Warning: no access to tty (Bad file descriptor). Thus no job control in this shell. 21-Dec-2005 13:30:06 n-1<22052> ssi:boot:base:linear: booting n0 (wolf01) n-1<22052> ssi:boot:base:linear: booting n1 (wolf02) n-1<22052> ssi:boot:base:linear: booting n2 (wolf03) n-1<22052> ssi:boot:base:linear: booting n3 (wolf04) n-1<22052> ssi:boot:base:linear: booting n4 (wolf05) n-1<22052> ssi:boot:base:linear: booting n5 (wolf06) n-1<22052> ssi:boot:base:linear: booting n6 (wolf07) n-1<22052> ssi:boot:base:linear: booting n7 (wolf08) n-1<22052> ssi:boot:base:linear: booting n8 (wolf09) n-1<22052> ssi:boot:base:linear: booting n9 (wolf10) n-1<22052> ssi:boot:base:linear: booting n10 (wolf11) n-1<22052> ssi:boot:base:linear: booting n11 (wolf12) n-1<22052> ssi:boot:base:linear: booting n12 (wolf13) n-1<22052> 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, 3183 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 3183 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, 238 assignments. - peakcheck: peaks fit Deviations from chemical shift list: Dim Peaks Median Average Maximum RMSD Number Tolerance 1 238 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, 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, 1984 chemical shifts. - calibration: read peaks c13no format= Peak list "c13no.peaks" read, 3489 peaks, 3183 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, 238 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=2.5E7 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, 1984 chemical shifts. - calibration: read peaks fc12no format= append Peak list "fc12no.peaks" read, 233 peaks, 143 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 4169 upper limits added, 2/691 at lower/upper bound, average 4.58 A. - znf42: write upl znf42-in.upl Distance constraint file "znf42-in.upl" written, 4169 upper limits, 4169 assignments. - znf42: distance modify Number of modified constraints: 2150 - znf42: write upl znf42.upl Distance constraint file "znf42.upl" written, 2150 upper limits, 2150 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, 2150 upper limits, 2150 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 = 5.71034. Structure annealed in 38 s, f = 3.62578. Structure annealed in 38 s, f = 3.49900. Structure annealed in 38 s, f = 2.61539. Structure annealed in 38 s, f = 2.63921. Structure annealed in 39 s, f = 7.20230. Structure annealed in 38 s, f = 2.39989. Structure annealed in 38 s, f = 8.54568. Structure annealed in 38 s, f = 15.0496. Structure annealed in 39 s, f = 2.89274. Structure annealed in 39 s, f = 13.6398. Structure annealed in 38 s, f = 4.30165. Structure annealed in 38 s, f = 4.41117. Structure annealed in 38 s, f = 7.93195. Structure annealed in 38 s, f = 2.87108. Structure annealed in 38 s, f = 8.21643. Structure annealed in 38 s, f = 3.98427. Structure annealed in 38 s, f = 4.68876. Structure annealed in 38 s, f = 3.05747. Structure annealed in 38 s, f = 3.75337. Structure annealed in 39 s, f = 3.56908. Structure annealed in 38 s, f = 3.10979. Structure annealed in 39 s, f = 128.452. Structure annealed in 38 s, f = 3.67915. Structure annealed in 38 s, f = 2.86967. Structure annealed in 38 s, f = 8.51413. Structure annealed in 38 s, f = 3.35006. Structure annealed in 38 s, f = 3.59478. Structure annealed in 38 s, f = 6.40207. Structure annealed in 38 s, f = 4.38104. Structure annealed in 38 s, f = 2.67543. Structure annealed in 38 s, f = 2.35775. Structure annealed in 38 s, f = 9.16529. Structure annealed in 38 s, f = 5.81097. Structure annealed in 38 s, f = 2.42638. Structure annealed in 38 s, f = 7.52292. Structure annealed in 38 s, f = 6.24124. Structure annealed in 38 s, f = 3.09776. Structure annealed in 38 s, f = 4.18058. Structure annealed in 38 s, f = 4.88283. Structure annealed in 38 s, f = 8.04463. Structure annealed in 39 s, f = 6.29830. Structure annealed in 39 s, f = 4.47382. Structure annealed in 38 s, f = 5.71976. Structure annealed in 38 s, f = 2.70470. Structure annealed in 38 s, f = 10.4144. Structure annealed in 38 s, f = 6.87466. Structure annealed in 39 s, f = 2.77829. Structure annealed in 39 s, f = 2.89614. Structure annealed in 39 s, f = 7.96418. Structure annealed in 38 s, f = 7.38813. Structure annealed in 38 s, f = 3.47838. Structure annealed in 38 s, f = 4.96033. Structure annealed in 38 s, f = 3.39530. Structure annealed in 38 s, f = 6.03247. Structure annealed in 38 s, f = 2.51799. Structure annealed in 38 s, f = 3.88883. Structure annealed in 38 s, f = 9.42499. Structure annealed in 39 s, f = 8.26171. Structure annealed in 38 s, f = 16.5603. Structure annealed in 38 s, f = 3.70254. Structure annealed in 38 s, f = 2.54046. Structure annealed in 38 s, f = 4.87356. Structure annealed in 38 s, f = 3.02158. Structure annealed in 39 s, f = 6.60183. Structure annealed in 38 s, f = 5.27905. Structure annealed in 38 s, f = 3.25359. Structure annealed in 38 s, f = 6.44392. Structure annealed in 38 s, f = 4.06086. Structure annealed in 38 s, f = 6.39597. Structure annealed in 39 s, f = 24.7031. Structure annealed in 38 s, f = 6.34454. Structure annealed in 39 s, f = 4.60041. Structure annealed in 39 s, f = 3.40034. Structure annealed in 39 s, f = 7.08805. Structure annealed in 38 s, f = 3.48117. Structure annealed in 38 s, f = 7.35839. Structure annealed in 38 s, f = 3.15297. Structure annealed in 38 s, f = 2.70752. Structure annealed in 38 s, f = 3.68254. Structure annealed in 38 s, f = 3.27719. Structure annealed in 39 s, f = 3.53481. Structure annealed in 38 s, f = 5.83477. Structure annealed in 38 s, f = 6.23491. Structure annealed in 38 s, f = 3.12888. Structure annealed in 38 s, f = 7.40514. Structure annealed in 38 s, f = 7.35291. Structure annealed in 39 s, f = 3.17750. Structure annealed in 38 s, f = 7.89925. Structure annealed in 39 s, f = 3.50383. Structure annealed in 38 s, f = 9.31653. Structure annealed in 38 s, f = 8.33569. Structure annealed in 38 s, f = 6.53536. Structure annealed in 38 s, f = 3.81867. Structure annealed in 38 s, f = 4.50728. Structure annealed in 38 s, f = 3.65349. Structure annealed in 38 s, f = 6.04562. Structure annealed in 39 s, f = 3.78467. Structure annealed in 39 s, f = 7.93482. Structure annealed in 39 s, f = 7.56963. 100 structures finished in 160 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 2.36 0 0.0092 0.19 3 7.5 0.25 0 0.4080 3.59 2 2.40 1 0.0098 0.20 1 8.1 0.21 0 0.3474 2.49 3 2.43 0 0.0096 0.20 1 7.9 0.22 0 0.4620 3.75 4 2.52 1 0.0099 0.26 1 8.1 0.24 0 0.3104 2.28 5 2.54 0 0.0095 0.19 2 8.0 0.23 0 0.4586 3.10 6 2.62 1 0.0093 0.20 1 8.1 0.23 0 0.4492 3.50 7 2.64 1 0.0100 0.21 1 8.3 0.24 0 0.3279 3.15 8 2.68 3 0.0110 0.28 1 8.3 0.21 0 0.3461 3.14 9 2.70 2 0.0103 0.23 1 9.2 0.24 0 0.5366 3.51 10 2.71 1 0.0093 0.23 2 8.0 0.24 0 0.4556 3.08 11 2.78 1 0.0106 0.21 4 8.7 0.28 0 0.2676 1.85 12 2.87 0 0.0093 0.20 2 7.7 0.23 0 0.4170 2.90 13 2.87 1 0.0103 0.20 0 9.1 0.17 0 0.3741 2.80 14 2.89 0 0.0105 0.19 1 8.0 0.22 0 0.3660 2.76 15 2.90 1 0.0106 0.20 1 9.0 0.23 0 0.3118 2.20 16 3.02 4 0.0111 0.32 2 8.6 0.20 0 0.5070 4.78 17 3.06 3 0.0115 0.39 3 8.9 0.29 0 0.3351 2.41 18 3.10 3 0.0117 0.27 1 9.1 0.23 0 0.5604 3.56 19 3.11 0 0.0101 0.19 4 8.6 0.25 0 0.3751 3.03 20 3.13 7 0.0128 0.27 1 8.5 0.22 0 0.4429 3.05 Ave 2.77 2 0.0103 0.23 2 8.4 0.23 0 0.4029 3.05 +/- 0.24 2 0.0009 0.05 1 0.5 0.03 0 0.0779 0.64 Min 2.36 0 0.0092 0.19 0 7.5 0.17 0 0.2676 1.85 Max 3.13 7 0.0128 0.39 4 9.2 0.29 0 0.5604 4.78 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 10 0 4 (ARG 124, GLU 125, ARG 424, GLU 425) 3 135 17 0 0 4 137 12 3 0 5 136 12 2 2 (GLU 125, GLU 425) 6 142 8 0 2 (SER 36, SER 336) 7 134 16 1 1 (SER 36) 8 138 14 0 0 9 140 12 0 0 10 138 12 2 0 11 136 16 0 0 forrtl: Stale NFS file handle forrtl: severe (38): error during write, unit 41, file /user/francis/znf42/8cyana/150a-stereo/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 22134 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() 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 13:33:18