Warning: no access to tty (Bad file descriptor). Thus no job control in this shell. 06-Dec-2005 00:32:47 n-1<19524> ssi:boot:base:linear: booting n0 (wolf01) n-1<19524> ssi:boot:base:linear: booting n1 (wolf02) n-1<19524> ssi:boot:base:linear: booting n2 (wolf03) n-1<19524> ssi:boot:base:linear: booting n3 (wolf04) n-1<19524> ssi:boot:base:linear: booting n4 (wolf05) n-1<19524> ssi:boot:base:linear: booting n5 (wolf06) n-1<19524> ssi:boot:base:linear: booting n6 (wolf07) n-1<19524> ssi:boot:base:linear: booting n7 (wolf08) n-1<19524> ssi:boot:base:linear: booting n8 (wolf09) n-1<19524> ssi:boot:base:linear: booting n9 (wolf10) n-1<19524> ssi:boot:base:linear: booting n10 (wolf11) n-1<19524> ssi:boot:base:linear: booting n11 (wolf12) n-1<19524> ssi:boot:base:linear: booting n12 (wolf13) n-1<19524> 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 E7,3.0E7,1.0E7 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=3.0E7 Calibration constant for peak list 3: 3.00E+07 Upper limit set for 292 peaks. - calibration: caltab peaks Distance bounds: -2.99 A: 18 6.2% 3.00-3.99 A: 40 13.7% 4.00-4.99 A: 141 48.3% 5.00-5.99 A: 93 31.8% 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, 3/604 at lower/upper bound, average 4.53 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: 2198 - znf42: write upl znf42.upl Distance constraint file "znf42.upl" written, 2198 upper limits, 2198 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, 2198 upper limits, 2198 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 = 4.30254. Structure annealed in 39 s, f = 10.5192. Structure annealed in 39 s, f = 7.42876. Structure annealed in 39 s, f = 3.78661. Structure annealed in 39 s, f = 4.49268. Structure annealed in 39 s, f = 3.78999. Structure annealed in 39 s, f = 11.5328. Structure annealed in 39 s, f = 3.62029. Structure annealed in 39 s, f = 3.24616. Structure annealed in 39 s, f = 4.46133. Structure annealed in 39 s, f = 3.82421. Structure annealed in 39 s, f = 8.21543. Structure annealed in 39 s, f = 3.82064. Structure annealed in 39 s, f = 4.33496. Structure annealed in 39 s, f = 6.29700. Structure annealed in 39 s, f = 3.75572. Structure annealed in 39 s, f = 3.70304. Structure annealed in 39 s, f = 3.41767. Structure annealed in 39 s, f = 4.27925. Structure annealed in 39 s, f = 3.22177. Structure annealed in 39 s, f = 3.95780. Structure annealed in 39 s, f = 9.06389. Structure annealed in 39 s, f = 4.77566. Structure annealed in 39 s, f = 8.14915. Structure annealed in 40 s, f = 5.12442. Structure annealed in 38 s, f = 6.20918. Structure annealed in 39 s, f = 3.02054. Structure annealed in 39 s, f = 8.52323. Structure annealed in 38 s, f = 6.89291. Structure annealed in 39 s, f = 10.5495. Structure annealed in 39 s, f = 3.66779. Structure annealed in 39 s, f = 6.23470. Structure annealed in 39 s, f = 8.76002. Structure annealed in 39 s, f = 3.10448. Structure annealed in 40 s, f = 3.69625. Structure annealed in 39 s, f = 5.05416. Structure annealed in 39 s, f = 10.0299. Structure annealed in 39 s, f = 3.03035. Structure annealed in 39 s, f = 4.95484. Structure annealed in 39 s, f = 6.68267. Structure annealed in 39 s, f = 4.17942. Structure annealed in 39 s, f = 4.49209. Structure annealed in 39 s, f = 4.28044. Structure annealed in 39 s, f = 4.48031. Structure annealed in 39 s, f = 23.9000. Structure annealed in 39 s, f = 7.69187. Structure annealed in 39 s, f = 4.72565. Structure annealed in 41 s, f = 394.616. Structure annealed in 39 s, f = 2.41716. Structure annealed in 39 s, f = 4.74590. Structure annealed in 39 s, f = 8.28377. Structure annealed in 39 s, f = 3.01252. Structure annealed in 39 s, f = 8.23593. Structure annealed in 39 s, f = 4.66222. Structure annealed in 39 s, f = 8.90239. Structure annealed in 39 s, f = 2.99361. Structure annealed in 39 s, f = 7.67569. Structure annealed in 39 s, f = 4.44339. Structure annealed in 39 s, f = 7.76870. Structure annealed in 39 s, f = 3.42947. Structure annealed in 39 s, f = 4.51170. Structure annealed in 39 s, f = 3.15028. Structure annealed in 39 s, f = 9.49031. Structure annealed in 39 s, f = 10.7043. Structure annealed in 39 s, f = 5.18893. Structure annealed in 39 s, f = 6.32749. Structure annealed in 39 s, f = 4.19189. Structure annealed in 39 s, f = 5.89703. Structure annealed in 39 s, f = 4.29993. Structure annealed in 39 s, f = 5.62896. Structure annealed in 39 s, f = 4.95884. Structure annealed in 39 s, f = 3.17054. Structure annealed in 40 s, f = 6.97348. Structure annealed in 39 s, f = 7.57381. Structure annealed in 39 s, f = 3.10401. Structure annealed in 38 s, f = 3.71209. Structure annealed in 39 s, f = 7.36880. Structure annealed in 39 s, f = 3.79830. Structure annealed in 39 s, f = 3.98113. Structure annealed in 39 s, f = 4.27291. Structure annealed in 39 s, f = 3.69446. Structure annealed in 39 s, f = 10.5246. Structure annealed in 39 s, f = 7.00586. Structure annealed in 39 s, f = 4.36741. Structure annealed in 39 s, f = 8.96440. Structure annealed in 39 s, f = 2.93092. Structure annealed in 39 s, f = 4.01760. Structure annealed in 39 s, f = 4.52733. Structure annealed in 39 s, f = 8.08750. Structure annealed in 39 s, f = 6.85550. Structure annealed in 39 s, f = 3.35488. Structure annealed in 39 s, f = 8.38778. Structure annealed in 39 s, f = 5.35780. Structure annealed in 39 s, f = 4.98371. Structure annealed in 39 s, f = 5.32331. Structure annealed in 39 s, f = 13.5149. Structure annealed in 40 s, f = 43.0564. Structure annealed in 39 s, f = 6.72284. Structure annealed in 39 s, f = 3.54536. Structure annealed in 39 s, f = 3.82962. 100 structures finished in 163 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 2.42 0 0.0072 0.16 0 7.6 0.19 0 0.2867 2.21 2 2.93 3 0.0099 0.29 1 8.4 0.21 0 0.3924 2.67 3 2.99 2 0.0090 0.21 2 7.8 0.30 0 0.3472 3.44 4 3.01 1 0.0086 0.34 4 8.4 0.25 0 0.3897 3.45 5 3.02 3 0.0089 0.32 3 8.1 0.29 0 0.2882 2.11 6 3.03 4 0.0103 0.33 0 7.3 0.16 0 0.4011 2.76 7 3.10 3 0.0103 0.26 0 7.5 0.19 0 0.4433 2.89 8 3.10 5 0.0094 0.23 1 8.1 0.22 0 0.3386 2.06 9 3.15 4 0.0094 0.25 1 7.5 0.20 1 0.6669 7.41 10 3.17 3 0.0092 0.29 2 7.4 0.31 0 0.3896 2.55 11 3.22 4 0.0122 0.40 0 8.9 0.19 0 0.4955 3.94 12 3.25 2 0.0091 0.29 3 8.6 0.28 0 0.3909 3.56 13 3.36 2 0.0097 0.22 0 7.9 0.19 0 0.3777 2.37 14 3.42 3 0.0093 0.28 0 7.7 0.18 0 0.2891 1.75 15 3.43 3 0.0099 0.34 2 9.0 0.26 0 0.4464 3.26 16 3.55 1 0.0086 0.21 1 8.5 0.25 0 0.4612 3.25 17 3.62 4 0.0115 0.31 1 8.5 0.21 0 0.5538 3.86 18 3.67 0 0.0086 0.19 3 8.9 0.28 1 0.5464 5.03 19 3.69 10 0.0114 0.30 4 9.3 0.29 0 0.3361 2.40 20 3.70 10 0.0136 0.46 2 8.7 0.29 0 0.5440 4.68 Ave 3.24 3 0.0098 0.28 2 8.2 0.24 0 0.4192 3.28 +/- 0.31 3 0.0014 0.07 1 0.6 0.05 0 0.0989 1.27 Min 2.42 0 0.0072 0.16 0 7.3 0.16 0 0.2867 1.75 Max 3.70 10 0.0136 0.46 4 9.3 0.31 1 0.6669 7.41 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 13 2 0 2 140 12 0 0 forrtl: Stale NFS file handle forrtl: severe (38): error during write, unit 41, file /user/francis/znf42/8cyana/116h/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 1, comm 3) MPI_Recv: process in local group is dead (rank 4, 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 19606 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 00:36:01