diff --git a/src/colvar/PathMSDBase.cpp b/src/colvar/PathMSDBase.cpp
index 2aab621ac4a43b8d8b0b0bce6ed4d4d6d0ff0e4d..7daf8a429536a5d18a68eeab7cc01b07af134135 100644
--- a/src/colvar/PathMSDBase.cpp
+++ b/src/colvar/PathMSDBase.cpp
@@ -86,14 +86,14 @@ PathMSDBase::PathMSDBase(const ActionOptions&ao):
         unsigned nat=mypdb.getAtomNumbers().size();
         if(nat!=mypdb.getAtomNumbers().size()) error("frames should have the same number of atoms");
         if(aaa.empty()) {
-           aaa=mypdb.getAtomNumbers();
-           log.printf("  found %d atoms in input \n",aaa.size());
-           log.printf("  with indices : ");
-           for(unsigned i=0; i<aaa.size(); ++i) {
-             if(i%25==0) log<<"\n";
-             log.printf("%d ",aaa[i].serial());
-           }
-           log.printf("\n");
+          aaa=mypdb.getAtomNumbers();
+          log.printf("  found %d atoms in input \n",aaa.size());
+          log.printf("  with indices : ");
+          for(unsigned i=0; i<aaa.size(); ++i) {
+            if(i%25==0) log<<"\n";
+            log.printf("%d ",aaa[i].serial());
+          }
+          log.printf("\n");
         }
         if(aaa!=mypdb.getAtomNumbers()) error("frames should contain same atoms in same order");
         log<<"Found PDB: "<<nframes<<" containing  "<<mypdb.getAtomNumbers().size()<<" atoms\n";
diff --git a/src/mapping/Mapping.cpp b/src/mapping/Mapping.cpp
index da3beb758fdf1b9413daf09454f4168b49bacc0e..10c6b3d1dcba823f3d13a85b408191031e83c6b6 100644
--- a/src/mapping/Mapping.cpp
+++ b/src/mapping/Mapping.cpp
@@ -109,14 +109,14 @@ Mapping::Mapping(const ActionOptions&ao):
   if( req_args.size()>0 && atoms.size()>0 ) error("cannot mix atoms and arguments");
   if( req_args.size()>0 ) requestArguments( req_args );
   if( atoms.size()>0 ) {
-      log.printf("  found %d atoms in input \n",atoms.size());
-      log.printf("  with indices : ");
-      for(unsigned i=0; i<atoms.size(); ++i) {
-        if(i%25==0) log<<"\n";
-        log.printf("%d ",atoms[i].serial());
-      }
-      log.printf("\n");
-      requestAtoms( atoms );
+    log.printf("  found %d atoms in input \n",atoms.size());
+    log.printf("  with indices : ");
+    for(unsigned i=0; i<atoms.size(); ++i) {
+      if(i%25==0) log<<"\n";
+      log.printf("%d ",atoms[i].serial());
+    }
+    log.printf("\n");
+    requestAtoms( atoms );
   }
   // Duplicate all frames (duplicates are used by sketch-map)
   // mymap->duplicateFrameList();
diff --git a/src/mapping/PCAVars.cpp b/src/mapping/PCAVars.cpp
index 18c6828a17f4d711bc065e3dde2dae6eb32dd697..224dfb7493b34491f291e9398d00454eefe482dc 100644
--- a/src/mapping/PCAVars.cpp
+++ b/src/mapping/PCAVars.cpp
@@ -268,14 +268,14 @@ PCAVars::PCAVars(const ActionOptions& ao):
   // Get the arguments and atoms that are required
   std::vector<AtomNumber> atoms; myref->getAtomRequests( atoms, false );
   std::vector<std::string> args; myref->getArgumentRequests( args, false );
-  if( atoms.size()>0 ) { 
-      log.printf("  found %d atoms in input \n",atoms.size());
-      log.printf("  with indices : ");
-      for(unsigned i=0; i<atoms.size(); ++i) {
-        if(i%25==0) log<<"\n";
-        log.printf("%d ",atoms[i].serial());
-      }
-      log.printf("\n");
+  if( atoms.size()>0 ) {
+    log.printf("  found %d atoms in input \n",atoms.size());
+    log.printf("  with indices : ");
+    for(unsigned i=0; i<atoms.size(); ++i) {
+      if(i%25==0) log<<"\n";
+      log.printf("%d ",atoms[i].serial());
+    }
+    log.printf("\n");
   }
   requestAtoms( atoms ); std::vector<Value*> req_args;
   interpretArgumentList( args, req_args ); requestArguments( req_args );