Warning: no access to tty (Bad file descriptor). Thus no job control in this shell. 13-Dec-2005 14:31:37 n-1<13682> ssi:boot:base:linear: booting n0 (wolf01) n-1<13682> ssi:boot:base:linear: booting n1 (wolf02) n-1<13682> ssi:boot:base:linear: booting n2 (wolf03) n-1<13682> ssi:boot:base:linear: booting n3 (wolf04) n-1<13682> ssi:boot:base:linear: booting n4 (wolf05) n-1<13682> ssi:boot:base:linear: booting n5 (wolf06) n-1<13682> ssi:boot:base:linear: booting n6 (wolf07) n-1<13682> ssi:boot:base:linear: booting n7 (wolf08) n-1<13682> ssi:boot:base:linear: booting n8 (wolf09) n-1<13682> ssi:boot:base:linear: booting n9 (wolf10) n-1<13682> ssi:boot:base:linear: booting n10 (wolf11) n-1<13682> ssi:boot:base:linear: booting n11 (wolf12) n-1<13682> ssi:boot:base:linear: booting n12 (wolf13) n-1<13682> 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, 3180 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 3180 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, 1273 peaks, 1105 assignments. - peakcheck: peaks fit Deviations from chemical shift list: Dim Peaks Median Average Maximum RMSD Number Tolerance 1 1105 0.002 0.002 0.030 0.011 0 0.030 2 1271 0.000 0.000 0.011 0.001 0 0.030 3 1271 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 0.016 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, 3180 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, 1273 peaks, 1105 assignments. - calibration: peaks select "** list=2" 1273 of 4756 peaks, 1273 of 4756 assignments selected. - calibration: peaks set volume=abs(volume) Volume of 1273 peaks set. - calibration: peaks simplecal constant=1.7E7 Calibration constant for peak list 2: 1.70E+07 Upper limit set for 1273 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: 493 38.7% 5.00-5.99 A: 479 37.6% 6.00- A: 0 0.0% All: 1273 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 5048 peaks, 292 of 5048 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 5281 peaks, 233 of 5281 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 ** 5281 of 5281 peaks, 5281 of 5281 assignments selected. - znf42: peaks calibrate ** simple 4172 upper limits added, 2/693 at lower/upper bound, average 4.58 A. - znf42: write upl znf42-in.upl Distance constraint file "znf42-in.upl" written, 4172 upper limits, 4172 assignments. - znf42: distance modify Number of modified constraints: 2131 - znf42: write upl znf42.upl Distance constraint file "znf42.upl" written, 2131 upper limits, 2131 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, 2131 upper limits, 2131 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 = 4.07465. Structure annealed in 38 s, f = 5.76922. Structure annealed in 39 s, f = 2.44997. Structure annealed in 39 s, f = 1.81651. Structure annealed in 39 s, f = 5.14239. Structure annealed in 39 s, f = 49.5586. Structure annealed in 39 s, f = 6.32480. Structure annealed in 39 s, f = 3.53203. Structure annealed in 39 s, f = 2.32212. Structure annealed in 39 s, f = 2.48935. Structure annealed in 39 s, f = 5.47290. Structure annealed in 39 s, f = 1.78164. Structure annealed in 39 s, f = 1.45646. Structure annealed in 39 s, f = 1.75407. Structure annealed in 40 s, f = 3.03377. Structure annealed in 39 s, f = 2.15986. Structure annealed in 39 s, f = 101.755. Structure annealed in 39 s, f = 1.64698. Structure annealed in 39 s, f = 2.04076. Structure annealed in 39 s, f = 2.56381. Structure annealed in 39 s, f = 2.02389. Structure annealed in 39 s, f = 1.70099. Structure annealed in 39 s, f = 4.64386. Structure annealed in 39 s, f = 5.53170. Structure annealed in 39 s, f = 2.62426. Structure annealed in 39 s, f = 6.02810. Structure annealed in 39 s, f = 5.64614. Structure annealed in 38 s, f = 3.34319. Structure annealed in 38 s, f = 2.09510. Structure annealed in 39 s, f = 3.47159. Structure annealed in 39 s, f = 1.64934. Structure annealed in 39 s, f = 6.91489. Structure annealed in 39 s, f = 5.88209. Structure annealed in 39 s, f = 6.72161. Structure annealed in 39 s, f = 2.11389. Structure annealed in 39 s, f = 3.47559. Structure annealed in 39 s, f = 2.41658. Structure annealed in 39 s, f = 1.77897. Structure annealed in 39 s, f = 6.73094. Structure annealed in 39 s, f = 2.47445. Structure annealed in 39 s, f = 1.67087. Structure annealed in 39 s, f = 2.53423. Structure annealed in 39 s, f = 6.22127. Structure annealed in 39 s, f = 5.56889. Structure annealed in 39 s, f = 6.88228. Structure annealed in 39 s, f = 1.79231. Structure annealed in 39 s, f = 2.01415. Structure annealed in 39 s, f = 6.15643. Structure annealed in 39 s, f = 6.82951. Structure annealed in 39 s, f = 5.31935. Structure annealed in 38 s, f = 5.77302. Structure annealed in 39 s, f = 3.63700. Structure annealed in 38 s, f = 9.53524. Structure annealed in 39 s, f = 3.73747. Structure annealed in 39 s, f = 1.42665. Structure annealed in 39 s, f = 1.32277. Structure annealed in 39 s, f = 7.24302. Structure annealed in 39 s, f = 3.40593. Structure annealed in 39 s, f = 7.74005. Structure annealed in 39 s, f = 3.43896. Structure annealed in 39 s, f = 2.56726. Structure annealed in 39 s, f = 2.23350. Structure annealed in 39 s, f = 3.43226. Structure annealed in 39 s, f = 2.80085. Structure annealed in 39 s, f = 4.71904. Structure annealed in 39 s, f = 2.67797. Structure annealed in 39 s, f = 1.81192. Structure annealed in 38 s, f = 2.11486. Structure annealed in 39 s, f = 2.42904. Structure annealed in 40 s, f = 2.09937. Structure annealed in 40 s, f = 139.004. Structure annealed in 39 s, f = 3.12934. Structure annealed in 39 s, f = 2.08085. Structure annealed in 39 s, f = 2.88267. Structure annealed in 39 s, f = 10.8986. Structure annealed in 38 s, f = 8.33101. Structure annealed in 39 s, f = 3.23411. Structure annealed in 39 s, f = 2.41613. Structure annealed in 39 s, f = 3.43484. Structure annealed in 39 s, f = 3.33252. Structure annealed in 38 s, f = 3.99077. Structure annealed in 39 s, f = 5.94999. Structure annealed in 39 s, f = 2.86338. Structure annealed in 39 s, f = 2.80260. Structure annealed in 39 s, f = 6.21013. Structure annealed in 39 s, f = 5.06869. Structure annealed in 39 s, f = 4.68206. Structure annealed in 39 s, f = 32.1716. Structure annealed in 41 s, f = 321.806. Structure annealed in 39 s, f = 2.86395. Structure annealed in 39 s, f = 5.66696. Structure annealed in 39 s, f = 2.02284. Structure annealed in 39 s, f = 2.49266. Structure annealed in 39 s, f = 3.30463. Structure annealed in 41 s, f = 320.222. Structure annealed in 39 s, f = 2.21637. Structure annealed in 39 s, f = 2.67186. Structure annealed in 39 s, f = 2.99213. Structure annealed in 39 s, f = 3.05472. Structure annealed in 39 s, f = 6.02402. 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 1.32 1 0.0058 0.23 2 5.2 0.24 0 0.2537 1.93 2 1.43 1 0.0056 0.20 0 5.5 0.14 0 0.1968 0.93 3 1.46 0 0.0059 0.16 1 5.2 0.25 0 0.3239 3.20 4 1.65 0 0.0058 0.19 3 5.9 0.29 0 0.2796 2.80 5 1.65 0 0.0050 0.15 1 5.9 0.21 0 0.3041 2.30 6 1.67 0 0.0071 0.20 1 5.9 0.20 0 0.3369 2.39 7 1.70 2 0.0083 0.38 0 5.0 0.16 0 0.3075 2.21 8 1.75 2 0.0076 0.31 0 5.8 0.15 0 0.2989 1.82 9 1.78 1 0.0067 0.20 0 7.3 0.16 0 0.2770 2.25 10 1.78 1 0.0056 0.24 2 6.7 0.29 0 0.2977 2.29 11 1.79 2 0.0079 0.38 1 5.4 0.20 0 0.3365 2.32 12 1.81 1 0.0070 0.33 1 6.2 0.23 0 0.3010 2.37 13 1.82 1 0.0068 0.20 1 7.3 0.22 0 0.3695 3.02 14 2.01 0 0.0057 0.17 2 6.0 0.29 0 0.2427 1.13 15 2.02 1 0.0066 0.20 2 6.7 0.21 0 0.2973 2.53 16 2.02 1 0.0062 0.27 1 5.8 0.21 0 0.3195 2.48 17 2.04 2 0.0075 0.35 1 6.6 0.24 0 0.3068 2.33 18 2.08 0 0.0056 0.19 2 6.6 0.23 0 0.2914 2.11 19 2.10 0 0.0062 0.17 1 7.2 0.21 0 0.3630 2.66 20 2.10 0 0.0056 0.19 3 7.4 0.29 0 0.2408 1.77 Ave 1.80 1 0.0064 0.24 1 6.2 0.22 0 0.2972 2.24 +/- 0.23 1 0.0009 0.07 1 0.7 0.04 0 0.0406 0.53 Min 1.32 0 0.0050 0.15 0 5.0 0.14 0 0.1968 0.93 Max 2.10 2 0.0083 0.38 3 7.4 0.29 0 0.3695 3.20 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 2 138 12 2 0 3 141 11 0 0 forrtl: Stale NFS file handle forrtl: severe (38): error during write, unit 41, file /user/francis/znf42/8cyana/122a/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 13764 failed on node n0 (192.168.96.101) with exit status 28. ----------------------------------------------------------------------------- MPI_Recv: process in local group is dead (rank 8, comm 3) 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() 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 13-Dec-2005 14:34:50