Warning: no access to tty (Bad file descriptor). Thus no job control in this shell. 06-Dec-2005 00:14:34 n-1<18870> ssi:boot:base:linear: booting n0 (wolf01) n-1<18870> ssi:boot:base:linear: booting n1 (wolf02) n-1<18870> ssi:boot:base:linear: booting n2 (wolf03) n-1<18870> ssi:boot:base:linear: booting n3 (wolf04) n-1<18870> ssi:boot:base:linear: booting n4 (wolf05) n-1<18870> ssi:boot:base:linear: booting n5 (wolf06) n-1<18870> ssi:boot:base:linear: booting n6 (wolf07) n-1<18870> ssi:boot:base:linear: booting n7 (wolf08) n-1<18870> ssi:boot:base:linear: booting n8 (wolf09) n-1<18870> ssi:boot:base:linear: booting n9 (wolf10) n-1<18870> ssi:boot:base:linear: booting n10 (wolf11) n-1<18870> ssi:boot:base:linear: booting n11 (wolf12) n-1<18870> ssi:boot:base:linear: booting n12 (wolf13) n-1<18870> 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 E7,2.0E7,1.0E7 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=2.0E7 Calibration constant for peak list 3: 2.00E+07 Upper limit set for 292 peaks. - calibration: caltab peaks Distance bounds: -2.99 A: 22 7.5% 3.00-3.99 A: 61 20.9% 4.00-4.99 A: 174 59.6% 5.00-5.99 A: 35 12.0% 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, 2/699 at lower/upper bound, average 4.57 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: 2155 - znf42: write upl znf42.upl Distance constraint file "znf42.upl" written, 2155 upper limits, 2155 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, 2155 upper limits, 2155 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 = 3.04671. Structure annealed in 39 s, f = 6.39297. Structure annealed in 39 s, f = 4.87078. Structure annealed in 39 s, f = 7.13797. Structure annealed in 39 s, f = 7.17212. Structure annealed in 39 s, f = 4.04141. Structure annealed in 39 s, f = 3.66600. Structure annealed in 39 s, f = 8.16755. Structure annealed in 38 s, f = 3.77001. Structure annealed in 39 s, f = 2.53953. Structure annealed in 39 s, f = 54.3417. Structure annealed in 39 s, f = 4.74638. Structure annealed in 39 s, f = 5.29420. Structure annealed in 39 s, f = 7.66374. Structure annealed in 39 s, f = 5.69887. Structure annealed in 39 s, f = 5.16189. Structure annealed in 39 s, f = 5.13084. Structure annealed in 39 s, f = 3.34414. Structure annealed in 39 s, f = 2.98039. Structure annealed in 39 s, f = 4.51068. Structure annealed in 39 s, f = 5.52300. Structure annealed in 39 s, f = 3.91972. Structure annealed in 39 s, f = 6.02957. Structure annealed in 39 s, f = 3.15226. Structure annealed in 39 s, f = 10.7530. Structure annealed in 39 s, f = 3.95297. Structure annealed in 39 s, f = 7.34181. Structure annealed in 39 s, f = 3.95037. Structure annealed in 39 s, f = 4.60773. Structure annealed in 39 s, f = 6.86346. Structure annealed in 39 s, f = 4.31995. Structure annealed in 39 s, f = 3.05003. Structure annealed in 39 s, f = 3.33271. Structure annealed in 39 s, f = 2.79408. Structure annealed in 39 s, f = 3.82973. Structure annealed in 39 s, f = 24.9779. Structure annealed in 39 s, f = 8.16302. Structure annealed in 39 s, f = 2.85921. Structure annealed in 39 s, f = 4.29401. Structure annealed in 39 s, f = 6.10772. Structure annealed in 39 s, f = 7.35253. Structure annealed in 39 s, f = 9.36511. Structure annealed in 39 s, f = 108.497. Structure annealed in 39 s, f = 4.28033. Structure annealed in 39 s, f = 6.54895. Structure annealed in 39 s, f = 3.47360. Structure annealed in 40 s, f = 4.18860. Structure annealed in 39 s, f = 3.93923. Structure annealed in 39 s, f = 5.06922. Structure annealed in 39 s, f = 5.94687. Structure annealed in 38 s, f = 3.70914. Structure annealed in 39 s, f = 3.24546. Structure annealed in 41 s, f = 190.681. Structure annealed in 39 s, f = 5.71177. Structure annealed in 39 s, f = 4.47805. Structure annealed in 39 s, f = 4.73162. Structure annealed in 39 s, f = 5.46005. Structure annealed in 38 s, f = 3.10443. Structure annealed in 39 s, f = 4.05622. Structure annealed in 39 s, f = 4.40154. Structure annealed in 39 s, f = 8.41451. Structure annealed in 39 s, f = 10.9624. Structure annealed in 39 s, f = 5.09060. Structure annealed in 39 s, f = 4.92408. Structure annealed in 39 s, f = 2.07254. Structure annealed in 39 s, f = 4.75728. Structure annealed in 39 s, f = 3.85091. Structure annealed in 39 s, f = 4.85386. Structure annealed in 39 s, f = 4.35046. Structure annealed in 39 s, f = 2.77322. Structure annealed in 39 s, f = 3.72005. Structure annealed in 39 s, f = 5.73711. Structure annealed in 39 s, f = 3.62219. Structure annealed in 39 s, f = 3.16500. Structure annealed in 39 s, f = 9.39701. Structure annealed in 38 s, f = 14.4194. Structure annealed in 39 s, f = 10.3641. Structure annealed in 39 s, f = 2.34783. Structure annealed in 39 s, f = 3.15398. Structure annealed in 39 s, f = 13.0324. Structure annealed in 39 s, f = 6.13472. Structure annealed in 39 s, f = 3.14573. Structure annealed in 39 s, f = 7.03052. Structure annealed in 39 s, f = 4.25451. Structure annealed in 39 s, f = 6.41152. Structure annealed in 39 s, f = 5.55619. Structure annealed in 39 s, f = 4.00130. Structure annealed in 39 s, f = 3.48193. Structure annealed in 39 s, f = 4.20716. Structure annealed in 39 s, f = 8.38454. Structure annealed in 39 s, f = 7.20992. Structure annealed in 39 s, f = 4.29653. Structure annealed in 39 s, f = 3.93408. Structure annealed in 39 s, f = 4.00115. Structure annealed in 39 s, f = 4.16250. Structure annealed in 39 s, f = 9.07034. Structure annealed in 39 s, f = 3.72052. Structure annealed in 39 s, f = 2.92156. Structure annealed in 39 s, f = 3.70628. Structure annealed in 39 s, f = 5.74035. 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 2.07 0 0.0080 0.19 1 7.4 0.22 0 0.3549 2.35 2 2.35 3 0.0096 0.31 0 7.0 0.14 0 0.3909 2.51 3 2.54 1 0.0090 0.22 0 7.6 0.17 0 0.5205 4.66 4 2.77 2 0.0089 0.22 0 8.1 0.19 0 0.3636 2.94 5 2.79 4 0.0096 0.27 2 8.9 0.22 0 0.3884 2.27 6 2.86 2 0.0088 0.23 0 7.8 0.15 0 0.3296 2.47 7 2.92 2 0.0092 0.23 4 8.5 0.29 0 0.3487 2.14 8 2.98 0 0.0084 0.18 3 8.2 0.29 0 0.4001 2.61 9 3.05 2 0.0091 0.22 2 8.9 0.28 0 0.4343 3.01 10 3.05 1 0.0082 0.23 4 8.2 0.29 0 0.3649 2.71 11 3.10 2 0.0087 0.21 1 8.1 0.22 0 0.3495 2.10 12 3.15 5 0.0124 0.41 0 7.9 0.19 0 0.4305 4.13 13 3.15 3 0.0085 0.25 4 9.2 0.23 0 0.3289 2.26 14 3.15 1 0.0094 0.20 0 8.3 0.15 0 0.4098 2.33 15 3.17 0 0.0085 0.19 1 8.4 0.24 0 0.4582 3.22 16 3.25 4 0.0102 0.31 5 9.0 0.29 0 0.3760 2.34 17 3.33 3 0.0101 0.22 1 8.9 0.24 0 0.3913 2.45 18 3.34 1 0.0091 0.29 0 8.2 0.18 0 0.4006 2.68 19 3.47 3 0.0107 0.27 1 10.2 0.20 0 0.4158 2.70 20 3.48 4 0.0102 0.24 1 8.7 0.23 0 0.3649 2.31 Ave 3.00 2 0.0093 0.24 2 8.4 0.22 0 0.3911 2.71 +/- 0.35 1 0.0010 0.05 2 0.7 0.05 0 0.0451 0.64 Min 2.07 0 0.0080 0.18 0 7.0 0.14 0 0.3289 2.10 Max 3.48 5 0.0124 0.41 5 10.2 0.29 0 0.5205 4.66 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 ------ --- --- --- --- 1 142 10 0 0 2 141 11 0 0 3 138 14 0 0 4 139 13 0 0 5 139 11 2 0 6 142 10 0 0 7 133 19 0 0 8 138 14 0 0 9 139 13 0 0 10 140 12 0 0 11 138 12 0 2 (GLU 125, GLU 425) 12 139 13 0 0 13 138 14 0 0 14 136 14 2 0 15 135 15 2 0 16 141 11 0 0 17 134 16 2 0 18 139 13 0 0 19 140 10 0 2 (ARG 123, ARG 423) 20 135 15 0 2 (ARG 124, ARG 424) all 91.0% 8.6% 0.3% 0.2% *** 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 18953 failed on node n0 (192.168.96.101) with exit status 1. ----------------------------------------------------------------------------- MPI_Recv: process in local group is dead (rank 8, comm 3) 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() forrtl: error (78): process killed (SIGTERM) forrtl: error (78): process killed (SIGTERM) LAM 7.2b1svn10112005/MPI 2 C++/ROMIO - Indiana University 06-Dec-2005 00:17:52