Error running RosettaAntibodyDesign application

Hi,

I'm trying to replicate one of the runs from the paper "Rosetta Antibody Design (RAbD): A General Framework for Computational Antibody Design".  I'm trying to replicate the run for the pdb 2j88 using the protocol and flags as described in the supplementary material.  The application runs for about 10 hours and then crashes.  The last 50 lines are pasted below (the log file is too large to upload to this forum).  I've attached the files common_flags.txt, experimental_flags.txt, and cdr_instructions.txt.  I pre-processed the complexed starting from 2j88 (which was renumbered to AHo scheme using the pyigclassify server) and following the protocol and flags as listed in the supp. materials.  I'm running rosetta_src_2017.39, which is the latest version that's currently available.

Any ideas what could be going wrong?

Thanks

>ROSETTA_DIR=/opt/software/rosetta/rosetta_src_2017.39.59729_bundle/main

>export ROSETTA3_DB=${ROSETTA_DIR}/database

>${ROSETTA_DIR}/source/bin/antibody_designer.linuxgccrelease -database ${ROSETTA_DIR}/database @common_flags.txt @experimental_flags.txt -cdr_instructions cdr_instructions.txt -s 2j88_pareto_optimal.pdb -nstruct 5

....

protocols.relax.FastRelax: MRP: 4  -521.406  -525.718  1.63405  1.63405  
protocols.relax.FastRelax: CMD: accept_to_best  -521.406  1.71513  1.71513  0.55
protocols.relax.FastRelax: CMD: endrepeat  -521.406  1.71513  1.71513  0.55
protocols::checkpoint: Deleting checkpoints of FastRelax
protocols.antibody.design.AntibodyDesignProtocol: start:            -1110.12
protocols.antibody.design.AntibodyDesignProtocol: postDsREL:        -1805.08
protocols::checkpoint: Deleting checkpoints of FastRelax
protocols.antibody.design.AntibodyDesignProtocol: Native: -1117.84
protocols.antibody.design.AntibodyDesignProtocol: Pose 1
protocols.antibody.design.AntibodyDesignProtocol: 
------------------------------------------------------------
 Scores                       Weight   Raw Score Wghtd.Score
------------------------------------------------------------
 fa_atr                       1.000   -3396.194   -3396.194
 fa_rep                       0.550     697.558     383.657
 fa_sol                       1.000    1951.133    1951.133
 fa_intra_rep                 0.005    1311.326       6.557
 fa_intra_sol_xover4          1.000     105.062     105.062
 lk_ball_wtd                  1.000     -68.700     -68.700
 fa_elec                      1.000   -1041.850   -1041.850
 pro_close                    1.250      73.671      92.088
 hbond_sr_bb                  1.000    -177.286    -177.286
 hbond_lr_bb                  1.000    -170.676    -170.676
 hbond_bb_sc                  1.000    -132.466    -132.466
 hbond_sc                     1.000    -131.506    -131.506
 dslf_fa13                    1.250      -2.640      -3.300
 atom_pair_constraint         0.010    1192.252      11.923
 omega                        0.400      33.594      13.438
 fa_dun                       0.700     930.455     651.318
 p_aa_pp                      0.600    -188.772    -113.263
 yhh_planarity                0.625       0.347       0.217
 ref                          1.000     170.176     170.176
 rama_prepro                  0.450      99.102      44.596
---------------------------------------------------
 Total weighted score:                    -1805.076
antibody.AntibodyInfo: Setting up CDR Cluster for H1
protocols.jd2.JobDistributor: [ ERROR ] 

[ERROR] Exception caught by JobDistributor for job 2j88_pareto_optimal_0001
H1 end resnum not found in pose: 42 H  
Please check pdb is renumbered properly and the passed -numbering_scheme option matches the PDB. 
This could also mean missing density in the cdr loop.  Loop modeling applications can be used to fill missing residues 

protocols.jd2.JobDistributor: [ ERROR ] 
protocols.jd2.JobDistributor: [ WARNING ] 2j88_pareto_optimal_0001 reported that its input was bad and will not retry
protocols.jd2.FileSystemJobDistributor: job failed, reporting bad input; other jobs of same input will be canceled: 2j88_pareto_optimal_0001
protocols.jd2.JobDistributor: no more batches to process... 
protocols.jd2.JobDistributor: 5 jobs considered, 1 jobs attempted in 40115 seconds
Error: [ ERROR ] ERROR: Exception caught by antibody_design application:1 jobs failed; check output for error messages
Error: [ ERROR ]