This program performs the same geometric checks that are carried out at the PDBe when a structure is submitted. Geometry is checked against a dictionary standard_geometry.cif which has values based on the references given below. The atom names must match the dictionary which uses the naming conventions of pdb version 3.0. (These are NOT the same as pdb version 2.0 for the nucleic acids.) There is a program checknames.f which converts old names to new names
It returns a list of bad contacts and unexpected geometric features.
e.g pdb4tst.ent is the input coordinate file.
If you dont have a file with this name use
ln -s your_coordinate_file pdb4tst.ent
r500 4tst
or
if using a PDB entry, run as
r500 IDCODE(lowercase)
1.608 all_angle_rmsd
0.016 all_bond_rmsd
The following bond classes show an overall poor rmsd -check your dictionary
Total Observed Expected E&H99 Example Example
Class RMSD RMSD Value Bond Residue
80 0.137 0.007 1.339 C5 - C6 T
80 0.081 0.007 1.378 N1 - C6 T
80 0.056 0.009 1.445 C4 - C5 T
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT
SUBTOPIC: CLOSE CONTACTS
SUBTOPIC: COVALENT BOND LENGTHS
SUBTOPIC: COVALENT BOND ANGLES
SUBTOPIC: TORSION ANGLES
SUBTOPIC: NON-CIS, NON-TRANS
SUBTOPIC: PLANAR GROUPS
SUBTOPIC: MAIN CHAIN PLANARITY
SUBTOPIC: CHIRAL CENTERS
_pdbx_validate_close_contact
_pdbx_validate_symm_contact
_pdbx_validate_rmsd_bond
_pdbx_validate_rmsd_angle
_pdbx_validate_torsion
_pdbx_validate_peptide_omega
_pdbx_validate_planes
_pdbx_validate_main_chain_plane
_pdbx_validate_planes_atom
_pdbx_validate_chiral
_struct_mon_nucl
_struct_mon_prot_cis
CISPEP 1 THR A 284 ASP A 285 0 15.64 CISPEP 2 ASP A 285 LYS A 286 0 -17.48 CISPEP 3 ASN A 493 PRO A 494 0 -6.46 CISPEP 4 ASP B 285 LYS B 286 0 -14.41 CISPEP 5 LYS B 286 GLY B 287 0 8.65 CISPEP 6 GLY B 383 VAL B 384 0 -5.75 CISPEP 7 ASN B 493 PRO B 494 0 4.93
CAVEAT 3KWH ARG A 40 C-ALPHA IS PLANAR CAVEAT 3I3L MODEL 0 VAL A 483 C-ALPHA IS PLANAR CAVEAT 3I3L MODEL 0 GLU A 510 C-ALPHA IS PLANAR CAVEAT 3I3L MODEL 0 LEU A 543 C-ALPHA IS PLANAR CAVEAT 3JYV ILE H 34 CBETA WRONG HAND
REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 S SO4 E 2 LIES ON A SPECIAL POSITION. suggested occupancy = 0.50
the above is a warning that the occupancy in the atoms is wrong
HETATM 660 S SO4 E 1 8.082 21.623 75.689 1.00 38.66 S HETATM 661 O1 SO4 E 1 7.927 20.196 75.427 1.00 36.18 O HETATM 662 O2 SO4 E 1 7.675 22.436 74.562 1.00 41.62 O HETATM 663 O3 SO4 E 1 9.476 21.880 75.938 1.00 46.97 O HETATM 664 O4 SO4 E 1 7.269 22.000 76.841 1.00 49.11 O HETATM 665 S SO4 E 2 19.803 15.042 81.509 1.00 73.42 S HETATM 666 O1 SO4 E 2 20.434 14.490 80.305 1.00 73.42 O HETATM 667 O2 SO4 E 2 20.691 14.754 82.647 1.00 73.42 O HETATM 668 O3 SO4 E 2 18.507 14.438 81.719 1.00 73.42 O HETATM 669 O4 SO4 E 2 19.709 16.492 81.352 1.00 73.42 O
on a DBREF if non-standard residue found as a check, and there is a mismatch in chirality of a residue and the uniprot entry has either a FT or KW that mentions any type of modified residue. If this happens then the uniprot file is written in current directory .e.g. as P43683.txt, e.g. for 1mqx\
D-/L-aa mismatch look in Uniprot 1 ABA A 2 UNIPROT has D-aa in Chain A for P43683 ** check stereo 1 ABA A 4 UNIPROT has D-aa in Chain A for P43683 ** check stereo 1 ABA A 13 UNIPROT has D-aa in Chain A for P43683 ** check stereo 1 ABA A 15 UNIPROT has D-aa in Chain A for P43683 ** check stereo <...> 12 ABA A 15 UNIPROT has D-aa in Chain A for P43683 ** check stereo
Available keywords are:
Environment variable STANDDATA must point to standard_geometry.cif
uses
/usr/bin/elinks --source HTTP://ebi.uniprot.org/uniprot/
To run correctly input file should have SEQRES, DBREF, LINK, REMARK 465, SEQADV i.e. after DOHLC run and all atom names should be standard PDB names if not run checknames first
If input file has LINK records these distances are removed from close contacts
If REMARK 465 given - extra check is done on chain break
If not Xray then EXPDTA should give method, i.e. to turn off symmetry in NMR
Microhet requires a PDB SEQADV to process only one residue in Linkages
Only the 1st of an alt_atom set is done
DBREF is used as check on UniProt features to see if a non-standard amino acid is present
Linking angles in the PDB format are given with the residue name of the central atom
For Chirality Cbeta is done for ILE and THR derivatives, i.e.
L-THR 2S,3R D-THR 2R,3S L-allo-THR 2S,3S D-allo-THR 2R,3R L-ILE 2S,3S L-alloILE 2S,3R D-ILE 2R,3R D-allo-ILE 2R,3S
these include
4TP 4-hydroxy-L-Threonine-5-monophosphate (2S,3S)
ALO L-allothreonine (2S,3S)
B2I Isoleucine boronic acid (1R,2R)
BIU 5-bromo-L-Isoleucine (2S,3S)
BMT 4-methyl-4-[(E)-2-butenyl]-4,N-methyl-threonine (E,2S,3R,4R)
CTH 4-chloro-L-threonine (2S,3S)
D11 O-phosphono-D-threonine (2R,3S)
DIL D-Isoleucine (2R,3R)
DTH D-threonine (2R,3S)
IIL L-alloIsoleucine (2S,3R)
ILE L-Isoleucine (2S,3S)
ILP N-[O-phosphono-pyridoxyl]-Isoleucine (2R,3S)
ILX 4,5-dihydroxyIsoleucine (2S,3R,4R)
IML N-methyl-Isoleucine (2S,3S)
LNT N-[(2S)-2-amino-1,1-dihydroxy-4-methylpentyl]-L-threonine (2S,3R)
OLT O-methyl-L-threonine (2S,3R)
TH5 O-acetyl-L-threonine (2S,3R)
THC N-acetyl-L-threonine (2S,3R)
THO reduced threonine [diol] (2R,3R)
THR L-threonine (2S,3R)
TPO O-phosphono-L-threonine (2S,3R)
VLL (2S,3R)-2,3-diaminobutanoic acid
VDL (2R,3R)-2,3-diaminobutanoic acid
Calpha is done for standard and non-standard amino acids. The PDB has a range of atom names for the equivalent to Calpha for non-standard amino acids, these are given in $STANDATA and possible Calpha types are:
Standard use CA C CB N and Type = D or L or . or P
B3E B3K B3X B3Y use CB CA CG N and L Type = 1
B3A use CE CA CG N and L Type = 2
CAV use CA CH CB N and L Type = 3
use CA C CB OHN and L Type = 4
B2I use CA B CB N and L Type = 6
use CA C C1 N and L Type = 7
use CA C C1 N and D Type = 8
LOV use CA C CB CT and L Type = 5
PRQ use CAM CAJ CAK NAA and L Type = 0
PRV use CA C CG N and L Type = 9
X2W use CA C CB N1 and L Type = a
If type is blank - no C-alpha chirality e.g. GLY and SAR
If type is P then C-alpha is sp2 no chirality but extra check that the Calpha is planar example 23F
Nucleic acid chirality of C1' of ribiose is checked
e.g. 1asy
REMARK 500 M RES CSSEQI IMPROPER EXPECTED FOUND DETAILS
REMARK 500 PSU R 632 -21.4 D D OUTSIDE RANGE
REMARK 500 PSU R 655 -19.0 D D OUTSIDE RANGE
REMARK 500 PSU S 613 -23.4 D D OUTSIDE RANGE
REMARK 500 PSU S 655 -20.0 D D OUTSIDE RANGE
REMARK 500 ILE A 206 24.5 L L OUTSIDE RANGE
REMARK 500 PHE A 389 24.4 L L OUTSIDE RANGE
REMARK 500 LEU A 547 19.8 L L OUTSIDE RANGE
REMARK 500 ASP B 313 23.8 L L OUTSIDE RANGE
REMARK 500 ASP B 446 24.9 L L OUTSIDE RANGE
Nucleic Acid C1' chirality types are
N1 C1' O4' N1 C2'
N9 C1' O4' N9 C2'
N5 C5 O4 N1 C4
NA C1' O5' N9A C2'
NC C1' C' N1 C2'
NM C1' O4' N1M C2'
NS C1' S4' N1 C2'
NX C1' CX' N9 C2'
C1 C1' O4' C1 C2'
C5 C1' O4' C5 C2'
F5 C1' O4' C5 C2'
NP C1D O4D N9 C2D
N7 C1' O4' N7 C2'
NR CR1 OR1 N1 CR2
C1 C1' C N1 C2'
S1 C1' S N1 C2'
NT C1T O4T N1 C2T
NH C1' O5' N1 C2'
Output may have for Found Expected
D/L or R/S with description
'EXPECTING PLANAR'
'WRONG HAND'
'OUTSIDE RANGE'
'EXPECTING SP3'
'CBETA WRONG HAND'
**WARNING CAVEAT WRITTEN (see 1a70) **WARNING SEE FEATURE FILE (see 1mqx) **WARNING CHECK REM375 FILE OCCUPANCY ERROR (see 1a7g)
Potential error messages are:
STOP 'File name not found'
STOP 'PDB File not found'
STOP 'Only 4 pairs allowed in -n'
STOP 'MaxMicrohet exceeded'
STOP 'MaxDBREF exceeded'
STOP 'max links exceeded'
STOP 'Max atoms exceeded'
STOP 'Too many boxes'
STOP 'STANDATA not found'
STOP 'QQstan gt MaxStandard'
STOP 'residue name not found _chem_comp_atom.'
STOP 'MaxAtoms exceeded 2'
STOP 'residue name not found in plane definition'
STOP 'resid not found in bonds '
STOP 'Too many Non-standard AA from STANDATA'
STOP 'Too many Non-standard NA from STANDATA'
STOP 'SYMMETRY OPERATOR ERROR'
STOP 'error in symmetry'
STOP 'identity error'
STOP 'no SYMMETRY '
STOP ' no symmop set'
STOP 'error in SYMOP'
STOP 'max atoms exceeded'
STOP 'Max CYS exceeded'
STOP 'Too many atoms on special positions'
At run time chain breaks are printed, e.g.
r500 2j0k
bond break: 0 PRO A 362 THR A 394 Ca(-1)--Ca = 25.996 C(-1)--N = 26.701
bond break: 0 GLU A 403 THR A 412 Ca(-1)--Ca = 16.095 C(-1)--N = 13.564
bond break: 0 LEU A 567 LYS A 583 Ca(-1)--Ca = 13.546 C(-1)--N = 13.078
bond break: 0 PRO B 362 GLY B 383 Ca(-1)--Ca = 21.518 C(-1)--N = 19.418
bond break: 0 THR B 388 ASP B 395 Ca(-1)--Ca = 16.654 C(-1)--N = 17.263
bond break: 0 ARG B 569 LEU B 584 Ca(-1)--Ca = 11.745 C(-1)--N = 12.929
Bond distances > 20xRMS are also written at run time e.g. 3fin
NOTE the P--O3' of 2.052 this may be not a chain break but is outside expected limits of a P--O bond
bond break: 0 HIS 6 46 THR 6 47 Ca(-1)--Ca = 4.114
C(-1)--N = 4.894
bond break: 0 G A1051 C A1052 P--O3' = 2.052
bond break: 0 G A1107 U A1108 P--O3' = 2.612
bond break: 0 A A2126 G A2127 P--O3' = 4.818
bond break: 0 C A2161 G A2162 P--O3' = 2.541
bond break: 0 ARG C 27 THR C 34 Ca(-1)--Ca = 7.430
C(-1)--N = 5.015
bond break: 0 PHE C 110 VAL C 119 Ca(-1)--Ca = 12.729
C(-1)--N = 11.810
bond break: 0 LEU C 136 ASN C 139 Ca(-1)--Ca = 6.345
C(-1)--N = 4.988
bond break: 0 GLN V 80 TYR V 81 Ca(-1)--Ca = 4.140
C(-1)--N = 3.010
**ERROR expected Bond Dist >20x RMSD in Model 0
for atom pair G A2190 O3' and G A2191 P
with distance 1.254
**ERROR expected Bond Dist >20x RMSD in Model 0
for atom pair U A2653 O3' and A A2654 P
with distance 1.278
**ERROR expected Bond Dist >20x RMSD in Model 0
for atom pair PRO G 112 C and ARG G 113 N
with distance 4.013
Kim Henrick.