2.17 *******************
* GREF WRITE-UP *
*******************
GREF is program for the refinement of rigid groups against x-ray
diffraction data. It can be used to refine entire protein domains,
substructures or even individual atoms. It is space group general and
can refine up to 24 groups with a total of up to 20000 atoms in the
asymmetric unit. Each input atom must belong to a group, but the
atoms can be partitioned into groups in any possible manner. The
program is also used to refine heavy atom positions by defining each
heavy atom to be a "one atom group", and refining only the group
centroid position, occupancy and (possibly) thermal factor (e.g. omit
refinement of the group orientation parameters). The program can read
any of the "merged" reflection files input to PHASIT (for heavy atom
refinement against isomorphous or anomalous scattering differences) or
a general file for protein group refinement against native data.
Scattering factors can be either the normal type for refinement
against native data or isomorphous differences, or 2*delta f" for
refinement against anomalous scattering differences. One can select
all data, only centric data, or only acentric data for the
calculations. The output refined coordinate file can be used as input
to PHASIT for subsequent phase calculations.
INPUT DATA (UNIT 5)
CARD 1 PAMFIL (free format)
PAMFIL = Name of input file containing cell parameters,
symmetry information etc.
CARD 2 INPCDS (free format)
INPCDS = Name of file containing input atomic coordinates.
CARD 3 INPREF (free format)
INPREF = Name of file containing input reflection data.
CARD 4 NCYCLS,IFOUR,SC,TO,CUTS,CUTMN,CUTMX,IWGHT,NXSCAT (free format)
NCYCLS = # of refinement cycles (= 0 for
a single structure factor calculation)
IFOUR = 0 for no Fourier coefficient output.
= 1 to write final Fourier coefficients
to file.
SC = scale factor, such that Fobs=SC*Fcalc.
TO = Overall isotropic thermal factor. If
zero, then individual thermal factors
for each group must be supplied. If
non-zero, applies to all atoms, and
thermal factors for each group SHOULD
NOT be input.
CUTS = Data selection cutoff. Rejects data
with Fobs < CUTS*Sig(Fobs).
CUTMN = Data selection cutoff. Rejects data
with sin(theta)/lambda < CUTMN.
CUTMX = Data selection cutoff. Rejects data
with sin(theta)/lambda > CUTMX.
IWGHT = Weighting factor indicator.
= 0 for weights of 1./Sig(Fobs)**2
= 1 for unit weights.
NXSCAT = number of additional atomic
types for which scattering
factors will be input. Note
that 20 types are already
stored in the program (see
below), thus this is usually
nonzero only for exotic
atoms or wavelengths other
than CU K alpha.
CARD 4A OUTREF (free format)
***** Include this card ONLY if IFOUR=1 *****
OUTREF = Name of output phased reflection file
CARD 4B OUTCDS (free format)
***** Include this card ONLY if NCYCLS > 0 *****
OUTCDS = Name of output coordinate file
CARDS 4C Extra scattering factors (all free format)
***** Include this set of records ONLY if NXSCAT > 0 *****
Up to 5 additional atomic types may be input. For each additional
atomic type, include the following 3 records
REC 1 (A(J),J=1,4) (free format)
A(J) = Coefficients for analytical
approximation to scattering
factors, as in Int. Tables,
Vol IV, pages 99-101.
REC 2 (B(J),J=1,4) , C (free format)
B(J) = Coefficients for analytical
approximation to scattering
C = factors, as in Int. Tables,
Vol IV, pages 99-101.
REC 3 DEL f' , DEL f'' (free format)
DEL f' = real part of anomalous
scattering correction term.
DEL f'' = imaginary part of anomalous
scattering correction term.
CARD 5 IFLTYP,ICLTYP,ISFTYP,MINCEN,IMODE (free format)
These parameters indicate what type of
reflection file is input, what type of
data is to be used, and what scattering
factors are to be used.
IFLTYP = 0 for h,k,l,FO,Sig(FO) input, uses
FOBS=FO and SIG= Sig(FO).
= 1 for h,k,l,FP,Sig(FP),FPH,Sig(FPH)
input, uses FOBS=ABS(FP-FPH) and
SIG=mean Sig.
= 2 for h,k,l,FP+,Sig(FP+),FP-,Sig(FP-)
input, uses FOBS=ABS(FP+ - FP-) and
SIG=mean Sig.
= 3 for h,k,l,FP,Sig(FP),FPH+,Sig(FPH+),
FPH-,Sig(FPH-) input, uses
FOBS=ABS(FPH+ - FPH-) and SIG=
(Sig(FPH+)+Sig(FPH-))/2.
ICLTYP = 0 to use all data types.
= 1 to use only centric data.
= 2 to use only acentric data.
ISFTYP = 0 to use normal scattering factors.
= 1 to use only 2.*delta f" as
scattering factors.
MINCEN = minimum number of centric reflections
to be used without including 25%
strongest differences for acentric
reflections. Applied only if ICLTYP=1
(suggested value=75, but space group
considerations may dictate otherwise,
see NOTES).
IMODE = 0 If atom types derived from first
character in atom name (only C,N,O,S,
Fe recognized).
= 1 If atom type code number explicitly
input for each atom.
CARD 6 (NGP, NAG(I), I=1,NGP) (free format)
NGP = # of groups (each atom must belong to
a group)
NAG(I) = # of atoms in group I. It is assumed
that the first NAG(1) atoms form group
1, the next NAG(2) atoms form group 2
etc.
CARD 7 (OCC(I), I=1,NGP) (free format)
OCC(I) = Occupancy factor for group I.
CARD 8 (BETA(I), I=1,NGP) (free format)
BETA(I) = Isotropic thermal factor for group I.
NOTE! Include this card only if TO
is zero.
FOLLOWING CARDS ARE TO BE INCLUDED ONLY IF REFINING ( NCYCLS > 0 )
CARD 9 ISC,ITO (free format)
ISC = 0 to hold scale factor fixed.
= 1 to refine
ITO = 0 to hold overall thermal factor
fixed.
= 1 to refine. (it can be refined only
if TO > 0 ).
The following card must be repeated for each of the NGP groups.
CARDS 10 ITX,ITY,ITZ,IRX,IRY,IRZ,IBT,IOC (free format)
ITX = 0 to hold group centroid fixed
at respective x,y, or z coordinate.
ITY = 1 to refine group centroid
translation for respective coordinate.
ITZ =
IRX = 0 to hold group orientation angle
fixed with respect to x,y,or z
IRY = axis (orthogonal axes).
1 to refine group rotation angle
IRZ = about corresponding axis (all
rotations about group centroid).
IBT = 0 to hold group thermal factor
fixed.
= 1 to refine. (applicable only if
TO is non zero.)
IOC = 0 to hold group occupancy factor
fixed.
= 1 to refine.
***** FILES *****
INPREF - INPUT REFLECTION DATA (free format)
This file can have any of 4 types of structures, with the particular
type designated by IFLTYP. All types are read in free format, i.e.
each item must be separated by at least one blank or a comma. For all
types there should be data for one reflection in each record.
For IFLTYP=0 records with h, k, l, FP, Sig(FP) and the data used
as input. Typically native data for protein refinement.
For IFLTYP=1 records with h, k, l, FP, Sig(FP), FPH, Sig(FPH) and
the data used is ABS(FP-FPH), mean Sigma. Typically
isomorphous replacement data for heavy atom refinement.
For IFLTYP=2 records with h, k, l, FP(h,k,l), Sig( FP(h,k,l) ),
FP(-h,-k,-l), Sig( FP(-h,-k,-l) ) and the data used
as ABS( FP(h,k,l) - FP(-h,-k,-l) ), mean Sigma.
Typically native anomalous scattering data for heavy
atom refinement.
For IFLTYP=3 records with h,k,l,FP,Sig(FP),FPH(h,k,l),
Sig( FPH(h,k,l) ),FPH(-h,-k,-l), Sig( FPH(-h,-k,-l) )
and the data used is ABS( FPH(h,k,l) - FPH(-h,-k,-l) )
and (Sig( FPH(h,k,l) ) + Sig( FPH(-h,-k,-l) ) )/2.
Typically derivative anomalous scattering data for
heavy atom refinement.
INPCDS - INPUT ATOMIC PARAMETERS FORMAT (1X,A1,5X,A1,I3,A4,5F10.5,I5)
One atom per record, containing CHN,RTYPE,IRES,ATOM,X,Y,Z,B,OC,ITYP
CHN = Single character chain identifier (not
used)
RTYPE = One letter amino acid code (not used)
IRES = Sequence number (not used)
ATOM = Atom name (used only if IMODE=0)
X =
Y = Fractional atomic coordinates
Z =
B = Isotropic thermal factor (not used as
TO or BETA values superseed it)
OC = Occupancy factor (not used as OCC
value superseeds it)
ITYP = 1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,
16,17,18,19 or 20 for C,N,O,S,Fe,Pt,
Hg,Au,Pb,Os,I,Zn,Ca,Mg,Cd,U,P,Br,Cl,
or Sm, respectively. ITYP= 21
through 20+NXSCAT for the additional
types, in same order as originally
input. (This field used only if
IMODE=1)
OUTCDS - OUTPUT ATOMIC PARAMETER FILE (same data and format as INPCDS)
Generated only if NCYCLS > 0. Contains the new parameters. If heavy
atom refinement was done this file can be inserted in a PHASIT deck
for phase calculations. It can also be input back into GREF for
further refinement. The format is compatible with the Hendrickson-
Konnert program PROTIN, or with PHASIT's structure factor calculation
mode.
Note that this file may have the same name as INPCDS, although
the original contents will then be destroyed.
OUTREF - OUTPUT FOURIER COEFFICIENTS (BINARY)
Generated following last structure calculation only if IFOUR=1.
Contains records of h, k, l, FOBS, FCAL, PHI where the indices
are INTEGERS and the other data REALS. PHI is in degrees. This file
can be used in program FSFOUR for Fourier calculations, and converted
to ASCII by program RD31.
***** NOTES *****
1) Generally when refining heavy atom parameters against isomorphous
differences only centric data is used. In space groups where there is
an insufficent number of centric reflections to refine all needed
parameters, the program will include the 25% strongest differences for
acentric reflections. The input parameter MINCEN determines how many
acceptable centric reflections MUST be found to SUPPRESS the automatic
inclusion of the acentric data. A good value of MINCEN is 75, but in
some space groups it may be necessary to set it to a large
(unobtainable) number to force automatic inclusion of the strongest
differences for acentric data. An example of this would be space group
P2(1) with more than one heavy atom input. In that case there might be
a hundred or more centric reflections, but all will be h,0,l
reflections, thus the y coordinate of the second atom can not be
refined without including some acentric data. Similarly, in space
group P1 only centric reflections should be requested (even though
there aren't any), but MINCEN should be nonzero. This will force ONLY
THE 25% LARGEST ACENTRIC DIFFERENCES to be used. For orthorhombic
space groups there generally are enough centric reflections to refine
all parameters, thus MINCEN=75 is usually sufficient. The MINCEN
parameter is used only if ICLTYP=1, i.e when only centric reflections
are requested.
2) When refining heavy atom parameters against anomalous scattering
differences, one should use only a certain percentage of the largest
differences. If ICLTYP=2 and ISFTYP=1, then heavy atom refinement
against anomalous scattering differences is assumed and the program
will automatically select the 25% strongest Bijvoet differences for
use in the calculations.
3) If anomalous scattering data is used (ISFTYP=1), then the output
phases on file 31 are not correct as they are 90 degrees less than
their true values. This results from use of scattering factors of
2*delta f" instead of i*(2*delta f"). The computed structure factor
amplitudes however, are correct thus the refinement is still valid.
Note also that the structure factor calculation is insensitive to the
hand of the heavy atoms.
4) Although the refined values of the thermal factors and occupancies
are output on the new parameter file, they are ignored on input as
these parameters are set based on values in the input control file.
Accordingly, one must update the control file if additional cycles are
to resume where previous cycles left off. Only the new positional
parameters are used from the input coordinate file. One must also
update the scale factor in the input control file in a similar manner.
The new values of the scale, thermal and occupancy factors are listed
on the log file.
5) If a group contains only a single atom, then the three orientation
angles can not be refined. If a group contains only two atoms, then
only two of the orientation angles can be refined (it usually doesn't
matter which two, although it may if the inter-atom vector happens to
be parallel to one of the orthogonal axes ). If only one atom is
input, then the scale factor and occupancy factor can not both be
refined as they are identical in that situation.
6) With low resolution data, occupancy and thermal factors are highly
correlated and often can not be refined simultaneously.