Warning: no access to tty (Bad file descriptor). Thus no job control in this shell. 02-Dec-2005 19:47:19 n-1<20961> ssi:boot:base:linear: booting n0 (wolf01) n-1<20961> ssi:boot:base:linear: booting n1 (wolf02) n-1<20961> ssi:boot:base:linear: booting n2 (wolf03) n-1<20961> ssi:boot:base:linear: booting n3 (wolf04) n-1<20961> ssi:boot:base:linear: booting n4 (wolf05) n-1<20961> ssi:boot:base:linear: booting n5 (wolf06) n-1<20961> ssi:boot:base:linear: booting n6 (wolf07) n-1<20961> ssi:boot:base:linear: booting n7 (wolf08) n-1<20961> ssi:boot:base:linear: booting n8 (wolf09) n-1<20961> ssi:boot:base:linear: booting n9 (wolf10) n-1<20961> ssi:boot:base:linear: booting n10 (wolf11) n-1<20961> ssi:boot:base:linear: booting n11 (wolf12) n-1<20961> ssi:boot:base:linear: booting n12 (wolf13) n-1<20961> ssi:boot:base:linear: finished LAM 7.2b1svn10112005/MPI 2 C++/ROMIO - Indiana University ___________________________________________________________________ CYANA 2.1 (intel-lam) Copyright (c) 2002-05 Peter Guntert. All rights reserved. ___________________________________________________________________ Library file "/user/cyana-2.1/lib/cyana.lib" read, 37 residue types. Sequence file "znf42.seq" read, 219 residues. Symmetric dimer: Molecule 1: residues 35..128 Molecule 2: residues 335..428 403 identity constraints created. 8836 symmetry constraints created. cyana> cyana> cyana> - znf42: peakcheck peaks=c13no,n15no,c13ar,fc12no prot=znf42 ------------------------------------------------------------ Proton list: znf42 - peakcheck: read prot znf42 unknown=warn Chemical shift list "znf42.prot" read, 1980 chemical shifts. - peakcheck: shifts missing "H* Q* - HYDROXYL - AMIDE + H HN / &H_* &PSEUD" Residue missing shifts GLY 35 H QA SER 36 H HA QB ASP 37 H CYS 49 HG PHE 50 HZ CYS 69 HG LEU 84 QD2 GLY 335 H QA SER 336 H HA QB ASP 337 H CYS 349 HG PHE 350 HZ CYS 369 HG LEU 384 QD2 20 missing chemical shifts, completeness 98.0%. ------------------------------------------------------------ Peak list : c13no Proton list: znf42 - peakcheck: read prot znf42 unknown=skip Chemical shift list "znf42.prot" read, 1980 chemical shifts. - peakcheck: read peaks c13no format= Peak list "c13no.peaks" read, 3477 peaks, 3197 assignments. - peakcheck: atom shift unusual Atom Shift Dev Mean +/- Minimum Maximum HG3 ARG 44 -0.750 5.11 1.50 0.44 -0.72 3.30 NE ARG 44 113.446 16.64 84.33 1.75 78.96 89.30 NE ARG 48 118.117 19.31 84.33 1.75 78.96 89.30 NE ARG 66 116.949 18.64 84.33 1.75 78.96 89.30 QD2 LEU 73 -0.640 4.25 0.72 0.32 -1.03 1.31 HG3 ARG 344 -0.750 5.11 1.50 0.44 -0.72 3.30 NE ARG 344 113.446 16.64 84.33 1.75 78.96 89.30 NE ARG 348 118.117 19.31 84.33 1.75 78.96 89.30 NE ARG 366 116.949 18.64 84.33 1.75 78.96 89.30 QD2 LEU 373 -0.640 4.25 0.72 0.32 -1.03 1.31 10 shifts outside expected range. - peakcheck: peaks fit Deviations from chemical shift list: Dim Peaks Median Average Maximum RMSD Number Tolerance 1 3197 0.000 0.002 0.048 0.009 2 0.030 2 3473 0.000 0.000 0.331 0.006 1 0.030 3 3473 0.000 0.000 0.297 0.023 0 0.450 - peakcheck: atom shift check Atom Residue Shift Median Deviation Peaks HB2 PRO 126 2.312 2.312 0.331 9 HB2 PHE 392 3.102 3.093 0.048 4 HG2 GLU 413 2.465 2.495 0.030 2 3 shifts with spread larger than tolerance. - peakcheck: peak deviations Peak Dim Deviation Atom Residue 2276 1 0.030 HG2 GLU 413 2360 1 -0.048 HB2 PHE 392 4075 2 -0.331 HB2 PRO 126 3 deviations larger than tolerance. ------------------------------------------------------------ Peak list : n15no Proton list: znf42 - peakcheck: read prot znf42 unknown=skip Chemical shift list "znf42.prot" read, 1980 chemical shifts. - peakcheck: read peaks n15no format= Peak list "n15no.peaks" read, 1273 peaks, 1113 assignments. - peakcheck: peaks fit Deviations from chemical shift list: Dim Peaks Median Average Maximum RMSD Number Tolerance 1 1113 0.002 0.002 0.030 0.011 0 0.030 2 1269 0.000 0.000 0.011 0.001 0 0.030 3 1269 0.000 -0.001 0.186 0.009 0 0.450 - peakcheck: atom shift check Atom Residue Shift Median Deviation Peaks 0 shifts with spread larger than tolerance. - peakcheck: peak deviations Peak Dim Deviation Atom Residue 0 deviations larger than tolerance. ------------------------------------------------------------ Peak list : c13ar Proton list: znf42 - peakcheck: read prot znf42 unknown=skip Chemical shift list "znf42.prot" read, 1980 chemical shifts. - peakcheck: read peaks c13ar format= Peak list "c13ar.peaks" read, 281 peaks, 223 assignments. - peakcheck: peaks fit Deviations from chemical shift list: Dim Peaks Median Average Maximum RMSD Number Tolerance 1 223 0.004 0.005 0.030 0.013 1 0.030 2 280 0.000 0.000 0.000 0.000 0 0.030 3 280 0.000 0.000 0.000 0.000 0 0.450 - peakcheck: atom shift check Atom Residue Shift Median Deviation Peaks HB3 ARG 44 0.295 0.325 0.030 1 1 shift with spread larger than tolerance. - peakcheck: peak deviations Peak Dim Deviation Atom Residue 226 1 0.030 HB3 ARG 44 1 deviations larger than tolerance. ------------------------------------------------------------ Peak list : fc12no Proton list: znf42 - peakcheck: read prot znf42 unknown=skip Chemical shift list "znf42.prot" read, 1980 chemical shifts. - peakcheck: read peaks fc12no format= Peak list "fc12no.peaks" read, 225 peaks, 150 assignments. - peakcheck: peaks fit Deviations from chemical shift list: Dim Peaks Median Average Maximum RMSD Number Tolerance 1 150 0.000 -0.001 0.029 0.016 0 0.030 2 169 0.000 -0.001 0.014 0.005 0 0.030 3 169 0.000 -0.005 0.297 0.034 0 0.450 - peakcheck: atom shift check Atom Residue Shift Median Deviation Peaks 0 shifts with spread larger than tolerance. - peakcheck: peak deviations Peak Dim Deviation Atom Residue 0 deviations larger than tolerance. - znf42: calibration prot=znf42 peaks=c13no,n15no,c13ar,fc12no constant=3.0E7,1.2 E7,2.0E7,1.0E7 dref=4.2 - calibration: read prot znf42 unknown=warn Chemical shift list "znf42.prot" read, 1980 chemical shifts. - calibration: read peaks c13no format= Peak list "c13no.peaks" read, 3477 peaks, 3197 assignments. - calibration: peaks select "** list=1" 3477 of 3477 peaks, 3477 of 3477 assignments selected. - calibration: peaks set volume=abs(volume) Volume of 3477 peaks set. - calibration: peaks simplecal constant=3.0E7 Calibration constant for peak list 1: 3.00E+07 Upper limit set for 3477 peaks. - calibration: caltab peaks Distance bounds: -2.99 A: 329 9.5% 3.00-3.99 A: 768 22.1% 4.00-4.99 A: 1384 39.8% 5.00-5.99 A: 994 28.6% 6.00- A: 0 0.0% All: 3477 100.0% - calibration: read prot znf42 unknown=warn append Chemical shift list "znf42.prot" read, 1980 chemical shifts. - calibration: read peaks n15no format= append Peak list "n15no.peaks" read, 1273 peaks, 1113 assignments. - calibration: peaks select "** list=2" 1273 of 4750 peaks, 1273 of 4750 assignments selected. - calibration: peaks set volume=abs(volume) Volume of 1273 peaks set. - calibration: peaks simplecal constant=1.2E7 Calibration constant for peak list 2: 1.20E+07 Upper limit set for 1273 peaks. - calibration: caltab peaks Distance bounds: -2.99 A: 93 7.3% 3.00-3.99 A: 339 26.6% 4.00-4.99 A: 492 38.6% 5.00-5.99 A: 347 27.3% 6.00- A: 0 0.0% All: 1273 100.0% - calibration: read prot znf42 unknown=warn append Chemical shift list "znf42.prot" read, 1980 chemical shifts. - calibration: read peaks c13ar format= append Peak list "c13ar.peaks" read, 281 peaks, 223 assignments. - calibration: peaks select "** list=3" 281 of 5031 peaks, 281 of 5031 assignments selected. - calibration: peaks set volume=abs(volume) Volume of 281 peaks set. - calibration: peaks simplecal constant=2.0E7 Calibration constant for peak list 3: 2.00E+07 Upper limit set for 281 peaks. - calibration: caltab peaks Distance bounds: -2.99 A: 21 7.5% 3.00-3.99 A: 57 20.3% 4.00-4.99 A: 161 57.3% 5.00-5.99 A: 42 14.9% 6.00- A: 0 0.0% All: 281 100.0% - calibration: read prot znf42 unknown=warn append Chemical shift list "znf42.prot" read, 1980 chemical shifts. - calibration: read peaks fc12no format= append Peak list "fc12no.peaks" read, 225 peaks, 150 assignments. - calibration: peaks select "** list=4" 225 of 5256 peaks, 225 of 5256 assignments selected. - calibration: peaks set volume=abs(volume) Volume of 225 peaks set. - calibration: peaks simplecal constant=1.0E7 Calibration constant for peak list 4: 1.00E+07 Upper limit set for 225 peaks. - calibration: caltab peaks Distance bounds: -2.99 A: 2 0.9% 3.00-3.99 A: 48 21.3% 4.00-4.99 A: 156 69.3% 5.00-5.99 A: 19 8.4% 6.00- A: 0 0.0% All: 225 100.0% - calibration: peaks select ** 5256 of 5256 peaks, 5256 of 5256 assignments selected. - znf42: peaks calibrate ** simple 4188 upper limits added, 8/498 at lower/upper bound, average 4.47 A. - znf42: write upl znf42-in.upl Distance constraint file "znf42-in.upl" written, 4188 upper limits, 4188 assignments. - znf42: distance modify Number of modified constraints: 2237 - znf42: write upl znf42.upl Distance constraint file "znf42.upl" written, 2237 upper limits, 2237 assignments. - znf42: ./init - init: read lib /user/cyana-2.1/lib/cyana.lib Library file "/user/cyana-2.1/lib/cyana.lib" read, 37 residue types. - init: read seq znf42.seq Sequence file "znf42.seq" read, 219 residues. - init: molecules define 35..128 335..428 Symmetric dimer: Molecule 1: residues 35..128 Molecule 2: residues 335..428 - init: molecule identity 403 identity constraints created. - init: molecule symdist "CA 35..128" "CA 335..428" 8836 symmetry constraints created. - znf42: read upl znf42.upl Distance constraint file "znf42.upl" read, 2237 upper limits, 2237 assignments. - znf42: read aco znf42.aco Angle constraint file "znf42.aco" read, 267 constraints for 267 angles. - znf42: calc_all structures=100 command=anneal steps=10000 100 structures selected. 100 random structures created (seed 35671). Structure annealed in 39 s, f = 12.7908. Structure annealed in 40 s, f = 16.4752. Structure annealed in 39 s, f = 14.3412. Structure annealed in 40 s, f = 179.575. Structure annealed in 41 s, f = 420.377. Structure annealed in 39 s, f = 24.1808. Structure annealed in 39 s, f = 13.2466. Structure annealed in 39 s, f = 14.0292. Structure annealed in 40 s, f = 16.4978. Structure annealed in 40 s, f = 13.6336. Structure annealed in 40 s, f = 34.3926. Structure annealed in 39 s, f = 12.8072. Structure annealed in 39 s, f = 13.0064. Structure annealed in 40 s, f = 12.6612. Structure annealed in 40 s, f = 10.6588. Structure annealed in 40 s, f = 11.8268. Structure annealed in 40 s, f = 16.2941. Structure annealed in 39 s, f = 15.5167. Structure annealed in 39 s, f = 14.1634. Structure annealed in 40 s, f = 10.7935. Structure annealed in 40 s, f = 16.7300. Structure annealed in 40 s, f = 136.646. Structure annealed in 40 s, f = 11.4049. Structure annealed in 40 s, f = 13.9985. Structure annealed in 40 s, f = 12.2439. Structure annealed in 39 s, f = 12.0619. Structure annealed in 39 s, f = 9.66520. Structure annealed in 39 s, f = 13.4191. Structure annealed in 39 s, f = 13.0994. Structure annealed in 39 s, f = 10.3494. Structure annealed in 39 s, f = 16.4539. Structure annealed in 40 s, f = 23.4979. Structure annealed in 40 s, f = 14.4339. Structure annealed in 40 s, f = 12.4831. Structure annealed in 42 s, f = 399.778. Structure annealed in 40 s, f = 13.9898. Structure annealed in 39 s, f = 12.5940. Structure annealed in 40 s, f = 10.6434. Structure annealed in 40 s, f = 19.3682. Structure annealed in 39 s, f = 12.6442. Structure annealed in 40 s, f = 17.0815. Structure annealed in 40 s, f = 32.3517. Structure annealed in 40 s, f = 13.6254. Structure annealed in 39 s, f = 13.1165. Structure annealed in 39 s, f = 16.5187. Structure annealed in 40 s, f = 10.0520. Structure annealed in 40 s, f = 10.8815. Structure annealed in 40 s, f = 12.9044. Structure annealed in 39 s, f = 10.7151. Structure annealed in 39 s, f = 10.8077. Structure annealed in 39 s, f = 13.3504. Structure annealed in 39 s, f = 16.6552. Structure annealed in 39 s, f = 12.4367. Structure annealed in 39 s, f = 14.1429. Structure annealed in 39 s, f = 11.2881. Structure annealed in 39 s, f = 12.8307. Structure annealed in 40 s, f = 11.8621. Structure annealed in 39 s, f = 16.2028. Structure annealed in 39 s, f = 12.3530. Structure annealed in 39 s, f = 12.0852. Structure annealed in 39 s, f = 11.3436. Structure annealed in 39 s, f = 10.7540. Structure annealed in 40 s, f = 22.1556. Structure annealed in 40 s, f = 177.274. Structure annealed in 40 s, f = 10.4772. Structure annealed in 40 s, f = 49.3878. Structure annealed in 40 s, f = 15.7135. Structure annealed in 40 s, f = 25.5190. Structure annealed in 40 s, f = 12.6242. Structure annealed in 40 s, f = 11.6082. Structure annealed in 40 s, f = 12.2157. Structure annealed in 40 s, f = 12.3960. Structure annealed in 40 s, f = 21.0988. Structure annealed in 39 s, f = 13.7492. Structure annealed in 39 s, f = 13.1713. Structure annealed in 39 s, f = 17.0197. Structure annealed in 39 s, f = 10.8459. Structure annealed in 39 s, f = 14.8855. Structure annealed in 39 s, f = 13.4755. Structure annealed in 39 s, f = 13.4803. Structure annealed in 39 s, f = 15.6969. Structure annealed in 40 s, f = 11.2285. Structure annealed in 40 s, f = 10.5931. Structure annealed in 39 s, f = 10.9144. Structure annealed in 40 s, f = 12.6340. Structure annealed in 40 s, f = 14.8181. Structure annealed in 39 s, f = 11.9227. Structure annealed in 39 s, f = 11.2510. Structure annealed in 39 s, f = 10.1173. Structure annealed in 40 s, f = 14.8921. Structure annealed in 39 s, f = 16.0654. Structure annealed in 40 s, f = 11.5917. Structure annealed in 39 s, f = 11.6876. Structure annealed in 40 s, f = 12.9152. Structure annealed in 41 s, f = 186.289. Structure annealed in 41 s, f = 445.192. Structure annealed in 40 s, f = 11.3743. Structure annealed in 40 s, f = 16.4889. Structure annealed in 39 s, f = 14.3020. Structure annealed in 40 s, f = 13.9312. 100 structures finished in 165 s (1 s/structure). - znf42: overview znf42.ovw structures=20 pdb Structural statistics: str target upper limits van der Waals torsion angles function # rms max # sum max # rms max 1 9.67 37 0.0231 0.47 4 16.5 0.30 2 1.0438 5.59 2 10.05 33 0.0232 0.49 6 15.6 0.39 1 0.9969 5.78 3 10.12 37 0.0241 0.49 6 15.8 0.30 1 0.8597 5.29 4 10.35 39 0.0244 0.46 5 17.4 0.26 1 0.8792 5.83 5 10.48 38 0.0250 0.56 4 16.7 0.23 2 1.0492 6.10 6 10.59 38 0.0232 0.47 6 17.0 0.48 2 1.0023 5.39 7 10.64 32 0.0238 0.64 6 17.6 0.48 0 0.8807 4.71 8 10.66 35 0.0244 0.56 4 16.8 0.28 3 1.1584 7.36 9 10.72 31 0.0247 0.58 5 17.5 0.28 5 1.2127 7.45 10 10.75 38 0.0251 0.52 3 16.5 0.24 1 0.9497 5.79 11 10.79 32 0.0231 0.57 6 17.2 0.30 3 1.0615 7.40 12 10.81 35 0.0235 0.47 8 17.2 0.28 1 0.9058 5.47 13 10.85 38 0.0238 0.55 6 17.5 0.24 2 1.1014 5.38 14 10.88 32 0.0239 0.50 7 17.8 0.35 1 0.9686 5.44 15 10.91 40 0.0244 0.45 6 17.8 0.30 2 0.9568 5.22 16 11.23 35 0.0241 0.56 8 19.0 0.33 1 0.9923 5.89 17 11.25 33 0.0239 0.63 9 19.8 0.30 2 1.0154 6.09 18 11.29 29 0.0239 0.56 8 18.8 0.30 1 1.0384 6.09 19 11.34 38 0.0249 0.54 5 18.4 0.40 2 0.9513 5.71 20 11.37 36 0.0258 0.58 4 18.1 0.22 2 1.1556 7.50 Ave 10.74 35 0.0241 0.53 6 17.5 0.31 2 1.0090 5.98 +/- 0.44 3 0.0007 0.05 2 1.0 0.07 1 0.0944 0.80 Min 9.67 29 0.0231 0.45 3 15.6 0.22 0 0.8597 4.71 Max 11.37 40 0.0258 0.64 9 19.8 0.48 5 1.2127 7.50 Cut 0.20 0.20 5.00 Overview file "znf42.ovw" written. PDB coordinate file "znf42.pdb" written, 20 conformers. - znf42: ramaplot znf42.rama nobackground label Struct fav add gen dis ------ --- --- --- --- 1 138 14 0 0 2 143 9 0 0 3 142 10 0 0 4 134 18 0 0 forrtl: Stale NFS file handle forrtl: severe (38): error during write, unit 41, file /user/francis/znf42/8cyana/113b/znf42.grf Image PC Routine Line Source cyanaexe.intel-la 40000000004FC670 Unknown Unknown Unknown cyanaexe.intel-la 40000000004F8A50 Unknown Unknown Unknown cyanaexe.intel-la 40000000004A0250 Unknown Unknown Unknown cyanaexe.intel-la 40000000004207C0 Unknown Unknown Unknown cyanaexe.intel-la 400000000041FB70 Unknown Unknown Unknown cyanaexe.intel-la 4000000000473F90 Unknown Unknown Unknown cyanaexe.intel-la 4000000000470770 Unknown Unknown Unknown cyanaexe.intel-la 40000000002C5A30 Unknown Unknown Unknown cyanaexe.intel-la 40000000002C51E0 Unknown Unknown Unknown cyanaexe.intel-la 40000000002B08B0 Unknown Unknown Unknown cyanaexe.intel-la 4000000000295780 Unknown Unknown Unknown cyanaexe.intel-la 4000000000007370 Unknown Unknown Unknown cyanaexe.intel-la 4000000000006A90 Unknown Unknown Unknown libc.so.6.1 2000000000456970 Unknown Unknown Unknown cyanaexe.intel-la 40000000000068C0 Unknown Unknown Unknown forrtl: severe (28): CLOSE error, unit 41, file "Unknown" Image PC Routine Line Source cyanaexe.intel-la 40000000004FC670 Unknown Unknown Unknown cyanaexe.intel-la 40000000004F8A50 Unknown Unknown Unknown cyanaexe.intel-la 40000000004A0250 Unknown Unknown Unknown cyanaexe.intel-la 40000000004207C0 Unknown Unknown Unknown cyanaexe.intel-la 4000000000423180 Unknown Unknown Unknown cyanaexe.intel-la 4000000000420620 Unknown Unknown Unknown cyanaexe.intel-la 400000000041FB70 Unknown Unknown Unknown cyanaexe.intel-la 4000000000473F90 Unknown Unknown Unknown cyanaexe.intel-la 4000000000470770 Unknown Unknown Unknown cyanaexe.intel-la 40000000002C5A30 Unknown Unknown Unknown cyanaexe.intel-la 40000000002C51E0 Unknown Unknown Unknown cyanaexe.intel-la 40000000002B08B0 Unknown Unknown Unknown cyanaexe.intel-la 4000000000295780 Unknown Unknown Unknown cyanaexe.intel-la 4000000000007370 Unknown Unknown Unknown cyanaexe.intel-la 4000000000006A90 Unknown Unknown Unknown libc.so.6.1 2000000000456970 Unknown Unknown Unknown cyanaexe.intel-la 40000000000068C0 Unknown Unknown Unknown getRegFromUnwindContext: Can't get Gr0 from UnwindContext, using 0 getRegFromUnwindContext: Can't get Gr0 from UnwindContext, using 0 MPI_Recv: process in local group is dead (rank 1, comm 3) MPI_Recv: process in local group is dead (rank 2, comm 3) MPI_Recv: process in local group is dead (rank 4, comm 3) Rank (4, MPI_COMM_WORLD): Call stack within LAM: Rank (4, MPI_COMM_WORLD): - MPI_Recv() Rank (4, MPI_COMM_WORLD): - MPI_Bcast() Rank (4, MPI_COMM_WORLD): - MPI_Bcast() Rank (4, MPI_COMM_WORLD): - main() Rank (2, MPI_COMM_WORLD): Call stack within LAM: Rank (2, MPI_COMM_WORLD): - MPI_Recv() Rank (2, MPI_COMM_WORLD): - MPI_Bcast() Rank (2, MPI_COMM_WORLD): - MPI_Bcast() Rank (2, MPI_COMM_WORLD): - main() ----------------------------------------------------------------------------- One of the processes started by mpirun has exited with a nonzero exit code. This typically indicates that the process finished in error. If your process did not finish in error, be sure to include a "return 0" or "exit(0)" in your C code before exiting the application. PID 21043 failed on node n0 (192.168.96.101) with exit status 28. ----------------------------------------------------------------------------- MPI_Recv: process in local group is dead (rank 3, comm 3) Rank (6, MPI_COMM_WORLD): Call stack within LAM: Rank (6, MPI_COMM_WORLD): - MPI_Recv() Rank (6, MPI_COMM_WORLD): - MPI_Bcast() Rank (6, MPI_COMM_WORLD): - MPI_Bcast() Rank (6, MPI_COMM_WORLD): - main() Rank (8, MPI_COMM_WORLD): Call stack within LAM: Rank (8, MPI_COMM_WORLD): - MPI_Recv() Rank (8, MPI_COMM_WORLD): - MPI_Bcast() Rank (8, MPI_COMM_WORLD): - MPI_Bcast() Rank (8, MPI_COMM_WORLD): - main() LAM 7.2b1svn10112005/MPI 2 C++/ROMIO - Indiana University 02-Dec-2005 19:50:37