Warning: no access to tty (Bad file descriptor). Thus no job control in this shell. 13-Dec-2005 16:39:16 n-1<14671> ssi:boot:base:linear: booting n0 (wolf01) n-1<14671> ssi:boot:base:linear: booting n1 (wolf02) n-1<14671> ssi:boot:base:linear: booting n2 (wolf03) n-1<14671> ssi:boot:base:linear: booting n3 (wolf04) n-1<14671> ssi:boot:base:linear: booting n4 (wolf05) n-1<14671> ssi:boot:base:linear: booting n5 (wolf06) n-1<14671> ssi:boot:base:linear: booting n6 (wolf07) n-1<14671> ssi:boot:base:linear: booting n7 (wolf08) n-1<14671> ssi:boot:base:linear: booting n8 (wolf09) n-1<14671> ssi:boot:base:linear: booting n9 (wolf10) n-1<14671> ssi:boot:base:linear: booting n10 (wolf11) n-1<14671> ssi:boot:base:linear: booting n11 (wolf12) n-1<14671> ssi:boot:base:linear: booting n12 (wolf13) n-1<14671> 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, 1983 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, 1983 chemical shifts. - peakcheck: read peaks c13no format= *** WARNING: Assignment of peak 378 not found in chemical shift list. *** WARNING: Assignment of peak 3211 not found in chemical shift list. *** WARNING: Assignment of peak 3212 not found in chemical shift list. Peak list "c13no.peaks" read, 3489 peaks, 3184 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 3184 0.000 0.002 0.032 0.009 1 0.030 2 3485 0.000 0.000 0.026 0.002 0 0.030 3 3485 0.000 -0.001 0.297 0.025 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, 1983 chemical shifts. - peakcheck: read peaks n15no format= Peak list "n15no.peaks" read, 1274 peaks, 1106 assignments. - peakcheck: peaks fit Deviations from chemical shift list: Dim Peaks Median Average Maximum RMSD Number Tolerance 1 1106 0.002 0.002 0.030 0.011 0 0.030 2 1272 0.000 0.000 0.011 0.001 0 0.030 3 1272 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, 1983 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, 1983 chemical shifts. - peakcheck: read peaks fc12no format= Peak list "fc12no.peaks" read, 233 peaks, 143 assignments. - peakcheck: peaks fit Deviations from chemical shift list: Dim Peaks Median Average Maximum RMSD Number Tolerance 1 143 -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 dref=4.2 - calibration: read prot znf42 unknown=warn Chemical shift list "znf42.prot" read, 1983 chemical shifts. - calibration: read peaks c13no format= *** WARNING: Assignment of peak 378 not found in chemical shift list. *** WARNING: Assignment of peak 3211 not found in chemical shift list. *** WARNING: Assignment of peak 3212 not found in chemical shift list. Peak list "c13no.peaks" read, 3489 peaks, 3184 assignments. - calibration: peaks select "** list=1" 3489 of 3489 peaks, 3489 of 3489 assignments selected. - calibration: peaks set volume=abs(volume) Volume of 3489 peaks set. - calibration: peaks simplecal dref=4.2 Calibration constant for peak list 1: 1.84E+07 Upper limit set for 3489 peaks. - calibration: caltab peaks Distance bounds: -2.99 A: 441 12.6% 3.00-3.99 A: 1173 33.6% 4.00-4.99 A: 1308 37.5% 5.00-5.99 A: 567 16.3% 6.00- A: 0 0.0% All: 3489 100.0% - calibration: read prot znf42 unknown=warn append Chemical shift list "znf42.prot" read, 1983 chemical shifts. - calibration: read peaks n15no format= append Peak list "n15no.peaks" read, 1274 peaks, 1106 assignments. - calibration: peaks select "** list=2" 1274 of 4763 peaks, 1274 of 4763 assignments selected. - calibration: peaks set volume=abs(volume) Volume of 1274 peaks set. - calibration: peaks simplecal dref=4.2 Calibration constant for peak list 2: 8.44E+06 Upper limit set for 1274 peaks. - calibration: caltab peaks Distance bounds: -2.99 A: 111 8.7% 3.00-3.99 A: 470 36.9% 4.00-4.99 A: 478 37.5% 5.00-5.99 A: 215 16.9% 6.00- A: 0 0.0% All: 1274 100.0% - calibration: read prot znf42 unknown=warn append Chemical shift list "znf42.prot" read, 1983 chemical shifts. - calibration: read peaks c13ar format= append Peak list "c13ar.peaks" read, 292 peaks, 238 assignments. - calibration: peaks select "** list=3" 292 of 5055 peaks, 292 of 5055 assignments selected. - calibration: peaks set volume=abs(volume) Volume of 292 peaks set. - calibration: peaks simplecal dref=4.2 Calibration constant for peak list 3: 1.44E+07 Upper limit set for 292 peaks. - calibration: caltab peaks Distance bounds: -2.99 A: 26 8.9% 3.00-3.99 A: 93 31.8% 4.00-4.99 A: 166 56.8% 5.00-5.99 A: 7 2.4% 6.00- A: 0 0.0% All: 292 100.0% - calibration: read prot znf42 unknown=warn append Chemical shift list "znf42.prot" read, 1983 chemical shifts. - calibration: read peaks fc12no format= append Peak list "fc12no.peaks" read, 233 peaks, 143 assignments. - calibration: peaks select "** list=4" 233 of 5288 peaks, 233 of 5288 assignments selected. - calibration: peaks set volume=abs(volume) Volume of 233 peaks set. - calibration: peaks simplecal dref=4.2 Calibration constant for peak list 4: 7.23E+06 Upper limit set for 233 peaks. - calibration: caltab peaks Distance bounds: -2.99 A: 8 3.4% 3.00-3.99 A: 80 34.3% 4.00-4.99 A: 145 62.2% 5.00-5.99 A: 0 0.0% 6.00- A: 0 0.0% All: 233 100.0% - calibration: peaks select ** 5288 of 5288 peaks, 5288 of 5288 assignments selected. - znf42: peaks calibrate ** simple 4176 upper limits added, 18/141 at lower/upper bound, average 4.17 A. - znf42: write upl znf42-in.upl Distance constraint file "znf42-in.upl" written, 4176 upper limits, 4176 assignments. - znf42: distance modify Too restrictive distance constraints: limit dmin dmax Upper HA ASP 37 - QG PRO 38 3.96 4.11 6.06 Number of modified constraints: 2352 - znf42: write upl znf42.upl Distance constraint file "znf42.upl" written, 2352 upper limits, 2352 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, 2352 upper limits, 2352 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 40 s, f = 23.9495. Structure annealed in 40 s, f = 24.3733. Structure annealed in 40 s, f = 17.6653. Structure annealed in 40 s, f = 20.1943. Structure annealed in 41 s, f = 25.4142. Structure annealed in 40 s, f = 17.9603. Structure annealed in 40 s, f = 17.5511. Structure annealed in 40 s, f = 18.1325. Structure annealed in 40 s, f = 18.2269. Structure annealed in 40 s, f = 25.4077. Structure annealed in 40 s, f = 23.0375. Structure annealed in 40 s, f = 22.8325. Structure annealed in 40 s, f = 54.4113. Structure annealed in 40 s, f = 19.1027. Structure annealed in 40 s, f = 19.5510. Structure annealed in 40 s, f = 20.2163. Structure annealed in 40 s, f = 19.2749. Structure annealed in 40 s, f = 24.5808. Structure annealed in 40 s, f = 26.9657. Structure annealed in 40 s, f = 17.6300. Structure annealed in 40 s, f = 22.2275. Structure annealed in 41 s, f = 44.9031. Structure annealed in 40 s, f = 24.4888. Structure annealed in 40 s, f = 18.4659. Structure annealed in 40 s, f = 23.2127. Structure annealed in 40 s, f = 24.6822. Structure annealed in 40 s, f = 18.6782. Structure annealed in 40 s, f = 21.3629. Structure annealed in 40 s, f = 23.4771. Structure annealed in 40 s, f = 22.3692. Structure annealed in 40 s, f = 20.1688. Structure annealed in 40 s, f = 19.1317. Structure annealed in 40 s, f = 23.3184. Structure annealed in 40 s, f = 18.8164. Structure annealed in 40 s, f = 29.3664. Structure annealed in 41 s, f = 31.3916. Structure annealed in 40 s, f = 20.9786. Structure annealed in 40 s, f = 18.2811. Structure annealed in 40 s, f = 20.7898. Structure annealed in 40 s, f = 22.5447. Structure annealed in 40 s, f = 23.6297. Structure annealed in 40 s, f = 24.7949. Structure annealed in 41 s, f = 17.3264. Structure annealed in 40 s, f = 20.1528. Structure annealed in 40 s, f = 18.8288. Structure annealed in 40 s, f = 25.5128. Structure annealed in 40 s, f = 24.1203. Structure annealed in 40 s, f = 20.2884. Structure annealed in 40 s, f = 18.0698. Structure annealed in 41 s, f = 35.9486. Structure annealed in 40 s, f = 19.1378. Structure annealed in 40 s, f = 23.7688. Structure annealed in 40 s, f = 19.3068. Structure annealed in 40 s, f = 21.2955. Structure annealed in 40 s, f = 26.2938. Structure annealed in 40 s, f = 22.4971. Structure annealed in 40 s, f = 25.7959. Structure annealed in 40 s, f = 27.7583. Structure annealed in 40 s, f = 21.1922. Structure annealed in 41 s, f = 26.0433. Structure annealed in 40 s, f = 22.7689. Structure annealed in 40 s, f = 20.0880. Structure annealed in 40 s, f = 24.4750. Structure annealed in 40 s, f = 20.4963. Structure annealed in 40 s, f = 20.7758. Structure annealed in 40 s, f = 20.6451. Structure annealed in 41 s, f = 24.3836. Structure annealed in 40 s, f = 17.6724. Structure annealed in 40 s, f = 21.5236. Structure annealed in 41 s, f = 18.3596. Structure annealed in 40 s, f = 28.8396. Structure annealed in 40 s, f = 24.6138. Structure annealed in 40 s, f = 18.1529. Structure annealed in 40 s, f = 25.1098. Structure annealed in 40 s, f = 19.7917. Structure annealed in 40 s, f = 26.3356. Structure annealed in 40 s, f = 18.1003. Structure annealed in 40 s, f = 18.1572. Structure annealed in 40 s, f = 19.9015. Structure annealed in 40 s, f = 21.6645. Structure annealed in 40 s, f = 20.5409. Structure annealed in 43 s, f = 469.745. Structure annealed in 40 s, f = 19.5380. Structure annealed in 40 s, f = 29.6196. Structure annealed in 41 s, f = 22.6294. Structure annealed in 41 s, f = 397.710. Structure annealed in 40 s, f = 25.6752. Structure annealed in 40 s, f = 20.6244. Structure annealed in 40 s, f = 19.6672. Structure annealed in 43 s, f = 452.520. Structure annealed in 40 s, f = 19.6705. Structure annealed in 40 s, f = 18.5618. Structure annealed in 40 s, f = 26.2961. Structure annealed in 40 s, f = 21.6700. Structure annealed in 40 s, f = 17.1895. Structure annealed in 40 s, f = 19.1606. Structure annealed in 40 s, f = 21.3607. Structure annealed in 40 s, f = 20.3175. Structure annealed in 41 s, f = 164.172. Structure annealed in 41 s, f = 26.8306. 100 structures finished in 168 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 17.19 82 0.0358 0.55 7 20.3 0.30 2 0.9337 6.47 2 17.33 87 0.0364 0.58 10 19.4 0.33 0 0.8262 4.55 3 17.55 86 0.0359 0.52 10 21.0 0.51 0 0.7889 4.27 4 17.63 82 0.0366 0.60 4 18.2 0.32 2 1.0639 9.66 5 17.67 81 0.0372 0.71 6 20.1 0.52 2 1.0147 5.72 6 17.67 77 0.0357 0.60 11 20.0 0.51 2 1.1078 9.66 7 17.96 85 0.0368 0.55 11 21.4 0.51 2 1.0627 7.63 8 18.07 85 0.0364 0.55 12 21.7 0.51 0 0.8721 4.20 9 18.10 79 0.0354 0.57 7 20.5 0.50 4 1.0994 5.86 10 18.13 77 0.0365 0.60 7 21.1 0.32 2 0.9873 6.13 11 18.15 81 0.0356 0.61 15 21.3 0.40 2 1.0298 7.64 12 18.16 81 0.0355 0.59 7 21.4 0.51 1 0.9834 6.40 13 18.23 84 0.0354 0.51 6 20.6 0.51 2 1.0005 5.47 14 18.28 81 0.0384 0.62 8 19.4 0.31 1 0.9879 5.76 15 18.36 86 0.0364 0.52 11 21.3 0.51 2 0.9714 7.35 16 18.47 86 0.0362 0.53 9 20.9 0.51 0 0.8495 4.74 17 18.56 86 0.0365 0.52 7 21.7 0.32 2 0.9639 5.59 18 18.68 78 0.0366 0.61 11 22.2 0.47 1 0.9530 5.64 19 18.82 79 0.0354 0.52 12 21.4 0.52 2 1.0691 7.75 20 18.83 97 0.0391 0.70 2 19.7 0.32 1 1.0582 6.25 Ave 18.09 83 0.0364 0.58 9 20.7 0.44 2 0.9812 6.34 +/- 0.46 4 0.0010 0.06 3 1.0 0.09 1 0.0880 1.51 Min 17.19 77 0.0354 0.51 2 18.2 0.30 0 0.7889 4.20 Max 18.83 97 0.0391 0.71 15 22.2 0.52 4 1.1078 9.66 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 ------ --- --- --- --- 1 138 14 0 0 2 136 16 0 0 3 138 14 0 0 4 137 15 0 0 5 140 10 0 2 (GLU 125, GLU 425) 6 140 12 0 0 7 140 12 0 0 8 139 11 2 0 9 136 16 0 0 forrtl: Stale NFS file handle forrtl: severe (39): error during read, unit 51, file /user/francis/znf42/8cyana/122c_auto/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 400000000045AAA0 Unknown Unknown Unknown cyanaexe.intel-la 40000000002EC8C0 Unknown Unknown Unknown cyanaexe.intel-la 4000000000296560 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 MPI_Recv: process in local group is dead (rank 3, 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. PID 23727 failed on node n2 (192.168.96.103) with exit status 39. ----------------------------------------------------------------------------- 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() LAM 7.2b1svn10112005/MPI 2 C++/ROMIO - Indiana University 13-Dec-2005 16:42:37