update of auth chain output for 3vi4

Issue 107 adapting to long chain & residue names & molfile fixes

.github/workflows/c-cpp.yml

@@ -15,10 +15,10 @@ jobs:
       run: sudo apt-get install libnetcdf-dev
     - name: make
       run: make fpocket
-    - name: Set up Python 3.7
+    - name: Set up Python 3.12
       uses: actions/setup-python@v2
       with:
-        python-version: 3.7
+        python-version: 3.12
     - name: create conda environment
       run: conda env update -f ./tests/environment.yml   
     - name : activate

Dockerfile-debian-slim

@@ -1,4 +1,4 @@
-FROM debian:bullseye-slim
+FROM debian:bookworm-slim
 RUN groupadd -r fpocket && useradd --no-log-init -r -g fpocket fpocket
 RUN apt update -y && apt install -y gcc g++ make libnetcdf-dev && rm -rf /var/lib/apt/lists/*
 

headers/fparams.h

@@ -55,6 +55,8 @@ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLI
 #define M_DB_RUN 0 /**< default value for running fpocket for populating a database, 0 default*/
 
 #define M_MAX_CHAINS_DELETE 20
+#define M_MAX_CHAIN_NAME_LENGTH 20
+#define M_MAX_LIG_RESNAME_LENGTH 20
 
 #define M_MIN_AS_DENSITY 0.7
 
@@ -121,7 +123,7 @@ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLI
 #define M_PAR_CHAIN_AS_LIGAND 'a' /**flag, to define which chains are defined as a ligand*/
 #define M_PAR_CHAIN_AS_LIGAND_LONG "chain_as_ligand"
 
-#define M_PAR_WRITE_MODE 'w' /**flag, to define which chains are defined as a ligand*/
+#define M_PAR_WRITE_MODE 'w' /**flag, to define write mode for pocket output: d->same as input, b or both -> both (pdb & cif), p or pdb ->pdb, m or cif -> mmcif*/
 #define M_PAR_WRITE_MODE_LONG "write_mode"
 
 #define M_PAR_MIN_N_EXPLICIT_POCKET 'u'
@@ -184,8 +186,8 @@ typedef struct s_fparams
 	char custom_ligand[M_MAX_PDB_NAME_LEN]; /**container for custom pocket detection using a particular ligand*/
 	char custom_pocket_arg[M_MAX_CUSTOM_POCKET_LEN];
 	char **pdb_lst;
-	char xlig_chain_code[3];
-	char xlig_resname[3];
+	char *xlig_chain_code;
+	char *xlig_resname;
 	int xlig_resnumber;
 	int xpocket_n; /**number of residues defining the pocket to consider*/
 	char *xpocket_chain_code;
@@ -204,7 +206,8 @@ typedef struct s_fparams
 												 to be an apolar a-sphere */
 		nb_mcv_iter,						  /**< Number of iteration for the Monte Carlo volume
 												 calculation */
-		basic_volume_div,					  /**< Box division factor for basic volume calculation */
+		basic_volume_div;					  /**< Box division factor for basic volume calculation */
+	unsigned short
 		min_pock_nb_asph;					  /**< Minimump number of alpha spheres per pocket */
 
 	float clust_max_dist,				/**< First clustering distance criteria */
@@ -214,8 +217,10 @@ typedef struct s_fparams
 		asph_min_size,						/**< Minimum size of alpha spheres to keep */
 		min_as_density,						/**<Minimum alpha sphere density for a pocket to be retained*/
 		asph_max_size;						/**< Maximum size of alpha spheres to keep */
-	char chain_delete[M_MAX_CHAINS_DELETE]; /*chosen chain to delete before calculation*/
-	char chain_as_ligand[M_MAX_CHAINS_DELETE];
+	char *chain_delete[M_MAX_CHAINS_DELETE]; /*chosen chain to delete before calculation*/
+	unsigned short n_chains_to_delete;
+	unsigned short n_chains_as_ligand;
+	char *chain_as_ligand[M_MAX_CHAINS_DELETE];
 	int chain_is_kept;	/* To choose if we keep the chains or not*/
 	char write_par[10]; /*write mode : d -> default | b -> both pdb and mmcif | p ->pdb | m  -> mmcif*/
 

headers/refine.h

@@ -31,7 +31,7 @@ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLI
 /* --------------------------PROTOTYPES---------------------------------------*/
 
 void refinePockets(c_lst_pockets *pockets, s_fparams *params);
-void apply_clustering(c_lst_pockets *pockets, s_fparams *params);
+void apply_clustering(c_lst_pockets *pockets);
 void reIndexPockets(c_lst_pockets *pockets);
 void dropSmallNpolarPockets(c_lst_pockets *pockets, s_fparams *params);
 void drop_tiny(c_lst_pockets *pockets, s_fparams *params) ;

headers/rpdb.h

@@ -146,6 +146,6 @@ void fill_coord_grid(s_pdb *pdb);
 
 
 short get_mm_type_from_element(char *symbol);
-int chains_to_delete(char *chains_selected, char current_line_chain, int is_chain_kept);
-int is_ligand(char *chains_selected, char current_line_chain);
+int chains_to_delete(char *chains_selected[20], char *current_line_chain, int is_chain_kept,unsigned short n_chains_to_delete);
+int is_ligand(char *chains_selected[20], char *current_line_chain, unsigned short n_chains_as_ligand);
 #endif

makefile

@@ -47,7 +47,7 @@ COS         = -DM_OS_LINUX
 CDEBUG      = -DMNO_MEM_DEBUG
 CWARN       = -W -Wextra -Wwrite-strings -Wstrict-prototypes
 
-CFLAGS      = $(CWARN) $(COS) $(CDEBUG) -O2 -g -pg -std=c99 -I$(PLUGINDIR)/include -I$(PLUGINDIR)/$(ARCH)/molfile
+CFLAGS      = $(CWARN) $(COS) $(CDEBUG) -O2 -g -pg -std=gnu99 -I$(PLUGINDIR)/include -I$(PLUGINDIR)/$(ARCH)/molfile
 QCFLAGS     = -O -g -pg -ansi
 
 LGSL        = -L$(PATH_GSL)lib -lgsl -lgslcblas 

src/fparams.c

@@ -89,6 +89,8 @@ s_fparams *init_def_fparams(void)
     par->write_par[0] = 'd';
     par->xpocket_n = 0;
     par->min_n_explicit_pocket_atoms = M_MIN_N_EXPLICIT_POCKET;
+    par->n_chains_to_delete=0;
+    par->n_chains_as_ligand=0;
     return par;
 }
 
@@ -122,7 +124,7 @@ s_fparams *get_fpocket_args(int nargs, char **args)
     char *apt;
     char *residue_string[M_MAX_CUSTOM_POCKET_LEN];
     short custom_ligand_i = 0;
-
+    const char *separators = ",:";
     static struct option fplong_options[] = {/*long options args located in fparams.h*/
                                              {"file", required_argument, 0, M_PAR_PDB_FILE},
                                              {"min_alpha_size", required_argument, 0, M_PAR_MIN_ASHAPE_SIZE},
@@ -185,54 +187,53 @@ s_fparams *get_fpocket_args(int nargs, char **args)
         case M_PAR_CHAIN_AS_LIGAND: /*option with -a "name of the chain" to be specified as a ligand*/
             /*select the chains as ligand*/
             status++;
-            strcpy(par->chain_as_ligand, optarg); /*par->chain_as_ligand contains the arg given in cmd line*/
-            const char *separatorss = ",";        /* defining separators*/
-            pt = strtok(par->chain_as_ligand, separatorss);
+            pt = strtok(optarg, separators);
             int nn = 0;
             while (pt != NULL)
             {
-                strncpy(&(par->chain_as_ligand[nn]), pt, 1);
+                par->chain_as_ligand[nn] = (char *)malloc((M_MAX_CHAIN_NAME_LENGTH + 1) * sizeof(char));
+                strncpy(par->chain_as_ligand[nn], pt, M_MAX_CHAIN_NAME_LENGTH);
+                par->chain_as_ligand[nn][M_MAX_CHAIN_NAME_LENGTH]='\0';
                 nn++;
-                pt = strtok(NULL, separatorss);
+                pt = strtok(NULL, separators);
             }
+            par->n_chains_as_ligand=nn;
             par->xlig_resnumber = 0;
-            // printf("lig %s\n",par->chain_as_ligand);
             break;
 
         case M_PAR_DROP_CHAINS:                /*option with -c "name of the chains"*/
                                                /*drop the selected chains from the pdb file*/
-            strcpy(par->chain_delete, optarg); /*par->custom_ligand contains the arg given in cmd line*/
-            // printf("%s and %s",par->custom_ligand,optarg);
-            const char *separators = ",:"; /* defining separators for drop chains args*/
-            pt = strtok(par->chain_delete, separators);
+            pt = strtok(optarg, separators);
             int n = 0;
             while (pt != NULL)
             {
-                strncpy(&(par->chain_delete[n]), pt, 1);
+                par->chain_delete[n] = (char *)malloc((M_MAX_CHAIN_NAME_LENGTH + 1) * sizeof(char));
+                strncpy(par->chain_delete[n], pt, M_MAX_CHAIN_NAME_LENGTH);
+                par->chain_delete[n][M_MAX_CHAIN_NAME_LENGTH]='\0';
 
                 n++;
                 pt = strtok(NULL, separators);
             }
             par->chain_is_kept = 0;
-
-            // printf("%s\n",par->chain_delete);
+            par->n_chains_to_delete=n;
             status++;
             break;
 
         case M_PAR_KEEP_CHAINS: /*option with -k "name of the chains"*/
                                 /*drop the selected chains from the pdb file*/
 
-            strcpy(par->chain_delete, optarg); /*par->custom_ligand contains the arg given in cmd line*/
-            // printf("%s and %s",par->custom_ligand,optarg);
-            const char *separator = ",:"; /* defining separators for drop chains args*/
-            pt = strtok(par->chain_delete, separator);
+            pt = strtok(optarg, separators);
             int nk = 0;
             while (pt != NULL)
             {
-                strncpy(&(par->chain_delete[nk]), pt, 1);
+                
+                par->chain_delete[nk] = (char *)malloc((M_MAX_CHAIN_NAME_LENGTH + 1) * sizeof(char));
+                strncpy(par->chain_delete[nk], pt, M_MAX_CHAIN_NAME_LENGTH);
+                par->chain_delete[nk][M_MAX_CHAIN_NAME_LENGTH]='\0';
                 nk++;
-                pt = strtok(NULL, separator);
+                pt = strtok(NULL, separators);
             }
+            par->n_chains_to_delete=nk;
             // printf("%s\n",par->chain_delete);
             par->chain_is_kept = 1;
             status++;
@@ -246,26 +247,29 @@ s_fparams *get_fpocket_args(int nargs, char **args)
 
             status++;
 
-            strcpy(par->custom_ligand, optarg);
+            // strcpy(par->custom_ligand, optarg);
             // printf("%s and %s",par->custom_ligand,optarg);
-            pt = strtok(par->custom_ligand, ":");
+            pt = strtok(optarg, ":");
 
             while (pt != NULL)
             {
                 custom_ligand_i++;
                 if (custom_ligand_i == 1)
                     par->xlig_resnumber = atoi(pt);
-                else if (custom_ligand_i == 2)
-                    strncpy(&(par->xlig_resname), pt, 3);
-                else if (custom_ligand_i == 3)
-                    strncpy(&(par->xlig_chain_code), pt, 1);
-                /*int a = atoi(pt);
-                    printf("%d\n", a);*/
+                else if (custom_ligand_i == 2){
+                    par->xlig_resname= (char *)malloc((M_MAX_LIG_RESNAME_LENGTH + 1) * sizeof(char));
+                    strncpy(par->xlig_resname, pt, M_MAX_LIG_RESNAME_LENGTH);
+                    par->xlig_resname[M_MAX_LIG_RESNAME_LENGTH]='\0';
+                }
+                else if (custom_ligand_i == 3){
+                    par->xlig_chain_code= (char *)malloc((M_MAX_CHAIN_NAME_LENGTH + 1) * sizeof(char));
+                    strncpy(par->xlig_chain_code, pt, M_MAX_CHAIN_NAME_LENGTH);
+                    par->xlig_chain_code[M_MAX_CHAIN_NAME_LENGTH]='\0';
+                }
                 pt = strtok(NULL, ":");
             }
 
             break;
-
         case M_PAR_CUSTOM_POCKET:
 
             // parse pocket specification that has to be given as
@@ -292,7 +296,7 @@ s_fparams *get_fpocket_args(int nargs, char **args)
                 strcpy(&residue_string, pt);
                 rest2 = residue_string;
                 apti = 0;
-                while (apt = strtok_r(rest2, ":", &rest2))
+                while ((apt = strtok_r(rest2, ":", &rest2)))
                 {
                     switch (apti)
                     {
@@ -971,10 +975,10 @@ void print_pocket_usage(FILE *f)
     fprintf(f, "\t-%c --%s (string)\t\t: String specifying a ligand like: \n\
 \t\t\t\t\t\t  residuenumber:residuename:chain_code (ie. 1224:PU8:A).\t\n",
             M_PAR_CUSTOM_LIGAND, M_PAR_CUSTOM_LIGAND_LONG);
-    fprintf(f, "\t-%c --%s (string)\t\t: String specifying a pocket like: \n\ 
+    fprintf(f, "\t-%c --%s (string)\t\t: String specifying a pocket like: \n\
 \t\t\t\t\t\t  residuenumber1:insertion_code1('-' if empty):chain_code1.residuenumber2:insertion_code2:chain_code2 (ie. 138:-:A.139:-:A).\t\n",
             M_PAR_CUSTOM_POCKET, M_PAR_CUSTOM_POCKET_LONG);
-    fprintf(f, "\t-%c --%s (int)\t: If explicit pocket provided, minimum number \n\ 
+    fprintf(f, "\t-%c --%s (int)\t: If explicit pocket provided, minimum number \n\
 \t\t\t\t\t\t  of atoms of an alpha sphere that have to be in the selected pocket.\t\n",
             M_PAR_MIN_N_EXPLICIT_POCKET, M_PAR_MIN_N_EXPLICIT_POCKET_LONG);
     fprintf(f, "\t-%c --%s (char)\t\t: Character specifying a chain as a ligand\t\n", M_PAR_CHAIN_AS_LIGAND, M_PAR_CHAIN_AS_LIGAND_LONG);

src/fpmain.c

@@ -76,7 +76,7 @@ int main(int argc, char *argv[])
                 }
                 else
                 {
-                        if (params->pdb_path == NULL || strlen(params->pdb_path) <= 0)
+                        if (!params->pdb_path[0] || strlen(params->pdb_path) <= 0)
                         {
                                 fprintf(stdout, "! Invalid pdb name given.\n");
                                 print_pocket_usage(stdout);
@@ -222,8 +222,10 @@ void process_pdb(char *pdbname, s_fparams *params)
                         print_number_of_objects_in_memory();
                 }
         }
-        else
-                fprintf(stderr, "! PDB reading failed!\n");
+        else {
+                fprintf(stderr, "! Structure reading failed!\n");
+                exit( EXIT_FAILURE );
+        }
 }
 
 s_pdb *open_file_format(char *fpath, const char *ligan, const int keep_lig, int model_number, s_fparams *par)

src/fpocket.c

@@ -165,7 +165,7 @@ c_lst_pockets *search_pocket(s_pdb *pdb, s_fparams *params, s_pdb *pdb_w_lig)
         fflush(DEBUG_STREAM);
     }
 
-    apply_clustering(pockets, params);
+    apply_clustering(pockets);
     if (DEBUG)
     {
         fprintf(DEBUG_STREAM, "applied clustering to pockets");
@@ -216,7 +216,7 @@ c_lst_pockets *search_pocket(s_pdb *pdb, s_fparams *params, s_pdb *pdb_w_lig)
             print_number_of_objects_in_memory();
         //        int i;
 
-        if (params->fpocket_running && params->flag_do_grid_calculations && params->topology_path)
+        if (params->fpocket_running && params->flag_do_grid_calculations && params->topology_path[0])
             calculate_pocket_energy_grids(pockets, params, pdb);
         // params->fpocket_running &&
     }

src/mdparams.c

@@ -256,7 +256,7 @@ s_mdparams* get_mdpocket_args(int nargs, char **args) {
                 par = NULL;
                 print_mdpocket_usage(stdout);
             }
-        } else if ((!traj_file_defined || !traj_format_defined || !par->fpar->pdb_path)) {
+        } else if ((!traj_file_defined || !traj_format_defined || !par->fpar->pdb_path[0])) {
             fprintf(stdout, "! No input file given... Try again :).%d %d %s\n",traj_file_defined,traj_format_defined,par->fpar->pdb_path);
             free_mdparams(par);
             par = NULL;

src/pertable.c

@@ -265,10 +265,13 @@ char *pte_get_element_from_number(int atomicnumber)
 	
 		tmp[0] = ST_pte_symbol[atomicnumber][0] ;
 		tmp[1] = ST_pte_symbol[atomicnumber][1] ;
-		tmp[2] = '\0';
 		return tmp;
-	} 
-	return -1 ;
+	} else {
+		tmp[0]='-';
+		tmp[1]='1';
+	}
+	tmp[2]='\0';
+	return tmp;
 }
 
 /**

src/qhull/src/qconvex/qconvex.c

@@ -42,7 +42,7 @@ int run_qconvex(FILE *fin,FILE *fout) {
   boolT ismalloc;
 
   int argc=2;
-  char *argv[2];
+  const char *argv[2];
   argv[0]=malloc(sizeof(char)*200);
   argv[0]="src/qhull/qconvex\0";
   argv[1]=malloc(sizeof(char)*2);

src/qhull/src/qvoronoi/qvoronoi.c

@@ -239,7 +239,7 @@ int run_qvoronoi(FILE *fin,FILE *fout) {
   coordT *points;
   boolT ismalloc;
   int argc=6;
-  char *argv[6];
+  const char *argv[6];
   argv[0]=malloc(sizeof(char)*200);
   argv[0]="src/qhull/qvoronoi\0";
   argv[1]=malloc(sizeof(char)*2);

src/read_mmcif.c

@@ -56,7 +56,7 @@ s_pdb *open_mmcif(char *fpath, const char *ligan, const int keep_lig, int model_
 
     molfile_pdbxplugin_init();
     molfile_pdbxplugin_register(NULL, register_cb);
-    char *filetype = "cif";
+    const char *filetype = "cif";
     int inatoms; /*number of atoms in the  file determined by molfile api*/
     // printf("%s | %s |%d", fpath, filetype, inatoms);
     // printf("\n");
@@ -68,8 +68,11 @@ s_pdb *open_mmcif(char *fpath, const char *ligan, const int keep_lig, int model_
     int rc2;
     int j;
     int k;
-
     h_in = api->open_file_read(fpath, filetype, &inatoms);
+    if(inatoms==0){
+        fprintf(stderr, "! Structure reading failed or file is empty!\n");
+        exit( EXIT_FAILURE );
+    }
     at_in = (molfile_atom_t *)malloc(inatoms * sizeof(molfile_atom_t));
     ts_in.coords = (float *)malloc(3 * inatoms * sizeof(float)); /*allocating space for the coords*/
     rc2 = api->read_structure(h_in, &optflags, at_in);
@@ -79,15 +82,13 @@ s_pdb *open_mmcif(char *fpath, const char *ligan, const int keep_lig, int model_
     model_flag = 1;
     for (i = 0; i < inatoms; i++) /*loop to go through all atoms*/
     {
-
         if (at_in[i].altloc[0] == '.' || at_in[i].altloc[0] == '\0')
             at_in[i].altloc[0] = ' ';
-        if (at_in[i].modelnumber == model_number && !strncmp(at_in[i].atom_type, "ATOM", 4) && !is_ligand(par->chain_as_ligand, at_in[i].chain[0]))
+        if (at_in[i].modelnumber == model_number && !strncmp(at_in[i].atom_type, "ATOM", 4) && !is_ligand(par->chain_as_ligand, at_in[i].chain_auth,par->n_chains_as_ligand))
         {
-            if (at_in[i].altloc[0] == ' ' || at_in[i].altloc[0] == 'A')
-
+            if (at_in[i].altloc[0] == ' ' || at_in[i].altloc[0] == 'A' || at_in[i].altloc[0] == '?')
             {
-                if (chains_to_delete(par->chain_delete, at_in[i].chain[0], par->chain_is_kept))
+                if (chains_to_delete(par->chain_delete, at_in[i].chain_auth, par->chain_is_kept,par->n_chains_to_delete))
                 {
                     /* Atom entry: check if there is a ligand in there (just in case)... */
                     if (ligan && strlen(ligan) > 1 && ligan[0] == at_in[i].resname[0] && ligan[1] == at_in[i].resname[1] && ligan[2] == at_in[i].resname[2])
@@ -99,7 +100,7 @@ s_pdb *open_mmcif(char *fpath, const char *ligan, const int keep_lig, int model_
                         }
                         /*check this function*/
                     }
-                    else if (ligan && strlen(ligan) == 1 && at_in[i].chain[0] == ligan[0])
+                    else if (ligan && strlen(ligan) == 1 && at_in[i].chain_auth[0] == ligan[0])
                     { /*here we have a protein chain defined as ligand...a bit more complex then*/
                         if (keep_lig)
                         {
@@ -114,13 +115,7 @@ s_pdb *open_mmcif(char *fpath, const char *ligan, const int keep_lig, int model_
                 }
                 if (par->xlig_resnumber > -1)
                 {
-
-                    // if ((at_in[i].chain[0] == par->xlig_chain_code[0] && at_in[i].resid == par->xlig_resnumber && par->xlig_resname[0] == at_in[i].resname[0] && par->xlig_resname[1] == at_in[i].resname[1] && par->xlig_resname[2] == at_in[i].resname[2]) || (at_in[i].chain_auth[0] == par->xlig_chain_code[0] && at_in[i].resid_auth == par->xlig_resnumber && par->xlig_resname[0] == at_in[i].resname[0] && par->xlig_resname[1] == at_in[i].resname[1] && par->xlig_resname[2] == at_in[i].resname[2]))
-                    // {
-                    //     pdb->n_xlig_atoms++;
-                    // }
-
-                    if (is_ligand(par->chain_as_ligand, at_in[i].chain[0]))
+                    if (is_ligand(par->chain_as_ligand, at_in[i].chain_auth,par->n_chains_as_ligand))
                     {
                         pdb->n_xlig_atoms++;
                     }
@@ -129,26 +124,25 @@ s_pdb *open_mmcif(char *fpath, const char *ligan, const int keep_lig, int model_
             if (par->xlig_resnumber > -1)
             {
 
-                if ((at_in[i].chain[0] == par->xlig_chain_code[0] && at_in[i].resid == par->xlig_resnumber && par->xlig_resname[0] == at_in[i].resname[0] && par->xlig_resname[1] == at_in[i].resname[1] && par->xlig_resname[2] == at_in[i].resname[2]) || (at_in[i].chain_auth[0] == par->xlig_chain_code[0] && at_in[i].resid_auth == par->xlig_resnumber && par->xlig_resname[0] == at_in[i].resname[0] && par->xlig_resname[1] == at_in[i].resname[1] && par->xlig_resname[2] == at_in[i].resname[2]))
+                if (((is_ligand(par->chain_as_ligand, at_in[i].chain_auth,par->n_chains_as_ligand)) || (par->xlig_chain_code !=NULL && at_in[i].chain_auth[0] == par->xlig_chain_code[0] && at_in[i].resid == par->xlig_resnumber && par->xlig_resname[0] == at_in[i].resname[0] && par->xlig_resname[1] == at_in[i].resname[1] && par->xlig_resname[2] == at_in[i].resname[2]) || (par->xlig_chain_code!=NULL && at_in[i].chain_auth[0] == par->xlig_chain_code[0] && at_in[i].resid_auth == par->xlig_resnumber && par->xlig_resname[0] == at_in[i].resname[0] && par->xlig_resname[1] == at_in[i].resname[1] && par->xlig_resname[2] == at_in[i].resname[2])))
                 {
                     pdb->n_xlig_atoms++;
                 }
             }
         }
-        else if (at_in[i].modelnumber == model_number && !strncmp(at_in[i].atom_type, "HETATM", 6) || (!strncmp(at_in[i].atom_type, "ATOM", 4) && is_ligand(par->chain_as_ligand, at_in[i].chain[0])))
+        else if ((at_in[i].modelnumber == model_number && !strncmp(at_in[i].atom_type, "HETATM", 6)) || (!strncmp(at_in[i].atom_type, "ATOM", 4) && is_ligand(par->chain_as_ligand, at_in[i].chain_auth,par->n_chains_as_ligand)))
         {
 
-            if (at_in[i].altloc[0] == ' ' || at_in[i].altloc[0] == 'A' || at_in[i].altloc[0] == '1')
+            if (at_in[i].altloc[0] == '?' || at_in[i].altloc[0] == ' ' || at_in[i].altloc[0] == 'A' || at_in[i].altloc[0] == '1')
             {
-
-                if (chains_to_delete(par->chain_delete, at_in[i].chain[0], par->chain_is_kept))
+                if (chains_to_delete(par->chain_delete, at_in[i].chain_auth, par->chain_is_kept,par->n_chains_to_delete))
                 {
                     if (ligan && strlen(ligan) > 1 && keep_lig && ligan[0] == at_in[i].resname[0] && ligan[1] == at_in[i].resname[1] && ligan[2] == at_in[i].resname[2])
                     {
                         natm_lig++;
                         natoms++;
                     }
-                    else if (ligan && strlen(ligan) == 1 && ligan[0] == at_in[i].chain[0])
+                    else if (ligan && strlen(ligan) == 1 && ligan[0] == at_in[i].chain_auth[0])
                     {
                         if (keep_lig)
                             natm_lig++;
@@ -157,13 +151,13 @@ s_pdb *open_mmcif(char *fpath, const char *ligan, const int keep_lig, int model_
                     else
                     {
                         /* Keep specific HETATM given in the static list ST_keep_hetatm */
-                        if ((keep_lig && !ligan && strncmp(at_in[i].resname, "HOH", 3) && strncmp(at_in[i].resname, "WAT", 3) && strncmp(at_in[i].resname, "TIP", 3)) || (keep_lig && is_ligand(par->chain_as_ligand, at_in[i].chain[0])))
+                        if ((keep_lig && !ligan && strncmp(at_in[i].resname, "HOH", 3) && strncmp(at_in[i].resname, "WAT", 3) && strncmp(at_in[i].resname, "TIP", 3)) || (keep_lig && is_ligand(par->chain_as_ligand, at_in[i].chain_auth,par->n_chains_as_ligand)))
                         {
 
                             natoms++;
                             nhetatm++;
                         }
-                        else if (!is_ligand(par->chain_as_ligand, at_in[i].chain[0]))
+                        else if (!is_ligand(par->chain_as_ligand, at_in[i].chain_auth,par->n_chains_as_ligand))
                         {
                             for (j = 0; j < ST_nb_keep_hetatm; j++)
                             {
@@ -178,14 +172,14 @@ s_pdb *open_mmcif(char *fpath, const char *ligan, const int keep_lig, int model_
                     }
                 }
 
-                if (is_ligand(par->chain_as_ligand, at_in[i].chain[0]))
+                if (is_ligand(par->chain_as_ligand, at_in[i].chain_auth,par->n_chains_as_ligand))
                 {
                     pdb->n_xlig_atoms++;
                 }
             }
             if (par->xlig_resnumber > -1)
-            {
-                if ((at_in[i].chain[0] == par->xlig_chain_code[0] && at_in[i].resid == par->xlig_resnumber && par->xlig_resname[0] == at_in[i].resname[0] && par->xlig_resname[1] == at_in[i].resname[1] && par->xlig_resname[2] == at_in[i].resname[2]) || (at_in[i].chain_auth[0] == par->xlig_chain_code[0] && at_in[i].resid_auth == par->xlig_resnumber && par->xlig_resname[0] == at_in[i].resname[0] && par->xlig_resname[1] == at_in[i].resname[1] && par->xlig_resname[2] == at_in[i].resname[2]))
+            {   
+                if ((is_ligand(par->chain_as_ligand, at_in[i].chain_auth,par->n_chains_as_ligand)) || (par->xlig_chain_code !=NULL && !strcmp(at_in[i].chain_auth,par->xlig_chain_code) && (at_in[i].resid == par->xlig_resnumber) && (par->xlig_resname[0] == at_in[i].resname[0]) && (par->xlig_resname[1] == at_in[i].resname[1]) && (par->xlig_resname[2] == at_in[i].resname[2])) || (par->xlig_chain_code!=NULL && !strcmp(at_in[i].chain_auth, par->xlig_chain_code) && at_in[i].resid_auth == par->xlig_resnumber && par->xlig_resname[0] == at_in[i].resname[0] && par->xlig_resname[1] == at_in[i].resname[1] && par->xlig_resname[2] == at_in[i].resname[2]))
                 {
                     pdb->n_xlig_atoms++;
                 }
@@ -260,7 +254,7 @@ void read_mmcif(s_pdb *pdb, const char *ligan, const int keep_lig, int model_num
     /*******************************************************************************/
     molfile_pdbxplugin_init();
     molfile_pdbxplugin_register(NULL, register_cb);
-    char *filetype = "cif";
+    const char *filetype = "cif";
     int inatoms; /*number of atoms in the  file determined by molfile api*/
 
     void *h_in;
@@ -277,6 +271,7 @@ void read_mmcif(s_pdb *pdb, const char *ligan, const int keep_lig, int model_num
     ts_in.coords = (float *)malloc(3 * inatoms * sizeof(float)); /*allocating space for the coords*/
     rc2 = api->read_structure(h_in, &optflags, at_in);
     rc = api->read_next_timestep(h_in, inatoms, &ts_in);
+
     // printf("READ : %s | %s |%d\n", pdb->fname, filetype, inatoms);
     /* Loop over the pdb file */
     model_flag = 1;
@@ -285,25 +280,26 @@ void read_mmcif(s_pdb *pdb, const char *ligan, const int keep_lig, int model_num
     ; /*here we indicate that a particular model should be read only*/
     for (i = 0; i < inatoms; i++)
     {
+
         if (at_in[i].altloc[0] == '.' || at_in[i].altloc[0] == '\0')
             at_in[i].altloc[0] = ' ';
 
-        if (at_in[i].modelnumber == model_number && !strncmp(at_in[i].atom_type, "ATOM", 4) && !is_ligand(params->chain_as_ligand, at_in[i].chain[0]))
+        if (at_in[i].modelnumber == model_number && !strncmp(at_in[i].atom_type, "ATOM", 4) && !is_ligand(params->chain_as_ligand, at_in[i].chain_auth,params->n_chains_as_ligand))
         {
 
-            if (at_in[i].altloc[0] == ' ' || at_in[i].altloc[0] == 'A' || at_in[i].altloc[0] == '1')
+            if (at_in[i].altloc[0] == ' ' || at_in[i].altloc[0] == 'A' || at_in[i].altloc[0] == '1' || at_in[i].altloc[0] == '?')
             { /*if within first occurence*/
                 /* Enter this if when arg in command line is -r */
 
                 /* Enter this if when arg in command line is -a */
-                if (is_ligand(params->chain_as_ligand, at_in[i].chain[0]))
+                if (is_ligand(params->chain_as_ligand, at_in[i].chain_auth,params->n_chains_as_ligand))
                 {
                     *(pdb->xlig_x + i_explicit_ligand_atom) = ts_in.coords[3 * i];
                     *(pdb->xlig_y + i_explicit_ligand_atom) = ts_in.coords[(3 * i) + 1];
                     *(pdb->xlig_z + i_explicit_ligand_atom) = ts_in.coords[(3 * i) + 2];
                     i_explicit_ligand_atom++;
                 }
-                if (chains_to_delete(params->chain_delete, at_in[i].chain[0], params->chain_is_kept)) // deleting the chains we want to delete from pdb file
+                if (chains_to_delete(params->chain_delete, at_in[i].chain_auth, params->chain_is_kept,params->n_chains_to_delete)) // deleting the chains we want to delete from pdb file
                 {
                     /* Check if the desired ligand is in such an entry */
                     if (ligan && strlen(ligan) > 1 && ligan[0] == at_in[i].resname[0] && ligan[1] == at_in[i].resname[1] && ligan[2] == at_in[i].resname[2])
@@ -317,7 +313,7 @@ void read_mmcif(s_pdb *pdb, const char *ligan, const int keep_lig, int model_num
                             strcpy(atom->name, at_in[i].type);
                             atom->pdb_aloc = at_in[i].altloc[0];
                             strcpy(atom->res_name, at_in[i].resname);
-                            strncpy(atom->chain, at_in[i].chain, 2);
+                            strcpy(atom->chain, at_in[i].chain_auth);
                             atom->res_id = at_in[i].resid;
                             atom->pdb_insert = at_in[i].insertion[0];
                             atom->x = ts_in.coords[(3 * i)];
@@ -342,7 +338,7 @@ void read_mmcif(s_pdb *pdb, const char *ligan, const int keep_lig, int model_num
                             ligfound = 1;
                         }
                     }
-                    else if (ligan && strlen(ligan) == 1 && at_in[i].chain[0] == ligan[0])
+                    else if (ligan && strlen(ligan) == 1 && at_in[i].chain_auth[0] == ligan[0])
                     { /*here we have a protein chain defined as ligand...a bit more complex then*/
                         if (keep_lig)
                         {
@@ -354,9 +350,8 @@ void read_mmcif(s_pdb *pdb, const char *ligan, const int keep_lig, int model_num
                             strcpy(atom->name, at_in[i].type);
                             atom->pdb_aloc = at_in[i].altloc[0];
                             strcpy(atom->res_name, at_in[i].resname);
-                            strncpy(atom->chain, at_in[i].chain, 2);
+                            strcpy(atom->chain, at_in[i].chain_auth);
                             atom->res_id = at_in[i].resid;
-                            // fprintf(stdout, " here : %c\n", at_in[i].insertion[0]);
                             atom->pdb_insert = at_in[i].insertion[0];
                             atom->x = ts_in.coords[(3 * i)];
                             atom->y = ts_in.coords[(3 * i) + 1];
@@ -399,13 +394,10 @@ void read_mmcif(s_pdb *pdb, const char *ligan, const int keep_lig, int model_num
                         strcpy(atom->name, at_in[i].type);
                         atom->pdb_aloc = at_in[i].altloc[0];
                         strcpy(atom->res_name, at_in[i].resname);
-                        // fprintf(stdout,"%s |%s|%d\n", atom->chain, at_in[i].chain,i);
-                        // fflush(stdout);
-                        strncpy(atom->chain, at_in[i].chain, 2);
-                        // fprintf(stdout,"%s |%s|%d\n", atom->chain, at_in[i].chain,i);
+
+                        strcpy(atom->chain, at_in[i].chain_auth);
                         atom->res_id = at_in[i].resid;
                         atom->pdb_insert = at_in[i].insertion[0];
-                        // printf("ins:%s",at_in[i].insertion);
 
                         atom->x = ts_in.coords[(3 * i)];
                         atom->y = ts_in.coords[(3 * i) + 1];
@@ -435,9 +427,10 @@ void read_mmcif(s_pdb *pdb, const char *ligan, const int keep_lig, int model_num
             }
             if (pdb->n_xlig_atoms)
             {
-                if (at_in[i].chain[0] == params->xlig_chain_code[0] && at_in[i].resid == params->xlig_resnumber && params->xlig_resname[0] == at_in[i].resname[0] && params->xlig_resname[1] == at_in[i].resname[1] && params->xlig_resname[2] == at_in[i].resname[2])
-                {
+                unsigned short is_chain_ligand=(is_ligand(params->chain_as_ligand, at_in[i].chain_auth,params->n_chains_as_ligand) &&  strncmp(at_in[i].resname, "HOH", 3) && strncmp(at_in[i].resname, "WAT", 3) && strncmp(at_in[i].resname, "TIP", 3));
 
+                if (is_chain_ligand || (params->xlig_chain_code !=NULL && at_in[i].chain_auth[0] == params->xlig_chain_code[0] && at_in[i].resid == params->xlig_resnumber && params->xlig_resname[0] == at_in[i].resname[0] && params->xlig_resname[1] == at_in[i].resname[1] && params->xlig_resname[2] == at_in[i].resname[2]))
+                {
                     *(pdb->xlig_x + i_explicit_ligand_atom) = ts_in.coords[3 * i];
                     *(pdb->xlig_y + i_explicit_ligand_atom) = ts_in.coords[(3 * i) + 1];
                     *(pdb->xlig_z + i_explicit_ligand_atom) = ts_in.coords[(3 * i) + 2];
@@ -445,23 +438,22 @@ void read_mmcif(s_pdb *pdb, const char *ligan, const int keep_lig, int model_num
                 }
             }
         }
-        else if (at_in[i].modelnumber == model_number && !strncmp(at_in[i].atom_type, "HETATM", 6) || (!strncmp(at_in[i].atom_type, "ATOM", 4) && is_ligand(params->chain_as_ligand, at_in[i].chain[0])))
+        else if ((at_in[i].modelnumber == model_number && !strncmp(at_in[i].atom_type, "HETATM", 6)) || (!strncmp(at_in[i].atom_type, "ATOM", 4) && is_ligand(params->chain_as_ligand, at_in[i].chain_auth,params->n_chains_as_ligand)))
         {
 
-            if (at_in[i].altloc[0] == ' ' || at_in[i].altloc[0] == 'A' || at_in[i].altloc[0] == '1')
+            if (at_in[i].altloc[0] == ' ' || at_in[i].altloc[0] == 'A' || at_in[i].altloc[0] == '1' || at_in[i].altloc[0] =='?')
             { /*first occurence*/
 
-                if (is_ligand(params->chain_as_ligand, at_in[i].chain[0]))
+                if (is_ligand(params->chain_as_ligand, at_in[i].chain_auth,params->n_chains_as_ligand))
                 {
                     *(pdb->xlig_x + i_explicit_ligand_atom) = ts_in.coords[3 * i];
                     *(pdb->xlig_y + i_explicit_ligand_atom) = ts_in.coords[(3 * i) + 1];
                     *(pdb->xlig_z + i_explicit_ligand_atom) = ts_in.coords[(3 * i) + 2];
 
-                    // printf("%d\n", i_explicit_ligand_atom);
                     i_explicit_ligand_atom++;
                 }
                 // fflush(stdout);
-                if (chains_to_delete(params->chain_delete, at_in[i].chain[0], params->chain_is_kept)) // deleting the chains we want to delete from pdb file
+                if (chains_to_delete(params->chain_delete, at_in[i].chain_auth, params->chain_is_kept,params->n_chains_to_delete)) // deleting the chains we want to delete from pdb file
                 {
                     /* Check if the desired ligand is in HETATM entry */
                     if (ligan && strlen(ligan) > 1 && keep_lig && ligan[0] == at_in[i].resname[0] && ligan[1] == at_in[i].resname[1] && ligan[2] == at_in[i].resname[2])
@@ -473,7 +465,7 @@ void read_mmcif(s_pdb *pdb, const char *ligan, const int keep_lig, int model_num
                         strcpy(atom->name, at_in[i].type);
                         atom->pdb_aloc = at_in[i].altloc[0];
                         strcpy(atom->res_name, at_in[i].resname);
-                        strncpy(atom->chain, at_in[i].chain, 2);
+                        strcpy(atom->chain, at_in[i].chain_auth);
                         atom->res_id = at_in[i].resid;
                         atom->pdb_insert = at_in[i].insertion[0];
                         atom->x = ts_in.coords[(3 * i)];
@@ -497,7 +489,7 @@ void read_mmcif(s_pdb *pdb, const char *ligan, const int keep_lig, int model_num
                         iatoms++;
                         ligfound = 1;
                     }
-                    else if (ligan && strlen(ligan) == 1 && ligan[0] == at_in[i].chain[0])
+                    else if (ligan && strlen(ligan) == 1 && ligan[0] == at_in[i].chain_auth[0])
                     {
 
                         if (keep_lig)
@@ -510,7 +502,7 @@ void read_mmcif(s_pdb *pdb, const char *ligan, const int keep_lig, int model_num
                             strcpy(atom->name, at_in[i].type);
                             atom->pdb_aloc = at_in[i].altloc[0];
                             strcpy(atom->res_name, at_in[i].resname);
-                            strncpy(atom->chain, at_in[i].chain, 2);
+                            strcpy(atom->chain, at_in[i].chain_auth);
                             atom->res_id = at_in[i].resid;
                             atom->pdb_insert = at_in[i].insertion[0];
                             atom->x = ts_in.coords[(3 * i)];
@@ -539,7 +531,7 @@ void read_mmcif(s_pdb *pdb, const char *ligan, const int keep_lig, int model_num
                     {
 
                         /* Keep specific HETATM given in the static list ST_keep_hetatm. */
-                        if ((keep_lig && !ligan && strncmp(at_in[i].resname, "HOH", 3) && strncmp(at_in[i].resname, "WAT", 3) && strncmp(at_in[i].resname, "TIP", 3)) || (keep_lig && is_ligand(params->chain_as_ligand, at_in[i].chain[0])))
+                        if ((keep_lig && !ligan && strncmp(at_in[i].resname, "HOH", 3) && strncmp(at_in[i].resname, "WAT", 3) && strncmp(at_in[i].resname, "TIP", 3)) || (keep_lig && is_ligand(params->chain_as_ligand, at_in[i].chain_auth,params->n_chains_as_ligand)))
                         {
 
                             atom = atoms + iatoms;
@@ -548,7 +540,7 @@ void read_mmcif(s_pdb *pdb, const char *ligan, const int keep_lig, int model_num
                             strcpy(atom->name, at_in[i].type);
                             atom->pdb_aloc = at_in[i].altloc[0];
                             strcpy(atom->res_name, at_in[i].resname);
-                            strncpy(atom->chain, at_in[i].chain, 2);
+                            strcpy(atom->chain, at_in[i].chain_auth);
                             atom->res_id = at_in[i].resid;
                             atom->pdb_insert = at_in[i].insertion[0];
                             atom->x = ts_in.coords[(3 * i)];
@@ -570,7 +562,7 @@ void read_mmcif(s_pdb *pdb, const char *ligan, const int keep_lig, int model_num
                             ihetatm++;
                             iatoms++;
                         }
-                        else if (!is_ligand(params->chain_as_ligand, at_in[i].chain[0]))
+                        else if (!is_ligand(params->chain_as_ligand, at_in[i].chain_auth,params->n_chains_as_ligand))
                         {
 
                             for (j = 0; j < ST_nb_keep_hetatm; j++)
@@ -586,7 +578,7 @@ void read_mmcif(s_pdb *pdb, const char *ligan, const int keep_lig, int model_num
                                     strcpy(atom->name, at_in[i].type);
                                     atom->pdb_aloc = at_in[i].altloc[0];
                                     strcpy(atom->res_name, at_in[i].resname);
-                                    strncpy(atom->chain, at_in[i].chain, 2);
+                                    strcpy(atom->chain, at_in[i].chain_auth);
                                     atom->res_id = at_in[i].resid;
                                     atom->pdb_insert = at_in[i].insertion[0];
                                     atom->x = ts_in.coords[(3 * i)];
@@ -615,16 +607,18 @@ void read_mmcif(s_pdb *pdb, const char *ligan, const int keep_lig, int model_num
                     }
                 }
             }
+
             if (pdb->n_xlig_atoms)
             {
-                if ((at_in[i].chain[0] == params->xlig_chain_code[0] && at_in[i].resid == params->xlig_resnumber && params->xlig_resname[0] == at_in[i].resname[0] && params->xlig_resname[1] == at_in[i].resname[1] && params->xlig_resname[2] == at_in[i].resname[2]) || (at_in[i].chain_auth[0] == params->xlig_chain_code[0] && at_in[i].resid_auth == params->xlig_resnumber && params->xlig_resname[0] == at_in[i].resname[0] && params->xlig_resname[1] == at_in[i].resname[1] && params->xlig_resname[2] == at_in[i].resname[2]))
-                {
-                    // if (params->xlig_resname[0] == resb[0] && params->xlig_resname[1] == resb[1] && params->xlig_resname[2] == resb[2]) {
 
+                unsigned short is_chain_ligand=(is_ligand(params->chain_as_ligand, at_in[i].chain_auth,params->n_chains_as_ligand) &&  strncmp(at_in[i].resname, "HOH", 3) && strncmp(at_in[i].resname, "WAT", 3) && strncmp(at_in[i].resname, "TIP", 3));
+
+                if (is_chain_ligand || (params->xlig_chain_code !=NULL && at_in[i].chain_auth[0] == params->xlig_chain_code[0] && at_in[i].resid == params->xlig_resnumber && params->xlig_resname[0] == at_in[i].resname[0] && params->xlig_resname[1] == at_in[i].resname[1] && params->xlig_resname[2] == at_in[i].resname[2]) || (params->xlig_chain_code!=NULL && at_in[i].chain_auth[0] == params->xlig_chain_code[0] && at_in[i].resid_auth == params->xlig_resnumber && params->xlig_resname[0] == at_in[i].resname[0] && params->xlig_resname[1] == at_in[i].resname[1] && params->xlig_resname[2] == at_in[i].resname[2]))
+                {
+                                        
                     *(pdb->xlig_x + i_explicit_ligand_atom) = ts_in.coords[3 * i];
                     *(pdb->xlig_y + i_explicit_ligand_atom) = ts_in.coords[(3 * i) + 1];
                     *(pdb->xlig_z + i_explicit_ligand_atom) = ts_in.coords[(3 * i) + 2];
-
                     i_explicit_ligand_atom++;
                 }
             }

src/refine.c

@@ -55,7 +55,7 @@ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLI
 	void
 
 */
-void apply_clustering(c_lst_pockets *pockets, s_fparams *params)
+void apply_clustering(c_lst_pockets *pockets)
 {
 	node_pocket *nextPocket;
 	node_pocket *curMobilePocket;

src/rpdb.c

@@ -803,6 +803,8 @@ s_pdb *rpdb_open(char *fpath, const char *ligan, const int keep_lig, int model_n
     int i;
     float x, y, z;
     int resnbuf = 0;
+    char *chainbuf=(char *)my_malloc(sizeof(char)*2);
+    chainbuf[1]='\0';
     int model_flag = 0;      /*by default we consider that no particular model is read*/
     int model_read = 0;      /*flag tracking the status if a current line is read or not*/
     int cur_model_count = 0; /*when reading NMR models, then count on which model you currently are*/
@@ -848,12 +850,12 @@ s_pdb *rpdb_open(char *fpath, const char *ligan, const int keep_lig, int model_n
         }
         if (pdb->model_flag == 0 || model_read == 1)
         {
-
-            if (!strncmp(buf, "ATOM ", 5) && !is_ligand(par->chain_as_ligand, buf[21]))
+            chainbuf[0]=buf[21];
+            if (!strncmp(buf, "ATOM ", 5) && !is_ligand(par->chain_as_ligand, chainbuf,par->n_chains_as_ligand))
             {
 
                 // printf("%s",par->chain_delete ); // deleting the chains we want to delete from pdb file
-                if (chains_to_delete(par->chain_delete, buf[21], par->chain_is_kept))
+                if (chains_to_delete(par->chain_delete, chainbuf, par->chain_is_kept,par->n_chains_to_delete))
                 {
                     /* Check if this is the first occurence of this atom*/
                     rpdb_extract_atm_resname(buf, resb);
@@ -862,7 +864,7 @@ s_pdb *rpdb_open(char *fpath, const char *ligan, const int keep_lig, int model_n
                 }
                 if ((buf[16] == ' ' || buf[16] == 'A') && x < 9990 && y < 9990 && z < 9990)
                 {
-                    if (chains_to_delete(par->chain_delete, buf[21], par->chain_is_kept))
+                    if (chains_to_delete(par->chain_delete, chainbuf, par->chain_is_kept,par->n_chains_to_delete))
                     {
                         /* Atom entry: check if there is a ligand in there (just in case)... */
                         if (ligan && strlen(ligan) > 1 && ligan[0] == resb[0] && ligan[1] == resb[1] && ligan[2] == resb[2])
@@ -891,20 +893,9 @@ s_pdb *rpdb_open(char *fpath, const char *ligan, const int keep_lig, int model_n
                     /*handle explicit ligand input here*/
                     if (par->xlig_resnumber > -1)
                     {
-
-                        //                        if (resb[0] == par->xlig_resname[0] && resb[1] == par->xlig_resname[1] && resb[2] == par->xlig_resname[2]) {
-                        // fprintf(stdout,"%s\t%s\n",buf[16],par->xlig_chain_code);
-
-                        // if (buf[21] == par->xlig_chain_code[0] && resnbuf == par->xlig_resnumber && par->xlig_resname[0] == resb[0] && par->xlig_resname[1] == resb[1] && par->xlig_resname[2] == resb[2])
-                        // {
-                        //     pdb->n_xlig_atoms++;
-                        //     fprintf(stdout, "%d\n", pdb->n_xlig_atoms);
-                        // }
-
-                        if (is_ligand(par->chain_as_ligand, buf[21]))
+                        if (is_ligand(par->chain_as_ligand, chainbuf,par->n_chains_as_ligand))
                         {
                             pdb->n_xlig_atoms++;
-                            // fprintf(stdout, "%d\t", pdb->n_xlig_atoms);
                         }
                     }
                 }
@@ -912,7 +903,11 @@ s_pdb *rpdb_open(char *fpath, const char *ligan, const int keep_lig, int model_n
                 {
                     if (par->xlig_resnumber > -1)
                     {
-                        if (buf[21] == par->xlig_chain_code[0] && resnbuf == par->xlig_resnumber && par->xlig_resname[0] == resb[0] && par->xlig_resname[1] == resb[1] && par->xlig_resname[2] == resb[2])
+                        if (is_ligand(par->chain_as_ligand, chainbuf,par->n_chains_as_ligand))
+                        {
+                            pdb->n_xlig_atoms++;
+                        }
+                        else if (par->xlig_chain_code!=NULL && buf[21] == par->xlig_chain_code[0] && resnbuf == par->xlig_resnumber && par->xlig_resname[0] == resb[0] && par->xlig_resname[1] == resb[1] && par->xlig_resname[2] == resb[2])
                         {
                             pdb->n_xlig_atoms++;
                         }
@@ -920,11 +915,11 @@ s_pdb *rpdb_open(char *fpath, const char *ligan, const int keep_lig, int model_n
                 }
             }
 
-            else if (!strncmp(buf, "HETATM", 6) || (!strncmp(buf, "ATOM ", 5) && is_ligand(par->chain_as_ligand, buf[21])))
+            else if (!strncmp(buf, "HETATM", 6) || (!strncmp(buf, "ATOM ", 5) && is_ligand(par->chain_as_ligand, chainbuf,par->n_chains_as_ligand)))
             {
-                if (chains_to_delete(par->chain_delete, buf[21], par->chain_is_kept))
-                {
 
+                if (chains_to_delete(par->chain_delete, chainbuf, par->chain_is_kept,par->n_chains_to_delete))
+                {
                     /*Check again for the first occurence*/
                     rpdb_extract_atom_coordinates(buf, &x, &y, &z); /*extract and double check coordinates to avoid issues with wrong coordinates*/
                     resnbuf = rpdb_extract_atm_resumber(buf);
@@ -932,11 +927,12 @@ s_pdb *rpdb_open(char *fpath, const char *ligan, const int keep_lig, int model_n
                 if ((buf[16] == ' ' || buf[16] == 'A') && x < 9990 && y < 9990 && z < 9990)
                 {
                     /* Hetatom entry: check if there is a ligand in there too... */
-                    if (chains_to_delete(par->chain_delete, buf[21], par->chain_is_kept))
+
+                    if (chains_to_delete(par->chain_delete, chainbuf, par->chain_is_kept,par->n_chains_to_delete))
                     {
                         rpdb_extract_atm_resname(buf, resb);
 
-                        // printf("%s ",ligan);
+                        
                         if (ligan && strlen(ligan) > 1 && keep_lig && ligan[0] == resb[0] && ligan[1] == resb[1] && ligan[2] == resb[2])
                         {
                             natm_lig++;
@@ -951,13 +947,12 @@ s_pdb *rpdb_open(char *fpath, const char *ligan, const int keep_lig, int model_n
                         else
                         {
                             /* Keep specific HETATM given in the static list ST_keep_hetatm */
-                            if ((keep_lig && !ligan && strncmp(resb, "HOH", 3) && strncmp(resb, "WAT", 3) && strncmp(resb, "TIP", 3)) || (keep_lig && is_ligand(par->chain_as_ligand, buf[21])))
+                            if ((keep_lig && !ligan && strncmp(resb, "HOH", 3) && strncmp(resb, "WAT", 3) && strncmp(resb, "TIP", 3)) || (keep_lig && is_ligand(par->chain_as_ligand, chainbuf,par->n_chains_as_ligand)))
                             {
-                                // printf("%s|%c ",resb,buf[21]);
                                 natoms++;
                                 nhetatm++;
                             }
-                            else if (!is_ligand(par->chain_as_ligand, buf[21]))
+                            else if (!is_ligand(par->chain_as_ligand, chainbuf,par->n_chains_as_ligand))
                             {
                                 for (i = 0; i < ST_nb_keep_hetatm; i++)
                                 {
@@ -972,19 +967,9 @@ s_pdb *rpdb_open(char *fpath, const char *ligan, const int keep_lig, int model_n
                         }
                     }
 
-                    /*handle explicit ligand input here*/
-
-                    // if (par->xlig_resnumber > -1)
-                    // {
-                    //     if (buf[21] == par->xlig_chain_code[0] && resnbuf == par->xlig_resnumber && par->xlig_resname[0] == resb[0] && par->xlig_resname[1] == resb[1] && par->xlig_resname[2] == resb[2])
-                    //     {
-                    //         pdb->n_xlig_atoms++;
-                    //     }
-                    // }
-                    if (is_ligand(par->chain_as_ligand, buf[21]))
+                    if (is_ligand(par->chain_as_ligand, chainbuf,par->n_chains_as_ligand))
                     {
                         pdb->n_xlig_atoms++;
-                        // fprintf(stdout, "H%d\t", pdb->n_xlig_atoms);
                     }
                 }
                 if (x < 9990 && y < 9990 && z < 9990)
@@ -994,9 +979,9 @@ s_pdb *rpdb_open(char *fpath, const char *ligan, const int keep_lig, int model_n
 
                     if (par->xlig_resnumber > -1)
                     {
-                        if (buf[21] == par->xlig_chain_code[0] && resnbuf == par->xlig_resnumber && par->xlig_resname[0] == resb[0] && par->xlig_resname[1] == resb[1] && par->xlig_resname[2] == resb[2])
+                        unsigned short is_chain_ligand=(is_ligand(par->chain_as_ligand, chainbuf,par->n_chains_as_ligand) && strncmp(resb, "HOH", 3) && strncmp(resb, "WAT", 3) && strncmp(resb, "TIP", 3));
+                        if (is_chain_ligand || (par->xlig_chain_code!=NULL && buf[21] == par->xlig_chain_code[0] && resnbuf == par->xlig_resnumber && par->xlig_resname[0] == resb[0] && par->xlig_resname[1] == resb[1] && par->xlig_resname[2] == resb[2]))
                         {
-
                             pdb->n_xlig_atoms++;
                         }
                     }
@@ -1099,6 +1084,8 @@ void rpdb_read(s_pdb *pdb, const char *ligan, const int keep_lig, int model_numb
     int model_flag = 0;      /*by default we consider that no particular model is read*/
     int model_read = 0;      /*flag tracking the status if a current line is read or not*/
     int cur_model_count = 0; /*when reading NMR models, then count on which model you currently are*/
+    char *chainbuf=(char *)my_malloc(sizeof(char)*2);
+    chainbuf[1]='\0';
     s_atm *atom = NULL;
     s_atm *atoms = pdb->latoms;
     s_atm **atoms_p = pdb->latoms_p;
@@ -1125,10 +1112,10 @@ void rpdb_read(s_pdb *pdb, const char *ligan, const int keep_lig, int model_numb
         if (pdb->model_flag == 0 || model_read == 1)
         {
 
-            if (strncmp(pdb_line, "ATOM ", 5) == 0 && !is_ligand(params->chain_as_ligand, pdb_line[21]))
+            if (strncmp(pdb_line, "ATOM ", 5) == 0 && !is_ligand(params->chain_as_ligand, chainbuf,params->n_chains_as_ligand))
             {
-
-                if (chains_to_delete(params->chain_delete, pdb_line[21], params->chain_is_kept)) // deleting the chains we want to delete from pdb file
+                chainbuf[0]=pdb_line[21];
+                if (chains_to_delete(params->chain_delete, chainbuf, params->chain_is_kept,params->n_chains_to_delete)) // deleting the chains we want to delete from pdb file
                 {
                     // printf("%s\n",params->chain_delete);
 
@@ -1139,30 +1126,20 @@ void rpdb_read(s_pdb *pdb, const char *ligan, const int keep_lig, int model_numb
                 if ((pdb_line[16] == ' ' || pdb_line[16] == 'A') && tmpx < 9990 && tmpy < 9990 && tmpz < 9990)
                 { /*if within first occurence*/
                     /* Store ATOM entry */
-                    if (chains_to_delete(params->chain_delete, pdb_line[21], params->chain_is_kept)) // deleting the chains we want to delete from pdb file
+                    if (chains_to_delete(params->chain_delete, chainbuf, params->chain_is_kept,params->n_chains_to_delete)) // deleting the chains we want to delete from pdb file
                     {
                         rpdb_extract_atm_resname(pdb_line, resb);
 
                         resnbuf = rpdb_extract_atm_resumber(pdb_line);
                     }
-                    /* Enter this if when arg in command line is -r */
-                    // if (pdb->n_xlig_atoms)
-                    // {
-                    //     if (pdb_line[21] == params->xlig_chain_code[0] && resnbuf == params->xlig_resnumber && params->xlig_resname[0] == resb[0] && params->xlig_resname[1] == resb[1] && params->xlig_resname[2] == resb[2])
-                    //     {
-
-                    //         rpdb_extract_atom_coordinates(pdb_line, (pdb->xlig_x + i_explicit_ligand_atom), (pdb->xlig_y + i_explicit_ligand_atom), (pdb->xlig_z + i_explicit_ligand_atom));
-                    //         i_explicit_ligand_atom++;
-                    //     }
-                    // }
 
                     /* Enter this if when arg in command line is -a */
-                    if (is_ligand(params->chain_as_ligand, pdb_line[21]))
+                    if (is_ligand(params->chain_as_ligand, chainbuf,params->n_chains_as_ligand))
                     {
                         rpdb_extract_atom_coordinates(pdb_line, (pdb->xlig_x + i_explicit_ligand_atom), (pdb->xlig_y + i_explicit_ligand_atom), (pdb->xlig_z + i_explicit_ligand_atom));
                         i_explicit_ligand_atom++;
                     }
-                    if (chains_to_delete(params->chain_delete, pdb_line[21], params->chain_is_kept)) // deleting the chains we want to delete from pdb file
+                    if (chains_to_delete(params->chain_delete, chainbuf, params->chain_is_kept,params->n_chains_to_delete)) // deleting the chains we want to delete from pdb file
                     {
                         /* Check if the desired ligand is in such an entry */
                         if (ligan && strlen(ligan) > 1 && ligan[0] == resb[0] && ligan[1] == resb[1] && ligan[2] == resb[2])
@@ -1252,8 +1229,10 @@ void rpdb_read(s_pdb *pdb, const char *ligan, const int keep_lig, int model_numb
                     {
                         rpdb_extract_atm_resname(pdb_line, resb);
                         resnbuf = rpdb_extract_atm_resumber(pdb_line);
+                        
+                        unsigned short is_chain_ligand=(is_ligand(params->chain_as_ligand, chainbuf,params->n_chains_as_ligand) && strncmp(resb, "HOH", 3) && strncmp(resb, "WAT", 3) && strncmp(resb, "TIP", 3));
 
-                        if (pdb_line[21] == params->xlig_chain_code[0] && resnbuf == params->xlig_resnumber && params->xlig_resname[0] == resb[0] && params->xlig_resname[1] == resb[1] && params->xlig_resname[2] == resb[2])
+                        if (is_chain_ligand || (params->xlig_chain_code!=NULL && (pdb_line[21] == params->xlig_chain_code[0] && resnbuf == params->xlig_resnumber && params->xlig_resname[0] == resb[0] && params->xlig_resname[1] == resb[1] && params->xlig_resname[2] == resb[2])))
                         {
 
                             rpdb_extract_atom_coordinates(pdb_line, (pdb->xlig_x + i_explicit_ligand_atom), (pdb->xlig_y + i_explicit_ligand_atom), (pdb->xlig_z + i_explicit_ligand_atom));
@@ -1262,33 +1241,25 @@ void rpdb_read(s_pdb *pdb, const char *ligan, const int keep_lig, int model_numb
                     }
                 }
             }
-            else if (strncmp(pdb_line, "HETATM", 6) == 0 || (strncmp(pdb_line, "ATOM ", 5) == 0 && is_ligand(params->chain_as_ligand, pdb_line[21])))
+
+            else if (strncmp(pdb_line, "HETATM", 6) == 0 || (strncmp(pdb_line, "ATOM ", 5) == 0 && is_ligand(params->chain_as_ligand, chainbuf,params->n_chains_as_ligand)))
             {
-                if (chains_to_delete(params->chain_delete, pdb_line[21], params->chain_is_kept)) // deleting the chains we want to delete from pdb file
+                chainbuf[0]=pdb_line[21];
+                if (chains_to_delete(params->chain_delete, chainbuf, params->chain_is_kept,params->n_chains_to_delete)) // deleting the chains we want to delete from pdb file
                 {
                     rpdb_extract_atom_coordinates(pdb_line, &tmpx, &tmpy, &tmpz); /*extract and double check coordinates to avoid issues with wrong coordinates*/
+                    resnbuf = rpdb_extract_atm_resumber(pdb_line);
                 }
                 if ((pdb_line[16] == ' ' || pdb_line[16] == 'A') && tmpx < 9990 && tmpy < 9990 && tmpz < 9990)
                 { /*first occurence*/
                     /* Check HETATM entry */
-                    if (chains_to_delete(params->chain_delete, pdb_line[21], params->chain_is_kept)) // deleting the chains we want to delete from pdb file
+
+                    if (chains_to_delete(params->chain_delete, chainbuf, params->chain_is_kept,params->n_chains_to_delete)) // deleting the chains we want to delete from pdb file
                     {
                         rpdb_extract_atm_resname(pdb_line, resb);
-                        resnbuf = rpdb_extract_atm_resumber(pdb_line);
                     }
 
-                    // if (pdb->n_xlig_atoms)
-                    // {
-                    //     if (pdb_line[21] == params->xlig_chain_code[0] && resnbuf == params->xlig_resnumber && params->xlig_resname[0] == resb[0] && params->xlig_resname[1] == resb[1] && params->xlig_resname[2] == resb[2])
-                    //     {
-                    //         // if (params->xlig_resname[0] == resb[0] && params->xlig_resname[1] == resb[1] && params->xlig_resname[2] == resb[2]) {
-
-                    //         rpdb_extract_atom_coordinates(pdb_line, (pdb->xlig_x + i_explicit_ligand_atom), (pdb->xlig_y + i_explicit_ligand_atom), (pdb->xlig_z + i_explicit_ligand_atom));
-
-                    //         i_explicit_ligand_atom++;
-                    //     }
-                    // }
-                    if (is_ligand(params->chain_as_ligand, pdb_line[21]))
+                    if (is_ligand(params->chain_as_ligand, chainbuf,params->n_chains_as_ligand))
                     {
 
                         rpdb_extract_atom_coordinates(pdb_line, (pdb->xlig_x + i_explicit_ligand_atom), (pdb->xlig_y + i_explicit_ligand_atom), (pdb->xlig_z + i_explicit_ligand_atom));
@@ -1296,7 +1267,7 @@ void rpdb_read(s_pdb *pdb, const char *ligan, const int keep_lig, int model_numb
                         i_explicit_ligand_atom++;
                     }
                     // fflush(stdout);
-                    if (chains_to_delete(params->chain_delete, pdb_line[21], params->chain_is_kept)) // deleting the chains we want to delete from pdb file
+                    if (chains_to_delete(params->chain_delete, chainbuf, params->chain_is_kept,params->n_chains_to_delete)) // deleting the chains we want to delete from pdb file
                     {
                         /* Check if the desired ligand is in HETATM entry */
                         if (ligan && strlen(ligan) > 1 && keep_lig && ligan[0] == resb[0] && ligan[1] == resb[1] && ligan[2] == resb[2])
@@ -1350,9 +1321,8 @@ void rpdb_read(s_pdb *pdb, const char *ligan, const int keep_lig, int model_numb
                         }
                         else if (pdb->lhetatm)
                         {
-
                             /* Keep specific HETATM given in the static list ST_keep_hetatm. */
-                            if ((keep_lig && !ligan && strncmp(resb, "HOH", 3) && strncmp(resb, "WAT", 3) && strncmp(resb, "TIP", 3)) || (keep_lig && is_ligand(params->chain_as_ligand, pdb_line[21])))
+                            if ((keep_lig && !ligan && strncmp(resb, "HOH", 3) && strncmp(resb, "WAT", 3) && strncmp(resb, "TIP", 3)) || (keep_lig && is_ligand(params->chain_as_ligand, chainbuf,params->n_chains_as_ligand)))
                             {
 
                                 atom = atoms + iatoms;
@@ -1374,7 +1344,7 @@ void rpdb_read(s_pdb *pdb, const char *ligan, const int keep_lig, int model_numb
                                 ihetatm++;
                                 iatoms++;
                             }
-                            else if (!is_ligand(params->chain_as_ligand, pdb_line[21]))
+                            else if (!is_ligand(params->chain_as_ligand, chainbuf,params->n_chains_as_ligand))
                             {
 
                                 for (i = 0; i < ST_nb_keep_hetatm; i++)
@@ -1416,7 +1386,9 @@ void rpdb_read(s_pdb *pdb, const char *ligan, const int keep_lig, int model_numb
                     {
                         resnbuf = rpdb_extract_atm_resumber(pdb_line);
                         rpdb_extract_atm_resname(pdb_line, resb);
-                        if (pdb_line[21] == params->xlig_chain_code[0] && resnbuf == params->xlig_resnumber && params->xlig_resname[0] == resb[0] && params->xlig_resname[1] == resb[1] && params->xlig_resname[2] == resb[2])
+                        unsigned short is_chain_ligand=(is_ligand(params->chain_as_ligand, chainbuf,params->n_chains_as_ligand) && strncmp(resb, "HOH", 3) && strncmp(resb, "WAT", 3) && strncmp(resb, "TIP", 3));
+
+                        if (is_chain_ligand || (params->xlig_chain_code!=NULL && (pdb_line[21] == params->xlig_chain_code[0] && resnbuf == params->xlig_resnumber && params->xlig_resname[0] == resb[0] && params->xlig_resname[1] == resb[1] && params->xlig_resname[2] == resb[2])))
                         {
 
                             rpdb_extract_atom_coordinates(pdb_line, (pdb->xlig_x + i_explicit_ligand_atom), (pdb->xlig_y + i_explicit_ligand_atom), (pdb->xlig_z + i_explicit_ligand_atom));
@@ -1426,6 +1398,7 @@ void rpdb_read(s_pdb *pdb, const char *ligan, const int keep_lig, int model_numb
                     }
                 }
             }
+            
             else if (strncmp(pdb_line, "CRYST1", 6) == 0)
             {
                 rpdb_extract_cryst1(pdb_line, &(pdb->alpha), &(pdb->beta), &(pdb->gamma),
@@ -1463,11 +1436,6 @@ void rpdb_read(s_pdb *pdb, const char *ligan, const int keep_lig, int model_numb
     int num_h_atoms = get_number_of_h_atoms(pdb);
     pdb->natoms_h = num_h_atoms;
     pdb->avg_bfactor /= (iatoms - num_h_atoms);
-    //        pdb->avg_bfactor=0.0;
-
-    /*if(guess_flag>0) {
-        fprintf(stderr, ">! Warning: You did not provide a standard PDB file.\nElements were guessed by fpocket, because not provided in the PDB file. \nThere is no guarantee on the results!\n");
-    }*/
 
     if (ligan && keep_lig && (ligfound == 0 || pdb->natm_lig <= 0))
     {
@@ -1574,50 +1542,49 @@ void free_pdb_atoms(s_pdb *pdb)
         int
 
  */
-int chains_to_delete(char *chains_selected, char current_line_chain, int is_chain_kept)
+int chains_to_delete(char *chains_selected[20], char *current_line_chain, int is_chain_kept,unsigned short n_chains_to_delete)
 { /*deletes the chains selected by command -c, returns true if the chain correspond false if not*/
 
     if (is_chain_kept == 0)
     {
         int is_deleted = 1;
         int i = 0;
-        for (i = 0; i < M_MAX_CHAINS_DELETE; i++)
+        for (i = 0; i < n_chains_to_delete; i++)
         {
-            if (chains_selected[i] == current_line_chain)
+            if (!strcmp(chains_selected[i], current_line_chain))
             {
-                // printf("%c_%c ", chains_selected[i],current_line_chain);
                 is_deleted = 0;
             }
         }
-        // printf("\n");
         return is_deleted;
     }
     else
     {
-        int is_deleted = 0;
+        int is_kept = 0;
+
         int i = 0;
-        for (i = 0; i < M_MAX_CHAINS_DELETE; i++)
+        for (i = 0; i < n_chains_to_delete; i++)
         {
-            if (chains_selected[i] == current_line_chain)
+            if (!strcmp(chains_selected[i], current_line_chain))
             {
-                // printf("%c_%c ", chains_selected[i],current_line_chain);
-                is_deleted = 1;
+                is_kept = 1;
             }
         }
-        // printf("\n");
-        return is_deleted;
+        return is_kept;
     }
 }
 
-int is_ligand(char *chains_selected, char current_line_chain)
+
+
+int is_ligand(char *chains_selected[20], char *current_line_chain, unsigned short n_chains_as_ligand)
 {
+    
     int is_a_ligand = 0;
     int i;
-    for (i = 0; i < M_MAX_CHAINS_DELETE; i++)
+    for (i = 0; i < n_chains_as_ligand; i++)
     {
-        if (chains_selected[i] == current_line_chain)
+        if (!strcmp(chains_selected[i],current_line_chain))
         {
-            // printf("%c_%c ", chains_selected[i],current_line_chain);
             is_a_ligand = 1;
         }
     }

src/write_visu.c

@@ -61,7 +61,7 @@ void write_visualization(char *pdb_name, char *pdb_out_name)
 	}
 
 	if(write_mode[0] == 'm' || write_mode[0] == 'b'){
-	char *ext_cif = ".cif";
+	const char *ext_cif = ".cif";
 	remove_ext(pdb_out_name); 
 	strcat(pdb_out_name,ext_cif); /*put the .cif file extension*/
 	

tests/environment.yml

@@ -2,5 +2,5 @@ name: fpocket_test
 channels:
   - defaults
 dependencies:
-  - python=3.7
+  - python=3.12
   - pytest

tests/reference_output/1QNH_out/1QNH_info.txt

@@ -1,21 +1,21 @@
 Pocket 1 :
-	Score : 	5.845
+	Score : 	6.128
 	Druggability Score : 	1.000
-	Number of Alpha Spheres : 	217
-	Total SASA : 	319.981
-	Polar SASA : 	172.651
-	Apolar SASA : 	147.331
-	Volume : 	4956.883
-	Mean local hydrophobic density : 	13.444
-	Mean alpha sphere radius :	4.302
-	Mean alp. sph. solvent access : 	0.583
-	Apolar alpha sphere proportion : 	0.249
-	Hydrophobicity score:	16.815
-	Volume score: 	 3.889
-	Polarity score:	 16
+	Number of Alpha Spheres : 	225
+	Total SASA : 	353.188
+	Polar SASA : 	186.535
+	Apolar SASA : 	166.653
+	Volume : 	5738.319
+	Mean local hydrophobic density : 	13.345
+	Mean alpha sphere radius :	4.321
+	Mean alp. sph. solvent access : 	0.581
+	Apolar alpha sphere proportion : 	0.244
+	Hydrophobicity score:	18.464
+	Volume score: 	 4.000
+	Polarity score:	 17
 	Charge score :	 6
-	Proportion of polar atoms: 	43.262
-	Alpha sphere density : 	29.044
+	Proportion of polar atoms: 	42.857
+	Alpha sphere density : 	29.333
 	Cent. of mass - Alpha Sphere max dist: 	66.371
 	Flexibility : 	0.000
 

tests/reference_output/1QNH_out/1QNH_out.cif

@@ -481,7 +481,7 @@ ATOM      461    C   CZ .  PHE   A .   59 ?   16.521  46.943  23.448  0.00  0
 ATOM      462    N    N .  HIS   A .   60 ?   21.685  41.894  24.095  0.00  0   A
 ATOM      463    C   CA .  HIS   A .   60 ?   22.877  41.116  24.412  0.00  0   A
 ATOM      464    C    C .  HIS   A .   60 ?   24.158  41.904  24.638  0.00  0   A
-ATOM      465    O    O .  HIS   A .   60 ?   25.158  41.344  25.078  0.00  0   A
+ATOM      465    O    O .  HIS   A .   60 ?   25.158  41.344  25.078 -1.62  0   A
 ATOM      466    C   CB .  HIS   A .   60 ?   23.129  40.084  23.309  0.00  0   A
 ATOM      467    C   CG .  HIS   A .   60 ?   23.547  40.688  22.003  0.00  0   A
 ATOM      468    N  ND1 .  HIS   A .   60 ?   22.643  41.187  21.089  0.00  0   A
@@ -629,7 +629,7 @@ ATOM      609    O   OG .  SER   A .   79 ?   25.802  34.452  16.172  0.00  0
 ATOM      610    N    N .  GLY   A .   80 ?   23.617  36.549  14.815  0.00  0   A
 ATOM      611    C   CA .  GLY   A .   80 ?   22.490  36.294  13.936  0.00  0   A
 ATOM      612    C    C .  GLY   A .   80 ?   21.685  37.488  13.466  0.00  0   A
-ATOM      613    O    O .  GLY   A .   80 ?   22.190  38.611  13.380 -1.07  0   A
+ATOM      613    O    O .  GLY   A .   80 ?   22.190  38.611  13.380  0.00  0   A
 ATOM      614    N    N .  GLY   A .   81 ?   20.416  37.230  13.161  0.00  0   A
 ATOM      615    C   CA .  GLY   A .   81 ?   19.529  38.276  12.689  0.00  0   A
 ATOM      616    C    C .  GLY   A .   81 ?   18.939  37.935  11.332  0.00  0   A
@@ -682,8 +682,8 @@ ATOM      662    C   CG .  ARG   A .   87 ?   21.394  36.553   6.201  0.00  0
 ATOM      663    C   CD .  ARG   A .   87 ?   20.856  36.029   7.533  0.00  0   A
 ATOM      664    N   NE .  ARG   A .   87 ?   21.879  35.978   8.574  0.00  0   A
 ATOM      665    C   CZ .  ARG   A .   87 ?   22.430  37.047   9.144  0.00  0   A
-ATOM      666    N  NH1 .  ARG   A .   87 ?   22.062  38.269   8.777 -2.61  0   A
-ATOM      667    N  NH2 .  ARG   A .   87 ?   23.345  36.894  10.092 -4.12  0   A
+ATOM      666    N  NH1 .  ARG   A .   87 ?   22.062  38.269   8.777 -4.12  0   A
+ATOM      667    N  NH2 .  ARG   A .   87 ?   23.345  36.894  10.092 -1.93  0   A
 ATOM      668    N    N .  SER   A .   88 ?   19.796  39.808   4.725  0.00  0   A
 ATOM      669    C   CA .  SER   A .   88 ?   20.319  41.168   4.848  0.00  0   A
 ATOM      670    C    C .  SER   A .   88 ?   19.779  42.086   3.763  0.00  0   A
@@ -877,7 +877,7 @@ ATOM      857    N  ND2 .  ASN   A .  112 ?   25.973  47.831  -0.009  0.00  0
 ATOM      858    N    N .  THR   A .  113 ?   24.686  45.203   5.123  0.00  0   A
 ATOM      859    C   CA .  THR   A .  113 ?   24.527  43.954   5.854  0.00  0   A
 ATOM      860    C    C .  THR   A .  113 ?   23.498  44.091   6.974  0.00  0   A
-ATOM      861    O    O .  THR   A .  113 ?   23.582  43.411   7.996 -4.69  0   A
+ATOM      861    O    O .  THR   A .  113 ?   23.582  43.411   7.996 -5.36  0   A
 ATOM      862    C   CB .  THR   A .  113 ?   25.860  43.490   6.456  0.00  0   A
 ATOM      863    O  OG1 .  THR   A .  113 ?   26.407  44.539   7.260  0.00  0   A
 ATOM      864    C  CG2 .  THR   A .  113 ?   26.850  43.117   5.347  0.00  0   A
@@ -1807,7 +1807,7 @@ ATOM     1787    C   CD .  ARG   B .   61 ?   15.961  88.260  38.521  0.00  0
 ATOM     1788    N   NE .  ARG   B .   61 ?   14.906  89.269  38.594  0.00  0   B
 ATOM     1789    C   CZ .  ARG   B .   61 ?   13.831  89.292  37.808  0.00  0   B
 ATOM     1790    N  NH1 .  ARG   B .   61 ?   13.659  88.360  36.879  0.00  0   B
-ATOM     1791    N  NH2 .  ARG   B .   61 ?   12.927  90.252  37.946 -4.37  0   B
+ATOM     1791    N  NH2 .  ARG   B .   61 ?   12.927  90.252  37.946 -1.09  0   B
 ATOM     1792    N    N .  ILE   B .   62 ?   15.192  84.329  41.806  0.00  0   B
 ATOM     1793    C   CA .  ILE   B .   62 ?   13.926  83.743  42.225  0.00  0   B
 ATOM     1794    C    C .  ILE   B .   62 ?   13.156  84.764  43.053  0.00  0   B
@@ -2498,12 +2498,12 @@ ATOM     2478    C   CB .  ALA   B .  153 ?   15.056  87.549  48.607  0.00  0
 ATOM     2479    N    N .  LYS   B .  154 ?   12.406  88.974  47.844  0.00  0   B
 ATOM     2480    C   CA .  LYS   B .  154 ?   11.675  90.001  47.104  0.00  0   B
 ATOM     2481    C    C .  LYS   B .  154 ?   12.565  90.692  46.075  0.00  0   B
-ATOM     2482    O    O .  LYS   B .  154 ?   12.088  91.141  45.036  0.00  0   B
+ATOM     2482    O    O .  LYS   B .  154 ?   12.088  91.141  45.036 -0.54  0   B
 ATOM     2483    C   CB .  LYS   B .  154 ?   11.096  91.033  48.071  0.00  0   B
 ATOM     2484    N    N .  SER   B .  155 ?   13.858  90.777  46.370  0.00  0   B
 ATOM     2485    C   CA .  SER   B .  155 ?   14.806  91.415  45.464  0.00  0   B
 ATOM     2486    C    C .  SER   B .  155 ?   15.208  90.467  44.338  0.00  0   B
-ATOM     2487    O    O .  SER   B .  155 ?   15.773  90.893  43.331 -1.62  0   B
+ATOM     2487    O    O .  SER   B .  155 ?   15.773  90.893  43.331 -3.35  0   B
 ATOM     2488    C   CB .  SER   B .  155 ?   16.059  91.844  46.226  0.00  0   B
 ATOM     2489    O   OG .  SER   B .  155 ?   16.736  90.715  46.751  0.00  0   B
 ATOM     2490    N    N .  GLY   B .  156 ?   14.919  89.180  44.521  0.00  0   B
@@ -2689,154 +2689,162 @@ HETATM     64    V APOL .  STP   C .    1 ?   10.093  87.611  33.467  0.00  0
 HETATM     65    V APOL .  STP   C .    1 ?   10.538  87.926  33.379  0.00  0   C
 HETATM     66    V APOL .  STP   C .    1 ?   33.888  49.647  16.687  0.00  0   C
 HETATM     67    V APOL .  STP   C .    1 ?   17.468  87.092  29.886  0.00  0   C
-HETATM     68    V APOL .  STP   C .    1 ?   33.220  49.873  17.122  0.00  0   C
-HETATM     69    V APOL .  STP   C .    1 ?    9.423  86.425  34.239  0.00  0   C
-HETATM     70    V APOL .  STP   C .    1 ?    9.363  86.402  34.268  0.00  0   C
-HETATM     71    V APOL .  STP   C .    1 ?   17.156  90.553  34.548  0.00  0   C
-HETATM     72    V APOL .  STP   C .    1 ?   18.977  88.996  36.323  0.00  0   C
-HETATM     73    V APOL .  STP   C .    1 ?   18.801  90.804  35.327  0.00  0   C
-HETATM     74    V APOL .  STP   C .    1 ?   18.268  89.945  34.975  0.00  0   C
-HETATM     75    V APOL .  STP   C .    1 ?   18.868  89.208  35.945  0.00  0   C
-HETATM     76    V APOL .  STP   C .    1 ?   18.065  88.657  35.595  0.00  0   C
-HETATM     77    V APOL .  STP   C .    1 ?   18.379  89.193  35.362  0.00  0   C
-HETATM     78    V APOL .  STP   C .    1 ?   18.882  87.605  27.239  0.00  0   C
-HETATM     79    V APOL .  STP   C .    1 ?   13.300  94.652  30.063  0.00  0   C
-HETATM     80    V APOL .  STP   C .    1 ?   13.169  88.280  31.543  0.00  0   C
-HETATM     81    V APOL .  STP   C .    1 ?   12.965  87.866  31.201  0.00  0   C
-HETATM     82    V APOL .  STP   C .    1 ?   17.206  86.955  29.975  0.00  0   C
-HETATM     83    V APOL .  STP   C .    1 ?   17.313  86.932  29.848  0.00  0   C
-HETATM     84    V APOL .  STP   C .    1 ?   17.260  86.826  29.857  0.00  0   C
-HETATM     85    V APOL .  STP   C .    1 ?   17.647  86.903  29.170  0.00  0   C
-HETATM     86    V APOL .  STP   C .    1 ?   17.446  86.914  29.625  0.00  0   C
-HETATM     87    V APOL .  STP   C .    1 ?   17.540  86.349  29.071  0.00  0   C
-HETATM     88    V APOL .  STP   C .    1 ?   17.825  86.147  28.464  0.00  0   C
-HETATM     89    V APOL .  STP   C .    1 ?   17.638  86.291  28.817  0.00  0   C
-HETATM     90    V APOL .  STP   C .    1 ?   17.589  86.200  28.737  0.00  0   C
-HETATM     91    V APOL .  STP   C .    1 ?   17.310  86.348  29.432  0.00  0   C
-HETATM     92    V APOL .  STP   C .    1 ?   24.622  40.674  10.795  0.00  0   C
-HETATM     93    V APOL .  STP   C .    1 ?   27.005  49.985  17.993  0.00  0   C
-HETATM     94    V APOL .  STP   C .    1 ?   26.839  50.582  18.014  0.00  0   C
-HETATM     95    V APOL .  STP   C .    1 ?   27.676  50.218  16.945  0.00  0   C
-HETATM     96    V APOL .  STP   C .    1 ?   26.991  50.900  17.679  0.00  0   C
-HETATM     97    V APOL .  STP   C .    1 ?   30.592  49.040  16.768  0.00  0   C
-HETATM     98    V APOL .  STP   C .    1 ?   31.112  44.097  16.205  0.00  0   C
-HETATM     99    V APOL .  STP   C .    1 ?   26.685  48.719  17.768  0.00  0   C
-HETATM    100    V APOL .  STP   C .    1 ?   27.314  49.434  17.751  0.00  0   C
-HETATM    101    V APOL .  STP   C .    1 ?   30.711  48.752  16.393  0.00  0   C
-HETATM    102    V APOL .  STP   C .    1 ?   31.020  47.339  15.614  0.00  0   C
-HETATM    103    V APOL .  STP   C .    1 ?   29.111  49.193  16.737  0.00  0   C
-HETATM    104    V APOL .  STP   C .    1 ?   27.150  48.349  16.835  0.00  0   C
-HETATM    105    V APOL .  STP   C .    1 ?   28.085  46.923  16.028  0.00  0   C
-HETATM    106    V APOL .  STP   C .    1 ?   29.429  38.000  16.814  0.00  0   C
-HETATM    107    V APOL .  STP   C .    1 ?   25.337  41.857  10.796  0.00  0   C
-HETATM    108    V APOL .  STP   C .    1 ?   10.851  87.154  34.207  0.00  0   C
-HETATM    109    V APOL .  STP   C .    1 ?   10.692  87.013  34.265  0.00  0   C
-HETATM    110    V APOL .  STP   C .    1 ?   11.818  86.568  34.068  0.00  0   C
-HETATM    111    V APOL .  STP   C .    1 ?   12.318  85.510  34.106  0.00  0   C
-HETATM    112    V APOL .  STP   C .    1 ?    5.545  90.375  43.119  0.00  0   C
-HETATM    113    V APOL .  STP   C .    1 ?    4.561  89.333  40.639  0.00  0   C
-HETATM    114    V APOL .  STP   C .    1 ?    4.611  89.401  40.637  0.00  0   C
-HETATM    115    V APOL .  STP   C .    1 ?    6.032  91.564  41.830  0.00  0   C
-HETATM    116    V APOL .  STP   C .    1 ?    6.186  90.504  39.052  0.00  0   C
-HETATM    117    V APOL .  STP   C .    1 ?    6.160  90.509  39.113  0.00  0   C
-HETATM    118    V APOL .  STP   C .    1 ?   17.990  86.008  28.210  0.00  0   C
-HETATM    119    V APOL .  STP   C .    1 ?   18.006  86.098  28.176  0.00  0   C
-HETATM    120    V APOL .  STP   C .    1 ?   19.521  87.572  27.205  0.00  0   C
-HETATM    121    V APOL .  STP   C .    1 ?   19.240  87.483  27.521  0.00  0   C
-HETATM    122    V APOL .  STP   C .    1 ?   18.718  87.116  27.484  0.00  0   C
-HETATM    123    V APOL .  STP   C .    1 ?   18.711  87.054  27.742  0.00  0   C
-HETATM    124    V APOL .  STP   C .    1 ?   19.118  87.451  27.484  0.00  0   C
-HETATM    125    V APOL .  STP   C .    1 ?   19.138  87.454  27.544  0.00  0   C
-HETATM    126    V APOL .  STP   C .    1 ?   17.547  86.179  28.768  0.00  0   C
-HETATM    127    V APOL .  STP   C .    1 ?   24.404  40.531  10.860  0.00  0   C
-HETATM    128    V APOL .  STP   C .    1 ?   24.678  40.696  10.870  0.00  0   C
-HETATM    129    V APOL .  STP   C .    1 ?   25.061  40.721  10.992  0.00  0   C
-HETATM    130    V APOL .  STP   C .    1 ?   34.434  54.099  24.046  0.00  0   C
-HETATM    131    V APOL .  STP   C .    1 ?   34.785  54.066  24.214  0.00  0   C
-HETATM    132    V APOL .  STP   C .    1 ?   30.243  49.144  18.082  0.00  0   C
-HETATM    133    V APOL .  STP   C .    1 ?   33.629  50.117  17.900  0.00  0   C
-HETATM    134    V APOL .  STP   C .    1 ?   32.643  53.327  21.021  0.00  0   C
-HETATM    135    V APOL .  STP   C .    1 ?   33.259  50.367  13.555  0.00  0   C
-HETATM    136    V APOL .  STP   C .    1 ?   32.796  52.509  13.407  0.00  0   C
-HETATM    137    V APOL .  STP   C .    1 ?   31.179  49.730  10.161  0.00  0   C
-HETATM    138    V APOL .  STP   C .    1 ?   25.397  48.219  17.846  0.00  0   C
-HETATM    139    V APOL .  STP   C .    1 ?   25.657  48.105  17.477  0.00  0   C
-HETATM    140    V APOL .  STP   C .    1 ?   32.744  47.500  12.564  0.00  0   C
-HETATM    141    V APOL .  STP   C .    1 ?   32.680  48.711  11.135  0.00  0   C
-HETATM    142    V APOL .  STP   C .    1 ?   30.293  34.983  19.208  0.00  0   C
-HETATM    143    V APOL .  STP   C .    1 ?   30.515  37.558  12.012  0.00  0   C
-HETATM    144    V APOL .  STP   C .    1 ?   28.816  38.796  12.429  0.00  0   C
-HETATM    145    V APOL .  STP   C .    1 ?   25.694  40.137  11.519  0.00  0   C
-HETATM    146    V APOL .  STP   C .    1 ?   25.745  40.188  11.663  0.00  0   C
-HETATM    147    V APOL .  STP   C .    1 ?   30.778  40.864  18.244  0.00  0   C
-HETATM    148    V APOL .  STP   C .    1 ?   29.300  41.260  18.522  0.00  0   C
-HETATM    149    V APOL .  STP   C .    1 ?   29.435  42.951  17.876  0.00  0   C
-HETATM    150    V APOL .  STP   C .    1 ?   17.364  91.328  34.163  0.00  0   C
-HETATM    151    V APOL .  STP   C .    1 ?   17.378  91.256  34.191  0.00  0   C
-HETATM    152    V APOL .  STP   C .    1 ?   17.444  91.177  34.269  0.00  0   C
-HETATM    153    V APOL .  STP   C .    1 ?   17.348  91.074  34.310  0.00  0   C
-HETATM    154    V APOL .  STP   C .    1 ?   30.062  47.686  12.765  0.00  0   C
-HETATM    155    V APOL .  STP   C .    1 ?   26.323  48.692  15.710  0.00  0   C
-HETATM    156    V APOL .  STP   C .    1 ?   30.408  47.380  15.676  0.00  0   C
-HETATM    157    V APOL .  STP   C .    1 ?   28.125  47.095  15.991  0.00  0   C
-HETATM    158    V APOL .  STP   C .    1 ?   27.417  50.537  16.276  0.00  0   C
-HETATM    159    V APOL .  STP   C .    1 ?   27.373  50.707  16.089  0.00  0   C
-HETATM    160    V APOL .  STP   C .    1 ?   27.302  48.395  16.701  0.00  0   C
-HETATM    161    V APOL .  STP   C .    1 ?   27.841  49.832  16.849  0.00  0   C
-HETATM    162    V APOL .  STP   C .    1 ?   28.558  49.429  16.774  0.00  0   C
-HETATM    163    V APOL .  STP   C .    1 ?   27.865  49.337  16.994  0.00  0   C
-HETATM    164    V APOL .  STP   C .    1 ?   28.735  49.235  16.785  0.00  0   C
-HETATM    165    V APOL .  STP   C .    1 ?   31.288  55.409  23.269  0.00  0   C
-HETATM    166    V APOL .  STP   C .    1 ?   32.312  48.943  10.498  0.00  0   C
-HETATM    167    V APOL .  STP   C .    1 ?   34.237  48.223  11.050  0.00  0   C
-HETATM    168    V APOL .  STP   C .    1 ?   24.685  41.731  11.638  0.00  0   C
-HETATM    169    V APOL .  STP   C .    1 ?   23.857  42.701  11.472  0.00  0   C
-HETATM    170    V APOL .  STP   C .    1 ?   28.622  41.347  18.970  0.00  0   C
-HETATM    171    V APOL .  STP   C .    1 ?   28.182  41.101  20.281  0.00  0   C
-HETATM    172    V APOL .  STP   C .    1 ?   24.517  43.394  13.603  0.00  0   C
-HETATM    173    V APOL .  STP   C .    1 ?   24.414  43.155  13.231  0.00  0   C
-HETATM    174    V APOL .  STP   C .    1 ?   27.454  47.131  15.066  0.00  0   C
-HETATM    175    V APOL .  STP   C .    1 ?   25.046  43.340  13.819  0.00  0   C
-HETATM    176    V APOL .  STP   C .    1 ?   24.700  43.363  13.625  0.00  0   C
-HETATM    177    V APOL .  STP   C .    1 ?   28.073  46.895  16.026  0.00  0   C
-HETATM    178    V APOL .  STP   C .    1 ?   28.133  46.815  16.042  0.00  0   C
-HETATM    179    V APOL .  STP   C .    1 ?   30.376  42.824  16.523  0.00  0   C
-HETATM    180    V APOL .  STP   C .    1 ?   30.365  42.854  16.522  0.00  0   C
-HETATM    181    V APOL .  STP   C .    1 ?   30.061  42.491  17.173  0.00  0   C
-HETATM    182    V APOL .  STP   C .    1 ?   29.539  42.849  17.699  0.00  0   C
-HETATM    183    V APOL .  STP   C .    1 ?   29.681  42.794  17.547  0.00  0   C
-HETATM    184    V APOL .  STP   C .    1 ?   28.734  41.753  18.363  0.00  0   C
-HETATM    185    V APOL .  STP   C .    1 ?   27.985  42.238  18.956  0.00  0   C
-HETATM    186    V APOL .  STP   C .    1 ?   28.539  41.757  18.517  0.00  0   C
-HETATM    187    V APOL .  STP   C .    1 ?   29.507  42.806  17.744  0.00  0   C
-HETATM    188    V APOL .  STP   C .    1 ?   29.791  42.296  17.519  0.00  0   C
-HETATM    189    V APOL .  STP   C .    1 ?   25.552  40.651  11.800  0.00  0   C
-HETATM    190    V APOL .  STP   C .    1 ?   25.702  41.429  12.209  0.00  0   C
-HETATM    191    V APOL .  STP   C .    1 ?   25.788  41.400  12.282  0.00  0   C
-HETATM    192    V APOL .  STP   C .    1 ?   25.003  41.310  11.497  0.00  0   C
-HETATM    193    V APOL .  STP   C .    1 ?   25.002  41.301  11.494  0.00  0   C
-HETATM    194    V APOL .  STP   C .    1 ?   24.966  42.497  12.680  0.00  0   C
-HETATM    195    V APOL .  STP   C .    1 ?   24.684  41.731  11.659  0.00  0   C
-HETATM    196    V APOL .  STP   C .    1 ?   24.715  41.678  11.631  0.00  0   C
-HETATM    197    V APOL .  STP   C .    1 ?   24.813  41.386  11.520  0.00  0   C
-HETATM    198    V APOL .  STP   C .    1 ?   24.837  43.023  13.213  0.00  0   C
-HETATM    199    V APOL .  STP   C .    1 ?   24.938  43.175  13.547  0.00  0   C
-HETATM    200    V APOL .  STP   C .    1 ?   24.059  42.452  12.156  0.00  0   C
-HETATM    201    V APOL .  STP   C .    1 ?   24.523  43.068  13.102  0.00  0   C
-HETATM    202    V APOL .  STP   C .    1 ?   23.664  42.606  12.414  0.00  0   C
-HETATM    203    V APOL .  STP   C .    1 ?   24.396  43.128  13.200  0.00  0   C
-HETATM    204    V APOL .  STP   C .    1 ?   24.435  43.138  13.214  0.00  0   C
-HETATM    205    V APOL .  STP   C .    1 ?   24.518  43.086  13.129  0.00  0   C
-HETATM    206    V APOL .  STP   C .    1 ?   24.575  43.157  13.291  0.00  0   C
-HETATM    207    V APOL .  STP   C .    1 ?   31.063  55.664  23.330  0.00  0   C
-HETATM    208    V APOL .  STP   C .    1 ?   33.721  54.466  25.554  0.00  0   C
-HETATM    209    V APOL .  STP   C .    1 ?   25.197  43.355  14.014  0.00  0   C
-HETATM    210    V APOL .  STP   C .    1 ?   25.635  43.546  14.505  0.00  0   C
-HETATM    211    V APOL .  STP   C .    1 ?   25.403  43.098  14.044  0.00  0   C
-HETATM    212    V APOL .  STP   C .    1 ?   26.324  42.901  14.728  0.00  0   C
-HETATM    213    V APOL .  STP   C .    1 ?   26.006  42.758  14.370  0.00  0   C
-HETATM    214    V APOL .  STP   C .    1 ?   28.626  39.926  18.156  0.00  0   C
-HETATM    215    V APOL .  STP   C .    1 ?   30.514  38.191  17.400  0.00  0   C
-HETATM    216    V APOL .  STP   C .    1 ?   29.885  37.934  17.493  0.00  0   C
-HETATM    217    V APOL .  STP   C .    1 ?   29.459  38.005  16.840  0.00  0   C
+HETATM     68    V APOL .  STP   C .    1 ?   26.368  39.013   7.356  0.00  0   C
+HETATM     69    V APOL .  STP   C .    1 ?   33.220  49.873  17.122  0.00  0   C
+HETATM     70    V APOL .  STP   C .    1 ?   30.363  38.669  24.413  0.00  0   C
+HETATM     71    V APOL .  STP   C .    1 ?    9.423  86.425  34.239  0.00  0   C
+HETATM     72    V APOL .  STP   C .    1 ?    9.363  86.402  34.268  0.00  0   C
+HETATM     73    V APOL .  STP   C .    1 ?   17.156  90.553  34.548  0.00  0   C
+HETATM     74    V APOL .  STP   C .    1 ?   18.977  88.996  36.323  0.00  0   C
+HETATM     75    V APOL .  STP   C .    1 ?   18.801  90.804  35.327  0.00  0   C
+HETATM     76    V APOL .  STP   C .    1 ?   18.268  89.945  34.975  0.00  0   C
+HETATM     77    V APOL .  STP   C .    1 ?   18.868  89.208  35.945  0.00  0   C
+HETATM     78    V APOL .  STP   C .    1 ?   18.065  88.657  35.595  0.00  0   C
+HETATM     79    V APOL .  STP   C .    1 ?   18.379  89.193  35.362  0.00  0   C
+HETATM     80    V APOL .  STP   C .    1 ?   18.882  87.605  27.239  0.00  0   C
+HETATM     81    V APOL .  STP   C .    1 ?   13.300  94.652  30.063  0.00  0   C
+HETATM     82    V APOL .  STP   C .    1 ?   13.169  88.280  31.543  0.00  0   C
+HETATM     83    V APOL .  STP   C .    1 ?   12.965  87.866  31.201  0.00  0   C
+HETATM     84    V APOL .  STP   C .    1 ?   17.206  86.955  29.975  0.00  0   C
+HETATM     85    V APOL .  STP   C .    1 ?   17.313  86.932  29.848  0.00  0   C
+HETATM     86    V APOL .  STP   C .    1 ?   17.260  86.826  29.857  0.00  0   C
+HETATM     87    V APOL .  STP   C .    1 ?   17.647  86.903  29.170  0.00  0   C
+HETATM     88    V APOL .  STP   C .    1 ?   17.446  86.914  29.625  0.00  0   C
+HETATM     89    V APOL .  STP   C .    1 ?   17.540  86.349  29.071  0.00  0   C
+HETATM     90    V APOL .  STP   C .    1 ?   17.825  86.147  28.464  0.00  0   C
+HETATM     91    V APOL .  STP   C .    1 ?   17.638  86.291  28.817  0.00  0   C
+HETATM     92    V APOL .  STP   C .    1 ?   17.589  86.200  28.737  0.00  0   C
+HETATM     93    V APOL .  STP   C .    1 ?   17.310  86.348  29.432  0.00  0   C
+HETATM     94    V APOL .  STP   C .    1 ?   24.622  40.674  10.795  0.00  0   C
+HETATM     95    V APOL .  STP   C .    1 ?   27.005  49.985  17.993  0.00  0   C
+HETATM     96    V APOL .  STP   C .    1 ?   26.839  50.582  18.014  0.00  0   C
+HETATM     97    V APOL .  STP   C .    1 ?   27.676  50.218  16.945  0.00  0   C
+HETATM     98    V APOL .  STP   C .    1 ?   26.991  50.900  17.679  0.00  0   C
+HETATM     99    V APOL .  STP   C .    1 ?   30.592  49.040  16.768  0.00  0   C
+HETATM    100    V APOL .  STP   C .    1 ?   31.112  44.097  16.205  0.00  0   C
+HETATM    101    V APOL .  STP   C .    1 ?   26.685  48.719  17.768  0.00  0   C
+HETATM    102    V APOL .  STP   C .    1 ?   27.314  49.434  17.751  0.00  0   C
+HETATM    103    V APOL .  STP   C .    1 ?   30.711  48.752  16.393  0.00  0   C
+HETATM    104    V APOL .  STP   C .    1 ?   31.020  47.339  15.614  0.00  0   C
+HETATM    105    V APOL .  STP   C .    1 ?   29.111  49.193  16.737  0.00  0   C
+HETATM    106    V APOL .  STP   C .    1 ?   27.150  48.349  16.835  0.00  0   C
+HETATM    107    V APOL .  STP   C .    1 ?   28.085  46.923  16.028  0.00  0   C
+HETATM    108    V APOL .  STP   C .    1 ?   29.429  38.000  16.814  0.00  0   C
+HETATM    109    V APOL .  STP   C .    1 ?   25.337  41.857  10.796  0.00  0   C
+HETATM    110    V APOL .  STP   C .    1 ?   26.549  39.030   7.512  0.00  0   C
+HETATM    111    V APOL .  STP   C .    1 ?   25.458  40.233   9.519  0.00  0   C
+HETATM    112    V APOL .  STP   C .    1 ?   26.179  39.423   7.970  0.00  0   C
+HETATM    113    V APOL .  STP   C .    1 ?   25.736  40.004   8.551  0.00  0   C
+HETATM    114    V APOL .  STP   C .    1 ?   10.851  87.154  34.207  0.00  0   C
+HETATM    115    V APOL .  STP   C .    1 ?   10.692  87.013  34.265  0.00  0   C
+HETATM    116    V APOL .  STP   C .    1 ?   11.818  86.568  34.068  0.00  0   C
+HETATM    117    V APOL .  STP   C .    1 ?   12.318  85.510  34.106  0.00  0   C
+HETATM    118    V APOL .  STP   C .    1 ?    5.545  90.375  43.119  0.00  0   C
+HETATM    119    V APOL .  STP   C .    1 ?    4.561  89.333  40.639  0.00  0   C
+HETATM    120    V APOL .  STP   C .    1 ?    4.611  89.401  40.637  0.00  0   C
+HETATM    121    V APOL .  STP   C .    1 ?    6.032  91.564  41.830  0.00  0   C
+HETATM    122    V APOL .  STP   C .    1 ?    6.186  90.504  39.052  0.00  0   C
+HETATM    123    V APOL .  STP   C .    1 ?    6.160  90.509  39.113  0.00  0   C
+HETATM    124    V APOL .  STP   C .    1 ?   17.990  86.008  28.210  0.00  0   C
+HETATM    125    V APOL .  STP   C .    1 ?   18.006  86.098  28.176  0.00  0   C
+HETATM    126    V APOL .  STP   C .    1 ?   19.521  87.572  27.205  0.00  0   C
+HETATM    127    V APOL .  STP   C .    1 ?   19.240  87.483  27.521  0.00  0   C
+HETATM    128    V APOL .  STP   C .    1 ?   18.718  87.116  27.484  0.00  0   C
+HETATM    129    V APOL .  STP   C .    1 ?   18.711  87.054  27.742  0.00  0   C
+HETATM    130    V APOL .  STP   C .    1 ?   19.118  87.451  27.484  0.00  0   C
+HETATM    131    V APOL .  STP   C .    1 ?   19.138  87.454  27.544  0.00  0   C
+HETATM    132    V APOL .  STP   C .    1 ?   17.547  86.179  28.768  0.00  0   C
+HETATM    133    V APOL .  STP   C .    1 ?   24.404  40.531  10.860  0.00  0   C
+HETATM    134    V APOL .  STP   C .    1 ?   24.678  40.696  10.870  0.00  0   C
+HETATM    135    V APOL .  STP   C .    1 ?   25.061  40.721  10.992  0.00  0   C
+HETATM    136    V APOL .  STP   C .    1 ?   34.434  54.099  24.046  0.00  0   C
+HETATM    137    V APOL .  STP   C .    1 ?   34.785  54.066  24.214  0.00  0   C
+HETATM    138    V APOL .  STP   C .    1 ?   30.243  49.144  18.082  0.00  0   C
+HETATM    139    V APOL .  STP   C .    1 ?   33.629  50.117  17.900  0.00  0   C
+HETATM    140    V APOL .  STP   C .    1 ?   32.643  53.327  21.021  0.00  0   C
+HETATM    141    V APOL .  STP   C .    1 ?   33.259  50.367  13.555  0.00  0   C
+HETATM    142    V APOL .  STP   C .    1 ?   32.796  52.509  13.407  0.00  0   C
+HETATM    143    V APOL .  STP   C .    1 ?   31.179  49.730  10.161  0.00  0   C
+HETATM    144    V APOL .  STP   C .    1 ?   25.397  48.219  17.846  0.00  0   C
+HETATM    145    V APOL .  STP   C .    1 ?   25.657  48.105  17.477  0.00  0   C
+HETATM    146    V APOL .  STP   C .    1 ?   32.744  47.500  12.564  0.00  0   C
+HETATM    147    V APOL .  STP   C .    1 ?   32.680  48.711  11.135  0.00  0   C
+HETATM    148    V APOL .  STP   C .    1 ?   30.293  34.983  19.208  0.00  0   C
+HETATM    149    V APOL .  STP   C .    1 ?   30.515  37.558  12.012  0.00  0   C
+HETATM    150    V APOL .  STP   C .    1 ?   28.816  38.796  12.429  0.00  0   C
+HETATM    151    V APOL .  STP   C .    1 ?   25.694  40.137  11.519  0.00  0   C
+HETATM    152    V APOL .  STP   C .    1 ?   25.745  40.188  11.663  0.00  0   C
+HETATM    153    V APOL .  STP   C .    1 ?   30.778  40.864  18.244  0.00  0   C
+HETATM    154    V APOL .  STP   C .    1 ?   29.300  41.260  18.522  0.00  0   C
+HETATM    155    V APOL .  STP   C .    1 ?   30.155  39.400  23.865  0.00  0   C
+HETATM    156    V APOL .  STP   C .    1 ?   29.435  42.951  17.876  0.00  0   C
+HETATM    157    V APOL .  STP   C .    1 ?   17.364  91.328  34.163  0.00  0   C
+HETATM    158    V APOL .  STP   C .    1 ?   17.378  91.256  34.191  0.00  0   C
+HETATM    159    V APOL .  STP   C .    1 ?   17.444  91.177  34.269  0.00  0   C
+HETATM    160    V APOL .  STP   C .    1 ?   17.348  91.074  34.310  0.00  0   C
+HETATM    161    V APOL .  STP   C .    1 ?   30.062  47.686  12.765  0.00  0   C
+HETATM    162    V APOL .  STP   C .    1 ?   26.323  48.692  15.710  0.00  0   C
+HETATM    163    V APOL .  STP   C .    1 ?   30.408  47.380  15.676  0.00  0   C
+HETATM    164    V APOL .  STP   C .    1 ?   28.125  47.095  15.991  0.00  0   C
+HETATM    165    V APOL .  STP   C .    1 ?   27.417  50.537  16.276  0.00  0   C
+HETATM    166    V APOL .  STP   C .    1 ?   27.373  50.707  16.089  0.00  0   C
+HETATM    167    V APOL .  STP   C .    1 ?   27.302  48.395  16.701  0.00  0   C
+HETATM    168    V APOL .  STP   C .    1 ?   27.841  49.832  16.849  0.00  0   C
+HETATM    169    V APOL .  STP   C .    1 ?   28.558  49.429  16.774  0.00  0   C
+HETATM    170    V APOL .  STP   C .    1 ?   27.865  49.337  16.994  0.00  0   C
+HETATM    171    V APOL .  STP   C .    1 ?   28.735  49.235  16.785  0.00  0   C
+HETATM    172    V APOL .  STP   C .    1 ?   30.286  38.810  24.532  0.00  0   C
+HETATM    173    V APOL .  STP   C .    1 ?   31.288  55.409  23.269  0.00  0   C
+HETATM    174    V APOL .  STP   C .    1 ?   32.312  48.943  10.498  0.00  0   C
+HETATM    175    V APOL .  STP   C .    1 ?   34.237  48.223  11.050  0.00  0   C
+HETATM    176    V APOL .  STP   C .    1 ?   24.685  41.731  11.638  0.00  0   C
+HETATM    177    V APOL .  STP   C .    1 ?   23.857  42.701  11.472  0.00  0   C
+HETATM    178    V APOL .  STP   C .    1 ?   28.622  41.347  18.970  0.00  0   C
+HETATM    179    V APOL .  STP   C .    1 ?   28.182  41.101  20.281  0.00  0   C
+HETATM    180    V APOL .  STP   C .    1 ?   24.517  43.394  13.603  0.00  0   C
+HETATM    181    V APOL .  STP   C .    1 ?   24.414  43.155  13.231  0.00  0   C
+HETATM    182    V APOL .  STP   C .    1 ?   27.454  47.131  15.066  0.00  0   C
+HETATM    183    V APOL .  STP   C .    1 ?   25.046  43.340  13.819  0.00  0   C
+HETATM    184    V APOL .  STP   C .    1 ?   24.700  43.363  13.625  0.00  0   C
+HETATM    185    V APOL .  STP   C .    1 ?   28.073  46.895  16.026  0.00  0   C
+HETATM    186    V APOL .  STP   C .    1 ?   28.133  46.815  16.042  0.00  0   C
+HETATM    187    V APOL .  STP   C .    1 ?   30.376  42.824  16.523  0.00  0   C
+HETATM    188    V APOL .  STP   C .    1 ?   30.365  42.854  16.522  0.00  0   C
+HETATM    189    V APOL .  STP   C .    1 ?   30.061  42.491  17.173  0.00  0   C
+HETATM    190    V APOL .  STP   C .    1 ?   29.539  42.849  17.699  0.00  0   C
+HETATM    191    V APOL .  STP   C .    1 ?   29.681  42.794  17.547  0.00  0   C
+HETATM    192    V APOL .  STP   C .    1 ?   28.734  41.753  18.363  0.00  0   C
+HETATM    193    V APOL .  STP   C .    1 ?   27.985  42.238  18.956  0.00  0   C
+HETATM    194    V APOL .  STP   C .    1 ?   28.539  41.757  18.517  0.00  0   C
+HETATM    195    V APOL .  STP   C .    1 ?   29.507  42.806  17.744  0.00  0   C
+HETATM    196    V APOL .  STP   C .    1 ?   29.791  42.296  17.519  0.00  0   C
+HETATM    197    V APOL .  STP   C .    1 ?   25.552  40.651  11.800  0.00  0   C
+HETATM    198    V APOL .  STP   C .    1 ?   25.702  41.429  12.209  0.00  0   C
+HETATM    199    V APOL .  STP   C .    1 ?   25.788  41.400  12.282  0.00  0   C
+HETATM    200    V APOL .  STP   C .    1 ?   25.003  41.310  11.497  0.00  0   C
+HETATM    201    V APOL .  STP   C .    1 ?   25.002  41.301  11.494  0.00  0   C
+HETATM    202    V APOL .  STP   C .    1 ?   24.966  42.497  12.680  0.00  0   C
+HETATM    203    V APOL .  STP   C .    1 ?   24.684  41.731  11.659  0.00  0   C
+HETATM    204    V APOL .  STP   C .    1 ?   24.715  41.678  11.631  0.00  0   C
+HETATM    205    V APOL .  STP   C .    1 ?   24.813  41.386  11.520  0.00  0   C
+HETATM    206    V APOL .  STP   C .    1 ?   24.837  43.023  13.213  0.00  0   C
+HETATM    207    V APOL .  STP   C .    1 ?   24.938  43.175  13.547  0.00  0   C
+HETATM    208    V APOL .  STP   C .    1 ?   24.059  42.452  12.156  0.00  0   C
+HETATM    209    V APOL .  STP   C .    1 ?   24.523  43.068  13.102  0.00  0   C
+HETATM    210    V APOL .  STP   C .    1 ?   23.664  42.606  12.414  0.00  0   C
+HETATM    211    V APOL .  STP   C .    1 ?   24.396  43.128  13.200  0.00  0   C
+HETATM    212    V APOL .  STP   C .    1 ?   24.435  43.138  13.214  0.00  0   C
+HETATM    213    V APOL .  STP   C .    1 ?   24.518  43.086  13.129  0.00  0   C
+HETATM    214    V APOL .  STP   C .    1 ?   24.575  43.157  13.291  0.00  0   C
+HETATM    215    V APOL .  STP   C .    1 ?   31.063  55.664  23.330  0.00  0   C
+HETATM    216    V APOL .  STP   C .    1 ?   33.721  54.466  25.554  0.00  0   C
+HETATM    217    V APOL .  STP   C .    1 ?   25.197  43.355  14.014  0.00  0   C
+HETATM    218    V APOL .  STP   C .    1 ?   25.635  43.546  14.505  0.00  0   C
+HETATM    219    V APOL .  STP   C .    1 ?   25.403  43.098  14.044  0.00  0   C
+HETATM    220    V APOL .  STP   C .    1 ?   26.324  42.901  14.728  0.00  0   C
+HETATM    221    V APOL .  STP   C .    1 ?   26.006  42.758  14.370  0.00  0   C
+HETATM    222    V APOL .  STP   C .    1 ?   28.626  39.926  18.156  0.00  0   C
+HETATM    223    V APOL .  STP   C .    1 ?   30.514  38.191  17.400  0.00  0   C
+HETATM    224    V APOL .  STP   C .    1 ?   29.885  37.934  17.493  0.00  0   C
+HETATM    225    V APOL .  STP   C .    1 ?   29.459  38.005  16.840  0.00  0   C
 # 

tests/reference_output/1QNH_out/1QNH_pockets.pqr

@@ -68,155 +68,163 @@ ATOM     64    C STP     1      10.093  87.611  33.467    0.00     4.07
 ATOM     65    C STP     1      10.538  87.926  33.379    0.00     4.35
 ATOM     66    O STP     1      33.888  49.647  16.687    0.00     6.03
 ATOM     67    O STP     1      17.468  87.092  29.886    0.00     3.61
-ATOM     68    O STP     1      33.220  49.873  17.122    0.00     5.53
-ATOM     69    C STP     1       9.423  86.425  34.239    0.00     3.53
-ATOM     70    C STP     1       9.363  86.402  34.268    0.00     3.50
-ATOM     71    O STP     1      17.156  90.553  34.548    0.00     4.74
-ATOM     72    O STP     1      18.977  88.996  36.323    0.00     3.80
-ATOM     73    O STP     1      18.801  90.804  35.327    0.00     4.97
-ATOM     74    O STP     1      18.268  89.945  34.975    0.00     4.55
-ATOM     75    O STP     1      18.868  89.208  35.945    0.00     4.00
-ATOM     76    O STP     1      18.065  88.657  35.595    0.00     3.63
-ATOM     77    O STP     1      18.379  89.193  35.362    0.00     4.09
-ATOM     78    O STP     1      18.882  87.605  27.239    0.00     3.92
-ATOM     79    O STP     1      13.300  94.652  30.063    0.00     5.74
-ATOM     80    O STP     1      13.169  88.280  31.543    0.00     3.79
-ATOM     81    C STP     1      12.965  87.866  31.201    0.00     3.42
-ATOM     82    O STP     1      17.206  86.955  29.975    0.00     3.57
-ATOM     83    O STP     1      17.313  86.932  29.848    0.00     3.60
-ATOM     84    O STP     1      17.260  86.826  29.857    0.00     3.56
-ATOM     85    O STP     1      17.647  86.903  29.170    0.00     3.65
-ATOM     86    O STP     1      17.446  86.914  29.625    0.00     3.62
-ATOM     87    O STP     1      17.540  86.349  29.071    0.00     3.57
-ATOM     88    O STP     1      17.825  86.147  28.464    0.00     3.66
-ATOM     89    O STP     1      17.638  86.291  28.817    0.00     3.62
-ATOM     90    O STP     1      17.589  86.200  28.737    0.00     3.57
-ATOM     91    C STP     1      17.310  86.348  29.432    0.00     3.47
-ATOM     92    O STP     1      24.622  40.674  10.795    0.00     4.05
-ATOM     93    C STP     1      27.005  49.985  17.993    0.00     3.82
-ATOM     94    C STP     1      26.839  50.582  18.014    0.00     3.60
-ATOM     95    C STP     1      27.676  50.218  16.945    0.00     4.09
-ATOM     96    C STP     1      26.991  50.900  17.679    0.00     3.59
-ATOM     97    O STP     1      30.592  49.040  16.768    0.00     4.84
-ATOM     98    O STP     1      31.112  44.097  16.205    0.00     5.49
-ATOM     99    O STP     1      26.685  48.719  17.768    0.00     3.95
-ATOM    100    C STP     1      27.314  49.434  17.751    0.00     4.15
-ATOM    101    O STP     1      30.711  48.752  16.393    0.00     5.04
-ATOM    102    O STP     1      31.020  47.339  15.614    0.00     5.44
-ATOM    103    O STP     1      29.111  49.193  16.737    0.00     4.56
-ATOM    104    O STP     1      27.150  48.349  16.835    0.00     4.29
-ATOM    105    O STP     1      28.085  46.923  16.028    0.00     4.46
-ATOM    106    O STP     1      29.429  38.000  16.814    0.00     3.95
-ATOM    107    O STP     1      25.337  41.857  10.796    0.00     3.65
-ATOM    108    C STP     1      10.851  87.154  34.207    0.00     4.06
-ATOM    109    C STP     1      10.692  87.013  34.265    0.00     3.95
-ATOM    110    O STP     1      11.818  86.568  34.068    0.00     3.81
-ATOM    111    C STP     1      12.318  85.510  34.106    0.00     3.44
-ATOM    112    O STP     1       5.545  90.375  43.119    0.00     4.74
-ATOM    113    C STP     1       4.561  89.333  40.639    0.00     3.85
-ATOM    114    C STP     1       4.611  89.401  40.637    0.00     3.86
-ATOM    115    C STP     1       6.032  91.564  41.830    0.00     5.21
-ATOM    116    C STP     1       6.186  90.504  39.052    0.00     3.61
-ATOM    117    C STP     1       6.160  90.509  39.113    0.00     3.63
-ATOM    118    O STP     1      17.990  86.008  28.210    0.00     3.70
-ATOM    119    O STP     1      18.006  86.098  28.176    0.00     3.73
-ATOM    120    O STP     1      19.521  87.572  27.205    0.00     4.19
-ATOM    121    O STP     1      19.240  87.483  27.521    0.00     4.22
-ATOM    122    O STP     1      18.718  87.116  27.484    0.00     3.98
-ATOM    123    O STP     1      18.711  87.054  27.742    0.00     4.02
-ATOM    124    O STP     1      19.118  87.451  27.484    0.00     4.20
-ATOM    125    O STP     1      19.138  87.454  27.544    0.00     4.22
-ATOM    126    O STP     1      17.547  86.179  28.768    0.00     3.54
-ATOM    127    O STP     1      24.404  40.531  10.860    0.00     3.87
-ATOM    128    O STP     1      24.678  40.696  10.870    0.00     4.10
-ATOM    129    O STP     1      25.061  40.721  10.992    0.00     4.29
-ATOM    130    C STP     1      34.434  54.099  24.046    0.00     5.83
-ATOM    131    C STP     1      34.785  54.066  24.214    0.00     6.17
-ATOM    132    O STP     1      30.243  49.144  18.082    0.00     3.84
-ATOM    133    O STP     1      33.629  50.117  17.900    0.00     5.37
-ATOM    134    C STP     1      32.643  53.327  21.021    0.00     3.69
-ATOM    135    O STP     1      33.259  50.367  13.555    0.00     5.25
-ATOM    136    O STP     1      32.796  52.509  13.407    0.00     3.99
-ATOM    137    O STP     1      31.179  49.730  10.161    0.00     4.05
-ATOM    138    C STP     1      25.397  48.219  17.846    0.00     3.48
-ATOM    139    C STP     1      25.657  48.105  17.477    0.00     3.55
-ATOM    140    O STP     1      32.744  47.500  12.564    0.00     5.68
-ATOM    141    O STP     1      32.680  48.711  11.135    0.00     5.22
-ATOM    142    O STP     1      30.293  34.983  19.208    0.00     5.09
-ATOM    143    C STP     1      30.515  37.558  12.012    0.00     5.68
-ATOM    144    O STP     1      28.816  38.796  12.429    0.00     4.55
-ATOM    145    O STP     1      25.694  40.137  11.519    0.00     4.25
-ATOM    146    O STP     1      25.745  40.188  11.663    0.00     4.25
-ATOM    147    O STP     1      30.778  40.864  18.244    0.00     5.65
-ATOM    148    O STP     1      29.300  41.260  18.522    0.00     4.72
-ATOM    149    O STP     1      29.435  42.951  17.876    0.00     4.50
-ATOM    150    O STP     1      17.364  91.328  34.163    0.00     5.47
-ATOM    151    O STP     1      17.378  91.256  34.191    0.00     5.43
-ATOM    152    O STP     1      17.444  91.177  34.269    0.00     5.37
-ATOM    153    O STP     1      17.348  91.074  34.310    0.00     5.25
-ATOM    154    O STP     1      30.062  47.686  12.765    0.00     3.67
-ATOM    155    C STP     1      26.323  48.692  15.710    0.00     3.43
-ATOM    156    O STP     1      30.408  47.380  15.676    0.00     5.15
-ATOM    157    O STP     1      28.125  47.095  15.991    0.00     4.51
-ATOM    158    C STP     1      27.417  50.537  16.276    0.00     3.74
-ATOM    159    C STP     1      27.373  50.707  16.089    0.00     3.59
-ATOM    160    C STP     1      27.302  48.395  16.701    0.00     4.37
-ATOM    161    C STP     1      27.841  49.832  16.849    0.00     4.30
-ATOM    162    C STP     1      28.558  49.429  16.774    0.00     4.43
-ATOM    163    C STP     1      27.865  49.337  16.994    0.00     4.49
-ATOM    164    O STP     1      28.735  49.235  16.785    0.00     4.53
-ATOM    165    C STP     1      31.288  55.409  23.269    0.00     3.49
-ATOM    166    O STP     1      32.312  48.943  10.498    0.00     4.81
-ATOM    167    O STP     1      34.237  48.223  11.050    0.00     6.07
-ATOM    168    O STP     1      24.685  41.731  11.638    0.00     4.16
-ATOM    169    O STP     1      23.857  42.701  11.472    0.00     3.56
-ATOM    170    O STP     1      28.622  41.347  18.970    0.00     4.24
-ATOM    171    O STP     1      28.182  41.101  20.281    0.00     3.62
-ATOM    172    C STP     1      24.517  43.394  13.603    0.00     3.46
-ATOM    173    C STP     1      24.414  43.155  13.231    0.00     3.58
-ATOM    174    O STP     1      27.454  47.131  15.066    0.00     3.72
-ATOM    175    O STP     1      25.046  43.340  13.819    0.00     3.59
-ATOM    176    C STP     1      24.700  43.363  13.625    0.00     3.53
-ATOM    177    O STP     1      28.073  46.895  16.026    0.00     4.44
-ATOM    178    O STP     1      28.133  46.815  16.042    0.00     4.43
-ATOM    179    O STP     1      30.376  42.824  16.523    0.00     5.68
-ATOM    180    O STP     1      30.365  42.854  16.522    0.00     5.67
-ATOM    181    O STP     1      30.061  42.491  17.173    0.00     5.36
-ATOM    182    O STP     1      29.539  42.849  17.699    0.00     4.70
-ATOM    183    O STP     1      29.681  42.794  17.547    0.00     4.87
-ATOM    184    O STP     1      28.734  41.753  18.363    0.00     4.47
-ATOM    185    O STP     1      27.985  42.238  18.956    0.00     3.70
-ATOM    186    O STP     1      28.539  41.757  18.517    0.00     4.33
-ATOM    187    O STP     1      29.507  42.806  17.744    0.00     4.69
-ATOM    188    O STP     1      29.791  42.296  17.519    0.00     5.14
-ATOM    189    O STP     1      25.552  40.651  11.800    0.00     4.24
-ATOM    190    O STP     1      25.702  41.429  12.209    0.00     4.09
-ATOM    191    O STP     1      25.788  41.400  12.282    0.00     4.07
-ATOM    192    O STP     1      25.003  41.310  11.497    0.00     4.32
-ATOM    193    O STP     1      25.002  41.301  11.494    0.00     4.32
-ATOM    194    O STP     1      24.966  42.497  12.680    0.00     3.75
-ATOM    195    O STP     1      24.684  41.731  11.659    0.00     4.16
-ATOM    196    O STP     1      24.715  41.678  11.631    0.00     4.18
-ATOM    197    O STP     1      24.813  41.386  11.520    0.00     4.25
-ATOM    198    O STP     1      24.837  43.023  13.213    0.00     3.66
-ATOM    199    O STP     1      24.938  43.175  13.547    0.00     3.62
-ATOM    200    O STP     1      24.059  42.452  12.156    0.00     3.85
-ATOM    201    O STP     1      24.523  43.068  13.102    0.00     3.64
-ATOM    202    O STP     1      23.664  42.606  12.414    0.00     3.66
-ATOM    203    O STP     1      24.396  43.128  13.200    0.00     3.58
-ATOM    204    O STP     1      24.435  43.138  13.214    0.00     3.59
-ATOM    205    O STP     1      24.518  43.086  13.129    0.00     3.63
-ATOM    206    O STP     1      24.575  43.157  13.291    0.00     3.61
-ATOM    207    C STP     1      31.063  55.664  23.330    0.00     3.47
-ATOM    208    O STP     1      33.721  54.466  25.554    0.00     5.34
-ATOM    209    O STP     1      25.197  43.355  14.014    0.00     3.58
-ATOM    210    O STP     1      25.635  43.546  14.505    0.00     3.53
-ATOM    211    O STP     1      25.403  43.098  14.044    0.00     3.59
-ATOM    212    O STP     1      26.324  42.901  14.728    0.00     3.68
-ATOM    213    O STP     1      26.006  42.758  14.370    0.00     3.65
-ATOM    214    O STP     1      28.626  39.926  18.156    0.00     3.63
-ATOM    215    O STP     1      30.514  38.191  17.400    0.00     5.05
-ATOM    216    O STP     1      29.885  37.934  17.493    0.00     4.48
-ATOM    217    O STP     1      29.459  38.005  16.840    0.00     3.98
+ATOM     68    O STP     1      26.368  39.013   7.356    0.00     4.59
+ATOM     69    O STP     1      33.220  49.873  17.122    0.00     5.53
+ATOM     70    O STP     1      30.363  38.669  24.413    0.00     5.89
+ATOM     71    C STP     1       9.423  86.425  34.239    0.00     3.53
+ATOM     72    C STP     1       9.363  86.402  34.268    0.00     3.50
+ATOM     73    O STP     1      17.156  90.553  34.548    0.00     4.74
+ATOM     74    O STP     1      18.977  88.996  36.323    0.00     3.80
+ATOM     75    O STP     1      18.801  90.804  35.327    0.00     4.97
+ATOM     76    O STP     1      18.268  89.945  34.975    0.00     4.55
+ATOM     77    O STP     1      18.868  89.208  35.945    0.00     4.00
+ATOM     78    O STP     1      18.065  88.657  35.595    0.00     3.63
+ATOM     79    O STP     1      18.379  89.193  35.362    0.00     4.09
+ATOM     80    O STP     1      18.882  87.605  27.239    0.00     3.92
+ATOM     81    O STP     1      13.300  94.652  30.063    0.00     5.74
+ATOM     82    O STP     1      13.169  88.280  31.543    0.00     3.79
+ATOM     83    C STP     1      12.965  87.866  31.201    0.00     3.42
+ATOM     84    O STP     1      17.206  86.955  29.975    0.00     3.57
+ATOM     85    O STP     1      17.313  86.932  29.848    0.00     3.60
+ATOM     86    O STP     1      17.260  86.826  29.857    0.00     3.56
+ATOM     87    O STP     1      17.647  86.903  29.170    0.00     3.65
+ATOM     88    O STP     1      17.446  86.914  29.625    0.00     3.62
+ATOM     89    O STP     1      17.540  86.349  29.071    0.00     3.57
+ATOM     90    O STP     1      17.825  86.147  28.464    0.00     3.66
+ATOM     91    O STP     1      17.638  86.291  28.817    0.00     3.62
+ATOM     92    O STP     1      17.589  86.200  28.737    0.00     3.57
+ATOM     93    C STP     1      17.310  86.348  29.432    0.00     3.47
+ATOM     94    O STP     1      24.622  40.674  10.795    0.00     4.05
+ATOM     95    C STP     1      27.005  49.985  17.993    0.00     3.82
+ATOM     96    C STP     1      26.839  50.582  18.014    0.00     3.60
+ATOM     97    C STP     1      27.676  50.218  16.945    0.00     4.09
+ATOM     98    C STP     1      26.991  50.900  17.679    0.00     3.59
+ATOM     99    O STP     1      30.592  49.040  16.768    0.00     4.84
+ATOM    100    O STP     1      31.112  44.097  16.205    0.00     5.49
+ATOM    101    O STP     1      26.685  48.719  17.768    0.00     3.95
+ATOM    102    C STP     1      27.314  49.434  17.751    0.00     4.15
+ATOM    103    O STP     1      30.711  48.752  16.393    0.00     5.04
+ATOM    104    O STP     1      31.020  47.339  15.614    0.00     5.44
+ATOM    105    O STP     1      29.111  49.193  16.737    0.00     4.56
+ATOM    106    O STP     1      27.150  48.349  16.835    0.00     4.29
+ATOM    107    O STP     1      28.085  46.923  16.028    0.00     4.46
+ATOM    108    O STP     1      29.429  38.000  16.814    0.00     3.95
+ATOM    109    O STP     1      25.337  41.857  10.796    0.00     3.65
+ATOM    110    C STP     1      26.549  39.030   7.512    0.00     4.64
+ATOM    111    O STP     1      25.458  40.233   9.519    0.00     3.99
+ATOM    112    O STP     1      26.179  39.423   7.970    0.00     4.35
+ATOM    113    O STP     1      25.736  40.004   8.551    0.00     4.07
+ATOM    114    C STP     1      10.851  87.154  34.207    0.00     4.06
+ATOM    115    C STP     1      10.692  87.013  34.265    0.00     3.95
+ATOM    116    O STP     1      11.818  86.568  34.068    0.00     3.81
+ATOM    117    C STP     1      12.318  85.510  34.106    0.00     3.44
+ATOM    118    O STP     1       5.545  90.375  43.119    0.00     4.74
+ATOM    119    C STP     1       4.561  89.333  40.639    0.00     3.85
+ATOM    120    C STP     1       4.611  89.401  40.637    0.00     3.86
+ATOM    121    C STP     1       6.032  91.564  41.830    0.00     5.21
+ATOM    122    C STP     1       6.186  90.504  39.052    0.00     3.61
+ATOM    123    C STP     1       6.160  90.509  39.113    0.00     3.63
+ATOM    124    O STP     1      17.990  86.008  28.210    0.00     3.70
+ATOM    125    O STP     1      18.006  86.098  28.176    0.00     3.73
+ATOM    126    O STP     1      19.521  87.572  27.205    0.00     4.19
+ATOM    127    O STP     1      19.240  87.483  27.521    0.00     4.22
+ATOM    128    O STP     1      18.718  87.116  27.484    0.00     3.98
+ATOM    129    O STP     1      18.711  87.054  27.742    0.00     4.02
+ATOM    130    O STP     1      19.118  87.451  27.484    0.00     4.20
+ATOM    131    O STP     1      19.138  87.454  27.544    0.00     4.22
+ATOM    132    O STP     1      17.547  86.179  28.768    0.00     3.54
+ATOM    133    O STP     1      24.404  40.531  10.860    0.00     3.87
+ATOM    134    O STP     1      24.678  40.696  10.870    0.00     4.10
+ATOM    135    O STP     1      25.061  40.721  10.992    0.00     4.29
+ATOM    136    C STP     1      34.434  54.099  24.046    0.00     5.83
+ATOM    137    C STP     1      34.785  54.066  24.214    0.00     6.17
+ATOM    138    O STP     1      30.243  49.144  18.082    0.00     3.84
+ATOM    139    O STP     1      33.629  50.117  17.900    0.00     5.37
+ATOM    140    C STP     1      32.643  53.327  21.021    0.00     3.69
+ATOM    141    O STP     1      33.259  50.367  13.555    0.00     5.25
+ATOM    142    O STP     1      32.796  52.509  13.407    0.00     3.99
+ATOM    143    O STP     1      31.179  49.730  10.161    0.00     4.05
+ATOM    144    C STP     1      25.397  48.219  17.846    0.00     3.48
+ATOM    145    C STP     1      25.657  48.105  17.477    0.00     3.55
+ATOM    146    O STP     1      32.744  47.500  12.564    0.00     5.68
+ATOM    147    O STP     1      32.680  48.711  11.135    0.00     5.22
+ATOM    148    O STP     1      30.293  34.983  19.208    0.00     5.09
+ATOM    149    C STP     1      30.515  37.558  12.012    0.00     5.68
+ATOM    150    O STP     1      28.816  38.796  12.429    0.00     4.55
+ATOM    151    O STP     1      25.694  40.137  11.519    0.00     4.25
+ATOM    152    O STP     1      25.745  40.188  11.663    0.00     4.25
+ATOM    153    O STP     1      30.778  40.864  18.244    0.00     5.65
+ATOM    154    O STP     1      29.300  41.260  18.522    0.00     4.72
+ATOM    155    O STP     1      30.155  39.400  23.865    0.00     5.50
+ATOM    156    O STP     1      29.435  42.951  17.876    0.00     4.50
+ATOM    157    O STP     1      17.364  91.328  34.163    0.00     5.47
+ATOM    158    O STP     1      17.378  91.256  34.191    0.00     5.43
+ATOM    159    O STP     1      17.444  91.177  34.269    0.00     5.37
+ATOM    160    O STP     1      17.348  91.074  34.310    0.00     5.25
+ATOM    161    O STP     1      30.062  47.686  12.765    0.00     3.67
+ATOM    162    C STP     1      26.323  48.692  15.710    0.00     3.43
+ATOM    163    O STP     1      30.408  47.380  15.676    0.00     5.15
+ATOM    164    O STP     1      28.125  47.095  15.991    0.00     4.51
+ATOM    165    C STP     1      27.417  50.537  16.276    0.00     3.74
+ATOM    166    C STP     1      27.373  50.707  16.089    0.00     3.59
+ATOM    167    C STP     1      27.302  48.395  16.701    0.00     4.37
+ATOM    168    C STP     1      27.841  49.832  16.849    0.00     4.30
+ATOM    169    C STP     1      28.558  49.429  16.774    0.00     4.43
+ATOM    170    C STP     1      27.865  49.337  16.994    0.00     4.49
+ATOM    171    O STP     1      28.735  49.235  16.785    0.00     4.53
+ATOM    172    O STP     1      30.286  38.810  24.532    0.00     5.75
+ATOM    173    C STP     1      31.288  55.409  23.269    0.00     3.49
+ATOM    174    O STP     1      32.312  48.943  10.498    0.00     4.81
+ATOM    175    O STP     1      34.237  48.223  11.050    0.00     6.07
+ATOM    176    O STP     1      24.685  41.731  11.638    0.00     4.16
+ATOM    177    O STP     1      23.857  42.701  11.472    0.00     3.56
+ATOM    178    O STP     1      28.622  41.347  18.970    0.00     4.24
+ATOM    179    O STP     1      28.182  41.101  20.281    0.00     3.62
+ATOM    180    C STP     1      24.517  43.394  13.603    0.00     3.46
+ATOM    181    C STP     1      24.414  43.155  13.231    0.00     3.58
+ATOM    182    O STP     1      27.454  47.131  15.066    0.00     3.72
+ATOM    183    O STP     1      25.046  43.340  13.819    0.00     3.59
+ATOM    184    C STP     1      24.700  43.363  13.625    0.00     3.53
+ATOM    185    O STP     1      28.073  46.895  16.026    0.00     4.44
+ATOM    186    O STP     1      28.133  46.815  16.042    0.00     4.43
+ATOM    187    O STP     1      30.376  42.824  16.523    0.00     5.68
+ATOM    188    O STP     1      30.365  42.854  16.522    0.00     5.67
+ATOM    189    O STP     1      30.061  42.491  17.173    0.00     5.36
+ATOM    190    O STP     1      29.539  42.849  17.699    0.00     4.70
+ATOM    191    O STP     1      29.681  42.794  17.547    0.00     4.87
+ATOM    192    O STP     1      28.734  41.753  18.363    0.00     4.47
+ATOM    193    O STP     1      27.985  42.238  18.956    0.00     3.70
+ATOM    194    O STP     1      28.539  41.757  18.517    0.00     4.33
+ATOM    195    O STP     1      29.507  42.806  17.744    0.00     4.69
+ATOM    196    O STP     1      29.791  42.296  17.519    0.00     5.14
+ATOM    197    O STP     1      25.552  40.651  11.800    0.00     4.24
+ATOM    198    O STP     1      25.702  41.429  12.209    0.00     4.09
+ATOM    199    O STP     1      25.788  41.400  12.282    0.00     4.07
+ATOM    200    O STP     1      25.003  41.310  11.497    0.00     4.32
+ATOM    201    O STP     1      25.002  41.301  11.494    0.00     4.32
+ATOM    202    O STP     1      24.966  42.497  12.680    0.00     3.75
+ATOM    203    O STP     1      24.684  41.731  11.659    0.00     4.16
+ATOM    204    O STP     1      24.715  41.678  11.631    0.00     4.18
+ATOM    205    O STP     1      24.813  41.386  11.520    0.00     4.25
+ATOM    206    O STP     1      24.837  43.023  13.213    0.00     3.66
+ATOM    207    O STP     1      24.938  43.175  13.547    0.00     3.62
+ATOM    208    O STP     1      24.059  42.452  12.156    0.00     3.85
+ATOM    209    O STP     1      24.523  43.068  13.102    0.00     3.64
+ATOM    210    O STP     1      23.664  42.606  12.414    0.00     3.66
+ATOM    211    O STP     1      24.396  43.128  13.200    0.00     3.58
+ATOM    212    O STP     1      24.435  43.138  13.214    0.00     3.59
+ATOM    213    O STP     1      24.518  43.086  13.129    0.00     3.63
+ATOM    214    O STP     1      24.575  43.157  13.291    0.00     3.61
+ATOM    215    C STP     1      31.063  55.664  23.330    0.00     3.47
+ATOM    216    O STP     1      33.721  54.466  25.554    0.00     5.34
+ATOM    217    O STP     1      25.197  43.355  14.014    0.00     3.58
+ATOM    218    O STP     1      25.635  43.546  14.505    0.00     3.53
+ATOM    219    O STP     1      25.403  43.098  14.044    0.00     3.59
+ATOM    220    O STP     1      26.324  42.901  14.728    0.00     3.68
+ATOM    221    O STP     1      26.006  42.758  14.370    0.00     3.65
+ATOM    222    O STP     1      28.626  39.926  18.156    0.00     3.63
+ATOM    223    O STP     1      30.514  38.191  17.400    0.00     5.05
+ATOM    224    O STP     1      29.885  37.934  17.493    0.00     4.48
+ATOM    225    O STP     1      29.459  38.005  16.840    0.00     3.98
 TER
 END

tests/reference_output/1QNH_out/pockets/pocket1_atm.cif

@@ -6,21 +6,21 @@ This is a mmcif format file writen by the programm fpocket.
 It represents the atoms contacted by the voronoi vertices of the pocket.  
                                                                            
 Information about the pocket     1:
-0  - Pocket Score                      : 5.8454
+0  - Pocket Score                      : 6.1285
 1  - Drug Score                        : 1.0000
-2  - Number of alpha spheres           :   217
-3  - Mean alpha-sphere radius          : 4.3019
-4  - Mean alpha-sphere Solvent Acc.    : 0.5830
+2  - Number of alpha spheres           :   225
+3  - Mean alpha-sphere radius          : 4.3213
+4  - Mean alpha-sphere Solvent Acc.    : 0.5807
 5  - Mean B-factor of pocket residues  : 0.0000
-6  - Hydrophobicity Score              : 16.8148
-7  - Polarity Score                    :    16
-8  - Amino Acid based volume Score     : 3.8889
-9  - Pocket volume (Monte Carlo)       : 4956.8828
-10  -Pocket volume (convex hull)       : 10904.4561
+6  - Hydrophobicity Score              : 18.4643
+7  - Polarity Score                    :    17
+8  - Amino Acid based volume Score     : 4.0000
+9  - Pocket volume (Monte Carlo)       : 5738.3193
+10  -Pocket volume (convex hull)       : 11845.1973
 11 - Charge Score                      :     6
-12 - Local hydrophobic density Score   : 13.4444
-13 - Number of apolar alpha sphere     :    54
-14 - Proportion of apolar alpha sphere : 0.2488
+12 - Local hydrophobic density Score   : 13.3455
+13 - Number of apolar alpha sphere     :    55
+14 - Proportion of apolar alpha sphere : 0.2444
 # 
 loop_
 _atom_site.group_PDB
@@ -50,7 +50,7 @@ ATOM     2286    C  CD1 .  LEU   B .  128 ?    6.202  86.633  32.781  0.00  0
 ATOM     2318    N  NE2 .  HIS   B .  132 ?    9.242  88.831  29.145 -5.47  0   B
 ATOM     2317    C  CE1 .  HIS   B .  132 ?   10.323  88.078  29.041  0.00  0   B
 ATOM     2135    O  OD1 .  ASN   B .  108 ?   12.641  89.570  26.461 -2.14  0   B
-ATOM     1791    N  NH2 .  ARG   B .   61 ?   12.927  90.252  37.946 -4.37  0   B
+ATOM     1791    N  NH2 .  ARG   B .   61 ?   12.927  90.252  37.946 -1.09  0   B
 ATOM     1855    C   CD .  GLN   B .   69 ?   15.725  85.545  34.857  0.00  0   B
 ATOM     1833    C  CE2 .  PHE   B .   66 ?    8.952  88.462  37.965  0.00  0   B
 ATOM     2274    N  NE1 .  TRP   B .  127 ?    4.665  90.424  35.013  0.00  0   B
@@ -66,9 +66,9 @@ ATOM     2277    C  CZ2 .  TRP   B .  127 ?    3.617  89.154  36.912  0.00  0
 ATOM     1830    C  CD1 .  PHE   B .   66 ?    6.646  86.985  38.413  0.00  0   B
 ATOM     1818    O    O .  GLN   B .   65 ?    4.153  85.911  42.353  0.00  0   B
 ATOM     2279    C  CH2 .  TRP   B .  127 ?    2.401  88.785  37.428  0.00  0   B
-ATOM     2482    O    O .  LYS   B .  154 ?   12.088  91.141  45.036  0.00  0   B
+ATOM     2482    O    O .  LYS   B .  154 ?   12.088  91.141  45.036 -0.54  0   B
 ATOM     1807    C  CD1 .  ILE   B .   63 ?   11.752  89.132  41.153  0.00  0   B
-ATOM     2487    O    O .  SER   B .  155 ?   15.773  90.893  43.331 -1.62  0   B
+ATOM     2487    O    O .  SER   B .  155 ?   15.773  90.893  43.331 -3.35  0   B
 ATOM     1789    C   CZ .  ARG   B .   61 ?   13.831  89.292  37.808  0.00  0   B
 ATOM     1911    C    C .  GLY   B .   78 ?   21.795  87.544  32.811  0.00  0   B
 ATOM     1904    O    O .  ASN   B .   77 ?   22.544  87.676  36.296  0.00  0   B
@@ -104,7 +104,15 @@ ATOM     2272    C  CD1 .  TRP   B .  127 ?    4.169  91.116  33.936  0.00  0
 ATOM      971    N  NE1 .  TRP   A .  127 ?   31.690  55.125  17.941  0.00  0   A
 ATOM      482    N  NH2 .  ARG   A .   61 ?   30.854  46.734  21.014 -1.09  0   A
 ATOM     2194    C   CD .  GLN   B .  117 ?   19.437  84.530  31.487  0.00  0   B
+ATOM      862    C   CB .  THR   A .  113 ?   25.860  43.490   6.456  0.00  0   A
+ATOM      666    N  NH1 .  ARG   A .   87 ?   22.062  38.269   8.777 -4.12  0   A
+ATOM      864    C  CG2 .  THR   A .  113 ?   26.850  43.117   5.347  0.00  0   A
+ATOM      667    N  NH2 .  ARG   A .   87 ?   23.345  36.894  10.092 -1.93  0   A
 ATOM      525    C   CZ .  PHE   A .   66 ?   29.230  52.224  20.147  0.00  0   A
+ATOM      465    O    O .  HIS   A .   60 ?   25.158  41.344  25.078 -1.62  0   A
+ATOM      595    O    O .  ASN   A .   77 ?   26.312  38.006  20.189  0.00  0   A
+ATOM     1184    O    O .  SER   A .  155 ?   31.853  44.086  26.183  0.00  0   A
+ATOM     1197    C  CD1 .  TYR   A .  157 ?   28.532  39.033  29.999  0.00  0   A
 ATOM     1840    C   CG .  MET   B .   67 ?    9.633  84.822  37.381  0.00  0   B
 ATOM     1787    C   CD .  ARG   B .   61 ?   15.961  88.260  38.521  0.00  0   B
 ATOM     1778    C  CD2 .  HIS   B .   60 ?   19.860  85.375  37.081  0.00  0   B
@@ -116,9 +124,7 @@ ATOM     2129    N    N .  ASN   B .  108 ?   14.150  86.948  28.128  0.00  0
 ATOM     2192    C   CB .  GLN   B .  117 ?   17.733  83.041  30.399  0.00  0   B
 ATOM     2127    O    O .  ALA   B .  107 ?   14.577  84.908  27.317  0.00  0   B
 ATOM      878    O   OG .  SER   A .  115 ?   20.631  41.367  10.780 -3.21  0   A
-ATOM      666    N  NH1 .  ARG   A .   87 ?   22.062  38.269   8.777 -2.61  0   A
-ATOM      861    O    O .  THR   A .  113 ?   23.582  43.411   7.996 -4.69  0   A
-ATOM      667    N  NH2 .  ARG   A .   87 ?   23.345  36.894  10.092 -4.12  0   A
+ATOM      861    O    O .  THR   A .  113 ?   23.582  43.411   7.996 -5.36  0   A
 ATOM      531    C   CG .  MET   A .   67 ?   25.856  51.243  21.414  0.00  0   A
 ATOM      911    C  CD1 .  LEU   A .  119 ?   23.851  52.591  18.054  0.00  0   A
 ATOM      983    C  CD1 .  LEU   A .  128 ?   27.372  54.269  16.512  0.00  0   A
@@ -142,7 +148,7 @@ ATOM     1829    C   CG .  PHE   B .   66 ?    7.541  87.175  39.460  0.00  0
 ATOM     1831    C  CD2 .  PHE   B .   66 ?    8.694  87.919  39.225  0.00  0   B
 ATOM     2181    O   OG .  SER   B .  115 ?   19.809  83.527  26.162 -4.29  0   B
 ATOM     2126    C    C .  ALA   B .  107 ?   14.097  85.624  28.193  0.00  0   B
-ATOM      613    O    O .  GLY   A .   80 ?   22.190  38.611  13.380 -1.07  0   A
+ATOM      613    O    O .  GLY   A .   80 ?   22.190  38.611  13.380  0.00  0   A
 ATOM      520    C   CG .  PHE   A .   66 ?   28.847  52.956  22.827  0.00  0   A
 ATOM      974    C  CZ2 .  TRP   A .  127 ?   31.017  56.465  19.955  0.00  0   A
 ATOM      519    C   CB .  PHE   A .   66 ?   28.655  53.352  24.272  0.00  0   A
@@ -156,7 +162,6 @@ ATOM      546    C   CD .  GLN   A .   69 ?   25.009  44.971  19.024  0.00  0
 ATOM      839    N    N .  GLY   A .  110 ?   29.407  45.801   8.294  0.00  0   A
 ATOM      597    C   CG .  ASN   A .   77 ?   25.222  34.668  19.575  0.00  0   A
 ATOM      598    O  OD1 .  ASN   A .   77 ?   25.256  35.283  18.510 -1.07  0   A
-ATOM      595    O    O .  ASN   A .   77 ?   26.312  38.006  20.189  0.00  0   A
 ATOM      607    O    O .  SER   A .   79 ?   25.110  36.261  13.164  0.00  0   A
 ATOM      479    N   NE .  ARG   A .   61 ?   29.569  45.021  21.872 -2.19  0   A
 ATOM      478    C   CD .  ARG   A .   61 ?   28.334  44.256  22.042  0.00  0   A
@@ -164,6 +169,7 @@ ATOM      601    C   CA .  GLY   A .   78 ?   25.067  39.217  18.072  0.00  0
 ATOM     1788    N   NE .  ARG   B .   61 ?   14.906  89.269  38.594  0.00  0   B
 ATOM     1014    C  CE1 .  HIS   A .  132 ?   27.139  49.898  12.602  0.00  0   A
 ATOM      822    C   CA .  ALA   A .  107 ?   23.846  47.439  13.692  0.00  0   A
+ATOM     1192    C   CA .  TYR   A .  157 ?   28.602  42.056  28.964  0.00  0   A
 ATOM      521    C  CD1 .  PHE   A .   66 ?   28.541  53.842  21.796  0.00  0   A
 ATOM      840    C   CA .  GLY   A .  110 ?   29.978  46.428   7.122  0.00  0   A
 ATOM      827    C   CA .  ASN   A .  108 ?   25.685  45.693  10.863  0.00  0   A

tests/reference_output/1QNH_out/pockets/pocket1_vert.pqr

@@ -4,20 +4,20 @@ HEADER It represent the voronoi vertices of a single pocket found by the
 HEADER algorithm.                                                                
 HEADER                                                                           
 HEADER Information about the pocket     1:
-HEADER 0  - Pocket Score                      : 5.8454
+HEADER 0  - Pocket Score                      : 6.1285
 HEADER 1  - Drug Score                        : 1.0000
-HEADER 2  - Number of V. Vertices             :   217
-HEADER 3  - Mean alpha-sphere radius          : 4.3019
-HEADER 4  - Mean alpha-sphere SA              : 0.5830
+HEADER 2  - Number of V. Vertices             :   225
+HEADER 3  - Mean alpha-sphere radius          : 4.3213
+HEADER 4  - Mean alpha-sphere SA              : 0.5807
 HEADER 5  - Mean B-factor                     : 0.0000
-HEADER 6  - Hydrophobicity Score              : 16.8148
-HEADER 7  - Polarity Score                    :    16
-HEADER 8  - Volume Score                      : 3.8889
-HEADER 9  - Real volume (approximation)       : 4956.8828
+HEADER 6  - Hydrophobicity Score              : 18.4643
+HEADER 7  - Polarity Score                    :    17
+HEADER 8  - Volume Score                      : 4.0000
+HEADER 9  - Real volume (approximation)       : 5738.3193
 HEADER 10 - Charge Score                      :     6
-HEADER 11 - Local hydrophobic density Score   : 13.4444
-HEADER 12 - Number of apolar alpha sphere     :    54
-HEADER 13 - Proportion of apolar alpha sphere : 0.2488
+HEADER 11 - Local hydrophobic density Score   : 13.3455
+HEADER 12 - Number of apolar alpha sphere     :    55
+HEADER 13 - Proportion of apolar alpha sphere : 0.2444
 ATOM      1    O STP     1      13.304  88.665  32.454    0.00     4.42
 ATOM      2    C STP     1       9.417  86.428  34.234    0.00     3.53
 ATOM      3    O STP     1      12.036  91.586  29.846    0.00     3.99
@@ -85,155 +85,163 @@ ATOM     64    C STP     1      10.093  87.611  33.467    0.00     4.07
 ATOM     65    C STP     1      10.538  87.926  33.379    0.00     4.35
 ATOM     66    O STP     1      33.888  49.647  16.687    0.00     6.03
 ATOM     67    O STP     1      17.468  87.092  29.886    0.00     3.61
-ATOM     68    O STP     1      33.220  49.873  17.122    0.00     5.53
-ATOM     69    C STP     1       9.423  86.425  34.239    0.00     3.53
-ATOM     70    C STP     1       9.363  86.402  34.268    0.00     3.50
-ATOM     71    O STP     1      17.156  90.553  34.548    0.00     4.74
-ATOM     72    O STP     1      18.977  88.996  36.323    0.00     3.80
-ATOM     73    O STP     1      18.801  90.804  35.327    0.00     4.97
-ATOM     74    O STP     1      18.268  89.945  34.975    0.00     4.55
-ATOM     75    O STP     1      18.868  89.208  35.945    0.00     4.00
-ATOM     76    O STP     1      18.065  88.657  35.595    0.00     3.63
-ATOM     77    O STP     1      18.379  89.193  35.362    0.00     4.09
-ATOM     78    O STP     1      18.882  87.605  27.239    0.00     3.92
-ATOM     79    O STP     1      13.300  94.652  30.063    0.00     5.74
-ATOM     80    O STP     1      13.169  88.280  31.543    0.00     3.79
-ATOM     81    C STP     1      12.965  87.866  31.201    0.00     3.42
-ATOM     82    O STP     1      17.206  86.955  29.975    0.00     3.57
-ATOM     83    O STP     1      17.313  86.932  29.848    0.00     3.60
-ATOM     84    O STP     1      17.260  86.826  29.857    0.00     3.56
-ATOM     85    O STP     1      17.647  86.903  29.170    0.00     3.65
-ATOM     86    O STP     1      17.446  86.914  29.625    0.00     3.62
-ATOM     87    O STP     1      17.540  86.349  29.071    0.00     3.57
-ATOM     88    O STP     1      17.825  86.147  28.464    0.00     3.66
-ATOM     89    O STP     1      17.638  86.291  28.817    0.00     3.62
-ATOM     90    O STP     1      17.589  86.200  28.737    0.00     3.57
-ATOM     91    C STP     1      17.310  86.348  29.432    0.00     3.47
-ATOM     92    O STP     1      24.622  40.674  10.795    0.00     4.05
-ATOM     93    C STP     1      27.005  49.985  17.993    0.00     3.82
-ATOM     94    C STP     1      26.839  50.582  18.014    0.00     3.60
-ATOM     95    C STP     1      27.676  50.218  16.945    0.00     4.09
-ATOM     96    C STP     1      26.991  50.900  17.679    0.00     3.59
-ATOM     97    O STP     1      30.592  49.040  16.768    0.00     4.84
-ATOM     98    O STP     1      31.112  44.097  16.205    0.00     5.49
-ATOM     99    O STP     1      26.685  48.719  17.768    0.00     3.95
-ATOM    100    C STP     1      27.314  49.434  17.751    0.00     4.15
-ATOM    101    O STP     1      30.711  48.752  16.393    0.00     5.04
-ATOM    102    O STP     1      31.020  47.339  15.614    0.00     5.44
-ATOM    103    O STP     1      29.111  49.193  16.737    0.00     4.56
-ATOM    104    O STP     1      27.150  48.349  16.835    0.00     4.29
-ATOM    105    O STP     1      28.085  46.923  16.028    0.00     4.46
-ATOM    106    O STP     1      29.429  38.000  16.814    0.00     3.95
-ATOM    107    O STP     1      25.337  41.857  10.796    0.00     3.65
-ATOM    108    C STP     1      10.851  87.154  34.207    0.00     4.06
-ATOM    109    C STP     1      10.692  87.013  34.265    0.00     3.95
-ATOM    110    O STP     1      11.818  86.568  34.068    0.00     3.81
-ATOM    111    C STP     1      12.318  85.510  34.106    0.00     3.44
-ATOM    112    O STP     1       5.545  90.375  43.119    0.00     4.74
-ATOM    113    C STP     1       4.561  89.333  40.639    0.00     3.85
-ATOM    114    C STP     1       4.611  89.401  40.637    0.00     3.86
-ATOM    115    C STP     1       6.032  91.564  41.830    0.00     5.21
-ATOM    116    C STP     1       6.186  90.504  39.052    0.00     3.61
-ATOM    117    C STP     1       6.160  90.509  39.113    0.00     3.63
-ATOM    118    O STP     1      17.990  86.008  28.210    0.00     3.70
-ATOM    119    O STP     1      18.006  86.098  28.176    0.00     3.73
-ATOM    120    O STP     1      19.521  87.572  27.205    0.00     4.19
-ATOM    121    O STP     1      19.240  87.483  27.521    0.00     4.22
-ATOM    122    O STP     1      18.718  87.116  27.484    0.00     3.98
-ATOM    123    O STP     1      18.711  87.054  27.742    0.00     4.02
-ATOM    124    O STP     1      19.118  87.451  27.484    0.00     4.20
-ATOM    125    O STP     1      19.138  87.454  27.544    0.00     4.22
-ATOM    126    O STP     1      17.547  86.179  28.768    0.00     3.54
-ATOM    127    O STP     1      24.404  40.531  10.860    0.00     3.87
-ATOM    128    O STP     1      24.678  40.696  10.870    0.00     4.10
-ATOM    129    O STP     1      25.061  40.721  10.992    0.00     4.29
-ATOM    130    C STP     1      34.434  54.099  24.046    0.00     5.83
-ATOM    131    C STP     1      34.785  54.066  24.214    0.00     6.17
-ATOM    132    O STP     1      30.243  49.144  18.082    0.00     3.84
-ATOM    133    O STP     1      33.629  50.117  17.900    0.00     5.37
-ATOM    134    C STP     1      32.643  53.327  21.021    0.00     3.69
-ATOM    135    O STP     1      33.259  50.367  13.555    0.00     5.25
-ATOM    136    O STP     1      32.796  52.509  13.407    0.00     3.99
-ATOM    137    O STP     1      31.179  49.730  10.161    0.00     4.05
-ATOM    138    C STP     1      25.397  48.219  17.846    0.00     3.48
-ATOM    139    C STP     1      25.657  48.105  17.477    0.00     3.55
-ATOM    140    O STP     1      32.744  47.500  12.564    0.00     5.68
-ATOM    141    O STP     1      32.680  48.711  11.135    0.00     5.22
-ATOM    142    O STP     1      30.293  34.983  19.208    0.00     5.09
-ATOM    143    C STP     1      30.515  37.558  12.012    0.00     5.68
-ATOM    144    O STP     1      28.816  38.796  12.429    0.00     4.55
-ATOM    145    O STP     1      25.694  40.137  11.519    0.00     4.25
-ATOM    146    O STP     1      25.745  40.188  11.663    0.00     4.25
-ATOM    147    O STP     1      30.778  40.864  18.244    0.00     5.65
-ATOM    148    O STP     1      29.300  41.260  18.522    0.00     4.72
-ATOM    149    O STP     1      29.435  42.951  17.876    0.00     4.50
-ATOM    150    O STP     1      17.364  91.328  34.163    0.00     5.47
-ATOM    151    O STP     1      17.378  91.256  34.191    0.00     5.43
-ATOM    152    O STP     1      17.444  91.177  34.269    0.00     5.37
-ATOM    153    O STP     1      17.348  91.074  34.310    0.00     5.25
-ATOM    154    O STP     1      30.062  47.686  12.765    0.00     3.67
-ATOM    155    C STP     1      26.323  48.692  15.710    0.00     3.43
-ATOM    156    O STP     1      30.408  47.380  15.676    0.00     5.15
-ATOM    157    O STP     1      28.125  47.095  15.991    0.00     4.51
-ATOM    158    C STP     1      27.417  50.537  16.276    0.00     3.74
-ATOM    159    C STP     1      27.373  50.707  16.089    0.00     3.59
-ATOM    160    C STP     1      27.302  48.395  16.701    0.00     4.37
-ATOM    161    C STP     1      27.841  49.832  16.849    0.00     4.30
-ATOM    162    C STP     1      28.558  49.429  16.774    0.00     4.43
-ATOM    163    C STP     1      27.865  49.337  16.994    0.00     4.49
-ATOM    164    O STP     1      28.735  49.235  16.785    0.00     4.53
-ATOM    165    C STP     1      31.288  55.409  23.269    0.00     3.49
-ATOM    166    O STP     1      32.312  48.943  10.498    0.00     4.81
-ATOM    167    O STP     1      34.237  48.223  11.050    0.00     6.07
-ATOM    168    O STP     1      24.685  41.731  11.638    0.00     4.16
-ATOM    169    O STP     1      23.857  42.701  11.472    0.00     3.56
-ATOM    170    O STP     1      28.622  41.347  18.970    0.00     4.24
-ATOM    171    O STP     1      28.182  41.101  20.281    0.00     3.62
-ATOM    172    C STP     1      24.517  43.394  13.603    0.00     3.46
-ATOM    173    C STP     1      24.414  43.155  13.231    0.00     3.58
-ATOM    174    O STP     1      27.454  47.131  15.066    0.00     3.72
-ATOM    175    O STP     1      25.046  43.340  13.819    0.00     3.59
-ATOM    176    C STP     1      24.700  43.363  13.625    0.00     3.53
-ATOM    177    O STP     1      28.073  46.895  16.026    0.00     4.44
-ATOM    178    O STP     1      28.133  46.815  16.042    0.00     4.43
-ATOM    179    O STP     1      30.376  42.824  16.523    0.00     5.68
-ATOM    180    O STP     1      30.365  42.854  16.522    0.00     5.67
-ATOM    181    O STP     1      30.061  42.491  17.173    0.00     5.36
-ATOM    182    O STP     1      29.539  42.849  17.699    0.00     4.70
-ATOM    183    O STP     1      29.681  42.794  17.547    0.00     4.87
-ATOM    184    O STP     1      28.734  41.753  18.363    0.00     4.47
-ATOM    185    O STP     1      27.985  42.238  18.956    0.00     3.70
-ATOM    186    O STP     1      28.539  41.757  18.517    0.00     4.33
-ATOM    187    O STP     1      29.507  42.806  17.744    0.00     4.69
-ATOM    188    O STP     1      29.791  42.296  17.519    0.00     5.14
-ATOM    189    O STP     1      25.552  40.651  11.800    0.00     4.24
-ATOM    190    O STP     1      25.702  41.429  12.209    0.00     4.09
-ATOM    191    O STP     1      25.788  41.400  12.282    0.00     4.07
-ATOM    192    O STP     1      25.003  41.310  11.497    0.00     4.32
-ATOM    193    O STP     1      25.002  41.301  11.494    0.00     4.32
-ATOM    194    O STP     1      24.966  42.497  12.680    0.00     3.75
-ATOM    195    O STP     1      24.684  41.731  11.659    0.00     4.16
-ATOM    196    O STP     1      24.715  41.678  11.631    0.00     4.18
-ATOM    197    O STP     1      24.813  41.386  11.520    0.00     4.25
-ATOM    198    O STP     1      24.837  43.023  13.213    0.00     3.66
-ATOM    199    O STP     1      24.938  43.175  13.547    0.00     3.62
-ATOM    200    O STP     1      24.059  42.452  12.156    0.00     3.85
-ATOM    201    O STP     1      24.523  43.068  13.102    0.00     3.64
-ATOM    202    O STP     1      23.664  42.606  12.414    0.00     3.66
-ATOM    203    O STP     1      24.396  43.128  13.200    0.00     3.58
-ATOM    204    O STP     1      24.435  43.138  13.214    0.00     3.59
-ATOM    205    O STP     1      24.518  43.086  13.129    0.00     3.63
-ATOM    206    O STP     1      24.575  43.157  13.291    0.00     3.61
-ATOM    207    C STP     1      31.063  55.664  23.330    0.00     3.47
-ATOM    208    O STP     1      33.721  54.466  25.554    0.00     5.34
-ATOM    209    O STP     1      25.197  43.355  14.014    0.00     3.58
-ATOM    210    O STP     1      25.635  43.546  14.505    0.00     3.53
-ATOM    211    O STP     1      25.403  43.098  14.044    0.00     3.59
-ATOM    212    O STP     1      26.324  42.901  14.728    0.00     3.68
-ATOM    213    O STP     1      26.006  42.758  14.370    0.00     3.65
-ATOM    214    O STP     1      28.626  39.926  18.156    0.00     3.63
-ATOM    215    O STP     1      30.514  38.191  17.400    0.00     5.05
-ATOM    216    O STP     1      29.885  37.934  17.493    0.00     4.48
-ATOM    217    O STP     1      29.459  38.005  16.840    0.00     3.98
+ATOM     68    O STP     1      26.368  39.013   7.356    0.00     4.59
+ATOM     69    O STP     1      33.220  49.873  17.122    0.00     5.53
+ATOM     70    O STP     1      30.363  38.669  24.413    0.00     5.89
+ATOM     71    C STP     1       9.423  86.425  34.239    0.00     3.53
+ATOM     72    C STP     1       9.363  86.402  34.268    0.00     3.50
+ATOM     73    O STP     1      17.156  90.553  34.548    0.00     4.74
+ATOM     74    O STP     1      18.977  88.996  36.323    0.00     3.80
+ATOM     75    O STP     1      18.801  90.804  35.327    0.00     4.97
+ATOM     76    O STP     1      18.268  89.945  34.975    0.00     4.55
+ATOM     77    O STP     1      18.868  89.208  35.945    0.00     4.00
+ATOM     78    O STP     1      18.065  88.657  35.595    0.00     3.63
+ATOM     79    O STP     1      18.379  89.193  35.362    0.00     4.09
+ATOM     80    O STP     1      18.882  87.605  27.239    0.00     3.92
+ATOM     81    O STP     1      13.300  94.652  30.063    0.00     5.74
+ATOM     82    O STP     1      13.169  88.280  31.543    0.00     3.79
+ATOM     83    C STP     1      12.965  87.866  31.201    0.00     3.42
+ATOM     84    O STP     1      17.206  86.955  29.975    0.00     3.57
+ATOM     85    O STP     1      17.313  86.932  29.848    0.00     3.60
+ATOM     86    O STP     1      17.260  86.826  29.857    0.00     3.56
+ATOM     87    O STP     1      17.647  86.903  29.170    0.00     3.65
+ATOM     88    O STP     1      17.446  86.914  29.625    0.00     3.62
+ATOM     89    O STP     1      17.540  86.349  29.071    0.00     3.57
+ATOM     90    O STP     1      17.825  86.147  28.464    0.00     3.66
+ATOM     91    O STP     1      17.638  86.291  28.817    0.00     3.62
+ATOM     92    O STP     1      17.589  86.200  28.737    0.00     3.57
+ATOM     93    C STP     1      17.310  86.348  29.432    0.00     3.47
+ATOM     94    O STP     1      24.622  40.674  10.795    0.00     4.05
+ATOM     95    C STP     1      27.005  49.985  17.993    0.00     3.82
+ATOM     96    C STP     1      26.839  50.582  18.014    0.00     3.60
+ATOM     97    C STP     1      27.676  50.218  16.945    0.00     4.09
+ATOM     98    C STP     1      26.991  50.900  17.679    0.00     3.59
+ATOM     99    O STP     1      30.592  49.040  16.768    0.00     4.84
+ATOM    100    O STP     1      31.112  44.097  16.205    0.00     5.49
+ATOM    101    O STP     1      26.685  48.719  17.768    0.00     3.95
+ATOM    102    C STP     1      27.314  49.434  17.751    0.00     4.15
+ATOM    103    O STP     1      30.711  48.752  16.393    0.00     5.04
+ATOM    104    O STP     1      31.020  47.339  15.614    0.00     5.44
+ATOM    105    O STP     1      29.111  49.193  16.737    0.00     4.56
+ATOM    106    O STP     1      27.150  48.349  16.835    0.00     4.29
+ATOM    107    O STP     1      28.085  46.923  16.028    0.00     4.46
+ATOM    108    O STP     1      29.429  38.000  16.814    0.00     3.95
+ATOM    109    O STP     1      25.337  41.857  10.796    0.00     3.65
+ATOM    110    C STP     1      26.549  39.030   7.512    0.00     4.64
+ATOM    111    O STP     1      25.458  40.233   9.519    0.00     3.99
+ATOM    112    O STP     1      26.179  39.423   7.970    0.00     4.35
+ATOM    113    O STP     1      25.736  40.004   8.551    0.00     4.07
+ATOM    114    C STP     1      10.851  87.154  34.207    0.00     4.06
+ATOM    115    C STP     1      10.692  87.013  34.265    0.00     3.95
+ATOM    116    O STP     1      11.818  86.568  34.068    0.00     3.81
+ATOM    117    C STP     1      12.318  85.510  34.106    0.00     3.44
+ATOM    118    O STP     1       5.545  90.375  43.119    0.00     4.74
+ATOM    119    C STP     1       4.561  89.333  40.639    0.00     3.85
+ATOM    120    C STP     1       4.611  89.401  40.637    0.00     3.86
+ATOM    121    C STP     1       6.032  91.564  41.830    0.00     5.21
+ATOM    122    C STP     1       6.186  90.504  39.052    0.00     3.61
+ATOM    123    C STP     1       6.160  90.509  39.113    0.00     3.63
+ATOM    124    O STP     1      17.990  86.008  28.210    0.00     3.70
+ATOM    125    O STP     1      18.006  86.098  28.176    0.00     3.73
+ATOM    126    O STP     1      19.521  87.572  27.205    0.00     4.19
+ATOM    127    O STP     1      19.240  87.483  27.521    0.00     4.22
+ATOM    128    O STP     1      18.718  87.116  27.484    0.00     3.98
+ATOM    129    O STP     1      18.711  87.054  27.742    0.00     4.02
+ATOM    130    O STP     1      19.118  87.451  27.484    0.00     4.20
+ATOM    131    O STP     1      19.138  87.454  27.544    0.00     4.22
+ATOM    132    O STP     1      17.547  86.179  28.768    0.00     3.54
+ATOM    133    O STP     1      24.404  40.531  10.860    0.00     3.87
+ATOM    134    O STP     1      24.678  40.696  10.870    0.00     4.10
+ATOM    135    O STP     1      25.061  40.721  10.992    0.00     4.29
+ATOM    136    C STP     1      34.434  54.099  24.046    0.00     5.83
+ATOM    137    C STP     1      34.785  54.066  24.214    0.00     6.17
+ATOM    138    O STP     1      30.243  49.144  18.082    0.00     3.84
+ATOM    139    O STP     1      33.629  50.117  17.900    0.00     5.37
+ATOM    140    C STP     1      32.643  53.327  21.021    0.00     3.69
+ATOM    141    O STP     1      33.259  50.367  13.555    0.00     5.25
+ATOM    142    O STP     1      32.796  52.509  13.407    0.00     3.99
+ATOM    143    O STP     1      31.179  49.730  10.161    0.00     4.05
+ATOM    144    C STP     1      25.397  48.219  17.846    0.00     3.48
+ATOM    145    C STP     1      25.657  48.105  17.477    0.00     3.55
+ATOM    146    O STP     1      32.744  47.500  12.564    0.00     5.68
+ATOM    147    O STP     1      32.680  48.711  11.135    0.00     5.22
+ATOM    148    O STP     1      30.293  34.983  19.208    0.00     5.09
+ATOM    149    C STP     1      30.515  37.558  12.012    0.00     5.68
+ATOM    150    O STP     1      28.816  38.796  12.429    0.00     4.55
+ATOM    151    O STP     1      25.694  40.137  11.519    0.00     4.25
+ATOM    152    O STP     1      25.745  40.188  11.663    0.00     4.25
+ATOM    153    O STP     1      30.778  40.864  18.244    0.00     5.65
+ATOM    154    O STP     1      29.300  41.260  18.522    0.00     4.72
+ATOM    155    O STP     1      30.155  39.400  23.865    0.00     5.50
+ATOM    156    O STP     1      29.435  42.951  17.876    0.00     4.50
+ATOM    157    O STP     1      17.364  91.328  34.163    0.00     5.47
+ATOM    158    O STP     1      17.378  91.256  34.191    0.00     5.43
+ATOM    159    O STP     1      17.444  91.177  34.269    0.00     5.37
+ATOM    160    O STP     1      17.348  91.074  34.310    0.00     5.25
+ATOM    161    O STP     1      30.062  47.686  12.765    0.00     3.67
+ATOM    162    C STP     1      26.323  48.692  15.710    0.00     3.43
+ATOM    163    O STP     1      30.408  47.380  15.676    0.00     5.15
+ATOM    164    O STP     1      28.125  47.095  15.991    0.00     4.51
+ATOM    165    C STP     1      27.417  50.537  16.276    0.00     3.74
+ATOM    166    C STP     1      27.373  50.707  16.089    0.00     3.59
+ATOM    167    C STP     1      27.302  48.395  16.701    0.00     4.37
+ATOM    168    C STP     1      27.841  49.832  16.849    0.00     4.30
+ATOM    169    C STP     1      28.558  49.429  16.774    0.00     4.43
+ATOM    170    C STP     1      27.865  49.337  16.994    0.00     4.49
+ATOM    171    O STP     1      28.735  49.235  16.785    0.00     4.53
+ATOM    172    O STP     1      30.286  38.810  24.532    0.00     5.75
+ATOM    173    C STP     1      31.288  55.409  23.269    0.00     3.49
+ATOM    174    O STP     1      32.312  48.943  10.498    0.00     4.81
+ATOM    175    O STP     1      34.237  48.223  11.050    0.00     6.07
+ATOM    176    O STP     1      24.685  41.731  11.638    0.00     4.16
+ATOM    177    O STP     1      23.857  42.701  11.472    0.00     3.56
+ATOM    178    O STP     1      28.622  41.347  18.970    0.00     4.24
+ATOM    179    O STP     1      28.182  41.101  20.281    0.00     3.62
+ATOM    180    C STP     1      24.517  43.394  13.603    0.00     3.46
+ATOM    181    C STP     1      24.414  43.155  13.231    0.00     3.58
+ATOM    182    O STP     1      27.454  47.131  15.066    0.00     3.72
+ATOM    183    O STP     1      25.046  43.340  13.819    0.00     3.59
+ATOM    184    C STP     1      24.700  43.363  13.625    0.00     3.53
+ATOM    185    O STP     1      28.073  46.895  16.026    0.00     4.44
+ATOM    186    O STP     1      28.133  46.815  16.042    0.00     4.43
+ATOM    187    O STP     1      30.376  42.824  16.523    0.00     5.68
+ATOM    188    O STP     1      30.365  42.854  16.522    0.00     5.67
+ATOM    189    O STP     1      30.061  42.491  17.173    0.00     5.36
+ATOM    190    O STP     1      29.539  42.849  17.699    0.00     4.70
+ATOM    191    O STP     1      29.681  42.794  17.547    0.00     4.87
+ATOM    192    O STP     1      28.734  41.753  18.363    0.00     4.47
+ATOM    193    O STP     1      27.985  42.238  18.956    0.00     3.70
+ATOM    194    O STP     1      28.539  41.757  18.517    0.00     4.33
+ATOM    195    O STP     1      29.507  42.806  17.744    0.00     4.69
+ATOM    196    O STP     1      29.791  42.296  17.519    0.00     5.14
+ATOM    197    O STP     1      25.552  40.651  11.800    0.00     4.24
+ATOM    198    O STP     1      25.702  41.429  12.209    0.00     4.09
+ATOM    199    O STP     1      25.788  41.400  12.282    0.00     4.07
+ATOM    200    O STP     1      25.003  41.310  11.497    0.00     4.32
+ATOM    201    O STP     1      25.002  41.301  11.494    0.00     4.32
+ATOM    202    O STP     1      24.966  42.497  12.680    0.00     3.75
+ATOM    203    O STP     1      24.684  41.731  11.659    0.00     4.16
+ATOM    204    O STP     1      24.715  41.678  11.631    0.00     4.18
+ATOM    205    O STP     1      24.813  41.386  11.520    0.00     4.25
+ATOM    206    O STP     1      24.837  43.023  13.213    0.00     3.66
+ATOM    207    O STP     1      24.938  43.175  13.547    0.00     3.62
+ATOM    208    O STP     1      24.059  42.452  12.156    0.00     3.85
+ATOM    209    O STP     1      24.523  43.068  13.102    0.00     3.64
+ATOM    210    O STP     1      23.664  42.606  12.414    0.00     3.66
+ATOM    211    O STP     1      24.396  43.128  13.200    0.00     3.58
+ATOM    212    O STP     1      24.435  43.138  13.214    0.00     3.59
+ATOM    213    O STP     1      24.518  43.086  13.129    0.00     3.63
+ATOM    214    O STP     1      24.575  43.157  13.291    0.00     3.61
+ATOM    215    C STP     1      31.063  55.664  23.330    0.00     3.47
+ATOM    216    O STP     1      33.721  54.466  25.554    0.00     5.34
+ATOM    217    O STP     1      25.197  43.355  14.014    0.00     3.58
+ATOM    218    O STP     1      25.635  43.546  14.505    0.00     3.53
+ATOM    219    O STP     1      25.403  43.098  14.044    0.00     3.59
+ATOM    220    O STP     1      26.324  42.901  14.728    0.00     3.68
+ATOM    221    O STP     1      26.006  42.758  14.370    0.00     3.65
+ATOM    222    O STP     1      28.626  39.926  18.156    0.00     3.63
+ATOM    223    O STP     1      30.514  38.191  17.400    0.00     5.05
+ATOM    224    O STP     1      29.885  37.934  17.493    0.00     4.48
+ATOM    225    O STP     1      29.459  38.005  16.840    0.00     3.98
 TER
 END

tests/reference_output/3VI4_out/pockets/pocket100_atm.cif

@@ -15,7 +15,7 @@ Information about the pocket   100:
 6  - Hydrophobicity Score              : -9.1111
 7  - Polarity Score                    :     4
 8  - Amino Acid based volume Score     : 3.7778
-9  - Pocket volume (Monte Carlo)       : 311.2629
+9  - Pocket volume (Monte Carlo)       : 310.5818
 10  -Pocket volume (convex hull)       : 23.0368
 11 - Charge Score                      :     1
 12 - Local hydrophobic density Score   : 12.0000

tests/reference_output/3VI4_out/pockets/pocket100_vert.pqr

@@ -13,7 +13,7 @@ HEADER 5  - Mean B-factor                     : 0.4798
 HEADER 6  - Hydrophobicity Score              : -9.1111
 HEADER 7  - Polarity Score                    :     4
 HEADER 8  - Volume Score                      : 3.7778
-HEADER 9  - Real volume (approximation)       : 311.2629
+HEADER 9  - Real volume (approximation)       : 310.5818
 HEADER 10 - Charge Score                      :     1
 HEADER 11 - Local hydrophobic density Score   : 12.0000
 HEADER 12 - Number of apolar alpha sphere     :    13

tests/reference_output/3VI4_out/pockets/pocket101_atm.cif

@@ -15,7 +15,7 @@ Information about the pocket   101:
 6  - Hydrophobicity Score              : 1.5455
 7  - Polarity Score                    :     8
 8  - Amino Acid based volume Score     : 3.8182
-9  - Pocket volume (Monte Carlo)       : 437.7543
+9  - Pocket volume (Monte Carlo)       : 435.1609
 10  -Pocket volume (convex hull)       : 50.2388
 11 - Charge Score                      :     0
 12 - Local hydrophobic density Score   : 3.0000
@@ -39,27 +39,27 @@ _atom_site.Cartn_z
 _atom_site.occupancy
 _atom_site.pdbx_formal_charge
 _atom_site.auth_asym_id
-ATOM    17677    O    O .  THR   F .   30 ?  -52.637 -33.822  -4.105 -0.40  0   F
-ATOM    17881    C   CA .  GLY   F .   54 ?  -52.321 -29.162  -1.309  0.00  0   F
-ATOM    17884    N    N .  SER   F .   55 ?  -54.587 -28.344  -1.337  0.00  0   F
-ATOM    17872    C  CD2 .  LEU   F .   52 ?  -57.139 -32.118  -3.703  0.00  0   F
-ATOM    17870    C   CG .  LEU   F .   52 ?  -56.402 -32.713  -2.512  0.00  0   F
-ATOM    17680    C  CG2 .  THR   F .   30 ?  -49.551 -31.699  -2.081  0.00  0   F
-ATOM    17678    C   CB .  THR   F .   30 ?  -50.220 -32.477  -3.191  0.00  0   F
-ATOM    17679    O  OG1 .  THR   F .   30 ?  -49.279 -32.680  -4.239 -1.88  0   F
+ATOM    17677    O    O .  THR   H .   30 ?  -52.637 -33.822  -4.105 -0.40  0   H
+ATOM    17881    C   CA .  GLY   H .   54 ?  -52.321 -29.162  -1.309  0.00  0   H
+ATOM    17884    N    N .  SER   H .   55 ?  -54.587 -28.344  -1.337  0.00  0   H
+ATOM    17872    C  CD2 .  LEU   H .   52 ?  -57.139 -32.118  -3.703  0.00  0   H
+ATOM    17870    C   CG .  LEU   H .   52 ?  -56.402 -32.713  -2.512  0.00  0   H
+ATOM    17680    C  CG2 .  THR   H .   30 ?  -49.551 -31.699  -2.081  0.00  0   H
+ATOM    17678    C   CB .  THR   H .   30 ?  -50.220 -32.477  -3.191  0.00  0   H
+ATOM    17679    O  OG1 .  THR   H .   30 ?  -49.279 -32.680  -4.239 -1.88  0   H
 ATOM    13194    N   NZ .  LYS   D .  116 ?  -55.107 -29.089  -9.088 -2.35  0   D
-ATOM    17888    C   CB .  SER   F .   55 ?  -56.852 -27.995  -2.041  0.00  0   F
-ATOM    17903    C  CE2 .  TYR   F .   57 ?  -59.740 -28.055  -4.247  0.00  0   F
+ATOM    17888    C   CB .  SER   H .   55 ?  -56.852 -27.995  -2.041  0.00  0   H
+ATOM    17903    C  CE2 .  TYR   H .   57 ?  -59.740 -28.055  -4.247  0.00  0   H
 ATOM    15419    O  OE2 .  GLU   D .  403 ?  -54.096 -26.103  -9.993  0.00  0   D
-ATOM    17885    C   CA .  SER   F .   55 ?  -55.671 -27.386  -1.310  0.00  0   F
+ATOM    17885    C   CA .  SER   H .   55 ?  -55.671 -27.386  -1.310  0.00  0   H
 ATOM    12875    N    N .  ARG   D .   78 ?  -60.377 -30.303  -7.599  0.00  0   D
 ATOM    15402    O    O .  GLY   D .  401 ?  -52.580 -30.729  -9.617  0.00  0   D
-ATOM    17882    C    C .  GLY   F .   54 ?  -53.320 -28.034  -1.091  0.00  0   F
+ATOM    17882    C    C .  GLY   H .   54 ?  -53.320 -28.034  -1.091  0.00  0   H
 ATOM    15416    C   CG .  GLU   D .  403 ?  -52.230 -27.156 -11.039  0.00  0   D
 ATOM    12884    N  NH1 .  ARG   D .   78 ?  -55.708 -34.552  -6.275 -2.19  0   D
 ATOM    15400    C   CA .  GLY   D .  401 ?  -53.294 -32.992  -9.696  0.00  0   D
 ATOM    15401    C    C .  GLY   D .  401 ?  -52.253 -31.906  -9.782  0.00  0   D
-ATOM    17905    O   OH .  TYR   F .   57 ?  -60.080 -25.871  -5.220  0.00  0   F
+ATOM    17905    O   OH .  TYR   H .   57 ?  -60.080 -25.871  -5.220  0.00  0   H
 ATOM    12871    C   CB .  ASN   D .   77 ?  -60.289 -27.204  -8.363  0.00  0   D
 ATOM    12881    C   CD .  ARG   D .   78 ?  -57.822 -33.318  -7.660  0.00  0   D
 ATOM    15409    O  OD1 .  ASP   D .  402 ?  -48.489 -32.553  -8.164 -1.88  0   D

tests/reference_output/3VI4_out/pockets/pocket101_vert.pqr

@@ -13,7 +13,7 @@ HEADER 5  - Mean B-factor                     : 0.0836
 HEADER 6  - Hydrophobicity Score              : 1.5455
 HEADER 7  - Polarity Score                    :     8
 HEADER 8  - Volume Score                      : 3.8182
-HEADER 9  - Real volume (approximation)       : 437.7543
+HEADER 9  - Real volume (approximation)       : 435.1609
 HEADER 10 - Charge Score                      :     0
 HEADER 11 - Local hydrophobic density Score   : 3.0000
 HEADER 12 - Number of apolar alpha sphere     :     4

tests/reference_output/3VI4_out/pockets/pocket102_atm.cif

@@ -15,7 +15,7 @@ Information about the pocket   102:
 6  - Hydrophobicity Score              : 4.3333
 7  - Polarity Score                    :     9
 8  - Amino Acid based volume Score     : 4.7500
-9  - Pocket volume (Monte Carlo)       : 511.1440
+9  - Pocket volume (Monte Carlo)       : 512.9062
 10  -Pocket volume (convex hull)       : 46.7281
 11 - Charge Score                      :     2
 12 - Local hydrophobic density Score   : 10.9231

tests/reference_output/3VI4_out/pockets/pocket102_vert.pqr

@@ -13,7 +13,7 @@ HEADER 5  - Mean B-factor                     : 0.2953
 HEADER 6  - Hydrophobicity Score              : 4.3333
 HEADER 7  - Polarity Score                    :     9
 HEADER 8  - Volume Score                      : 4.7500
-HEADER 9  - Real volume (approximation)       : 511.1440
+HEADER 9  - Real volume (approximation)       : 512.9062
 HEADER 10 - Charge Score                      :     2
 HEADER 11 - Local hydrophobic density Score   : 10.9231
 HEADER 12 - Number of apolar alpha sphere     :    13

tests/reference_output/3VI4_out/pockets/pocket103_atm.cif

@@ -15,7 +15,7 @@ Information about the pocket   103:
 6  - Hydrophobicity Score              : 33.0000
 7  - Polarity Score                    :     3
 8  - Amino Acid based volume Score     : 4.0000
-9  - Pocket volume (Monte Carlo)       : 408.1248
+9  - Pocket volume (Monte Carlo)       : 405.8968
 10  -Pocket volume (convex hull)       : 30.6056
 11 - Charge Score                      :     0
 12 - Local hydrophobic density Score   : 11.8571

tests/reference_output/3VI4_out/pockets/pocket103_vert.pqr

@@ -13,7 +13,7 @@ HEADER 5  - Mean B-factor                     : 0.3957
 HEADER 6  - Hydrophobicity Score              : 33.0000
 HEADER 7  - Polarity Score                    :     3
 HEADER 8  - Volume Score                      : 4.0000
-HEADER 9  - Real volume (approximation)       : 408.1248
+HEADER 9  - Real volume (approximation)       : 405.8968
 HEADER 10 - Charge Score                      :     0
 HEADER 11 - Local hydrophobic density Score   : 11.8571
 HEADER 12 - Number of apolar alpha sphere     :    14

tests/reference_output/3VI4_out/pockets/pocket104_atm.cif

@@ -15,7 +15,7 @@ Information about the pocket   104:
 6  - Hydrophobicity Score              : 23.4000
 7  - Polarity Score                    :     2
 8  - Amino Acid based volume Score     : 3.2000
-9  - Pocket volume (Monte Carlo)       : 174.9672
+9  - Pocket volume (Monte Carlo)       : 174.2773
 10  -Pocket volume (convex hull)       : 1.7370
 11 - Charge Score                      :     0
 12 - Local hydrophobic density Score   : 6.0000

tests/reference_output/3VI4_out/pockets/pocket104_vert.pqr

@@ -13,7 +13,7 @@ HEADER 5  - Mean B-factor                     : 0.2803
 HEADER 6  - Hydrophobicity Score              : 23.4000
 HEADER 7  - Polarity Score                    :     2
 HEADER 8  - Volume Score                      : 3.2000
-HEADER 9  - Real volume (approximation)       : 174.9672
+HEADER 9  - Real volume (approximation)       : 174.2773
 HEADER 10 - Charge Score                      :     0
 HEADER 11 - Local hydrophobic density Score   : 6.0000
 HEADER 12 - Number of apolar alpha sphere     :     7

tests/reference_output/3VI4_out/pockets/pocket105_atm.cif

@@ -15,7 +15,7 @@ Information about the pocket   105:
 6  - Hydrophobicity Score              : -17.1429
 7  - Polarity Score                    :     7
 8  - Amino Acid based volume Score     : 4.5714
-9  - Pocket volume (Monte Carlo)       : 340.4088
+9  - Pocket volume (Monte Carlo)       : 336.3605
 10  -Pocket volume (convex hull)       : 22.7726
 11 - Charge Score                      :     1
 12 - Local hydrophobic density Score   : 3.0000

tests/reference_output/3VI4_out/pockets/pocket105_vert.pqr

@@ -13,7 +13,7 @@ HEADER 5  - Mean B-factor                     : 0.2744
 HEADER 6  - Hydrophobicity Score              : -17.1429
 HEADER 7  - Polarity Score                    :     7
 HEADER 8  - Volume Score                      : 4.5714
-HEADER 9  - Real volume (approximation)       : 340.4088
+HEADER 9  - Real volume (approximation)       : 336.3605
 HEADER 10 - Charge Score                      :     1
 HEADER 11 - Local hydrophobic density Score   : 3.0000
 HEADER 12 - Number of apolar alpha sphere     :     4

tests/reference_output/3VI4_out/pockets/pocket106_atm.cif

@@ -15,7 +15,7 @@ Information about the pocket   106:
 6  - Hydrophobicity Score              : 50.5714
 7  - Polarity Score                    :     3
 8  - Amino Acid based volume Score     : 3.8571
-9  - Pocket volume (Monte Carlo)       : 126.8368
+9  - Pocket volume (Monte Carlo)       : 125.3750
 10  -Pocket volume (convex hull)       : 1.7687
 11 - Charge Score                      :     0
 12 - Local hydrophobic density Score   : 6.0000
@@ -39,17 +39,17 @@ _atom_site.Cartn_z
 _atom_site.occupancy
 _atom_site.pdbx_formal_charge
 _atom_site.auth_asym_id
-ATOM    18706    O    O .  LEU   F .  164 ?  -44.196 -70.373  28.776 -1.07  0   F
-ATOM    18663    O  OG1 .  THR   F .  158 ?  -43.218 -63.423  28.849 -5.09  0   F
-ATOM    18694    C   CA .  GLY   F .  162 ?  -40.106 -67.515  28.240  0.00  0   F
-ATOM    18715    C   CB .  SER   F .  165 ?  -44.337 -70.268  25.265  0.00  0   F
-ATOM    18665    N    N .  TRP   F .  159 ?  -44.435 -66.719  31.226  0.00  0   F
-ATOM    18733    C  CG2 .  VAL   F .  168 ?  -48.420 -70.232  28.312  0.00  0   F
-ATOM    18671    C  CD1 .  TRP   F .  159 ?  -47.791 -67.852  31.462  0.00  0   F
-ATOM    18714    O    O .  SER   F .  165 ?  -47.350 -70.972  25.224  0.00  0   F
-ATOM    18712    C   CA .  SER   F .  165 ?  -45.207 -71.003  26.292  0.00  0   F
-ATOM    18732    C  CG1 .  VAL   F .  168 ?  -49.763 -68.146  28.385  0.00  0   F
-ATOM    18654    O    O .  VAL   F .  157 ?  -46.916 -63.352  29.360 -1.21  0   F
-ATOM    18659    C   CA .  THR   F .  158 ?  -44.601 -64.361  30.625  0.00  0   F
-ATOM    18731    C   CB .  VAL   F .  168 ?  -49.615 -69.504  27.714  0.00  0   F
+ATOM    18706    O    O .  LEU   H .  164 ?  -44.196 -70.373  28.776 -1.07  0   H
+ATOM    18663    O  OG1 .  THR   H .  158 ?  -43.218 -63.423  28.849 -5.09  0   H
+ATOM    18694    C   CA .  GLY   H .  162 ?  -40.106 -67.515  28.240  0.00  0   H
+ATOM    18715    C   CB .  SER   H .  165 ?  -44.337 -70.268  25.265  0.00  0   H
+ATOM    18665    N    N .  TRP   H .  159 ?  -44.435 -66.719  31.226  0.00  0   H
+ATOM    18733    C  CG2 .  VAL   H .  168 ?  -48.420 -70.232  28.312  0.00  0   H
+ATOM    18671    C  CD1 .  TRP   H .  159 ?  -47.791 -67.852  31.462  0.00  0   H
+ATOM    18714    O    O .  SER   H .  165 ?  -47.350 -70.972  25.224  0.00  0   H
+ATOM    18712    C   CA .  SER   H .  165 ?  -45.207 -71.003  26.292  0.00  0   H
+ATOM    18732    C  CG1 .  VAL   H .  168 ?  -49.763 -68.146  28.385  0.00  0   H
+ATOM    18654    O    O .  VAL   H .  157 ?  -46.916 -63.352  29.360 -1.21  0   H
+ATOM    18659    C   CA .  THR   H .  158 ?  -44.601 -64.361  30.625  0.00  0   H
+ATOM    18731    C   CB .  VAL   H .  168 ?  -49.615 -69.504  27.714  0.00  0   H
 # 

tests/reference_output/3VI4_out/pockets/pocket106_vert.pqr

@@ -13,7 +13,7 @@ HEADER 5  - Mean B-factor                     : 0.2315
 HEADER 6  - Hydrophobicity Score              : 50.5714
 HEADER 7  - Polarity Score                    :     3
 HEADER 8  - Volume Score                      : 3.8571
-HEADER 9  - Real volume (approximation)       : 126.8368
+HEADER 9  - Real volume (approximation)       : 125.3750
 HEADER 10 - Charge Score                      :     0
 HEADER 11 - Local hydrophobic density Score   : 6.0000
 HEADER 12 - Number of apolar alpha sphere     :     7

tests/reference_output/3VI4_out/pockets/pocket107_atm.cif

@@ -15,7 +15,7 @@ Information about the pocket   107:
 6  - Hydrophobicity Score              : 3.5455
 7  - Polarity Score                    :     8
 8  - Amino Acid based volume Score     : 3.3636
-9  - Pocket volume (Monte Carlo)       : 395.0145
+9  - Pocket volume (Monte Carlo)       : 383.6299
 10  -Pocket volume (convex hull)       : 27.1766
 11 - Charge Score                      :     0
 12 - Local hydrophobic density Score   : 2.0000

tests/reference_output/3VI4_out/pockets/pocket107_vert.pqr

@@ -13,7 +13,7 @@ HEADER 5  - Mean B-factor                     : 0.1316
 HEADER 6  - Hydrophobicity Score              : 3.5455
 HEADER 7  - Polarity Score                    :     8
 HEADER 8  - Volume Score                      : 3.3636
-HEADER 9  - Real volume (approximation)       : 395.0145
+HEADER 9  - Real volume (approximation)       : 383.6299
 HEADER 10 - Charge Score                      :     0
 HEADER 11 - Local hydrophobic density Score   : 2.0000
 HEADER 12 - Number of apolar alpha sphere     :     3

tests/reference_output/3VI4_out/pockets/pocket108_atm.cif

@@ -15,7 +15,7 @@ Information about the pocket   108:
 6  - Hydrophobicity Score              : -20.7143
 7  - Polarity Score                    :     6
 8  - Amino Acid based volume Score     : 4.1429
-9  - Pocket volume (Monte Carlo)       : 184.0723
+9  - Pocket volume (Monte Carlo)       : 185.1816
 10  -Pocket volume (convex hull)       : 3.7328
 11 - Charge Score                      :     2
 12 - Local hydrophobic density Score   : 4.0000

tests/reference_output/3VI4_out/pockets/pocket108_vert.pqr

@@ -13,7 +13,7 @@ HEADER 5  - Mean B-factor                     : 0.3888
 HEADER 6  - Hydrophobicity Score              : -20.7143
 HEADER 7  - Polarity Score                    :     6
 HEADER 8  - Volume Score                      : 4.1429
-HEADER 9  - Real volume (approximation)       : 184.0723
+HEADER 9  - Real volume (approximation)       : 185.1816
 HEADER 10 - Charge Score                      :     2
 HEADER 11 - Local hydrophobic density Score   : 4.0000
 HEADER 12 - Number of apolar alpha sphere     :     5

tests/reference_output/3VI4_out/pockets/pocket109_atm.cif

@@ -15,7 +15,7 @@ Information about the pocket   109:
 6  - Hydrophobicity Score              : 24.6667
 7  - Polarity Score                    :     3
 8  - Amino Acid based volume Score     : 3.3333
-9  - Pocket volume (Monte Carlo)       : 247.6693
+9  - Pocket volume (Monte Carlo)       : 242.3332
 10  -Pocket volume (convex hull)       : 5.0058
 11 - Charge Score                      :     0
 12 - Local hydrophobic density Score   : 8.0000
@@ -39,18 +39,18 @@ _atom_site.Cartn_z
 _atom_site.occupancy
 _atom_site.pdbx_formal_charge
 _atom_site.auth_asym_id
-ATOM    17025    C  CD2 .  LEU   E .  165 ?  -66.251 -56.454  34.125  0.00  0   E
-ATOM    17023    C   CG .  LEU   E .  165 ?  -65.372 -56.932  35.276  0.00  0   E
-ATOM    17002    O    O .  ASN   E .  162 ?  -70.749 -57.245  39.009 -0.14  0   E
-ATOM    17014    O    O .  VAL   E .  164 ?  -68.166 -58.504  36.036 -0.95  0   E
-ATOM    17010    O    O .  GLY   E .  163 ?  -66.841 -59.260  39.999 -1.07  0   E
-ATOM    17024    C  CD1 .  LEU   E .  165 ?  -64.254 -55.932  35.504  0.00  0   E
-ATOM    18797    N  NE2 .  GLN   F .  176 ?  -62.293 -56.470  39.498 -0.84  0   F
-ATOM    18792    O    O .  GLN   F .  176 ?  -64.396 -51.488  37.035  0.00  0   F
-ATOM    17008    C   CA .  GLY   E .  163 ?  -68.735 -58.000  40.718  0.00  0   E
-ATOM    17009    C    C .  GLY   E .  163 ?  -68.001 -58.906  39.760  0.00  0   E
-ATOM    18794    C   CG .  GLN   F .  176 ?  -62.371 -54.451  38.162  0.00  0   F
-ATOM    17179    C   CB .  THR   E .  185 ?  -63.771 -58.536  42.126  0.00  0   E
-ATOM    17178    O    O .  THR   E .  185 ?  -66.416 -58.298  43.574  0.00  0   E
-ATOM    17181    C  CG2 .  THR   E .  185 ?  -62.726 -57.936  43.060  0.00  0   E
+ATOM    17025    C  CD2 .  LEU   L .  165 ?  -66.251 -56.454  34.125  0.00  0   L
+ATOM    17023    C   CG .  LEU   L .  165 ?  -65.372 -56.932  35.276  0.00  0   L
+ATOM    17002    O    O .  ASN   L .  162 ?  -70.749 -57.245  39.009 -0.14  0   L
+ATOM    17014    O    O .  VAL   L .  164 ?  -68.166 -58.504  36.036 -0.95  0   L
+ATOM    17010    O    O .  GLY   L .  163 ?  -66.841 -59.260  39.999 -1.07  0   L
+ATOM    17024    C  CD1 .  LEU   L .  165 ?  -64.254 -55.932  35.504  0.00  0   L
+ATOM    18797    N  NE2 .  GLN   H .  176 ?  -62.293 -56.470  39.498 -0.84  0   H
+ATOM    18792    O    O .  GLN   H .  176 ?  -64.396 -51.488  37.035  0.00  0   H
+ATOM    17008    C   CA .  GLY   L .  163 ?  -68.735 -58.000  40.718  0.00  0   L
+ATOM    17009    C    C .  GLY   L .  163 ?  -68.001 -58.906  39.760  0.00  0   L
+ATOM    18794    C   CG .  GLN   H .  176 ?  -62.371 -54.451  38.162  0.00  0   H
+ATOM    17179    C   CB .  THR   L .  185 ?  -63.771 -58.536  42.126  0.00  0   L
+ATOM    17178    O    O .  THR   L .  185 ?  -66.416 -58.298  43.574  0.00  0   L
+ATOM    17181    C  CG2 .  THR   L .  185 ?  -62.726 -57.936  43.060  0.00  0   L
 # 

tests/reference_output/3VI4_out/pockets/pocket109_vert.pqr

@@ -13,7 +13,7 @@ HEADER 5  - Mean B-factor                     : 0.1617
 HEADER 6  - Hydrophobicity Score              : 24.6667
 HEADER 7  - Polarity Score                    :     3
 HEADER 8  - Volume Score                      : 3.3333
-HEADER 9  - Real volume (approximation)       : 247.6693
+HEADER 9  - Real volume (approximation)       : 242.3332
 HEADER 10 - Charge Score                      :     0
 HEADER 11 - Local hydrophobic density Score   : 8.0000
 HEADER 12 - Number of apolar alpha sphere     :     9

tests/reference_output/3VI4_out/pockets/pocket10_atm.cif

@@ -15,7 +15,7 @@ Information about the pocket    10:
 6  - Hydrophobicity Score              : 50.1818
 7  - Polarity Score                    :     3
 8  - Amino Acid based volume Score     : 4.4545
-9  - Pocket volume (Monte Carlo)       : 219.1696
+9  - Pocket volume (Monte Carlo)       : 219.6118
 10  -Pocket volume (convex hull)       : 16.0192
 11 - Charge Score                      :     1
 12 - Local hydrophobic density Score   : 32.0000

tests/reference_output/3VI4_out/pockets/pocket10_vert.pqr

@@ -13,7 +13,7 @@ HEADER 5  - Mean B-factor                     : 0.0756
 HEADER 6  - Hydrophobicity Score              : 50.1818
 HEADER 7  - Polarity Score                    :     3
 HEADER 8  - Volume Score                      : 4.4545
-HEADER 9  - Real volume (approximation)       : 219.1696
+HEADER 9  - Real volume (approximation)       : 219.6118
 HEADER 10 - Charge Score                      :     1
 HEADER 11 - Local hydrophobic density Score   : 32.0000
 HEADER 12 - Number of apolar alpha sphere     :    33

tests/reference_output/3VI4_out/pockets/pocket110_atm.cif

@@ -15,7 +15,7 @@ Information about the pocket   110:
 6  - Hydrophobicity Score              : 4.5000
 7  - Polarity Score                    :     6
 8  - Amino Acid based volume Score     : 3.7500
-9  - Pocket volume (Monte Carlo)       : 313.0909
+9  - Pocket volume (Monte Carlo)       : 307.5981
 10  -Pocket volume (convex hull)       : 21.1442
 11 - Charge Score                      :    -1
 12 - Local hydrophobic density Score   : 6.0000

tests/reference_output/3VI4_out/pockets/pocket110_vert.pqr

@@ -13,7 +13,7 @@ HEADER 5  - Mean B-factor                     : 0.1650
 HEADER 6  - Hydrophobicity Score              : 4.5000
 HEADER 7  - Polarity Score                    :     6
 HEADER 8  - Volume Score                      : 3.7500
-HEADER 9  - Real volume (approximation)       : 313.0909
+HEADER 9  - Real volume (approximation)       : 307.5981
 HEADER 10 - Charge Score                      :    -1
 HEADER 11 - Local hydrophobic density Score   : 6.0000
 HEADER 12 - Number of apolar alpha sphere     :     7

tests/reference_output/3VI4_out/pockets/pocket111_atm.cif

@@ -15,7 +15,7 @@ Information about the pocket   111:
 6  - Hydrophobicity Score              : 34.8462
 7  - Polarity Score                    :     4
 8  - Amino Acid based volume Score     : 4.0000
-9  - Pocket volume (Monte Carlo)       : 198.5655
+9  - Pocket volume (Monte Carlo)       : 196.2901
 10  -Pocket volume (convex hull)       : 11.2587
 11 - Charge Score                      :     1
 12 - Local hydrophobic density Score   : 1.0000

tests/reference_output/3VI4_out/pockets/pocket111_vert.pqr

@@ -13,7 +13,7 @@ HEADER 5  - Mean B-factor                     : 0.1605
 HEADER 6  - Hydrophobicity Score              : 34.8462
 HEADER 7  - Polarity Score                    :     4
 HEADER 8  - Volume Score                      : 4.0000
-HEADER 9  - Real volume (approximation)       : 198.5655
+HEADER 9  - Real volume (approximation)       : 196.2901
 HEADER 10 - Charge Score                      :     1
 HEADER 11 - Local hydrophobic density Score   : 1.0000
 HEADER 12 - Number of apolar alpha sphere     :     2

tests/reference_output/3VI4_out/pockets/pocket112_atm.cif

@@ -15,7 +15,7 @@ Information about the pocket   112:
 6  - Hydrophobicity Score              : -26.8571
 7  - Polarity Score                    :     5
 8  - Amino Acid based volume Score     : 4.0000
-9  - Pocket volume (Monte Carlo)       : 96.2154
+9  - Pocket volume (Monte Carlo)       : 101.3422
 10  -Pocket volume (convex hull)       : 0.6463
 11 - Charge Score                      :     0
 12 - Local hydrophobic density Score   : 3.0000

tests/reference_output/3VI4_out/pockets/pocket112_vert.pqr

@@ -13,7 +13,7 @@ HEADER 5  - Mean B-factor                     : 0.1606
 HEADER 6  - Hydrophobicity Score              : -26.8571
 HEADER 7  - Polarity Score                    :     5
 HEADER 8  - Volume Score                      : 4.0000
-HEADER 9  - Real volume (approximation)       : 96.2154
+HEADER 9  - Real volume (approximation)       : 101.3422
 HEADER 10 - Charge Score                      :     0
 HEADER 11 - Local hydrophobic density Score   : 3.0000
 HEADER 12 - Number of apolar alpha sphere     :     4

tests/reference_output/3VI4_out/pockets/pocket113_atm.cif

@@ -15,7 +15,7 @@ Information about the pocket   113:
 6  - Hydrophobicity Score              : -9.6667
 7  - Polarity Score                    :     8
 8  - Amino Acid based volume Score     : 5.0000
-9  - Pocket volume (Monte Carlo)       : 305.5177
+9  - Pocket volume (Monte Carlo)       : 296.7589
 10  -Pocket volume (convex hull)       : 12.9262
 11 - Charge Score                      :     1
 12 - Local hydrophobic density Score   : 11.0000
@@ -39,23 +39,23 @@ _atom_site.Cartn_z
 _atom_site.occupancy
 _atom_site.pdbx_formal_charge
 _atom_site.auth_asym_id
-ATOM    21506    C   CG .  GLU   H .   89 ?   27.567 -19.652 -78.035  0.00  0   H
-ATOM    21493    O  OG1 .  THR   H .   87 ?   27.198 -16.638 -79.404 -1.07  0   H
-ATOM    21345    C   CE .  LYS   H .   67 ?   28.427 -13.397 -75.202  0.00  0   H
-ATOM    21346    N   NZ .  LYS   H .   67 ?   29.066 -12.797 -76.407 -1.26  0   H
-ATOM    21505    C   CB .  GLU   H .   89 ?   26.534 -19.165 -77.036  0.00  0   H
-ATOM    21344    C   CD .  LYS   H .   67 ?   29.356 -13.432 -74.001  0.00  0   H
-ATOM    21308    O    O .  LYS   H .   63 ?   32.034 -16.546 -69.862 -7.90  0   H
-ATOM    21323    C  CE2 .  PHE   H .   64 ?   26.443 -16.639 -70.107  0.00  0   H
-ATOM    21343    C   CG .  LYS   H .   67 ?   28.589 -13.156 -72.719  0.00  0   H
-ATOM    21324    C   CZ .  PHE   H .   64 ?   26.595 -17.924 -69.607  0.00  0   H
-ATOM    21111    N   NZ .  LYS   H .   38 ?   24.535 -18.820 -72.917 -2.61  0   H
-ATOM    21172    O  OE1 .  GLU   H .   46 ?   25.380 -21.501 -69.187 -3.21  0   H
-ATOM    21130    N  NH1 .  ARG   H .   40 ?   24.702 -22.157 -74.301 -4.54  0   H
-ATOM    21173    O  OE2 .  GLU   H .   46 ?   27.134 -20.777 -68.059 -4.29  0   H
-ATOM    21309    C   CB .  LYS   H .   63 ?   31.454 -19.087 -67.985  0.00  0   H
-ATOM    21322    C  CE1 .  PHE   H .   64 ?   27.510 -18.162 -68.594  0.00  0   H
-ATOM    21516    O  OD1 .  ASP   H .   90 ?   26.017 -15.491 -75.470 -2.14  0   H
-ATOM    21321    C  CD2 .  PHE   H .   64 ?   27.206 -15.595 -69.594  0.00  0   H
-ATOM    21311    C   CD .  LYS   H .   63 ?   31.038 -21.555 -67.748  0.00  0   H
+ATOM    21506    C   CG .  GLU   F .   89 ?   27.567 -19.652 -78.035  0.00  0   F
+ATOM    21493    O  OG1 .  THR   F .   87 ?   27.198 -16.638 -79.404 -1.07  0   F
+ATOM    21345    C   CE .  LYS   F .   67 ?   28.427 -13.397 -75.202  0.00  0   F
+ATOM    21346    N   NZ .  LYS   F .   67 ?   29.066 -12.797 -76.407 -1.26  0   F
+ATOM    21505    C   CB .  GLU   F .   89 ?   26.534 -19.165 -77.036  0.00  0   F
+ATOM    21344    C   CD .  LYS   F .   67 ?   29.356 -13.432 -74.001  0.00  0   F
+ATOM    21308    O    O .  LYS   F .   63 ?   32.034 -16.546 -69.862 -7.90  0   F
+ATOM    21323    C  CE2 .  PHE   F .   64 ?   26.443 -16.639 -70.107  0.00  0   F
+ATOM    21343    C   CG .  LYS   F .   67 ?   28.589 -13.156 -72.719  0.00  0   F
+ATOM    21324    C   CZ .  PHE   F .   64 ?   26.595 -17.924 -69.607  0.00  0   F
+ATOM    21111    N   NZ .  LYS   F .   38 ?   24.535 -18.820 -72.917 -2.61  0   F
+ATOM    21172    O  OE1 .  GLU   F .   46 ?   25.380 -21.501 -69.187 -3.21  0   F
+ATOM    21130    N  NH1 .  ARG   F .   40 ?   24.702 -22.157 -74.301 -4.54  0   F
+ATOM    21173    O  OE2 .  GLU   F .   46 ?   27.134 -20.777 -68.059 -4.29  0   F
+ATOM    21309    C   CB .  LYS   F .   63 ?   31.454 -19.087 -67.985  0.00  0   F
+ATOM    21322    C  CE1 .  PHE   F .   64 ?   27.510 -18.162 -68.594  0.00  0   F
+ATOM    21516    O  OD1 .  ASP   F .   90 ?   26.017 -15.491 -75.470 -2.14  0   F
+ATOM    21321    C  CD2 .  PHE   F .   64 ?   27.206 -15.595 -69.594  0.00  0   F
+ATOM    21311    C   CD .  LYS   F .   63 ?   31.038 -21.555 -67.748  0.00  0   F
 # 

tests/reference_output/3VI4_out/pockets/pocket113_vert.pqr

@@ -13,7 +13,7 @@ HEADER 5  - Mean B-factor                     : 0.2096
 HEADER 6  - Hydrophobicity Score              : -9.6667
 HEADER 7  - Polarity Score                    :     8
 HEADER 8  - Volume Score                      : 5.0000
-HEADER 9  - Real volume (approximation)       : 305.5177
+HEADER 9  - Real volume (approximation)       : 296.7589
 HEADER 10 - Charge Score                      :     1
 HEADER 11 - Local hydrophobic density Score   : 11.0000
 HEADER 12 - Number of apolar alpha sphere     :    12

tests/reference_output/3VI4_out/pockets/pocket114_atm.cif

@@ -15,7 +15,7 @@ Information about the pocket   114:
 6  - Hydrophobicity Score              : 31.3636
 7  - Polarity Score                    :     4
 8  - Amino Acid based volume Score     : 3.6364
-9  - Pocket volume (Monte Carlo)       : 314.5858
+9  - Pocket volume (Monte Carlo)       : 315.9565
 10  -Pocket volume (convex hull)       : 17.2749
 11 - Charge Score                      :     1
 12 - Local hydrophobic density Score   : 1.0000

tests/reference_output/3VI4_out/pockets/pocket114_vert.pqr

@@ -13,7 +13,7 @@ HEADER 5  - Mean B-factor                     : 0.2224
 HEADER 6  - Hydrophobicity Score              : 31.3636
 HEADER 7  - Polarity Score                    :     4
 HEADER 8  - Volume Score                      : 3.6364
-HEADER 9  - Real volume (approximation)       : 314.5858
+HEADER 9  - Real volume (approximation)       : 315.9565
 HEADER 10 - Charge Score                      :     1
 HEADER 11 - Local hydrophobic density Score   : 1.0000
 HEADER 12 - Number of apolar alpha sphere     :     2

tests/reference_output/3VI4_out/pockets/pocket115_atm.cif

@@ -15,7 +15,7 @@ Information about the pocket   115:
 6  - Hydrophobicity Score              : 24.6667
 7  - Polarity Score                    :     4
 8  - Amino Acid based volume Score     : 3.8333
-9  - Pocket volume (Monte Carlo)       : 232.8985
+9  - Pocket volume (Monte Carlo)       : 238.3594
 10  -Pocket volume (convex hull)       : 17.8626
 11 - Charge Score                      :    -1
 12 - Local hydrophobic density Score   : 10.0000

tests/reference_output/3VI4_out/pockets/pocket115_vert.pqr

@@ -13,7 +13,7 @@ HEADER 5  - Mean B-factor                     : 0.5100
 HEADER 6  - Hydrophobicity Score              : 24.6667
 HEADER 7  - Polarity Score                    :     4
 HEADER 8  - Volume Score                      : 3.8333
-HEADER 9  - Real volume (approximation)       : 232.8985
+HEADER 9  - Real volume (approximation)       : 238.3594
 HEADER 10 - Charge Score                      :    -1
 HEADER 11 - Local hydrophobic density Score   : 10.0000
 HEADER 12 - Number of apolar alpha sphere     :    11

tests/reference_output/3VI4_out/pockets/pocket116_atm.cif

@@ -15,7 +15,7 @@ Information about the pocket   116:
 6  - Hydrophobicity Score              : -2.3333
 7  - Polarity Score                    :     6
 8  - Amino Acid based volume Score     : 4.8333
-9  - Pocket volume (Monte Carlo)       : 195.1483
+9  - Pocket volume (Monte Carlo)       : 193.0439
 10  -Pocket volume (convex hull)       : 4.3541
 11 - Charge Score                      :     0
 12 - Local hydrophobic density Score   : 5.0000

tests/reference_output/3VI4_out/pockets/pocket116_vert.pqr

@@ -13,7 +13,7 @@ HEADER 5  - Mean B-factor                     : 0.3765
 HEADER 6  - Hydrophobicity Score              : -2.3333
 HEADER 7  - Polarity Score                    :     6
 HEADER 8  - Volume Score                      : 4.8333
-HEADER 9  - Real volume (approximation)       : 195.1483
+HEADER 9  - Real volume (approximation)       : 193.0439
 HEADER 10 - Charge Score                      :     0
 HEADER 11 - Local hydrophobic density Score   : 5.0000
 HEADER 12 - Number of apolar alpha sphere     :     6

tests/reference_output/3VI4_out/pockets/pocket117_atm.cif

@@ -15,7 +15,7 @@ Information about the pocket   117:
 6  - Hydrophobicity Score              : 3.4444
 7  - Polarity Score                    :     5
 8  - Amino Acid based volume Score     : 3.3333
-9  - Pocket volume (Monte Carlo)       : 451.8676
+9  - Pocket volume (Monte Carlo)       : 463.4369
 10  -Pocket volume (convex hull)       : 46.5028
 11 - Charge Score                      :     2
 12 - Local hydrophobic density Score   : 10.2857
@@ -39,33 +39,33 @@ _atom_site.Cartn_z
 _atom_site.occupancy
 _atom_site.pdbx_formal_charge
 _atom_site.auth_asym_id
-ATOM    22358    C   CA .  PRO   H .  205 ?    1.310 -11.573 -85.487  0.00  0   H
-ATOM    22376    C   CA .  SER   H .  208 ?    0.225  -9.372 -89.696  0.00  0   H
-ATOM    22384    O    O .  THR   H .  209 ?   -1.906 -13.993 -89.884 -2.14  0   H
-ATOM    22396    N   NZ .  LYS   H .  210 ?   -7.433 -10.828 -88.444  0.00  0   H
-ATOM    22379    C   CB .  SER   H .  208 ?   -0.011  -7.884 -89.987  0.00  0   H
-ATOM    22380    O   OG .  SER   H .  208 ?    0.136  -7.106 -88.808 -0.95  0   H
-ATOM    22360    O    O .  PRO   H .  205 ?    2.022  -9.602 -86.637 -0.14  0   H
-ATOM    22392    C   CB .  LYS   H .  210 ?   -5.421 -13.480 -91.493  0.00  0   H
-ATOM    22394    C   CD .  LYS   H .  210 ?   -7.323 -12.762 -90.032  0.00  0   H
-ATOM    22393    C   CG .  LYS   H .  210 ?   -5.846 -13.145 -90.071  0.00  0   H
-ATOM    22378    O    O .  SER   H .  208 ?   -0.453  -9.823 -91.966  0.00  0   H
-ATOM    22381    N    N .  THR   H .  209 ?   -0.415 -11.543 -90.491 -1.09  0   H
-ATOM    22350    O    O .  HIS   H .  204 ?    1.148 -12.439 -88.132  0.00  0   H
-ATOM    22346    C   CB .  ALA   H .  203 ?   -2.788 -16.094 -86.399  0.00  0   H
-ATOM    22395    C   CE .  LYS   H .  210 ?   -7.757 -12.266 -88.660  0.00  0   H
-ATOM    22357    N    N .  PRO   H .  205 ?    1.524 -12.939 -85.949  0.00  0   H
-ATOM    22361    C   CB .  PRO   H .  205 ?    1.399 -11.702 -83.963  0.00  0   H
-ATOM    22363    C   CD .  PRO   H .  205 ?    1.962 -13.833 -84.858  0.00  0   H
-ATOM    21984    C    C .  PRO   H .  154 ?    4.195 -17.223 -83.525  0.00  0   H
-ATOM    21989    N    N .  VAL   H .  155 ?    3.456 -18.330 -83.555 -1.09  0   H
-ATOM    21986    C   CB .  PRO   H .  154 ?    4.494 -15.717 -81.532  0.00  0   H
-ATOM    22002    C  CG2 .  THR   H .  156 ?   -1.288 -18.736 -81.601  0.00  0   H
-ATOM    21996    N    N .  THR   H .  156 ?    0.151 -19.270 -84.261  0.00  0   H
-ATOM    22362    C   CG .  PRO   H .  205 ?    2.265 -12.894 -83.728  0.00  0   H
-ATOM    22377    C    C .  SER   H .  208 ?   -0.254 -10.267 -90.831  0.00  0   H
-ATOM    22349    C    C .  HIS   H .  204 ?    1.383 -13.272 -87.247  0.00  0   H
-ATOM    22388    N    N .  LYS   H .  210 ?   -2.974 -13.392 -91.783 -3.28  0   H
-ATOM    22001    O  OG1 .  THR   H .  156 ?   -2.459 -18.179 -83.653 -0.14  0   H
-ATOM    22345    O    O .  ALA   H .  203 ?    0.171 -16.781 -86.260  0.00  0   H
+ATOM    22358    C   CA .  PRO   F .  205 ?    1.310 -11.573 -85.487  0.00  0   F
+ATOM    22376    C   CA .  SER   F .  208 ?    0.225  -9.372 -89.696  0.00  0   F
+ATOM    22384    O    O .  THR   F .  209 ?   -1.906 -13.993 -89.884 -2.14  0   F
+ATOM    22396    N   NZ .  LYS   F .  210 ?   -7.433 -10.828 -88.444  0.00  0   F
+ATOM    22379    C   CB .  SER   F .  208 ?   -0.011  -7.884 -89.987  0.00  0   F
+ATOM    22380    O   OG .  SER   F .  208 ?    0.136  -7.106 -88.808 -0.95  0   F
+ATOM    22360    O    O .  PRO   F .  205 ?    2.022  -9.602 -86.637 -0.14  0   F
+ATOM    22392    C   CB .  LYS   F .  210 ?   -5.421 -13.480 -91.493  0.00  0   F
+ATOM    22394    C   CD .  LYS   F .  210 ?   -7.323 -12.762 -90.032  0.00  0   F
+ATOM    22393    C   CG .  LYS   F .  210 ?   -5.846 -13.145 -90.071  0.00  0   F
+ATOM    22378    O    O .  SER   F .  208 ?   -0.453  -9.823 -91.966  0.00  0   F
+ATOM    22381    N    N .  THR   F .  209 ?   -0.415 -11.543 -90.491 -1.09  0   F
+ATOM    22350    O    O .  HIS   F .  204 ?    1.148 -12.439 -88.132  0.00  0   F
+ATOM    22346    C   CB .  ALA   F .  203 ?   -2.788 -16.094 -86.399  0.00  0   F
+ATOM    22395    C   CE .  LYS   F .  210 ?   -7.757 -12.266 -88.660  0.00  0   F
+ATOM    22357    N    N .  PRO   F .  205 ?    1.524 -12.939 -85.949  0.00  0   F
+ATOM    22361    C   CB .  PRO   F .  205 ?    1.399 -11.702 -83.963  0.00  0   F
+ATOM    22363    C   CD .  PRO   F .  205 ?    1.962 -13.833 -84.858  0.00  0   F
+ATOM    21984    C    C .  PRO   F .  154 ?    4.195 -17.223 -83.525  0.00  0   F
+ATOM    21989    N    N .  VAL   F .  155 ?    3.456 -18.330 -83.555 -1.09  0   F
+ATOM    21986    C   CB .  PRO   F .  154 ?    4.494 -15.717 -81.532  0.00  0   F
+ATOM    22002    C  CG2 .  THR   F .  156 ?   -1.288 -18.736 -81.601  0.00  0   F
+ATOM    21996    N    N .  THR   F .  156 ?    0.151 -19.270 -84.261  0.00  0   F
+ATOM    22362    C   CG .  PRO   F .  205 ?    2.265 -12.894 -83.728  0.00  0   F
+ATOM    22377    C    C .  SER   F .  208 ?   -0.254 -10.267 -90.831  0.00  0   F
+ATOM    22349    C    C .  HIS   F .  204 ?    1.383 -13.272 -87.247  0.00  0   F
+ATOM    22388    N    N .  LYS   F .  210 ?   -2.974 -13.392 -91.783 -3.28  0   F
+ATOM    22001    O  OG1 .  THR   F .  156 ?   -2.459 -18.179 -83.653 -0.14  0   F
+ATOM    22345    O    O .  ALA   F .  203 ?    0.171 -16.781 -86.260  0.00  0   F
 # 

tests/reference_output/3VI4_out/pockets/pocket117_vert.pqr

@@ -13,7 +13,7 @@ HEADER 5  - Mean B-factor                     : 0.3292
 HEADER 6  - Hydrophobicity Score              : 3.4444
 HEADER 7  - Polarity Score                    :     5
 HEADER 8  - Volume Score                      : 3.3333
-HEADER 9  - Real volume (approximation)       : 451.8676
+HEADER 9  - Real volume (approximation)       : 463.4369
 HEADER 10 - Charge Score                      :     2
 HEADER 11 - Local hydrophobic density Score   : 10.2857
 HEADER 12 - Number of apolar alpha sphere     :    14

tests/reference_output/3VI4_out/pockets/pocket118_atm.cif

@@ -15,7 +15,7 @@ Information about the pocket   118:
 6  - Hydrophobicity Score              : 16.2500
 7  - Polarity Score                    :     6
 8  - Amino Acid based volume Score     : 5.0000
-9  - Pocket volume (Monte Carlo)       : 306.1676
+9  - Pocket volume (Monte Carlo)       : 297.8879
 10  -Pocket volume (convex hull)       : 20.3241
 11 - Charge Score                      :     3
 12 - Local hydrophobic density Score   : 14.0000

tests/reference_output/3VI4_out/pockets/pocket118_vert.pqr

@@ -13,7 +13,7 @@ HEADER 5  - Mean B-factor                     : 0.1701
 HEADER 6  - Hydrophobicity Score              : 16.2500
 HEADER 7  - Polarity Score                    :     6
 HEADER 8  - Volume Score                      : 5.0000
-HEADER 9  - Real volume (approximation)       : 306.1676
+HEADER 9  - Real volume (approximation)       : 297.8879
 HEADER 10 - Charge Score                      :     3
 HEADER 11 - Local hydrophobic density Score   : 14.0000
 HEADER 12 - Number of apolar alpha sphere     :    15

tests/reference_output/3VI4_out/pockets/pocket119_atm.cif

@@ -15,7 +15,7 @@ Information about the pocket   119:
 6  - Hydrophobicity Score              : 46.3333
 7  - Polarity Score                    :     2
 8  - Amino Acid based volume Score     : 4.5000
-9  - Pocket volume (Monte Carlo)       : 206.9675
+9  - Pocket volume (Monte Carlo)       : 201.4158
 10  -Pocket volume (convex hull)       : 5.4763
 11 - Charge Score                      :     1
 12 - Local hydrophobic density Score   : 12.0000

tests/reference_output/3VI4_out/pockets/pocket119_vert.pqr

@@ -13,7 +13,7 @@ HEADER 5  - Mean B-factor                     : 0.8433
 HEADER 6  - Hydrophobicity Score              : 46.3333
 HEADER 7  - Polarity Score                    :     2
 HEADER 8  - Volume Score                      : 4.5000
-HEADER 9  - Real volume (approximation)       : 206.9675
+HEADER 9  - Real volume (approximation)       : 201.4158
 HEADER 10 - Charge Score                      :     1
 HEADER 11 - Local hydrophobic density Score   : 12.0000
 HEADER 12 - Number of apolar alpha sphere     :    13

tests/reference_output/3VI4_out/pockets/pocket11_atm.cif

@@ -15,7 +15,7 @@ Information about the pocket    11:
 6  - Hydrophobicity Score              : 39.8064
 7  - Polarity Score                    :    14
 8  - Amino Acid based volume Score     : 4.0968
-9  - Pocket volume (Monte Carlo)       : 792.6983
+9  - Pocket volume (Monte Carlo)       : 799.6038
 10  -Pocket volume (convex hull)       : 271.3904
 11 - Charge Score                      :     2
 12 - Local hydrophobic density Score   : 23.2941

tests/reference_output/3VI4_out/pockets/pocket11_vert.pqr

@@ -13,7 +13,7 @@ HEADER 5  - Mean B-factor                     : 0.1092
 HEADER 6  - Hydrophobicity Score              : 39.8064
 HEADER 7  - Polarity Score                    :    14
 HEADER 8  - Volume Score                      : 4.0968
-HEADER 9  - Real volume (approximation)       : 792.6983
+HEADER 9  - Real volume (approximation)       : 799.6038
 HEADER 10 - Charge Score                      :     2
 HEADER 11 - Local hydrophobic density Score   : 23.2941
 HEADER 12 - Number of apolar alpha sphere     :    34

tests/reference_output/3VI4_out/pockets/pocket120_atm.cif

@@ -15,7 +15,7 @@ Information about the pocket   120:
 6  - Hydrophobicity Score              : 19.0000
 7  - Polarity Score                    :     5
 8  - Amino Acid based volume Score     : 3.5455
-9  - Pocket volume (Monte Carlo)       : 424.9396
+9  - Pocket volume (Monte Carlo)       : 422.3725
 10  -Pocket volume (convex hull)       : 43.6686
 11 - Charge Score                      :     2
 12 - Local hydrophobic density Score   : 6.0000

tests/reference_output/3VI4_out/pockets/pocket120_vert.pqr

@@ -13,7 +13,7 @@ HEADER 5  - Mean B-factor                     : 0.4277
 HEADER 6  - Hydrophobicity Score              : 19.0000
 HEADER 7  - Polarity Score                    :     5
 HEADER 8  - Volume Score                      : 3.5455
-HEADER 9  - Real volume (approximation)       : 424.9396
+HEADER 9  - Real volume (approximation)       : 422.3725
 HEADER 10 - Charge Score                      :     2
 HEADER 11 - Local hydrophobic density Score   : 6.0000
 HEADER 12 - Number of apolar alpha sphere     :     7

tests/reference_output/3VI4_out/pockets/pocket121_atm.cif

@@ -15,7 +15,7 @@ Information about the pocket   121:
 6  - Hydrophobicity Score              : 14.7500
 7  - Polarity Score                    :     7
 8  - Amino Acid based volume Score     : 3.8750
-9  - Pocket volume (Monte Carlo)       : 268.8548
+9  - Pocket volume (Monte Carlo)       : 277.9102
 10  -Pocket volume (convex hull)       : 11.2359
 11 - Charge Score                      :     1
 12 - Local hydrophobic density Score   : 3.0000
@@ -39,21 +39,21 @@ _atom_site.Cartn_z
 _atom_site.occupancy
 _atom_site.pdbx_formal_charge
 _atom_site.auth_asym_id
-ATOM    21050    O   OH .  TYR   H .   32 ?   13.073 -11.192 -47.720  0.00  0   H
+ATOM    21050    O   OH .  TYR   F .   32 ?   13.073 -11.192 -47.720  0.00  0   F
 ATOM     5367    N  NH2 .  ARG   B .  117 ?   13.629  -7.764 -40.531 -2.19  0   B
 ATOM     7237    O  OD1 .  ASN   B .  356 ?    9.103 -10.251 -40.742  0.00  0   B
 ATOM     7560    C  CD1 .  ILE   B .  400 ?   15.834  -9.409 -44.206  0.00  0   B
-ATOM    21047    C  CE1 .  TYR   H .   32 ?   13.988  -9.386 -48.971  0.00  0   H
+ATOM    21047    C  CE1 .  TYR   F .   32 ?   13.988  -9.386 -48.971  0.00  0   F
 ATOM     7551    C   CB .  SER   B .  399 ?   13.399  -3.782 -44.780  0.00  0   B
-ATOM    21038    O   OG .  SER   H .   31 ?   15.325  -5.680 -48.513 -1.07  0   H
+ATOM    21038    O   OG .  SER   F .   31 ?   15.325  -5.680 -48.513 -1.07  0   F
 ATOM     5366    N  NH1 .  ARG   B .  117 ?   13.557  -5.487 -40.729 -2.19  0   B
 ATOM     7235    C   CB .  ASN   B .  356 ?    7.800  -8.404 -39.834  0.00  0   B
 ATOM     7263    C   CB .  SER   B .  360 ?   11.141  -3.612 -39.367  0.00  0   B
 ATOM     7236    C   CG .  ASN   B .  356 ?    8.010  -9.664 -40.686  0.00  0   B
 ATOM     7553    N    N .  ILE   B .  400 ?   15.898  -5.269 -43.802  0.00  0   B
-ATOM    21013    O  OG1 .  THR   H .   28 ?   13.458  -3.388 -48.217  0.00  0   H
-ATOM    21008    N    N .  THR   H .   28 ?   11.175  -4.594 -50.156  0.00  0   H
-ATOM    21014    C  CG2 .  THR   H .   28 ?   11.123  -2.705 -48.023  0.00  0   H
+ATOM    21013    O  OG1 .  THR   F .   28 ?   13.458  -3.388 -48.217  0.00  0   F
+ATOM    21008    N    N .  THR   F .   28 ?   11.175  -4.594 -50.156  0.00  0   F
+ATOM    21014    C  CG2 .  THR   F .   28 ?   11.123  -2.705 -48.023  0.00  0   F
 ATOM     7234    O    O .  ASN   B .  356 ?    9.734  -6.265 -38.070 -1.07  0   B
 ATOM     7264    O   OG .  SER   B .  360 ?    9.861  -3.657 -38.800  0.00  0   B
 ATOM     7558    C  CG1 .  ILE   B .  400 ?   16.435  -8.204 -43.505  0.00  0   B

tests/reference_output/3VI4_out/pockets/pocket121_vert.pqr

@@ -13,7 +13,7 @@ HEADER 5  - Mean B-factor                     : 0.0692
 HEADER 6  - Hydrophobicity Score              : 14.7500
 HEADER 7  - Polarity Score                    :     7
 HEADER 8  - Volume Score                      : 3.8750
-HEADER 9  - Real volume (approximation)       : 268.8548
+HEADER 9  - Real volume (approximation)       : 277.9102
 HEADER 10 - Charge Score                      :     1
 HEADER 11 - Local hydrophobic density Score   : 3.0000
 HEADER 12 - Number of apolar alpha sphere     :     4

tests/reference_output/3VI4_out/pockets/pocket122_atm.cif

@@ -15,7 +15,7 @@ Information about the pocket   122:
 6  - Hydrophobicity Score              : -25.6667
 7  - Polarity Score                    :     3
 8  - Amino Acid based volume Score     : 5.3333
-9  - Pocket volume (Monte Carlo)       : 157.5379
+9  - Pocket volume (Monte Carlo)       : 156.9713
 10  -Pocket volume (convex hull)       : 0.7748
 11 - Charge Score                      :     1
 12 - Local hydrophobic density Score   : 10.0000

tests/reference_output/3VI4_out/pockets/pocket122_vert.pqr

@@ -13,7 +13,7 @@ HEADER 5  - Mean B-factor                     : 0.6382
 HEADER 6  - Hydrophobicity Score              : -25.6667
 HEADER 7  - Polarity Score                    :     3
 HEADER 8  - Volume Score                      : 5.3333
-HEADER 9  - Real volume (approximation)       : 157.5379
+HEADER 9  - Real volume (approximation)       : 156.9713
 HEADER 10 - Charge Score                      :     1
 HEADER 11 - Local hydrophobic density Score   : 10.0000
 HEADER 12 - Number of apolar alpha sphere     :    11

tests/reference_output/3VI4_out/pockets/pocket123_atm.cif

@@ -15,7 +15,7 @@ Information about the pocket   123:
 6  - Hydrophobicity Score              : 33.2500
 7  - Polarity Score                    :     6
 8  - Amino Acid based volume Score     : 4.6667
-9  - Pocket volume (Monte Carlo)       : 367.6850
+9  - Pocket volume (Monte Carlo)       : 364.4446
 10  -Pocket volume (convex hull)       : 27.1672
 11 - Charge Score                      :    -1
 12 - Local hydrophobic density Score   : 4.0000
@@ -39,25 +39,25 @@ _atom_site.Cartn_z
 _atom_site.occupancy
 _atom_site.pdbx_formal_charge
 _atom_site.auth_asym_id
-ATOM    21174    N    N .  TRP   H .   47 ?   23.873 -20.274 -63.702  0.00  0   H
-ATOM    19886    O    O .  PHE   G .  101 ?   26.188 -22.003 -60.476 -6.43  0   G
-ATOM    21166    C   CA .  GLU   H .   46 ?   23.051 -21.596 -65.552  0.00  0   H
-ATOM    21170    C   CG .  GLU   H .   46 ?   25.280 -21.513 -66.780  0.00  0   H
-ATOM    19895    C   CA .  THR   G .  102 ?   25.758 -24.694 -59.994  0.00  0   G
-ATOM    19900    C  CG2 .  THR   G .  102 ?   26.890 -26.689 -61.045  0.00  0   G
-ATOM    21295    N  ND2 .  ASN   H .   61 ?   28.799 -19.246 -64.990 -2.19  0   H
-ATOM    21313    N   NZ .  LYS   H .   63 ?   30.558 -23.878 -66.980  0.00  0   H
-ATOM    19899    O  OG1 .  THR   G .  102 ?   28.156 -24.834 -60.223 -5.36  0   G
-ATOM    19881    C   CG .  PRO   G .  100 ?   30.984 -20.801 -61.017  0.00  0   G
-ATOM    21294    O  OD1 .  ASN   H .   61 ?   30.757 -19.071 -63.904 -2.14  0   H
-ATOM    19111    N    N .  ASP   G .    1 ?   33.160 -24.445 -60.466 -2.77  0   G
-ATOM    21312    C   CE .  LYS   H .   63 ?   31.616 -22.848 -67.189  0.00  0   H
-ATOM    19133    C  CG2 .  VAL   G .    3 ?   31.749 -30.359 -61.603  0.00  0   G
-ATOM    19132    C  CG1 .  VAL   G .    3 ?   29.650 -31.606 -62.134  0.00  0   G
-ATOM    21160    O    O .  LEU   H .   45 ?   22.122 -24.178 -65.229 -4.69  0   H
-ATOM    19901    N    N .  PHE   G .  103 ?   23.706 -25.594 -60.880 -2.19  0   G
-ATOM    19904    O    O .  PHE   G .  103 ?   24.161 -27.782 -62.399 -0.95  0   G
-ATOM    19122    O    O .  ILE   G .    2 ?   29.752 -27.348 -59.464  0.00  0   G
-ATOM    19114    O    O .  ASP   G .    1 ?   33.092 -27.780 -59.996 -1.48  0   G
-ATOM    19128    C   CA .  VAL   G .    3 ?   29.714 -30.047 -60.139  0.00  0   G
+ATOM    21174    N    N .  TRP   F .   47 ?   23.873 -20.274 -63.702  0.00  0   F
+ATOM    19886    O    O .  PHE   E .  101 ?   26.188 -22.003 -60.476 -6.43  0   E
+ATOM    21166    C   CA .  GLU   F .   46 ?   23.051 -21.596 -65.552  0.00  0   F
+ATOM    21170    C   CG .  GLU   F .   46 ?   25.280 -21.513 -66.780  0.00  0   F
+ATOM    19895    C   CA .  THR   E .  102 ?   25.758 -24.694 -59.994  0.00  0   E
+ATOM    19900    C  CG2 .  THR   E .  102 ?   26.890 -26.689 -61.045  0.00  0   E
+ATOM    21295    N  ND2 .  ASN   F .   61 ?   28.799 -19.246 -64.990 -2.19  0   F
+ATOM    21313    N   NZ .  LYS   F .   63 ?   30.558 -23.878 -66.980  0.00  0   F
+ATOM    19899    O  OG1 .  THR   E .  102 ?   28.156 -24.834 -60.223 -5.36  0   E
+ATOM    19881    C   CG .  PRO   E .  100 ?   30.984 -20.801 -61.017  0.00  0   E
+ATOM    21294    O  OD1 .  ASN   F .   61 ?   30.757 -19.071 -63.904 -2.14  0   F
+ATOM    19111    N    N .  ASP   E .    1 ?   33.160 -24.445 -60.466 -2.77  0   E
+ATOM    21312    C   CE .  LYS   F .   63 ?   31.616 -22.848 -67.189  0.00  0   F
+ATOM    19133    C  CG2 .  VAL   E .    3 ?   31.749 -30.359 -61.603  0.00  0   E
+ATOM    19132    C  CG1 .  VAL   E .    3 ?   29.650 -31.606 -62.134  0.00  0   E
+ATOM    21160    O    O .  LEU   F .   45 ?   22.122 -24.178 -65.229 -4.69  0   F
+ATOM    19901    N    N .  PHE   E .  103 ?   23.706 -25.594 -60.880 -2.19  0   E
+ATOM    19904    O    O .  PHE   E .  103 ?   24.161 -27.782 -62.399 -0.95  0   E
+ATOM    19122    O    O .  ILE   E .    2 ?   29.752 -27.348 -59.464  0.00  0   E
+ATOM    19114    O    O .  ASP   E .    1 ?   33.092 -27.780 -59.996 -1.48  0   E
+ATOM    19128    C   CA .  VAL   E .    3 ?   29.714 -30.047 -60.139  0.00  0   E
 # 

tests/reference_output/3VI4_out/pockets/pocket123_vert.pqr

@@ -13,7 +13,7 @@ HEADER 5  - Mean B-factor                     : 0.1684
 HEADER 6  - Hydrophobicity Score              : 33.2500
 HEADER 7  - Polarity Score                    :     6
 HEADER 8  - Volume Score                      : 4.6667
-HEADER 9  - Real volume (approximation)       : 367.6850
+HEADER 9  - Real volume (approximation)       : 364.4446
 HEADER 10 - Charge Score                      :    -1
 HEADER 11 - Local hydrophobic density Score   : 4.0000
 HEADER 12 - Number of apolar alpha sphere     :     5

tests/reference_output/3VI4_out/pockets/pocket124_atm.cif

@@ -15,7 +15,7 @@ Information about the pocket   124:
 6  - Hydrophobicity Score              : 26.3846
 7  - Polarity Score                    :     5
 8  - Amino Acid based volume Score     : 3.8462
-9  - Pocket volume (Monte Carlo)       : 517.4641
+9  - Pocket volume (Monte Carlo)       : 505.6645
 10  -Pocket volume (convex hull)       : 108.2540
 11 - Charge Score                      :     0
 12 - Local hydrophobic density Score   : 7.4000

tests/reference_output/3VI4_out/pockets/pocket124_vert.pqr

@@ -13,7 +13,7 @@ HEADER 5  - Mean B-factor                     : 0.4141
 HEADER 6  - Hydrophobicity Score              : 26.3846
 HEADER 7  - Polarity Score                    :     5
 HEADER 8  - Volume Score                      : 3.8462
-HEADER 9  - Real volume (approximation)       : 517.4641
+HEADER 9  - Real volume (approximation)       : 505.6645
 HEADER 10 - Charge Score                      :     0
 HEADER 11 - Local hydrophobic density Score   : 7.4000
 HEADER 12 - Number of apolar alpha sphere     :    10

tests/reference_output/3VI4_out/pockets/pocket125_atm.cif

@@ -15,7 +15,7 @@ Information about the pocket   125:
 6  - Hydrophobicity Score              : 25.7000
 7  - Polarity Score                    :     4
 8  - Amino Acid based volume Score     : 3.9000
-9  - Pocket volume (Monte Carlo)       : 359.7047
+9  - Pocket volume (Monte Carlo)       : 356.9362
 10  -Pocket volume (convex hull)       : 25.8922
 11 - Charge Score                      :     1
 12 - Local hydrophobic density Score   : 14.0000

tests/reference_output/3VI4_out/pockets/pocket125_vert.pqr

@@ -13,7 +13,7 @@ HEADER 5  - Mean B-factor                     : 0.6543
 HEADER 6  - Hydrophobicity Score              : 25.7000
 HEADER 7  - Polarity Score                    :     4
 HEADER 8  - Volume Score                      : 3.9000
-HEADER 9  - Real volume (approximation)       : 359.7047
+HEADER 9  - Real volume (approximation)       : 356.9362
 HEADER 10 - Charge Score                      :     1
 HEADER 11 - Local hydrophobic density Score   : 14.0000
 HEADER 12 - Number of apolar alpha sphere     :    15

tests/reference_output/3VI4_out/pockets/pocket126_atm.cif

@@ -15,7 +15,7 @@ Information about the pocket   126:
 6  - Hydrophobicity Score              : 13.5714
 7  - Polarity Score                    :     6
 8  - Amino Acid based volume Score     : 4.4286
-9  - Pocket volume (Monte Carlo)       : 264.7911
+9  - Pocket volume (Monte Carlo)       : 267.1677
 10  -Pocket volume (convex hull)       : 13.5489
 11 - Charge Score                      :    -1
 12 - Local hydrophobic density Score   : 12.0000

tests/reference_output/3VI4_out/pockets/pocket126_vert.pqr

@@ -13,7 +13,7 @@ HEADER 5  - Mean B-factor                     : 0.1544
 HEADER 6  - Hydrophobicity Score              : 13.5714
 HEADER 7  - Polarity Score                    :     6
 HEADER 8  - Volume Score                      : 4.4286
-HEADER 9  - Real volume (approximation)       : 264.7911
+HEADER 9  - Real volume (approximation)       : 267.1677
 HEADER 10 - Charge Score                      :    -1
 HEADER 11 - Local hydrophobic density Score   : 12.0000
 HEADER 12 - Number of apolar alpha sphere     :    13

tests/reference_output/3VI4_out/pockets/pocket127_atm.cif

@@ -15,7 +15,7 @@ Information about the pocket   127:
 6  - Hydrophobicity Score              : -7.4000
 7  - Polarity Score                    :     8
 8  - Amino Acid based volume Score     : 3.1000
-9  - Pocket volume (Monte Carlo)       : 491.8675
+9  - Pocket volume (Monte Carlo)       : 474.6230
 10  -Pocket volume (convex hull)       : 51.9391
 11 - Charge Score                      :     0
 12 - Local hydrophobic density Score   : 6.0000
@@ -39,31 +39,31 @@ _atom_site.Cartn_z
 _atom_site.occupancy
 _atom_site.pdbx_formal_charge
 _atom_site.auth_asym_id
-ATOM    18743    N  NE2 .  HIS   F .  169 ?  -56.352 -70.926  25.084 -5.47  0   F
-ATOM    18742    C  CE1 .  HIS   F .  169 ?  -56.136 -71.834  26.051  0.00  0   F
-ATOM    16841    N  ND2 .  ASN   E .  143 ?  -57.095 -74.460  24.075 -2.61  0   E
-ATOM    17085    O  OD2 .  ASP   E .  172 ?  -54.514 -70.230  20.436  0.00  0   E
-ATOM    17097    C   CG .  LYS   E .  174 ?  -51.088 -74.026  17.307  0.00  0   E
-ATOM    18721    C   CB .  SER   F .  166 ?  -47.112 -75.061  24.324  0.00  0   F
-ATOM    17099    C   CE .  LYS   E .  174 ?  -48.630 -74.357  16.901  0.00  0   E
-ATOM    17098    C   CD .  LYS   E .  174 ?  -49.779 -73.357  16.913  0.00  0   E
-ATOM    18723    N    N .  GLY   F .  167 ?  -49.755 -73.956  25.910 -3.28  0   F
-ATOM    18727    N    N .  VAL   F .  168 ?  -50.792 -71.627  27.171  0.00  0   F
-ATOM    18730    O    O .  VAL   F .  168 ?  -52.340 -69.624  26.068  0.00  0   F
-ATOM    18724    C   CA .  GLY   F .  167 ?  -50.763 -74.044  26.966  0.00  0   F
-ATOM    17108    O  OD2 .  ASP   E .  175 ?  -56.215 -75.381  20.840  0.00  0   E
-ATOM    18877    O  OG1 .  THR   F .  187 ?  -52.404 -76.633  30.003 -4.29  0   F
-ATOM    18740    N  ND1 .  HIS   F .  169 ?  -55.757 -71.177  27.163 -3.28  0   F
-ATOM    18726    O    O .  GLY   F .  167 ?  -50.900 -72.862  29.052 -2.14  0   F
-ATOM    18878    C  CG2 .  THR   F .  187 ?  -54.010 -75.645  31.468  0.00  0   F
-ATOM    17084    O  OD1 .  ASP   E .  172 ?  -54.634 -72.083  19.283 -1.48  0   E
-ATOM    18725    C    C .  GLY   F .  167 ?  -50.829 -72.786  27.822  0.00  0   F
-ATOM    18714    O    O .  SER   F .  165 ?  -47.350 -70.972  25.224  0.00  0   F
-ATOM    16840    O  OD1 .  ASN   E .  143 ?  -57.295 -74.737  26.292 -3.62  0   E
-ATOM    17096    C   CB .  LYS   E .  174 ?  -52.234 -73.030  17.371  0.00  0   E
-ATOM    18713    C    C .  SER   F .  165 ?  -46.400 -71.661  25.605  0.00  0   F
-ATOM    18717    N    N .  SER   F .  166 ?  -46.346 -72.980  25.434  0.00  0   F
-ATOM    18716    O   OG .  SER   F .  165 ?  -43.359 -71.131  24.714  0.00  0   F
-ATOM    17100    N   NZ .  LYS   E .  174 ?  -47.317 -73.683  16.709  0.00  0   E
-ATOM    18718    C   CA .  SER   F .  166 ?  -47.517 -73.735  24.981  0.00  0   F
+ATOM    18743    N  NE2 .  HIS   H .  169 ?  -56.352 -70.926  25.084 -5.47  0   H
+ATOM    18742    C  CE1 .  HIS   H .  169 ?  -56.136 -71.834  26.051  0.00  0   H
+ATOM    16841    N  ND2 .  ASN   L .  143 ?  -57.095 -74.460  24.075 -2.61  0   L
+ATOM    17085    O  OD2 .  ASP   L .  172 ?  -54.514 -70.230  20.436  0.00  0   L
+ATOM    17097    C   CG .  LYS   L .  174 ?  -51.088 -74.026  17.307  0.00  0   L
+ATOM    18721    C   CB .  SER   H .  166 ?  -47.112 -75.061  24.324  0.00  0   H
+ATOM    17099    C   CE .  LYS   L .  174 ?  -48.630 -74.357  16.901  0.00  0   L
+ATOM    17098    C   CD .  LYS   L .  174 ?  -49.779 -73.357  16.913  0.00  0   L
+ATOM    18723    N    N .  GLY   H .  167 ?  -49.755 -73.956  25.910 -3.28  0   H
+ATOM    18727    N    N .  VAL   H .  168 ?  -50.792 -71.627  27.171  0.00  0   H
+ATOM    18730    O    O .  VAL   H .  168 ?  -52.340 -69.624  26.068  0.00  0   H
+ATOM    18724    C   CA .  GLY   H .  167 ?  -50.763 -74.044  26.966  0.00  0   H
+ATOM    17108    O  OD2 .  ASP   L .  175 ?  -56.215 -75.381  20.840  0.00  0   L
+ATOM    18877    O  OG1 .  THR   H .  187 ?  -52.404 -76.633  30.003 -4.29  0   H
+ATOM    18740    N  ND1 .  HIS   H .  169 ?  -55.757 -71.177  27.163 -3.28  0   H
+ATOM    18726    O    O .  GLY   H .  167 ?  -50.900 -72.862  29.052 -2.14  0   H
+ATOM    18878    C  CG2 .  THR   H .  187 ?  -54.010 -75.645  31.468  0.00  0   H
+ATOM    17084    O  OD1 .  ASP   L .  172 ?  -54.634 -72.083  19.283 -1.48  0   L
+ATOM    18725    C    C .  GLY   H .  167 ?  -50.829 -72.786  27.822  0.00  0   H
+ATOM    18714    O    O .  SER   H .  165 ?  -47.350 -70.972  25.224  0.00  0   H
+ATOM    16840    O  OD1 .  ASN   L .  143 ?  -57.295 -74.737  26.292 -3.62  0   L
+ATOM    17096    C   CB .  LYS   L .  174 ?  -52.234 -73.030  17.371  0.00  0   L
+ATOM    18713    C    C .  SER   H .  165 ?  -46.400 -71.661  25.605  0.00  0   H
+ATOM    18717    N    N .  SER   H .  166 ?  -46.346 -72.980  25.434  0.00  0   H
+ATOM    18716    O   OG .  SER   H .  165 ?  -43.359 -71.131  24.714  0.00  0   H
+ATOM    17100    N   NZ .  LYS   L .  174 ?  -47.317 -73.683  16.709  0.00  0   L
+ATOM    18718    C   CA .  SER   H .  166 ?  -47.517 -73.735  24.981  0.00  0   H
 # 

tests/reference_output/3VI4_out/pockets/pocket127_vert.pqr

@@ -13,7 +13,7 @@ HEADER 5  - Mean B-factor                     : 0.2447
 HEADER 6  - Hydrophobicity Score              : -7.4000
 HEADER 7  - Polarity Score                    :     8
 HEADER 8  - Volume Score                      : 3.1000
-HEADER 9  - Real volume (approximation)       : 491.8675
+HEADER 9  - Real volume (approximation)       : 474.6230
 HEADER 10 - Charge Score                      :     0
 HEADER 11 - Local hydrophobic density Score   : 6.0000
 HEADER 12 - Number of apolar alpha sphere     :     7

tests/reference_output/3VI4_out/pockets/pocket128_atm.cif

@@ -15,7 +15,7 @@ Information about the pocket   128:
 6  - Hydrophobicity Score              : 25.0000
 7  - Polarity Score                    :     8
 8  - Amino Acid based volume Score     : 4.5000
-9  - Pocket volume (Monte Carlo)       : 433.0090
+9  - Pocket volume (Monte Carlo)       : 422.8404
 10  -Pocket volume (convex hull)       : 45.7449
 11 - Charge Score                      :    -1
 12 - Local hydrophobic density Score   : 20.6087

tests/reference_output/3VI4_out/pockets/pocket128_vert.pqr

@@ -13,7 +13,7 @@ HEADER 5  - Mean B-factor                     : 0.1752
 HEADER 6  - Hydrophobicity Score              : 25.0000
 HEADER 7  - Polarity Score                    :     8
 HEADER 8  - Volume Score                      : 4.5000
-HEADER 9  - Real volume (approximation)       : 433.0090
+HEADER 9  - Real volume (approximation)       : 422.8404
 HEADER 10 - Charge Score                      :    -1
 HEADER 11 - Local hydrophobic density Score   : 20.6087
 HEADER 12 - Number of apolar alpha sphere     :    23

tests/reference_output/3VI4_out/pockets/pocket129_atm.cif

@@ -15,7 +15,7 @@ Information about the pocket   129:
 6  - Hydrophobicity Score              : -9.5714
 7  - Polarity Score                    :     6
 8  - Amino Acid based volume Score     : 4.2857
-9  - Pocket volume (Monte Carlo)       : 213.8664
+9  - Pocket volume (Monte Carlo)       : 214.5620
 10  -Pocket volume (convex hull)       : 6.5323
 11 - Charge Score                      :     1
 12 - Local hydrophobic density Score   : 1.0000

tests/reference_output/3VI4_out/pockets/pocket129_vert.pqr

@@ -13,7 +13,7 @@ HEADER 5  - Mean B-factor                     : 0.1051
 HEADER 6  - Hydrophobicity Score              : -9.5714
 HEADER 7  - Polarity Score                    :     6
 HEADER 8  - Volume Score                      : 4.2857
-HEADER 9  - Real volume (approximation)       : 213.8664
+HEADER 9  - Real volume (approximation)       : 214.5620
 HEADER 10 - Charge Score                      :     1
 HEADER 11 - Local hydrophobic density Score   : 1.0000
 HEADER 12 - Number of apolar alpha sphere     :     2

tests/reference_output/3VI4_out/pockets/pocket12_atm.cif

@@ -15,7 +15,7 @@ Information about the pocket    12:
 6  - Hydrophobicity Score              : 28.8750
 7  - Polarity Score                    :     5
 8  - Amino Acid based volume Score     : 4.1250
-9  - Pocket volume (Monte Carlo)       : 311.3338
+9  - Pocket volume (Monte Carlo)       : 302.7495
 10  -Pocket volume (convex hull)       : 9.5733
 11 - Charge Score                      :    -1
 12 - Local hydrophobic density Score   : 15.0000

tests/reference_output/3VI4_out/pockets/pocket12_vert.pqr

@@ -13,7 +13,7 @@ HEADER 5  - Mean B-factor                     : 0.1060
 HEADER 6  - Hydrophobicity Score              : 28.8750
 HEADER 7  - Polarity Score                    :     5
 HEADER 8  - Volume Score                      : 4.1250
-HEADER 9  - Real volume (approximation)       : 311.3338
+HEADER 9  - Real volume (approximation)       : 302.7495
 HEADER 10 - Charge Score                      :    -1
 HEADER 11 - Local hydrophobic density Score   : 15.0000
 HEADER 12 - Number of apolar alpha sphere     :    16

tests/reference_output/3VI4_out/pockets/pocket130_atm.cif

@@ -15,7 +15,7 @@ Information about the pocket   130:
 6  - Hydrophobicity Score              : 16.8571
 7  - Polarity Score                    :     5
 8  - Amino Acid based volume Score     : 4.4286
-9  - Pocket volume (Monte Carlo)       : 358.9691
+9  - Pocket volume (Monte Carlo)       : 357.2821
 10  -Pocket volume (convex hull)       : 23.5281
 11 - Charge Score                      :     2
 12 - Local hydrophobic density Score   : 7.0000

tests/reference_output/3VI4_out/pockets/pocket130_vert.pqr

@@ -13,7 +13,7 @@ HEADER 5  - Mean B-factor                     : 0.3034
 HEADER 6  - Hydrophobicity Score              : 16.8571
 HEADER 7  - Polarity Score                    :     5
 HEADER 8  - Volume Score                      : 4.4286
-HEADER 9  - Real volume (approximation)       : 358.9691
+HEADER 9  - Real volume (approximation)       : 357.2821
 HEADER 10 - Charge Score                      :     2
 HEADER 11 - Local hydrophobic density Score   : 7.0000
 HEADER 12 - Number of apolar alpha sphere     :     8