb2d6b.ent
    11  1291 (  129)  1291 (  129) A L O2 <-   129  1    pdb2d6b.ent
    12  1292 (  140)  1292 (  140) A  CL       Mod  1    pdb2d6b.ent
    13  1293 (  141)  1293 (  141) A  CL       Mod  1    pdb2d6b.ent
    14  1294 (  142)  1294 (  142) A  NA       Mod  1    pdb2d6b.ent
    15  1295 (  131)  1295 (  131) A 202       Mod  1    pdb2d6b.ent
    16  1296 (  132)  1296 (  132) A 202       Mod  1    pdb2d6b.ent
    17  1297 (  133)  1297 (  133) A 202       Mod  1    pdb2d6b.ent
    18  1298 (  134)  1298 (  134) A A10       Mod  1    pdb2d6b.ent
    19  1299 (  135)  1299 (  135) A A11       Mod  1    pdb2d6b.ent
    20  1300 (  136)  1300 (  136) A A12       Mod  1    pdb2d6b.ent
    21  1301 (  137)  1301 (  137) A A13       Mod  1    pdb2d6b.ent
    22  1302 (  138)  1302 (  138) A A14       Mod  1    pdb2d6b.ent
    23  1303 (  139)  1303 (  139) A A15       Mod  1    pdb2d6b.ent
    24  1304 (  129)  1304 (  129) A L O2 <-   258  2    pdb2d6b.ent
    25  1305 (  140)  1305 (  140) A  CL       Mod  2    pdb2d6b.ent
And so on for a total of 150 lines.

Note: Some notes regarding the PDB file contents

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

This NMR ensemble consists of 10 MODELs.
The total number of amino acids found is 1290.
Amino acids per NMR MODEL: 129.
Number of water molecules 2963

Note: Chain identifiers seem OK

All ions seem to have a logical chain identifier, or there are no ions present in the input file.

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; Model number 1

Note: Ramachandran plot

Chain identifier: A; Model number 2

Note: Ramachandran plot

Chain identifier: A; Model number 3

Note: Ramachandran plot

Chain identifier: A; Model number 4

Note: Ramachandran plot

Chain identifier: A; Model number 5

Note: Ramachandran plot

Chain identifier: A; Model number 6

Note: Ramachandran plot

Chain identifier: A; Model number 7

Note: Ramachandran plot

Chain identifier: A; Model number 8

Note: Ramachandran plot

Chain identifier: A; Model number 9

Note: Ramachandran plot

Chain identifier: A; Model number 10

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 KVFGRCELAAAMKRHGLDNYRGYSLGNWVCAAKFESNFNTQATNRNTDGSTDYGILQINS
(   1)-(  60)    HHHHHHHHHHTT TT TT  HHHHHHHHHHHHTT TT SSS TTT SSSTTTTSST
                     70        80        90       100       110       120
                      |         |         |         |         |         |
   61 -  120 RWWCNDGRTPGSRNLCNIPCSALLSSDITASVNCAKKIVSDGNGMNAWVAWRNRCKGTDV
(  61)-( 120)TTT   T TTT   TT T 33333TTTTHHHHHHHHHHHTTTT3333THHHHHHTTTT 3
 
 
  121 -  129 QAWIRGCRL
( 121)-( 129)3333TT
 
           130       140       150       160       170       180
             |         |         |         |         |         |
  130 -  189 KVFGRCELAAAMKRHGLDNYRGYSLGNWVCAAKFESNFNTQATNRNTDGSTDYGILQINS
(   1)-(  60)    HHHHHHHHHHTT TT TT  HHHHHHHHHHHHTT TT SSS TTT SSSTTTTSST
           190       200       210       220       230       240
             |         |         |         |         |         |
  190 -  249 RWWCNDGRTPGSRNLCNIPCSALLSSDITASVNCAKKIVSDGNGMNAWVAWRNRCKGTDV
(  61)-( 120)TTT   T TTT   TT T 33333TTTTHHHHHHHHHHHTTTT3333THHHHHHTTTT 3
           250
             |
  250 -  258 QAWIRGCRL
( 121)-( 129)3333TT
 
            260       270       280       290       300       310
              |         |         |         |         |         |
  259 -  318 KVFGRCELAAAMKRHGLDNYRGYSLGNWVCAAKFESNFNTQATNRNTDGSTDYGILQINS
(   1)-(  60)    HHHHHHHHHHTT TT TT  HHHHHHHHHHHHTT TT SSS TTT SSSTTTTSST
            320       330       340       350       360       370
              |         |         |         |         |         |
  319 -  378 RWWCNDGRTPGSRNLCNIPCSALLSSDITASVNCAKKIVSDGNGMNAWVAWRNRCKGTDV
(  61)-( 120)TTT   T TTT   TT T 33333TTTTHHHHHHHHHHHTTTT3333THHHHHHTTTT 3
            380
              |
  379 -  387 QAWIRGCRL
( 121)-( 129)3333TT
 
             390       400       410       420       430       440
               |         |         |         |         |         |
  388 -  447 KVFGRCELAAAMKRHGLDNYRGYSLGNWVCAAKFESNFNTQATNRNTDGSTDYGILQINS
(   1)-(  60)    HHHHHHHHHHTT TT TT  HHHHHHHHHHHHTT TT SSS TTT SSSTTTTSST
             450       460       470       480       490       500
               |         |         |         |         |         |
  448 -  507 RWWCNDGRTPGSRNLCNIPCSALLSSDITASVNCAKKIVSDGNGMNAWVAWRNRCKGTDV
(  61)-( 120)TTT   T TTT   TT T 33333TTTTHHHHHHHHHHHTTTT3333THHHHHHTTTT 3
             510
               |
  508 -  516 QAWIRGCRL
( 121)-( 129)3333TT
 
              520       530       540       550       560       570
                |         |         |         |         |         |
  517 -  576 KVFGRCELAAAMKRHGLDNYRGYSLGNWVCAAKFESNFNTQATNRNTDGSTDYGILQINS
(   1)-(  60)    HHHHHHHHHHTT TT TT  HHHHHHHHHHHHTT TT SSS TTT SSSTTTTSST
              580       590       600       610       620       630
                |         |         |         |         |         |
  577 -  636 RWWCNDGRTPGSRNLCNIPCSALLSSDITASVNCAKKIVSDGNGMNAWVAWRNRCKGTDV
(  61)-( 120)TTT   T TTT   TT T 33333TTTTHHHHHHHHHHHTTTT3333THHHHHHTTTT 3
              640
                |
  637 -  645 QAWIRGCRL
( 121)-( 129)3333TT
 
               650       660       670       680       690       700
                 |         |         |         |         |         |
  646 -  705 KVFGRCELAAAMKRHGLDNYRGYSLGNWVCAAKFESNFNTQATNRNTDGSTDYGILQINS
(   1)-(  60)    HHHHHHHHHHTT TT TT  HHHHHHHHHHHHTT TT SSS TTT SSSTTTTSST
               710       720       730       740       750       760
                 |         |         |         |         |         |
  706 -  765 RWWCNDGRTPGSRNLCNIPCSALLSSDITASVNCAKKIVSDGNGMNAWVAWRNRCKGTDV
(  61)-( 120)TTT   T TTT   TT T 33333TTTTHHHHHHHHHHHTTTT3333THHHHHHTTTT 3
               770
                 |
  766 -  774 QAWIRGCRL
( 121)-( 129)3333TT
 
                780       790       800       810       820       830
                  |         |         |         |         |         |
  775 -  834 KVFGRCELAAAMKRHGLDNYRGYSLGNWVCAAKFESNFNTQATNRNTDGSTDYGILQINS
(   1)-(  60)    HHHHHHHHHHTT TT TT  HHHHHHHHHHHHTT TT SSS TTT SSSTTTTSST
                840       850       860       870       880       890
                  |         |         |         |         |         |
  835 -  894 RWWCNDGRTPGSRNLCNIPCSALLSSDITASVNCAKKIVSDGNGMNAWVAWRNRCKGTDV
(  61)-( 120)TTT   T TTT   TT T 33333TTTTHHHHHHHHHHHTTTT3333THHHHHHTTTT 3
                900
                  |
  895 -  903 QAWIRGCRL
( 121)-( 129)3333TT
 
                 910       920       930       940       950       960
                   |         |         |         |         |         |
  904 -  963 KVFGRCELAAAMKRHGLDNYRGYSLGNWVCAAKFESNFNTQATNRNTDGSTDYGILQINS
(   1)-(  60)    HHHHHHHHHHTT TT TT  HHHHHHHHHHHHTT TT SSS TTT SSSTTTTSST
                 970       980       990      1000      1010      1020
                   |         |         |         |         |         |
  964 - 1023 RWWCNDGRTPGSRNLCNIPCSALLSSDITASVNCAKKIVSDGNGMNAWVAWRNRCKGTDV
(  61)-( 120)TTT   T TTT   TT T 33333TTT HHHHHHHHHHHTTTT3333THHHHHHTTTT 3
                1030
                   |
 1024 - 1032 QAWIRGCRL
( 121)-( 129)3333TT
 
                 1040      1050      1060      1070      1080      1090
                    |         |         |         |         |         |
 1033 - 1092 KVFGRCELAAAMKRHGLDNYRGYSLGNWVCAAKFESNFNTQATNRNTDGSTDYGILQINS
(   1)-(  60)    HHHHHHHHHHTT TT TT  HHHHHHHHHHHHTT TT SSS TTT SSSTTTTSST
                 1100      1110      1120      1130      1140      1150
                    |         |         |         |         |         |
 1093 - 1152 RWWCNDGRTPGSRNLCNIPCSALLSSDITASVNCAKKIVSDGNGMNAWVAWRNRCKGTDV
(  61)-( 120)TTT   T TTT   TT T 33333TTTTHHHHHHHHHHHTTTT3333THHHHHHTTTT 3
                 1160
                    |
 1153 - 1161 QAWIRGCRL
( 121)-( 129)3333TT
 
                  1170      1180      1190      1200      1210      1220
                     |         |         |         |         |         |
 1162 - 1221 KVFGRCELAAAMKRHGLDNYRGYSLGNWVCAAKFESNFNTQATNRNTDGSTDYGILQINS
(   1)-(  60)    HHHHHHHHHHTT TT TT  HHHHHHHHHHHHTT TT SSS TTT SSSTTTTSST
                  1230      1240      1250      1260      1270      1280
                     |         |         |         |         |         |
 1222 - 1281 RWWCNDGRTPGSRNLCNIPCSALLSSDITASVNCAKKIVSDGNGMNAWVAWRNRCKGTDV
(  61)-( 120)TTT   T TTT   TT T 33333TTTTHHHHHHHHHHHTTTT3333THHHHHHTTTT 3
                  1290
                     |
 1282 - 1290 QAWIRGCRL
( 121)-( 129)3333TT
 
 
 

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.

Note: No missing atoms detected in residues

All expected atoms are present in residues. This validation option has not looked at 'things' that can or should be attached to the elemantary building blocks (amino acids, nucleotides). Even the C-terminal oxygens are treated separately.

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: Test capping of (pseudo) C-termini

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

Note: No OXT found in the middle of chains

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

Note: Weights checked OK

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

Note: Normal distribution of occupancy values

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

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

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

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

Note: B-factors irrelevant in NMR structures

B-factors are a way to describe the motion or positional inhomogeneity of atoms in crystal structures. B-factors, therefore, are irrelevant for NMR structures, so we do not check them.

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.

  45 ARG   (  45-)  A
  61 ARG   (  61-)  A
  73 ARG   (  73-)  A
 125 ARG   ( 125-)  A
 174 ARG   (  45-)  A
 190 ARG   (  61-)  A
 202 ARG   (  73-)  A
 254 ARG   ( 125-)  A
 303 ARG   (  45-)  A
 319 ARG   (  61-)  A
 331 ARG   (  73-)  A
 383 ARG   ( 125-)  A
 432 ARG   (  45-)  A
 448 ARG   (  61-)  A
 460 ARG   (  73-)  A
 512 ARG   ( 125-)  A
 561 ARG   (  45-)  A
 577 ARG   (  61-)  A
 589 ARG   (  73-)  A
 641 ARG   ( 125-)  A
 690 ARG   (  45-)  A
 706 ARG   (  61-)  A
 718 ARG   (  73-)  A
 770 ARG   ( 125-)  A
 819 ARG   (  45-)  A
 835 ARG   (  61-)  A
 847 ARG   (  73-)  A
 899 ARG   ( 125-)  A
 948 ARG   (  45-)  A
 964 ARG   (  61-)  A
 976 ARG   (  73-)  A
1028 ARG   ( 125-)  A
1077 ARG   (  45-)  A
1093 ARG   (  61-)  A
1105 ARG   (  73-)  A
1157 ARG   ( 125-)  A
1206 ARG   (  45-)  A 1
1222 ARG   (  61-)  A 1
1234 ARG   (  73-)  A 1
1286 ARG   ( 125-)  A 1

Warning: Tyrosine convention problem

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

 407 TYR   (  20-)  A
1052 TYR   (  20-)  A

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

No errors were detected in phosphate group naming conventions.

Note: Heavy atom naming OK

No errors were detected in the atom names for non-hydrogen atoms. Please be aware that the PDB wants us to deliberately make some nomenclature errors; especially in non-canonical amino acids.

Note: Chain names are OK

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

Geometric checks

Warning: Unusual bond lengths

The bond lengths listed in the table below were found to deviate more than 4 sigma from standard bond lengths (both standard values and sigmas for amino acid residues have been taken from Engh and Huber [REF], for DNA they were taken from Parkinson et al [REF]). In the table below for each unusual bond the bond length and the number of standard deviations it differs from the normal value is given.

Atom names starting with "-" belong to the previous residue in the chain. If the second atom name is "-SG*", the disulphide bridge has a deviating length.

 160 ALA   (  31-)  A      N   -C     1.25   -4.1
 237 TRP   ( 108-)  A      NE1  CE2   1.42    4.5
 366 TRP   ( 108-)  A      NE1  CE2   1.42    4.5
 495 TRP   ( 108-)  A      NE1  CE2   1.42    4.2
 624 TRP   ( 108-)  A      NE1  CE2   1.42    4.3
 676 ALA   (  31-)  A      N   -C     1.25   -4.1
1192 ALA   (  31-)  A 1    N   -C     1.24   -4.3
1269 TRP   ( 108-)  A 1    NE1  CE2   1.42    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: 0.964
RMS-deviation in bond distances: 0.020

Note: Per-model averages for bond-length check

The table below gives the per-model bond-length RMS Z-scores.

Model 1 : 0.968
Model 2 : 0.965
Model 3 : 0.956
Model 4 : 0.947
Model 5 : 0.963
Model 6 : 0.964
Model 7 : 0.955
Model 8 : 0.964
Model 9 : 0.980
Model 10 : 0.980

Warning: Possible cell scaling problem

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

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

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

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

Unit Cell deformation matrix

 |  0.992314  0.003534 -0.002516|
 |  0.003534  0.993530 -0.000152|
 | -0.002516 -0.000152  1.009394|
Proposed new scale matrix

 |  0.013053 -0.000046  0.000033|
 | -0.000046  0.013037  0.000002|
 |  0.000066  0.000004  0.025940|
With corresponding cell

    A    =  76.615  B   =  76.709  C    =  38.550
    Alpha=  90.018  Beta=  90.288  Gamma=  89.592

The CRYST1 cell dimensions

    A    =  77.210  B   =  77.210  C    =  38.191
    Alpha=  90.000  Beta=  90.000  Gamma=  90.000

Variance: 1346.220
(Under-)estimated Z-score: 27.041

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.

   5 ARG   (   5-)  A      CG   CD   NE  118.21    4.5
  13 LYS   (  13-)  A     -O   -C    N   132.67    6.0
  13 LYS   (  13-)  A     -C    N    CA  112.33   -5.2
  14 ARG   (  14-)  A      CB   CG   CD  105.69   -4.2
  14 ARG   (  14-)  A      NH1  CZ   NH2 127.74    4.5
  18 ASP   (  18-)  A      C    CA   CB  117.74    4.0
  18 ASP   (  18-)  A      CB   CG   OD2 103.07   -6.7
  18 ASP   (  18-)  A      CB   CG   OD1 130.49    5.3
  37 ASN   (  37-)  A      ND2  CG   OD1 127.55    5.0
  45 ARG   (  45-)  A      CD   NE   CZ  129.85    4.5
  46 ASN   (  46-)  A      ND2  CG   OD1 127.46    4.9
  59 ASN   (  59-)  A      CA   CB   CG  117.69    5.1
  65 ASN   (  65-)  A      CA   CB   CG  107.63   -5.0
  66 ASP   (  66-)  A      CA   CB   CG  117.38    4.8
  67 GLY   (  67-)  A     -O   -C    N   129.46    4.0
  68 ARG   (  68-)  A      CG   CD   NE  103.53   -4.1
  73 ARG   (  73-)  A      CD   NE   CZ  129.24    4.2
  77 ASN   (  77-)  A      CA   CB   CG  108.57   -4.0
  78 ILE   (  78-)  A     -O   -C    N   115.22   -4.9
 101 ASP   ( 101-)  A     -CA  -C    N   124.51    4.2
 101 ASP   ( 101-)  A      CA   C    O   112.97   -4.6
 103 ASN   ( 103-)  A      CA   CB   CG  108.33   -4.3
 108 TRP   ( 108-)  A     -O   -C    N   116.18   -4.3
 110 ALA   ( 110-)  A      N    CA   CB  116.55    4.1
 111 TRP   ( 111-)  A      CE3  CD2  CG  138.66    4.8
And so on for a total of 325 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: 1.643
RMS-deviation in bond angles: 2.876

Note: Per-model averages for bond-angle check

The table below gives the per-model bond-angle RMS Z-scores.

Model 1 : 1.639
Model 2 : 1.641
Model 3 : 1.677
Model 4 : 1.662
Model 5 : 1.637
Model 6 : 1.638
Model 7 : 1.640
Model 8 : 1.621
Model 9 : 1.632
Model 10 : 1.641

Error: Nomenclature error(s)

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

  45 ARG   (  45-)  A
  61 ARG   (  61-)  A
  73 ARG   (  73-)  A
 125 ARG   ( 125-)  A
 174 ARG   (  45-)  A
 190 ARG   (  61-)  A
 202 ARG   (  73-)  A
 254 ARG   ( 125-)  A
 303 ARG   (  45-)  A
 319 ARG   (  61-)  A
 331 ARG   (  73-)  A
 383 ARG   ( 125-)  A
 432 ARG   (  45-)  A
 448 ARG   (  61-)  A
 460 ARG   (  73-)  A
 512 ARG   ( 125-)  A
 561 ARG   (  45-)  A
 577 ARG   (  61-)  A
 589 ARG   (  73-)  A
 641 ARG   ( 125-)  A
 690 ARG   (  45-)  A
 706 ARG   (  61-)  A
 718 ARG   (  73-)  A
 770 ARG   ( 125-)  A
 819 ARG   (  45-)  A
 835 ARG   (  61-)  A
 847 ARG   (  73-)  A
 899 ARG   ( 125-)  A
 948 ARG   (  45-)  A
 964 ARG   (  61-)  A
 976 ARG   (  73-)  A
1028 ARG   ( 125-)  A
1077 ARG   (  45-)  A
1093 ARG   (  61-)  A
1105 ARG   (  73-)  A
1157 ARG   ( 125-)  A
1206 ARG   (  45-)  A 1
1222 ARG   (  61-)  A 1
1234 ARG   (  73-)  A 1
1286 ARG   ( 125-)  A 1

Note: Chirality OK

All protein atoms have proper chirality. But, look at the previous table to see a series of administrative chirality problems that were corrected automatically upon reading-in the PDB file.

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 : 1.074

Note: Per-model averages for chirality check

The table below gives the per-model improper dihedral RMS Z-scores.

Model 1 : 1.078
Model 2 : 1.071
Model 3 : 1.072
Model 4 : 1.075
Model 5 : 1.087
Model 6 : 1.067
Model 7 : 1.068
Model 8 : 1.071
Model 9 : 1.072
Model 10 : 1.075

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.

 908 ARG   (   5-)  A    4.60
1166 ARG   (   5-)  A 1   4.47
1037 ARG   (   5-)  A    4.31
 128 ARG   ( 128-)  A    4.18
1160 ARG   ( 128-)  A    4.08
 779 ARG   (   5-)  A    4.05
 134 ARG   (   5-)  A    4.00

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 : 1.165

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.

 581 ASN   (  65-)  A    4.69
1198 ASN   (  37-)  A 1   4.62
1069 ASN   (  37-)  A    4.47
 940 ASN   (  37-)  A    4.37
 194 ASN   (  65-)  A    4.16
 811 ASN   (  37-)  A    4.08

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 : 0.070

Note: Per-model averages for Ramachandran check

The table below gives the per-model Ramachandran Z-scores.

Model 1 : 0.045
Model 2 : 0.006
Model 3 : 0.065
Model 4 : 0.187
Model 5 : 0.121
Model 6 : 0.049
Model 7 : 0.091
Model 8 : 0.076
Model 9 : -0.013
Model 10 : 0.072

Warning: Torsion angle evaluation shows unusual residues

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

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

  38 PHE   (  38-)  A    -2.3
 812 PHE   (  38-)  A    -2.3
1070 PHE   (  38-)  A    -2.3
 197 ARG   (  68-)  A    -2.3
 326 ARG   (  68-)  A    -2.3
  68 ARG   (  68-)  A    -2.2
 584 ARG   (  68-)  A    -2.2
 455 ARG   (  68-)  A    -2.2
1199 PHE   (  38-)  A 1   -2.2
 683 PHE   (  38-)  A    -2.2
1100 ARG   (  68-)  A    -2.2
 296 PHE   (  38-)  A    -2.2
1031 ARG   ( 128-)  A    -2.2
 842 ARG   (  68-)  A    -2.2
 128 ARG   ( 128-)  A    -2.2
1289 ARG   ( 128-)  A 1   -2.2
 257 ARG   ( 128-)  A    -2.2
 971 ARG   (  68-)  A    -2.1
 386 ARG   ( 128-)  A    -2.1
1160 ARG   ( 128-)  A    -2.1
 167 PHE   (  38-)  A    -2.1
1053 ARG   (  21-)  A    -2.1
 425 PHE   (  38-)  A    -2.1
 515 ARG   ( 128-)  A    -2.1
 941 PHE   (  38-)  A    -2.1
 713 ARG   (  68-)  A    -2.1
1229 ARG   (  68-)  A 1   -2.1
 718 ARG   (  73-)  A    -2.1
 554 PHE   (  38-)  A    -2.1
 644 ARG   ( 128-)  A    -2.1
 331 ARG   (  73-)  A    -2.1
 847 ARG   (  73-)  A    -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.

   3 PHE   (   3-)  A  omega poor
  19 ASN   (  19-)  A  Poor phi/psi
  38 PHE   (  38-)  A  Poor phi/psi
  62 TRP   (  62-)  A  omega poor
 132 PHE   (   3-)  A  omega poor
 148 ASN   (  19-)  A  Poor phi/psi
 150 ARG   (  21-)  A  Poor phi/psi
 167 PHE   (  38-)  A  Poor phi/psi
 191 TRP   (  62-)  A  omega poor
 206 ASN   (  77-)  A  Poor phi/psi
 261 PHE   (   3-)  A  omega poor
 277 ASN   (  19-)  A  Poor phi/psi
 296 PHE   (  38-)  A  Poor phi/psi
 320 TRP   (  62-)  A  Poor phi/psi, omega poor
 335 ASN   (  77-)  A  Poor phi/psi
 390 PHE   (   3-)  A  omega poor
 406 ASN   (  19-)  A  Poor phi/psi
 408 ARG   (  21-)  A  Poor phi/psi
 425 PHE   (  38-)  A  Poor phi/psi
 449 TRP   (  62-)  A  omega poor
 519 PHE   (   3-)  A  omega poor
 535 ASN   (  19-)  A  Poor phi/psi
 537 ARG   (  21-)  A  Poor phi/psi
 554 PHE   (  38-)  A  Poor phi/psi
 578 TRP   (  62-)  A  omega poor
And so on for a total of 55 lines.

Note: chi-1/chi-2 angle correlation Z-score OK

The score expressing how well the chi-1/chi-2 angles of all residues correspond to the populated areas in the database is within expected ranges for well-refined structures.

chi-1/chi-2 correlation Z-score : -1.271

Note: Per-model averages for chi-1/chi-2 angle check

The table below gives the per-model chi-1/chi-2 correlation Z-scores.

Model 1 : -1.234
Model 2 : -1.144
Model 3 : -1.461
Model 4 : -1.425
Model 5 : -1.479
Model 6 : -1.212
Model 7 : -1.140
Model 8 : -1.153
Model 9 : -1.296
Model 10 : -1.164

Note: Rotamers checked OK

None of the residues that have a normal backbone environment have abnormal rotamers.

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!

  18 ASP   (  18-)  A      0
  19 ASN   (  19-)  A      0
  20 TYR   (  20-)  A      0
  21 ARG   (  21-)  A      0
  36 SER   (  36-)  A      0
  37 ASN   (  37-)  A      0
  38 PHE   (  38-)  A      0
  42 ALA   (  42-)  A      0
  50 SER   (  50-)  A      0
  53 TYR   (  53-)  A      0
  61 ARG   (  61-)  A      0
  62 TRP   (  62-)  A      0
  63 TRP   (  63-)  A      0
  66 ASP   (  66-)  A      0
  68 ARG   (  68-)  A      0
  70 PRO   (  70-)  A      0
  74 ASN   (  74-)  A      0
  76 CYS   (  76-)  A      0
 101 ASP   ( 101-)  A      0
 105 MET   ( 105-)  A      0
 106 ASN   ( 106-)  A      0
 108 TRP   ( 108-)  A      0
 113 ASN   ( 113-)  A      0
 114 ARG   ( 114-)  A      0
 116 LYS   ( 116-)  A      0
And so on for a total of 557 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 : -0.611

Note: Omega angle restraint OK

The omega angles for trans-peptide bonds in a structure is expected to give a gaussian distribution with the average around +178 degrees, and a standard deviation around 5.5. In the current structure the standard deviation agrees with this expectation.

Standard deviation of omega values : 6.494

Note: Per-model averages for omega angle check

The table below gives the per-model omega angle standard deviations.

Model 1 : 6.491
Model 2 : 6.543
Model 3 : 6.392
Model 4 : 6.521
Model 5 : 6.455
Model 6 : 6.431
Model 7 : 6.590
Model 8 : 6.563
Model 9 : 6.571
Model 10 : 6.539

Note: Backbone oxygen evaluation OK

All residues for which the local backbone conformation could be found in the WHAT IF database have a normal backbone oxygen position.

Note: Peptide bond conformations

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

Note: PRO puckering amplitude OK

Puckering amplitudes for all PRO residues are within normal ranges.

Note: PRO puckering phases OK

Puckering phases for all PRO residues are normal

Bump checks

Error: Abnormally short interatomic distances

The pairs of atoms listed in the table below have an unusually short distance.

The contact distances of all atom pairs have been checked. Two atoms are said to `bump' if they are closer than the sum of their Van der Waals radii minus 0.40 Angstrom. For hydrogen bonded pairs a tolerance of 0.55 Angstrom is used. The first number in the table tells you how much shorter that specific contact is than the acceptable limit. The second distance is the distance between the centres of the two atoms. Although we believe that two water atoms at 2.4 A distance are too close, we only report water pairs that are closer than this rather short distance.

The last text-item on each line represents the status of the atom pair. 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).

Bumps between atoms for which the sum of their occupancies is lower than one are not reported. In any case, each bump is listed in only one direction. However, as this seems to be an NMR structure, this is unlikely to happen in this report.

 882 TRP   ( 108-)  A      CE2 <-> 1427 HOH   (1264 )  A      O      1.46    1.34
1160 ARG   ( 128-)  A      CZ  <-> 1429 HOH   (1274 )  A      O      1.26    1.54
 515 ARG   ( 128-)  A      CZ  <-> 1424 HOH   (1245 )  A      O      1.24    1.56
 871 LYS   (  97-)  A    A NZ  <-> 1427 HOH   (1278 )  A      O      1.21    1.49
1289 ARG   ( 128-)  A 1    CZ  <-> 1430 HOH   (1264 )  A 1    O      1.21    1.59
 386 ARG   ( 128-)  A      CZ  <-> 1423 HOH   (1255 )  A      O      1.20    1.60
  45 ARG   (  45-)  A      NH1 <-> 1421 HOH   (1267 )  A      O      1.17    1.53
 746 ASP   ( 101-)  A      CB  <-> 1426 HOH   (1162 )  A      O      1.16    1.64
 303 ARG   (  45-)  A      NH1 <-> 1423 HOH   (1284 )  A      O      1.15    1.55
1077 ARG   (  45-)  A      NH1 <-> 1429 HOH   (1275 )  A      O      1.13    1.57
 166 ASN   (  37-)  A      CB  <-> 1422 HOH   (1261 )  A      O      1.12    1.68
 617 ASP   ( 101-)  A      CB  <-> 1425 HOH   (1163 )  A      O      1.09    1.71
 230 ASP   ( 101-)  A      CB  <-> 1422 HOH   (1173 )  A      O      1.09    1.71
 128 ARG   ( 128-)  A      CZ  <-> 1421 HOH   (1282 )  A      O      1.08    1.72
 101 ASP   ( 101-)  A      CB  <-> 1421 HOH   (1176 )  A      O      1.07    1.73
 819 ARG   (  45-)  A      NH1 <-> 1427 HOH   (1272 )  A      O      1.07    1.63
1004 ASP   ( 101-)  A      CB  <-> 1428 HOH   (1157 )  A      O      1.07    1.73
 257 ARG   ( 128-)  A      CZ  <-> 1422 HOH   (1269 )  A      O      1.06    1.74
1137 MET   ( 105-)  A      CE  <-> 1429 HOH   (1286 )  A      O      1.05    1.75
 882 TRP   ( 108-)  A      CD2 <-> 1427 HOH   (1264 )  A      O      1.04    1.76
1115 LEU   (  83-)  A      CB  <-> 1429 HOH   (1239 )  A      O      1.03    1.77
 488 ASP   ( 101-)  A      CB  <-> 1424 HOH   (1164 )  A      O      1.02    1.78
 599 LEU   (  83-)  A      CB  <-> 1425 HOH   (1303 )  A      O      1.02    1.78
 875 ASP   ( 101-)  A      CB  <-> 1427 HOH   (1159 )  A      O      1.02    1.78
 986 LEU   (  83-)  A      CB  <-> 1428 HOH   (1245 )  A      O      1.01    1.79
And so on for a total of 677 lines.

Packing, accessibility and threading

Note: Inside/Outside residue distribution normal

The distribution of residue types over the inside and the outside of the protein is normal.

inside/outside RMS Z-score : 0.903

Note: Per-model averages for inside/outside residue distributi ...heck










Note: Inside/Outside RMS Z-score plot

Chain identifier: A; Model number 1

Note: Inside/Outside RMS Z-score plot

Chain identifier: A; Model number 2

Note: Inside/Outside RMS Z-score plot

Chain identifier: A; Model number 3

Note: Inside/Outside RMS Z-score plot

Chain identifier: A; Model number 4

Note: Inside/Outside RMS Z-score plot

Chain identifier: A; Model number 5

Note: Inside/Outside RMS Z-score plot

Chain identifier: A; Model number 6

Note: Inside/Outside RMS Z-score plot

Chain identifier: A; Model number 7

Note: Inside/Outside RMS Z-score plot

Chain identifier: A; Model number 8

Note: Inside/Outside RMS Z-score plot

Chain identifier: A; Model number 9

Note: Inside/Outside RMS Z-score plot

Chain identifier: A; Model number 10

Warning: Abnormal packing environment for some residues


Note: No series of residues with bad packing environment

Note: Structural average packing environment OK

Note: Quality value plot

Chain identifier: A; Model number 1

Note: Quality value plot

Chain identifier: A; Model number 2

Note: Quality value plot

Chain identifier: A; Model number 3

Note: Quality value plot

Chain identifier: A; Model number 4

Note: Quality value plot

Chain identifier: A; Model number 5

Note: Quality value plot

Chain identifier: A; Model number 6

Note: Quality value plot

Chain identifier: A; Model number 7

Note: Quality value plot

Chain identifier: A; Model number 8

Note: Quality value plot

Chain identifier: A; Model number 9

Note: Quality value plot

Chain identifier: A; Model number 10

Warning: Low packing Z-score for some residues


Note: No series of residues with abnormal new packing environment

Note: Per-model averages for NQA










Note: Second generation quality Z-score plot

Chain identifier: A; Model number 1

Note: Second generation quality Z-score plot

Chain identifier: A; Model number 2

Note: Second generation quality Z-score plot

Chain identifier: A; Model number 3

Note: Second generation quality Z-score plot

Chain identifier: A; Model number 4

Note: Second generation quality Z-score plot

Chain identifier: A; Model number 5

Note: Second generation quality Z-score plot

Chain identifier: A; Model number 6

Note: Second generation quality Z-score plot

Chain identifier: A; Model number 7

Note: Second generation quality Z-score plot

Chain identifier: A; Model number 8

Note: Second generation quality Z-score plot

Chain identifier: A; Model number 9

Note: Second generation quality Z-score plot

Chain identifier: A; Model number 10

Water, ion, and hydrogenbond related checks

Note: Water contacts OK

Warning: Water molecules need moving


Error: Water molecules without hydrogen bonds


Error: HIS, ASN, GLN side chain flips


Note: Histidine type assignments


Warning: Buried unsatisfied hydrogen bond donors


Warning: Buried unsatisfied hydrogen bond acceptors


Note: Crystallisation conditions from REMARK 280


Note: Overview of ions

Note: Ion packing OK

Warning: Unusual water packing


Warning: Possible wrong residue type


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


Final summary

Note: Summary report for users of a structure







Note: Summary report for depositors of a structure