Warning: no access to tty (Bad file descriptor). Thus no job control in this shell. 06-Dec-2005 21:51:06 n-1<27442> ssi:boot:base:linear: booting n0 (wolf01) n-1<27442> ssi:boot:base:linear: booting n1 (wolf02) n-1<27442> ssi:boot:base:linear: booting n2 (wolf03) n-1<27442> ssi:boot:base:linear: booting n3 (wolf04) n-1<27442> ssi:boot:base:linear: booting n4 (wolf05) n-1<27442> ssi:boot:base:linear: booting n5 (wolf06) n-1<27442> ssi:boot:base:linear: booting n6 (wolf07) n-1<27442> ssi:boot:base:linear: booting n7 (wolf08) n-1<27442> ssi:boot:base:linear: booting n8 (wolf09) n-1<27442> ssi:boot:base:linear: booting n9 (wolf10) n-1<27442> ssi:boot:base:linear: booting n10 (wolf11) n-1<27442> ssi:boot:base:linear: booting n11 (wolf12) n-1<27442> ssi:boot:base:linear: booting n12 (wolf13) n-1<27442> 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, 3183 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 3183 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, 1982 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, 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, 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, 1982 chemical shifts. - calibration: read peaks c13no format= Peak list "c13no.peaks" read, 3483 peaks, 3183 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, 1982 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, 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 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, 1982 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 4179 upper limits added, 2/699 at lower/upper bound, average 4.58 A. - znf42: write upl znf42-in.upl Distance constraint file "znf42-in.upl" written, 4179 upper limits, 4179 assignments. - znf42: distance modify Number of modified constraints: 2148 - znf42: write upl znf42.upl Distance constraint file "znf42.upl" written, 2148 upper limits, 2148 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, 2148 upper limits, 2148 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 = 6.23160. Structure annealed in 39 s, f = 8.09459. Structure annealed in 39 s, f = 2.02650. Structure annealed in 39 s, f = 6.33614. Structure annealed in 39 s, f = 6.18506. Structure annealed in 39 s, f = 6.26534. Structure annealed in 38 s, f = 6.96183. Structure annealed in 39 s, f = 3.15110. Structure annealed in 38 s, f = 7.80117. Structure annealed in 39 s, f = 3.68140. Structure annealed in 38 s, f = 6.66954. Structure annealed in 39 s, f = 2.27016. Structure annealed in 39 s, f = 4.29896. Structure annealed in 39 s, f = 3.91781. Structure annealed in 39 s, f = 3.20793. Structure annealed in 39 s, f = 3.33060. Structure annealed in 39 s, f = 2.36536. Structure annealed in 39 s, f = 2.21510. Structure annealed in 39 s, f = 3.14645. Structure annealed in 39 s, f = 4.08957. Structure annealed in 39 s, f = 6.57385. Structure annealed in 40 s, f = 104.849. Structure annealed in 39 s, f = 3.25044. Structure annealed in 39 s, f = 7.43095. Structure annealed in 39 s, f = 3.35193. Structure annealed in 39 s, f = 8.61103. Structure annealed in 38 s, f = 2.77486. Structure annealed in 39 s, f = 4.03782. Structure annealed in 39 s, f = 6.56401. Structure annealed in 39 s, f = 8.58408. Structure annealed in 39 s, f = 4.95647. Structure annealed in 39 s, f = 6.92903. Structure annealed in 39 s, f = 3.10124. Structure annealed in 40 s, f = 3.15726. Structure annealed in 39 s, f = 8.00808. Structure annealed in 39 s, f = 3.01104. Structure annealed in 39 s, f = 3.93589. Structure annealed in 39 s, f = 7.76338. Structure annealed in 39 s, f = 107.752. Structure annealed in 39 s, f = 5.74052. Structure annealed in 39 s, f = 8.82203. Structure annealed in 39 s, f = 3.01891. Structure annealed in 39 s, f = 8.73667. Structure annealed in 39 s, f = 3.86914. Structure annealed in 39 s, f = 5.18460. Structure annealed in 39 s, f = 3.17355. Structure annealed in 39 s, f = 2.49909. Structure annealed in 39 s, f = 3.86077. Structure annealed in 39 s, f = 3.57316. Structure annealed in 39 s, f = 101.202. Structure annealed in 38 s, f = 3.52663. Structure annealed in 39 s, f = 6.04293. Structure annealed in 39 s, f = 4.31343. Structure annealed in 39 s, f = 4.92122. Structure annealed in 39 s, f = 6.54443. Structure annealed in 39 s, f = 11.3952. Structure annealed in 39 s, f = 4.40710. Structure annealed in 40 s, f = 102.281. Structure annealed in 39 s, f = 2.40354. Structure annealed in 39 s, f = 4.90744. Structure annealed in 39 s, f = 5.38673. Structure annealed in 39 s, f = 3.24119. Structure annealed in 39 s, f = 26.5154. Structure annealed in 39 s, f = 3.24531. Structure annealed in 39 s, f = 2.76244. Structure annealed in 39 s, f = 3.21810. Structure annealed in 39 s, f = 7.30535. Structure annealed in 39 s, f = 4.15576. Structure annealed in 39 s, f = 9.34942. Structure annealed in 39 s, f = 6.69488. Structure annealed in 39 s, f = 2.58550. Structure annealed in 39 s, f = 3.92602. Structure annealed in 39 s, f = 6.51206. Structure annealed in 39 s, f = 4.44741. Structure annealed in 39 s, f = 3.04257. Structure annealed in 38 s, f = 6.96723. Structure annealed in 39 s, f = 3.82819. Structure annealed in 39 s, f = 6.51322. Structure annealed in 39 s, f = 3.08562. Structure annealed in 39 s, f = 2.92208. Structure annealed in 39 s, f = 4.44854. Structure annealed in 39 s, f = 9.34160. Structure annealed in 39 s, f = 4.26688. Structure annealed in 39 s, f = 4.42229. Structure annealed in 38 s, f = 3.89558. Structure annealed in 39 s, f = 3.13536. Structure annealed in 39 s, f = 6.52240. Structure annealed in 39 s, f = 5.85541. Structure annealed in 39 s, f = 2.12037. Structure annealed in 39 s, f = 6.46919. Structure annealed in 39 s, f = 7.16282. Structure annealed in 39 s, f = 6.74873. Structure annealed in 39 s, f = 3.35429. Structure annealed in 41 s, f = 366.739. Structure annealed in 39 s, f = 3.97130. Structure annealed in 39 s, f = 7.32990. Structure annealed in 39 s, f = 2.67866. Structure annealed in 39 s, f = 2.80062. Structure annealed in 39 s, f = 4.08210. Structure annealed in 39 s, f = 8.31083. 100 structures finished in 163 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 2.03 0 0.0075 0.20 1 7.1 0.21 0 0.3154 2.46 2 2.12 2 0.0077 0.33 0 5.8 0.14 0 0.2263 1.33 3 2.22 1 0.0077 0.22 1 7.0 0.25 0 0.3714 2.38 4 2.27 0 0.0076 0.20 0 6.7 0.18 0 0.3176 2.14 5 2.37 2 0.0085 0.30 2 8.3 0.29 0 0.2879 2.24 6 2.40 1 0.0077 0.25 1 7.3 0.20 0 0.4203 2.35 7 2.50 2 0.0080 0.21 2 8.9 0.23 0 0.3342 2.19 8 2.59 2 0.0085 0.31 0 7.7 0.15 0 0.3124 2.04 9 2.68 0 0.0080 0.19 2 8.5 0.30 0 0.3545 2.36 10 2.76 2 0.0083 0.23 3 8.4 0.25 0 0.3631 2.69 11 2.78 3 0.0105 0.41 0 8.0 0.19 0 0.4182 2.74 12 2.80 1 0.0074 0.22 1 7.3 0.24 0 0.3325 2.15 13 2.92 3 0.0103 0.34 0 7.8 0.19 0 0.3585 2.18 14 3.01 1 0.0074 0.26 3 7.7 0.29 0 0.3134 2.21 15 3.02 4 0.0089 0.33 2 7.9 0.30 0 0.2940 2.22 16 3.04 3 0.0091 0.27 0 8.0 0.17 0 0.4043 3.07 17 3.09 0 0.0078 0.19 1 7.7 0.23 0 0.3852 2.01 18 3.10 2 0.0081 0.27 2 7.7 0.29 0 0.3727 2.45 19 3.14 2 0.0097 0.39 1 7.9 0.22 0 0.4193 2.15 20 3.15 3 0.0086 0.23 0 7.5 0.18 0 0.3145 1.96 Ave 2.70 2 0.0084 0.27 1 7.7 0.22 0 0.3458 2.27 +/- 0.36 1 0.0009 0.07 1 0.7 0.05 0 0.0493 0.34 Min 2.03 0 0.0074 0.19 0 5.8 0.14 0 0.2263 1.33 Max 3.15 4 0.0105 0.41 3 8.9 0.30 0 0.4203 3.07 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 ------ --- --- --- --- 1 135 17 0 0 2 144 8 0 0 3 134 18 0 0 4 136 15 1 0 5 141 11 0 0 6 143 9 0 0 7 134 16 0 2 (GLU 125, GLU 425) 8 140 10 2 0 9 133 19 0 0 10 143 9 0 0 11 137 13 2 0 12 140 12 0 0 13 139 9 4 0 forrtl: Stale NFS file handle forrtl: severe (38): error during write, unit 41, file /user/francis/znf42/8cyana/120a/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 (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() 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() ----------------------------------------------------------------------------- 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 27524 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() 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 21:54:22