[ccp4bb]: problem with special distance in PROTIN

[Tom Lee <tomlee@msg.ucsf.edu>]

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Dear ccp4 users:

I am having a trouble in refining a structure with ligands.  I included 
special distances within a ligand as well as between residues and ligands.
But PROTIN cannot identify these distances and excludes them.

My PROTIN file:
------------------
...
CHNNAM ID A CHNTYP 1
CHNNAM ID B CHNTYP 1
CHNNAM ID W CHNTYP 2
CHNNAM ID C CHNTYP 3
CHNNAM ID D CHNTYP 3
CHNNAM ID E CHNTYP 5
CHNNAM ID F CHNTYP 5
CHNNAM ID G CHNTYP 6
CHNNAM ID H CHNTYP 6
CHNTYP 1 NTERM  1 MET  3 CTERM 263 ALA 2 
CHNTYP 2 WAT
CHNTYP 3 WAT
CHNTYP 5 WAT
CHNTYP 6 WAT 
CHNTYP 5 MULPLN 1 501
CHNTYP 5 MULPLN 1 502
CHNTYP 6 SPEC RESN 601 601 ATNA N1 C6 DIST 1.47  1 1
CHNTYP 6 SPEC RESN 601 601 ATNA N1 C2 DIST 1.444 1 1
CHNTYP 6 SPEC RESN 601 601 ATNA C2 N3 DIST 1.38  1 1
CHNTYP 6 SPEC RESN 601 601 ATNA N3 C4 DIST 1.38  1 1
CHNTYP 6 SPEC RESN 601 601 ATNA C4 C5 DIST 1.516 1 1 
CHNTYP 6 SPEC RESN 601 601 ATNA C5 C6 DIST 1.53  1 1
SPEC CHNNAM A C RESN 1 301 ATNA N C DIST 1.330 1 1
SPEC CHNNAM B D RESN 1 302 ATNA N C DIST 1.330 1 1
SPEC CHNNAM A G RESN 146 601 ATNA SG C6 DIST 1.81 1 1
...
-----------------

The log file:
-----------------
...
***Warning:  Not ALL Atoms specified in the Special Distance Restraints 
  are Present in the Input Coordinates
    (Remember ZERO Occupancy Atoms are Ignored)
     check atom identifiers given on spec cards
     for reference,  0 Intra-Chain Special Distances out of   6 Specified
 have been found and   3 Inter-Chain Distances out of   3 Specified


 The following Atoms are missing from the deck  of atomic Coordinates ---


 OT   of ALAC 263
 OE   of ALAC 263
 OT   of ALAC 263
 OE   of ALAC 263


 EXTERNALLY DESIGNATED DISTANCES
 Exclude      IRES IATOM        JRES JATOM   ICH APACK
              601    0          601    6      6    45993269108.0
 Exclude      IRES IATOM        JRES JATOM   ICH APACK
              601    0          601    2      6    45993269104.0
 Exclude      IRES IATOM        JRES JATOM   ICH APACK
              601    0          601    3      6    45993269105.0
 Exclude      IRES IATOM        JRES JATOM   ICH APACK
              601    0          601    4      6    45993269106.0
 Exclude      IRES IATOM        JRES JATOM   ICH APACK
              601    0          601    5      6    45993269107.0
 Exclude      IRES IATOM        JRES JATOM   ICH APACK
              601    0          601    6      6    45993269108.0
 12191    7 4285   1N    to  301C      1.330   1.347   1   1   
 Exclude ICHN IRES IATOM   JCHN JRES JATOM   IPR APACK
           1    1    1       4  301    1      3       79588304.0
 12192 2149 4288   1N    to  302C      1.330   1.352   1   1   
 Exclude ICHN IRES IATOM   JCHN JRES JATOM   IPR APACK
           2    1    1       5  302    1     11       79598505.0
 12193 1187 4365 146SG   to  601C6     1.810   1.843   1   1   
 Exclude ICHN IRES IATOM   JCHN JRES JATOM   IPR APACK
           1  146    6       8  601    6      7    11177715759.0
...
---------------

In the case of Intra-Chain Distances, why is the IATOM's are set to 0 
instead of the correct atom order number set in protin.dict? The log
says "3 Inter-Chain Distances out of 3 Specified", but later excludes
them.  What does "exclude" mean?  BTW, atom occupancies have been checked.
Could anyone help me?  Thanks in advance.

Tom Lee