Warning: no access to tty (Bad file descriptor). Thus no job control in this shell. 11-Nov-2005 14:26:08 LAM 6.5.9/MPI 2 C++/ROMIO - Indiana University Executing hboot on n0 (cesg-node13.biochem.wisc.edu - 2 CPUs)... Executing hboot on n1 (cesg-node12.biochem.wisc.edu - 2 CPUs)... Executing hboot on n2 (cesg-node11.biochem.wisc.edu - 2 CPUs)... Executing hboot on n3 (cesg-node10.biochem.wisc.edu - 2 CPUs)... Executing hboot on n4 (cesg-node9.biochem.wisc.edu - 2 CPUs)... Executing hboot on n5 (cesg-node8.biochem.wisc.edu - 2 CPUs)... Executing hboot on n6 (cesg-node7.biochem.wisc.edu - 2 CPUs)... Executing hboot on n7 (cesg-node6.biochem.wisc.edu - 2 CPUs)... Executing hboot on n8 (cesg-node5.biochem.wisc.edu - 2 CPUs)... Executing hboot on n9 (cesg-node4.biochem.wisc.edu - 2 CPUs)... topology n0 (o)... n1... n2... n3... n4... n5... n6... n7... n8... n9... done ___________________________________________________________________ CYANA 2.1 (intel-lam) Copyright (c) 2002-05 Peter Guntert. All rights reserved. ___________________________________________________________________ Library file "/s/src/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, 1980 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, 1980 chemical shifts. - peakcheck: read peaks c13no format= Peak list "c13no.peaks" read, 3503 peaks, 2971 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 2971 0.000 0.002 0.030 0.009 0 0.030 2 3321 0.000 0.000 0.029 0.003 0 0.030 3 3321 0.000 0.000 0.297 0.031 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, 1980 chemical shifts. - peakcheck: read peaks n15no format= Peak list "n15no.peaks" read, 1292 peaks, 1081 assignments. - peakcheck: peaks fit Deviations from chemical shift list: Dim Peaks Median Average Maximum RMSD Number Tolerance 1 1081 0.002 0.002 0.030 0.011 0 0.030 2 1222 0.000 0.000 0.011 0.001 0 0.030 3 1222 0.000 0.000 0.234 0.016 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, 1980 chemical shifts. - peakcheck: read peaks c13ar format= Peak list "c13ar.peaks" read, 281 peaks, 222 assignments. - peakcheck: peaks fit Deviations from chemical shift list: Dim Peaks Median Average Maximum RMSD Number Tolerance 1 222 0.004 0.005 0.030 0.013 0 0.030 2 280 0.000 0.000 0.000 0.000 0 0.030 3 280 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, 1980 chemical shifts. - peakcheck: read peaks fc12no format= Peak list "fc12no.peaks" read, 227 peaks, 147 assignments. - peakcheck: peaks fit Deviations from chemical shift list: Dim Peaks Median Average Maximum RMSD Number Tolerance 1 147 0.000 -0.001 0.029 0.016 0 0.030 2 161 0.000 0.000 0.014 0.005 0 0.030 3 161 0.000 -0.005 0.297 0.035 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=3.0E7,1.2 E7,2.0E7,1.0E7 dref=4.2 - calibration: read prot znf42 unknown=warn Chemical shift list "znf42.prot" read, 1980 chemical shifts. - calibration: read peaks c13no format= Peak list "c13no.peaks" read, 3503 peaks, 2971 assignments. - calibration: peaks select "** list=1" 3503 of 3503 peaks, 3503 of 3503 assignments selected. - calibration: peaks set volume=abs(volume) Volume of 3503 peaks set. - calibration: peaks simplecal constant=3.0E7 Calibration constant for peak list 1: 3.00E+07 Upper limit set for 3503 peaks. - calibration: caltab peaks Distance bounds: -2.99 A: 326 9.3% 3.00-3.99 A: 771 22.0% 4.00-4.99 A: 1391 39.7% 5.00-5.99 A: 1013 28.9% 6.00- A: 0 0.0% All: 3503 100.0% - calibration: read prot znf42 unknown=warn append Chemical shift list "znf42.prot" read, 1980 chemical shifts. - calibration: read peaks n15no format= append Peak list "n15no.peaks" read, 1292 peaks, 1081 assignments. - calibration: peaks select "** list=2" 1292 of 4795 peaks, 1292 of 4795 assignments selected. - calibration: peaks set volume=abs(volume) Volume of 1292 peaks set. - calibration: peaks simplecal constant=1.2E7 Calibration constant for peak list 2: 1.20E+07 Upper limit set for 1292 peaks. - calibration: caltab peaks Distance bounds: -2.99 A: 93 7.2% 3.00-3.99 A: 340 26.3% 4.00-4.99 A: 499 38.6% 5.00-5.99 A: 358 27.7% 6.00- A: 0 0.0% All: 1292 100.0% - calibration: read prot znf42 unknown=warn append Chemical shift list "znf42.prot" read, 1980 chemical shifts. - calibration: read peaks c13ar format= append Peak list "c13ar.peaks" read, 281 peaks, 222 assignments. - calibration: peaks select "** list=3" 281 of 5076 peaks, 281 of 5076 assignments selected. - calibration: peaks set volume=abs(volume) Volume of 281 peaks set. - calibration: peaks simplecal constant=2.0E7 Calibration constant for peak list 3: 2.00E+07 Upper limit set for 281 peaks. - calibration: caltab peaks Distance bounds: -2.99 A: 21 7.5% 3.00-3.99 A: 57 20.3% 4.00-4.99 A: 161 57.3% 5.00-5.99 A: 42 14.9% 6.00- A: 0 0.0% All: 281 100.0% - calibration: read prot znf42 unknown=warn append Chemical shift list "znf42.prot" read, 1980 chemical shifts. - calibration: read peaks fc12no format= append Peak list "fc12no.peaks" read, 227 peaks, 147 assignments. - calibration: peaks select "** list=4" 227 of 5303 peaks, 227 of 5303 assignments selected. - calibration: peaks set volume=abs(volume) Volume of 227 peaks set. - calibration: peaks simplecal constant=1.0E7 Calibration constant for peak list 4: 1.00E+07 Upper limit set for 227 peaks. - calibration: caltab peaks Distance bounds: -2.99 A: 1 0.4% 3.00-3.99 A: 50 22.0% 4.00-4.99 A: 157 69.2% 5.00-5.99 A: 19 8.4% 6.00- A: 0 0.0% All: 227 100.0% - calibration: peaks select ** 5303 of 5303 peaks, 5303 of 5303 assignments selected. - znf42: peaks calibrate ** simple 3965 upper limits added, 9/469 at lower/upper bound, average 4.46 A. - znf42: write upl znf42-in.upl Distance constraint file "znf42-in.upl" written, 3965 upper limits, 3965 assignments. - znf42: distance modify Number of modified constraints: 2080 - znf42: write upl znf42.upl Distance constraint file "znf42.upl" written, 2080 upper limits, 2080 assignments. - znf42: ./init - init: read lib /s/src/cyana-2.1/lib/cyana.lib Library file "/s/src/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, 2080 upper limits, 2080 assignments. - znf42: read aco znf42.aco Angle constraint file "znf42.aco" read, 267 constraints for 267 angles. - znf42: calc_all structures=100 command=anneal steps=10000 100 structures selected. 100 random structures created (seed 35671). Structure annealed in 129 s, f = 15.9969. Structure annealed in 133 s, f = 8.37856. Structure annealed in 133 s, f = 10.9569. Structure annealed in 131 s, f = 30.4124. Structure annealed in 132 s, f = 12.2073. Structure annealed in 128 s, f = 17.3899. Structure annealed in 137 s, f = 13.4483. Structure annealed in 129 s, f = 9.46432. Structure annealed in 129 s, f = 11.6201. Structure annealed in 136 s, f = 13.0118. Structure annealed in 111 s, f = 9.81924. Structure annealed in 118 s, f = 11.4701. Structure annealed in 131 s, f = 8.66347. Structure annealed in 129 s, f = 15.2176. Structure annealed in 132 s, f = 8.93171. Structure annealed in 132 s, f = 8.39514. Structure annealed in 130 s, f = 9.57076. Structure annealed in 135 s, f = 15.3191. Structure annealed in 131 s, f = 9.67832. Structure annealed in 136 s, f = 23.6801. Structure annealed in 110 s, f = 8.97829. Structure annealed in 135 s, f = 13.2190. Structure annealed in 131 s, f = 13.1710. Structure annealed in 131 s, f = 10.0608. Structure annealed in 131 s, f = 9.61332. Structure annealed in 130 s, f = 13.9851. Structure annealed in 132 s, f = 9.51138. Structure annealed in 130 s, f = 9.32474. Structure annealed in 129 s, f = 13.4354. Structure annealed in 133 s, f = 9.64027. Structure annealed in 135 s, f = 10.6458. Structure annealed in 131 s, f = 13.4543. Structure annealed in 131 s, f = 13.2248. Structure annealed in 132 s, f = 13.3447. Structure annealed in 132 s, f = 10.8708. Structure annealed in 131 s, f = 9.23432. Structure annealed in 131 s, f = 13.2245. Structure annealed in 133 s, f = 13.2951. Structure annealed in 133 s, f = 13.1061. Structure annealed in 98 s, f = 11.6201. Structure annealed in 98 s, f = 91.6975. Structure annealed in 134 s, f = 13.0046. Structure annealed in 131 s, f = 11.2170. Structure annealed in 132 s, f = 12.4961. Structure annealed in 127 s, f = 9.98120. Structure annealed in 130 s, f = 18.5780. Structure annealed in 130 s, f = 9.75223. Structure annealed in 132 s, f = 9.41088. Structure annealed in 130 s, f = 23.3281. Structure annealed in 130 s, f = 10.1141. Structure annealed in 135 s, f = 15.0095. Structure annealed in 132 s, f = 9.64817. Structure annealed in 134 s, f = 9.16359. Structure annealed in 134 s, f = 90.1605. Structure annealed in 133 s, f = 8.51779. Structure annealed in 133 s, f = 9.46827. Structure annealed in 136 s, f = 12.2262. Structure annealed in 134 s, f = 14.6895. Structure annealed in 134 s, f = 12.6034. Structure annealed in 131 s, f = 11.5221. Structure annealed in 132 s, f = 14.5829. Structure annealed in 132 s, f = 12.1789. Structure annealed in 130 s, f = 15.3442. Structure annealed in 132 s, f = 9.34792. Structure annealed in 133 s, f = 12.1275. Structure annealed in 135 s, f = 14.1651. Structure annealed in 130 s, f = 7.82148. Structure annealed in 133 s, f = 10.8090. Structure annealed in 134 s, f = 8.49248. Structure annealed in 137 s, f = 10.8218. Structure annealed in 130 s, f = 10.1882. Structure annealed in 132 s, f = 12.2813. Structure annealed in 135 s, f = 10.4986. Structure annealed in 133 s, f = 8.78380. Structure annealed in 134 s, f = 8.01147. Structure annealed in 133 s, f = 10.2492. Structure annealed in 129 s, f = 10.5377. Structure annealed in 106 s, f = 8.12348. Structure annealed in 127 s, f = 393.904. Structure annealed in 130 s, f = 10.9234. Structure annealed in 132 s, f = 13.4292. Structure annealed in 129 s, f = 10.9399. Structure annealed in 133 s, f = 9.29798. Structure annealed in 128 s, f = 13.5080. Structure annealed in 129 s, f = 13.3702. Structure annealed in 133 s, f = 9.76314. Structure annealed in 132 s, f = 8.38467. Structure annealed in 130 s, f = 8.21308. Structure annealed in 133 s, f = 12.2937. Structure annealed in 131 s, f = 15.1106. Structure annealed in 130 s, f = 9.72017. Structure annealed in 129 s, f = 11.6105. Structure annealed in 132 s, f = 16.2929. Structure annealed in 131 s, f = 8.91893. Structure annealed in 132 s, f = 11.4493. Structure annealed in 134 s, f = 10.6963. Structure annealed in 136 s, f = 9.64783. Structure annealed in 108 s, f = 10.1928. Structure annealed in 103 s, f = 16.3320. Structure annealed in 98 s, f = 11.7147. 100 structures finished in 761 s (7 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 7.82 24 0.0216 0.68 7 14.8 0.32 0 0.8318 4.16 2 8.01 28 0.0227 0.62 5 14.8 0.25 0 0.8365 4.46 3 8.12 28 0.0237 0.70 5 14.9 0.33 2 0.9523 5.16 4 8.21 23 0.0222 0.72 9 15.2 0.25 2 0.9358 5.80 5 8.38 25 0.0227 0.67 7 15.3 0.30 1 0.8922 6.00 6 8.38 24 0.0219 0.62 4 14.5 0.25 0 0.8374 4.11 7 8.40 27 0.0215 0.55 4 16.1 0.27 2 0.9663 5.70 8 8.49 30 0.0224 0.58 4 14.8 0.30 0 0.8439 4.30 9 8.52 24 0.0214 0.67 6 15.0 0.31 0 0.8405 3.74 10 8.66 24 0.0218 0.57 5 13.8 0.27 0 0.8541 4.66 11 8.78 27 0.0238 0.73 2 15.9 0.24 1 0.8483 5.71 12 8.92 30 0.0234 0.63 7 14.9 0.30 2 0.9459 6.07 13 8.93 30 0.0228 0.55 4 16.0 0.23 0 0.8086 4.95 14 8.98 26 0.0218 0.59 4 14.9 0.23 2 0.9210 5.59 15 9.16 25 0.0239 0.76 6 13.7 0.34 2 1.0236 7.27 16 9.23 26 0.0238 0.67 5 16.0 0.31 0 0.8381 4.30 17 9.30 29 0.0235 0.60 5 14.5 0.25 1 1.0116 5.37 18 9.33 28 0.0251 0.74 5 16.0 0.30 1 1.0162 6.00 19 9.35 20 0.0219 0.69 9 16.1 0.32 0 0.8111 4.38 20 9.41 27 0.0252 0.99 7 15.2 0.30 0 0.8609 4.29 Ave 8.72 26 0.0229 0.67 6 15.1 0.28 1 0.8938 5.10 +/- 0.48 3 0.0011 0.10 2 0.7 0.03 1 0.0697 0.88 Min 7.82 20 0.0214 0.55 2 13.7 0.23 0 0.8086 3.74 Max 9.41 30 0.0252 0.99 9 16.1 0.34 2 1.0236 7.27 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 ------ --- --- --- --- 1 143 9 0 0 2 136 14 2 0 3 139 11 2 0 4 138 12 2 0 5 139 13 0 0 6 135 17 0 0 7 131 17 4 0 8 136 16 0 0 9 138 12 2 0 10 141 11 0 0 11 136 14 2 0 12 137 15 0 0 13 133 19 0 0 14 141 11 0 0 15 144 8 0 0 16 142 10 0 0 17 134 17 1 0 18 138 14 0 0 19 138 14 0 0 20 139 11 2 0 all 90.7% 8.7% 0.6% 0.0% *** ERROR: Graphics file "znf42.grf" not found. *** FATAL ERROR: Program aborted. ----------------------------------------------------------------------------- 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 8898 failed on node n0 with exit status 1. ----------------------------------------------------------------------------- MPI_Recv: process in local group is dead (rank 9, MPI_COMM_WORLD) MPI_Recv: process in local group is dead (rank 17, MPI_COMM_WORLD) MPI_Recv: process in local group is dead (rank 10, MPI_COMM_WORLD) MPI_Recv: process in local group is dead (rank 18, MPI_COMM_WORLD) MPI_Recv: process in local group is dead (rank 14, MPI_COMM_WORLD) MPI_Recv: process in local group is dead (rank 20, MPI_COMM_WORLD) MPI_Recv: process in local group is dead (rank 12, MPI_COMM_WORLD) MPI_Recv: process in local group is dead (rank 8, MPI_COMM_WORLD) MPI_Recv: process in local group is dead (rank 16, MPI_COMM_WORLD) 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): - main() MPI_Recv: process in local group is dead (rank 11, MPI_COMM_WORLD) MPI_Recv: process in local group is dead (rank 19, MPI_COMM_WORLD) Rank (9, MPI_COMM_WORLD): Call stack within LAM: Rank (9, MPI_COMM_WORLD): - MPI_Recv() Rank (9, MPI_COMM_WORLD): - MPI_Bcast() Rank (9, MPI_COMM_WORLD): - main() Rank (10, MPI_COMM_WORLD): Call stack within LAM: Rank (10, MPI_COMM_WORLD): - MPI_Recv() Rank (10, MPI_COMM_WORLD): - MPI_Bcast() Rank (10, MPI_COMM_WORLD): - main() MPI_Recv: process in local group is dead (rank 13, MPI_COMM_WORLD) Rank (11, MPI_COMM_WORLD): Call stack within LAM: Rank (11, MPI_COMM_WORLD): - MPI_Recv() Rank (11, MPI_COMM_WORLD): - MPI_Bcast() Rank (11, MPI_COMM_WORLD): - main() 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): - main() Rank (13, MPI_COMM_WORLD): Call stack within LAM: Rank (13, MPI_COMM_WORLD): - MPI_Recv() Rank (13, MPI_COMM_WORLD): - MPI_Bcast() Rank (13, MPI_COMM_WORLD): - main() Rank (20, MPI_COMM_WORLD): Call stack within LAM: Rank (20, MPI_COMM_WORLD): - MPI_Recv() Rank (20, MPI_COMM_WORLD): - MPI_Bcast() Rank (20, MPI_COMM_WORLD): - main() Rank (17, MPI_COMM_WORLD): Call stack within LAM: Rank (17, MPI_COMM_WORLD): - MPI_Recv() Rank (17, MPI_COMM_WORLD): - MPI_Bcast() Rank (17, 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): - main() Rank (14, MPI_COMM_WORLD): Call stack within LAM: Rank (14, MPI_COMM_WORLD): - MPI_Recv() Rank (14, MPI_COMM_WORLD): - MPI_Bcast() Rank (14, MPI_COMM_WORLD): - main() Rank (18, MPI_COMM_WORLD): Call stack within LAM: Rank (18, MPI_COMM_WORLD): - MPI_Recv() Rank (18, MPI_COMM_WORLD): - MPI_Bcast() Rank (18, MPI_COMM_WORLD): - main() Rank (19, MPI_COMM_WORLD): Call stack within LAM: Rank (19, MPI_COMM_WORLD): - MPI_Recv() Rank (19, MPI_COMM_WORLD): - MPI_Bcast() Rank (19, MPI_COMM_WORLD): - main() LAM 6.5.9/MPI 2 C++/ROMIO - Indiana University 11-Nov-2005 14:40:50