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diff --git a/makefile_refmac.inc1 b/makefile_refmac.inc1
index 3f858c8..a8ab515 100644
--- a/makefile_refmac.inc1
+++ b/makefile_refmac.inc1
@@ -89,9 +89,7 @@ messy_pdb.o                 \
 bridge.o                    \
 i0.o                        \
 i1.o                        \
-chbevl.o                    \
-$(LLIBCIF)                  \
-$(LLIBLAPACK)
+chbevl.o
 
 
 SUBL =                      \
@@ -124,9 +122,7 @@ cell_symm_subrs.o           \
 iheap_sort.o                \
 linalgebra.o                \
 math_refmac.o               \
-subnumrec.o                 \
-$(LLIBLAPACK)               \
-$(LLIBCCP)
+subnumrec.o
 
 #--------------------------------------------------------------------------------
 
@@ -150,20 +146,20 @@ twin77mod.o:  twin77mod.f
 	$(FC) $(FFLAGS) -c twin77mod.f
 
 
-optimise_solvent_all.o: optimise_solvent_all.f90
+optimise_solvent_all.o: optimise_solvent_all.f90 atomf77mod.o
 	$(FC) $(FFLAGS) -c optimise_solvent_all.f90
 
-ncs_rest.o: ncs_ncs_generate.f90 ncs_rest.f
-	$(FC) $(FFLAGS) -c ncs_ncs_generate.f90 ncs_rest.f
+ncs_rest.o: ncs_ncs_generate.o ncs_rest.f
+	$(FC) $(FFLAGS) -c ncs_rest.f
 
-ncs_ncs_generate.o: ncs_ncs_generate.f90 align_refmac.f90
-	$(FC) $(FFLAGS) -c ncs_ncs_generate.f90 align_refmac.f90
+ncs_ncs_generate.o: ncs_ncs_generate.f90 align_refmac.o
+	$(FC) $(FFLAGS) -c ncs_ncs_generate.f90
 
-lsq_exp2.o: dist_routines.f90 ncs_simil.f90 ridge.f90 local_tls.f90 lsq_exp2.f
-	$(FC) $(FFLAGS) -c dist_routines.f90 ncs_simil.f90 ridge.f90 local_tls.f90  lsq_exp2.f
+lsq_exp2.o: dist_routines.o ncs_simil.o ridge.o local_tls.o lsq_exp2.f
+	$(FC) $(FFLAGS) -c lsq_exp2.f
 
-vdw_and_contacts.o: vdw_and_contacts.f local_tls.f90 ridge.f90 
-	$(FC) $(FFLAGS) -c ridge.f90 local_tls.f90 vdw_and_contacts.f
+vdw_and_contacts.o: vdw_and_contacts.f local_tls.o ridge.o
+	$(FC) $(FFLAGS) -c vdw_and_contacts.f
 
 dist_routines.o: dist_routines.f90
 	$(FC) $(FFLAGS) -c dist_routines.f90
@@ -178,8 +174,8 @@ align_refmac.o: align_refmac.f90
 	$(FC) $(FFLAGS) -c align_refmac.f90
 
 
-hkon_secder_tch.o: hkon_secder_tch.f local_tls.f90 ncs_simil.f90 optimise_solvent_all.f90
-	$(FC) $(FFLAGS) -c optimise_solvent_all.f90 ncs_simil.f90 local_tls.f90 hkon_secder_tch.f
+hkon_secder_tch.o: hkon_secder_tch.f local_tls.o ncs_simil.o optimise_solvent_all.o optimise_solvent_all.o
+	$(FC) $(FFLAGS) -c hkon_secder_tch.f
 
 oppro_allocate.o: oppro_allocate.f filter_params.f90 optimise_solvent_all.f90
 	$(FC) $(FFLAGS) -c optimise_solvent_all.f90 filter_params.f90 oppro_allocate.f
@@ -187,50 +183,50 @@ oppro_allocate.o: oppro_allocate.f filter_params.f90 optimise_solvent_all.f90
 coords.o: coords.f90 atomf77mod.f
 	$(FC) $(FFLAGS) -c atomf77mod.f coords.f90
 
-refpre_twin.o: refpre_twin.f coords.f90 automorphism.f90
-	$(FC) $(FFLAGS) -c coords.f90 automorphism.f90 refpre_twin.f
+refpre_twin.o: refpre_twin.f coords.o automorphism.o
+	$(FC) $(FFLAGS) -c refpre_twin.f
 
 automorphism.o: automorphism.f90
 	$(FC) $(FFLAGS) -c automorphism.f90
 
-mtz_write_twin.o: mtz_write_twin.f filter_params.f90
-	$(FC) $(FFLAGS) -c filter_params.f90 mtz_write_twin.f
+mtz_write_twin.o: mtz_write_twin.f filter_params.o
+	$(FC) $(FFLAGS) -c mtz_write_twin.f
 
 filter_params.o: filter_params.f90
 	$(FC) $(FFLAGS) -c filter_params.f90
 
-rcard_tor1.o: rcard_tor1.f filter_params.f90 local_tls.f90 ridge.f90 optimise_solvent_all.f90
-	$(FC) $(FFLAGS) -c optimise_solvent_all.f90 filter_params.f90 local_tls.f90 ridge.f90 rcard_tor1.f
+rcard_tor1.o: rcard_tor1.f filter_params.o local_tls.o ridge.o optimise_solvent_all.o
+	$(FC) $(FFLAGS) -c rcard_tor1.f
 
-local_tls.o: local_tls.f90 linalgebra_f90.f90
-	$(FC) $(FFLAGS) -c linalgebra_f90.f90 local_tls.f90
+local_tls.o: local_tls.f90 linalgebra_f90.o
+	$(FC) $(FFLAGS) -c local_tls.f90
 
 linalgebra_f90.o: linalgebra_f90.f90 
 	$(FC) $(FFLAGS) -c linalgebra_f90.f90
 
-make_refmac_dummy.o: make_refmac_dummy.f optimise_solvent_all.f90
-	$(FC) $(FFLAGS) -c optimise_solvent_all.f90 make_refmac_dummy.f
+make_refmac_dummy.o: make_refmac_dummy.f optimise_solvent_all.o
+	$(FC) $(FFLAGS) -c make_refmac_dummy.f
 
-ml_scaling_double.o: ml_scaling_double.f optimise_solvent_all.f90
-	$(FC) $(FFLAGS) -c optimise_solvent_all.f90 ml_scaling_double.f
+ml_scaling_double.o: ml_scaling_double.f optimise_solvent_all.o
+	$(FC) $(FFLAGS) -c ml_scaling_double.f
 
-refall_twin.o: refall_twin.f optimise_solvent_all.f90
-	$(FC) $(FFLAGS) -c optimise_solvent_all.f90 refall_twin.f
+refall_twin.o: refall_twin.f optimise_solvent_all.o
+	$(FC) $(FFLAGS) -c refall_twin.f
 
-rharvest.o: rharvest.f optimise_solvent_all.f90
-	$(FC) $(FFLAGS) -c optimise_solvent_all.f90 rharvest.f
+rharvest.o: rharvest.f optimise_solvent_all.o
+	$(FC) $(FFLAGS) -c rharvest.f
 
-solvent_contr_mask.o: solvent_contr_mask.f optimise_solvent_all.f90
-	$(FC) $(FFLAGS) -c optimise_solvent_all.f90 solvent_contr_mask.f
+solvent_contr_mask.o: solvent_contr_mask.f optimise_solvent_all.o atomf77mod.o
+	$(FC) $(FFLAGS) -c  atomf77mod.f solvent_contr_mask.f
 
-subag_scale_hessian.o: subag_scale_hessian.f optimise_solvent_all.f90
-	$(FC) $(FFLAGS) -c optimise_solvent_all.f90 subag_scale_hessian.f
+subag_scale_hessian.o: subag_scale_hessian.f optimise_solvent_all.o
+	$(FC) $(FFLAGS) -c subag_scale_hessian.f
 
-subcf_scale1.o: subcf_scale1.f optimise_solvent_all.f90
-	$(FC) $(FFLAGS) -c optimise_solvent_all.f90 subcf_scale1.f
+subcf_scale1.o: subcf_scale1.f optimise_solvent_all.o
+	$(FC) $(FFLAGS) -c subcf_scale1.f
 
-refmac_xml.o: refmac_xml.f optimise_solvent_all.f90
-	$(FC) $(FFLAGS) -c optimise_solvent_all.f90 refmac_xml.f
+refmac_xml.o: refmac_xml.f optimise_solvent_all.o
+	$(FC) $(FFLAGS) -c refmac_xml.f
 
 hkl_pack.o:  hkl_pack.f90
 	$(FC) $(FFLAGS) -c hkl_pack.f90
@@ -239,30 +235,31 @@ subvag.o: subvag.f hkl_pack.f90
 	$(FC) $(FFLAGS) -c hkl_pack.f90 subvag.f
 
 refmac:	$(SUBR)
-	$(FC) $(FFLAGS) -o refmac${VERSION}   ${SUBR} $(LLIBOTHERS) $(LLIBCCP)
+	$(FC) $(FFLAGS) $(LDFLAGS) -o refmac${VERSION}   ${SUBR} $(LLIBOTHERS) $(LLIBCCP) $(LLIBCIF) $(LLIBLAPACK)
 
-mol2_file.o:	mol2_file.f odb_files.f90
-	$(FC) $(FFLAGS) -c odb_files.f90 mol2_file.f
+mol2_file.o:	mol2_file.f odb_files.o
+	$(FC) $(FFLAGS) -c mol2_file.f
 
-odb_files.o:	odb_files.f90 elements_module.f90 enerf77mod.f
-	$(FC) $(FFLAGS) -c elements_module.f90 enerf77mod.f odb_files.f90
+odb_files.o:	odb_files.f90 elements_module.o enerf77mod.f
+	$(FC) $(FFLAGS) -c enerf77mod.f odb_files.f90
 
 elements_module.o:	elements_module.f90
 	$(FC) $(FFLAGS) -c elements_module.f90
 
-make_lib2.o:	make_lib2.f odb_files.f90 
-	$(FC) $(FFLAGS) -c odb_files.f90 make_lib2.f
+make_lib2.o:	make_lib2.f odb_files.o
+	$(FC) $(FFLAGS) -c make_lib2.f
 
 pdb2libcheck.o:	pdb2libcheck.f90
 	$(FC) $(FFLAGS) -c pdb2libcheck.f90
 
-libcheck.o:	libcheck.f elements_module.f90 pdb2libcheck.f90
-	$(FC) $(FFLAGS) -c elements_module.f90 pdb2libcheck.f90 libcheck.f
+libcheck.o:	libcheck.f elements_module.o pdb2libcheck.o
+	$(FC) $(FFLAGS) -c libcheck.f
 
 libcheck:	$(SUBL)
-	$(FC) $(FFLAGS) -o libcheck${VERSION} $(SUBL)
+	$(FC) $(FFLAGS) $(LDFLAGS) -o libcheck${VERSION} $(SUBL) $(LLIBCCP) $(LLIBCIF) $(LLIBLAPACK)
 
 clean:
 	/bin/rm *.o
 
 bridge.o:			bridge.cpp llhood.h covmat.h Gauss.h tabfunc.h
+	$(CXX) $(CXXFLAGS) -c bridge.cpp