Warning: no access to tty (Bad file descriptor). Thus no job control in this shell. 16-Dec-2005 13:54:36 LAM 6.5.9/MPI 2 C++/ROMIO - Indiana University Executing hboot on n0 (cesg-node13.biochem.wisc.edu - 2 CPUs)... Executing hboot on n1 (cesg-node12.biochem.wisc.edu - 2 CPUs)... Executing hboot on n2 (cesg-node11.biochem.wisc.edu - 2 CPUs)... Executing hboot on n3 (cesg-node10.biochem.wisc.edu - 2 CPUs)... Executing hboot on n4 (cesg-node9.biochem.wisc.edu - 2 CPUs)... Executing hboot on n5 (cesg-node8.biochem.wisc.edu - 2 CPUs)... Executing hboot on n6 (cesg-node7.biochem.wisc.edu - 2 CPUs)... Executing hboot on n7 (cesg-node6.biochem.wisc.edu - 2 CPUs)... Executing hboot on n8 (cesg-node5.biochem.wisc.edu - 2 CPUs)... Executing hboot on n9 (cesg-node4.biochem.wisc.edu - 2 CPUs)... topology n0 (o)... n1... n2... n3... n4... n5... n6... n7... n8... n9... 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, 1645 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 83 HG2 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 186 missing chemical shifts, completeness 81.1%. ------------------------------------------------------------ Peak list : c13no_new Proton list: at5g39720 - peakcheck: read prot at5g39720 unknown=skip Chemical shift list "at5g39720.prot" read, 1645 chemical shifts. - peakcheck: read peaks c13no_new format= Peak list "c13no_new.peaks" read, 3501 peaks, 2936 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 2936 0.003 0.003 0.030 0.013 0 0.040 2 2936 -0.003 -0.004 0.030 0.009 0 0.030 3 2936 0.000 -0.020 0.299 0.091 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, 1645 chemical shifts. - peakcheck: read peaks n15no_new format= Peak list "n15no_new.peaks" read, 1847 peaks, 1520 assignments. - peakcheck: peaks fit Deviations from chemical shift list: Dim Peaks Median Average Maximum RMSD Number Tolerance 1 1520 0.005 0.005 0.032 0.013 0 0.040 2 1520 0.000 0.000 0.029 0.005 0 0.030 3 1520 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, 1645 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: read seq at5g39720.seq Sequence file "at5g39720.seq" read, 173 residues. - CALC: read upl sort_cycle7.upl Distance constraint file "sort_cycle7.upl" read, 2150 upper limits, 2150 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 72 s, f = 26.0697. Structure annealed in 68 s, f = 23.2814. Structure annealed in 71 s, f = 25.6678. Structure annealed in 70 s, f = 22.8962. Structure annealed in 70 s, f = 37.6833. Structure annealed in 69 s, f = 28.4760. Structure annealed in 69 s, f = 23.5963. Structure annealed in 65 s, f = 27.4564. Structure annealed in 70 s, f = 26.7936. Structure annealed in 70 s, f = 21.4098. Structure annealed in 70 s, f = 23.3282. Structure annealed in 73 s, f = 24.7453. Structure annealed in 70 s, f = 21.0220. Structure annealed in 67 s, f = 23.3931. Structure annealed in 69 s, f = 21.3289. Structure annealed in 68 s, f = 38.1306. Structure annealed in 68 s, f = 26.6669. Structure annealed in 68 s, f = 27.3637. Structure annealed in 71 s, f = 27.0654. Structure annealed in 68 s, f = 23.4045. Structure annealed in 67 s, f = 23.6671. Structure annealed in 70 s, f = 51.7451. Structure annealed in 68 s, f = 51.1903. Structure annealed in 68 s, f = 24.5140. Structure annealed in 68 s, f = 24.3279. Structure annealed in 67 s, f = 23.0759. Structure annealed in 68 s, f = 26.1273. Structure annealed in 72 s, f = 24.0536. Structure annealed in 69 s, f = 23.0110. Structure annealed in 70 s, f = 28.4238. Structure annealed in 69 s, f = 22.1062. Structure annealed in 71 s, f = 25.5341. Structure annealed in 70 s, f = 24.5467. Structure annealed in 70 s, f = 26.6120. Structure annealed in 68 s, f = 25.1565. Structure annealed in 68 s, f = 24.5491. Structure annealed in 70 s, f = 25.7862. Structure annealed in 68 s, f = 42.2738. Structure annealed in 68 s, f = 26.3007. Structure annealed in 68 s, f = 23.1021. Structure annealed in 64 s, f = 23.7162. Structure annealed in 68 s, f = 30.9611. Structure annealed in 68 s, f = 22.3767. Structure annealed in 67 s, f = 24.1391. Structure annealed in 65 s, f = 22.9790. Structure annealed in 68 s, f = 25.2345. Structure annealed in 68 s, f = 28.5647. Structure annealed in 68 s, f = 25.5155. Structure annealed in 68 s, f = 50.1951. Structure annealed in 65 s, f = 23.6641. Structure annealed in 68 s, f = 26.5651. Structure annealed in 71 s, f = 27.3708. Structure annealed in 69 s, f = 23.7764. Structure annealed in 70 s, f = 24.5441. Structure annealed in 72 s, f = 28.6681. Structure annealed in 73 s, f = 70.6086. Structure annealed in 70 s, f = 22.0809. Structure annealed in 69 s, f = 20.8389. Structure annealed in 69 s, f = 23.0267. Structure annealed in 68 s, f = 23.9846. Structure annealed in 68 s, f = 21.1904. Structure annealed in 69 s, f = 23.6717. Structure annealed in 67 s, f = 23.8363. Structure annealed in 69 s, f = 44.6081. Structure annealed in 72 s, f = 72.3310. Structure annealed in 67 s, f = 21.9838. Structure annealed in 69 s, f = 22.0835. Structure annealed in 68 s, f = 27.8728. Structure annealed in 68 s, f = 26.5127. Structure annealed in 69 s, f = 21.4323. Structure annealed in 69 s, f = 26.9877. Structure annealed in 69 s, f = 44.7481. Structure annealed in 69 s, f = 26.0530. Structure annealed in 67 s, f = 25.1237. Structure annealed in 69 s, f = 23.4160. Structure annealed in 73 s, f = 23.6646. Structure annealed in 72 s, f = 27.4542. Structure annealed in 71 s, f = 26.7007. Structure annealed in 68 s, f = 21.6944. Structure annealed in 70 s, f = 24.1357. Structure annealed in 68 s, f = 24.6309. Structure annealed in 68 s, f = 31.7972. Structure annealed in 68 s, f = 24.3033. Structure annealed in 67 s, f = 39.7449. Structure annealed in 65 s, f = 24.8306. Structure annealed in 68 s, f = 21.8694. Structure annealed in 68 s, f = 23.0994. Structure annealed in 68 s, f = 45.8756. Structure annealed in 70 s, f = 47.4591. Structure annealed in 67 s, f = 23.5733. Structure annealed in 69 s, f = 31.4828. Structure annealed in 68 s, f = 27.7017. Structure annealed in 67 s, f = 22.9630. Structure annealed in 65 s, f = 23.2635. Structure annealed in 67 s, f = 22.8787. Structure annealed in 68 s, f = 24.0558. Structure annealed in 68 s, f = 21.9004. Structure annealed in 59 s, f = 26.6280. Structure annealed in 72 s, f = 51.0366. Structure annealed in 71 s, f = 315.357. 100 structures finished in 369 s (3 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 20.84 64 0.0574 1.24 15 19.2 0.30 17 2.8093 11.66 2 21.02 66 0.0575 1.13 16 20.0 0.30 15 2.6988 11.79 3 21.19 66 0.0570 1.22 13 21.7 0.38 16 2.6889 13.44 4 21.33 64 0.0580 1.23 11 20.3 0.33 16 2.7492 13.04 5 21.41 64 0.0574 1.14 16 21.2 0.36 17 2.7221 11.94 6 21.43 73 0.0581 1.16 15 21.2 0.30 15 2.7976 12.61 7 21.69 68 0.0584 1.13 14 20.9 0.31 17 2.7745 12.96 8 21.87 64 0.0574 1.23 15 22.8 0.31 18 2.8404 13.92 9 21.90 66 0.0578 1.15 16 22.7 0.32 17 2.7433 12.37 10 21.98 68 0.0586 1.23 15 21.0 0.32 15 2.7789 11.47 11 22.08 64 0.0582 1.14 16 22.5 0.31 18 2.8070 11.55 12 22.08 70 0.0588 1.15 13 22.0 0.31 17 2.8277 12.45 13 22.11 71 0.0588 1.14 14 22.0 0.34 16 2.7429 12.21 14 22.38 66 0.0590 1.22 14 22.1 0.30 17 2.8136 12.81 15 22.88 67 0.0593 1.15 17 23.3 0.30 17 2.8578 14.41 16 22.90 75 0.0597 1.14 15 23.4 0.32 16 2.7132 13.78 17 22.96 65 0.0596 1.14 17 22.6 0.30 19 2.8930 15.82 18 22.98 71 0.0590 1.22 17 23.3 0.31 19 2.8900 12.29 19 23.01 71 0.0592 1.14 16 24.1 0.32 15 2.7934 13.25 20 23.03 76 0.0592 1.15 17 23.8 0.31 14 2.7535 12.60 Ave 22.05 68 0.0584 1.17 15 22.0 0.32 17 2.7848 12.82 +/- 0.70 4 0.0008 0.04 2 1.3 0.02 1 0.0577 1.05 Min 20.84 64 0.0570 1.13 11 19.2 0.30 14 2.6889 11.47 Max 23.03 76 0.0597 1.24 17 24.1 0.38 19 2.8930 15.82 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 ------ --- --- --- --- 1 113 35 4 1 (GLN 16) 2 113 34 5 1 (HIS 5) 3 121 28 4 0 4 114 34 3 2 (HIS 6, GLN 16) 5 123 24 5 1 (GLN 16) 6 115 33 5 0 7 118 28 6 1 (GLN 16) 8 117 31 4 1 (GLN 16) 9 120 29 3 1 (GLN 16) 10 117 30 5 1 (SER 11) 11 117 30 4 2 (ASP 13, GLN 16) 12 114 29 8 2 (ASP 13, ASN 162) 13 114 33 5 1 (GLN 16) 14 115 29 8 1 (VAL 168) 15 115 33 4 1 (GLN 16) 16 116 34 3 0 17 120 29 2 2 (GLN 16, LYS 156) 18 116 31 5 1 (GLN 16) 19 115 36 2 0 20 117 29 6 1 (GLN 16) all 76.1% 20.2% 3.0% 0.7% Postscript file "at5g39720.rama" written. cyana> LAM 6.5.9/MPI 2 C++/ROMIO - Indiana University 16-Dec-2005 14:02:39