Warning: no access to tty (Bad file descriptor). Thus no job control in this shell. 01-Dec-2005 14:39:30 n-1<11605> ssi:boot:base:linear: booting n0 (wolf01) n-1<11605> ssi:boot:base:linear: booting n1 (wolf02) n-1<11605> ssi:boot:base:linear: booting n2 (wolf03) n-1<11605> ssi:boot:base:linear: booting n3 (wolf04) n-1<11605> ssi:boot:base:linear: booting n4 (wolf05) n-1<11605> ssi:boot:base:linear: booting n5 (wolf06) n-1<11605> ssi:boot:base:linear: booting n6 (wolf07) n-1<11605> ssi:boot:base:linear: booting n7 (wolf08) n-1<11605> ssi:boot:base:linear: booting n8 (wolf09) n-1<11605> ssi:boot:base:linear: booting n9 (wolf10) n-1<11605> ssi:boot:base:linear: booting n10 (wolf11) n-1<11605> ssi:boot:base:linear: booting n11 (wolf12) n-1<11605> ssi:boot:base:linear: booting n12 (wolf13) n-1<11605> 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 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, 3485 peaks, 3082 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 3082 0.000 0.002 0.131 0.009 1 0.030 2 3410 0.000 0.000 0.027 0.003 0 0.030 3 3410 0.000 0.001 0.297 0.027 0 0.450 - peakcheck: atom shift check Atom Residue Shift Median Deviation Peaks QD PHE 92 6.917 6.925 0.131 10 1 shift with spread larger than tolerance. - peakcheck: peak deviations Peak Dim Deviation Atom Residue 3240 1 0.131 QD PHE 92 1 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, 1110 assignments. - peakcheck: peaks fit Deviations from chemical shift list: Dim Peaks Median Average Maximum RMSD Number Tolerance 1 1110 0.002 0.002 0.030 0.011 1 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 QD1 LEU 118 0.930 0.902 0.030 3 1 shift with spread larger than tolerance. - peakcheck: peak deviations Peak Dim Deviation Atom Residue 1240 1 -0.030 QD1 LEU 118 1 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, 222 assignments. - peakcheck: peaks fit Deviations from chemical shift list: Dim Peaks Median Average Maximum RMSD Number Tolerance 1 222 0.004 0.005 0.030 0.013 0 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 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 constant=3.0E7,1.2E7,2.0E 7 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, 3485 peaks, 3082 assignments. - calibration: peaks select "** list=1" 3485 of 3485 peaks, 3485 of 3485 assignments selected. - calibration: peaks set volume=abs(volume) Volume of 3485 peaks set. - calibration: peaks simplecal constant=3.0E7 Calibration constant for peak list 1: 3.00E+07 Upper limit set for 3485 peaks. - calibration: caltab peaks Distance bounds: -2.99 A: 330 9.5% 3.00-3.99 A: 764 21.9% 4.00-4.99 A: 1365 39.2% 5.00-5.99 A: 1024 29.4% 6.00- A: 0 0.0% All: 3485 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, 1110 assignments. - calibration: peaks select "** list=2" 1273 of 4758 peaks, 1273 of 4758 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, 222 assignments. - calibration: peaks select "** list=3" 281 of 5039 peaks, 281 of 5039 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: peaks select ** 5039 of 5039 peaks, 5039 of 5039 assignments selected. - znf42: peaks calibrate ** simple 3935 upper limits added, 9/503 at lower/upper bound, average 4.47 A. - znf42: write upl znf42-in.upl Distance constraint file "znf42-in.upl" written, 3935 upper limits, 3935 assignments. - znf42: distance modify Number of modified constraints: 2099 - znf42: write upl znf42.upl Distance constraint file "znf42.upl" written, 2099 upper limits, 2099 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, 2099 upper limits, 2099 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 = 11.5692. Structure annealed in 39 s, f = 11.6423. Structure annealed in 40 s, f = 13.2757. Structure annealed in 39 s, f = 11.9239. Structure annealed in 39 s, f = 10.5607. Structure annealed in 39 s, f = 17.3448. Structure annealed in 39 s, f = 51.5028. Structure annealed in 40 s, f = 17.7375. Structure annealed in 39 s, f = 19.7795. Structure annealed in 39 s, f = 13.1177. Structure annealed in 39 s, f = 11.9203. Structure annealed in 39 s, f = 9.93481. Structure annealed in 39 s, f = 14.7769. Structure annealed in 39 s, f = 10.4808. Structure annealed in 39 s, f = 16.8249. Structure annealed in 40 s, f = 10.6497. Structure annealed in 39 s, f = 9.74995. Structure annealed in 41 s, f = 402.542. Structure annealed in 39 s, f = 21.9072. Structure annealed in 39 s, f = 10.3567. Structure annealed in 39 s, f = 18.1275. Structure annealed in 39 s, f = 12.7212. Structure annealed in 39 s, f = 42.7169. Structure annealed in 39 s, f = 11.5467. Structure annealed in 39 s, f = 9.62648. Structure annealed in 39 s, f = 15.2761. Structure annealed in 39 s, f = 11.8630. Structure annealed in 39 s, f = 11.0841. Structure annealed in 39 s, f = 9.46056. Structure annealed in 39 s, f = 17.4922. Structure annealed in 41 s, f = 166.771. Structure annealed in 39 s, f = 10.2368. Structure annealed in 40 s, f = 17.8886. Structure annealed in 39 s, f = 16.9712. Structure annealed in 39 s, f = 19.9292. Structure annealed in 39 s, f = 10.3367. Structure annealed in 39 s, f = 10.6433. Structure annealed in 39 s, f = 9.91767. Structure annealed in 39 s, f = 15.2784. Structure annealed in 39 s, f = 16.0033. Structure annealed in 39 s, f = 13.3689. Structure annealed in 39 s, f = 9.21612. Structure annealed in 39 s, f = 15.2543. Structure annealed in 39 s, f = 10.5810. Structure annealed in 39 s, f = 10.2968. Structure annealed in 39 s, f = 12.2331. Structure annealed in 42 s, f = 414.404. Structure annealed in 39 s, f = 30.6834. Structure annealed in 40 s, f = 182.242. Structure annealed in 39 s, f = 14.1828. Structure annealed in 39 s, f = 10.1677. Structure annealed in 39 s, f = 17.2836. Structure annealed in 39 s, f = 13.1726. Structure annealed in 39 s, f = 8.51002. Structure annealed in 40 s, f = 21.6418. Structure annealed in 39 s, f = 8.00005. Structure annealed in 40 s, f = 16.6396. Structure annealed in 39 s, f = 14.8005. Structure annealed in 40 s, f = 13.3835. Structure annealed in 39 s, f = 16.5192. Structure annealed in 39 s, f = 20.0381. Structure annealed in 39 s, f = 16.6567. Structure annealed in 39 s, f = 8.46011. Structure annealed in 39 s, f = 10.4713. Structure annealed in 41 s, f = 372.173. Structure annealed in 39 s, f = 10.5649. Structure annealed in 41 s, f = 193.434. Structure annealed in 41 s, f = 300.838. Structure annealed in 39 s, f = 13.4012. Structure annealed in 40 s, f = 20.2300. Structure annealed in 39 s, f = 14.4558. Structure annealed in 39 s, f = 12.9850. Structure annealed in 39 s, f = 9.85712. Structure annealed in 39 s, f = 9.94684. Structure annealed in 39 s, f = 21.1699. Structure annealed in 40 s, f = 428.756. Structure annealed in 39 s, f = 18.6167. Structure annealed in 39 s, f = 25.2178. Structure annealed in 39 s, f = 16.9753. Structure annealed in 39 s, f = 15.9744. Structure annealed in 39 s, f = 8.70363. Structure annealed in 39 s, f = 10.0605. Structure annealed in 39 s, f = 14.9358. Structure annealed in 39 s, f = 10.0895. Structure annealed in 39 s, f = 15.3313. Structure annealed in 39 s, f = 11.8629. Structure annealed in 39 s, f = 11.3152. Structure annealed in 39 s, f = 9.33790. Structure annealed in 39 s, f = 10.7458. Structure annealed in 40 s, f = 58.7554. Structure annealed in 39 s, f = 13.6857. Structure annealed in 39 s, f = 16.0120. Structure annealed in 40 s, f = 10.3110. Structure annealed in 39 s, f = 11.4843. Structure annealed in 40 s, f = 69.9841. Structure annealed in 39 s, f = 10.3231. Structure annealed in 41 s, f = 318.205. Structure annealed in 39 s, f = 10.5889. Structure annealed in 39 s, f = 14.6924. Structure annealed in 39 s, f = 9.28712. 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 8.00 22 0.0234 0.58 3 14.3 0.28 0 0.7634 4.06 2 8.46 29 0.0229 0.54 3 15.7 0.28 0 0.7528 3.60 3 8.51 30 0.0244 0.83 5 14.3 0.28 0 0.6586 3.34 4 8.70 25 0.0246 0.78 3 14.6 0.24 0 0.8331 4.46 5 9.22 25 0.0234 0.75 6 15.7 0.28 1 0.9783 5.46 6 9.29 30 0.0250 0.60 3 15.9 0.29 0 0.8315 4.47 7 9.34 33 0.0241 0.81 7 15.9 0.26 0 0.7761 3.86 8 9.46 31 0.0237 0.53 5 15.7 0.27 1 0.9298 5.42 9 9.63 30 0.0242 0.59 4 16.1 0.24 0 0.8312 4.37 10 9.75 32 0.0256 0.62 5 16.8 0.22 1 0.8111 5.38 11 9.86 25 0.0230 0.58 7 17.6 0.28 2 0.9001 5.64 12 9.92 35 0.0258 0.69 4 14.2 0.22 1 0.9176 6.10 13 9.94 28 0.0251 0.69 4 16.7 0.23 2 0.9876 6.26 14 9.95 24 0.0249 0.85 9 17.0 0.30 0 0.7134 3.68 15 10.06 31 0.0243 0.71 7 15.7 0.28 0 0.9210 4.14 16 10.09 35 0.0259 0.54 6 16.6 0.27 3 0.9145 5.82 17 10.17 32 0.0257 0.72 7 15.6 0.26 1 0.9761 6.19 18 10.24 36 0.0253 0.61 7 16.8 0.28 0 0.8099 3.78 19 10.30 30 0.0239 0.75 6 16.1 0.28 0 0.8952 4.47 20 10.31 32 0.0264 0.58 6 16.9 0.27 0 0.8266 4.80 Ave 9.56 30 0.0246 0.67 5 15.9 0.27 1 0.8514 4.76 +/- 0.66 4 0.0010 0.10 2 1.0 0.02 1 0.0890 0.92 Min 8.00 22 0.0229 0.53 3 14.2 0.22 0 0.6586 3.34 Max 10.31 36 0.0264 0.85 9 17.6 0.30 3 0.9876 6.26 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 2 138 11 3 0 3 136 16 0 0 4 138 14 0 0 forrtl: Stale NFS file handle forrtl: severe (38): error during write, unit 41, file /user/francis/znf42/8cyana/111a_nofc/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 2, comm 3) MPI_Recv: process in local group is dead (rank 4, comm 3) MPI_Recv: process in local group is dead (rank 8, comm 3) MPI_Recv: process in local group is dead (rank 1, comm 3) 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 11687 failed on node n0 (192.168.96.101) with exit status 28. ----------------------------------------------------------------------------- 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() 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() MPI_Recv: process in local group is dead (rank 5, comm 3) MPI_Recv: process in local group is dead (rank 6, comm 3) Rank (10, MPI_COMM_WORLD): Call stack within LAM: Rank (10, MPI_COMM_WORLD): - MPI_Recv() Rank (10, MPI_COMM_WORLD): - MPI_Bcast() Rank (10, MPI_COMM_WORLD): - MPI_Bcast() Rank (10, MPI_COMM_WORLD): - main() Rank (12, MPI_COMM_WORLD): Call stack within LAM: Rank (12, MPI_COMM_WORLD): - MPI_Recv() Rank (12, MPI_COMM_WORLD): - MPI_Bcast() Rank (12, MPI_COMM_WORLD): - MPI_Bcast() Rank (12, MPI_COMM_WORLD): - main() Rank (16, MPI_COMM_WORLD): Call stack within LAM: Rank (16, MPI_COMM_WORLD): - MPI_Recv() Rank (16, MPI_COMM_WORLD): - MPI_Bcast() Rank (16, MPI_COMM_WORLD): - MPI_Bcast() Rank (16, MPI_COMM_WORLD): - main() LAM 7.2b1svn10112005/MPI 2 C++/ROMIO - Indiana University 01-Dec-2005 14:42:48