Warning: no access to tty (Bad file descriptor). Thus no job control in this shell. 13-Dec-2005 23:11:04 n-1<17730> ssi:boot:base:linear: booting n0 (wolf01) n-1<17730> ssi:boot:base:linear: booting n1 (wolf02) n-1<17730> ssi:boot:base:linear: booting n2 (wolf03) n-1<17730> ssi:boot:base:linear: booting n3 (wolf04) n-1<17730> ssi:boot:base:linear: booting n4 (wolf05) n-1<17730> ssi:boot:base:linear: booting n5 (wolf06) n-1<17730> ssi:boot:base:linear: booting n6 (wolf07) n-1<17730> ssi:boot:base:linear: booting n7 (wolf08) n-1<17730> ssi:boot:base:linear: booting n8 (wolf09) n-1<17730> ssi:boot:base:linear: booting n9 (wolf10) n-1<17730> ssi:boot:base:linear: booting n10 (wolf11) n-1<17730> ssi:boot:base:linear: booting n11 (wolf12) n-1<17730> ssi:boot:base:linear: booting n12 (wolf13) n-1<17730> 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, 1983 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, 1983 chemical shifts. - peakcheck: read peaks c13no format= Peak list "c13no.peaks" read, 3489 peaks, 3187 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 3187 0.000 0.002 0.030 0.009 0 0.030 2 3485 0.000 0.000 0.026 0.002 0 0.030 3 3485 0.000 -0.001 0.297 0.025 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 : n15no Proton list: znf42 - peakcheck: read prot znf42 unknown=skip Chemical shift list "znf42.prot" read, 1983 chemical shifts. - peakcheck: read peaks n15no format= *** WARNING: Inconsistent heavy atom assignment for peak 1410. Peak list "n15no.peaks" read, 1274 peaks, 1100 assignments. - peakcheck: peaks fit Deviations from chemical shift list: Dim Peaks Median Average Maximum RMSD Number Tolerance 1 1100 0.002 0.002 0.030 0.011 0 0.030 2 1272 0.000 0.000 0.011 0.001 0 0.030 3 1272 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, 1983 chemical shifts. - peakcheck: read peaks c13ar format= Peak list "c13ar.peaks" read, 292 peaks, 238 assignments. - peakcheck: peaks fit Deviations from chemical shift list: Dim Peaks Median Average Maximum RMSD Number Tolerance 1 238 0.005 0.005 0.030 0.012 0 0.030 2 291 0.000 0.000 0.000 0.000 0 0.030 3 291 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, 1983 chemical shifts. - peakcheck: read peaks fc12no format= Peak list "fc12no.peaks" read, 233 peaks, 143 assignments. - peakcheck: peaks fit Deviations from chemical shift list: Dim Peaks Median Average Maximum RMSD Number Tolerance 1 143 -0.005 -0.002 0.029 0.016 0 0.030 2 225 0.000 -0.001 0.014 0.005 0 0.030 3 225 0.000 -0.005 0.111 0.026 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=3.5E7,1.7 E7,2.5E7,1.0E7 dref=4.2 - calibration: read prot znf42 unknown=warn Chemical shift list "znf42.prot" read, 1983 chemical shifts. - calibration: read peaks c13no format= Peak list "c13no.peaks" read, 3489 peaks, 3187 assignments. - calibration: peaks select "** list=1" 3489 of 3489 peaks, 3489 of 3489 assignments selected. - calibration: peaks set volume=abs(volume) Volume of 3489 peaks set. - calibration: peaks simplecal constant=3.5E7 Calibration constant for peak list 1: 3.50E+07 Upper limit set for 3489 peaks. - calibration: caltab peaks Distance bounds: -2.99 A: 297 8.5% 3.00-3.99 A: 679 19.5% 4.00-4.99 A: 1372 39.3% 5.00-5.99 A: 1141 32.7% 6.00- A: 0 0.0% All: 3489 100.0% - calibration: read prot znf42 unknown=warn append Chemical shift list "znf42.prot" read, 1983 chemical shifts. - calibration: read peaks n15no format= append *** WARNING: Inconsistent heavy atom assignment for peak 1410. Peak list "n15no.peaks" read, 1274 peaks, 1100 assignments. - calibration: peaks select "** list=2" 1274 of 4763 peaks, 1274 of 4763 assignments selected. - calibration: peaks set volume=abs(volume) Volume of 1274 peaks set. - calibration: peaks simplecal constant=1.7E7 Calibration constant for peak list 2: 1.70E+07 Upper limit set for 1274 peaks. - calibration: caltab peaks Distance bounds: -2.99 A: 74 5.8% 3.00-3.99 A: 227 17.8% 4.00-4.99 A: 493 38.7% 5.00-5.99 A: 480 37.7% 6.00- A: 0 0.0% All: 1274 100.0% - calibration: read prot znf42 unknown=warn append Chemical shift list "znf42.prot" read, 1983 chemical shifts. - calibration: read peaks c13ar format= append Peak list "c13ar.peaks" read, 292 peaks, 238 assignments. - calibration: peaks select "** list=3" 292 of 5055 peaks, 292 of 5055 assignments selected. - calibration: peaks set volume=abs(volume) Volume of 292 peaks set. - calibration: peaks simplecal constant=2.5E7 Calibration constant for peak list 3: 2.50E+07 Upper limit set for 292 peaks. - calibration: caltab peaks Distance bounds: -2.99 A: 19 6.5% 3.00-3.99 A: 47 16.1% 4.00-4.99 A: 160 54.8% 5.00-5.99 A: 66 22.6% 6.00- A: 0 0.0% All: 292 100.0% - calibration: read prot znf42 unknown=warn append Chemical shift list "znf42.prot" read, 1983 chemical shifts. - calibration: read peaks fc12no format= append Peak list "fc12no.peaks" read, 233 peaks, 143 assignments. - calibration: peaks select "** list=4" 233 of 5288 peaks, 233 of 5288 assignments selected. - calibration: peaks set volume=abs(volume) Volume of 233 peaks set. - calibration: peaks simplecal constant=1.0E7 Calibration constant for peak list 4: 1.00E+07 Upper limit set for 233 peaks. - calibration: caltab peaks Distance bounds: -2.99 A: 3 1.3% 3.00-3.99 A: 55 23.6% 4.00-4.99 A: 159 68.2% 5.00-5.99 A: 16 6.9% 6.00- A: 0 0.0% All: 233 100.0% - calibration: peaks select ** 5288 of 5288 peaks, 5288 of 5288 assignments selected. - znf42: peaks calibrate ** simple 4173 upper limits added, 2/695 at lower/upper bound, average 4.58 A. - znf42: write upl znf42-in.upl Distance constraint file "znf42-in.upl" written, 4173 upper limits, 4173 assignments. - znf42: distance modify Number of modified constraints: 2128 - znf42: write upl znf42.upl Distance constraint file "znf42.upl" written, 2128 upper limits, 2128 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, 2128 upper limits, 2128 assignments. - znf42: read aco znf42.aco Angle constraint file "znf42.aco" read, 264 constraints for 264 angles. - znf42: calc_all structures=100 command=anneal steps=10000 100 structures selected. 100 random structures created (seed 35671). Structure annealed in 38 s, f = 5.53739. Structure annealed in 38 s, f = 2.58613. Structure annealed in 39 s, f = 6.94447. Structure annealed in 38 s, f = 3.10315. Structure annealed in 39 s, f = 1.90457. Structure annealed in 39 s, f = 2.66146. Structure annealed in 39 s, f = 4.04874. Structure annealed in 39 s, f = 1.43958. Structure annealed in 39 s, f = 1.38214. Structure annealed in 39 s, f = 10.2927. Structure annealed in 39 s, f = 2.63201. Structure annealed in 38 s, f = 8.18864. Structure annealed in 39 s, f = 3.03893. Structure annealed in 38 s, f = 2.10508. Structure annealed in 39 s, f = 6.89110. Structure annealed in 39 s, f = 4.48379. Structure annealed in 39 s, f = 2.11736. Structure annealed in 39 s, f = 1.77834. Structure annealed in 39 s, f = 4.37026. Structure annealed in 39 s, f = 4.34771. Structure annealed in 39 s, f = 1.64506. Structure annealed in 39 s, f = 2.13727. Structure annealed in 39 s, f = 2.04848. Structure annealed in 39 s, f = 2.81708. Structure annealed in 39 s, f = 1.34909. Structure annealed in 39 s, f = 6.31747. Structure annealed in 38 s, f = 6.76050. Structure annealed in 39 s, f = 97.7339. Structure annealed in 39 s, f = 7.41385. Structure annealed in 39 s, f = 1.71370. Structure annealed in 39 s, f = 3.14036. Structure annealed in 38 s, f = 1.96993. Structure annealed in 40 s, f = 108.097. Structure annealed in 39 s, f = 2.62246. Structure annealed in 38 s, f = 3.07832. Structure annealed in 39 s, f = 5.77258. Structure annealed in 39 s, f = 2.15033. Structure annealed in 39 s, f = 2.08482. Structure annealed in 38 s, f = 3.17250. Structure annealed in 39 s, f = 4.17002. Structure annealed in 39 s, f = 3.23640. Structure annealed in 39 s, f = 10.7485. Structure annealed in 39 s, f = 1.55001. Structure annealed in 38 s, f = 6.86639. Structure annealed in 39 s, f = 2.05720. Structure annealed in 39 s, f = 3.65688. Structure annealed in 39 s, f = 3.51743. Structure annealed in 39 s, f = 7.65850. Structure annealed in 39 s, f = 1.88863. Structure annealed in 39 s, f = 3.02043. Structure annealed in 38 s, f = 2.26354. Structure annealed in 39 s, f = 6.31951. Structure annealed in 39 s, f = 2.31898. Structure annealed in 39 s, f = 1.75450. Structure annealed in 39 s, f = 2.79327. Structure annealed in 39 s, f = 6.48984. Structure annealed in 39 s, f = 1.57882. Structure annealed in 38 s, f = 5.53116. Structure annealed in 39 s, f = 2.14675. Structure annealed in 39 s, f = 1.16884. Structure annealed in 38 s, f = 7.37125. Structure annealed in 39 s, f = 5.55918. Structure annealed in 38 s, f = 2.44893. Structure annealed in 39 s, f = 0.963712. Structure annealed in 39 s, f = 1.96594. Structure annealed in 39 s, f = 2.36042. Structure annealed in 39 s, f = 3.36804. Structure annealed in 39 s, f = 1.94635. Structure annealed in 39 s, f = 2.75559. Structure annealed in 39 s, f = 1.44210. Structure annealed in 39 s, f = 6.84442. Structure annealed in 39 s, f = 4.35844. Structure annealed in 39 s, f = 4.30019. Structure annealed in 39 s, f = 3.26643. Structure annealed in 39 s, f = 7.28055. Structure annealed in 38 s, f = 6.20296. Structure annealed in 38 s, f = 1.26546. Structure annealed in 39 s, f = 2.15710. Structure annealed in 38 s, f = 4.55347. Structure annealed in 39 s, f = 2.20128. Structure annealed in 38 s, f = 2.76892. Structure annealed in 40 s, f = 22.6807. Structure annealed in 39 s, f = 2.84767. Structure annealed in 38 s, f = 1.16122. Structure annealed in 38 s, f = 3.34018. Structure annealed in 39 s, f = 2.32682. Structure annealed in 39 s, f = 5.35411. Structure annealed in 39 s, f = 3.06736. Structure annealed in 39 s, f = 2.25025. Structure annealed in 39 s, f = 5.89834. Structure annealed in 39 s, f = 3.75017. Structure annealed in 38 s, f = 2.18675. Structure annealed in 39 s, f = 1.46839. Structure annealed in 39 s, f = 6.69343. Structure annealed in 39 s, f = 6.83154. Structure annealed in 39 s, f = 6.13082. Structure annealed in 39 s, f = 6.88240. Structure annealed in 39 s, f = 2.35306. Structure annealed in 39 s, f = 1.61716. Structure annealed in 39 s, f = 6.27763. 100 structures finished in 160 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 0.96 0 0.0050 0.15 0 4.7 0.17 0 0.2598 2.14 2 1.16 0 0.0044 0.13 2 5.4 0.29 0 0.2062 1.71 3 1.17 1 0.0062 0.20 0 5.0 0.17 0 0.2702 2.73 4 1.27 0 0.0046 0.15 0 4.8 0.16 0 0.2752 2.02 5 1.35 1 0.0060 0.25 1 6.3 0.22 0 0.2923 2.06 6 1.38 0 0.0058 0.19 1 5.6 0.23 0 0.3323 2.85 7 1.44 1 0.0064 0.22 1 5.5 0.20 0 0.3273 3.06 8 1.44 0 0.0049 0.16 2 5.4 0.29 0 0.2464 1.80 9 1.47 0 0.0058 0.20 2 6.1 0.29 0 0.2462 2.55 10 1.55 0 0.0043 0.16 2 5.3 0.29 0 0.3180 2.72 11 1.58 1 0.0064 0.20 0 6.4 0.17 0 0.2406 1.75 12 1.62 0 0.0054 0.14 0 5.2 0.17 0 0.3294 2.43 13 1.65 1 0.0052 0.21 0 5.3 0.14 0 0.2261 1.75 14 1.71 1 0.0059 0.26 2 7.2 0.21 0 0.2971 2.56 15 1.75 0 0.0062 0.16 1 6.2 0.22 0 0.3342 3.06 16 1.78 1 0.0061 0.23 1 5.8 0.23 0 0.2517 2.23 17 1.89 0 0.0058 0.17 2 6.5 0.29 0 0.2650 2.04 18 1.90 1 0.0073 0.23 0 6.0 0.17 0 0.3496 2.00 19 1.95 0 0.0061 0.20 3 7.3 0.29 0 0.2641 1.77 20 1.97 0 0.0060 0.20 2 6.1 0.30 0 0.2878 2.30 Ave 1.55 0 0.0057 0.19 1 5.8 0.22 0 0.2810 2.28 +/- 0.28 0 0.0007 0.04 1 0.7 0.05 0 0.0395 0.43 Min 0.96 0 0.0043 0.13 0 4.7 0.14 0 0.2062 1.71 Max 1.97 1 0.0073 0.26 3 7.3 0.30 0 0.3496 3.06 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 ------ --- --- --- --- 1 139 13 0 0 2 135 17 0 0 3 138 12 2 0 forrtl: Stale NFS file handle forrtl: severe (38): error during write, unit 41, file /user/francis/znf42/8cyana/123a/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 17812 failed on node n0 (192.168.96.101) with exit status 28. ----------------------------------------------------------------------------- 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 (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() 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 13-Dec-2005 23:14:16