Warning: no access to tty (Bad file descriptor). Thus no job control in this shell. 30-Nov-2005 17:53:06 n-1<5766> ssi:boot:base:linear: booting n0 (wolf01) n-1<5766> ssi:boot:base:linear: booting n1 (wolf02) n-1<5766> ssi:boot:base:linear: booting n2 (wolf03) n-1<5766> ssi:boot:base:linear: booting n3 (wolf04) n-1<5766> ssi:boot:base:linear: booting n4 (wolf05) n-1<5766> ssi:boot:base:linear: booting n5 (wolf06) n-1<5766> ssi:boot:base:linear: booting n6 (wolf07) n-1<5766> ssi:boot:base:linear: booting n7 (wolf08) n-1<5766> ssi:boot:base:linear: booting n8 (wolf09) n-1<5766> ssi:boot:base:linear: booting n9 (wolf10) n-1<5766> ssi:boot:base:linear: booting n10 (wolf11) n-1<5766> ssi:boot:base:linear: booting n11 (wolf12) n-1<5766> ssi:boot:base:linear: booting n12 (wolf13) n-1<5766> ssi:boot:base:linear: booting n13 (wolf14) n-1<5766> ssi:boot:base:linear: booting n14 (wolf15) n-1<5766> ssi:boot:base:linear: booting n15 (wolf16) n-1<5766> ssi:boot:base:linear: finished LAM 7.2b1svn10112005/MPI 2 C++/ROMIO - Indiana University ___________________________________________________________________ CYANA 2.1 (intel-lam) Copyright (c) 2002-05 Peter Guntert. All rights reserved. ___________________________________________________________________ Library file "/user/cyana-2.1/lib/cyana.lib" read, 37 residue types. Sequence file "znf42.seq" read, 219 residues. Symmetric dimer: Molecule 1: residues 35..128 Molecule 2: residues 335..428 403 identity constraints created. 8836 symmetry constraints created. cyana> cyana> cyana> - znf42: peakcheck peaks=c13no,n15no,c13ar,fc12no prot=znf42 ------------------------------------------------------------ Proton list: znf42 - peakcheck: read prot znf42 unknown=warn Chemical shift list "znf42.prot" read, 1980 chemical shifts. - peakcheck: shifts missing "H* Q* - HYDROXYL - AMIDE + H HN / &H_* &PSEUD" Residue missing shifts GLY 35 H QA SER 36 H HA QB ASP 37 H CYS 49 HG PHE 50 HZ CYS 69 HG LEU 84 QD2 GLY 335 H QA SER 336 H HA QB ASP 337 H CYS 349 HG PHE 350 HZ CYS 369 HG LEU 384 QD2 20 missing chemical shifts, completeness 98.0%. ------------------------------------------------------------ Peak list : c13no Proton list: znf42 - peakcheck: read prot znf42 unknown=skip Chemical shift list "znf42.prot" read, 1980 chemical shifts. - peakcheck: read peaks c13no format= Peak list "c13no.peaks" read, 3485 peaks, 3082 assignments. - peakcheck: atom shift unusual Atom Shift Dev Mean +/- Minimum Maximum HG3 ARG 44 -0.750 5.11 1.50 0.44 -0.72 3.30 NE ARG 44 113.446 16.64 84.33 1.75 78.96 89.30 NE ARG 48 118.117 19.31 84.33 1.75 78.96 89.30 NE ARG 66 116.949 18.64 84.33 1.75 78.96 89.30 QD2 LEU 73 -0.640 4.25 0.72 0.32 -1.03 1.31 HG3 ARG 344 -0.750 5.11 1.50 0.44 -0.72 3.30 NE ARG 344 113.446 16.64 84.33 1.75 78.96 89.30 NE ARG 348 118.117 19.31 84.33 1.75 78.96 89.30 NE ARG 366 116.949 18.64 84.33 1.75 78.96 89.30 QD2 LEU 373 -0.640 4.25 0.72 0.32 -1.03 1.31 10 shifts outside expected range. - peakcheck: peaks fit Deviations from chemical shift list: Dim Peaks Median Average Maximum RMSD Number Tolerance 1 3082 0.000 0.002 0.131 0.009 1 0.030 2 3410 0.000 0.000 0.027 0.003 0 0.030 3 3410 0.000 0.001 0.297 0.027 0 0.450 - peakcheck: atom shift check Atom Residue Shift Median Deviation Peaks QD PHE 92 6.917 6.925 0.131 10 1 shift with spread larger than tolerance. - peakcheck: peak deviations Peak Dim Deviation Atom Residue 3240 1 0.131 QD PHE 92 1 deviations larger than tolerance. ------------------------------------------------------------ Peak list : n15no Proton list: znf42 - peakcheck: read prot znf42 unknown=skip Chemical shift list "znf42.prot" read, 1980 chemical shifts. - peakcheck: read peaks n15no format= Peak list "n15no.peaks" read, 1273 peaks, 1110 assignments. - peakcheck: peaks fit Deviations from chemical shift list: Dim Peaks Median Average Maximum RMSD Number Tolerance 1 1110 0.002 0.002 0.030 0.011 1 0.030 2 1269 0.000 0.000 0.011 0.001 0 0.030 3 1269 0.000 -0.001 0.186 0.009 0 0.450 - peakcheck: atom shift check Atom Residue Shift Median Deviation Peaks QD1 LEU 118 0.930 0.902 0.030 3 1 shift with spread larger than tolerance. - peakcheck: peak deviations Peak Dim Deviation Atom Residue 1240 1 -0.030 QD1 LEU 118 1 deviations larger than tolerance. ------------------------------------------------------------ Peak list : c13ar Proton list: znf42 - peakcheck: read prot znf42 unknown=skip Chemical shift list "znf42.prot" read, 1980 chemical shifts. - peakcheck: read peaks c13ar format= Peak list "c13ar.peaks" read, 281 peaks, 222 assignments. - peakcheck: peaks fit Deviations from chemical shift list: Dim Peaks Median Average Maximum RMSD Number Tolerance 1 222 0.004 0.005 0.030 0.013 0 0.030 2 280 0.000 0.000 0.000 0.000 0 0.030 3 280 0.000 0.000 0.000 0.000 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 : fc12no Proton list: znf42 - peakcheck: read prot znf42 unknown=skip Chemical shift list "znf42.prot" read, 1980 chemical shifts. - peakcheck: read peaks fc12no format= Peak list "fc12no.peaks" read, 225 peaks, 150 assignments. - peakcheck: peaks fit Deviations from chemical shift list: Dim Peaks Median Average Maximum RMSD Number Tolerance 1 150 0.000 -0.001 0.029 0.016 0 0.030 2 169 0.000 -0.001 0.014 0.005 0 0.030 3 169 0.000 -0.005 0.297 0.034 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. - znf42: calibration prot=znf42 peaks=c13no,n15no,c13ar,fc12no dref=4.2 - calibration: read prot znf42 unknown=warn Chemical shift list "znf42.prot" read, 1980 chemical shifts. - calibration: read peaks c13no format= Peak list "c13no.peaks" read, 3485 peaks, 3082 assignments. - calibration: peaks select "** list=1" 3485 of 3485 peaks, 3485 of 3485 assignments selected. - calibration: peaks set volume=abs(volume) Volume of 3485 peaks set. - calibration: peaks simplecal dref=4.2 Calibration constant for peak list 1: 1.83E+07 Upper limit set for 3485 peaks. - calibration: caltab peaks Distance bounds: -2.99 A: 446 12.8% 3.00-3.99 A: 1153 33.1% 4.00-4.99 A: 1295 37.2% 5.00-5.99 A: 591 17.0% 6.00- A: 0 0.0% All: 3485 100.0% - calibration: read prot znf42 unknown=warn append Chemical shift list "znf42.prot" read, 1980 chemical shifts. - calibration: read peaks n15no format= append Peak list "n15no.peaks" read, 1273 peaks, 1110 assignments. - calibration: peaks select "** list=2" 1273 of 4758 peaks, 1273 of 4758 assignments selected. - calibration: peaks set volume=abs(volume) Volume of 1273 peaks set. - calibration: peaks simplecal dref=4.2 Calibration constant for peak list 2: 8.42E+06 Upper limit set for 1273 peaks. - calibration: caltab peaks Distance bounds: -2.99 A: 111 8.7% 3.00-3.99 A: 468 36.8% 4.00-4.99 A: 480 37.7% 5.00-5.99 A: 214 16.8% 6.00- A: 0 0.0% All: 1273 100.0% - calibration: read prot znf42 unknown=warn append Chemical shift list "znf42.prot" read, 1980 chemical shifts. - calibration: read peaks c13ar format= append Peak list "c13ar.peaks" read, 281 peaks, 222 assignments. - calibration: peaks select "** list=3" 281 of 5039 peaks, 281 of 5039 assignments selected. - calibration: peaks set volume=abs(volume) Volume of 281 peaks set. - calibration: peaks simplecal dref=4.2 Calibration constant for peak list 3: 1.40E+07 Upper limit set for 281 peaks. - calibration: caltab peaks Distance bounds: -2.99 A: 26 9.3% 3.00-3.99 A: 87 31.0% 4.00-4.99 A: 150 53.4% 5.00-5.99 A: 18 6.4% 6.00- A: 0 0.0% All: 281 100.0% - calibration: read prot znf42 unknown=warn append Chemical shift list "znf42.prot" read, 1980 chemical shifts. - calibration: read peaks fc12no format= append Peak list "fc12no.peaks" read, 225 peaks, 150 assignments. - calibration: peaks select "** list=4" 225 of 5264 peaks, 225 of 5264 assignments selected. - calibration: peaks set volume=abs(volume) Volume of 225 peaks set. - calibration: peaks simplecal dref=4.2 Calibration constant for peak list 4: 7.01E+06 Upper limit set for 225 peaks. - calibration: caltab peaks Distance bounds: -2.99 A: 6 2.7% 3.00-3.99 A: 77 34.2% 4.00-4.99 A: 140 62.2% 5.00-5.99 A: 2 0.9% 6.00- A: 0 0.0% All: 225 100.0% - calibration: peaks select ** 5264 of 5264 peaks, 5264 of 5264 assignments selected. - znf42: peaks calibrate ** simple 4083 upper limits added, 18/160 at lower/upper bound, average 4.18 A. - znf42: write upl znf42-in.upl Distance constraint file "znf42-in.upl" written, 4083 upper limits, 4083 assignments. - znf42: distance modify Too restrictive distance constraints: limit dmin dmax Upper HA ASP 37 - QG PRO 38 3.95 4.11 6.06 Number of modified constraints: 2286 - znf42: write upl znf42.upl Distance constraint file "znf42.upl" written, 2286 upper limits, 2286 assignments. - znf42: ./init - init: read lib /user/cyana-2.1/lib/cyana.lib Library file "/user/cyana-2.1/lib/cyana.lib" read, 37 residue types. - init: read seq znf42.seq Sequence file "znf42.seq" read, 219 residues. - init: molecules define 35..128 335..428 Symmetric dimer: Molecule 1: residues 35..128 Molecule 2: residues 335..428 - init: molecule identity 403 identity constraints created. - init: molecule symdist "CA 35..128" "CA 335..428" 8836 symmetry constraints created. - znf42: read upl znf42.upl Distance constraint file "znf42.upl" read, 2286 upper limits, 2286 assignments. - znf42: read aco znf42.aco Angle constraint file "znf42.aco" read, 267 constraints for 267 angles. - znf42: calc_all structures=100 command=anneal steps=10000 100 structures selected. 100 random structures created (seed 35671). Structure annealed in 40 s, f = 37.5615. Structure annealed in 40 s, f = 36.8991. Structure annealed in 41 s, f = 42.5286. Structure annealed in 40 s, f = 36.8784. Structure annealed in 40 s, f = 39.4481. Structure annealed in 40 s, f = 53.0267. Structure annealed in 40 s, f = 34.5708. Structure annealed in 40 s, f = 43.1513. Structure annealed in 40 s, f = 37.3856. Structure annealed in 41 s, f = 34.5652. Structure annealed in 41 s, f = 39.5085. Structure annealed in 40 s, f = 37.2394. Structure annealed in 40 s, f = 39.5980. Structure annealed in 40 s, f = 38.3381. Structure annealed in 41 s, f = 33.2443. Structure annealed in 41 s, f = 39.0408. Structure annealed in 41 s, f = 37.5729. Structure annealed in 40 s, f = 37.0420. Structure annealed in 40 s, f = 33.7632. Structure annealed in 40 s, f = 41.3019. Structure annealed in 40 s, f = 57.2843. Structure annealed in 40 s, f = 45.1464. Structure annealed in 40 s, f = 40.5113. Structure annealed in 40 s, f = 35.6755. Structure annealed in 41 s, f = 36.5303. Structure annealed in 40 s, f = 32.4261. Structure annealed in 40 s, f = 35.9057. Structure annealed in 40 s, f = 40.3588. Structure annealed in 40 s, f = 34.5657. Structure annealed in 40 s, f = 42.6481. Structure annealed in 40 s, f = 37.7394. Structure annealed in 40 s, f = 39.5046. Structure annealed in 40 s, f = 34.6933. Structure annealed in 40 s, f = 41.5657. Structure annealed in 41 s, f = 56.7196. Structure annealed in 40 s, f = 34.7178. Structure annealed in 40 s, f = 34.5954. Structure annealed in 40 s, f = 40.0308. Structure annealed in 40 s, f = 36.2470. Structure annealed in 40 s, f = 37.3702. Structure annealed in 40 s, f = 32.8675. Structure annealed in 41 s, f = 45.3834. Structure annealed in 40 s, f = 44.6571. Structure annealed in 40 s, f = 36.4312. Structure annealed in 40 s, f = 34.9161. Structure annealed in 41 s, f = 40.8161. Structure annealed in 41 s, f = 36.6395. Structure annealed in 40 s, f = 39.9832. Structure annealed in 40 s, f = 36.6618. Structure annealed in 40 s, f = 39.4668. Structure annealed in 40 s, f = 38.1054. Structure annealed in 40 s, f = 53.9012. Structure annealed in 40 s, f = 40.2146. Structure annealed in 40 s, f = 42.6540. Structure annealed in 41 s, f = 38.5445. Structure annealed in 40 s, f = 39.8028. Structure annealed in 41 s, f = 65.6520. Structure annealed in 40 s, f = 40.0250. Structure annealed in 40 s, f = 39.6683. Structure annealed in 41 s, f = 41.7470. Structure annealed in 40 s, f = 39.1700. Structure annealed in 40 s, f = 35.6490. Structure annealed in 40 s, f = 37.2477. Structure annealed in 40 s, f = 37.4805. Structure annealed in 40 s, f = 39.4480. Structure annealed in 40 s, f = 41.7235. Structure annealed in 40 s, f = 38.2155. Structure annealed in 41 s, f = 56.0765. Structure annealed in 41 s, f = 39.2232. Structure annealed in 40 s, f = 43.0983. Structure annealed in 40 s, f = 39.0177. Structure annealed in 40 s, f = 36.8174. Structure annealed in 40 s, f = 35.1792. Structure annealed in 40 s, f = 38.4019. Structure annealed in 40 s, f = 49.9760. Structure annealed in 40 s, f = 50.2299. Structure annealed in 40 s, f = 34.5540. Structure annealed in 41 s, f = 37.7925. Structure annealed in 40 s, f = 40.1714. Structure annealed in 41 s, f = 43.3446. Structure annealed in 40 s, f = 41.4971. Structure annealed in 40 s, f = 40.3681. Structure annealed in 41 s, f = 46.5615. Structure annealed in 41 s, f = 39.4333. Structure annealed in 40 s, f = 43.7911. Structure annealed in 41 s, f = 80.4291. Structure annealed in 41 s, f = 39.3937. Structure annealed in 40 s, f = 40.6073. Structure annealed in 40 s, f = 41.2521. Structure annealed in 40 s, f = 40.4033. Structure annealed in 40 s, f = 39.3155. Structure annealed in 40 s, f = 41.3167. Structure annealed in 40 s, f = 35.7356. Structure annealed in 40 s, f = 40.5392. Structure annealed in 40 s, f = 39.1414. Structure annealed in 40 s, f = 37.1876. Structure annealed in 40 s, f = 34.3996. Structure annealed in 40 s, f = 36.3918. Structure annealed in 40 s, f = 41.2825. Structure annealed in 40 s, f = 36.6286. 100 structures finished in 187 s (1 s/structure). - znf42: overview znf42.ovw structures=20 pdb Structural statistics: str target upper limits van der Waals torsion angles function # rms max # sum max # rms max 1 32.43 126 0.0511 1.17 17 28.9 0.36 5 1.4562 7.41 2 32.87 117 0.0505 1.19 17 29.7 0.34 9 1.6259 8.29 3 33.24 121 0.0506 1.27 18 29.9 0.41 10 1.6600 8.62 4 33.76 135 0.0510 1.19 14 29.9 0.33 7 1.6048 8.29 5 34.40 124 0.0513 1.22 22 31.7 0.37 7 1.6598 10.45 6 34.55 127 0.0503 1.11 28 33.4 0.41 8 1.5350 7.60 7 34.57 111 0.0511 1.20 17 29.3 0.48 6 1.6340 10.16 8 34.57 133 0.0521 1.00 21 32.6 0.40 5 1.4186 8.09 9 34.57 134 0.0515 0.80 19 32.1 0.33 8 1.5000 7.53 10 34.60 126 0.0527 1.10 18 31.4 0.38 4 1.3384 8.47 11 34.69 129 0.0511 1.17 17 33.2 0.34 9 1.6283 8.24 12 34.72 120 0.0522 0.96 16 30.8 0.39 8 1.4948 7.46 13 34.92 135 0.0534 0.98 12 31.8 0.28 5 1.4808 8.60 14 35.18 137 0.0524 0.95 17 32.3 0.43 6 1.4508 8.35 15 35.65 129 0.0508 0.93 23 33.6 0.41 6 1.4577 7.62 16 35.68 122 0.0539 1.19 17 29.4 0.34 9 1.7505 10.83 17 35.74 126 0.0516 1.18 17 34.0 0.47 9 1.5865 8.94 18 35.91 131 0.0522 1.41 23 33.5 0.39 9 1.7165 8.68 19 36.25 120 0.0525 1.09 16 32.6 0.34 7 1.4393 7.35 20 36.39 130 0.0525 1.18 18 34.4 0.31 8 1.6379 7.53 Ave 34.73 127 0.0517 1.12 18 31.7 0.38 7 1.5538 8.43 +/- 1.04 7 0.0010 0.14 3 1.7 0.05 2 0.1084 0.99 Min 32.43 111 0.0503 0.80 12 28.9 0.28 4 1.3384 7.35 Max 36.39 137 0.0539 1.41 28 34.4 0.48 10 1.7505 10.83 Cut 0.20 0.20 5.00 Overview file "znf42.ovw" written. PDB coordinate file "znf42.pdb" written, 20 conformers. - znf42: ramaplot znf42.rama nobackground label Struct fav add gen dis ------ --- --- --- --- 1 139 13 0 0 2 142 9 1 0 3 141 10 1 0 4 137 10 3 2 (ASP 37, ASP 337) 5 133 18 1 0 6 136 16 0 0 7 138 13 1 0 8 138 14 0 0 9 136 16 0 0 10 135 17 0 0 11 133 19 0 0 12 137 15 0 0 13 137 15 0 0 14 141 11 0 0 15 139 12 1 0 16 137 14 1 0 17 135 13 2 2 (ASP 37, ASP 337) 18 137 14 1 0 19 138 14 0 0 20 133 19 0 0 all 90.2% 9.3% 0.4% 0.1% Postscript file "znf42.rama" written. cyana> LAM 7.2b1svn10112005/MPI 2 C++/ROMIO - Indiana University 30-Nov-2005 17:56:50