Warning: no access to tty (Bad file descriptor). Thus no job control in this shell. 21-Dec-2005 14:57:48 n-1<23783> ssi:boot:base:linear: booting n0 (wolf01) n-1<23783> ssi:boot:base:linear: booting n1 (wolf02) n-1<23783> ssi:boot:base:linear: booting n2 (wolf03) n-1<23783> ssi:boot:base:linear: booting n3 (wolf04) n-1<23783> ssi:boot:base:linear: booting n4 (wolf05) n-1<23783> ssi:boot:base:linear: booting n5 (wolf06) n-1<23783> ssi:boot:base:linear: booting n6 (wolf07) n-1<23783> ssi:boot:base:linear: booting n7 (wolf08) n-1<23783> ssi:boot:base:linear: booting n8 (wolf09) n-1<23783> ssi:boot:base:linear: booting n9 (wolf10) n-1<23783> ssi:boot:base:linear: booting n10 (wolf11) n-1<23783> ssi:boot:base:linear: booting n11 (wolf12) n-1<23783> ssi:boot:base:linear: booting n12 (wolf13) n-1<23783> 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: finalstereo 125 stereospecific assignments defined. - znf42: peakcheck peaks=c13no,n15no,c13ar,fc12no prot=znf42 ------------------------------------------------------------ Proton list: znf42 - peakcheck: read prot znf42 unknown=warn Chemical shift list "znf42.prot" read, 1984 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, 1984 chemical shifts. - peakcheck: read peaks c13no format= Peak list "c13no.peaks" read, 3489 peaks, 3181 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 3181 0.000 0.002 0.030 0.009 0 0.030 2 3485 0.000 0.000 0.026 0.002 0 0.030 3 3485 0.000 -0.001 0.297 0.025 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, 1984 chemical shifts. - peakcheck: read peaks n15no format= Peak list "n15no.peaks" read, 1274 peaks, 1100 assignments. - peakcheck: peaks fit Deviations from chemical shift list: Dim Peaks Median Average Maximum RMSD Number Tolerance 1 1100 0.002 0.002 0.030 0.011 0 0.030 2 1272 0.000 0.000 0.011 0.001 0 0.030 3 1272 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, 1984 chemical shifts. - peakcheck: read peaks c13ar format= Peak list "c13ar.peaks" read, 292 peaks, 237 assignments. - peakcheck: peaks fit Deviations from chemical shift list: Dim Peaks Median Average Maximum RMSD Number Tolerance 1 237 0.005 0.006 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, 1984 chemical shifts. - peakcheck: read peaks fc12no format= Peak list "fc12no.peaks" read, 233 peaks, 142 assignments. - peakcheck: peaks fit Deviations from chemical shift list: Dim Peaks Median Average Maximum RMSD Number Tolerance 1 142 -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 E7,2.75E7,1.0E7 dref=4.2 - calibration: read prot znf42 unknown=warn Chemical shift list "znf42.prot" read, 1984 chemical shifts. - calibration: read peaks c13no format= Peak list "c13no.peaks" read, 3489 peaks, 3181 assignments. - calibration: peaks select "** list=1" 3489 of 3489 peaks, 3489 of 3489 assignments selected. - calibration: peaks set volume=abs(volume) Volume of 3489 peaks set. - calibration: peaks simplecal constant=3.5E7 Calibration constant for peak list 1: 3.50E+07 Upper limit set for 3489 peaks. - calibration: caltab peaks Distance bounds: -2.99 A: 298 8.5% 3.00-3.99 A: 680 19.5% 4.00-4.99 A: 1373 39.4% 5.00-5.99 A: 1138 32.6% 6.00- A: 0 0.0% All: 3489 100.0% - calibration: read prot znf42 unknown=warn append Chemical shift list "znf42.prot" read, 1984 chemical shifts. - calibration: read peaks n15no format= append Peak list "n15no.peaks" read, 1274 peaks, 1100 assignments. - calibration: peaks select "** list=2" 1274 of 4763 peaks, 1274 of 4763 assignments selected. - calibration: peaks set volume=abs(volume) Volume of 1274 peaks set. - calibration: peaks simplecal constant=1.7E7 Calibration constant for peak list 2: 1.70E+07 Upper limit set for 1274 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: 480 37.7% 6.00- A: 0 0.0% All: 1274 100.0% - calibration: read prot znf42 unknown=warn append Chemical shift list "znf42.prot" read, 1984 chemical shifts. - calibration: read peaks c13ar format= append Peak list "c13ar.peaks" read, 292 peaks, 237 assignments. - calibration: peaks select "** list=3" 292 of 5055 peaks, 292 of 5055 assignments selected. - calibration: peaks set volume=abs(volume) Volume of 292 peaks set. - calibration: peaks simplecal constant=2.75E7 Calibration constant for peak list 3: 2.75E+07 Upper limit set for 292 peaks. - calibration: caltab peaks Distance bounds: -2.99 A: 18 6.2% 3.00-3.99 A: 43 14.7% 4.00-4.99 A: 158 54.1% 5.00-5.99 A: 73 25.0% 6.00- A: 0 0.0% All: 292 100.0% - calibration: read prot znf42 unknown=warn append Chemical shift list "znf42.prot" read, 1984 chemical shifts. - calibration: read peaks fc12no format= append Peak list "fc12no.peaks" read, 233 peaks, 142 assignments. - calibration: peaks select "** list=4" 233 of 5288 peaks, 233 of 5288 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 ** 5288 of 5288 peaks, 5288 of 5288 assignments selected. - znf42: peaks calibrate ** simple 4165 upper limits added, 2/692 at lower/upper bound, average 4.58 A. - znf42: write upl znf42-in.upl Distance constraint file "znf42-in.upl" written, 4165 upper limits, 4165 assignments. - znf42: distance modify Number of modified constraints: 2144 - znf42: write upl znf42.upl Distance constraint file "znf42.upl" written, 2144 upper limits, 2144 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, 2144 upper limits, 2144 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 = 170.528. Structure annealed in 38 s, f = 6.73408. Structure annealed in 38 s, f = 3.34242. Structure annealed in 38 s, f = 4.06275. Structure annealed in 38 s, f = 2.52102. Structure annealed in 38 s, f = 9.96626. Structure annealed in 39 s, f = 65.5767. Structure annealed in 38 s, f = 1.88620. Structure annealed in 38 s, f = 9.72499. Structure annealed in 39 s, f = 3.65991. Structure annealed in 38 s, f = 5.94523. Structure annealed in 38 s, f = 3.21404. Structure annealed in 39 s, f = 39.9371. Structure annealed in 38 s, f = 8.37538. Structure annealed in 38 s, f = 6.77749. Structure annealed in 39 s, f = 50.0116. Structure annealed in 38 s, f = 5.89813. Structure annealed in 38 s, f = 1.99583. Structure annealed in 38 s, f = 4.26129. Structure annealed in 39 s, f = 6.75227. Structure annealed in 38 s, f = 2.54611. Structure annealed in 39 s, f = 2.03782. Structure annealed in 39 s, f = 229.646. Structure annealed in 39 s, f = 1.79652. Structure annealed in 39 s, f = 2.51485. Structure annealed in 38 s, f = 7.67682. Structure annealed in 38 s, f = 2.85980. Structure annealed in 38 s, f = 3.34606. Structure annealed in 38 s, f = 4.08399. Structure annealed in 38 s, f = 3.63810. Structure annealed in 38 s, f = 2.39511. Structure annealed in 38 s, f = 2.12554. Structure annealed in 38 s, f = 2.86843. Structure annealed in 38 s, f = 3.25119. Structure annealed in 38 s, f = 15.5497. Structure annealed in 38 s, f = 5.81399. Structure annealed in 39 s, f = 7.50574. Structure annealed in 38 s, f = 2.51870. Structure annealed in 38 s, f = 3.95195. Structure annealed in 39 s, f = 150.397. Structure annealed in 38 s, f = 4.62402. Structure annealed in 38 s, f = 2.83980. Structure annealed in 38 s, f = 8.30228. Structure annealed in 38 s, f = 3.28482. Structure annealed in 38 s, f = 1.99219. Structure annealed in 38 s, f = 7.73020. Structure annealed in 39 s, f = 2.87182. Structure annealed in 39 s, f = 6.52139. Structure annealed in 39 s, f = 4.54160. Structure annealed in 38 s, f = 4.09583. Structure annealed in 38 s, f = 3.08536. Structure annealed in 38 s, f = 2.89692. Structure annealed in 38 s, f = 5.96088. Structure annealed in 38 s, f = 5.14003. Structure annealed in 39 s, f = 3.47252. Structure annealed in 38 s, f = 6.45177. Structure annealed in 38 s, f = 2.44253. Structure annealed in 38 s, f = 2.73594. Structure annealed in 38 s, f = 3.03886. Structure annealed in 38 s, f = 9.01616. Structure annealed in 38 s, f = 1.95066. Structure annealed in 38 s, f = 2.54221. Structure annealed in 38 s, f = 3.30631. Structure annealed in 38 s, f = 5.42389. Structure annealed in 38 s, f = 3.10611. Structure annealed in 39 s, f = 4.11068. Structure annealed in 38 s, f = 5.39806. Structure annealed in 38 s, f = 3.88174. Structure annealed in 38 s, f = 3.50802. Structure annealed in 38 s, f = 3.88034. Structure annealed in 38 s, f = 3.47310. Structure annealed in 39 s, f = 8.75034. Structure annealed in 39 s, f = 5.95741. Structure annealed in 38 s, f = 8.34979. Structure annealed in 38 s, f = 4.91229. Structure annealed in 38 s, f = 2.65903. Structure annealed in 38 s, f = 2.59033. Structure annealed in 38 s, f = 2.67335. Structure annealed in 38 s, f = 7.64580. Structure annealed in 38 s, f = 11.8088. Structure annealed in 38 s, f = 3.73323. Structure annealed in 38 s, f = 2.67880. Structure annealed in 38 s, f = 3.95914. Structure annealed in 39 s, f = 4.91650. Structure annealed in 38 s, f = 6.64942. Structure annealed in 38 s, f = 8.06742. Structure annealed in 38 s, f = 2.39468. Structure annealed in 38 s, f = 2.31512. Structure annealed in 38 s, f = 3.53099. Structure annealed in 38 s, f = 2.22618. Structure annealed in 38 s, f = 2.42081. Structure annealed in 38 s, f = 7.60496. Structure annealed in 38 s, f = 3.82232. Structure annealed in 39 s, f = 5.31215. Structure annealed in 38 s, f = 3.03624. Structure annealed in 38 s, f = 5.63722. Structure annealed in 38 s, f = 2.21984. Structure annealed in 39 s, f = 150.680. Structure annealed in 38 s, f = 3.53319. Structure annealed in 38 s, f = 2.50032. 100 structures finished in 159 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 1.80 0 0.0084 0.18 1 6.7 0.23 0 0.4519 3.51 2 1.89 0 0.0093 0.20 0 7.8 0.18 0 0.3238 2.92 3 1.95 0 0.0078 0.16 0 7.7 0.17 0 0.3221 2.70 4 1.99 0 0.0087 0.18 0 8.3 0.18 0 0.2745 1.44 5 2.00 0 0.0083 0.18 1 7.1 0.23 0 0.3795 3.61 6 2.04 1 0.0076 0.23 2 6.7 0.24 0 0.3974 3.39 7 2.13 1 0.0089 0.22 0 7.1 0.16 0 0.3270 2.56 8 2.22 1 0.0094 0.31 2 7.2 0.23 0 0.4520 3.60 9 2.23 1 0.0098 0.22 0 7.8 0.16 0 0.3366 3.01 10 2.32 0 0.0088 0.18 1 9.1 0.23 0 0.3872 3.01 11 2.39 3 0.0101 0.22 3 8.7 0.28 0 0.3253 2.76 12 2.40 2 0.0103 0.24 1 8.6 0.24 0 0.3924 3.66 13 2.42 2 0.0090 0.22 2 7.7 0.22 0 0.5342 3.66 14 2.44 3 0.0104 0.26 0 8.3 0.17 0 0.3968 3.79 15 2.50 1 0.0097 0.21 0 8.3 0.17 0 0.3773 3.02 16 2.52 0 0.0085 0.17 1 7.8 0.23 0 0.4492 3.76 17 2.52 1 0.0091 0.21 2 8.1 0.28 0 0.3194 2.59 18 2.52 2 0.0097 0.21 1 8.2 0.23 0 0.4855 3.77 19 2.54 1 0.0101 0.21 0 8.7 0.18 0 0.3168 1.98 20 2.55 1 0.0096 0.20 0 8.1 0.18 0 0.3634 2.91 Ave 2.27 1 0.0092 0.21 1 7.9 0.21 0 0.3806 3.08 +/- 0.24 1 0.0008 0.03 1 0.7 0.04 0 0.0648 0.62 Min 1.80 0 0.0076 0.16 0 6.7 0.16 0 0.2745 1.44 Max 2.55 3 0.0104 0.31 3 9.1 0.28 0 0.5342 3.79 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 ------ --- --- --- --- 1 138 14 0 0 2 137 15 0 0 3 136 16 0 0 4 135 17 0 0 forrtl: Stale NFS file handle forrtl: severe (38): error during write, unit 41, file /user/francis/znf42/8cyana/160c/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 (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() 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() ----------------------------------------------------------------------------- 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 23865 failed on node n0 (192.168.96.101) with exit status 28. ----------------------------------------------------------------------------- MPI_Recv: process in local group is dead (rank 3, comm 3) Rank (6, MPI_COMM_WORLD): Call stack within LAM: Rank (6, MPI_COMM_WORLD): - MPI_Recv() Rank (6, MPI_COMM_WORLD): - MPI_Bcast() Rank (6, MPI_COMM_WORLD): - MPI_Bcast() Rank (6, 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 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 21-Dec-2005 15:01:00