Warning: no access to tty (Bad file descriptor). Thus no job control in this shell. 14-Jan-2006 13:52:56 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, 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= *** WARNING: Assignment of peak 3015 not found in chemical shift list. Peak list "c13no_new.peaks" read, 3517 peaks, 2924 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 0.033 0.013 0 0.040 2 2958 -0.003 -0.004 0.030 0.009 0 0.030 3 2958 0.000 -0.022 0.431 0.092 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, 1821 peaks, 1501 assignments. - peakcheck: peaks fit Deviations from chemical shift list: Dim Peaks Median Average Maximum RMSD Number Tolerance 1 1503 0.005 0.005 0.049 0.013 1 0.040 2 1508 0.000 0.000 0.029 0.005 0 0.030 3 1508 0.001 0.010 0.276 0.055 0 0.450 - peakcheck: atom shift check Atom Residue Shift Median Deviation Peaks HA VAL 43 4.640 4.659 0.049 3 1 shift with spread larger than tolerance. - peakcheck: peak deviations Peak Dim Deviation Atom Residue 834 1 0.049 HA VAL 43 1 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, 571 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 2 273 -0.006 -0.006 0.019 0.009 0 0.030 3 273 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 constant=1 .0E7,1.4E07,7.0E6 dref=4.2 - calibration: read prot at5g39720 unknown=warn Chemical shift list "at5g39720.prot" read, 1646 chemical shifts. - calibration: read peaks c13no_new format= *** WARNING: Assignment of peak 3015 not found in chemical shift list. Peak list "c13no_new.peaks" read, 3517 peaks, 2924 assignments. - calibration: peaks select "** list=1" 3517 of 3517 peaks, 3517 of 3517 assignments selected. - calibration: peaks set volume=abs(volume) Volume of 3517 peaks set. - calibration: peaks simplecal constant=1.0E7 Calibration constant for peak list 1: 1.00E+07 Upper limit set for 3517 peaks. - calibration: caltab peaks Distance bounds: -2.99 A: 459 13.1% 3.00-3.99 A: 1187 33.8% 4.00-4.99 A: 1537 43.7% 5.00-5.99 A: 333 9.5% 6.00- A: 0 0.0% All: 3517 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, 1821 peaks, 1501 assignments. - calibration: peaks select "** list=2" 1821 of 5338 peaks, 1821 of 5338 assignments selected. - calibration: peaks set volume=abs(volume) Volume of 1821 peaks set. - calibration: peaks simplecal constant=1.4E07 Calibration constant for peak list 2: 1.40E+07 Upper limit set for 1821 peaks. - calibration: caltab peaks Distance bounds: -2.99 A: 121 6.6% 3.00-3.99 A: 347 19.1% 4.00-4.99 A: 886 48.7% 5.00-5.99 A: 465 25.5% 6.00- A: 0 0.0% All: 1821 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, 571 peaks, 272 assignments. - calibration: peaks select "** list=3" 571 of 5909 peaks, 571 of 5909 assignments selected. - calibration: peaks set volume=abs(volume) Volume of 571 peaks set. - calibration: peaks simplecal constant=7.0E6 Calibration constant for peak list 3: 7.00E+06 Upper limit set for 571 peaks. - calibration: caltab peaks Distance bounds: -2.99 A: 53 9.3% 3.00-3.99 A: 109 19.1% 4.00-4.99 A: 324 56.7% 5.00-5.99 A: 82 14.4% 6.00- A: 0 0.0% All: 571 100.0% - calibration: peaks select ** 5909 of 5909 peaks, 5909 of 5909 assignments selected. - CALC: peaks calibrate ** simple 4060 upper limits added, 4/135 at lower/upper bound, average 4.30 A. - CALC: write upl at5g39720-in.upl Distance constraint file "at5g39720-in.upl" written, 4060 upper limits, 4060 assignments. - CALC: distance modify Number of modified constraints: 2019 - CALC: write upl at5g39720.upl Distance constraint file "at5g39720.upl" written, 2019 upper limits, 2019 assignments. - CALC: read seq at5g39720.seq Sequence file "at5g39720.seq" read, 173 residues. - CALC: read upl at5g39720.upl Distance constraint file "at5g39720.upl" read, 2019 upper limits, 2019 assignments. - CALC: read aco at5g39720.aco Angle constraint file "at5g39720.aco" read, 193 constraints for 193 angles. - CALC: calc_all structures=100 command=anneal steps=10000 100 structures selected. 100 random structures created (seed 5671). Structure annealed in 70 s, f = 2.24095. Structure annealed in 73 s, f = 26.1114. Structure annealed in 74 s, f = 12.1061. Structure annealed in 73 s, f = 4.15532. Structure annealed in 76 s, f = 26.6191. Structure annealed in 74 s, f = 10.4062. Structure annealed in 75 s, f = 3.54563. Structure annealed in 73 s, f = 2.92467. Structure annealed in 73 s, f = 3.94305. Structure annealed in 71 s, f = 5.69104. Structure annealed in 89 s, f = 901.336. Structure annealed in 73 s, f = 3.03058. Structure annealed in 71 s, f = 3.27296. Structure annealed in 67 s, f = 19.7209. Structure annealed in 71 s, f = 3.08130. Structure annealed in 73 s, f = 3.23738. Structure annealed in 74 s, f = 2.23374. Structure annealed in 73 s, f = 5.54160. Structure annealed in 72 s, f = 2.44756. Structure annealed in 74 s, f = 12.6718. Structure annealed in 70 s, f = 5.56201. Structure annealed in 69 s, f = 2.39856. Structure annealed in 74 s, f = 2.95627. Structure annealed in 70 s, f = 2.64082. Structure annealed in 70 s, f = 7.54109. Structure annealed in 71 s, f = 4.38398. Structure annealed in 69 s, f = 4.06494. Structure annealed in 76 s, f = 12.6099. Structure annealed in 71 s, f = 4.45986. Structure annealed in 71 s, f = 4.94011. Structure annealed in 73 s, f = 2.00482. Structure annealed in 74 s, f = 4.67344. Structure annealed in 72 s, f = 2.26266. Structure annealed in 73 s, f = 4.15066. Structure annealed in 70 s, f = 3.05627. Structure annealed in 72 s, f = 2.97403. Structure annealed in 75 s, f = 4.34332. Structure annealed in 70 s, f = 2.97313. Structure annealed in 83 s, f = 669.448. Structure annealed in 74 s, f = 3.20279. Structure annealed in 77 s, f = 578.337. Structure annealed in 71 s, f = 13.3468. Structure annealed in 65 s, f = 2.61099. Structure annealed in 71 s, f = 11.0098. Structure annealed in 71 s, f = 4.72473. Structure annealed in 74 s, f = 3.68209. Structure annealed in 73 s, f = 4.14975. Structure annealed in 72 s, f = 4.02843. Structure annealed in 72 s, f = 5.47623. Structure annealed in 72 s, f = 2.61901. Structure annealed in 75 s, f = 26.9108. Structure annealed in 75 s, f = 11.2780. Structure annealed in 74 s, f = 3.86270. Structure annealed in 74 s, f = 3.51238. Structure annealed in 73 s, f = 1.71851. Structure annealed in 75 s, f = 2.64813. Structure annealed in 73 s, f = 2.02604. Structure annealed in 72 s, f = 1.87518. Structure annealed in 73 s, f = 3.03586. Structure annealed in 74 s, f = 2.82260. Structure annealed in 70 s, f = 2.56274. Structure annealed in 73 s, f = 2.66031. Structure annealed in 70 s, f = 3.58331. Structure annealed in 70 s, f = 4.46095. Structure annealed in 71 s, f = 29.3504. Structure annealed in 71 s, f = 2.79196. Structure annealed in 73 s, f = 4.54245. Structure annealed in 70 s, f = 3.33098. Structure annealed in 74 s, f = 5.48712. Structure annealed in 71 s, f = 2.97803. Structure annealed in 81 s, f = 659.397. Structure annealed in 77 s, f = 5.01143. Structure annealed in 67 s, f = 3.77299. Structure annealed in 75 s, f = 3.34698. Structure annealed in 72 s, f = 2.48009. Structure annealed in 73 s, f = 3.48780. Structure annealed in 74 s, f = 4.04491. Structure annealed in 74 s, f = 2.77224. Structure annealed in 73 s, f = 2.87846. Structure annealed in 72 s, f = 4.79697. Structure annealed in 70 s, f = 3.26853. Structure annealed in 74 s, f = 2.59333. Structure annealed in 74 s, f = 3.78099. Structure annealed in 72 s, f = 33.7640. Structure annealed in 69 s, f = 3.33508. Structure annealed in 70 s, f = 12.1169. Structure annealed in 70 s, f = 2.54720. Structure annealed in 74 s, f = 2.50289. Structure annealed in 74 s, f = 45.2300. Structure annealed in 70 s, f = 11.2751. Structure annealed in 73 s, f = 10.3979. Structure annealed in 69 s, f = 1.89330. Structure annealed in 72 s, f = 3.09970. Structure annealed in 73 s, f = 3.58552. Structure annealed in 72 s, f = 15.1843. Structure annealed in 69 s, f = 1.66668. Structure annealed in 71 s, f = 26.8240. Structure annealed in 74 s, f = 29.3614. Structure annealed in 68 s, f = 2.39126. Structure annealed in 69 s, f = 4.03400. 100 structures finished in 386 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 1.67 0 0.0081 0.17 2 6.8 0.31 0 0.6365 3.70 2 1.72 0 0.0075 0.20 4 6.5 0.30 0 0.6990 3.58 3 1.88 0 0.0087 0.18 3 6.9 0.30 0 0.8554 4.70 4 1.89 2 0.0084 0.24 4 7.6 0.25 1 0.7359 5.18 5 2.00 0 0.0078 0.20 3 7.7 0.30 0 0.6687 3.50 6 2.03 1 0.0083 0.20 4 8.0 0.29 1 0.8137 5.13 7 2.23 1 0.0098 0.26 5 8.2 0.27 1 0.8838 5.86 8 2.24 3 0.0105 0.45 3 8.5 0.30 0 0.7621 4.38 9 2.26 1 0.0098 0.41 4 8.1 0.29 0 0.7974 4.81 10 2.39 2 0.0100 0.28 4 8.6 0.30 0 0.9020 4.81 11 2.40 4 0.0103 0.27 5 8.7 0.30 0 0.6912 3.16 12 2.45 2 0.0101 0.31 5 8.5 0.30 1 0.8435 5.70 13 2.48 3 0.0099 0.22 4 9.3 0.24 0 0.8750 4.79 14 2.50 5 0.0116 0.47 3 8.0 0.30 2 0.9177 6.71 15 2.55 3 0.0125 0.47 2 8.2 0.26 0 0.8537 4.79 16 2.56 3 0.0108 0.31 5 8.5 0.30 0 0.7552 3.83 17 2.59 2 0.0119 0.58 3 8.7 0.30 1 0.8229 5.03 18 2.61 2 0.0108 0.35 3 9.0 0.30 0 0.7656 3.69 19 2.62 4 0.0120 0.33 3 9.1 0.30 0 0.7985 4.47 20 2.64 3 0.0110 0.28 6 8.7 0.30 0 0.7384 3.70 Ave 2.29 2 0.0100 0.31 4 8.2 0.29 0 0.7908 4.58 +/- 0.31 1 0.0014 0.11 1 0.7 0.02 1 0.0782 0.88 Min 1.67 0 0.0075 0.17 2 6.5 0.24 0 0.6365 3.16 Max 2.64 5 0.0125 0.58 6 9.3 0.31 2 0.9177 6.71 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 ------ --- --- --- --- 1 125 26 2 0 2 120 29 4 0 3 112 38 2 1 (LYS 56) 4 123 26 4 0 5 124 26 3 0 6 122 27 4 0 7 123 28 2 0 8 121 29 3 0 9 116 30 4 3 (ASN 131, LYS 156, ASP 172) 10 120 31 2 0 11 113 37 2 1 (ARG 58) 12 127 22 3 1 (LYS 155) 13 116 31 6 0 14 110 39 3 1 (HIS 2) 15 117 28 7 1 (LYS 155) 16 123 25 5 0 17 120 30 2 1 (GLN 160) 18 120 27 6 0 19 121 27 5 0 20 127 22 4 0 all 78.4% 18.9% 2.4% 0.3% Postscript file "at5g39720.rama" written. cyana> LAM 6.5.9/MPI 2 C++/ROMIO - Indiana University 14-Jan-2006 14:01:18