diff --git a/eppic-cli/pom.xml b/eppic-cli/pom.xml
index 660bf4256..c0ee4f81a 100644
--- a/eppic-cli/pom.xml
+++ b/eppic-cli/pom.xml
@@ -1,67 +1,67 @@
 <project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
 	xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
 	<modelVersion>4.0.0</modelVersion>
-        <parent>
-                <groupId>org.eppic-web</groupId>
-                <artifactId>eppic</artifactId>
-                <version>3.0-SNAPSHOT</version>
-        </parent>
-        <artifactId>eppic-cli</artifactId>
+	<parent>
+		<groupId>org.eppic-web</groupId>
+		<artifactId>eppic</artifactId>
+		<version>3.0-SNAPSHOT</version>
+	</parent>
+	<artifactId>eppic-cli</artifactId>
 
 	<properties>
 		<biojava.version>4.2.3</biojava.version>
 	</properties>
-	
+
 	<repositories>
 		<!-- for uniprot japi -->
 		<repository>
-        	<id>ebi-repo</id>
-        	<name>ebi-repo</name>
-        	<url>http://www.ebi.ac.uk/~maven/m2repo</url>
-    	</repository>		 
+			<id>ebi-repo</id>
+			<name>ebi-repo</name>
+			<url>http://www.ebi.ac.uk/~maven/m2repo</url>
+		</repository>
 	</repositories>
-	
-	
+
+
 	<dependencies>
 		<dependency>
 			<groupId>com.github.spullara.mustache.java</groupId>
 			<artifactId>compiler</artifactId>
 			<version>0.8.18</version>
 		</dependency>
-		
-	    <dependency>
+
+		<dependency>
 			<groupId>org.eppic-web</groupId>
 			<artifactId>eppic-model</artifactId>
 			<version>${project.version}</version>
 			<scope>compile</scope>
 		</dependency>
-		
+
 		<dependency>
 			<groupId>java3d</groupId>
 			<artifactId>vecmath</artifactId>
 			<version>1.3.1</version>
 		</dependency>
-		
+
 		<dependency>
 			<groupId>org.biojava</groupId>
-       		<artifactId>biojava-core</artifactId>
-        	<version>${biojava.version}</version>
+			<artifactId>biojava-core</artifactId>
+			<version>${biojava.version}</version>
 		</dependency>
-		
+
 		<dependency>
 			<groupId>org.biojava</groupId>
-       		<artifactId>biojava-structure-gui</artifactId>
-        	<version>${biojava.version}</version>
+			<artifactId>biojava-structure-gui</artifactId>
+			<version>${biojava.version}</version>
 		</dependency>
 
 		<dependency>
 			<groupId>org.biojava</groupId>
-       		<artifactId>biojava-structure</artifactId>
-        	<version>${biojava.version}</version>
+			<artifactId>biojava-structure</artifactId>
+			<version>${biojava.version}</version>
 		</dependency>
-	
+
 		<!-- junit -->
-		
+
 		<dependency>
 			<groupId>junit</groupId>
 			<artifactId>junit</artifactId>
@@ -97,7 +97,7 @@
 			<version>${log4j.version}</version>
 			<scope>compile</scope>
 		</dependency>
-	
+
 		<!-- jgrapht for assembly package -->
 		<dependency>
 			<groupId>org.jgrapht</groupId>
@@ -123,7 +123,7 @@
 			<artifactId>java-getopt</artifactId>
 			<version>1.0.13</version>
 		</dependency>
-                        
+
 		<dependency>
 			<groupId>org.apache.commons</groupId>
 			<artifactId>commons-math</artifactId>
@@ -132,70 +132,69 @@
 
 		<!-- uniprot -->
 		<dependency>
-	        <groupId>uk.ac.ebi.uniprot</groupId>
-    	    <artifactId>japi</artifactId>
-        	<version>1.0.8</version> 	
-    	</dependency>
-		
-		
+			<groupId>uk.ac.ebi.uniprot</groupId>
+			<artifactId>japi</artifactId>
+			<version>1.0.8</version>
+			<exclusions>
+			<!-- This should fix the problem of multiple bindings (warning at startup). But it doesn't because something 
+			in the UniProt japi calls a logback function at runtime and then the JVM crashes with a NoClassDefFoundError.
+			I've submitted a bug report to the UniProt people - JD 2016-09-23 -->
+			<!-- 
+				<exclusion>
+					<groupId>ch.qos.logback</groupId>
+					<artifactId>logback-classic</artifactId>					
+				</exclusion>
+			-->
+			</exclusions>
+		</dependency>
+
+
 		<dependency>
 			<groupId>mysql</groupId>
 			<artifactId>mysql-connector-java</artifactId>
 			<version>5.1.14</version>
 		</dependency>
-		
-				
+
+
 	</dependencies>
-	
+
 	<build>
-		
-		<!-- one possible way to include sources in jar for gwt compiler to be able to work in eppic-wui -->
-		<!-- 
-     	<resources>
-        	<resource>
-            <directory>src/main/java</directory>
-            <includes>
-                <include>**/*.java</include>
-            </includes>
-        	</resource>
-        	<resource>
-            <directory>src/main/resources</directory>
-            <includes>
-                <include>**/*.*xml</include>
-                <include>**/*.*properties</include>
-            </includes>
-        	</resource>
-    	</resources>
-    	-->
-    			
+
+		<!-- one possible way to include sources in jar for gwt compiler to be 
+			able to work in eppic-wui -->
+		<!-- <resources> <resource> <directory>src/main/java</directory> <includes> 
+			<include>**/*.java</include> </includes> </resource> <resource> <directory>src/main/resources</directory> 
+			<includes> <include>**/*.*xml</include> <include>**/*.*properties</include> 
+			</includes> </resource> </resources> -->
+
 		<plugins>
 			<!-- jar plugin to add eppic's main class, so that the jar is executable -->
 			<plugin>
-        		<groupId>org.apache.maven.plugins</groupId>
-        		<artifactId>maven-jar-plugin</artifactId>
-        		<version>2.4</version>
-        		<configuration>
-			    	<archive>
-            			<manifest>
-              				<addClasspath>true</addClasspath>
+				<groupId>org.apache.maven.plugins</groupId>
+				<artifactId>maven-jar-plugin</artifactId>
+				<version>2.4</version>
+				<configuration>
+					<archive>
+						<manifest>
+							<addClasspath>true</addClasspath>
 							<mainClass>eppic.Main</mainClass>
-            			</manifest>
-          			</archive>
-		        </configuration>
+						</manifest>
+					</archive>
+				</configuration>
+			</plugin>
+
+			<plugin>
+				<groupId>org.apache.maven.plugins</groupId>
+				<artifactId>maven-compiler-plugin</artifactId>
+				<version>3.1</version>
+				<configuration>
+					<source>${java.version}</source>
+					<target>${java.version}</target>
+				</configuration>
 			</plugin>
 
-       		<plugin>
-             		<groupId>org.apache.maven.plugins</groupId>
-              		<artifactId>maven-compiler-plugin</artifactId>
-               		<version>3.1</version>
-               		<configuration>
-                    		<source>${java.version}</source>
-                    		<target>${java.version}</target>
-               		</configuration>
-          	</plugin>
-
-		
-			<!-- the shade plugin to repack all jars into one uber-jar -->			
+
+			<!-- the shade plugin to repack all jars into one uber-jar -->
 			<plugin>
 				<groupId>org.apache.maven.plugins</groupId>
 				<artifactId>maven-shade-plugin</artifactId>
@@ -206,57 +205,58 @@
 							<goal>shade</goal>
 						</goals>
 						<configuration>
-	              			<filters>
-        						<filter>
-        							<!-- solution to the signature repackaging problem is this filter: exclude the signatures!  -->
-            						<artifact>*:*</artifact>
-            						<excludes>
-                						<exclude>META-INF/*.SF</exclude>
-                						<exclude>META-INF/*.DSA</exclude>
-                						<exclude>META-INF/*.RSA</exclude>
-            						</excludes>
-        						</filter>
-    						</filters>
-           				</configuration>
+							<filters>
+								<filter>
+									<!-- solution to the signature repackaging problem is this filter: 
+										exclude the signatures! -->
+									<artifact>*:*</artifact>
+									<excludes>
+										<exclude>META-INF/*.SF</exclude>
+										<exclude>META-INF/*.DSA</exclude>
+										<exclude>META-INF/*.RSA</exclude>
+									</excludes>
+								</filter>
+							</filters>
+						</configuration>
 					</execution>
 				</executions>
 				<configuration>
 					<finalName>uber-${project.artifactId}-${project.version}</finalName>
 				</configuration>
 			</plugin>
-			
+
 			<!-- assembly plugin for final packaging -->
 			<plugin>
-  				<groupId>org.apache.maven.plugins</groupId>
-  				<artifactId>maven-assembly-plugin</artifactId>
-  				<version>2.6</version>
-  				<configuration>
-    				<descriptor>src/assembly/bin.xml</descriptor>
-    				<finalName>${project.artifactId}-${project.version}</finalName>
-    
+				<groupId>org.apache.maven.plugins</groupId>
+				<artifactId>maven-assembly-plugin</artifactId>
+				<version>2.6</version>
+				<configuration>
+					<descriptor>src/assembly/bin.xml</descriptor>
+					<finalName>${project.artifactId}-${project.version}</finalName>
+
 					<archiverConfig>
 						<fileMode>0644</fileMode>
 						<directoryMode>0755</directoryMode>
 						<defaultDirectoryMode>0755</defaultDirectoryMode>
 					</archiverConfig>
-					
-  				</configuration>
-  				
-  				<executions>
-    				<execution>
-
-      					<phase>package</phase>
-      					<goals>
-        					<goal>single</goal>
-      					</goals>
-    				</execution>
-  				</executions>
+
+				</configuration>
+
+				<executions>
+					<execution>
+
+						<phase>package</phase>
+						<goals>
+							<goal>single</goal>
+						</goals>
+					</execution>
+				</executions>
 			</plugin>
-			
+
 		</plugins>
 	</build>
-	
-	
-	
-	
+
+
+
+
 </project>