WARNING: Required bond angle not found between atoms CD , N , and C in group PROThis warning will be issued when a bond angle definition is missing. You should add to your geometry definition the line
GEOMETRY PRO ANGLE ??? ?? C, N, CD
substituting the proper values for the angle and its standard deviation.
WARNING: Required torsion angle not found between atoms CG , CD , N , and C in group PROThis warning will be issued when a additional torsion angle definition is required. You should add
GEOMETRY PRO TORSION ??? ?? C, N, CD, CG
substituting the proper values for the torsion angle and its standard deviation.
WARNING: In group HIS the torsion angle for the atoms CB , CG , ND1 , and CE1 is either cis or trans because all the atoms are in the same plane. The REFI dictionary will assume they are trans.This warning is issued when a torsion angle must be either cis or trans because all the atoms are in a plane. There is no way for the program to distinguish these two possibilities but I have found that trans is more probable. If the angle is trans you need do nothing. If the angle is cis you must enter a GEOMETRY statement similar to
GEOMETRY PRO TORSION 1000 5 CB, CG, ND1, CE1
In this particular example the angle is properly trans and no changes need be made.
WARNING: In group HIS the torsion angle for the atoms CG , CD2 , NE2 , and CE1X is either cis or trans because all the atoms are in the same plane. The REFI dictionary will assume they are cis because the last atom is a ring closure atom.This warning is also produced when there is an ambiguity between cis and trans but in this case the program guesses that cis is correct. The difference is that the last atom in the list is marked (with the appended `X') as a ``ring closure" atom. If the angle really is trans you must enter the GEOMETRY statement
GEOMETRY PRO TORSION 1180 5 CG, CD2, NE2, CE1
(Note that the `X' is left off the name of `CE1'.) If the angle is properly cis no changes need to be made. In this example the program's guess is correct and no action is required.
WARNING: Required torsion angle not found between atoms C4A , CHB , C1B , and NBX in group PRF . This angle could be defined by either the definition of a plane covering (at least) C2B , CHB , C1B , and NBX or a chiral center located at C1B , or failing that provide the value of the torsion angle.This warning is issued when a torsion angle has not been defined but the angle could have been inferred from either a plane or a chiral center definition. You have to examine the structure of the group and chose the appropriate response. In this case all of these atoms should be in a common plane - the plane of the bacteriochlorophyll-a ring.
If neither a plane or a chiral center definition is appropriate for this group of atoms you can define a torsion angle. Usually, however, it is proper in these cases to leave the angle undefined and allow this angle to be classified as ``variable".
WARNING: Required torsion angle not found between atoms NA , MG , NB , and C1BX in group PRF . This angle is not the 'primary' angle at this location. To define this angle you need to define a plane or chiral center, or as a last resort provide the value of the torsion angle.This angle is similar to the last except for its relationship to another torsion angle - here NA-MG-NB-C4B. If you want to define this angle with a chiral center or plane you must also define a single valued torsion angle for this other group. In almost all cases this is the proper response. If there is no chiral center or plane here then either leave this angle as ``variable" or defined it with a single valued torsion angle.