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.
Space group as read from CRYST card: P 41 21 2
Number of matrices in space group: 8
Highest polymer chain multiplicity in structure: 1
Highest polymer chain multiplicity according to SEQRES: 2
Such multiplicity differences are not by definition worrisome as it is very
well possible that this merely indicates that it is difficult to superpose
chains due to crystal induced differences
No explicit MTRIX NCS matrices found in the input file
Value of Z as found on the CRYST1 card: 8
Polymer chain multiplicity and SEQRES multiplicity disagree 1 2
Z and NCS seem to support the 3D multiplicity
There is strong evidence, though, for multiplicity and Z: 1 8
Error: Matthews Coefficient (Vm) very high
The Matthews coefficient [REF] is defined as the density of the protein structure in cubic Angstroms per Dalton. Normal values are between 1.5 (tightly packed, little room for solvent) and 4.0 (loosely packed, much space for solvent). Some very loosely packed structures can get values a bit higher than that.
Numbers this high are almost always caused by giving the wrong value for Z on the CRYST1 card (or not giving this number at all).
Molecular weight of all polymer chains: 39793.297
Volume of the Unit Cell V= 1222731.1
Space group multiplicity: 8
No NCS symmetry matrices (MTRIX records) found in PDB file
Matthews coefficient for observed atoms and Z high: Vm= 7.682
Vm by authors and this calculated Vm do not agree very well
Matthews coefficient read from REMARK 280 Vm= 3.520 SEQRES and ATOM multiplicities disagree. Error-reasoning thus is difficult.
(and the absence of MTRIX records doesn't help)
There is strong evidence, though, for multiplicity and Z: 1 8
which would result in the much more normal Vm= 3.841
and which also agrees with the number of NCS matrices (labeled `don't use')
that the user provided in the MTRIX records 1
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.
302 FOX ( 7-) 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: Missing atoms
The atoms listed in the table below are missing from the entry. If many atoms
are missing, the other checks can become less sensitive. Be aware that it
often happens that groups at the termini of DNA or RNA are really missing,
so that the absence of these atoms normally is neither an error nor the
result of poor electron density. Some of the atoms listed here might also be
listed by other checks, most noticeably by the options in the previous
section that list missing atoms in several categories. The plausible atoms
with zero occupancy are not listed here, as they already got assigned a
non-zero occupancy, and thus are no longer 'missing'.
42 LYS ( 15-) A CD 42 LYS ( 15-) A CE 42 LYS ( 15-) A NZ 58 ARG ( 31-) A CZ 58 ARG ( 31-) A NH1 58 ARG ( 31-) A NH2 69 LYS ( 42-) A CD 69 LYS ( 42-) A CE 69 LYS ( 42-) A NZ 92 ASP ( 65-) A CG 92 ASP ( 65-) A OD1 92 ASP ( 65-) A OD2 93 ASP ( 66-) A CG 93 ASP ( 66-) A OD1 93 ASP ( 66-) A OD2 105 LYS ( 78-) A CD 105 LYS ( 78-) A CE 105 LYS ( 78-) A NZ 115 ARG ( 88-) A CG 115 ARG ( 88-) A CD 115 ARG ( 88-) A NE 115 ARG ( 88-) A CZ 115 ARG ( 88-) A NH1 115 ARG ( 88-) A NH2 127 ASP ( 100-) A CGAnd so on for a total of 59 lines.
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
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.
1 DCYT ( 1-) B C1' N1 1.53 4.7 6 DTHY ( 6-) B C3' C2' 1.56 4.1 7 DTHY ( 8-) B C5' C4' 1.55 4.9 7 DTHY ( 8-) B N1 C6 1.41 4.1 7 DTHY ( 8-) B C5 C7 1.53 6.4 8 DTHY ( 9-) B N1 C6 1.41 4.3 9 DTHY ( 10-) B C5 C7 1.52 4.8 12 DCYT ( 13-) B C1' N1 1.52 4.0 15 DCYT ( 16-) C C1' N1 1.52 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
| 0.997066 0.001166 -0.000452| | 0.001166 0.996429 -0.001492| | -0.000452 -0.001492 0.993659|Proposed new scale matrix
| 0.010841 -0.000013 0.000005| | -0.000013 0.010848 0.000016| | 0.000003 0.000011 0.007045|With corresponding cell
A = 92.244 B = 92.185 C = 141.951 Alpha= 90.172 Beta= 90.052 Gamma= 89.866
The CRYST1 cell dimensions
A = 92.513 B = 92.513 C = 142.867 Alpha= 90.000 Beta= 90.000 Gamma= 90.000
(Under-)estimated Z-score: 14.617
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.
4 DTHY ( 4-) B N3 C2 O2 119.85 -4.1 6 DTHY ( 6-) B C6 C5 C7 119.69 -5.3 6 DTHY ( 6-) B C4 C5 C7 123.27 7.1 7 DTHY ( 8-) B P O5' C5' 113.32 -4.7 7 DTHY ( 8-) B O4' C1' N1 103.64 -5.2 8 DTHY ( 9-) B N3 C2 O2 119.44 -4.8 9 DTHY ( 10-) B C4 C5 C7 121.82 4.7 10 DCYT ( 11-) B N3 C2 O2 118.79 -4.4 11 DTHY ( 12-) B C5 C4 O4 120.38 -6.5 11 DTHY ( 12-) B C4 C5 C7 122.04 5.1 11 DTHY ( 12-) B O4 C4 N3 122.37 4.1 12 DCYT ( 13-) B O4' C1' C2' 100.74 -4.9 12 DCYT ( 13-) B O4' C1' N1 103.33 -5.6 13 DGUA ( 14-) B C5 C6 O6 125.90 -4.5 14 DGUA ( 15-) C O4' C1' N9 112.23 5.5 14 DGUA ( 15-) C N9 C8 N7 114.35 6.5 14 DGUA ( 15-) C N9 C4 C5 107.16 4.4 14 DGUA ( 15-) C C8 N9 C4 104.55 -4.6 16 DGUA ( 17-) C P -C3* -O3* 126.81 5.9 16 DGUA ( 17-) C O5' C5' C4' 103.36 -4.9 17 DADE ( 18-) C O4' C1' N9 103.40 -5.5 17 DADE ( 18-) C C2 N3 C4 108.54 -4.1 18 DGUA ( 19-) C N9 C8 N7 113.33 4.5 19 DADE ( 20-) C O4' C1' N9 112.89 6.4 19 DADE ( 20-) C N6 C6 N1 121.54 4.9 22 DCYT ( 23-) C OP1 P OP2 126.09 4.3 22 DCYT ( 23-) C C4' O4' C1' 103.72 -4.3 22 DCYT ( 23-) C O4' C1' N1 103.92 -4.8 22 DCYT ( 23-) C N1 C2 O2 121.97 5.1 26 DGUA ( 27-) C O4' C1' N9 112.50 5.9 26 DGUA ( 27-) C N9 C8 N7 113.77 5.3 27 DADE ( 28-) C O4' C1' N9 112.84 6.3 67 LEU ( 40-) A CA CB CG 133.68 5.0 95 ARG ( 68-) A CG CD NE 118.54 4.7 225 HIS ( 198-) A CG ND1 CE1 109.61 4.0 236 GLN ( 209-) A CB CG CD 119.72 4.2
43 ARG ( 16-) A 5.21
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.
193 VAL ( 166-) 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.
60 VAL ( 33-) A omega poor 90 ILE ( 63-) A omega poor 91 GLY ( 64-) A Poor phi/psi 101 ARG ( 74-) A Poor phi/psi 137 LYS ( 110-) A Poor phi/psi 157 LYS ( 130-) A Poor phi/psi 162 PRO ( 135-) A Poor phi/psi 190 GLN ( 163-) A Poor phi/psi 194 ALA ( 167-) A omega poor 209 LYS ( 182-) A Poor phi/psi 247 ARG ( 220-) A omega poor 248 THR ( 221-) A Poor phi/psi 249 TYR ( 222-) A omega poor 288 GLY ( 261-) A omega poor chi-1/chi-2 correlation Z-score : -0.347
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 DCYT ( 3-) B 0 4 DTHY ( 4-) B 0 5 DTHY ( 5-) B 0 6 DTHY ( 6-) B 0 7 DTHY ( 8-) B 0 8 DTHY ( 9-) B 0 9 DTHY ( 10-) B 0 10 DCYT ( 11-) B 0 11 DTHY ( 12-) B 0 12 DCYT ( 13-) B 0 13 DGUA ( 14-) B 0 14 DGUA ( 15-) C 0 15 DCYT ( 16-) C 0 16 DGUA ( 17-) C 0 17 DADE ( 18-) C 0 18 DGUA ( 19-) C 0 19 DADE ( 20-) C 0 20 DADE ( 21-) C 0 21 DADE ( 22-) C 0 22 DCYT ( 23-) C 0 23 DADE ( 24-) C 0 24 DADE ( 25-) C 0 25 DADE ( 26-) C 0 26 DGUA ( 27-) C 0 27 DADE ( 28-) C 0And so on for a total of 123 lines.
28 PRO ( 1-) A 0.46 HIGH
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.
6 DTHY ( 6-) B O3' <-> 302 FOX ( 7-) B P 1.00 1.60 INTRA BL 6 DTHY ( 6-) B C3' <-> 302 FOX ( 7-) B P 0.81 2.59 INTRA BL 13 DGUA ( 14-) B N1 <-> 15 DCYT ( 16-) C N3 0.26 2.74 INTRA BF 2 DTHY ( 2-) B N3 <-> 27 DADE ( 28-) C N1 0.25 2.75 INTRA BF 5 DTHY ( 5-) B N3 <-> 24 DADE ( 25-) C N1 0.25 2.75 INTRA 162 PRO ( 135-) A O <-> 236 GLN ( 209-) A NE2 0.24 2.46 INTRA 4 DTHY ( 4-) B N3 <-> 25 DADE ( 26-) C N1 0.24 2.76 INTRA BF 20 DADE ( 21-) C N7 <-> 304 HOH ( 196 ) C O 0.22 2.48 INTRA BF 271 LYS ( 244-) A NZ <-> 278 GLU ( 251-) A OE2 0.21 2.49 INTRA BF 21 DADE ( 22-) C OP2 <-> 304 HOH ( 372 ) C O 0.21 2.19 INTRA BF 92 ASP ( 65-) A CB <-> 305 HOH (5269 ) A O 0.20 2.60 INTRA BF 175 LYS ( 148-) A NZ <-> 305 HOH (5113 ) A O 0.19 2.51 INTRA 180 THR ( 153-) A N <-> 305 HOH (5297 ) A O 0.19 2.51 INTRA BF 11 DTHY ( 12-) B N3 <-> 17 DADE ( 18-) C N1 0.18 2.82 INTRA BF 53 GLU ( 26-) A OE2 <-> 305 HOH (5181 ) A O 0.18 2.22 INTRA BF 275 CYS ( 248-) A SG <-> 292 CYS ( 265-) A SG 0.18 3.27 INTRA 6 DTHY ( 6-) B N3 <-> 23 DADE ( 24-) C N1 0.16 2.84 INTRA BL 15 DCYT ( 16-) C C2' <-> 16 DGUA ( 17-) C C8 0.16 3.04 INTRA BF 9 DTHY ( 10-) B N3 <-> 19 DADE ( 20-) C N1 0.15 2.85 INTRA 24 DADE ( 25-) C N7 <-> 304 HOH ( 178 ) C O 0.15 2.55 INTRA BF 12 DCYT ( 13-) B N3 <-> 16 DGUA ( 17-) C N1 0.12 2.88 INTRA BF 10 DCYT ( 11-) B N3 <-> 18 DGUA ( 19-) C N1 0.12 2.88 INTRA 272 CYS ( 245-) A N <-> 277 ALA ( 250-) A O 0.12 2.58 INTRA 94 PHE ( 67-) A CD1 <-> 305 HOH (5218 ) A O 0.11 2.69 INTRA BF 76 ILE ( 49-) A CD1 <-> 123 MET ( 96-) A CE 0.11 3.09 INTRAAnd so on for a total of 54 lines.
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.
102 MET ( 75-) A -6.70 274 ARG ( 247-) A -6.56 297 GLN ( 270-) A -6.47
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.
247 ARG ( 220-) A -2.91 100 LEU ( 73-) A -2.89 136 ARG ( 109-) A -2.73 298 LYS ( 271-) A -2.65 103 GLU ( 76-) A -2.52
The table below lists the first and last residue in each stretch found, as well as the average residue Z-score of the series.
99 HIS ( 72-) A - 103 GLU ( 76-) A -1.90
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.
305 HOH (5278 ) A O 23.49 71.73 7.29
305 HOH (5242 ) A O 305 HOH (5318 ) A O 305 HOH (5323 ) A O 305 HOH (5325 ) A O
280 GLN ( 253-) 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.
28 PRO ( 1-) A N 45 VAL ( 18-) A N 95 ARG ( 68-) A NH1 127 ASP ( 100-) A N 138 PHE ( 111-) A N 198 ASN ( 171-) A ND2 246 ILE ( 219-) A N 247 ARG ( 220-) A N 266 GLY ( 239-) A N 287 ARG ( 260-) A NH2
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.
305 HOH (5015 ) A O 0.98 K 4 305 HOH (5046 ) A O 1.06 K 4 305 HOH (5155 ) A O 0.86 NA 4 *2 ION-B 305 HOH (5199 ) A O 0.97 K 5 Ion-B 305 HOH (5270 ) A O 1.03 K 5
29 GLU ( 2-) A H-bonding suggests Gln 32 GLU ( 5-) A H-bonding suggests Gln 39 GLU ( 12-) A H-bonding suggests Gln; but Alt-Rotamer
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 : -0.485 2nd generation packing quality : -1.441 Ramachandran plot appearance : 0.031 chi-1/chi-2 rotamer normality : -0.347 Backbone conformation : -0.281
Bond lengths : 0.983 Bond angles : 1.110 Omega angle restraints : 1.088 Side chain planarity : 0.904 Improper dihedral distribution : 0.943 B-factor distribution : 0.504 Inside/Outside distribution : 1.003
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 : 1.95
Structure Z-scores, positive is better than average:
1st generation packing quality : 0.1 2nd generation packing quality : -1.4 Ramachandran plot appearance : 0.1 chi-1/chi-2 rotamer normality : 0.1 Backbone conformation : -1.1
Bond lengths : 0.983 Bond angles : 1.110 Omega angle restraints : 1.088 Side chain planarity : 0.904 Improper dihedral distribution : 0.943 B-factor distribution : 0.504 Inside/Outside distribution : 1.003 ==============
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.