diff --git a/biology/dsr-pdb/Makefile b/biology/dsr-pdb/Makefile
index c73b661acd4f..b17e471da589 100644
--- a/biology/dsr-pdb/Makefile
+++ b/biology/dsr-pdb/Makefile
@@ -1,38 +1,39 @@
 PORTNAME=	dsr-pdb
 DISTVERSION=	1.0.3
-PORTREVISION=	5
+PORTREVISION=	6
 CATEGORIES=	biology
 MASTER_SITES=	https://graphics.stanford.edu/~drussel/
 DISTNAME=	${PORTNAME}
 DIST_SUBDIR=	${PORTNAME}-${DISTVERSION}
 
 MAINTAINER=	yuri@FreeBSD.org
 COMMENT=	Simple C++ PDB reader (reads the protein description format)
 
 LICENSE=	LGPL21
 LICENSE_FILE=	${WRKSRC}/COPYING.txt
 
 BROKEN_aarch64=	ld: error: undefined symbol: .mcount (see bug#262709)
 
 LIB_DEPENDS=	libboost_program_options.so:devel/boost-libs
 
 USES=		compiler:c++11-lang gmake libtool localbase:ldflags tar:tgz
-GNU_CONFIGURE=	yes
 USE_LDCONFIG=	yes
 
+GNU_CONFIGURE=	yes
+
 WRKSRC=		${WRKDIR}/${PORTNAME}-${PORTVERSION}
 CXXFLAGS+=	-fPIC --std=c++11 # libboost_program_options.so isn't found without --std=c++11
 
 post-patch:
 .for dir in lib tools test
 	@cd ${WRKSRC}/${dir} && ${LN} -s ../ dsrpdb
 .endfor
 
 post-build: # the project itself doesn't support shared libraries in a regular way
 	@cd ${WRKSRC}/lib && ${CXX} ${LDFLAGS} --shared -Wl,-soname,libdsrpdb.so -o libdsrpdb.so *.o
 
 post-install:
 	${INSTALL_DATA} ${WRKSRC}/config.h ${STAGEDIR}${PREFIX}/include/dsrpdb
 	${INSTALL_LIB} ${WRKSRC}/lib/libdsrpdb.so ${STAGEDIR}${PREFIX}/lib
 
 .include <bsd.port.mk>
diff --git a/biology/dsr-pdb/files/patch-lib_Makefile.in b/biology/dsr-pdb/files/patch-lib_Makefile.in
new file mode 100644
index 000000000000..58a5ed2003b5
--- /dev/null
+++ b/biology/dsr-pdb/files/patch-lib_Makefile.in
@@ -0,0 +1,13 @@
+- workaround for https://bugs.freebsd.org/bugzilla/show_bug.cgi?id=262709
+
+--- lib/Makefile.in.orig	2022-03-22 00:02:00 UTC
++++ lib/Makefile.in
+@@ -180,7 +180,7 @@ sysconfdir = @sysconfdir@
+ target_alias = @target_alias@
+ lib_LTLIBRARIES = libdsrpdb.la
+ noinst_HEADERS = pdb_utils.h Residue_data.h
+-AM_CPPFLAGS = -I../include -pg
++AM_CPPFLAGS = -I../include
+ libdsrpdb_la_SOURCES = Residue.cc Protein.cc Residue_data.cc Protein_pdb.cc pdb_utils.cc Model.cc PDB.cc align.cc distance.cc Error_logger.cc
+ libdsrpdb_la_LDFLAGS = -static
+ all: all-am