Warning: no access to tty (Bad file descriptor). Thus no job control in this shell. 06-Dec-2005 23:51:53 n-1<28980> ssi:boot:base:linear: booting n0 (wolf01) n-1<28980> ssi:boot:base:linear: booting n1 (wolf02) n-1<28980> ssi:boot:base:linear: booting n2 (wolf03) n-1<28980> ssi:boot:base:linear: booting n3 (wolf04) n-1<28980> ssi:boot:base:linear: booting n4 (wolf05) n-1<28980> ssi:boot:base:linear: booting n5 (wolf06) n-1<28980> ssi:boot:base:linear: booting n6 (wolf07) n-1<28980> ssi:boot:base:linear: booting n7 (wolf08) n-1<28980> ssi:boot:base:linear: booting n8 (wolf09) n-1<28980> ssi:boot:base:linear: booting n9 (wolf10) n-1<28980> ssi:boot:base:linear: booting n10 (wolf11) n-1<28980> ssi:boot:base:linear: booting n11 (wolf12) n-1<28980> ssi:boot:base:linear: booting n12 (wolf13) n-1<28980> 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, 3180 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 3180 0.000 0.002 0.032 0.009 1 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 HB3 LEU 89 1.333 1.333 0.032 19 1 shift with spread larger than tolerance. - peakcheck: peak deviations Peak Dim Deviation Atom Residue 3779 1 0.032 HB3 LEU 89 1 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, 1271 peaks, 1105 assignments. - peakcheck: peaks fit Deviations from chemical shift list: Dim Peaks Median Average Maximum RMSD Number Tolerance 1 1105 0.002 0.002 0.030 0.011 0 0.030 2 1269 0.000 0.000 0.011 0.001 0 0.030 3 1269 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, 142 assignments. - peakcheck: peaks fit Deviations from chemical shift list: Dim Peaks Median Average Maximum RMSD Number Tolerance 1 142 -0.005 -0.002 0.029 0.016 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=3.0E7,1.7 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, 3180 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=3.0E7 Calibration constant for peak list 1: 3.00E+07 Upper limit set for 3483 peaks. - calibration: caltab peaks Distance bounds: -2.99 A: 330 9.5% 3.00-3.99 A: 772 22.2% 4.00-4.99 A: 1385 39.8% 5.00-5.99 A: 994 28.5% 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, 1271 peaks, 1105 assignments. - calibration: peaks select "** list=2" 1271 of 4754 peaks, 1271 of 4754 assignments selected. - calibration: peaks set volume=abs(volume) Volume of 1271 peaks set. - calibration: peaks simplecal constant=1.7E7 Calibration constant for peak list 2: 1.70E+07 Upper limit set for 1271 peaks. - calibration: caltab peaks Distance bounds: -2.99 A: 74 5.8% 3.00-3.99 A: 227 17.9% 4.00-4.99 A: 491 38.6% 5.00-5.99 A: 479 37.7% 6.00- A: 0 0.0% All: 1271 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 5046 peaks, 292 of 5046 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, 142 assignments. - calibration: peaks select "** list=4" 233 of 5279 peaks, 233 of 5279 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 ** 5279 of 5279 peaks, 5279 of 5279 assignments selected. - znf42: peaks calibrate ** simple 4171 upper limits added, 3/592 at lower/upper bound, average 4.52 A. - znf42: write upl znf42-in.upl Distance constraint file "znf42-in.upl" written, 4171 upper limits, 4171 assignments. - znf42: distance modify Number of modified constraints: 2177 - znf42: write upl znf42.upl Distance constraint file "znf42.upl" written, 2177 upper limits, 2177 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, 2177 upper limits, 2177 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 = 3.97554. Structure annealed in 39 s, f = 8.02394. Structure annealed in 39 s, f = 12.2984. Structure annealed in 39 s, f = 8.24400. Structure annealed in 39 s, f = 7.58035. Structure annealed in 39 s, f = 12.4140. Structure annealed in 39 s, f = 4.63291. Structure annealed in 39 s, f = 8.69576. Structure annealed in 39 s, f = 3.58340. Structure annealed in 39 s, f = 4.67523. Structure annealed in 39 s, f = 7.06045. Structure annealed in 41 s, f = 172.526. Structure annealed in 39 s, f = 13.8838. Structure annealed in 39 s, f = 2.18055. Structure annealed in 39 s, f = 2.07626. Structure annealed in 39 s, f = 5.56854. Structure annealed in 39 s, f = 3.05953. Structure annealed in 39 s, f = 5.02933. Structure annealed in 39 s, f = 1.64649. Structure annealed in 39 s, f = 2.09012. Structure annealed in 39 s, f = 7.13347. Structure annealed in 39 s, f = 2.78306. Structure annealed in 39 s, f = 5.93037. Structure annealed in 39 s, f = 1.87715. Structure annealed in 39 s, f = 6.56615. Structure annealed in 38 s, f = 2.14983. Structure annealed in 39 s, f = 1.72476. Structure annealed in 39 s, f = 3.40508. Structure annealed in 38 s, f = 2.44753. Structure annealed in 39 s, f = 22.2315. Structure annealed in 39 s, f = 45.9699. Structure annealed in 39 s, f = 3.13840. Structure annealed in 39 s, f = 2.38386. Structure annealed in 39 s, f = 5.64202. Structure annealed in 39 s, f = 11.7555. Structure annealed in 39 s, f = 2.54151. Structure annealed in 39 s, f = 12.5254. Structure annealed in 39 s, f = 1.80541. Structure annealed in 39 s, f = 5.08358. Structure annealed in 39 s, f = 2.68036. Structure annealed in 39 s, f = 2.05812. Structure annealed in 39 s, f = 6.73761. Structure annealed in 39 s, f = 7.95553. Structure annealed in 39 s, f = 3.40715. Structure annealed in 39 s, f = 2.57768. Structure annealed in 39 s, f = 7.61643. Structure annealed in 39 s, f = 3.33280. Structure annealed in 39 s, f = 3.19705. Structure annealed in 39 s, f = 6.18095. Structure annealed in 42 s, f = 321.599. Structure annealed in 38 s, f = 4.96615. Structure annealed in 39 s, f = 8.67220. Structure annealed in 39 s, f = 6.49558. Structure annealed in 39 s, f = 2.54447. Structure annealed in 39 s, f = 109.172. Structure annealed in 38 s, f = 3.42402. Structure annealed in 39 s, f = 6.91945. Structure annealed in 39 s, f = 3.51457. Structure annealed in 39 s, f = 11.4649. Structure annealed in 39 s, f = 3.75097. Structure annealed in 39 s, f = 9.00355. Structure annealed in 39 s, f = 6.28392. Structure annealed in 39 s, f = 3.68448. Structure annealed in 39 s, f = 5.12258. Structure annealed in 39 s, f = 2.28538. Structure annealed in 39 s, f = 6.45962. Structure annealed in 39 s, f = 11.7602. Structure annealed in 39 s, f = 4.04337. Structure annealed in 39 s, f = 3.41998. Structure annealed in 39 s, f = 3.26598. Structure annealed in 39 s, f = 5.56807. Structure annealed in 39 s, f = 6.55346. Structure annealed in 39 s, f = 2.71731. Structure annealed in 40 s, f = 4.87117. Structure annealed in 39 s, f = 5.36157. Structure annealed in 39 s, f = 9.61496. Structure annealed in 38 s, f = 6.34855. Structure annealed in 39 s, f = 2.07185. Structure annealed in 38 s, f = 5.60690. Structure annealed in 39 s, f = 2.52064. Structure annealed in 39 s, f = 3.63082. Structure annealed in 39 s, f = 8.55534. Structure annealed in 39 s, f = 4.48992. Structure annealed in 39 s, f = 7.74974. Structure annealed in 39 s, f = 4.55798. Structure annealed in 39 s, f = 4.55473. Structure annealed in 38 s, f = 5.92305. Structure annealed in 39 s, f = 1.80920. Structure annealed in 39 s, f = 2.67928. Structure annealed in 39 s, f = 4.22993. Structure annealed in 39 s, f = 2.88071. Structure annealed in 39 s, f = 23.2081. Structure annealed in 39 s, f = 3.02270. Structure annealed in 39 s, f = 2.43905. Structure annealed in 39 s, f = 2.07374. Structure annealed in 39 s, f = 2.23056. Structure annealed in 39 s, f = 2.73116. Structure annealed in 39 s, f = 6.77540. Structure annealed in 39 s, f = 2.54534. Structure annealed in 39 s, f = 6.49889. 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 1.65 1 0.0067 0.30 1 5.5 0.22 0 0.3508 2.64 2 1.72 0 0.0065 0.19 1 6.1 0.24 0 0.3757 3.61 3 1.81 0 0.0067 0.16 2 7.8 0.25 0 0.3444 2.85 4 1.81 1 0.0076 0.25 0 7.0 0.18 0 0.4232 3.66 5 1.88 0 0.0072 0.17 2 7.1 0.29 0 0.3895 4.19 6 2.06 2 0.0078 0.30 0 6.9 0.15 0 0.4137 2.65 7 2.07 0 0.0071 0.20 4 6.7 0.29 0 0.2750 2.12 8 2.07 0 0.0081 0.20 2 7.3 0.29 0 0.3321 2.81 9 2.08 0 0.0084 0.20 1 7.6 0.22 0 0.4307 2.68 10 2.09 1 0.0072 0.27 0 6.5 0.14 0 0.4536 3.60 11 2.15 3 0.0081 0.25 3 7.1 0.29 0 0.3048 2.80 12 2.18 0 0.0068 0.17 2 7.0 0.29 0 0.3138 2.33 13 2.23 1 0.0080 0.22 2 7.3 0.29 0 0.4100 3.67 14 2.29 1 0.0092 0.39 0 6.8 0.17 0 0.3871 2.61 15 2.38 0 0.0089 0.18 2 7.7 0.25 0 0.4171 2.95 16 2.44 0 0.0081 0.18 2 7.4 0.29 0 0.3224 1.91 17 2.45 0 0.0077 0.19 3 7.5 0.28 0 0.3748 2.68 18 2.52 2 0.0082 0.33 2 7.6 0.28 0 0.3721 3.28 19 2.54 1 0.0087 0.21 4 8.3 0.29 0 0.3387 2.66 20 2.54 4 0.0102 0.40 1 7.3 0.21 0 0.5618 4.68 Ave 2.15 1 0.0078 0.24 2 7.1 0.25 0 0.3796 3.02 +/- 0.27 1 0.0009 0.07 1 0.6 0.05 0 0.0621 0.68 Min 1.65 0 0.0065 0.16 0 5.5 0.14 0 0.2750 1.91 Max 2.54 4 0.0102 0.40 4 8.3 0.29 0 0.5618 4.68 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 ------ --- --- --- --- 1 138 12 0 2 (ARG 124, ARG 424) 2 139 13 0 0 forrtl: Stale NFS file handle forrtl: severe (38): error during write, unit 41, file /user/francis/znf42/8cyana/120e/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 29062 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() MPI_Recv: process in local group is dead (rank 6, comm 3) 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): - MPI_Bcast() Rank (12, 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 23:55:09