Warning: no access to tty (Bad file descriptor). Thus no job control in this shell. 21-Dec-2005 13:23:11 n-1<21898> ssi:boot:base:linear: booting n0 (wolf01) n-1<21898> ssi:boot:base:linear: booting n1 (wolf02) n-1<21898> ssi:boot:base:linear: booting n2 (wolf03) n-1<21898> ssi:boot:base:linear: booting n3 (wolf04) n-1<21898> ssi:boot:base:linear: booting n4 (wolf05) n-1<21898> ssi:boot:base:linear: booting n5 (wolf06) n-1<21898> ssi:boot:base:linear: booting n6 (wolf07) n-1<21898> ssi:boot:base:linear: booting n7 (wolf08) n-1<21898> ssi:boot:base:linear: booting n8 (wolf09) n-1<21898> ssi:boot:base:linear: booting n9 (wolf10) n-1<21898> ssi:boot:base:linear: booting n10 (wolf11) n-1<21898> ssi:boot:base:linear: booting n11 (wolf12) n-1<21898> ssi:boot:base:linear: booting n12 (wolf13) n-1<21898> 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: finalstereo 125 stereospecific assignments defined. - znf42: peakcheck peaks=c13no,n15no,c13ar,fc12no prot=znf42 ------------------------------------------------------------ Proton list: znf42 - peakcheck: read prot znf42 unknown=warn Chemical shift list "znf42.prot" read, 1984 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, 1984 chemical shifts. - peakcheck: read peaks c13no format= Peak list "c13no.peaks" read, 3489 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 3485 0.000 0.000 0.026 0.002 0 0.030 3 3485 0.000 -0.001 0.297 0.025 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, 1984 chemical shifts. - peakcheck: read peaks n15no format= Peak list "n15no.peaks" read, 1274 peaks, 1101 assignments. - peakcheck: peaks fit Deviations from chemical shift list: Dim Peaks Median Average Maximum RMSD Number Tolerance 1 1101 0.002 0.002 0.030 0.011 0 0.030 2 1272 0.000 0.000 0.011 0.001 0 0.030 3 1272 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, 1984 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 0.006 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, 1984 chemical shifts. - peakcheck: read peaks fc12no format= Peak list "fc12no.peaks" read, 233 peaks, 143 assignments. - peakcheck: peaks fit Deviations from chemical shift list: Dim Peaks Median Average Maximum RMSD Number Tolerance 1 143 -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=3.5E7,1.7 E7,2.5E7,1.0E7 dref=4.2 - calibration: read prot znf42 unknown=warn Chemical shift list "znf42.prot" read, 1984 chemical shifts. - calibration: read peaks c13no format= Peak list "c13no.peaks" read, 3489 peaks, 3185 assignments. - calibration: peaks select "** list=1" 3489 of 3489 peaks, 3489 of 3489 assignments selected. - calibration: peaks set volume=abs(volume) Volume of 3489 peaks set. - calibration: peaks simplecal constant=3.5E7 Calibration constant for peak list 1: 3.50E+07 Upper limit set for 3489 peaks. - calibration: caltab peaks Distance bounds: -2.99 A: 298 8.5% 3.00-3.99 A: 680 19.5% 4.00-4.99 A: 1373 39.4% 5.00-5.99 A: 1138 32.6% 6.00- A: 0 0.0% All: 3489 100.0% - calibration: read prot znf42 unknown=warn append Chemical shift list "znf42.prot" read, 1984 chemical shifts. - calibration: read peaks n15no format= append Peak list "n15no.peaks" read, 1274 peaks, 1101 assignments. - calibration: peaks select "** list=2" 1274 of 4763 peaks, 1274 of 4763 assignments selected. - calibration: peaks set volume=abs(volume) Volume of 1274 peaks set. - calibration: peaks simplecal constant=1.7E7 Calibration constant for peak list 2: 1.70E+07 Upper limit set for 1274 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: 493 38.7% 5.00-5.99 A: 480 37.7% 6.00- A: 0 0.0% All: 1274 100.0% - calibration: read prot znf42 unknown=warn append Chemical shift list "znf42.prot" read, 1984 chemical shifts. - calibration: read peaks c13ar format= append Peak list "c13ar.peaks" read, 292 peaks, 238 assignments. - calibration: peaks select "** list=3" 292 of 5055 peaks, 292 of 5055 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, 1984 chemical shifts. - calibration: read peaks fc12no format= append Peak list "fc12no.peaks" read, 233 peaks, 143 assignments. - calibration: peaks select "** list=4" 233 of 5288 peaks, 233 of 5288 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 ** 5288 of 5288 peaks, 5288 of 5288 assignments selected. - znf42: peaks calibrate ** simple 4172 upper limits added, 2/691 at lower/upper bound, average 4.58 A. - znf42: write upl znf42-in.upl Distance constraint file "znf42-in.upl" written, 4172 upper limits, 4172 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, 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 = 4.80200. Structure annealed in 38 s, f = 9.95424. Structure annealed in 38 s, f = 6.46939. Structure annealed in 38 s, f = 8.78368. Structure annealed in 39 s, f = 121.507. Structure annealed in 38 s, f = 4.19465. Structure annealed in 39 s, f = 3.84307. Structure annealed in 38 s, f = 4.91087. Structure annealed in 38 s, f = 3.47294. Structure annealed in 38 s, f = 7.87170. Structure annealed in 39 s, f = 111.491. Structure annealed in 38 s, f = 3.72979. Structure annealed in 39 s, f = 4.92955. Structure annealed in 38 s, f = 4.45148. Structure annealed in 38 s, f = 3.59956. Structure annealed in 38 s, f = 8.39766. Structure annealed in 39 s, f = 9.09600. Structure annealed in 38 s, f = 8.47984. Structure annealed in 38 s, f = 3.18200. Structure annealed in 39 s, f = 4.40247. Structure annealed in 38 s, f = 5.30482. Structure annealed in 39 s, f = 15.2613. Structure annealed in 38 s, f = 4.14805. Structure annealed in 38 s, f = 3.04051. Structure annealed in 38 s, f = 7.66744. Structure annealed in 38 s, f = 7.33986. Structure annealed in 38 s, f = 8.26953. Structure annealed in 38 s, f = 4.07483. Structure annealed in 39 s, f = 8.07882. Structure annealed in 38 s, f = 8.96106. Structure annealed in 39 s, f = 4.74389. Structure annealed in 38 s, f = 4.57761. Structure annealed in 38 s, f = 3.18164. Structure annealed in 38 s, f = 3.96146. Structure annealed in 39 s, f = 3.87425. Structure annealed in 38 s, f = 3.95666. Structure annealed in 39 s, f = 46.3142. Structure annealed in 39 s, f = 3.46456. Structure annealed in 41 s, f = 459.457. Structure annealed in 38 s, f = 3.83039. Structure annealed in 38 s, f = 4.24018. Structure annealed in 38 s, f = 8.56977. Structure annealed in 38 s, f = 4.81898. Structure annealed in 38 s, f = 10.2256. Structure annealed in 40 s, f = 309.478. Structure annealed in 38 s, f = 3.53899. Structure annealed in 38 s, f = 4.33298. Structure annealed in 38 s, f = 7.30938. Structure annealed in 38 s, f = 5.60830. Structure annealed in 38 s, f = 10.1167. Structure annealed in 38 s, f = 8.11995. Structure annealed in 38 s, f = 8.21239. Structure annealed in 38 s, f = 2.54823. Structure annealed in 38 s, f = 3.67606. Structure annealed in 38 s, f = 3.13749. Structure annealed in 38 s, f = 3.74401. Structure annealed in 38 s, f = 15.3503. Structure annealed in 38 s, f = 3.25955. Structure annealed in 41 s, f = 410.501. Structure annealed in 38 s, f = 8.93225. Structure annealed in 38 s, f = 6.39589. Structure annealed in 38 s, f = 4.43573. Structure annealed in 38 s, f = 3.01786. Structure annealed in 39 s, f = 7.72846. Structure annealed in 38 s, f = 2.98790. Structure annealed in 38 s, f = 4.69764. Structure annealed in 38 s, f = 4.14732. Structure annealed in 38 s, f = 47.7409. Structure annealed in 38 s, f = 4.55465. Structure annealed in 38 s, f = 3.93124. Structure annealed in 39 s, f = 4.85510. Structure annealed in 38 s, f = 12.3043. Structure annealed in 38 s, f = 8.18210. Structure annealed in 40 s, f = 383.387. Structure annealed in 38 s, f = 3.82227. Structure annealed in 38 s, f = 7.05222. Structure annealed in 39 s, f = 4.13050. Structure annealed in 38 s, f = 4.29035. Structure annealed in 38 s, f = 5.25382. Structure annealed in 38 s, f = 7.62593. Structure annealed in 38 s, f = 10.8205. Structure annealed in 39 s, f = 3.76810. Structure annealed in 38 s, f = 3.38347. Structure annealed in 38 s, f = 4.23186. Structure annealed in 38 s, f = 4.09312. Structure annealed in 39 s, f = 7.74920. Structure annealed in 38 s, f = 4.92977. Structure annealed in 38 s, f = 9.52399. Structure annealed in 38 s, f = 9.07443. Structure annealed in 38 s, f = 6.03508. Structure annealed in 38 s, f = 7.21781. Structure annealed in 38 s, f = 3.74445. Structure annealed in 38 s, f = 2.65526. Structure annealed in 38 s, f = 6.95517. Structure annealed in 38 s, f = 3.45311. Structure annealed in 39 s, f = 7.43005. Structure annealed in 38 s, f = 7.49251. Structure annealed in 38 s, f = 3.33250. Structure annealed in 38 s, f = 5.90763. Structure annealed in 38 s, f = 12.0957. 100 structures finished in 162 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 2.55 3 0.0120 0.49 1 7.0 0.23 0 0.4151 3.50 2 2.66 4 0.0113 0.35 0 7.6 0.19 0 0.5232 4.78 3 2.99 4 0.0120 0.36 1 9.1 0.20 0 0.5511 4.84 4 3.02 4 0.0123 0.47 1 8.7 0.22 0 0.4265 2.96 5 3.04 2 0.0113 0.47 2 7.7 0.22 0 0.4038 3.14 6 3.14 4 0.0122 0.47 1 8.1 0.21 0 0.4563 3.28 7 3.18 3 0.0119 0.48 3 7.6 0.25 0 0.4165 3.47 8 3.18 3 0.0120 0.46 0 8.6 0.17 0 0.3906 2.60 9 3.26 2 0.0121 0.47 1 8.0 0.22 0 0.3442 3.17 10 3.33 4 0.0126 0.49 3 9.8 0.23 0 0.4079 2.84 11 3.38 5 0.0126 0.48 2 9.0 0.21 0 0.4381 2.67 12 3.45 3 0.0114 0.41 2 9.5 0.23 0 0.5088 4.46 13 3.46 2 0.0124 0.46 1 9.3 0.24 0 0.4122 3.28 14 3.47 3 0.0133 0.46 1 8.9 0.21 0 0.3994 2.74 15 3.54 2 0.0118 0.47 5 9.8 0.25 1 0.5592 5.39 16 3.60 4 0.0126 0.46 3 9.2 0.29 0 0.3846 2.99 17 3.68 4 0.0124 0.47 1 8.4 0.23 0 0.4414 3.28 18 3.73 4 0.0128 0.48 1 9.4 0.23 0 0.4118 3.24 19 3.74 3 0.0129 0.45 1 8.8 0.20 0 0.3763 2.49 20 3.74 4 0.0136 0.51 3 8.5 0.28 0 0.3552 2.65 Ave 3.31 3 0.0123 0.46 2 8.7 0.23 0 0.4311 3.39 +/- 0.33 1 0.0006 0.04 1 0.8 0.03 0 0.0591 0.80 Min 2.55 2 0.0113 0.35 0 7.0 0.17 0 0.3442 2.49 Max 3.74 5 0.0136 0.51 5 9.8 0.29 1 0.5592 5.39 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 14 0 0 2 142 10 0 0 3 136 14 2 0 4 138 14 0 0 forrtl: Stale NFS file handle forrtl: severe (38): error during write, unit 41, file /user/francis/znf42/8cyana/150-stereo/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 21980 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() 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 21-Dec-2005 13:26:25