Warning: no access to tty (Bad file descriptor). Thus no job control in this shell. 21-Dec-2005 14:51:20 n-1<23534> ssi:boot:base:linear: booting n0 (wolf01) n-1<23534> ssi:boot:base:linear: booting n1 (wolf02) n-1<23534> ssi:boot:base:linear: booting n2 (wolf03) n-1<23534> ssi:boot:base:linear: booting n3 (wolf04) n-1<23534> ssi:boot:base:linear: booting n4 (wolf05) n-1<23534> ssi:boot:base:linear: booting n5 (wolf06) n-1<23534> ssi:boot:base:linear: booting n6 (wolf07) n-1<23534> ssi:boot:base:linear: booting n7 (wolf08) n-1<23534> ssi:boot:base:linear: booting n8 (wolf09) n-1<23534> ssi:boot:base:linear: booting n9 (wolf10) n-1<23534> ssi:boot:base:linear: booting n10 (wolf11) n-1<23534> ssi:boot:base:linear: booting n11 (wolf12) n-1<23534> ssi:boot:base:linear: booting n12 (wolf13) n-1<23534> 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=3.75E7,1. 7E7,2.5E7,1.0E7 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=3.75E7 Calibration constant for peak list 1: 3.75E+07 Upper limit set for 3489 peaks. - calibration: caltab peaks Distance bounds: -2.99 A: 283 8.1% 3.00-3.99 A: 651 18.7% 4.00-4.99 A: 1336 38.3% 5.00-5.99 A: 1218 34.9% 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=1.0E7 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 4165 upper limits added, 2/737 at lower/upper bound, average 4.61 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: 2135 - znf42: write upl znf42.upl Distance constraint file "znf42.upl" written, 2135 upper limits, 2135 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, 2135 upper limits, 2135 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 = 2.01073. Structure annealed in 38 s, f = 8.13064. Structure annealed in 38 s, f = 7.00442. Structure annealed in 38 s, f = 2.39991. Structure annealed in 38 s, f = 7.93011. Structure annealed in 38 s, f = 15.1584. Structure annealed in 38 s, f = 3.38486. Structure annealed in 38 s, f = 3.61379. Structure annealed in 38 s, f = 2.18209. Structure annealed in 38 s, f = 2.18450. Structure annealed in 39 s, f = 3.76163. Structure annealed in 38 s, f = 3.03028. Structure annealed in 38 s, f = 3.19839. Structure annealed in 38 s, f = 2.61633. Structure annealed in 38 s, f = 3.94452. Structure annealed in 38 s, f = 3.46450. Structure annealed in 38 s, f = 6.31521. Structure annealed in 38 s, f = 5.39958. Structure annealed in 38 s, f = 3.79791. Structure annealed in 38 s, f = 3.28804. Structure annealed in 39 s, f = 2.96888. Structure annealed in 38 s, f = 9.14556. Structure annealed in 38 s, f = 3.27280. Structure annealed in 38 s, f = 7.26982. Structure annealed in 39 s, f = 6.62190. Structure annealed in 38 s, f = 6.54831. Structure annealed in 38 s, f = 4.22265. Structure annealed in 38 s, f = 3.45879. Structure annealed in 38 s, f = 3.23325. Structure annealed in 38 s, f = 2.30215. Structure annealed in 38 s, f = 6.38001. Structure annealed in 38 s, f = 7.70364. Structure annealed in 38 s, f = 5.33259. Structure annealed in 38 s, f = 3.64759. Structure annealed in 38 s, f = 3.89833. Structure annealed in 38 s, f = 1.62484. Structure annealed in 38 s, f = 4.88291. Structure annealed in 38 s, f = 10.5609. Structure annealed in 38 s, f = 2.56663. Structure annealed in 38 s, f = 7.97492. Structure annealed in 38 s, f = 2.21055. Structure annealed in 38 s, f = 3.72500. Structure annealed in 39 s, f = 9.29565. Structure annealed in 38 s, f = 2.60619. Structure annealed in 38 s, f = 2.68502. Structure annealed in 38 s, f = 2.35827. Structure annealed in 39 s, f = 107.764. Structure annealed in 38 s, f = 3.64949. Structure annealed in 38 s, f = 6.21895. Structure annealed in 38 s, f = 3.47192. Structure annealed in 38 s, f = 4.24110. Structure annealed in 38 s, f = 2.20023. Structure annealed in 38 s, f = 3.10234. Structure annealed in 38 s, f = 4.39047. Structure annealed in 38 s, f = 4.57231. Structure annealed in 38 s, f = 3.42695. Structure annealed in 38 s, f = 6.37729. Structure annealed in 38 s, f = 5.01104. Structure annealed in 38 s, f = 4.58407. Structure annealed in 38 s, f = 3.35403. Structure annealed in 38 s, f = 2.29981. Structure annealed in 38 s, f = 5.89661. Structure annealed in 38 s, f = 2.63013. Structure annealed in 38 s, f = 2.84132. Structure annealed in 38 s, f = 2.85692. Structure annealed in 39 s, f = 3.79770. Structure annealed in 38 s, f = 2.82950. Structure annealed in 38 s, f = 8.31620. Structure annealed in 38 s, f = 3.54078. Structure annealed in 38 s, f = 4.56642. Structure annealed in 39 s, f = 4.24258. Structure annealed in 38 s, f = 10.5560. Structure annealed in 38 s, f = 3.18062. Structure annealed in 38 s, f = 4.19719. Structure annealed in 38 s, f = 2.44771. Structure annealed in 38 s, f = 2.09397. Structure annealed in 38 s, f = 13.2008. Structure annealed in 38 s, f = 4.24849. Structure annealed in 38 s, f = 3.50073. Structure annealed in 38 s, f = 8.61348. Structure annealed in 41 s, f = 631.483. Structure annealed in 38 s, f = 4.25521. Structure annealed in 39 s, f = 3.83789. Structure annealed in 38 s, f = 5.99215. Structure annealed in 39 s, f = 2.99710. Structure annealed in 38 s, f = 6.39631. Structure annealed in 38 s, f = 5.05011. Structure annealed in 38 s, f = 2.99563. Structure annealed in 38 s, f = 7.49069. Structure annealed in 39 s, f = 22.5563. Structure annealed in 38 s, f = 3.36386. Structure annealed in 38 s, f = 2.78746. Structure annealed in 39 s, f = 2.09091. Structure annealed in 39 s, f = 107.149. Structure annealed in 38 s, f = 10.6992. Structure annealed in 38 s, f = 2.38021. Structure annealed in 38 s, f = 2.20084. Structure annealed in 38 s, f = 2.46830. Structure annealed in 39 s, f = 3.31923. Structure annealed in 39 s, f = 9.21027. 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 1.62 0 0.0069 0.16 2 6.7 0.24 0 0.4058 3.23 2 2.01 0 0.0074 0.16 0 7.5 0.18 0 0.3910 2.37 3 2.09 1 0.0086 0.20 0 7.8 0.17 0 0.3673 3.34 4 2.09 0 0.0076 0.17 2 8.3 0.22 0 0.5210 3.82 5 2.18 0 0.0069 0.16 3 7.9 0.23 0 0.4996 3.46 6 2.18 1 0.0091 0.20 1 7.1 0.20 0 0.3527 2.74 7 2.20 1 0.0090 0.22 0 7.5 0.16 0 0.3484 2.14 8 2.20 0 0.0089 0.17 0 8.1 0.16 0 0.4104 2.92 9 2.21 1 0.0090 0.22 0 7.1 0.14 0 0.2731 1.45 10 2.30 0 0.0088 0.20 0 7.2 0.17 0 0.3081 2.88 11 2.30 1 0.0076 0.21 1 7.8 0.23 0 0.4285 3.19 12 2.36 2 0.0094 0.24 0 6.9 0.17 0 0.3461 2.36 13 2.38 2 0.0091 0.30 6 8.6 0.28 0 0.4595 3.70 14 2.40 1 0.0090 0.20 2 7.7 0.24 0 0.3343 2.69 15 2.45 1 0.0095 0.21 0 8.6 0.17 0 0.4176 3.29 16 2.47 0 0.0087 0.18 2 9.0 0.22 0 0.6494 4.79 17 2.57 2 0.0100 0.22 0 8.6 0.18 0 0.3041 2.49 18 2.61 1 0.0091 0.23 0 7.8 0.18 0 0.3381 2.21 19 2.62 2 0.0103 0.25 0 8.9 0.19 0 0.4008 3.30 20 2.63 2 0.0110 0.24 0 9.0 0.18 0 0.4767 4.70 Ave 2.29 1 0.0088 0.21 1 7.9 0.20 0 0.4016 3.05 +/- 0.24 1 0.0010 0.04 1 0.7 0.04 0 0.0861 0.80 Min 1.62 0 0.0069 0.16 0 6.7 0.14 0 0.2731 1.45 Max 2.63 2 0.0110 0.30 6 9.0 0.28 0 0.6494 4.79 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 2 133 15 2 2 (GLU 125, GLU 425) 3 133 17 2 0 4 142 10 0 0 5 140 12 0 0 6 136 14 2 0 7 138 12 2 0 8 140 10 2 0 9 139 13 0 0 10 141 11 0 0 11 138 12 0 2 (ARG 124, ARG 424) 12 140 12 0 0 13 132 18 2 0 forrtl: Stale NFS file handle forrtl: severe (38): error during write, unit 41, file /user/francis/znf42/8cyana/160a/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() MPI_Recv: process in local group is dead (rank 3, 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 23616 failed on node n0 (192.168.96.101) with exit status 28. ----------------------------------------------------------------------------- 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() 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 14:54:33