Warning: no access to tty (Bad file descriptor). Thus no job control in this shell. 05-Dec-2005 23:58:48 n-1<18576> ssi:boot:base:linear: booting n0 (wolf01) n-1<18576> ssi:boot:base:linear: booting n1 (wolf02) n-1<18576> ssi:boot:base:linear: booting n2 (wolf03) n-1<18576> ssi:boot:base:linear: booting n3 (wolf04) n-1<18576> ssi:boot:base:linear: booting n4 (wolf05) n-1<18576> ssi:boot:base:linear: booting n5 (wolf06) n-1<18576> ssi:boot:base:linear: booting n6 (wolf07) n-1<18576> ssi:boot:base:linear: booting n7 (wolf08) n-1<18576> ssi:boot:base:linear: booting n8 (wolf09) n-1<18576> ssi:boot:base:linear: booting n9 (wolf10) n-1<18576> ssi:boot:base:linear: booting n10 (wolf11) n-1<18576> ssi:boot:base:linear: booting n11 (wolf12) n-1<18576> ssi:boot:base:linear: booting n12 (wolf13) n-1<18576> 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 E7,2.0E7,1.0E7 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=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=1.0E7 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, 3/596 at lower/upper bound, average 4.51 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: 2203 - znf42: write upl znf42.upl Distance constraint file "znf42.upl" written, 2203 upper limits, 2203 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, 2203 upper limits, 2203 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 = 9.26120. Structure annealed in 39 s, f = 4.51313. Structure annealed in 39 s, f = 8.69259. Structure annealed in 41 s, f = 386.169. Structure annealed in 39 s, f = 20.2591. Structure annealed in 39 s, f = 6.90835. Structure annealed in 39 s, f = 3.67438. Structure annealed in 39 s, f = 3.35723. Structure annealed in 39 s, f = 4.78493. Structure annealed in 39 s, f = 4.11684. Structure annealed in 39 s, f = 4.51473. Structure annealed in 39 s, f = 4.15423. Structure annealed in 39 s, f = 9.29668. Structure annealed in 39 s, f = 5.35021. Structure annealed in 39 s, f = 4.59776. Structure annealed in 39 s, f = 7.85334. Structure annealed in 40 s, f = 5.97943. Structure annealed in 39 s, f = 6.02950. Structure annealed in 39 s, f = 10.7598. Structure annealed in 39 s, f = 5.58515. Structure annealed in 39 s, f = 4.54758. Structure annealed in 39 s, f = 4.69643. Structure annealed in 39 s, f = 3.14740. Structure annealed in 39 s, f = 6.89654. Structure annealed in 39 s, f = 9.61768. Structure annealed in 38 s, f = 3.84073. Structure annealed in 39 s, f = 11.9405. Structure annealed in 39 s, f = 4.16597. Structure annealed in 39 s, f = 18.3673. Structure annealed in 39 s, f = 8.55328. Structure annealed in 39 s, f = 4.51551. Structure annealed in 39 s, f = 8.89223. Structure annealed in 39 s, f = 12.1953. Structure annealed in 39 s, f = 4.65550. Structure annealed in 39 s, f = 5.15363. Structure annealed in 39 s, f = 8.07517. Structure annealed in 39 s, f = 9.41526. Structure annealed in 39 s, f = 5.13484. Structure annealed in 39 s, f = 2.84954. Structure annealed in 39 s, f = 7.80939. Structure annealed in 39 s, f = 4.88574. Structure annealed in 39 s, f = 8.09410. Structure annealed in 39 s, f = 3.32199. Structure annealed in 41 s, f = 190.971. Structure annealed in 39 s, f = 8.20745. Structure annealed in 39 s, f = 8.60093. Structure annealed in 39 s, f = 3.83851. Structure annealed in 39 s, f = 6.03957. Structure annealed in 39 s, f = 6.91642. Structure annealed in 39 s, f = 3.28106. Structure annealed in 38 s, f = 4.02394. Structure annealed in 39 s, f = 8.26536. Structure annealed in 39 s, f = 7.23363. Structure annealed in 39 s, f = 4.87461. Structure annealed in 39 s, f = 12.0289. Structure annealed in 39 s, f = 18.2740. Structure annealed in 39 s, f = 5.07960. Structure annealed in 39 s, f = 4.88501. Structure annealed in 39 s, f = 14.2304. Structure annealed in 39 s, f = 7.18322. Structure annealed in 39 s, f = 7.46684. Structure annealed in 39 s, f = 4.51526. Structure annealed in 39 s, f = 5.59597. Structure annealed in 39 s, f = 4.28505. Structure annealed in 39 s, f = 9.19448. Structure annealed in 39 s, f = 4.06485. Structure annealed in 39 s, f = 5.15559. Structure annealed in 39 s, f = 4.22796. Structure annealed in 39 s, f = 6.67131. Structure annealed in 39 s, f = 5.49393. Structure annealed in 40 s, f = 6.31965. Structure annealed in 39 s, f = 3.98567. Structure annealed in 39 s, f = 7.11969. Structure annealed in 42 s, f = 393.013. Structure annealed in 39 s, f = 5.93574. Structure annealed in 39 s, f = 3.58540. Structure annealed in 39 s, f = 3.73066. Structure annealed in 39 s, f = 4.64854. Structure annealed in 39 s, f = 10.0842. Structure annealed in 39 s, f = 5.14612. Structure annealed in 39 s, f = 4.71426. Structure annealed in 39 s, f = 4.57359. Structure annealed in 39 s, f = 4.33584. Structure annealed in 40 s, f = 9.37253. Structure annealed in 39 s, f = 4.96372. Structure annealed in 39 s, f = 3.52039. Structure annealed in 39 s, f = 6.82567. Structure annealed in 39 s, f = 3.62087. Structure annealed in 39 s, f = 3.27272. Structure annealed in 39 s, f = 9.70367. Structure annealed in 39 s, f = 24.2880. Structure annealed in 39 s, f = 6.39172. Structure annealed in 39 s, f = 7.36917. Structure annealed in 39 s, f = 5.39258. Structure annealed in 39 s, f = 6.07488. Structure annealed in 39 s, f = 6.97282. Structure annealed in 39 s, f = 9.46677. Structure annealed in 39 s, f = 4.19248. Structure annealed in 39 s, f = 7.78119. Structure annealed in 39 s, f = 5.32478. 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 2.85 2 0.0104 0.28 0 8.3 0.17 0 0.3748 2.13 2 3.15 2 0.0108 0.39 1 9.0 0.22 0 0.3820 2.34 3 3.27 2 0.0101 0.27 1 9.3 0.22 0 0.4131 2.62 4 3.28 1 0.0104 0.21 2 9.1 0.29 0 0.3230 1.90 5 3.32 6 0.0119 0.32 1 9.3 0.23 0 0.4320 2.54 6 3.36 3 0.0107 0.27 2 8.7 0.25 1 0.6413 6.92 7 3.52 6 0.0118 0.33 3 9.2 0.22 0 0.4562 3.98 8 3.59 3 0.0103 0.23 3 9.4 0.24 0 0.3799 2.59 9 3.62 2 0.0098 0.22 0 8.6 0.18 0 0.4850 4.80 10 3.67 2 0.0108 0.32 3 9.1 0.29 0 0.3567 2.35 11 3.73 4 0.0114 0.32 3 9.6 0.23 0 0.4615 2.83 12 3.84 1 0.0095 0.22 3 9.7 0.29 0 0.3367 2.06 13 3.84 3 0.0110 0.23 3 10.0 0.29 0 0.3935 2.88 14 3.99 2 0.0110 0.28 0 10.5 0.17 0 0.4087 2.54 15 4.02 3 0.0115 0.27 2 9.9 0.29 0 0.4483 2.44 16 4.06 2 0.0125 0.51 2 9.3 0.24 1 0.6546 5.27 17 4.12 6 0.0118 0.42 1 8.5 0.22 0 0.5147 3.60 18 4.15 9 0.0139 0.34 3 10.6 0.25 0 0.5601 3.45 19 4.17 2 0.0115 0.23 0 9.6 0.17 0 0.4325 2.61 20 4.19 3 0.0117 0.36 3 9.6 0.28 0 0.5219 4.53 Ave 3.69 3 0.0111 0.30 2 9.4 0.24 0 0.4488 3.22 +/- 0.38 2 0.0010 0.08 1 0.6 0.04 0 0.0897 1.26 Min 2.85 1 0.0095 0.21 0 8.3 0.17 0 0.3230 1.90 Max 4.19 9 0.0139 0.51 3 10.6 0.29 1 0.6546 6.92 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 2 138 14 0 0 forrtl: Stale NFS file handle forrtl: severe (38): error during write, unit 41, file /user/francis/znf42/8cyana/116b/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 18658 failed on node n0 (192.168.96.101) with exit status 28. ----------------------------------------------------------------------------- MPI_Recv: process in local group is dead (rank 3, comm 3) Rank (6, MPI_COMM_WORLD): Call stack within LAM: Rank (6, MPI_COMM_WORLD): - MPI_Recv() Rank (6, MPI_COMM_WORLD): - MPI_Bcast() Rank (6, MPI_COMM_WORLD): - MPI_Bcast() Rank (6, 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() 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 00:02:04