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.
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.
Very high numbers are most often caused by giving the wrong value for Z on the CRYST1 card (or not giving this number at all), but can also result from large fractions missing out of the molecular weight (e.g. a lot of UNK residues, or DNA/RNA missing from virus structures).
Molecular weight of all polymer chains: 70356.023
Volume of the Unit Cell V= 2638629.5
Space group multiplicity: 9
No NCS symmetry matrices (MTRIX records) found in PDB file
Matthews coefficient for observed atoms and Z a bit high: Vm= 4.167
Vm by authors and this calculated Vm agree remarkably well
Matthews coefficient read from REMARK 280 Vm= 4.200
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.
608 MAN (1618-) A - 609 BMA (1619-) A - 610 FLC (1624-) A - 611 BMA (1620-) A - 612 MAN (1621-) 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.
603 NAG (1616-) A - O4 bound to 604 NAG (1617-) A - C1 604 NAG (1617-) A - O4 bound to 609 BMA (1619-) A - C1
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: C-terminal nitrogen atoms detected.
It is becoming habit to indicate that a residue is not the true C-terminus
by including only the backbone N of the next residue. This has been
observed in this PDB file.
In X-ray the coordinates must be located in density. Mobility or disorder sometimes cause this density to be so poor that the positions of the atoms cannot be determined. Crystallographers tend to leave out the atoms in such cases. In many cases the N- or C-terminal residues are too disordered to see. In case of the N-terminus, you can see from the residue numbers if there are missing residues, but at the C-terminus this is impossible. Therefore, often the position of the backbone nitrogen of the first residue missing at the C-terminal end is calculated and added to indicate that there are missing residues. As a single N causes validation trouble, we remove these single-N-residues before doing the validation. But, if you get weird errors at, or near, the left-over incomplete C-terminal residue, please check by hand if a missing Oxt or removed N is the cause.
602 GLY ( 4-) P
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.
52 GLU ( 68-) A 0.50 59 GLU ( 75-) A 0.50 94 GLU ( 110-) A 0.50 135 GLU ( 151-) A 0.50 195 ASP ( 211-) A 0.50 213 GLN ( 229-) A 0.50 263 GLU ( 279-) A 0.50 604 NAG (1622-) A 0.40 605 NAG (1623-) A 0.70
Obviously, the temperature at which the X-ray data was collected has some importance too:
Number of TLS groups mentione in PDB file header: 1
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: Low bond length variability
Bond lengths were found to deviate less than normal from the mean Engh and
Huber [REF] and/or Parkinson et al [REF] standard bond lengths. The RMS
Z-score given below is expected to be near 1.0 for a normally restrained
data set. The fact that it is lower than 0.667 in this structure might
indicate that too-strong restraints have been used in the refinement. This
can only be a problem for high resolution X-ray structures.
RMS Z-score for bond lengths: 0.326
RMS-deviation in bond distances: 0.008
Warning: Possible cell scaling problem
Comparison of bond distances with Engh and Huber [REF] standard values for
protein residues and Parkinson et al [REF] values for DNA/RNA shows a
significant systematic deviation. It could be that the unit cell used in
refinement was not accurate enough. The deformation matrix given below gives
the deviations found: the three numbers on the diagonal represent the
relative corrections needed along the A, B and C cell axis. These values are
1.000 in a normal case, but have significant deviations here (significant at
the 99.99 percent confidence level)
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
| 0.996809 0.000164 -0.000018| | 0.000164 0.997438 -0.000092| | -0.000018 -0.000092 0.996998|Proposed new scale matrix
| 0.005789 0.003340 0.000000| | -0.000001 0.006680 0.000000| | 0.000000 0.000000 0.009886|With corresponding cell
A = 172.727 B = 172.806 C = 101.156 Alpha= 90.001 Beta= 90.001 Gamma= 119.971
The CRYST1 cell dimensions
A = 173.292 B = 173.292 C = 101.458 Alpha= 90.000 Beta= 90.000 Gamma= 120.000
(Under-)estimated Z-score: 9.735
Warning: Low bond angle variability
Bond angles were found to deviate less than normal from the standard bond
angles (normal values for protein residues were taken from Engh and Huber
[REF], for DNA/RNA from Parkinson et al [REF]). The RMS Z-score given below
is expected to be near 1.0 for a normally restrained data set. The fact that
it is lower than 0.667 in this structure might indicate that too-strong
restraints have been used in the refinement. This can only be a problem for
high resolution X-ray structures.
RMS Z-score for bond angles: 0.486
RMS-deviation in bond angles: 1.017
Warning: Torsion angle evaluation shows unusual residues
The residues listed in the table below contain bad or abnormal
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.
131 PRO ( 147-) A -2.7 371 THR ( 387-) A -2.6 318 LEU ( 334-) A -2.5 362 TYR ( 378-) A -2.1 463 ILE ( 479-) 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.
68 GLN ( 84-) A Poor phi/psi 130 ASP ( 146-) A PRO omega poor 180 ASN ( 196-) A Poor phi/psi 239 PRO ( 255-) A omega poor 295 ASN ( 311-) A Poor phi/psi 328 TYR ( 344-) A Poor phi/psi 329 LEU ( 345-) A Poor phi/psi 331 ASP ( 347-) A Poor phi/psi 370 ARG ( 386-) A Poor phi/psi 373 ALA ( 389-) A omega poor 474 PHE ( 490-) A omega poor chi-1/chi-2 correlation Z-score : 0.147
It is not necessarily an error if a few residues have rotamer values below 0.3, but careful inspection of all residues with these low values could be worth it.
438 SER ( 454-) A 0.36 483 SER ( 499-) A 0.36 504 SER ( 520-) A 0.36
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!
36 SER ( 52-) A 0 37 ASN ( 53-) A 0 68 GLN ( 84-) A 0 69 TRP ( 85-) A 0 72 TYR ( 88-) A 0 73 GLN ( 89-) A 0 89 TYR ( 105-) A 0 124 LYS ( 140-) A 0 125 CYS ( 141-) A 0 126 ASP ( 142-) A 0 141 ARG ( 157-) A 0 143 HIS ( 159-) A 0 180 ASN ( 196-) A 0 181 PHE ( 197-) A 0 226 HIS ( 242-) A 0 227 TYR ( 243-) A 0 231 VAL ( 247-) A 0 235 THR ( 251-) A 0 240 MET ( 256-) A 0 245 ASN ( 261-) A 0 247 TRP ( 263-) A 0 249 GLN ( 265-) A 0 250 GLN ( 266-) A 0 251 TRP ( 267-) A 0 261 PHE ( 277-) A 0And so on for a total of 170 lines.
131 PRO ( 147-) A -44.3 envelop C-alpha (-36 degrees) 265 PRO ( 281-) A -119.1 half-chair C-delta/C-gamma (-126 degrees) 366 PRO ( 382-) A -120.8 half-chair C-delta/C-gamma (-126 degrees) 427 PRO ( 443-) A -114.5 envelop C-gamma (-108 degrees) 601 PRO ( 3-) P -113.7 envelop C-gamma (-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.
The last text-item on each line represents the status of the atom pair. The text `INTRA' means that the bump is between atoms that are explicitly listed in the PDB file. `INTER' means it is an inter-symmetry bump. 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). If the last column is 'BF', the sum of the B-factors of the atoms is higher than 80, which makes the appearance of the bump somewhat less severe because the atoms probably are not there anyway. BL, on the other hand, indicates that the bumping atoms both have a low B-factor, and that makes the bumps more worrisome.
It seems likely that at least some of the reported bumps are caused by administrative errors in the chain names. I.e. covalently bound atoms with different non-blank chain-names are reported as bumps. In rare cases this is not an error.
Bumps between atoms for which the sum of their occupancies is lower than one are not reported. If the MODEL number does not exist (as is the case in most X-ray files), a minus sign is printed instead.
608 BMA (1619-) A O6 <-> 611 MAN (1621-) A C1 0.96 1.44 INTRA B3 607 MAN (1618-) A O6 <-> 610 BMA (1620-) A C1 0.96 1.44 INTRA B3 608 BMA (1619-) A C6 <-> 611 MAN (1621-) A C1 0.86 2.34 INTRA 607 MAN (1618-) A C6 <-> 610 BMA (1620-) A C1 0.84 2.36 INTRA 406 ARG ( 422-) A NH1 <-> 612 HOH (2447 ) A O 0.29 2.41 INTRA 355 HIS ( 371-) A ND1 <-> 378 HIS ( 394-) A ND1 0.22 2.78 INTRA BL 162 ARG ( 178-) A NH2 <-> 612 HOH (2210 ) A O 0.16 2.54 INTRA 309 ILE ( 325-) A O <-> 339 THR ( 355-) A CG2 0.15 2.65 INTRA 278 TYR ( 294-) A CE2 <-> 286 MET ( 302-) A SD 0.13 3.27 INTRA 141 ARG ( 157-) A NH2 <-> 256 ASP ( 272-) A OD1 0.12 2.58 INTRA 457 ARG ( 473-) A NH2 <-> 612 HOH (2326 ) A O 0.10 2.60 INTRA BL 361 GLN ( 377-) A NE2 <-> 537 HIS ( 553-) A CD2 0.10 3.00 INTRA 96 ASP ( 112-) A OD2 <-> 174 LYS ( 190-) A NZ 0.08 2.62 INTRA 548 TRP ( 564-) A N <-> 549 PRO ( 565-) A CD 0.07 2.93 INTRA BL 550 ASP ( 566-) A OD1 <-> 559 ARG ( 575-) A NH1 0.06 2.64 INTRA 462 GLY ( 478-) A CA <-> 590 TRP ( 606-) A CE2 0.04 3.16 INTRA BL 158 GLY ( 174-) A C <-> 474 PHE ( 490-) A O 0.04 2.76 INTRA BL 325 TRP ( 341-) A N <-> 334 ARG ( 350-) A O 0.03 2.67 INTRA BL 222 ARG ( 238-) A NH1 <-> 259 SER ( 275-) A O 0.03 2.67 INTRA 599 ARG ( 1-) P N <-> 609 FLC (1624-) A OA1 0.02 2.68 INTRA BL 202 GLU ( 218-) A OE2 <-> 434 LYS ( 450-) A NZ 0.02 2.68 INTRA BL 213 GLN ( 229-) A NE2 <-> 612 HOH (2286 ) A O 0.02 2.68 INTRA 469 ARG ( 485-) A NH2 <-> 475 ASP ( 491-) A OD1 0.02 2.68 INTRA BL 58 LYS ( 74-) A NZ <-> 92 LEU ( 108-) A O 0.02 2.68 INTRA 209 ARG ( 225-) A N <-> 210 PRO ( 226-) A CD 0.01 2.99 INTRA BL 320 CYS ( 336-) A O <-> 612 HOH (2375 ) A O 0.01 2.39 INTRA 220 ARG ( 236-) A NH2 <-> 589 GLY ( 605-) A O 0.01 2.69 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.
226 HIS ( 242-) A -5.87 119 TYR ( 135-) A -5.30 587 HIS ( 603-) A -5.21 556 ASN ( 572-) A -5.17 588 ILE ( 604-) A -5.12 263 GLU ( 279-) A -5.06
The table below lists the first and last residue in each stretch found, as well as the average residue score of the series.
459 GLU ( 475-) A 461 - SER 477- ( A) -4.26
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.
257 ILE ( 273-) A -2.63
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.
612 HOH (2271 ) A O 48.64 0.97 64.80
17 ASN ( 33-) A 25 ASN ( 41-) A 110 ASN ( 126-) A 213 GLN ( 229-) A 214 GLN ( 230-) A 343 GLN ( 359-) A 350 HIS ( 366-) A 357 GLN ( 373-) A 363 GLN ( 379-) A 364 HIS ( 380-) A 413 ASN ( 429-) A 450 ASN ( 466-) A 500 GLN ( 516-) A 511 GLN ( 527-) A 537 HIS ( 553-) A 587 HIS ( 603-) 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.
3 VAL ( 19-) A N 39 THR ( 55-) A OG1 143 HIS ( 159-) A N 150 TRP ( 166-) A NE1 224 ARG ( 240-) A NE 241 HIS ( 257-) A N 241 HIS ( 257-) A ND1 245 ASN ( 261-) A N 250 GLN ( 266-) A N 279 THR ( 295-) A N 324 ALA ( 340-) A N 330 THR ( 346-) A N 337 GLN ( 353-) A NE2 374 ASN ( 390-) A N 383 ASP ( 399-) A N 404 TYR ( 420-) A N 409 GLU ( 425-) A N 425 PHE ( 441-) A N 428 PHE ( 444-) A N 467 VAL ( 483-) A N 526 ILE ( 542-) A N 556 ASN ( 572-) A ND2 Only metal coordination for 351 HIS ( 367-) A NE2 Only metal coordination for 379 GLU ( 395-) A OE1
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.
337 GLN ( 353-) A OE1 352 GLU ( 368-) A OE1 581 ASN ( 597-) A OD1
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.
612 HOH (2246 ) A O 0.88 K 4 ION-B 612 HOH (2262 ) A O 0.93 K 5 612 HOH (2272 ) A O 1.04 K 4 612 HOH (2274 ) A O 1.02 K 4 612 HOH (2383 ) A O 0.88 K 5 612 HOH (2475 ) A O 0.89 K 4 612 HOH (2483 ) A O 0.95 K 6 612 HOH (2522 ) A O 1.05 K 4 Ion-B
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 : 0.052 2nd generation packing quality : -0.900 Ramachandran plot appearance : 0.482 chi-1/chi-2 rotamer normality : 0.147 Backbone conformation : -0.296
Bond lengths : 0.326 (tight) Bond angles : 0.486 (tight) Omega angle restraints : 0.811 Side chain planarity : 0.247 (tight) Improper dihedral distribution : 0.459 B-factor distribution : 0.324 Inside/Outside distribution : 1.000
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 : -0.8 Ramachandran plot appearance : 1.0 chi-1/chi-2 rotamer normality : 0.6 Backbone conformation : -0.6
Bond lengths : 0.326 (tight) Bond angles : 0.486 (tight) Omega angle restraints : 0.811 Side chain planarity : 0.247 (tight) Improper dihedral distribution : 0.459 B-factor distribution : 0.324 Inside/Outside distribution : 1.000 ==============
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.