Warning: no access to tty (Bad file descriptor). Thus no job control in this shell. 05-Dec-2005 12:04:20 n-1<13925> ssi:boot:base:linear: booting n0 (wolf01) n-1<13925> ssi:boot:base:linear: booting n1 (wolf02) n-1<13925> ssi:boot:base:linear: booting n2 (wolf03) n-1<13925> ssi:boot:base:linear: booting n3 (wolf04) n-1<13925> ssi:boot:base:linear: booting n4 (wolf05) n-1<13925> ssi:boot:base:linear: booting n5 (wolf06) n-1<13925> ssi:boot:base:linear: booting n6 (wolf07) n-1<13925> ssi:boot:base:linear: booting n7 (wolf08) n-1<13925> ssi:boot:base:linear: booting n8 (wolf09) n-1<13925> ssi:boot:base:linear: booting n9 (wolf10) n-1<13925> ssi:boot:base:linear: booting n10 (wolf11) n-1<13925> ssi:boot:base:linear: booting n11 (wolf12) n-1<13925> ssi:boot:base:linear: booting n12 (wolf13) n-1<13925> 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= *** WARNING: Assignment of peak 1812 not found in chemical shift list. *** WARNING: Assignment of peak 4135 not found in chemical shift list. Peak list "c13no.peaks" read, 3483 peaks, 3199 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 3200 0.000 0.002 0.030 0.009 0 0.030 2 3478 0.000 0.000 0.026 0.002 0 0.030 3 3478 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= *** WARNING: Assignment of peak 695 not found in chemical shift list. *** WARNING: Assignment of peak 730 not found in chemical shift list. Peak list "n15no.peaks" read, 1272 peaks, 1111 assignments. - peakcheck: peaks fit Deviations from chemical shift list: Dim Peaks Median Average Maximum RMSD Number Tolerance 1 1111 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, 240 assignments. - peakcheck: peaks fit Deviations from chemical shift list: Dim Peaks Median Average Maximum RMSD Number Tolerance 1 240 0.005 0.005 0.030 0.012 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 HB3 ARG 44 0.295 0.325 0.030 1 1 shift with spread larger than tolerance. - peakcheck: peak deviations Peak Dim Deviation Atom Residue 226 1 0.030 HB3 ARG 44 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, 227 peaks, 151 assignments. - peakcheck: peaks fit Deviations from chemical shift list: Dim Peaks Median Average Maximum RMSD Number Tolerance 1 151 0.000 -0.001 0.040 0.016 1 0.030 2 173 0.000 -0.001 0.014 0.005 0 0.030 3 173 0.000 -0.005 0.297 0.034 0 0.450 - peakcheck: atom shift check Atom Residue Shift Median Deviation Peaks HD2 ARG 366 3.089 3.129 0.040 1 1 shift with spread larger than tolerance. - peakcheck: peak deviations Peak Dim Deviation Atom Residue 8233 1 0.040 HD2 ARG 366 1 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, 1981 chemical shifts. - calibration: read peaks c13no format= *** WARNING: Assignment of peak 1812 not found in chemical shift list. *** WARNING: Assignment of peak 4135 not found in chemical shift list. Peak list "c13no.peaks" read, 3483 peaks, 3199 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: 329 9.4% 3.00-3.99 A: 768 22.1% 4.00-4.99 A: 1384 39.7% 5.00-5.99 A: 1000 28.7% 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 *** WARNING: Assignment of peak 695 not found in chemical shift list. *** WARNING: Assignment of peak 730 not found in chemical shift list. Peak list "n15no.peaks" read, 1272 peaks, 1111 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=1.2E7 Calibration constant for peak list 2: 1.20E+07 Upper limit set for 1272 peaks. - calibration: caltab peaks Distance bounds: -2.99 A: 93 7.3% 3.00-3.99 A: 339 26.7% 4.00-4.99 A: 491 38.6% 5.00-5.99 A: 347 27.3% 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, 240 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, 227 peaks, 151 assignments. - calibration: peaks select "** list=4" 227 of 5274 peaks, 227 of 5274 assignments selected. - calibration: peaks set volume=abs(volume) Volume of 227 peaks set. - calibration: peaks simplecal constant=1.0E7 Calibration constant for peak list 4: 1.00E+07 Upper limit set for 227 peaks. - calibration: caltab peaks Distance bounds: -2.99 A: 2 0.9% 3.00-3.99 A: 49 21.6% 4.00-4.99 A: 158 69.6% 5.00-5.99 A: 18 7.9% 6.00- A: 0 0.0% All: 227 100.0% - calibration: peaks select ** 5274 of 5274 peaks, 5274 of 5274 assignments selected. - znf42: peaks calibrate ** simple 4205 upper limits added, 8/493 at lower/upper bound, average 4.46 A. - znf42: write upl znf42-in.upl Distance constraint file "znf42-in.upl" written, 4205 upper limits, 4205 assignments. - znf42: distance modify Too restrictive distance constraints: limit dmin dmax Upper HA TYR 52 - QE TYR 52 3.88 3.96 6.78 Number of modified constraints: 2247 - znf42: write upl znf42.upl Distance constraint file "znf42.upl" written, 2247 upper limits, 2247 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, 2247 upper limits, 2247 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 = 11.9756. Structure annealed in 40 s, f = 9.55727. Structure annealed in 40 s, f = 16.9263. Structure annealed in 40 s, f = 9.75754. Structure annealed in 40 s, f = 19.7608. Structure annealed in 39 s, f = 9.19899. Structure annealed in 40 s, f = 11.7902. Structure annealed in 39 s, f = 11.9573. Structure annealed in 39 s, f = 13.0167. Structure annealed in 39 s, f = 20.3188. Structure annealed in 39 s, f = 8.03255. Structure annealed in 40 s, f = 9.22047. Structure annealed in 40 s, f = 19.9843. Structure annealed in 39 s, f = 9.20430. Structure annealed in 39 s, f = 15.8692. Structure annealed in 39 s, f = 13.2722. Structure annealed in 39 s, f = 9.69426. Structure annealed in 39 s, f = 8.56533. Structure annealed in 39 s, f = 13.3557. Structure annealed in 42 s, f = 333.755. Structure annealed in 40 s, f = 9.64716. Structure annealed in 40 s, f = 12.0065. Structure annealed in 39 s, f = 14.3059. Structure annealed in 41 s, f = 276.717. Structure annealed in 40 s, f = 10.8748. Structure annealed in 39 s, f = 15.0345. Structure annealed in 40 s, f = 8.39583. Structure annealed in 39 s, f = 19.6224. Structure annealed in 39 s, f = 9.22217. Structure annealed in 40 s, f = 13.1109. Structure annealed in 39 s, f = 8.97427. Structure annealed in 41 s, f = 193.417. Structure annealed in 39 s, f = 13.5336. Structure annealed in 39 s, f = 9.00150. Structure annealed in 39 s, f = 8.48463. Structure annealed in 40 s, f = 9.14073. Structure annealed in 40 s, f = 15.5816. Structure annealed in 39 s, f = 8.81679. Structure annealed in 39 s, f = 9.92585. Structure annealed in 39 s, f = 8.13765. Structure annealed in 39 s, f = 19.0734. Structure annealed in 42 s, f = 302.437. Structure annealed in 39 s, f = 9.26058. Structure annealed in 39 s, f = 13.4565. Structure annealed in 40 s, f = 9.03313. Structure annealed in 39 s, f = 13.3758. Structure annealed in 39 s, f = 8.85313. Structure annealed in 40 s, f = 9.47016. Structure annealed in 39 s, f = 8.76518. Structure annealed in 39 s, f = 8.12249. Structure annealed in 39 s, f = 9.51101. Structure annealed in 39 s, f = 10.2134. Structure annealed in 39 s, f = 12.3004. Structure annealed in 39 s, f = 15.2490. Structure annealed in 40 s, f = 9.08971. Structure annealed in 39 s, f = 13.9763. Structure annealed in 40 s, f = 8.88158. Structure annealed in 39 s, f = 12.9135. Structure annealed in 39 s, f = 9.05730. Structure annealed in 39 s, f = 13.6729. Structure annealed in 39 s, f = 12.7093. Structure annealed in 40 s, f = 10.7656. Structure annealed in 39 s, f = 11.6047. Structure annealed in 40 s, f = 22.5875. Structure annealed in 40 s, f = 37.7939. Structure annealed in 39 s, f = 9.07471. Structure annealed in 39 s, f = 10.2364. Structure annealed in 39 s, f = 12.0182. Structure annealed in 40 s, f = 8.73299. Structure annealed in 40 s, f = 10.2932. Structure annealed in 40 s, f = 11.4236. Structure annealed in 39 s, f = 23.9262. Structure annealed in 40 s, f = 10.1929. Structure annealed in 39 s, f = 9.82901. Structure annealed in 40 s, f = 9.67654. Structure annealed in 39 s, f = 10.2926. Structure annealed in 39 s, f = 11.5675. Structure annealed in 39 s, f = 9.26105. Structure annealed in 39 s, f = 30.1124. Structure annealed in 39 s, f = 13.8185. Structure annealed in 39 s, f = 11.7499. Structure annealed in 40 s, f = 14.5127. Structure annealed in 39 s, f = 10.9449. Structure annealed in 39 s, f = 11.5058. Structure annealed in 40 s, f = 127.864. Structure annealed in 39 s, f = 9.13064. Structure annealed in 40 s, f = 21.4867. Structure annealed in 39 s, f = 9.61047. Structure annealed in 39 s, f = 8.54507. Structure annealed in 40 s, f = 15.9916. Structure annealed in 39 s, f = 11.4581. Structure annealed in 39 s, f = 15.7859. Structure annealed in 40 s, f = 10.5205. Structure annealed in 39 s, f = 10.5052. Structure annealed in 42 s, f = 448.751. Structure annealed in 40 s, f = 29.1599. Structure annealed in 40 s, f = 21.5688. Structure annealed in 39 s, f = 12.3450. Structure annealed in 40 s, f = 8.68077. Structure annealed in 40 s, f = 12.2617. 100 structures finished in 166 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 8.03 33 0.0218 0.53 4 14.3 0.25 0 0.7750 3.85 2 8.12 27 0.0213 0.46 1 13.1 0.22 0 0.8807 4.89 3 8.14 27 0.0203 0.48 3 14.2 0.24 0 0.7965 4.53 4 8.40 23 0.0209 0.64 4 14.4 0.25 0 0.8729 4.04 5 8.48 28 0.0213 0.53 4 15.0 0.28 0 0.7420 4.75 6 8.55 29 0.0207 0.49 0 13.7 0.20 1 0.9724 6.69 7 8.57 29 0.0210 0.46 4 15.0 0.24 1 1.0011 6.00 8 8.68 30 0.0211 0.43 4 15.1 0.30 0 0.6979 3.99 9 8.73 29 0.0210 0.49 8 15.6 0.28 1 0.9800 7.16 10 8.77 30 0.0217 0.49 7 15.8 0.29 1 0.9072 5.51 11 8.82 28 0.0203 0.38 4 14.8 0.24 1 0.7870 5.48 12 8.85 29 0.0228 0.60 0 14.0 0.20 0 0.8159 4.73 13 8.88 35 0.0214 0.46 1 16.4 0.20 1 0.9840 5.94 14 8.97 30 0.0213 0.58 3 15.6 0.26 2 0.9684 5.67 15 9.00 29 0.0225 0.59 4 15.6 0.26 0 0.7603 3.29 16 9.03 27 0.0213 0.43 1 14.4 0.21 0 0.8951 4.91 17 9.06 36 0.0230 0.56 3 15.2 0.49 0 0.7032 3.54 18 9.07 38 0.0231 0.47 1 15.4 0.22 1 0.9290 6.75 19 9.09 24 0.0218 0.51 3 15.6 0.28 1 0.8979 6.09 20 9.13 27 0.0222 0.52 6 14.2 0.28 0 0.8774 4.67 Ave 8.72 29 0.0215 0.51 3 14.9 0.26 1 0.8622 5.12 +/- 0.33 4 0.0008 0.06 2 0.8 0.06 1 0.0943 1.08 Min 8.03 23 0.0203 0.38 0 13.1 0.20 0 0.6979 3.29 Max 9.13 38 0.0231 0.64 8 16.4 0.49 2 1.0011 7.16 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 2 137 13 2 0 3 140 10 2 0 forrtl: Stale NFS file handle forrtl: severe (38): error during write, unit 41, file /user/francis/znf42/8cyana/115a/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 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) ----------------------------------------------------------------------------- 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. 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() PID 14007 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() 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 05-Dec-2005 12:07:37