Warning: no access to tty (Bad file descriptor). Thus no job control in this shell. 30-Nov-2005 17:38:42 n-1<5587> ssi:boot:base:linear: booting n0 (wolf01) n-1<5587> ssi:boot:base:linear: booting n1 (wolf02) n-1<5587> ssi:boot:base:linear: booting n2 (wolf03) n-1<5587> ssi:boot:base:linear: booting n3 (wolf04) n-1<5587> ssi:boot:base:linear: booting n4 (wolf05) n-1<5587> ssi:boot:base:linear: booting n5 (wolf06) n-1<5587> ssi:boot:base:linear: booting n6 (wolf07) n-1<5587> ssi:boot:base:linear: booting n7 (wolf08) n-1<5587> ssi:boot:base:linear: booting n8 (wolf09) n-1<5587> ssi:boot:base:linear: booting n9 (wolf10) n-1<5587> ssi:boot:base:linear: booting n10 (wolf11) n-1<5587> ssi:boot:base:linear: booting n11 (wolf12) n-1<5587> ssi:boot:base:linear: booting n12 (wolf13) n-1<5587> 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, 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, 3485 peaks, 3082 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 3082 0.000 0.002 0.131 0.009 1 0.030 2 3410 0.000 0.000 0.027 0.003 0 0.030 3 3410 0.000 0.001 0.297 0.027 0 0.450 - peakcheck: atom shift check Atom Residue Shift Median Deviation Peaks QD PHE 92 6.917 6.925 0.131 10 1 shift with spread larger than tolerance. - peakcheck: peak deviations Peak Dim Deviation Atom Residue 3240 1 0.131 QD PHE 92 1 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, 1273 peaks, 1110 assignments. - peakcheck: peaks fit Deviations from chemical shift list: Dim Peaks Median Average Maximum RMSD Number Tolerance 1 1110 0.002 0.002 0.030 0.011 1 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 QD1 LEU 118 0.930 0.902 0.030 3 1 shift with spread larger than tolerance. - peakcheck: peak deviations Peak Dim Deviation Atom Residue 1240 1 -0.030 QD1 LEU 118 1 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, 225 peaks, 150 assignments. - peakcheck: peaks fit Deviations from chemical shift list: Dim Peaks Median Average Maximum RMSD Number Tolerance 1 150 0.000 -0.001 0.029 0.016 0 0.030 2 169 0.000 -0.001 0.014 0.005 0 0.030 3 169 0.000 -0.005 0.297 0.034 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, 3485 peaks, 3082 assignments. - calibration: peaks select "** list=1" 3485 of 3485 peaks, 3485 of 3485 assignments selected. - calibration: peaks set volume=abs(volume) Volume of 3485 peaks set. - calibration: peaks simplecal constant=3.0E7 Calibration constant for peak list 1: 3.00E+07 Upper limit set for 3485 peaks. - calibration: caltab peaks Distance bounds: -2.99 A: 330 9.5% 3.00-3.99 A: 764 21.9% 4.00-4.99 A: 1365 39.2% 5.00-5.99 A: 1024 29.4% 6.00- A: 0 0.0% All: 3485 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, 1273 peaks, 1110 assignments. - calibration: peaks select "** list=2" 1273 of 4758 peaks, 1273 of 4758 assignments selected. - calibration: peaks set volume=abs(volume) Volume of 1273 peaks set. - calibration: peaks simplecal constant=1.2E7 Calibration constant for peak list 2: 1.20E+07 Upper limit set for 1273 peaks. - calibration: caltab peaks Distance bounds: -2.99 A: 93 7.3% 3.00-3.99 A: 339 26.6% 4.00-4.99 A: 492 38.6% 5.00-5.99 A: 347 27.3% 6.00- A: 0 0.0% All: 1273 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 5039 peaks, 281 of 5039 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, 225 peaks, 150 assignments. - calibration: peaks select "** list=4" 225 of 5264 peaks, 225 of 5264 assignments selected. - calibration: peaks set volume=abs(volume) Volume of 225 peaks set. - calibration: peaks simplecal constant=1.0E7 Calibration constant for peak list 4: 1.00E+07 Upper limit set for 225 peaks. - calibration: caltab peaks Distance bounds: -2.99 A: 2 0.9% 3.00-3.99 A: 48 21.3% 4.00-4.99 A: 156 69.3% 5.00-5.99 A: 19 8.4% 6.00- A: 0 0.0% All: 225 100.0% - calibration: peaks select ** 5264 of 5264 peaks, 5264 of 5264 assignments selected. - znf42: peaks calibrate ** simple 4083 upper limits added, 9/503 at lower/upper bound, average 4.46 A. - znf42: write upl znf42-in.upl Distance constraint file "znf42-in.upl" written, 4083 upper limits, 4083 assignments. - znf42: distance modify Number of modified constraints: 2152 - znf42: write upl znf42.upl Distance constraint file "znf42.upl" written, 2152 upper limits, 2152 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, 2152 upper limits, 2152 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 39 s, f = 15.5384. Structure annealed in 39 s, f = 12.6873. Structure annealed in 40 s, f = 26.0768. Structure annealed in 39 s, f = 16.1294. Structure annealed in 39 s, f = 13.6748. Structure annealed in 39 s, f = 15.1135. Structure annealed in 39 s, f = 15.4897. Structure annealed in 39 s, f = 22.8663. Structure annealed in 41 s, f = 391.558. Structure annealed in 39 s, f = 16.6290. Structure annealed in 40 s, f = 20.4956. Structure annealed in 39 s, f = 26.7038. Structure annealed in 40 s, f = 223.428. Structure annealed in 39 s, f = 12.8167. Structure annealed in 39 s, f = 12.4980. Structure annealed in 39 s, f = 16.5370. Structure annealed in 39 s, f = 10.8055. Structure annealed in 39 s, f = 11.8190. Structure annealed in 39 s, f = 13.3969. Structure annealed in 39 s, f = 11.2956. Structure annealed in 39 s, f = 14.9080. Structure annealed in 39 s, f = 18.2814. Structure annealed in 39 s, f = 11.0910. Structure annealed in 39 s, f = 16.1603. Structure annealed in 39 s, f = 13.4461. Structure annealed in 39 s, f = 15.0138. Structure annealed in 39 s, f = 13.6346. Structure annealed in 39 s, f = 17.0655. Structure annealed in 39 s, f = 14.8604. Structure annealed in 39 s, f = 13.9755. Structure annealed in 39 s, f = 15.3521. Structure annealed in 40 s, f = 11.8031. Structure annealed in 39 s, f = 11.2819. Structure annealed in 40 s, f = 12.3218. Structure annealed in 39 s, f = 18.6839. Structure annealed in 39 s, f = 16.5246. Structure annealed in 39 s, f = 14.5534. Structure annealed in 39 s, f = 12.3720. Structure annealed in 40 s, f = 14.5132. Structure annealed in 39 s, f = 16.6973. Structure annealed in 39 s, f = 15.4676. Structure annealed in 39 s, f = 16.7029. Structure annealed in 39 s, f = 14.6138. Structure annealed in 39 s, f = 19.3497. Structure annealed in 40 s, f = 16.8448. Structure annealed in 39 s, f = 12.6422. Structure annealed in 40 s, f = 13.2045. Structure annealed in 39 s, f = 13.0684. Structure annealed in 40 s, f = 14.2924. Structure annealed in 39 s, f = 11.1704. Structure annealed in 40 s, f = 16.2106. Structure annealed in 39 s, f = 12.1738. Structure annealed in 39 s, f = 14.3150. Structure annealed in 39 s, f = 35.6162. Structure annealed in 39 s, f = 16.3011. Structure annealed in 40 s, f = 16.5232. Structure annealed in 41 s, f = 333.973. Structure annealed in 40 s, f = 19.6896. Structure annealed in 39 s, f = 13.2620. Structure annealed in 39 s, f = 14.4913. Structure annealed in 40 s, f = 13.1242. Structure annealed in 39 s, f = 16.3010. Structure annealed in 39 s, f = 13.4164. Structure annealed in 39 s, f = 15.1098. Structure annealed in 39 s, f = 12.9108. Structure annealed in 40 s, f = 59.8669. Structure annealed in 39 s, f = 14.1637. Structure annealed in 39 s, f = 17.7616. Structure annealed in 39 s, f = 23.2435. Structure annealed in 39 s, f = 13.6896. Structure annealed in 40 s, f = 11.0077. Structure annealed in 40 s, f = 13.9705. Structure annealed in 40 s, f = 13.2411. Structure annealed in 39 s, f = 11.8508. Structure annealed in 39 s, f = 16.6652. Structure annealed in 39 s, f = 13.0267. Structure annealed in 39 s, f = 12.7831. Structure annealed in 39 s, f = 12.2080. Structure annealed in 39 s, f = 15.0045. Structure annealed in 39 s, f = 13.3364. Structure annealed in 40 s, f = 19.0433. Structure annealed in 39 s, f = 24.9573. Structure annealed in 40 s, f = 19.7044. Structure annealed in 39 s, f = 14.9228. Structure annealed in 39 s, f = 19.7177. Structure annealed in 40 s, f = 14.9100. Structure annealed in 39 s, f = 13.6928. Structure annealed in 39 s, f = 11.1910. Structure annealed in 39 s, f = 13.9145. Structure annealed in 41 s, f = 201.653. Structure annealed in 39 s, f = 13.6864. Structure annealed in 40 s, f = 19.2417. Structure annealed in 40 s, f = 16.7892. Structure annealed in 39 s, f = 15.3772. Structure annealed in 40 s, f = 14.9709. Structure annealed in 39 s, f = 12.9652. Structure annealed in 39 s, f = 17.3841. Structure annealed in 40 s, f = 15.2468. Structure annealed in 39 s, f = 17.8974. Structure annealed in 40 s, f = 18.3671. 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 10.81 38 0.0261 0.77 7 15.9 0.33 1 0.9443 5.28 2 11.01 39 0.0262 0.81 8 16.7 0.30 2 1.0980 6.40 3 11.09 39 0.0279 0.82 4 15.9 0.30 1 1.0094 5.04 4 11.17 37 0.0258 0.78 8 18.0 0.24 1 0.9715 5.06 5 11.19 39 0.0262 0.75 8 16.6 0.28 1 1.0555 6.48 6 11.28 36 0.0251 0.75 5 16.0 0.28 2 1.0678 6.62 7 11.30 33 0.0268 0.82 5 18.1 0.27 2 0.9132 5.26 8 11.80 37 0.0274 0.96 9 18.7 0.28 4 1.1150 5.84 9 11.82 39 0.0273 0.77 4 17.2 0.38 0 0.8816 4.37 10 11.85 42 0.0275 0.68 7 18.1 0.29 0 0.9226 4.71 11 12.17 37 0.0287 0.66 4 16.8 0.28 1 1.0683 5.64 12 12.21 32 0.0256 0.80 9 18.5 0.28 5 1.1741 6.46 13 12.32 45 0.0276 0.61 6 17.6 0.30 0 0.9721 4.41 14 12.37 31 0.0279 0.89 8 18.5 0.29 2 0.9843 5.74 15 12.50 39 0.0283 0.94 9 19.9 0.40 5 1.2464 6.10 16 12.64 39 0.0291 0.75 4 19.0 0.31 2 1.1439 7.17 17 12.69 39 0.0269 0.81 6 19.2 0.28 1 1.0971 5.18 18 12.78 38 0.0265 0.91 11 18.6 0.41 2 0.9998 6.25 19 12.82 36 0.0281 0.95 8 17.2 0.40 5 1.2140 6.56 20 12.91 39 0.0268 0.75 10 19.5 0.34 3 1.1424 6.15 Ave 11.94 38 0.0271 0.80 7 17.8 0.31 2 1.0511 5.74 +/- 0.68 3 0.0011 0.09 2 1.2 0.05 2 0.1007 0.77 Min 10.81 31 0.0251 0.61 4 15.9 0.24 0 0.8816 4.37 Max 12.91 45 0.0291 0.96 11 19.9 0.41 5 1.2464 7.17 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 ------ --- --- --- --- 1 137 15 0 0 2 138 14 0 0 3 136 16 0 0 4 137 14 1 0 5 139 13 0 0 6 136 12 2 2 (ASP 37, ASP 337) 7 136 16 0 0 8 139 11 2 0 9 136 13 3 0 10 136 14 2 0 11 137 15 0 0 12 137 13 2 0 13 137 15 0 0 forrtl: Stale NFS file handle forrtl: severe (38): error during write, unit 41, file /user/francis/znf42/8cyana/111a/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 5669 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 30-Nov-2005 17:41:59