Warning: no access to tty (Bad file descriptor). Thus no job control in this shell. 02-Dec-2005 12:27:22 n-1<18285> ssi:boot:base:linear: booting n0 (wolf01) n-1<18285> ssi:boot:base:linear: booting n1 (wolf02) n-1<18285> ssi:boot:base:linear: booting n2 (wolf03) n-1<18285> ssi:boot:base:linear: booting n3 (wolf04) n-1<18285> ssi:boot:base:linear: booting n4 (wolf05) n-1<18285> ssi:boot:base:linear: booting n5 (wolf06) n-1<18285> ssi:boot:base:linear: booting n6 (wolf07) n-1<18285> ssi:boot:base:linear: booting n7 (wolf08) n-1<18285> ssi:boot:base:linear: booting n8 (wolf09) n-1<18285> ssi:boot:base:linear: booting n9 (wolf10) n-1<18285> ssi:boot:base:linear: booting n10 (wolf11) n-1<18285> ssi:boot:base:linear: booting n11 (wolf12) n-1<18285> ssi:boot:base:linear: booting n12 (wolf13) n-1<18285> 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, 1980 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, 1980 chemical shifts. - peakcheck: read peaks c13no format= Peak list "c13no.peaks" read, 3480 peaks, 3128 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 3128 0.000 0.002 0.044 0.009 1 0.030 2 3431 0.000 0.000 0.026 0.003 0 0.030 3 3431 0.000 0.000 0.297 0.025 0 0.450 - peakcheck: atom shift check Atom Residue Shift Median Deviation Peaks QG GLU 99 2.338 2.343 0.044 13 1 shift with spread larger than tolerance. - peakcheck: peak deviations Peak Dim Deviation Atom Residue 2726 1 -0.044 QG GLU 99 1 deviations larger than tolerance. ------------------------------------------------------------ Peak list : n15no Proton list: znf42 - peakcheck: read prot znf42 unknown=skip Chemical shift list "znf42.prot" read, 1980 chemical shifts. - peakcheck: read peaks n15no format= Peak list "n15no.peaks" read, 1273 peaks, 1112 assignments. - peakcheck: peaks fit Deviations from chemical shift list: Dim Peaks Median Average Maximum RMSD Number Tolerance 1 1112 0.002 0.002 0.033 0.011 1 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 QB GLN 82 2.338 2.361 0.033 2 1 shift with spread larger than tolerance. - peakcheck: peak deviations Peak Dim Deviation Atom Residue 1057 1 0.033 QB GLN 82 1 deviations larger than tolerance. ------------------------------------------------------------ Peak list : c13ar Proton list: znf42 - peakcheck: read prot znf42 unknown=skip Chemical shift list "znf42.prot" read, 1980 chemical shifts. - peakcheck: read peaks c13ar format= Peak list "c13ar.peaks" read, 281 peaks, 222 assignments. - peakcheck: peaks fit Deviations from chemical shift list: Dim Peaks Median Average Maximum RMSD Number Tolerance 1 222 0.004 0.005 0.030 0.013 0 0.030 2 280 0.000 0.000 0.000 0.000 0 0.030 3 280 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, 1980 chemical shifts. - peakcheck: read peaks fc12no format= Peak list "fc12no.peaks" read, 225 peaks, 150 assignments. - peakcheck: peaks fit Deviations from chemical shift list: Dim Peaks Median Average Maximum RMSD Number Tolerance 1 150 0.000 -0.001 0.029 0.016 0 0.030 2 169 0.000 -0.001 0.014 0.005 0 0.030 3 169 0.000 -0.005 0.297 0.034 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=3.0E7,1.2 E7,2.0E7,1.0E7 dref=4.2 - calibration: read prot znf42 unknown=warn Chemical shift list "znf42.prot" read, 1980 chemical shifts. - calibration: read peaks c13no format= Peak list "c13no.peaks" read, 3480 peaks, 3128 assignments. - calibration: peaks select "** list=1" 3480 of 3480 peaks, 3480 of 3480 assignments selected. - calibration: peaks set volume=abs(volume) Volume of 3480 peaks set. - calibration: peaks simplecal constant=3.0E7 Calibration constant for peak list 1: 3.00E+07 Upper limit set for 3480 peaks. - calibration: caltab peaks Distance bounds: -2.99 A: 328 9.4% 3.00-3.99 A: 773 22.2% 4.00-4.99 A: 1384 39.8% 5.00-5.99 A: 993 28.5% 6.00- A: 0 0.0% All: 3480 100.0% - calibration: read prot znf42 unknown=warn append Chemical shift list "znf42.prot" read, 1980 chemical shifts. - calibration: read peaks n15no format= append Peak list "n15no.peaks" read, 1273 peaks, 1112 assignments. - calibration: peaks select "** list=2" 1273 of 4753 peaks, 1273 of 4753 assignments selected. - calibration: peaks set volume=abs(volume) Volume of 1273 peaks set. - calibration: peaks simplecal constant=1.2E7 Calibration constant for peak list 2: 1.20E+07 Upper limit set for 1273 peaks. - calibration: caltab peaks Distance bounds: -2.99 A: 93 7.3% 3.00-3.99 A: 339 26.6% 4.00-4.99 A: 492 38.6% 5.00-5.99 A: 347 27.3% 6.00- A: 0 0.0% All: 1273 100.0% - calibration: read prot znf42 unknown=warn append Chemical shift list "znf42.prot" read, 1980 chemical shifts. - calibration: read peaks c13ar format= append Peak list "c13ar.peaks" read, 281 peaks, 222 assignments. - calibration: peaks select "** list=3" 281 of 5034 peaks, 281 of 5034 assignments selected. - calibration: peaks set volume=abs(volume) Volume of 281 peaks set. - calibration: peaks simplecal constant=2.0E7 Calibration constant for peak list 3: 2.00E+07 Upper limit set for 281 peaks. - calibration: caltab peaks Distance bounds: -2.99 A: 21 7.5% 3.00-3.99 A: 57 20.3% 4.00-4.99 A: 161 57.3% 5.00-5.99 A: 42 14.9% 6.00- A: 0 0.0% All: 281 100.0% - calibration: read prot znf42 unknown=warn append Chemical shift list "znf42.prot" read, 1980 chemical shifts. - calibration: read peaks fc12no format= append Peak list "fc12no.peaks" read, 225 peaks, 150 assignments. - calibration: peaks select "** list=4" 225 of 5259 peaks, 225 of 5259 assignments selected. - calibration: peaks set volume=abs(volume) Volume of 225 peaks set. - calibration: peaks simplecal constant=1.0E7 Calibration constant for peak list 4: 1.00E+07 Upper limit set for 225 peaks. - calibration: caltab peaks Distance bounds: -2.99 A: 2 0.9% 3.00-3.99 A: 48 21.3% 4.00-4.99 A: 156 69.3% 5.00-5.99 A: 19 8.4% 6.00- A: 0 0.0% All: 225 100.0% - calibration: peaks select ** 5259 of 5259 peaks, 5259 of 5259 assignments selected. - znf42: peaks calibrate ** simple 4127 upper limits added, 8/489 at lower/upper bound, average 4.46 A. - znf42: write upl znf42-in.upl Distance constraint file "znf42-in.upl" written, 4127 upper limits, 4127 assignments. - znf42: distance modify Number of modified constraints: 2192 - znf42: write upl znf42.upl Distance constraint file "znf42.upl" written, 2192 upper limits, 2192 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, 2192 upper limits, 2192 assignments. - znf42: read aco znf42.aco Angle constraint file "znf42.aco" read, 267 constraints for 267 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 = 14.2233. Structure annealed in 40 s, f = 13.5802. Structure annealed in 41 s, f = 361.651. Structure annealed in 40 s, f = 16.9090. Structure annealed in 39 s, f = 15.4809. Structure annealed in 40 s, f = 18.3198. Structure annealed in 40 s, f = 10.1607. Structure annealed in 39 s, f = 13.1333. Structure annealed in 39 s, f = 20.2136. Structure annealed in 39 s, f = 12.4056. Structure annealed in 40 s, f = 17.0334. Structure annealed in 39 s, f = 16.9029. Structure annealed in 39 s, f = 12.7291. Structure annealed in 40 s, f = 15.7868. Structure annealed in 39 s, f = 14.2262. Structure annealed in 39 s, f = 15.0374. Structure annealed in 39 s, f = 12.9281. Structure annealed in 39 s, f = 18.3822. Structure annealed in 39 s, f = 15.5669. Structure annealed in 39 s, f = 12.4164. Structure annealed in 39 s, f = 16.4733. Structure annealed in 40 s, f = 16.9992. Structure annealed in 40 s, f = 12.1210. Structure annealed in 40 s, f = 17.7390. Structure annealed in 40 s, f = 13.9326. Structure annealed in 39 s, f = 19.1128. Structure annealed in 39 s, f = 11.9899. Structure annealed in 39 s, f = 17.8576. Structure annealed in 39 s, f = 16.9844. Structure annealed in 39 s, f = 14.2212. Structure annealed in 39 s, f = 11.5883. Structure annealed in 39 s, f = 12.3058. Structure annealed in 40 s, f = 20.0401. Structure annealed in 39 s, f = 16.3617. Structure annealed in 39 s, f = 15.2027. Structure annealed in 40 s, f = 25.9352. Structure annealed in 39 s, f = 11.5407. Structure annealed in 39 s, f = 12.0883. Structure annealed in 40 s, f = 14.2000. Structure annealed in 39 s, f = 13.3771. Structure annealed in 40 s, f = 15.2031. Structure annealed in 40 s, f = 11.7118. Structure annealed in 39 s, f = 14.8437. Structure annealed in 40 s, f = 15.5986. Structure annealed in 41 s, f = 337.103. Structure annealed in 40 s, f = 11.0855. Structure annealed in 40 s, f = 15.7233. Structure annealed in 40 s, f = 22.9691. Structure annealed in 39 s, f = 17.8418. Structure annealed in 40 s, f = 13.6978. Structure annealed in 39 s, f = 12.7096. Structure annealed in 39 s, f = 21.0411. Structure annealed in 39 s, f = 14.1237. Structure annealed in 39 s, f = 17.4201. Structure annealed in 39 s, f = 18.4551. Structure annealed in 40 s, f = 12.8003. Structure annealed in 39 s, f = 16.8982. Structure annealed in 39 s, f = 13.6637. Structure annealed in 40 s, f = 12.2743. Structure annealed in 39 s, f = 11.6451. Structure annealed in 40 s, f = 17.3468. Structure annealed in 39 s, f = 12.2349. Structure annealed in 39 s, f = 15.4764. Structure annealed in 40 s, f = 15.4486. Structure annealed in 40 s, f = 213.800. Structure annealed in 40 s, f = 16.1993. Structure annealed in 39 s, f = 26.8952. Structure annealed in 39 s, f = 15.3575. Structure annealed in 40 s, f = 21.8921. Structure annealed in 39 s, f = 16.1131. Structure annealed in 40 s, f = 12.5626. Structure annealed in 39 s, f = 16.8109. Structure annealed in 40 s, f = 15.7015. Structure annealed in 40 s, f = 18.2087. Structure annealed in 39 s, f = 12.9369. Structure annealed in 39 s, f = 14.3025. Structure annealed in 39 s, f = 14.6063. Structure annealed in 39 s, f = 17.3151. Structure annealed in 39 s, f = 15.5519. Structure annealed in 39 s, f = 12.2511. Structure annealed in 39 s, f = 16.0270. Structure annealed in 39 s, f = 12.7664. Structure annealed in 39 s, f = 12.8536. Structure annealed in 39 s, f = 19.9059. Structure annealed in 39 s, f = 12.2138. Structure annealed in 39 s, f = 15.4838. Structure annealed in 41 s, f = 184.398. Structure annealed in 40 s, f = 27.1816. Structure annealed in 42 s, f = 374.422. Structure annealed in 40 s, f = 16.4474. Structure annealed in 39 s, f = 13.5187. Structure annealed in 39 s, f = 12.2696. Structure annealed in 40 s, f = 12.5007. Structure annealed in 40 s, f = 19.7048. Structure annealed in 40 s, f = 16.0907. Structure annealed in 40 s, f = 14.2863. Structure annealed in 40 s, f = 13.0567. Structure annealed in 40 s, f = 13.7275. Structure annealed in 39 s, f = 15.6813. Structure annealed in 39 s, f = 16.8055. 100 structures finished in 165 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 10.16 29 0.0244 0.65 5 16.3 0.24 1 1.0267 5.58 2 11.09 30 0.0253 0.79 9 17.3 0.28 1 0.9226 5.71 3 11.54 35 0.0271 1.01 7 17.1 0.36 0 0.9251 4.68 4 11.59 34 0.0255 0.82 5 16.8 0.31 1 0.9879 5.40 5 11.65 31 0.0263 0.64 8 18.1 0.24 1 1.0315 5.02 6 11.71 36 0.0247 0.72 9 16.0 0.29 1 1.1017 6.44 7 11.99 29 0.0254 0.72 11 16.8 0.36 4 1.1377 6.29 8 12.09 34 0.0261 0.74 4 17.0 0.39 1 1.0900 6.56 9 12.12 39 0.0262 0.67 8 18.1 0.26 0 1.0021 4.98 10 12.21 39 0.0272 0.86 7 19.1 0.29 0 0.9439 4.24 11 12.24 38 0.0277 0.85 4 17.9 0.24 1 1.0349 8.16 12 12.25 42 0.0280 0.81 10 18.4 0.33 0 0.9865 4.85 13 12.27 38 0.0264 0.66 9 18.4 0.26 4 1.0778 6.47 14 12.27 38 0.0262 0.79 7 17.8 0.33 0 0.9383 4.76 15 12.31 33 0.0259 0.63 9 18.5 0.46 3 1.1496 6.27 16 12.41 37 0.0272 0.64 10 17.7 0.27 0 0.9417 4.59 17 12.42 35 0.0259 0.78 8 16.8 0.25 1 1.0912 5.56 18 12.50 34 0.0280 0.83 7 18.3 0.32 0 0.9172 4.42 19 12.56 36 0.0273 0.66 7 18.1 0.33 1 1.0799 5.38 20 12.71 39 0.0274 0.74 8 18.4 0.32 1 1.0778 7.48 Ave 12.00 35 0.0264 0.75 8 17.6 0.31 1 1.0232 5.64 +/- 0.58 4 0.0010 0.09 2 0.8 0.06 1 0.0734 1.01 Min 10.16 29 0.0244 0.63 4 16.0 0.24 0 0.9172 4.24 Max 12.71 42 0.0280 1.01 11 19.1 0.46 4 1.1496 8.16 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 ------ --- --- --- --- 1 137 15 0 0 2 135 14 1 2 (ASP 37, ASP 337) 3 137 13 0 2 (GLU 125, GLU 425) 4 137 14 1 0 5 138 14 0 0 6 143 9 0 0 7 142 10 0 0 8 137 12 3 0 9 133 19 0 0 10 135 15 0 2 (GLU 125, GLU 425) 11 137 15 0 0 12 137 12 3 0 13 139 11 2 0 forrtl: Stale NFS file handle forrtl: severe (38): error during write, unit 41, file /user/francis/znf42/8cyana/113/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 18367 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 (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 02-Dec-2005 12:30:40