diff --git a/image_analysis/structure_refinement/ModelValidation.cpp b/image_analysis/structure_refinement/ModelValidation.cpp
index 14bc6ed39..17d4f39e6 100644
--- a/image_analysis/structure_refinement/ModelValidation.cpp
+++ b/image_analysis/structure_refinement/ModelValidation.cpp
@@ -7,6 +7,7 @@
 #include <algorithm>
 #include <cmath>
 #include <complex>
+#include <cstdio>
 #include <array>
 #include <atomic>
 #include <functional>
@@ -59,11 +60,20 @@ gemmi::Grid<float> map_from_coefficients(gemmi::AsuData<std::complex<float>> &co
     return MapFromFPhi(gemmi::get_f_phi_on_grid<float>(coef, size, true));
 }
 
+// A file this run may already have written - the validation in the model's setting writes over the
+// first one's maps - is removed before it is written again, not truncated: XFS (and ext4) flush a file
+// truncated and rewritten when it is closed, and three 150 MB maps forced out to a disk that way cost
+// seconds where a fresh file costs nothing.
+void remove_before_rewriting(const std::string &path) {
+    std::remove(path.c_str());
+}
+
 // Write a map as CCP4; return its RMS (the sigma the map is read in).
 double write_ccp4(const gemmi::Grid<float> &map, const std::string &path) {
     gemmi::Ccp4<float> ccp4;
     ccp4.grid = map;
     ccp4.update_ccp4_header(2);
+    remove_before_rewriting(path);
     ccp4.write_ccp4_map(path);
     return ccp4.hstats.rms;
 }
@@ -1466,6 +1476,7 @@ ModelValidationResult Validate(const std::vector<MergedReflection> &merged,
         }
         mtz.nreflections = static_cast<int>(terms.size());
         mtz.data = std::move(data);
+        remove_before_rewriting(output_prefix + "_maps.mtz");
         mtz.write_to_file(output_prefix + "_maps.mtz");
     } catch (const std::exception &e) {
         logger.Warning("Model validation: could not write map MTZ: {}", e.what());