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.
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.
62 HIS ( 64-) A 0.70
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 : 18.02
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
56 ARG ( 58-) A
73 ASP ( 75-) A
24 GLU ( 26-) A 67 GLU ( 69-) A
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.
39 ASP ( 41-) A C O 1.15 -4.1 184 GLU ( 187-) A CD OE1 1.16 -4.7 234 PRO ( 237-) A CD N 1.55 5.3
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
| 1.001319 0.000783 -0.000749| | 0.000783 1.002601 -0.000248| | -0.000749 -0.000248 1.001336|Proposed new scale matrix
| 0.023698 -0.000018 0.006088| | -0.000019 0.024254 0.000005| | 0.000011 0.000004 0.014316|With corresponding cell
A = 42.205 B = 41.230 C = 72.134 Alpha= 90.048 Beta= 104.450 Gamma= 89.908
The CRYST1 cell dimensions
A = 42.149 B = 41.124 C = 72.014 Alpha= 90.000 Beta= 104.370 Gamma= 90.000
(Under-)estimated Z-score: 4.170
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.
8 HIS ( 10-) A CG ND1 CE1 109.82 4.2 75 ALA ( 77-) A -O -C N 115.57 -4.6 75 ALA ( 77-) A -C N CA 129.81 4.5
24 GLU ( 26-) A 56 ARG ( 58-) A 67 GLU ( 69-) A 73 ASP ( 75-) A
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.
Please also see the previous table that lists a series of administrative chirality problems that were corrected automatically upon reading-in the PDB file.
66 VAL ( 68-) A C -6.0 -8.09 0.15 74 LYS ( 76-) A C -7.8 -11.66 0.11 205 THR ( 208-) A C -6.3 -9.08 0.30 The average deviation= 1.223
204 VAL ( 207-) A 4.95
32 ASP ( 34-) A 4.20
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.
173 PHE ( 176-) A -2.4 81 PRO ( 83-) A -2.4 43 LYS ( 45-) A -2.2 2 HIS ( 4-) A -2.2 90 GLN ( 92-) A -2.1 148 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 ( 4-) A Poor phi/psi 27 SER ( 29-) A PRO omega poor 58 LEU ( 60-) A omega poor 63 ALA ( 65-) A Poor phi/psi 109 LYS ( 111-) A Poor phi/psi 175 ASN ( 178-) A Poor phi/psi 198 PRO ( 201-) A PRO omega poor 200 LEU ( 203-) A Poor phi/psi 240 ASP ( 243-) A Poor phi/psi 249 LYS ( 252-) A Poor phi/psi chi-1/chi-2 correlation Z-score : -0.357
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 TRP ( 5-) A 0 5 TYR ( 7-) A 0 8 HIS ( 10-) A 0 17 ASP ( 19-) A 0 18 PHE ( 20-) A 0 22 LYS ( 24-) A 0 25 ARG ( 27-) A 0 26 GLN ( 28-) A 0 27 SER ( 29-) A 0 48 SER ( 50-) A 0 52 ALA ( 54-) A 0 60 ASN ( 62-) A 0 62 HIS ( 64-) A 0 70 ASP ( 72-) A 0 71 SER ( 73-) A 0 73 ASP ( 75-) A 0 74 LYS ( 76-) A 0 75 ALA ( 77-) A 0 78 LYS ( 80-) A 0 81 PRO ( 83-) A 0 83 ASP ( 85-) A 0 90 GLN ( 92-) A 0 97 SER ( 99-) A 0 101 GLN ( 103-) A 0 104 GLU ( 106-) A 0And so on for a total of 116 lines.
19 PRO ( 21-) A 0.12 LOW 40 PRO ( 42-) A 0.45 HIGH 135 PRO ( 138-) A 0.17 LOW 212 PRO ( 215-) A 0.16 LOW
11 PRO ( 13-) A 103.1 envelop C-beta (108 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.
1 HIS ( 3-) A ND1 <-> 2 HIS ( 4-) A N 0.62 2.28 INTRA 124 LYS ( 127-) A CE <-> 125 TYR ( 128-) A CZ 0.53 2.67 INTRA 7 LYS ( 9-) A NZ <-> 8 HIS ( 10-) A NE2 0.49 2.51 INTRA 124 LYS ( 127-) A NZ <-> 260 HOH ( 457 ) A O 0.48 2.22 INTRA 72 GLN ( 74-) A NE2 <-> 74 LYS ( 76-) A CE 0.41 2.69 INTRA 249 LYS ( 252-) A NZ <-> 260 HOH ( 403 ) A O 0.40 2.30 INTRA 1 HIS ( 3-) A O <-> 2 HIS ( 4-) A CD2 0.32 2.38 INTRA 124 LYS ( 127-) A CE <-> 125 TYR ( 128-) A CE2 0.32 2.88 INTRA 87 ARG ( 89-) A NH2 <-> 260 HOH ( 441 ) A O 0.28 2.42 INTRA 172 ASP ( 175-) A OD1 <-> 260 HOH ( 436 ) A O 0.25 2.15 INTRA 249 LYS ( 252-) A NZ <-> 260 HOH ( 468 ) A O 0.24 2.46 INTRA 124 LYS ( 127-) A CE <-> 125 TYR ( 128-) A OH 0.23 2.57 INTRA 38 TYR ( 40-) A CE2 <-> 40 PRO ( 42-) A CG 0.23 2.97 INTRA 73 ASP ( 75-) A OD2 <-> 87 ARG ( 89-) A NH2 0.22 2.48 INTRA 172 ASP ( 175-) A CG <-> 260 HOH ( 485 ) A O 0.22 2.58 INTRA 74 LYS ( 76-) A O <-> 260 HOH ( 369 ) A O 0.19 2.21 INTRA 124 LYS ( 127-) A NZ <-> 136 ASP ( 139-) A OD2 0.18 2.52 INTRA 1 HIS ( 3-) A O <-> 2 HIS ( 4-) A CG 0.16 2.54 INTRA 172 ASP ( 175-) A OD1 <-> 260 HOH ( 485 ) A O 0.14 2.26 INTRA 13 HIS ( 15-) A ND1 <-> 16 LYS ( 18-) A NZ 0.12 2.88 INTRA BL 1 HIS ( 3-) A CG <-> 2 HIS ( 4-) A N 0.12 2.88 INTRA 7 LYS ( 9-) A NZ <-> 8 HIS ( 10-) A CD2 0.12 2.98 INTRA 43 LYS ( 45-) A CB <-> 44 PRO ( 46-) A CD 0.11 2.99 INTRA 260 HOH ( 386 ) A O <-> 260 HOH ( 602 ) A O 0.10 2.10 INTRA 41 SER ( 43-) A O <-> 43 LYS ( 45-) A CD 0.10 2.70 INTRA 115 GLU ( 117-) A OE2 <-> 117 HIS ( 119-) A NE2 0.09 2.61 INTRA BL 87 ARG ( 89-) A CG <-> 123 THR ( 125-) A CG2 0.08 3.12 INTRA BL 22 LYS ( 24-) A NZ <-> 260 HOH ( 374 ) A O 0.08 2.62 INTRA 105 HIS ( 107-) A NE2 <-> 191 TYR ( 194-) A OH 0.07 2.63 INTRA BL 25 ARG ( 27-) A CG <-> 202 GLU ( 205-) A CD 0.05 3.15 INTRA BL 19 PRO ( 21-) A C <-> 21 ALA ( 23-) A N 0.05 2.85 INTRA BL 2 HIS ( 4-) A ND1 <-> 260 HOH ( 432 ) A O 0.05 2.65 INTRA 158 VAL ( 161-) A CG1 <-> 222 LYS ( 225-) A CD 0.04 3.16 INTRA 15 HIS ( 17-) A ND1 <-> 260 HOH ( 388 ) A O 0.03 2.67 INTRA 24 GLU ( 26-) A OE2 <-> 260 HOH ( 468 ) A O 0.03 2.37 INTRA 97 SER ( 99-) A N <-> 98 LEU ( 100-) A N 0.02 2.58 INTRA BL 70 ASP ( 72-) A OD2 <-> 121 TRP ( 123-) A NE1 0.02 2.68 INTRA BL 10 GLY ( 12-) A CA <-> 11 PRO ( 13-) A CD 0.01 2.79 INTRA BL 73 ASP ( 75-) A CG <-> 87 ARG ( 89-) A NE 0.01 3.09 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.
8 HIS ( 10-) A -6.35 2 HIS ( 4-) A -5.76 98 LEU ( 100-) A -5.16
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.
16 LYS ( 18-) A -2.59 249 LYS ( 252-) 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.
260 HOH ( 395 ) A O -18.94 -21.56 5.14 260 HOH ( 564 ) A O -13.05 12.96 31.95
175 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.
8 HIS ( 10-) A NE2 29 VAL ( 31-) A N 72 GLN ( 74-) A N 87 ARG ( 89-) A NE 98 LEU ( 100-) A N 150 ALA ( 153-) A N 155 GLN ( 158-) A NE2 201 LEU ( 204-) A N 227 ASN ( 230-) A ND2 242 TRP ( 245-) A N 257 PHE ( 260-) A N Only metal coordination for 94 HIS ( 96-) A NE2 Only metal coordination for 117 HIS ( 119-) A ND1
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.
1 HIS ( 3-) A ND1 73 ASP ( 75-) A OD1
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 : -0.011 2nd generation packing quality : 0.777 Ramachandran plot appearance : -1.499 chi-1/chi-2 rotamer normality : -0.357 Backbone conformation : -0.840
Bond lengths : 0.764 Bond angles : 0.839 Omega angle restraints : 0.750 Side chain planarity : 1.072 Improper dihedral distribution : 1.088 Inside/Outside distribution : 0.944
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 : -0.2 Ramachandran plot appearance : -1.8 chi-1/chi-2 rotamer normality : -0.9 Backbone conformation : -1.3
Bond lengths : 0.764 Bond angles : 0.839 Omega angle restraints : 0.750 Side chain planarity : 1.072 Improper dihedral distribution : 1.088 Inside/Outside distribution : 0.944 ==============
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.