update with output in mmCIF, PPII helices

GNUmakefile.in

@@ -16,12 +16,13 @@ firstTarget: all
 CXX					= @CXX@
 CXXFLAGS			= @CXXFLAGS@ @CPPFLAGS@ @BOOST_CPPFLAGS@ @PTHREAD_CFLAGS@
 LDFLAGS				= @LDFLAGS@ @BOOST_LDFLAGS@ @PTHREAD_CFLAGS@
-LIBS				= @LIBS@ \
+LIBS				= -lcif++ \
 					  @BOOST_IOSTREAMS_LIB@ \
 					  @BOOST_THREAD_LIB@ \
 					  @BOOST_REGEX_LIB@ \
 					  @BOOST_PROGRAM_OPTIONS_LIB@ \
-					  -lboost_timer -lboost_chrono
+					  -lboost_timer -lboost_chrono \
+					  @LIBS@
 
 prefix				= @prefix@
 exec_prefix			= @exec_prefix@

configure.ac

@@ -29,12 +29,6 @@ fi
 
 AX_PTHREAD
 
-AX_BOOST_BASE([1.65.1], [], [AC_MSG_ERROR([Could not find a recent version of boost])])
-AX_BOOST_IOSTREAMS
-AX_BOOST_THREAD
-AX_BOOST_REGEX
-AX_BOOST_PROGRAM_OPTIONS
-
 AC_ARG_WITH([cif++],
 	AS_HELP_STRING([--with-cif++=@<:@location@:>@],
 		[Use the cif++ library as specified.]),
@@ -42,15 +36,19 @@ AC_ARG_WITH([cif++],
 			CPPFLAGS="$CPPFLAGS -I ${withval}/include"
 			CXXFLAGS="$CXXFLAGS -I ${withval}/include"
 			LDFLAGS="$LDFLAGS -L${withval}/.libs"
-			LIBS="$LIBS -lcif++"
 			AC_SUBST([CIFPP_RSRC], [${withval}/rsrc]) 
 		])
 
-
 AX_CHECK_LIBRARY([LIBCIFPP], [cif++/Config.hpp], [cif++],
 	[],
 	[AC_MSG_ERROR([libcif++ not found - cannot continue])])
 
+AX_BOOST_BASE([1.65.1], [], [AC_MSG_ERROR([Could not find a recent version of boost])])
+AX_BOOST_IOSTREAMS
+AX_BOOST_THREAD
+AX_BOOST_REGEX
+AX_BOOST_PROGRAM_OPTIONS
+
 AC_ARG_VAR([CCP4], [The location where CCP4 is installed])
 
 AS_IF([test x"$CCP4" != x""],