Warning: no access to tty (Bad file descriptor). Thus no job control in this shell. 06-Dec-2005 22:08:09 n-1<27621> ssi:boot:base:linear: booting n0 (wolf01) n-1<27621> ssi:boot:base:linear: booting n1 (wolf02) n-1<27621> ssi:boot:base:linear: booting n2 (wolf03) n-1<27621> ssi:boot:base:linear: booting n3 (wolf04) n-1<27621> ssi:boot:base:linear: booting n4 (wolf05) n-1<27621> ssi:boot:base:linear: booting n5 (wolf06) n-1<27621> ssi:boot:base:linear: booting n6 (wolf07) n-1<27621> ssi:boot:base:linear: booting n7 (wolf08) n-1<27621> ssi:boot:base:linear: booting n8 (wolf09) n-1<27621> ssi:boot:base:linear: booting n9 (wolf10) n-1<27621> ssi:boot:base:linear: booting n10 (wolf11) n-1<27621> ssi:boot:base:linear: booting n11 (wolf12) n-1<27621> ssi:boot:base:linear: booting n12 (wolf13) n-1<27621> 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, 1982 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, 1982 chemical shifts. - peakcheck: read peaks c13no format= Peak list "c13no.peaks" read, 3483 peaks, 3183 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 3183 0.000 0.002 0.030 0.009 0 0.030 2 3479 0.000 0.000 0.026 0.002 0 0.030 3 3479 0.000 0.000 0.297 0.023 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, 1982 chemical shifts. - peakcheck: read peaks n15no format= Peak list "n15no.peaks" read, 1272 peaks, 1108 assignments. - peakcheck: peaks fit Deviations from chemical shift list: Dim Peaks Median Average Maximum RMSD Number Tolerance 1 1108 0.002 0.002 0.030 0.011 0 0.030 2 1270 0.000 0.000 0.011 0.001 0 0.030 3 1270 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, 1982 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, 1982 chemical shifts. - peakcheck: read peaks fc12no format= Peak list "fc12no.peaks" read, 233 peaks, 144 assignments. - peakcheck: peaks fit Deviations from chemical shift list: Dim Peaks Median Average Maximum RMSD Number Tolerance 1 144 -0.004 -0.002 0.029 0.015 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 dref=4.2 - calibration: read prot znf42 unknown=warn Chemical shift list "znf42.prot" read, 1982 chemical shifts. - calibration: read peaks c13no format= Peak list "c13no.peaks" read, 3483 peaks, 3183 assignments. - calibration: peaks select "** list=1" 3483 of 3483 peaks, 3483 of 3483 assignments selected. - calibration: peaks set volume=abs(volume) Volume of 3483 peaks set. - calibration: peaks simplecal dref=4.2 Calibration constant for peak list 1: 1.85E+07 Upper limit set for 3483 peaks. - calibration: caltab peaks Distance bounds: -2.99 A: 439 12.6% 3.00-3.99 A: 1173 33.7% 4.00-4.99 A: 1307 37.5% 5.00-5.99 A: 562 16.1% 6.00- A: 0 0.0% All: 3483 100.0% - calibration: read prot znf42 unknown=warn append Chemical shift list "znf42.prot" read, 1982 chemical shifts. - calibration: read peaks n15no format= append Peak list "n15no.peaks" read, 1272 peaks, 1108 assignments. - calibration: peaks select "** list=2" 1272 of 4755 peaks, 1272 of 4755 assignments selected. - calibration: peaks set volume=abs(volume) Volume of 1272 peaks set. - calibration: peaks simplecal dref=4.2 Calibration constant for peak list 2: 8.42E+06 Upper limit set for 1272 peaks. - calibration: caltab peaks Distance bounds: -2.99 A: 111 8.7% 3.00-3.99 A: 468 36.8% 4.00-4.99 A: 479 37.7% 5.00-5.99 A: 214 16.8% 6.00- A: 0 0.0% All: 1272 100.0% - calibration: read prot znf42 unknown=warn append Chemical shift list "znf42.prot" read, 1982 chemical shifts. - calibration: read peaks c13ar format= append Peak list "c13ar.peaks" read, 292 peaks, 238 assignments. - calibration: peaks select "** list=3" 292 of 5047 peaks, 292 of 5047 assignments selected. - calibration: peaks set volume=abs(volume) Volume of 292 peaks set. - calibration: peaks simplecal dref=4.2 Calibration constant for peak list 3: 1.44E+07 Upper limit set for 292 peaks. - calibration: caltab peaks Distance bounds: -2.99 A: 26 8.9% 3.00-3.99 A: 93 31.8% 4.00-4.99 A: 166 56.8% 5.00-5.99 A: 7 2.4% 6.00- A: 0 0.0% All: 292 100.0% - calibration: read prot znf42 unknown=warn append Chemical shift list "znf42.prot" read, 1982 chemical shifts. - calibration: read peaks fc12no format= append Peak list "fc12no.peaks" read, 233 peaks, 144 assignments. - calibration: peaks select "** list=4" 233 of 5280 peaks, 233 of 5280 assignments selected. - calibration: peaks set volume=abs(volume) Volume of 233 peaks set. - calibration: peaks simplecal dref=4.2 Calibration constant for peak list 4: 7.23E+06 Upper limit set for 233 peaks. - calibration: caltab peaks Distance bounds: -2.99 A: 8 3.4% 3.00-3.99 A: 80 34.3% 4.00-4.99 A: 145 62.2% 5.00-5.99 A: 0 0.0% 6.00- A: 0 0.0% All: 233 100.0% - calibration: peaks select ** 5280 of 5280 peaks, 5280 of 5280 assignments selected. - znf42: peaks calibrate ** simple 4179 upper limits added, 18/139 at lower/upper bound, average 4.17 A. - znf42: write upl znf42-in.upl Distance constraint file "znf42-in.upl" written, 4179 upper limits, 4179 assignments. - znf42: distance modify Too restrictive distance constraints: limit dmin dmax Upper HA ASP 37 - QG PRO 38 3.96 4.11 6.06 Number of modified constraints: 2371 - znf42: write upl znf42.upl Distance constraint file "znf42.upl" written, 2371 upper limits, 2371 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, 2371 upper limits, 2371 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 40 s, f = 20.4678. Structure annealed in 41 s, f = 39.4894. Structure annealed in 40 s, f = 25.7540. Structure annealed in 40 s, f = 26.7521. Structure annealed in 40 s, f = 21.1858. Structure annealed in 41 s, f = 174.930. Structure annealed in 40 s, f = 26.7032. Structure annealed in 41 s, f = 25.3542. Structure annealed in 40 s, f = 32.2359. Structure annealed in 40 s, f = 29.7133. Structure annealed in 40 s, f = 24.6231. Structure annealed in 41 s, f = 24.7080. Structure annealed in 40 s, f = 20.6269. Structure annealed in 40 s, f = 26.3525. Structure annealed in 40 s, f = 27.3063. Structure annealed in 40 s, f = 28.3890. Structure annealed in 40 s, f = 20.7547. Structure annealed in 41 s, f = 21.6621. Structure annealed in 41 s, f = 24.2246. Structure annealed in 41 s, f = 25.4278. Structure annealed in 40 s, f = 27.6781. Structure annealed in 41 s, f = 26.4376. Structure annealed in 40 s, f = 29.6218. Structure annealed in 40 s, f = 25.3786. Structure annealed in 40 s, f = 23.3012. Structure annealed in 40 s, f = 22.5716. Structure annealed in 40 s, f = 22.4672. Structure annealed in 40 s, f = 29.1109. Structure annealed in 40 s, f = 24.0067. Structure annealed in 41 s, f = 28.4703. Structure annealed in 40 s, f = 28.0784. Structure annealed in 40 s, f = 31.2116. Structure annealed in 40 s, f = 22.9613. Structure annealed in 40 s, f = 23.5815. Structure annealed in 40 s, f = 25.3596. Structure annealed in 40 s, f = 26.0079. Structure annealed in 40 s, f = 32.5942. Structure annealed in 40 s, f = 22.9578. Structure annealed in 40 s, f = 22.9539. Structure annealed in 40 s, f = 30.7649. Structure annealed in 41 s, f = 25.4964. Structure annealed in 40 s, f = 24.5750. Structure annealed in 41 s, f = 38.5859. Structure annealed in 40 s, f = 26.4053. Structure annealed in 41 s, f = 25.2580. Structure annealed in 40 s, f = 29.8410. Structure annealed in 40 s, f = 25.1355. Structure annealed in 40 s, f = 21.7949. Structure annealed in 40 s, f = 30.0276. Structure annealed in 40 s, f = 23.3947. Structure annealed in 40 s, f = 102.688. Structure annealed in 40 s, f = 28.4196. Structure annealed in 40 s, f = 22.7253. Structure annealed in 40 s, f = 24.9609. Structure annealed in 41 s, f = 278.287. Structure annealed in 41 s, f = 19.6415. Structure annealed in 40 s, f = 21.2309. Structure annealed in 40 s, f = 23.1393. Structure annealed in 40 s, f = 33.4756. Structure annealed in 40 s, f = 21.3006. Structure annealed in 41 s, f = 23.8233. Structure annealed in 41 s, f = 211.091. Structure annealed in 40 s, f = 34.1503. Structure annealed in 40 s, f = 24.4814. Structure annealed in 40 s, f = 21.3783. Structure annealed in 41 s, f = 22.1339. Structure annealed in 40 s, f = 21.5157. Structure annealed in 40 s, f = 28.4664. Structure annealed in 40 s, f = 23.1224. Structure annealed in 40 s, f = 28.0802. Structure annealed in 40 s, f = 24.5868. Structure annealed in 41 s, f = 17.8713. Structure annealed in 40 s, f = 22.1486. Structure annealed in 40 s, f = 22.0834. Structure annealed in 40 s, f = 26.9790. Structure annealed in 40 s, f = 22.4268. Structure annealed in 40 s, f = 25.3650. Structure annealed in 40 s, f = 24.2301. Structure annealed in 40 s, f = 24.4202. Structure annealed in 40 s, f = 20.2800. Structure annealed in 40 s, f = 27.1237. Structure annealed in 42 s, f = 484.152. Structure annealed in 40 s, f = 22.4287. Structure annealed in 40 s, f = 30.3836. Structure annealed in 41 s, f = 23.2123. Structure annealed in 40 s, f = 23.6761. Structure annealed in 41 s, f = 22.3841. Structure annealed in 40 s, f = 20.4336. Structure annealed in 40 s, f = 24.8072. Structure annealed in 40 s, f = 24.9501. Structure annealed in 40 s, f = 28.3931. Structure annealed in 40 s, f = 25.8019. Structure annealed in 40 s, f = 27.3572. Structure annealed in 40 s, f = 25.2282. Structure annealed in 40 s, f = 25.9131. Structure annealed in 40 s, f = 26.9392. Structure annealed in 40 s, f = 27.4060. Structure annealed in 41 s, f = 22.1089. Structure annealed in 40 s, f = 21.8764. Structure annealed in 40 s, f = 27.6349. 100 structures finished in 168 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 17.87 88 0.0380 0.63 7 18.0 0.52 2 1.0338 6.05 2 19.64 89 0.0387 0.64 6 20.2 0.32 1 1.0107 5.87 3 20.28 82 0.0386 0.63 9 22.4 0.30 1 1.0850 5.53 4 20.43 85 0.0380 0.70 14 21.7 0.46 3 1.1695 7.40 5 20.47 92 0.0377 0.66 10 20.6 0.31 0 0.9437 4.86 6 20.63 93 0.0382 0.67 7 21.6 0.23 1 1.1223 5.31 7 20.75 89 0.0390 0.65 12 22.5 0.33 2 1.1445 10.34 8 21.19 94 0.0389 0.66 12 21.2 0.52 2 1.0533 7.94 9 21.23 90 0.0388 0.69 14 23.6 0.33 2 1.0959 7.82 10 21.30 90 0.0383 0.62 10 22.7 0.35 2 1.0632 6.10 11 21.38 102 0.0392 0.62 14 23.8 0.48 0 0.9386 4.92 12 21.52 83 0.0390 0.78 15 25.6 0.31 2 1.0236 6.34 13 21.66 89 0.0397 0.80 10 23.7 0.27 2 1.1489 5.34 14 21.80 89 0.0399 1.10 9 21.6 0.46 2 1.1426 8.81 15 21.88 89 0.0394 0.75 13 22.6 0.54 3 1.1313 8.72 16 22.08 91 0.0399 1.16 9 22.9 0.49 3 1.1408 7.61 17 22.11 101 0.0415 0.87 10 23.1 0.25 5 1.1903 6.10 18 22.13 97 0.0406 0.67 10 22.3 0.52 2 1.0684 7.45 19 22.15 91 0.0402 1.15 11 22.9 0.49 3 1.1135 8.59 20 22.38 99 0.0395 0.85 9 25.4 0.28 2 1.1390 6.52 Ave 21.14 91 0.0392 0.77 11 22.4 0.39 2 1.0879 6.88 +/- 1.05 5 0.0009 0.17 2 1.7 0.10 1 0.0688 1.47 Min 17.87 82 0.0377 0.62 6 18.0 0.23 0 0.9386 4.86 Max 22.38 102 0.0415 1.16 15 25.6 0.54 5 1.1903 10.34 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 ------ --- --- --- --- 1 140 12 0 0 2 138 14 0 0 3 144 8 0 0 forrtl: Stale NFS file handle forrtl: severe (38): error during write, unit 41, file /user/francis/znf42/8cyana/120a_auto/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 27703 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() 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 06-Dec-2005 22:11:29