WHAT IF Check report

This file was created 2011-12-13 from WHAT_CHECK output by a conversion script. If you are new to WHAT_CHECK, please study the pdbreport pages. There also exists a legend to the output.

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.

Verification log for pdb3cye.ent

Checks that need to be done early-on in validation

Note: Non crystallographic symmetry RMS plot

The plot shows the RMS differences between two similar chains on a residue- by-residue basis. Individual "spikes" can be indicative of interesting or wrong residues. If all residues show a high RMS value, the structure could be incorrectly refined.

Chain identifiers of the two chains: A and B

All-atom RMS fit for the two chains : 0.224
CA-only RMS fit for the two chains : 0.069

Note: Non crystallographic symmetry backbone difference plot

The plot shows the differences in backbone torsion angles between two similar chains on a residue-by-residue basis. Individual "spikes" can be indicative of interesting or wrong residues. If all residues show high differences, the structure could be incorrectly refined.

Chain identifiers of the two chains: A and B

Note: Non crystallographic symmetry backbone difference plot

The plot shows the differences in backbone torsion angles between two similar chains on a residue-by-residue basis. Individual "spikes" can be indicative of interesting or wrong residues. If all residues show high differences, the structure could be incorrectly refined.

Chain identifiers of the two chains: A and A

Note: Non crystallographic symmetry RMS plot

The plot shows the RMS differences between two similar chains on a residue- by-residue basis. Individual "spikes" can be indicative of interesting or wrong residues. If all residues show a high RMS value, the structure could be incorrectly refined.

Chain identifiers of the two chains: A and B

All-atom RMS fit for the two chains : 0.258
CA-only RMS fit for the two chains : 0.112

Note: Non crystallographic symmetry backbone difference plot

The plot shows the differences in backbone torsion angles between two similar chains on a residue-by-residue basis. Individual "spikes" can be indicative of interesting or wrong residues. If all residues show high differences, the structure could be incorrectly refined.

Chain identifiers of the two chains: A and B

Note: Non crystallographic symmetry RMS plot

The plot shows the RMS differences between two similar chains on a residue- by-residue basis. Individual "spikes" can be indicative of interesting or wrong residues. If all residues show a high RMS value, the structure could be incorrectly refined.

Chain identifiers of the two chains: B and A

All-atom RMS fit for the two chains : 0.267
CA-only RMS fit for the two chains : 0.115

Note: Non crystallographic symmetry backbone difference plot

The plot shows the differences in backbone torsion angles between two similar chains on a residue-by-residue basis. Individual "spikes" can be indicative of interesting or wrong residues. If all residues show high differences, the structure could be incorrectly refined.

Chain identifiers of the two chains: B and A

Note: Non crystallographic symmetry RMS plot

The plot shows the RMS differences between two similar chains on a residue- by-residue basis. Individual "spikes" can be indicative of interesting or wrong residues. If all residues show a high RMS value, the structure could be incorrectly refined.

Chain identifiers of the two chains: B and B

All-atom RMS fit for the two chains : 0.172
CA-only RMS fit for the two chains : 0.115

Note: Non crystallographic symmetry backbone difference plot

The plot shows the differences in backbone torsion angles between two similar chains on a residue-by-residue basis. Individual "spikes" can be indicative of interesting or wrong residues. If all residues show high differences, the structure could be incorrectly refined.

Chain identifiers of the two chains: B and B

Warning: Problem detected upon counting molecules and matrices

The parameter Z as given on the CRYST card represents the molecular multiplicity in the crystallographic cell. Normally, Z equals the number of matrices of the space group multiplied by the number of NCS relations. The value of Z is multiplied by the integrated molecular weight of the molecules in the file to determine the Matthews coefficient. This relation is being validated in this option. Be aware that the validation can get confused if both multiple copies of the molecule are present in the ATOM records and MTRIX records are present in the header of the PDB file.

Space group as read from CRYST card: C 2 2 21
Number of matrices in space group: 8
Highest polymer chain multiplicity in structure: 4
Highest polymer chain multiplicity according to SEQRES: 2
No explicit MTRIX NCS matrices found in the input file
Value of Z as found on the CRYST1 card: 16
Polymer chain multiplicity and SEQRES multiplicity disagree 4 2
Z and NCS seem to support the SEQRES multiplicity (so the matrix counting
problems seem not overly severe)

Error: Matthews Coefficient (Vm) too low

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.

The fact that it is lower than 1.5 in this structure might be caused by a miscalculated value of Z on the CRYST1 card.

Molecular weight of all polymer chains: 170281.953
Volume of the Unit Cell V= 1921226.0
Space group multiplicity: 8
No NCS symmetry matrices (MTRIX records) found in PDB file
Matthews coefficient for observed atoms and Z a bit low: Vm= 1.410
Vm by authors and this calculated Vm do not agree very well
Matthews coefficient read from REMARK 280 Vm= 2.830 Could it be that Z must be: 8
This number is the multiplication of the spacegroup and NCS symmetry count
Matthews coefficient for observed atoms and corrected Z: Vm= 2.821

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.

1554 ACT   (3000-)  A  1
1555 ACT   (3002-)  A  1
1556 ACT   (3003-)  A  1
1561 MAN   (2003-)  B  1
1562 MAN   (2004-)  B  1
1567 ACT   (3001-)  B  1
1568 ACT   (3004-)  B  1
1579 ACT   (3000-)  A  2
1580 ACT   (3001-)  B  2
1581 ACT   (3002-)  A  2
1582 ACT   (3003-)  A  2
1584 MAN   (2003-)  B  2
1591 ACT   (3004-)  B  1
1592 MAN   (2004-)  B  1

Administrative problems that can generate validation failures

Warning: Alternate atom problems encountered

The residues listed in the table below have alternate atoms. One of two problems might have been encountered: 1) The software did not properly deal with the alternate atoms; 2) The alternate atom indicators are too wrong to sort out.

Alternate atom indicators in PDB files are known to often be erroneous. It has been observed that alternate atom indicators are missing, or that there are too many of them. It is common to see that the distance between two atoms that should be covalently bound is far too big, but the distance between the alternate A of one of them and alternate B of the other is proper for a covalent bond. We have discovered many, many ways in which alternate atoms can be abused. The software tries to deal with most cases, but we know for sure that it cannot deal with all cases. If an alternate atom indicator problem is not properly solved, subsequent checks will list errors that are based on wrong coordinate combinations. So, any problem listed in this table should be solved before error messages further down in this report can be trusted.

  86 SER   ( 168-)  A  1
 258 SER   ( 343-)  A  1
 471 SER   ( 168-)  B  1
 859 SER   ( 168-)  A  2
1031 SER   ( 343-)  A  2
1244 SER   ( 168-)  B  2

Warning: Alternate atom problems quasi solved

The residues listed in the table below have alternate atoms that WHAT IF decided to correct (e.g. take alternate atom B instead of A for one or more of the atoms). Residues for which the use of alternate atoms is non-standard, but WHAT IF left it that way because he liked the non-standard situation better than other solutions, are listed too in this table.

In case any of these residues shows up as poor or bad in checks further down this report, please check the consistency of the alternate atoms in this residue first, correct it yourself if needed, and run the validation again.

 258 SER   ( 343-)  A  1

Warning: Groups attached to potentially hydrogenbonding atoms

Residues were observed with groups attached to (or very near to) atoms that potentially can form hydrogen bonds. WHAT IF is not very good at dealing with such exceptional cases (Mainly because it's author is not...). So be warned that the hydrogenbonding-related analyses of these residues might be in error.

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.

 772 NAG   (2001-)  B  1 A O4  bound to  773 NAG   (2002-)  B  1 A C1
 773 NAG   (2002-)  B  1 A O4  bound to 1561 MAN   (2003-)  B  1 A C1
1545 NAG   (2001-)  B  2 B O4  bound to 1546 NAG   (2002-)  B  2 B C1
1546 NAG   (2002-)  B  2 B O4  bound to 1584 MAN   (2003-)  B  2 B C1

Non-validating, descriptive output paragraph

Note: Ramachandran plot

In this Ramachandran plot x-signs represent glycines, squares represent prolines, and plus-signs represent the other residues. If too many plus- signs fall outside the contoured areas then the molecule is poorly refined (or worse). Proline can only occur in the narrow region around phi=-60 that also falls within the other contour islands.

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; Model number 1

Note: Ramachandran plot

Chain identifier: B; Model number 1

Note: Ramachandran plot

Chain identifier: A; Model number 2

Note: Ramachandran plot

Chain identifier: B; Model number 2

Coordinate problems, unexpected atoms, B-factor and occupancy checks

Warning: Very strange distribution of occupancy values

The distribution of the occupancy values in this file differs very much from distributions commonly observed in well-refined PDB files. This does not need to mean anything, but please look at it. This file should not be used in training sets that need to hold 'good' PDB files.

Be aware that this evaluation is merely the result of comparing this file with about 500 well-refined high-resolution files in the PDB. If this file has much higher or much lower resolution than the PDB files used in WHAT IF's training set, non-normal values might very well be perfectly fine, or normal values might actually be not so normal...

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.

   1 VAL   (  83-)  A    0.77
   2 ILE   (  84-)  A    0.77
   3 LEU   (  85-)  A    0.77
   4 THR   (  86-)  A    0.77
   5 GLY   (  87-)  A    0.77
   6 ASN   (  88-)  A    0.77
   7 SER   (  89-)  A    0.77
   8 SER   (  90-)  A    0.77
   9 LEU   (  91-)  A    0.77
  10 CYS   (  92-)  A    0.77
  11 PRO   (  93-)  A    0.77
  12 ILE   (  94-)  A    0.77
  13 SER   (  95-)  A    0.77
  14 GLY   (  96-)  A    0.77
  15 TRP   (  97-)  A    0.77
  16 ALA   (  98-)  A    0.77
  17 ILE   (  99-)  A    0.77
  18 TYR   ( 100-)  A    0.77
  19 SER   ( 101-)  A    0.77
  20 LYS   ( 102-)  A    0.77
  21 ASP   ( 103-)  A    0.77
  22 ASN   ( 104-)  A    0.77
  23 GLY   ( 105-)  A    0.77
  24 ILE   ( 106-)  A    0.77
  25 ARG   ( 107-)  A    0.77
And so on for a total of 1546 lines.

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

 944 TYR   ( 252-)  A
 973 TYR   ( 281-)  A
1358 TYR   ( 281-)  B

Warning: Phenylalanine convention problem

The phenylalanine residues listed in the table below have their chi-2 not between -90.0 and 90.0.

 824 PHE   ( 133-)  A
 930 PHE   ( 238-)  A
 997 PHE   ( 305-)  A
1209 PHE   ( 133-)  B
1382 PHE   ( 305-)  B

Geometric checks

Note: Per-model averages for bond-length check

The table below gives the per-model bond-length RMS Z-scores.

Model 1 : 0.660
Model 2 : 0.394

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

 |  0.997212  0.000192  0.000074|
 |  0.000192  0.997604  0.000165|
 |  0.000074  0.000165  0.996832|
Proposed new scale matrix

 |  0.008518 -0.000002  0.000000|
 | -0.000001  0.007239 -0.000001|
 |  0.000000 -0.000001  0.008512|
With corresponding cell

    A    = 117.402  B   = 138.134  C    = 117.482
    Alpha=  89.981  Beta=  90.001  Gamma=  89.978

The CRYST1 cell dimensions

    A    = 117.728  B   = 138.472  C    = 117.860
    Alpha=  90.000  Beta=  90.000  Gamma=  90.000

Variance: 399.056
(Under-)estimated Z-score: 14.723

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.

 447 HIS   ( 144-)  B      CG   ND1  CE1 109.61    4.0

Note: Per-model averages for bond-angle check

The table below gives the per-model bond-angle RMS Z-scores.

Model 1 : 0.736
Model 2 : 0.571

Torsion-related checks

Note: Per-model averages for Ramachandran check

The table below gives the per-model Ramachandran Z-scores.

Model 1 : -0.626
Model 2 : -0.894

Warning: Torsion angle evaluation shows unusual residues

The residues listed in the table below contain bad or abnormal torsion angles.

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.

 976 THR   ( 284-)  A    -3.5
 203 THR   ( 284-)  A    -3.4
1361 THR   ( 284-)  B    -3.4
 588 THR   ( 284-)  B    -3.2
1146 TRP   ( 456-)  A    -2.7
1531 TRP   ( 456-)  B    -2.6
 543 THR   ( 239-)  B    -2.5
 158 THR   ( 239-)  A    -2.5
 758 TRP   ( 456-)  B    -2.4
 373 TRP   ( 456-)  A    -2.4
 917 THR   ( 225-)  A    -2.4
 144 THR   ( 225-)  A    -2.4
 808 ILE   ( 117-)  A    -2.4
 529 THR   ( 225-)  B    -2.4
 988 HIS   ( 296-)  A    -2.4
1302 THR   ( 225-)  B    -2.4
1373 HIS   ( 296-)  B    -2.4
1196 PRO   ( 120-)  B    -2.3
  35 ILE   ( 117-)  A    -2.3
  88 TYR   ( 169-)  A    -2.3
1540 PRO   ( 465-)  B    -2.3
 215 HIS   ( 296-)  A    -2.3
1122 PRO   ( 431-)  A    -2.3
 376 PRO   ( 459-)  A    -2.3
1246 TYR   ( 169-)  B    -2.3
 600 HIS   ( 296-)  B    -2.3
1316 THR   ( 239-)  B    -2.3
 563 LYS   ( 259-)  B    -2.2
 473 TYR   ( 169-)  B    -2.2
 420 ILE   ( 117-)  B    -2.2
1343 ILE   ( 266-)  B    -2.1
 861 TYR   ( 169-)  A    -2.1
 931 THR   ( 239-)  A    -2.1
 989 GLY   ( 297-)  A    -2.1
1144 VAL   ( 454-)  A    -2.1
 919 GLU   ( 227-)  A    -2.1
 756 VAL   ( 454-)  B    -2.0
1304 GLU   ( 227-)  B    -2.0
 146 GLU   ( 227-)  A    -2.0

Warning: Backbone evaluation reveals unusual conformations

The residues listed in the table below have abnormal backbone torsion angles.

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.

  33 PHE   ( 115-)  A  omega poor
  35 ILE   ( 117-)  A  omega poor
  43 SER   ( 125-)  A  Poor phi/psi
  45 LEU   ( 127-)  A  Poor phi/psi
  59 ASN   ( 141-)  A  Poor phi/psi
  96 ALA   ( 177-)  A  omega poor
 139 ASN   ( 220-)  A  Poor phi/psi
 141 ILE   ( 222-)  A  Poor phi/psi
 144 THR   ( 225-)  A  Poor phi/psi, omega poor
 145 GLN   ( 226-)  A  omega poor
 146 GLU   ( 227-)  A  Poor phi/psi
 153 ASN   ( 234-)  A  Poor phi/psi
 191 ASN   ( 272-)  A  Poor phi/psi
 195 GLU   ( 276-)  A  omega poor
 196 GLU   ( 277-)  A  Poor phi/psi
 209 VAL   ( 290-)  A  omega poor
 217 SER   ( 298-)  A  omega poor
 228 LEU   ( 310-)  A  Poor phi/psi, omega poor
 233 GLY   ( 315-)  A  omega poor
 243 ASN   ( 325-)  A  PRO omega poor
 262 ASN   ( 347-)  A  Poor phi/psi
 272 ASP   ( 357-)  A  Poor phi/psi
 275 VAL   ( 360-)  A  omega poor
 296 ASN   ( 381-)  A  omega poor
 318 SER   ( 404-)  A  Poor phi/psi
And so on for a total of 110 lines.

Note: Per-model averages for chi-1/chi-2 angle check

The table below gives the per-model chi-1/chi-2 correlation Z-scores.

Model 1 : -1.437
Model 2 : -2.191

Warning: Unusual backbone conformations

For the residues listed in the table below, the backbone formed by itself and two neighbouring residues on either side is in a conformation that is not seen very often in the database of solved protein structures. The number given in the table is the number of similar backbone conformations in the database with the same amino acid in the centre.

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!

   4 THR   (  86-)  A      0
   6 ASN   (  88-)  A      0
  19 SER   ( 101-)  A      0
  28 SER   ( 110-)  A      0
  29 LYS   ( 111-)  A      0
  33 PHE   ( 115-)  A      0
  36 ARG   ( 118-)  A      0
  37 GLU   ( 119-)  A      0
  38 PRO   ( 120-)  A      0
  44 HIS   ( 126-)  A      0
  45 LEU   ( 127-)  A      0
  46 GLU   ( 128-)  A      0
  54 GLN   ( 136-)  A      0
  58 LEU   ( 140-)  A      0
  59 ASN   ( 141-)  A      0
  63 SER   ( 145-)  A      0
  66 THR   ( 148-)  A      0
  70 ARG   ( 152-)  A      0
  74 ARG   ( 156-)  A      0
  81 VAL   ( 163-)  A      0
  86 SER   ( 168-)  A      0
  93 GLU   ( 174-)  A      0
  94 SER   ( 175-)  A      0
  95 VAL   ( 176-)  A      0
  96 ALA   ( 177-)  A      0
And so on for a total of 846 lines.

Note: Per-model averages for omega angle check

The table below gives the per-model omega angle standard deviations.

Model 1 : 7.105
Model 2 : 6.213

Warning: Backbone oxygen evaluation

The residues listed in the table below have an unusual backbone oxygen position.

For each of the residues in the structure, a search was performed to find 5-residue stretches in the WHAT IF database with superposable C-alpha coordinates, and some restraining on the neighbouring backbone oxygens.

In the following table the RMS distance between the backbone oxygen positions of these matching structures in the database and the position of the backbone oxygen atom in the current residue is given. If this number is larger than 1.5 a significant number of structures in the database show an alternative position for the backbone oxygen. If the number is larger than 2.0 most matching backbone fragments in the database have the peptide plane flipped. A manual check needs to be performed to assess whether the experimental data can support that alternative as well. The number in the last column is the number of database hits (maximum 80) used in the calculation. It is "normal" that some glycine residues show up in this list, but they are still worth checking!

1265 GLY   ( 188-)  B   1.58   13
1409 GLY   ( 333-)  B   1.54   49
 636 GLY   ( 333-)  B   1.54   41
 880 GLY   ( 188-)  A   1.52   14
 263 GLY   ( 348-)  A   1.51   67

Warning: Unusual PRO puckering amplitudes

The proline residues listed in the table below have a puckering amplitude that is outside of normal ranges. Puckering parameters were calculated by the method of Cremer and Pople [REF]. Normal PRO rings have a puckering amplitude Q between 0.20 and 0.45 Angstrom. If Q is lower than 0.20 Angstrom for a PRO residue, this could indicate disorder between the two different normal ring forms (with C-gamma below and above the ring, respectively). If Q is higher than 0.45 Angstrom something could have gone wrong during the refinement. Be aware that this is a warning with a low confidence level. See: Who checks the checkers? Four validation tools applied to eight atomic resolution structures [REF]

 246 PRO   ( 328-)  A    0.16 LOW
 631 PRO   ( 328-)  B    0.17 LOW
 845 PRO   ( 154-)  A    0.18 LOW

Warning: Unusual PRO puckering phases

The proline residues listed in the table below have a puckering phase that is not expected to occur in protein structures. Puckering parameters were calculated by the method of Cremer and Pople [REF]. Normal PRO rings approximately show a so-called envelope conformation with the C-gamma atom above the plane of the ring (phi=+72 degrees), or a half-chair conformation with C-gamma below and C-beta above the plane of the ring (phi=-90 degrees). If phi deviates strongly from these values, this is indicative of a very strange conformation for a PRO residue, and definitely requires a manual check of the data. Be aware that this is a warning with a low confidence level. See: Who checks the checkers? Four validation tools applied to eight atomic resolution structures [REF].

 328 PRO   ( 412-)  A   100.6 envelop C-beta (108 degrees)
 349 PRO   ( 431-)  A   -42.6 envelop C-alpha (-36 degrees)
 713 PRO   ( 412-)  B   104.5 envelop C-beta (108 degrees)
 734 PRO   ( 431-)  B   -55.1 half-chair C-beta/C-alpha (-54 degrees)
 811 PRO   ( 120-)  A   -61.1 half-chair C-beta/C-alpha (-54 degrees)
1111 PRO   ( 420-)  A   -49.9 half-chair C-beta/C-alpha (-54 degrees)
1122 PRO   ( 431-)  A   -55.8 half-chair C-beta/C-alpha (-54 degrees)
1196 PRO   ( 120-)  B   -23.3 half-chair C-alpha/N (-18 degrees)
1496 PRO   ( 420-)  B   -61.4 half-chair C-beta/C-alpha (-54 degrees)
1540 PRO   ( 465-)  B   -65.1 envelop C-beta (-72 degrees)

Bump checks

Error: Abnormally short interatomic distances

The pairs of atoms listed in the table below have an unusually short distance.

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).

Bumps between atoms for which the sum of their occupancies is lower than one are not reported. In any case, each bump is listed in only one direction. However, as this seems to be an NMR structure, this is unlikely to happen in this report.

 131 THR   ( 212-)  A    A O   <->  180 LYS   ( 261-)  A    A NZ     0.29    2.41
 380 GLU   ( 463-)  A    A N   <->  447 HIS   ( 144-)  B    A NE2    0.19    2.81
1564 GOL   (1004-)  B    A O1  <-> 1568 ACT   (3004-)  B    A O2     0.18    2.22
 146 GLU   ( 227-)  A    A OE2 <-> 1555 ACT   (3002-)  A    A CH3    0.18    2.62
1593 HOH   (3380 )  A    A O   <-> 1594 HOH   (3337 )  B    A O      0.16    2.24
 134 ILE   ( 215-)  A    A CD1 <->  174 LEU   ( 255-)  A    A CD1    0.15    3.05
  68 LYS   ( 150-)  A    A NZ  <-> 1593 HOH   (3331 )  A    A O      0.15    2.55
 138 ARG   ( 219-)  A    A NH1 <-> 1593 HOH   (3292 )  A    A O      0.14    2.56
 101 ALA   ( 182-)  A    A C   <->  149 CYS   ( 230-)  A    A SG     0.13    3.27
 138 ARG   ( 219-)  A    A NH2 <-> 1593 HOH   (3149 )  A    A O      0.12    2.58
 180 LYS   ( 261-)  A    A NZ  <-> 1593 HOH   (3132 )  A    A O      0.12    2.58
 581 GLU   ( 277-)  B    A OE2 <-> 1568 ACT   (3004-)  B    A O2     0.12    2.28
 531 GLU   ( 227-)  B    A OE2 <-> 1568 ACT   (3004-)  B    A CH3    0.12    2.68
 655 ARG   ( 355-)  B    A NH2 <-> 1565 GOL   (1006-)  B    A C3     0.12    2.98
  46 GLU   ( 128-)  A    A OE1 <-> 1593 HOH   (3315 )  A    A O      0.11    2.29
 421 ARG   ( 118-)  B    A NE  <->  728 GLU   ( 425-)  B    A OE2    0.11    2.59
 733 GLN   ( 430-)  B    A NE2 <->  738 THR   ( 436-)  B    A O      0.10    2.60
 327 HIS   ( 412-)  A    A CD2 <-> 1593 HOH   (3013 )  A    A O      0.10    2.70
 486 ALA   ( 182-)  B    A C   <->  534 CYS   ( 230-)  B    A SG     0.10    3.30
 189 ALA   ( 270-)  A    A N   <-> 1554 ACT   (3000-)  A    A O2     0.10    2.60
 519 ILE   ( 215-)  B    A CD1 <->  559 LEU   ( 255-)  B    A CD1    0.10    3.10
  25 ARG   ( 107-)  A    A NH2 <->  439 GLN   ( 136-)  B    A O      0.09    2.61
 439 GLN   ( 136-)  B    A NE2 <-> 1594 HOH   (3110 )  B    A O      0.09    2.61
1593 HOH   (3391 )  A    A O   <-> 1594 HOH   (3235 )  B    A O      0.09    2.31
 439 GLN   ( 136-)  B    A CB  <-> 1594 HOH   (3091 )  B    A O      0.08    2.72
And so on for a total of 56 lines.

Packing, accessibility and threading

Note: Per-model averages for inside/outside residue distributi ...heck


Note: Inside/Outside RMS Z-score plot

Chain identifier: A; Model number 1

Note: Inside/Outside RMS Z-score plot

Chain identifier: B; Model number 1

Note: Inside/Outside RMS Z-score plot

Chain identifier: A; Model number 2

Note: Inside/Outside RMS Z-score plot

Chain identifier: B; Model number 2

Warning: Abnormal packing environment for some residues


Note: Quality value plot

Chain identifier: A; Model number 1

Note: Quality value plot

Chain identifier: B; Model number 1

Note: Quality value plot

Chain identifier: A; Model number 2

Note: Quality value plot

Chain identifier: B; Model number 2

Warning: Low packing Z-score for some residues


Note: Per-model averages for NQA


Note: Second generation quality Z-score plot

Chain identifier: A; Model number 1

Note: Second generation quality Z-score plot

Chain identifier: B; Model number 1

Note: Second generation quality Z-score plot

Chain identifier: A; Model number 2

Note: Second generation quality Z-score plot

Chain identifier: B; Model number 2

Water, ion, and hydrogenbond related checks

Warning: Water molecules need moving


Error: Water molecules without hydrogen bonds


Error: HIS, ASN, GLN side chain flips


Warning: Buried unsatisfied hydrogen bond donors


Warning: Buried unsatisfied hydrogen bond acceptors


Warning: Unusual ion packing


Warning: Unusual water packing


Warning: Possible wrong residue type


Final summary

Note: Summary report for users of a structure







Note: Summary report for depositors of a structure