Warning: no access to tty (Bad file descriptor). Thus no job control in this shell. 06-Dec-2005 00:26:18 n-1<19275> ssi:boot:base:linear: booting n0 (wolf01) n-1<19275> ssi:boot:base:linear: booting n1 (wolf02) n-1<19275> ssi:boot:base:linear: booting n2 (wolf03) n-1<19275> ssi:boot:base:linear: booting n3 (wolf04) n-1<19275> ssi:boot:base:linear: booting n4 (wolf05) n-1<19275> ssi:boot:base:linear: booting n5 (wolf06) n-1<19275> ssi:boot:base:linear: booting n6 (wolf07) n-1<19275> ssi:boot:base:linear: booting n7 (wolf08) n-1<19275> ssi:boot:base:linear: booting n8 (wolf09) n-1<19275> ssi:boot:base:linear: booting n9 (wolf10) n-1<19275> ssi:boot:base:linear: booting n10 (wolf11) n-1<19275> ssi:boot:base:linear: booting n11 (wolf12) n-1<19275> ssi:boot:base:linear: booting n12 (wolf13) n-1<19275> 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=3.0E7,2.5 E7,2.0E7,1.0E7 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=2.5E7 Calibration constant for peak list 2: 2.50E+07 Upper limit set for 1272 peaks. - calibration: caltab peaks Distance bounds: -2.99 A: 47 3.7% 3.00-3.99 A: 144 11.3% 4.00-4.99 A: 477 37.5% 5.00-5.99 A: 604 47.5% 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=2.0E7 Calibration constant for peak list 3: 2.00E+07 Upper limit set for 292 peaks. - calibration: caltab peaks Distance bounds: -2.99 A: 22 7.5% 3.00-3.99 A: 61 20.9% 4.00-4.99 A: 174 59.6% 5.00-5.99 A: 35 12.0% 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, 3/712 at lower/upper bound, average 4.56 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: 2179 - znf42: write upl znf42.upl Distance constraint file "znf42.upl" written, 2179 upper limits, 2179 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, 2179 upper limits, 2179 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 = 8.09913. Structure annealed in 39 s, f = 9.43655. Structure annealed in 39 s, f = 5.43643. Structure annealed in 39 s, f = 4.02766. Structure annealed in 39 s, f = 4.66228. Structure annealed in 39 s, f = 2.98963. Structure annealed in 39 s, f = 3.20603. Structure annealed in 39 s, f = 4.22859. Structure annealed in 39 s, f = 7.20100. Structure annealed in 39 s, f = 4.09627. Structure annealed in 39 s, f = 7.93289. Structure annealed in 39 s, f = 3.63975. Structure annealed in 39 s, f = 106.426. Structure annealed in 39 s, f = 6.79596. Structure annealed in 39 s, f = 5.25431. Structure annealed in 39 s, f = 4.17112. Structure annealed in 39 s, f = 4.12365. Structure annealed in 39 s, f = 9.12512. Structure annealed in 39 s, f = 4.43365. Structure annealed in 39 s, f = 8.98789. Structure annealed in 39 s, f = 5.01342. Structure annealed in 40 s, f = 9.07220. Structure annealed in 39 s, f = 9.64337. Structure annealed in 39 s, f = 4.19742. Structure annealed in 39 s, f = 8.48273. Structure annealed in 39 s, f = 5.26097. Structure annealed in 38 s, f = 4.55250. Structure annealed in 39 s, f = 113.405. Structure annealed in 39 s, f = 5.36181. Structure annealed in 39 s, f = 5.57851. Structure annealed in 39 s, f = 10.6183. Structure annealed in 39 s, f = 4.14604. Structure annealed in 39 s, f = 4.11941. Structure annealed in 39 s, f = 10.9261. Structure annealed in 39 s, f = 5.39349. Structure annealed in 39 s, f = 5.67239. Structure annealed in 39 s, f = 4.10874. Structure annealed in 39 s, f = 3.81790. Structure annealed in 39 s, f = 2.98526. Structure annealed in 38 s, f = 4.32183. Structure annealed in 39 s, f = 3.31451. Structure annealed in 39 s, f = 19.5181. Structure annealed in 39 s, f = 7.94978. Structure annealed in 39 s, f = 2.96721. Structure annealed in 39 s, f = 6.89742. Structure annealed in 39 s, f = 4.26144. Structure annealed in 39 s, f = 9.28569. Structure annealed in 39 s, f = 5.60337. Structure annealed in 39 s, f = 4.33067. Structure annealed in 39 s, f = 3.71660. Structure annealed in 38 s, f = 3.59866. Structure annealed in 39 s, f = 4.04270. Structure annealed in 39 s, f = 5.02102. Structure annealed in 39 s, f = 144.768. Structure annealed in 39 s, f = 4.24172. Structure annealed in 39 s, f = 5.78590. Structure annealed in 39 s, f = 3.96051. Structure annealed in 39 s, f = 4.14220. Structure annealed in 39 s, f = 11.8423. Structure annealed in 39 s, f = 5.98569. Structure annealed in 39 s, f = 4.17293. Structure annealed in 39 s, f = 5.14864. Structure annealed in 39 s, f = 7.87379. Structure annealed in 39 s, f = 4.33274. Structure annealed in 39 s, f = 3.83851. Structure annealed in 39 s, f = 7.72279. Structure annealed in 39 s, f = 4.82325. Structure annealed in 39 s, f = 3.15973. Structure annealed in 39 s, f = 3.52207. Structure annealed in 39 s, f = 4.22386. Structure annealed in 39 s, f = 8.75909. Structure annealed in 40 s, f = 145.778. Structure annealed in 39 s, f = 3.18680. Structure annealed in 39 s, f = 5.25886. Structure annealed in 39 s, f = 6.92059. Structure annealed in 39 s, f = 5.03686. Structure annealed in 39 s, f = 2.96971. Structure annealed in 38 s, f = 3.50553. Structure annealed in 39 s, f = 3.28971. Structure annealed in 39 s, f = 7.63432. Structure annealed in 39 s, f = 4.50572. Structure annealed in 39 s, f = 8.18594. Structure annealed in 39 s, f = 5.29978. Structure annealed in 39 s, f = 7.97930. Structure annealed in 39 s, f = 4.75746. Structure annealed in 39 s, f = 4.66302. Structure annealed in 39 s, f = 5.86616. Structure annealed in 40 s, f = 30.3699. Structure annealed in 39 s, f = 3.48014. Structure annealed in 39 s, f = 9.54986. Structure annealed in 39 s, f = 4.95769. Structure annealed in 39 s, f = 5.42477. Structure annealed in 39 s, f = 4.54699. Structure annealed in 39 s, f = 5.28202. Structure annealed in 38 s, f = 3.98671. Structure annealed in 39 s, f = 7.35077. Structure annealed in 39 s, f = 8.14809. Structure annealed in 39 s, f = 3.27359. Structure annealed in 39 s, f = 7.37619. Structure annealed in 39 s, f = 3.69168. 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 2.97 3 0.0109 0.39 0 7.8 0.17 0 0.3597 2.21 2 2.97 1 0.0086 0.21 2 8.6 0.22 0 0.3621 2.57 3 2.99 1 0.0092 0.20 1 8.4 0.23 0 0.3533 2.51 4 2.99 2 0.0096 0.30 1 8.7 0.21 0 0.3551 2.26 5 3.16 7 0.0110 0.26 0 8.5 0.17 0 0.4285 2.87 6 3.19 0 0.0089 0.19 3 7.9 0.29 0 0.4039 2.54 7 3.21 5 0.0119 0.35 2 8.2 0.24 0 0.4355 3.25 8 3.27 3 0.0100 0.29 0 8.6 0.19 0 0.3773 2.12 9 3.29 0 0.0090 0.19 2 8.8 0.29 0 0.4055 3.22 10 3.31 8 0.0120 0.36 2 8.4 0.25 0 0.4415 2.63 11 3.48 2 0.0102 0.25 3 9.2 0.29 0 0.4098 3.51 12 3.51 3 0.0098 0.33 3 8.9 0.29 0 0.3774 2.87 13 3.52 0 0.0095 0.20 3 8.7 0.29 0 0.3936 2.98 14 3.60 4 0.0114 0.37 0 9.0 0.17 0 0.4605 4.14 15 3.64 5 0.0113 0.39 3 8.8 0.29 0 0.5557 4.47 16 3.69 1 0.0096 0.26 2 9.5 0.29 0 0.3600 2.66 17 3.72 2 0.0106 0.26 2 10.1 0.23 0 0.4412 2.51 18 3.82 6 0.0114 0.27 1 8.9 0.20 0 0.4159 3.14 19 3.84 6 0.0114 0.30 3 9.7 0.29 0 0.4387 2.96 20 3.96 4 0.0109 0.29 0 8.4 0.18 0 0.4906 3.39 Ave 3.41 3 0.0104 0.28 2 8.8 0.24 0 0.4133 2.94 +/- 0.31 2 0.0010 0.06 1 0.6 0.05 0 0.0499 0.59 Min 2.97 0 0.0086 0.19 0 7.8 0.17 0 0.3533 2.12 Max 3.96 8 0.0120 0.39 3 10.1 0.29 0 0.5557 4.47 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 ------ --- --- --- --- 1 135 17 0 0 2 136 14 0 2 (ARG 124, ARG 424) 3 136 16 0 0 forrtl: Stale NFS file handle forrtl: severe (38): error during write, unit 41, file /user/francis/znf42/8cyana/116f/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 4, comm 3) MPI_Recv: process in local group is dead (rank 8, comm 3) ----------------------------------------------------------------------------- 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 19357 failed on node n0 (192.168.96.101) with exit status 28. ----------------------------------------------------------------------------- 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 (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 06-Dec-2005 00:29:31