Warning: no access to tty (Bad file descriptor). Thus no job control in this shell. 29-Dec-2005 22:07:46 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 238. *** WARNING: Inconsistent heavy atom assignment for peak 3034. *** WARNING: Inconsistent heavy atom assignment for peak 3038. *** WARNING: Inconsistent heavy atom assignment for peak 3612. Peak list "c13no_new.peaks" read, 3519 peaks, 2939 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 2940 0.003 0.003 0.044 0.013 2 0.040 2 2957 -0.003 -0.004 0.030 0.009 0 0.030 3 2957 0.000 -0.021 0.431 0.092 0 0.450 - peakcheck: atom shift check Atom Residue Shift Median Deviation Peaks QG1 VAL 75 0.748 0.753 0.042 19 HA MET 77 5.144 5.164 0.044 8 2 shifts with spread larger than tolerance. - peakcheck: peak deviations Peak Dim Deviation Atom Residue 4406 1 0.044 HA MET 77 4702 1 0.042 QG1 VAL 75 2 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, 1838 peaks, 1508 assignments. - peakcheck: peaks fit Deviations from chemical shift list: Dim Peaks Median Average Maximum RMSD Number Tolerance 1 1510 0.004 0.005 0.049 0.013 1 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 HA VAL 43 4.640 4.656 0.049 4 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 .0E7,1.2E07,6.0E6 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 238. *** WARNING: Inconsistent heavy atom assignment for peak 3034. *** WARNING: Inconsistent heavy atom assignment for peak 3038. *** WARNING: Inconsistent heavy atom assignment for peak 3612. Peak list "c13no_new.peaks" read, 3519 peaks, 2939 assignments. - calibration: peaks select "** list=1" 3519 of 3519 peaks, 3519 of 3519 assignments selected. - calibration: peaks set volume=abs(volume) Volume of 3519 peaks set. - calibration: peaks simplecal constant=1.0E7 Calibration constant for peak list 1: 1.00E+07 Upper limit set for 3519 peaks. - calibration: caltab peaks Distance bounds: -2.99 A: 460 13.1% 3.00-3.99 A: 1185 33.7% 4.00-4.99 A: 1534 43.6% 5.00-5.99 A: 339 9.6% 6.00- A: 0 0.0% All: 3519 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, 1838 peaks, 1508 assignments. - calibration: peaks select "** list=2" 1838 of 5357 peaks, 1838 of 5357 assignments selected. - calibration: peaks set volume=abs(volume) Volume of 1838 peaks set. - calibration: peaks simplecal constant=1.2E07 Calibration constant for peak list 2: 1.20E+07 Upper limit set for 1838 peaks. - calibration: caltab peaks Distance bounds: -2.99 A: 133 7.2% 3.00-3.99 A: 424 23.1% 4.00-4.99 A: 905 49.2% 5.00-5.99 A: 376 20.5% 6.00- A: 0 0.0% All: 1838 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 5928 peaks, 571 of 5928 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 ** 5928 of 5928 peaks, 5928 of 5928 assignments selected. - CALC: peaks calibrate ** simple 4083 upper limits added, 5/97 at lower/upper bound, average 4.26 A. - CALC: write upl at5g39720-in.upl Distance constraint file "at5g39720-in.upl" written, 4083 upper limits, 4083 assignments. - CALC: distance modify Number of modified constraints: 2049 - CALC: write upl at5g39720.upl Distance constraint file "at5g39720.upl" written, 2049 upper limits, 2049 assignments. - CALC: read seq at5g39720.seq Sequence file "at5g39720.seq" read, 173 residues. - CALC: read upl at5g39720.upl Distance constraint file "at5g39720.upl" read, 2049 upper limits, 2049 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 = 6.27132. Structure annealed in 73 s, f = 16.2939. Structure annealed in 77 s, f = 8.24153. Structure annealed in 73 s, f = 8.49068. Structure annealed in 75 s, f = 9.60018. Structure annealed in 74 s, f = 9.39576. Structure annealed in 76 s, f = 10.0696. Structure annealed in 75 s, f = 6.45108. Structure annealed in 76 s, f = 9.23169. Structure annealed in 75 s, f = 10.9947. Structure annealed in 70 s, f = 9.35416. Structure annealed in 76 s, f = 60.3466. Structure annealed in 70 s, f = 7.61483. Structure annealed in 75 s, f = 5.97344. Structure annealed in 70 s, f = 19.0861. Structure annealed in 74 s, f = 7.34101. Structure annealed in 76 s, f = 16.5696. Structure annealed in 76 s, f = 6.91196. Structure annealed in 71 s, f = 7.22390. Structure annealed in 72 s, f = 17.0570. Structure annealed in 71 s, f = 6.25968. Structure annealed in 70 s, f = 7.15233. Structure annealed in 70 s, f = 6.68368. Structure annealed in 68 s, f = 5.88168. Structure annealed in 72 s, f = 6.30163. Structure annealed in 73 s, f = 7.57470. Structure annealed in 76 s, f = 7.29310. Structure annealed in 72 s, f = 6.40644. Structure annealed in 74 s, f = 6.49215. Structure annealed in 73 s, f = 7.97999. Structure annealed in 76 s, f = 30.3592. Structure annealed in 75 s, f = 18.4796. Structure annealed in 75 s, f = 8.11889. Structure annealed in 70 s, f = 6.68142. Structure annealed in 73 s, f = 7.03791. Structure annealed in 73 s, f = 13.9564. Structure annealed in 69 s, f = 10.2615. Structure annealed in 84 s, f = 695.258. Structure annealed in 76 s, f = 9.30450. Structure annealed in 70 s, f = 9.37573. Structure annealed in 73 s, f = 7.88090. Structure annealed in 75 s, f = 6.36165. Structure annealed in 73 s, f = 7.66533. Structure annealed in 70 s, f = 7.50447. Structure annealed in 70 s, f = 6.09011. Structure annealed in 70 s, f = 7.89521. Structure annealed in 73 s, f = 9.25642. Structure annealed in 72 s, f = 10.7722. Structure annealed in 76 s, f = 33.3284. Structure annealed in 68 s, f = 6.44558. Structure annealed in 72 s, f = 9.04449. Structure annealed in 72 s, f = 18.0108. Structure annealed in 74 s, f = 8.38618. Structure annealed in 77 s, f = 16.3105. Structure annealed in 71 s, f = 7.12198. Structure annealed in 73 s, f = 6.63311. Structure annealed in 74 s, f = 5.81228. Structure annealed in 73 s, f = 5.58534. Structure annealed in 75 s, f = 5.44763. Structure annealed in 76 s, f = 7.66964. Structure annealed in 72 s, f = 9.39843. Structure annealed in 71 s, f = 5.69477. Structure annealed in 67 s, f = 6.60968. Structure annealed in 73 s, f = 16.1314. Structure annealed in 74 s, f = 7.30909. Structure annealed in 74 s, f = 8.72081. Structure annealed in 74 s, f = 6.81328. Structure annealed in 71 s, f = 5.87732. Structure annealed in 72 s, f = 6.36976. Structure annealed in 73 s, f = 6.23961. Structure annealed in 74 s, f = 5.93291. Structure annealed in 74 s, f = 6.82323. Structure annealed in 74 s, f = 6.61001. Structure annealed in 75 s, f = 5.97982. Structure annealed in 73 s, f = 7.99035. Structure annealed in 76 s, f = 8.23342. Structure annealed in 72 s, f = 8.77780. Structure annealed in 76 s, f = 9.21821. Structure annealed in 75 s, f = 8.90547. Structure annealed in 72 s, f = 7.87091. Structure annealed in 68 s, f = 7.85323. Structure annealed in 73 s, f = 8.17424. Structure annealed in 70 s, f = 31.5518. Structure annealed in 73 s, f = 9.67254. Structure annealed in 75 s, f = 5.87338. Structure annealed in 73 s, f = 13.6716. Structure annealed in 67 s, f = 5.99730. Structure annealed in 68 s, f = 11.1844. Structure annealed in 73 s, f = 15.3947. Structure annealed in 73 s, f = 8.93837. Structure annealed in 74 s, f = 7.16575. Structure annealed in 74 s, f = 6.75836. Structure annealed in 69 s, f = 7.24881. Structure annealed in 75 s, f = 30.4399. Structure annealed in 74 s, f = 35.3061. Structure annealed in 70 s, f = 7.75971. Structure annealed in 73 s, f = 6.79167. Structure annealed in 74 s, f = 32.5456. Structure annealed in 71 s, f = 6.64781. Structure annealed in 73 s, f = 12.5740. 100 structures finished in 393 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 5.45 13 0.0164 0.43 6 13.0 0.29 6 1.9888 12.73 2 5.59 11 0.0173 0.39 8 12.3 0.29 9 1.9725 12.64 3 5.69 12 0.0173 0.39 8 12.0 0.37 9 1.9637 12.34 4 5.81 17 0.0178 0.56 6 13.0 0.30 8 1.9487 11.33 5 5.87 13 0.0183 0.45 8 12.7 0.35 8 1.9435 13.15 6 5.88 12 0.0182 0.44 7 12.6 0.31 8 1.9290 12.83 7 5.88 13 0.0169 0.38 6 13.6 0.44 7 1.8799 11.83 8 5.93 13 0.0177 0.36 9 13.2 0.36 6 1.8347 11.58 9 5.97 16 0.0174 0.38 9 13.2 0.31 8 1.9420 13.26 10 5.98 13 0.0182 0.44 6 13.6 0.37 6 1.9620 11.75 11 6.00 16 0.0178 0.38 5 13.9 0.30 9 2.0531 12.45 12 6.09 14 0.0178 0.45 10 13.1 0.48 5 1.7999 11.80 13 6.24 17 0.0186 0.35 7 14.3 0.29 8 2.0652 12.42 14 6.26 13 0.0183 0.46 6 14.4 0.29 9 2.0137 11.26 15 6.27 13 0.0178 0.40 8 14.0 0.44 7 1.9030 12.09 16 6.30 15 0.0174 0.38 9 14.3 0.44 7 1.9242 12.50 17 6.36 16 0.0187 0.39 7 14.4 0.48 6 1.9271 13.05 18 6.37 16 0.0180 0.41 9 13.9 0.30 10 2.0597 11.43 19 6.41 15 0.0184 0.41 9 14.1 0.32 9 1.9916 11.54 20 6.45 18 0.0189 0.39 9 14.5 0.41 5 1.7784 12.98 Ave 6.04 14 0.0179 0.41 8 13.5 0.36 8 1.9440 12.25 +/- 0.28 2 0.0006 0.05 1 0.7 0.07 1 0.0766 0.63 Min 5.45 11 0.0164 0.35 5 12.0 0.29 5 1.7784 11.26 Max 6.45 18 0.0189 0.56 10 14.5 0.48 10 2.0652 13.26 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 ------ --- --- --- --- 1 117 30 5 1 (HIS 2) 2 120 27 6 0 3 115 30 8 0 4 116 33 4 0 5 114 33 6 0 6 117 32 4 0 7 110 32 10 1 (ARG 170) 8 122 26 4 1 (ASP 13) 9 114 33 6 0 10 116 32 4 1 (ASP 13) 11 113 36 4 0 12 111 34 6 2 (HIS 2, GLN 16) 13 116 35 2 0 14 113 33 7 0 15 123 22 8 0 16 121 29 3 0 17 118 30 3 2 (ASP 13, GLN 158) 18 115 31 5 2 (HIS 3, ASN 131) 19 114 33 6 0 20 116 33 3 1 (ASP 172) all 75.8% 20.4% 3.4% 0.4% Postscript file "at5g39720.rama" written. cyana> LAM 6.5.9/MPI 2 C++/ROMIO - Indiana University 29-Dec-2005 22:16:14