Warning: no access to tty (Bad file descriptor). Thus no job control in this shell. 21-Dec-2005 12:03:54 n-1<21215> ssi:boot:base:linear: booting n0 (wolf01) n-1<21215> ssi:boot:base:linear: booting n1 (wolf02) n-1<21215> ssi:boot:base:linear: booting n2 (wolf03) n-1<21215> ssi:boot:base:linear: booting n3 (wolf04) n-1<21215> ssi:boot:base:linear: booting n4 (wolf05) n-1<21215> ssi:boot:base:linear: booting n5 (wolf06) n-1<21215> ssi:boot:base:linear: booting n6 (wolf07) n-1<21215> ssi:boot:base:linear: booting n7 (wolf08) n-1<21215> ssi:boot:base:linear: booting n8 (wolf09) n-1<21215> ssi:boot:base:linear: booting n9 (wolf10) n-1<21215> ssi:boot:base:linear: booting n10 (wolf11) n-1<21215> ssi:boot:base:linear: booting n11 (wolf12) n-1<21215> ssi:boot:base:linear: booting n12 (wolf13) n-1<21215> 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, 3187 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 3187 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, 1102 assignments. - peakcheck: peaks fit Deviations from chemical shift list: Dim Peaks Median Average Maximum RMSD Number Tolerance 1 1102 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, 3187 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, 1102 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 4175 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, 4175 upper limits, 4175 assignments. - znf42: distance modify Number of modified constraints: 2153 - znf42: write upl znf42.upl Distance constraint file "znf42.upl" written, 2153 upper limits, 2153 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, 2153 upper limits, 2153 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 = 7.58017. Structure annealed in 38 s, f = 3.56963. Structure annealed in 39 s, f = 4.68500. Structure annealed in 39 s, f = 9.60065. Structure annealed in 39 s, f = 149.576. Structure annealed in 38 s, f = 5.31386. Structure annealed in 38 s, f = 4.09436. Structure annealed in 39 s, f = 7.83344. Structure annealed in 38 s, f = 10.3459. Structure annealed in 38 s, f = 5.82506. Structure annealed in 38 s, f = 3.14828. Structure annealed in 38 s, f = 4.14910. Structure annealed in 38 s, f = 6.52591. Structure annealed in 38 s, f = 3.59556. Structure annealed in 38 s, f = 9.27689. Structure annealed in 38 s, f = 4.31843. Structure annealed in 38 s, f = 7.64620. Structure annealed in 38 s, f = 4.86428. Structure annealed in 39 s, f = 7.44019. Structure annealed in 39 s, f = 16.4600. Structure annealed in 38 s, f = 7.03329. Structure annealed in 38 s, f = 5.47661. Structure annealed in 38 s, f = 4.52517. Structure annealed in 38 s, f = 3.44557. Structure annealed in 39 s, f = 5.04020. Structure annealed in 38 s, f = 8.24048. Structure annealed in 38 s, f = 5.77086. Structure annealed in 38 s, f = 3.93102. Structure annealed in 38 s, f = 8.52405. Structure annealed in 38 s, f = 7.56556. Structure annealed in 38 s, f = 3.63547. Structure annealed in 41 s, f = 518.054. Structure annealed in 38 s, f = 11.3734. Structure annealed in 38 s, f = 4.17819. Structure annealed in 39 s, f = 42.5722. Structure annealed in 38 s, f = 9.30991. Structure annealed in 39 s, f = 11.3820. Structure annealed in 38 s, f = 14.3040. Structure annealed in 38 s, f = 19.6258. Structure annealed in 39 s, f = 8.98783. Structure annealed in 38 s, f = 4.71734. Structure annealed in 38 s, f = 4.19445. Structure annealed in 38 s, f = 4.80239. Structure annealed in 38 s, f = 8.23178. Structure annealed in 39 s, f = 8.46337. Structure annealed in 38 s, f = 9.50579. Structure annealed in 39 s, f = 5.62523. Structure annealed in 39 s, f = 5.32329. Structure annealed in 38 s, f = 5.40256. Structure annealed in 38 s, f = 5.33731. Structure annealed in 38 s, f = 4.61430. Structure annealed in 38 s, f = 3.88443. Structure annealed in 38 s, f = 7.98606. Structure annealed in 38 s, f = 7.68910. Structure annealed in 38 s, f = 5.50450. Structure annealed in 38 s, f = 5.53546. Structure annealed in 38 s, f = 4.50535. Structure annealed in 38 s, f = 7.30303. Structure annealed in 38 s, f = 6.59957. Structure annealed in 38 s, f = 9.37446. Structure annealed in 39 s, f = 3.24722. Structure annealed in 38 s, f = 9.97741. Structure annealed in 38 s, f = 4.44449. Structure annealed in 38 s, f = 4.29778. Structure annealed in 38 s, f = 9.91412. Structure annealed in 38 s, f = 4.20933. Structure annealed in 39 s, f = 5.07540. Structure annealed in 41 s, f = 239.748. Structure annealed in 39 s, f = 5.74778. Structure annealed in 39 s, f = 4.50952. Structure annealed in 38 s, f = 7.57541. Structure annealed in 38 s, f = 4.22405. Structure annealed in 38 s, f = 16.8077. Structure annealed in 39 s, f = 5.60639. Structure annealed in 38 s, f = 5.08445. Structure annealed in 38 s, f = 5.45069. Structure annealed in 38 s, f = 4.26272. Structure annealed in 39 s, f = 24.6858. Structure annealed in 38 s, f = 3.75267. Structure annealed in 38 s, f = 5.02000. Structure annealed in 38 s, f = 4.04202. Structure annealed in 38 s, f = 5.33200. Structure annealed in 38 s, f = 13.4658. Structure annealed in 38 s, f = 3.86807. Structure annealed in 38 s, f = 3.81015. Structure annealed in 38 s, f = 5.12102. Structure annealed in 38 s, f = 8.78662. Structure annealed in 38 s, f = 12.4708. Structure annealed in 38 s, f = 4.14755. Structure annealed in 38 s, f = 3.85734. Structure annealed in 38 s, f = 4.84463. Structure annealed in 39 s, f = 5.56673. Structure annealed in 39 s, f = 8.13093. Structure annealed in 38 s, f = 7.00695. Structure annealed in 38 s, f = 5.37424. Structure annealed in 38 s, f = 5.00081. Structure annealed in 38 s, f = 13.7882. Structure annealed in 38 s, f = 4.35003. Structure annealed in 39 s, f = 8.06463. Structure annealed in 38 s, f = 3.83189. 100 structures finished in 161 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 3.15 6 0.0138 0.52 1 7.4 0.24 0 0.4176 2.98 2 3.25 7 0.0146 0.54 0 8.2 0.16 0 0.3384 2.61 3 3.45 6 0.0147 0.55 2 8.3 0.23 0 0.4415 3.22 4 3.57 6 0.0145 0.53 1 9.4 0.21 0 0.4963 3.47 5 3.60 7 0.0148 0.53 1 8.7 0.24 0 0.4657 3.48 6 3.64 7 0.0153 0.55 0 9.1 0.18 0 0.4754 3.27 7 3.75 6 0.0142 0.53 2 8.8 0.23 0 0.4376 3.14 8 3.81 5 0.0142 0.56 2 9.2 0.23 0 0.4688 3.42 9 3.83 6 0.0144 0.42 1 10.2 0.23 0 0.5454 4.59 10 3.86 7 0.0144 0.54 4 9.7 0.25 0 0.4344 2.91 11 3.87 5 0.0155 0.55 1 9.9 0.21 0 0.5484 3.23 12 3.88 6 0.0153 0.55 0 9.9 0.17 0 0.4385 3.21 13 3.93 7 0.0154 0.54 0 9.2 0.18 0 0.4598 3.93 14 4.04 6 0.0133 0.42 2 9.6 0.25 0 0.5187 4.48 15 4.09 7 0.0154 0.52 0 9.7 0.17 1 0.5570 5.07 16 4.15 7 0.0152 0.54 2 9.8 0.25 0 0.4368 2.88 17 4.15 6 0.0144 0.41 3 10.2 0.28 0 0.5306 4.45 18 4.18 5 0.0143 0.43 1 8.8 0.20 0 0.5572 4.60 19 4.19 5 0.0150 0.53 3 10.4 0.28 0 0.4953 3.33 20 4.21 7 0.0148 0.42 0 10.3 0.19 0 0.6253 4.89 Ave 3.83 6 0.0147 0.51 1 9.3 0.22 0 0.4844 3.66 +/- 0.30 1 0.0006 0.05 1 0.8 0.04 0 0.0632 0.73 Min 3.15 5 0.0133 0.41 0 7.4 0.16 0 0.3384 2.61 Max 4.21 7 0.0155 0.56 4 10.4 0.28 1 0.6253 5.07 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 2 141 11 0 0 3 136 15 1 0 4 134 16 2 0 forrtl: Stale NFS file handle forrtl: severe (38): error during write, unit 41, file /user/francis/znf42/8cyana/140-final/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 1, comm 3) MPI_Recv: process in local group is dead (rank 4, 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 21297 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 12, comm 3) Rank (24, MPI_COMM_WORLD): Call stack within LAM: Rank (24, MPI_COMM_WORLD): - MPI_Recv() Rank (24, MPI_COMM_WORLD): - MPI_Bcast() Rank (24, MPI_COMM_WORLD): - MPI_Bcast() Rank (24, MPI_COMM_WORLD): - main() LAM 7.2b1svn10112005/MPI 2 C++/ROMIO - Indiana University 21-Dec-2005 12:07:06