Warning: no access to tty (Bad file descriptor). Thus no job control in this shell. 06-Dec-2005 00:29:32 n-1<19389> ssi:boot:base:linear: booting n0 (wolf01) n-1<19389> ssi:boot:base:linear: booting n1 (wolf02) n-1<19389> ssi:boot:base:linear: booting n2 (wolf03) n-1<19389> ssi:boot:base:linear: booting n3 (wolf04) n-1<19389> ssi:boot:base:linear: booting n4 (wolf05) n-1<19389> ssi:boot:base:linear: booting n5 (wolf06) n-1<19389> ssi:boot:base:linear: booting n6 (wolf07) n-1<19389> ssi:boot:base:linear: booting n7 (wolf08) n-1<19389> ssi:boot:base:linear: booting n8 (wolf09) n-1<19389> ssi:boot:base:linear: booting n9 (wolf10) n-1<19389> ssi:boot:base:linear: booting n10 (wolf11) n-1<19389> ssi:boot:base:linear: booting n11 (wolf12) n-1<19389> ssi:boot:base:linear: booting n12 (wolf13) n-1<19389> 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, 1981 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, 1981 chemical shifts. - peakcheck: read peaks c13no format= Peak list "c13no.peaks" read, 3483 peaks, 3185 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 3185 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, 1981 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, 1981 chemical shifts. - peakcheck: read peaks c13ar format= Peak list "c13ar.peaks" read, 292 peaks, 239 assignments. - peakcheck: peaks fit Deviations from chemical shift list: Dim Peaks Median Average Maximum RMSD Number Tolerance 1 239 0.005 0.004 0.271 0.021 1 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 HG LEU 396 1.874 1.603 0.271 1 1 shift with spread larger than tolerance. - peakcheck: peak deviations Peak Dim Deviation Atom Residue 234 1 -0.271 HG LEU 396 1 deviations larger than tolerance. ------------------------------------------------------------ Peak list : fc12no Proton list: znf42 - peakcheck: read prot znf42 unknown=skip Chemical shift list "znf42.prot" read, 1981 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 constant=3.0E7,1.7 E7,2.5E7,1.0E7 dref=4.2 - calibration: read prot znf42 unknown=warn Chemical shift list "znf42.prot" read, 1981 chemical shifts. - calibration: read peaks c13no format= Peak list "c13no.peaks" read, 3483 peaks, 3185 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 constant=3.0E7 Calibration constant for peak list 1: 3.00E+07 Upper limit set for 3483 peaks. - calibration: caltab peaks Distance bounds: -2.99 A: 330 9.5% 3.00-3.99 A: 772 22.2% 4.00-4.99 A: 1385 39.8% 5.00-5.99 A: 994 28.5% 6.00- A: 0 0.0% All: 3483 100.0% - calibration: read prot znf42 unknown=warn append Chemical shift list "znf42.prot" read, 1981 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 constant=1.7E7 Calibration constant for peak list 2: 1.70E+07 Upper limit set for 1272 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: 491 38.6% 5.00-5.99 A: 480 37.7% 6.00- A: 0 0.0% All: 1272 100.0% - calibration: read prot znf42 unknown=warn append Chemical shift list "znf42.prot" read, 1981 chemical shifts. - calibration: read peaks c13ar format= append Peak list "c13ar.peaks" read, 292 peaks, 239 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 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, 1981 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 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 ** 5280 of 5280 peaks, 5280 of 5280 assignments selected. - znf42: peaks calibrate ** simple 4182 upper limits added, 3/597 at lower/upper bound, average 4.52 A. - znf42: write upl znf42-in.upl Distance constraint file "znf42-in.upl" written, 4182 upper limits, 4182 assignments. - znf42: distance modify Number of modified constraints: 2201 - znf42: write upl znf42.upl Distance constraint file "znf42.upl" written, 2201 upper limits, 2201 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, 2201 upper limits, 2201 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 39 s, f = 53.9768. Structure annealed in 39 s, f = 8.91620. Structure annealed in 39 s, f = 4.68280. Structure annealed in 39 s, f = 13.2917. Structure annealed in 39 s, f = 5.22384. Structure annealed in 39 s, f = 4.49758. Structure annealed in 40 s, f = 148.831. Structure annealed in 39 s, f = 13.1610. Structure annealed in 39 s, f = 4.03073. Structure annealed in 39 s, f = 4.85960. Structure annealed in 39 s, f = 12.9123. Structure annealed in 39 s, f = 4.62188. Structure annealed in 41 s, f = 180.750. Structure annealed in 39 s, f = 5.70964. Structure annealed in 39 s, f = 8.85554. Structure annealed in 39 s, f = 7.02532. Structure annealed in 39 s, f = 3.62247. Structure annealed in 40 s, f = 155.327. Structure annealed in 40 s, f = 3.74943. Structure annealed in 39 s, f = 4.52013. Structure annealed in 39 s, f = 7.32613. Structure annealed in 39 s, f = 4.65383. Structure annealed in 39 s, f = 7.88141. Structure annealed in 39 s, f = 6.85393. Structure annealed in 41 s, f = 382.577. Structure annealed in 39 s, f = 5.05997. Structure annealed in 38 s, f = 3.24532. Structure annealed in 39 s, f = 5.26144. Structure annealed in 39 s, f = 4.55916. Structure annealed in 39 s, f = 3.54757. Structure annealed in 39 s, f = 4.12991. Structure annealed in 39 s, f = 5.13540. Structure annealed in 39 s, f = 4.62238. Structure annealed in 39 s, f = 5.33277. Structure annealed in 39 s, f = 2.97765. Structure annealed in 39 s, f = 12.4762. Structure annealed in 39 s, f = 8.44660. Structure annealed in 39 s, f = 3.74977. Structure annealed in 39 s, f = 5.76951. Structure annealed in 39 s, f = 17.4516. Structure annealed in 39 s, f = 7.41819. Structure annealed in 39 s, f = 7.99263. Structure annealed in 39 s, f = 4.37372. Structure annealed in 39 s, f = 4.37446. Structure annealed in 39 s, f = 4.52277. Structure annealed in 40 s, f = 3.79066. Structure annealed in 40 s, f = 148.447. Structure annealed in 39 s, f = 5.38646. Structure annealed in 39 s, f = 20.6036. Structure annealed in 39 s, f = 9.85966. Structure annealed in 39 s, f = 11.5957. Structure annealed in 39 s, f = 4.10350. Structure annealed in 39 s, f = 5.92503. Structure annealed in 39 s, f = 7.07250. Structure annealed in 39 s, f = 4.35997. Structure annealed in 39 s, f = 5.50956. Structure annealed in 39 s, f = 3.92303. Structure annealed in 41 s, f = 192.700. Structure annealed in 39 s, f = 4.52275. Structure annealed in 39 s, f = 2.72685. Structure annealed in 39 s, f = 7.21530. Structure annealed in 39 s, f = 4.56568. Structure annealed in 39 s, f = 2.67264. Structure annealed in 39 s, f = 5.34399. Structure annealed in 39 s, f = 4.03075. Structure annealed in 39 s, f = 6.77993. Structure annealed in 39 s, f = 4.02020. Structure annealed in 39 s, f = 4.72477. Structure annealed in 39 s, f = 4.70799. Structure annealed in 39 s, f = 3.80350. Structure annealed in 39 s, f = 3.70541. Structure annealed in 39 s, f = 4.33413. Structure annealed in 39 s, f = 4.41626. Structure annealed in 39 s, f = 7.03257. Structure annealed in 39 s, f = 4.79179. Structure annealed in 39 s, f = 7.64475. Structure annealed in 39 s, f = 10.8465. Structure annealed in 39 s, f = 3.50275. Structure annealed in 39 s, f = 4.35766. Structure annealed in 39 s, f = 7.58280. Structure annealed in 39 s, f = 10.8873. Structure annealed in 39 s, f = 3.09400. Structure annealed in 39 s, f = 4.78799. Structure annealed in 39 s, f = 4.95130. Structure annealed in 39 s, f = 3.78311. Structure annealed in 39 s, f = 3.22757. Structure annealed in 39 s, f = 5.29791. Structure annealed in 39 s, f = 13.3692. Structure annealed in 39 s, f = 8.20658. Structure annealed in 39 s, f = 7.08791. Structure annealed in 39 s, f = 5.26630. Structure annealed in 39 s, f = 7.85781. Structure annealed in 39 s, f = 9.37855. Structure annealed in 39 s, f = 5.61255. Structure annealed in 39 s, f = 3.86188. Structure annealed in 39 s, f = 4.17961. Structure annealed in 39 s, f = 7.70611. Structure annealed in 39 s, f = 7.64971. Structure annealed in 39 s, f = 8.81480. Structure annealed in 39 s, f = 4.65351. 100 structures finished in 164 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 2.67 0 0.0079 0.18 2 8.3 0.22 0 0.3570 2.72 2 2.73 3 0.0100 0.32 0 7.0 0.17 0 0.4183 3.10 3 2.98 2 0.0092 0.24 1 8.6 0.22 0 0.4204 3.69 4 3.09 5 0.0112 0.28 0 9.2 0.19 0 0.4149 2.77 5 3.23 6 0.0110 0.42 1 7.9 0.21 0 0.3517 2.44 6 3.25 5 0.0100 0.24 1 8.7 0.23 0 0.3838 2.56 7 3.50 2 0.0099 0.25 3 9.6 0.30 0 0.4348 3.59 8 3.55 3 0.0092 0.26 2 9.3 0.29 0 0.2840 2.43 9 3.62 4 0.0101 0.33 0 8.1 0.17 0 0.4256 2.51 10 3.71 8 0.0127 0.38 0 9.3 0.17 0 0.3758 2.11 11 3.75 3 0.0115 0.32 0 11.2 0.20 0 0.4672 2.73 12 3.75 3 0.0098 0.28 1 8.7 0.24 0 0.3816 2.96 13 3.78 3 0.0102 0.35 4 9.3 0.29 0 0.3278 2.22 14 3.79 7 0.0125 0.34 1 10.1 0.21 0 0.4180 2.45 15 3.80 6 0.0118 0.37 3 9.5 0.29 0 0.4811 3.75 16 3.86 2 0.0096 0.23 4 8.7 0.29 0 0.4431 2.83 17 3.92 4 0.0105 0.28 3 10.0 0.30 0 0.4991 2.74 18 4.02 2 0.0099 0.24 3 9.8 0.29 0 0.3791 3.28 19 4.03 5 0.0111 0.34 1 9.6 0.24 0 0.4685 3.64 20 4.03 5 0.0110 0.26 1 8.8 0.21 0 0.5786 4.29 Ave 3.55 4 0.0105 0.30 2 9.1 0.24 0 0.4155 2.94 +/- 0.41 2 0.0011 0.06 1 0.9 0.04 0 0.0641 0.57 Min 2.67 0 0.0079 0.18 0 7.0 0.17 0 0.2840 2.11 Max 4.03 8 0.0127 0.42 4 11.2 0.30 0 0.5786 4.29 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 2 141 11 0 0 forrtl: Stale NFS file handle forrtl: severe (38): error during write, unit 41, file /user/francis/znf42/8cyana/116g/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 4, comm 3) 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 19471 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() MPI_Recv: process in local group is dead (rank 12, comm 3) Rank (24, MPI_COMM_WORLD): Call stack within LAM: Rank (24, MPI_COMM_WORLD): - MPI_Recv() Rank (24, MPI_COMM_WORLD): - MPI_Bcast() Rank (24, MPI_COMM_WORLD): - MPI_Bcast() Rank (24, MPI_COMM_WORLD): - main() LAM 7.2b1svn10112005/MPI 2 C++/ROMIO - Indiana University 06-Dec-2005 00:32:47