[ccp4bb]: REFMAC, PDB deposit

[skarthik@caregroup.harvard.edu]

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Dear all,

  I refined couple of structures using REFMAC. The question is 
while depositing the coordinates to PDB. If I choose the Refinement
program as REFMAC, an option in the ADIT tool, then the required
parameters for RMS deviation from ideal values are as follows:

REMARK   3  RMS DEVIATIONS FROM IDEAL VALUES.
REMARK   3   DISTANCE RESTRAINTS.                    RMS    SIGMA
REMARK   3    BOND LENGTH                     (A) : 0.018 ; 0.021
REMARK   3    ANGLE DISTANCE                  (A) : NULL  ; NULL
REMARK   3    INTRAPLANAR 1-4 DISTANCE        (A) : NULL  ; NULL
REMARK   3    H-BOND OR METAL COORDINATION    (A) : NULL  ; NULL
REMARK   3
REMARK   3   PLANE RESTRAINT                  (A) : 0.008 ; 0.020
REMARK   3   CHIRAL-CENTER RESTRAINT       (A**3) : 0.100 ; 0.200
REMARK   3
REMARK   3   NON-BONDED CONTACT RESTRAINTS.
REMARK   3    SINGLE TORSION                  (A) : NULL  ; NULL
REMARK   3    MULTIPLE TORSION                (A) : NULL  ; NULL
REMARK   3    H-BOND (X...Y)                  (A) : NULL  ; NULL
REMARK   3    H-BOND (X-H...Y)                (A) : NULL  ; NULL
REMARK   3
REMARK   3   CONFORMATIONAL TORSION ANGLE RESTRAINTS.
REMARK   3    SPECIFIED                 (DEGREES) : NULL  ; NULL
REMARK   3    PLANAR                    (DEGREES) : NULL  ; NULL
REMARK   3    STAGGERED                 (DEGREES) : NULL  ; NULL
REMARK   3    TRANSVERSE                (DEGREES) : NULL  ; NULL
REMARK   3

   I guess these values are from the output of PROLSQ format. But the
output PDB file from REFMAC has a different values from this (as shown 
below):
REMARK   3  RMS DEVIATIONS FROM IDEAL VALUES        COUNT    RMS    WEIGHT
REMARK   3   BOND LENGTHS REFINED ATOMS        (A):   693 ; 0.016 ; 0.021
REMARK   3   BOND ANGLES REFINED ATOMS   (DEGREES):   938 ; 1.707 ; 1.986
REMARK   3   TORSION ANGLES, PERIOD 1    (DEGREES):    90 ; 4.155 ; 3.000
REMARK   3   TORSION ANGLES, PERIOD 3    (DEGREES):   121 ;14.452 ;15.000
REMARK   3   CHIRAL-CENTER RESTRAINTS       (A**3):   105 ; 0.099 ; 0.200
REMARK   3   GENERAL PLANES REFINED ATOMS      (A):   538 ; 0.006 ; 0.020
REMARK   3   NON-BONDED CONTACTS REFINED ATOMS (A):   310 ; 0.243 ; 0.300
REMARK   3   H-BOND (X...Y) REFINED ATOMS      (A):    75 ; 0.142 ; 0.500
REMARK   3   SYMMETRY VDW REFINED ATOMS        (A):    45 ; 0.241 ; 0.300
REMARK   3   SYMMETRY H-BOND REFINED ATOMS     (A):    10 ; 0.235 ; 0.500

   Could somebody help me to get the values as compatible to PDB
format (instead of saying "NULL"). I am not sure whether these values
are in the REFMAC output.  using REFINEMENT TARGET as 
MAXIMUM LIKELIHOOD.

Thanks in advance
karthik