Warning: no access to tty (Bad file descriptor). Thus no job control in this shell. ##sourcing /farm/software/bin/cshrc.all from Linux n009.bw03.cabm.rutgers.edu 2.6.23.1-21.fc7 #1 SMP Thu Nov 1 20:28:15 EDT 2007 x86_64 x86_64 x86_64 GNU/Linux. ##DISPLAY not set. ##running Linux LAM 7.1.2/MPI 2 C++/ROMIO - Indiana University ]2;n009.bw03.cabm.rutgers.edu:/farm/data/gliu/projects/HR4394/cyana/calc25ali4abs.peaks final.ovw noec_sw.prot aliabs-cycle7.peaks final.pdb noefold.prot aliabs-cycle7-ref.peaks finalstereo.cya noe.prot aliabs.peaks final.upl noe.seq alimod.peaks FindTensor.cya* noe_sw.prot ali.peaks getfil overint.peaks aromod.peaks hb1.cya pegrdc aronoe.peaks hb.awk pred1.tab aro.peaks hr4394rdc1 ramaplot.ps atomsw.cya* hr43hb1.upl rama.ps AUTO.cya* hr43.rdc rdc1 autorun.cya* hy2.cya rdc2 CALC.cya* init.cya* rdc3 cleanlogali modali rdc.awk cleanlogaro modali1 runcleanAli* cleanlogC modaro runcleanAro* cleanlogN modaro1 runcleansim* cleanlogsim modC simc.peaks cnoe1.peaks modC1 simnoemod.peaks cnoe2.peaks modN simnoe.peaks cnoe4abs.peaks modN1 sr115c.pdb cnoeabs-cycle7.peaks modsim ssa.cya cnoeabs-cycle7-ref.peaks modsim1 submit_cyana* cnoeabs.peaks nnoe1.peaks talos2.aco cnoe.peaks nnoe2.peaks talos.aco cyanalog nnoe4abs.peaks tensor d2oc.prot nnoeabs-cycle7.peaks test.ovw d2oc_sw-final.prot nnoeabs-cycle7-ref.peaks unc.peaks d2oc_sw.prot nnoeabs.peaks unn.peaks d2o.prot nnoe.peaks upl_c2d.cya* demo.ovw noeall.prot upl_d2c.cya* demo.pdb noec.prot final.aco noec_sw-final.prot ___________________________________________________________________ CYANA 3.0 (gfortran-openmpi) Copyright (c) 2002-08 Peter Guntert. All rights reserved. ___________________________________________________________________ Library file "/farm/software/cyana-3.0-mpi/lib/cyana.lib" read, 38 residue types. Sequence file "noe.seq" read, 145 residues. 1 stereospecific assignment added. 5 stereospecific assignments added. 6 stereospecific assignments added. 9 stereospecific assignments added. Restraints for hydrogen bond H GLU 28 - O LYS 24 added. Restraints for hydrogen bond H PHE 38 - O LYS 34 added. Restraints for hydrogen bond H LEU 39 - O ARG 35 added. Restraints for hydrogen bond H ASP 40 - O LYS 36 added. Restraints for hydrogen bond H ASP 41 - O GLU 37 added. Restraints for hydrogen bond H LEU 42 - O PHE 38 added. Restraints for hydrogen bond H PHE 43 - O LEU 39 added. Restraints for hydrogen bond H SER 44 - O ASP 40 added. Restraints for hydrogen bond H PHE 45 - O ASP 41 added. Restraints for hydrogen bond H MET 46 - O LEU 42 added. Restraints for hydrogen bond H GLN 47 - O PHE 43 added. Restraints for hydrogen bond H MET 59 - O GLN 62 added. Restraints for hydrogen bond H GLN 62 - O MET 59 added. Restraints for hydrogen bond H LEU 69 - O ASP 65 added. Restraints for hydrogen bond H TYR 70 - O LEU 66 added. Restraints for hydrogen bond H VAL 71 - O PHE 67 added. Restraints for hydrogen bond H LEU 72 - O MET 68 added. Restraints for hydrogen bond H VAL 73 - O LEU 69 added. Restraints for hydrogen bond H THR 74 - O TYR 70 added. Restraints for hydrogen bond H GLU 75 - O VAL 71 added. Restraints for hydrogen bond H VAL 82 - O GLY 78 added. Restraints for hydrogen bond H ILE 83 - O LEU 79 added. Restraints for hydrogen bond H ASN 84 - O VAL 80 added. Restraints for hydrogen bond H LYS 85 - O GLU 81 added. Restraints for hydrogen bond H THR 92 - O TRP 88 added. Restraints for hydrogen bond H LYS 93 - O ARG 89 added. Restraints for hydrogen bond H GLY 94 - O GLU 90 added. Restraints for hydrogen bond H THR 107 - O SER 103 added. Restraints for hydrogen bond H LEU 108 - O ALA 104 added. Restraints for hydrogen bond H GLN 111 - O THR 107 added. Restraints for hydrogen bond H TYR 112 - O LEU 108 added. Restraints for hydrogen bond H LYS 114 - O THR 110 added. Restraints for hydrogen bond H GLU 122 - O PRO 118 added. Restraints for hydrogen bond H LYS 123 - O TYR 119 added. Restraints for hydrogen bond H ALA 135 - O GLU 131 added. Restraints for hydrogen bond H ILE 136 - O LEU 132 added. Restraints for hydrogen bond H ASP 137 - O GLN 133 added. Restraints for hydrogen bond H SER 138 - O ALA 134 added. Restraints for hydrogen bond H ARG 140 - O ILE 136 added. Restraints for hydrogen bond H ARG 141 - O ASP 137 added. ======================= Check ======================== ------------------------------------------------------------ Proton list: noec_sw Chemical shift list "noec_sw.prot" read, 1422 chemical shifts. Residue missing shifts MET 1 H HA QB QG QE GLY 2 H HIS 3 H HA QB HD2 HE1 HIS 4 H HA QB HD2 HE1 HIS 5 H HA QB HD2 HE1 HIS 6 H HA QB HD2 HE1 HIS 7 H HA QB HD2 HE1 HIS 8 H HA QB HD2 HE1 SER 9 H HA QB HIS 10 H HE1 HIS 14 HE1 TYR 19 H HA QB QR GLU 20 H HA QB QG GLU 21 H HA QB QG GLN 22 H HA QB QG PHE 23 H HA QB LYS 24 H HD3 QE ASN 54 H ARG 55 HB2 VAL 63 H ARG 89 H CYS 121 HG 69 missing chemical shifts, completeness 91.9%. ------------------------------------------------------------ Proton list: noec_sw Chemical shift list "noec_sw.prot" read, 1422 chemical shifts. Residue missing shifts MET 1 H HA QB QG QE GLY 2 H HIS 3 H HA QB HD2 HE1 HIS 4 H HA QB HD2 HE1 HIS 5 H HA QB HD2 HE1 HIS 6 H HA QB HD2 HE1 HIS 7 H HA QB HD2 HE1 HIS 8 H HA QB HD2 HE1 SER 9 H HA QB HIS 10 H HE1 HIS 14 HE1 TYR 19 H HA QB QR GLU 20 H HA QB QG GLU 21 H HA QB QG GLN 22 H HA QB QG PHE 23 H HA QB LYS 24 H HD3 QE ASN 54 H ARG 55 HB2 VAL 63 H ARG 89 H CYS 121 HG 69 missing chemical shifts, completeness 91.9%. ------------------------------------------------------------ Proton list: d2oc_sw Chemical shift list "d2oc_sw.prot" read, 1162 chemical shifts. Residue missing shifts MET 1 H HA QB QG QE GLY 2 H HIS 3 H HA QB HD2 HE1 HIS 4 H HA QB HD2 HE1 HIS 5 H HA QB HD2 HE1 HIS 6 H HA QB HD2 HE1 HIS 7 H HA QB HD2 HE1 HIS 8 H HA QB HD2 HE1 SER 9 H HA QB HIS 10 H HE1 MET 11 H ASP 13 H HIS 14 H HE1 GLY 15 H ASP 16 H TRP 17 H HD1 HE3 THR 18 H TYR 19 H HA QB QR GLU 20 H HA QB QG GLU 21 H HA QB QG GLN 22 H HA QB QG PHE 23 H HA QB LYS 24 H HD3 QE GLN 25 H LEU 26 H TYR 27 H GLU 28 H LEU 29 H GLY 31 H ASP 32 H LYS 34 H ARG 35 H QD PHE 43 H SER 44 H LYS 48 H ARG 49 H GLY 50 H THR 51 H VAL 53 H ASN 54 H ARG 55 H HB2 ILE 56 H ILE 58 H MET 59 H ALA 60 H LYS 61 H GLN 62 H VAL 63 H LEU 64 H ASP 65 H TYR 70 QE LEU 79 H ASN 84 H LYS 85 H LYS 86 H TRP 88 H ARG 89 H GLU 90 H ILE 91 H THR 92 H LYS 93 H GLY 94 H LEU 95 H ASN 96 H THR 99 H SER 100 H ILE 101 H THR 102 H SER 103 H ALA 104 H ALA 105 H PHE 106 H THR 107 H LEU 108 H ARG 109 H THR 110 H GLN 111 H TYR 117 HB2 CYS 121 H HG GLU 122 H LYS 123 H ARG 124 H GLY 125 H LEU 126 H SER 127 H ASN 128 H ASN 130 H GLU 131 H LEU 132 H GLN 133 H ALA 134 H ALA 135 H ILE 136 H ASP 137 H SER 138 H ASN 139 H ARG 140 H ARG 141 H GLU 142 H GLY 143 H ARG 144 H ARG 145 H 155 missing chemical shifts, completeness 81.9%. ------------------------------------------------------------ Peak list : cnoeabs.peaks Proton list: noec_sw Chemical shift list "noec_sw.prot" read, 1422 chemical shifts. Peak list "cnoeabs.peaks" read, 7481 peaks, 4794 assignments. Atom Shift Dev Mean +/- Minimum Maximum HB2 LEU 42 -0.228 4.02 1.54 0.44 -1.40 2.43 QG1 VAL 82 -1.122 7.43 0.81 0.26 -0.27 1.54 2 shifts outside expected range. Deviations from chemical shift list: Dim Peaks Median Average Maximum RMSD Number Tolerance 1 4795 0.000 0.000 0.022 0.001 4 0.020 2 7470 0.000 0.000 0.017 0.001 14 0.010 3 7470 0.000 0.000 0.262 0.015 0 0.400 Atom Residue Shift Median Deviation Peaks HB2 HIS 14 2.926 2.928 0.021 12 HB3 HIS 14 2.991 2.992 0.021 14 HE1 TRP 17 9.983 9.981 0.020 5 QD PHE 23 6.938 6.938 0.022 26 4 shifts with spread larger than tolerance. Peak Dim Deviation Atom Residue 5656 2 -0.017 QE TYR 112 5657 2 -0.017 QE TYR 112 8261 1 0.022 QD PHE 23 10950 1 -0.020 HE1 TRP 17 4502 1 -0.021 HB2 HIS 14 4503 1 -0.021 HB3 HIS 14 4580 2 -0.011 QD PHE 45 4581 2 -0.011 QD PHE 45 4582 2 -0.011 QD PHE 45 4583 2 -0.011 QD PHE 45 4584 2 -0.011 QD PHE 45 4656 2 0.013 QE TYR 112 4657 2 0.013 QE TYR 112 4689 2 -0.011 QD PHE 45 4690 2 -0.011 QD PHE 45 4758 2 -0.011 QD PHE 45 4759 2 -0.011 QD PHE 45 4822 2 -0.011 QD PHE 45 18 deviations larger than tolerance. ------------------------------------------------------------ Peak list : nnoeabs.peaks Proton list: noec_sw Chemical shift list "noec_sw.prot" read, 1422 chemical shifts. Peak list "nnoeabs.peaks" read, 2339 peaks, 1697 assignments. Atom Shift Dev Mean +/- Minimum Maximum HB2 LEU 42 -0.228 4.02 1.54 0.44 -1.40 2.43 QG1 VAL 82 -1.122 7.43 0.81 0.26 -0.27 1.54 2 shifts outside expected range. Deviations from chemical shift list: Dim Peaks Median Average Maximum RMSD Number Tolerance 1 1697 0.000 0.000 0.026 0.002 4 0.020 2 2339 0.000 0.000 0.003 0.000 0 0.010 3 2339 0.000 0.000 0.000 0.000 0 0.400 Atom Residue Shift Median Deviation Peaks HB2 PRO 12 1.759 1.769 0.021 2 HB3 PRO 12 2.215 2.204 0.023 2 HG2 PRO 12 1.925 1.936 0.023 2 HE22 GLN 47 6.879 6.882 0.026 9 4 shifts with spread larger than tolerance. Peak Dim Deviation Atom Residue 8038 1 -0.023 HB3 PRO 12 8039 1 0.023 HG2 PRO 12 8040 1 0.021 HB2 PRO 12 11651 1 -0.026 HE22 GLN 47 4 deviations larger than tolerance. ------------------------------------------------------------ Peak list : aliabs.peaks Proton list: d2oc_sw Chemical shift list "d2oc_sw.prot" read, 1162 chemical shifts. Peak list "aliabs.peaks" read, 5987 peaks, 3804 assignments. Atom Shift Dev Mean +/- Minimum Maximum QG1 VAL 82 -1.114 7.40 0.81 0.26 -0.27 1.54 1 shift outside expected range. Deviations from chemical shift list: Dim Peaks Median Average Maximum RMSD Number Tolerance 1 3804 0.000 0.000 0.019 0.001 0 0.020 2 5987 0.000 0.000 0.021 0.000 1 0.010 3 5987 0.000 0.000 0.148 0.002 0 0.400 Atom Residue Shift Median Deviation Peaks HD3 ARG 109 3.325 3.326 0.021 22 1 shift with spread larger than tolerance. Peak Dim Deviation Atom Residue 10740 2 -0.021 HD3 ARG 109 1 deviations larger than tolerance. ------------------------------------------------------------ Proton lists: noec_sw <-> d2oc_sw Chemical shift list "noec_sw.prot" read, 1422 chemical shifts. Deviation of 0.503 ppm in atom CA TRP 17 Deviation of -0.045 ppm in atom QG2 THR 18 Deviation of 0.530 ppm in atom CB LYS 24 Deviation of 0.470 ppm in atom CG GLN 25 Deviation of 0.415 ppm in atom CE LYS 36 Deviation of -0.022 ppm in atom QE PHE 38 Deviation of -0.031 ppm in atom QD2 LEU 39 Deviation of -0.031 ppm in atom QD1 LEU 42 Deviation of -0.042 ppm in atom QD2 LEU 42 Deviation of -0.492 ppm in atom CZ PHE 43 Deviation of 0.522 ppm in atom CZ PHE 45 Deviation of 0.525 ppm in atom CA PRO 52 Deviation of -0.031 ppm in atom QG1 VAL 53 Deviation of 0.027 ppm in atom QG2 VAL 53 Deviation of 0.540 ppm in atom CB ASN 54 Deviation of -0.024 ppm in atom QG2 ILE 56 Deviation of 0.499 ppm in atom CG2 ILE 56 Deviation of -0.053 ppm in atom QD1 ILE 56 Deviation of -0.020 ppm in atom QE MET 59 Deviation of 0.435 ppm in atom CE MET 59 Deviation of -0.025 ppm in atom QG1 VAL 63 Deviation of -0.028 ppm in atom QG2 VAL 63 Deviation of -0.024 ppm in atom QD2 LEU 64 Deviation of -0.027 ppm in atom QD1 LEU 66 Deviation of -0.021 ppm in atom QD2 LEU 66 Deviation of -0.029 ppm in atom QD2 LEU 72 Deviation of -0.028 ppm in atom QD2 LEU 108 Deviation of -0.026 ppm in atom QD2 LEU 116 28 significant deviations, average deviation 0.027 ppm. New proton list should be shifted by 0.011 ppm. Chemical shift list "d2oc_sw.prot" read, 1 chemical shift. ------------------------------------------------------------ Proton lists: noec_sw <-> d2oc_sw Chemical shift list "noec_sw.prot" read, 1422 chemical shifts. Deviation of 0.503 ppm in atom CA TRP 17 Deviation of -0.045 ppm in atom QG2 THR 18 Deviation of 0.530 ppm in atom CB LYS 24 Deviation of 0.470 ppm in atom CG GLN 25 Deviation of 0.415 ppm in atom CE LYS 36 Deviation of -0.022 ppm in atom QE PHE 38 Deviation of -0.031 ppm in atom QD2 LEU 39 Deviation of -0.031 ppm in atom QD1 LEU 42 Deviation of -0.042 ppm in atom QD2 LEU 42 Deviation of -0.492 ppm in atom CZ PHE 43 Deviation of 0.522 ppm in atom CZ PHE 45 Deviation of 0.525 ppm in atom CA PRO 52 Deviation of -0.031 ppm in atom QG1 VAL 53 Deviation of 0.027 ppm in atom QG2 VAL 53 Deviation of 0.540 ppm in atom CB ASN 54 Deviation of -0.024 ppm in atom QG2 ILE 56 Deviation of 0.499 ppm in atom CG2 ILE 56 Deviation of -0.053 ppm in atom QD1 ILE 56 Deviation of -0.020 ppm in atom QE MET 59 Deviation of 0.435 ppm in atom CE MET 59 Deviation of -0.025 ppm in atom QG1 VAL 63 Deviation of -0.028 ppm in atom QG2 VAL 63 Deviation of -0.024 ppm in atom QD2 LEU 64 Deviation of -0.027 ppm in atom QD1 LEU 66 Deviation of -0.021 ppm in atom QD2 LEU 66 Deviation of -0.029 ppm in atom QD2 LEU 72 Deviation of -0.028 ppm in atom QD2 LEU 108 Deviation of -0.026 ppm in atom QD2 LEU 116 28 significant deviations, average deviation 0.027 ppm. New proton list should be shifted by 0.011 ppm. Chemical shift list "d2oc_sw.prot" read, 1 chemical shift. CB CG CB-CG Ptrans Pcis Result PRO 12: 31.89 27.30 4.59 1.000 0.000 trans PRO 33: 32.01 27.30 4.71 0.999 0.001 trans PRO 52: 32.05 27.30 4.75 0.999 0.001 trans PRO 57: 31.87 27.60 4.27 1.000 0.000 trans PRO 98: 32.00 27.30 4.70 1.000 0.000 trans PRO 118: 30.04 28.90 1.14 1.000 0.000 trans PRO 129: 31.98 27.79 4.19 1.000 0.000 trans Library file "/farm/software/cyana-3.0-mpi/lib/cyana.lib" read, 38 residue types. Sequence file "noe.seq" read, 145 residues. 1 stereospecific assignment added. 5 stereospecific assignments added. 6 stereospecific assignments added. 9 stereospecific assignments added. Restraints for hydrogen bond H GLU 28 - O LYS 24 added. Restraints for hydrogen bond H PHE 38 - O LYS 34 added. Restraints for hydrogen bond H LEU 39 - O ARG 35 added. Restraints for hydrogen bond H ASP 40 - O LYS 36 added. Restraints for hydrogen bond H ASP 41 - O GLU 37 added. Restraints for hydrogen bond H LEU 42 - O PHE 38 added. Restraints for hydrogen bond H PHE 43 - O LEU 39 added. Restraints for hydrogen bond H SER 44 - O ASP 40 added. Restraints for hydrogen bond H PHE 45 - O ASP 41 added. Restraints for hydrogen bond H MET 46 - O LEU 42 added. Restraints for hydrogen bond H GLN 47 - O PHE 43 added. Restraints for hydrogen bond H MET 59 - O GLN 62 added. Restraints for hydrogen bond H GLN 62 - O MET 59 added. Restraints for hydrogen bond H LEU 69 - O ASP 65 added. Restraints for hydrogen bond H TYR 70 - O LEU 66 added. Restraints for hydrogen bond H VAL 71 - O PHE 67 added. Restraints for hydrogen bond H LEU 72 - O MET 68 added. Restraints for hydrogen bond H VAL 73 - O LEU 69 added. Restraints for hydrogen bond H THR 74 - O TYR 70 added. Restraints for hydrogen bond H GLU 75 - O VAL 71 added. Restraints for hydrogen bond H VAL 82 - O GLY 78 added. Restraints for hydrogen bond H ILE 83 - O LEU 79 added. Restraints for hydrogen bond H ASN 84 - O VAL 80 added. Restraints for hydrogen bond H LYS 85 - O GLU 81 added. Restraints for hydrogen bond H THR 92 - O TRP 88 added. Restraints for hydrogen bond H LYS 93 - O ARG 89 added. Restraints for hydrogen bond H GLY 94 - O GLU 90 added. Restraints for hydrogen bond H THR 107 - O SER 103 added. Restraints for hydrogen bond H LEU 108 - O ALA 104 added. Restraints for hydrogen bond H GLN 111 - O THR 107 added. Restraints for hydrogen bond H TYR 112 - O LEU 108 added. Restraints for hydrogen bond H LYS 114 - O THR 110 added. Restraints for hydrogen bond H GLU 122 - O PRO 118 added. Restraints for hydrogen bond H LYS 123 - O TYR 119 added. Restraints for hydrogen bond H ALA 135 - O GLU 131 added. Restraints for hydrogen bond H ILE 136 - O LEU 132 added. Restraints for hydrogen bond H ASP 137 - O GLN 133 added. Restraints for hydrogen bond H SER 138 - O ALA 134 added. Restraints for hydrogen bond H ARG 140 - O ILE 136 added. Restraints for hydrogen bond H ARG 141 - O ASP 137 added. 100 structures selected. 100 random structures created (seed 3771). Terminated