Warning: no access to tty (Bad file descriptor). Thus no job control in this shell. 05-Dec-2005 16:37:22 n-1<16012> ssi:boot:base:linear: booting n0 (wolf01) n-1<16012> ssi:boot:base:linear: booting n1 (wolf02) n-1<16012> ssi:boot:base:linear: booting n2 (wolf03) n-1<16012> ssi:boot:base:linear: booting n3 (wolf04) n-1<16012> ssi:boot:base:linear: booting n4 (wolf05) n-1<16012> ssi:boot:base:linear: booting n5 (wolf06) n-1<16012> ssi:boot:base:linear: booting n6 (wolf07) n-1<16012> ssi:boot:base:linear: booting n7 (wolf08) n-1<16012> ssi:boot:base:linear: booting n8 (wolf09) n-1<16012> ssi:boot:base:linear: booting n9 (wolf10) n-1<16012> ssi:boot:base:linear: booting n10 (wolf11) n-1<16012> ssi:boot:base:linear: booting n11 (wolf12) n-1<16012> ssi:boot:base:linear: booting n12 (wolf13) n-1<16012> 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, 3194 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 3194 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, 1111 assignments. - peakcheck: peaks fit Deviations from chemical shift list: Dim Peaks Median Average Maximum RMSD Number Tolerance 1 1111 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, 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, 1981 chemical shifts. - peakcheck: read peaks fc12no format= Peak list "fc12no.peaks" read, 227 peaks, 138 assignments. - peakcheck: peaks fit Deviations from chemical shift list: Dim Peaks Median Average Maximum RMSD Number Tolerance 1 138 0.000 -0.001 0.029 0.015 0 0.030 2 186 0.000 -0.001 0.014 0.005 0 0.030 3 186 0.000 -0.006 0.297 0.035 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 E7,2.0E7,1.0E7 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, 3194 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, 1111 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, 238 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, 227 peaks, 138 assignments. - calibration: peaks select "** list=4" 227 of 5274 peaks, 227 of 5274 assignments selected. - calibration: peaks set volume=abs(volume) Volume of 227 peaks set. - calibration: peaks simplecal constant=1.0E7 Calibration constant for peak list 4: 1.00E+07 Upper limit set for 227 peaks. - calibration: caltab peaks Distance bounds: -2.99 A: 2 0.9% 3.00-3.99 A: 49 21.6% 4.00-4.99 A: 157 69.2% 5.00-5.99 A: 19 8.4% 6.00- A: 0 0.0% All: 227 100.0% - calibration: peaks select ** 5274 of 5274 peaks, 5274 of 5274 assignments selected. - znf42: peaks calibrate ** simple 4186 upper limits added, 3/598 at lower/upper bound, average 4.51 A. - znf42: write upl znf42-in.upl Distance constraint file "znf42-in.upl" written, 4186 upper limits, 4186 assignments. - znf42: distance modify Number of modified constraints: 2197 - znf42: write upl znf42.upl Distance constraint file "znf42.upl" written, 2197 upper limits, 2197 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, 2197 upper limits, 2197 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 = 8.51707. Structure annealed in 39 s, f = 6.01031. Structure annealed in 39 s, f = 5.88791. Structure annealed in 39 s, f = 5.39121. Structure annealed in 39 s, f = 6.24756. Structure annealed in 39 s, f = 8.85222. Structure annealed in 39 s, f = 5.99090. Structure annealed in 39 s, f = 10.8417. Structure annealed in 40 s, f = 42.6249. Structure annealed in 39 s, f = 11.0897. Structure annealed in 39 s, f = 11.3332. Structure annealed in 39 s, f = 7.83432. Structure annealed in 39 s, f = 12.2429. Structure annealed in 39 s, f = 13.3788. Structure annealed in 39 s, f = 6.55126. Structure annealed in 39 s, f = 5.56856. Structure annealed in 39 s, f = 9.63763. Structure annealed in 39 s, f = 115.449. Structure annealed in 39 s, f = 6.91264. Structure annealed in 39 s, f = 8.95178. Structure annealed in 39 s, f = 7.49189. Structure annealed in 39 s, f = 10.5413. Structure annealed in 39 s, f = 6.75267. Structure annealed in 39 s, f = 6.08014. Structure annealed in 39 s, f = 7.25254. Structure annealed in 39 s, f = 4.88153. Structure annealed in 39 s, f = 5.63230. Structure annealed in 39 s, f = 10.5533. Structure annealed in 39 s, f = 9.38681. Structure annealed in 40 s, f = 10.8785. Structure annealed in 39 s, f = 5.90787. Structure annealed in 39 s, f = 7.19146. Structure annealed in 39 s, f = 7.14818. Structure annealed in 39 s, f = 6.85093. Structure annealed in 39 s, f = 9.47045. Structure annealed in 39 s, f = 6.82717. Structure annealed in 39 s, f = 6.85481. Structure annealed in 39 s, f = 7.22469. Structure annealed in 39 s, f = 6.39926. Structure annealed in 39 s, f = 5.90493. Structure annealed in 39 s, f = 8.07130. Structure annealed in 39 s, f = 4.70181. Structure annealed in 39 s, f = 16.2757. Structure annealed in 39 s, f = 6.57706. Structure annealed in 39 s, f = 6.33750. Structure annealed in 39 s, f = 8.26184. Structure annealed in 40 s, f = 5.59900. Structure annealed in 39 s, f = 5.40158. Structure annealed in 39 s, f = 5.12453. Structure annealed in 39 s, f = 8.68780. Structure annealed in 39 s, f = 7.62119. Structure annealed in 39 s, f = 5.83083. Structure annealed in 39 s, f = 12.1914. Structure annealed in 39 s, f = 7.78144. Structure annealed in 39 s, f = 6.34239. Structure annealed in 39 s, f = 4.97974. Structure annealed in 39 s, f = 9.39903. Structure annealed in 39 s, f = 8.41225. Structure annealed in 39 s, f = 4.59016. Structure annealed in 39 s, f = 4.84799. Structure annealed in 39 s, f = 7.49587. Structure annealed in 39 s, f = 9.69441. Structure annealed in 40 s, f = 6.09771. Structure annealed in 40 s, f = 10.5643. Structure annealed in 39 s, f = 6.21957. Structure annealed in 39 s, f = 5.95305. Structure annealed in 39 s, f = 5.42783. Structure annealed in 39 s, f = 4.89783. Structure annealed in 39 s, f = 5.38407. Structure annealed in 39 s, f = 9.46062. Structure annealed in 39 s, f = 6.11169. Structure annealed in 39 s, f = 5.73309. Structure annealed in 39 s, f = 5.25542. Structure annealed in 39 s, f = 7.51677. Structure annealed in 39 s, f = 6.79524. Structure annealed in 39 s, f = 4.89272. Structure annealed in 39 s, f = 8.20504. Structure annealed in 39 s, f = 6.28113. Structure annealed in 39 s, f = 7.40760. Structure annealed in 39 s, f = 11.5569. Structure annealed in 39 s, f = 10.3122. Structure annealed in 42 s, f = 350.623. Structure annealed in 39 s, f = 10.3907. Structure annealed in 39 s, f = 6.67921. Structure annealed in 41 s, f = 276.565. Structure annealed in 39 s, f = 6.28500. Structure annealed in 39 s, f = 5.84378. Structure annealed in 39 s, f = 6.29820. Structure annealed in 39 s, f = 8.13771. Structure annealed in 39 s, f = 5.19886. Structure annealed in 39 s, f = 9.24452. Structure annealed in 39 s, f = 12.1282. Structure annealed in 39 s, f = 6.18627. Structure annealed in 39 s, f = 16.0415. Structure annealed in 40 s, f = 6.13070. Structure annealed in 39 s, f = 5.19109. Structure annealed in 39 s, f = 8.75349. Structure annealed in 39 s, f = 5.36576. Structure annealed in 39 s, f = 5.16336. Structure annealed in 39 s, f = 11.2236. 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 4.59 6 0.0129 0.29 2 10.1 0.21 0 0.5401 3.39 2 4.70 11 0.0149 0.53 1 9.4 0.25 0 0.6743 4.72 3 4.85 11 0.0150 0.37 0 11.6 0.19 0 0.6091 3.47 4 4.88 10 0.0134 0.28 2 10.8 0.29 0 0.5541 4.17 5 4.89 16 0.0164 0.40 1 11.6 0.29 0 0.6275 3.96 6 4.90 13 0.0154 0.34 1 11.5 0.20 0 0.6729 4.90 7 4.98 20 0.0173 0.49 2 11.0 0.21 0 0.6839 4.31 8 5.12 9 0.0135 0.29 4 11.9 0.28 0 0.6218 4.17 9 5.16 13 0.0149 0.42 2 11.7 0.24 1 0.6736 5.43 10 5.19 15 0.0148 0.40 0 10.5 0.18 0 0.6288 4.34 11 5.20 10 0.0144 0.33 2 11.3 0.27 0 0.6731 3.88 12 5.26 9 0.0141 0.39 0 10.6 0.20 0 0.5519 3.33 13 5.37 14 0.0148 0.30 4 12.0 0.29 0 0.6061 3.81 14 5.38 12 0.0149 0.41 0 11.4 0.17 0 0.5845 3.64 15 5.39 11 0.0140 0.34 3 11.8 0.28 0 0.6946 3.72 16 5.40 18 0.0162 0.31 1 12.1 0.23 0 0.6189 3.28 17 5.43 11 0.0141 0.30 4 11.7 0.27 0 0.5335 3.37 18 5.57 13 0.0146 0.34 3 10.5 0.24 0 0.5185 4.05 19 5.60 14 0.0157 0.49 2 12.1 0.25 1 0.7281 5.72 20 5.63 18 0.0164 0.34 4 12.8 0.28 0 0.5659 3.22 Ave 5.17 13 0.0149 0.37 2 11.3 0.24 0 0.6181 4.04 +/- 0.30 3 0.0011 0.07 1 0.8 0.04 0 0.0594 0.69 Min 4.59 6 0.0129 0.28 0 9.4 0.17 0 0.5185 3.22 Max 5.63 20 0.0173 0.53 4 12.8 0.29 1 0.7281 5.72 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 ------ --- --- --- --- 1 140 12 0 0 2 135 17 0 0 forrtl: Stale NFS file handle forrtl: severe (38): error during write, unit 41, file /user/francis/znf42/8cyana/115f/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 16094 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() 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 05-Dec-2005 16:40:36