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.
260 ACE ( 1-) A -
For example, an aspartic acid can be protonated on one of its delta oxygens. This is possible because the one delta oxygen 'helps' the other one holding that proton. However, if a delta oxygen has a group bound to it, then it can no longer 'help' the other delta oxygen bind the proton. However, both delta oxygens, in principle, can still be hydrogen bond acceptors. Such problems can occur in the amino acids Asp, Glu, and His. I have opted, for now to simply allow no hydrogen bonds at all for any atom in any side chain that somewhere has a 'funny' group attached to it. I know this is wrong, but there are only 12 hours in a day.
1 SER ( 2-) A - N bound to 260 ACE ( 1-) A - CH3
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: 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 SER ( 2-) A 0.55 2 HIS ( 3-) A 0.58 63 HIS ( 64-) A 1.20
Obviously, the temperature at which the X-ray data was collected has some importance too:
Temperature cannot be read from the PDB file. This most likely means that
the temperature is listed as NULL (meaning unknown) in the PDB file.
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 : 21.34
Note: B-factor plot
The average atomic B-factor per residue is plotted as function of the residue
Chain identifier: A
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.
92 PHE ( 93-) A CG CD1 1.47 4.2
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
| 0.995484 0.000023 -0.001252| | 0.000023 0.996075 -0.000871| | -0.001252 -0.000871 0.995783|Proposed new scale matrix
| 0.023533 0.000005 0.006155| | 0.000000 0.024076 0.000021| | 0.000018 0.000012 0.014216|With corresponding cell
A = 42.508 B = 41.536 C = 72.734 Alpha= 90.097 Beta= 104.730 Gamma= 89.999
The CRYST1 cell dimensions
A = 42.700 B = 41.700 C = 73.000 Alpha= 90.000 Beta= 104.600 Gamma= 90.000
(Under-)estimated Z-score: 9.501
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.
1 SER ( 2-) A N CA CB 118.82 4.9 2 HIS ( 3-) A -C N CA 145.17 13.0 2 HIS ( 3-) A N CA C 93.63 -6.3 2 HIS ( 3-) A CA C O 110.43 -6.1 2 HIS ( 3-) A C CA CB 119.31 4.8 2 HIS ( 3-) A CA CB CG 117.81 4.0 2 HIS ( 3-) A CG ND1 CE1 109.82 4.2 3 HIS ( 4-) A -CA -C N 128.40 6.1 3 HIS ( 4-) A CA CB CG 123.11 9.3 9 HIS ( 10-) A CA CB CG 109.29 -4.5 13 GLU ( 14-) A CB CG CD 129.66 10.0 25 GLU ( 26-) A CG CD OE1 128.43 4.4 26 ARG ( 27-) A CA CB CG 130.20 8.0 26 ARG ( 27-) A CG CD NE 122.08 6.8 36 THR ( 37-) A N CA CB 102.82 -4.5 36 THR ( 37-) A C CA CB 120.01 5.2 36 THR ( 37-) A CA CB CG2 119.61 5.4 36 THR ( 37-) A CG2 CB OG1 117.66 4.2 49 SER ( 50-) A CA CB OG 100.86 -5.1 52 GLN ( 53-) A CB CG CD 103.78 -5.2 52 GLN ( 53-) A CG CD NE2 108.53 -5.2 52 GLN ( 53-) A NE2 CD OE1 128.66 6.1 54 THR ( 55-) A CA CB OG1 103.43 -4.1 57 ARG ( 58-) A N CA CB 99.51 -6.5 61 ASN ( 62-) A ND2 CG OD1 117.63 -5.0And so on for a total of 67 lines.
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.
208 ILE ( 210-) A C -6.2 -8.03 0.03 The average deviation= 1.946
2 HIS ( 3-) A 5.79 149 GLY ( 151-) A 4.03
93 HIS ( 94-) A 5.73 156 GLN ( 158-) A 4.81 242 ASN ( 244-) A 4.61 118 HIS ( 119-) A 4.56
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.
2 HIS ( 3-) A -3.1 82 PRO ( 83-) A -2.6 59 LEU ( 60-) A -2.2 174 PHE ( 176-) A -2.2 165 ILE ( 167-) A -2.2 161 VAL ( 163-) A -2.1 189 TYR ( 191-) A -2.1 237 GLU ( 239-) A -2.1 79 LYS ( 80-) A -2.1 110 LYS ( 111-) A -2.1 78 LEU ( 79-) A -2.1
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.
2 HIS ( 3-) A Poor phi/psi 28 SER ( 29-) A PRO omega poor 74 ASP ( 75-) A Poor phi/psi 110 LYS ( 111-) A Poor phi/psi 127 GLY ( 129-) A Poor phi/psi 176 ASN ( 178-) A Poor phi/psi 199 PRO ( 201-) A PRO omega poor 241 ASP ( 243-) A Poor phi/psi 250 LYS ( 252-) A Poor phi/psi chi-1/chi-2 correlation Z-score : -1.738
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 HIS ( 4-) A 0 4 TRP ( 5-) A 0 6 TYR ( 7-) A 0 9 HIS ( 10-) A 0 18 ASP ( 19-) A 0 19 PHE ( 20-) A 0 23 LYS ( 24-) A 0 26 ARG ( 27-) A 0 27 GLN ( 28-) A 0 28 SER ( 29-) A 0 49 SER ( 50-) A 0 51 ASP ( 52-) A 0 53 ALA ( 54-) A 0 61 ASN ( 62-) A 0 63 HIS ( 64-) A 0 71 ASP ( 72-) A 0 72 SER ( 73-) A 0 74 ASP ( 75-) A 0 75 LYS ( 76-) A 0 76 ALA ( 77-) A 0 79 LYS ( 80-) A 0 82 PRO ( 83-) A 0 84 ASP ( 85-) A 0 91 GLN ( 92-) A 0 102 GLN ( 103-) A 0And so on for a total of 117 lines.
Standard deviation of omega values : 3.920
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]
20 PRO ( 21-) A 0.49 HIGH 41 PRO ( 42-) A 0.46 HIGH 45 PRO ( 46-) A 0.46 HIGH 136 PRO ( 138-) A 0.08 LOW 153 PRO ( 155-) A 0.09 LOW 245 PRO ( 247-) A 0.09 LOW
193 PRO ( 195-) A -65.3 envelop C-beta (-72 degrees)
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.
14 HIS ( 15-) A ND1 <-> 17 LYS ( 18-) A NZ 0.26 2.74 INTRA BL 111 LYS ( 112-) A NZ <-> 264 HOH ( 423 ) A O 0.20 2.50 INTRA 223 LYS ( 225-) A NZ <-> 264 HOH ( 383 ) A O 0.15 2.55 INTRA 74 ASP ( 75-) A OD1 <-> 88 ARG ( 89-) A NE 0.13 2.57 INTRA 23 LYS ( 24-) A NZ <-> 264 HOH ( 503 ) A O 0.12 2.58 INTRA BF 116 GLU ( 117-) A OE2 <-> 118 HIS ( 119-) A NE2 0.11 2.59 INTRA BL 197 THR ( 199-) A OG1 <-> 263 H2S ( 263-) A S 0.11 2.89 INTRA 263 H2S ( 263-) A S <-> 264 HOH ( 318 ) A O 0.11 2.79 INTRA 63 HIS ( 64-) A A NE2 <-> 264 HOH ( 490 ) A O 0.09 2.61 INTRA 1 SER ( 2-) A N <-> 9 HIS ( 10-) A O 0.07 2.63 INTRA 27 GLN ( 28-) A OE1 <-> 244 ARG ( 246-) A NH1 0.06 2.64 INTRA BL 6 TYR ( 7-) A N <-> 264 HOH ( 293 ) A O 0.06 2.64 INTRA BL 263 H2S ( 263-) A S <-> 264 HOH ( 338 ) A O 0.06 2.84 INTRA 149 GLY ( 151-) A N <-> 216 VAL ( 218-) A O 0.06 2.64 INTRA BL 50 TYR ( 51-) A OH <-> 121 HIS ( 122-) A NE2 0.05 2.65 INTRA BL 250 LYS ( 252-) A NZ <-> 264 HOH ( 363 ) A O 0.04 2.66 INTRA 91 GLN ( 92-) A OE1 <-> 93 HIS ( 94-) A ND1 0.03 2.67 INTRA BL 106 HIS ( 107-) A NE2 <-> 192 TYR ( 194-) A OH 0.03 2.67 INTRA BL
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.
3 HIS ( 4-) A -5.40 99 LEU ( 100-) A -5.12 2 HIS ( 3-) A -5.09 134 GLN ( 136-) A -5.02
Chain identifier: A
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 LYS ( 18-) A -2.54
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.
264 HOH ( 303 ) A O -19.65 -20.94 5.14 264 HOH ( 317 ) A O -13.72 -18.74 15.17 264 HOH ( 349 ) A O -3.07 -17.90 5.18 264 HOH ( 373 ) A O -21.21 -6.87 -2.44 264 HOH ( 382 ) A O -18.83 -3.20 -2.34 264 HOH ( 426 ) A O 16.50 -6.04 13.00 264 HOH ( 481 ) A O -11.71 -0.46 42.81
264 HOH ( 488 ) A O Metal-coordinating Histidine residue 93 fixed to 1 Metal-coordinating Histidine residue 95 fixed to 1 Metal-coordinating Histidine residue 118 fixed to 1
52 GLN ( 53-) A 135 GLN ( 137-) A 176 ASN ( 178-) 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.
30 VAL ( 31-) A N 44 LYS ( 45-) A N 73 GLN ( 74-) A N 99 LEU ( 100-) A N 128 ASP ( 130-) A N 198 THR ( 200-) A N 202 LEU ( 204-) A N 219 GLU ( 221-) A N 242 ASN ( 244-) A ND2 243 TRP ( 245-) A N 258 PHE ( 260-) A N Only metal coordination for 95 HIS ( 96-) A NE2 Only metal coordination for 118 HIS ( 119-) A ND1
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.
264 HOH ( 282 ) A O 0.90 K 4 264 HOH ( 291 ) A O 0.98 K 4 264 HOH ( 392 ) A O 1.02 K 4 Ion-B 264 HOH ( 436 ) A O 0.86 K 4
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 : -0.345 2nd generation packing quality : 0.294 Ramachandran plot appearance : -1.421 chi-1/chi-2 rotamer normality : -1.738 Backbone conformation : -1.110
Bond lengths : 0.881 Bond angles : 1.618 Omega angle restraints : 0.713 (tight) Side chain planarity : 1.808 Improper dihedral distribution : 1.610 (loose) Inside/Outside distribution : 0.948
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 : 1.90
Structure Z-scores, positive is better than average:
1st generation packing quality : 0.1 2nd generation packing quality : -0.1 Ramachandran plot appearance : -1.2 chi-1/chi-2 rotamer normality : -1.1 Backbone conformation : -1.5
Bond lengths : 0.881 Bond angles : 1.618 Omega angle restraints : 0.713 (tight) Side chain planarity : 1.808 Improper dihedral distribution : 1.610 (loose) Inside/Outside distribution : 0.948 ==============
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.