diff --git a/wwpdb/apps/ann_tasks_v2/__init__.py b/wwpdb/apps/ann_tasks_v2/__init__.py
index 3638c83..7be2b04 100644
--- a/wwpdb/apps/ann_tasks_v2/__init__.py
+++ b/wwpdb/apps/ann_tasks_v2/__init__.py
@@ -2,4 +2,4 @@
 __author__ = "Ezra Peisach"
 __email__ = "ezra.peisach@rcsb.org"
 __license__ = "Apache 2.0"
-__version__ = "0.41.1"
+__version__ = "0.41.2"
diff --git a/wwpdb/apps/ann_tasks_v2/assembly/AssemblyInput.py b/wwpdb/apps/ann_tasks_v2/assembly/AssemblyInput.py
index 5f210e2..1b74c57 100644
--- a/wwpdb/apps/ann_tasks_v2/assembly/AssemblyInput.py
+++ b/wwpdb/apps/ann_tasks_v2/assembly/AssemblyInput.py
@@ -347,6 +347,8 @@ def makeSymopInfoTable(self, entryId="1ABC", entryFileName=None):
             #
         #
         symopFile = os.path.join(self.__sessionPath, entryId + "-symop-info.txt")
+        if os.access(symopFile, os.R_OK):
+            os.remove(symopFile)
         #
         try:
             dp = RcsbDpUtility(tmpPath=self.__sessionPath, siteId=self.__siteId, verbose=self.__verbose, log=self.__lfh)
diff --git a/wwpdb/apps/ann_tasks_v2/assembly/AssemblySelect.py b/wwpdb/apps/ann_tasks_v2/assembly/AssemblySelect.py
index 1609f57..d482953 100644
--- a/wwpdb/apps/ann_tasks_v2/assembly/AssemblySelect.py
+++ b/wwpdb/apps/ann_tasks_v2/assembly/AssemblySelect.py
@@ -96,11 +96,16 @@ def run(self, entryId, inpFile, sessionName, maxAssems=50):
             inpPath = os.path.join(self.__sessionPath, inpFile)
             reportPath = os.path.join(self.__sessionPath, entryId + "_assembly-report_P1.xml")
             logPath = os.path.join(self.__sessionPath, entryId + "-assembly-report.log")
+            for filePath in ( reportPath, logPath ):
+                if os.access(filePath, os.R_OK):
+                    os.remove(filePath)
+                #
             #
             dp = RcsbDpUtility(tmpPath=self.__sessionPath, siteId=self.__siteId, verbose=self.__verbose, log=self.__lfh)
             dp.imp(inpPath)
             if self.__assemblyArgs is not None and len(self.__assemblyArgs) > 0:
                 dp.addInput(name="pisa_assembly_arguments", value=self.__assemblyArgs)
+            #
             dp.addInput(name="pisa_session_name", value=sessionName)
             dp.op("pisa-analysis")
             dp.expLog(logPath)
@@ -127,7 +132,10 @@ def run(self, entryId, inpFile, sessionName, maxAssems=50):
                     dp.exp(assemModelFileName)
                     if self.__verbose:
                         self.__lfh.write("+AssemblySelect.run - creating assembly model %r file %s\n" % (assemblyUid, assemModelFileName))
-                # dp.cleanup()
+                    #
+                #
+            #
+            # dp.cleanup()
             return True
         except:  # noqa: E722 pylint: disable=bare-except
             if self.__verbose:
@@ -273,6 +281,11 @@ def updateModelFile(self, entryId, inpFile, assignPath, updateInput=True):
             retPath = os.path.join(self.__sessionPath, entryId + "_model-updated_P1.cif")
             logPath = os.path.join(self.__sessionPath, entryId + "_assembly-merge.log")
             reportPath = os.path.join(self.__sessionPath, entryId + "_assembly-report_P1.xml")
+            for filePath in ( retPath, logPath ):
+                if os.access(filePath, os.R_OK):
+                    os.remove(filePath)
+                #
+            #
             if self.__verbose:
                 self.__lfh.write("+AssemblySelect.updateModelFile() input  path %s\n" % inpPath)
                 self.__lfh.write("+AssemblySelect.updateModelFile() return path %s\n" % retPath)
@@ -288,14 +301,14 @@ def updateModelFile(self, entryId, inpFile, assignPath, updateInput=True):
             #
             dp.op("pisa-assembly-merge-cif")
             dp.exp(retPath)
-            if updateInput:
+            if updateInput and os.access(retPath, os.R_OK):
                 dp.exp(inpPath)
+            #
             dp.expLog(logPath)
             #
             #  Added generation of assembly files to the model update.
             if os.access(retPath, os.R_OK):
                 self.generateAssemblies(entryId, modelFilePath=retPath)
-
             #
             # dp.cleanup()
             return True
@@ -314,6 +327,10 @@ def autoAssignDefaultAssembly(self, entryId, inpFile):
             logPath = os.path.join(self.__sessionPath, entryId + "_assembly-merge.log")
             assignPath = os.path.join(self.__sessionPath, entryId + "_assembly-assign_P1.cif")
             reportPath = os.path.join(self.__sessionPath, entryId + "_assembly-report_P1.xml")
+            for filePath in ( retPath, logPath ):
+                if os.access(filePath, os.R_OK):
+                    os.remove(filePath)
+                #
             #
             dp = RcsbDpUtility(tmpPath=self.__sessionPath, siteId=self.__siteId, verbose=self.__verbose, log=self.__lfh)
             dp.imp(inpPath)
@@ -339,7 +356,6 @@ def autoAssignDefaultAssembly(self, entryId, inpFile):
             #  Added generation of assembly files to the model update.
             if os.access(retPath, os.R_OK):
                 self.generateAssemblies(entryId, modelFilePath=retPath)
-
             #
             # dp.cleanup()
             return True
@@ -539,6 +555,10 @@ def runPdb(self, entryId, inpFile, sessionName):
             inpPath = os.path.join(self.__sessionPath, inpFile)
             reportPath = os.path.join(self.__sessionPath, entryId + "_assembly-report_P1.xml")
             logPath = os.path.join(self.__sessionPath, entryId + "_assembly-report.log")
+            for filePath in ( reportPath, logPath ):
+                if os.access(filePath, os.R_OK):
+                    os.remove(filePath)
+                #
             #
             dp = RcsbDpUtility(tmpPath=self.__sessionPath, siteId=self.__siteId, verbose=self.__verbose, log=self.__lfh)
             dp.imp(inpPath)
diff --git a/wwpdb/apps/ann_tasks_v2/check/ExtraCheck.py b/wwpdb/apps/ann_tasks_v2/check/ExtraCheck.py
index 1921a28..e85d67d 100644
--- a/wwpdb/apps/ann_tasks_v2/check/ExtraCheck.py
+++ b/wwpdb/apps/ann_tasks_v2/check/ExtraCheck.py
@@ -42,7 +42,7 @@ def __init__(self, reqObj=None, verbose=False, log=sys.stderr):
         #
         self.__exportPath = None
         self.__checkArgs = None
-        self.__cleanup = False
+        self.__cleanup = True
         self.__reportFileSize = 0
         self.__reportPath = None
         #
diff --git a/wwpdb/apps/ann_tasks_v2/check/FormatCheck.py b/wwpdb/apps/ann_tasks_v2/check/FormatCheck.py
index fb64c88..878b4a0 100644
--- a/wwpdb/apps/ann_tasks_v2/check/FormatCheck.py
+++ b/wwpdb/apps/ann_tasks_v2/check/FormatCheck.py
@@ -42,7 +42,7 @@ def __init__(self, reqObj=None, verbose=False, log=sys.stderr):
 
         self.__exportPath = None
         self.__checkArgs = None
-        self.__cleanup = False
+        self.__cleanup = True
         self.__reportFileSize = 0
         self.__reportPath = None
 
diff --git a/wwpdb/apps/ann_tasks_v2/check/GeometryCalc.py b/wwpdb/apps/ann_tasks_v2/check/GeometryCalc.py
index d8eac7b..90aec43 100644
--- a/wwpdb/apps/ann_tasks_v2/check/GeometryCalc.py
+++ b/wwpdb/apps/ann_tasks_v2/check/GeometryCalc.py
@@ -49,7 +49,7 @@ def __setup(self):
         self.__siteId = self.__reqObj.getValue("WWPDB_SITE_ID")
         self.__sObj = self.__reqObj.getSessionObj()
         self.__sessionPath = self.__sObj.getPath()
-        self.__cleanup = False
+        self.__cleanup = True
 
     def setArguments(self, checkArgs):
         self.__checkArgs = checkArgs
@@ -76,7 +76,7 @@ def run(self, entryId, inpFile, updateInput=True):
             dp.exp(retPath)
             self.addDownloadPath(retPath)
             self.addDownloadPath(logPath)
-            if updateInput:
+            if updateInput and os.access(retPath, os.R_OK):
                 dp.exp(inpPath)
             #
             if self.__verbose:
@@ -84,7 +84,12 @@ def run(self, entryId, inpFile, updateInput=True):
 
             if self.__cleanup:
                 dp.cleanup()
-            return True
+            #
+            if os.access(retPath, os.R_OK):
+                return True
+            else:
+                return False
+            #
         except:  # noqa: E722 pylint: disable=bare-except
             if self.__verbose:
                 self.__lfh.write("+%s.%s geometry calc failed for entryId %s file %s\n" % (self.__class__.__name__, inspect.currentframe().f_code.co_name, entryId, inpFile))
diff --git a/wwpdb/apps/ann_tasks_v2/check/GeometryCheck.py b/wwpdb/apps/ann_tasks_v2/check/GeometryCheck.py
index 40177cb..630fe67 100644
--- a/wwpdb/apps/ann_tasks_v2/check/GeometryCheck.py
+++ b/wwpdb/apps/ann_tasks_v2/check/GeometryCheck.py
@@ -44,7 +44,7 @@ def __init__(self, reqObj=None, verbose=False, log=sys.stderr):
         self.__checkArgs = None
         self.__reportFileSize = 0
         self.__reportPath = None
-        self.__cleanup = False
+        self.__cleanup = True
 
         self.__setup()
 
diff --git a/wwpdb/apps/ann_tasks_v2/correspnd/CorresPNDTemplate.py b/wwpdb/apps/ann_tasks_v2/correspnd/CorresPNDTemplate.py
index ed5ef10..ba21513 100644
--- a/wwpdb/apps/ann_tasks_v2/correspnd/CorresPNDTemplate.py
+++ b/wwpdb/apps/ann_tasks_v2/correspnd/CorresPNDTemplate.py
@@ -86,6 +86,10 @@ def __runGetCorresInfo(self):
         try:
             resultfile = os.path.join(self.__sessionPath, "corres_1.cif")
             logfilename = os.path.join(self.__sessionPath, "corres_1.log")
+            for filePath in ( resultfile, logfilename ):
+                if os.access(filePath, os.R_OK):
+                    os.remove(filePath)
+                #
             #
             dp = RcsbDpUtility(tmpPath=self.__sessionPath, siteId=self.__siteId, verbose=self.__verbose, log=self.__lfh)
             dp.imp(os.path.join(self.__sessionPath, self.__entryFile))
diff --git a/wwpdb/apps/ann_tasks_v2/editCoord/CSEditorForm.py b/wwpdb/apps/ann_tasks_v2/editCoord/CSEditorForm.py
index 3ed4fb5..870da95 100644
--- a/wwpdb/apps/ann_tasks_v2/editCoord/CSEditorForm.py
+++ b/wwpdb/apps/ann_tasks_v2/editCoord/CSEditorForm.py
@@ -63,11 +63,18 @@ def get(self):
     def __runScript(self):
         """ """
         try:
+            retPath = os.path.join(self.__sessionPath, self.__entryId + "_cs_html.txt")
+            logPath = os.path.join(self.__sessionPath, self.__entryId + "_cs_summary.log")
+            for filePath in ( retPath, logPath ):
+                if os.access(filePath, os.R_OK):
+                    os.remove(filePath)
+                #
+            #
             dp = RcsbDpUtility(tmpPath=self.__sessionPath, siteId=self.__siteId, verbose=self.__verbose, log=self.__lfh)
             dp.imp(os.path.join(self.__sessionPath, self.__entryFile))
             dp.op("annot-depict-chemical-shift")
-            dp.exp(os.path.join(self.__sessionPath, self.__entryId + "_cs_html.txt"))
-            dp.expLog(os.path.join(self.__sessionPath, self.__entryId + "_cs_summary.log"))
+            dp.exp(retPath)
+            dp.expLog(logPath)
             dp.cleanup()
         except:  # noqa: E722 pylint: disable=bare-except
             traceback.print_exc(file=self.__lfh)
diff --git a/wwpdb/apps/ann_tasks_v2/editCoord/CSEditorUpdate.py b/wwpdb/apps/ann_tasks_v2/editCoord/CSEditorUpdate.py
index cf0ffd3..40b8108 100644
--- a/wwpdb/apps/ann_tasks_v2/editCoord/CSEditorUpdate.py
+++ b/wwpdb/apps/ann_tasks_v2/editCoord/CSEditorUpdate.py
@@ -103,12 +103,16 @@ def __writeSelectInfo(self, cmap):
     def __runUpdateScript(self):
         """ """
         try:
+            logPath = os.path.join(self.__sessionPath, self.__entryId + "_cs_update.log")
+            if os.access(logPath, os.R_OK):
+                os.remove(logPath)
+            #
             dp = RcsbDpUtility(tmpPath=self.__sessionPath, siteId=self.__siteId, verbose=self.__verbose, log=self.__lfh)
             dp.imp(os.path.join(self.__sessionPath, self.__entryFile))
             dp.addInput(name="assign", value=os.path.join(self.__sessionPath, self.__entryId + "_cs_select.cif"))
             dp.op("annot-edit-chemical-shift")
             dp.exp(os.path.join(self.__sessionPath, self.__entryFile))
-            dp.expLog(os.path.join(self.__sessionPath, self.__entryId + "_cs_update.log"))
+            dp.expLog(logPath)
             dp.cleanup()
             #
             return self.__readLogFile("_cs_update.log", "Update failed!")
diff --git a/wwpdb/apps/ann_tasks_v2/editCoord/CoordEditorForm_v2.py b/wwpdb/apps/ann_tasks_v2/editCoord/CoordEditorForm_v2.py
index 116a43a..6c10c77 100644
--- a/wwpdb/apps/ann_tasks_v2/editCoord/CoordEditorForm_v2.py
+++ b/wwpdb/apps/ann_tasks_v2/editCoord/CoordEditorForm_v2.py
@@ -157,8 +157,14 @@ def __runScript(self):
             jsonPath = os.path.join(self.__jsonPath, self.__entryId + ".json")
             textPath = os.path.join(self.__sessionPath, self.__entryId + "_chainids.txt")
             indxPath = os.path.join(self.__sessionPath, self.__entryId + "_index.cif")
+            logPath = os.path.join(self.__sessionPath, self.__entryId + "_summary.log")
+            for filePath in ( jsonPath, textPath, indxPath, logPath ):
+                if os.access(filePath, os.R_OK):
+                    os.remove(filePath)
+                #
+            #
             dp.expList(dstPathList=[jsonPath, textPath, indxPath])
-            dp.expLog(os.path.join(self.__sessionPath, self.__entryId + "_summary.log"))
+            dp.expLog(logPath)
             dp.cleanup()
         except:  # noqa: E722 pylint: disable=bare-except
             traceback.print_exc(file=self.__lfh)
diff --git a/wwpdb/apps/ann_tasks_v2/editCoord/CoordEditorUpdate.py b/wwpdb/apps/ann_tasks_v2/editCoord/CoordEditorUpdate.py
index d937cb4..1f3051d 100644
--- a/wwpdb/apps/ann_tasks_v2/editCoord/CoordEditorUpdate.py
+++ b/wwpdb/apps/ann_tasks_v2/editCoord/CoordEditorUpdate.py
@@ -114,11 +114,15 @@ def __writeSelectInfo(self, smap):
     def __runCheckScript(self):
         """ """
         try:
+            logPath = os.path.join(self.__sessionPath, self.__entryId + "_check.log")
+            if os.access(logPath, os.R_OK):
+                os.remove(logPath)
+            #
             dp = RcsbDpUtility(tmpPath=self.__sessionPath, siteId=self.__siteId, verbose=self.__verbose, log=self.__lfh)
             dp.imp(os.path.join(self.__sessionPath, self.__entryId + "_index.cif"))
             dp.addInput(name="select", value=os.path.join(self.__sessionPath, self.__entryId + "_select.cif"))
             dp.op("annot-check-select-number")
-            dp.expLog(dstPath=os.path.join(self.__sessionPath, self.__entryId + "_check.log"), appendMode=False)
+            dp.expLog(dstPath=logPath, appendMode=False)
             dp.cleanup()
             #
             return self.__readLogFile("_check.log", "Run numbering checking failed")
@@ -131,12 +135,16 @@ def __runCheckScript(self):
     def __runUpdateScript(self):
         """ """
         try:
+            logPath = os.path.join(self.__sessionPath, self.__entryId + "_update.log")
+            if os.access(logPath, os.R_OK):
+                os.remove(logPath)
+            #
             dp = RcsbDpUtility(tmpPath=self.__sessionPath, siteId=self.__siteId, verbose=self.__verbose, log=self.__lfh)
             dp.imp(os.path.join(self.__sessionPath, self.__entryFile))
             dp.addInput(name="assign", value=os.path.join(self.__sessionPath, self.__entryId + "_select.cif"))
             dp.op("annot-update-molecule")
             dp.exp(os.path.join(self.__sessionPath, self.__entryFile))
-            dp.expLog(dstPath=os.path.join(self.__sessionPath, self.__entryId + "_update.log"), appendMode=False)
+            dp.expLog(dstPath=logPath, appendMode=False)
             dp.cleanup()
             #
             return self.__readLogFile("_update.log", "Update failed!")
diff --git a/wwpdb/apps/ann_tasks_v2/em3d/EmAutoFix.py b/wwpdb/apps/ann_tasks_v2/em3d/EmAutoFix.py
index a6a4ccd..c7c44d1 100644
--- a/wwpdb/apps/ann_tasks_v2/em3d/EmAutoFix.py
+++ b/wwpdb/apps/ann_tasks_v2/em3d/EmAutoFix.py
@@ -31,7 +31,7 @@ def __init__(self, sessionPath, siteId=None, verbose=True, log=sys.stderr):
         self.__lfh = log
         self.__siteId = siteId
         self.__sessionPath = sessionPath
-        self.__cleanup = False
+        self.__cleanup = True
         self.__pI = PathInfo(sessionPath=sessionPath, verbose=self.__verbose, log=self.__lfh)
         self.__mD = {"primary map": "em-volume", "mask": "em-mask-volume", "additional map": "em-additional-volume", "half map": "em-half-volume", "map header": "em-volume-header"}
 
@@ -53,6 +53,11 @@ def __getEmdDbCode(blockobj):
     def __mapfix(self, depsetid, emdbid, volin, volout, voxel):
         resultPath = os.path.join(self.__sessionPath, depsetid + "_mapfix-header-report_P1.json")
         logPath = os.path.join(self.__sessionPath, depsetid + "_mapfix-report_P1.txt")
+        for filePath in ( resultPath, logPath ):
+            if os.access(filePath, os.R_OK):
+                os.remove(filePath)
+            #
+        #
         dp = RcsbDpUtility(tmpPath=self.__sessionPath, siteId=self.__siteId, verbose=self.__verbose, log=self.__lfh)
         dp.setDebugMode(flag=True)
         dp.addInput(name="input_map_file_path", value=volin, type="file")
@@ -65,7 +70,7 @@ def __mapfix(self, depsetid, emdbid, volin, volout, voxel):
 
         if self.__cleanup:
             dp.cleanup()
-
+        #
         return resultPath
 
     def autoFixMapLabels(self, datasetid, modelin, modelout, vollocation="archive"):
diff --git a/wwpdb/apps/ann_tasks_v2/em3d/EmEditUtils.py b/wwpdb/apps/ann_tasks_v2/em3d/EmEditUtils.py
index d1966b7..df40fef 100644
--- a/wwpdb/apps/ann_tasks_v2/em3d/EmEditUtils.py
+++ b/wwpdb/apps/ann_tasks_v2/em3d/EmEditUtils.py
@@ -47,7 +47,7 @@ def __setup(self):
         self.__sessionId = self.__sObj.getId()
         self.__sessionPath = self.__sObj.getPath()
         self.__pI = PathInfo(siteId=self.__siteId, sessionPath=self.__sessionPath, verbose=self.__verbose, log=self.__lfh)
-        self.__cleanup = False
+        self.__cleanup = True
 
         self.__headerKeyList = [
             ("Map title", "label", True),
@@ -107,6 +107,10 @@ def getMapHeader(self, entryId, mapFilePath):
         try:
             resultPath = os.path.join(self.__sessionPath, entryId + "_mapfix-header-report_P1.json")
             logPath = os.path.join(self.__sessionPath, entryId + "_mapfix-report_P1.txt")
+            for filePath in ( resultPath, logPath ):
+                if os.access(filePath, os.R_OK):
+                    os.remove(filePath)
+                #
             #
             dp = RcsbDpUtility(tmpPath=self.__sessionPath, siteId=self.__siteId, verbose=self.__verbose, log=self.__lfh)
             dp.setDebugMode(flag=True)
@@ -289,6 +293,10 @@ def updateMapHeader(self, entryId, inputMapFileName, outputMapFilePath=None):
 
             resultPath = os.path.join(self.__sessionPath, entryId + "_mapfix-header-report_P1.json")
             logPath = os.path.join(self.__sessionPath, entryId + "_mapfix-report_P1.txt")
+            for filePath in ( resultPath, logPath ):
+                if os.access(filePath, os.R_OK):
+                    os.remove(filePath)
+                #
             #
             dp = RcsbDpUtility(tmpPath=self.__sessionPath, siteId=self.__siteId, verbose=self.__verbose, log=self.__lfh)
             dp.setDebugMode(flag=True)
diff --git a/wwpdb/apps/ann_tasks_v2/link/Link.py b/wwpdb/apps/ann_tasks_v2/link/Link.py
index d781ca2..5bda399 100644
--- a/wwpdb/apps/ann_tasks_v2/link/Link.py
+++ b/wwpdb/apps/ann_tasks_v2/link/Link.py
@@ -60,14 +60,16 @@ def run(self, entryId, inpFile, updateInput=True):
             pI = PathInfo(siteId=self.__siteId, sessionPath=self.__sessionPath, verbose=self.__verbose, log=self.__lfh)
             csvFile = pI.getFileName(entryId, contentType="pcm-missing-data", formatType="csv", versionId="none", partNumber="1")
             csvPath = os.path.join(self.__sessionPath, csvFile)
-            if os.access(csvPath, os.F_OK):
-                os.remove(csvPath)
             #
             inpPath = os.path.join(self.__sessionPath, inpFile)
             logPath1 = os.path.join(self.__sessionPath, entryId + "-link-anal.log")
             logPath2 = os.path.join(self.__sessionPath, entryId + "-cispeptide-anal.log")
             retPath1 = os.path.join(self.__sessionPath, entryId + "_model-updated_P1.cif")
             retPath2 = os.path.join(self.__sessionPath, entryId + "_model-updated_P2.cif")
+            for filePath in ( csvPath, retPath1, retPath2, logPath1, logPath2 ):
+                if os.access(filePath, os.R_OK):
+                    os.remove(filePath)
+                #
             #
             dp = RcsbDpUtility(tmpPath=self.__sessionPath, siteId=self.__siteId, verbose=self.__verbose, log=self.__lfh)
             dp.imp(inpPath)
diff --git a/wwpdb/apps/ann_tasks_v2/mapcalc/BisoFullCalc.py b/wwpdb/apps/ann_tasks_v2/mapcalc/BisoFullCalc.py
index 9c2393c..d1a39d0 100644
--- a/wwpdb/apps/ann_tasks_v2/mapcalc/BisoFullCalc.py
+++ b/wwpdb/apps/ann_tasks_v2/mapcalc/BisoFullCalc.py
@@ -37,7 +37,7 @@ def __init__(self, reqObj=None, verbose=False, log=sys.stderr):
         self.__lfh = log
         self.__reqObj = reqObj
         self.__dccArgs = None
-        self.__cleanup = False
+        self.__cleanup = True
         #
         self.__setup()
 
@@ -67,6 +67,10 @@ def run(self, entryId, modelInputFile=None, expInputFile=None, updateInput=True)
             #
             logPath = os.path.join(self.__sessionPath, entryId + "_biso-full-calc.log")
             retPath = os.path.join(self.__sessionPath, entryId + "_model-updated_P1.cif")
+            for filePath in ( retPath, logPath ):
+                if os.access(filePath, os.R_OK):
+                    os.remove(filePath)
+                #
             #
             dp = RcsbDpUtility(tmpPath=self.__sessionPath, siteId=self.__siteId, verbose=self.__verbose, log=self.__lfh)
             dp.imp(inpPath)
@@ -79,7 +83,7 @@ def run(self, entryId, modelInputFile=None, expInputFile=None, updateInput=True)
             dp.expLog(logPath)
             dp.exp(retPath)
 
-            if updateInput:
+            if updateInput and os.access(retPath, os.R_OK):
                 dp.exp(inpPath)
             #
             if self.__verbose:
@@ -87,7 +91,12 @@ def run(self, entryId, modelInputFile=None, expInputFile=None, updateInput=True)
 
             if self.__cleanup:
                 dp.cleanup()
-            return True
+            #
+            if os.access(retPath, os.R_OK):
+                return True
+            else:
+                return False
+            #
         except:  # noqa: E722 pylint: disable=bare-except
             if self.__verbose:
                 self.__lfh.write("+BisoFullCalc.run-  failed with exception for entryId %s file %s\n" % (entryId, inpPath))
diff --git a/wwpdb/apps/ann_tasks_v2/mapcalc/DccCalc.py b/wwpdb/apps/ann_tasks_v2/mapcalc/DccCalc.py
index e843918..6dcba28 100644
--- a/wwpdb/apps/ann_tasks_v2/mapcalc/DccCalc.py
+++ b/wwpdb/apps/ann_tasks_v2/mapcalc/DccCalc.py
@@ -37,7 +37,7 @@ def __init__(self, reqObj=None, verbose=False, log=sys.stderr):
         self.__lfh = log
         self.__reqObj = reqObj
         self.__dccArgs = None
-        self.__cleanup = False
+        self.__cleanup = True
         self.__exportPath = None
         self.__reportPath = None
         #
diff --git a/wwpdb/apps/ann_tasks_v2/mapcalc/DccRefineCalc.py b/wwpdb/apps/ann_tasks_v2/mapcalc/DccRefineCalc.py
index cbc11fa..3469517 100644
--- a/wwpdb/apps/ann_tasks_v2/mapcalc/DccRefineCalc.py
+++ b/wwpdb/apps/ann_tasks_v2/mapcalc/DccRefineCalc.py
@@ -37,7 +37,7 @@ def __init__(self, reqObj=None, verbose=False, log=sys.stderr):
         self.__lfh = log
         self.__reqObj = reqObj
         self.__dccArgs = None
-        self.__cleanup = False
+        self.__cleanup = True
         #
         self.__setup()
 
@@ -67,6 +67,10 @@ def run(self, entryId, modelInputFile=None, expInputFile=None, updateInput=True)
             #
             logPath = os.path.join(self.__sessionPath, entryId + "_dcc-refine-calc.log")
             reportPath = os.path.join(self.__sessionPath, entryId + "_dcc-refine-report.cif")
+            for filePath in ( reportPath, logPath ):
+                if os.access(filePath, os.R_OK):
+                    os.remove(filePath)
+                #
             #
             dp = RcsbDpUtility(tmpPath=self.__sessionPath, siteId=self.__siteId, verbose=self.__verbose, log=self.__lfh)
             dp.imp(inpPath)
diff --git a/wwpdb/apps/ann_tasks_v2/mapcalc/MapCalc.py b/wwpdb/apps/ann_tasks_v2/mapcalc/MapCalc.py
index dfbbcdb..3edee18 100644
--- a/wwpdb/apps/ann_tasks_v2/mapcalc/MapCalc.py
+++ b/wwpdb/apps/ann_tasks_v2/mapcalc/MapCalc.py
@@ -37,7 +37,7 @@ def __init__(self, reqObj=None, verbose=False, log=sys.stderr):
         self.__lfh = log
         self.__reqObj = reqObj
         self.__mapArgs = None
-        self.__cleanup = False
+        self.__cleanup = True
         #
         self.__setup()
 
@@ -66,6 +66,9 @@ def run(self, entryId, modelInputFile=None, expInputFile=None, updateInput=True,
             #
             #
             logPath = os.path.join(self.__sessionPath, entryId + "_map-calc.log")
+            if os.access(logPath, os.R_OK):
+                os.remove(logPath)
+            #
             result2fofcPath = os.path.join(self.__sessionPath, entryId + "_map-2fofc_P1.map")
             resultfofcPath = os.path.join(self.__sessionPath, entryId + "_map-fofc_P1.map")
             #
@@ -90,6 +93,9 @@ def run(self, entryId, modelInputFile=None, expInputFile=None, updateInput=True,
             #
             if doOmit:
                 logPath = os.path.join(self.__sessionPath, entryId + "_map-omit-calc.log")
+                if os.access(logPath, os.R_OK):
+                    os.remove(logPath)
+                #
                 result2fofcPath = os.path.join(self.__sessionPath, entryId + "_map-omit-2fofc_P1.map")
                 resultfofcPath = os.path.join(self.__sessionPath, entryId + "_map-omit-fofc_P1.map")
                 #
diff --git a/wwpdb/apps/ann_tasks_v2/mapcalc/NpCcMapCalc.py b/wwpdb/apps/ann_tasks_v2/mapcalc/NpCcMapCalc.py
index 8f1433d..89d812e 100644
--- a/wwpdb/apps/ann_tasks_v2/mapcalc/NpCcMapCalc.py
+++ b/wwpdb/apps/ann_tasks_v2/mapcalc/NpCcMapCalc.py
@@ -37,7 +37,7 @@ def __init__(self, reqObj=None, verbose=False, log=sys.stderr):
         self.__reqObj = reqObj
         #
         self.__mapArgs = None
-        self.__cleanup = False
+        self.__cleanup = True
         #
         self.__setup()
 
@@ -65,6 +65,9 @@ def run(self, entryId, modelInputFile=None, expInputFile=None, updateInput=True,
                 sfPath = os.path.join(self.__sessionPath, expInputFile)
             #
             logPath = os.path.join(self.__sessionPath, entryId + "_map-npcc-calc.log")
+            if os.access(logPath, os.R_OK):
+                os.remove(logPath)
+            #
             outDataPath = os.path.join(self.__sessionPath, "np-cc-maps")
             outIndexPath = os.path.join(self.__sessionPath, "np-cc-maps", "np-cc-maps-index.cif")
             #
@@ -93,6 +96,9 @@ def run(self, entryId, modelInputFile=None, expInputFile=None, updateInput=True,
                 dp.setDebugMode(flag=True)
                 #
                 logPath = os.path.join(self.__sessionPath, entryId + "_map-omit-npcc-calc.log")
+                if os.access(logPath, os.R_OK):
+                    os.remove(logPath)
+                #
                 outDataPath = os.path.join(self.__sessionPath, "np-cc-omit-maps")
                 outIndexPath = os.path.join(self.__sessionPath, "np-cc-omit-maps", "np-cc-omit-maps-index.cif")
                 dp.imp(inpPath)
diff --git a/wwpdb/apps/ann_tasks_v2/mapcalc/ReassignAltIdsCalc.py b/wwpdb/apps/ann_tasks_v2/mapcalc/ReassignAltIdsCalc.py
index a4b2ba1..4765cbc 100644
--- a/wwpdb/apps/ann_tasks_v2/mapcalc/ReassignAltIdsCalc.py
+++ b/wwpdb/apps/ann_tasks_v2/mapcalc/ReassignAltIdsCalc.py
@@ -37,7 +37,7 @@ def __init__(self, reqObj=None, verbose=False, log=sys.stderr):
         self.__lfh = log
         self.__reqObj = reqObj
         self.__dccArgs = None
-        self.__cleanup = False
+        self.__cleanup = True
         #
         self.__setup()
 
@@ -57,16 +57,19 @@ def run(self, entryId, modelInputFile=None, expInputFile=None, updateInput=True)
                 inpPath = os.path.join(self.__sessionPath, modelFileName)
             else:
                 inpPath = os.path.join(self.__sessionPath, modelInputFile)
-
+            #
             if expInputFile is None:
                 expFileName = entryId + "_sf_P1.cif"
                 sfPath = os.path.join(self.__sessionPath, expFileName)
             else:
                 sfPath = os.path.join(self.__sessionPath, expInputFile)
             #
-            #
             logPath = os.path.join(self.__sessionPath, entryId + "_reassign-alt-ids-calc.log")
             retPath = os.path.join(self.__sessionPath, entryId + "_model-updated_P1.cif")
+            for filePath in ( retPath, logPath ):
+                if os.access(filePath, os.R_OK):
+                    os.remove(filePath)
+                #
             #
             dp = RcsbDpUtility(tmpPath=self.__sessionPath, siteId=self.__siteId, verbose=self.__verbose, log=self.__lfh)
             dp.imp(inpPath)
@@ -78,15 +81,20 @@ def run(self, entryId, modelInputFile=None, expInputFile=None, updateInput=True)
             dp.exp(retPath)
             self.addDownloadPath(retPath)
             self.addDownloadPath(logPath)
-            if updateInput:
+            if updateInput and os.access(retPath, os.R_OK):
                 dp.exp(inpPath)
             #
             if self.__verbose:
                 self.__lfh.write("+ReassignAltIdsCalc.run-  completed for entryId %s file %s\n" % (entryId, inpPath))
-
+            #
             if self.__cleanup:
                 dp.cleanup()
-            return True
+            #
+            if os.access(retPath, os.R_OK):
+                return True
+            else:
+                return False
+            #
         except:  # noqa: E722 pylint: disable=bare-except
             if self.__verbose:
                 self.__lfh.write("+ReassignAltIdsCalc.run-  failed with exception for entryId %s file %s\n" % (entryId, inpPath))
diff --git a/wwpdb/apps/ann_tasks_v2/mapcalc/SpecialPositionCalc.py b/wwpdb/apps/ann_tasks_v2/mapcalc/SpecialPositionCalc.py
index 40dafe8..c7c01bc 100644
--- a/wwpdb/apps/ann_tasks_v2/mapcalc/SpecialPositionCalc.py
+++ b/wwpdb/apps/ann_tasks_v2/mapcalc/SpecialPositionCalc.py
@@ -47,7 +47,7 @@ def __setup(self):
         self.__siteId = self.__reqObj.getValue("WWPDB_SITE_ID")
         self.__sObj = self.__reqObj.getSessionObj()
         self.__sessionPath = self.__sObj.getPath()
-        self.__cleanup = False
+        self.__cleanup = True
 
     def setArguments(self, dccArgs):  # pylint: disable=unused-argument
         # self.__dccArgs = dccArgs
@@ -97,6 +97,7 @@ def run(self, entryId, modelInputFile=None):
 
             if self.__cleanup:
                 dp.cleanup()
+            #
             return True
         except:  # noqa: E722 pylint: disable=bare-except
             if self.__verbose:
diff --git a/wwpdb/apps/ann_tasks_v2/mapcalc/SpecialPositionUpdate.py b/wwpdb/apps/ann_tasks_v2/mapcalc/SpecialPositionUpdate.py
index 325ff40..05fb7fe 100644
--- a/wwpdb/apps/ann_tasks_v2/mapcalc/SpecialPositionUpdate.py
+++ b/wwpdb/apps/ann_tasks_v2/mapcalc/SpecialPositionUpdate.py
@@ -40,7 +40,7 @@ def __init__(self, reqObj=None, verbose=False, log=sys.stderr):
         self.__lfh = log
         self.__reqObj = reqObj
         # self.__checkArgs = None
-        self.__cleanup = False
+        self.__cleanup = True
         self.__modelUpdated = False
         #
         self.__setup()
@@ -69,6 +69,10 @@ def run(self, entryId, inpFile, updateInput=True):
             inpPath = os.path.join(self.__sessionPath, inpFile)
             logPath = os.path.join(self.__sessionPath, entryId + "_special-position-update.log")
             retPath = os.path.join(self.__sessionPath, entryId + "_model-updated_P1.cif")
+            for filePath in ( retPath, logPath ):
+                if os.access(filePath, os.R_OK):
+                    os.remove(filePath)
+                #
             #
             dp = RcsbDpUtility(tmpPath=self.__sessionPath, siteId=self.__siteId, verbose=self.__verbose, log=self.__lfh)
             dp.imp(inpPath)
@@ -81,17 +85,22 @@ def run(self, entryId, inpFile, updateInput=True):
                 self.__modelUpdated = True
 
             self.addDownloadPath(logPath)
-            if updateInput:
+            if updateInput and os.access(retPath, os.R_OK):
                 dp.expList(dstPathList=[inpPath])
             #
             if self.__verbose:
                 self.__lfh.write(
                     "+%s.%s special position update calc completed for entryId %s file %s\n" % (self.__class__.__name__, inspect.currentframe().f_code.co_name, entryId, inpFile)
                 )
-
+            #
             if self.__cleanup:
                 dp.cleanup()
-            return True
+            #
+            if os.access(retPath, os.R_OK):
+                return True
+            else:
+                return False
+            #
         except:  # noqa: E722 pylint: disable=bare-except
             if self.__verbose:
                 self.__lfh.write(
diff --git a/wwpdb/apps/ann_tasks_v2/nafeatures/NAFeatures.py b/wwpdb/apps/ann_tasks_v2/nafeatures/NAFeatures.py
index bcc7176..64fd182 100644
--- a/wwpdb/apps/ann_tasks_v2/nafeatures/NAFeatures.py
+++ b/wwpdb/apps/ann_tasks_v2/nafeatures/NAFeatures.py
@@ -55,6 +55,10 @@ def run(self, entryId, inpFile, updateInput=True):
             inpPath = os.path.join(self.__sessionPath, inpFile)
             logPath1 = os.path.join(self.__sessionPath, entryId + "-na-anal.log")
             retPath = os.path.join(self.__sessionPath, entryId + "_model-updated_P1.cif")
+            for filePath in ( retPath, logPath1 ):
+                if os.access(filePath, os.R_OK):
+                    os.remove(filePath)
+                #
             #
             dp = RcsbDpUtility(tmpPath=self.__sessionPath, siteId=self.__siteId, verbose=self.__verbose, log=self.__lfh)
             dp.imp(inpPath)
@@ -66,13 +70,18 @@ def run(self, entryId, inpFile, updateInput=True):
             #
             self.addDownloadPath(retPath)
             self.addDownloadPath(logPath1)
-            if updateInput:
+            if updateInput and os.access(retPath, os.R_OK):
                 dp.exp(inpPath)
+            #
             if self.__verbose:
                 self.__lfh.write("+NAFeatures.run-  completed for entryId %s file %s\n" % (entryId, inpPath))
-
+            #
             dp.cleanup()
-            return True
+            if os.access(retPath, os.R_OK):
+                return True
+            else:
+                return False
+            #
         except:  # noqa: E722 pylint: disable=bare-except
             traceback.print_exc(file=self.__lfh)
             return False
diff --git a/wwpdb/apps/ann_tasks_v2/nmr/NmrChemShiftsMiscChecks.py b/wwpdb/apps/ann_tasks_v2/nmr/NmrChemShiftsMiscChecks.py
index 22c6b3c..e48cc99 100644
--- a/wwpdb/apps/ann_tasks_v2/nmr/NmrChemShiftsMiscChecks.py
+++ b/wwpdb/apps/ann_tasks_v2/nmr/NmrChemShiftsMiscChecks.py
@@ -61,6 +61,10 @@ def run(self, entryId, csInpFilePath, xyzFilePath):
             ofpng = os.path.join(self.__sessionPath, entryId + "-nmr-val-slider.png")
             ofsvg = os.path.join(self.__sessionPath, entryId + "-nmr-val-slider.svg")
             logPath = os.path.join(self.__sessionPath, entryId + "-nmr-cs-check-rpt.log")
+            for filePath in ( ofpdf, ofxml, offullpdf, ofpng, ofsvg, logPath ):
+                if os.access(filePath, os.R_OK):
+                    os.remove(filePath)
+                #
             # ------------
             dp.addInput(name="request_annotation_context", value="yes")
             # adding explicit selection of steps --
@@ -87,6 +91,7 @@ def run(self, entryId, csInpFilePath, xyzFilePath):
             #
             if self.__cleanUp:
                 dp.cleanup()
+            #
             return True
         except:  # noqa: E722 pylint: disable=bare-except
             traceback.print_exc(file=self.__lfh)
diff --git a/wwpdb/apps/ann_tasks_v2/nmr/NmrChemShiftsUtils.py b/wwpdb/apps/ann_tasks_v2/nmr/NmrChemShiftsUtils.py
index 1c8714c..7028d32 100644
--- a/wwpdb/apps/ann_tasks_v2/nmr/NmrChemShiftsUtils.py
+++ b/wwpdb/apps/ann_tasks_v2/nmr/NmrChemShiftsUtils.py
@@ -82,6 +82,8 @@ def runPrep(self, entryId):
             csFilePath = pI.getChemcialShiftsFilePath(entryId, formatType="pdbx", fileSource="session", versionId="none", mileStone=None)
             # outPath=os.path.join(self.__sessionPath, entryId + "_cs_P1.cif")
             logPath = os.path.join(self.__sessionPath, entryId + "-annot-chem-shifts-upload-check.log")
+            if os.access(logPath, os.R_OK):
+                os.remove(logPath)
             #
             chkPath = os.path.join(self.__sessionPath, entryId + "_nmr-chemical-shifts-upload-report_P1.cif")
             dp.addInput(name="chemical_shifts_upload_check_file_path", value=chkPath)
@@ -90,7 +92,6 @@ def runPrep(self, entryId):
             dp.expLog(logPath)
             dp.exp(csFilePath)
             #
-            #
             wPath = os.path.join(self.__sessionPath, "Warnings-combine.txt")
             ePath = os.path.join(self.__sessionPath, "Errors-combine.txt")
             self.__processReport(chkPath, wPath, ePath)
@@ -101,6 +102,7 @@ def runPrep(self, entryId):
 
             if self.__cleanUp:
                 dp.cleanup()
+            #
             return True
         except:  # noqa: E722 pylint: disable=bare-except
             traceback.print_exc(file=self.__lfh)
@@ -122,6 +124,9 @@ def runAtomNameCheck(self, entryId, csInpFilePath, xyzFilePath, csOutFilePath):
             dp.addInput(name="coordinate_file_path", value=xyzFilePath)
             #
             logPath = os.path.join(self.__sessionPath, entryId + "-chem-shifts-atom-name-check.log")
+            if os.access(logPath, os.R_OK):
+                os.remove(logPath)
+            #
             chkPath = os.path.join(self.__sessionPath, entryId + "_nmr-chemical-shifts-atom-name-report_P1.cif")
 
             dp.addInput(name="chemical_shifts_coord_check_file_path", value=chkPath)
@@ -130,7 +135,6 @@ def runAtomNameCheck(self, entryId, csInpFilePath, xyzFilePath, csOutFilePath):
             dp.expLog(logPath)
             dp.exp(csOutFilePath)
             #
-            #
             wPath = os.path.join(self.__sessionPath, "Warnings-atom-name.txt")
             ePath = os.path.join(self.__sessionPath, "Errors-atom-name.txt")
             self.__processReport(chkPath, wPath, ePath)
@@ -138,10 +142,10 @@ def runAtomNameCheck(self, entryId, csInpFilePath, xyzFilePath, csOutFilePath):
             self.addDownloadPath(chkPath)
             self.addDownloadPath(logPath)
             self.addDownloadPath(csOutFilePath)
-
             #
             if self.__cleanUp:
                 dp.cleanup()
+            #
             return True
         except:  # noqa: E722 pylint: disable=bare-except
             traceback.print_exc(file=self.__lfh)
@@ -163,7 +167,9 @@ def runUpdate(self, entryId, csInpFilePath, xyzFilePath, csOutFilePath):
             dp.addInput(name="coordinate_file_path", value=xyzFilePath)
             #
             logPath = os.path.join(self.__sessionPath, entryId + "-chem-shifts-update.log")
-
+            if os.access(logPath, os.R_OK):
+                os.remove(logPath)
+            #
             dp.op("annot-chem-shifts-update")
             dp.expLog(logPath)
             dp.exp(csOutFilePath)
@@ -173,6 +179,7 @@ def runUpdate(self, entryId, csInpFilePath, xyzFilePath, csOutFilePath):
             #
             if self.__cleanUp:
                 dp.cleanup()
+            #
             return True
         except:  # noqa: E722 pylint: disable=bare-except
             traceback.print_exc(file=self.__lfh)
@@ -200,7 +207,7 @@ def __processReport(self, chkPath, warningPath=None, errorPath=None):
                 ofh.write("%s" % ("\n").join(self.__errors))
                 ofh.close()
                 self.addDownloadPath(errorPath)
-
+            #
             return True
         except:  # noqa: E722 pylint: disable=bare-except
             traceback.print_exc(file=self.__lfh)
diff --git a/wwpdb/apps/ann_tasks_v2/nmr/NmrModelUtils.py b/wwpdb/apps/ann_tasks_v2/nmr/NmrModelUtils.py
index 53b0b64..b22bc68 100644
--- a/wwpdb/apps/ann_tasks_v2/nmr/NmrModelUtils.py
+++ b/wwpdb/apps/ann_tasks_v2/nmr/NmrModelUtils.py
@@ -95,7 +95,7 @@ def run(self, entryId, inpFile, updateInput=True):
             if updateInput and (self.__status == "ok"):
                 dp.exp(inpPath)
             #
-            # dp.cleanup()
+            dp.cleanup()
             if self.__status == "ok":
                 return True
             else:
diff --git a/wwpdb/apps/ann_tasks_v2/secstruct/SecondaryStructure.py b/wwpdb/apps/ann_tasks_v2/secstruct/SecondaryStructure.py
index d810a5b..ddabc92 100644
--- a/wwpdb/apps/ann_tasks_v2/secstruct/SecondaryStructure.py
+++ b/wwpdb/apps/ann_tasks_v2/secstruct/SecondaryStructure.py
@@ -76,26 +76,34 @@ def run(self, entryId, inpFile, updateInput=True):
             inpPath = os.path.join(self.__sessionPath, inpFile)
             logPath1 = os.path.join(self.__sessionPath, entryId + "-sec-struct-anal.log")
             retPath = os.path.join(self.__sessionPath, entryId + "_model-updated_P1.cif")
+            for filePath in ( retPath, logPath1 ):
+                if os.access(filePath, os.R_OK):
+                    os.remove(filePath)
+                #
             #
             dp = RcsbDpUtility(tmpPath=self.__sessionPath, siteId=self.__siteId, verbose=self.__verbose, log=self.__lfh)
             dp.imp(inpPath)
             if self.__topFilePath is not None:
                 dp.addInput(name="ss_topology_file_path", value=self.__topFilePath)
+            #
             dp.op("annot-secondary-structure")
             dp.expLog(logPath1)
             dp.exp(retPath)
             self.addDownloadPath(retPath)
             self.addDownloadPath(logPath1)
-            if updateInput:
+            if updateInput and os.access(retPath, os.R_OK):
                 dp.exp(inpPath)
-
             #
             self.__status = self.__checkStatus(logPath1)
             if self.__verbose:
                 self.__lfh.write("+SecondaryStructure.run-  completed with status %s for entryId %s file %s\n" % (self.__status, entryId, inpPath))
-
+            #
             dp.cleanup()
-            return True
+            if os.access(retPath, os.R_OK):
+                return True
+            else:
+                return False
+            #
         except:  # noqa: E722 pylint: disable=bare-except
             traceback.print_exc(file=self.__lfh)
             return False
diff --git a/wwpdb/apps/ann_tasks_v2/site/Site.py b/wwpdb/apps/ann_tasks_v2/site/Site.py
index a9004a7..098ddc7 100644
--- a/wwpdb/apps/ann_tasks_v2/site/Site.py
+++ b/wwpdb/apps/ann_tasks_v2/site/Site.py
@@ -57,6 +57,10 @@ def run(self, entryId, inpFile, updateInput=True):
             logPath2 = os.path.join(self.__sessionPath, entryId + "_site-merge.log")
             resultPath = os.path.join(self.__sessionPath, entryId + "_site-anal_P1.cif")
             retPath = os.path.join(self.__sessionPath, entryId + "_model-updated_P1.cif")
+            for filePath in ( resultPath, retPath, logPath1, logPath2 ):
+                if os.access(filePath, os.R_OK):
+                    os.remove(filePath)
+                #
             #
             dp = RcsbDpUtility(tmpPath=self.__sessionPath, siteId=self.__siteId, verbose=self.__verbose, log=self.__lfh)
             dp.imp(inpPath)
@@ -78,12 +82,12 @@ def run(self, entryId, inpFile, updateInput=True):
             dp.exp(retPath)
             self.addDownloadPath(retPath)
             self.addDownloadPath(logPath2)
-            if updateInput:
+            if updateInput and os.access(retPath, os.R_OK):
                 dp.exp(inpPath)
             #
             if self.__verbose:
                 self.__lfh.write("+Site.run-  completed for entryId %s file %s\n" % (entryId, inpPath))
-
+            #
             dp.cleanup()
             return True
         except:  # noqa: E722 pylint: disable=bare-except
diff --git a/wwpdb/apps/ann_tasks_v2/solvent/Solvent.py b/wwpdb/apps/ann_tasks_v2/solvent/Solvent.py
index 3bbbf9f..05a5030 100644
--- a/wwpdb/apps/ann_tasks_v2/solvent/Solvent.py
+++ b/wwpdb/apps/ann_tasks_v2/solvent/Solvent.py
@@ -58,6 +58,10 @@ def run(self, entryId, inpFile, updateInput=True):
             inpPath = os.path.join(self.__sessionPath, inpFile)
             logPath1 = os.path.join(self.__sessionPath, entryId + "-solvent-anal.log")
             retPath = os.path.join(self.__sessionPath, entryId + "_model-updated_P1.cif")
+            for filePath in ( retPath, logPath1 ):
+                if os.access(filePath, os.R_OK):
+                    os.remove(filePath)
+                #
             #
             dp = RcsbDpUtility(tmpPath=self.__sessionPath, siteId=self.__siteId, verbose=self.__verbose, log=self.__lfh)
             dp.imp(inpPath)
@@ -72,13 +76,18 @@ def run(self, entryId, inpFile, updateInput=True):
             dp.exp(retPath)
             self.addDownloadPath(retPath)
             self.addDownloadPath(logPath1)
-            if updateInput:
+            if updateInput and os.access(retPath, os.R_OK):
                 dp.exp(inpPath)
+            #
             if self.__verbose:
                 self.__lfh.write("+Solvent.run-  completed for entryId %s file %s\n" % (entryId, inpPath))
-
+            #
             dp.cleanup()
-            return True
+            if os.access(retPath, os.R_OK):
+                return True
+            else:
+                return False
+            #
         except:  # noqa: E722 pylint: disable=bare-except
             traceback.print_exc(file=self.__lfh)
             return False
diff --git a/wwpdb/apps/ann_tasks_v2/transformCoord/TransformCoord.py b/wwpdb/apps/ann_tasks_v2/transformCoord/TransformCoord.py
index 508a9d2..8341bff 100644
--- a/wwpdb/apps/ann_tasks_v2/transformCoord/TransformCoord.py
+++ b/wwpdb/apps/ann_tasks_v2/transformCoord/TransformCoord.py
@@ -63,6 +63,10 @@ def run(self, entryId, inpFile, fileType="symop", updateInput=True):
             inpPath = os.path.join(self.__sessionPath, inpFile)
             logPath1 = os.path.join(self.__sessionPath, entryId + "-trans-coord.log")
             retPath = os.path.join(self.__sessionPath, entryId + "_model-updated_P1.cif")
+            for filePath in ( retPath, logPath1 ):
+                if os.access(filePath, os.R_OK):
+                    os.remove(filePath)
+                #
             #
             dp = RcsbDpUtility(tmpPath=self.__sessionPath, siteId=self.__siteId, verbose=self.__verbose, log=self.__lfh)
             dp.imp(inpPath)
@@ -74,6 +78,7 @@ def run(self, entryId, inpFile, fileType="symop", updateInput=True):
                 dp.op("annot-move-xyz-by-matrix")
             else:
                 dp.op("annot-move-xyz-by-symop")
+            #
             dp.expLog(logPath1)
             dp.exp(retPath)
             self.addDownloadPath(retPath)
@@ -91,7 +96,7 @@ def run(self, entryId, inpFile, fileType="symop", updateInput=True):
                 status = False
             else:
                 status = False
-
+            #
             dp.cleanup()
             return status
         except:  # noqa: E722 pylint: disable=bare-except
diff --git a/wwpdb/apps/ann_tasks_v2/utils/PublicPdbxFile.py b/wwpdb/apps/ann_tasks_v2/utils/PublicPdbxFile.py
index eb3c913..aa1f261 100644
--- a/wwpdb/apps/ann_tasks_v2/utils/PublicPdbxFile.py
+++ b/wwpdb/apps/ann_tasks_v2/utils/PublicPdbxFile.py
@@ -51,7 +51,7 @@ def __setup(self):
         self.__sObj = self.__reqObj.getSessionObj()
         self._sessionPath = self.__sObj.getPath()
         self._exportPath = self._sessionPath  # pylint: disable=attribute-defined-outside-init
-        self._cleanup = False
+        self._cleanup = True
 
     def setExportPath(self, exportPath):
         """Set the path where output files are copyied."""
diff --git a/wwpdb/apps/ann_tasks_v2/utils/TerminalAtoms.py b/wwpdb/apps/ann_tasks_v2/utils/TerminalAtoms.py
index 4657955..9d0b54e 100644
--- a/wwpdb/apps/ann_tasks_v2/utils/TerminalAtoms.py
+++ b/wwpdb/apps/ann_tasks_v2/utils/TerminalAtoms.py
@@ -68,6 +68,10 @@ def run(self, entryId, inpFile, updateInput=True, updateOption="delete"):
             inpPath = os.path.join(self.__sessionPath, inpFile)
             logPath1 = os.path.join(self.__sessionPath, entryId + "-terminal-atoms.log")
             retPath = os.path.join(self.__sessionPath, entryId + "_model-updated_P1.cif")
+            for filePath in ( retPath, logPath1 ):
+                if os.access(filePath, os.R_OK):
+                    os.remove(filePath)
+                #
             #
             dp = RcsbDpUtility(tmpPath=self.__sessionPath, siteId=self.__siteId, verbose=self.__verbose, log=self.__lfh)
             dp.imp(inpPath)
@@ -78,16 +82,19 @@ def run(self, entryId, inpFile, updateInput=True, updateOption="delete"):
             dp.exp(retPath)
             self.addDownloadPath(retPath)
             self.addDownloadPath(logPath1)
-            if updateInput:
+            if updateInput and os.access(retPath, os.R_OK):
                 dp.exp(inpPath)
-
             #
             self.__status = self.__checkStatus(logPath1)
             if self.__verbose:
                 self.__lfh.write("+TerminalAtoms.run-  completed with status %s for entryId %s file %s\n" % (self.__status, entryId, inpPath))
-
+            #
             dp.cleanup()
-            return True
+            if os.access(retPath, os.R_OK):
+                return True
+            else:
+                return False
+            #
         except:  # noqa: E722 pylint: disable=bare-except
             traceback.print_exc(file=self.__lfh)
             return False
diff --git a/wwpdb/apps/ann_tasks_v2/utils/TlsRange.py b/wwpdb/apps/ann_tasks_v2/utils/TlsRange.py
index c0b935b..94119ba 100644
--- a/wwpdb/apps/ann_tasks_v2/utils/TlsRange.py
+++ b/wwpdb/apps/ann_tasks_v2/utils/TlsRange.py
@@ -65,8 +65,10 @@ def run(self, entryId, depFileName, inpFile):
             inpPath = os.path.join(self.__sessionPath, inpFile)
             logPath = os.path.join(self.__sessionPath, entryId + "-tls-range.log")
             retPath = os.path.join(self.__sessionPath, entryId + "-tls-correction.cif")
-            if os.access(retPath, os.R_OK):
-                os.remove(retPath)
+            for filePath in ( retPath, logPath ):
+                if os.access(filePath, os.R_OK):
+                    os.remove(filePath)
+                #
             #
             dp = RcsbDpUtility(tmpPath=self.__sessionPath, siteId=self.__siteId, verbose=self.__verbose, log=self.__lfh)
             #
@@ -95,7 +97,7 @@ def run(self, entryId, depFileName, inpFile):
             if self.__verbose:
                 self.__lfh.write("+TlsRange.run-  completed with status %s for entryId %s file %s\n" % (self.__status, entryId, inpPath))
             #
-            # dp.cleanup()
+            dp.cleanup()
             return True
         except:  # noqa: E722 pylint: disable=bare-except
             traceback.print_exc(file=self.__lfh)
diff --git a/wwpdb/apps/ann_tasks_v2/webapp/AnnTasksWebAppWorker.py b/wwpdb/apps/ann_tasks_v2/webapp/AnnTasksWebAppWorker.py
index bf47e44..941d6b6 100644
--- a/wwpdb/apps/ann_tasks_v2/webapp/AnnTasksWebAppWorker.py
+++ b/wwpdb/apps/ann_tasks_v2/webapp/AnnTasksWebAppWorker.py
@@ -315,8 +315,9 @@ def _launchOp(self):
             #
         #
         auto_assembly_status = ""
+        assembly_inferred = ""
         if bIsWorkflow:
-            hasAssemblyInfo = self.__checkAssemblyInfo(os.path.join(self._sessionPath, entryFileName))
+            hasAssemblyInfo,assembly_inferred = self.__checkAssemblyInfo(os.path.join(self._sessionPath, entryFileName))
             if hasAssemblyInfo:
                 auto_assembly_status = "existed"
             method = str(self._reqObj.getValue("method")).strip().upper()
@@ -332,7 +333,7 @@ def _launchOp(self):
                     assem.autoAssignDefaultAssembly(entryId, entryFileName)
                     #
                     updatedModelPath = os.path.join(self._sessionPath, entryId + "_model-assembly-updated_P1.cif")
-                    hasAssemblyInfo = self.__checkAssemblyInfo(updatedModelPath)
+                    hasAssemblyInfo,assembly_inferred = self.__checkAssemblyInfo(updatedModelPath)
                     if hasAssemblyInfo:
                         auto_assembly_status = "updated"
                         os.rename(updatedModelPath, os.path.join(self._sessionPath, entryFileName))
@@ -353,6 +354,9 @@ def _launchOp(self):
         if missingpcmstatus == "yes":
             auto_assembly_status_url += "&missingpcmstatus=" + missingpcmstatus
         #
+        if assembly_inferred != "":
+            auto_assembly_status_url += "&provenance=" + assembly_inferred.strip().upper()
+        #
         htmlList = []
         htmlList.append("<!DOCTYPE html>")
         htmlList.append('<html lang="en">')
@@ -869,10 +873,11 @@ def __checkAssemblyInfo(self, modelFile):
         assemblyList = cifObj.GetValue("pdbx_struct_assembly")
         genList = cifObj.GetValue("pdbx_struct_assembly_gen")
         operList = cifObj.GetValue("pdbx_struct_oper_list")
+        assembly_inferred = cifObj.GetSingleValue("pdbx_depui_status_flags", "assembly_inferred")
         if (len(assemblyList) > 0) and (len(genList) > 0) and (len(operList) > 0):
-            return True
+            return True,assembly_inferred
         #
-        return False
+        return False,assembly_inferred
 
     def __getNmrDiagnosticsHtmlText(self, entryId):
         """Get diagnostics from validation xml and nmr-shift-error-report json files"""