Warning: no access to tty (Bad file descriptor). Thus no job control in this shell. 27-Dec-2005 22:18:46 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: Inconsistent heavy atom assignment for peak 3034. *** WARNING: Inconsistent heavy atom assignment for peak 3038. Peak list "c13no_new.peaks" read, 3506 peaks, 2932 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 2933 0.003 0.003 0.030 0.013 0 0.040 2 2942 -0.003 -0.004 0.030 0.009 0 0.030 3 2942 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= *** WARNING: Inconsistent heavy atom assignment for peak 247. Peak list "n15no_new.peaks" read, 1837 peaks, 1509 assignments. - peakcheck: peaks fit Deviations from chemical shift list: Dim Peaks Median Average Maximum RMSD Number Tolerance 1 1510 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, 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 .0E7,1.0E07,6.0E6 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: Inconsistent heavy atom assignment for peak 3034. *** WARNING: Inconsistent heavy atom assignment for peak 3038. Peak list "c13no_new.peaks" read, 3506 peaks, 2932 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 constant=1.0E7 Calibration constant for peak list 1: 1.00E+07 Upper limit set for 3506 peaks. - calibration: caltab peaks Distance bounds: -2.99 A: 457 13.0% 3.00-3.99 A: 1180 33.7% 4.00-4.99 A: 1530 43.6% 5.00-5.99 A: 338 9.6% 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 *** WARNING: Inconsistent heavy atom assignment for peak 247. Peak list "n15no_new.peaks" read, 1837 peaks, 1509 assignments. - calibration: peaks select "** list=2" 1837 of 5343 peaks, 1837 of 5343 assignments selected. - calibration: peaks set volume=abs(volume) Volume of 1837 peaks set. - calibration: peaks simplecal constant=1.0E07 Calibration constant for peak list 2: 1.00E+07 Upper limit set for 1837 peaks. - calibration: caltab peaks Distance bounds: -2.99 A: 143 7.8% 3.00-3.99 A: 520 28.3% 4.00-4.99 A: 898 48.9% 5.00-5.99 A: 274 14.9% 6.00- A: 0 0.0% All: 1837 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 5914 peaks, 571 of 5914 assignments selected. - calibration: peaks set volume=abs(volume) Volume of 571 peaks set. - calibration: peaks simplecal constant=6.0E6 Calibration constant for peak list 3: 6.00E+06 Upper limit set for 571 peaks. - calibration: caltab peaks Distance bounds: -2.99 A: 53 9.3% 3.00-3.99 A: 140 24.5% 4.00-4.99 A: 324 56.7% 5.00-5.99 A: 53 9.3% 6.00- A: 0 0.0% All: 571 100.0% - calibration: peaks select ** 5914 of 5914 peaks, 5914 of 5914 assignments selected. - CALC: peaks calibrate ** simple 4080 upper limits added, 6/63 at lower/upper bound, average 4.22 A. - CALC: write upl at5g39720-in.upl Distance constraint file "at5g39720-in.upl" written, 4080 upper limits, 4080 assignments. - CALC: distance modify Number of modified constraints: 2086 - CALC: write upl at5g39720.upl Distance constraint file "at5g39720.upl" written, 2086 upper limits, 2086 assignments. - CALC: read seq at5g39720.seq Sequence file "at5g39720.seq" read, 173 residues. - CALC: read upl at5g39720.upl Distance constraint file "at5g39720.upl" read, 2086 upper limits, 2086 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 75 s, f = 12.9896. Structure annealed in 77 s, f = 8.76793. Structure annealed in 73 s, f = 9.04128. Structure annealed in 73 s, f = 7.71187. Structure annealed in 76 s, f = 11.5803. Structure annealed in 75 s, f = 28.8208. Structure annealed in 72 s, f = 7.80063. Structure annealed in 74 s, f = 19.1629. Structure annealed in 73 s, f = 8.20214. Structure annealed in 73 s, f = 10.0498. Structure annealed in 75 s, f = 11.8146. Structure annealed in 74 s, f = 9.01580. Structure annealed in 76 s, f = 9.26982. Structure annealed in 73 s, f = 9.07399. Structure annealed in 72 s, f = 8.20654. Structure annealed in 72 s, f = 8.47295. Structure annealed in 72 s, f = 18.6511. Structure annealed in 75 s, f = 8.00320. Structure annealed in 72 s, f = 9.13417. Structure annealed in 72 s, f = 15.6858. Structure annealed in 77 s, f = 7.76518. Structure annealed in 76 s, f = 8.34392. Structure annealed in 75 s, f = 19.2660. Structure annealed in 70 s, f = 32.2956. Structure annealed in 73 s, f = 9.58905. Structure annealed in 86 s, f = 818.550. Structure annealed in 75 s, f = 12.7112. Structure annealed in 74 s, f = 8.57633. Structure annealed in 75 s, f = 11.5303. Structure annealed in 75 s, f = 7.09219. Structure annealed in 74 s, f = 8.26526. Structure annealed in 75 s, f = 10.6224. Structure annealed in 75 s, f = 19.5968. Structure annealed in 75 s, f = 19.5642. Structure annealed in 76 s, f = 8.81639. Structure annealed in 74 s, f = 7.85200. Structure annealed in 75 s, f = 8.16401. Structure annealed in 69 s, f = 7.83494. Structure annealed in 74 s, f = 9.71426. Structure annealed in 74 s, f = 7.47474. Structure annealed in 70 s, f = 9.43286. Structure annealed in 77 s, f = 9.20186. Structure annealed in 67 s, f = 6.98167. Structure annealed in 74 s, f = 6.92932. Structure annealed in 77 s, f = 7.59510. Structure annealed in 74 s, f = 6.61479. Structure annealed in 74 s, f = 9.50522. Structure annealed in 72 s, f = 8.01513. Structure annealed in 72 s, f = 8.13382. Structure annealed in 75 s, f = 10.7595. Structure annealed in 74 s, f = 8.45699. Structure annealed in 83 s, f = 737.801. Structure annealed in 73 s, f = 8.47203. Structure annealed in 75 s, f = 7.06285. Structure annealed in 76 s, f = 8.91669. Structure annealed in 72 s, f = 7.59369. Structure annealed in 76 s, f = 10.5395. Structure annealed in 77 s, f = 9.41484. Structure annealed in 76 s, f = 7.83975. Structure annealed in 67 s, f = 10.4222. Structure annealed in 76 s, f = 8.78048. Structure annealed in 68 s, f = 9.15395. Structure annealed in 73 s, f = 8.35946. Structure annealed in 76 s, f = 22.0781. Structure annealed in 74 s, f = 7.01471. Structure annealed in 74 s, f = 10.6750. Structure annealed in 71 s, f = 9.14246. Structure annealed in 76 s, f = 19.9969. Structure annealed in 69 s, f = 7.52976. Structure annealed in 73 s, f = 9.21601. Structure annealed in 72 s, f = 9.56249. Structure annealed in 72 s, f = 7.83172. Structure annealed in 76 s, f = 8.12320. Structure annealed in 77 s, f = 19.5669. Structure annealed in 73 s, f = 8.31790. Structure annealed in 76 s, f = 7.83802. Structure annealed in 75 s, f = 7.75832. Structure annealed in 67 s, f = 11.0201. Structure annealed in 75 s, f = 10.4157. Structure annealed in 75 s, f = 7.53968. Structure annealed in 71 s, f = 19.2782. Structure annealed in 69 s, f = 7.53257. Structure annealed in 69 s, f = 9.87450. Structure annealed in 74 s, f = 8.16944. Structure annealed in 71 s, f = 10.0786. Structure annealed in 76 s, f = 7.19696. Structure annealed in 72 s, f = 8.93972. Structure annealed in 74 s, f = 11.8268. Structure annealed in 73 s, f = 8.65159. Structure annealed in 69 s, f = 8.35344. Structure annealed in 72 s, f = 8.97957. Structure annealed in 71 s, f = 8.76418. Structure annealed in 75 s, f = 10.1262. Structure annealed in 68 s, f = 11.5616. Structure annealed in 71 s, f = 6.99351. Structure annealed in 69 s, f = 7.75135. Structure annealed in 73 s, f = 8.35497. Structure annealed in 75 s, f = 41.8308. Structure annealed in 76 s, f = 11.3943. Structure annealed in 75 s, f = 7.55554. 100 structures finished in 395 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 6.61 15 0.0193 0.36 7 14.4 0.35 7 2.0284 11.05 2 6.93 15 0.0195 0.35 12 15.2 0.36 8 1.9116 10.59 3 6.98 20 0.0197 0.34 10 14.3 0.42 6 1.9183 11.39 4 6.99 17 0.0209 0.64 7 13.4 0.35 9 2.0685 11.30 5 7.01 19 0.0209 0.59 5 14.5 0.35 10 2.0558 12.69 6 7.06 17 0.0200 0.36 7 15.0 0.36 7 1.9957 11.01 7 7.09 19 0.0194 0.33 8 14.7 0.48 8 1.9808 10.99 8 7.20 19 0.0205 0.40 8 14.8 0.36 8 2.0317 11.34 9 7.47 19 0.0204 0.35 6 15.9 0.37 10 2.0769 11.61 10 7.53 21 0.0213 0.58 6 15.9 0.34 10 2.0489 11.56 11 7.53 21 0.0210 0.36 7 15.5 0.44 7 2.0354 13.84 12 7.54 22 0.0217 0.61 7 16.0 0.32 10 2.1248 11.42 13 7.56 19 0.0219 0.61 8 14.7 0.44 7 1.9466 11.79 14 7.59 21 0.0200 0.43 9 15.8 0.38 8 2.0480 12.35 15 7.60 19 0.0224 0.57 8 16.5 0.34 7 1.8067 8.86 16 7.71 20 0.0220 0.59 9 17.6 0.41 7 1.7643 8.72 17 7.75 21 0.0218 0.43 7 15.9 0.33 13 2.2371 12.84 18 7.76 24 0.0212 0.34 11 16.3 0.35 9 2.0008 12.47 19 7.77 18 0.0210 0.63 11 16.8 0.35 10 1.8808 9.45 20 7.80 21 0.0204 0.35 11 16.0 0.47 8 2.0339 11.56 Ave 7.37 19 0.0208 0.46 8 15.5 0.38 8 1.9998 11.34 +/- 0.34 2 0.0009 0.12 2 1.0 0.05 2 0.1047 1.23 Min 6.61 15 0.0193 0.33 5 13.4 0.32 6 1.7643 8.72 Max 7.80 24 0.0224 0.64 12 17.6 0.48 13 2.2371 13.84 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 ------ --- --- --- --- 1 109 39 4 1 (ASN 131) 2 119 28 5 1 (VAL 168) 3 116 31 4 2 (ASP 13, LYS 156) 4 118 29 6 0 5 118 31 4 0 6 113 35 5 0 7 117 29 7 0 8 111 37 5 0 9 113 34 6 0 10 114 30 8 1 (ARG 170) 11 116 30 5 2 (ASP 13, LYS 155) 12 112 37 4 0 13 114 33 5 1 (HIS 4) 14 115 28 6 4 (LYS 156, GLN 160, ILE 165, GLU 171) 15 112 34 6 1 (LYS 156) 16 112 34 5 2 (ASN 131, VAL 168) 17 122 26 5 0 18 115 31 7 0 19 116 33 4 0 20 115 31 7 0 all 75.1% 20.9% 3.5% 0.5% Postscript file "at5g39720.rama" written. cyana> LAM 6.5.9/MPI 2 C++/ROMIO - Indiana University 27-Dec-2005 22:27:14