Warning: no access to tty (Bad file descriptor). Thus no job control in this shell. 20-Dec-2005 17:53:14 n-1<11939> ssi:boot:base:linear: booting n0 (wolf01) n-1<11939> ssi:boot:base:linear: booting n1 (wolf02) n-1<11939> ssi:boot:base:linear: booting n2 (wolf03) n-1<11939> ssi:boot:base:linear: booting n3 (wolf04) n-1<11939> ssi:boot:base:linear: booting n4 (wolf05) n-1<11939> ssi:boot:base:linear: booting n5 (wolf06) n-1<11939> ssi:boot:base:linear: booting n6 (wolf07) n-1<11939> ssi:boot:base:linear: booting n7 (wolf08) n-1<11939> ssi:boot:base:linear: booting n8 (wolf09) n-1<11939> ssi:boot:base:linear: booting n9 (wolf10) n-1<11939> ssi:boot:base:linear: booting n10 (wolf11) n-1<11939> ssi:boot:base:linear: booting n11 (wolf12) n-1<11939> ssi:boot:base:linear: booting n12 (wolf13) n-1<11939> 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, 1984 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, 1984 chemical shifts. - peakcheck: read peaks c13no format= Peak list "c13no.peaks" read, 3489 peaks, 3187 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 3187 0.000 0.002 0.030 0.009 0 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 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, 1984 chemical shifts. - peakcheck: read peaks n15no format= Peak list "n15no.peaks" read, 1274 peaks, 1102 assignments. - peakcheck: peaks fit Deviations from chemical shift list: Dim Peaks Median Average Maximum RMSD Number Tolerance 1 1102 0.002 0.002 0.034 0.011 1 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 QD1 LEU 118 0.930 0.905 0.034 4 1 shift with spread larger than tolerance. - peakcheck: peak deviations Peak Dim Deviation Atom Residue 1278 1 -0.034 QD1 LEU 118 1 deviations larger than tolerance. ------------------------------------------------------------ Peak list : c13ar Proton list: znf42 - peakcheck: read prot znf42 unknown=skip Chemical shift list "znf42.prot" read, 1984 chemical shifts. - peakcheck: read peaks c13ar format= *** WARNING: Assignment of peak 288 not found in chemical shift list. *** WARNING: Assignment of peak 314 not found in chemical shift list. Peak list "c13ar.peaks" read, 292 peaks, 236 assignments. - peakcheck: peaks fit Deviations from chemical shift list: Dim Peaks Median Average Maximum RMSD Number Tolerance 1 236 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, 1984 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 constant=3.5E7,1.7 E7,2.5E7,1.0E7 dref=4.2 - calibration: read prot znf42 unknown=warn Chemical shift list "znf42.prot" read, 1984 chemical shifts. - calibration: read peaks c13no format= Peak list "c13no.peaks" read, 3489 peaks, 3187 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 constant=3.5E7 Calibration constant for peak list 1: 3.50E+07 Upper limit set for 3489 peaks. - calibration: caltab peaks Distance bounds: -2.99 A: 298 8.5% 3.00-3.99 A: 680 19.5% 4.00-4.99 A: 1373 39.4% 5.00-5.99 A: 1138 32.6% 6.00- A: 0 0.0% All: 3489 100.0% - calibration: read prot znf42 unknown=warn append Chemical shift list "znf42.prot" read, 1984 chemical shifts. - calibration: read peaks n15no format= append Peak list "n15no.peaks" read, 1274 peaks, 1102 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 constant=1.7E7 Calibration constant for peak list 2: 1.70E+07 Upper limit set for 1274 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: 493 38.7% 5.00-5.99 A: 480 37.7% 6.00- A: 0 0.0% All: 1274 100.0% - calibration: read prot znf42 unknown=warn append Chemical shift list "znf42.prot" read, 1984 chemical shifts. - calibration: read peaks c13ar format= append *** WARNING: Assignment of peak 288 not found in chemical shift list. *** WARNING: Assignment of peak 314 not found in chemical shift list. Peak list "c13ar.peaks" read, 292 peaks, 236 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 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, 1984 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 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 ** 5288 of 5288 peaks, 5288 of 5288 assignments selected. - znf42: peaks calibrate ** simple 4173 upper limits added, 2/691 at lower/upper bound, average 4.58 A. - znf42: write upl znf42-in.upl Distance constraint file "znf42-in.upl" written, 4173 upper limits, 4173 assignments. - znf42: distance modify Number of modified constraints: 2128 - znf42: write upl znf42.upl Distance constraint file "znf42.upl" written, 2128 upper limits, 2128 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, 2128 upper limits, 2128 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 = 3.06594. Structure annealed in 39 s, f = 1.70755. Structure annealed in 39 s, f = 1.71172. Structure annealed in 39 s, f = 2.87307. Structure annealed in 38 s, f = 1.75609. Structure annealed in 39 s, f = 5.85212. Structure annealed in 39 s, f = 2.45739. Structure annealed in 38 s, f = 2.17839. Structure annealed in 39 s, f = 2.33629. Structure annealed in 39 s, f = 9.67803. Structure annealed in 39 s, f = 2.59316. Structure annealed in 38 s, f = 3.17983. Structure annealed in 41 s, f = 287.783. Structure annealed in 39 s, f = 2.31727. Structure annealed in 39 s, f = 2.49199. Structure annealed in 38 s, f = 5.53086. Structure annealed in 38 s, f = 2.67043. Structure annealed in 39 s, f = 6.17995. Structure annealed in 39 s, f = 1.99448. Structure annealed in 38 s, f = 3.07377. Structure annealed in 39 s, f = 3.80907. Structure annealed in 39 s, f = 7.11461. Structure annealed in 39 s, f = 2.22601. Structure annealed in 39 s, f = 5.63060. Structure annealed in 41 s, f = 320.817. Structure annealed in 39 s, f = 2.63871. Structure annealed in 39 s, f = 1.89988. Structure annealed in 39 s, f = 2.35809. Structure annealed in 38 s, f = 3.85474. Structure annealed in 38 s, f = 2.14885. Structure annealed in 39 s, f = 3.53064. Structure annealed in 39 s, f = 2.47721. Structure annealed in 39 s, f = 6.06779. Structure annealed in 39 s, f = 2.55944. Structure annealed in 39 s, f = 5.36303. Structure annealed in 39 s, f = 2.24937. Structure annealed in 39 s, f = 1.74717. Structure annealed in 39 s, f = 1.65087. Structure annealed in 39 s, f = 1.56648. Structure annealed in 39 s, f = 2.50720. Structure annealed in 39 s, f = 3.90853. Structure annealed in 39 s, f = 7.14579. Structure annealed in 39 s, f = 4.64737. Structure annealed in 39 s, f = 8.68966. Structure annealed in 38 s, f = 1.68939. Structure annealed in 39 s, f = 1.66576. Structure annealed in 39 s, f = 6.04793. Structure annealed in 38 s, f = 2.94512. Structure annealed in 39 s, f = 1.46430. Structure annealed in 41 s, f = 197.561. Structure annealed in 39 s, f = 5.04259. Structure annealed in 38 s, f = 3.11368. Structure annealed in 38 s, f = 1.95605. Structure annealed in 39 s, f = 1.52773. Structure annealed in 38 s, f = 2.29748. Structure annealed in 38 s, f = 2.42339. Structure annealed in 39 s, f = 1.52571. Structure annealed in 39 s, f = 8.41111. Structure annealed in 38 s, f = 1.99721. Structure annealed in 39 s, f = 2.33561. Structure annealed in 39 s, f = 2.03769. Structure annealed in 38 s, f = 1.86255. Structure annealed in 39 s, f = 6.59646. Structure annealed in 38 s, f = 4.97806. Structure annealed in 39 s, f = 3.12045. Structure annealed in 39 s, f = 23.6129. Structure annealed in 38 s, f = 5.78998. Structure annealed in 39 s, f = 3.24728. Structure annealed in 38 s, f = 1.48455. Structure annealed in 39 s, f = 2.65118. Structure annealed in 39 s, f = 3.16294. Structure annealed in 39 s, f = 1.88045. Structure annealed in 39 s, f = 1.65167. Structure annealed in 39 s, f = 2.35602. Structure annealed in 39 s, f = 1.34853. Structure annealed in 39 s, f = 2.61783. Structure annealed in 39 s, f = 1.55021. Structure annealed in 39 s, f = 2.90168. Structure annealed in 39 s, f = 2.88058. Structure annealed in 38 s, f = 7.75522. Structure annealed in 39 s, f = 8.39881. Structure annealed in 39 s, f = 2.12678. Structure annealed in 39 s, f = 3.01874. Structure annealed in 39 s, f = 2.63600. Structure annealed in 38 s, f = 1.96043. Structure annealed in 39 s, f = 2.86646. Structure annealed in 39 s, f = 2.97432. Structure annealed in 39 s, f = 3.56045. Structure annealed in 39 s, f = 2.96308. Structure annealed in 38 s, f = 1.09882. Structure annealed in 39 s, f = 2.78532. Structure annealed in 38 s, f = 3.50419. Structure annealed in 41 s, f = 434.648. Structure annealed in 39 s, f = 5.54204. Structure annealed in 39 s, f = 1.56609. Structure annealed in 39 s, f = 2.99099. Structure annealed in 39 s, f = 2.99693. Structure annealed in 39 s, f = 1.96440. Structure annealed in 39 s, f = 2.77143. Structure annealed in 39 s, f = 4.80432. 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 1.10 0 0.0057 0.18 0 5.8 0.17 0 0.2779 2.19 2 1.35 0 0.0056 0.19 1 5.3 0.21 0 0.2737 2.15 3 1.46 2 0.0068 0.21 1 6.3 0.23 0 0.2766 1.94 4 1.48 0 0.0046 0.16 2 5.7 0.29 0 0.2857 2.12 5 1.53 0 0.0060 0.15 1 5.8 0.22 0 0.3067 2.75 6 1.53 0 0.0059 0.18 1 5.9 0.22 0 0.2945 2.09 7 1.55 0 0.0061 0.20 1 5.3 0.21 0 0.2897 2.10 8 1.57 0 0.0053 0.18 1 5.5 0.20 0 0.3071 2.96 9 1.57 0 0.0053 0.17 1 5.3 0.22 0 0.3179 3.53 10 1.65 0 0.0060 0.18 3 5.9 0.30 0 0.2589 2.49 11 1.65 0 0.0062 0.20 2 6.2 0.29 0 0.3013 2.83 12 1.67 1 0.0067 0.20 2 6.1 0.29 0 0.2755 2.60 13 1.69 0 0.0050 0.18 3 5.8 0.29 0 0.2401 2.21 14 1.71 0 0.0058 0.16 3 6.0 0.29 0 0.2550 2.23 15 1.71 1 0.0070 0.21 1 6.2 0.21 0 0.2560 1.79 16 1.75 1 0.0064 0.21 0 5.9 0.19 0 0.3240 2.40 17 1.76 0 0.0062 0.19 1 6.1 0.23 0 0.3105 2.30 18 1.86 3 0.0079 0.38 2 6.4 0.25 0 0.3360 2.89 19 1.88 2 0.0081 0.24 3 7.6 0.29 0 0.2980 2.28 20 1.90 2 0.0069 0.22 3 6.5 0.29 0 0.2001 1.27 Ave 1.62 1 0.0062 0.20 2 6.0 0.24 0 0.2843 2.36 +/- 0.18 1 0.0009 0.05 1 0.5 0.04 0 0.0311 0.47 Min 1.10 0 0.0046 0.15 0 5.3 0.17 0 0.2001 1.27 Max 1.90 3 0.0081 0.38 3 7.6 0.30 0 0.3360 3.53 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 3 133 17 0 2 (ASP 37, ASP 337) forrtl: Stale NFS file handle forrtl: severe (38): error during write, unit 41, file /user/francis/znf42/8cyana/130/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) ----------------------------------------------------------------------------- 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 12021 failed on node n0 (192.168.96.101) with exit status 28. ----------------------------------------------------------------------------- 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 (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 11, comm 3) Rank (22, MPI_COMM_WORLD): Call stack within LAM: Rank (22, MPI_COMM_WORLD): - MPI_Recv() Rank (22, MPI_COMM_WORLD): - MPI_Bcast() Rank (22, MPI_COMM_WORLD): - MPI_Bcast() Rank (22, MPI_COMM_WORLD): - main() MPI_Recv: process in local group is dead (rank 12, comm 3) Rank (24, MPI_COMM_WORLD): Call stack within LAM: Rank (24, MPI_COMM_WORLD): - MPI_Recv() Rank (24, MPI_COMM_WORLD): - MPI_Bcast() Rank (24, MPI_COMM_WORLD): - MPI_Bcast() Rank (24, MPI_COMM_WORLD): - main() LAM 7.2b1svn10112005/MPI 2 C++/ROMIO - Indiana University 20-Dec-2005 17:56:29