Warning: no access to tty (Bad file descriptor). Thus no job control in this shell. 29-Nov-2005 22:24:22 n-1<32304> ssi:boot:base:linear: booting n0 (wolf01) n-1<32304> ssi:boot:base:linear: booting n1 (wolf02) n-1<32304> ssi:boot:base:linear: booting n2 (wolf03) n-1<32304> ssi:boot:base:linear: booting n3 (wolf04) n-1<32304> ssi:boot:base:linear: booting n4 (wolf05) n-1<32304> ssi:boot:base:linear: booting n5 (wolf06) n-1<32304> ssi:boot:base:linear: booting n6 (wolf07) n-1<32304> ssi:boot:base:linear: booting n7 (wolf08) n-1<32304> ssi:boot:base:linear: booting n8 (wolf09) n-1<32304> ssi:boot:base:linear: booting n9 (wolf10) n-1<32304> ssi:boot:base:linear: booting n10 (wolf11) n-1<32304> ssi:boot:base:linear: booting n11 (wolf12) n-1<32304> ssi:boot:base:linear: booting n12 (wolf13) n-1<32304> 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= *** WARNING: Inconsistent heavy atom assignment for peak 4284. Peak list "c13no.peaks" read, 3489 peaks, 3015 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 3015 0.000 0.003 0.460 0.012 2 0.030 2 3362 0.000 0.000 0.291 0.006 1 0.030 3 3362 0.000 0.001 0.324 0.030 0 0.450 - peakcheck: atom shift check Atom Residue Shift Median Deviation Peaks HB2 LEU 73 1.257 1.257 0.044 17 QD1 LEU 73 0.281 0.281 0.460 25 HD3 ARG 78 2.772 2.772 0.291 19 3 shifts with spread larger than tolerance. - peakcheck: peak deviations Peak Dim Deviation Atom Residue 1210 2 0.291 HD3 ARG 78 1781 1 0.044 HB2 LEU 73 2948 1 0.460 QD1 LEU 73 3 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, 227 peaks, 147 assignments. - peakcheck: peaks fit Deviations from chemical shift list: Dim Peaks Median Average Maximum RMSD Number Tolerance 1 147 0.000 -0.001 0.029 0.016 0 0.030 2 161 0.000 0.000 0.014 0.005 0 0.030 3 161 0.000 -0.005 0.297 0.035 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= *** WARNING: Inconsistent heavy atom assignment for peak 4284. Peak list "c13no.peaks" read, 3489 peaks, 3015 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=3.0E7 Calibration constant for peak list 1: 3.00E+07 Upper limit set for 3489 peaks. - calibration: caltab peaks Distance bounds: -2.99 A: 330 9.5% 3.00-3.99 A: 771 22.1% 4.00-4.99 A: 1385 39.7% 5.00-5.99 A: 1001 28.7% 6.00- A: 0 0.0% All: 3489 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 4762 peaks, 1273 of 4762 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 5043 peaks, 281 of 5043 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, 227 peaks, 147 assignments. - calibration: peaks select "** list=4" 227 of 5270 peaks, 227 of 5270 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: 1 0.4% 3.00-3.99 A: 50 22.0% 4.00-4.99 A: 157 69.2% 5.00-5.99 A: 19 8.4% 6.00- A: 0 0.0% All: 227 100.0% - calibration: peaks select ** 5270 of 5270 peaks, 5270 of 5270 assignments selected. - znf42: peaks calibrate ** simple 4033 upper limits added, 9/473 at lower/upper bound, average 4.46 A. - znf42: write upl znf42-in.upl Distance constraint file "znf42-in.upl" written, 4033 upper limits, 4033 assignments. - znf42: distance modify Number of modified constraints: 2128 - znf42: write upl znf42.upl Distance constraint file "znf42.upl" written, 2128 upper limits, 2128 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, 2128 upper limits, 2128 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 = 133.146. Structure annealed in 40 s, f = 20.9390. Structure annealed in 40 s, f = 19.4441. Structure annealed in 40 s, f = 21.8839. Structure annealed in 39 s, f = 16.1817. Structure annealed in 40 s, f = 13.9920. Structure annealed in 40 s, f = 35.2014. Structure annealed in 40 s, f = 12.8169. Structure annealed in 39 s, f = 20.4292. Structure annealed in 40 s, f = 20.6884. Structure annealed in 40 s, f = 14.7338. Structure annealed in 39 s, f = 16.6557. Structure annealed in 40 s, f = 14.3253. Structure annealed in 39 s, f = 13.8561. Structure annealed in 39 s, f = 17.5657. Structure annealed in 39 s, f = 20.4071. Structure annealed in 39 s, f = 16.0810. Structure annealed in 40 s, f = 13.9739. Structure annealed in 40 s, f = 18.1516. Structure annealed in 39 s, f = 15.0757. Structure annealed in 40 s, f = 14.9895. Structure annealed in 40 s, f = 15.5995. Structure annealed in 40 s, f = 18.8277. Structure annealed in 39 s, f = 20.6239. Structure annealed in 40 s, f = 16.9387. Structure annealed in 41 s, f = 192.361. Structure annealed in 39 s, f = 22.5476. Structure annealed in 39 s, f = 20.3504. Structure annealed in 39 s, f = 15.4767. Structure annealed in 40 s, f = 24.0517. Structure annealed in 39 s, f = 14.1284. Structure annealed in 39 s, f = 21.0264. Structure annealed in 39 s, f = 16.0049. Structure annealed in 39 s, f = 16.6924. Structure annealed in 39 s, f = 15.9184. Structure annealed in 39 s, f = 17.4076. Structure annealed in 39 s, f = 21.4244. Structure annealed in 39 s, f = 27.9935. Structure annealed in 39 s, f = 18.5524. Structure annealed in 39 s, f = 13.7316. Structure annealed in 40 s, f = 13.4157. Structure annealed in 40 s, f = 20.4195. Structure annealed in 40 s, f = 13.9667. Structure annealed in 40 s, f = 20.2387. Structure annealed in 40 s, f = 15.5675. Structure annealed in 40 s, f = 12.3941. Structure annealed in 40 s, f = 20.3380. Structure annealed in 39 s, f = 18.7789. Structure annealed in 42 s, f = 310.716. Structure annealed in 40 s, f = 134.814. Structure annealed in 39 s, f = 12.0246. Structure annealed in 40 s, f = 13.1447. Structure annealed in 40 s, f = 14.6198. Structure annealed in 39 s, f = 18.5395. Structure annealed in 39 s, f = 27.4909. Structure annealed in 40 s, f = 30.3756. Structure annealed in 40 s, f = 14.8648. Structure annealed in 39 s, f = 18.9448. Structure annealed in 39 s, f = 20.2679. Structure annealed in 41 s, f = 418.633. Structure annealed in 39 s, f = 21.4432. Structure annealed in 39 s, f = 15.6630. Structure annealed in 39 s, f = 15.9154. Structure annealed in 39 s, f = 14.3237. Structure annealed in 39 s, f = 12.9864. Structure annealed in 39 s, f = 16.2436. Structure annealed in 39 s, f = 14.0597. Structure annealed in 39 s, f = 15.6235. Structure annealed in 40 s, f = 15.4432. Structure annealed in 40 s, f = 14.4833. Structure annealed in 40 s, f = 15.6907. Structure annealed in 40 s, f = 13.3280. Structure annealed in 39 s, f = 18.5502. Structure annealed in 40 s, f = 14.1385. Structure annealed in 40 s, f = 13.0337. Structure annealed in 39 s, f = 15.8024. Structure annealed in 39 s, f = 16.4614. Structure annealed in 39 s, f = 16.0400. Structure annealed in 39 s, f = 16.0742. Structure annealed in 39 s, f = 20.6240. Structure annealed in 39 s, f = 15.6742. Structure annealed in 39 s, f = 21.9883. Structure annealed in 39 s, f = 18.6098. Structure annealed in 39 s, f = 13.9945. Structure annealed in 39 s, f = 14.8694. Structure annealed in 40 s, f = 16.0061. Structure annealed in 40 s, f = 19.6900. Structure annealed in 39 s, f = 20.3672. Structure annealed in 39 s, f = 12.7333. Structure annealed in 39 s, f = 27.3937. Structure annealed in 40 s, f = 14.6004. Structure annealed in 39 s, f = 25.1746. Structure annealed in 39 s, f = 19.6078. Structure annealed in 40 s, f = 20.4923. Structure annealed in 39 s, f = 14.6642. Structure annealed in 39 s, f = 14.8046. Structure annealed in 40 s, f = 12.6337. Structure annealed in 39 s, f = 20.1629. Structure annealed in 40 s, f = 13.6888. Structure annealed in 40 s, f = 18.6360. 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 12.02 40 0.0266 0.77 7 19.8 0.34 1 1.0596 6.07 2 12.39 36 0.0271 0.71 9 18.4 0.36 2 1.1776 5.64 3 12.63 36 0.0274 0.67 9 17.1 0.32 1 1.0489 5.20 4 12.73 40 0.0288 0.86 7 18.7 0.35 1 0.9999 7.56 5 12.82 35 0.0271 0.72 6 18.1 0.35 2 1.0973 6.49 6 12.99 42 0.0274 0.63 9 19.6 0.33 4 1.2374 7.47 7 13.03 37 0.0267 0.67 12 19.7 0.35 4 1.1656 6.58 8 13.14 37 0.0301 0.85 4 17.9 0.33 2 1.1329 7.54 9 13.33 34 0.0278 0.65 7 19.3 0.30 2 1.1550 5.55 10 13.42 38 0.0276 0.69 7 19.1 0.37 1 1.0304 5.03 11 13.69 38 0.0276 0.77 15 21.5 0.37 0 0.9856 4.61 12 13.73 41 0.0276 0.78 12 19.8 0.38 1 0.9619 5.42 13 13.86 35 0.0274 0.79 7 19.7 0.36 3 1.2659 7.36 14 13.97 45 0.0302 0.97 8 18.6 0.39 3 1.1574 6.97 15 13.97 45 0.0285 0.72 8 19.4 0.38 0 1.0871 4.99 16 13.99 38 0.0274 0.81 13 22.2 0.38 5 1.3035 7.43 17 13.99 40 0.0299 0.75 9 18.9 0.34 2 1.1269 5.99 18 14.06 40 0.0279 0.84 8 21.6 0.33 2 1.1978 8.25 19 14.13 41 0.0280 0.65 13 20.8 0.34 3 1.1523 6.31 20 14.14 41 0.0297 0.77 6 19.5 0.31 0 1.0020 4.83 Ave 13.40 39 0.0280 0.75 9 19.5 0.35 2 1.1173 6.26 +/- 0.63 3 0.0011 0.08 3 1.3 0.02 1 0.0932 1.07 Min 12.02 34 0.0266 0.63 4 17.1 0.30 0 0.9619 4.61 Max 14.14 45 0.0302 0.97 15 22.2 0.39 5 1.3035 8.25 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 ------ --- --- --- --- 1 140 9 1 2 (GLU 125, GLU 425) 2 140 9 3 0 forrtl: Stale NFS file handle forrtl: severe (38): error during write, unit 41, file /user/francis/znf42/8cyana/110b/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) ----------------------------------------------------------------------------- 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 32386 failed on node n0 (192.168.96.101) with exit status 28. ----------------------------------------------------------------------------- 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() 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() LAM 7.2b1svn10112005/MPI 2 C++/ROMIO - Indiana University 29-Nov-2005 22:27:39