Please note that you are looking at an abridged version of the output (all checks that gave normal results have been removed from this report). You can have a look at the Full report instead.
The CRYST1 cell dimensions
A = 22.329 B = 18.471 C = 40.769 Alpha= 90.000 Beta= 90.550 Gamma= 90.000
Dimensions of a reduced cell
A = 18.471 B = 22.329 C = 40.769 Alpha= 90.550 Beta= 90.000 Gamma= 90.000
Dimensions of the conventional cell
A = 18.471 B = 22.329 C = 40.769 Alpha= 89.450 Beta= 90.000 Gamma= 90.000
Transformation to conventional cell
| 0.000000 1.000000 0.000000| | -1.000000 0.000000 0.000000| | 0.000000 0.000000 1.000000|
Crystal class of the cell: MONOCLINIC
Crystal class of the conventional CELL: ORTHORHOMBIC
Space group name: P 1 21 1
Bravais type of conventional cell is: P
Warning: Conventional cell is pseudo-cell
The extra symmetry that would be implied by the transition to the previously
mentioned conventional cell has not been observed. It must be concluded that
the crystal lattice has pseudo-symmetry.
Warning: Ligands for which a topology was generated automatically
The topology for the ligands in the table below were determined
automatically. WHAT IF uses a local copy of Daan van Aalten's Dundee PRODRG
server to automatically generate topology information for ligands. For this
PDB file that seems to have gone fine, but 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 first.
48 EOH (2001-) A - 49 EOH (2002-) A - 50 EOH (2003-) A - 51 EOH (2004-) A -
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.
7 ILE ( 7-) A - 8 VAL ( 8-) A -
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.
7 ILE ( 7-) A - 8 VAL ( 8-) A - REMOVED.LIS BUG. File already open at 77 Delete overlapping entity 22 PRO ( 22-) A - Delete overlapping entity 25 LEU ( 25-) A - Delete overlapping entity 49 EOH (2002-) A -
Overlapping residues or molecules (for short entities) are occasionally observed in the PDB. Often these are cases like, for example, two sugars that bind equally well in the same active site, are both seen overlapping in the density, and are both entered in the PDB file as separate entities. This can cause some false positive error messsages further down the validation path, and therefore the second of the overlapping entities has been deleted before the validation continued. If you want to validate both situations, make it two PDB files, one for each sugar. And fudge reality a bit by making the occupancy of the sugar atoms 1.0 in both cases, because many validation options are not executed on atoms with low occupancy. If you go for this two-file option, please make sure that any side chains that have alternate locations depending on the sugar bound are selected in each of the two cases in agreement with the sugar that you keep for validation in that particular file.
22 PRO ( 22-) A - 25 LEU ( 25-) A - 49 EOH (2002-) A -
Please also see the previous check
Please see the user course on the WHAT CHECK website if you want to know why this table and the previous one have not been merged.
Non-validating, descriptive output paragraph
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
Coordinate problems, unexpected atoms, B-factor and occupancy checks
Warning: Very strange distribution of occupancy values
The distribution of the occupancy values in this file differs very much from distributions commonly observed in well-refined PDB files. This does not need to mean anything, but please look at it. This file should not be used in training sets that need to hold 'good' PDB files.
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...
Warning: Occupancies atoms do not add up to 1.0.
In principle, the occupancy of all alternates of one atom should add up till
1.0. A valid exception is the missing atom (i.e. an atom not seen in the
electron density) that is allowed to have a 0.0 occupancy. Sometimes this
even happens when there are no alternate atoms given...
Atoms want to move. That is the direct result of the second law of thermodynamics, in a somewhat weird way of thinking. Any way, many atoms seem to have more than one position where they like to sit, and they jump between them. The population difference between those sites (which is related to their energy differences) is seen in the occupancy factors. As also for atoms it is 'to be or not to be', these occupancies should add up to 1.0. Obviously, it is possible that they add up to a number less than 1.0, in cases where there are yet more, but undetected' rotamers/positions in play, but also in those cases a warning is in place as the information shown in the PDB file is less certain than it could have been. The residues listed below contain atoms that have an occupancy greater than zero, but all their alternates do not add up to one.
WARNING. Presently WHAT CHECK only deals with a maximum of two alternate positions. A small number of atoms in the PDB has three alternates. In those cases the warning given here should obviously be neglected! In a next release we will try to fix this.
1 THR ( 1-) A 1.12 2 THR ( 2-) A 1.05 7 ILE ( 7-) A 1.03 8 VAL ( 8-) A 1.10 11 ASN ( 12-) A 1.03 12 PHE ( 13-) A 0.96 18 PRO ( 19-) A 1.02 21 PRO ( 22-) A 0.70 24 LEU ( 25-) A 0.65 28 TYR ( 29-) A 0.75 33 ILE ( 34-) A 0.91 36 GLY ( 37-) A 0.91 37 ALA ( 38-) A 1.11 38 THR ( 39-) A 1.04 42 ASP ( 43-) A 0.95
Obviously, the temperature at which the X-ray data was collected has some importance too:
Crystal temperature (K) :100.000
Warning: More than 5 percent of buried atoms has low B-factor
For normal protein structures, no more than about 1 percent of the B factors
of buried atoms is below 5.0. The fact that this value is much higher in the
current structure could be a signal that the B-factors were restraints or
constraints to too-low values, misuse of B-factor field in the PDB file, or
a TLS/scaling problem. If the average B factor is low too, it is probably a
low temperature structure determination.
Percentage of buried atoms with B less than 5 : 93.04
Note: B-factor plot
The average atomic B-factor per residue is plotted as function of the residue
Chain identifier: A
Nomenclature related problems
Warning: Phenylalanine convention problem
The phenylalanine residues listed in the table below have their chi-2 not
between -90.0 and 90.0.
12 PHE ( 13-) A
42 ASP ( 43-) A
RMS Z-score for bond lengths: 0.581
RMS-deviation in bond distances: 0.013
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.
2 THR ( 2-) A CG2 CB OG1 117.73 4.2 9 ALA ( 9-) A -O -C N 130.47 4.7 13 ASN ( 14-) A -O -C N 129.63 4.1 28 TYR ( 29-) A -C N CA 113.19 -4.7 28 TYR ( 29-) A N CA CB 103.12 -4.3 42 ASP ( 43-) A CA CB CG 116.76 4.2
42 ASP ( 43-) A
28 TYR ( 29-) A 4.35
28 TYR ( 29-) A 4.14
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.
43 TYR ( 44-) A omega poor chi-1/chi-2 correlation Z-score : -0.209
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!
5 PRO ( 5-) A 0 9 ALA ( 9-) A 0 10 ARG ( 10-) A 0 11 ASN ( 12-) A 0 12 PHE ( 13-) A 0 18 PRO ( 19-) A 0 4 CYS ( 4-) A 1 29 THR ( 30-) A 1 35 PRO ( 36-) A 1 43 TYR ( 44-) A 1 31 CYS ( 32-) A 2 37 ALA ( 38-) A 2 39 CYS ( 40-) A 2
The contact distances of all atom pairs have been checked. Two atoms are said to `bump' if they are closer than the sum of their Van der Waals radii minus 0.40 Angstrom. For hydrogen bonded pairs a tolerance of 0.55 Angstrom is used. The first number in the table tells you how much shorter that specific contact is than the acceptable limit. The second distance is the distance between the centres of the two atoms. Although we believe that two water atoms at 2.4 A distance are too close, we only report water pairs that are closer than this rather short distance.
The last text-item on each line represents the status of the atom pair. If the final column contains the text 'HB', the bump criterion was relaxed because there could be a hydrogen bond. Similarly relaxed criteria are used for 1-3 and 1-4 interactions (listed as 'B2' and 'B3', respectively). BL indicates that the B-factors of the clashing atoms have a low B-factor thereby making this clash even more worrisome. INTRA and INTER indicate whether the clashes are between atoms in the same asymmetric unit, or atoms in symmetry related asymmetric units, respectively.
21 PRO ( 22-) A A CD <-> 50 HOH (3112 ) A B O 1.27 1.53 INTRA BL 21 PRO ( 22-) A A CG <-> 50 HOH (3112 ) A B O 0.81 1.99 INTRA BL 50 HOH (3022 ) A O <-> 50 HOH (3114 ) A O 0.50 1.70 INTRA 50 HOH (3053 ) A O <-> 50 HOH (3117 ) A O 0.46 1.74 INTRA BF 50 HOH (3031 ) A O <-> 50 HOH (3121 ) A O 0.40 1.80 INTRA BF 50 HOH (3073 ) A A O <-> 50 HOH (3102 ) A A O 0.39 1.81 INTRA BL 47 EOH (2001-) A C2 <-> 50 HOH (3087 ) A O 0.35 2.45 INTRA 50 HOH (3101 ) A O <-> 50 HOH (3120 ) A O 0.29 1.91 INTRA BF 50 HOH (3074 ) A O <-> 50 HOH (3115 ) A A O 0.18 2.02 INTRA 50 HOH (3096 ) A O <-> 50 HOH (3109 ) A O 0.17 2.03 INTRA BF 50 HOH (3090 ) A O <-> 50 HOH (3121 ) A O 0.15 2.05 INTRA BF 45 ASN ( 46-) A OD1 <-> 47 EOH (2001-) A C1 0.09 2.71 INTRA BL 50 HOH (3082 ) A A O <-> 50 HOH (3109 ) A O 0.09 2.11 INTRA 1 THR ( 1-) A A N <-> 50 HOH (3082 ) A B O 0.07 2.63 INTRA 50 HOH (3082 ) A B O <-> 50 HOH (3109 ) A O 0.07 2.13 INTRA BF 50 HOH (3086 ) A O <-> 50 HOH (3119 ) A O 0.06 2.14 INTRA BF 36 GLY ( 37-) A N <-> 50 HOH (3024 ) A B O 0.06 2.64 INTRA BL
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
Chain identifier: A
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
Water, ion, and hydrogenbond related checks
Warning: Water molecules need moving
The water molecules listed in the table below were found to be significantly
closer to a symmetry related non-water molecule than to the ones given in the
coordinate file. For optimal viewing convenience revised coordinates for
these water molecules should be given.
The number in brackets is the identifier of the water molecule in the input file. Suggested coordinates are also given in the table. Please note that alternative conformations for protein residues are not taken into account for this calculation. If you are using WHAT IF / WHAT-CHECK interactively, then the moved waters can be found in PDB format in the file: MOVEDH2O.pdb.
50 HOH (3010 ) A O 5.94 -8.21 -5.76 50 HOH (3011 ) A O -4.13 0.16 9.79 50 HOH (3015 ) A O 7.83 -17.91 9.65 50 HOH (3048 ) A B O 20.68 -15.37 11.32 50 HOH (3085 ) A O -0.13 0.41 12.76 50 HOH (3091 ) A O 20.00 0.14 14.37 50 HOH (3095 ) A O 19.18 -1.75 15.53 50 HOH (3118 ) A O 14.38 -15.55 20.76 50 HOH (3119 ) A O 2.88 -23.12 16.59
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.
6 SER ( 6-) A N 14 VAL ( 15-) A N 36 GLY ( 37-) A N 39 CYS ( 40-) A N 45 ASN ( 46-) A ND2
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.
45 ASN ( 46-) A OD1
The score listed is the valency score. This number should be close to (preferably a bit above) 1.0 for the suggested ion to be a likely alternative for the water molecule. Ions listed in brackets are good alternate choices. *1 indicates that the suggested ion-type has been observed elsewhere in the PDB file too. *2 indicates that the suggested ion-type has been observed in the REMARK 280 cards of the PDB file. Ion-B and ION-B indicate that the B-factor of this water is high, or very high, respectively. H2O-B indicates that the B-factors of atoms that surround this water/ion are suspicious. See: swift.cmbi.ru.nl/teach/theory/ for a detailed explanation.
50 HOH (3048 ) A A O 1.02 NA 5 (or CA) 50 HOH (3071 ) A O 1.00 K 6 50 HOH (3106 ) A A O 1.13 K 7 Ion-B
42 ASP ( 43-) A H-bonding suggests Asn
The second part of the table mostly gives an impression of how well the model conforms to common refinement restraint values. The first part of the table shows a number of global quality indicators.
Structure Z-scores, positive is better than average:
1st generation packing quality : -0.435 2nd generation packing quality : -2.415 Ramachandran plot appearance : -2.201 chi-1/chi-2 rotamer normality : -0.209 Backbone conformation : 1.990
Bond lengths : 0.581 (tight) Bond angles : 1.217 Omega angle restraints : 1.006 Side chain planarity : 1.479 Improper dihedral distribution : 1.051 Inside/Outside distribution : 1.021
The second part of the table mostly gives an impression of how well the model conforms to common refinement restraint values. The first part of the table shows a number of global quality indicators, which have been calibrated against structures of similar resolution.
Resolution found in PDB file : 0.48
Structure Z-scores, positive is better than average:
1st generation packing quality : -0.1 2nd generation packing quality : -1.8 Ramachandran plot appearance : -2.4 chi-1/chi-2 rotamer normality : -0.8 Backbone conformation : 1.5
Bond lengths : 0.581 (tight) Bond angles : 1.217 Omega angle restraints : 1.006 Side chain planarity : 1.479 Improper dihedral distribution : 1.051 Inside/Outside distribution : 1.021 ==============
WHAT IF G.Vriend, WHAT IF: a molecular modelling and drug design program, J. Mol. Graph. 8, 52--56 (1990). WHAT_CHECK (verification routines from WHAT IF) R.W.W.Hooft, G.Vriend, C.Sander and E.E.Abola, Errors in protein structures Nature 381, 272 (1996). (see also http://swift.cmbi.ru.nl/gv/whatcheck for a course and extra inform Bond lengths and angles, protein residues R.Engh and R.Huber, Accurate bond and angle parameters for X-ray protein structure refinement, Acta Crystallogr. A47, 392--400 (1991). Bond lengths and angles, DNA/RNA G.Parkinson, J.Voitechovsky, L.Clowney, A.T.Bruenger and H.Berman, New parameters for the refinement of nucleic acid-containing structures Acta Crystallogr. D52, 57--64 (1996). DSSP W.Kabsch and C.Sander, Dictionary of protein secondary structure: pattern recognition of hydrogen bond and geometrical features Biopolymers 22, 2577--2637 (1983). Hydrogen bond networks R.W.W.Hooft, C.Sander and G.Vriend, Positioning hydrogen atoms by optimizing hydrogen bond networks in protein structures PROTEINS, 26, 363--376 (1996). Matthews' Coefficient B.W.Matthews Solvent content of Protein Crystals J. Mol. Biol. 33, 491--497 (1968). Protein side chain planarity R.W.W. Hooft, C. Sander and G. Vriend, Verification of protein structures: side-chain planarity J. Appl. Cryst. 29, 714--716 (1996). Puckering parameters D.Cremer and J.A.Pople, A general definition of ring puckering coordinates J. Am. Chem. Soc. 97, 1354--1358 (1975). Quality Control G.Vriend and C.Sander, Quality control of protein models: directional atomic contact analysis, J. Appl. Cryst. 26, 47--60 (1993). Ramachandran plot G.N.Ramachandran, C.Ramakrishnan and V.Sasisekharan, Stereochemistry of Polypeptide Chain Conformations J. Mol. Biol. 7, 95--99 (1963). Symmetry Checks R.W.W.Hooft, C.Sander and G.Vriend, Reconstruction of symmetry related molecules from protein data bank (PDB) files J. Appl. Cryst. 27, 1006--1009 (1994). Ion Checks I.D.Brown and K.K.Wu, Empirical Parameters for Calculating Cation-Oxygen Bond Valences Acta Cryst. B32, 1957--1959 (1975). M.Nayal and E.Di Cera, Valence Screening of Water in Protein Crystals Reveals Potential Na+ Binding Sites J.Mol.Biol. 256 228--234 (1996). P.Mueller, S.Koepke and G.M.Sheldrick, Is the bond-valence method able to identify metal atoms in protein structures? Acta Cryst. D 59 32--37 (2003). Checking checks K.Wilson, C.Sander, R.W.W.Hooft, G.Vriend, et al. Who checks the checkers J.Mol.Biol. (1998) 276,417-436.