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: 39660.070
Volume of the Unit Cell V= 1202772.6
Space group multiplicity: 8
No NCS symmetry matrices (MTRIX records) found in PDB file
Matthews coefficient for observed atoms and Z high: Vm= 7.582
Vm by authors and this calculated Vm do not agree very well
Matthews coefficient read from REMARK 280 Vm= 3.780 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= 3.791
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 GOL (1002-) A - 303 GOL (1003-) A - 304 GOL (1004-) A -
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'.
248 ARG ( 220-) A CB 248 ARG ( 220-) A CG 248 ARG ( 220-) A CD 248 ARG ( 220-) A NE 248 ARG ( 220-) A CZ 248 ARG ( 220-) A NH1 248 ARG ( 220-) A NH2 249 THR ( 221-) A CB 249 THR ( 221-) A OG1 249 THR ( 221-) A CG2 250 TYR ( 222-) A CB 250 TYR ( 222-) A CG 250 TYR ( 222-) A CD1 250 TYR ( 222-) A CD2 250 TYR ( 222-) A CE1 250 TYR ( 222-) A CE2 250 TYR ( 222-) A CZ 250 TYR ( 222-) A OH 251 SER ( 223-) A CB 251 SER ( 223-) A OG
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.
93 ASP ( 65-) A 0.50 94 ASP ( 66-) A 0.50 234 GLU ( 206-) A 0.50 247 ILE ( 219-) A 0.50 248 ARG ( 220-) A 0.50 249 THR ( 221-) A 0.50 250 TYR ( 222-) A 0.50 251 SER ( 223-) A 0.50
Obviously, the temperature at which the X-ray data was collected has some importance too:
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: Tyrosine convention problem
The tyrosine residues listed in the table below have their chi-2 not between
-90.0 and 90.0
57 TYR ( 29-) A 86 TYR ( 58-) A 153 TYR ( 125-) A 201 TYR ( 173-) A
89 PHE ( 61-) A 168 PHE ( 140-) A 173 PHE ( 145-) A 292 PHE ( 264-) A
135 ASP ( 107-) A
33 GLU ( 5-) A 35 GLU ( 7-) A 66 GLU ( 38-) A 166 GLU ( 138-) A 216 GLU ( 188-) A 279 GLU ( 251-) A
RMS Z-score for bond lengths: 0.300
RMS-deviation in bond distances: 0.006
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.
15 DGUA ( 15-) E N9 C8 N7 113.13 4.1 17 DGUA ( 17-) E N9 C8 N7 113.15 4.1 19 DGUA ( 19-) E N9 C8 N7 113.12 4.0 27 DGUA ( 27-) E N9 C8 N7 113.10 4.0
RMS Z-score for bond angles: 0.630
RMS-deviation in bond angles: 1.270
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.
33 GLU ( 5-) A 35 GLU ( 7-) A 66 GLU ( 38-) A 135 ASP ( 107-) A 166 GLU ( 138-) A 216 GLU ( 188-) A 279 GLU ( 251-) A
44 ARG ( 16-) A 6.47 72 LEU ( 44-) A 4.69 45 ILE ( 17-) A 4.44 184 ILE ( 156-) A 4.21
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.
168 PHE ( 140-) A -2.3 104 GLU ( 76-) A -2.2 258 LYS ( 230-) A -2.2 194 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.
102 ARG ( 74-) A Poor phi/psi 138 LYS ( 110-) A Poor phi/psi 158 LYS ( 130-) A Poor phi/psi 191 GLN ( 163-) A Poor phi/psi 249 THR ( 221-) A Poor phi/psi 250 TYR ( 222-) A Poor phi/psi 270 GLY ( 242-) A Poor phi/psi chi-1/chi-2 correlation Z-score : -0.128
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-) D 0 4 DTHY ( 4-) D 0 5 DTHY ( 5-) D 0 6 DTHY ( 6-) D 0 7 3DR ( 7-) D 0 8 DTHY ( 8-) D 0 9 DTHY ( 9-) D 0 10 DTHY ( 10-) D 0 11 DCYT ( 11-) D 0 12 DTHY ( 12-) D 0 13 DCYT ( 13-) D 0 14 DGUA ( 14-) D 0 15 DGUA ( 15-) E 0 16 DCYT ( 16-) E 0 17 DGUA ( 17-) E 0 18 DADE ( 18-) E 0 19 DGUA ( 19-) E 0 20 DADE ( 20-) E 0 21 DADE ( 21-) E 0 22 DADE ( 22-) E 0 23 DCYT ( 23-) E 0 24 DADE ( 24-) E 0 25 DADE ( 25-) E 0 26 DADE ( 26-) E 0 27 DGUA ( 27-) E 0And so on for a total of 126 lines.
Standard deviation of omega values : 1.391
Error: Abnormally short interatomic distances
The pairs of atoms listed in the table below have an unusually short
interactomic distance; each bump is listed in only one direction.
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.
116 ARG ( 88-) A NH1 <-> 307 HOH (1125 ) A O 0.24 2.46 INTRA BF 5 DTHY ( 5-) D N3 <-> 25 DADE ( 25-) E N1 0.17 2.83 INTRA 258 LYS ( 230-) A NZ <-> 261 ASN ( 233-) A ND2 0.17 2.68 INTRA BF 2 DTHY ( 2-) D N3 <-> 28 DADE ( 28-) E N1 0.17 2.83 INTRA 6 DTHY ( 6-) D N3 <-> 24 DADE ( 24-) E N1 0.17 2.83 INTRA BL 183 LYS ( 155-) A NZ <-> 307 HOH (1200 ) A O 0.17 2.53 INTRA 215 LYS ( 187-) A NZ <-> 307 HOH (1090 ) A O 0.15 2.55 INTRA 116 ARG ( 88-) A NH1 <-> 120 ASP ( 92-) A CB 0.15 2.95 INTRA 69 LYS ( 41-) A NZ <-> 307 HOH (1023 ) A O 0.14 2.56 INTRA 284 LYS ( 256-) A NZ <-> 307 HOH (1082 ) A O 0.12 2.58 INTRA 1 DCYT ( 1-) D C2' <-> 2 DTHY ( 2-) D C7 0.11 3.09 INTRA BF 151 LEU ( 123-) A N <-> 152 PRO ( 124-) A CD 0.11 2.89 INTRA BL 10 DTHY ( 10-) D N3 <-> 20 DADE ( 20-) E N1 0.11 2.89 INTRA BL 119 HIS ( 91-) A N <-> 307 HOH (1129 ) A O 0.10 2.60 INTRA 56 THR ( 28-) A N <-> 57 TYR ( 29-) A N 0.09 2.51 INTRA BL 176 LYS ( 148-) A NZ <-> 307 HOH (1037 ) A O 0.09 2.61 INTRA 100 HIS ( 72-) A ND1 <-> 102 ARG ( 74-) A N 0.09 2.91 INTRA BL 24 DADE ( 24-) E N7 <-> 306 HOH ( 267 ) E O 0.09 2.61 INTRA 4 DTHY ( 4-) D N3 <-> 26 DADE ( 26-) E N1 0.09 2.91 INTRA 8 DTHY ( 8-) D N3 <-> 22 DADE ( 22-) E N1 0.08 2.92 INTRA BL 8 DTHY ( 8-) D OP1 <-> 85 LYS ( 57-) A NZ 0.08 2.62 INTRA BL 25 DADE ( 25-) E N7 <-> 306 HOH ( 110 ) E O 0.07 2.63 INTRA BF 202 VAL ( 174-) A CG1 <-> 203 ASP ( 175-) A N 0.07 2.93 INTRA BL 12 DTHY ( 12-) D N3 <-> 18 DADE ( 18-) E N1 0.07 2.93 INTRA 9 DTHY ( 9-) D N3 <-> 21 DADE ( 21-) E N1 0.07 2.93 INTRA BL 14 DGUA ( 14-) D N1 <-> 16 DCYT ( 16-) E N3 0.05 2.95 INTRA 11 DCYT ( 11-) D C2' <-> 12 DTHY ( 12-) D C7 0.05 3.15 INTRA BF 182 LYS ( 154-) A NZ <-> 190 GLU ( 162-) A OE2 0.05 2.65 INTRA 160 GLY ( 132-) A N <-> 191 GLN ( 163-) A O 0.04 2.66 INTRA BL 250 TYR ( 222-) A O <-> 252 ALA ( 224-) A N 0.04 2.66 INTRA BF 143 GLU ( 115-) A OE1 <-> 304 GOL (1004-) A A O3 0.04 2.36 INTRA 121 HIS ( 93-) A NE2 <-> 135 ASP ( 107-) A O 0.04 2.66 INTRA BL 104 GLU ( 76-) A N <-> 307 HOH (1006 ) A O 0.03 2.67 INTRA BL 20 DADE ( 20-) E N7 <-> 306 HOH ( 220 ) E O 0.03 2.67 INTRA BF 212 HIS ( 184-) A ND1 <-> 214 GLU ( 186-) A N 0.02 2.98 INTRA BL 30 GLU ( 2-) A CD <-> 198 GLY ( 170-) A CA 0.02 3.18 INTRA BL 181 THR ( 153-) A N <-> 182 LYS ( 154-) A N 0.02 2.58 INTRA B3 246 SER ( 218-) A C <-> 248 ARG ( 220-) A N 0.01 2.89 INTRA BF 69 LYS ( 41-) A NZ <-> 307 HOH (1097 ) A O 0.01 2.69 INTRA BF
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.
103 MET ( 75-) A -6.72 275 ARG ( 247-) A -6.64 298 GLN ( 270-) A -5.85 219 GLN ( 191-) A -5.49
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.
250 TYR ( 222-) A -3.07 248 ARG ( 220-) A -3.04 101 LEU ( 73-) A -2.84 286 ALA ( 258-) A -2.81 137 ARG ( 109-) A -2.65
The table below lists the first and last residue in each stretch found, as well as the average residue Z-score of the series.
100 HIS ( 72-) A - 103 MET ( 75-) A -1.83
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.
307 HOH (1220 ) A O 81.22 83.64 69.38
307 HOH (1212 ) A O ERROR. Strange cone in HB2INI Affected atom 7 3DR ( 7-) D P Expected ambiguity-2 in FILL1HARR 0 24 455
48 GLN ( 20-) A 261 ASN ( 233-) 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.
102 ARG ( 74-) A NE 128 ASP ( 100-) A N 139 PHE ( 111-) A N 194 VAL ( 166-) A N 260 GLN ( 232-) A N 267 GLY ( 239-) A N 288 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.
307 HOH (1054 ) A O 0.99 K 4
30 GLU ( 2-) A H-bonding suggests Gln 33 GLU ( 5-) A H-bonding suggests Gln 128 ASP ( 100-) A H-bonding suggests Asn; Ligand-contact
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 : 0.029 2nd generation packing quality : -1.023 Ramachandran plot appearance : -0.260 chi-1/chi-2 rotamer normality : -0.128 Backbone conformation : -0.518
Bond lengths : 0.300 (tight) Bond angles : 0.630 (tight) Omega angle restraints : 0.253 (tight) Side chain planarity : 0.236 (tight) Improper dihedral distribution : 0.575 B-factor distribution : 0.458 Inside/Outside distribution : 1.010
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 : 0.5 2nd generation packing quality : -0.9 Ramachandran plot appearance : 0.1 chi-1/chi-2 rotamer normality : 0.4 Backbone conformation : -0.9
Bond lengths : 0.300 (tight) Bond angles : 0.630 (tight) Omega angle restraints : 0.253 (tight) Side chain planarity : 0.236 (tight) Improper dihedral distribution : 0.575 B-factor distribution : 0.458 Inside/Outside distribution : 1.010 ==============
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.