Warning: no access to tty (Bad file descriptor). Thus no job control in this shell. 05-Dec-2005 16:24:54 n-1<15835> ssi:boot:base:linear: booting n0 (wolf01) n-1<15835> ssi:boot:base:linear: booting n1 (wolf02) n-1<15835> ssi:boot:base:linear: booting n2 (wolf03) n-1<15835> ssi:boot:base:linear: booting n3 (wolf04) n-1<15835> ssi:boot:base:linear: booting n4 (wolf05) n-1<15835> ssi:boot:base:linear: booting n5 (wolf06) n-1<15835> ssi:boot:base:linear: booting n6 (wolf07) n-1<15835> ssi:boot:base:linear: booting n7 (wolf08) n-1<15835> ssi:boot:base:linear: booting n8 (wolf09) n-1<15835> ssi:boot:base:linear: booting n9 (wolf10) n-1<15835> ssi:boot:base:linear: booting n10 (wolf11) n-1<15835> ssi:boot:base:linear: booting n11 (wolf12) n-1<15835> ssi:boot:base:linear: booting n12 (wolf13) n-1<15835> 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, 3197 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 3197 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, 3197 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 4189 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, 4189 upper limits, 4189 assignments. - znf42: distance modify Number of modified constraints: 2198 - znf42: write upl znf42.upl Distance constraint file "znf42.upl" written, 2198 upper limits, 2198 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, 2198 upper limits, 2198 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 = 6.18893. Structure annealed in 39 s, f = 116.812. Structure annealed in 41 s, f = 281.309. Structure annealed in 39 s, f = 7.84829. Structure annealed in 39 s, f = 5.54609. Structure annealed in 39 s, f = 10.3954. Structure annealed in 39 s, f = 10.6462. Structure annealed in 39 s, f = 20.5343. Structure annealed in 39 s, f = 4.34743. Structure annealed in 39 s, f = 5.60614. Structure annealed in 40 s, f = 29.9814. Structure annealed in 39 s, f = 6.46221. Structure annealed in 39 s, f = 9.32107. Structure annealed in 39 s, f = 7.22396. Structure annealed in 39 s, f = 6.61448. Structure annealed in 39 s, f = 10.9512. Structure annealed in 40 s, f = 5.32598. Structure annealed in 39 s, f = 8.79446. Structure annealed in 39 s, f = 5.55773. Structure annealed in 39 s, f = 5.65359. Structure annealed in 39 s, f = 8.87554. Structure annealed in 39 s, f = 5.25776. Structure annealed in 39 s, f = 5.20501. Structure annealed in 40 s, f = 114.818. Structure annealed in 40 s, f = 4.75558. Structure annealed in 39 s, f = 13.0146. Structure annealed in 39 s, f = 10.6062. Structure annealed in 39 s, f = 8.04162. Structure annealed in 39 s, f = 6.35110. Structure annealed in 39 s, f = 4.76206. Structure annealed in 40 s, f = 8.73974. Structure annealed in 39 s, f = 127.588. Structure annealed in 39 s, f = 5.69057. Structure annealed in 39 s, f = 8.58651. Structure annealed in 39 s, f = 6.43660. Structure annealed in 40 s, f = 7.32507. Structure annealed in 39 s, f = 25.7405. Structure annealed in 39 s, f = 7.27892. Structure annealed in 39 s, f = 5.18020. Structure annealed in 39 s, f = 7.30362. Structure annealed in 39 s, f = 6.85211. Structure annealed in 40 s, f = 114.371. Structure annealed in 40 s, f = 6.46909. Structure annealed in 39 s, f = 56.1250. Structure annealed in 39 s, f = 5.03229. Structure annealed in 39 s, f = 9.43876. Structure annealed in 39 s, f = 5.75487. Structure annealed in 39 s, f = 10.6693. Structure annealed in 39 s, f = 9.11897. Structure annealed in 39 s, f = 5.13376. Structure annealed in 38 s, f = 8.44111. Structure annealed in 39 s, f = 5.34418. Structure annealed in 39 s, f = 8.50217. Structure annealed in 39 s, f = 10.1280. Structure annealed in 39 s, f = 8.57397. Structure annealed in 39 s, f = 6.61493. Structure annealed in 39 s, f = 8.98797. Structure annealed in 39 s, f = 9.48491. Structure annealed in 39 s, f = 6.15022. Structure annealed in 41 s, f = 188.173. Structure annealed in 39 s, f = 9.45610. Structure annealed in 39 s, f = 7.71532. Structure annealed in 39 s, f = 10.2558. Structure annealed in 39 s, f = 10.0255. Structure annealed in 39 s, f = 10.3651. Structure annealed in 39 s, f = 6.23826. Structure annealed in 39 s, f = 13.5630. Structure annealed in 39 s, f = 7.64549. Structure annealed in 41 s, f = 303.593. Structure annealed in 39 s, f = 7.26653. Structure annealed in 40 s, f = 5.08350. Structure annealed in 39 s, f = 9.56531. Structure annealed in 39 s, f = 6.04504. Structure annealed in 39 s, f = 9.55104. Structure annealed in 39 s, f = 5.67962. Structure annealed in 38 s, f = 5.42769. Structure annealed in 39 s, f = 6.42940. Structure annealed in 39 s, f = 5.66880. Structure annealed in 39 s, f = 10.4561. Structure annealed in 39 s, f = 8.58638. Structure annealed in 39 s, f = 5.63862. Structure annealed in 39 s, f = 5.81143. Structure annealed in 39 s, f = 11.6337. Structure annealed in 39 s, f = 6.06751. Structure annealed in 39 s, f = 5.85666. Structure annealed in 39 s, f = 12.4455. Structure annealed in 41 s, f = 275.374. Structure annealed in 39 s, f = 6.69795. Structure annealed in 40 s, f = 9.45186. Structure annealed in 40 s, f = 160.008. Structure annealed in 39 s, f = 5.41615. Structure annealed in 39 s, f = 10.6736. Structure annealed in 39 s, f = 8.61032. Structure annealed in 40 s, f = 5.44437. Structure annealed in 39 s, f = 7.23040. Structure annealed in 39 s, f = 11.6990. Structure annealed in 39 s, f = 6.54488. Structure annealed in 39 s, f = 5.33036. Structure annealed in 39 s, f = 8.37434. Structure annealed in 39 s, f = 6.35259. 100 structures finished in 164 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 4.35 10 0.0139 0.42 1 9.9 0.24 0 0.4788 4.06 2 4.76 13 0.0144 0.33 1 10.8 0.20 0 0.5548 3.45 3 4.76 11 0.0142 0.36 2 10.0 0.27 0 0.4924 3.23 4 5.03 14 0.0145 0.29 3 11.0 0.21 0 0.6140 3.49 5 5.08 13 0.0160 0.37 4 11.3 0.29 0 0.6049 4.05 6 5.13 12 0.0164 0.79 0 9.6 0.15 0 0.5306 3.17 7 5.18 20 0.0171 0.50 2 10.3 0.24 0 0.6370 3.77 8 5.21 13 0.0164 0.79 2 10.6 0.29 0 0.5493 3.48 9 5.26 11 0.0138 0.30 3 11.4 0.29 0 0.5822 4.26 10 5.33 15 0.0149 0.29 3 12.1 0.29 0 0.5996 4.57 11 5.33 14 0.0150 0.31 5 11.8 0.28 0 0.6542 4.22 12 5.34 12 0.0144 0.37 0 12.1 0.18 0 0.5952 3.42 13 5.42 14 0.0148 0.30 2 11.9 0.30 2 0.7640 5.94 14 5.43 15 0.0161 0.47 3 11.4 0.28 0 0.6190 3.50 15 5.44 13 0.0159 0.36 5 11.2 0.29 0 0.5929 3.89 16 5.55 10 0.0146 0.37 2 11.7 0.24 0 0.6093 3.84 17 5.56 15 0.0165 0.50 3 11.8 0.24 0 0.6520 3.66 18 5.61 12 0.0145 0.29 5 12.1 0.29 0 0.6168 4.02 19 5.64 10 0.0139 0.29 2 11.8 0.28 0 0.6465 3.98 20 5.65 15 0.0150 0.41 4 12.2 0.28 0 0.6782 4.17 Ave 5.25 13 0.0151 0.41 3 11.2 0.26 0 0.6036 3.91 +/- 0.33 2 0.0010 0.14 1 0.8 0.04 0 0.0628 0.59 Min 4.35 10 0.0138 0.29 0 9.6 0.15 0 0.4788 3.17 Max 5.65 20 0.0171 0.79 5 12.2 0.30 2 0.7640 5.94 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 2 139 13 0 0 forrtl: Stale NFS file handle forrtl: severe (38): error during write, unit 41, file /user/francis/znf42/8cyana/115e/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 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() ----------------------------------------------------------------------------- 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 15936 failed on node n0 (192.168.96.101) with exit status 28. ----------------------------------------------------------------------------- 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 16:28:09