Warning: no access to tty (Bad file descriptor). Thus no job control in this shell. 06-Dec-2005 00:45:45 n-1<20043> ssi:boot:base:linear: booting n0 (wolf01) n-1<20043> ssi:boot:base:linear: booting n1 (wolf02) n-1<20043> ssi:boot:base:linear: booting n2 (wolf03) n-1<20043> ssi:boot:base:linear: booting n3 (wolf04) n-1<20043> ssi:boot:base:linear: booting n4 (wolf05) n-1<20043> ssi:boot:base:linear: booting n5 (wolf06) n-1<20043> ssi:boot:base:linear: booting n6 (wolf07) n-1<20043> ssi:boot:base:linear: booting n7 (wolf08) n-1<20043> ssi:boot:base:linear: booting n8 (wolf09) n-1<20043> ssi:boot:base:linear: booting n9 (wolf10) n-1<20043> ssi:boot:base:linear: booting n10 (wolf11) n-1<20043> ssi:boot:base:linear: booting n11 (wolf12) n-1<20043> ssi:boot:base:linear: booting n12 (wolf13) n-1<20043> 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 E7,2.0E7,0.5E7 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=2.0E7 Calibration constant for peak list 3: 2.00E+07 Upper limit set for 292 peaks. - calibration: caltab peaks Distance bounds: -2.99 A: 22 7.5% 3.00-3.99 A: 61 20.9% 4.00-4.99 A: 174 59.6% 5.00-5.99 A: 35 12.0% 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=0.5E7 Calibration constant for peak list 4: 5.00E+06 Upper limit set for 233 peaks. - calibration: caltab peaks Distance bounds: -2.99 A: 11 4.7% 3.00-3.99 A: 118 50.6% 4.00-4.99 A: 104 44.6% 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 4182 upper limits added, 3/596 at lower/upper bound, average 4.49 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: 2208 - znf42: write upl znf42.upl Distance constraint file "znf42.upl" written, 2208 upper limits, 2208 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, 2208 upper limits, 2208 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 = 5.70978. Structure annealed in 40 s, f = 9.28915. Structure annealed in 39 s, f = 8.68734. Structure annealed in 39 s, f = 7.89468. Structure annealed in 39 s, f = 13.2383. Structure annealed in 39 s, f = 4.35138. Structure annealed in 39 s, f = 8.31356. Structure annealed in 39 s, f = 3.72618. Structure annealed in 39 s, f = 9.74580. Structure annealed in 39 s, f = 4.22779. Structure annealed in 39 s, f = 10.6204. Structure annealed in 40 s, f = 8.91788. Structure annealed in 39 s, f = 5.93015. Structure annealed in 39 s, f = 4.92673. Structure annealed in 39 s, f = 5.68374. Structure annealed in 39 s, f = 5.40846. Structure annealed in 40 s, f = 5.03753. Structure annealed in 39 s, f = 10.5043. Structure annealed in 40 s, f = 121.858. Structure annealed in 39 s, f = 9.25255. Structure annealed in 39 s, f = 10.4649. Structure annealed in 39 s, f = 14.1227. Structure annealed in 39 s, f = 5.06674. Structure annealed in 39 s, f = 6.60926. Structure annealed in 40 s, f = 12.2726. Structure annealed in 39 s, f = 11.2051. Structure annealed in 39 s, f = 5.33006. Structure annealed in 39 s, f = 10.5827. Structure annealed in 39 s, f = 11.8455. Structure annealed in 40 s, f = 6.41984. Structure annealed in 39 s, f = 5.51729. Structure annealed in 39 s, f = 9.49528. Structure annealed in 39 s, f = 7.19103. Structure annealed in 39 s, f = 4.81978. Structure annealed in 39 s, f = 6.15215. Structure annealed in 39 s, f = 6.85608. Structure annealed in 39 s, f = 9.14186. Structure annealed in 40 s, f = 8.38790. Structure annealed in 39 s, f = 10.0568. Structure annealed in 39 s, f = 28.3526. Structure annealed in 39 s, f = 6.44863. Structure annealed in 39 s, f = 9.91089. Structure annealed in 39 s, f = 6.53654. Structure annealed in 39 s, f = 9.25678. Structure annealed in 39 s, f = 7.79920. Structure annealed in 39 s, f = 9.20975. Structure annealed in 39 s, f = 6.49408. Structure annealed in 40 s, f = 4.61858. Structure annealed in 39 s, f = 8.05108. Structure annealed in 39 s, f = 4.95260. Structure annealed in 39 s, f = 9.27318. Structure annealed in 39 s, f = 6.48935. Structure annealed in 39 s, f = 5.37297. Structure annealed in 39 s, f = 6.47065. Structure annealed in 39 s, f = 10.0208. Structure annealed in 39 s, f = 6.20613. Structure annealed in 39 s, f = 8.29060. Structure annealed in 39 s, f = 5.04462. Structure annealed in 39 s, f = 9.49676. Structure annealed in 39 s, f = 5.76972. Structure annealed in 39 s, f = 4.57108. Structure annealed in 39 s, f = 5.98200. Structure annealed in 39 s, f = 5.43951. Structure annealed in 39 s, f = 5.43761. Structure annealed in 41 s, f = 6.58523. Structure annealed in 40 s, f = 44.5488. Structure annealed in 39 s, f = 13.0029. Structure annealed in 39 s, f = 4.87019. Structure annealed in 39 s, f = 4.70291. Structure annealed in 39 s, f = 4.68892. Structure annealed in 39 s, f = 6.63672. Structure annealed in 39 s, f = 6.22860. Structure annealed in 39 s, f = 5.07833. Structure annealed in 40 s, f = 4.63790. Structure annealed in 39 s, f = 7.10880. Structure annealed in 38 s, f = 5.56496. Structure annealed in 39 s, f = 6.03225. Structure annealed in 39 s, f = 6.18089. Structure annealed in 39 s, f = 5.14763. Structure annealed in 39 s, f = 10.0299. Structure annealed in 39 s, f = 33.6762. Structure annealed in 39 s, f = 6.48395. Structure annealed in 39 s, f = 6.62048. Structure annealed in 39 s, f = 4.69892. Structure annealed in 39 s, f = 6.90457. Structure annealed in 40 s, f = 6.59454. Structure annealed in 39 s, f = 5.90933. Structure annealed in 39 s, f = 5.74396. Structure annealed in 39 s, f = 5.09260. Structure annealed in 39 s, f = 4.57852. Structure annealed in 39 s, f = 4.14154. Structure annealed in 39 s, f = 12.7458. Structure annealed in 40 s, f = 155.502. Structure annealed in 39 s, f = 5.99519. Structure annealed in 39 s, f = 6.32290. Structure annealed in 39 s, f = 5.86567. Structure annealed in 39 s, f = 9.06630. Structure annealed in 39 s, f = 13.3080. Structure annealed in 39 s, f = 11.9058. Structure annealed in 39 s, f = 5.35111. 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 3.73 6 0.0122 0.33 0 9.1 0.19 0 0.4765 2.69 2 4.14 8 0.0131 0.34 3 10.3 0.21 0 0.4533 2.91 3 4.23 2 0.0112 0.23 4 10.2 0.28 0 0.3990 2.81 4 4.35 3 0.0124 0.39 1 11.0 0.24 0 0.4905 3.60 5 4.57 4 0.0129 0.34 2 11.3 0.26 0 0.4678 2.82 6 4.58 5 0.0115 0.35 3 10.4 0.29 0 0.6057 4.79 7 4.62 6 0.0121 0.34 1 10.1 0.24 0 0.4994 3.09 8 4.64 8 0.0140 0.43 0 9.7 0.20 0 0.6108 4.15 9 4.69 4 0.0132 0.44 4 11.1 0.29 0 0.3932 2.97 10 4.70 7 0.0126 0.26 3 11.6 0.25 0 0.4815 2.97 11 4.70 3 0.0129 0.38 3 11.1 0.28 0 0.5596 3.91 12 4.82 4 0.0144 0.52 1 10.6 0.22 1 0.6961 5.81 13 4.87 6 0.0132 0.36 1 10.6 0.20 1 0.7599 8.11 14 4.93 7 0.0148 0.40 1 10.5 0.25 0 0.5917 3.52 15 4.95 5 0.0132 0.36 2 11.0 0.24 0 0.4792 2.66 16 5.04 4 0.0124 0.33 2 10.9 0.26 0 0.5024 3.17 17 5.04 7 0.0133 0.44 5 12.6 0.29 0 0.5234 3.06 18 5.07 6 0.0139 0.40 2 11.4 0.30 0 0.6144 4.91 19 5.08 8 0.0142 0.48 3 11.3 0.24 0 0.5319 3.69 20 5.09 7 0.0133 0.33 3 11.4 0.29 0 0.5503 3.87 Ave 4.69 6 0.0130 0.37 2 10.8 0.25 0 0.5343 3.78 +/- 0.35 2 0.0009 0.07 1 0.7 0.03 0 0.0898 1.29 Min 3.73 2 0.0112 0.23 0 9.1 0.19 0 0.3932 2.66 Max 5.09 8 0.0148 0.52 5 12.6 0.30 1 0.7599 8.11 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 forrtl: Stale NFS file handle forrtl: severe (38): error during write, unit 41, file /user/francis/znf42/8cyana/116l/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 20125 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 00:49:00