Warning: no access to tty (Bad file descriptor). Thus no job control in this shell. 21-Dec-2005 15:01:00 n-1<23918> ssi:boot:base:linear: booting n0 (wolf01) n-1<23918> ssi:boot:base:linear: booting n1 (wolf02) n-1<23918> ssi:boot:base:linear: booting n2 (wolf03) n-1<23918> ssi:boot:base:linear: booting n3 (wolf04) n-1<23918> ssi:boot:base:linear: booting n4 (wolf05) n-1<23918> ssi:boot:base:linear: booting n5 (wolf06) n-1<23918> ssi:boot:base:linear: booting n6 (wolf07) n-1<23918> ssi:boot:base:linear: booting n7 (wolf08) n-1<23918> ssi:boot:base:linear: booting n8 (wolf09) n-1<23918> ssi:boot:base:linear: booting n9 (wolf10) n-1<23918> ssi:boot:base:linear: booting n10 (wolf11) n-1<23918> ssi:boot:base:linear: booting n11 (wolf12) n-1<23918> ssi:boot:base:linear: booting n12 (wolf13) n-1<23918> 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: finalstereo 125 stereospecific assignments defined. - znf42: peakcheck peaks=c13no,n15no,c13ar,fc12no prot=znf42 ------------------------------------------------------------ Proton list: znf42 - peakcheck: read prot znf42 unknown=warn Chemical shift list "znf42.prot" read, 1984 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, 1984 chemical shifts. - peakcheck: read peaks c13no format= Peak list "c13no.peaks" read, 3489 peaks, 3181 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 3181 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, 1984 chemical shifts. - peakcheck: read peaks n15no format= 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, 1984 chemical shifts. - peakcheck: read peaks c13ar format= Peak list "c13ar.peaks" read, 292 peaks, 237 assignments. - peakcheck: peaks fit Deviations from chemical shift list: Dim Peaks Median Average Maximum RMSD Number Tolerance 1 237 0.005 0.006 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, 1984 chemical shifts. - peakcheck: read peaks fc12no format= Peak list "fc12no.peaks" read, 233 peaks, 142 assignments. - peakcheck: peaks fit Deviations from chemical shift list: Dim Peaks Median Average Maximum RMSD Number Tolerance 1 142 -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 E7,2.5E7,1.25E7 dref=4.2 - calibration: read prot znf42 unknown=warn Chemical shift list "znf42.prot" read, 1984 chemical shifts. - calibration: read peaks c13no format= Peak list "c13no.peaks" read, 3489 peaks, 3181 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: 298 8.5% 3.00-3.99 A: 680 19.5% 4.00-4.99 A: 1373 39.4% 5.00-5.99 A: 1138 32.6% 6.00- A: 0 0.0% All: 3489 100.0% - calibration: read prot znf42 unknown=warn append Chemical shift list "znf42.prot" read, 1984 chemical shifts. - calibration: read peaks n15no format= append 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, 1984 chemical shifts. - calibration: read peaks c13ar format= append Peak list "c13ar.peaks" read, 292 peaks, 237 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, 1984 chemical shifts. - calibration: read peaks fc12no format= append Peak list "fc12no.peaks" read, 233 peaks, 142 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=1.25E7 Calibration constant for peak list 4: 1.25E+07 Upper limit set for 233 peaks. - calibration: caltab peaks Distance bounds: -2.99 A: 2 0.9% 3.00-3.99 A: 43 18.5% 4.00-4.99 A: 149 63.9% 5.00-5.99 A: 39 16.7% 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 4165 upper limits added, 2/690 at lower/upper bound, average 4.59 A. - znf42: write upl znf42-in.upl Distance constraint file "znf42-in.upl" written, 4165 upper limits, 4165 assignments. - znf42: distance modify Number of modified constraints: 2146 - znf42: write upl znf42.upl Distance constraint file "znf42.upl" written, 2146 upper limits, 2146 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, 2146 upper limits, 2146 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 = 3.43757. Structure annealed in 39 s, f = 8.67870. Structure annealed in 38 s, f = 2.48410. Structure annealed in 38 s, f = 5.04027. Structure annealed in 39 s, f = 2.76192. Structure annealed in 38 s, f = 10.6296. Structure annealed in 38 s, f = 6.74703. Structure annealed in 39 s, f = 3.37133. Structure annealed in 38 s, f = 3.37815. Structure annealed in 38 s, f = 3.21473. Structure annealed in 41 s, f = 347.600. Structure annealed in 38 s, f = 3.15453. Structure annealed in 39 s, f = 3.29354. Structure annealed in 38 s, f = 3.55801. Structure annealed in 38 s, f = 4.44790. Structure annealed in 38 s, f = 6.51596. Structure annealed in 38 s, f = 8.05724. Structure annealed in 39 s, f = 3.03255. Structure annealed in 38 s, f = 9.30657. Structure annealed in 38 s, f = 6.52375. Structure annealed in 39 s, f = 2.97701. Structure annealed in 38 s, f = 7.10925. Structure annealed in 38 s, f = 2.56605. Structure annealed in 39 s, f = 234.517. Structure annealed in 38 s, f = 5.82924. Structure annealed in 38 s, f = 3.67289. Structure annealed in 38 s, f = 1.94875. Structure annealed in 38 s, f = 1.95718. Structure annealed in 38 s, f = 2.13111. Structure annealed in 38 s, f = 3.57228. Structure annealed in 38 s, f = 2.28513. Structure annealed in 38 s, f = 3.44395. Structure annealed in 38 s, f = 3.31033. Structure annealed in 38 s, f = 2.66014. Structure annealed in 38 s, f = 6.01193. Structure annealed in 38 s, f = 4.53235. Structure annealed in 38 s, f = 3.81595. Structure annealed in 38 s, f = 6.00531. Structure annealed in 39 s, f = 151.799. Structure annealed in 38 s, f = 2.54748. Structure annealed in 39 s, f = 49.4230. Structure annealed in 39 s, f = 3.43517. Structure annealed in 38 s, f = 7.56386. Structure annealed in 38 s, f = 3.04265. Structure annealed in 38 s, f = 6.90206. Structure annealed in 39 s, f = 2.49150. Structure annealed in 38 s, f = 2.95042. Structure annealed in 38 s, f = 5.98823. Structure annealed in 38 s, f = 2.78075. Structure annealed in 39 s, f = 6.35114. Structure annealed in 38 s, f = 2.60622. Structure annealed in 38 s, f = 17.9290. Structure annealed in 38 s, f = 3.41767. Structure annealed in 39 s, f = 108.628. Structure annealed in 38 s, f = 1.82417. Structure annealed in 39 s, f = 7.27513. Structure annealed in 38 s, f = 6.75888. Structure annealed in 38 s, f = 4.70313. Structure annealed in 38 s, f = 2.82941. Structure annealed in 38 s, f = 2.24915. Structure annealed in 38 s, f = 9.97961. Structure annealed in 38 s, f = 11.0925. Structure annealed in 38 s, f = 2.26183. Structure annealed in 38 s, f = 4.81406. Structure annealed in 38 s, f = 2.61415. Structure annealed in 38 s, f = 5.25451. Structure annealed in 38 s, f = 6.62959. Structure annealed in 38 s, f = 41.1984. Structure annealed in 38 s, f = 2.31818. Structure annealed in 39 s, f = 8.23840. Structure annealed in 38 s, f = 2.38101. Structure annealed in 39 s, f = 7.72979. Structure annealed in 38 s, f = 8.14846. Structure annealed in 39 s, f = 2.61711. Structure annealed in 39 s, f = 3.15765. Structure annealed in 38 s, f = 151.821. Structure annealed in 38 s, f = 3.21682. Structure annealed in 38 s, f = 15.8127. Structure annealed in 38 s, f = 2.72179. Structure annealed in 38 s, f = 3.56057. Structure annealed in 38 s, f = 2.43081. Structure annealed in 38 s, f = 3.12601. Structure annealed in 39 s, f = 116.503. Structure annealed in 40 s, f = 187.417. Structure annealed in 38 s, f = 3.60012. Structure annealed in 38 s, f = 3.14014. Structure annealed in 39 s, f = 4.43051. Structure annealed in 38 s, f = 7.60766. Structure annealed in 38 s, f = 2.74774. Structure annealed in 38 s, f = 2.82539. Structure annealed in 38 s, f = 3.34972. Structure annealed in 38 s, f = 3.30269. Structure annealed in 38 s, f = 3.57865. Structure annealed in 38 s, f = 3.45113. Structure annealed in 38 s, f = 3.52670. Structure annealed in 38 s, f = 2.83179. Structure annealed in 38 s, f = 2.66239. Structure annealed in 39 s, f = 6.47294. Structure annealed in 38 s, f = 4.09284. Structure annealed in 40 s, f = 130.903. 100 structures finished in 163 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 1.82 0 0.0090 0.20 0 7.8 0.16 0 0.4034 3.40 2 1.95 0 0.0101 0.20 0 7.3 0.20 0 0.3797 4.12 3 1.96 1 0.0089 0.21 0 7.0 0.18 0 0.2851 2.47 4 2.13 0 0.0076 0.16 2 7.6 0.22 0 0.5245 3.70 5 2.25 1 0.0096 0.21 3 8.2 0.28 0 0.3031 2.93 6 2.26 1 0.0096 0.21 0 7.6 0.17 0 0.3570 2.66 7 2.29 0 0.0090 0.19 0 6.8 0.16 0 0.3616 3.28 8 2.32 0 0.0092 0.19 1 7.7 0.21 0 0.3304 2.46 9 2.38 1 0.0093 0.22 0 7.8 0.16 0 0.3337 2.75 10 2.43 1 0.0096 0.21 1 8.0 0.21 0 0.2777 2.15 11 2.48 0 0.0092 0.19 2 8.3 0.28 0 0.3450 2.74 12 2.49 0 0.0096 0.19 0 6.6 0.17 0 0.3210 2.59 13 2.55 1 0.0093 0.21 0 8.3 0.19 0 0.3783 3.33 14 2.57 0 0.0084 0.19 2 6.8 0.23 0 0.3945 2.94 15 2.61 2 0.0095 0.21 0 8.1 0.18 0 0.4067 2.83 16 2.61 2 0.0108 0.37 2 8.3 0.25 0 0.6039 4.98 17 2.62 0 0.0092 0.18 0 7.9 0.18 0 0.3877 3.40 18 2.66 1 0.0093 0.24 0 7.5 0.18 0 0.2616 1.73 19 2.66 1 0.0097 0.20 1 9.4 0.21 0 0.5464 3.69 20 2.72 0 0.0100 0.20 0 7.1 0.18 0 0.3166 2.48 Ave 2.39 1 0.0093 0.21 1 7.7 0.20 0 0.3759 3.03 +/- 0.26 1 0.0006 0.04 1 0.6 0.04 0 0.0876 0.72 Min 1.82 0 0.0076 0.16 0 6.6 0.16 0 0.2616 1.73 Max 2.72 2 0.0108 0.37 3 9.4 0.28 0 0.6039 4.98 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 ------ --- --- --- --- 1 144 6 2 0 2 140 12 0 0 3 136 16 0 0 4 144 8 0 0 5 136 14 2 0 6 141 11 0 0 7 139 11 0 2 (ASP 37, ASP 337) 8 138 14 0 0 9 141 11 0 0 10 139 13 0 0 11 140 12 0 0 12 138 12 2 0 13 139 13 0 0 forrtl: Stale NFS file handle forrtl: severe (38): error during write, unit 41, file /user/francis/znf42/8cyana/160d/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) MPI_Recv: process in local group is dead (rank 8, 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 24002 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 (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 21-Dec-2005 15:04:16