Warning: no access to tty (Bad file descriptor). Thus no job control in this shell. 06-Dec-2005 00:42:32 n-1<19908> ssi:boot:base:linear: booting n0 (wolf01) n-1<19908> ssi:boot:base:linear: booting n1 (wolf02) n-1<19908> ssi:boot:base:linear: booting n2 (wolf03) n-1<19908> ssi:boot:base:linear: booting n3 (wolf04) n-1<19908> ssi:boot:base:linear: booting n4 (wolf05) n-1<19908> ssi:boot:base:linear: booting n5 (wolf06) n-1<19908> ssi:boot:base:linear: booting n6 (wolf07) n-1<19908> ssi:boot:base:linear: booting n7 (wolf08) n-1<19908> ssi:boot:base:linear: booting n8 (wolf09) n-1<19908> ssi:boot:base:linear: booting n9 (wolf10) n-1<19908> ssi:boot:base:linear: booting n10 (wolf11) n-1<19908> ssi:boot:base:linear: booting n11 (wolf12) n-1<19908> ssi:boot:base:linear: booting n12 (wolf13) n-1<19908> 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=3.5E7,1.7 E7,2.5E7,1.0E7 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=3.5E7 Calibration constant for peak list 1: 3.50E+07 Upper limit set for 3483 peaks. - calibration: caltab peaks Distance bounds: -2.99 A: 297 8.5% 3.00-3.99 A: 679 19.5% 4.00-4.99 A: 1372 39.4% 5.00-5.99 A: 1135 32.6% 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=2.5E7 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, 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, 2/700 at lower/upper bound, average 4.58 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: 2153 - znf42: write upl znf42.upl Distance constraint file "znf42.upl" written, 2153 upper limits, 2153 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, 2153 upper limits, 2153 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 = 1.37568. Structure annealed in 39 s, f = 2.60493. Structure annealed in 39 s, f = 4.26855. Structure annealed in 39 s, f = 5.66061. Structure annealed in 39 s, f = 5.89631. Structure annealed in 39 s, f = 4.28728. Structure annealed in 39 s, f = 4.54508. Structure annealed in 39 s, f = 11.0666. Structure annealed in 39 s, f = 2.42820. Structure annealed in 39 s, f = 4.47335. Structure annealed in 39 s, f = 6.05498. Structure annealed in 39 s, f = 5.92967. Structure annealed in 39 s, f = 4.19061. Structure annealed in 39 s, f = 2.95046. Structure annealed in 39 s, f = 4.05940. Structure annealed in 39 s, f = 4.22895. Structure annealed in 39 s, f = 3.43271. Structure annealed in 39 s, f = 7.64162. Structure annealed in 39 s, f = 3.51272. Structure annealed in 39 s, f = 4.30071. Structure annealed in 39 s, f = 3.69402. Structure annealed in 39 s, f = 7.75273. Structure annealed in 39 s, f = 3.46583. Structure annealed in 39 s, f = 10.3590. Structure annealed in 39 s, f = 11.0615. Structure annealed in 38 s, f = 3.50801. Structure annealed in 39 s, f = 3.82434. Structure annealed in 39 s, f = 2.86453. Structure annealed in 38 s, f = 3.81672. Structure annealed in 39 s, f = 5.12047. Structure annealed in 39 s, f = 5.82590. Structure annealed in 39 s, f = 4.04652. Structure annealed in 38 s, f = 5.47835. Structure annealed in 39 s, f = 3.02729. Structure annealed in 39 s, f = 18.9555. Structure annealed in 39 s, f = 5.37716. Structure annealed in 39 s, f = 6.28417. Structure annealed in 39 s, f = 3.13855. Structure annealed in 41 s, f = 299.435. Structure annealed in 38 s, f = 5.94256. Structure annealed in 39 s, f = 4.78822. Structure annealed in 39 s, f = 3.50300. Structure annealed in 39 s, f = 7.29179. Structure annealed in 39 s, f = 8.21148. Structure annealed in 39 s, f = 7.89532. Structure annealed in 39 s, f = 3.61938. Structure annealed in 39 s, f = 5.84791. Structure annealed in 39 s, f = 4.38674. Structure annealed in 39 s, f = 5.98107. Structure annealed in 39 s, f = 3.73211. Structure annealed in 38 s, f = 2.68983. Structure annealed in 39 s, f = 3.64987. Structure annealed in 39 s, f = 4.15864. Structure annealed in 39 s, f = 3.76948. Structure annealed in 39 s, f = 8.47571. Structure annealed in 39 s, f = 3.37444. Structure annealed in 39 s, f = 4.16555. Structure annealed in 39 s, f = 3.97354. Structure annealed in 39 s, f = 10.0008. Structure annealed in 39 s, f = 2.11129. Structure annealed in 39 s, f = 7.52668. Structure annealed in 39 s, f = 2.82967. Structure annealed in 39 s, f = 7.26092. Structure annealed in 39 s, f = 6.36849. Structure annealed in 39 s, f = 4.72640. Structure annealed in 39 s, f = 4.03628. Structure annealed in 39 s, f = 5.44784. Structure annealed in 39 s, f = 5.32915. Structure annealed in 39 s, f = 7.07398. Structure annealed in 39 s, f = 9.18515. Structure annealed in 39 s, f = 3.36537. Structure annealed in 39 s, f = 7.79010. Structure annealed in 40 s, f = 106.799. Structure annealed in 39 s, f = 5.11991. Structure annealed in 38 s, f = 2.56274. Structure annealed in 38 s, f = 3.18621. Structure annealed in 39 s, f = 6.18218. Structure annealed in 39 s, f = 5.41524. Structure annealed in 39 s, f = 3.08119. Structure annealed in 39 s, f = 2.65721. Structure annealed in 39 s, f = 4.74460. Structure annealed in 39 s, f = 7.96904. Structure annealed in 39 s, f = 3.07287. Structure annealed in 39 s, f = 7.11637. Structure annealed in 39 s, f = 2.60790. Structure annealed in 39 s, f = 3.11205. Structure annealed in 39 s, f = 2.77288. Structure annealed in 39 s, f = 5.65944. Structure annealed in 39 s, f = 6.39912. Structure annealed in 39 s, f = 7.80650. Structure annealed in 39 s, f = 3.54259. Structure annealed in 39 s, f = 4.85390. Structure annealed in 39 s, f = 5.78423. Structure annealed in 39 s, f = 8.50236. Structure annealed in 39 s, f = 3.48406. Structure annealed in 39 s, f = 3.51425. Structure annealed in 39 s, f = 3.67601. Structure annealed in 39 s, f = 3.87333. Structure annealed in 39 s, f = 6.87094. Structure annealed in 39 s, f = 5.85593. 100 structures finished in 162 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 1.38 0 0.0054 0.13 0 5.3 0.19 0 0.2492 2.11 2 2.11 3 0.0082 0.21 0 6.8 0.17 0 0.3370 2.30 3 2.43 0 0.0068 0.20 0 7.0 0.18 0 0.2456 2.16 4 2.56 3 0.0084 0.28 0 7.2 0.16 0 0.3523 2.25 5 2.60 0 0.0070 0.20 3 8.2 0.29 0 0.2854 2.09 6 2.61 1 0.0083 0.24 2 8.3 0.29 0 0.3293 2.66 7 2.66 0 0.0077 0.19 2 8.4 0.29 0 0.3798 2.86 8 2.69 1 0.0082 0.21 3 8.4 0.29 0 0.3569 2.66 9 2.77 1 0.0081 0.21 0 7.6 0.20 0 0.4040 2.21 10 2.83 3 0.0091 0.37 0 7.5 0.18 0 0.3774 2.44 11 2.86 0 0.0070 0.19 3 8.0 0.29 0 0.3917 3.28 12 2.95 2 0.0078 0.22 1 8.4 0.21 0 0.4106 2.49 13 3.03 1 0.0090 0.28 0 8.9 0.14 0 0.3405 2.34 14 3.07 4 0.0099 0.31 0 7.5 0.19 0 0.4018 2.18 15 3.08 1 0.0090 0.21 2 9.8 0.29 0 0.4806 4.35 16 3.11 3 0.0097 0.23 3 10.0 0.28 0 0.4288 3.17 17 3.14 2 0.0089 0.23 3 7.9 0.29 0 0.3750 2.30 18 3.19 1 0.0084 0.28 2 8.3 0.29 0 0.3295 2.63 19 3.37 3 0.0086 0.22 2 9.1 0.29 0 0.4820 3.75 20 3.37 1 0.0089 0.29 3 9.0 0.29 0 0.3203 2.76 Ave 2.79 2 0.0082 0.23 1 8.1 0.24 0 0.3639 2.65 +/- 0.45 1 0.0010 0.05 1 1.0 0.05 0 0.0622 0.58 Min 1.38 0 0.0054 0.13 0 5.3 0.14 0 0.2456 2.09 Max 3.37 4 0.0099 0.37 3 10.0 0.29 0 0.4820 4.35 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 ------ --- --- --- --- 1 141 11 0 0 2 143 9 0 0 3 137 15 0 0 forrtl: Stale NFS file handle forrtl: severe (38): error during write, unit 41, file /user/francis/znf42/8cyana/116k/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 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. PID 19990 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 (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 00:45:45