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.
264 TRI ( 494-) 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 - C
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 13 GLU ( 14-) A 0.50 63 HIS ( 64-) A 0.90 134 GLN ( 136-) A 0.40
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 : 19.65
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.
9 HIS ( 10-) A CG CD2 1.41 4.6 25 GLU ( 26-) A CD OE2 1.33 4.1 122 TRP ( 123-) A NE1 CE2 1.42 4.5 163 ASP ( 165-) A CG OD2 1.34 4.9 185 GLU ( 187-) A CD OE1 1.33 4.5 232 GLU ( 234-) A CD OE1 1.34 4.6 237 GLU ( 239-) A CD OE1 1.33 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
| 0.997634 0.000507 -0.002706| | 0.000507 0.999751 -0.001049| | -0.002706 -0.001049 0.993132|Proposed new scale matrix
| 0.023491 -0.000005 0.006206| | -0.000012 0.023987 0.000025| | 0.000039 0.000015 0.014254|With corresponding cell
A = 42.600 B = 41.689 C = 72.615 Alpha= 90.131 Beta= 104.954 Gamma= 89.942
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: 8.620
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 HIS ( 3-) A -C N CA 134.06 6.9 2 HIS ( 3-) A N CA C 97.05 -5.1 2 HIS ( 3-) A CA C O 111.31 -5.6 2 HIS ( 3-) A C CA CB 119.45 4.9 2 HIS ( 3-) A CA CB CG 118.43 4.6 3 HIS ( 4-) A -C N CA 104.78 -9.4 3 HIS ( 4-) A CA CB CG 121.25 7.4 9 HIS ( 10-) A CA CB CG 109.36 -4.4 13 GLU ( 14-) A CB CG CD 127.48 8.8 19 PHE ( 20-) A CA CB CG 109.53 -4.3 25 GLU ( 26-) A C CA CB 102.45 -4.0 26 ARG ( 27-) A C CA CB 119.29 4.8 36 THR ( 37-) A CA CB CG2 119.46 5.3 36 THR ( 37-) A CG2 CB OG1 117.65 4.2 46 LEU ( 47-) A C CA CB 101.75 -4.4 49 SER ( 50-) A CA CB OG 101.70 -4.7 51 ASP ( 52-) A CA CB CG 107.29 -5.3 52 GLN ( 53-) A CB CG CD 102.92 -5.7 52 GLN ( 53-) A CG CD NE2 105.85 -7.0 52 GLN ( 53-) A NE2 CD OE1 129.23 6.6 57 ARG ( 58-) A N CA CB 102.16 -4.9 60 ASN ( 61-) A ND2 CG OD1 126.89 4.3 63 HIS ( 64-) A N CA CB 118.98 5.0 65 PHE ( 66-) A CA CB CG 118.30 4.5 66 ASN ( 67-) A CA CB CG 118.23 5.6And so on for a total of 69 lines.
2 HIS ( 3-) A 4.67 149 GLY ( 151-) A 4.15
14 HIS ( 15-) A 5.87 52 GLN ( 53-) A 5.16 33 ASP ( 34-) A 5.11 94 PHE ( 95-) A 4.46
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 -2.6 237 GLU ( 239-) A -2.3 161 VAL ( 163-) A -2.1 91 GLN ( 92-) A -2.1 200 PRO ( 202-) A -2.0 149 GLY ( 151-) 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.
2 HIS ( 3-) A Poor phi/psi 28 SER ( 29-) A PRO omega poor 63 HIS ( 64-) A Poor phi/psi 109 ASP ( 110-) A Poor phi/psi 110 LYS ( 111-) A Poor phi/psi 176 ASN ( 178-) A Poor phi/psi 189 TYR ( 191-) A omega poor 199 PRO ( 201-) A PRO omega poor 201 LEU ( 203-) A Poor phi/psi 241 ASP ( 243-) A Poor phi/psi 250 LYS ( 252-) A Poor phi/psi chi-1/chi-2 correlation Z-score : -1.146
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 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 0 106 HIS ( 107-) A 0And so on for a total of 119 lines.
136 PRO ( 138-) A 0.17 LOW 193 PRO ( 195-) A 0.18 LOW 245 PRO ( 247-) A 0.08 LOW
213 PRO ( 215-) A 50.7 half-chair C-delta/C-gamma (54 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 0.33 2.67 INTRA BL 111 LYS ( 112-) A NZ <-> 265 HOH ( 423 ) A O 0.29 2.41 INTRA 112 LYS ( 113-) A CE <-> 265 HOH ( 486 ) A O 0.26 2.54 INTRA 1 SER ( 2-) A OG <-> 2 HIS ( 3-) A N 0.17 2.43 INTRA BF 250 LYS ( 252-) A NZ <-> 265 HOH ( 363 ) A O 0.16 2.54 INTRA 74 ASP ( 75-) A OD1 <-> 88 ARG ( 89-) A NE 0.15 2.55 INTRA 116 GLU ( 117-) A OE2 <-> 118 HIS ( 119-) A NE2 0.15 2.55 INTRA BL 147 LYS ( 149-) A NZ <-> 215 SER ( 217-) A OG 0.11 2.59 INTRA 265 HOH ( 381 ) A O <-> 265 HOH ( 389 ) A O 0.11 2.09 INTRA BF 1 SER ( 2-) A CB <-> 260 ACE ( 1-) A O 0.08 2.72 INTRA BF 197 THR ( 199-) A N <-> 264 TRI ( 494-) A N2 0.07 2.93 INTRA 79 LYS ( 80-) A NZ <-> 265 HOH ( 416 ) A O 0.06 2.64 INTRA BF 106 HIS ( 107-) A NE2 <-> 192 TYR ( 194-) A OH 0.05 2.65 INTRA BL 223 LYS ( 225-) A NZ <-> 265 HOH ( 383 ) A O 0.05 2.65 INTRA BF 17 LYS ( 18-) A NZ <-> 260 ACE ( 1-) A O 0.05 2.65 INTRA 2 HIS ( 3-) A C <-> 3 HIS ( 4-) A CA 0.05 2.25 INTRA B2 7 GLY ( 8-) A N <-> 10 ASN ( 11-) A OD1 0.02 2.68 INTRA 234 GLU ( 236-) A CB <-> 235 PRO ( 237-) A CD 0.02 3.08 INTRA 250 LYS ( 252-) A CB <-> 251 ASN ( 253-) A N 0.01 2.69 INTRA BL 20 PRO ( 21-) A C <-> 22 ALA ( 23-) A N 0.01 2.89 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 -5.35 99 LEU ( 100-) A -5.18 134 GLN ( 136-) A -5.14 2 HIS ( 3-) A -5.05
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 -2.53
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.
265 HOH ( 315 ) A O -14.64 -18.84 18.96 265 HOH ( 317 ) A O -13.60 -18.55 15.27 265 HOH ( 349 ) A O -3.08 -17.96 5.60 265 HOH ( 373 ) A O -21.45 -6.71 -2.34 265 HOH ( 382 ) A O -18.68 -3.40 -2.51 265 HOH ( 386 ) A O -11.31 -15.31 34.61 265 HOH ( 445 ) A O 1.15 -6.14 35.02 265 HOH ( 447 ) A O -1.25 -8.61 33.49 265 HOH ( 481 ) A O -12.10 -0.54 42.69 265 HOH ( 487 ) A O -25.43 12.35 6.13 265 HOH ( 488 ) A O -25.96 -6.56 34.29
265 HOH ( 345 ) A O 265 HOH ( 461 ) A O 265 HOH ( 489 ) 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
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 99 LEU ( 100-) A N 167 THR ( 169-) A N 198 THR ( 200-) A N 202 LEU ( 204-) A N 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 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 : -0.234 2nd generation packing quality : 0.378 Ramachandran plot appearance : -1.375 chi-1/chi-2 rotamer normality : -1.146 Backbone conformation : -1.017
Bond lengths : 1.123 Bond angles : 1.610 Omega angle restraints : 1.005 Side chain planarity : 2.281 (loose) Improper dihedral distribution : 1.839 (loose) Inside/Outside distribution : 0.947
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 : 0.2 2nd generation packing quality : -0.1 Ramachandran plot appearance : -1.2 chi-1/chi-2 rotamer normality : -0.5 Backbone conformation : -1.4
Bond lengths : 1.123 Bond angles : 1.610 Omega angle restraints : 1.005 Side chain planarity : 2.281 (loose) Improper dihedral distribution : 1.839 (loose) Inside/Outside distribution : 0.947 ==============
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.