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: 69824.266
Volume of the Unit Cell V= 2636605.0
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= 4.196
Vm by authors and this calculated Vm agree well
Matthews coefficient read from REMARK 280 Vm= 4.250
Warning: Topology could not be determined for some ligands
Some ligands in the table below are too complicated for the automatic
topology determination. WHAT IF uses a local copy of Daan van Aalten's
Dundee PRODRG server to automatically generate topology information
for ligands. Some molecules are too complicated for this software. If that
happens, WHAT IF / WHAT-CHECK continue with a simplified topology that
lacks certain information. Ligands with a simplified topology can, for
example, not form hydrogen bonds, and that reduces the accuracy of all
hydrogen bond related checking facilities.
The reason for topology generation failure is indicated. 'Atom types' indicates that the ligand contains atom types not known to PRODRUG. 'Attached' means that the ligand is covalently attached to a macromolecule. 'Size' indicates that the ligand has either too many atoms (or two or less which PRODRUG also cannot cope with), or too many bonds, angles, or torsion angles. 'Fragmented' is written when the ligand is not one fully covalently connected molecule but consists of multiple fragments. 'N/O only' is given when the ligand contains only N and/or O atoms. 'OK' indicates that the automatic topology generation succeeded.
602 BMA (1619-) A - OK 603 MAN (1620-) A - OK 604 SLC (1626-) A - Atom types 605 BMA (1624-) A - OK 606 MAN (1623-) A - OK
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.
597 NAG (1617-) A - O4 bound to 598 NAG (1618-) A - C1 598 NAG (1618-) A - O4 bound to 602 BMA (1619-) A - C1
1 VAL ( 19-) A CG1 1 VAL ( 19-) A CG2 2 LYS ( 20-) A CG 2 LYS ( 20-) A CD 2 LYS ( 20-) A CE 2 LYS ( 20-) A NZ 6 GLN ( 24-) A CG 6 GLN ( 24-) A CD 6 GLN ( 24-) A OE1 6 GLN ( 24-) A NE2 470 LYS ( 488-) A CD 470 LYS ( 488-) A CE 470 LYS ( 488-) A NZ
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.
50 GLU ( 68-) A 0.50 57 GLU ( 75-) A 0.50 92 GLU ( 110-) A 0.50 133 GLU ( 151-) A 0.50 193 ASP ( 211-) A 0.50 211 GLN ( 229-) A 0.50 261 GLU ( 279-) A 0.50 599 NAG (1621-) A 0.40 600 NAG (1622-) A 0.50
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
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.
597 NAG (1617-) A C1 O5 1.24 -4.6
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
| 0.997260 -0.000067 -0.000238| | -0.000067 0.998380 -0.000053| | -0.000238 -0.000053 0.995671|Proposed new scale matrix
| 0.005770 0.003328 0.000002| | 0.000000 0.006655 0.000000| | 0.000002 0.000000 0.009964|With corresponding cell
A = 173.311 B = 173.470 C = 100.360 Alpha= 89.987 Beta= 90.029 Gamma= 119.974
The CRYST1 cell dimensions
A = 173.797 B = 173.797 C = 100.795 Alpha= 90.000 Beta= 90.000 Gamma= 120.000
(Under-)estimated Z-score: 9.951
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.
129 PRO ( 147-) A -2.9 369 THR ( 387-) A -2.8 316 LEU ( 334-) A -2.6 360 TYR ( 378-) A -2.2 544 LYS ( 562-) A -2.1 461 ILE ( 479-) A -2.1 267 VAL ( 285-) 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.
66 GLN ( 84-) A Poor phi/psi, omega poor 128 ASP ( 146-) A PRO omega poor 137 LYS ( 155-) A Poor phi/psi 178 ASN ( 196-) A Poor phi/psi, omega poor 237 PRO ( 255-) A omega poor 246 ALA ( 264-) A Poor phi/psi 293 ASN ( 311-) A Poor phi/psi 294 LEU ( 312-) A omega poor 303 ASP ( 321-) A omega poor 311 THR ( 329-) A omega poor 326 TYR ( 344-) A Poor phi/psi 327 LEU ( 345-) A Poor phi/psi 329 ASP ( 347-) A Poor phi/psi 336 CYS ( 354-) A omega poor 371 ALA ( 389-) A omega poor 378 ALA ( 396-) A omega poor 401 ASP ( 419-) A Poor phi/psi 419 ASP ( 437-) A omega poor 446 ASN ( 464-) A omega poor 472 PHE ( 490-) A omega poor 483 ASP ( 501-) A Poor phi/psi 592 ASN ( 610-) A omega poor chi-1/chi-2 correlation Z-score : -2.130
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.
481 SER ( 499-) A 0.38 161 SER ( 179-) A 0.39
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!
34 SER ( 52-) A 0 35 ASN ( 53-) A 0 66 GLN ( 84-) A 0 67 TRP ( 85-) A 0 70 TYR ( 88-) A 0 71 GLN ( 89-) A 0 84 LYS ( 102-) A 0 87 TYR ( 105-) A 0 122 LYS ( 140-) A 0 123 CYS ( 141-) A 0 124 ASP ( 142-) A 0 136 SER ( 154-) A 0 137 LYS ( 155-) A 0 138 SER ( 156-) A 0 139 ARG ( 157-) A 0 141 HIS ( 159-) A 0 157 THR ( 175-) A 0 224 HIS ( 242-) A 0 225 TYR ( 243-) A 0 229 VAL ( 247-) A 0 233 THR ( 251-) A 0 238 MET ( 256-) A 0 243 ASN ( 261-) A 0 245 TRP ( 263-) A 0 247 GLN ( 265-) A 0And so on for a total of 168 lines.
129 PRO ( 147-) A -34.8 envelop C-alpha (-36 degrees) 258 PRO ( 276-) A 100.6 envelop C-beta (108 degrees) 278 PRO ( 296-) A 109.3 envelop C-beta (108 degrees) 364 PRO ( 382-) A 107.9 envelop C-beta (108 degrees) 425 PRO ( 443-) A -115.4 envelop C-gamma (-108 degrees) 518 PRO ( 536-) A -42.3 envelop C-alpha (-36 degrees) 547 PRO ( 565-) A 104.4 envelop C-beta (108 degrees) 570 PRO ( 588-) A -123.6 half-chair C-delta/C-gamma (-126 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.
602 BMA (1619-) A O3 <-> 606 MAN (1623-) A C1 0.95 1.45 INTRA BF 602 BMA (1619-) A C3 <-> 606 MAN (1623-) A C1 0.83 2.37 INTRA BF 601 ZN (1001-) A ZN <-> 604 SLC (1626-) A SE 0.47 2.73 INTRA BF 601 ZN (1001-) A ZN <-> 604 SLC (1626-) A C1 0.44 2.76 INTRA BF 455 ARG ( 473-) A NH1 <-> 607 HOH (2147 ) A O 0.33 2.37 INTRA BL 431 ASP ( 449-) A OD1 <-> 434 ARG ( 452-) A NH2 0.29 2.41 INTRA BL 139 ARG ( 157-) A NH2 <-> 254 ASP ( 272-) A OD1 0.24 2.46 INTRA BF 467 ARG ( 485-) A NH2 <-> 473 ASP ( 491-) A OD1 0.23 2.47 INTRA BL 319 HIS ( 337-) A NE2 <-> 604 SLC (1626-) A O1 0.23 2.47 INTRA BF 293 ASN ( 311-) A ND2 <-> 599 NAG (1621-) A C2 0.22 1.98 INTRA BF 474 ALA ( 492-) A N <-> 475 PRO ( 493-) A CD 0.16 2.84 INTRA BL 431 ASP ( 449-) A O <-> 435 TRP ( 453-) A N 0.15 2.55 INTRA BL 598 NAG (1618-) A N2 <-> 607 HOH (2199 ) A O 0.14 2.56 INTRA BF 200 GLU ( 218-) A OE2 <-> 432 LYS ( 450-) A NZ 0.14 2.56 INTRA BL 319 HIS ( 337-) A ND1 <-> 607 HOH (2120 ) A O 0.14 2.56 INTRA BL 207 ARG ( 225-) A N <-> 208 PRO ( 226-) A CD 0.14 2.86 INTRA BL 492 SER ( 510-) A O <-> 496 GLN ( 514-) A N 0.13 2.57 INTRA BL 349 HIS ( 367-) A NE2 <-> 604 SLC (1626-) A C1 0.13 2.97 INTRA BF 207 ARG ( 225-) A NE <-> 607 HOH (2085 ) A O 0.12 2.58 INTRA BL 431 ASP ( 449-) A OD2 <-> 487 LEU ( 505-) A N 0.12 2.58 INTRA BL 455 ARG ( 473-) A CZ <-> 607 HOH (2147 ) A O 0.11 2.69 INTRA BL 353 HIS ( 371-) A ND1 <-> 376 HIS ( 394-) A ND1 0.11 2.89 INTRA BL 546 TRP ( 564-) A CG <-> 547 PRO ( 565-) A CD 0.10 3.10 INTRA BL 546 TRP ( 564-) A N <-> 547 PRO ( 565-) A CD 0.10 2.90 INTRA BL 467 ARG ( 485-) A N <-> 593 LYS ( 611-) A O 0.09 2.61 INTRA BLAnd so on for a total of 60 lines.
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.
224 HIS ( 242-) A -5.90 404 ARG ( 422-) A -5.29 296 LYS ( 314-) A -5.24 554 ASN ( 572-) A -5.16 117 TYR ( 135-) A -5.13 586 ILE ( 604-) A -5.12 261 GLU ( 279-) A -5.10
The table below lists the first and last residue in each stretch found, as well as the average residue score of the series.
457 GLU ( 475-) A 459 - SER 477- ( A) -4.17
482 ALA ( 500-) A -3.10 1 VAL ( 19-) A -3.08
607 HOH (2022 ) A O 607 HOH (2097 ) A O 607 HOH (2200 ) A O 607 HOH (2201 ) A O Bound group on Asn; dont flip 35 ASN ( 53-) A Bound to: 600 NAG (1622-) A Bound group on Asn; dont flip 178 ASN ( 196-) A Bound to: 597 NAG (1617-) A Bound group on Asn; dont flip 293 ASN ( 311-) A Bound to: 599 NAG (1621-) A Metal-coordinating Histidine residue 349 fixed to 1 Metal-coordinating Histidine residue 353 fixed to 1
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.
37 THR ( 55-) A N 122 LYS ( 140-) A N 243 ASN ( 261-) A N 248 GLN ( 266-) A N 277 THR ( 295-) A N 319 HIS ( 337-) A NE2 328 THR ( 346-) A N 372 ASN ( 390-) A N 384 SER ( 402-) A OG 397 GLY ( 415-) A N 404 ARG ( 422-) A NH1 442 VAL ( 460-) A N 448 ASN ( 466-) A ND2 455 ARG ( 473-) A NH1 465 VAL ( 483-) A N 483 ASP ( 501-) A N 486 TYR ( 504-) A OH 587 GLY ( 605-) A N Only metal coordination for 349 HIS ( 367-) A NE2 Only metal coordination for 377 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.
214 HIS ( 232-) A ND1 335 GLN ( 353-) A OE1 350 GLU ( 368-) A OE1 350 GLU ( 368-) A OE2 412 GLN ( 430-) A OE1 579 ASN ( 597-) A OD1
4 GLU ( 22-) A H-bonding suggests Gln; but Alt-Rotamer 100 ASP ( 118-) A H-bonding suggests Asn 184 GLU ( 202-) A H-bonding suggests Gln 205 ASP ( 223-) A H-bonding suggests Asn 350 GLU ( 368-) A H-bonding suggests Gln; but Alt-Rotamer; Ligand-contact 469 GLU ( 487-) A H-bonding suggests Gln
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 : -0.255 2nd generation packing quality : -1.193 Ramachandran plot appearance : -1.584 chi-1/chi-2 rotamer normality : -2.130 Backbone conformation : -0.125
Bond lengths : 0.455 (tight) Bond angles : 0.425 (tight) Omega angle restraints : 1.062 Side chain planarity : 0.354 (tight) Improper dihedral distribution : 0.504 B-factor distribution : 0.396 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 : 2.35
Structure Z-scores, positive is better than average:
1st generation packing quality : 0.8 2nd generation packing quality : -0.0 Ramachandran plot appearance : -0.0 chi-1/chi-2 rotamer normality : -1.1 Backbone conformation : -0.2
Bond lengths : 0.455 (tight) Bond angles : 0.425 (tight) Omega angle restraints : 1.062 Side chain planarity : 0.354 (tight) Improper dihedral distribution : 0.504 B-factor distribution : 0.396 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.