Warning: no access to tty (Bad file descriptor). Thus no job control in this shell. 27-Dec-2005 17:04:54 LAM 6.5.9/MPI 2 C++/ROMIO - Indiana University Executing hboot on n0 (cesg-node9.biochem.wisc.edu - 2 CPUs)... Executing hboot on n1 (cesg-node7.biochem.wisc.edu - 2 CPUs)... Executing hboot on n2 (cesg-node6.biochem.wisc.edu - 2 CPUs)... Executing hboot on n3 (cesg-node5.biochem.wisc.edu - 2 CPUs)... Executing hboot on n4 (cesg-node4.biochem.wisc.edu - 2 CPUs)... topology n0 (o)... n1... n2... n3... n4... done ___________________________________________________________________ CYANA 2.1 (intel-lam) Copyright (c) 2002-05 Peter Guntert. All rights reserved. ___________________________________________________________________ Library file "/s/src/cyana-2.1/lib/cyana.lib" read, 37 residue types. Sequence file "at5g39720.seq" read, 173 residues. cyana> cyana> cyana> - CALC: peakcheck peaks=c13no_new,n15no_new,c13ar_new prot=at5g39720 ------------------------------------------------------------ Proton list: at5g39720 - peakcheck: read prot at5g39720 unknown=warn Chemical shift list "at5g39720.prot" read, 1646 chemical shifts. - peakcheck: shifts missing "H* Q* - HYDROXYL - AMIDE + H HN / &H_* &PSEUD" Residue missing shifts GLY 1 H QA HIS 2 H HA QB HD2 HE1 HIS 3 H HA QB HD2 HE1 HIS 4 H HA QB HD2 HE1 HIS 5 HA QB HD2 HE1 HIS 6 H HA QB HD2 HE1 HIS 7 H HB2 HD2 HE1 LEU 8 HB2 GLU 9 HG2 CYS 10 HG SER 11 HB2 ASP 13 HB2 SER 14 HB2 GLN 16 HG2 HIS 18 HB2 PHE 21 HZ GLY 24 H QA SER 25 H HA QB PHE 26 HZ MET 35 HB2 HG2 LEU 36 QD1 ARG 38 HD3 PRO 40 HB2 GLU 41 HB2 PHE 50 HZ ARG 52 QG QD PHE 53 HZ ARG 54 HG2 LEU 55 H HA QB HG QQD LYS 56 H HA QB QG QD QE GLY 57 H QA ARG 58 QB QG TYR 60 HB2 QE PRO 61 QB QG QD CYS 62 HG GLU 67 HB2 HG2 LYS 68 HG2 HD2 HE2 LEU 76 QD1 SER 81 QB GLU 85 HB2 GLU 96 HG2 VAL 103 QG1 ARG 104 HD2 GLU 105 HG2 SER 108 HB2 LYS 110 HD2 HE2 LYS 114 QG HE2 TYR 116 HB2 MET 117 HB2 LYS 121 HG2 HD2 ASP 123 HB2 PRO 124 HG2 HD2 PHE 127 HB2 QE HZ GLU 129 HB2 HG2 TRP 130 HE3 ASN 131 HA PHE 132 QE HZ GLU 134 HB2 TRP 135 HZ3 LYS 136 HA HB2 HG2 QD HE2 ARG 137 HB2 HIS 139 HD2 HE1 LYS 140 HB2 HG2 HD2 HE2 LYS 141 HB2 HG2 HE2 LYS 142 HB2 HG2 QD HE2 PHE 143 QE HZ GLU 145 HB2 LYS 148 HB2 HG2 HD2 HE2 LYS 149 HA QB QG QD QE MET 151 HB2 QE GLU 152 HB2 CYS 153 HB2 HG LYS 154 HB2 HG2 HD2 HE2 LYS 155 HG2 HD2 HE2 LYS 156 HA QB QG QD QE PRO 157 HG2 GLY 161 HA2 ASN 162 HB2 ASP 163 HB2 ASP 164 HA QB ILE 165 H QG1 SER 166 H HA QB HIS 167 H VAL 168 QG1 LEU 169 HG QD1 ARG 170 HA QB QG QD GLU 171 H HG2 ASP 172 HB2 GLN 173 HA QB QG 185 missing chemical shifts, completeness 81.2%. ------------------------------------------------------------ Peak list : c13no_new Proton list: at5g39720 - peakcheck: read prot at5g39720 unknown=skip Chemical shift list "at5g39720.prot" read, 1646 chemical shifts. - peakcheck: read peaks c13no_new format= Peak list "c13no_new.peaks" read, 3506 peaks, 2935 assignments. - peakcheck: atom shift unusual Atom Shift Dev Mean +/- Minimum Maximum HG2 GLU 91 0.205 10.42 2.29 0.20 1.48 2.79 HB2 GLU 94 0.734 5.63 2.03 0.23 0.72 2.90 2 shifts outside expected range. - peakcheck: peaks fit Deviations from chemical shift list: Dim Peaks Median Average Maximum RMSD Number Tolerance 1 2935 0.003 0.003 0.030 0.013 0 0.040 2 2943 -0.003 -0.004 0.030 0.009 0 0.030 3 2943 0.000 -0.021 0.431 0.093 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_new Proton list: at5g39720 - peakcheck: read prot at5g39720 unknown=skip Chemical shift list "at5g39720.prot" read, 1646 chemical shifts. - peakcheck: read peaks n15no_new format= Peak list "n15no_new.peaks" read, 1839 peaks, 1511 assignments. - peakcheck: peaks fit Deviations from chemical shift list: Dim Peaks Median Average Maximum RMSD Number Tolerance 1 1511 0.004 0.005 0.032 0.013 0 0.040 2 1513 0.000 0.000 0.029 0.005 0 0.030 3 1513 0.001 0.010 0.276 0.055 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_new Proton list: at5g39720 - peakcheck: read prot at5g39720 unknown=skip Chemical shift list "at5g39720.prot" read, 1646 chemical shifts. - peakcheck: read peaks c13ar_new format= Peak list "c13ar_new.peaks" read, 570 peaks, 272 assignments. - peakcheck: peaks fit Deviations from chemical shift list: Dim Peaks Median Average Maximum RMSD Number Tolerance 1 272 0.005 0.004 0.029 0.013 0 0.040 2 272 -0.006 -0.006 0.019 0.009 0 0.030 3 272 0.000 0.000 0.120 0.007 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. - CALC: calibration prot=at5g39720 peaks=c13no_new,n15no_new,c13ar_new dref=4.2 - calibration: read prot at5g39720 unknown=warn Chemical shift list "at5g39720.prot" read, 1646 chemical shifts. - calibration: read peaks c13no_new format= Peak list "c13no_new.peaks" read, 3506 peaks, 2935 assignments. - calibration: peaks select "** list=1" 3506 of 3506 peaks, 3506 of 3506 assignments selected. - calibration: peaks set volume=abs(volume) Volume of 3506 peaks set. - calibration: peaks simplecal dref=4.2 Calibration constant for peak list 1: 1.01E+07 Upper limit set for 3506 peaks. - calibration: caltab peaks Distance bounds: -2.99 A: 457 13.0% 3.00-3.99 A: 1166 33.3% 4.00-4.99 A: 1526 43.5% 5.00-5.99 A: 354 10.1% 6.00- A: 0 0.0% All: 3506 100.0% - calibration: read prot at5g39720 unknown=warn append Chemical shift list "at5g39720.prot" read, 1646 chemical shifts. - calibration: read peaks n15no_new format= append Peak list "n15no_new.peaks" read, 1839 peaks, 1511 assignments. - calibration: peaks select "** list=2" 1839 of 5345 peaks, 1839 of 5345 assignments selected. - calibration: peaks set volume=abs(volume) Volume of 1839 peaks set. - calibration: peaks simplecal dref=4.2 Calibration constant for peak list 2: 8.27E+06 Upper limit set for 1839 peaks. - calibration: caltab peaks Distance bounds: -2.99 A: 163 8.9% 3.00-3.99 A: 636 34.6% 4.00-4.99 A: 862 46.9% 5.00-5.99 A: 178 9.7% 6.00- A: 0 0.0% All: 1839 100.0% - calibration: read prot at5g39720 unknown=warn append Chemical shift list "at5g39720.prot" read, 1646 chemical shifts. - calibration: read peaks c13ar_new format= append Peak list "c13ar_new.peaks" read, 570 peaks, 272 assignments. - calibration: peaks select "** list=3" 570 of 5915 peaks, 570 of 5915 assignments selected. - calibration: peaks set volume=abs(volume) Volume of 570 peaks set. - calibration: peaks simplecal dref=4.2 Calibration constant for peak list 3: 4.83E+06 Upper limit set for 570 peaks. - calibration: caltab peaks Distance bounds: -2.99 A: 56 9.8% 3.00-3.99 A: 176 30.9% 4.00-4.99 A: 313 54.9% 5.00-5.99 A: 25 4.4% 6.00- A: 0 0.0% All: 570 100.0% - calibration: peaks select ** 5915 of 5915 peaks, 5915 of 5915 assignments selected. - CALC: peaks calibrate ** simple 4084 upper limits added, 7/59 at lower/upper bound, average 4.17 A. - CALC: write upl at5g39720-in.upl Distance constraint file "at5g39720-in.upl" written, 4084 upper limits, 4084 assignments. - CALC: distance modify Too restrictive distance constraints: limit dmin dmax Upper HA PHE 147 - QE PHE 147 3.84 3.94 6.76 Number of modified constraints: 2135 - CALC: write upl at5g39720.upl Distance constraint file "at5g39720.upl" written, 2135 upper limits, 2135 assignments. - CALC: read seq at5g39720.seq Sequence file "at5g39720.seq" read, 173 residues. - CALC: read upl at5g39720.upl Distance constraint file "at5g39720.upl" read, 2135 upper limits, 2135 assignments. - CALC: read aco at5g39720.aco Angle constraint file "at5g39720.aco" read, 203 constraints for 203 angles. - CALC: calc_all structures=100 command=anneal steps=10000 100 structures selected. 100 random structures created (seed 5671). Structure annealed in 79 s, f = 15.9089. Structure annealed in 77 s, f = 12.7365. Structure annealed in 76 s, f = 47.1826. Structure annealed in 74 s, f = 23.8699. Structure annealed in 78 s, f = 10.9794. Structure annealed in 77 s, f = 12.1669. Structure annealed in 74 s, f = 11.5224. Structure annealed in 76 s, f = 12.5796. Structure annealed in 76 s, f = 12.0190. Structure annealed in 76 s, f = 14.4265. Structure annealed in 73 s, f = 14.5574. Structure annealed in 75 s, f = 12.3413. Structure annealed in 76 s, f = 25.5674. Structure annealed in 75 s, f = 12.2987. Structure annealed in 74 s, f = 11.9375. Structure annealed in 74 s, f = 14.4042. Structure annealed in 76 s, f = 22.6091. Structure annealed in 77 s, f = 13.4907. Structure annealed in 76 s, f = 12.8174. Structure annealed in 78 s, f = 13.5430. Structure annealed in 73 s, f = 20.9740. Structure annealed in 73 s, f = 10.8098. Structure annealed in 75 s, f = 32.3544. Structure annealed in 73 s, f = 13.9725. Structure annealed in 75 s, f = 9.97313. Structure annealed in 77 s, f = 13.0977. Structure annealed in 76 s, f = 16.1934. Structure annealed in 74 s, f = 21.8260. Structure annealed in 74 s, f = 11.5804. Structure annealed in 73 s, f = 12.5155. Structure annealed in 75 s, f = 13.7540. Structure annealed in 75 s, f = 13.0608. Structure annealed in 68 s, f = 15.2231. Structure annealed in 75 s, f = 23.9622. Structure annealed in 74 s, f = 11.5669. Structure annealed in 75 s, f = 14.8684. Structure annealed in 77 s, f = 29.1630. Structure annealed in 76 s, f = 13.2973. Structure annealed in 74 s, f = 32.5839. Structure annealed in 74 s, f = 11.9204. Structure annealed in 69 s, f = 12.0948. Structure annealed in 76 s, f = 13.1833. Structure annealed in 75 s, f = 12.2351. Structure annealed in 72 s, f = 16.2856. Structure annealed in 72 s, f = 13.5673. Structure annealed in 75 s, f = 11.2839. Structure annealed in 74 s, f = 11.5104. Structure annealed in 77 s, f = 12.9897. Structure annealed in 76 s, f = 25.9042. Structure annealed in 75 s, f = 13.8368. Structure annealed in 69 s, f = 44.6349. Structure annealed in 79 s, f = 829.447. Structure annealed in 74 s, f = 16.3905. Structure annealed in 78 s, f = 21.3330. Structure annealed in 75 s, f = 13.0644. Structure annealed in 76 s, f = 12.7653. Structure annealed in 72 s, f = 11.8238. Structure annealed in 78 s, f = 15.0945. Structure annealed in 74 s, f = 11.7781. Structure annealed in 75 s, f = 14.0288. Structure annealed in 70 s, f = 26.2366. Structure annealed in 74 s, f = 12.9632. Structure annealed in 76 s, f = 22.2044. Structure annealed in 77 s, f = 12.5650. Structure annealed in 69 s, f = 13.6360. Structure annealed in 75 s, f = 13.3674. Structure annealed in 76 s, f = 13.2117. Structure annealed in 77 s, f = 13.6006. Structure annealed in 78 s, f = 56.8539. Structure annealed in 76 s, f = 39.0141. Structure annealed in 73 s, f = 13.3125. Structure annealed in 73 s, f = 12.9529. Structure annealed in 73 s, f = 22.3174. Structure annealed in 81 s, f = 836.274. Structure annealed in 75 s, f = 11.1828. Structure annealed in 74 s, f = 13.1595. Structure annealed in 76 s, f = 12.3971. Structure annealed in 73 s, f = 12.4327. Structure annealed in 77 s, f = 11.7581. Structure annealed in 76 s, f = 12.9333. Structure annealed in 74 s, f = 15.4990. Structure annealed in 74 s, f = 13.9105. Structure annealed in 69 s, f = 13.4382. Structure annealed in 75 s, f = 12.4550. Structure annealed in 77 s, f = 12.6695. Structure annealed in 73 s, f = 12.0001. Structure annealed in 76 s, f = 12.0959. Structure annealed in 71 s, f = 16.5157. Structure annealed in 75 s, f = 17.5796. Structure annealed in 76 s, f = 28.0343. Structure annealed in 68 s, f = 11.8263. Structure annealed in 74 s, f = 13.0163. Structure annealed in 75 s, f = 11.7315. Structure annealed in 73 s, f = 13.7386. Structure annealed in 77 s, f = 23.3621. Structure annealed in 71 s, f = 12.9118. Structure annealed in 76 s, f = 12.9004. Structure annealed in 68 s, f = 14.1667. Structure annealed in 73 s, f = 13.0736. Structure annealed in 71 s, f = 17.0800. 100 structures finished in 772 s (7 s/structure). - CALC: overview at5g39720.ovw structures=20 pdb Structural statistics: str target upper limits van der Waals torsion angles function # rms max # sum max # rms max 1 9.97 36 0.0273 0.42 8 17.0 0.31 10 2.2094 12.02 2 10.81 43 0.0284 0.47 10 18.4 0.32 10 2.2097 11.90 3 10.98 43 0.0281 0.47 11 18.8 0.36 9 2.2555 11.67 4 11.18 44 0.0293 0.59 10 18.9 0.33 12 2.1438 11.89 5 11.28 47 0.0281 0.52 13 19.7 0.34 7 2.1678 14.87 6 11.51 40 0.0285 0.49 12 19.3 0.40 12 2.3126 11.87 7 11.52 52 0.0297 0.49 9 19.2 0.34 13 2.3561 12.02 8 11.57 50 0.0298 0.47 9 18.8 0.35 10 2.2564 11.72 9 11.58 49 0.0294 0.52 9 19.6 0.35 14 2.2746 12.02 10 11.73 48 0.0295 0.60 13 20.3 0.36 11 2.2125 11.86 11 11.76 36 0.0301 0.79 10 19.6 0.31 13 2.3294 11.84 12 11.78 51 0.0306 0.47 9 18.5 0.30 11 2.3684 13.82 13 11.82 51 0.0299 0.47 8 19.8 0.35 13 2.3785 11.41 14 11.83 47 0.0292 0.49 13 20.7 0.37 11 2.1303 10.82 15 11.92 50 0.0295 0.46 11 19.8 0.32 12 2.3975 13.21 16 11.94 52 0.0296 0.42 10 21.7 0.37 12 2.2135 11.28 17 12.00 49 0.0317 0.79 7 19.6 0.31 15 2.2614 9.03 18 12.02 51 0.0292 0.52 12 20.4 0.40 14 2.3361 11.23 19 12.09 55 0.0308 0.44 9 19.5 0.34 12 2.2818 10.70 20 12.10 46 0.0310 0.52 8 19.7 0.31 12 2.2856 14.11 Ave 11.57 47 0.0295 0.52 10 19.5 0.34 12 2.2691 11.96 +/- 0.51 5 0.0010 0.10 2 1.0 0.03 2 0.0759 1.25 Min 9.97 36 0.0273 0.42 7 17.0 0.30 7 2.1303 9.03 Max 12.10 55 0.0317 0.79 13 21.7 0.40 15 2.3975 14.87 Cut 0.20 0.20 5.00 Overview file "at5g39720.ovw" written. PDB coordinate file "at5g39720.pdb" written, 20 conformers. - CALC: ramaplot at5g39720.rama nobackground label Struct fav add gen dis ------ --- --- --- --- 1 114 31 5 3 (HIS 7, ASP 164, ILE 165) 2 117 34 2 0 3 115 31 6 1 (SER 14) 4 114 36 3 0 5 114 34 5 0 6 109 42 2 0 7 113 36 4 0 8 116 30 6 1 (LYS 156) 9 117 33 2 1 (LYS 156) 10 110 41 2 0 11 116 31 6 0 12 111 40 2 0 13 117 30 4 2 (LYS 155, LYS 156) 14 117 28 8 0 15 109 40 4 0 16 118 32 3 0 17 111 41 1 0 18 114 35 4 0 19 109 42 2 0 20 117 32 4 0 all 74.4% 22.8% 2.5% 0.3% *** ERROR: Graphics file "at5g39720.grf" not found. *** FATAL ERROR: Program aborted. MPI_Recv: process in local group is dead (rank 9, MPI_COMM_WORLD) MPI_Recv: process in local group is dead (rank 10, MPI_COMM_WORLD) ----------------------------------------------------------------------------- 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 23214 failed on node n0 with exit status 1. ----------------------------------------------------------------------------- MPI_Recv: process in local group is dead (rank 8, MPI_COMM_WORLD) Rank (10, MPI_COMM_WORLD): Call stack within LAM: Rank (10, MPI_COMM_WORLD): - MPI_Recv() Rank (10, MPI_COMM_WORLD): - MPI_Bcast() Rank (10, 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): - main() Rank (9, MPI_COMM_WORLD): Call stack within LAM: Rank (9, MPI_COMM_WORLD): - MPI_Recv() Rank (9, MPI_COMM_WORLD): - MPI_Bcast() Rank (9, MPI_COMM_WORLD): - main() LAM 6.5.9/MPI 2 C++/ROMIO - Indiana University 27-Dec-2005 17:19:03