mkdir und2 /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR Cannot open partial pdb file for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/T0098-1a3lL.0.1.pdb: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR write_partial_pdb_file failed. gmake: *** [und2/T0098-1a3lL.0.1.index] Error 1 mkdir und2 /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end Debugging on ! Reading sequence file Reading input structure 12 residues read Measuring phi and psi Getting chi values ASP 1 5 ASN 2 4 LYS 3 31 PRO 4 2 LYS 5 22 ASN 6 4 LEU 7 3 ASP 8 5 SER 10 2 Building many copies of each residue Checking backbone and frame clashes Finding the lowest Also, print out the first version, pre-bump Finding disulfide bonds. Found 0 disulfide bonds. Residue clashes: 0 clashing residues after turn Residue clashes: Still clashes at these sidechain pairs: Residual clashes = 0.00000 Printing mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.0.5.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.0.5.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.0.5 -outdir und2 partial PDB gets fragment 202 through 211 extending start extending end Debugging on ! Reading sequence file Reading input structure 12 residues read Measuring phi and psi Getting chi values ASP 1 8 ASN 2 5 LYS 3 22 PRO 4 2 LYS 5 29 ASN 6 5 LEU 7 3 ASP 8 5 SER 10 3 Building many copies of each residue Checking backbone and frame clashes Finding the lowest Also, print out the first version, pre-bump Finding disulfide bonds. Found 0 disulfide bonds. Residue clashes: 0 clashing residues after turn Residue clashes: Still clashes at these sidechain pairs: Residual clashes = 0.00000 Printing mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.1.0.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.1.0.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.1.0 -outdir und2 partial PDB gets fragment 199 through 208 extending start extending end Debugging on ! Reading sequence file Reading input structure 12 residues read Measuring phi and psi Getting chi values ASN 1 5 LYS 2 27 PRO 3 2 LYS 4 31 ASN 5 5 LEU 6 2 ASP 7 3 ILE 10 5 Building many copies of each residue Checking backbone and frame clashes Finding the lowest Also, print out the first version, pre-bump Finding disulfide bonds. Found 0 disulfide bonds. Residue clashes: 0 clashing residues after turn Residue clashes: Still clashes at these sidechain pairs: Residual clashes = 1.02280 Printing mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.1.3.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.1.3.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.1.3 -outdir und2 partial PDB gets fragment 201 through 210 extending start extending end Debugging on ! Reading sequence file Reading input structure 12 residues read Measuring phi and psi Getting chi values ASN 1 4 LYS 2 31 PRO 3 2 LYS 4 22 ASN 5 4 LEU 6 3 ASP 7 5 SER 9 2 ILE 10 3 Building many copies of each residue Checking backbone and frame clashes Finding the lowest Also, print out the first version, pre-bump Finding disulfide bonds. Found 0 disulfide bonds. Residue clashes: 0 clashing residues after turn Residue clashes: Still clashes at these sidechain pairs: Residual clashes = 0.00000 Printing mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.2.0.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.2.0.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.2.0 -outdir und2 partial PDB gets fragment 198 through 207 extending start extending end Debugging on ! Reading sequence file Reading input structure 12 residues read Measuring phi and psi Getting chi values LYS 1 27 PRO 2 2 LYS 3 27 ASN 4 4 LEU 5 5 ASP 6 5 ILE 9 5 THR 10 2 Building many copies of each residue Checking backbone and frame clashes Finding the lowest Also, print out the first version, pre-bump Finding disulfide bonds. Found 0 disulfide bonds. Residue clashes: 0 clashing residues after turn Residue clashes: Still clashes at these sidechain pairs: Residual clashes = 0.00000 Printing mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.2.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.2.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.2.1 -outdir und2 partial PDB gets fragment 200 through 209 extending start extending end Debugging on ! Reading sequence file Reading input structure 12 residues read Measuring phi and psi Getting chi values LYS 1 27 PRO 2 2 LYS 3 31 ASN 4 5 LEU 5 2 ASP 6 3 ILE 9 5 THR 10 2 Building many copies of each residue Checking backbone and frame clashes Finding the lowest Also, print out the first version, pre-bump Finding disulfide bonds. Found 0 disulfide bonds. Residue clashes: 0 clashing residues after turn Residue clashes: Still clashes at these sidechain pairs: Residual clashes = 0.00000 Printing mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.3.0.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.3.0.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.3.0 -outdir und2 partial PDB gets fragment 197 through 206 extending start extending end Debugging on ! Reading sequence file Reading input structure 12 residues read Measuring phi and psi Getting chi values PRO 1 2 LYS 2 27 ASN 3 5 LEU 4 3 ASP 5 5 SER 7 2 ILE 8 3 THR 9 2 SER 10 2 Building many copies of each residue Checking backbone and frame clashes Finding the lowest Also, print out the first version, pre-bump Finding disulfide bonds. Found 0 disulfide bonds. Residue clashes: 0 clashing residues after turn Residue clashes: Still clashes at these sidechain pairs: Residual clashes = 0.00000 Printing mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.3.2.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.3.2.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.3.2 -outdir und2 partial PDB gets fragment 199 through 208 extending start extending end Debugging on ! Reading sequence file Reading input structure 12 residues read Measuring phi and psi Getting chi values PRO 1 2 LYS 2 27 ASN 3 4 LEU 4 5 ASP 5 5 ILE 8 5 THR 9 2 SER 10 3 Building many copies of each residue Checking backbone and frame clashes Finding the lowest Also, print out the first version, pre-bump Finding disulfide bonds. Found 0 disulfide bonds. Residue clashes: 0 clashing residues after turn Residue clashes: Still clashes at these sidechain pairs: Residual clashes = 0.00000 Printing mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.4.0.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.4.0.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.4.0 -outdir und2 partial PDB gets fragment 196 through 205 extending start extending end Debugging on ! Reading sequence file Reading input structure 12 residues read Measuring phi and psi Getting chi values LYS 1 26 ASN 2 6 LEU 3 3 ASP 4 5 SER 6 2 ILE 7 5 THR 8 2 SER 9 2 ILE 10 3 Building many copies of each residue Checking backbone and frame clashes Finding the lowest Also, print out the first version, pre-bump Finding disulfide bonds. Found 0 disulfide bonds. Residue clashes: 0 clashing residues after turn Residue clashes: Still clashes at these sidechain pairs: Residual clashes = 5.88568 Printing mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.4.2.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.4.2.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.4.2 -outdir und2 partial PDB gets fragment 198 through 207 extending start extending end Debugging on ! Reading sequence file Reading input structure 12 residues read Measuring phi and psi Getting chi values LYS 1 27 ASN 2 5 LEU 3 3 ASP 4 5 SER 6 2 ILE 7 3 THR 8 2 SER 9 2 ILE 10 3 Building many copies of each residue Checking backbone and frame clashes Finding the lowest Also, print out the first version, pre-bump Finding disulfide bonds. Found 0 disulfide bonds. Residue clashes: 0 clashing residues after turn Residue clashes: Still clashes at these sidechain pairs: Residual clashes = 0.00000 Printing mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.5.0.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.5.0.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.5.0 -outdir und2 partial PDB gets fragment 195 through 204 extending start extending end Debugging on ! Reading sequence file Reading input structure 12 residues read Measuring phi and psi Getting chi values ASN 1 5 LEU 2 3 ASP 3 6 SER 5 3 ILE 6 3 SER 8 3 ILE 9 4 ILE 10 3 Building many copies of each residue Checking backbone and frame clashes Finding the lowest Also, print out the first version, pre-bump Finding disulfide bonds. Found 0 disulfide bonds. Residue clashes: 0 clashing residues after turn Residue clashes: Still clashes at these sidechain pairs: Residual clashes = 0.00000 Printing mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.5.2.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.5.2.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.5.2 -outdir und2 partial PDB gets fragment 197 through 206 extending start extending end Debugging on ! Reading sequence file Reading input structure 12 residues read Measuring phi and psi Getting chi values ASN 1 6 LEU 2 3 ASP 3 5 SER 5 2 ILE 6 5 THR 7 2 SER 8 2 ILE 9 3 ILE 10 4 Building many copies of each residue Checking backbone and frame clashes Finding the lowest Also, print out the first version, pre-bump Finding disulfide bonds. Found 0 disulfide bonds. Residue clashes: 0 clashing residues after turn Residue clashes: Still clashes at these sidechain pairs: Residual clashes = 5.88568 Printing mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.5.5.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.5.5.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.5.5 -outdir und2 partial PDB gets fragment 199 through 208 extending start extending end Debugging on ! Reading sequence file Reading input structure 12 residues read Measuring phi and psi Getting chi values ASN 1 5 LEU 2 3 ASP 3 5 SER 5 2 ILE 6 3 THR 7 2 SER 8 2 ILE 9 3 ILE 10 5 Building many copies of each residue Checking backbone and frame clashes Finding the lowest Also, print out the first version, pre-bump Finding disulfide bonds. Found 0 disulfide bonds. Residue clashes: 0 clashing residues after turn Residue clashes: Still clashes at these sidechain pairs: Residual clashes = 0.00000 Printing mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.6.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.6.1.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.6.1 -outdir und2 partial PDB gets fragment 194 through 203 extending start extending end Debugging on ! Reading sequence file Reading input structure 12 residues read Measuring phi and psi Getting chi values LEU 1 3 ASP 2 5 SER 4 3 ILE 5 3 THR 6 2 SER 7 3 ILE 8 2 ILE 9 5 HIS 10 3 Building many copies of each residue Checking backbone and frame clashes Finding the lowest Also, print out the first version, pre-bump Finding disulfide bonds. Found 0 disulfide bonds. Residue clashes: 0 clashing residues after turn Residue clashes: Still clashes at these sidechain pairs: Residual clashes = 0.00000 Printing mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.6.2.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.6.2.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.6.2 -outdir und2 partial PDB gets fragment 196 through 205 extending start extending end Debugging on ! Reading sequence file Reading input structure 12 residues read Measuring phi and psi Getting chi values LEU 1 3 ASP 2 6 SER 4 3 ILE 5 3 SER 7 3 ILE 8 4 ILE 9 3 HIS 10 4 Building many copies of each residue Checking backbone and frame clashes Finding the lowest Also, print out the first version, pre-bump Finding disulfide bonds. Found 0 disulfide bonds. Residue clashes: 0 clashing residues after turn Residue clashes: Still clashes at these sidechain pairs: Residual clashes = 0.00000 Printing mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.7.3.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.7.3.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.7.3 -outdir und2 partial PDB gets fragment 193 through 202 extending start extending end Debugging on ! Reading sequence file Reading input structure 12 residues read Measuring phi and psi Getting chi values ASP 1 5 ILE 4 2 SER 6 3 ILE 7 3 ILE 8 3 HIS 9 3 GLU 10 16 Building many copies of each residue Checking backbone and frame clashes Finding the lowest Also, print out the first version, pre-bump Finding disulfide bonds. Found 0 disulfide bonds. Residue clashes: 0 clashing residues after turn Residue clashes: Still clashes at these sidechain pairs: Residual clashes = 0.00000 Printing mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a3lL.7.5.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a3lL.7.5.a2m \ -target T0098 -template 1a3lL \ -out T0098-1a3lL.7.5 -outdir und2 partial PDB gets fragment 195 through 204 extending start extending end Debugging on ! Reading sequence file Reading input structure 12 residues read Measuring phi and psi Getting chi values ASP 1 5 SER 3 3 ILE 4 3 THR 5 2 SER 6 3 ILE 7 2 ILE 8 5 HIS 9 3 GLU 10 13 Building many copies of each residue Checking backbone and frame clashes Finding the lowest Also, print out the first version, pre-bump Finding disulfide bonds. Found 0 disulfide bonds. Residue clashes: 0 clashing residues after turn Residue clashes: Still clashes at these sidechain pairs: Residual clashes = 0.00000 Printing mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a4iA.38.4.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a4iA.38.4.a2m \ -target T0098 -template 1a4iA \ -out T0098-1a4iA.38.4 -outdir und2 PDB sequence and aligned sequence are not exact. /projects/kestrel/users/karplus/burial/slicer/slicer: Error: Cannot open file tmp/1a4iA-orig.a2m for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/1a4iA-orig.a2m: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR align_unmatched failed. gmake: *** [und2/T0098-1a4iA.38.4.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a4iA.39.2.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a4iA.39.2.a2m \ -target T0098 -template 1a4iA \ -out T0098-1a4iA.39.2 -outdir und2 PDB sequence and aligned sequence are not exact. /projects/kestrel/users/karplus/burial/slicer/slicer: Error: Cannot open file tmp/1a4iA-orig.a2m for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/1a4iA-orig.a2m: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR align_unmatched failed. gmake: *** [und2/T0098-1a4iA.39.2.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a4iA.40.4.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a4iA.40.4.a2m \ -target T0098 -template 1a4iA \ -out T0098-1a4iA.40.4 -outdir und2 PDB sequence and aligned sequence are not exact. /projects/kestrel/users/karplus/burial/slicer/slicer: Error: Cannot open file tmp/1a4iA-orig.a2m for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/1a4iA-orig.a2m: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR align_unmatched failed. gmake: *** [und2/T0098-1a4iA.40.4.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a4iA.41.5.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a4iA.41.5.a2m \ -target T0098 -template 1a4iA \ -out T0098-1a4iA.41.5 -outdir und2 PDB sequence and aligned sequence are not exact. /projects/kestrel/users/karplus/burial/slicer/slicer: Error: Cannot open file tmp/1a4iA-orig.a2m for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/1a4iA-orig.a2m: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR align_unmatched failed. gmake: *** [und2/T0098-1a4iA.41.5.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a4iA.42.5.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a4iA.42.5.a2m \ -target T0098 -template 1a4iA \ -out T0098-1a4iA.42.5 -outdir und2 PDB sequence and aligned sequence are not exact. /projects/kestrel/users/karplus/burial/slicer/slicer: Error: Cannot open file tmp/1a4iA-orig.a2m for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/1a4iA-orig.a2m: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR align_unmatched failed. gmake: *** [und2/T0098-1a4iA.42.5.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a4iA.43.4.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a4iA.43.4.a2m \ -target T0098 -template 1a4iA \ -out T0098-1a4iA.43.4 -outdir und2 PDB sequence and aligned sequence are not exact. /projects/kestrel/users/karplus/burial/slicer/slicer: Error: Cannot open file tmp/1a4iA-orig.a2m for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/1a4iA-orig.a2m: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR align_unmatched failed. gmake: *** [und2/T0098-1a4iA.43.4.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a4iA.44.2.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a4iA.44.2.a2m \ -target T0098 -template 1a4iA \ -out T0098-1a4iA.44.2 -outdir und2 PDB sequence and aligned sequence are not exact. /projects/kestrel/users/karplus/burial/slicer/slicer: Error: Cannot open file tmp/1a4iA-orig.a2m for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/1a4iA-orig.a2m: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR align_unmatched failed. gmake: *** [und2/T0098-1a4iA.44.2.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a4iA.45.2.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a4iA.45.2.a2m \ -target T0098 -template 1a4iA \ -out T0098-1a4iA.45.2 -outdir und2 PDB sequence and aligned sequence are not exact. /projects/kestrel/users/karplus/burial/slicer/slicer: Error: Cannot open file tmp/1a4iA-orig.a2m for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/1a4iA-orig.a2m: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR align_unmatched failed. gmake: *** [und2/T0098-1a4iA.45.2.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a4iA.45.4.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a4iA.45.4.a2m \ -target T0098 -template 1a4iA \ -out T0098-1a4iA.45.4 -outdir und2 PDB sequence and aligned sequence are not exact. /projects/kestrel/users/karplus/burial/slicer/slicer: Error: Cannot open file tmp/1a4iA-orig.a2m for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/1a4iA-orig.a2m: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR align_unmatched failed. gmake: *** [und2/T0098-1a4iA.45.4.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a4iA.46.3.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a4iA.46.3.a2m \ -target T0098 -template 1a4iA \ -out T0098-1a4iA.46.3 -outdir und2 PDB sequence and aligned sequence are not exact. /projects/kestrel/users/karplus/burial/slicer/slicer: Error: Cannot open file tmp/1a4iA-orig.a2m for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/1a4iA-orig.a2m: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR align_unmatched failed. gmake: *** [und2/T0098-1a4iA.46.3.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a4iA.46.4.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a4iA.46.4.a2m \ -target T0098 -template 1a4iA \ -out T0098-1a4iA.46.4 -outdir und2 PDB sequence and aligned sequence are not exact. /projects/kestrel/users/karplus/burial/slicer/slicer: Error: Cannot open file tmp/1a4iA-orig.a2m for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/1a4iA-orig.a2m: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR align_unmatched failed. gmake: *** [und2/T0098-1a4iA.46.4.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a4iA.47.4.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a4iA.47.4.a2m \ -target T0098 -template 1a4iA \ -out T0098-1a4iA.47.4 -outdir und2 PDB sequence and aligned sequence are not exact. /projects/kestrel/users/karplus/burial/slicer/slicer: Error: Cannot open file tmp/1a4iA-orig.a2m for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/1a4iA-orig.a2m: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR align_unmatched failed. gmake: *** [und2/T0098-1a4iA.47.4.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a6m.0.0.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a6m.0.0.a2m \ -target T0098 -template 1a6m \ -out T0098-1a6m.0.0 -outdir und2 Skipped atom 27, because occupancy 0.43 <= existing 0.570001 Skipped atom 29, because occupancy 0.43 <= existing 0.570001 Skipped atom 31, because occupancy 0.43 <= existing 0.570001 Skipped atom 33, because occupancy 0.43 <= existing 0.570001 Skipped atom 35, because occupancy 0.43 <= existing 0.570001 Skipped atom 68, because occupancy 0.43 <= existing 0.570001 Skipped atom 70, because occupancy 0.43 <= existing 0.570001 Skipped atom 72, because occupancy 0.43 <= existing 0.570001 Skipped atom 74, because occupancy 0.43 <= existing 0.570001 Skipped atom 76, because occupancy 0.43 <= existing 0.570001 Skipped atom 209, because occupancy 0.35 <= existing 0.650001 Skipped atom 211, because occupancy 0.35 <= existing 0.650001 Skipped atom 213, because occupancy 0.35 <= existing 0.650001 Skipped atom 215, because occupancy 0.35 <= existing 0.650001 Skipped atom 217, because occupancy 0.35 <= existing 0.650001 Skipped atom 348, because occupancy 0.49 <= existing 0.510001 Skipped atom 350, because occupancy 0.49 <= existing 0.510001 Skipped atom 352, because occupancy 0.49 <= existing 0.510001 Skipped atom 354, because occupancy 0.49 <= existing 0.510001 Skipped atom 356, because occupancy 0.49 <= existing 0.510001 Skipped atom 412, because occupancy 0.32 <= existing 0.680001 Skipped atom 414, because occupancy 0.32 <= existing 0.680001 Skipped atom 416, because occupancy 0.32 <= existing 0.680001 Skipped atom 418, because occupancy 0.32 <= existing 0.680001 Skipped atom 420, because occupancy 0.32 <= existing 0.680001 Skipped atom 533, because occupancy 0.34 <= existing 0.660001 Skipped atom 535, because occupancy 0.34 <= existing 0.660001 Skipped atom 537, because occupancy 0.34 <= existing 0.660001 Skipped atom 539, because occupancy 0.34 <= existing 0.660001 Skipped atom 554, because occupancy 0.41 <= existing 0.590001 Skipped atom 556, because occupancy 0.41 <= existing 0.590001 Skipped atom 558, because occupancy 0.41 <= existing 0.590001 Skipped atom 560, because occupancy 0.41 <= existing 0.590001 Skipped atom 562, because occupancy 0.41 <= existing 0.590001 Skipped atom 568, because occupancy 0.5 <= existing 0.500001 Skipped atom 570, because occupancy 0.5 <= existing 0.500001 Skipped atom 572, because occupancy 0.5 <= existing 0.500001 Skipped atom 574, because occupancy 0.5 <= existing 0.500001 Skipped atom 576, because occupancy 0.5 <= existing 0.500001 Skipped atom 578, because occupancy 0.5 <= existing 0.500001 Skipped atom 773, because occupancy 0.47 <= existing 0.530001 Skipped atom 775, because occupancy 0.47 <= existing 0.530001 Skipped atom 777, because occupancy 0.47 <= existing 0.530001 Skipped atom 779, because occupancy 0.47 <= existing 0.530001 Skipped atom 781, because occupancy 0.47 <= existing 0.530001 Skipped atom 815, because occupancy 0.45 <= existing 0.550001 Skipped atom 817, because occupancy 0.45 <= existing 0.550001 Skipped atom 819, because occupancy 0.45 <= existing 0.550001 Skipped atom 821, because occupancy 0.45 <= existing 0.550001 Skipped atom 823, because occupancy 0.45 <= existing 0.550001 Skipped atom 934, because occupancy 0.34 <= existing 0.660001 Skipped atom 936, because occupancy 0.34 <= existing 0.660001 Skipped atom 938, because occupancy 0.34 <= existing 0.660001 Skipped atom 940, because occupancy 0.34 <= existing 0.660001 Skipped atom 942, because occupancy 0.34 <= existing 0.660001 Skipped atom 998, because occupancy 0.46 <= existing 0.540001 Skipped atom 1000, because occupancy 0.46 <= existing 0.540001 Skipped atom 1002, because occupancy 0.46 <= existing 0.540001 Skipped atom 1004, because occupancy 0.46 <= existing 0.540001 Skipped atom 1006, because occupancy 0.46 <= existing 0.540001 Skipped atom 1008, because occupancy 0.46 <= existing 0.540001 Skipped atom 1014, because occupancy 0.44 <= existing 0.560001 Skipped atom 1016, because occupancy 0.44 <= existing 0.560001 Skipped atom 1089, because occupancy 0.34 <= existing 0.660001 Skipped atom 1091, because occupancy 0.34 <= existing 0.660001 Skipped atom 1093, because occupancy 0.34 <= existing 0.660001 Skipped atom 1095, because occupancy 0.34 <= existing 0.660001 Skipped atom 1106, because occupancy 0.44 <= existing 0.560001 Skipped atom 1108, because occupancy 0.44 <= existing 0.560001 Skipped atom 1110, because occupancy 0.44 <= existing 0.560001 Skipped atom 1112, because occupancy 0.44 <= existing 0.560001 Skipped atom 1114, because occupancy 0.44 <= existing 0.560001 Skipped atom 1145, because occupancy 0.45 <= existing 0.550001 Skipped atom 1147, because occupancy 0.45 <= existing 0.550001 Skipped atom 1149, because occupancy 0.45 <= existing 0.550001 Skipped atom 1151, because occupancy 0.45 <= existing 0.550001 Skipped atom 1153, because occupancy 0.45 <= existing 0.550001 Skipped atom 1172, because occupancy 0.43 <= existing 0.570001 Skipped atom 1174, because occupancy 0.43 <= existing 0.570001 Skipped atom 1176, because occupancy 0.43 <= existing 0.570001 Skipped atom 1178, because occupancy 0.43 <= existing 0.570001 Skipped atom 1180, because occupancy 0.43 <= existing 0.570001 Skipped atom 1240, because occupancy 0.33 <= existing 0.670001 Skipped atom 1242, because occupancy 0.33 <= existing 0.670001 Skipped atom 1244, because occupancy 0.33 <= existing 0.670001 Skipped atom 1246, because occupancy 0.33 <= existing 0.670001 Skipped atom 1321, because occupancy 0.5 <= existing 0.500001 Skipped atom 1323, because occupancy 0.5 <= existing 0.500001 Skipped atom 1325, because occupancy 0.5 <= existing 0.500001 Skipped atom 1327, because occupancy 0.5 <= existing 0.500001 Skipped atom 1329, because occupancy 0.5 <= existing 0.500001 Skipped atom 1331, because occupancy 0.5 <= existing 0.500001 Skipped atom 1333, because occupancy 0.5 <= existing 0.500001 Skipped atom 1335, because occupancy 0.5 <= existing 0.500001 partial PDB gets fragment 136 through 145 extending start extending end Debugging on ! Reading sequence file Reading input structure 12 residues read Measuring phi and psi Getting chi values ASP 1 4 ASN 2 4 LYS 3 26 PRO 4 2 LYS 5 26 ASN 6 4 LEU 7 3 ASP 8 4 SER 10 3 Building many copies of each residue Checking backbone and frame clashes Finding the lowest Also, print out the first version, pre-bump All 2 rotamers of residue P 5 conflict with the backbone. This may be a problem with the backbone,or a subtle problem with the rotamers. Please be aware of this, and examine it. Finding disulfide bonds. Found 0 disulfide bonds. Residue clashes: 0 clashing residues after turn Residue clashes: Still clashes at these sidechain pairs: Residual clashes = 0.00000 Printing mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a6m.1.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a6m.1.1.a2m \ -target T0098 -template 1a6m \ -out T0098-1a6m.1.1 -outdir und2 Skipped atom 27, because occupancy 0.43 <= existing 0.570001 Skipped atom 29, because occupancy 0.43 <= existing 0.570001 Skipped atom 31, because occupancy 0.43 <= existing 0.570001 Skipped atom 33, because occupancy 0.43 <= existing 0.570001 Skipped atom 35, because occupancy 0.43 <= existing 0.570001 Skipped atom 68, because occupancy 0.43 <= existing 0.570001 Skipped atom 70, because occupancy 0.43 <= existing 0.570001 Skipped atom 72, because occupancy 0.43 <= existing 0.570001 Skipped atom 74, because occupancy 0.43 <= existing 0.570001 Skipped atom 76, because occupancy 0.43 <= existing 0.570001 Skipped atom 209, because occupancy 0.35 <= existing 0.650001 Skipped atom 211, because occupancy 0.35 <= existing 0.650001 Skipped atom 213, because occupancy 0.35 <= existing 0.650001 Skipped atom 215, because occupancy 0.35 <= existing 0.650001 Skipped atom 217, because occupancy 0.35 <= existing 0.650001 Skipped atom 348, because occupancy 0.49 <= existing 0.510001 Skipped atom 350, because occupancy 0.49 <= existing 0.510001 Skipped atom 352, because occupancy 0.49 <= existing 0.510001 Skipped atom 354, because occupancy 0.49 <= existing 0.510001 Skipped atom 356, because occupancy 0.49 <= existing 0.510001 Skipped atom 412, because occupancy 0.32 <= existing 0.680001 Skipped atom 414, because occupancy 0.32 <= existing 0.680001 Skipped atom 416, because occupancy 0.32 <= existing 0.680001 Skipped atom 418, because occupancy 0.32 <= existing 0.680001 Skipped atom 420, because occupancy 0.32 <= existing 0.680001 Skipped atom 533, because occupancy 0.34 <= existing 0.660001 Skipped atom 535, because occupancy 0.34 <= existing 0.660001 Skipped atom 537, because occupancy 0.34 <= existing 0.660001 Skipped atom 539, because occupancy 0.34 <= existing 0.660001 Skipped atom 554, because occupancy 0.41 <= existing 0.590001 Skipped atom 556, because occupancy 0.41 <= existing 0.590001 Skipped atom 558, because occupancy 0.41 <= existing 0.590001 Skipped atom 560, because occupancy 0.41 <= existing 0.590001 Skipped atom 562, because occupancy 0.41 <= existing 0.590001 Skipped atom 568, because occupancy 0.5 <= existing 0.500001 Skipped atom 570, because occupancy 0.5 <= existing 0.500001 Skipped atom 572, because occupancy 0.5 <= existing 0.500001 Skipped atom 574, because occupancy 0.5 <= existing 0.500001 Skipped atom 576, because occupancy 0.5 <= existing 0.500001 Skipped atom 578, because occupancy 0.5 <= existing 0.500001 Skipped atom 773, because occupancy 0.47 <= existing 0.530001 Skipped atom 775, because occupancy 0.47 <= existing 0.530001 Skipped atom 777, because occupancy 0.47 <= existing 0.530001 Skipped atom 779, because occupancy 0.47 <= existing 0.530001 Skipped atom 781, because occupancy 0.47 <= existing 0.530001 Skipped atom 815, because occupancy 0.45 <= existing 0.550001 Skipped atom 817, because occupancy 0.45 <= existing 0.550001 Skipped atom 819, because occupancy 0.45 <= existing 0.550001 Skipped atom 821, because occupancy 0.45 <= existing 0.550001 Skipped atom 823, because occupancy 0.45 <= existing 0.550001 Skipped atom 934, because occupancy 0.34 <= existing 0.660001 Skipped atom 936, because occupancy 0.34 <= existing 0.660001 Skipped atom 938, because occupancy 0.34 <= existing 0.660001 Skipped atom 940, because occupancy 0.34 <= existing 0.660001 Skipped atom 942, because occupancy 0.34 <= existing 0.660001 Skipped atom 998, because occupancy 0.46 <= existing 0.540001 Skipped atom 1000, because occupancy 0.46 <= existing 0.540001 Skipped atom 1002, because occupancy 0.46 <= existing 0.540001 Skipped atom 1004, because occupancy 0.46 <= existing 0.540001 Skipped atom 1006, because occupancy 0.46 <= existing 0.540001 Skipped atom 1008, because occupancy 0.46 <= existing 0.540001 Skipped atom 1014, because occupancy 0.44 <= existing 0.560001 Skipped atom 1016, because occupancy 0.44 <= existing 0.560001 Skipped atom 1089, because occupancy 0.34 <= existing 0.660001 Skipped atom 1091, because occupancy 0.34 <= existing 0.660001 Skipped atom 1093, because occupancy 0.34 <= existing 0.660001 Skipped atom 1095, because occupancy 0.34 <= existing 0.660001 Skipped atom 1106, because occupancy 0.44 <= existing 0.560001 Skipped atom 1108, because occupancy 0.44 <= existing 0.560001 Skipped atom 1110, because occupancy 0.44 <= existing 0.560001 Skipped atom 1112, because occupancy 0.44 <= existing 0.560001 Skipped atom 1114, because occupancy 0.44 <= existing 0.560001 Skipped atom 1145, because occupancy 0.45 <= existing 0.550001 Skipped atom 1147, because occupancy 0.45 <= existing 0.550001 Skipped atom 1149, because occupancy 0.45 <= existing 0.550001 Skipped atom 1151, because occupancy 0.45 <= existing 0.550001 Skipped atom 1153, because occupancy 0.45 <= existing 0.550001 Skipped atom 1172, because occupancy 0.43 <= existing 0.570001 Skipped atom 1174, because occupancy 0.43 <= existing 0.570001 Skipped atom 1176, because occupancy 0.43 <= existing 0.570001 Skipped atom 1178, because occupancy 0.43 <= existing 0.570001 Skipped atom 1180, because occupancy 0.43 <= existing 0.570001 Skipped atom 1240, because occupancy 0.33 <= existing 0.670001 Skipped atom 1242, because occupancy 0.33 <= existing 0.670001 Skipped atom 1244, because occupancy 0.33 <= existing 0.670001 Skipped atom 1246, because occupancy 0.33 <= existing 0.670001 Skipped atom 1321, because occupancy 0.5 <= existing 0.500001 Skipped atom 1323, because occupancy 0.5 <= existing 0.500001 Skipped atom 1325, because occupancy 0.5 <= existing 0.500001 Skipped atom 1327, because occupancy 0.5 <= existing 0.500001 Skipped atom 1329, because occupancy 0.5 <= existing 0.500001 Skipped atom 1331, because occupancy 0.5 <= existing 0.500001 Skipped atom 1333, because occupancy 0.5 <= existing 0.500001 Skipped atom 1335, because occupancy 0.5 <= existing 0.500001 partial PDB gets fragment 135 through 144 extending start extending end Debugging on ! Reading sequence file Reading input structure 12 residues read Measuring phi and psi Getting chi values ASN 1 4 LYS 2 26 PRO 3 2 LYS 4 26 ASN 5 4 LEU 6 3 ASP 7 4 SER 9 3 ILE 10 3 Building many copies of each residue Checking backbone and frame clashes Finding the lowest Also, print out the first version, pre-bump All 2 rotamers of residue P 4 conflict with the backbone. This may be a problem with the backbone,or a subtle problem with the rotamers. Please be aware of this, and examine it. Finding disulfide bonds. Found 0 disulfide bonds. Residue clashes: 0 clashing residues after turn Residue clashes: Still clashes at these sidechain pairs: Residual clashes = 0.00000 Printing mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a6m.100.3.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a6m.100.3.a2m \ -target T0098 -template 1a6m \ -out T0098-1a6m.100.3 -outdir und2 Skipped atom 27, because occupancy 0.43 <= existing 0.570001 Skipped atom 29, because occupancy 0.43 <= existing 0.570001 Skipped atom 31, because occupancy 0.43 <= existing 0.570001 Skipped atom 33, because occupancy 0.43 <= existing 0.570001 Skipped atom 35, because occupancy 0.43 <= existing 0.570001 Skipped atom 68, because occupancy 0.43 <= existing 0.570001 Skipped atom 70, because occupancy 0.43 <= existing 0.570001 Skipped atom 72, because occupancy 0.43 <= existing 0.570001 Skipped atom 74, because occupancy 0.43 <= existing 0.570001 Skipped atom 76, because occupancy 0.43 <= existing 0.570001 Skipped atom 209, because occupancy 0.35 <= existing 0.650001 Skipped atom 211, because occupancy 0.35 <= existing 0.650001 Skipped atom 213, because occupancy 0.35 <= existing 0.650001 Skipped atom 215, because occupancy 0.35 <= existing 0.650001 Skipped atom 217, because occupancy 0.35 <= existing 0.650001 Skipped atom 348, because occupancy 0.49 <= existing 0.510001 Skipped atom 350, because occupancy 0.49 <= existing 0.510001 Skipped atom 352, because occupancy 0.49 <= existing 0.510001 Skipped atom 354, because occupancy 0.49 <= existing 0.510001 Skipped atom 356, because occupancy 0.49 <= existing 0.510001 Skipped atom 412, because occupancy 0.32 <= existing 0.680001 Skipped atom 414, because occupancy 0.32 <= existing 0.680001 Skipped atom 416, because occupancy 0.32 <= existing 0.680001 Skipped atom 418, because occupancy 0.32 <= existing 0.680001 Skipped atom 420, because occupancy 0.32 <= existing 0.680001 Skipped atom 533, because occupancy 0.34 <= existing 0.660001 Skipped atom 535, because occupancy 0.34 <= existing 0.660001 Skipped atom 537, because occupancy 0.34 <= existing 0.660001 Skipped atom 539, because occupancy 0.34 <= existing 0.660001 Skipped atom 554, because occupancy 0.41 <= existing 0.590001 Skipped atom 556, because occupancy 0.41 <= existing 0.590001 Skipped atom 558, because occupancy 0.41 <= existing 0.590001 Skipped atom 560, because occupancy 0.41 <= existing 0.590001 Skipped atom 562, because occupancy 0.41 <= existing 0.590001 Skipped atom 568, because occupancy 0.5 <= existing 0.500001 Skipped atom 570, because occupancy 0.5 <= existing 0.500001 Skipped atom 572, because occupancy 0.5 <= existing 0.500001 Skipped atom 574, because occupancy 0.5 <= existing 0.500001 Skipped atom 576, because occupancy 0.5 <= existing 0.500001 Skipped atom 578, because occupancy 0.5 <= existing 0.500001 Skipped atom 773, because occupancy 0.47 <= existing 0.530001 Skipped atom 775, because occupancy 0.47 <= existing 0.530001 Skipped atom 777, because occupancy 0.47 <= existing 0.530001 Skipped atom 779, because occupancy 0.47 <= existing 0.530001 Skipped atom 781, because occupancy 0.47 <= existing 0.530001 Skipped atom 815, because occupancy 0.45 <= existing 0.550001 Skipped atom 817, because occupancy 0.45 <= existing 0.550001 Skipped atom 819, because occupancy 0.45 <= existing 0.550001 Skipped atom 821, because occupancy 0.45 <= existing 0.550001 Skipped atom 823, because occupancy 0.45 <= existing 0.550001 Skipped atom 934, because occupancy 0.34 <= existing 0.660001 Skipped atom 936, because occupancy 0.34 <= existing 0.660001 Skipped atom 938, because occupancy 0.34 <= existing 0.660001 Skipped atom 940, because occupancy 0.34 <= existing 0.660001 Skipped atom 942, because occupancy 0.34 <= existing 0.660001 Skipped atom 998, because occupancy 0.46 <= existing 0.540001 Skipped atom 1000, because occupancy 0.46 <= existing 0.540001 Skipped atom 1002, because occupancy 0.46 <= existing 0.540001 Skipped atom 1004, because occupancy 0.46 <= existing 0.540001 Skipped atom 1006, because occupancy 0.46 <= existing 0.540001 Skipped atom 1008, because occupancy 0.46 <= existing 0.540001 Skipped atom 1014, because occupancy 0.44 <= existing 0.560001 Skipped atom 1016, because occupancy 0.44 <= existing 0.560001 Skipped atom 1089, because occupancy 0.34 <= existing 0.660001 Skipped atom 1091, because occupancy 0.34 <= existing 0.660001 Skipped atom 1093, because occupancy 0.34 <= existing 0.660001 Skipped atom 1095, because occupancy 0.34 <= existing 0.660001 Skipped atom 1106, because occupancy 0.44 <= existing 0.560001 Skipped atom 1108, because occupancy 0.44 <= existing 0.560001 Skipped atom 1110, because occupancy 0.44 <= existing 0.560001 Skipped atom 1112, because occupancy 0.44 <= existing 0.560001 Skipped atom 1114, because occupancy 0.44 <= existing 0.560001 Skipped atom 1145, because occupancy 0.45 <= existing 0.550001 Skipped atom 1147, because occupancy 0.45 <= existing 0.550001 Skipped atom 1149, because occupancy 0.45 <= existing 0.550001 Skipped atom 1151, because occupancy 0.45 <= existing 0.550001 Skipped atom 1153, because occupancy 0.45 <= existing 0.550001 Skipped atom 1172, because occupancy 0.43 <= existing 0.570001 Skipped atom 1174, because occupancy 0.43 <= existing 0.570001 Skipped atom 1176, because occupancy 0.43 <= existing 0.570001 Skipped atom 1178, because occupancy 0.43 <= existing 0.570001 Skipped atom 1180, because occupancy 0.43 <= existing 0.570001 Skipped atom 1240, because occupancy 0.33 <= existing 0.670001 Skipped atom 1242, because occupancy 0.33 <= existing 0.670001 Skipped atom 1244, because occupancy 0.33 <= existing 0.670001 Skipped atom 1246, because occupancy 0.33 <= existing 0.670001 Skipped atom 1321, because occupancy 0.5 <= existing 0.500001 Skipped atom 1323, because occupancy 0.5 <= existing 0.500001 Skipped atom 1325, because occupancy 0.5 <= existing 0.500001 Skipped atom 1327, because occupancy 0.5 <= existing 0.500001 Skipped atom 1329, because occupancy 0.5 <= existing 0.500001 Skipped atom 1331, because occupancy 0.5 <= existing 0.500001 Skipped atom 1333, because occupancy 0.5 <= existing 0.500001 Skipped atom 1335, because occupancy 0.5 <= existing 0.500001 partial PDB gets fragment 15 through 24 extending start extending end Debugging on ! Reading sequence file Reading input structure 12 residues read Measuring phi and psi Getting chi values PRO 1 2 THR 2 2 ASN 3 5 SER 4 2 GLU 5 15 PHE 6 2 ILE 7 3 MET 9 10 VAL 10 1 Building many copies of each residue Checking backbone and frame clashes Finding the lowest Also, print out the first version, pre-bump Finding disulfide bonds. Found 0 disulfide bonds. Residue clashes: 0 clashing residues after turn Residue clashes: Still clashes at these sidechain pairs: Residual clashes = 0.00000 Printing mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a6m.102.4.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a6m.102.4.a2m \ -target T0098 -template 1a6m \ -out T0098-1a6m.102.4 -outdir und2 Skipped atom 27, because occupancy 0.43 <= existing 0.570001 Skipped atom 29, because occupancy 0.43 <= existing 0.570001 Skipped atom 31, because occupancy 0.43 <= existing 0.570001 Skipped atom 33, because occupancy 0.43 <= existing 0.570001 Skipped atom 35, because occupancy 0.43 <= existing 0.570001 Skipped atom 68, because occupancy 0.43 <= existing 0.570001 Skipped atom 70, because occupancy 0.43 <= existing 0.570001 Skipped atom 72, because occupancy 0.43 <= existing 0.570001 Skipped atom 74, because occupancy 0.43 <= existing 0.570001 Skipped atom 76, because occupancy 0.43 <= existing 0.570001 Skipped atom 209, because occupancy 0.35 <= existing 0.650001 Skipped atom 211, because occupancy 0.35 <= existing 0.650001 Skipped atom 213, because occupancy 0.35 <= existing 0.650001 Skipped atom 215, because occupancy 0.35 <= existing 0.650001 Skipped atom 217, because occupancy 0.35 <= existing 0.650001 Skipped atom 348, because occupancy 0.49 <= existing 0.510001 Skipped atom 350, because occupancy 0.49 <= existing 0.510001 Skipped atom 352, because occupancy 0.49 <= existing 0.510001 Skipped atom 354, because occupancy 0.49 <= existing 0.510001 Skipped atom 356, because occupancy 0.49 <= existing 0.510001 Skipped atom 412, because occupancy 0.32 <= existing 0.680001 Skipped atom 414, because occupancy 0.32 <= existing 0.680001 Skipped atom 416, because occupancy 0.32 <= existing 0.680001 Skipped atom 418, because occupancy 0.32 <= existing 0.680001 Skipped atom 420, because occupancy 0.32 <= existing 0.680001 Skipped atom 533, because occupancy 0.34 <= existing 0.660001 Skipped atom 535, because occupancy 0.34 <= existing 0.660001 Skipped atom 537, because occupancy 0.34 <= existing 0.660001 Skipped atom 539, because occupancy 0.34 <= existing 0.660001 Skipped atom 554, because occupancy 0.41 <= existing 0.590001 Skipped atom 556, because occupancy 0.41 <= existing 0.590001 Skipped atom 558, because occupancy 0.41 <= existing 0.590001 Skipped atom 560, because occupancy 0.41 <= existing 0.590001 Skipped atom 562, because occupancy 0.41 <= existing 0.590001 Skipped atom 568, because occupancy 0.5 <= existing 0.500001 Skipped atom 570, because occupancy 0.5 <= existing 0.500001 Skipped atom 572, because occupancy 0.5 <= existing 0.500001 Skipped atom 574, because occupancy 0.5 <= existing 0.500001 Skipped atom 576, because occupancy 0.5 <= existing 0.500001 Skipped atom 578, because occupancy 0.5 <= existing 0.500001 Skipped atom 773, because occupancy 0.47 <= existing 0.530001 Skipped atom 775, because occupancy 0.47 <= existing 0.530001 Skipped atom 777, because occupancy 0.47 <= existing 0.530001 Skipped atom 779, because occupancy 0.47 <= existing 0.530001 Skipped atom 781, because occupancy 0.47 <= existing 0.530001 Skipped atom 815, because occupancy 0.45 <= existing 0.550001 Skipped atom 817, because occupancy 0.45 <= existing 0.550001 Skipped atom 819, because occupancy 0.45 <= existing 0.550001 Skipped atom 821, because occupancy 0.45 <= existing 0.550001 Skipped atom 823, because occupancy 0.45 <= existing 0.550001 Skipped atom 934, because occupancy 0.34 <= existing 0.660001 Skipped atom 936, because occupancy 0.34 <= existing 0.660001 Skipped atom 938, because occupancy 0.34 <= existing 0.660001 Skipped atom 940, because occupancy 0.34 <= existing 0.660001 Skipped atom 942, because occupancy 0.34 <= existing 0.660001 Skipped atom 998, because occupancy 0.46 <= existing 0.540001 Skipped atom 1000, because occupancy 0.46 <= existing 0.540001 Skipped atom 1002, because occupancy 0.46 <= existing 0.540001 Skipped atom 1004, because occupancy 0.46 <= existing 0.540001 Skipped atom 1006, because occupancy 0.46 <= existing 0.540001 Skipped atom 1008, because occupancy 0.46 <= existing 0.540001 Skipped atom 1014, because occupancy 0.44 <= existing 0.560001 Skipped atom 1016, because occupancy 0.44 <= existing 0.560001 Skipped atom 1089, because occupancy 0.34 <= existing 0.660001 Skipped atom 1091, because occupancy 0.34 <= existing 0.660001 Skipped atom 1093, because occupancy 0.34 <= existing 0.660001 Skipped atom 1095, because occupancy 0.34 <= existing 0.660001 Skipped atom 1106, because occupancy 0.44 <= existing 0.560001 Skipped atom 1108, because occupancy 0.44 <= existing 0.560001 Skipped atom 1110, because occupancy 0.44 <= existing 0.560001 Skipped atom 1112, because occupancy 0.44 <= existing 0.560001 Skipped atom 1114, because occupancy 0.44 <= existing 0.560001 Skipped atom 1145, because occupancy 0.45 <= existing 0.550001 Skipped atom 1147, because occupancy 0.45 <= existing 0.550001 Skipped atom 1149, because occupancy 0.45 <= existing 0.550001 Skipped atom 1151, because occupancy 0.45 <= existing 0.550001 Skipped atom 1153, because occupancy 0.45 <= existing 0.550001 Skipped atom 1172, because occupancy 0.43 <= existing 0.570001 Skipped atom 1174, because occupancy 0.43 <= existing 0.570001 Skipped atom 1176, because occupancy 0.43 <= existing 0.570001 Skipped atom 1178, because occupancy 0.43 <= existing 0.570001 Skipped atom 1180, because occupancy 0.43 <= existing 0.570001 Skipped atom 1240, because occupancy 0.33 <= existing 0.670001 Skipped atom 1242, because occupancy 0.33 <= existing 0.670001 Skipped atom 1244, because occupancy 0.33 <= existing 0.670001 Skipped atom 1246, because occupancy 0.33 <= existing 0.670001 Skipped atom 1321, because occupancy 0.5 <= existing 0.500001 Skipped atom 1323, because occupancy 0.5 <= existing 0.500001 Skipped atom 1325, because occupancy 0.5 <= existing 0.500001 Skipped atom 1327, because occupancy 0.5 <= existing 0.500001 Skipped atom 1329, because occupancy 0.5 <= existing 0.500001 Skipped atom 1331, because occupancy 0.5 <= existing 0.500001 Skipped atom 1333, because occupancy 0.5 <= existing 0.500001 Skipped atom 1335, because occupancy 0.5 <= existing 0.500001 partial PDB gets fragment 13 through 22 extending start extending end Debugging on ! Reading sequence file Reading input structure 12 residues read Measuring phi and psi Getting chi values ASN 1 4 SER 2 2 GLU 3 12 PHE 4 3 ILE 5 4 MET 7 14 ASP 10 5 Building many copies of each residue Checking backbone and frame clashes Finding the lowest Also, print out the first version, pre-bump Finding disulfide bonds. Found 0 disulfide bonds. Residue clashes: 0 clashing residues after turn Residue clashes: Still clashes at these sidechain pairs: Residual clashes = 0.00000 Printing mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a6m.104.5.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a6m.104.5.a2m \ -target T0098 -template 1a6m \ -out T0098-1a6m.104.5 -outdir und2 Skipped atom 27, because occupancy 0.43 <= existing 0.570001 Skipped atom 29, because occupancy 0.43 <= existing 0.570001 Skipped atom 31, because occupancy 0.43 <= existing 0.570001 Skipped atom 33, because occupancy 0.43 <= existing 0.570001 Skipped atom 35, because occupancy 0.43 <= existing 0.570001 Skipped atom 68, because occupancy 0.43 <= existing 0.570001 Skipped atom 70, because occupancy 0.43 <= existing 0.570001 Skipped atom 72, because occupancy 0.43 <= existing 0.570001 Skipped atom 74, because occupancy 0.43 <= existing 0.570001 Skipped atom 76, because occupancy 0.43 <= existing 0.570001 Skipped atom 209, because occupancy 0.35 <= existing 0.650001 Skipped atom 211, because occupancy 0.35 <= existing 0.650001 Skipped atom 213, because occupancy 0.35 <= existing 0.650001 Skipped atom 215, because occupancy 0.35 <= existing 0.650001 Skipped atom 217, because occupancy 0.35 <= existing 0.650001 Skipped atom 348, because occupancy 0.49 <= existing 0.510001 Skipped atom 350, because occupancy 0.49 <= existing 0.510001 Skipped atom 352, because occupancy 0.49 <= existing 0.510001 Skipped atom 354, because occupancy 0.49 <= existing 0.510001 Skipped atom 356, because occupancy 0.49 <= existing 0.510001 Skipped atom 412, because occupancy 0.32 <= existing 0.680001 Skipped atom 414, because occupancy 0.32 <= existing 0.680001 Skipped atom 416, because occupancy 0.32 <= existing 0.680001 Skipped atom 418, because occupancy 0.32 <= existing 0.680001 Skipped atom 420, because occupancy 0.32 <= existing 0.680001 Skipped atom 533, because occupancy 0.34 <= existing 0.660001 Skipped atom 535, because occupancy 0.34 <= existing 0.660001 Skipped atom 537, because occupancy 0.34 <= existing 0.660001 Skipped atom 539, because occupancy 0.34 <= existing 0.660001 Skipped atom 554, because occupancy 0.41 <= existing 0.590001 Skipped atom 556, because occupancy 0.41 <= existing 0.590001 Skipped atom 558, because occupancy 0.41 <= existing 0.590001 Skipped atom 560, because occupancy 0.41 <= existing 0.590001 Skipped atom 562, because occupancy 0.41 <= existing 0.590001 Skipped atom 568, because occupancy 0.5 <= existing 0.500001 Skipped atom 570, because occupancy 0.5 <= existing 0.500001 Skipped atom 572, because occupancy 0.5 <= existing 0.500001 Skipped atom 574, because occupancy 0.5 <= existing 0.500001 Skipped atom 576, because occupancy 0.5 <= existing 0.500001 Skipped atom 578, because occupancy 0.5 <= existing 0.500001 Skipped atom 773, because occupancy 0.47 <= existing 0.530001 Skipped atom 775, because occupancy 0.47 <= existing 0.530001 Skipped atom 777, because occupancy 0.47 <= existing 0.530001 Skipped atom 779, because occupancy 0.47 <= existing 0.530001 Skipped atom 781, because occupancy 0.47 <= existing 0.530001 Skipped atom 815, because occupancy 0.45 <= existing 0.550001 Skipped atom 817, because occupancy 0.45 <= existing 0.550001 Skipped atom 819, because occupancy 0.45 <= existing 0.550001 Skipped atom 821, because occupancy 0.45 <= existing 0.550001 Skipped atom 823, because occupancy 0.45 <= existing 0.550001 Skipped atom 934, because occupancy 0.34 <= existing 0.660001 Skipped atom 936, because occupancy 0.34 <= existing 0.660001 Skipped atom 938, because occupancy 0.34 <= existing 0.660001 Skipped atom 940, because occupancy 0.34 <= existing 0.660001 Skipped atom 942, because occupancy 0.34 <= existing 0.660001 Skipped atom 998, because occupancy 0.46 <= existing 0.540001 Skipped atom 1000, because occupancy 0.46 <= existing 0.540001 Skipped atom 1002, because occupancy 0.46 <= existing 0.540001 Skipped atom 1004, because occupancy 0.46 <= existing 0.540001 Skipped atom 1006, because occupancy 0.46 <= existing 0.540001 Skipped atom 1008, because occupancy 0.46 <= existing 0.540001 Skipped atom 1014, because occupancy 0.44 <= existing 0.560001 Skipped atom 1016, because occupancy 0.44 <= existing 0.560001 Skipped atom 1089, because occupancy 0.34 <= existing 0.660001 Skipped atom 1091, because occupancy 0.34 <= existing 0.660001 Skipped atom 1093, because occupancy 0.34 <= existing 0.660001 Skipped atom 1095, because occupancy 0.34 <= existing 0.660001 Skipped atom 1106, because occupancy 0.44 <= existing 0.560001 Skipped atom 1108, because occupancy 0.44 <= existing 0.560001 Skipped atom 1110, because occupancy 0.44 <= existing 0.560001 Skipped atom 1112, because occupancy 0.44 <= existing 0.560001 Skipped atom 1114, because occupancy 0.44 <= existing 0.560001 Skipped atom 1145, because occupancy 0.45 <= existing 0.550001 Skipped atom 1147, because occupancy 0.45 <= existing 0.550001 Skipped atom 1149, because occupancy 0.45 <= existing 0.550001 Skipped atom 1151, because occupancy 0.45 <= existing 0.550001 Skipped atom 1153, because occupancy 0.45 <= existing 0.550001 Skipped atom 1172, because occupancy 0.43 <= existing 0.570001 Skipped atom 1174, because occupancy 0.43 <= existing 0.570001 Skipped atom 1176, because occupancy 0.43 <= existing 0.570001 Skipped atom 1178, because occupancy 0.43 <= existing 0.570001 Skipped atom 1180, because occupancy 0.43 <= existing 0.570001 Skipped atom 1240, because occupancy 0.33 <= existing 0.670001 Skipped atom 1242, because occupancy 0.33 <= existing 0.670001 Skipped atom 1244, because occupancy 0.33 <= existing 0.670001 Skipped atom 1246, because occupancy 0.33 <= existing 0.670001 Skipped atom 1321, because occupancy 0.5 <= existing 0.500001 Skipped atom 1323, because occupancy 0.5 <= existing 0.500001 Skipped atom 1325, because occupancy 0.5 <= existing 0.500001 Skipped atom 1327, because occupancy 0.5 <= existing 0.500001 Skipped atom 1329, because occupancy 0.5 <= existing 0.500001 Skipped atom 1331, because occupancy 0.5 <= existing 0.500001 Skipped atom 1333, because occupancy 0.5 <= existing 0.500001 Skipped atom 1335, because occupancy 0.5 <= existing 0.500001 partial PDB gets fragment 11 through 20 extending start extending end Debugging on ! Reading sequence file Reading input structure 12 residues read Measuring phi and psi Getting chi values GLU 1 12 PHE 2 3 ILE 3 5 MET 5 10 ASP 8 5 LYS 9 26 LEU 10 3 Building many copies of each residue Checking backbone and frame clashes Finding the lowest Also, print out the first version, pre-bump Finding disulfide bonds. Found 0 disulfide bonds. Residue clashes: 0 clashing residues after turn Residue clashes: Still clashes at these sidechain pairs: Residual clashes = 0.00000 Printing mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a6m.2.2.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a6m.2.2.a2m \ -target T0098 -template 1a6m \ -out T0098-1a6m.2.2 -outdir und2 Skipped atom 27, because occupancy 0.43 <= existing 0.570001 Skipped atom 29, because occupancy 0.43 <= existing 0.570001 Skipped atom 31, because occupancy 0.43 <= existing 0.570001 Skipped atom 33, because occupancy 0.43 <= existing 0.570001 Skipped atom 35, because occupancy 0.43 <= existing 0.570001 Skipped atom 68, because occupancy 0.43 <= existing 0.570001 Skipped atom 70, because occupancy 0.43 <= existing 0.570001 Skipped atom 72, because occupancy 0.43 <= existing 0.570001 Skipped atom 74, because occupancy 0.43 <= existing 0.570001 Skipped atom 76, because occupancy 0.43 <= existing 0.570001 Skipped atom 209, because occupancy 0.35 <= existing 0.650001 Skipped atom 211, because occupancy 0.35 <= existing 0.650001 Skipped atom 213, because occupancy 0.35 <= existing 0.650001 Skipped atom 215, because occupancy 0.35 <= existing 0.650001 Skipped atom 217, because occupancy 0.35 <= existing 0.650001 Skipped atom 348, because occupancy 0.49 <= existing 0.510001 Skipped atom 350, because occupancy 0.49 <= existing 0.510001 Skipped atom 352, because occupancy 0.49 <= existing 0.510001 Skipped atom 354, because occupancy 0.49 <= existing 0.510001 Skipped atom 356, because occupancy 0.49 <= existing 0.510001 Skipped atom 412, because occupancy 0.32 <= existing 0.680001 Skipped atom 414, because occupancy 0.32 <= existing 0.680001 Skipped atom 416, because occupancy 0.32 <= existing 0.680001 Skipped atom 418, because occupancy 0.32 <= existing 0.680001 Skipped atom 420, because occupancy 0.32 <= existing 0.680001 Skipped atom 533, because occupancy 0.34 <= existing 0.660001 Skipped atom 535, because occupancy 0.34 <= existing 0.660001 Skipped atom 537, because occupancy 0.34 <= existing 0.660001 Skipped atom 539, because occupancy 0.34 <= existing 0.660001 Skipped atom 554, because occupancy 0.41 <= existing 0.590001 Skipped atom 556, because occupancy 0.41 <= existing 0.590001 Skipped atom 558, because occupancy 0.41 <= existing 0.590001 Skipped atom 560, because occupancy 0.41 <= existing 0.590001 Skipped atom 562, because occupancy 0.41 <= existing 0.590001 Skipped atom 568, because occupancy 0.5 <= existing 0.500001 Skipped atom 570, because occupancy 0.5 <= existing 0.500001 Skipped atom 572, because occupancy 0.5 <= existing 0.500001 Skipped atom 574, because occupancy 0.5 <= existing 0.500001 Skipped atom 576, because occupancy 0.5 <= existing 0.500001 Skipped atom 578, because occupancy 0.5 <= existing 0.500001 Skipped atom 773, because occupancy 0.47 <= existing 0.530001 Skipped atom 775, because occupancy 0.47 <= existing 0.530001 Skipped atom 777, because occupancy 0.47 <= existing 0.530001 Skipped atom 779, because occupancy 0.47 <= existing 0.530001 Skipped atom 781, because occupancy 0.47 <= existing 0.530001 Skipped atom 815, because occupancy 0.45 <= existing 0.550001 Skipped atom 817, because occupancy 0.45 <= existing 0.550001 Skipped atom 819, because occupancy 0.45 <= existing 0.550001 Skipped atom 821, because occupancy 0.45 <= existing 0.550001 Skipped atom 823, because occupancy 0.45 <= existing 0.550001 Skipped atom 934, because occupancy 0.34 <= existing 0.660001 Skipped atom 936, because occupancy 0.34 <= existing 0.660001 Skipped atom 938, because occupancy 0.34 <= existing 0.660001 Skipped atom 940, because occupancy 0.34 <= existing 0.660001 Skipped atom 942, because occupancy 0.34 <= existing 0.660001 Skipped atom 998, because occupancy 0.46 <= existing 0.540001 Skipped atom 1000, because occupancy 0.46 <= existing 0.540001 Skipped atom 1002, because occupancy 0.46 <= existing 0.540001 Skipped atom 1004, because occupancy 0.46 <= existing 0.540001 Skipped atom 1006, because occupancy 0.46 <= existing 0.540001 Skipped atom 1008, because occupancy 0.46 <= existing 0.540001 Skipped atom 1014, because occupancy 0.44 <= existing 0.560001 Skipped atom 1016, because occupancy 0.44 <= existing 0.560001 Skipped atom 1089, because occupancy 0.34 <= existing 0.660001 Skipped atom 1091, because occupancy 0.34 <= existing 0.660001 Skipped atom 1093, because occupancy 0.34 <= existing 0.660001 Skipped atom 1095, because occupancy 0.34 <= existing 0.660001 Skipped atom 1106, because occupancy 0.44 <= existing 0.560001 Skipped atom 1108, because occupancy 0.44 <= existing 0.560001 Skipped atom 1110, because occupancy 0.44 <= existing 0.560001 Skipped atom 1112, because occupancy 0.44 <= existing 0.560001 Skipped atom 1114, because occupancy 0.44 <= existing 0.560001 Skipped atom 1145, because occupancy 0.45 <= existing 0.550001 Skipped atom 1147, because occupancy 0.45 <= existing 0.550001 Skipped atom 1149, because occupancy 0.45 <= existing 0.550001 Skipped atom 1151, because occupancy 0.45 <= existing 0.550001 Skipped atom 1153, because occupancy 0.45 <= existing 0.550001 Skipped atom 1172, because occupancy 0.43 <= existing 0.570001 Skipped atom 1174, because occupancy 0.43 <= existing 0.570001 Skipped atom 1176, because occupancy 0.43 <= existing 0.570001 Skipped atom 1178, because occupancy 0.43 <= existing 0.570001 Skipped atom 1180, because occupancy 0.43 <= existing 0.570001 Skipped atom 1240, because occupancy 0.33 <= existing 0.670001 Skipped atom 1242, because occupancy 0.33 <= existing 0.670001 Skipped atom 1244, because occupancy 0.33 <= existing 0.670001 Skipped atom 1246, because occupancy 0.33 <= existing 0.670001 Skipped atom 1321, because occupancy 0.5 <= existing 0.500001 Skipped atom 1323, because occupancy 0.5 <= existing 0.500001 Skipped atom 1325, because occupancy 0.5 <= existing 0.500001 Skipped atom 1327, because occupancy 0.5 <= existing 0.500001 Skipped atom 1329, because occupancy 0.5 <= existing 0.500001 Skipped atom 1331, because occupancy 0.5 <= existing 0.500001 Skipped atom 1333, because occupancy 0.5 <= existing 0.500001 Skipped atom 1335, because occupancy 0.5 <= existing 0.500001 partial PDB gets fragment 134 through 143 extending start extending end Debugging on ! Reading sequence file Reading input structure 12 residues read Measuring phi and psi Getting chi values LYS 1 30 PRO 2 2 LYS 3 26 ASN 4 4 LEU 5 3 ASP 6 4 SER 8 3 ILE 9 3 THR 10 2 Building many copies of each residue Checking backbone and frame clashes Finding the lowest Also, print out the first version, pre-bump Finding disulfide bonds. Found 0 disulfide bonds. Residue clashes: 0 clashing residues after turn Residue clashes: Still clashes at these sidechain pairs: Residual clashes = 0.00000 Printing mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a6m.3.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a6m.3.1.a2m \ -target T0098 -template 1a6m \ -out T0098-1a6m.3.1 -outdir und2 Skipped atom 27, because occupancy 0.43 <= existing 0.570001 Skipped atom 29, because occupancy 0.43 <= existing 0.570001 Skipped atom 31, because occupancy 0.43 <= existing 0.570001 Skipped atom 33, because occupancy 0.43 <= existing 0.570001 Skipped atom 35, because occupancy 0.43 <= existing 0.570001 Skipped atom 68, because occupancy 0.43 <= existing 0.570001 Skipped atom 70, because occupancy 0.43 <= existing 0.570001 Skipped atom 72, because occupancy 0.43 <= existing 0.570001 Skipped atom 74, because occupancy 0.43 <= existing 0.570001 Skipped atom 76, because occupancy 0.43 <= existing 0.570001 Skipped atom 209, because occupancy 0.35 <= existing 0.650001 Skipped atom 211, because occupancy 0.35 <= existing 0.650001 Skipped atom 213, because occupancy 0.35 <= existing 0.650001 Skipped atom 215, because occupancy 0.35 <= existing 0.650001 Skipped atom 217, because occupancy 0.35 <= existing 0.650001 Skipped atom 348, because occupancy 0.49 <= existing 0.510001 Skipped atom 350, because occupancy 0.49 <= existing 0.510001 Skipped atom 352, because occupancy 0.49 <= existing 0.510001 Skipped atom 354, because occupancy 0.49 <= existing 0.510001 Skipped atom 356, because occupancy 0.49 <= existing 0.510001 Skipped atom 412, because occupancy 0.32 <= existing 0.680001 Skipped atom 414, because occupancy 0.32 <= existing 0.680001 Skipped atom 416, because occupancy 0.32 <= existing 0.680001 Skipped atom 418, because occupancy 0.32 <= existing 0.680001 Skipped atom 420, because occupancy 0.32 <= existing 0.680001 Skipped atom 533, because occupancy 0.34 <= existing 0.660001 Skipped atom 535, because occupancy 0.34 <= existing 0.660001 Skipped atom 537, because occupancy 0.34 <= existing 0.660001 Skipped atom 539, because occupancy 0.34 <= existing 0.660001 Skipped atom 554, because occupancy 0.41 <= existing 0.590001 Skipped atom 556, because occupancy 0.41 <= existing 0.590001 Skipped atom 558, because occupancy 0.41 <= existing 0.590001 Skipped atom 560, because occupancy 0.41 <= existing 0.590001 Skipped atom 562, because occupancy 0.41 <= existing 0.590001 Skipped atom 568, because occupancy 0.5 <= existing 0.500001 Skipped atom 570, because occupancy 0.5 <= existing 0.500001 Skipped atom 572, because occupancy 0.5 <= existing 0.500001 Skipped atom 574, because occupancy 0.5 <= existing 0.500001 Skipped atom 576, because occupancy 0.5 <= existing 0.500001 Skipped atom 578, because occupancy 0.5 <= existing 0.500001 Skipped atom 773, because occupancy 0.47 <= existing 0.530001 Skipped atom 775, because occupancy 0.47 <= existing 0.530001 Skipped atom 777, because occupancy 0.47 <= existing 0.530001 Skipped atom 779, because occupancy 0.47 <= existing 0.530001 Skipped atom 781, because occupancy 0.47 <= existing 0.530001 Skipped atom 815, because occupancy 0.45 <= existing 0.550001 Skipped atom 817, because occupancy 0.45 <= existing 0.550001 Skipped atom 819, because occupancy 0.45 <= existing 0.550001 Skipped atom 821, because occupancy 0.45 <= existing 0.550001 Skipped atom 823, because occupancy 0.45 <= existing 0.550001 Skipped atom 934, because occupancy 0.34 <= existing 0.660001 Skipped atom 936, because occupancy 0.34 <= existing 0.660001 Skipped atom 938, because occupancy 0.34 <= existing 0.660001 Skipped atom 940, because occupancy 0.34 <= existing 0.660001 Skipped atom 942, because occupancy 0.34 <= existing 0.660001 Skipped atom 998, because occupancy 0.46 <= existing 0.540001 Skipped atom 1000, because occupancy 0.46 <= existing 0.540001 Skipped atom 1002, because occupancy 0.46 <= existing 0.540001 Skipped atom 1004, because occupancy 0.46 <= existing 0.540001 Skipped atom 1006, because occupancy 0.46 <= existing 0.540001 Skipped atom 1008, because occupancy 0.46 <= existing 0.540001 Skipped atom 1014, because occupancy 0.44 <= existing 0.560001 Skipped atom 1016, because occupancy 0.44 <= existing 0.560001 Skipped atom 1089, because occupancy 0.34 <= existing 0.660001 Skipped atom 1091, because occupancy 0.34 <= existing 0.660001 Skipped atom 1093, because occupancy 0.34 <= existing 0.660001 Skipped atom 1095, because occupancy 0.34 <= existing 0.660001 Skipped atom 1106, because occupancy 0.44 <= existing 0.560001 Skipped atom 1108, because occupancy 0.44 <= existing 0.560001 Skipped atom 1110, because occupancy 0.44 <= existing 0.560001 Skipped atom 1112, because occupancy 0.44 <= existing 0.560001 Skipped atom 1114, because occupancy 0.44 <= existing 0.560001 Skipped atom 1145, because occupancy 0.45 <= existing 0.550001 Skipped atom 1147, because occupancy 0.45 <= existing 0.550001 Skipped atom 1149, because occupancy 0.45 <= existing 0.550001 Skipped atom 1151, because occupancy 0.45 <= existing 0.550001 Skipped atom 1153, because occupancy 0.45 <= existing 0.550001 Skipped atom 1172, because occupancy 0.43 <= existing 0.570001 Skipped atom 1174, because occupancy 0.43 <= existing 0.570001 Skipped atom 1176, because occupancy 0.43 <= existing 0.570001 Skipped atom 1178, because occupancy 0.43 <= existing 0.570001 Skipped atom 1180, because occupancy 0.43 <= existing 0.570001 Skipped atom 1240, because occupancy 0.33 <= existing 0.670001 Skipped atom 1242, because occupancy 0.33 <= existing 0.670001 Skipped atom 1244, because occupancy 0.33 <= existing 0.670001 Skipped atom 1246, because occupancy 0.33 <= existing 0.670001 Skipped atom 1321, because occupancy 0.5 <= existing 0.500001 Skipped atom 1323, because occupancy 0.5 <= existing 0.500001 Skipped atom 1325, because occupancy 0.5 <= existing 0.500001 Skipped atom 1327, because occupancy 0.5 <= existing 0.500001 Skipped atom 1329, because occupancy 0.5 <= existing 0.500001 Skipped atom 1331, because occupancy 0.5 <= existing 0.500001 Skipped atom 1333, because occupancy 0.5 <= existing 0.500001 Skipped atom 1335, because occupancy 0.5 <= existing 0.500001 partial PDB gets fragment 133 through 142 extending start extending end Debugging on ! Reading sequence file Reading input structure 12 residues read Measuring phi and psi Getting chi values PRO 1 2 LYS 2 30 ASN 3 4 ASP 5 5 SER 7 3 ILE 8 3 THR 9 2 SER 10 3 Building many copies of each residue Checking backbone and frame clashes Finding the lowest Also, print out the first version, pre-bump Finding disulfide bonds. Found 0 disulfide bonds. Residue clashes: 0 clashing residues after turn Residue clashes: Still clashes at these sidechain pairs: Residual clashes = 0.00000 Printing mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a6m.4.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a6m.4.1.a2m \ -target T0098 -template 1a6m \ -out T0098-1a6m.4.1 -outdir und2 Skipped atom 27, because occupancy 0.43 <= existing 0.570001 Skipped atom 29, because occupancy 0.43 <= existing 0.570001 Skipped atom 31, because occupancy 0.43 <= existing 0.570001 Skipped atom 33, because occupancy 0.43 <= existing 0.570001 Skipped atom 35, because occupancy 0.43 <= existing 0.570001 Skipped atom 68, because occupancy 0.43 <= existing 0.570001 Skipped atom 70, because occupancy 0.43 <= existing 0.570001 Skipped atom 72, because occupancy 0.43 <= existing 0.570001 Skipped atom 74, because occupancy 0.43 <= existing 0.570001 Skipped atom 76, because occupancy 0.43 <= existing 0.570001 Skipped atom 209, because occupancy 0.35 <= existing 0.650001 Skipped atom 211, because occupancy 0.35 <= existing 0.650001 Skipped atom 213, because occupancy 0.35 <= existing 0.650001 Skipped atom 215, because occupancy 0.35 <= existing 0.650001 Skipped atom 217, because occupancy 0.35 <= existing 0.650001 Skipped atom 348, because occupancy 0.49 <= existing 0.510001 Skipped atom 350, because occupancy 0.49 <= existing 0.510001 Skipped atom 352, because occupancy 0.49 <= existing 0.510001 Skipped atom 354, because occupancy 0.49 <= existing 0.510001 Skipped atom 356, because occupancy 0.49 <= existing 0.510001 Skipped atom 412, because occupancy 0.32 <= existing 0.680001 Skipped atom 414, because occupancy 0.32 <= existing 0.680001 Skipped atom 416, because occupancy 0.32 <= existing 0.680001 Skipped atom 418, because occupancy 0.32 <= existing 0.680001 Skipped atom 420, because occupancy 0.32 <= existing 0.680001 Skipped atom 533, because occupancy 0.34 <= existing 0.660001 Skipped atom 535, because occupancy 0.34 <= existing 0.660001 Skipped atom 537, because occupancy 0.34 <= existing 0.660001 Skipped atom 539, because occupancy 0.34 <= existing 0.660001 Skipped atom 554, because occupancy 0.41 <= existing 0.590001 Skipped atom 556, because occupancy 0.41 <= existing 0.590001 Skipped atom 558, because occupancy 0.41 <= existing 0.590001 Skipped atom 560, because occupancy 0.41 <= existing 0.590001 Skipped atom 562, because occupancy 0.41 <= existing 0.590001 Skipped atom 568, because occupancy 0.5 <= existing 0.500001 Skipped atom 570, because occupancy 0.5 <= existing 0.500001 Skipped atom 572, because occupancy 0.5 <= existing 0.500001 Skipped atom 574, because occupancy 0.5 <= existing 0.500001 Skipped atom 576, because occupancy 0.5 <= existing 0.500001 Skipped atom 578, because occupancy 0.5 <= existing 0.500001 Skipped atom 773, because occupancy 0.47 <= existing 0.530001 Skipped atom 775, because occupancy 0.47 <= existing 0.530001 Skipped atom 777, because occupancy 0.47 <= existing 0.530001 Skipped atom 779, because occupancy 0.47 <= existing 0.530001 Skipped atom 781, because occupancy 0.47 <= existing 0.530001 Skipped atom 815, because occupancy 0.45 <= existing 0.550001 Skipped atom 817, because occupancy 0.45 <= existing 0.550001 Skipped atom 819, because occupancy 0.45 <= existing 0.550001 Skipped atom 821, because occupancy 0.45 <= existing 0.550001 Skipped atom 823, because occupancy 0.45 <= existing 0.550001 Skipped atom 934, because occupancy 0.34 <= existing 0.660001 Skipped atom 936, because occupancy 0.34 <= existing 0.660001 Skipped atom 938, because occupancy 0.34 <= existing 0.660001 Skipped atom 940, because occupancy 0.34 <= existing 0.660001 Skipped atom 942, because occupancy 0.34 <= existing 0.660001 Skipped atom 998, because occupancy 0.46 <= existing 0.540001 Skipped atom 1000, because occupancy 0.46 <= existing 0.540001 Skipped atom 1002, because occupancy 0.46 <= existing 0.540001 Skipped atom 1004, because occupancy 0.46 <= existing 0.540001 Skipped atom 1006, because occupancy 0.46 <= existing 0.540001 Skipped atom 1008, because occupancy 0.46 <= existing 0.540001 Skipped atom 1014, because occupancy 0.44 <= existing 0.560001 Skipped atom 1016, because occupancy 0.44 <= existing 0.560001 Skipped atom 1089, because occupancy 0.34 <= existing 0.660001 Skipped atom 1091, because occupancy 0.34 <= existing 0.660001 Skipped atom 1093, because occupancy 0.34 <= existing 0.660001 Skipped atom 1095, because occupancy 0.34 <= existing 0.660001 Skipped atom 1106, because occupancy 0.44 <= existing 0.560001 Skipped atom 1108, because occupancy 0.44 <= existing 0.560001 Skipped atom 1110, because occupancy 0.44 <= existing 0.560001 Skipped atom 1112, because occupancy 0.44 <= existing 0.560001 Skipped atom 1114, because occupancy 0.44 <= existing 0.560001 Skipped atom 1145, because occupancy 0.45 <= existing 0.550001 Skipped atom 1147, because occupancy 0.45 <= existing 0.550001 Skipped atom 1149, because occupancy 0.45 <= existing 0.550001 Skipped atom 1151, because occupancy 0.45 <= existing 0.550001 Skipped atom 1153, because occupancy 0.45 <= existing 0.550001 Skipped atom 1172, because occupancy 0.43 <= existing 0.570001 Skipped atom 1174, because occupancy 0.43 <= existing 0.570001 Skipped atom 1176, because occupancy 0.43 <= existing 0.570001 Skipped atom 1178, because occupancy 0.43 <= existing 0.570001 Skipped atom 1180, because occupancy 0.43 <= existing 0.570001 Skipped atom 1240, because occupancy 0.33 <= existing 0.670001 Skipped atom 1242, because occupancy 0.33 <= existing 0.670001 Skipped atom 1244, because occupancy 0.33 <= existing 0.670001 Skipped atom 1246, because occupancy 0.33 <= existing 0.670001 Skipped atom 1321, because occupancy 0.5 <= existing 0.500001 Skipped atom 1323, because occupancy 0.5 <= existing 0.500001 Skipped atom 1325, because occupancy 0.5 <= existing 0.500001 Skipped atom 1327, because occupancy 0.5 <= existing 0.500001 Skipped atom 1329, because occupancy 0.5 <= existing 0.500001 Skipped atom 1331, because occupancy 0.5 <= existing 0.500001 Skipped atom 1333, because occupancy 0.5 <= existing 0.500001 Skipped atom 1335, because occupancy 0.5 <= existing 0.500001 partial PDB gets fragment 132 through 141 extending start extending end Debugging on ! Reading sequence file Reading input structure 12 residues read Measuring phi and psi Getting chi values ASN 2 5 ASP 4 5 SER 6 3 ILE 7 3 THR 8 1 SER 9 3 Building many copies of each residue Checking backbone and frame clashes Finding the lowest Also, print out the first version, pre-bump Finding disulfide bonds. Found 0 disulfide bonds. Residue clashes: 0 clashing residues after turn Residue clashes: Still clashes at these sidechain pairs: Residual clashes = 0.00000 Printing mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a6m.5.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a6m.5.1.a2m \ -target T0098 -template 1a6m \ -out T0098-1a6m.5.1 -outdir und2 Skipped atom 27, because occupancy 0.43 <= existing 0.570001 Skipped atom 29, because occupancy 0.43 <= existing 0.570001 Skipped atom 31, because occupancy 0.43 <= existing 0.570001 Skipped atom 33, because occupancy 0.43 <= existing 0.570001 Skipped atom 35, because occupancy 0.43 <= existing 0.570001 Skipped atom 68, because occupancy 0.43 <= existing 0.570001 Skipped atom 70, because occupancy 0.43 <= existing 0.570001 Skipped atom 72, because occupancy 0.43 <= existing 0.570001 Skipped atom 74, because occupancy 0.43 <= existing 0.570001 Skipped atom 76, because occupancy 0.43 <= existing 0.570001 Skipped atom 209, because occupancy 0.35 <= existing 0.650001 Skipped atom 211, because occupancy 0.35 <= existing 0.650001 Skipped atom 213, because occupancy 0.35 <= existing 0.650001 Skipped atom 215, because occupancy 0.35 <= existing 0.650001 Skipped atom 217, because occupancy 0.35 <= existing 0.650001 Skipped atom 348, because occupancy 0.49 <= existing 0.510001 Skipped atom 350, because occupancy 0.49 <= existing 0.510001 Skipped atom 352, because occupancy 0.49 <= existing 0.510001 Skipped atom 354, because occupancy 0.49 <= existing 0.510001 Skipped atom 356, because occupancy 0.49 <= existing 0.510001 Skipped atom 412, because occupancy 0.32 <= existing 0.680001 Skipped atom 414, because occupancy 0.32 <= existing 0.680001 Skipped atom 416, because occupancy 0.32 <= existing 0.680001 Skipped atom 418, because occupancy 0.32 <= existing 0.680001 Skipped atom 420, because occupancy 0.32 <= existing 0.680001 Skipped atom 533, because occupancy 0.34 <= existing 0.660001 Skipped atom 535, because occupancy 0.34 <= existing 0.660001 Skipped atom 537, because occupancy 0.34 <= existing 0.660001 Skipped atom 539, because occupancy 0.34 <= existing 0.660001 Skipped atom 554, because occupancy 0.41 <= existing 0.590001 Skipped atom 556, because occupancy 0.41 <= existing 0.590001 Skipped atom 558, because occupancy 0.41 <= existing 0.590001 Skipped atom 560, because occupancy 0.41 <= existing 0.590001 Skipped atom 562, because occupancy 0.41 <= existing 0.590001 Skipped atom 568, because occupancy 0.5 <= existing 0.500001 Skipped atom 570, because occupancy 0.5 <= existing 0.500001 Skipped atom 572, because occupancy 0.5 <= existing 0.500001 Skipped atom 574, because occupancy 0.5 <= existing 0.500001 Skipped atom 576, because occupancy 0.5 <= existing 0.500001 Skipped atom 578, because occupancy 0.5 <= existing 0.500001 Skipped atom 773, because occupancy 0.47 <= existing 0.530001 Skipped atom 775, because occupancy 0.47 <= existing 0.530001 Skipped atom 777, because occupancy 0.47 <= existing 0.530001 Skipped atom 779, because occupancy 0.47 <= existing 0.530001 Skipped atom 781, because occupancy 0.47 <= existing 0.530001 Skipped atom 815, because occupancy 0.45 <= existing 0.550001 Skipped atom 817, because occupancy 0.45 <= existing 0.550001 Skipped atom 819, because occupancy 0.45 <= existing 0.550001 Skipped atom 821, because occupancy 0.45 <= existing 0.550001 Skipped atom 823, because occupancy 0.45 <= existing 0.550001 Skipped atom 934, because occupancy 0.34 <= existing 0.660001 Skipped atom 936, because occupancy 0.34 <= existing 0.660001 Skipped atom 938, because occupancy 0.34 <= existing 0.660001 Skipped atom 940, because occupancy 0.34 <= existing 0.660001 Skipped atom 942, because occupancy 0.34 <= existing 0.660001 Skipped atom 998, because occupancy 0.46 <= existing 0.540001 Skipped atom 1000, because occupancy 0.46 <= existing 0.540001 Skipped atom 1002, because occupancy 0.46 <= existing 0.540001 Skipped atom 1004, because occupancy 0.46 <= existing 0.540001 Skipped atom 1006, because occupancy 0.46 <= existing 0.540001 Skipped atom 1008, because occupancy 0.46 <= existing 0.540001 Skipped atom 1014, because occupancy 0.44 <= existing 0.560001 Skipped atom 1016, because occupancy 0.44 <= existing 0.560001 Skipped atom 1089, because occupancy 0.34 <= existing 0.660001 Skipped atom 1091, because occupancy 0.34 <= existing 0.660001 Skipped atom 1093, because occupancy 0.34 <= existing 0.660001 Skipped atom 1095, because occupancy 0.34 <= existing 0.660001 Skipped atom 1106, because occupancy 0.44 <= existing 0.560001 Skipped atom 1108, because occupancy 0.44 <= existing 0.560001 Skipped atom 1110, because occupancy 0.44 <= existing 0.560001 Skipped atom 1112, because occupancy 0.44 <= existing 0.560001 Skipped atom 1114, because occupancy 0.44 <= existing 0.560001 Skipped atom 1145, because occupancy 0.45 <= existing 0.550001 Skipped atom 1147, because occupancy 0.45 <= existing 0.550001 Skipped atom 1149, because occupancy 0.45 <= existing 0.550001 Skipped atom 1151, because occupancy 0.45 <= existing 0.550001 Skipped atom 1153, because occupancy 0.45 <= existing 0.550001 Skipped atom 1172, because occupancy 0.43 <= existing 0.570001 Skipped atom 1174, because occupancy 0.43 <= existing 0.570001 Skipped atom 1176, because occupancy 0.43 <= existing 0.570001 Skipped atom 1178, because occupancy 0.43 <= existing 0.570001 Skipped atom 1180, because occupancy 0.43 <= existing 0.570001 Skipped atom 1240, because occupancy 0.33 <= existing 0.670001 Skipped atom 1242, because occupancy 0.33 <= existing 0.670001 Skipped atom 1244, because occupancy 0.33 <= existing 0.670001 Skipped atom 1246, because occupancy 0.33 <= existing 0.670001 Skipped atom 1321, because occupancy 0.5 <= existing 0.500001 Skipped atom 1323, because occupancy 0.5 <= existing 0.500001 Skipped atom 1325, because occupancy 0.5 <= existing 0.500001 Skipped atom 1327, because occupancy 0.5 <= existing 0.500001 Skipped atom 1329, because occupancy 0.5 <= existing 0.500001 Skipped atom 1331, because occupancy 0.5 <= existing 0.500001 Skipped atom 1333, because occupancy 0.5 <= existing 0.500001 Skipped atom 1335, because occupancy 0.5 <= existing 0.500001 partial PDB gets fragment 131 through 140 extending start extending end Debugging on ! Reading sequence file Reading input structure 12 residues read Measuring phi and psi Getting chi values LEU 2 3 ASP 3 4 SER 5 3 ILE 6 3 THR 7 1 SER 8 3 ILE 9 2 ILE 10 3 Building many copies of each residue Checking backbone and frame clashes Finding the lowest Also, print out the first version, pre-bump Finding disulfide bonds. Found 0 disulfide bonds. Residue clashes: 0 clashing residues after turn Residue clashes: Still clashes at these sidechain pairs: Residual clashes = 0.00000 Printing mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a6m.6.0.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a6m.6.0.a2m \ -target T0098 -template 1a6m \ -out T0098-1a6m.6.0 -outdir und2 Skipped atom 27, because occupancy 0.43 <= existing 0.570001 Skipped atom 29, because occupancy 0.43 <= existing 0.570001 Skipped atom 31, because occupancy 0.43 <= existing 0.570001 Skipped atom 33, because occupancy 0.43 <= existing 0.570001 Skipped atom 35, because occupancy 0.43 <= existing 0.570001 Skipped atom 68, because occupancy 0.43 <= existing 0.570001 Skipped atom 70, because occupancy 0.43 <= existing 0.570001 Skipped atom 72, because occupancy 0.43 <= existing 0.570001 Skipped atom 74, because occupancy 0.43 <= existing 0.570001 Skipped atom 76, because occupancy 0.43 <= existing 0.570001 Skipped atom 209, because occupancy 0.35 <= existing 0.650001 Skipped atom 211, because occupancy 0.35 <= existing 0.650001 Skipped atom 213, because occupancy 0.35 <= existing 0.650001 Skipped atom 215, because occupancy 0.35 <= existing 0.650001 Skipped atom 217, because occupancy 0.35 <= existing 0.650001 Skipped atom 348, because occupancy 0.49 <= existing 0.510001 Skipped atom 350, because occupancy 0.49 <= existing 0.510001 Skipped atom 352, because occupancy 0.49 <= existing 0.510001 Skipped atom 354, because occupancy 0.49 <= existing 0.510001 Skipped atom 356, because occupancy 0.49 <= existing 0.510001 Skipped atom 412, because occupancy 0.32 <= existing 0.680001 Skipped atom 414, because occupancy 0.32 <= existing 0.680001 Skipped atom 416, because occupancy 0.32 <= existing 0.680001 Skipped atom 418, because occupancy 0.32 <= existing 0.680001 Skipped atom 420, because occupancy 0.32 <= existing 0.680001 Skipped atom 533, because occupancy 0.34 <= existing 0.660001 Skipped atom 535, because occupancy 0.34 <= existing 0.660001 Skipped atom 537, because occupancy 0.34 <= existing 0.660001 Skipped atom 539, because occupancy 0.34 <= existing 0.660001 Skipped atom 554, because occupancy 0.41 <= existing 0.590001 Skipped atom 556, because occupancy 0.41 <= existing 0.590001 Skipped atom 558, because occupancy 0.41 <= existing 0.590001 Skipped atom 560, because occupancy 0.41 <= existing 0.590001 Skipped atom 562, because occupancy 0.41 <= existing 0.590001 Skipped atom 568, because occupancy 0.5 <= existing 0.500001 Skipped atom 570, because occupancy 0.5 <= existing 0.500001 Skipped atom 572, because occupancy 0.5 <= existing 0.500001 Skipped atom 574, because occupancy 0.5 <= existing 0.500001 Skipped atom 576, because occupancy 0.5 <= existing 0.500001 Skipped atom 578, because occupancy 0.5 <= existing 0.500001 Skipped atom 773, because occupancy 0.47 <= existing 0.530001 Skipped atom 775, because occupancy 0.47 <= existing 0.530001 Skipped atom 777, because occupancy 0.47 <= existing 0.530001 Skipped atom 779, because occupancy 0.47 <= existing 0.530001 Skipped atom 781, because occupancy 0.47 <= existing 0.530001 Skipped atom 815, because occupancy 0.45 <= existing 0.550001 Skipped atom 817, because occupancy 0.45 <= existing 0.550001 Skipped atom 819, because occupancy 0.45 <= existing 0.550001 Skipped atom 821, because occupancy 0.45 <= existing 0.550001 Skipped atom 823, because occupancy 0.45 <= existing 0.550001 Skipped atom 934, because occupancy 0.34 <= existing 0.660001 Skipped atom 936, because occupancy 0.34 <= existing 0.660001 Skipped atom 938, because occupancy 0.34 <= existing 0.660001 Skipped atom 940, because occupancy 0.34 <= existing 0.660001 Skipped atom 942, because occupancy 0.34 <= existing 0.660001 Skipped atom 998, because occupancy 0.46 <= existing 0.540001 Skipped atom 1000, because occupancy 0.46 <= existing 0.540001 Skipped atom 1002, because occupancy 0.46 <= existing 0.540001 Skipped atom 1004, because occupancy 0.46 <= existing 0.540001 Skipped atom 1006, because occupancy 0.46 <= existing 0.540001 Skipped atom 1008, because occupancy 0.46 <= existing 0.540001 Skipped atom 1014, because occupancy 0.44 <= existing 0.560001 Skipped atom 1016, because occupancy 0.44 <= existing 0.560001 Skipped atom 1089, because occupancy 0.34 <= existing 0.660001 Skipped atom 1091, because occupancy 0.34 <= existing 0.660001 Skipped atom 1093, because occupancy 0.34 <= existing 0.660001 Skipped atom 1095, because occupancy 0.34 <= existing 0.660001 Skipped atom 1106, because occupancy 0.44 <= existing 0.560001 Skipped atom 1108, because occupancy 0.44 <= existing 0.560001 Skipped atom 1110, because occupancy 0.44 <= existing 0.560001 Skipped atom 1112, because occupancy 0.44 <= existing 0.560001 Skipped atom 1114, because occupancy 0.44 <= existing 0.560001 Skipped atom 1145, because occupancy 0.45 <= existing 0.550001 Skipped atom 1147, because occupancy 0.45 <= existing 0.550001 Skipped atom 1149, because occupancy 0.45 <= existing 0.550001 Skipped atom 1151, because occupancy 0.45 <= existing 0.550001 Skipped atom 1153, because occupancy 0.45 <= existing 0.550001 Skipped atom 1172, because occupancy 0.43 <= existing 0.570001 Skipped atom 1174, because occupancy 0.43 <= existing 0.570001 Skipped atom 1176, because occupancy 0.43 <= existing 0.570001 Skipped atom 1178, because occupancy 0.43 <= existing 0.570001 Skipped atom 1180, because occupancy 0.43 <= existing 0.570001 Skipped atom 1240, because occupancy 0.33 <= existing 0.670001 Skipped atom 1242, because occupancy 0.33 <= existing 0.670001 Skipped atom 1244, because occupancy 0.33 <= existing 0.670001 Skipped atom 1246, because occupancy 0.33 <= existing 0.670001 Skipped atom 1321, because occupancy 0.5 <= existing 0.500001 Skipped atom 1323, because occupancy 0.5 <= existing 0.500001 Skipped atom 1325, because occupancy 0.5 <= existing 0.500001 Skipped atom 1327, because occupancy 0.5 <= existing 0.500001 Skipped atom 1329, because occupancy 0.5 <= existing 0.500001 Skipped atom 1331, because occupancy 0.5 <= existing 0.500001 Skipped atom 1333, because occupancy 0.5 <= existing 0.500001 Skipped atom 1335, because occupancy 0.5 <= existing 0.500001 partial PDB gets fragment 130 through 139 extending start extending end Debugging on ! Reading sequence file Reading input structure 12 residues read Measuring phi and psi Getting chi values LEU 1 3 ASP 2 4 SER 4 3 ILE 5 5 THR 6 2 SER 7 3 ILE 8 3 ILE 9 3 HIS 10 3 Building many copies of each residue Checking backbone and frame clashes Finding the lowest Also, print out the first version, pre-bump Finding disulfide bonds. Found 0 disulfide bonds. Residue clashes: 0 clashing residues after turn Residue clashes: Still clashes at these sidechain pairs: Residual clashes = 0.00000 Printing mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a6m.7.0.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a6m.7.0.a2m \ -target T0098 -template 1a6m \ -out T0098-1a6m.7.0 -outdir und2 Skipped atom 27, because occupancy 0.43 <= existing 0.570001 Skipped atom 29, because occupancy 0.43 <= existing 0.570001 Skipped atom 31, because occupancy 0.43 <= existing 0.570001 Skipped atom 33, because occupancy 0.43 <= existing 0.570001 Skipped atom 35, because occupancy 0.43 <= existing 0.570001 Skipped atom 68, because occupancy 0.43 <= existing 0.570001 Skipped atom 70, because occupancy 0.43 <= existing 0.570001 Skipped atom 72, because occupancy 0.43 <= existing 0.570001 Skipped atom 74, because occupancy 0.43 <= existing 0.570001 Skipped atom 76, because occupancy 0.43 <= existing 0.570001 Skipped atom 209, because occupancy 0.35 <= existing 0.650001 Skipped atom 211, because occupancy 0.35 <= existing 0.650001 Skipped atom 213, because occupancy 0.35 <= existing 0.650001 Skipped atom 215, because occupancy 0.35 <= existing 0.650001 Skipped atom 217, because occupancy 0.35 <= existing 0.650001 Skipped atom 348, because occupancy 0.49 <= existing 0.510001 Skipped atom 350, because occupancy 0.49 <= existing 0.510001 Skipped atom 352, because occupancy 0.49 <= existing 0.510001 Skipped atom 354, because occupancy 0.49 <= existing 0.510001 Skipped atom 356, because occupancy 0.49 <= existing 0.510001 Skipped atom 412, because occupancy 0.32 <= existing 0.680001 Skipped atom 414, because occupancy 0.32 <= existing 0.680001 Skipped atom 416, because occupancy 0.32 <= existing 0.680001 Skipped atom 418, because occupancy 0.32 <= existing 0.680001 Skipped atom 420, because occupancy 0.32 <= existing 0.680001 Skipped atom 533, because occupancy 0.34 <= existing 0.660001 Skipped atom 535, because occupancy 0.34 <= existing 0.660001 Skipped atom 537, because occupancy 0.34 <= existing 0.660001 Skipped atom 539, because occupancy 0.34 <= existing 0.660001 Skipped atom 554, because occupancy 0.41 <= existing 0.590001 Skipped atom 556, because occupancy 0.41 <= existing 0.590001 Skipped atom 558, because occupancy 0.41 <= existing 0.590001 Skipped atom 560, because occupancy 0.41 <= existing 0.590001 Skipped atom 562, because occupancy 0.41 <= existing 0.590001 Skipped atom 568, because occupancy 0.5 <= existing 0.500001 Skipped atom 570, because occupancy 0.5 <= existing 0.500001 Skipped atom 572, because occupancy 0.5 <= existing 0.500001 Skipped atom 574, because occupancy 0.5 <= existing 0.500001 Skipped atom 576, because occupancy 0.5 <= existing 0.500001 Skipped atom 578, because occupancy 0.5 <= existing 0.500001 Skipped atom 773, because occupancy 0.47 <= existing 0.530001 Skipped atom 775, because occupancy 0.47 <= existing 0.530001 Skipped atom 777, because occupancy 0.47 <= existing 0.530001 Skipped atom 779, because occupancy 0.47 <= existing 0.530001 Skipped atom 781, because occupancy 0.47 <= existing 0.530001 Skipped atom 815, because occupancy 0.45 <= existing 0.550001 Skipped atom 817, because occupancy 0.45 <= existing 0.550001 Skipped atom 819, because occupancy 0.45 <= existing 0.550001 Skipped atom 821, because occupancy 0.45 <= existing 0.550001 Skipped atom 823, because occupancy 0.45 <= existing 0.550001 Skipped atom 934, because occupancy 0.34 <= existing 0.660001 Skipped atom 936, because occupancy 0.34 <= existing 0.660001 Skipped atom 938, because occupancy 0.34 <= existing 0.660001 Skipped atom 940, because occupancy 0.34 <= existing 0.660001 Skipped atom 942, because occupancy 0.34 <= existing 0.660001 Skipped atom 998, because occupancy 0.46 <= existing 0.540001 Skipped atom 1000, because occupancy 0.46 <= existing 0.540001 Skipped atom 1002, because occupancy 0.46 <= existing 0.540001 Skipped atom 1004, because occupancy 0.46 <= existing 0.540001 Skipped atom 1006, because occupancy 0.46 <= existing 0.540001 Skipped atom 1008, because occupancy 0.46 <= existing 0.540001 Skipped atom 1014, because occupancy 0.44 <= existing 0.560001 Skipped atom 1016, because occupancy 0.44 <= existing 0.560001 Skipped atom 1089, because occupancy 0.34 <= existing 0.660001 Skipped atom 1091, because occupancy 0.34 <= existing 0.660001 Skipped atom 1093, because occupancy 0.34 <= existing 0.660001 Skipped atom 1095, because occupancy 0.34 <= existing 0.660001 Skipped atom 1106, because occupancy 0.44 <= existing 0.560001 Skipped atom 1108, because occupancy 0.44 <= existing 0.560001 Skipped atom 1110, because occupancy 0.44 <= existing 0.560001 Skipped atom 1112, because occupancy 0.44 <= existing 0.560001 Skipped atom 1114, because occupancy 0.44 <= existing 0.560001 Skipped atom 1145, because occupancy 0.45 <= existing 0.550001 Skipped atom 1147, because occupancy 0.45 <= existing 0.550001 Skipped atom 1149, because occupancy 0.45 <= existing 0.550001 Skipped atom 1151, because occupancy 0.45 <= existing 0.550001 Skipped atom 1153, because occupancy 0.45 <= existing 0.550001 Skipped atom 1172, because occupancy 0.43 <= existing 0.570001 Skipped atom 1174, because occupancy 0.43 <= existing 0.570001 Skipped atom 1176, because occupancy 0.43 <= existing 0.570001 Skipped atom 1178, because occupancy 0.43 <= existing 0.570001 Skipped atom 1180, because occupancy 0.43 <= existing 0.570001 Skipped atom 1240, because occupancy 0.33 <= existing 0.670001 Skipped atom 1242, because occupancy 0.33 <= existing 0.670001 Skipped atom 1244, because occupancy 0.33 <= existing 0.670001 Skipped atom 1246, because occupancy 0.33 <= existing 0.670001 Skipped atom 1321, because occupancy 0.5 <= existing 0.500001 Skipped atom 1323, because occupancy 0.5 <= existing 0.500001 Skipped atom 1325, because occupancy 0.5 <= existing 0.500001 Skipped atom 1327, because occupancy 0.5 <= existing 0.500001 Skipped atom 1329, because occupancy 0.5 <= existing 0.500001 Skipped atom 1331, because occupancy 0.5 <= existing 0.500001 Skipped atom 1333, because occupancy 0.5 <= existing 0.500001 Skipped atom 1335, because occupancy 0.5 <= existing 0.500001 partial PDB gets fragment 129 through 138 extending start extending end Debugging on ! Reading sequence file Reading input structure 12 residues read Measuring phi and psi Getting chi values ASP 1 4 SER 3 3 ILE 4 3 THR 5 2 SER 6 2 ILE 7 3 ILE 8 3 HIS 9 3 GLU 10 12 Building many copies of each residue Checking backbone and frame clashes Finding the lowest Also, print out the first version, pre-bump Finding disulfide bonds. Found 0 disulfide bonds. Residue clashes: 0 clashing residues after turn Residue clashes: Still clashes at these sidechain pairs: Residual clashes = 0.00000 Printing mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a6m.8.5.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a6m.8.5.a2m \ -target T0098 -template 1a6m \ -out T0098-1a6m.8.5 -outdir und2 Skipped atom 27, because occupancy 0.43 <= existing 0.570001 Skipped atom 29, because occupancy 0.43 <= existing 0.570001 Skipped atom 31, because occupancy 0.43 <= existing 0.570001 Skipped atom 33, because occupancy 0.43 <= existing 0.570001 Skipped atom 35, because occupancy 0.43 <= existing 0.570001 Skipped atom 68, because occupancy 0.43 <= existing 0.570001 Skipped atom 70, because occupancy 0.43 <= existing 0.570001 Skipped atom 72, because occupancy 0.43 <= existing 0.570001 Skipped atom 74, because occupancy 0.43 <= existing 0.570001 Skipped atom 76, because occupancy 0.43 <= existing 0.570001 Skipped atom 209, because occupancy 0.35 <= existing 0.650001 Skipped atom 211, because occupancy 0.35 <= existing 0.650001 Skipped atom 213, because occupancy 0.35 <= existing 0.650001 Skipped atom 215, because occupancy 0.35 <= existing 0.650001 Skipped atom 217, because occupancy 0.35 <= existing 0.650001 Skipped atom 348, because occupancy 0.49 <= existing 0.510001 Skipped atom 350, because occupancy 0.49 <= existing 0.510001 Skipped atom 352, because occupancy 0.49 <= existing 0.510001 Skipped atom 354, because occupancy 0.49 <= existing 0.510001 Skipped atom 356, because occupancy 0.49 <= existing 0.510001 Skipped atom 412, because occupancy 0.32 <= existing 0.680001 Skipped atom 414, because occupancy 0.32 <= existing 0.680001 Skipped atom 416, because occupancy 0.32 <= existing 0.680001 Skipped atom 418, because occupancy 0.32 <= existing 0.680001 Skipped atom 420, because occupancy 0.32 <= existing 0.680001 Skipped atom 533, because occupancy 0.34 <= existing 0.660001 Skipped atom 535, because occupancy 0.34 <= existing 0.660001 Skipped atom 537, because occupancy 0.34 <= existing 0.660001 Skipped atom 539, because occupancy 0.34 <= existing 0.660001 Skipped atom 554, because occupancy 0.41 <= existing 0.590001 Skipped atom 556, because occupancy 0.41 <= existing 0.590001 Skipped atom 558, because occupancy 0.41 <= existing 0.590001 Skipped atom 560, because occupancy 0.41 <= existing 0.590001 Skipped atom 562, because occupancy 0.41 <= existing 0.590001 Skipped atom 568, because occupancy 0.5 <= existing 0.500001 Skipped atom 570, because occupancy 0.5 <= existing 0.500001 Skipped atom 572, because occupancy 0.5 <= existing 0.500001 Skipped atom 574, because occupancy 0.5 <= existing 0.500001 Skipped atom 576, because occupancy 0.5 <= existing 0.500001 Skipped atom 578, because occupancy 0.5 <= existing 0.500001 Skipped atom 773, because occupancy 0.47 <= existing 0.530001 Skipped atom 775, because occupancy 0.47 <= existing 0.530001 Skipped atom 777, because occupancy 0.47 <= existing 0.530001 Skipped atom 779, because occupancy 0.47 <= existing 0.530001 Skipped atom 781, because occupancy 0.47 <= existing 0.530001 Skipped atom 815, because occupancy 0.45 <= existing 0.550001 Skipped atom 817, because occupancy 0.45 <= existing 0.550001 Skipped atom 819, because occupancy 0.45 <= existing 0.550001 Skipped atom 821, because occupancy 0.45 <= existing 0.550001 Skipped atom 823, because occupancy 0.45 <= existing 0.550001 Skipped atom 934, because occupancy 0.34 <= existing 0.660001 Skipped atom 936, because occupancy 0.34 <= existing 0.660001 Skipped atom 938, because occupancy 0.34 <= existing 0.660001 Skipped atom 940, because occupancy 0.34 <= existing 0.660001 Skipped atom 942, because occupancy 0.34 <= existing 0.660001 Skipped atom 998, because occupancy 0.46 <= existing 0.540001 Skipped atom 1000, because occupancy 0.46 <= existing 0.540001 Skipped atom 1002, because occupancy 0.46 <= existing 0.540001 Skipped atom 1004, because occupancy 0.46 <= existing 0.540001 Skipped atom 1006, because occupancy 0.46 <= existing 0.540001 Skipped atom 1008, because occupancy 0.46 <= existing 0.540001 Skipped atom 1014, because occupancy 0.44 <= existing 0.560001 Skipped atom 1016, because occupancy 0.44 <= existing 0.560001 Skipped atom 1089, because occupancy 0.34 <= existing 0.660001 Skipped atom 1091, because occupancy 0.34 <= existing 0.660001 Skipped atom 1093, because occupancy 0.34 <= existing 0.660001 Skipped atom 1095, because occupancy 0.34 <= existing 0.660001 Skipped atom 1106, because occupancy 0.44 <= existing 0.560001 Skipped atom 1108, because occupancy 0.44 <= existing 0.560001 Skipped atom 1110, because occupancy 0.44 <= existing 0.560001 Skipped atom 1112, because occupancy 0.44 <= existing 0.560001 Skipped atom 1114, because occupancy 0.44 <= existing 0.560001 Skipped atom 1145, because occupancy 0.45 <= existing 0.550001 Skipped atom 1147, because occupancy 0.45 <= existing 0.550001 Skipped atom 1149, because occupancy 0.45 <= existing 0.550001 Skipped atom 1151, because occupancy 0.45 <= existing 0.550001 Skipped atom 1153, because occupancy 0.45 <= existing 0.550001 Skipped atom 1172, because occupancy 0.43 <= existing 0.570001 Skipped atom 1174, because occupancy 0.43 <= existing 0.570001 Skipped atom 1176, because occupancy 0.43 <= existing 0.570001 Skipped atom 1178, because occupancy 0.43 <= existing 0.570001 Skipped atom 1180, because occupancy 0.43 <= existing 0.570001 Skipped atom 1240, because occupancy 0.33 <= existing 0.670001 Skipped atom 1242, because occupancy 0.33 <= existing 0.670001 Skipped atom 1244, because occupancy 0.33 <= existing 0.670001 Skipped atom 1246, because occupancy 0.33 <= existing 0.670001 Skipped atom 1321, because occupancy 0.5 <= existing 0.500001 Skipped atom 1323, because occupancy 0.5 <= existing 0.500001 Skipped atom 1325, because occupancy 0.5 <= existing 0.500001 Skipped atom 1327, because occupancy 0.5 <= existing 0.500001 Skipped atom 1329, because occupancy 0.5 <= existing 0.500001 Skipped atom 1331, because occupancy 0.5 <= existing 0.500001 Skipped atom 1333, because occupancy 0.5 <= existing 0.500001 Skipped atom 1335, because occupancy 0.5 <= existing 0.500001 partial PDB gets fragment 128 through 137 extending start extending end Debugging on ! Reading sequence file Reading input structure 12 residues read Measuring phi and psi Getting chi values SER 2 3 ILE 3 3 THR 4 2 SER 5 3 ILE 6 3 ILE 7 5 HIS 8 4 GLU 9 12 ILE 10 3 Building many copies of each residue Checking backbone and frame clashes Finding the lowest Also, print out the first version, pre-bump Finding disulfide bonds. Found 0 disulfide bonds. Residue clashes: 0 clashing residues after turn Residue clashes: Still clashes at these sidechain pairs: Residual clashes = 0.00000 Printing mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a6m.93.5.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a6m.93.5.a2m \ -target T0098 -template 1a6m \ -out T0098-1a6m.93.5 -outdir und2 Skipped atom 27, because occupancy 0.43 <= existing 0.570001 Skipped atom 29, because occupancy 0.43 <= existing 0.570001 Skipped atom 31, because occupancy 0.43 <= existing 0.570001 Skipped atom 33, because occupancy 0.43 <= existing 0.570001 Skipped atom 35, because occupancy 0.43 <= existing 0.570001 Skipped atom 68, because occupancy 0.43 <= existing 0.570001 Skipped atom 70, because occupancy 0.43 <= existing 0.570001 Skipped atom 72, because occupancy 0.43 <= existing 0.570001 Skipped atom 74, because occupancy 0.43 <= existing 0.570001 Skipped atom 76, because occupancy 0.43 <= existing 0.570001 Skipped atom 209, because occupancy 0.35 <= existing 0.650001 Skipped atom 211, because occupancy 0.35 <= existing 0.650001 Skipped atom 213, because occupancy 0.35 <= existing 0.650001 Skipped atom 215, because occupancy 0.35 <= existing 0.650001 Skipped atom 217, because occupancy 0.35 <= existing 0.650001 Skipped atom 348, because occupancy 0.49 <= existing 0.510001 Skipped atom 350, because occupancy 0.49 <= existing 0.510001 Skipped atom 352, because occupancy 0.49 <= existing 0.510001 Skipped atom 354, because occupancy 0.49 <= existing 0.510001 Skipped atom 356, because occupancy 0.49 <= existing 0.510001 Skipped atom 412, because occupancy 0.32 <= existing 0.680001 Skipped atom 414, because occupancy 0.32 <= existing 0.680001 Skipped atom 416, because occupancy 0.32 <= existing 0.680001 Skipped atom 418, because occupancy 0.32 <= existing 0.680001 Skipped atom 420, because occupancy 0.32 <= existing 0.680001 Skipped atom 533, because occupancy 0.34 <= existing 0.660001 Skipped atom 535, because occupancy 0.34 <= existing 0.660001 Skipped atom 537, because occupancy 0.34 <= existing 0.660001 Skipped atom 539, because occupancy 0.34 <= existing 0.660001 Skipped atom 554, because occupancy 0.41 <= existing 0.590001 Skipped atom 556, because occupancy 0.41 <= existing 0.590001 Skipped atom 558, because occupancy 0.41 <= existing 0.590001 Skipped atom 560, because occupancy 0.41 <= existing 0.590001 Skipped atom 562, because occupancy 0.41 <= existing 0.590001 Skipped atom 568, because occupancy 0.5 <= existing 0.500001 Skipped atom 570, because occupancy 0.5 <= existing 0.500001 Skipped atom 572, because occupancy 0.5 <= existing 0.500001 Skipped atom 574, because occupancy 0.5 <= existing 0.500001 Skipped atom 576, because occupancy 0.5 <= existing 0.500001 Skipped atom 578, because occupancy 0.5 <= existing 0.500001 Skipped atom 773, because occupancy 0.47 <= existing 0.530001 Skipped atom 775, because occupancy 0.47 <= existing 0.530001 Skipped atom 777, because occupancy 0.47 <= existing 0.530001 Skipped atom 779, because occupancy 0.47 <= existing 0.530001 Skipped atom 781, because occupancy 0.47 <= existing 0.530001 Skipped atom 815, because occupancy 0.45 <= existing 0.550001 Skipped atom 817, because occupancy 0.45 <= existing 0.550001 Skipped atom 819, because occupancy 0.45 <= existing 0.550001 Skipped atom 821, because occupancy 0.45 <= existing 0.550001 Skipped atom 823, because occupancy 0.45 <= existing 0.550001 Skipped atom 934, because occupancy 0.34 <= existing 0.660001 Skipped atom 936, because occupancy 0.34 <= existing 0.660001 Skipped atom 938, because occupancy 0.34 <= existing 0.660001 Skipped atom 940, because occupancy 0.34 <= existing 0.660001 Skipped atom 942, because occupancy 0.34 <= existing 0.660001 Skipped atom 998, because occupancy 0.46 <= existing 0.540001 Skipped atom 1000, because occupancy 0.46 <= existing 0.540001 Skipped atom 1002, because occupancy 0.46 <= existing 0.540001 Skipped atom 1004, because occupancy 0.46 <= existing 0.540001 Skipped atom 1006, because occupancy 0.46 <= existing 0.540001 Skipped atom 1008, because occupancy 0.46 <= existing 0.540001 Skipped atom 1014, because occupancy 0.44 <= existing 0.560001 Skipped atom 1016, because occupancy 0.44 <= existing 0.560001 Skipped atom 1089, because occupancy 0.34 <= existing 0.660001 Skipped atom 1091, because occupancy 0.34 <= existing 0.660001 Skipped atom 1093, because occupancy 0.34 <= existing 0.660001 Skipped atom 1095, because occupancy 0.34 <= existing 0.660001 Skipped atom 1106, because occupancy 0.44 <= existing 0.560001 Skipped atom 1108, because occupancy 0.44 <= existing 0.560001 Skipped atom 1110, because occupancy 0.44 <= existing 0.560001 Skipped atom 1112, because occupancy 0.44 <= existing 0.560001 Skipped atom 1114, because occupancy 0.44 <= existing 0.560001 Skipped atom 1145, because occupancy 0.45 <= existing 0.550001 Skipped atom 1147, because occupancy 0.45 <= existing 0.550001 Skipped atom 1149, because occupancy 0.45 <= existing 0.550001 Skipped atom 1151, because occupancy 0.45 <= existing 0.550001 Skipped atom 1153, because occupancy 0.45 <= existing 0.550001 Skipped atom 1172, because occupancy 0.43 <= existing 0.570001 Skipped atom 1174, because occupancy 0.43 <= existing 0.570001 Skipped atom 1176, because occupancy 0.43 <= existing 0.570001 Skipped atom 1178, because occupancy 0.43 <= existing 0.570001 Skipped atom 1180, because occupancy 0.43 <= existing 0.570001 Skipped atom 1240, because occupancy 0.33 <= existing 0.670001 Skipped atom 1242, because occupancy 0.33 <= existing 0.670001 Skipped atom 1244, because occupancy 0.33 <= existing 0.670001 Skipped atom 1246, because occupancy 0.33 <= existing 0.670001 Skipped atom 1321, because occupancy 0.5 <= existing 0.500001 Skipped atom 1323, because occupancy 0.5 <= existing 0.500001 Skipped atom 1325, because occupancy 0.5 <= existing 0.500001 Skipped atom 1327, because occupancy 0.5 <= existing 0.500001 Skipped atom 1329, because occupancy 0.5 <= existing 0.500001 Skipped atom 1331, because occupancy 0.5 <= existing 0.500001 Skipped atom 1333, because occupancy 0.5 <= existing 0.500001 Skipped atom 1335, because occupancy 0.5 <= existing 0.500001 partial PDB gets fragment 22 through 31 extending start extending end Debugging on ! Reading sequence file Reading input structure 12 residues read Measuring phi and psi Getting chi values VAL 1 2 SER 2 3 VAL 3 1 SER 4 3 LYS 5 26 LYS 7 26 PRO 8 2 THR 9 1 ASN 10 4 Building many copies of each residue Checking backbone and frame clashes Finding the lowest Also, print out the first version, pre-bump All 2 rotamers of residue P 9 conflict with the backbone. This may be a problem with the backbone,or a subtle problem with the rotamers. Please be aware of this, and examine it. Finding disulfide bonds. Found 0 disulfide bonds. Residue clashes: 0 clashing residues after turn Residue clashes: Still clashes at these sidechain pairs: Residual clashes = 0.00000 Printing mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a6m.94.3.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a6m.94.3.a2m \ -target T0098 -template 1a6m \ -out T0098-1a6m.94.3 -outdir und2 Skipped atom 27, because occupancy 0.43 <= existing 0.570001 Skipped atom 29, because occupancy 0.43 <= existing 0.570001 Skipped atom 31, because occupancy 0.43 <= existing 0.570001 Skipped atom 33, because occupancy 0.43 <= existing 0.570001 Skipped atom 35, because occupancy 0.43 <= existing 0.570001 Skipped atom 68, because occupancy 0.43 <= existing 0.570001 Skipped atom 70, because occupancy 0.43 <= existing 0.570001 Skipped atom 72, because occupancy 0.43 <= existing 0.570001 Skipped atom 74, because occupancy 0.43 <= existing 0.570001 Skipped atom 76, because occupancy 0.43 <= existing 0.570001 Skipped atom 209, because occupancy 0.35 <= existing 0.650001 Skipped atom 211, because occupancy 0.35 <= existing 0.650001 Skipped atom 213, because occupancy 0.35 <= existing 0.650001 Skipped atom 215, because occupancy 0.35 <= existing 0.650001 Skipped atom 217, because occupancy 0.35 <= existing 0.650001 Skipped atom 348, because occupancy 0.49 <= existing 0.510001 Skipped atom 350, because occupancy 0.49 <= existing 0.510001 Skipped atom 352, because occupancy 0.49 <= existing 0.510001 Skipped atom 354, because occupancy 0.49 <= existing 0.510001 Skipped atom 356, because occupancy 0.49 <= existing 0.510001 Skipped atom 412, because occupancy 0.32 <= existing 0.680001 Skipped atom 414, because occupancy 0.32 <= existing 0.680001 Skipped atom 416, because occupancy 0.32 <= existing 0.680001 Skipped atom 418, because occupancy 0.32 <= existing 0.680001 Skipped atom 420, because occupancy 0.32 <= existing 0.680001 Skipped atom 533, because occupancy 0.34 <= existing 0.660001 Skipped atom 535, because occupancy 0.34 <= existing 0.660001 Skipped atom 537, because occupancy 0.34 <= existing 0.660001 Skipped atom 539, because occupancy 0.34 <= existing 0.660001 Skipped atom 554, because occupancy 0.41 <= existing 0.590001 Skipped atom 556, because occupancy 0.41 <= existing 0.590001 Skipped atom 558, because occupancy 0.41 <= existing 0.590001 Skipped atom 560, because occupancy 0.41 <= existing 0.590001 Skipped atom 562, because occupancy 0.41 <= existing 0.590001 Skipped atom 568, because occupancy 0.5 <= existing 0.500001 Skipped atom 570, because occupancy 0.5 <= existing 0.500001 Skipped atom 572, because occupancy 0.5 <= existing 0.500001 Skipped atom 574, because occupancy 0.5 <= existing 0.500001 Skipped atom 576, because occupancy 0.5 <= existing 0.500001 Skipped atom 578, because occupancy 0.5 <= existing 0.500001 Skipped atom 773, because occupancy 0.47 <= existing 0.530001 Skipped atom 775, because occupancy 0.47 <= existing 0.530001 Skipped atom 777, because occupancy 0.47 <= existing 0.530001 Skipped atom 779, because occupancy 0.47 <= existing 0.530001 Skipped atom 781, because occupancy 0.47 <= existing 0.530001 Skipped atom 815, because occupancy 0.45 <= existing 0.550001 Skipped atom 817, because occupancy 0.45 <= existing 0.550001 Skipped atom 819, because occupancy 0.45 <= existing 0.550001 Skipped atom 821, because occupancy 0.45 <= existing 0.550001 Skipped atom 823, because occupancy 0.45 <= existing 0.550001 Skipped atom 934, because occupancy 0.34 <= existing 0.660001 Skipped atom 936, because occupancy 0.34 <= existing 0.660001 Skipped atom 938, because occupancy 0.34 <= existing 0.660001 Skipped atom 940, because occupancy 0.34 <= existing 0.660001 Skipped atom 942, because occupancy 0.34 <= existing 0.660001 Skipped atom 998, because occupancy 0.46 <= existing 0.540001 Skipped atom 1000, because occupancy 0.46 <= existing 0.540001 Skipped atom 1002, because occupancy 0.46 <= existing 0.540001 Skipped atom 1004, because occupancy 0.46 <= existing 0.540001 Skipped atom 1006, because occupancy 0.46 <= existing 0.540001 Skipped atom 1008, because occupancy 0.46 <= existing 0.540001 Skipped atom 1014, because occupancy 0.44 <= existing 0.560001 Skipped atom 1016, because occupancy 0.44 <= existing 0.560001 Skipped atom 1089, because occupancy 0.34 <= existing 0.660001 Skipped atom 1091, because occupancy 0.34 <= existing 0.660001 Skipped atom 1093, because occupancy 0.34 <= existing 0.660001 Skipped atom 1095, because occupancy 0.34 <= existing 0.660001 Skipped atom 1106, because occupancy 0.44 <= existing 0.560001 Skipped atom 1108, because occupancy 0.44 <= existing 0.560001 Skipped atom 1110, because occupancy 0.44 <= existing 0.560001 Skipped atom 1112, because occupancy 0.44 <= existing 0.560001 Skipped atom 1114, because occupancy 0.44 <= existing 0.560001 Skipped atom 1145, because occupancy 0.45 <= existing 0.550001 Skipped atom 1147, because occupancy 0.45 <= existing 0.550001 Skipped atom 1149, because occupancy 0.45 <= existing 0.550001 Skipped atom 1151, because occupancy 0.45 <= existing 0.550001 Skipped atom 1153, because occupancy 0.45 <= existing 0.550001 Skipped atom 1172, because occupancy 0.43 <= existing 0.570001 Skipped atom 1174, because occupancy 0.43 <= existing 0.570001 Skipped atom 1176, because occupancy 0.43 <= existing 0.570001 Skipped atom 1178, because occupancy 0.43 <= existing 0.570001 Skipped atom 1180, because occupancy 0.43 <= existing 0.570001 Skipped atom 1240, because occupancy 0.33 <= existing 0.670001 Skipped atom 1242, because occupancy 0.33 <= existing 0.670001 Skipped atom 1244, because occupancy 0.33 <= existing 0.670001 Skipped atom 1246, because occupancy 0.33 <= existing 0.670001 Skipped atom 1321, because occupancy 0.5 <= existing 0.500001 Skipped atom 1323, because occupancy 0.5 <= existing 0.500001 Skipped atom 1325, because occupancy 0.5 <= existing 0.500001 Skipped atom 1327, because occupancy 0.5 <= existing 0.500001 Skipped atom 1329, because occupancy 0.5 <= existing 0.500001 Skipped atom 1331, because occupancy 0.5 <= existing 0.500001 Skipped atom 1333, because occupancy 0.5 <= existing 0.500001 Skipped atom 1335, because occupancy 0.5 <= existing 0.500001 partial PDB gets fragment 21 through 30 extending start extending end Debugging on ! Reading sequence file Reading input structure 12 residues read Measuring phi and psi Getting chi values SER 1 3 VAL 2 2 SER 3 3 LYS 4 26 LYS 6 26 PRO 7 2 THR 8 2 ASN 9 4 SER 10 3 Building many copies of each residue Checking backbone and frame clashes Finding the lowest Also, print out the first version, pre-bump All 2 rotamers of residue P 8 conflict with the backbone. This may be a problem with the backbone,or a subtle problem with the rotamers. Please be aware of this, and examine it. Finding disulfide bonds. Found 0 disulfide bonds. Residue clashes: 0 clashing residues after turn Residue clashes: Still clashes at these sidechain pairs: Residual clashes = 0.00000 Printing mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a6m.95.3.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a6m.95.3.a2m \ -target T0098 -template 1a6m \ -out T0098-1a6m.95.3 -outdir und2 Skipped atom 27, because occupancy 0.43 <= existing 0.570001 Skipped atom 29, because occupancy 0.43 <= existing 0.570001 Skipped atom 31, because occupancy 0.43 <= existing 0.570001 Skipped atom 33, because occupancy 0.43 <= existing 0.570001 Skipped atom 35, because occupancy 0.43 <= existing 0.570001 Skipped atom 68, because occupancy 0.43 <= existing 0.570001 Skipped atom 70, because occupancy 0.43 <= existing 0.570001 Skipped atom 72, because occupancy 0.43 <= existing 0.570001 Skipped atom 74, because occupancy 0.43 <= existing 0.570001 Skipped atom 76, because occupancy 0.43 <= existing 0.570001 Skipped atom 209, because occupancy 0.35 <= existing 0.650001 Skipped atom 211, because occupancy 0.35 <= existing 0.650001 Skipped atom 213, because occupancy 0.35 <= existing 0.650001 Skipped atom 215, because occupancy 0.35 <= existing 0.650001 Skipped atom 217, because occupancy 0.35 <= existing 0.650001 Skipped atom 348, because occupancy 0.49 <= existing 0.510001 Skipped atom 350, because occupancy 0.49 <= existing 0.510001 Skipped atom 352, because occupancy 0.49 <= existing 0.510001 Skipped atom 354, because occupancy 0.49 <= existing 0.510001 Skipped atom 356, because occupancy 0.49 <= existing 0.510001 Skipped atom 412, because occupancy 0.32 <= existing 0.680001 Skipped atom 414, because occupancy 0.32 <= existing 0.680001 Skipped atom 416, because occupancy 0.32 <= existing 0.680001 Skipped atom 418, because occupancy 0.32 <= existing 0.680001 Skipped atom 420, because occupancy 0.32 <= existing 0.680001 Skipped atom 533, because occupancy 0.34 <= existing 0.660001 Skipped atom 535, because occupancy 0.34 <= existing 0.660001 Skipped atom 537, because occupancy 0.34 <= existing 0.660001 Skipped atom 539, because occupancy 0.34 <= existing 0.660001 Skipped atom 554, because occupancy 0.41 <= existing 0.590001 Skipped atom 556, because occupancy 0.41 <= existing 0.590001 Skipped atom 558, because occupancy 0.41 <= existing 0.590001 Skipped atom 560, because occupancy 0.41 <= existing 0.590001 Skipped atom 562, because occupancy 0.41 <= existing 0.590001 Skipped atom 568, because occupancy 0.5 <= existing 0.500001 Skipped atom 570, because occupancy 0.5 <= existing 0.500001 Skipped atom 572, because occupancy 0.5 <= existing 0.500001 Skipped atom 574, because occupancy 0.5 <= existing 0.500001 Skipped atom 576, because occupancy 0.5 <= existing 0.500001 Skipped atom 578, because occupancy 0.5 <= existing 0.500001 Skipped atom 773, because occupancy 0.47 <= existing 0.530001 Skipped atom 775, because occupancy 0.47 <= existing 0.530001 Skipped atom 777, because occupancy 0.47 <= existing 0.530001 Skipped atom 779, because occupancy 0.47 <= existing 0.530001 Skipped atom 781, because occupancy 0.47 <= existing 0.530001 Skipped atom 815, because occupancy 0.45 <= existing 0.550001 Skipped atom 817, because occupancy 0.45 <= existing 0.550001 Skipped atom 819, because occupancy 0.45 <= existing 0.550001 Skipped atom 821, because occupancy 0.45 <= existing 0.550001 Skipped atom 823, because occupancy 0.45 <= existing 0.550001 Skipped atom 934, because occupancy 0.34 <= existing 0.660001 Skipped atom 936, because occupancy 0.34 <= existing 0.660001 Skipped atom 938, because occupancy 0.34 <= existing 0.660001 Skipped atom 940, because occupancy 0.34 <= existing 0.660001 Skipped atom 942, because occupancy 0.34 <= existing 0.660001 Skipped atom 998, because occupancy 0.46 <= existing 0.540001 Skipped atom 1000, because occupancy 0.46 <= existing 0.540001 Skipped atom 1002, because occupancy 0.46 <= existing 0.540001 Skipped atom 1004, because occupancy 0.46 <= existing 0.540001 Skipped atom 1006, because occupancy 0.46 <= existing 0.540001 Skipped atom 1008, because occupancy 0.46 <= existing 0.540001 Skipped atom 1014, because occupancy 0.44 <= existing 0.560001 Skipped atom 1016, because occupancy 0.44 <= existing 0.560001 Skipped atom 1089, because occupancy 0.34 <= existing 0.660001 Skipped atom 1091, because occupancy 0.34 <= existing 0.660001 Skipped atom 1093, because occupancy 0.34 <= existing 0.660001 Skipped atom 1095, because occupancy 0.34 <= existing 0.660001 Skipped atom 1106, because occupancy 0.44 <= existing 0.560001 Skipped atom 1108, because occupancy 0.44 <= existing 0.560001 Skipped atom 1110, because occupancy 0.44 <= existing 0.560001 Skipped atom 1112, because occupancy 0.44 <= existing 0.560001 Skipped atom 1114, because occupancy 0.44 <= existing 0.560001 Skipped atom 1145, because occupancy 0.45 <= existing 0.550001 Skipped atom 1147, because occupancy 0.45 <= existing 0.550001 Skipped atom 1149, because occupancy 0.45 <= existing 0.550001 Skipped atom 1151, because occupancy 0.45 <= existing 0.550001 Skipped atom 1153, because occupancy 0.45 <= existing 0.550001 Skipped atom 1172, because occupancy 0.43 <= existing 0.570001 Skipped atom 1174, because occupancy 0.43 <= existing 0.570001 Skipped atom 1176, because occupancy 0.43 <= existing 0.570001 Skipped atom 1178, because occupancy 0.43 <= existing 0.570001 Skipped atom 1180, because occupancy 0.43 <= existing 0.570001 Skipped atom 1240, because occupancy 0.33 <= existing 0.670001 Skipped atom 1242, because occupancy 0.33 <= existing 0.670001 Skipped atom 1244, because occupancy 0.33 <= existing 0.670001 Skipped atom 1246, because occupancy 0.33 <= existing 0.670001 Skipped atom 1321, because occupancy 0.5 <= existing 0.500001 Skipped atom 1323, because occupancy 0.5 <= existing 0.500001 Skipped atom 1325, because occupancy 0.5 <= existing 0.500001 Skipped atom 1327, because occupancy 0.5 <= existing 0.500001 Skipped atom 1329, because occupancy 0.5 <= existing 0.500001 Skipped atom 1331, because occupancy 0.5 <= existing 0.500001 Skipped atom 1333, because occupancy 0.5 <= existing 0.500001 Skipped atom 1335, because occupancy 0.5 <= existing 0.500001 partial PDB gets fragment 20 through 29 extending start extending end Debugging on ! Reading sequence file Reading input structure 12 residues read Measuring phi and psi Getting chi values SER 2 3 LYS 3 26 LYS 5 26 PRO 6 2 THR 7 2 ASN 8 4 SER 9 3 GLU 10 12 Building many copies of each residue Checking backbone and frame clashes Finding the lowest Also, print out the first version, pre-bump All 2 rotamers of residue P 7 conflict with the backbone. This may be a problem with the backbone,or a subtle problem with the rotamers. Please be aware of this, and examine it. Finding disulfide bonds. Found 0 disulfide bonds. Residue clashes: 0 clashing residues after turn Residue clashes: Still clashes at these sidechain pairs: Residual clashes = 0.00000 Printing mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a6m.96.2.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a6m.96.2.a2m \ -target T0098 -template 1a6m \ -out T0098-1a6m.96.2 -outdir und2 Skipped atom 27, because occupancy 0.43 <= existing 0.570001 Skipped atom 29, because occupancy 0.43 <= existing 0.570001 Skipped atom 31, because occupancy 0.43 <= existing 0.570001 Skipped atom 33, because occupancy 0.43 <= existing 0.570001 Skipped atom 35, because occupancy 0.43 <= existing 0.570001 Skipped atom 68, because occupancy 0.43 <= existing 0.570001 Skipped atom 70, because occupancy 0.43 <= existing 0.570001 Skipped atom 72, because occupancy 0.43 <= existing 0.570001 Skipped atom 74, because occupancy 0.43 <= existing 0.570001 Skipped atom 76, because occupancy 0.43 <= existing 0.570001 Skipped atom 209, because occupancy 0.35 <= existing 0.650001 Skipped atom 211, because occupancy 0.35 <= existing 0.650001 Skipped atom 213, because occupancy 0.35 <= existing 0.650001 Skipped atom 215, because occupancy 0.35 <= existing 0.650001 Skipped atom 217, because occupancy 0.35 <= existing 0.650001 Skipped atom 348, because occupancy 0.49 <= existing 0.510001 Skipped atom 350, because occupancy 0.49 <= existing 0.510001 Skipped atom 352, because occupancy 0.49 <= existing 0.510001 Skipped atom 354, because occupancy 0.49 <= existing 0.510001 Skipped atom 356, because occupancy 0.49 <= existing 0.510001 Skipped atom 412, because occupancy 0.32 <= existing 0.680001 Skipped atom 414, because occupancy 0.32 <= existing 0.680001 Skipped atom 416, because occupancy 0.32 <= existing 0.680001 Skipped atom 418, because occupancy 0.32 <= existing 0.680001 Skipped atom 420, because occupancy 0.32 <= existing 0.680001 Skipped atom 533, because occupancy 0.34 <= existing 0.660001 Skipped atom 535, because occupancy 0.34 <= existing 0.660001 Skipped atom 537, because occupancy 0.34 <= existing 0.660001 Skipped atom 539, because occupancy 0.34 <= existing 0.660001 Skipped atom 554, because occupancy 0.41 <= existing 0.590001 Skipped atom 556, because occupancy 0.41 <= existing 0.590001 Skipped atom 558, because occupancy 0.41 <= existing 0.590001 Skipped atom 560, because occupancy 0.41 <= existing 0.590001 Skipped atom 562, because occupancy 0.41 <= existing 0.590001 Skipped atom 568, because occupancy 0.5 <= existing 0.500001 Skipped atom 570, because occupancy 0.5 <= existing 0.500001 Skipped atom 572, because occupancy 0.5 <= existing 0.500001 Skipped atom 574, because occupancy 0.5 <= existing 0.500001 Skipped atom 576, because occupancy 0.5 <= existing 0.500001 Skipped atom 578, because occupancy 0.5 <= existing 0.500001 Skipped atom 773, because occupancy 0.47 <= existing 0.530001 Skipped atom 775, because occupancy 0.47 <= existing 0.530001 Skipped atom 777, because occupancy 0.47 <= existing 0.530001 Skipped atom 779, because occupancy 0.47 <= existing 0.530001 Skipped atom 781, because occupancy 0.47 <= existing 0.530001 Skipped atom 815, because occupancy 0.45 <= existing 0.550001 Skipped atom 817, because occupancy 0.45 <= existing 0.550001 Skipped atom 819, because occupancy 0.45 <= existing 0.550001 Skipped atom 821, because occupancy 0.45 <= existing 0.550001 Skipped atom 823, because occupancy 0.45 <= existing 0.550001 Skipped atom 934, because occupancy 0.34 <= existing 0.660001 Skipped atom 936, because occupancy 0.34 <= existing 0.660001 Skipped atom 938, because occupancy 0.34 <= existing 0.660001 Skipped atom 940, because occupancy 0.34 <= existing 0.660001 Skipped atom 942, because occupancy 0.34 <= existing 0.660001 Skipped atom 998, because occupancy 0.46 <= existing 0.540001 Skipped atom 1000, because occupancy 0.46 <= existing 0.540001 Skipped atom 1002, because occupancy 0.46 <= existing 0.540001 Skipped atom 1004, because occupancy 0.46 <= existing 0.540001 Skipped atom 1006, because occupancy 0.46 <= existing 0.540001 Skipped atom 1008, because occupancy 0.46 <= existing 0.540001 Skipped atom 1014, because occupancy 0.44 <= existing 0.560001 Skipped atom 1016, because occupancy 0.44 <= existing 0.560001 Skipped atom 1089, because occupancy 0.34 <= existing 0.660001 Skipped atom 1091, because occupancy 0.34 <= existing 0.660001 Skipped atom 1093, because occupancy 0.34 <= existing 0.660001 Skipped atom 1095, because occupancy 0.34 <= existing 0.660001 Skipped atom 1106, because occupancy 0.44 <= existing 0.560001 Skipped atom 1108, because occupancy 0.44 <= existing 0.560001 Skipped atom 1110, because occupancy 0.44 <= existing 0.560001 Skipped atom 1112, because occupancy 0.44 <= existing 0.560001 Skipped atom 1114, because occupancy 0.44 <= existing 0.560001 Skipped atom 1145, because occupancy 0.45 <= existing 0.550001 Skipped atom 1147, because occupancy 0.45 <= existing 0.550001 Skipped atom 1149, because occupancy 0.45 <= existing 0.550001 Skipped atom 1151, because occupancy 0.45 <= existing 0.550001 Skipped atom 1153, because occupancy 0.45 <= existing 0.550001 Skipped atom 1172, because occupancy 0.43 <= existing 0.570001 Skipped atom 1174, because occupancy 0.43 <= existing 0.570001 Skipped atom 1176, because occupancy 0.43 <= existing 0.570001 Skipped atom 1178, because occupancy 0.43 <= existing 0.570001 Skipped atom 1180, because occupancy 0.43 <= existing 0.570001 Skipped atom 1240, because occupancy 0.33 <= existing 0.670001 Skipped atom 1242, because occupancy 0.33 <= existing 0.670001 Skipped atom 1244, because occupancy 0.33 <= existing 0.670001 Skipped atom 1246, because occupancy 0.33 <= existing 0.670001 Skipped atom 1321, because occupancy 0.5 <= existing 0.500001 Skipped atom 1323, because occupancy 0.5 <= existing 0.500001 Skipped atom 1325, because occupancy 0.5 <= existing 0.500001 Skipped atom 1327, because occupancy 0.5 <= existing 0.500001 Skipped atom 1329, because occupancy 0.5 <= existing 0.500001 Skipped atom 1331, because occupancy 0.5 <= existing 0.500001 Skipped atom 1333, because occupancy 0.5 <= existing 0.500001 Skipped atom 1335, because occupancy 0.5 <= existing 0.500001 partial PDB gets fragment 19 through 28 extending start extending end Debugging on ! Reading sequence file Reading input structure 12 residues read Measuring phi and psi Getting chi values SER 1 3 LYS 2 24 LYS 4 29 PRO 5 2 THR 6 2 ASN 7 4 SER 8 3 GLU 9 12 PHE 10 3 Building many copies of each residue Checking backbone and frame clashes Finding the lowest Also, print out the first version, pre-bump All 2 rotamers of residue P 6 conflict with the backbone. This may be a problem with the backbone,or a subtle problem with the rotamers. Please be aware of this, and examine it. Finding disulfide bonds. Found 0 disulfide bonds. Residue clashes: 0 clashing residues after turn Residue clashes: Still clashes at these sidechain pairs: Residual clashes = 0.00000 Printing mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a6m.97.2.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a6m.97.2.a2m \ -target T0098 -template 1a6m \ -out T0098-1a6m.97.2 -outdir und2 Skipped atom 27, because occupancy 0.43 <= existing 0.570001 Skipped atom 29, because occupancy 0.43 <= existing 0.570001 Skipped atom 31, because occupancy 0.43 <= existing 0.570001 Skipped atom 33, because occupancy 0.43 <= existing 0.570001 Skipped atom 35, because occupancy 0.43 <= existing 0.570001 Skipped atom 68, because occupancy 0.43 <= existing 0.570001 Skipped atom 70, because occupancy 0.43 <= existing 0.570001 Skipped atom 72, because occupancy 0.43 <= existing 0.570001 Skipped atom 74, because occupancy 0.43 <= existing 0.570001 Skipped atom 76, because occupancy 0.43 <= existing 0.570001 Skipped atom 209, because occupancy 0.35 <= existing 0.650001 Skipped atom 211, because occupancy 0.35 <= existing 0.650001 Skipped atom 213, because occupancy 0.35 <= existing 0.650001 Skipped atom 215, because occupancy 0.35 <= existing 0.650001 Skipped atom 217, because occupancy 0.35 <= existing 0.650001 Skipped atom 348, because occupancy 0.49 <= existing 0.510001 Skipped atom 350, because occupancy 0.49 <= existing 0.510001 Skipped atom 352, because occupancy 0.49 <= existing 0.510001 Skipped atom 354, because occupancy 0.49 <= existing 0.510001 Skipped atom 356, because occupancy 0.49 <= existing 0.510001 Skipped atom 412, because occupancy 0.32 <= existing 0.680001 Skipped atom 414, because occupancy 0.32 <= existing 0.680001 Skipped atom 416, because occupancy 0.32 <= existing 0.680001 Skipped atom 418, because occupancy 0.32 <= existing 0.680001 Skipped atom 420, because occupancy 0.32 <= existing 0.680001 Skipped atom 533, because occupancy 0.34 <= existing 0.660001 Skipped atom 535, because occupancy 0.34 <= existing 0.660001 Skipped atom 537, because occupancy 0.34 <= existing 0.660001 Skipped atom 539, because occupancy 0.34 <= existing 0.660001 Skipped atom 554, because occupancy 0.41 <= existing 0.590001 Skipped atom 556, because occupancy 0.41 <= existing 0.590001 Skipped atom 558, because occupancy 0.41 <= existing 0.590001 Skipped atom 560, because occupancy 0.41 <= existing 0.590001 Skipped atom 562, because occupancy 0.41 <= existing 0.590001 Skipped atom 568, because occupancy 0.5 <= existing 0.500001 Skipped atom 570, because occupancy 0.5 <= existing 0.500001 Skipped atom 572, because occupancy 0.5 <= existing 0.500001 Skipped atom 574, because occupancy 0.5 <= existing 0.500001 Skipped atom 576, because occupancy 0.5 <= existing 0.500001 Skipped atom 578, because occupancy 0.5 <= existing 0.500001 Skipped atom 773, because occupancy 0.47 <= existing 0.530001 Skipped atom 775, because occupancy 0.47 <= existing 0.530001 Skipped atom 777, because occupancy 0.47 <= existing 0.530001 Skipped atom 779, because occupancy 0.47 <= existing 0.530001 Skipped atom 781, because occupancy 0.47 <= existing 0.530001 Skipped atom 815, because occupancy 0.45 <= existing 0.550001 Skipped atom 817, because occupancy 0.45 <= existing 0.550001 Skipped atom 819, because occupancy 0.45 <= existing 0.550001 Skipped atom 821, because occupancy 0.45 <= existing 0.550001 Skipped atom 823, because occupancy 0.45 <= existing 0.550001 Skipped atom 934, because occupancy 0.34 <= existing 0.660001 Skipped atom 936, because occupancy 0.34 <= existing 0.660001 Skipped atom 938, because occupancy 0.34 <= existing 0.660001 Skipped atom 940, because occupancy 0.34 <= existing 0.660001 Skipped atom 942, because occupancy 0.34 <= existing 0.660001 Skipped atom 998, because occupancy 0.46 <= existing 0.540001 Skipped atom 1000, because occupancy 0.46 <= existing 0.540001 Skipped atom 1002, because occupancy 0.46 <= existing 0.540001 Skipped atom 1004, because occupancy 0.46 <= existing 0.540001 Skipped atom 1006, because occupancy 0.46 <= existing 0.540001 Skipped atom 1008, because occupancy 0.46 <= existing 0.540001 Skipped atom 1014, because occupancy 0.44 <= existing 0.560001 Skipped atom 1016, because occupancy 0.44 <= existing 0.560001 Skipped atom 1089, because occupancy 0.34 <= existing 0.660001 Skipped atom 1091, because occupancy 0.34 <= existing 0.660001 Skipped atom 1093, because occupancy 0.34 <= existing 0.660001 Skipped atom 1095, because occupancy 0.34 <= existing 0.660001 Skipped atom 1106, because occupancy 0.44 <= existing 0.560001 Skipped atom 1108, because occupancy 0.44 <= existing 0.560001 Skipped atom 1110, because occupancy 0.44 <= existing 0.560001 Skipped atom 1112, because occupancy 0.44 <= existing 0.560001 Skipped atom 1114, because occupancy 0.44 <= existing 0.560001 Skipped atom 1145, because occupancy 0.45 <= existing 0.550001 Skipped atom 1147, because occupancy 0.45 <= existing 0.550001 Skipped atom 1149, because occupancy 0.45 <= existing 0.550001 Skipped atom 1151, because occupancy 0.45 <= existing 0.550001 Skipped atom 1153, because occupancy 0.45 <= existing 0.550001 Skipped atom 1172, because occupancy 0.43 <= existing 0.570001 Skipped atom 1174, because occupancy 0.43 <= existing 0.570001 Skipped atom 1176, because occupancy 0.43 <= existing 0.570001 Skipped atom 1178, because occupancy 0.43 <= existing 0.570001 Skipped atom 1180, because occupancy 0.43 <= existing 0.570001 Skipped atom 1240, because occupancy 0.33 <= existing 0.670001 Skipped atom 1242, because occupancy 0.33 <= existing 0.670001 Skipped atom 1244, because occupancy 0.33 <= existing 0.670001 Skipped atom 1246, because occupancy 0.33 <= existing 0.670001 Skipped atom 1321, because occupancy 0.5 <= existing 0.500001 Skipped atom 1323, because occupancy 0.5 <= existing 0.500001 Skipped atom 1325, because occupancy 0.5 <= existing 0.500001 Skipped atom 1327, because occupancy 0.5 <= existing 0.500001 Skipped atom 1329, because occupancy 0.5 <= existing 0.500001 Skipped atom 1331, because occupancy 0.5 <= existing 0.500001 Skipped atom 1333, because occupancy 0.5 <= existing 0.500001 Skipped atom 1335, because occupancy 0.5 <= existing 0.500001 partial PDB gets fragment 18 through 27 extending start extending end Debugging on ! Reading sequence file Reading input structure 12 residues read Measuring phi and psi Getting chi values LYS 1 27 LYS 3 24 PRO 4 2 THR 5 2 ASN 6 4 SER 7 3 GLU 8 12 PHE 9 3 Building many copies of each residue Checking backbone and frame clashes Finding the lowest Also, print out the first version, pre-bump Finding disulfide bonds. Found 0 disulfide bonds. Residue clashes: 0 clashing residues after turn Residue clashes: Still clashes at these sidechain pairs: Residual clashes = 0.00000 Printing mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a6m.98.2.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a6m.98.2.a2m \ -target T0098 -template 1a6m \ -out T0098-1a6m.98.2 -outdir und2 Skipped atom 27, because occupancy 0.43 <= existing 0.570001 Skipped atom 29, because occupancy 0.43 <= existing 0.570001 Skipped atom 31, because occupancy 0.43 <= existing 0.570001 Skipped atom 33, because occupancy 0.43 <= existing 0.570001 Skipped atom 35, because occupancy 0.43 <= existing 0.570001 Skipped atom 68, because occupancy 0.43 <= existing 0.570001 Skipped atom 70, because occupancy 0.43 <= existing 0.570001 Skipped atom 72, because occupancy 0.43 <= existing 0.570001 Skipped atom 74, because occupancy 0.43 <= existing 0.570001 Skipped atom 76, because occupancy 0.43 <= existing 0.570001 Skipped atom 209, because occupancy 0.35 <= existing 0.650001 Skipped atom 211, because occupancy 0.35 <= existing 0.650001 Skipped atom 213, because occupancy 0.35 <= existing 0.650001 Skipped atom 215, because occupancy 0.35 <= existing 0.650001 Skipped atom 217, because occupancy 0.35 <= existing 0.650001 Skipped atom 348, because occupancy 0.49 <= existing 0.510001 Skipped atom 350, because occupancy 0.49 <= existing 0.510001 Skipped atom 352, because occupancy 0.49 <= existing 0.510001 Skipped atom 354, because occupancy 0.49 <= existing 0.510001 Skipped atom 356, because occupancy 0.49 <= existing 0.510001 Skipped atom 412, because occupancy 0.32 <= existing 0.680001 Skipped atom 414, because occupancy 0.32 <= existing 0.680001 Skipped atom 416, because occupancy 0.32 <= existing 0.680001 Skipped atom 418, because occupancy 0.32 <= existing 0.680001 Skipped atom 420, because occupancy 0.32 <= existing 0.680001 Skipped atom 533, because occupancy 0.34 <= existing 0.660001 Skipped atom 535, because occupancy 0.34 <= existing 0.660001 Skipped atom 537, because occupancy 0.34 <= existing 0.660001 Skipped atom 539, because occupancy 0.34 <= existing 0.660001 Skipped atom 554, because occupancy 0.41 <= existing 0.590001 Skipped atom 556, because occupancy 0.41 <= existing 0.590001 Skipped atom 558, because occupancy 0.41 <= existing 0.590001 Skipped atom 560, because occupancy 0.41 <= existing 0.590001 Skipped atom 562, because occupancy 0.41 <= existing 0.590001 Skipped atom 568, because occupancy 0.5 <= existing 0.500001 Skipped atom 570, because occupancy 0.5 <= existing 0.500001 Skipped atom 572, because occupancy 0.5 <= existing 0.500001 Skipped atom 574, because occupancy 0.5 <= existing 0.500001 Skipped atom 576, because occupancy 0.5 <= existing 0.500001 Skipped atom 578, because occupancy 0.5 <= existing 0.500001 Skipped atom 773, because occupancy 0.47 <= existing 0.530001 Skipped atom 775, because occupancy 0.47 <= existing 0.530001 Skipped atom 777, because occupancy 0.47 <= existing 0.530001 Skipped atom 779, because occupancy 0.47 <= existing 0.530001 Skipped atom 781, because occupancy 0.47 <= existing 0.530001 Skipped atom 815, because occupancy 0.45 <= existing 0.550001 Skipped atom 817, because occupancy 0.45 <= existing 0.550001 Skipped atom 819, because occupancy 0.45 <= existing 0.550001 Skipped atom 821, because occupancy 0.45 <= existing 0.550001 Skipped atom 823, because occupancy 0.45 <= existing 0.550001 Skipped atom 934, because occupancy 0.34 <= existing 0.660001 Skipped atom 936, because occupancy 0.34 <= existing 0.660001 Skipped atom 938, because occupancy 0.34 <= existing 0.660001 Skipped atom 940, because occupancy 0.34 <= existing 0.660001 Skipped atom 942, because occupancy 0.34 <= existing 0.660001 Skipped atom 998, because occupancy 0.46 <= existing 0.540001 Skipped atom 1000, because occupancy 0.46 <= existing 0.540001 Skipped atom 1002, because occupancy 0.46 <= existing 0.540001 Skipped atom 1004, because occupancy 0.46 <= existing 0.540001 Skipped atom 1006, because occupancy 0.46 <= existing 0.540001 Skipped atom 1008, because occupancy 0.46 <= existing 0.540001 Skipped atom 1014, because occupancy 0.44 <= existing 0.560001 Skipped atom 1016, because occupancy 0.44 <= existing 0.560001 Skipped atom 1089, because occupancy 0.34 <= existing 0.660001 Skipped atom 1091, because occupancy 0.34 <= existing 0.660001 Skipped atom 1093, because occupancy 0.34 <= existing 0.660001 Skipped atom 1095, because occupancy 0.34 <= existing 0.660001 Skipped atom 1106, because occupancy 0.44 <= existing 0.560001 Skipped atom 1108, because occupancy 0.44 <= existing 0.560001 Skipped atom 1110, because occupancy 0.44 <= existing 0.560001 Skipped atom 1112, because occupancy 0.44 <= existing 0.560001 Skipped atom 1114, because occupancy 0.44 <= existing 0.560001 Skipped atom 1145, because occupancy 0.45 <= existing 0.550001 Skipped atom 1147, because occupancy 0.45 <= existing 0.550001 Skipped atom 1149, because occupancy 0.45 <= existing 0.550001 Skipped atom 1151, because occupancy 0.45 <= existing 0.550001 Skipped atom 1153, because occupancy 0.45 <= existing 0.550001 Skipped atom 1172, because occupancy 0.43 <= existing 0.570001 Skipped atom 1174, because occupancy 0.43 <= existing 0.570001 Skipped atom 1176, because occupancy 0.43 <= existing 0.570001 Skipped atom 1178, because occupancy 0.43 <= existing 0.570001 Skipped atom 1180, because occupancy 0.43 <= existing 0.570001 Skipped atom 1240, because occupancy 0.33 <= existing 0.670001 Skipped atom 1242, because occupancy 0.33 <= existing 0.670001 Skipped atom 1244, because occupancy 0.33 <= existing 0.670001 Skipped atom 1246, because occupancy 0.33 <= existing 0.670001 Skipped atom 1321, because occupancy 0.5 <= existing 0.500001 Skipped atom 1323, because occupancy 0.5 <= existing 0.500001 Skipped atom 1325, because occupancy 0.5 <= existing 0.500001 Skipped atom 1327, because occupancy 0.5 <= existing 0.500001 Skipped atom 1329, because occupancy 0.5 <= existing 0.500001 Skipped atom 1331, because occupancy 0.5 <= existing 0.500001 Skipped atom 1333, because occupancy 0.5 <= existing 0.500001 Skipped atom 1335, because occupancy 0.5 <= existing 0.500001 partial PDB gets fragment 17 through 26 extending start extending end Debugging on ! Reading sequence file Reading input structure 12 residues read Measuring phi and psi Getting chi values LYS 2 27 PRO 3 2 THR 4 1 ASN 5 4 SER 6 3 GLU 7 12 PHE 8 3 ILE 9 2 Building many copies of each residue Checking backbone and frame clashes Finding the lowest Also, print out the first version, pre-bump Finding disulfide bonds. Found 0 disulfide bonds. Residue clashes: 0 clashing residues after turn Residue clashes: Still clashes at these sidechain pairs: Residual clashes = 0.00000 Printing mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1a6m.99.2.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1a6m.99.2.a2m \ -target T0098 -template 1a6m \ -out T0098-1a6m.99.2 -outdir und2 Skipped atom 27, because occupancy 0.43 <= existing 0.570001 Skipped atom 29, because occupancy 0.43 <= existing 0.570001 Skipped atom 31, because occupancy 0.43 <= existing 0.570001 Skipped atom 33, because occupancy 0.43 <= existing 0.570001 Skipped atom 35, because occupancy 0.43 <= existing 0.570001 Skipped atom 68, because occupancy 0.43 <= existing 0.570001 Skipped atom 70, because occupancy 0.43 <= existing 0.570001 Skipped atom 72, because occupancy 0.43 <= existing 0.570001 Skipped atom 74, because occupancy 0.43 <= existing 0.570001 Skipped atom 76, because occupancy 0.43 <= existing 0.570001 Skipped atom 209, because occupancy 0.35 <= existing 0.650001 Skipped atom 211, because occupancy 0.35 <= existing 0.650001 Skipped atom 213, because occupancy 0.35 <= existing 0.650001 Skipped atom 215, because occupancy 0.35 <= existing 0.650001 Skipped atom 217, because occupancy 0.35 <= existing 0.650001 Skipped atom 348, because occupancy 0.49 <= existing 0.510001 Skipped atom 350, because occupancy 0.49 <= existing 0.510001 Skipped atom 352, because occupancy 0.49 <= existing 0.510001 Skipped atom 354, because occupancy 0.49 <= existing 0.510001 Skipped atom 356, because occupancy 0.49 <= existing 0.510001 Skipped atom 412, because occupancy 0.32 <= existing 0.680001 Skipped atom 414, because occupancy 0.32 <= existing 0.680001 Skipped atom 416, because occupancy 0.32 <= existing 0.680001 Skipped atom 418, because occupancy 0.32 <= existing 0.680001 Skipped atom 420, because occupancy 0.32 <= existing 0.680001 Skipped atom 533, because occupancy 0.34 <= existing 0.660001 Skipped atom 535, because occupancy 0.34 <= existing 0.660001 Skipped atom 537, because occupancy 0.34 <= existing 0.660001 Skipped atom 539, because occupancy 0.34 <= existing 0.660001 Skipped atom 554, because occupancy 0.41 <= existing 0.590001 Skipped atom 556, because occupancy 0.41 <= existing 0.590001 Skipped atom 558, because occupancy 0.41 <= existing 0.590001 Skipped atom 560, because occupancy 0.41 <= existing 0.590001 Skipped atom 562, because occupancy 0.41 <= existing 0.590001 Skipped atom 568, because occupancy 0.5 <= existing 0.500001 Skipped atom 570, because occupancy 0.5 <= existing 0.500001 Skipped atom 572, because occupancy 0.5 <= existing 0.500001 Skipped atom 574, because occupancy 0.5 <= existing 0.500001 Skipped atom 576, because occupancy 0.5 <= existing 0.500001 Skipped atom 578, because occupancy 0.5 <= existing 0.500001 Skipped atom 773, because occupancy 0.47 <= existing 0.530001 Skipped atom 775, because occupancy 0.47 <= existing 0.530001 Skipped atom 777, because occupancy 0.47 <= existing 0.530001 Skipped atom 779, because occupancy 0.47 <= existing 0.530001 Skipped atom 781, because occupancy 0.47 <= existing 0.530001 Skipped atom 815, because occupancy 0.45 <= existing 0.550001 Skipped atom 817, because occupancy 0.45 <= existing 0.550001 Skipped atom 819, because occupancy 0.45 <= existing 0.550001 Skipped atom 821, because occupancy 0.45 <= existing 0.550001 Skipped atom 823, because occupancy 0.45 <= existing 0.550001 Skipped atom 934, because occupancy 0.34 <= existing 0.660001 Skipped atom 936, because occupancy 0.34 <= existing 0.660001 Skipped atom 938, because occupancy 0.34 <= existing 0.660001 Skipped atom 940, because occupancy 0.34 <= existing 0.660001 Skipped atom 942, because occupancy 0.34 <= existing 0.660001 Skipped atom 998, because occupancy 0.46 <= existing 0.540001 Skipped atom 1000, because occupancy 0.46 <= existing 0.540001 Skipped atom 1002, because occupancy 0.46 <= existing 0.540001 Skipped atom 1004, because occupancy 0.46 <= existing 0.540001 Skipped atom 1006, because occupancy 0.46 <= existing 0.540001 Skipped atom 1008, because occupancy 0.46 <= existing 0.540001 Skipped atom 1014, because occupancy 0.44 <= existing 0.560001 Skipped atom 1016, because occupancy 0.44 <= existing 0.560001 Skipped atom 1089, because occupancy 0.34 <= existing 0.660001 Skipped atom 1091, because occupancy 0.34 <= existing 0.660001 Skipped atom 1093, because occupancy 0.34 <= existing 0.660001 Skipped atom 1095, because occupancy 0.34 <= existing 0.660001 Skipped atom 1106, because occupancy 0.44 <= existing 0.560001 Skipped atom 1108, because occupancy 0.44 <= existing 0.560001 Skipped atom 1110, because occupancy 0.44 <= existing 0.560001 Skipped atom 1112, because occupancy 0.44 <= existing 0.560001 Skipped atom 1114, because occupancy 0.44 <= existing 0.560001 Skipped atom 1145, because occupancy 0.45 <= existing 0.550001 Skipped atom 1147, because occupancy 0.45 <= existing 0.550001 Skipped atom 1149, because occupancy 0.45 <= existing 0.550001 Skipped atom 1151, because occupancy 0.45 <= existing 0.550001 Skipped atom 1153, because occupancy 0.45 <= existing 0.550001 Skipped atom 1172, because occupancy 0.43 <= existing 0.570001 Skipped atom 1174, because occupancy 0.43 <= existing 0.570001 Skipped atom 1176, because occupancy 0.43 <= existing 0.570001 Skipped atom 1178, because occupancy 0.43 <= existing 0.570001 Skipped atom 1180, because occupancy 0.43 <= existing 0.570001 Skipped atom 1240, because occupancy 0.33 <= existing 0.670001 Skipped atom 1242, because occupancy 0.33 <= existing 0.670001 Skipped atom 1244, because occupancy 0.33 <= existing 0.670001 Skipped atom 1246, because occupancy 0.33 <= existing 0.670001 Skipped atom 1321, because occupancy 0.5 <= existing 0.500001 Skipped atom 1323, because occupancy 0.5 <= existing 0.500001 Skipped atom 1325, because occupancy 0.5 <= existing 0.500001 Skipped atom 1327, because occupancy 0.5 <= existing 0.500001 Skipped atom 1329, because occupancy 0.5 <= existing 0.500001 Skipped atom 1331, because occupancy 0.5 <= existing 0.500001 Skipped atom 1333, because occupancy 0.5 <= existing 0.500001 Skipped atom 1335, because occupancy 0.5 <= existing 0.500001 partial PDB gets fragment 16 through 25 extending start extending end Debugging on ! Reading sequence file Reading input structure 12 residues read Measuring phi and psi Getting chi values LYS 1 26 PRO 2 2 THR 3 2 ASN 4 3 SER 5 3 GLU 6 12 PHE 7 3 ILE 8 3 MET 10 10 Building many copies of each residue Checking backbone and frame clashes Finding the lowest Also, print out the first version, pre-bump Finding disulfide bonds. Found 0 disulfide bonds. Residue clashes: 0 clashing residues after turn Residue clashes: Still clashes at these sidechain pairs: Residual clashes = 0.00000 Printing mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1aba.68.2.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1aba.68.2.a2m \ -target T0098 -template 1aba \ -out T0098-1aba.68.2 -outdir und2 Skipped atom 110, because occupancy 0.5 <= existing 0.500001 Skipped atom 112, because occupancy 0.5 <= existing 0.500001 Skipped atom 114, because occupancy 0.5 <= existing 0.500001 Skipped atom 116, because occupancy 0.5 <= existing 0.500001 Skipped atom 169, because occupancy 0.5 <= existing 0.500001 Skipped atom 171, because occupancy 0.5 <= existing 0.500001 Skipped atom 246, because occupancy 0.5 <= existing 0.500001 Skipped atom 287, because occupancy 0.5 <= existing 0.500001 Skipped atom 334, because occupancy 0.5 <= existing 0.500001 Skipped atom 336, because occupancy 0.5 <= existing 0.500001 Skipped atom 338, because occupancy 0.5 <= existing 0.500001 Skipped atom 340, because occupancy 0.5 <= existing 0.500001 Skipped atom 385, because occupancy 0.5 <= existing 0.500001 Skipped atom 387, because occupancy 0.5 <= existing 0.500001 Skipped atom 389, because occupancy 0.5 <= existing 0.500001 Skipped atom 391, because occupancy 0.5 <= existing 0.500001 Skipped atom 520, because occupancy 0.5 <= existing 0.500001 Skipped atom 522, because occupancy 0.5 <= existing 0.500001 Skipped atom 524, because occupancy 0.5 <= existing 0.500001 Skipped atom 592, because occupancy 0.5 <= existing 0.500001 Skipped atom 594, because occupancy 0.5 <= existing 0.500001 Skipped atom 596, because occupancy 0.5 <= existing 0.500001 Skipped atom 695, because occupancy 0.5 <= existing 0.500001 Skipped atom 697, because occupancy 0.5 <= existing 0.500001 Skipped atom 699, because occupancy 0.5 <= existing 0.500001 Skipped atom 701, because occupancy 0.5 <= existing 0.500001 Skipped atom 703, because occupancy 0.5 <= existing 0.500001 Skipped atom 705, because occupancy 0.5 <= existing 0.500001 Skipped atom 707, because occupancy 0.5 <= existing 0.500001 partial PDB gets fragment 25 through 34 extending start extending end Debugging on ! Reading sequence file Reading input structure 12 residues read Measuring phi and psi Getting chi values ILE 2 3 ARG 3 16 HIS 4 3 ILE 6 4 VAL 8 1 TRP 10 5 Building many copies of each residue Checking backbone and frame clashes Finding the lowest Also, print out the first version, pre-bump Finding disulfide bonds. Found 0 disulfide bonds. Residue clashes: 0 clashing residues after turn Residue clashes: Still clashes at these sidechain pairs: Residual clashes = 0.00000 Printing mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1aba.69.0.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1aba.69.0.a2m \ -target T0098 -template 1aba \ -out T0098-1aba.69.0 -outdir und2 Skipped atom 110, because occupancy 0.5 <= existing 0.500001 Skipped atom 112, because occupancy 0.5 <= existing 0.500001 Skipped atom 114, because occupancy 0.5 <= existing 0.500001 Skipped atom 116, because occupancy 0.5 <= existing 0.500001 Skipped atom 169, because occupancy 0.5 <= existing 0.500001 Skipped atom 171, because occupancy 0.5 <= existing 0.500001 Skipped atom 246, because occupancy 0.5 <= existing 0.500001 Skipped atom 287, because occupancy 0.5 <= existing 0.500001 Skipped atom 334, because occupancy 0.5 <= existing 0.500001 Skipped atom 336, because occupancy 0.5 <= existing 0.500001 Skipped atom 338, because occupancy 0.5 <= existing 0.500001 Skipped atom 340, because occupancy 0.5 <= existing 0.500001 Skipped atom 385, because occupancy 0.5 <= existing 0.500001 Skipped atom 387, because occupancy 0.5 <= existing 0.500001 Skipped atom 389, because occupancy 0.5 <= existing 0.500001 Skipped atom 391, because occupancy 0.5 <= existing 0.500001 Skipped atom 520, because occupancy 0.5 <= existing 0.500001 Skipped atom 522, because occupancy 0.5 <= existing 0.500001 Skipped atom 524, because occupancy 0.5 <= existing 0.500001 Skipped atom 592, because occupancy 0.5 <= existing 0.500001 Skipped atom 594, because occupancy 0.5 <= existing 0.500001 Skipped atom 596, because occupancy 0.5 <= existing 0.500001 Skipped atom 695, because occupancy 0.5 <= existing 0.500001 Skipped atom 697, because occupancy 0.5 <= existing 0.500001 Skipped atom 699, because occupancy 0.5 <= existing 0.500001 Skipped atom 701, because occupancy 0.5 <= existing 0.500001 Skipped atom 703, because occupancy 0.5 <= existing 0.500001 Skipped atom 705, because occupancy 0.5 <= existing 0.500001 Skipped atom 707, because occupancy 0.5 <= existing 0.500001 partial PDB gets fragment 24 through 33 extending start extending end Debugging on ! Reading sequence file Reading input structure 12 residues read Measuring phi and psi Getting chi values ILE 1 2 ARG 2 32 HIS 3 3 ILE 5 2 GLU 6 15 VAL 7 2 TRP 9 5 SER 10 2 Building many copies of each residue Checking backbone and frame clashes Finding the lowest Also, print out the first version, pre-bump Finding disulfide bonds. Found 0 disulfide bonds. Residue clashes: 0 clashing residues after turn Residue clashes: Still clashes at these sidechain pairs: Residual clashes = 0.00000 Printing mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1aba.70.0.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1aba.70.0.a2m \ -target T0098 -template 1aba \ -out T0098-1aba.70.0 -outdir und2 Skipped atom 110, because occupancy 0.5 <= existing 0.500001 Skipped atom 112, because occupancy 0.5 <= existing 0.500001 Skipped atom 114, because occupancy 0.5 <= existing 0.500001 Skipped atom 116, because occupancy 0.5 <= existing 0.500001 Skipped atom 169, because occupancy 0.5 <= existing 0.500001 Skipped atom 171, because occupancy 0.5 <= existing 0.500001 Skipped atom 246, because occupancy 0.5 <= existing 0.500001 Skipped atom 287, because occupancy 0.5 <= existing 0.500001 Skipped atom 334, because occupancy 0.5 <= existing 0.500001 Skipped atom 336, because occupancy 0.5 <= existing 0.500001 Skipped atom 338, because occupancy 0.5 <= existing 0.500001 Skipped atom 340, because occupancy 0.5 <= existing 0.500001 Skipped atom 385, because occupancy 0.5 <= existing 0.500001 Skipped atom 387, because occupancy 0.5 <= existing 0.500001 Skipped atom 389, because occupancy 0.5 <= existing 0.500001 Skipped atom 391, because occupancy 0.5 <= existing 0.500001 Skipped atom 520, because occupancy 0.5 <= existing 0.500001 Skipped atom 522, because occupancy 0.5 <= existing 0.500001 Skipped atom 524, because occupancy 0.5 <= existing 0.500001 Skipped atom 592, because occupancy 0.5 <= existing 0.500001 Skipped atom 594, because occupancy 0.5 <= existing 0.500001 Skipped atom 596, because occupancy 0.5 <= existing 0.500001 Skipped atom 695, because occupancy 0.5 <= existing 0.500001 Skipped atom 697, because occupancy 0.5 <= existing 0.500001 Skipped atom 699, because occupancy 0.5 <= existing 0.500001 Skipped atom 701, because occupancy 0.5 <= existing 0.500001 Skipped atom 703, because occupancy 0.5 <= existing 0.500001 Skipped atom 705, because occupancy 0.5 <= existing 0.500001 Skipped atom 707, because occupancy 0.5 <= existing 0.500001 partial PDB gets fragment 23 through 32 extending start extending end Debugging on ! Reading sequence file Reading input structure 12 residues read Measuring phi and psi Getting chi values ARG 1 27 HIS 2 3 ILE 4 3 GLU 5 7 VAL 6 1 TRP 8 6 SER 9 3 ARG 10 27 Building many copies of each residue Checking backbone and frame clashes Finding the lowest Also, print out the first version, pre-bump Finding disulfide bonds. Found 0 disulfide bonds. Residue clashes: keepclash 2 9 56.0455 keepclash 5 7 12.6642 Cluster 1 = 2 5 7 9 4 clashing residues after turn Residue clashes: 2-7 2-9 5-7 cluster 1 has 4 members and 2.000e+01 combinations: 7 9 5 2 Energy 74.0703 Searching cluster 2 Combinations for 4 members in cluster 1 OK: 2.000e+01 - Sending to search 12.664165 < 74.070297: keeping 9.764316 < 18.698309: keeping Solved cluster 1: residual clashing 14.78 Still clashes at these sidechain pairs: Residual clashes = 9.76432 Printing mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1aba.70.5.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1aba.70.5.a2m \ -target T0098 -template 1aba \ -out T0098-1aba.70.5 -outdir und2 Skipped atom 110, because occupancy 0.5 <= existing 0.500001 Skipped atom 112, because occupancy 0.5 <= existing 0.500001 Skipped atom 114, because occupancy 0.5 <= existing 0.500001 Skipped atom 116, because occupancy 0.5 <= existing 0.500001 Skipped atom 169, because occupancy 0.5 <= existing 0.500001 Skipped atom 171, because occupancy 0.5 <= existing 0.500001 Skipped atom 246, because occupancy 0.5 <= existing 0.500001 Skipped atom 287, because occupancy 0.5 <= existing 0.500001 Skipped atom 334, because occupancy 0.5 <= existing 0.500001 Skipped atom 336, because occupancy 0.5 <= existing 0.500001 Skipped atom 338, because occupancy 0.5 <= existing 0.500001 Skipped atom 340, because occupancy 0.5 <= existing 0.500001 Skipped atom 385, because occupancy 0.5 <= existing 0.500001 Skipped atom 387, because occupancy 0.5 <= existing 0.500001 Skipped atom 389, because occupancy 0.5 <= existing 0.500001 Skipped atom 391, because occupancy 0.5 <= existing 0.500001 Skipped atom 520, because occupancy 0.5 <= existing 0.500001 Skipped atom 522, because occupancy 0.5 <= existing 0.500001 Skipped atom 524, because occupancy 0.5 <= existing 0.500001 Skipped atom 592, because occupancy 0.5 <= existing 0.500001 Skipped atom 594, because occupancy 0.5 <= existing 0.500001 Skipped atom 596, because occupancy 0.5 <= existing 0.500001 Skipped atom 695, because occupancy 0.5 <= existing 0.500001 Skipped atom 697, because occupancy 0.5 <= existing 0.500001 Skipped atom 699, because occupancy 0.5 <= existing 0.500001 Skipped atom 701, because occupancy 0.5 <= existing 0.500001 Skipped atom 703, because occupancy 0.5 <= existing 0.500001 Skipped atom 705, because occupancy 0.5 <= existing 0.500001 Skipped atom 707, because occupancy 0.5 <= existing 0.500001 partial PDB gets fragment 21 through 30 extending start extending end Debugging on ! Reading sequence file Reading input structure 12 residues read Measuring phi and psi Getting chi values HIS 2 3 ILE 4 2 GLU 5 15 VAL 6 2 TRP 8 5 SER 9 3 ARG 10 29 Building many copies of each residue Checking backbone and frame clashes Finding the lowest Also, print out the first version, pre-bump Finding disulfide bonds. Found 0 disulfide bonds. Residue clashes: 0 clashing residues after turn Residue clashes: Still clashes at these sidechain pairs: Residual clashes = 0.00000 Printing mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1aba.71.0.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1aba.71.0.a2m \ -target T0098 -template 1aba \ -out T0098-1aba.71.0 -outdir und2 Skipped atom 110, because occupancy 0.5 <= existing 0.500001 Skipped atom 112, because occupancy 0.5 <= existing 0.500001 Skipped atom 114, because occupancy 0.5 <= existing 0.500001 Skipped atom 116, because occupancy 0.5 <= existing 0.500001 Skipped atom 169, because occupancy 0.5 <= existing 0.500001 Skipped atom 171, because occupancy 0.5 <= existing 0.500001 Skipped atom 246, because occupancy 0.5 <= existing 0.500001 Skipped atom 287, because occupancy 0.5 <= existing 0.500001 Skipped atom 334, because occupancy 0.5 <= existing 0.500001 Skipped atom 336, because occupancy 0.5 <= existing 0.500001 Skipped atom 338, because occupancy 0.5 <= existing 0.500001 Skipped atom 340, because occupancy 0.5 <= existing 0.500001 Skipped atom 385, because occupancy 0.5 <= existing 0.500001 Skipped atom 387, because occupancy 0.5 <= existing 0.500001 Skipped atom 389, because occupancy 0.5 <= existing 0.500001 Skipped atom 391, because occupancy 0.5 <= existing 0.500001 Skipped atom 520, because occupancy 0.5 <= existing 0.500001 Skipped atom 522, because occupancy 0.5 <= existing 0.500001 Skipped atom 524, because occupancy 0.5 <= existing 0.500001 Skipped atom 592, because occupancy 0.5 <= existing 0.500001 Skipped atom 594, because occupancy 0.5 <= existing 0.500001 Skipped atom 596, because occupancy 0.5 <= existing 0.500001 Skipped atom 695, because occupancy 0.5 <= existing 0.500001 Skipped atom 697, because occupancy 0.5 <= existing 0.500001 Skipped atom 699, because occupancy 0.5 <= existing 0.500001 Skipped atom 701, because occupancy 0.5 <= existing 0.500001 Skipped atom 703, because occupancy 0.5 <= existing 0.500001 Skipped atom 705, because occupancy 0.5 <= existing 0.500001 Skipped atom 707, because occupancy 0.5 <= existing 0.500001 partial PDB gets fragment 22 through 31 extending start extending end Debugging on ! Reading sequence file Reading input structure 12 residues read Measuring phi and psi Getting chi values HIS 1 4 ILE 3 2 GLU 4 15 VAL 5 2 TRP 7 5 SER 8 3 ARG 9 29 Building many copies of each residue Checking backbone and frame clashes Finding the lowest Also, print out the first version, pre-bump Finding disulfide bonds. Found 0 disulfide bonds. Residue clashes: 0 clashing residues after turn Residue clashes: Still clashes at these sidechain pairs: Residual clashes = 0.00000 Printing mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1aba.72.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1aba.72.1.a2m \ -target T0098 -template 1aba \ -out T0098-1aba.72.1 -outdir und2 Skipped atom 110, because occupancy 0.5 <= existing 0.500001 Skipped atom 112, because occupancy 0.5 <= existing 0.500001 Skipped atom 114, because occupancy 0.5 <= existing 0.500001 Skipped atom 116, because occupancy 0.5 <= existing 0.500001 Skipped atom 169, because occupancy 0.5 <= existing 0.500001 Skipped atom 171, because occupancy 0.5 <= existing 0.500001 Skipped atom 246, because occupancy 0.5 <= existing 0.500001 Skipped atom 287, because occupancy 0.5 <= existing 0.500001 Skipped atom 334, because occupancy 0.5 <= existing 0.500001 Skipped atom 336, because occupancy 0.5 <= existing 0.500001 Skipped atom 338, because occupancy 0.5 <= existing 0.500001 Skipped atom 340, because occupancy 0.5 <= existing 0.500001 Skipped atom 385, because occupancy 0.5 <= existing 0.500001 Skipped atom 387, because occupancy 0.5 <= existing 0.500001 Skipped atom 389, because occupancy 0.5 <= existing 0.500001 Skipped atom 391, because occupancy 0.5 <= existing 0.500001 Skipped atom 520, because occupancy 0.5 <= existing 0.500001 Skipped atom 522, because occupancy 0.5 <= existing 0.500001 Skipped atom 524, because occupancy 0.5 <= existing 0.500001 Skipped atom 592, because occupancy 0.5 <= existing 0.500001 Skipped atom 594, because occupancy 0.5 <= existing 0.500001 Skipped atom 596, because occupancy 0.5 <= existing 0.500001 Skipped atom 695, because occupancy 0.5 <= existing 0.500001 Skipped atom 697, because occupancy 0.5 <= existing 0.500001 Skipped atom 699, because occupancy 0.5 <= existing 0.500001 Skipped atom 701, because occupancy 0.5 <= existing 0.500001 Skipped atom 703, because occupancy 0.5 <= existing 0.500001 Skipped atom 705, because occupancy 0.5 <= existing 0.500001 Skipped atom 707, because occupancy 0.5 <= existing 0.500001 partial PDB gets fragment 21 through 30 extending start extending end Debugging on ! Reading sequence file Reading input structure 12 residues read Measuring phi and psi Getting chi values ILE 2 3 GLU 3 12 VAL 4 1 TRP 6 4 SER 7 2 ARG 8 26 ASN 10 6 Building many copies of each residue Checking backbone and frame clashes Finding the lowest Also, print out the first version, pre-bump Finding disulfide bonds. Found 0 disulfide bonds. Residue clashes: 0 clashing residues after turn Residue clashes: Still clashes at these sidechain pairs: Residual clashes = 0.00000 Printing mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1aba.73.1.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1aba.73.1.a2m \ -target T0098 -template 1aba \ -out T0098-1aba.73.1 -outdir und2 Skipped atom 110, because occupancy 0.5 <= existing 0.500001 Skipped atom 112, because occupancy 0.5 <= existing 0.500001 Skipped atom 114, because occupancy 0.5 <= existing 0.500001 Skipped atom 116, because occupancy 0.5 <= existing 0.500001 Skipped atom 169, because occupancy 0.5 <= existing 0.500001 Skipped atom 171, because occupancy 0.5 <= existing 0.500001 Skipped atom 246, because occupancy 0.5 <= existing 0.500001 Skipped atom 287, because occupancy 0.5 <= existing 0.500001 Skipped atom 334, because occupancy 0.5 <= existing 0.500001 Skipped atom 336, because occupancy 0.5 <= existing 0.500001 Skipped atom 338, because occupancy 0.5 <= existing 0.500001 Skipped atom 340, because occupancy 0.5 <= existing 0.500001 Skipped atom 385, because occupancy 0.5 <= existing 0.500001 Skipped atom 387, because occupancy 0.5 <= existing 0.500001 Skipped atom 389, because occupancy 0.5 <= existing 0.500001 Skipped atom 391, because occupancy 0.5 <= existing 0.500001 Skipped atom 520, because occupancy 0.5 <= existing 0.500001 Skipped atom 522, because occupancy 0.5 <= existing 0.500001 Skipped atom 524, because occupancy 0.5 <= existing 0.500001 Skipped atom 592, because occupancy 0.5 <= existing 0.500001 Skipped atom 594, because occupancy 0.5 <= existing 0.500001 Skipped atom 596, because occupancy 0.5 <= existing 0.500001 Skipped atom 695, because occupancy 0.5 <= existing 0.500001 Skipped atom 697, because occupancy 0.5 <= existing 0.500001 Skipped atom 699, because occupancy 0.5 <= existing 0.500001 Skipped atom 701, because occupancy 0.5 <= existing 0.500001 Skipped atom 703, because occupancy 0.5 <= existing 0.500001 Skipped atom 705, because occupancy 0.5 <= existing 0.500001 Skipped atom 707, because occupancy 0.5 <= existing 0.500001 partial PDB gets fragment 20 through 29 extending start extending end Debugging on ! Reading sequence file Reading input structure 12 residues read Measuring phi and psi Getting chi values ILE 1 2 GLU 2 15 VAL 3 1 TRP 5 5 SER 6 2 ARG 7 24 ASN 9 4 LEU 10 3 Building many copies of each residue Checking backbone and frame clashes Finding the lowest Also, print out the first version, pre-bump Finding disulfide bonds. Found 0 disulfide bonds. Residue clashes: 0 clashing residues after turn Residue clashes: Still clashes at these sidechain pairs: Residual clashes = 0.00000 Printing mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1aba.74.2.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1aba.74.2.a2m \ -target T0098 -template 1aba \ -out T0098-1aba.74.2 -outdir und2 Skipped atom 110, because occupancy 0.5 <= existing 0.500001 Skipped atom 112, because occupancy 0.5 <= existing 0.500001 Skipped atom 114, because occupancy 0.5 <= existing 0.500001 Skipped atom 116, because occupancy 0.5 <= existing 0.500001 Skipped atom 169, because occupancy 0.5 <= existing 0.500001 Skipped atom 171, because occupancy 0.5 <= existing 0.500001 Skipped atom 246, because occupancy 0.5 <= existing 0.500001 Skipped atom 287, because occupancy 0.5 <= existing 0.500001 Skipped atom 334, because occupancy 0.5 <= existing 0.500001 Skipped atom 336, because occupancy 0.5 <= existing 0.500001 Skipped atom 338, because occupancy 0.5 <= existing 0.500001 Skipped atom 340, because occupancy 0.5 <= existing 0.500001 Skipped atom 385, because occupancy 0.5 <= existing 0.500001 Skipped atom 387, because occupancy 0.5 <= existing 0.500001 Skipped atom 389, because occupancy 0.5 <= existing 0.500001 Skipped atom 391, because occupancy 0.5 <= existing 0.500001 Skipped atom 520, because occupancy 0.5 <= existing 0.500001 Skipped atom 522, because occupancy 0.5 <= existing 0.500001 Skipped atom 524, because occupancy 0.5 <= existing 0.500001 Skipped atom 592, because occupancy 0.5 <= existing 0.500001 Skipped atom 594, because occupancy 0.5 <= existing 0.500001 Skipped atom 596, because occupancy 0.5 <= existing 0.500001 Skipped atom 695, because occupancy 0.5 <= existing 0.500001 Skipped atom 697, because occupancy 0.5 <= existing 0.500001 Skipped atom 699, because occupancy 0.5 <= existing 0.500001 Skipped atom 701, because occupancy 0.5 <= existing 0.500001 Skipped atom 703, because occupancy 0.5 <= existing 0.500001 Skipped atom 705, because occupancy 0.5 <= existing 0.500001 Skipped atom 707, because occupancy 0.5 <= existing 0.500001 partial PDB gets fragment 19 through 28 extending start extending end Debugging on ! Reading sequence file Reading input structure 12 residues read Measuring phi and psi Getting chi values GLU 1 12 VAL 2 1 TRP 4 6 SER 5 3 ARG 6 26 ASN 8 5 LEU 9 2 GLU 10 13 Building many copies of each residue Checking backbone and frame clashes Finding the lowest Also, print out the first version, pre-bump Finding disulfide bonds. Found 0 disulfide bonds. Residue clashes: 0 clashing residues after turn Residue clashes: Still clashes at these sidechain pairs: Residual clashes = 0.00000 Printing mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1ail.92.4.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1ail.92.4.a2m \ -target T0098 -template 1ail \ -out T0098-1ail.92.4 -outdir und2 PDB sequence and aligned sequence are not exact. /projects/kestrel/users/karplus/burial/slicer/slicer: Error: Cannot open file tmp/1ail-orig.a2m for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/1ail-orig.a2m: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR align_unmatched failed. gmake: *** [und2/T0098-1ail.92.4.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1ail.93.3.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1ail.93.3.a2m \ -target T0098 -template 1ail \ -out T0098-1ail.93.3 -outdir und2 PDB sequence and aligned sequence are not exact. /projects/kestrel/users/karplus/burial/slicer/slicer: Error: Cannot open file tmp/1ail-orig.a2m for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/1ail-orig.a2m: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR align_unmatched failed. gmake: *** [und2/T0098-1ail.93.3.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1ail.94.5.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1ail.94.5.a2m \ -target T0098 -template 1ail \ -out T0098-1ail.94.5 -outdir und2 PDB sequence and aligned sequence are not exact. /projects/kestrel/users/karplus/burial/slicer/slicer: Error: Cannot open file tmp/1ail-orig.a2m for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/1ail-orig.a2m: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR align_unmatched failed. gmake: *** [und2/T0098-1ail.94.5.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1ail.95.5.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1ail.95.5.a2m \ -target T0098 -template 1ail \ -out T0098-1ail.95.5 -outdir und2 PDB sequence and aligned sequence are not exact. /projects/kestrel/users/karplus/burial/slicer/slicer: Error: Cannot open file tmp/1ail-orig.a2m for writing. /projects/kestrel/users/karplus/burial/slicer/slicer: tmp/1ail-orig.a2m: Permission denied /projects/kestrel/users/karplus/burial/slicer/slicer: ERROR align_unmatched failed. gmake: *** [und2/T0098-1ail.95.5.index] Error 1 mkdir und2 mkdir: cannot create und2. und2: File exists gmake: [und2/T0098-1al3.103.5.index] Error 2 (ignored) /projects/kestrel/users/karplus/burial/slicer/slicer \ -a2m dunbrack_frags/T0098-1al3.103.5.a2m \ -target T0098 -template 1al3 \ -out T0098-1al3.103.5 -outdir und2 Skipped atom 38, because occupancy 0.3 <= existing 0.700001 Skipped atom 40, because occupancy 0.3 <= existing 0.700001 Skipped atom 42, because occupancy 0.3 <= existing 0.700001 Skipped atom 44, because occupancy 0.3 <= existing 0.700001 Skipped atom 46, because occupancy 0.3 <= existing 0.700001 Skipped atom 48, because occupancy 0.3 <= existing 0.700001 Skipped atom 50, because occupancy 0.3 <= existing 0.700001 Skipped atom 52, because occupancy 0.3 <= existing 0.700001 Skipped atom 54, because occupancy 0.3 <= existing 0.700001 Skipped atom 60, because occupancy 0.5 <= existing 0.500001 Skipped atom 62, because occupancy 0.5 <= existing 0.500001 Skipped atom 64, because occupancy 0.5 <= existing 0.500001 Skipped atom 66, because occupancy 0.5 <= existing 0.500001 Skipped atom 68, because occupancy 0.5 <= existing 0.500001 Skipped atom 70, because occupancy 0.5 <= existing 0.500001 Skipped atom 235, because occupancy 0.5 <= existing 0.500001 Skipped atom 237, because occupancy 0.5 <= existing 0.500001 Skipped atom 239, because occupancy 0.5 <= existing 0.500001 Skipped atom 241, because occupancy 0.5 <= existing 0.500001 Skipped atom 243, because occupancy 0.5 <= existing 0.500001 Skipped atom 245, because occupancy 0.5 <= existing 0.500001 Skipped atom 247, because occupancy 0.5 <= existing 0.500001 Skipped atom 249, because occupancy 0.5 <= existing 0.500001 Skipped atom 393, because occupancy 0.5 <= existing 0.500001 Skipped atom 395, because occupancy 0.5 <= existing 0.500001 Skipped atom 397, because occupancy 0.5 <= existing 0.500001 Skipped atom 399, because occupancy 0.5 <= existing 0.500001 Skipped atom 401, because occupancy 0.5 <= existing 0.500001 Skipped atom 403, because occupancy 0.5 <= existing 0.500001 Skipped atom 405, because occupancy 0.5 <= existing 0.500001 Skipped atom 416, because occupancy 0.5 <= existing 0.500001 Skipped atom 418, because occupancy 0.5 <= existing 0.500001 Skipped atom 420, because occupancy 0.5 <= existing 0.500001 Skipped atom 422, because occupancy 0.5 <= existing 0.500001 Skipped atom 424, because occupancy 0.5 <= existing 0.500001 Skipped atom 426, because occupancy 0.5 <= existing 0.500001 Skipped atom 428, because occupancy 0.5 <= existing 0.500001 Skipped atom 430, because occupancy 0.5 <= existing 0.500001 Skipped atom 432, because occupancy 0.5 <= existing 0.500001 Skipped atom 434, because occupancy 0.5 <= existing 0.500001 Skipped atom 436, because occupancy 0.5 <= existing 0.500001 Skipped atom 438, because occupancy 0.5 <= existing 0.500001 Skipped atom 440, because occupancy 0.5 <= existing 0.500001 Skipped atom 571, because occupancy 0.5 <= existing 0.500001 Skipped atom 573, because occupancy 0.5 <= existing 0.500001 Skipped atom 575, because occupancy 0.5 <= existing 0.500001 Skipped atom 577, because occupancy 0.5 <= existing 0.500001 Skipped atom 579, because occupancy 0.5 <= existing 0.500001 Skipped atom 581, because occupancy 0.5 <= existing 0.500001 Skipped atom 583, because occupancy 0.5 <= existing 0.500001 Skipped atom 585, because occupancy 0.5 <= existing 0.500001 Skipped atom 628, because occupancy 0.5 <= existing 0.500001 Skipped atom 630, because occupancy 0.5 <= existing 0.500001 Skipped atom 730, because occupancy 0.5 <= existing 0.500001 Skipped atom 732, because occupancy 0.5 <= existing 0.500001 Skipped atom 734, because occupancy 0.5 <= existing 0.500001 Skipped atom 736, because occupancy 0.5 <= existing 0.500001 Skipped atom 738, because occupancy 0.5 <= existing 0.500001 Skipped atom 740, because occupancy 0.5 <= existing 0.500001 Skipped atom 742, because occupancy 0.5 <= existing 0.500001 Skipped atom 824, because occupancy 0.3 <= existing 0.700001 Skipped atom 826, because occupancy 0.3 <= existing 0.700001 Skipped atom 828, because occupancy 0.3 <= existing 0.700001 Skipped atom 830, because occupancy 0.3 <= existing 0.700001 Skipped atom 832, because occupancy 0.3 <= existing 0.700001 Skipped atom 834, because occupancy 0.3 <= existing 0.700001 Skipped atom 836, because occupancy 0.5 <= existing 0.500001 Skipped atom 838, because occupancy 0.5 <= existing 0.500001 Skipped atom 840, because occupancy 0.5 <= existing 0.500001 Skipped atom 842, because occupancy 0.5 <= existing 0.500001 Skipped atom 844, because occupancy 0.5 <= existing 0.500001 Skipped atom 846, because occupancy 0.5 <= existing 0.500001 Skipped atom 848, because occupancy 0.5 <= existing 0.500001 Skipped atom 895, because occupancy 0.5 <= existing 0.500001 Skipped atom 897, because occupancy 0.5 <= existing 0.500001 Skipped atom 899, because occupancy 0.5 <= existing 0.500001 Skipped atom 901, because occupancy 0.5 <= existing 0.500001 Skipped atom 903, because occupancy 0.5 <= existing 0.500001 Skipped atom 905, because occupancy 0.5 <= existing 0.500001 Skipped atom 907, because occupancy 0.5 <= existing 0.500001 Skipped atom 909, because occupancy 0.5 <= existing 0.500001 Skipped atom 911, because occupancy 0.5 <= existing 0.500001 Skipped atom 1111, because occupancy 0.3 <= existing 0.700001 Skipped atom 1113, because occupancy 0.3 <= existing 0.700001 Skipped atom 1115, because occupancy 0.3 <= existing 0.700001 Skipped atom 1117, because occupancy 0.3 <= existing 0.700001 Skipped atom 1119, because occupancy 0.3 <= existing 0.700001 Skipped atom 1121, because occupancy 0.3 <= existing 0.700001 Skipped atom 1123, because occupancy 0.3 <= existing 0.700001 Skipped atom 1132, because occupancy 0.5 <= existing 0.500001 Skipped atom 1134, because occupancy 0.5 <= existing 0.500001 Skipped atom 1136, because occupancy 0.5 <= existing 0.500001 Skipped atom 1138, because occupancy 0.5 <= existing 0.500001 Skipped atom 1140, because occupancy 0.5 <= existing 0.500001 Skipped atom 1142, because occupancy 0.5 <= existing 0.500001 Skipped atom 1144, because occupancy 0.5 <= existing 0.500001 Skipped atom 1146, because occupancy 0.5 <= existing 0.500001 Skipped atom 1148, because occupancy 0.5 <= existing 0.500001 Skipped atom 1150, because occupancy 0.5 <= existing 0.500001 Skipped atom 1152, because occupancy 0.5 <= existing 0.500001 Skipped atom 1341, because occupancy 0.5 <= existing 0.500001 Skipped atom 1356, because occupancy 0.5 <= existing 0.500001 Skipped atom 1358, because occupancy 0.5 <= existing 0.500001 Skipped atom 1360, because occupancy 0.5 <= existing 0.500001 Skipped atom 1362, because occupancy 0.5 <= existing 0.500001 Skipped atom 1364, because occupancy 0.5 <= existing 0.500001 Skipped atom 1366, because occupancy 0.5 <= existing 0.500001 Skipped atom 1368, because occupancy 0.5 <= existing 0.500001 Skipped atom 1453, because occupancy 0.5 <= existing 0.500001 Skipped atom 1455, because occupancy 0.5 <= existing 0.500001 Skipped atom 1457, because occupancy 0.5 <= existing 0.500001 Skipped atom 1459, because occupancy 0.5 <= existing 0.500001 Skipped atom 1461, because occupancy 0.5 <= existing 0.500001 Skipped atom 1463, because occupancy 0.5 <= existing 0.500001 Skipped atom 1465, because occupancy 0.5 <= existing 0.500001 Skipped atom 1467, because occupancy 0.5 <= existing 0.500001 Skipped atom 1469, because occupancy 0.5 <= existing 0.500001 Skipped atom 1471, because occupancy 0.5 <= existing 0.500001 Skipped atom 1473, because occupancy 0.5 <= existing 0.500001 Skipped atom 1475, because occupancy 0.5 <= existing 0.500001 Skipped atom 1477, because occupancy 0.5 <= existing 0.500001 Skipped atom 1479, because occupancy 0.5 <= existing 0.500001 Skipped atom 1481, because occupancy 0.5 <= existing 0.500001 Skipped atom 1483, because occupancy 0.5 <= existing 0.500001 Skipped atom 1485, because occupancy 0.5 <= existing 0.500001 Skipped atom 1487, because occupancy 0.5 <= existing 0.500001 Skipped atom 1489, because occupancy 0.5 <= existing 0.500001 Skipped atom 1491, because occupancy 0.5 <= existing 0.500001 Skipped atom 1493, because occupancy 0.5 <= existing 0.500001 Skipped atom 1495, because occupancy 0.5 <= existing 0.500001 Skipped atom 1497, because occupancy 0.5 <= existing 0.500001 Skipped atom 1499, because occupancy 0.5 <= existing 0.500001 Skipped atom 1501, because occupancy 0.5 <= existing 0.500001 Skipped atom 1558, because occupancy 0.5 <= existing 0.500001 Skipped atom 1560, because occupancy 0.5 <= existing 0.500001 Skipped atom 1562, because occupancy 0.5 <= existing 0.500001 Skipped atom 1564, because occupancy 0.5 <= existing 0.500001 Skipped atom 1566, because occupancy 0.5 <= existing 0.500001 Skipped atom 1568, because occupancy 0.5 <= existing 0.500001 Skipped atom 1570, because occupancy 0.5 <= existing 0.500001 Skipped atom 1572, because occupancy 0.5 <= existing 0.500001 Skipped atom 1574, because occupancy 0.5 <= existing 0.500001 Skipped atom 1738, because occupancy 0.3 <= existing 0.700001 Skipped atom 1740, because occupancy 0.3 <= existing 0.700001 Skipped atom 1742, because occupancy 0.3 <= existing 0.700001 Skipped atom 1744, because occupancy 0.3 <= existing 0.700001 Skipped atom 1746, because occupancy 0.3 <= existing 0.700001 Skipped atom 1748, because occupancy 0.3 <= existing 0.700001 Skipped atom 1750, because occupancy 0.3 <= existing 0.700001 Skipped atom 1752, because occupancy 0.3 <= existing 0.700001 Skipped atom 1754, because occupancy 0.3 <= existing 0.700001 Skipped atom 1756, because occupancy 0.3 <= existing 0.700001 Skipped atom 1793, because occupancy 0.5 <= existing 0.500001 Skipped atom 1795, because occupancy 0.5 <= existing 0.500001 Skipped atom 1797, because occupancy 0.5 <= existing 0.500001 Skipped atom 1799, because occupancy 0.5 <= existing 0.500001 Skipped atom 1801, because occupancy 0.5 <= existing 0.500001 Skipped atom 1803, because occupancy 0.5 <= existing 0.500001 Skipped atom 1805, because occupancy 0.5 <= existing 0.500001 Skipped atom 1807, because occupancy 0.5 <= existing 0.500001 PDB sequence and aligned sequence are not exact. Writing a2m file: tmp/1al3-orig.a2m Writing a2m file: tmp/1al3-pdb.a2m Reading /projects/compbio/bin/scripts/sam-t99.conf @@@@ chgrp protein /projects/compbio/tmp/tmp-build-weighted-model-eclipse-14293 @@@@ uniqueseq /projects/compbio/tmp/tmp-build-weighted-model-eclipse-14293/tmp -alignfile tmp/1al3-orig.a2m \ -a protein -percent_id 0.8 SAM: uniqueseq v3.2 (July 31, 2000) compiled 07/31/00_14:08:59 Reading alignment file tmp/1al3-orig.a2m (1 sequences, 324 columns) as A2M alignment. Writing sequence output to /projects/compbio/tmp/tmp-build-weighted-model-eclipse-14293/tmp.a2m. No sequences have been dropped. @@@@ modelfromalign /projects/compbio/tmp/tmp-build-weighted-model-eclipse-14293/tmp -alignfile /projects/compbio/tmp/tmp-build-weighted-model-eclipse-14293/tmp.a2m \ -insert /projects/compbio/lib/fssp-trained.regularizer \ -ins_jump_conf 1 \ -match_jump_conf 1 \ -del_jump_conf 1 \ -prior_library /projects/compbio/lib/recode3.20comp \ -binary_output 1 -a protein -aweight_method 1 -aweight_bits 0.5 -aweight_exponent 10 Reading parameter file /projects/compbio/lib/fssp-trained.regularizer /projects/compbio/lib/fssp-trained.regularizer(1): Reading REGULARIZER: transitions from FSSP and pseudocounts for diverse weighted HSSP SAM: modelfromalign v3.2 (July 31, 2000) compiled 07/31/00_14:08:27 Reading alignment file /projects/compbio/tmp/tmp-build-weighted-model-eclipse-14293/tmp.a2m (1 sequences, 324 columns) as A2M alignment. @@@@ cp -f /projects/compbio/tmp/tmp-build-weighted-model-eclipse-14293/tmp.mod tmp/1al3-align.mod @@@@ rm -rf /projects/compbio/tmp/tmp-build-weighted-model-eclipse-14293