Warning: no access to tty (Bad file descriptor). Thus no job control in this shell. 06-Dec-2005 19:37:08 n-1<26408> ssi:boot:base:linear: booting n0 (wolf01) n-1<26408> ssi:boot:base:linear: booting n1 (wolf02) n-1<26408> ssi:boot:base:linear: booting n2 (wolf03) n-1<26408> ssi:boot:base:linear: booting n3 (wolf04) n-1<26408> ssi:boot:base:linear: booting n4 (wolf05) n-1<26408> ssi:boot:base:linear: booting n5 (wolf06) n-1<26408> ssi:boot:base:linear: booting n6 (wolf07) n-1<26408> ssi:boot:base:linear: booting n7 (wolf08) n-1<26408> ssi:boot:base:linear: booting n8 (wolf09) n-1<26408> ssi:boot:base:linear: booting n9 (wolf10) n-1<26408> ssi:boot:base:linear: booting n10 (wolf11) n-1<26408> ssi:boot:base:linear: booting n11 (wolf12) n-1<26408> ssi:boot:base:linear: booting n12 (wolf13) n-1<26408> 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=c13nob,n15nob,c13arb,fc12nob 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 : c13nob Proton list: znf42 - peakcheck: read prot znf42 unknown=skip Chemical shift list "znf42.prot" read, 1982 chemical shifts. - peakcheck: read peaks c13nob format= Peak list "c13nob.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 : n15nob Proton list: znf42 - peakcheck: read prot znf42 unknown=skip Chemical shift list "znf42.prot" read, 1982 chemical shifts. - peakcheck: read peaks n15nob format= Peak list "n15nob.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 : c13arb Proton list: znf42 - peakcheck: read prot znf42 unknown=skip Chemical shift list "znf42.prot" read, 1982 chemical shifts. - peakcheck: read peaks c13arb format= Peak list "c13arb.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 96 1.874 1.603 0.271 1 1 shift with spread larger than tolerance. - peakcheck: peak deviations Peak Dim Deviation Atom Residue 10234 1 -0.271 HG LEU 96 1 deviations larger than tolerance. ------------------------------------------------------------ Peak list : fc12nob Proton list: znf42 - peakcheck: read prot znf42 unknown=skip Chemical shift list "znf42.prot" read, 1982 chemical shifts. - peakcheck: read peaks fc12nob format= Peak list "fc12nob.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=c13nob,n15nob,c13arb,fc12nob constant=3.5E7 ,1.7E7,2.5E7,1.0E7 dref=4.2 - calibration: read prot znf42 unknown=warn Chemical shift list "znf42.prot" read, 1982 chemical shifts. - calibration: read peaks c13nob format= Peak list "c13nob.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, 1982 chemical shifts. - calibration: read peaks n15nob format= append Peak list "n15nob.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 c13arb format= append Peak list "c13arb.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, 1982 chemical shifts. - calibration: read peaks fc12nob format= append Peak list "fc12nob.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 39 s, f = 3.50750. Structure annealed in 39 s, f = 2.40823. Structure annealed in 39 s, f = 7.71395. Structure annealed in 41 s, f = 197.957. Structure annealed in 38 s, f = 3.77957. Structure annealed in 39 s, f = 8.78053. Structure annealed in 39 s, f = 9.16722. Structure annealed in 39 s, f = 7.86519. Structure annealed in 39 s, f = 2.96346. Structure annealed in 39 s, f = 2.53686. Structure annealed in 39 s, f = 5.79671. Structure annealed in 39 s, f = 3.50125. Structure annealed in 39 s, f = 2.88305. Structure annealed in 40 s, f = 3.46054. Structure annealed in 39 s, f = 3.97003. Structure annealed in 39 s, f = 3.02404. Structure annealed in 39 s, f = 3.48435. Structure annealed in 39 s, f = 6.25673. Structure annealed in 39 s, f = 5.06184. Structure annealed in 39 s, f = 3.68811. Structure annealed in 39 s, f = 4.37869. Structure annealed in 39 s, f = 7.68829. Structure annealed in 40 s, f = 101.441. Structure annealed in 41 s, f = 188.677. Structure annealed in 40 s, f = 7.12578. Structure annealed in 39 s, f = 7.00686. Structure annealed in 41 s, f = 336.067. Structure annealed in 39 s, f = 7.49571. Structure annealed in 39 s, f = 2.62638. Structure annealed in 39 s, f = 4.48462. Structure annealed in 39 s, f = 6.96157. Structure annealed in 39 s, f = 3.01477. Structure annealed in 39 s, f = 6.50800. Structure annealed in 39 s, f = 8.27333. Structure annealed in 39 s, f = 4.18769. Structure annealed in 40 s, f = 102.279. Structure annealed in 40 s, f = 103.132. Structure annealed in 40 s, f = 6.36254. Structure annealed in 39 s, f = 8.64106. Structure annealed in 39 s, f = 6.92685. Structure annealed in 39 s, f = 3.00493. Structure annealed in 39 s, f = 2.82898. Structure annealed in 39 s, f = 2.88623. Structure annealed in 39 s, f = 4.15152. Structure annealed in 39 s, f = 3.97333. Structure annealed in 40 s, f = 5.16088. Structure annealed in 39 s, f = 3.73314. Structure annealed in 40 s, f = 6.34399. Structure annealed in 39 s, f = 3.05315. Structure annealed in 40 s, f = 3.20725. Structure annealed in 38 s, f = 2.58339. Structure annealed in 39 s, f = 2.82302. Structure annealed in 39 s, f = 3.89535. Structure annealed in 41 s, f = 281.478. Structure annealed in 39 s, f = 3.51184. Structure annealed in 39 s, f = 3.15080. Structure annealed in 39 s, f = 3.90668. Structure annealed in 39 s, f = 3.90727. Structure annealed in 39 s, f = 3.67344. Structure annealed in 39 s, f = 4.04289. Structure annealed in 39 s, f = 4.37978. Structure annealed in 39 s, f = 3.86499. Structure annealed in 39 s, f = 11.9591. Structure annealed in 39 s, f = 4.52130. Structure annealed in 40 s, f = 143.318. Structure annealed in 39 s, f = 3.50189. Structure annealed in 39 s, f = 2.22080. Structure annealed in 39 s, f = 1.83100. Structure annealed in 39 s, f = 4.27413. Structure annealed in 39 s, f = 3.20329. Structure annealed in 40 s, f = 281.053. Structure annealed in 40 s, f = 4.79953. Structure annealed in 39 s, f = 2.74644. Structure annealed in 40 s, f = 7.82133. Structure annealed in 39 s, f = 6.49108. Structure annealed in 39 s, f = 3.13423. Structure annealed in 39 s, f = 3.31997. Structure annealed in 39 s, f = 3.03157. Structure annealed in 39 s, f = 3.65456. Structure annealed in 39 s, f = 3.12096. Structure annealed in 41 s, f = 294.834. Structure annealed in 39 s, f = 3.29935. Structure annealed in 39 s, f = 2.56619. Structure annealed in 39 s, f = 9.02013. Structure annealed in 39 s, f = 9.46879. Structure annealed in 39 s, f = 3.59453. Structure annealed in 39 s, f = 4.17133. Structure annealed in 39 s, f = 3.11534. Structure annealed in 39 s, f = 2.94293. Structure annealed in 39 s, f = 11.6878. Structure annealed in 39 s, f = 7.56650. Structure annealed in 39 s, f = 6.05076. Structure annealed in 41 s, f = 273.745. Structure annealed in 39 s, f = 4.02301. Structure annealed in 39 s, f = 3.29513. Structure annealed in 39 s, f = 7.82480. Structure annealed in 40 s, f = 12.1418. Structure annealed in 41 s, f = 303.363. Structure annealed in 39 s, f = 3.23177. Structure annealed in 39 s, f = 4.45466. 100 structures finished in 165 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 1.83 1 0.0071 0.25 1 6.9 0.20 0 0.2841 2.15 2 2.22 0 0.0073 0.18 2 7.5 0.22 0 0.3261 2.12 3 2.41 1 0.0086 0.37 1 6.4 0.21 0 0.3673 2.60 4 2.54 2 0.0076 0.21 0 7.4 0.19 0 0.3644 2.62 5 2.57 2 0.0078 0.22 0 6.7 0.16 0 0.2833 1.83 6 2.58 1 0.0073 0.29 1 7.2 0.24 0 0.2644 2.05 7 2.63 1 0.0081 0.23 1 8.4 0.23 0 0.4026 2.74 8 2.75 3 0.0098 0.38 0 7.1 0.16 0 0.3375 2.52 9 2.82 1 0.0088 0.23 2 8.0 0.29 0 0.2668 1.52 10 2.83 3 0.0089 0.26 0 7.1 0.16 0 0.4061 2.35 11 2.88 2 0.0091 0.22 4 8.8 0.29 0 0.3651 2.09 12 2.89 1 0.0091 0.22 2 9.4 0.29 0 0.4381 2.67 13 2.94 0 0.0073 0.18 1 7.2 0.21 0 0.3320 2.46 14 2.96 3 0.0095 0.31 1 7.9 0.21 0 0.4125 2.35 15 3.01 1 0.0078 0.21 3 7.7 0.37 0 0.4026 3.22 16 3.02 0 0.0081 0.18 3 9.7 0.29 0 0.5020 3.34 17 3.02 1 0.0072 0.21 1 6.8 0.21 0 0.2967 1.99 18 3.03 1 0.0084 0.21 3 8.0 0.29 0 0.3586 2.15 19 3.05 1 0.0077 0.28 0 7.7 0.19 0 0.3231 1.61 20 3.12 3 0.0094 0.33 2 8.6 0.29 0 0.3933 2.55 Ave 2.75 1 0.0082 0.25 1 7.7 0.23 0 0.3563 2.35 +/- 0.32 1 0.0008 0.06 1 0.9 0.05 0 0.0604 0.45 Min 1.83 0 0.0071 0.18 0 6.4 0.16 0 0.2644 1.52 Max 3.12 3 0.0098 0.38 4 9.7 0.37 0 0.5020 3.34 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 2 137 15 0 0 3 137 15 0 0 4 137 13 1 1 (SER 336) 5 142 10 0 0 6 139 13 0 0 7 137 15 0 0 8 138 12 2 0 9 142 10 0 0 10 140 12 0 0 11 135 15 2 0 12 135 17 0 0 13 139 13 0 0 forrtl: Stale NFS file handle forrtl: severe (38): error during write, unit 41, file /user/francis/znf42/8cyana/118a/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 (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 (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() ----------------------------------------------------------------------------- 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 26490 failed on node n0 (192.168.96.101) with exit status 28. ----------------------------------------------------------------------------- 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 19:40:26