Warning: no access to tty (Bad file descriptor). Thus no job control in this shell. 06-Dec-2005 23:37:09 n-1<28801> ssi:boot:base:linear: booting n0 (wolf01) n-1<28801> ssi:boot:base:linear: booting n1 (wolf02) n-1<28801> ssi:boot:base:linear: booting n2 (wolf03) n-1<28801> ssi:boot:base:linear: booting n3 (wolf04) n-1<28801> ssi:boot:base:linear: booting n4 (wolf05) n-1<28801> ssi:boot:base:linear: booting n5 (wolf06) n-1<28801> ssi:boot:base:linear: booting n6 (wolf07) n-1<28801> ssi:boot:base:linear: booting n7 (wolf08) n-1<28801> ssi:boot:base:linear: booting n8 (wolf09) n-1<28801> ssi:boot:base:linear: booting n9 (wolf10) n-1<28801> ssi:boot:base:linear: booting n10 (wolf11) n-1<28801> ssi:boot:base:linear: booting n11 (wolf12) n-1<28801> ssi:boot:base:linear: booting n12 (wolf13) n-1<28801> 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, 1982 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, 1982 chemical shifts. - peakcheck: read peaks c13no format= Peak list "c13no.peaks" read, 3483 peaks, 3180 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 3180 0.000 0.002 0.032 0.009 1 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 HB3 LEU 89 1.333 1.333 0.032 19 1 shift with spread larger than tolerance. - peakcheck: peak deviations Peak Dim Deviation Atom Residue 3779 1 0.032 HB3 LEU 89 1 deviations larger than tolerance. ------------------------------------------------------------ Peak list : n15no Proton list: znf42 - peakcheck: read prot znf42 unknown=skip Chemical shift list "znf42.prot" read, 1982 chemical shifts. - peakcheck: read peaks n15no format= Peak list "n15no.peaks" read, 1271 peaks, 1105 assignments. - peakcheck: peaks fit Deviations from chemical shift list: Dim Peaks Median Average Maximum RMSD Number Tolerance 1 1105 0.002 0.002 0.030 0.011 0 0.030 2 1269 0.000 0.000 0.011 0.001 0 0.030 3 1269 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, 1982 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, 1982 chemical shifts. - peakcheck: read peaks fc12no format= Peak list "fc12no.peaks" read, 233 peaks, 142 assignments. - peakcheck: peaks fit Deviations from chemical shift list: Dim Peaks Median Average Maximum RMSD Number Tolerance 1 142 -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=3.0E7,1.2 E7,2.5E7,1.0E7 dref=4.2 - calibration: read prot znf42 unknown=warn Chemical shift list "znf42.prot" read, 1982 chemical shifts. - calibration: read peaks c13no format= Peak list "c13no.peaks" read, 3483 peaks, 3180 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, 1982 chemical shifts. - calibration: read peaks n15no format= append Peak list "n15no.peaks" read, 1271 peaks, 1105 assignments. - calibration: peaks select "** list=2" 1271 of 4754 peaks, 1271 of 4754 assignments selected. - calibration: peaks set volume=abs(volume) Volume of 1271 peaks set. - calibration: peaks simplecal constant=1.2E7 Calibration constant for peak list 2: 1.20E+07 Upper limit set for 1271 peaks. - calibration: caltab peaks Distance bounds: -2.99 A: 93 7.3% 3.00-3.99 A: 339 26.7% 4.00-4.99 A: 491 38.6% 5.00-5.99 A: 346 27.2% 6.00- A: 0 0.0% All: 1271 100.0% - calibration: read prot znf42 unknown=warn append Chemical shift list "znf42.prot" read, 1982 chemical shifts. - calibration: read peaks c13ar format= append Peak list "c13ar.peaks" read, 292 peaks, 238 assignments. - calibration: peaks select "** list=3" 292 of 5046 peaks, 292 of 5046 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, 1982 chemical shifts. - calibration: read peaks fc12no format= append Peak list "fc12no.peaks" read, 233 peaks, 142 assignments. - calibration: peaks select "** list=4" 233 of 5279 peaks, 233 of 5279 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 ** 5279 of 5279 peaks, 5279 of 5279 assignments selected. - znf42: peaks calibrate ** simple 4171 upper limits added, 8/483 at lower/upper bound, average 4.47 A. - znf42: write upl znf42-in.upl Distance constraint file "znf42-in.upl" written, 4171 upper limits, 4171 assignments. - znf42: distance modify Number of modified constraints: 2216 - znf42: write upl znf42.upl Distance constraint file "znf42.upl" written, 2216 upper limits, 2216 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, 2216 upper limits, 2216 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 = 4.42512. Structure annealed in 39 s, f = 2.72797. Structure annealed in 39 s, f = 3.09331. Structure annealed in 39 s, f = 2.88431. Structure annealed in 39 s, f = 3.89345. Structure annealed in 39 s, f = 3.69923. Structure annealed in 39 s, f = 3.94714. Structure annealed in 39 s, f = 6.76716. Structure annealed in 39 s, f = 9.23457. Structure annealed in 39 s, f = 4.13394. Structure annealed in 39 s, f = 7.26416. Structure annealed in 39 s, f = 5.57881. Structure annealed in 39 s, f = 2.53987. Structure annealed in 39 s, f = 4.97152. Structure annealed in 39 s, f = 5.85038. Structure annealed in 40 s, f = 5.59048. Structure annealed in 39 s, f = 9.40748. Structure annealed in 39 s, f = 6.84417. Structure annealed in 39 s, f = 3.45071. Structure annealed in 39 s, f = 4.34611. Structure annealed in 40 s, f = 164.044. Structure annealed in 39 s, f = 4.42676. Structure annealed in 40 s, f = 8.57906. Structure annealed in 39 s, f = 7.57053. Structure annealed in 39 s, f = 6.59036. Structure annealed in 38 s, f = 6.80745. Structure annealed in 39 s, f = 3.25141. Structure annealed in 39 s, f = 8.05138. Structure annealed in 39 s, f = 3.29626. Structure annealed in 40 s, f = 151.767. Structure annealed in 39 s, f = 9.61237. Structure annealed in 39 s, f = 6.23783. Structure annealed in 39 s, f = 2.54846. Structure annealed in 39 s, f = 4.89243. Structure annealed in 39 s, f = 8.03985. Structure annealed in 39 s, f = 3.34739. Structure annealed in 39 s, f = 3.63532. Structure annealed in 39 s, f = 5.24465. Structure annealed in 40 s, f = 4.15762. Structure annealed in 40 s, f = 4.05286. Structure annealed in 39 s, f = 5.08016. Structure annealed in 39 s, f = 5.73171. Structure annealed in 39 s, f = 5.29082. Structure annealed in 39 s, f = 3.26723. Structure annealed in 39 s, f = 7.66870. Structure annealed in 39 s, f = 8.15441. Structure annealed in 41 s, f = 12.1498. Structure annealed in 39 s, f = 7.02505. Structure annealed in 39 s, f = 5.57202. Structure annealed in 39 s, f = 7.75717. Structure annealed in 39 s, f = 32.6658. Structure annealed in 39 s, f = 3.59227. Structure annealed in 39 s, f = 5.40878. Structure annealed in 39 s, f = 6.09448. Structure annealed in 39 s, f = 5.40750. Structure annealed in 39 s, f = 3.62672. Structure annealed in 39 s, f = 5.11814. Structure annealed in 39 s, f = 3.11402. Structure annealed in 39 s, f = 7.87292. Structure annealed in 39 s, f = 9.81860. Structure annealed in 39 s, f = 3.25080. Structure annealed in 39 s, f = 5.23545. Structure annealed in 39 s, f = 8.40975. Structure annealed in 41 s, f = 209.983. Structure annealed in 39 s, f = 7.40269. Structure annealed in 39 s, f = 3.12813. Structure annealed in 39 s, f = 7.26925. Structure annealed in 39 s, f = 4.22245. Structure annealed in 39 s, f = 4.54906. Structure annealed in 39 s, f = 7.30317. Structure annealed in 39 s, f = 8.53381. Structure annealed in 39 s, f = 4.03892. Structure annealed in 40 s, f = 3.36028. Structure annealed in 39 s, f = 3.53921. Structure annealed in 39 s, f = 4.42767. Structure annealed in 38 s, f = 4.03460. Structure annealed in 39 s, f = 3.70023. Structure annealed in 39 s, f = 11.0053. Structure annealed in 39 s, f = 4.06848. Structure annealed in 39 s, f = 10.0590. Structure annealed in 39 s, f = 8.89573. Structure annealed in 39 s, f = 3.89624. Structure annealed in 39 s, f = 4.38140. Structure annealed in 39 s, f = 4.03956. Structure annealed in 39 s, f = 4.04681. Structure annealed in 39 s, f = 9.20691. Structure annealed in 39 s, f = 4.63810. Structure annealed in 39 s, f = 5.06065. Structure annealed in 39 s, f = 3.46008. Structure annealed in 39 s, f = 3.65746. Structure annealed in 39 s, f = 4.48310. Structure annealed in 39 s, f = 4.47105. Structure annealed in 39 s, f = 2.43496. Structure annealed in 40 s, f = 3.54354. Structure annealed in 39 s, f = 5.73054. Structure annealed in 41 s, f = 230.506. Structure annealed in 39 s, f = 3.39644. Structure annealed in 40 s, f = 3.76989. Structure annealed in 39 s, f = 3.50798. Structure annealed in 39 s, f = 6.67600. 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 2.44 5 0.0092 0.25 1 7.3 0.23 0 0.3911 2.91 2 2.54 4 0.0101 0.27 0 7.3 0.19 0 0.3890 3.07 3 2.55 8 0.0109 0.27 1 7.1 0.21 0 0.4418 3.18 4 2.73 3 0.0105 0.26 4 8.0 0.30 0 0.3165 2.33 5 2.88 3 0.0110 0.26 0 9.2 0.19 0 0.4955 3.11 6 3.09 4 0.0108 0.25 3 8.5 0.25 0 0.4685 3.39 7 3.11 3 0.0104 0.24 5 8.3 0.29 0 0.3441 2.40 8 3.13 4 0.0110 0.25 3 8.4 0.28 0 0.4284 3.54 9 3.25 5 0.0104 0.27 4 9.4 0.31 0 0.4149 3.79 10 3.25 5 0.0137 0.54 1 8.4 0.20 0 0.4742 3.20 11 3.27 7 0.0129 0.53 2 8.1 0.26 0 0.4962 3.16 12 3.30 5 0.0107 0.37 3 8.9 0.31 0 0.3246 2.26 13 3.35 5 0.0110 0.25 5 9.1 0.29 0 0.3970 2.94 14 3.36 8 0.0123 0.35 1 9.5 0.24 0 0.4036 3.66 15 3.40 5 0.0123 0.30 2 9.6 0.24 0 0.4199 3.44 16 3.45 7 0.0120 0.44 1 9.8 0.24 0 0.4735 3.64 17 3.46 4 0.0118 0.35 4 11.2 0.29 0 0.5111 2.44 18 3.51 5 0.0111 0.26 3 9.9 0.29 0 0.4392 2.35 19 3.54 3 0.0111 0.35 5 9.1 0.28 0 0.4883 4.52 20 3.54 6 0.0110 0.27 3 9.3 0.25 0 0.4936 4.33 Ave 3.16 5 0.0112 0.32 3 8.8 0.26 0 0.4305 3.18 +/- 0.34 2 0.0010 0.09 2 1.0 0.04 0 0.0570 0.62 Min 2.44 3 0.0092 0.24 0 7.1 0.19 0 0.3165 2.26 Max 3.54 8 0.0137 0.54 5 11.2 0.31 0 0.5111 4.52 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 ------ --- --- --- --- 1 143 9 0 0 2 141 11 0 0 3 138 13 1 0 forrtl: Stale NFS file handle forrtl: severe (38): error during write, unit 41, file /user/francis/znf42/8cyana/120d/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. 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() PID 28883 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 06-Dec-2005 23:40:24