diff --git a/README.md b/README.md
index 7299284..3ebdc2d 100644
--- a/README.md
+++ b/README.md
@@ -5,7 +5,13 @@
 
 ## Installation
 
-Clone the repository, then install the necessary libraries with `pip`:
+With `pip`:
+
+```
+pip install DockQ
+```
+
+Or, if you want the latest commit: clone the repository and run `pip` within the repo directory:
 
 ```
 git clone https://github.com/bjornwallner/DockQ/
@@ -47,33 +53,30 @@ Total DockQ over 3 native interfaces: 0.653 with BAC:ABC model:native mapping
 Native chains: A, B
 	Model chains: B, A
 	DockQ: 0.994
-	irms: 0.000
-	Lrms: 0.000
+	iRMSD: 0.000
+	LRMSD: 0.000
 	fnat: 0.983
 	fnonnat: 0.008
-	clashes: 0.000
 	F1: 0.987
-	DockQ_F1: 0.996
+	clashes: 0
 Native chains: A, C
 	Model chains: B, C
 	DockQ: 0.511
-	irms: 1.237
-	Lrms: 6.864
+	iRMSD: 1.237
+	LRMSD: 6.864
 	fnat: 0.333
 	fnonnat: 0.000
-	clashes: 0.000
 	F1: 0.500
-	DockQ_F1: 0.567
+	clashes: 0
 Native chains: B, C
 	Model chains: A, C
 	DockQ: 0.453
-	irms: 2.104
-	Lrms: 8.131
+	iRMSD: 2.104
+	LRMSD: 8.131
 	fnat: 0.500
 	fnonnat: 0.107
-	clashes: 0.000
-	F1: 0.641
-	DockQ_F1: 0.500
+    F1: 0.641
+	clashes: 0
 ```
 
 A more compact output option is available with the flag `--short`:
@@ -81,10 +84,16 @@ A more compact output option is available with the flag `--short`:
 ```
 $ DockQ examples/1A2K_r_l_b.model.pdb examples/1A2K_r_l_b.pdb --short
 
-DockQ 0.994 DockQ_F1 0.996 Fnat 0.983 iRMS 0.000 LRMS 0.000 Fnonnat 0.008 clashes 0 mapping BA:AB examples/1A2K_r_l_b.model.pdb B A -> examples/1A2K_r_l_b.pdb A B
-DockQ 0.511 DockQ_F1 0.567 Fnat 0.333 iRMS 1.237 LRMS 6.864 Fnonnat 0.000 clashes 0 mapping BC:AC examples/1A2K_r_l_b.model.pdb B C -> examples/1A2K_r_l_b.pdb A C
-DockQ 0.453 DockQ_F1 0.500 Fnat 0.500 iRMS 2.104 LRMS 8.131 Fnonnat 0.107 clashes 0 mapping AC:BC examples/1A2K_r_l_b.model.pdb A C -> examples/1A2K_r_l_b.pdb B C
+Total DockQ over 3 native interfaces: 0.653 with BAC:ABC model:native mapping
+DockQ 0.994 iRMSD 0.000 LRMSD 0.000 fnat 0.983 fnonnat 0.008 F1 0.987 clashes 0 mapping BA:AB examples/1A2K_r_l_b.model.pdb B A -> examples/1A2K_r_l_b.pdb A B
+DockQ 0.511 iRMSD 1.237 LRMSD 6.864 fnat 0.333 fnonnat 0.000 F1 0.500 clashes 0 mapping BC:AC examples/1A2K_r_l_b.model.pdb B C -> examples/1A2K_r_l_b.pdb A C
+DockQ 0.453 iRMSD 2.104 LRMSD 8.131 fnat 0.500 fnonnat 0.107 F1 0.641 clashes 0 mapping AC:BC examples/1A2K_r_l_b.model.pdb A C -> examples/1A2K_r_l_b.pdb B C
+```
+
+A dictionary containing the complete results data can be dumped in JSON format with the `--json filename.json` flag:
 
+```
+$ DockQ examples/1A2K_r_l_b.model.pdb examples/1A2K_r_l_b.pdb --json filename.json
 ```
 
 ## Model/Native chain mapping
@@ -156,10 +165,10 @@ Small molecules in PDB or mmCIF files can be scored and the mapping optimized in
 $ DockQ examples/1HHO_hem.cif examples/2HHB_hem.cif --small_molecule --mapping :ABEFG --short
 
 Total DockQ-small_molecules over 4 native interfaces: 0.659 with ABDCF:ABEFG model:native mapping
-DockQ 0.950 irms 0.455 Lrms 1.451 fnat 0.964 fnonnat 0.070 clashes 0.000 F1 0.946 DockQ_F1 0.945 mapping AB:AB examples/1HHO_hem.cif A B -> examples/2HHB_hem.cif A B
-Lrms 0.585 mapping AD:AE (HEM) examples/1HHO_hem.cif A D -> examples/2HHB_hem.cif A E
-Lrms 28.096 mapping BC:BF (PO4) examples/1HHO_hem.cif B C -> examples/2HHB_hem.cif B F
-Lrms 1.311 mapping BF:BG (HEM) examples/1HHO_hem.cif B F -> examples/2HHB_hem.cif B G
+DockQ 0.950 iRMSD 0.455 LRMSD 1.451 fnat 0.964 fnonnat 0.070 clashes 0.000 F1 0.946 DockQ_F1 0.945 mapping AB:AB examples/1HHO_hem.cif A B -> examples/2HHB_hem.cif A B
+LRMSD 0.585 mapping AD:AE (HEM) examples/1HHO_hem.cif A D -> examples/2HHB_hem.cif A E
+LRMSD 28.096 mapping BC:BF (PO4) examples/1HHO_hem.cif B C -> examples/2HHB_hem.cif B F
+LRMSD 1.311 mapping BF:BG (HEM) examples/1HHO_hem.cif B F -> examples/2HHB_hem.cif B G
 ```
 
 Only LRMSD is reported for small molecules.
@@ -170,7 +179,7 @@ Only LRMSD is reported for small molecules.
 
 Interfaces involving nucleic acids are seamlessly scored along with protein interfaces. The DockQ score is calculated for protein-NA or NA-NA interfaces in the same way as for protein-protein interfaces (two DockQ scores are reported for double helix chains).
 
-**Other uses**
+## Other uses
 
 Run DockQ with `-h/--help` to see a list of the available flags:
 
@@ -218,8 +227,8 @@ run_on_all_native_interfaces(model, native, chain_map=chain_map)
 
 ({('A', 'B'): {'DockQ_F1': 0.9437927182141027,
    'DockQ': 0.9425398964102757,
-   'irms': 0.3753064373774967,
-   'Lrms': 0.5535111803522507,
+   'iRMSD': 0.3753064373774967,
+   'LRMSD': 0.5535111803522507,
    'fnat': 0.8907563025210085,
    'nat_correct': 106,
    'nat_total': 119,
@@ -241,6 +250,16 @@ run_on_all_native_interfaces(model, native, chain_map=chain_map)
 
 See issue [#33](https://github.com/bjornwallner/DockQ/issues/33) if you want to merge multiple chains (e.g. heavy and light antibody chains) into a single receptor or ligand
 
+## Legend of outputs
+
+* `DockQ`: DockQ score as defined in the [original DockQ paper](https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0161879)
+* `iRMSD`: RMSD of interfacial residues
+* `LRMSD`: Ligand RMSD
+* `fnat`: Fraction of retrieved native contacts (same as Recall or TPR)
+* `fnonnat`: Fraction of predicted contacts that are not native (same as FPR)
+* `F1`: Harmonic mean of the precision and recall in predicted interfacial contacts
+* `clashes`: number of clashing interfacial residues in model (distance between residues below 2Å)
+
 ## Citing DockQ v2
 
 If you use DockQ v2, please cite the preprint: https://doi.org/10.1101/2024.05.28.596225 
diff --git a/pyproject.toml b/pyproject.toml
index 773d651..6d7818a 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,23 +1,23 @@
 [build-system]
-requires = ["setuptools>=68", "cython", "numpy ~= 1.21",]
+requires = ["setuptools>=68", "cython", "numpy < 2.0"]
 build-backend = "setuptools.build_meta"
 
 [project]
 name = "dockq"
-version = "2.1"
+version = "2.1.2"
 authors = [
   { name="Claudio Mirabello", email="claudio.mirabello@scilifelab.se" },
   { name="Bjorn Wallner", email="bjorn.wallner@liu.se" },
 ]
 description = "A Quality Measure for Protein, Nucleic Acids and Small Ligand Docking Models"
 readme = "README.md"
-requires-python = ">=3.9"
+requires-python = ">=3.8"
 classifiers = [
     "Programming Language :: Python :: 3",
     "License :: OSI Approved :: MIT License",
     "Operating System :: OS Independent",
 ]
-dependencies = ["biopython >= 1.79", "networkx", "parallelbar"]
+dependencies = ["numpy < 2.0", "biopython >= 1.79", "networkx", "parallelbar"]
 
 [project.urls]
 Homepage = "https://github.com/bjornwallner/DockQ"
diff --git a/run_test.sh b/run_test.sh
index 047f6df..6ce07d0 100644
--- a/run_test.sh
+++ b/run_test.sh
@@ -3,10 +3,12 @@ set -euo pipefail
 
 rm -f test .coverage
 
+PYTHON=${1:-"python"}
+
 if command -v coverage &> /dev/null; then
     binary="coverage run --parallel-mode -m DockQ.DockQ "
 else
-    binary="DockQ"
+    binary="$PYTHON -m DockQ.DockQ"
 fi
 
 $binary examples/1A2K_r_l_b.model.pdb examples/1A2K_r_l_b.pdb > test
@@ -49,9 +51,11 @@ diff <(grep -v "*" test) <(grep -v "*" testdata/6q2n_peptide.dockq)
 $binary examples/1HHO_hem.cif examples/2HHB_hem.cif --small_molecule --mapping :ABEFG > test
 
 # Test that cython version behaves the same as nocython
-python src/DockQ/DockQ.py examples/1A2K_r_l_b.model.pdb examples/1A2K_r_l_b.pdb > test
+$PYTHON src/DockQ/DockQ.py examples/1A2K_r_l_b.model.pdb examples/1A2K_r_l_b.pdb > test
 diff <(grep -v "*" test) <(grep -v "*" testdata/1A2K.dockq)
-python src/DockQ/DockQ.py examples/1A2K_r_l_b.model.pdb examples/1A2K_r_l_b.pdb --no_align > test
+$PYTHON src/DockQ/DockQ.py examples/1A2K_r_l_b.model.pdb examples/1A2K_r_l_b.pdb --no_align > test
 diff <(grep -v "*" test) <(grep -v "*" testdata/1A2K.dockq)
 
-coverage combine
+if command -v coverage &> /dev/null; then
+	coverage combine
+fi
diff --git a/setup.cfg b/setup.cfg
index e506d1c..48082e0 100644
--- a/setup.cfg
+++ b/setup.cfg
@@ -1,6 +1,6 @@
 [metadata]
 name = DockQ
-version = 2.1
+version = 2.1.2
 
 [options]
 package_dir =
@@ -10,7 +10,7 @@ install_requires =
     setuptools
     cython
     parallelbar
-    numpy~=1.21
+    numpy<2.0
     biopython>=1.79
     networkx
 
diff --git a/src/DockQ/DockQ.py b/src/DockQ/DockQ.py
index 89dfdb1..de47f54 100755
--- a/src/DockQ/DockQ.py
+++ b/src/DockQ/DockQ.py
@@ -1,10 +1,12 @@
 #!/usr/bin/env python
 
 import sys
+import json
 import gzip
 import math
-import warnings
+import logging
 import itertools
+import traceback
 from collections import Counter
 from argparse import ArgumentParser
 from functools import lru_cache, partial
@@ -20,9 +22,8 @@
     from .parsers import PDBParser, MMCIFParser
     from .constants import *
 except ImportError:
-    warnings.warn(
-        """WARNING: It looks like cython is not working,
-         falling back on native python. This will make DockQ slower"""
+    logging.warning(
+        """Invoking DockQ as script rather than binary. This will slow down computations."""
     )
     from operations_nocy import residue_distances, get_fnat_stats
     from parsers import PDBParser, MMCIFParser
@@ -53,12 +54,14 @@ def parse_args():
     parser.add_argument(
         "--short", default=False, action="store_true", help="Short output"
     )
+    parser.add_argument(
+        "--json", default=None, metavar="out.json", help="Write outputs to a chosen json file"
+    )
     parser.add_argument(
         "--verbose", "-v", default=False, action="store_true", help="Verbose output"
     )
     parser.add_argument(
         "--no_align",
-        # default=False,
         action="store_true",
         help="Do not align native and model using sequence alignments, but use the numbering of residues instead",
     )
@@ -76,12 +79,6 @@ def parse_args():
         metavar="CHUNK",
         help="Maximum size of chunks given to the cores, actual chunksize is min(max_chunk,combos/cpus)",
     )
-    parser.add_argument(
-        "--optDockQF1",
-        default=False,
-        action="store_true",
-        help="Optimize on DockQ_F1 instead of DockQ",
-    )
     parser.add_argument(
         "--allowed_mismatches",
         default=0,
@@ -255,11 +252,10 @@ def calc_sym_corrected_lrmsd(
         if lrms < min_lrms:
             best_mapping = isomorphism
             min_lrms = lrms
-    dockq_f1 = dockq = dockq_formula(0, 0, min_lrms)
+    dockq = dockq_formula(0, 0, min_lrms)
     info = {
-        "DockQ_F1": dockq_f1,
         "DockQ": dockq,
-        "Lrms": min_lrms,
+        "LRMSD": min_lrms,
         "mapping": best_mapping,
         "is_het": sample_ligand.is_het,
     }
@@ -379,14 +375,13 @@ def calc_DockQ(
 
     info = {}
     F1 = f1(nat_correct, nonnat_count, nat_total)
-    info["DockQ_F1"] = dockq_formula(F1, irms, lrms)
     info["DockQ"] = dockq_formula(fnat, irms, lrms)
     if low_memory:
         return info
 
     info["F1"] = F1
-    info["irms"] = irms
-    info["Lrms"] = lrms
+    info["iRMSD"] = irms
+    info["LRMSD"] = lrms
     info["fnat"] = fnat
     info["nat_correct"] = nat_correct
     info["nat_total"] = nat_total
@@ -632,7 +627,6 @@ def run_on_all_native_interfaces(
     no_align=False,
     capri_peptide=False,
     low_memory=False,
-    optDockQF1=False,
 ):
     """Given a native-model chain map, finds all non-null native interfaces
     and runs DockQ for each native-model pair of interfaces"""
@@ -667,14 +661,13 @@ def run_on_all_native_interfaces(
                     chain_map[chain_pair[1]],
                 )
                 info["chain_map"] = chain_map  # diagnostics
-                result_mapping[chain_pair] = info
+                result_mapping["".join(chain_pair)] = info
     total_dockq = sum(
         [
-            result["DockQ_F1" if optDockQF1 else "DockQ"]
+            result["DockQ"]
             for result in result_mapping.values()
         ]
     )
-
     return result_mapping, total_dockq
 
 
@@ -717,9 +710,24 @@ def group_chains(
     chain_clusters = {chain: [] for chain in ref_chains}
 
     for query_chain, ref_chain in alignment_targets:
-        qc = query_structure[query_chain]
-        rc = ref_structure[ref_chain]
-
+        try:
+            qc = query_structure[query_chain]
+        except KeyError:
+            logging.error(f"""The specified model chain {query_chain} is not found in the PDB structure.
+This is possibly due to using the wrong chain identifier in --mapping,
+or forgetting to specify --small_molecule if this is a HETATM chain.
+If working with mmCIF files, make sure you use the right chain identifier.
+            """)
+            print(traceback.format_exc())
+            sys.exit(1)
+        try:
+            rc = ref_structure[ref_chain]
+        except KeyError:
+            logging.error(f"""The specified native chain {ref_chain} is not found in the PDB structure.
+This is possibly due to using the wrong chain identifier in --mapping,
+or forgetting to specify --small_molecule if this is a HETATM chain.
+If working with mmCIF files, make sure you use the right chain identifier.
+            """)    
         het_qc = qc.is_het
         het_rc = rc.is_het
 
@@ -740,16 +748,21 @@ def group_chains(
                 chain_clusters[ref_chain].append(query_chain)
         elif het_qc and het_rc and het_qc == het_rc:
             chain_clusters[ref_chain].append(query_chain)
-
     chains_without_match = [
         chain for chain in chain_clusters if not chain_clusters[chain]
     ]
 
+    if mismatch_dict:
+        logging.warning(f"""Some chains have a limited number of sequence mismatches and are treated as non-homologous. 
+Try increasing the --allowed_mismatches for the following: {", ".join(f"Model chain {c[1]}, native chain {c[0]}: {m} mismatches" for c, m in mismatch_dict.items())}
+if they should be treated as homologous.""")
+
     if chains_without_match:
-        print(
-            f"For these chains {chains_without_match} no match was found between model and native, try increasing the --allowed_mismatches from {allowed_mismatches}"
+        logging.error(
+            f"For chains {chains_without_match} no identical corresponding chain was found between in the native."
         )
-        print(f"Current number of alignments with 1-10 mismatches: {mismatch_dict}")
+        sys.exit(1)
+
 
     return chain_clusters, reverse_map
 
@@ -763,7 +776,7 @@ def format_mapping(mapping_str, small_molecule=None):
 
     model_mapping, native_mapping = mapping_str.split(":")
     if not native_mapping:
-        print("When using --mapping, native chains must be set (e.g. ABC:ABC or :ABC)")
+        logging.error("When using --mapping, native chains must be set (e.g. ABC:ABC or :ABC)")
         sys.exit()
     else:
         # :ABC or *:ABC only use those natives chains, permute model chains
@@ -812,13 +825,18 @@ def product_without_dupl(*args, repeat=1):
 
 
 def count_chain_combinations(chain_clusters):
-    clusters = [tuple(li) for li in chain_clusters.values()]
-    number_of_combinations = np.prod(
-        [
-            int(math.factorial(len(a)) / math.factorial(len(a) - b))
-            for a, b in Counter(clusters).items()
-        ]
-    )
+    try:
+        clusters = [tuple(li) for li in chain_clusters.values()]
+        number_of_combinations = np.prod(
+            [
+                int(math.factorial(len(a)) / math.factorial(len(a) - b))
+                for a, b in Counter(clusters).items()
+            ]
+        )
+    except ValueError:
+        logging.error("""Couldn't find a match between each model-native chain specified in the mapping.
+Make sure that all chains in your model have a homologous chain in the native, or specify the right subset of chains with --mapping""")
+        sys.exit()
     return number_of_combinations
 
 
@@ -959,6 +977,10 @@ def main():
         best_mapping = next(chain_maps)
         best_result, best_dockq = run_chain_map(best_mapping)
 
+    if not best_result:
+        logging.error("Could not find interfaces in the native model. Please double check the inputs or select different chains with the --mapping flag.")
+        sys.exit(1)
+
     info = dict()
     info["model"] = args.model
     info["native"] = args.native
@@ -967,6 +989,11 @@ def main():
     info["GlobalDockQ"] = best_dockq / len(best_result)
     info["best_mapping"] = best_mapping
     info["best_mapping_str"] = f"{format_mapping_string(best_mapping)}"
+    
+    if args.json:
+        with open(args.json, "w") as fp:
+            json.dump(info, fp)
+
     print_results(
         info, args.short, args.verbose, args.capri_peptide, args.small_molecule
     )
@@ -991,20 +1018,19 @@ def print_results(
             reported_measures = (
                 [
                     "DockQ",
-                    "irms",
-                    "Lrms",
+                    "iRMSD",
+                    "LRMSD",
                     "fnat",
                     "fnonnat",
-                    "clashes",
                     "F1",
-                    "DockQ_F1",
+                    "clashes",
                 ]
                 if not results["is_het"]
-                else ["Lrms"]
+                else ["LRMSD"]
             )
             hetname = f" ({results['is_het']})" if results["is_het"] else ""
             score_str = " ".join(
-                [f"{item} {results[item]:.3f}" for item in reported_measures]
+                [f"{item} {results[item]:.3f}" if item != "clashes" else f"{item} {results[item]}" for item in reported_measures]
             )
             print(
                 f"{score_str} mapping {results['chain1']}{results['chain2']}:{chains[0]}{chains[1]}{hetname} {info['model']} {results['chain1']} {results['chain2']} -> {info['native']} {chains[0]} {chains[1]}"
@@ -1020,23 +1046,22 @@ def print_results(
             reported_measures = (
                 [
                     "DockQ",
-                    "irms",
-                    "Lrms",
+                    "iRMSD",
+                    "LRMSD",
                     "fnat",
                     "fnonnat",
-                    "clashes",
                     "F1",
-                    "DockQ_F1",
+                    "clashes",
                 ]
                 if not results["is_het"]
-                else ["Lrms"]
+                else ["LRMSD"]
             )
             hetname = f" ({results['is_het']})" if results["is_het"] else ""
             print(f"Native chains: {chains[0]}, {chains[1]}{hetname}")
             print(f"\tModel chains: {results['chain1']}, {results['chain2']}")
             print(
                 "\n".join(
-                    [f"\t{item}: {results[item]:.3f}" for item in reported_measures]
+                    [f"\t{item}: {results[item]:.3f}" if item != "clashes" else f"\t{item}: {results[item]}" for item in reported_measures]
                 )
             )
 
@@ -1065,7 +1090,7 @@ def print_header(verbose=False, capri_peptide=False):
         notice = (
             "*   For the record:                                            *\n"
             f"*   Definition of contact <{'5A' if not capri_peptide else '4A'} (Fnat)                           *\n"
-            f"*   Definition of interface <{'10A all heavy atoms (iRMS)       ' if not capri_peptide else '8A CB (iRMS)                     '} *\n"
+            f"*   Definition of interface <{'10A all heavy atoms (iRMSD)      ' if not capri_peptide else '8A CB (iRMSD)                    '} *\n"
             "****************************************************************"
         )
     else:
diff --git a/testdata/1A2K.dockq b/testdata/1A2K.dockq
index ea05b54..0fe273c 100644
--- a/testdata/1A2K.dockq
+++ b/testdata/1A2K.dockq
@@ -17,30 +17,27 @@ Total DockQ over 3 native interfaces: 0.653 with BAC:ABC model:native mapping
 Native chains: A, B
 	Model chains: B, A
 	DockQ: 0.994
-	irms: 0.000
-	Lrms: 0.000
+	iRMSD: 0.000
+	LRMSD: 0.000
 	fnat: 0.983
 	fnonnat: 0.008
-	clashes: 0.000
 	F1: 0.987
-	DockQ_F1: 0.996
+	clashes: 0
 Native chains: A, C
 	Model chains: B, C
 	DockQ: 0.511
-	irms: 1.237
-	Lrms: 6.864
+	iRMSD: 1.237
+	LRMSD: 6.864
 	fnat: 0.333
 	fnonnat: 0.000
-	clashes: 0.000
 	F1: 0.500
-	DockQ_F1: 0.567
+	clashes: 0
 Native chains: B, C
 	Model chains: A, C
 	DockQ: 0.453
-	irms: 2.104
-	Lrms: 8.131
+	iRMSD: 2.104
+	LRMSD: 8.131
 	fnat: 0.500
 	fnonnat: 0.107
-	clashes: 0.000
 	F1: 0.641
-	DockQ_F1: 0.500
+	clashes: 0
diff --git a/testdata/1A2K.dockq2 b/testdata/1A2K.dockq2
new file mode 100644
index 0000000..4acd852
--- /dev/null
+++ b/testdata/1A2K.dockq2
@@ -0,0 +1,46 @@
+****************************************************************
+*                       DockQ                                  *
+*   Scoring function for protein-protein docking models        *
+*   Statistics on CAPRI data:                                  *
+*    0.00 <= DockQ <  0.23 - Incorrect                         *
+*    0.23 <= DockQ <  0.49 - Acceptable quality                *
+*    0.49 <= DockQ <  0.80 - Medium quality                    *
+*            DockQ >= 0.80 - High quality                      *
+*   Ref: S. Basu and B. Wallner, DockQ: A quality measure for  *
+*   protein-protein docking models                             *
+*                            doi:10.1371/journal.pone.0161879  *
+*   For comments, please email: bjorn.wallner@.liu.se          *
+****************************************************************
+Model  : examples/1A2K_r_l_b.model.pdb
+Native : examples/1A2K_r_l_b.pdb
+Total DockQ over 3 native interfaces: 0.653 with BAC:ABC model:native mapping
+Native chains: A, B
+	Model chains: B, A
+	DockQ: 0.994
+	iRMSD: 0.000
+	LRMSD: 0.000
+	fnat: 0.983
+	fnonnat: 0.008
+	clashes: 0.000
+	F1: 0.987
+	DockQ_F1: 0.996
+Native chains: A, C
+	Model chains: B, C
+	DockQ: 0.511
+	iRMSD: 1.237
+	LRMSD: 6.864
+	fnat: 0.333
+	fnonnat: 0.000
+	clashes: 0.000
+	F1: 0.500
+	DockQ_F1: 0.567
+Native chains: B, C
+	Model chains: A, C
+	DockQ: 0.453
+	iRMSD: 2.104
+	LRMSD: 8.131
+	fnat: 0.500
+	fnonnat: 0.107
+	clashes: 0.000
+	F1: 0.641
+	DockQ_F1: 0.500
diff --git a/testdata/1EXB.dockq b/testdata/1EXB.dockq
index 2e7f40e..fc27a57 100644
--- a/testdata/1EXB.dockq
+++ b/testdata/1EXB.dockq
@@ -1,17 +1,17 @@
 Total DockQ over 16 native interfaces: 0.852 with BACDFHEG:ABDCEGFH model:native mapping
-DockQ 1.000 irms 0.000 Lrms 0.000 fnat 1.000 fnonnat 0.000 clashes 0.000 F1 1.000 DockQ_F1 1.000 mapping BC:AD examples/1EXB_r_l_b.model.pdb B C -> examples/1EXB_r_l_b.pdb A D
-DockQ 0.995 irms 0.000 Lrms 0.000 fnat 0.985 fnonnat 0.000 clashes 0.000 F1 0.993 DockQ_F1 0.998 mapping BD:AC examples/1EXB_r_l_b.model.pdb B D -> examples/1EXB_r_l_b.pdb A C
-DockQ 0.552 irms 1.458 Lrms 3.757 fnat 0.304 fnonnat 0.000 clashes 0.000 F1 0.467 DockQ_F1 0.606 mapping BF:AE examples/1EXB_r_l_b.model.pdb B F -> examples/1EXB_r_l_b.pdb A E
-DockQ 0.694 irms 0.793 Lrms 2.831 fnat 0.400 fnonnat 0.000 clashes 0.000 F1 0.571 DockQ_F1 0.751 mapping BH:AG examples/1EXB_r_l_b.model.pdb B H -> examples/1EXB_r_l_b.pdb A G
-DockQ 0.995 irms 0.000 Lrms 0.000 fnat 0.985 fnonnat 0.000 clashes 0.000 F1 0.993 DockQ_F1 0.998 mapping AC:BD examples/1EXB_r_l_b.model.pdb A C -> examples/1EXB_r_l_b.pdb B D
-DockQ 0.995 irms 0.000 Lrms 0.000 fnat 0.985 fnonnat 0.000 clashes 0.000 F1 0.993 DockQ_F1 0.998 mapping AD:BC examples/1EXB_r_l_b.model.pdb A D -> examples/1EXB_r_l_b.pdb B C
-DockQ 0.742 irms 0.850 Lrms 3.426 fnat 0.609 fnonnat 0.176 clashes 0.000 F1 0.700 DockQ_F1 0.772 mapping AE:BF examples/1EXB_r_l_b.model.pdb A E -> examples/1EXB_r_l_b.pdb B F
-DockQ 0.824 irms 0.625 Lrms 3.994 fnat 0.800 fnonnat 0.000 clashes 0.000 F1 0.889 DockQ_F1 0.853 mapping AG:BH examples/1EXB_r_l_b.model.pdb A G -> examples/1EXB_r_l_b.pdb B H
-DockQ 0.687 irms 1.161 Lrms 3.757 fnat 0.600 fnonnat 0.000 clashes 0.000 F1 0.750 DockQ_F1 0.737 mapping CF:DE examples/1EXB_r_l_b.model.pdb C F -> examples/1EXB_r_l_b.pdb D E
-DockQ 0.477 irms 1.425 Lrms 3.994 fnat 0.087 fnonnat 0.000 clashes 0.000 F1 0.160 DockQ_F1 0.502 mapping CG:DH examples/1EXB_r_l_b.model.pdb C G -> examples/1EXB_r_l_b.pdb D H
-DockQ 0.775 irms 0.711 Lrms 2.831 fnat 0.609 fnonnat 0.125 clashes 0.000 F1 0.718 DockQ_F1 0.812 mapping DH:CG examples/1EXB_r_l_b.model.pdb D H -> examples/1EXB_r_l_b.pdb C G
-DockQ 0.914 irms 0.547 Lrms 3.426 fnat 1.000 fnonnat 0.000 clashes 0.000 F1 1.000 DockQ_F1 0.914 mapping DE:CF examples/1EXB_r_l_b.model.pdb D E -> examples/1EXB_r_l_b.pdb C F
-DockQ 0.992 irms 0.001 Lrms 0.000 fnat 0.976 fnonnat 0.000 clashes 0.000 F1 0.988 DockQ_F1 0.996 mapping FH:EG examples/1EXB_r_l_b.model.pdb F H -> examples/1EXB_r_l_b.pdb E G
-DockQ 0.992 irms 0.001 Lrms 0.000 fnat 0.976 fnonnat 0.000 clashes 0.000 F1 0.988 DockQ_F1 0.996 mapping FG:EH examples/1EXB_r_l_b.model.pdb F G -> examples/1EXB_r_l_b.pdb E H
-DockQ 0.992 irms 0.001 Lrms 0.001 fnat 0.976 fnonnat 0.000 clashes 0.000 F1 0.988 DockQ_F1 0.996 mapping HE:GF examples/1EXB_r_l_b.model.pdb H E -> examples/1EXB_r_l_b.pdb G F
-DockQ 1.000 irms 0.001 Lrms 0.001 fnat 1.000 fnonnat 0.024 clashes 0.000 F1 0.988 DockQ_F1 0.996 mapping EG:FH examples/1EXB_r_l_b.model.pdb E G -> examples/1EXB_r_l_b.pdb F H
+DockQ 1.000 iRMSD 0.000 LRMSD 0.000 fnat 1.000 fnonnat 0.000 F1 1.000 clashes 0 mapping BC:AD examples/1EXB_r_l_b.model.pdb B C -> examples/1EXB_r_l_b.pdb A D
+DockQ 0.995 iRMSD 0.000 LRMSD 0.000 fnat 0.985 fnonnat 0.000 F1 0.993 clashes 0 mapping BD:AC examples/1EXB_r_l_b.model.pdb B D -> examples/1EXB_r_l_b.pdb A C
+DockQ 0.552 iRMSD 1.458 LRMSD 3.757 fnat 0.304 fnonnat 0.000 F1 0.467 clashes 0 mapping BF:AE examples/1EXB_r_l_b.model.pdb B F -> examples/1EXB_r_l_b.pdb A E
+DockQ 0.694 iRMSD 0.793 LRMSD 2.831 fnat 0.400 fnonnat 0.000 F1 0.571 clashes 0 mapping BH:AG examples/1EXB_r_l_b.model.pdb B H -> examples/1EXB_r_l_b.pdb A G
+DockQ 0.995 iRMSD 0.000 LRMSD 0.000 fnat 0.985 fnonnat 0.000 F1 0.993 clashes 0 mapping AC:BD examples/1EXB_r_l_b.model.pdb A C -> examples/1EXB_r_l_b.pdb B D
+DockQ 0.995 iRMSD 0.000 LRMSD 0.000 fnat 0.985 fnonnat 0.000 F1 0.993 clashes 0 mapping AD:BC examples/1EXB_r_l_b.model.pdb A D -> examples/1EXB_r_l_b.pdb B C
+DockQ 0.742 iRMSD 0.850 LRMSD 3.426 fnat 0.609 fnonnat 0.176 F1 0.700 clashes 0 mapping AE:BF examples/1EXB_r_l_b.model.pdb A E -> examples/1EXB_r_l_b.pdb B F
+DockQ 0.824 iRMSD 0.625 LRMSD 3.994 fnat 0.800 fnonnat 0.000 F1 0.889 clashes 0 mapping AG:BH examples/1EXB_r_l_b.model.pdb A G -> examples/1EXB_r_l_b.pdb B H
+DockQ 0.687 iRMSD 1.161 LRMSD 3.757 fnat 0.600 fnonnat 0.000 F1 0.750 clashes 0 mapping CF:DE examples/1EXB_r_l_b.model.pdb C F -> examples/1EXB_r_l_b.pdb D E
+DockQ 0.477 iRMSD 1.425 LRMSD 3.994 fnat 0.087 fnonnat 0.000 F1 0.160 clashes 0 mapping CG:DH examples/1EXB_r_l_b.model.pdb C G -> examples/1EXB_r_l_b.pdb D H
+DockQ 0.775 iRMSD 0.711 LRMSD 2.831 fnat 0.609 fnonnat 0.125 F1 0.718 clashes 0 mapping DH:CG examples/1EXB_r_l_b.model.pdb D H -> examples/1EXB_r_l_b.pdb C G
+DockQ 0.914 iRMSD 0.547 LRMSD 3.426 fnat 1.000 fnonnat 0.000 F1 1.000 clashes 0 mapping DE:CF examples/1EXB_r_l_b.model.pdb D E -> examples/1EXB_r_l_b.pdb C F
+DockQ 0.992 iRMSD 0.001 LRMSD 0.000 fnat 0.976 fnonnat 0.000 F1 0.988 clashes 0 mapping FH:EG examples/1EXB_r_l_b.model.pdb F H -> examples/1EXB_r_l_b.pdb E G
+DockQ 0.992 iRMSD 0.001 LRMSD 0.000 fnat 0.976 fnonnat 0.000 F1 0.988 clashes 0 mapping FG:EH examples/1EXB_r_l_b.model.pdb F G -> examples/1EXB_r_l_b.pdb E H
+DockQ 0.992 iRMSD 0.001 LRMSD 0.001 fnat 0.976 fnonnat 0.000 F1 0.988 clashes 0 mapping HE:GF examples/1EXB_r_l_b.model.pdb H E -> examples/1EXB_r_l_b.pdb G F
+DockQ 1.000 iRMSD 0.001 LRMSD 0.001 fnat 1.000 fnonnat 0.024 F1 0.988 clashes 0 mapping EG:FH examples/1EXB_r_l_b.model.pdb E G -> examples/1EXB_r_l_b.pdb F H
diff --git a/testdata/1EXB_.ABC.dockq b/testdata/1EXB_.ABC.dockq
index 803de58..ffd2ecf 100644
--- a/testdata/1EXB_.ABC.dockq
+++ b/testdata/1EXB_.ABC.dockq
@@ -1,3 +1,3 @@
 Total DockQ over 2 native interfaces: 0.998 with ABC:ABC model:native mapping
-DockQ 0.995 irms 0.000 Lrms 0.000 fnat 0.985 fnonnat 0.000 clashes 0.000 F1 0.993 DockQ_F1 0.998 mapping AC:AC examples/1EXB_r_l_b.model.pdb A C -> examples/1EXB_r_l_b.pdb A C
-DockQ 1.000 irms 0.000 Lrms 0.000 fnat 1.000 fnonnat 0.000 clashes 0.000 F1 1.000 DockQ_F1 1.000 mapping BC:BC examples/1EXB_r_l_b.model.pdb B C -> examples/1EXB_r_l_b.pdb B C
+DockQ 0.995 iRMSD 0.000 LRMSD 0.000 fnat 0.985 fnonnat 0.000 F1 0.993 clashes 0 mapping AC:AC examples/1EXB_r_l_b.model.pdb A C -> examples/1EXB_r_l_b.pdb A C
+DockQ 1.000 iRMSD 0.000 LRMSD 0.000 fnat 1.000 fnonnat 0.000 F1 1.000 clashes 0 mapping BC:BC examples/1EXB_r_l_b.model.pdb B C -> examples/1EXB_r_l_b.pdb B C
diff --git a/testdata/1EXB_AB.BA.dockq b/testdata/1EXB_AB.BA.dockq
index 7525ac5..265ffed 100644
--- a/testdata/1EXB_AB.BA.dockq
+++ b/testdata/1EXB_AB.BA.dockq
@@ -1,17 +1,17 @@
 Total DockQ over 16 native interfaces: 0.852 with ABCDFHEG:BADCEGFH model:native mapping
-DockQ 0.995 irms 0.000 Lrms 0.000 fnat 0.985 fnonnat 0.000 clashes 0.000 F1 0.993 DockQ_F1 0.998 mapping AC:BD examples/1EXB_r_l_b.model.pdb A C -> examples/1EXB_r_l_b.pdb B D
-DockQ 0.995 irms 0.000 Lrms 0.000 fnat 0.985 fnonnat 0.000 clashes 0.000 F1 0.993 DockQ_F1 0.998 mapping AD:BC examples/1EXB_r_l_b.model.pdb A D -> examples/1EXB_r_l_b.pdb B C
-DockQ 0.742 irms 0.850 Lrms 3.426 fnat 0.609 fnonnat 0.176 clashes 0.000 F1 0.700 DockQ_F1 0.772 mapping AE:BF examples/1EXB_r_l_b.model.pdb A E -> examples/1EXB_r_l_b.pdb B F
-DockQ 0.824 irms 0.625 Lrms 3.994 fnat 0.800 fnonnat 0.000 clashes 0.000 F1 0.889 DockQ_F1 0.853 mapping AG:BH examples/1EXB_r_l_b.model.pdb A G -> examples/1EXB_r_l_b.pdb B H
-DockQ 1.000 irms 0.000 Lrms 0.000 fnat 1.000 fnonnat 0.000 clashes 0.000 F1 1.000 DockQ_F1 1.000 mapping BC:AD examples/1EXB_r_l_b.model.pdb B C -> examples/1EXB_r_l_b.pdb A D
-DockQ 0.995 irms 0.000 Lrms 0.000 fnat 0.985 fnonnat 0.000 clashes 0.000 F1 0.993 DockQ_F1 0.998 mapping BD:AC examples/1EXB_r_l_b.model.pdb B D -> examples/1EXB_r_l_b.pdb A C
-DockQ 0.552 irms 1.458 Lrms 3.757 fnat 0.304 fnonnat 0.000 clashes 0.000 F1 0.467 DockQ_F1 0.606 mapping BF:AE examples/1EXB_r_l_b.model.pdb B F -> examples/1EXB_r_l_b.pdb A E
-DockQ 0.694 irms 0.793 Lrms 2.831 fnat 0.400 fnonnat 0.000 clashes 0.000 F1 0.571 DockQ_F1 0.751 mapping BH:AG examples/1EXB_r_l_b.model.pdb B H -> examples/1EXB_r_l_b.pdb A G
-DockQ 0.687 irms 1.161 Lrms 3.757 fnat 0.600 fnonnat 0.000 clashes 0.000 F1 0.750 DockQ_F1 0.737 mapping CF:DE examples/1EXB_r_l_b.model.pdb C F -> examples/1EXB_r_l_b.pdb D E
-DockQ 0.477 irms 1.425 Lrms 3.994 fnat 0.087 fnonnat 0.000 clashes 0.000 F1 0.160 DockQ_F1 0.502 mapping CG:DH examples/1EXB_r_l_b.model.pdb C G -> examples/1EXB_r_l_b.pdb D H
-DockQ 0.775 irms 0.711 Lrms 2.831 fnat 0.609 fnonnat 0.125 clashes 0.000 F1 0.718 DockQ_F1 0.812 mapping DH:CG examples/1EXB_r_l_b.model.pdb D H -> examples/1EXB_r_l_b.pdb C G
-DockQ 0.914 irms 0.547 Lrms 3.426 fnat 1.000 fnonnat 0.000 clashes 0.000 F1 1.000 DockQ_F1 0.914 mapping DE:CF examples/1EXB_r_l_b.model.pdb D E -> examples/1EXB_r_l_b.pdb C F
-DockQ 0.992 irms 0.001 Lrms 0.000 fnat 0.976 fnonnat 0.000 clashes 0.000 F1 0.988 DockQ_F1 0.996 mapping FH:EG examples/1EXB_r_l_b.model.pdb F H -> examples/1EXB_r_l_b.pdb E G
-DockQ 0.992 irms 0.001 Lrms 0.000 fnat 0.976 fnonnat 0.000 clashes 0.000 F1 0.988 DockQ_F1 0.996 mapping FG:EH examples/1EXB_r_l_b.model.pdb F G -> examples/1EXB_r_l_b.pdb E H
-DockQ 0.992 irms 0.001 Lrms 0.001 fnat 0.976 fnonnat 0.000 clashes 0.000 F1 0.988 DockQ_F1 0.996 mapping HE:GF examples/1EXB_r_l_b.model.pdb H E -> examples/1EXB_r_l_b.pdb G F
-DockQ 1.000 irms 0.001 Lrms 0.001 fnat 1.000 fnonnat 0.024 clashes 0.000 F1 0.988 DockQ_F1 0.996 mapping EG:FH examples/1EXB_r_l_b.model.pdb E G -> examples/1EXB_r_l_b.pdb F H
+DockQ 0.995 iRMSD 0.000 LRMSD 0.000 fnat 0.985 fnonnat 0.000 F1 0.993 clashes 0 mapping AC:BD examples/1EXB_r_l_b.model.pdb A C -> examples/1EXB_r_l_b.pdb B D
+DockQ 0.995 iRMSD 0.000 LRMSD 0.000 fnat 0.985 fnonnat 0.000 F1 0.993 clashes 0 mapping AD:BC examples/1EXB_r_l_b.model.pdb A D -> examples/1EXB_r_l_b.pdb B C
+DockQ 0.742 iRMSD 0.850 LRMSD 3.426 fnat 0.609 fnonnat 0.176 F1 0.700 clashes 0 mapping AE:BF examples/1EXB_r_l_b.model.pdb A E -> examples/1EXB_r_l_b.pdb B F
+DockQ 0.824 iRMSD 0.625 LRMSD 3.994 fnat 0.800 fnonnat 0.000 F1 0.889 clashes 0 mapping AG:BH examples/1EXB_r_l_b.model.pdb A G -> examples/1EXB_r_l_b.pdb B H
+DockQ 1.000 iRMSD 0.000 LRMSD 0.000 fnat 1.000 fnonnat 0.000 F1 1.000 clashes 0 mapping BC:AD examples/1EXB_r_l_b.model.pdb B C -> examples/1EXB_r_l_b.pdb A D
+DockQ 0.995 iRMSD 0.000 LRMSD 0.000 fnat 0.985 fnonnat 0.000 F1 0.993 clashes 0 mapping BD:AC examples/1EXB_r_l_b.model.pdb B D -> examples/1EXB_r_l_b.pdb A C
+DockQ 0.552 iRMSD 1.458 LRMSD 3.757 fnat 0.304 fnonnat 0.000 F1 0.467 clashes 0 mapping BF:AE examples/1EXB_r_l_b.model.pdb B F -> examples/1EXB_r_l_b.pdb A E
+DockQ 0.694 iRMSD 0.793 LRMSD 2.831 fnat 0.400 fnonnat 0.000 F1 0.571 clashes 0 mapping BH:AG examples/1EXB_r_l_b.model.pdb B H -> examples/1EXB_r_l_b.pdb A G
+DockQ 0.687 iRMSD 1.161 LRMSD 3.757 fnat 0.600 fnonnat 0.000 F1 0.750 clashes 0 mapping CF:DE examples/1EXB_r_l_b.model.pdb C F -> examples/1EXB_r_l_b.pdb D E
+DockQ 0.477 iRMSD 1.425 LRMSD 3.994 fnat 0.087 fnonnat 0.000 F1 0.160 clashes 0 mapping CG:DH examples/1EXB_r_l_b.model.pdb C G -> examples/1EXB_r_l_b.pdb D H
+DockQ 0.775 iRMSD 0.711 LRMSD 2.831 fnat 0.609 fnonnat 0.125 F1 0.718 clashes 0 mapping DH:CG examples/1EXB_r_l_b.model.pdb D H -> examples/1EXB_r_l_b.pdb C G
+DockQ 0.914 iRMSD 0.547 LRMSD 3.426 fnat 1.000 fnonnat 0.000 F1 1.000 clashes 0 mapping DE:CF examples/1EXB_r_l_b.model.pdb D E -> examples/1EXB_r_l_b.pdb C F
+DockQ 0.992 iRMSD 0.001 LRMSD 0.000 fnat 0.976 fnonnat 0.000 F1 0.988 clashes 0 mapping FH:EG examples/1EXB_r_l_b.model.pdb F H -> examples/1EXB_r_l_b.pdb E G
+DockQ 0.992 iRMSD 0.001 LRMSD 0.000 fnat 0.976 fnonnat 0.000 F1 0.988 clashes 0 mapping FG:EH examples/1EXB_r_l_b.model.pdb F G -> examples/1EXB_r_l_b.pdb E H
+DockQ 0.992 iRMSD 0.001 LRMSD 0.001 fnat 0.976 fnonnat 0.000 F1 0.988 clashes 0 mapping HE:GF examples/1EXB_r_l_b.model.pdb H E -> examples/1EXB_r_l_b.pdb G F
+DockQ 1.000 iRMSD 0.001 LRMSD 0.001 fnat 1.000 fnonnat 0.024 F1 0.988 clashes 0 mapping EG:FH examples/1EXB_r_l_b.model.pdb E G -> examples/1EXB_r_l_b.pdb F H
diff --git a/testdata/1EXB_ABCDEFGH.BADCFEHG.dockq b/testdata/1EXB_ABCDEFGH.BADCFEHG.dockq
index 24e9bb4..0e67f96 100644
--- a/testdata/1EXB_ABCDEFGH.BADCFEHG.dockq
+++ b/testdata/1EXB_ABCDEFGH.BADCFEHG.dockq
@@ -1,17 +1,17 @@
 Total DockQ over 16 native interfaces: 0.852 with ABCDEFGH:BADCFEHG model:native mapping
-DockQ 0.995 irms 0.000 Lrms 0.000 fnat 0.985 fnonnat 0.000 clashes 0.000 F1 0.993 DockQ_F1 0.998 mapping AC:BD examples/1EXB_r_l_b.model.pdb A C -> examples/1EXB_r_l_b.pdb B D
-DockQ 0.995 irms 0.000 Lrms 0.000 fnat 0.985 fnonnat 0.000 clashes 0.000 F1 0.993 DockQ_F1 0.998 mapping AD:BC examples/1EXB_r_l_b.model.pdb A D -> examples/1EXB_r_l_b.pdb B C
-DockQ 0.742 irms 0.850 Lrms 3.426 fnat 0.609 fnonnat 0.176 clashes 0.000 F1 0.700 DockQ_F1 0.772 mapping AE:BF examples/1EXB_r_l_b.model.pdb A E -> examples/1EXB_r_l_b.pdb B F
-DockQ 0.824 irms 0.625 Lrms 3.994 fnat 0.800 fnonnat 0.000 clashes 0.000 F1 0.889 DockQ_F1 0.853 mapping AG:BH examples/1EXB_r_l_b.model.pdb A G -> examples/1EXB_r_l_b.pdb B H
-DockQ 1.000 irms 0.000 Lrms 0.000 fnat 1.000 fnonnat 0.000 clashes 0.000 F1 1.000 DockQ_F1 1.000 mapping BC:AD examples/1EXB_r_l_b.model.pdb B C -> examples/1EXB_r_l_b.pdb A D
-DockQ 0.995 irms 0.000 Lrms 0.000 fnat 0.985 fnonnat 0.000 clashes 0.000 F1 0.993 DockQ_F1 0.998 mapping BD:AC examples/1EXB_r_l_b.model.pdb B D -> examples/1EXB_r_l_b.pdb A C
-DockQ 0.552 irms 1.458 Lrms 3.757 fnat 0.304 fnonnat 0.000 clashes 0.000 F1 0.467 DockQ_F1 0.606 mapping BF:AE examples/1EXB_r_l_b.model.pdb B F -> examples/1EXB_r_l_b.pdb A E
-DockQ 0.694 irms 0.793 Lrms 2.831 fnat 0.400 fnonnat 0.000 clashes 0.000 F1 0.571 DockQ_F1 0.751 mapping BH:AG examples/1EXB_r_l_b.model.pdb B H -> examples/1EXB_r_l_b.pdb A G
-DockQ 0.687 irms 1.161 Lrms 3.757 fnat 0.600 fnonnat 0.000 clashes 0.000 F1 0.750 DockQ_F1 0.737 mapping CF:DE examples/1EXB_r_l_b.model.pdb C F -> examples/1EXB_r_l_b.pdb D E
-DockQ 0.477 irms 1.425 Lrms 3.994 fnat 0.087 fnonnat 0.000 clashes 0.000 F1 0.160 DockQ_F1 0.502 mapping CG:DH examples/1EXB_r_l_b.model.pdb C G -> examples/1EXB_r_l_b.pdb D H
-DockQ 0.914 irms 0.547 Lrms 3.426 fnat 1.000 fnonnat 0.000 clashes 0.000 F1 1.000 DockQ_F1 0.914 mapping DE:CF examples/1EXB_r_l_b.model.pdb D E -> examples/1EXB_r_l_b.pdb C F
-DockQ 0.775 irms 0.711 Lrms 2.831 fnat 0.609 fnonnat 0.125 clashes 0.000 F1 0.718 DockQ_F1 0.812 mapping DH:CG examples/1EXB_r_l_b.model.pdb D H -> examples/1EXB_r_l_b.pdb C G
-DockQ 1.000 irms 0.001 Lrms 0.001 fnat 1.000 fnonnat 0.024 clashes 0.000 F1 0.988 DockQ_F1 0.996 mapping EG:FH examples/1EXB_r_l_b.model.pdb E G -> examples/1EXB_r_l_b.pdb F H
-DockQ 0.992 irms 0.001 Lrms 0.001 fnat 0.976 fnonnat 0.000 clashes 0.000 F1 0.988 DockQ_F1 0.996 mapping EH:FG examples/1EXB_r_l_b.model.pdb E H -> examples/1EXB_r_l_b.pdb F G
-DockQ 0.992 irms 0.001 Lrms 0.000 fnat 0.976 fnonnat 0.000 clashes 0.000 F1 0.988 DockQ_F1 0.996 mapping FG:EH examples/1EXB_r_l_b.model.pdb F G -> examples/1EXB_r_l_b.pdb E H
-DockQ 0.992 irms 0.001 Lrms 0.000 fnat 0.976 fnonnat 0.000 clashes 0.000 F1 0.988 DockQ_F1 0.996 mapping FH:EG examples/1EXB_r_l_b.model.pdb F H -> examples/1EXB_r_l_b.pdb E G
+DockQ 0.995 iRMSD 0.000 LRMSD 0.000 fnat 0.985 fnonnat 0.000 F1 0.993 clashes 0 mapping AC:BD examples/1EXB_r_l_b.model.pdb A C -> examples/1EXB_r_l_b.pdb B D
+DockQ 0.995 iRMSD 0.000 LRMSD 0.000 fnat 0.985 fnonnat 0.000 F1 0.993 clashes 0 mapping AD:BC examples/1EXB_r_l_b.model.pdb A D -> examples/1EXB_r_l_b.pdb B C
+DockQ 0.742 iRMSD 0.850 LRMSD 3.426 fnat 0.609 fnonnat 0.176 F1 0.700 clashes 0 mapping AE:BF examples/1EXB_r_l_b.model.pdb A E -> examples/1EXB_r_l_b.pdb B F
+DockQ 0.824 iRMSD 0.625 LRMSD 3.994 fnat 0.800 fnonnat 0.000 F1 0.889 clashes 0 mapping AG:BH examples/1EXB_r_l_b.model.pdb A G -> examples/1EXB_r_l_b.pdb B H
+DockQ 1.000 iRMSD 0.000 LRMSD 0.000 fnat 1.000 fnonnat 0.000 F1 1.000 clashes 0 mapping BC:AD examples/1EXB_r_l_b.model.pdb B C -> examples/1EXB_r_l_b.pdb A D
+DockQ 0.995 iRMSD 0.000 LRMSD 0.000 fnat 0.985 fnonnat 0.000 F1 0.993 clashes 0 mapping BD:AC examples/1EXB_r_l_b.model.pdb B D -> examples/1EXB_r_l_b.pdb A C
+DockQ 0.552 iRMSD 1.458 LRMSD 3.757 fnat 0.304 fnonnat 0.000 F1 0.467 clashes 0 mapping BF:AE examples/1EXB_r_l_b.model.pdb B F -> examples/1EXB_r_l_b.pdb A E
+DockQ 0.694 iRMSD 0.793 LRMSD 2.831 fnat 0.400 fnonnat 0.000 F1 0.571 clashes 0 mapping BH:AG examples/1EXB_r_l_b.model.pdb B H -> examples/1EXB_r_l_b.pdb A G
+DockQ 0.687 iRMSD 1.161 LRMSD 3.757 fnat 0.600 fnonnat 0.000 F1 0.750 clashes 0 mapping CF:DE examples/1EXB_r_l_b.model.pdb C F -> examples/1EXB_r_l_b.pdb D E
+DockQ 0.477 iRMSD 1.425 LRMSD 3.994 fnat 0.087 fnonnat 0.000 F1 0.160 clashes 0 mapping CG:DH examples/1EXB_r_l_b.model.pdb C G -> examples/1EXB_r_l_b.pdb D H
+DockQ 0.914 iRMSD 0.547 LRMSD 3.426 fnat 1.000 fnonnat 0.000 F1 1.000 clashes 0 mapping DE:CF examples/1EXB_r_l_b.model.pdb D E -> examples/1EXB_r_l_b.pdb C F
+DockQ 0.775 iRMSD 0.711 LRMSD 2.831 fnat 0.609 fnonnat 0.125 F1 0.718 clashes 0 mapping DH:CG examples/1EXB_r_l_b.model.pdb D H -> examples/1EXB_r_l_b.pdb C G
+DockQ 1.000 iRMSD 0.001 LRMSD 0.001 fnat 1.000 fnonnat 0.024 F1 0.988 clashes 0 mapping EG:FH examples/1EXB_r_l_b.model.pdb E G -> examples/1EXB_r_l_b.pdb F H
+DockQ 0.992 iRMSD 0.001 LRMSD 0.001 fnat 0.976 fnonnat 0.000 F1 0.988 clashes 0 mapping EH:FG examples/1EXB_r_l_b.model.pdb E H -> examples/1EXB_r_l_b.pdb F G
+DockQ 0.992 iRMSD 0.001 LRMSD 0.000 fnat 0.976 fnonnat 0.000 F1 0.988 clashes 0 mapping FG:EH examples/1EXB_r_l_b.model.pdb F G -> examples/1EXB_r_l_b.pdb E H
+DockQ 0.992 iRMSD 0.001 LRMSD 0.000 fnat 0.976 fnonnat 0.000 F1 0.988 clashes 0 mapping FH:EG examples/1EXB_r_l_b.model.pdb F H -> examples/1EXB_r_l_b.pdb E G
diff --git a/testdata/1EXB_DH.AE.dockq b/testdata/1EXB_DH.AE.dockq
index 7c374d0..59dbee1 100644
--- a/testdata/1EXB_DH.AE.dockq
+++ b/testdata/1EXB_DH.AE.dockq
@@ -17,10 +17,9 @@ Total DockQ over 1 native interfaces: 0.775 with DH:AE model:native mapping
 Native chains: A, E
 	Model chains: D, H
 	DockQ: 0.775
-	irms: 0.711
-	Lrms: 2.831
+	iRMSD: 0.711
+	LRMSD: 2.831
 	fnat: 0.609
 	fnonnat: 0.125
-	clashes: 0.000
 	F1: 0.718
-	DockQ_F1: 0.812
+	clashes: 0
diff --git a/testdata/1EXB_DH.AE_cif.dockq b/testdata/1EXB_DH.AE_cif.dockq
index b734d70..10fe5d3 100644
--- a/testdata/1EXB_DH.AE_cif.dockq
+++ b/testdata/1EXB_DH.AE_cif.dockq
@@ -17,10 +17,9 @@ Total DockQ over 1 native interfaces: 0.775 with DH:AE model:native mapping
 Native chains: A, E
 	Model chains: D, H
 	DockQ: 0.775
-	irms: 0.711
-	Lrms: 2.831
+	iRMSD: 0.711
+	LRMSD: 2.831
 	fnat: 0.609
 	fnonnat: 0.125
-	clashes: 0.000
 	F1: 0.718
-	DockQ_F1: 0.812
+	clashes: 0
diff --git a/testdata/6q2n_peptide.dockq b/testdata/6q2n_peptide.dockq
index 497aec6..5f9fe51 100644
--- a/testdata/6q2n_peptide.dockq
+++ b/testdata/6q2n_peptide.dockq
@@ -15,10 +15,9 @@ Total DockQ-capri_peptide over 1 native interfaces: 0.872 with AF:BG model:nativ
 Native chains: B, G
 	Model chains: A, F
 	DockQ: 0.872
-	irms: 0.588
-	Lrms: 0.982
+	iRMSD: 0.588
+	LRMSD: 0.982
 	fnat: 0.762
 	fnonnat: 0.158
-	clashes: 0.000
 	F1: 0.800
-	DockQ_F1: 0.885
+	clashes: 0
diff --git a/testdata/dimer_dimer.dockq b/testdata/dimer_dimer.dockq
index 553d642..f259f5e 100644
--- a/testdata/dimer_dimer.dockq
+++ b/testdata/dimer_dimer.dockq
@@ -1,5 +1,5 @@
 Total DockQ over 4 native interfaces: 1.000 with ABLH:ABLH model:native mapping
-DockQ 1.000 irms 0.000 Lrms 0.000 fnat 1.000 fnonnat 0.000 clashes 0.000 F1 1.000 DockQ_F1 1.000 mapping AB:AB examples/dimer_dimer.model.pdb A B -> examples/dimer_dimer.pdb A B
-DockQ 1.000 irms 0.000 Lrms 0.000 fnat 1.000 fnonnat 0.000 clashes 0.000 F1 1.000 DockQ_F1 1.000 mapping AL:AL examples/dimer_dimer.model.pdb A L -> examples/dimer_dimer.pdb A L
-DockQ 1.000 irms 0.000 Lrms 0.000 fnat 1.000 fnonnat 0.000 clashes 0.000 F1 1.000 DockQ_F1 1.000 mapping AH:AH examples/dimer_dimer.model.pdb A H -> examples/dimer_dimer.pdb A H
-DockQ 1.000 irms 0.000 Lrms 0.000 fnat 1.000 fnonnat 0.000 clashes 0.000 F1 1.000 DockQ_F1 1.000 mapping LH:LH examples/dimer_dimer.model.pdb L H -> examples/dimer_dimer.pdb L H
+DockQ 1.000 iRMSD 0.000 LRMSD 0.000 fnat 1.000 fnonnat 0.000 F1 1.000 clashes 0 mapping AB:AB examples/dimer_dimer.model.pdb A B -> examples/dimer_dimer.pdb A B
+DockQ 1.000 iRMSD 0.000 LRMSD 0.000 fnat 1.000 fnonnat 0.000 F1 1.000 clashes 0 mapping AL:AL examples/dimer_dimer.model.pdb A L -> examples/dimer_dimer.pdb A L
+DockQ 1.000 iRMSD 0.000 LRMSD 0.000 fnat 1.000 fnonnat 0.000 F1 1.000 clashes 0 mapping AH:AH examples/dimer_dimer.model.pdb A H -> examples/dimer_dimer.pdb A H
+DockQ 1.000 iRMSD 0.000 LRMSD 0.000 fnat 1.000 fnonnat 0.000 F1 1.000 clashes 0 mapping LH:LH examples/dimer_dimer.model.pdb L H -> examples/dimer_dimer.pdb L H
diff --git a/testdata/model.dockq b/testdata/model.dockq
index 9c7b0aa..368468b 100644
--- a/testdata/model.dockq
+++ b/testdata/model.dockq
@@ -17,10 +17,9 @@ Total DockQ over 1 native interfaces: 0.700 with AB:AB model:native mapping
 Native chains: A, B
 	Model chains: A, B
 	DockQ: 0.700
-	irms: 1.232
-	Lrms: 1.516
+	iRMSD: 1.232
+	LRMSD: 1.516
 	fnat: 0.533
 	fnonnat: 0.238
-	clashes: 2.000
 	F1: 0.627
-	DockQ_F1: 0.731
+	clashes: 2