 makefile_refmac.inc1 |  215 ++++++++++++++++++++++++--------------------------
 1 files changed, 104 insertions(+), 111 deletions(-)

diff --git a/makefile_refmac.inc1 b/makefile_refmac.inc1
index 0f8bd63..e59fbfb 100644
--- a/makefile_refmac.inc1
+++ b/makefile_refmac.inc1
@@ -96,9 +96,7 @@ bridge.o                    \
 i0.o                        \
 i1.o                        \
 chbevl.o                    \
-make_unix_ccp4.o            \
-$(LLIBCIF)                  \
-$(LLIBLAPACK)
+make_unix_ccp4.o
 
 
 SUBL =                      \
@@ -133,9 +131,7 @@ cell_symm_subrs.o           \
 iheap_sort.o                \
 linalgebra.o                \
 math_refmac.o               \
-subnumrec.o                 \
-$(LLIBLAPACK)               \
-$(LLIBCCP)
+subnumrec.o
 
 SUB_FREE  =                 \
 freer_twin.o                 \
@@ -145,9 +141,7 @@ subnumrec.o                 \
 libT.o                      \
 iheap_sort.o                \
 cell_symm_subrs.o           \
-math_refmac.o               \
-$(LLIBLAPACK)               \
-$(LLIBCCP)
+math_refmac.o
 
 SUB_HEADER = header2matr.o
 #--------------------------------------------------------------------------------
@@ -185,41 +179,41 @@ rharvest_mod.o:  rharvest_mod.f90
 twin77mod.o:  twin77mod.f
 	$(FC) $(FFLAGS) -c twin77mod.f
 
-gibbs_gm_sampler.o:  linalgebra_f90.f90 gibbs_gm_sampler.f90
-	$(FC) $(FFLAGS) -c linalgebra_f90.f90 gibbs_gm_sampler.f90
+gibbs_gm_sampler.o:  linalgebra_f90.o gibbs_gm_sampler.f90
+	$(FC) $(FFLAGS) -c gibbs_gm_sampler.f90
 
-max_with_twins.o: restr_files.f90 max_with_twins.f weights.f90 agreem.f90
-	$(FC) $(FFLAGS) -c restr_files.f90 weights.f90 agreem.f90 max_with_twins.f
+max_with_twins.o: restr_files.o max_with_twins.f weights.o agreem.o
+	$(FC) $(FFLAGS) -c max_with_twins.f
 
-merohedr_twin.o: restr_files.f90 merohedr_twin.f
-	$(FC) $(FFLAGS) -c restr_files.f90 merohedr_twin.f
+merohedr_twin.o: restr_files.o merohedr_twin.f
+	$(FC) $(FFLAGS) -c merohedr_twin.f
 
-ls_scaling_twin_save.o: restr_files.f90 ls_scaling_twin_save.f weights.f90 agreem.f90
-	$(FC) $(FFLAGS) -c restr_files.f90 weights.f90 agreem.f90 ls_scaling_twin_save.f
+ls_scaling_twin_save.o: restr_files.o ls_scaling_twin_save.f weights.o agreem.o
+	$(FC) $(FFLAGS) -c ls_scaling_twin_save.f
 
-ml_params_refine.o: restr_files.f90 ml_params_refine.f weights.f90 agreem.f90
-	$(FC) $(FFLAGS) -c restr_files.f90 weights.f90 agreem.f90 ml_params_refine.f
+ml_params_refine.o: restr_files.o ml_params_refine.f weights.o agreem.o
+	$(FC) $(FFLAGS) -c ml_params_refine.f
 
-optimise_solvent_all.o: optimise_solvent_all.f90 agreem.f90
-	$(FC) $(FFLAGS) -c optimise_solvent_all.f90 agreem.f90
+optimise_solvent_all.o: optimise_solvent_all.f90 agreem.o
+	$(FC) $(FFLAGS) -c optimise_solvent_all.f90
 
-ncs_rest.o: ncs_rest_mod.f90 restr_files.f90 ncs_ncs_generate.f90 ncs_rest.f weights.f90
-	$(FC) $(FFLAGS) -c ncs_rest_mod.f90 restr_files.f90 ncs_ncs_generate.f90 weights.f90 ncs_rest.f
+ncs_rest.o: ncs_rest_mod.o restr_files.o ncs_ncs_generate.o ncs_rest.f weights.o
+	$(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: ncs_rest_mod.f90 restr_files.f90 dist_routines.f90 ncs_simil.f90 ridge.f90 local_tls.f90 lsq_exp2.f weights.f90 rharvest_mod.f90
-	$(FC) $(FFLAGS) -c ncs_rest_mod.f90 restr_files.f90 dist_routines.f90 ncs_simil.f90 ridge.f90 local_tls.f90  lsq_exp2.f weights.f90 rharvest_mod.f90
+lsq_exp2.o: ncs_rest_mod.o restr_files.o dist_routines.o ncs_simil.o ridge.o local_tls.o lsq_exp2.f weights.o rharvest_mod.o
+	$(FC) $(FFLAGS) -c lsq_exp2.f
 
-vdw_and_contacts.o: ncs_rest_mod.f90 vdw_and_contacts.f local_tls.f90 ridge.f90 restr_files.f90 weights.f90 agreem.f90
-	$(FC) $(FFLAGS) -c ncs_rest_mod.f90 restr_files.f90 ridge.f90 local_tls.f90 weights.f90 agreem.f90 vdw_and_contacts.f
+vdw_and_contacts.o: ncs_rest_mod.o vdw_and_contacts.f local_tls.o ridge.o restr_files.o weights.o agreem.o
+	$(FC) $(FFLAGS) -c vdw_and_contacts.f
 
 dist_routines.o: dist_routines.f90
 	$(FC) $(FFLAGS) -c dist_routines.f90
 
-ncs_simil.o: ncs_rest_mod.f90 ncs_simil.f90
-	$(FC) $(FFLAGS) -c ncs_rest_mod.f90 ncs_simil.f90
+ncs_simil.o: ncs_rest_mod.o ncs_simil.f90
+	$(FC) $(FFLAGS) -c ncs_simil.f90
 
 ridge.o: ridge.f90
 	$(FC) $(FFLAGS) -c ridge.f90
@@ -227,140 +221,138 @@ ridge.o: ridge.f90
 align_refmac.o: align_refmac.f90
 	$(FC) $(FFLAGS) -c align_refmac.f90
 
-rigid_allocate.o: restr_files.f90 rigid_allocate.f agreem.f90
-	$(FC) $(FFLAGS) -c restr_files.f90 agreem.f90 rigid_allocate.f
+rigid_allocate.o: restr_files.o rigid_allocate.f agreem.o
+	$(FC) $(FFLAGS) -c rigid_allocate.f
 
-tls_allocate.o: restr_files.f90 tls_allocate.f weights.f90 agreem.f90
-	$(FC) $(FFLAGS) -c restr_files.f90 weights.f90 agreem.f90 tls_allocate.f
+tls_allocate.o: restr_files.o tls_allocate.f weights.o agreem.o
+	$(FC) $(FFLAGS) -c tls_allocate.f
 
-hkon_secder_tch.o: ridge.f90 gibbs_gm_sampler.f90 ncs_rest_mod.f90 hkon_secder_tch.f local_tls.f90 ncs_simil.f90 optimise_solvent_all.f90 \
-                   restr_files.f90 weights.f90 agreem.f90 rharvest_mod.f90
-	$(FC) $(FFLAGS) -c ridge.f90 gibbs_gm_sampler.f90 ncs_rest_mod.f90 restr_files.f90 optimise_solvent_all.f90 ncs_simil.f90 local_tls.f90 \
-	                   hkon_secder_tch.f weights.f90 agreem.f90 rharvest_mod.f90
+hkon_secder_tch.o: ridge.o gibbs_gm_sampler.o ncs_rest_mod.o hkon_secder_tch.f local_tls.o ncs_simil.o optimise_solvent_all.o \
+                   restr_files.o weights.o agreem.o rharvest_mod.o
+	$(FC) $(FFLAGS) -c hkon_secder_tch.f
 
-oppro_allocate.o: ncs_rest_mod.f90 oppro_allocate.f filter_params.f90 optimise_solvent_all.f90 restr_files.f90 weights.f90
-	$(FC) $(FFLAGS) -c ncs_rest_mod.f90 restr_files.f90 optimise_solvent_all.f90 filter_params.f90 weights.f90 oppro_allocate.f
+oppro_allocate.o: ncs_rest_mod.o oppro_allocate.f filter_params.o optimise_solvent_all.o restr_files.o weights.o
+	$(FC) $(FFLAGS) -c oppro_allocate.f
 
-read_extra_restraints.o: restr_files.f90 read_extra_restraints.f weights.f90
-	$(FC) $(FFLAGS) -c restr_files.f90 weights.f90 read_extra_restraints.f
+read_extra_restraints.o: restr_files.o read_extra_restraints.f weights.o
+	$(FC) $(FFLAGS) -c read_extra_restraints.f
 
-coords.o: coords.f90 atomf77mod.f
-	$(FC) $(FFLAGS) -c atomf77mod.f coords.f90
+coords.o: coords.f90 atomf77mod.o
+	$(FC) $(FFLAGS) -c coords.f90
 
 
-ls_scaling_double.o: ls_scaling_double.f weights.f90 agreem.f90
-	$(FC) $(FFLAGS) -c ls_scaling_double.f weights.f90 agreem.f90
+ls_scaling_double.o: ls_scaling_double.f weights.o agreem.o
+	$(FC) $(FFLAGS) -c ls_scaling_double.f
 
-fast_hessian_tabulation.o: fast_hessian_tabulation.f weights.f90 
-	$(FC) $(FFLAGS) -c fast_hessian_tabulation.f weights.f90
+fast_hessian_tabulation.o: fast_hessian_tabulation.f weights.o
+	$(FC) $(FFLAGS) -c fast_hessian_tabulation.f
 
-calc_stats_twin.o: calc_stats_twin.f weights.f90 agreem.f90 rharvest_mod.f90
-	$(FC) $(FFLAGS) -c calc_stats_twin.f weights.f90 agreem.f90 rharvest_mod.f90
+calc_stats_twin.o: calc_stats_twin.f weights.o agreem.o rharvest_mod.o
+	$(FC) $(FFLAGS) -c calc_stats_twin.f
 
-refpre_twin.o: refpre_twin.f coords.f90 automorphism.f90 restr_files.f90 weights.f90 agreem.f90 rharvest_mod.f90
-	$(FC) $(FFLAGS) -c restr_files.f90 coords.f90 automorphism.f90 weights.f90 agreem.f90 rharvest_mod.f90 refpre_twin.f
+refpre_twin.o: refpre_twin.f coords.o automorphism.o restr_files.o weights.o agreem.o rharvest_mod.o
+	$(FC) $(FFLAGS) -c refpre_twin.f
 
 
-decide_twin_opers_0.o: restr_files.f90 decide_twin_opers_0.f
-	$(FC) $(FFLAGS) -c restr_files.f90 decide_twin_opers_0.f
+decide_twin_opers_0.o: restr_files.o decide_twin_opers_0.f
+	$(FC) $(FFLAGS) -c decide_twin_opers_0.f
 
 automorphism.o: automorphism.f90
 	$(FC) $(FFLAGS) -c automorphism.f90
 
-mtz_write_twin.o: mtz_write_twin.f filter_params.f90 restr_files.f90 weights.f90 agreem.f90
-	$(FC) $(FFLAGS) -c restr_files.f90 filter_params.f90 weights.f90 agreem.f90 mtz_write_twin.f
+mtz_write_twin.o: mtz_write_twin.f filter_params.o restr_files.o weights.o agreem.o
+	$(FC) $(FFLAGS) -c mtz_write_twin.f
 
 filter_params.o: filter_params.f90
 	$(FC) $(FFLAGS) -c filter_params.f90
 
-rcard_tor1.o: ncs_rest_mod.f90 rcard_tor1.f filter_params.f90 local_tls.f90 ridge.f90 optimise_solvent_all.f90 restr_files.f90 weights.f90 \
-              agreem.f90 rharvest_mod.f90 ncs_constr.f90
-	$(FC) $(FFLAGS) -c ncs_rest_mod.f90 restr_files.f90 optimise_solvent_all.f90 filter_params.f90 local_tls.f90 ridge.f90 weights.f90 \
-	                   agreem.f90 rharvest_mod.f90 ncs_constr.f90 rcard_tor1.f
+rcard_tor1.o: ncs_rest_mod.o rcard_tor1.f filter_params.o local_tls.o ridge.o optimise_solvent_all.o restr_files.o weights.o \
+              agreem.o rharvest_mod.o ncs_constr.o
+	$(FC) $(FFLAGS) -c rcard_tor1.f
 
-inout_routines.o: restr_files.f90 inout_routines.f
-	$(FC) $(FFLAGS) -c restr_files.f90 inout_routines.f
+inout_routines.o: restr_files.o inout_routines.f
+	$(FC) $(FFLAGS) -c inout_routines.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: restr_files.f90 ncs_rest_mod.f90 make_refmac_dummy.f optimise_solvent_all.f90 weights.f90 agreem.f90 rharvest_mod.f90
-	$(FC) $(FFLAGS) -c restr_files.f90 ncs_rest_mod.f90 weights.f90 agreem.f90 rharvest_mod.f90 optimise_solvent_all.f90 make_refmac_dummy.f
+make_refmac_dummy.o: restr_files.o ncs_rest_mod.o make_refmac_dummy.f optimise_solvent_all.o weights.o agreem.o rharvest_mod.o
+	$(FC) $(FFLAGS) -c make_refmac_dummy.f
 
-ml_scaling_double.o: ml_scaling_double.f optimise_solvent_all.f90 weights.f90 agreem.f90 rharvest_mod.f90
-	$(FC) $(FFLAGS) -c optimise_solvent_all.f90 weights.f90 agreem.f90 rharvest_mod.f90 ml_scaling_double.f
+ml_scaling_double.o: ml_scaling_double.f optimise_solvent_all.o weights.o agreem.o rharvest_mod.o
+	$(FC) $(FFLAGS) -c ml_scaling_double.f
 
-refall_twin.o: refall_twin.f optimise_solvent_all.f90 restr_files.f90 weights.f90 agreem.f90 rharvest_mod.f90
-	$(FC) $(FFLAGS) -c restr_files.f90 optimise_solvent_all.f90  weights.f90 agreem.f90 rharvest_mod.f90 refall_twin.f
+refall_twin.o: refall_twin.f optimise_solvent_all.o restr_files.f90 weights.o agreem.o rharvest_mod.o
+	$(FC) $(FFLAGS) -c refall_twin.f
 
-rharvest_subr.o: ncs_rest_mod.f90 rharvest_subr.f optimise_solvent_all.f90 weights.f90 agreem.f90 rharvest_mod.f90
-	$(FC) $(FFLAGS) -c ncs_rest_mod.f90 optimise_solvent_all.f90  weights.f90 agreem.f90 rharvest_mod.f90 rharvest_subr.f
+rharvest_subr.o: ncs_rest_mod.o rharvest_subr.f optimise_solvent_all.o weights.o agreem.o rharvest_mod.o
+	$(FC) $(FFLAGS) -c rharvest_subr.f
 
-solvent_contr_mask.o: solvent_contr_mask.f optimise_solvent_all.f90 weights.f90 agreem.f90 rharvest_mod.f90 ncs_constr.f90
-	$(FC) $(FFLAGS) -c optimise_solvent_all.f90 weights.f90 agreem.f90 rharvest_mod.f90 ncs_constr.f90 solvent_contr_mask.f
+solvent_contr_mask.o: solvent_contr_mask.f optimise_solvent_all.o weights.o agreem.o rharvest_mod.o ncs_constr.o
+	$(FC) $(FFLAGS) -c solvent_contr_mask.f
 
-subag_scale_hessian.o: subag_scale_hessian.f optimise_solvent_all.f90 restr_files.f90 weights.f90 agreem.f90 rharvest_mod.f90 ncs_constr.f90
-	$(FC) $(FFLAGS) -c restr_files.f90 optimise_solvent_all.f90 weights.f90 agreem.f90 rharvest_mod.f90 ncs_constr.f90 subag_scale_hessian.f
+subag_scale_hessian.o: subag_scale_hessian.f optimise_solvent_all.o restr_files.o weights.o agreem.o rharvest_mod.o ncs_constr.o
+	$(FC) $(FFLAGS) -c subag_scale_hessian.f
 
-aniso_ref_eigen.o: aniso_ref_eigen.f ncs_constr.f90
-	$(FC) $(FFLAGS) -c ncs_constr.f90 aniso_ref_eigen.f
+aniso_ref_eigen.o: aniso_ref_eigen.f ncs_constr.o
+	$(FC) $(FFLAGS) -c aniso_ref_eigen.f
 
-subcf_scale1.o: subcf_scale1.f optimise_solvent_all.f90 weights.f90 agreem.f90 rharvest_mod.f90
-	$(FC) $(FFLAGS) -c optimise_solvent_all.f90 weights.f90 agreem.f90 rharvest_mod.f90 subcf_scale1.f
+subcf_scale1.o: subcf_scale1.f optimise_solvent_all.o weights.o agreem.o rharvest_mod.o
+	$(FC) $(FFLAGS) -c subcf_scale1.f
 
-bvalue_routines.o: bvalue_routines.f90 restr_files.f90 atomf77mod.f
-	$(FC) $(FFLAGS) -c restr_files.f90 atomf77mod.f bvalue_routines.f90
+bvalue_routines.o: bvalue_routines.f90 restr_files.o atomf77mod.o
+	$(FC) $(FFLAGS) -c bvalue_routines.f90
 
-newentry_idealise.o:: newentry_idealise.f weights.f90
-	$(FC) $(FFLAGS) -c newentry_idealise.f weights.f90
+newentry_idealise.o:: newentry_idealise.f weights.o
+	$(FC) $(FFLAGS) -c newentry_idealise.f
 
-occupancy_only_refine.o: occupancy_only_refine.f agreem.f90 rharvest_mod.f90
-	$(FC) $(FFLAGS) -c occupancy_only_refine.f agreem.f90 rharvest_mod.f90
+occupancy_only_refine.o: occupancy_only_refine.f agreem.o rharvest_mod.o
+	$(FC) $(FFLAGS) -c occupancy_only_refine.f
 
-refmac_completeness.o: weights.f90 agreem.f90 rharvest_mod.f90  refmac_completeness.f90
-	$(FC) $(FFLAGS) -c weights.f90 agreem.f90 rharvest_mod.f90 refmac_completeness.f90
+refmac_completeness.o: weights.o agreem.o rharvest_mod.o refmac_completeness.f90
+	$(FC) $(FFLAGS) -c refmac_completeness.f90
 
-refmac_xml.o: refmac_xml.f optimise_solvent_all.f90 restr_files.f90 bvalue_routines.f90 weights.f90 agreem.f90 rharvest_mod.f90
-	$(FC) $(FFLAGS) -c bvalue_routines.f90 restr_files.f90 optimise_solvent_all.f90 weights.f90 agreem.f90 rharvest_mod.f90 refmac_xml.f
+refmac_xml.o: refmac_xml.f optimise_solvent_all.o restr_files.o bvalue_routines.o weights.o agreem.o rharvest_mod.o
+	$(FC) $(FFLAGS) -c refmac_xml.f
 
 hkl_pack.o:  hkl_pack.f90
 	$(FC) $(FFLAGS) -c hkl_pack.f90
 
-extra_eigen.o: extra_eigen.f agreem.f90 ncs_constr.f90
-	$(FC) $(FFLAGS) -c extra_eigen.f agreem.f90 ncs_constr.f90
+extra_eigen.o: extra_eigen.f agreem.o ncs_constr.o
+	$(FC) $(FFLAGS) -c extra_eigen.f
 
-subvag.o: subvag.f hkl_pack.f90
-	$(FC) $(FFLAGS) -c hkl_pack.f90 subvag.f
+subvag.o: subvag.f hkl_pack.o
+	$(FC) $(FFLAGS) -c subvag.f
 
-make_PDB.o: make_PDB.f ncs_constr.f90
-	$(FC) $(FFLAGS) -c ncs_constr.f90 make_PDB.f
+make_PDB.o: make_PDB.f ncs_constr.o
+	$(FC) $(FFLAGS) -c make_PDB.f
 
-make_CIF.o: make_CIF.f ncs_constr.f90
-	$(FC) $(FFLAGS) -c ncs_constr.f90 make_CIF.f
+make_CIF.o: make_CIF.f ncs_constr.o
+	$(FC) $(FFLAGS) -c make_CIF.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.o
+	$(FC) $(FFLAGS) -c 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
 
 header2matr.o:	header2matr.f90
 	$(FC) $(FFLAGS) -c header2matr.f90
@@ -369,16 +361,17 @@ freer_twin.o:	freer_twin.f90
 	$(FC) $(FFLAGS) -c  freer_twin.f90
 
 libcheck:	$(SUBL)
-	$(FC) $(FFLAGS) -o libcheck${VERSION} $(SUBL)
+	$(FC) $(FFLAGS) $(LDFLAGS) -o libcheck${VERSION} $(SUBL) $(LLIBCCP) $(LLIBCIF) $(LLIBLAPACK)
 
 free_twin:	$(SUB_FREE)
-	$(FC) $(FFLAGS) -o FreeTwin${VERSION} $(SUB_FREE)
+	$(FC) $(FFLAGS) $(LDFLAGS) -o FreeTwin${VERSION} $(SUB_FREE) $(LLIBCCP) $(LLIBLAPACK)
 
 
 header2matr:	$(SUB_HEADER)
-	$(FC) $(FFLAGS) -o header2matr${VERSION} $(SUB_HEADER)
+	$(FC) $(FFLAGS) $(LDFLAGS) -o header2matr${VERSION} $(SUB_HEADER)
 
 clean:
 	/bin/rm *.o *.mod
 
 bridge.o:			bridge.cpp llhood.h covmat.h Gauss.h tabfunc.h
+	$(CXX) $(CXXFLAGS) -c bridge.cpp