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.
222 ACT (1218-) A - 223 ACT (1219-) A - 225 ACT (1220-) A -
In X-ray the coordinates must be located in density. Mobility or disorder sometimes cause this density to be so poor that the positions of the atoms cannot be determined. Crystallographers tend to leave out the atoms in such cases. This is not an error, albeit that we would prefer them to give it their best shot and provide coordinates with an occupancy of zero in cases where only a few atoms are involved. Anyway, several checks depend on the presence of the backbone atoms, so if you find errors in, or directly adjacent to, residues with missing backbone atoms, then please check by hand what is going on.
215 THR ( 80-) B -
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: C-terminal nitrogen atoms detected.
It is becoming habit to indicate that a residue is not the true C-terminus
by including only the backbone N of the next residue. This has been
observed in this PDB file.
In X-ray the coordinates must be located in density. Mobility or disorder sometimes cause this density to be so poor that the positions of the atoms cannot be determined. Crystallographers tend to leave out the atoms in such cases. In many cases the N- or C-terminal residues are too disordered to see. In case of the N-terminus, you can see from the residue numbers if there are missing residues, but at the C-terminus this is impossible. Therefore, often the position of the backbone nitrogen of the first residue missing at the C-terminal end is calculated and added to indicate that there are missing residues. As a single N causes validation trouble, we remove these single-N-residues before doing the validation. But, if you get weird errors at, or near, the left-over incomplete C-terminal residue, please check by hand if a missing Oxt or removed N is the cause.
219 ALA ( 98-) B 215 THR ( 80-) B
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.
169 ASN ( 169-) A 0.50 208 TYR ( 208-) A 0.50
Obviously, the temperature at which the X-ray data was collected has some importance too:
Number of TLS groups mentione in PDB file header: 0
Crystal temperature (K) :100.000
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: Arginine nomenclature problem
The arginine residues listed in the table below have their N-H-1 and N-H-2
111 ARG ( 111-) A 145 ARG ( 145-) A
48 TYR ( 48-) A 67 TYR ( 67-) A 78 TYR ( 78-) A 86 TYR ( 86-) A 94 TYR ( 94-) A 103 TYR ( 103-) A 186 TYR ( 186-) A 197 TYR ( 197-) A 203 TYR ( 203-) A
141 PHE ( 141-) A
3 GLU ( 3-) A 89 GLU ( 89-) A 118 GLU ( 118-) A 135 GLU ( 135-) A
RMS Z-score for bond lengths: 0.594
RMS-deviation in bond distances: 0.013
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
| 0.994549 -0.000521 -0.000788| | -0.000521 0.998102 0.001219| | -0.000788 0.001219 0.996374|Proposed new scale matrix
| 0.023758 0.000012 0.000019| | 0.000011 0.021725 -0.000027| | 0.000008 -0.000013 0.010488|With corresponding cell
A = 42.092 B = 46.029 C = 95.347 Alpha= 89.860 Beta= 90.091 Gamma= 90.060
The CRYST1 cell dimensions
A = 42.323 B = 46.118 C = 95.697 Alpha= 90.000 Beta= 90.000 Gamma= 90.000
(Under-)estimated Z-score: 7.460
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.
3 GLU ( 3-) A 89 GLU ( 89-) A 111 ARG ( 111-) A 118 GLU ( 118-) A 135 GLU ( 135-) A 145 ARG ( 145-) A
211 LYS ( 211-) A 4.01
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.
86 TYR ( 86-) A -2.9 156 LYS ( 156-) A -2.5 134 LEU ( 134-) A -2.4 211 LYS ( 211-) A -2.3 116 TYR ( 116-) A -2.0
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.
48 TYR ( 48-) A omega poor 77 GLN ( 77-) A omega poor 78 TYR ( 78-) A Poor phi/psi 128 GLN ( 128-) A Poor phi/psi 151 GLY ( 151-) A PRO omega poor 158 ASP ( 158-) A Poor phi/psi 170 TYR ( 170-) A omega poor 184 ASN ( 184-) A Poor phi/psi 200 CYS ( 200-) A Poor phi/psi 211 LYS ( 211-) A omega poor chi-1/chi-2 correlation Z-score : -0.761
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!
3 GLU ( 3-) A 0 7 TRP ( 7-) A 0 10 LYS ( 10-) A 0 12 ALA ( 12-) A 0 21 SER ( 21-) A 0 24 SER ( 24-) A 0 25 OCS ( 25-) A 0 41 ARG ( 41-) A 0 46 ASN ( 46-) A 0 56 CYS ( 56-) A 0 58 ARG ( 58-) A 0 60 SER ( 60-) A 0 61 TYR ( 61-) A 0 63 CYS ( 63-) A 0 64 ASN ( 64-) A 0 77 GLN ( 77-) A 0 78 TYR ( 78-) A 0 86 TYR ( 86-) A 0 89 GLU ( 89-) A 0 93 ARG ( 93-) A 0 94 TYR ( 94-) A 0 95 CYS ( 95-) A 0 96 ARG ( 96-) A 0 100 LYS ( 100-) A 0 102 PRO ( 102-) A 0And so on for a total of 99 lines.
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.
76 ALA ( 76-) A CB <-> 224 HOH (2063 ) A O 0.76 2.04 INTRA 78 TYR ( 78-) A CE2 <-> 222 GOL (1217-) A O2 0.41 2.39 INTRA 41 ARG ( 41-) A CZ <-> 211 LYS ( 211-) A O 0.40 2.40 INTRA 41 ARG ( 41-) A NH2 <-> 211 LYS ( 211-) A O 0.35 2.35 INTRA 59 ARG ( 59-) A NH1 <-> 224 HOH (2050 ) A O 0.33 2.37 INTRA BF 109 GLY ( 109-) A CA <-> 224 HOH (2099 ) A O 0.31 2.49 INTRA 98 ARG ( 98-) A A NH1 <-> 223 ACT (1220-) A O2 0.28 2.42 INTRA 59 ARG ( 59-) A NH2 <-> 221 ACT (1219-) A O2 0.26 2.44 INTRA BF 224 HOH (2061 ) A O <-> 224 HOH (2156 ) A O 0.22 1.98 INTRA 153 CYS ( 153-) A SG <-> 200 CYS ( 200-) A N 0.22 3.08 INTRA 186 TYR ( 186-) A OH <-> 219 GOL (1216-) A O1 0.17 2.23 INTRA 159 HIS ( 159-) A ND1 <-> 215 LEU ( 95-) B N 0.17 2.83 INTRA 47 GLN ( 47-) A NE2 <-> 224 HOH (2036 ) A O 0.17 2.53 INTRA 73 GLN ( 73-) A A NE2 <-> 224 HOH (2063 ) A O 0.16 2.54 INTRA 156 LYS ( 156-) A NZ <-> 224 HOH (2127 ) A O 0.14 2.56 INTRA 145 ARG ( 145-) A O <-> 224 HOH (2116 ) A O 0.10 2.30 INTRA 153 CYS ( 153-) A SG <-> 224 HOH (2123 ) A O 0.09 2.91 INTRA 74 LEU ( 74-) A O <-> 78 TYR ( 78-) A N 0.07 2.63 INTRA 83 ARG ( 83-) A NH1 <-> 220 ACT (1218-) A A CH3 0.06 3.04 INTRA 222 GOL (1217-) A C3 <-> 224 HOH (2047 ) A O 0.05 2.75 INTRA 73 GLN ( 73-) A A OE1 <-> 77 GLN ( 77-) A NE2 0.04 2.66 INTRA 224 HOH (2071 ) A O <-> 224 HOH (2072 ) A O 0.04 2.16 INTRA 10 LYS ( 10-) A NZ <-> 224 HOH (2008 ) A O 0.04 2.66 INTRA 182 GLY ( 182-) A O <-> 224 HOH (2116 ) A O 0.03 2.37 INTRA 158 ASP ( 158-) A OD2 <-> 224 HOH (2127 ) A O 0.03 2.37 INTRA 130 VAL ( 130-) A O <-> 163 ALA ( 163-) A N 0.02 2.68 INTRA BL 25 OCS ( 25-) A OD3 <-> 215 LEU ( 95-) B N 0.01 2.69 INTRA 108 ASP ( 108-) A N <-> 210 VAL ( 210-) A O 0.01 2.69 INTRA
Chain identifier: A
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.
145 ARG ( 145-) A -7.79 94 TYR ( 94-) A -6.26 77 GLN ( 77-) A -5.47 127 ASN ( 127-) A -5.43 78 TYR ( 78-) A -5.39 41 ARG ( 41-) A -5.32 4 TYR ( 4-) A -5.06
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.
224 HOH (2004 ) A O -10.66 -2.55 16.82
224 HOH (2010 ) A O
81 HIS ( 81-) A 112 GLN ( 112-) A 155 ASN ( 155-) A
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.
4 TYR ( 4-) A N 18 ASN ( 18-) A N 19 GLN ( 19-) A NE2 25 OCS ( 25-) A N 26 TRP ( 26-) A N 59 ARG ( 59-) A NE 69 TRP ( 69-) A N 83 ARG ( 83-) A NH2 91 VAL ( 91-) A N 98 ARG ( 98-) A N 98 ARG ( 98-) A A NH1 139 LYS ( 139-) A NZ 140 ASP ( 140-) A N 146 GLY ( 146-) A N 151 GLY ( 151-) A N 160 ALA ( 160-) A N 175 ASN ( 175-) A ND2 188 ARG ( 188-) A NH1 197 TYR ( 197-) A N
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.
3 GLU ( 3-) A A OE2
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.
224 HOH (2040 ) A O 0.86 K 4 224 HOH (2121 ) A O 1.13 K 7
55 ASP ( 55-) A H-bonding suggests Asn 158 ASP ( 158-) 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 : -0.774 2nd generation packing quality : -1.567 Ramachandran plot appearance : -1.166 chi-1/chi-2 rotamer normality : -0.761 Backbone conformation : -0.006
Bond lengths : 0.594 (tight) Bond angles : 0.699 Omega angle restraints : 1.054 Side chain planarity : 0.553 (tight) Improper dihedral distribution : 0.797 B-factor distribution : 0.532 Inside/Outside distribution : 1.057
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 : 1.50
Structure Z-scores, positive is better than average:
1st generation packing quality : -0.3 2nd generation packing quality : -1.5 Ramachandran plot appearance : -1.5 chi-1/chi-2 rotamer normality : -1.3 Backbone conformation : -0.5
Bond lengths : 0.594 (tight) Bond angles : 0.699 Omega angle restraints : 1.054 Side chain planarity : 0.553 (tight) Improper dihedral distribution : 0.797 B-factor distribution : 0.532 Inside/Outside distribution : 1.057 ==============
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.