Warning: no access to tty (Bad file descriptor). Thus no job control in this shell. 01-Dec-2005 17:50:04 n-1<13006> ssi:boot:base:linear: booting n0 (wolf01) n-1<13006> ssi:boot:base:linear: booting n1 (wolf02) n-1<13006> ssi:boot:base:linear: booting n2 (wolf03) n-1<13006> ssi:boot:base:linear: booting n3 (wolf04) n-1<13006> ssi:boot:base:linear: booting n4 (wolf05) n-1<13006> ssi:boot:base:linear: booting n5 (wolf06) n-1<13006> ssi:boot:base:linear: booting n6 (wolf07) n-1<13006> ssi:boot:base:linear: booting n7 (wolf08) n-1<13006> ssi:boot:base:linear: booting n8 (wolf09) n-1<13006> ssi:boot:base:linear: booting n9 (wolf10) n-1<13006> ssi:boot:base:linear: booting n10 (wolf11) n-1<13006> ssi:boot:base:linear: booting n11 (wolf12) n-1<13006> ssi:boot:base:linear: booting n12 (wolf13) n-1<13006> 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, 3482 peaks, 3120 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 3120 0.000 0.003 0.340 0.012 2 0.030 2 3432 0.000 0.001 0.340 0.014 6 0.030 3 3432 0.000 0.000 0.297 0.025 0 0.450 - peakcheck: atom shift check Atom Residue Shift Median Deviation Peaks QB GLN 82 1.998 2.338 0.340 8 1 shift with spread larger than tolerance. - peakcheck: peak deviations Peak Dim Deviation Atom Residue 304 1 0.340 QB GLN 82 306 2 0.340 QB GLN 82 307 1 0.340 QB GLN 82 307 2 0.340 QB GLN 82 308 2 0.340 QB GLN 82 4442 2 0.340 QB GLN 82 4443 2 0.340 QB GLN 82 4444 2 0.340 QB GLN 82 8 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, 1111 assignments. - peakcheck: peaks fit Deviations from chemical shift list: Dim Peaks Median Average Maximum RMSD Number Tolerance 1 1111 0.002 0.003 0.353 0.015 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 QB GLN 82 1.998 2.351 0.353 1 1 shift with spread larger than tolerance. - peakcheck: peak deviations Peak Dim Deviation Atom Residue 1423 1 0.353 QB GLN 82 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. ------------------------------------------------------------ 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, 3482 peaks, 3120 assignments. - calibration: peaks select "** list=1" 3482 of 3482 peaks, 3482 of 3482 assignments selected. - calibration: peaks set volume=abs(volume) Volume of 3482 peaks set. - calibration: peaks simplecal constant=3.0E7 Calibration constant for peak list 1: 3.00E+07 Upper limit set for 3482 peaks. - calibration: caltab peaks Distance bounds: -2.99 A: 328 9.4% 3.00-3.99 A: 773 22.2% 4.00-4.99 A: 1387 39.8% 5.00-5.99 A: 992 28.5% 6.00- A: 0 0.0% All: 3482 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, 1111 assignments. - calibration: peaks select "** list=2" 1273 of 4755 peaks, 1273 of 4755 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 5036 peaks, 281 of 5036 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 5261 peaks, 225 of 5261 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 ** 5261 of 5261 peaks, 5261 of 5261 assignments selected. - znf42: peaks calibrate ** simple 4118 upper limits added, 8/486 at lower/upper bound, average 4.46 A. - znf42: write upl znf42-in.upl Distance constraint file "znf42-in.upl" written, 4118 upper limits, 4118 assignments. - znf42: distance modify Number of modified constraints: 2186 - znf42: write upl znf42.upl Distance constraint file "znf42.upl" written, 2186 upper limits, 2186 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, 2186 upper limits, 2186 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 = 18.6608. Structure annealed in 40 s, f = 18.0432. Structure annealed in 40 s, f = 26.4088. Structure annealed in 39 s, f = 18.9483. Structure annealed in 40 s, f = 179.147. Structure annealed in 40 s, f = 13.3972. Structure annealed in 39 s, f = 50.8097. Structure annealed in 39 s, f = 13.6891. Structure annealed in 39 s, f = 15.9579. Structure annealed in 40 s, f = 18.6563. Structure annealed in 39 s, f = 16.3827. Structure annealed in 39 s, f = 13.4178. Structure annealed in 39 s, f = 14.2690. Structure annealed in 39 s, f = 16.6847. Structure annealed in 39 s, f = 14.1904. Structure annealed in 40 s, f = 14.8497. Structure annealed in 40 s, f = 35.5221. Structure annealed in 39 s, f = 17.7854. Structure annealed in 39 s, f = 15.0041. Structure annealed in 39 s, f = 18.9275. Structure annealed in 40 s, f = 15.7983. Structure annealed in 40 s, f = 15.9956. Structure annealed in 39 s, f = 14.1072. Structure annealed in 39 s, f = 19.9516. Structure annealed in 40 s, f = 15.4933. Structure annealed in 39 s, f = 18.3469. Structure annealed in 40 s, f = 16.7417. Structure annealed in 39 s, f = 15.4542. Structure annealed in 39 s, f = 16.7584. Structure annealed in 39 s, f = 12.8005. Structure annealed in 39 s, f = 16.4963. Structure annealed in 39 s, f = 20.7623. Structure annealed in 39 s, f = 15.3644. Structure annealed in 39 s, f = 14.3062. Structure annealed in 39 s, f = 12.8375. Structure annealed in 39 s, f = 16.2899. Structure annealed in 40 s, f = 14.0326. Structure annealed in 39 s, f = 14.6932. Structure annealed in 40 s, f = 14.7926. Structure annealed in 39 s, f = 17.4366. Structure annealed in 39 s, f = 15.1783. Structure annealed in 40 s, f = 19.5789. Structure annealed in 40 s, f = 15.3404. Structure annealed in 40 s, f = 18.1740. Structure annealed in 39 s, f = 16.0201. Structure annealed in 40 s, f = 15.2869. Structure annealed in 42 s, f = 336.253. Structure annealed in 40 s, f = 17.9750. Structure annealed in 40 s, f = 14.1126. Structure annealed in 40 s, f = 13.9324. Structure annealed in 39 s, f = 11.9880. Structure annealed in 39 s, f = 14.1312. Structure annealed in 40 s, f = 13.6534. Structure annealed in 39 s, f = 14.4127. Structure annealed in 39 s, f = 15.1882. Structure annealed in 40 s, f = 18.1149. Structure annealed in 40 s, f = 17.1060. Structure annealed in 40 s, f = 15.5879. Structure annealed in 39 s, f = 13.9547. Structure annealed in 39 s, f = 14.2285. Structure annealed in 39 s, f = 21.6737. Structure annealed in 39 s, f = 21.7630. Structure annealed in 39 s, f = 16.9786. Structure annealed in 39 s, f = 11.8291. Structure annealed in 40 s, f = 15.1557. Structure annealed in 39 s, f = 16.9480. Structure annealed in 40 s, f = 15.7538. Structure annealed in 39 s, f = 19.5039. Structure annealed in 39 s, f = 12.7884. Structure annealed in 40 s, f = 14.1422. Structure annealed in 40 s, f = 13.5730. Structure annealed in 39 s, f = 13.1124. Structure annealed in 39 s, f = 14.4271. Structure annealed in 41 s, f = 133.043. Structure annealed in 39 s, f = 13.3289. Structure annealed in 39 s, f = 17.7181. Structure annealed in 39 s, f = 13.8663. Structure annealed in 39 s, f = 14.4502. Structure annealed in 39 s, f = 12.1889. Structure annealed in 39 s, f = 16.4088. Structure annealed in 39 s, f = 14.9167. Structure annealed in 40 s, f = 16.5640. Structure annealed in 39 s, f = 24.6190. Structure annealed in 39 s, f = 12.3509. Structure annealed in 39 s, f = 15.1712. Structure annealed in 39 s, f = 15.5316. Structure annealed in 39 s, f = 14.2998. Structure annealed in 39 s, f = 13.7607. Structure annealed in 39 s, f = 15.3636. Structure annealed in 39 s, f = 14.8817. Structure annealed in 40 s, f = 22.3321. Structure annealed in 39 s, f = 24.4712. Structure annealed in 39 s, f = 13.7501. Structure annealed in 39 s, f = 15.4561. Structure annealed in 39 s, f = 14.3737. Structure annealed in 40 s, f = 180.085. Structure annealed in 40 s, f = 14.1792. Structure annealed in 40 s, f = 19.8392. Structure annealed in 40 s, f = 15.0979. Structure annealed in 40 s, f = 14.2303. 100 structures finished in 166 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 11.83 38 0.0269 0.79 10 17.3 0.30 1 0.9660 6.17 2 11.99 43 0.0286 0.78 7 17.0 0.30 1 0.9709 6.28 3 12.19 42 0.0284 0.81 7 18.9 0.33 3 1.0524 6.40 4 12.35 40 0.0279 0.85 7 17.7 0.32 2 1.1548 7.47 5 12.79 42 0.0282 0.75 8 17.3 0.32 3 1.1273 6.37 6 12.80 36 0.0274 0.75 12 18.6 0.26 1 1.0901 6.11 7 12.84 37 0.0283 0.85 7 17.5 0.28 1 1.0553 6.51 8 13.11 42 0.0271 0.76 9 19.4 0.33 3 1.0995 6.10 9 13.33 39 0.0295 0.81 11 18.1 0.31 2 1.1096 6.24 10 13.40 39 0.0281 0.80 11 19.3 0.24 3 1.1747 7.25 11 13.42 43 0.0288 0.74 4 17.0 0.27 2 1.0670 5.80 12 13.57 42 0.0289 0.76 11 18.9 0.31 3 1.1683 7.45 13 13.65 47 0.0288 0.77 5 18.0 0.26 2 1.0653 6.56 14 13.69 42 0.0304 0.81 7 18.6 0.28 1 0.9483 5.77 15 13.75 46 0.0291 0.82 7 18.6 0.23 3 1.1304 6.30 16 13.76 44 0.0302 0.76 7 18.1 0.24 4 1.1752 8.45 17 13.87 40 0.0292 0.82 7 19.7 0.31 3 1.1353 7.33 18 13.93 39 0.0275 0.76 13 19.6 0.26 5 1.1338 6.41 19 13.95 48 0.0315 0.89 9 18.9 0.25 1 0.9970 7.82 20 14.03 39 0.0274 0.74 10 20.4 0.42 5 1.1914 6.76 Ave 13.21 41 0.0286 0.79 8 18.4 0.29 2 1.0906 6.68 +/- 0.67 3 0.0011 0.04 2 0.9 0.04 1 0.0723 0.70 Min 11.83 36 0.0269 0.74 4 17.0 0.23 1 0.9483 5.77 Max 14.03 48 0.0315 0.89 13 20.4 0.42 5 1.1914 8.45 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 ------ --- --- --- --- 1 137 15 0 0 2 136 14 2 0 forrtl: Stale NFS file handle forrtl: severe (38): error during write, unit 41, file /user/francis/znf42/8cyana/112a/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) ----------------------------------------------------------------------------- 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 13088 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 6, comm 3) 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 17:53:20