Sanitizing post computation checks

@@ -1286,46 +1286,37 @@ class Pipeline:
         conn = sqlite3.connect(runDir + "/results/RNANet.db")
         conn = sqlite3.connect(runDir + "/results/RNANet.db")
 
 
         # Assert every structure is used
         # Assert every structure is used
-        r = sql_ask_database(conn, """SELECT structure_id FROM structure 
-                                      LEFT JOIN chain ON structure.pdb_id = chain.structure_id 
-                                      WHERE chain_id IS NULL;""")
+        r = sql_ask_database(conn, """SELECT DISTINCT pdb_id FROM structure WHERE pdb_id NOT IN (SELECT DISTINCT structure_id FROM chain);""")
         if len(r) and r[0][0] is not None:
         if len(r) and r[0][0] is not None:
-            warn("Structures without referenced chains have been detected")
-            for x in r:
-                print(x)
+            warn("Structures without referenced chains have been detected. This happens if we have known issues, for example.")
+            print(" ".join([x[0] for x in r]))
 
 
         # Assert every chain is attached to a structure
         # Assert every chain is attached to a structure
-        r = sql_ask_database(conn, """SELECT chain_id, structure_id FROM chain 
-                                      LEFT JOIN structure ON chain.structure_id = structure.pdb_id
-                                      WHERE pdb_id IS NULL;""")
+        r = sql_ask_database(conn, """SELECT DISTINCT chain_id, structure_id FROM chain WHERE structure_id NOT IN (SELECT DISTINCT pdb_id FROM structure);""")
         if len(r) and r[0][0] is not None:
         if len(r) and r[0][0] is not None:
             warn("Chains without referenced structures have been detected")
             warn("Chains without referenced structures have been detected")
-            for x in r:
-                print(x)
-
+            print(" ".join([x[1]+'-'+x[0] for x in r]))
         
         
         if self.HOMOLOGY:
         if self.HOMOLOGY:
             # check if chains have been re_mapped:
             # check if chains have been re_mapped:
-            r = sql_ask_database(conn, """SELECT COUNT(chain.chain_id) as Count, rfam_acc
-                                            FROM chain LEFT JOIN re_mapping
-                                            ON chain.chain_id = re_mapping.chain_id
-                                            WHERE index_ali IS NULL GROUP BY rfam_acc;""")
+            r = sql_ask_database(conn, """SELECT COUNT(DISTINCT chain_id) AS Count, rfam_acc FROM chain 
+                                          WHERE chain_id NOT IN (SELECT DISTINCT chain_id FROM re_mapping)
+                                          GROUP BY rfam_acc;""")
             if len(r) and r[0][0] is not None:
             if len(r) and r[0][0] is not None:
-                warn("Structures were not remapped:")
+                warn("Chains were not remapped (This happens if we have known issues for example):")
                 for x in r:
                 for x in r:
                     print(str(x[0]) + " chains of family " + x[1])
                     print(str(x[0]) + " chains of family " + x[1])
 
 
-            # check if some columns are missing in the remappings:
-            r = sql_ask_database(conn, """SELECT c.chain_id, c.structure_id, c.chain_name, c.rfam_acc, re_mapping.index_chain, re_mapping.index_ali 
-                                            FROM chain as c
-                                            NATURAL JOIN re_mapping
-                                            LEFT JOIN align_column 
-                                            ON re_mapping.index_ali=align_column.index_ali AND c.rfam_acc=align_column.rfam_acc
-                                            WHERE freq_A IS NULL;""")
-            if len(r) and r[0][0] is not None:
-                warn("Structures were not remapped:")
-                for x in r:
-                    print(x)
+            # # TODO : Optimize this (too slow)
+            # # check if some columns are missing in the remappings:
+            # r = sql_ask_database(conn, """SELECT c.chain_id, c.structure_id, c.chain_name, c.rfam_acc, r.index_chain, r.index_ali 
+            #                                 FROM chain as c
+            #                                 NATURAL JOIN re_mapping as r
+            #                                 WHERE index_ali NOT IN (SELECT index_ali FROM align_column WHERE rfam_acc = c.rfam_acc);""")
+            # if len(r) and r[0][0] is not None:
+            #     warn("Missing positions in the re-mapping:")
+            #     for x in r:
+            #         print(x)
 
 
         conn.close()
         conn.close()
 
 
@@ -1806,7 +1797,7 @@ def work_mmcif(pdb_id):
     with sqlite3.connect(runDir + "/results/RNANet.db") as conn:
     with sqlite3.connect(runDir + "/results/RNANet.db") as conn:
         sql_execute(conn, """INSERT OR REPLACE INTO structure (pdb_id, pdb_model, date, exp_method, resolution)
         sql_execute(conn, """INSERT OR REPLACE INTO structure (pdb_id, pdb_model, date, exp_method, resolution)
                              VALUES (?, ?, DATE(?), ?, ?);""", data = (pdb_id, 1, date, exp_meth, reso))
                              VALUES (?, ?, DATE(?), ?, ?);""", data = (pdb_id, 1, date, exp_meth, reso))
-    
+
     # run DSSR (you need to have it in your $PATH, follow x3dna installation instructions)
     # run DSSR (you need to have it in your $PATH, follow x3dna installation instructions)
     output = subprocess.run(["x3dna-dssr", f"-i={final_filepath}", "--json", "--auxfile=no"], 
     output = subprocess.run(["x3dna-dssr", f"-i={final_filepath}", "--json", "--auxfile=no"], 
                              stdout=subprocess.PIPE, stderr=subprocess.PIPE)
                              stdout=subprocess.PIPE, stderr=subprocess.PIPE)
@@ -1964,11 +1955,12 @@ def work_realign(rfam_acc):
             notify("Aligned new sequences together")
             notify("Aligned new sequences together")
 
 
             # And we merge the two alignments
             # And we merge the two alignments
-            p2= subprocess.run(["esl-alimerge", "-o", path_to_seq_data + f"realigned/{rfam_acc}++.stk", "--rna",
+            p2= subprocess.run(["esl-alimerge", "-o", path_to_seq_data + f"realigned/{rfam_acc}_merged.stk", "--rna",
                                 path_to_seq_data + f"realigned/{rfam_acc}++.stk", 
                                 path_to_seq_data + f"realigned/{rfam_acc}++.stk", 
                                 path_to_seq_data + f"realigned/{rfam_acc}_new.stk" ], 
                                 path_to_seq_data + f"realigned/{rfam_acc}_new.stk" ], 
                                 stdout=subprocess.DEVNULL, stderr=subprocess.PIPE)
                                 stdout=subprocess.DEVNULL, stderr=subprocess.PIPE)
             stderr = p1.stderr.decode('utf-8') + p2.stderr.decode('utf-8')
             stderr = p1.stderr.decode('utf-8') + p2.stderr.decode('utf-8')
+            subprocess.run(["mv", path_to_seq_data + f"realigned/{rfam_acc}_merged.stk", path_to_seq_data + f"realigned/{rfam_acc}++.stk"])
             notify("Merged alignments into one")
             notify("Merged alignments into one")
 
 
             # remove the partial files
             # remove the partial files

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+2du3_1_D_1-71
+Could not find nucleotides of chain D in annotation 2du3.json. We expect a problem with 2du3 mmCIF download. Delete it and retry.
+
+2du4_1_C_1-71
+Could not find nucleotides of chain C in annotation 2du4.json. We expect a problem with 2du4 mmCIF download. Delete it and retry.
+
+2du5_1_D_1-71
+Could not find nucleotides of chain D in annotation 2du5.json. We expect a problem with 2du5 mmCIF download. Delete it and retry.
+
+2du6_1_D_1-71
+Could not find nucleotides of chain D in annotation 2du6.json. We expect a problem with 2du6 mmCIF download. Delete it and retry.
+
+1ml5_1_a_151-2903
+Could not find nucleotides of chain a in annotation 1ml5.json. We expect a problem with 1ml5 mmCIF download. Delete it and retry.
+
+1ml5_1_a_1-2914
+Could not find nucleotides of chain a in annotation 1ml5.json. We expect a problem with 1ml5 mmCIF download. Delete it and retry.
+
+1ml5_1_b_5-121
+Could not find nucleotides of chain b in annotation 1ml5.json. We expect a problem with 1ml5 mmCIF download. Delete it and retry.
+
+1ml5_1_A_2-1520
+Could not find nucleotides of chain A in annotation 1ml5.json. We expect a problem with 1ml5 mmCIF download. Delete it and retry.
+
+1ml5_1_A_7-1518
+Could not find nucleotides of chain A in annotation 1ml5.json. We expect a problem with 1ml5 mmCIF download. Delete it and retry.
+
+1ml5_1_A_7-1515
+Could not find nucleotides of chain A in annotation 1ml5.json. We expect a problem with 1ml5 mmCIF download. Delete it and retry.
+
+5b63_1_D_1-74
+Could not find nucleotides of chain D in annotation 5b63.json. We expect a problem with 5b63 mmCIF download. Delete it and retry.
+
+5b63_1_B_1-74
+Could not find nucleotides of chain B in annotation 5b63.json. We expect a problem with 5b63 mmCIF download. Delete it and retry.
+
+5yyn_1_D_1-74
+Could not find nucleotides of chain D in annotation 5yyn.json. We expect a problem with 5yyn mmCIF download. Delete it and retry.
+
+5yyn_1_B_1-74
+Could not find nucleotides of chain B in annotation 5yyn.json. We expect a problem with 5yyn mmCIF download. Delete it and retry.
+
+6prv_1_A_1-58
+Could not find nucleotides of chain A in annotation 6prv.json. We expect a problem with 6prv mmCIF download. Delete it and retry.
+
+6prv_1_B_1-58
+Could not find nucleotides of chain B in annotation 6prv.json. We expect a problem with 6prv mmCIF download. Delete it and retry.
+
+6prv_1_C_1-58
+Could not find nucleotides of chain C in annotation 6prv.json. We expect a problem with 6prv mmCIF download. Delete it and retry.
+
+6prv_1_D_1-58
+Could not find nucleotides of chain D in annotation 6prv.json. We expect a problem with 6prv mmCIF download. Delete it and retry.
+
+1hc8_1_C_1-58
+Could not find nucleotides of chain C in annotation 1hc8.json. We expect a problem with 1hc8 mmCIF download. Delete it and retry.
+
+1hc8_1_D_1-58
+Could not find nucleotides of chain D in annotation 1hc8.json. We expect a problem with 1hc8 mmCIF download. Delete it and retry.
+
+1y39_1_C_1-58
+Could not find nucleotides of chain C in annotation 1y39.json. We expect a problem with 1y39 mmCIF download. Delete it and retry.
+
+1y39_1_D_1-58
+Could not find nucleotides of chain D in annotation 1y39.json. We expect a problem with 1y39 mmCIF download. Delete it and retry.
+
+1qa6_1_C_1-58
+Could not find nucleotides of chain C in annotation 1qa6.json. We expect a problem with 1qa6 mmCIF download. Delete it and retry.
+
+1qa6_1_D_1-58
+Could not find nucleotides of chain D in annotation 1qa6.json. We expect a problem with 1qa6 mmCIF download. Delete it and retry.
+
+2go5_1_9_3-88
+Could not find nucleotides of chain 9 in annotation 2go5.json. We expect a problem with 2go5 mmCIF download. Delete it and retry.
+
+3ds7_1_B_1-67
+Could not find nucleotides of chain B in annotation 3ds7.json. We expect a problem with 3ds7 mmCIF download. Delete it and retry.
+
+6qzp_1_L8_1267-4755
+Could not find nucleotides of chain L8 in annotation 6qzp.json. We expect a problem with 6qzp mmCIF download. Delete it and retry.
+
+6ek0_1_L8_1267-4755
+Could not find nucleotides of chain L8 in annotation 6ek0.json. We expect a problem with 6ek0 mmCIF download. Delete it and retry.
+
+6ole_1_D_1267-4755
+Could not find nucleotides of chain D in annotation 6ole.json. We expect a problem with 6ole mmCIF download. Delete it and retry.
+
+6om0_1_D_1267-4755
+Could not find nucleotides of chain D in annotation 6om0.json. We expect a problem with 6om0 mmCIF download. Delete it and retry.
+
+6y2l_1_L8_1267-4755
+Could not find nucleotides of chain L8 in annotation 6y2l.json. We expect a problem with 6y2l mmCIF download. Delete it and retry.
+
+6y0g_1_L8_1267-4755
+Could not find nucleotides of chain L8 in annotation 6y0g.json. We expect a problem with 6y0g mmCIF download. Delete it and retry.
+
+6oli_1_D_1267-4755
+Could not find nucleotides of chain D in annotation 6oli.json. We expect a problem with 6oli mmCIF download. Delete it and retry.
+
+6olg_1_A3_1267-4755
+Could not find nucleotides of chain A3 in annotation 6olg.json. We expect a problem with 6olg mmCIF download. Delete it and retry.
+
+6y57_1_L8_1267-4755
+Could not find nucleotides of chain L8 in annotation 6y57.json. We expect a problem with 6y57 mmCIF download. Delete it and retry.
+
+5t2c_1_C_1267-4755
+Could not find nucleotides of chain C in annotation 5t2c.json. We expect a problem with 5t2c mmCIF download. Delete it and retry.
+
+6om7_1_D_1267-4755
+Could not find nucleotides of chain D in annotation 6om7.json. We expect a problem with 6om7 mmCIF download. Delete it and retry.
+
+4ug0_1_L8_1267-4755
+Could not find nucleotides of chain L8 in annotation 4ug0.json. We expect a problem with 4ug0 mmCIF download. Delete it and retry.
+
+6olf_1_D_1267-4755
+Could not find nucleotides of chain D in annotation 6olf.json. We expect a problem with 6olf mmCIF download. Delete it and retry.
+
+6ip5_1_1C_1267-4755
+Could not find nucleotides of chain 1C in annotation 6ip5.json. We expect a problem with 6ip5 mmCIF download. Delete it and retry.
+
+6ip8_1_1C_1267-4755
+Could not find nucleotides of chain 1C in annotation 6ip8.json. We expect a problem with 6ip8 mmCIF download. Delete it and retry.
+
+6olz_1_A3_1267-4755
+Could not find nucleotides of chain A3 in annotation 6olz.json. We expect a problem with 6olz mmCIF download. Delete it and retry.
+
+5aj0_1_A3_1267-4755
+Could not find nucleotides of chain A3 in annotation 5aj0.json. We expect a problem with 5aj0 mmCIF download. Delete it and retry.
+
+5lks_1_L8_1267-4755
+Could not find nucleotides of chain L8 in annotation 5lks.json. We expect a problem with 5lks mmCIF download. Delete it and retry.
+
+6ip6_1_1C_1267-4755
+Could not find nucleotides of chain 1C in annotation 6ip6.json. We expect a problem with 6ip6 mmCIF download. Delete it and retry.
+
+4v6x_1_A8_1267-4755
+Could not find nucleotides of chain A8 in annotation 4v6x.json. We expect a problem with 4v6x mmCIF download. Delete it and retry.
+
+4woi_1_BB_3-118
+Could not find nucleotides of chain BB in annotation 4woi.json. We expect a problem with 4woi mmCIF download. Delete it and retry.
+
+4woi_1_CB_3-118
+Could not find nucleotides of chain CB in annotation 4woi.json. We expect a problem with 4woi mmCIF download. Delete it and retry.
+
+2rdo_1_A_3-118
+DSSR warning 2rdo.json: no nucleotides found. Ignoring 2rdo_1_A_3-118.
+
+4v48_1_A9_3-118
+DSSR warning 4v48.json: no nucleotides found. Ignoring 4v48_1_A9_3-118.
+
+4v47_1_A9_3-118
+DSSR warning 4v47.json: no nucleotides found. Ignoring 4v47_1_A9_3-118.
+
+1vy7_1_AY_1-73
+Sequence is too short. (< 5 resolved nts)
+
+1vy7_1_CY_1-73
+Sequence is too short. (< 5 resolved nts)
+
+4w2h_1_CY_1-73
+Sequence is too short. (< 5 resolved nts)
+
+2z9q_1_A_1-72
+DSSR warning 2z9q.json: no nucleotides found. Ignoring 2z9q_1_A_1-72.
+
+4v42_1_BB_5-121
+Could not find nucleotides of chain BB in annotation 4v42.json. We expect a problem with 4v42 mmCIF download. Delete it and retry.
+
+1ls2_1_B_1-73
+DSSR warning 1ls2.json: no nucleotides found. Ignoring 1ls2_1_B_1-73.
+
+3u4m_1_B_1-80
+Could not find nucleotides of chain B in annotation 3u4m.json. We expect a problem with 3u4m mmCIF download. Delete it and retry.
+
+4qvi_1_B_1-80
+Could not find nucleotides of chain B in annotation 4qvi.json. We expect a problem with 4qvi mmCIF download. Delete it and retry.
+
+3umy_1_B_1-80
+Could not find nucleotides of chain B in annotation 3umy.json. We expect a problem with 3umy mmCIF download. Delete it and retry.
+
+4qg3_1_B_1-80
+Could not find nucleotides of chain B in annotation 4qg3.json. We expect a problem with 4qg3 mmCIF download. Delete it and retry.
+
+3u56_1_B_1-80
+Could not find nucleotides of chain B in annotation 3u56.json. We expect a problem with 3u56 mmCIF download. Delete it and retry.
+
+3ep2_1_Y_1-72
+DSSR warning 3ep2.json: no nucleotides found. Ignoring 3ep2_1_Y_1-72.
+
+3eq3_1_Y_1-72
+DSSR warning 3eq3.json: no nucleotides found. Ignoring 3eq3_1_Y_1-72.
+
+4v48_1_A6_1-73
+DSSR warning 4v48.json: no nucleotides found. Ignoring 4v48_1_A6_1-73.
+
+2qex_1_9_1-121
+Could not find nucleotides of chain 9 in annotation 2qex.json. We expect a problem with 2qex mmCIF download. Delete it and retry.
+
+2otl_1_9_1-121
+Could not find nucleotides of chain 9 in annotation 2otl.json. We expect a problem with 2otl mmCIF download. Delete it and retry.
+
+2otj_1_9_1-121
+Could not find nucleotides of chain 9 in annotation 2otj.json. We expect a problem with 2otj mmCIF download. Delete it and retry.
+
+1kqs_1_9_1-121
+Could not find nucleotides of chain 9 in annotation 1kqs.json. We expect a problem with 1kqs mmCIF download. Delete it and retry.
+
+3ow2_1_9_1-121
+Could not find nucleotides of chain 9 in annotation 3ow2.json. We expect a problem with 3ow2 mmCIF download. Delete it and retry.
+
+1vq8_1_9_1-121
+Could not find nucleotides of chain 9 in annotation 1vq8.json. We expect a problem with 1vq8 mmCIF download. Delete it and retry.
+
+1vqo_1_9_1-121
+Could not find nucleotides of chain 9 in annotation 1vqo.json. We expect a problem with 1vqo mmCIF download. Delete it and retry.
+
+1vqk_1_9_1-121
+Could not find nucleotides of chain 9 in annotation 1vqk.json. We expect a problem with 1vqk mmCIF download. Delete it and retry.
+
+1vq9_1_9_1-121
+Could not find nucleotides of chain 9 in annotation 1vq9.json. We expect a problem with 1vq9 mmCIF download. Delete it and retry.
+
+1vqp_1_9_1-121
+Could not find nucleotides of chain 9 in annotation 1vqp.json. We expect a problem with 1vqp mmCIF download. Delete it and retry.
+
+1vq7_1_9_1-121
+Could not find nucleotides of chain 9 in annotation 1vq7.json. We expect a problem with 1vq7 mmCIF download. Delete it and retry.
+
+1vqn_1_9_1-121
+Could not find nucleotides of chain 9 in annotation 1vqn.json. We expect a problem with 1vqn mmCIF download. Delete it and retry.
+
+1vq4_1_9_1-121
+Could not find nucleotides of chain 9 in annotation 1vq4.json. We expect a problem with 1vq4 mmCIF download. Delete it and retry.
+
+1vq6_1_9_1-121
+Could not find nucleotides of chain 9 in annotation 1vq6.json. We expect a problem with 1vq6 mmCIF download. Delete it and retry.
+
+1m90_1_B_1-121
+Could not find nucleotides of chain B in annotation 1m90.json. We expect a problem with 1m90 mmCIF download. Delete it and retry.
+
+1qvg_1_9_1-121
+Could not find nucleotides of chain 9 in annotation 1qvg.json. We expect a problem with 1qvg mmCIF download. Delete it and retry.
+
+1vq5_1_9_1-121
+Could not find nucleotides of chain 9 in annotation 1vq5.json. We expect a problem with 1vq5 mmCIF download. Delete it and retry.
+
+1nji_1_B_1-121
+Could not find nucleotides of chain B in annotation 1nji.json. We expect a problem with 1nji mmCIF download. Delete it and retry.
+
+3cxc_1_9_1-121
+Could not find nucleotides of chain 9 in annotation 3cxc.json. We expect a problem with 3cxc mmCIF download. Delete it and retry.
+
+3cpw_1_9_1-121
+Could not find nucleotides of chain 9 in annotation 3cpw.json. We expect a problem with 3cpw mmCIF download. Delete it and retry.
+
+1q81_1_B_1-121
+Could not find nucleotides of chain B in annotation 1q81.json. We expect a problem with 1q81 mmCIF download. Delete it and retry.
+
+1q86_1_B_1-121
+Could not find nucleotides of chain B in annotation 1q86.json. We expect a problem with 1q86 mmCIF download. Delete it and retry.
+
+1kc8_1_B_1-121
+Could not find nucleotides of chain B in annotation 1kc8.json. We expect a problem with 1kc8 mmCIF download. Delete it and retry.
+
+1k73_1_B_1-121
+Could not find nucleotides of chain B in annotation 1k73.json. We expect a problem with 1k73 mmCIF download. Delete it and retry.
+
+1q82_1_B_1-121
+Could not find nucleotides of chain B in annotation 1q82.json. We expect a problem with 1q82 mmCIF download. Delete it and retry.
+
+1k9m_1_B_1-121
+Could not find nucleotides of chain B in annotation 1k9m.json. We expect a problem with 1k9m mmCIF download. Delete it and retry.
+
+1qvf_1_9_1-121
+Could not find nucleotides of chain 9 in annotation 1qvf.json. We expect a problem with 1qvf mmCIF download. Delete it and retry.
+
+1m1k_1_B_1-121
+Could not find nucleotides of chain B in annotation 1m1k.json. We expect a problem with 1m1k mmCIF download. Delete it and retry.
+
+1kd1_1_B_1-121
+Could not find nucleotides of chain B in annotation 1kd1.json. We expect a problem with 1kd1 mmCIF download. Delete it and retry.
+
+1k8a_1_B_1-121
+Could not find nucleotides of chain B in annotation 1k8a.json. We expect a problem with 1k8a mmCIF download. Delete it and retry.
+
+1q7y_1_B_1-121
+Could not find nucleotides of chain B in annotation 1q7y.json. We expect a problem with 1q7y mmCIF download. Delete it and retry.
+
+1n8r_1_B_1-121
+Could not find nucleotides of chain B in annotation 1n8r.json. We expect a problem with 1n8r mmCIF download. Delete it and retry.
+
+1eg0_1_O_1-73
+DSSR warning 1eg0.json: no nucleotides found. Ignoring 1eg0_1_O_1-73.
+
+1qtq_1_B_1-72
+Could not find nucleotides of chain B in annotation 1qtq.json. We expect a problem with 1qtq mmCIF download. Delete it and retry.
+
+4jxx_1_B_1-72
+Could not find nucleotides of chain B in annotation 4jxx.json. We expect a problem with 4jxx mmCIF download. Delete it and retry.
+
+1zjw_1_B_1-72
+Could not find nucleotides of chain B in annotation 1zjw.json. We expect a problem with 1zjw mmCIF download. Delete it and retry.
+
+1euy_1_B_1-71
+Could not find nucleotides of chain B in annotation 1euy.json. We expect a problem with 1euy mmCIF download. Delete it and retry.
+
+1euq_1_B_1-69
+Could not find nucleotides of chain B in annotation 1euq.json. We expect a problem with 1euq mmCIF download. Delete it and retry.
+
+2rd2_1_B_1-72
+Could not find nucleotides of chain B in annotation 2rd2.json. We expect a problem with 2rd2 mmCIF download. Delete it and retry.
+
+2re8_1_B_1-72
+Could not find nucleotides of chain B in annotation 2re8.json. We expect a problem with 2re8 mmCIF download. Delete it and retry.
+
 1gsg_1_T_1-72
 1gsg_1_T_1-72
-DSSR warning for 1gsg_1_T_1-72: no nucleotides found
+DSSR warning 1gsg.json: no nucleotides found. Ignoring 1gsg_1_T_1-72.
+
+1o0c_1_B_1-72
+Could not find nucleotides of chain B in annotation 1o0c.json. We expect a problem with 1o0c mmCIF download. Delete it and retry.
+
+1o0b_1_B_1-72
+Could not find nucleotides of chain B in annotation 1o0b.json. We expect a problem with 1o0b mmCIF download. Delete it and retry.
+
+1exd_1_B_1-70
+Could not find nucleotides of chain B in annotation 1exd.json. We expect a problem with 1exd mmCIF download. Delete it and retry.
+
+1fg0_1_A_1-602
+Could not find nucleotides of chain A in annotation 1fg0.json. We expect a problem with 1fg0 mmCIF download. Delete it and retry.
+
+1ffz_1_A_1-602
+Could not find nucleotides of chain A in annotation 1ffz.json. We expect a problem with 1ffz mmCIF download. Delete it and retry.
+
+3ktv_1_C_2-106
+Could not find nucleotides of chain C in annotation 3ktv.json. We expect a problem with 3ktv mmCIF download. Delete it and retry.
+
+3ktv_1_A_2-106
+Could not find nucleotides of chain A in annotation 3ktv.json. We expect a problem with 3ktv mmCIF download. Delete it and retry.
+
+3jcr_1_H_1-115
+DSSR warning 3jcr.json: no nucleotides found. Ignoring 3jcr_1_H_1-115.
+
+6d9j_1_4_1-187
+Could not find nucleotides of chain 4 in annotation 6d9j.json. We expect a problem with 6d9j mmCIF download. Delete it and retry.
+
+4v42_1_BA_151-2903
+Could not find nucleotides of chain BA in annotation 4v42.json. We expect a problem with 4v42 mmCIF download. Delete it and retry.
+
+4v42_1_BA_1-2914
+Could not find nucleotides of chain BA in annotation 4v42.json. We expect a problem with 4v42 mmCIF download. Delete it and retry.
+
+3moj_1_A_1-73
+Could not find nucleotides of chain A in annotation 3moj.json. We expect a problem with 3moj mmCIF download. Delete it and retry.
+
+4v48_1_BA_1-91
+DSSR warning 4v48.json: no nucleotides found. Ignoring 4v48_1_BA_1-91.
+
+4v48_1_BA_6-1538
+DSSR warning 4v48.json: no nucleotides found. Ignoring 4v48_1_BA_6-1538.
+
+4v48_1_BA_1-1543
+DSSR warning 4v48.json: no nucleotides found. Ignoring 4v48_1_BA_1-1543.
+
+4v48_1_BA_6-1541
+DSSR warning 4v48.json: no nucleotides found. Ignoring 4v48_1_BA_6-1541.
+
+4v47_1_BA_1-91
+DSSR warning 4v47.json: no nucleotides found. Ignoring 4v47_1_BA_1-91.
+
+4v47_1_BA_6-1537
+DSSR warning 4v47.json: no nucleotides found. Ignoring 4v47_1_BA_6-1537.
+
+4v47_1_BA_1-1542
+DSSR warning 4v47.json: no nucleotides found. Ignoring 4v47_1_BA_1-1542.
+
+4v47_1_BA_6-1540
+DSSR warning 4v47.json: no nucleotides found. Ignoring 4v47_1_BA_6-1540.
+
+5u4j_1_A_6-1522
+Could not find nucleotides of chain A in annotation 5u4j.json. We expect a problem with 5u4j mmCIF download. Delete it and retry.
+
+5u4j_1_A_1-1528
+Could not find nucleotides of chain A in annotation 5u4j.json. We expect a problem with 5u4j mmCIF download. Delete it and retry.
+
+5u4j_1_A_6-1460
+Could not find nucleotides of chain A in annotation 5u4j.json. We expect a problem with 5u4j mmCIF download. Delete it and retry.
+
+5u4j_1_A_6-1457
+Could not find nucleotides of chain A in annotation 5u4j.json. We expect a problem with 5u4j mmCIF download. Delete it and retry.
+
+2rdo_1_B_1-2903
+DSSR warning 2rdo.json: no nucleotides found. Ignoring 2rdo_1_B_1-2903.
+
+2rdo_1_B_6-1522
+DSSR warning 2rdo.json: no nucleotides found. Ignoring 2rdo_1_B_6-1522.
+
+2rdo_1_B_1-1528
+DSSR warning 2rdo.json: no nucleotides found. Ignoring 2rdo_1_B_1-1528.
+
+2rdo_1_B_6-1460
+DSSR warning 2rdo.json: no nucleotides found. Ignoring 2rdo_1_B_6-1460.
+
+2rdo_1_B_160-2893
+DSSR warning 2rdo.json: no nucleotides found. Ignoring 2rdo_1_B_160-2893.
+
+2rdo_1_B_1-2904
+DSSR warning 2rdo.json: no nucleotides found. Ignoring 2rdo_1_B_1-2904.
+
+2rdo_1_B_6-1457
+DSSR warning 2rdo.json: no nucleotides found. Ignoring 2rdo_1_B_6-1457.
+
+4v48_1_A0_1-2903
+DSSR warning 4v48.json: no nucleotides found. Ignoring 4v48_1_A0_1-2903.
+
+4v48_1_A0_6-1522
+DSSR warning 4v48.json: no nucleotides found. Ignoring 4v48_1_A0_6-1522.
+
+4v48_1_A0_1-1528
+DSSR warning 4v48.json: no nucleotides found. Ignoring 4v48_1_A0_1-1528.
+
+4v48_1_A0_6-1460
+DSSR warning 4v48.json: no nucleotides found. Ignoring 4v48_1_A0_6-1460.
+
+4v48_1_A0_160-2893
+DSSR warning 4v48.json: no nucleotides found. Ignoring 4v48_1_A0_160-2893.
+
+4v48_1_A0_1-2904
+DSSR warning 4v48.json: no nucleotides found. Ignoring 4v48_1_A0_1-2904.
+
+4v48_1_A0_6-1457
+DSSR warning 4v48.json: no nucleotides found. Ignoring 4v48_1_A0_6-1457.
+
+4v47_1_A0_1-2903
+DSSR warning 4v47.json: no nucleotides found. Ignoring 4v47_1_A0_1-2903.
+
+4v47_1_A0_6-1522
+DSSR warning 4v47.json: no nucleotides found. Ignoring 4v47_1_A0_6-1522.
+
+4v47_1_A0_1-1528
+DSSR warning 4v47.json: no nucleotides found. Ignoring 4v47_1_A0_1-1528.
+
+4v47_1_A0_6-1460
+DSSR warning 4v47.json: no nucleotides found. Ignoring 4v47_1_A0_6-1460.
+
+4v47_1_A0_160-2893
+DSSR warning 4v47.json: no nucleotides found. Ignoring 4v47_1_A0_160-2893.
+
+4v47_1_A0_1-2904
+DSSR warning 4v47.json: no nucleotides found. Ignoring 4v47_1_A0_1-2904.
+
+4v47_1_A0_6-1457
+DSSR warning 4v47.json: no nucleotides found. Ignoring 4v47_1_A0_6-1457.
+
+1il2_1_C_1-72
+Could not find nucleotides of chain C in annotation 1il2.json. We expect a problem with 1il2 mmCIF download. Delete it and retry.
+
+1il2_1_D_1-72
+Could not find nucleotides of chain D in annotation 1il2.json. We expect a problem with 1il2 mmCIF download. Delete it and retry.
+
+1asz_1_S_1-72
+Could not find nucleotides of chain S in annotation 1asz.json. We expect a problem with 1asz mmCIF download. Delete it and retry.
+
+1asy_1_S_1-72
+Could not find nucleotides of chain S in annotation 1asy.json. We expect a problem with 1asy mmCIF download. Delete it and retry.
+
+1asz_1_R_1-72
+Could not find nucleotides of chain R in annotation 1asz.json. We expect a problem with 1asz mmCIF download. Delete it and retry.
+
+1asy_1_R_1-72
+Could not find nucleotides of chain R in annotation 1asy.json. We expect a problem with 1asy mmCIF download. Delete it and retry.
+
+2ob7_1_A_10-319
+DSSR warning 2ob7.json: no nucleotides found. Ignoring 2ob7_1_A_10-319.
+
+2om7_1_C_1-96
+Could not find nucleotides of chain C in annotation 2om7.json. We expect a problem with 2om7 mmCIF download. Delete it and retry.
+
+2om7_1_C_1-130
+Could not find nucleotides of chain C in annotation 2om7.json. We expect a problem with 2om7 mmCIF download. Delete it and retry.
+
+1x1l_1_A_1-130
+DSSR warning 1x1l.json: no nucleotides found. Ignoring 1x1l_1_A_1-130.
+
+1zc8_1_Z_1-91
+DSSR warning 1zc8.json: no nucleotides found. Ignoring 1zc8_1_Z_1-91.
+
+1zc8_1_Z_1-130
+DSSR warning 1zc8.json: no nucleotides found. Ignoring 1zc8_1_Z_1-130.
+
+2ob7_1_D_1-130
+DSSR warning 2ob7.json: no nucleotides found. Ignoring 2ob7_1_D_1-130.
+
+1wz2_1_D_1-85
+Could not find nucleotides of chain D in annotation 1wz2.json. We expect a problem with 1wz2 mmCIF download. Delete it and retry.
+
+1wz2_1_C_1-85
+Could not find nucleotides of chain C in annotation 1wz2.json. We expect a problem with 1wz2 mmCIF download. Delete it and retry.
+
+6b19_1_C_1-73
+Could not find nucleotides of chain C in annotation 6b19.json. We expect a problem with 6b19 mmCIF download. Delete it and retry.
+
+6b19_1_C_3-101
+Could not find nucleotides of chain C in annotation 6b19.json. We expect a problem with 6b19 mmCIF download. Delete it and retry.
+
+5ndk_1_1G_20-55
+Could not find nucleotides of chain 1G in annotation 5ndk.json. We expect a problem with 5ndk mmCIF download. Delete it and retry.
+
+5ndk_1_13_20-55
+Could not find nucleotides of chain 13 in annotation 5ndk.json. We expect a problem with 5ndk mmCIF download. Delete it and retry.
+
+5ndj_1_1G_20-55
+Could not find nucleotides of chain 1G in annotation 5ndj.json. We expect a problem with 5ndj mmCIF download. Delete it and retry.
+
+5ndj_1_13_20-55
+Could not find nucleotides of chain 13 in annotation 5ndj.json. We expect a problem with 5ndj mmCIF download. Delete it and retry.
+
+1jgq_1_A_7-1515
+Could not find nucleotides of chain A in annotation 1jgq.json. We expect a problem with 1jgq mmCIF download. Delete it and retry.
+
+1jgq_1_A_2-1520
+Could not find nucleotides of chain A in annotation 1jgq.json. We expect a problem with 1jgq mmCIF download. Delete it and retry.
+
+1jgq_1_A_7-1518
+Could not find nucleotides of chain A in annotation 1jgq.json. We expect a problem with 1jgq mmCIF download. Delete it and retry.
+
+1jgq_1_A_20-55
+Could not find nucleotides of chain A in annotation 1jgq.json. We expect a problem with 1jgq mmCIF download. Delete it and retry.
+
+4v42_1_AA_7-1515
+Could not find nucleotides of chain AA in annotation 4v42.json. We expect a problem with 4v42 mmCIF download. Delete it and retry.
+
+4v42_1_AA_2-1520
+Could not find nucleotides of chain AA in annotation 4v42.json. We expect a problem with 4v42 mmCIF download. Delete it and retry.
+
+4v42_1_AA_7-1518
+Could not find nucleotides of chain AA in annotation 4v42.json. We expect a problem with 4v42 mmCIF download. Delete it and retry.
+
+4v42_1_AA_20-55
+Could not find nucleotides of chain AA in annotation 4v42.json. We expect a problem with 4v42 mmCIF download. Delete it and retry.
+
+1jgo_1_A_7-1515
+Could not find nucleotides of chain A in annotation 1jgo.json. We expect a problem with 1jgo mmCIF download. Delete it and retry.
+
+1jgo_1_A_2-1520
+Could not find nucleotides of chain A in annotation 1jgo.json. We expect a problem with 1jgo mmCIF download. Delete it and retry.
+
+1jgo_1_A_7-1518
+Could not find nucleotides of chain A in annotation 1jgo.json. We expect a problem with 1jgo mmCIF download. Delete it and retry.
+
+1jgo_1_A_20-55
+Could not find nucleotides of chain A in annotation 1jgo.json. We expect a problem with 1jgo mmCIF download. Delete it and retry.
+
+1jgp_1_A_7-1515
+Could not find nucleotides of chain A in annotation 1jgp.json. We expect a problem with 1jgp mmCIF download. Delete it and retry.
+
+1jgp_1_A_2-1520
+Could not find nucleotides of chain A in annotation 1jgp.json. We expect a problem with 1jgp mmCIF download. Delete it and retry.
+
+1jgp_1_A_7-1518
+Could not find nucleotides of chain A in annotation 1jgp.json. We expect a problem with 1jgp mmCIF download. Delete it and retry.
+
+1jgp_1_A_20-55
+Could not find nucleotides of chain A in annotation 1jgp.json. We expect a problem with 1jgp mmCIF download. Delete it and retry.
+
+1mms_1_C_1-58
+Could not find nucleotides of chain C in annotation 1mms.json. We expect a problem with 1mms mmCIF download. Delete it and retry.
+
+1mms_1_D_1-58
+Could not find nucleotides of chain D in annotation 1mms.json. We expect a problem with 1mms mmCIF download. Delete it and retry.
+
+1r2x_1_C_1-58
+DSSR warning 1r2x.json: no nucleotides found. Ignoring 1r2x_1_C_1-58.
+
+1r2w_1_C_1-58
+DSSR warning 1r2w.json: no nucleotides found. Ignoring 1r2w_1_C_1-58.
+
+1eg0_1_L_1-56
+DSSR warning 1eg0.json: no nucleotides found. Ignoring 1eg0_1_L_1-56.
+
+1eg0_1_L_1-57
+DSSR warning 1eg0.json: no nucleotides found. Ignoring 1eg0_1_L_1-57.
+
+6rxu_1_C2_588-2383
+Could not find nucleotides of chain C2 in annotation 6rxu.json. We expect a problem with 6rxu mmCIF download. Delete it and retry.
+
+6rxu_1_C2_583-2388
+Could not find nucleotides of chain C2 in annotation 6rxu.json. We expect a problem with 6rxu mmCIF download. Delete it and retry.
+
+6rxu_1_C2_588-2386
+Could not find nucleotides of chain C2 in annotation 6rxu.json. We expect a problem with 6rxu mmCIF download. Delete it and retry.
+
+5oql_1_2_588-2383
+Could not find nucleotides of chain 2 in annotation 5oql.json. We expect a problem with 5oql mmCIF download. Delete it and retry.
+
+5oql_1_2_583-2388
+Could not find nucleotides of chain 2 in annotation 5oql.json. We expect a problem with 5oql mmCIF download. Delete it and retry.
+
+5oql_1_2_588-2386
+Could not find nucleotides of chain 2 in annotation 5oql.json. We expect a problem with 5oql mmCIF download. Delete it and retry.
+
+6rxv_1_C2_588-2383
+Could not find nucleotides of chain C2 in annotation 6rxv.json. We expect a problem with 6rxv mmCIF download. Delete it and retry.
+
+6rxv_1_C2_583-2388
+Could not find nucleotides of chain C2 in annotation 6rxv.json. We expect a problem with 6rxv mmCIF download. Delete it and retry.
+
+6rxv_1_C2_588-2386
+Could not find nucleotides of chain C2 in annotation 6rxv.json. We expect a problem with 6rxv mmCIF download. Delete it and retry.
+
+6rxz_1_C2_588-2383
+Could not find nucleotides of chain C2 in annotation 6rxz.json. We expect a problem with 6rxz mmCIF download. Delete it and retry.
+
+6rxz_1_C2_583-2388
+Could not find nucleotides of chain C2 in annotation 6rxz.json. We expect a problem with 6rxz mmCIF download. Delete it and retry.
+
+6rxz_1_C2_588-2386
+Could not find nucleotides of chain C2 in annotation 6rxz.json. We expect a problem with 6rxz mmCIF download. Delete it and retry.
+
+6rxy_1_C2_588-2383
+Could not find nucleotides of chain C2 in annotation 6rxy.json. We expect a problem with 6rxy mmCIF download. Delete it and retry.
+
+6rxy_1_C2_583-2388
+Could not find nucleotides of chain C2 in annotation 6rxy.json. We expect a problem with 6rxy mmCIF download. Delete it and retry.
+
+6rxy_1_C2_588-2386
+Could not find nucleotides of chain C2 in annotation 6rxy.json. We expect a problem with 6rxy mmCIF download. Delete it and retry.
+
+6rxt_1_C2_588-2383
+Could not find nucleotides of chain C2 in annotation 6rxt.json. We expect a problem with 6rxt mmCIF download. Delete it and retry.
+
+6rxt_1_C2_583-2388
+Could not find nucleotides of chain C2 in annotation 6rxt.json. We expect a problem with 6rxt mmCIF download. Delete it and retry.
+
+6rxt_1_C2_588-2386
+Could not find nucleotides of chain C2 in annotation 6rxt.json. We expect a problem with 6rxt mmCIF download. Delete it and retry.
+
+4d61_1_j_1-199
+Could not find nucleotides of chain j in annotation 4d61.json. We expect a problem with 4d61 mmCIF download. Delete it and retry.
+
+4d5n_1_X_1-199
+Could not find nucleotides of chain X in annotation 4d5n.json. We expect a problem with 4d5n mmCIF download. Delete it and retry.
+
+3k0j_1_F_2-86
+Could not find nucleotides of chain F in annotation 3k0j.json. We expect a problem with 3k0j mmCIF download. Delete it and retry.
+
+4jxz_1_B_1-72
+Could not find nucleotides of chain B in annotation 4jxz.json. We expect a problem with 4jxz mmCIF download. Delete it and retry.
+
+4jyz_1_B_1-72
+Could not find nucleotides of chain B in annotation 4jyz.json. We expect a problem with 4jyz mmCIF download. Delete it and retry.
+
+3wqy_1_C_1-72
+Could not find nucleotides of chain C in annotation 3wqy.json. We expect a problem with 3wqy mmCIF download. Delete it and retry.
+
+3wqz_1_C_1-72
+Could not find nucleotides of chain C in annotation 3wqz.json. We expect a problem with 3wqz mmCIF download. Delete it and retry.
+
+1zc8_1_A_1-59
+DSSR warning 1zc8.json: no nucleotides found. Ignoring 1zc8_1_A_1-59.
+
+1mvr_1_D_1-59
+DSSR warning 1mvr.json: no nucleotides found. Ignoring 1mvr_1_D_1-59.
+
+4c9d_1_D_29-1
+Could not find nucleotides of chain D in annotation 4c9d.json. We expect a problem with 4c9d mmCIF download. Delete it and retry.
+
+4c9d_1_C_29-1
+Could not find nucleotides of chain C in annotation 4c9d.json. We expect a problem with 4c9d mmCIF download. Delete it and retry.
+
+4xej_1_BIRE_4-193
+Could not find nucleotides of chain BIRE in annotation 4xej.json. We expect a problem with 4xej mmCIF download. Delete it and retry.
+
+4xej_1_AIRE_4-193
+Could not find nucleotides of chain AIRE in annotation 4xej.json. We expect a problem with 4xej mmCIF download. Delete it and retry.
+
+1zn1_1_B_1-59
+DSSR warning 1zn1.json: no nucleotides found. Ignoring 1zn1_1_B_1-59.
+
+1n78_1_C_1-72
+Could not find nucleotides of chain C in annotation 1n78.json. We expect a problem with 1n78 mmCIF download. Delete it and retry.
+
+1n78_1_D_1-72
+Could not find nucleotides of chain D in annotation 1n78.json. We expect a problem with 1n78 mmCIF download. Delete it and retry.
+
+2dxi_1_C_1-72
+Could not find nucleotides of chain C in annotation 2dxi.json. We expect a problem with 2dxi mmCIF download. Delete it and retry.
+
+1n77_1_C_1-72
+Could not find nucleotides of chain C in annotation 1n77.json. We expect a problem with 1n77 mmCIF download. Delete it and retry.
+
+2dxi_1_D_1-72
+Could not find nucleotides of chain D in annotation 2dxi.json. We expect a problem with 2dxi mmCIF download. Delete it and retry.
+
+2cv2_1_C_1-72
+Could not find nucleotides of chain C in annotation 2cv2.json. We expect a problem with 2cv2 mmCIF download. Delete it and retry.
+
+1n77_1_D_1-72
+Could not find nucleotides of chain D in annotation 1n77.json. We expect a problem with 1n77 mmCIF download. Delete it and retry.
+
+2cv2_1_D_1-72
+Could not find nucleotides of chain D in annotation 2cv2.json. We expect a problem with 2cv2 mmCIF download. Delete it and retry.
+
+2cv1_1_D_1-72
+Could not find nucleotides of chain D in annotation 2cv1.json. We expect a problem with 2cv1 mmCIF download. Delete it and retry.
+
+2cv1_1_C_1-72
+Could not find nucleotides of chain C in annotation 2cv1.json. We expect a problem with 2cv1 mmCIF download. Delete it and retry.
+
+2cv0_1_C_1-72
+Could not find nucleotides of chain C in annotation 2cv0.json. We expect a problem with 2cv0 mmCIF download. Delete it and retry.
+
+2cv0_1_D_1-72
+Could not find nucleotides of chain D in annotation 2cv0.json. We expect a problem with 2cv0 mmCIF download. Delete it and retry.
+
+1g59_1_B_1-72
+Could not find nucleotides of chain B in annotation 1g59.json. We expect a problem with 1g59 mmCIF download. Delete it and retry.
+
+1g59_1_D_1-72
+Could not find nucleotides of chain D in annotation 1g59.json. We expect a problem with 1g59 mmCIF download. Delete it and retry.
+
+1emi_1_B_1-108
+DSSR warning 1emi.json: no nucleotides found. Ignoring 1emi_1_B_1-108.
+
+3iy9_1_A_498-1027
+DSSR warning 3iy9.json: no nucleotides found. Ignoring 3iy9_1_A_498-1027.
+
+3j0o_1_2_1-112
+Could not find nucleotides of chain 2 in annotation 3j0o.json. We expect a problem with 3j0o mmCIF download. Delete it and retry.
+
+3j0o_1_2_1-111
+Could not find nucleotides of chain 2 in annotation 3j0o.json. We expect a problem with 3j0o mmCIF download. Delete it and retry.
+
+3j0l_1_2_1-112
+Could not find nucleotides of chain 2 in annotation 3j0l.json. We expect a problem with 3j0l mmCIF download. Delete it and retry.
+
+3j0l_1_2_1-111
+Could not find nucleotides of chain 2 in annotation 3j0l.json. We expect a problem with 3j0l mmCIF download. Delete it and retry.
+
+3j0p_1_2_1-112
+Could not find nucleotides of chain 2 in annotation 3j0p.json. We expect a problem with 3j0p mmCIF download. Delete it and retry.
+
+3j0p_1_2_1-111
+Could not find nucleotides of chain 2 in annotation 3j0p.json. We expect a problem with 3j0p mmCIF download. Delete it and retry.
+
+3j0q_1_2_1-112
+Could not find nucleotides of chain 2 in annotation 3j0q.json. We expect a problem with 3j0q mmCIF download. Delete it and retry.
+
+3j0q_1_2_1-111
+Could not find nucleotides of chain 2 in annotation 3j0q.json. We expect a problem with 3j0q mmCIF download. Delete it and retry.
+
+3ep2_1_B_1-50
+DSSR warning 3ep2.json: no nucleotides found. Ignoring 3ep2_1_B_1-50.
+
+3eq3_1_B_1-50
+DSSR warning 3eq3.json: no nucleotides found. Ignoring 3eq3_1_B_1-50.
+
+3eq4_1_B_1-50
+DSSR warning 3eq4.json: no nucleotides found. Ignoring 3eq4_1_B_1-50.
+
+3j0d_1_A_1-50
+Could not find nucleotides of chain A in annotation 3j0d.json. We expect a problem with 3j0d mmCIF download. Delete it and retry.
+
+1gax_1_D_1-72
+Could not find nucleotides of chain D in annotation 1gax.json. We expect a problem with 1gax mmCIF download. Delete it and retry.
+
+1gax_1_C_1-72
+Could not find nucleotides of chain C in annotation 1gax.json. We expect a problem with 1gax mmCIF download. Delete it and retry.
+
+1ivs_1_C_1-72
+Could not find nucleotides of chain C in annotation 1ivs.json. We expect a problem with 1ivs mmCIF download. Delete it and retry.
+
+1ivs_1_D_1-72
+Could not find nucleotides of chain D in annotation 1ivs.json. We expect a problem with 1ivs mmCIF download. Delete it and retry.
+
+5it9_1_i_1-191
+Could not find nucleotides of chain i in annotation 5it9.json. We expect a problem with 5it9 mmCIF download. Delete it and retry.
+
+3pgw_1_R_1-164
+DSSR warning 3pgw.json: no nucleotides found. Ignoring 3pgw_1_R_1-164.
+
+3pgw_1_N_1-164
+DSSR warning 3pgw.json: no nucleotides found. Ignoring 3pgw_1_N_1-164.
+
+3cw1_1_x_1-138
+DSSR warning 3cw1.json: no nucleotides found. Ignoring 3cw1_1_x_1-138.
+
+3cw1_1_w_1-138
+DSSR warning 3cw1.json: no nucleotides found. Ignoring 3cw1_1_w_1-138.
+
+3cw1_1_V_1-138
+DSSR warning 3cw1.json: no nucleotides found. Ignoring 3cw1_1_V_1-138.
+
+3cw1_1_v_1-138
+DSSR warning 3cw1.json: no nucleotides found. Ignoring 3cw1_1_v_1-138.
+
+2ftc_1_R_792-1568
+DSSR warning 2ftc.json: no nucleotides found. Ignoring 2ftc_1_R_792-1568.
+
+2ftc_1_R_81-1466
+DSSR warning 2ftc.json: no nucleotides found. Ignoring 2ftc_1_R_81-1466.
+
+2ftc_1_R_1-1568
+DSSR warning 2ftc.json: no nucleotides found. Ignoring 2ftc_1_R_1-1568.
+
+3j2c_1_O_1-144
+Could not find nucleotides of chain O in annotation 3j2c.json. We expect a problem with 3j2c mmCIF download. Delete it and retry.
+
+3j2c_1_M_1-462
+Could not find nucleotides of chain M in annotation 3j2c.json. We expect a problem with 3j2c mmCIF download. Delete it and retry.
+
+2dlc_1_Y_1-73
+Could not find nucleotides of chain Y in annotation 2dlc.json. We expect a problem with 2dlc mmCIF download. Delete it and retry.
+
+2iy3_1_B_9-105
+DSSR warning 2iy3.json: no nucleotides found. Ignoring 2iy3_1_B_9-105.
+
+2zue_1_B_1-75
+Could not find nucleotides of chain B in annotation 2zue.json. We expect a problem with 2zue mmCIF download. Delete it and retry.
+
+2zuf_1_B_1-75
+Could not find nucleotides of chain B in annotation 2zuf.json. We expect a problem with 2zuf mmCIF download. Delete it and retry.
+
+2d6f_1_F_1-72
+Could not find nucleotides of chain F in annotation 2d6f.json. We expect a problem with 2d6f mmCIF download. Delete it and retry.
+
+2d6f_1_E_1-72
+Could not find nucleotides of chain E in annotation 2d6f.json. We expect a problem with 2d6f mmCIF download. Delete it and retry.
+
+3jcr_1_N_1-106
+DSSR warning 3jcr.json: no nucleotides found. Ignoring 3jcr_1_N_1-106.
+
+3jcr_1_N_1-188
+DSSR warning 3jcr.json: no nucleotides found. Ignoring 3jcr_1_N_1-188.
+
+2vaz_1_A_64-177
+DSSR warning 2vaz.json: no nucleotides found. Ignoring 2vaz_1_A_64-177.
+
+5ool_1_A_747-1472
+Could not find nucleotides of chain A in annotation 5ool.json. We expect a problem with 5ool mmCIF download. Delete it and retry.
+
+5ool_1_A_1-1454
+Could not find nucleotides of chain A in annotation 5ool.json. We expect a problem with 5ool mmCIF download. Delete it and retry.
+
+5ool_1_A_771-1559
+Could not find nucleotides of chain A in annotation 5ool.json. We expect a problem with 5ool mmCIF download. Delete it and retry.
+
+3j9m_1_A_747-1472
+Could not find nucleotides of chain A in annotation 3j9m.json. We expect a problem with 3j9m mmCIF download. Delete it and retry.
+
+3j9m_1_A_1-1454
+Could not find nucleotides of chain A in annotation 3j9m.json. We expect a problem with 3j9m mmCIF download. Delete it and retry.
+
+3j9m_1_A_771-1559
+Could not find nucleotides of chain A in annotation 3j9m.json. We expect a problem with 3j9m mmCIF download. Delete it and retry.
+
+5oom_1_A_747-1472
+Could not find nucleotides of chain A in annotation 5oom.json. We expect a problem with 5oom mmCIF download. Delete it and retry.
+
+5oom_1_A_1-1454
+Could not find nucleotides of chain A in annotation 5oom.json. We expect a problem with 5oom mmCIF download. Delete it and retry.
+
+5oom_1_A_771-1559
+Could not find nucleotides of chain A in annotation 5oom.json. We expect a problem with 5oom mmCIF download. Delete it and retry.
+
+3j7y_1_A_747-1472
+Could not find nucleotides of chain A in annotation 3j7y.json. We expect a problem with 3j7y mmCIF download. Delete it and retry.
+
+3j7y_1_A_1-1454
+Could not find nucleotides of chain A in annotation 3j7y.json. We expect a problem with 3j7y mmCIF download. Delete it and retry.
+
+3j7y_1_A_771-1559
+Could not find nucleotides of chain A in annotation 3j7y.json. We expect a problem with 3j7y mmCIF download. Delete it and retry.
+
+6nu2_1_A_747-1472
+Could not find nucleotides of chain A in annotation 6nu2.json. We expect a problem with 6nu2 mmCIF download. Delete it and retry.
+
+6nu2_1_A_1-1381
+Could not find nucleotides of chain A in annotation 6nu2.json. We expect a problem with 6nu2 mmCIF download. Delete it and retry.
+
+6nu2_1_A_738-1472
+Could not find nucleotides of chain A in annotation 6nu2.json. We expect a problem with 6nu2 mmCIF download. Delete it and retry.
+
+6nu3_1_A_747-1472
+Could not find nucleotides of chain A in annotation 6nu3.json. We expect a problem with 6nu3 mmCIF download. Delete it and retry.
+
+6nu3_1_A_1-1381
+Could not find nucleotides of chain A in annotation 6nu3.json. We expect a problem with 6nu3 mmCIF download. Delete it and retry.
+
+6nu3_1_A_738-1472
+Could not find nucleotides of chain A in annotation 6nu3.json. We expect a problem with 6nu3 mmCIF download. Delete it and retry.
+
+5aka_1_7_1-74
+Could not find nucleotides of chain 7 in annotation 5aka.json. We expect a problem with 5aka mmCIF download. Delete it and retry.
+
+1f7u_1_B_1-73
+Could not find nucleotides of chain B in annotation 1f7u.json. We expect a problem with 1f7u mmCIF download. Delete it and retry.
+
+1f7v_1_B_1-73
+Could not find nucleotides of chain B in annotation 1f7v.json. We expect a problem with 1f7v mmCIF download. Delete it and retry.
+
+2om7_1_I_1-58
+Could not find nucleotides of chain I in annotation 2om7.json. We expect a problem with 2om7 mmCIF download. Delete it and retry.
+
+2om7_1_J_1-102
+Could not find nucleotides of chain J in annotation 2om7.json. We expect a problem with 2om7 mmCIF download. Delete it and retry.
+
+1ysh_1_B_1-101
+Could not find nucleotides of chain B in annotation 1ysh.json. We expect a problem with 1ysh mmCIF download. Delete it and retry.
+
+3iwn_1_B_1-91
+Could not find nucleotides of chain B in annotation 3iwn.json. We expect a problem with 3iwn mmCIF download. Delete it and retry.
+
+3ndb_1_M_65-109
+Could not find nucleotides of chain M in annotation 3ndb.json. We expect a problem with 3ndb mmCIF download. Delete it and retry.
+
+4xco_1_M_46-90
+Could not find nucleotides of chain M in annotation 4xco.json. We expect a problem with 4xco mmCIF download. Delete it and retry.
+
+4xco_1_M_1-136
+Could not find nucleotides of chain M in annotation 4xco.json. We expect a problem with 4xco mmCIF download. Delete it and retry.
+
+4xco_1_E_46-90
+Could not find nucleotides of chain E in annotation 4xco.json. We expect a problem with 4xco mmCIF download. Delete it and retry.
+
+4xco_1_E_1-136
+Could not find nucleotides of chain E in annotation 4xco.json. We expect a problem with 4xco mmCIF download. Delete it and retry.
+
+1z43_1_A_50-94
+Could not find nucleotides of chain A in annotation 1z43.json. We expect a problem with 1z43 mmCIF download. Delete it and retry.
+
+1z43_1_A_1-136
+Could not find nucleotides of chain A in annotation 1z43.json. We expect a problem with 1z43 mmCIF download. Delete it and retry.
+
+2v3c_1_N_46-90
+Could not find nucleotides of chain N in annotation 2v3c.json. We expect a problem with 2v3c mmCIF download. Delete it and retry.
+
+2v3c_1_N_1-136
+Could not find nucleotides of chain N in annotation 2v3c.json. We expect a problem with 2v3c mmCIF download. Delete it and retry.
+
+2v3c_1_M_46-90
+Could not find nucleotides of chain M in annotation 2v3c.json. We expect a problem with 2v3c mmCIF download. Delete it and retry.
+
+2v3c_1_M_1-136
+Could not find nucleotides of chain M in annotation 2v3c.json. We expect a problem with 2v3c mmCIF download. Delete it and retry.
+
+1lng_1_B_48-92
+Could not find nucleotides of chain B in annotation 1lng.json. We expect a problem with 1lng mmCIF download. Delete it and retry.
+
+1lng_1_B_1-136
+Could not find nucleotides of chain B in annotation 1lng.json. We expect a problem with 1lng mmCIF download. Delete it and retry.
+
+3j5s_1_B_1-101
+Could not find nucleotides of chain B in annotation 3j5s.json. We expect a problem with 3j5s mmCIF download. Delete it and retry.
+
+3j5s_1_B_1-99
+Could not find nucleotides of chain B in annotation 3j5s.json. We expect a problem with 3j5s mmCIF download. Delete it and retry.
+
+3j5s_1_A_1-360
+Could not find nucleotides of chain A in annotation 3j5s.json. We expect a problem with 3j5s mmCIF download. Delete it and retry.
+
+3j45_1_5_1-108
+Could not find nucleotides of chain 5 in annotation 3j45.json. We expect a problem with 3j45 mmCIF download. Delete it and retry.
+
+3j46_1_4_2-109
+Could not find nucleotides of chain 4 in annotation 3j46.json. We expect a problem with 3j46 mmCIF download. Delete it and retry.
+
+3jcr_1_M_1-141
+DSSR warning 3jcr.json: no nucleotides found. Ignoring 3jcr_1_M_1-141.
+
+3jcr_1_M_1-107
+DSSR warning 3jcr.json: no nucleotides found. Ignoring 3jcr_1_M_1-107.
+
+3jcr_1_M_1-188
+DSSR warning 3jcr.json: no nucleotides found. Ignoring 3jcr_1_M_1-188.
+
+4v5z_1_B0_1-2902
+DSSR warning 4v5z.json: no nucleotides found. Ignoring 4v5z_1_B0_1-2902.
+
+4v5z_1_B0_1-2840
+DSSR warning 4v5z.json: no nucleotides found. Ignoring 4v5z_1_B0_1-2840.
+
+4v5z_1_B0_1-2899
+DSSR warning 4v5z.json: no nucleotides found. Ignoring 4v5z_1_B0_1-2899.
+
+3deg_1_G_1-70
+Could not find nucleotides of chain G in annotation 3deg.json. We expect a problem with 3deg mmCIF download. Delete it and retry.
+
+5d8h_1_A_1-74
+Could not find nucleotides of chain A in annotation 5d8h.json. We expect a problem with 5d8h mmCIF download. Delete it and retry.
+
+5g2x_1_A_595-692
+Sequence is too short. (< 5 resolved nts)
+
+5g2y_1_A_595-692
+Could not find nucleotides of chain A in annotation 5g2y.json. We expect a problem with 5g2y mmCIF download. Delete it and retry.
+
+3j0o_1_h_1-111
+Could not find nucleotides of chain h in annotation 3j0o.json. We expect a problem with 3j0o mmCIF download. Delete it and retry.
+
+3j0l_1_h_1-111
+Could not find nucleotides of chain h in annotation 3j0l.json. We expect a problem with 3j0l mmCIF download. Delete it and retry.
+
+3j0p_1_h_1-111
+Could not find nucleotides of chain h in annotation 3j0p.json. We expect a problem with 3j0p mmCIF download. Delete it and retry.
+
+3j0q_1_h_1-111
+Could not find nucleotides of chain h in annotation 3j0q.json. We expect a problem with 3j0q mmCIF download. Delete it and retry.
+
+3iy8_1_A_1-540
+DSSR warning 3iy8.json: no nucleotides found. Ignoring 3iy8_1_A_1-540.
+
+1j1u_1_B_1-74
+Could not find nucleotides of chain B in annotation 1j1u.json. We expect a problem with 1j1u mmCIF download. Delete it and retry.
+
+4v5z_1_BY_2-113
+DSSR warning 4v5z.json: no nucleotides found. Ignoring 4v5z_1_BY_2-113.
+
+4v5z_1_BZ_1-70
+DSSR warning 4v5z.json: no nucleotides found. Ignoring 4v5z_1_BZ_1-70.
+
+4cxg_1_1_1-135
+Could not find nucleotides of chain 1 in annotation 4cxg.json. We expect a problem with 4cxg mmCIF download. Delete it and retry.
+
+4cxh_1_1_1-135
+Could not find nucleotides of chain 1 in annotation 4cxh.json. We expect a problem with 4cxh mmCIF download. Delete it and retry.
+
+4cxg_1_2_1-50
+Could not find nucleotides of chain 2 in annotation 4cxg.json. We expect a problem with 4cxg mmCIF download. Delete it and retry.
+
+4cxh_1_2_1-50
+Could not find nucleotides of chain 2 in annotation 4cxh.json. We expect a problem with 4cxh mmCIF download. Delete it and retry.
+
+4v8y_1_CN_1-87
+Could not find nucleotides of chain CN in annotation 4v8y.json. We expect a problem with 4v8y mmCIF download. Delete it and retry.
+
+1c0a_1_B_1-74
+Could not find nucleotides of chain B in annotation 1c0a.json. We expect a problem with 1c0a mmCIF download. Delete it and retry.
+
+1j2b_1_C_1-74
+Could not find nucleotides of chain C in annotation 1j2b.json. We expect a problem with 1j2b mmCIF download. Delete it and retry.
+
+1j2b_1_D_1-74
+Could not find nucleotides of chain D in annotation 1j2b.json. We expect a problem with 1j2b mmCIF download. Delete it and retry.
+
+6d90_1_4_1-187
+Could not find nucleotides of chain 4 in annotation 6d90.json. We expect a problem with 6d90 mmCIF download. Delete it and retry.
+
+3j16_1_K_1-60
+Could not find nucleotides of chain K in annotation 3j16.json. We expect a problem with 3j16 mmCIF download. Delete it and retry.
+
+1mvr_1_B_1-96
+DSSR warning 1mvr.json: no nucleotides found. Ignoring 1mvr_1_B_1-96.
+
+4adx_1_0_132-2915
+DSSR warning 4adx.json: no nucleotides found. Ignoring 4adx_1_0_132-2915.
+
+4adx_1_0_1-2923
+DSSR warning 4adx.json: no nucleotides found. Ignoring 4adx_1_0_1-2923.
+
+4adx_1_9_1-121
+DSSR warning 4adx.json: no nucleotides found. Ignoring 4adx_1_9_1-121.
+
+2azx_1_D_1-72
+Could not find nucleotides of chain D in annotation 2azx.json. We expect a problem with 2azx mmCIF download. Delete it and retry.
+
+2azx_1_C_1-72
+Could not find nucleotides of chain C in annotation 2azx.json. We expect a problem with 2azx mmCIF download. Delete it and retry.
+
+3eq4_1_Y_1-69
+DSSR warning 3eq4.json: no nucleotides found. Ignoring 3eq4_1_Y_1-69.
+
+2il9_1_A_2-142
+Could not find nucleotides of chain A in annotation 2il9.json. We expect a problem with 2il9 mmCIF download. Delete it and retry.
+
+2il9_1_M_2-142
+Could not find nucleotides of chain M in annotation 2il9.json. We expect a problem with 2il9 mmCIF download. Delete it and retry.
+
+4v92_1_AZ_1-184
+Could not find nucleotides of chain AZ in annotation 4v92.json. We expect a problem with 4v92 mmCIF download. Delete it and retry.
+
+3v7e_1_D_1-125
+Could not find nucleotides of chain D in annotation 3v7e.json. We expect a problem with 3v7e mmCIF download. Delete it and retry.
+
+4v5z_1_AA_1-1563
+DSSR warning 4v5z.json: no nucleotides found. Ignoring 4v5z_1_AA_1-1563.
+
+4v5z_1_AA_1-1562
+DSSR warning 4v5z.json: no nucleotides found. Ignoring 4v5z_1_AA_1-1562.