Warning: no access to tty (Bad file descriptor). Thus no job control in this shell. 06-Dec-2005 00:36:01 n-1<19659> ssi:boot:base:linear: booting n0 (wolf01) n-1<19659> ssi:boot:base:linear: booting n1 (wolf02) n-1<19659> ssi:boot:base:linear: booting n2 (wolf03) n-1<19659> ssi:boot:base:linear: booting n3 (wolf04) n-1<19659> ssi:boot:base:linear: booting n4 (wolf05) n-1<19659> ssi:boot:base:linear: booting n5 (wolf06) n-1<19659> ssi:boot:base:linear: booting n6 (wolf07) n-1<19659> ssi:boot:base:linear: booting n7 (wolf08) n-1<19659> ssi:boot:base:linear: booting n8 (wolf09) n-1<19659> ssi:boot:base:linear: booting n9 (wolf10) n-1<19659> ssi:boot:base:linear: booting n10 (wolf11) n-1<19659> ssi:boot:base:linear: booting n11 (wolf12) n-1<19659> ssi:boot:base:linear: booting n12 (wolf13) n-1<19659> 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=3.0E7,1.7 E7,2.0E7,1.5E7 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=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, 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=1.5E7 Calibration constant for peak list 4: 1.50E+07 Upper limit set for 233 peaks. - calibration: caltab peaks Distance bounds: -2.99 A: 0 0.0% 3.00-3.99 A: 32 13.7% 4.00-4.99 A: 140 60.1% 5.00-5.99 A: 61 26.2% 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, 3/596 at lower/upper bound, average 4.52 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: 2201 - znf42: write upl znf42.upl Distance constraint file "znf42.upl" written, 2201 upper limits, 2201 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, 2201 upper limits, 2201 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 = 3.49556. Structure annealed in 39 s, f = 7.68440. Structure annealed in 39 s, f = 5.46118. Structure annealed in 39 s, f = 4.78317. Structure annealed in 39 s, f = 5.47409. Structure annealed in 39 s, f = 13.0889. Structure annealed in 39 s, f = 5.58562. Structure annealed in 39 s, f = 5.94817. Structure annealed in 39 s, f = 9.78135. Structure annealed in 39 s, f = 4.34538. Structure annealed in 39 s, f = 8.46654. Structure annealed in 39 s, f = 6.02386. Structure annealed in 39 s, f = 4.57045. Structure annealed in 39 s, f = 8.94211. Structure annealed in 40 s, f = 42.3972. Structure annealed in 39 s, f = 7.73866. Structure annealed in 39 s, f = 4.26322. Structure annealed in 39 s, f = 6.35274. Structure annealed in 39 s, f = 4.18134. Structure annealed in 39 s, f = 5.13173. Structure annealed in 39 s, f = 4.33578. Structure annealed in 39 s, f = 4.80683. Structure annealed in 39 s, f = 13.4909. Structure annealed in 40 s, f = 5.15635. Structure annealed in 40 s, f = 5.36030. Structure annealed in 39 s, f = 3.92552. Structure annealed in 39 s, f = 3.23307. Structure annealed in 38 s, f = 3.70255. Structure annealed in 39 s, f = 8.12858. Structure annealed in 39 s, f = 4.32694. Structure annealed in 39 s, f = 4.39872. Structure annealed in 39 s, f = 6.51928. Structure annealed in 39 s, f = 7.84339. Structure annealed in 39 s, f = 13.8459. Structure annealed in 39 s, f = 4.53732. Structure annealed in 39 s, f = 8.85520. Structure annealed in 39 s, f = 6.19678. Structure annealed in 39 s, f = 6.21404. Structure annealed in 39 s, f = 7.47991. Structure annealed in 39 s, f = 5.65216. Structure annealed in 39 s, f = 3.96566. Structure annealed in 40 s, f = 152.210. Structure annealed in 39 s, f = 4.45330. Structure annealed in 39 s, f = 13.4075. Structure annealed in 39 s, f = 5.91056. Structure annealed in 40 s, f = 3.94064. Structure annealed in 39 s, f = 4.64102. Structure annealed in 39 s, f = 4.01612. Structure annealed in 39 s, f = 7.39492. Structure annealed in 39 s, f = 3.95909. Structure annealed in 39 s, f = 5.77399. Structure annealed in 39 s, f = 6.73345. Structure annealed in 39 s, f = 3.10134. Structure annealed in 39 s, f = 3.98483. Structure annealed in 39 s, f = 3.92195. Structure annealed in 39 s, f = 6.28172. Structure annealed in 39 s, f = 4.28086. Structure annealed in 39 s, f = 4.64853. Structure annealed in 39 s, f = 3.99371. Structure annealed in 39 s, f = 5.00003. Structure annealed in 39 s, f = 4.90727. Structure annealed in 39 s, f = 5.45056. Structure annealed in 39 s, f = 6.30915. Structure annealed in 39 s, f = 4.88070. Structure annealed in 39 s, f = 5.11143. Structure annealed in 39 s, f = 9.07719. Structure annealed in 39 s, f = 4.44315. Structure annealed in 39 s, f = 9.86466. Structure annealed in 39 s, f = 4.76631. Structure annealed in 39 s, f = 6.92922. Structure annealed in 39 s, f = 4.55686. Structure annealed in 39 s, f = 7.68440. Structure annealed in 39 s, f = 4.12930. Structure annealed in 39 s, f = 5.70026. Structure annealed in 39 s, f = 3.69264. Structure annealed in 39 s, f = 9.38357. Structure annealed in 39 s, f = 3.91588. Structure annealed in 38 s, f = 6.17624. Structure annealed in 39 s, f = 8.74659. Structure annealed in 39 s, f = 4.25376. Structure annealed in 39 s, f = 9.42311. Structure annealed in 39 s, f = 12.3161. Structure annealed in 39 s, f = 9.25700. Structure annealed in 39 s, f = 7.73915. Structure annealed in 39 s, f = 8.50851. Structure annealed in 39 s, f = 5.92366. Structure annealed in 39 s, f = 4.98864. Structure annealed in 39 s, f = 9.83069. Structure annealed in 39 s, f = 5.70870. Structure annealed in 39 s, f = 5.08089. Structure annealed in 39 s, f = 3.60846. Structure annealed in 39 s, f = 4.83214. Structure annealed in 40 s, f = 5.07667. Structure annealed in 39 s, f = 3.91842. Structure annealed in 39 s, f = 4.66551. Structure annealed in 39 s, f = 4.42654. Structure annealed in 39 s, f = 5.19404. Structure annealed in 39 s, f = 3.77651. Structure annealed in 42 s, f = 383.521. Structure annealed in 39 s, f = 3.71738. 100 structures finished in 165 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 3.10 3 0.0104 0.30 1 8.8 0.22 0 0.3997 2.27 2 3.23 1 0.0101 0.20 0 8.7 0.19 0 0.4637 3.27 3 3.50 4 0.0122 0.53 2 8.5 0.29 0 0.4807 4.41 4 3.61 8 0.0136 0.50 1 8.5 0.25 0 0.5324 4.12 5 3.69 8 0.0132 0.32 0 8.1 0.17 0 0.4815 3.81 6 3.70 0 0.0102 0.20 1 9.0 0.25 0 0.4065 2.73 7 3.72 3 0.0108 0.29 1 9.1 0.24 0 0.3925 2.39 8 3.78 5 0.0128 0.41 0 10.1 0.19 0 0.4671 3.08 9 3.92 2 0.0100 0.21 4 9.1 0.41 0 0.4460 3.61 10 3.92 3 0.0104 0.26 4 10.1 0.29 0 0.4018 3.53 11 3.92 6 0.0122 0.33 1 10.4 0.23 0 0.4800 2.63 12 3.93 5 0.0113 0.25 1 9.6 0.24 0 0.4345 2.08 13 3.94 3 0.0116 0.30 3 10.0 0.29 0 0.3743 2.21 14 3.96 3 0.0124 0.40 4 9.7 0.29 0 0.4960 3.38 15 3.97 4 0.0122 0.40 3 9.3 0.29 0 0.5024 2.77 16 3.98 7 0.0124 0.38 3 9.8 0.29 0 0.4293 2.97 17 3.99 5 0.0126 0.36 0 9.3 0.20 0 0.4429 2.90 18 4.02 5 0.0116 0.29 2 10.0 0.23 0 0.5281 3.64 19 4.13 1 0.0099 0.22 3 9.8 0.29 0 0.4849 3.69 20 4.18 7 0.0130 0.32 3 9.7 0.28 0 0.5405 2.92 Ave 3.81 4 0.0116 0.32 2 9.4 0.25 0 0.4592 3.12 +/- 0.27 2 0.0011 0.09 1 0.6 0.05 0 0.0476 0.63 Min 3.10 0 0.0099 0.20 0 8.1 0.17 0 0.3743 2.08 Max 4.18 8 0.0136 0.53 4 10.4 0.41 0 0.5405 4.41 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 2 134 18 0 0 forrtl: Stale NFS file handle forrtl: severe (38): error during write, unit 41, file /user/francis/znf42/8cyana/116i/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) 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 19741 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() 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 06-Dec-2005 00:39:17