[ccp4bb]: strange conformation

[warizaya masaichi <masaichi_warizaya@po.fujisawa.co.jp>]

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Hello,

Now I'm using refmac4 program.(At last refmac5 will introduced in this
spring!.)

Refining a native protein structure(not including metal-ions and
ligands) determined by MR
with Amore follwed by rigid-body refinement.
, problem happens.
Refined structure has very strange conformations.
For example...the ring of aromatic residues such as Tyr, Phe, Trp and
His  is not planar (chair form etc.)
                    value of bond length and angle are different from
that determined usually .

This protein has flexible loop (about 10 residues) in N-terminal region
not clearly
identified with electron-density in themodel structure( same protein
previously determined in our lab).
Thus this loop has trucated in the model structure.



I don't understand What's wrong?
I'm looking forward your reply.

program shell is as follows

#!/bin/csh -f

set last=0
set cycles=1
set count=0
rm ./temp/*

###########################################################################

###########################################################################

#  Step 1: protin and REFMAC.
#   NCS restrains on molecules A B C AND water chains W X Y
#
#
#
start:
#while ($count != $cycles)
@ curr = $last + 1
#
protin \
XYZIN ./temp/ref_cyc${last}.pdb \
PROTOUT ./temp/cut_protout${curr}.dat   \
PROTCOUNTS ./temp/cut_counts${curr}.dat \
<< eof
TITL  *** PROTIN ***
CHNNAM ID A CHNTYP 1 ROFFSET 199
CHNTYP 1 NTER 200 ALA 3   CTER 477 TYR 2
CHNTYP 1 MULP 0 CISPRO 0
SYMMETRY 96
#
VDWCUT 5
CONTACTS
PEPP 5          !no. of atoms restrained to be in a plane [5]
LIST FEW
END
eof
#
refmac   \
HKLIN  ./temp/ref_cyc${last}.mtz  \
PROTOUT ./temp/cut_protout${curr}.dat   \
PROTCOUNTS ./temp/cut_counts${curr}.dat \
PROTSCR ./temp/cut_counts${last}.scr \
XYZIN ./temp/ref_cyc${last}.pdb \
HKLOUT ./temp/ref_cyc${curr}.mtz     \
XYZOUT ./temp/ref_cyc${curr}.pdb  << eop
#
LABI FP=FP SIGFP=SIGFP FREE=FreeR_flag
LABO FC=FC PHIC=PHIC FWT=FWT DELFWT=DELFWT
!Refinement parameters
REFI TYPE RESTrained                   ! include restraints
REFI RESOLUTION  20.0 2.50             ! resolution limits
REFI RESI MLKF                         ! maximum likelihood residual
REFI BREF ISOTropic                    ! individual isotropic B factors
REFI METH CGMAT                        ! minimisation method
! ***** additional control data
SCAL TYPE BULK                  ! scaling with bulk solvent correction
WEIG MATRIX 0.25                 ! weighting scheme
NCYC 5                                ! 6 cycles of refinement
MONI FEW XSHI 0.5 BSHI 8.0      ! shifts above these values are reported

BINS 20                                   ! no. of resolution bins
END
eop
#
#
#mv ./temp/temp_arp.pdb    ./temp/ref_cyc${curr}.pdb
#
#/bin/rm *TMP*,*ARP*
#

#rm ./temp/ref_cyc${last}.pdb
#rm ./temp/ref_cyc${last}.mtz
rm ./temp/cut_protout* ./temp/cut_counts*

@ last++
@ count++
#if ($count<$cycles) goto start
#
#echo " check log file error in one step "
#
grep -i '_refine_overall_R_factor' ref.out > Rfactor
grep -i '_refine_free_R_factor' ref.out > R_Free
grep -i '_refine_ls_WR_factor' ref.out > R_Work
#
if ($count<$cycles) goto start





--
----------------------------------------------------
藤沢薬品工業株式会社
探索研究所 分子科学
割鞘雅一
E-mail:masaichi_warizaya@po.fujisawa.co.jp
TEL : (0298)47-8611　
FAX : (0298)47-8313
----------------------------------------------------
Masaichi Warizaya
Exploratory Research Laboratories
Fujisawa Pharmaceutical CO. LTD.
5-2-3, Tokodai, Tsukuba, Ibaraki 300-2698, Japan
E-mail:masaichi_warizaya@po.fujisawa.co.jp
TEL : +81-298-47-8611
FAX : +81-298-47-8313
----------------------------------------------------