Warning: no access to tty (Bad file descriptor). Thus no job control in this shell. 06-Dec-2005 23:00:51 n-1<28082> ssi:boot:base:linear: booting n0 (wolf01) n-1<28082> ssi:boot:base:linear: booting n1 (wolf02) n-1<28082> ssi:boot:base:linear: booting n2 (wolf03) n-1<28082> ssi:boot:base:linear: booting n3 (wolf04) n-1<28082> ssi:boot:base:linear: booting n4 (wolf05) n-1<28082> ssi:boot:base:linear: booting n5 (wolf06) n-1<28082> ssi:boot:base:linear: booting n6 (wolf07) n-1<28082> ssi:boot:base:linear: booting n7 (wolf08) n-1<28082> ssi:boot:base:linear: booting n8 (wolf09) n-1<28082> ssi:boot:base:linear: booting n9 (wolf10) n-1<28082> ssi:boot:base:linear: booting n10 (wolf11) n-1<28082> ssi:boot:base:linear: booting n11 (wolf12) n-1<28082> ssi:boot:base:linear: booting n12 (wolf13) n-1<28082> 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, 3182 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 3182 0.000 0.002 0.032 0.009 1 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 HB3 LEU 89 1.333 1.333 0.032 19 1 shift with spread larger than tolerance. - peakcheck: peak deviations Peak Dim Deviation Atom Residue 3779 1 0.032 HB3 LEU 89 1 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, 1271 peaks, 1106 assignments. - peakcheck: peaks fit Deviations from chemical shift list: Dim Peaks Median Average Maximum RMSD Number Tolerance 1 1106 0.002 0.002 0.030 0.011 0 0.030 2 1269 0.000 0.000 0.011 0.001 0 0.030 3 1269 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, 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 0.015 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=3.5E7,1.7 E7,2.5E7,1.0E7 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, 3182 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=3.5E7 Calibration constant for peak list 1: 3.50E+07 Upper limit set for 3483 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 39.4% 5.00-5.99 A: 1135 32.6% 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, 1271 peaks, 1106 assignments. - calibration: peaks select "** list=2" 1271 of 4754 peaks, 1271 of 4754 assignments selected. - calibration: peaks set volume=abs(volume) Volume of 1271 peaks set. - calibration: peaks simplecal constant=1.7E7 Calibration constant for peak list 2: 1.70E+07 Upper limit set for 1271 peaks. - calibration: caltab peaks Distance bounds: -2.99 A: 74 5.8% 3.00-3.99 A: 227 17.9% 4.00-4.99 A: 491 38.6% 5.00-5.99 A: 479 37.7% 6.00- A: 0 0.0% All: 1271 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 5046 peaks, 292 of 5046 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, 1982 chemical shifts. - calibration: read peaks fc12no format= append Peak list "fc12no.peaks" read, 233 peaks, 143 assignments. - calibration: peaks select "** list=4" 233 of 5279 peaks, 233 of 5279 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 ** 5279 of 5279 peaks, 5279 of 5279 assignments selected. - znf42: peaks calibrate ** simple 4175 upper limits added, 2/697 at lower/upper bound, average 4.58 A. - znf42: write upl znf42-in.upl Distance constraint file "znf42-in.upl" written, 4175 upper limits, 4175 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 = 3.34757. Structure annealed in 39 s, f = 2.20981. Structure annealed in 39 s, f = 2.97994. Structure annealed in 41 s, f = 313.154. Structure annealed in 39 s, f = 2.58230. Structure annealed in 39 s, f = 2.33109. Structure annealed in 39 s, f = 8.18803. Structure annealed in 39 s, f = 2.40520. Structure annealed in 39 s, f = 3.74853. Structure annealed in 39 s, f = 2.59511. Structure annealed in 39 s, f = 1.74601. Structure annealed in 39 s, f = 2.88247. Structure annealed in 39 s, f = 2.36820. Structure annealed in 39 s, f = 2.51641. Structure annealed in 39 s, f = 2.58286. Structure annealed in 39 s, f = 39.8613. Structure annealed in 39 s, f = 5.81607. Structure annealed in 38 s, f = 2.32722. Structure annealed in 39 s, f = 3.98582. Structure annealed in 41 s, f = 382.839. Structure annealed in 39 s, f = 2.10812. Structure annealed in 39 s, f = 4.82850. Structure annealed in 39 s, f = 12.3881. Structure annealed in 39 s, f = 3.11743. Structure annealed in 39 s, f = 3.69252. Structure annealed in 38 s, f = 3.56997. Structure annealed in 39 s, f = 3.66107. Structure annealed in 39 s, f = 3.13341. Structure annealed in 39 s, f = 7.05283. Structure annealed in 39 s, f = 3.11815. Structure annealed in 39 s, f = 2.53097. Structure annealed in 41 s, f = 333.511. Structure annealed in 39 s, f = 3.25525. Structure annealed in 39 s, f = 3.10190. Structure annealed in 39 s, f = 1.61194. Structure annealed in 42 s, f = 348.111. Structure annealed in 38 s, f = 4.91504. Structure annealed in 39 s, f = 2.49622. Structure annealed in 38 s, f = 2.05962. Structure annealed in 38 s, f = 1.48557. Structure annealed in 41 s, f = 192.127. Structure annealed in 39 s, f = 3.60799. Structure annealed in 39 s, f = 1.59191. Structure annealed in 38 s, f = 3.93521. Structure annealed in 39 s, f = 1.93380. Structure annealed in 38 s, f = 1.83361. Structure annealed in 39 s, f = 2.28998. Structure annealed in 39 s, f = 1.62066. Structure annealed in 39 s, f = 3.77401. Structure annealed in 39 s, f = 2.26118. Structure annealed in 38 s, f = 6.28999. Structure annealed in 39 s, f = 2.22457. Structure annealed in 39 s, f = 2.05348. Structure annealed in 39 s, f = 6.53516. Structure annealed in 39 s, f = 1.43887. Structure annealed in 39 s, f = 3.88708. Structure annealed in 39 s, f = 6.62745. Structure annealed in 38 s, f = 2.20679. Structure annealed in 39 s, f = 2.00680. Structure annealed in 38 s, f = 2.61497. Structure annealed in 40 s, f = 204.317. Structure annealed in 39 s, f = 2.31774. Structure annealed in 39 s, f = 6.30765. Structure annealed in 39 s, f = 6.77094. Structure annealed in 39 s, f = 6.62517. Structure annealed in 39 s, f = 3.13978. Structure annealed in 39 s, f = 8.65288. Structure annealed in 38 s, f = 1.92406. Structure annealed in 39 s, f = 3.28217. Structure annealed in 39 s, f = 2.51758. Structure annealed in 39 s, f = 2.43470. Structure annealed in 39 s, f = 2.92948. Structure annealed in 39 s, f = 2.48477. Structure annealed in 39 s, f = 2.54285. Structure annealed in 39 s, f = 2.79731. Structure annealed in 38 s, f = 6.20575. Structure annealed in 39 s, f = 9.26591. Structure annealed in 39 s, f = 2.53422. Structure annealed in 39 s, f = 1.66870. Structure annealed in 39 s, f = 4.63715. Structure annealed in 39 s, f = 2.07156. Structure annealed in 39 s, f = 2.74662. Structure annealed in 38 s, f = 2.43283. Structure annealed in 38 s, f = 4.57821. Structure annealed in 39 s, f = 8.97837. Structure annealed in 39 s, f = 5.14415. Structure annealed in 38 s, f = 1.32563. Structure annealed in 39 s, f = 11.6554. Structure annealed in 39 s, f = 3.04289. Structure annealed in 38 s, f = 2.85524. Structure annealed in 39 s, f = 28.6069. Structure annealed in 39 s, f = 3.83882. Structure annealed in 39 s, f = 4.45641. Structure annealed in 39 s, f = 2.71290. Structure annealed in 38 s, f = 1.96518. Structure annealed in 39 s, f = 6.38876. Structure annealed in 39 s, f = 2.73892. Structure annealed in 39 s, f = 2.39467. Structure annealed in 39 s, f = 5.64778. Structure annealed in 39 s, f = 7.19782. 100 structures finished in 167 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 1.33 0 0.0047 0.13 0 4.9 0.16 0 0.2886 2.06 2 1.44 0 0.0059 0.17 1 5.8 0.21 0 0.3230 2.39 3 1.49 1 0.0077 0.29 1 5.8 0.21 0 0.3945 2.32 4 1.59 0 0.0066 0.20 0 6.5 0.16 0 0.3743 2.26 5 1.61 0 0.0066 0.18 0 5.9 0.17 0 0.4271 2.72 6 1.62 0 0.0057 0.14 2 6.4 0.29 0 0.3125 2.63 7 1.67 0 0.0066 0.18 2 7.2 0.29 0 0.2668 2.43 8 1.75 1 0.0075 0.30 1 5.8 0.24 0 0.4039 2.43 9 1.83 0 0.0054 0.17 2 5.5 0.29 0 0.3307 2.63 10 1.92 0 0.0058 0.19 0 6.6 0.17 0 0.3378 2.24 11 1.93 2 0.0074 0.31 2 6.7 0.23 0 0.3326 2.69 12 1.97 0 0.0056 0.14 2 6.6 0.29 0 0.2740 2.26 13 2.01 0 0.0059 0.17 1 6.7 0.21 0 0.3916 2.85 14 2.05 1 0.0064 0.21 3 6.4 0.29 0 0.3228 1.89 15 2.06 1 0.0074 0.24 2 7.2 0.29 0 0.3535 2.71 16 2.07 0 0.0060 0.20 1 6.0 0.23 0 0.3860 2.49 17 2.11 0 0.0063 0.19 2 6.2 0.29 0 0.3379 2.17 18 2.21 0 0.0071 0.19 2 7.5 0.29 0 0.4006 2.94 19 2.21 0 0.0077 0.17 1 7.2 0.22 0 0.4283 2.68 20 2.22 0 0.0059 0.18 3 7.7 0.29 0 0.4015 2.84 Ave 1.85 0 0.0064 0.20 1 6.4 0.24 0 0.3544 2.48 +/- 0.27 1 0.0008 0.05 1 0.7 0.05 0 0.0478 0.28 Min 1.33 0 0.0047 0.13 0 4.9 0.16 0 0.2668 1.89 Max 2.22 2 0.0077 0.31 3 7.7 0.29 0 0.4283 2.94 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 ------ --- --- --- --- 1 143 5 2 2 (ASP 37, ASP 337) 2 141 11 0 0 3 137 15 0 0 forrtl: Stale NFS file handle forrtl: severe (38): error during write, unit 41, file /user/francis/znf42/8cyana/120b/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 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 28164 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 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 06-Dec-2005 23:04:09