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jH蒖Ãu< hhKhhKT5&藕jc jHjS@}U E*GjGj(FhFhC[C[C[C [ C([(C0[0C8[8C@[@A 9Mx؍e[^_UURRRB R PPPB@R@PPXB`E Z`EXEXXUWVSE]]uuU DB uGuՃE }u؃[^_UWVS] PӔƃus hhhShKT5&ؓjcN W蕔u, hhhhKT5&虓jcC9]t빃}~<륉e[^_UWVS u} ~t PC9ut V̕e[^_ÐUWVS [)Eue[^_1Puu uG;}re[^_UÐUSRtЋCuX[ÐUSP[fFX[Blosum62%s: cannot read extend wABCDEFGHIJKLMNOPQRSTUVWXYZ%s: option inexistante .set.pml exiting... rb%s:: error: cannot open %s rtp0 : pb format binaire ...probleme shuffle %s %s nmatch %d wtCan't open set file %s Print results for Gok in %s Can't open pymol file %s %s: cannot read 1st input file name %s: cannot read matrix (option -x) %s: cannot read P : type of analysis %s: cannot read gap open penalty (-G option) %s: cannot read gap extention penalty (-g option) %s: cannot read threshold (-W option) option -w: threshold is <= 0.0, setting it to %f %s: cannot read recovering ratio (-r option) option -r: recovering ratio is not in [0,1], setting it to %f %s: cannot read proba (-N option) option -N: proba is <= 0.0, setting it to %f %s: cannot read minimum score (-m option) %s: cannot read minimum rms (-M option) option -m: minimum rms is <= 0.0, setting it to %f %s: cannot read number of wanted best subalignments %s: subalignment number cannot be less than 1, setting it to %d %s: cannot read minimal length %s: minimal length cannot be less than 0, setting it to %d %s: cannot read number of shuffle Cannot open out file (-i option) Cannot open error file (-j option) %s: cannot read maximum rrmsd a:b:D:e:Fg:G:hi:j:lL:m:M:n:N:pP:qr:s:u:UvVw:Wx:z%s: cannot read matrix in file %s %s: cannot read matrix in file Blosum62 %s:: error: No input 1st file ! %s:: error: cannot open temporary file %s:: Problem uncompressing 1st file %s, exiting.... -> 1st file uncompressed (%s) Cannot open gz file %s, exiting.... %s:: Problem uncompressing 1st gz file %s, exiting.... %s:: Problem uncompressing 2nd file %s, exiting.... -> 2nd file uncompressed (%s) Problem uncompressing gz file %s, exiting.... Problem in reading protein structure in %s %d eme proteine , exiting...End of first database file, %d proteins have been read Problem in recoding protein %s angles exiting... **********Problem in reading sequence in %s %d th reading ... plus de %d residus, on passe a la suivante ... %s %d **************** reading %s temps %f num prot %d Problem in reading the %dth protein (ignored) End of second database file, %d proteins have been read Problem in recoding protein %s angles (ignored) ========Problem in reading sequence in %s %d th reading ...================ reading %s num prot %d score : %f nb match %d threshold score=%f (ERR_SHUFFLE=%d) Print results for pymol in %s ************************no match Pb in reading %d sequences/structures Pb in recoding %d sequences/structures No protein read in one of the database file : file1 : %d file2 : %d ********** fin du fichier ************* /55555n5555=55555#55555555588555O5˙5)Ut85ڛ5՘ACDEFGHIKLMNPQRSTVWYACGTDNA:3D-STRUCTURE:PROTEIN:sim.cCCDDRRSSEEFFHHWWIIJJXXYYsROWsROW[i]LISTLIST[i]--> K = %d Kwanted = %d sim: break unknown cause !!! z %5d . : . %5d %s %s %5d %s simalign:: not enough memory for swres! %s: match %d mismatch %d gap-open %d gap-ext %d SIM:: not enough memory for RMS computations (pp0,pp1) pb malloc avec %s (%d %s) (size=%d) SIM: not enough memory for salign There are no %d alignments between two sequences--> match count = %d score = %d probleme proba waterman_vingron break: limit score, probability or length given is reached added match (%4d,%4d) (%4d,%4d) (score=%.2f len=%d) alignment discarded too much overlap (%.3f), restarting... (%4d,%4d) (%4d,%4d) (score=%f len=%d) sim: break cause length (%d) < minlength (%d) sim: break cause score (%f) < minscore (%f) sim: break cause proba (%f) < proba limit (%f) sim: break cause number of matches reached sim: break cause no more matches swalign:: not enough memory for crossed rms swalign:: not enough memory for group Aswalign.cswresswres->posd0swres->posd1swres->posf0swres->posf1swres->scoreswres->score_freqswres->score_par_freqswres->score_GLswres->tm_scoreswres->score_blosangleswres->recoverswres->rmsswres->rev_rmsswres->saliswres->tProbaMTD_p0swres->tProbaMTD_p1swres->tProbaIndepswres->tProbaBiswres->alphaswres->betaswres->gammaswres->new_rmsswres->matrix4xpb realloc avec %s (%d %s) swres->sali[swres->nmatch]MYFREE null %s%-6c: %6d %6d %7.1f - ##3 %4d - Number %4d local alignment Begins at (%d,%d) [PDB=(%4d%c,%4d%c)] Ends at (%d,%d) Zscore %.3f RRMSD: %.2f Sequence alignment: Angle alignment: NUM GROUP %5d [%3d] %7.2f lg_match match1 match2 RRMSD%10s%c %10s%c %6d %6d %6d %7d %8.2f %11.2f %8d #1 %6d %7.2f %6d %4d %4d %4d %4d %6.2f ##1 %s%c %s%c %4d ##2 ==1 ==2 %6.1f %c*pp0*pp1---- p0= %s%c p1= %s%c RESULTS ---- ********************************************************* Length protein1 %4d protein2 %4d Score %10.2f Score/Alignement Length %8.3f RMS or Probability %7.2f Overlap %4.2f Alignment length %4d MTD Probability protein1 %4.3f protein2 %4.3f Blosum score: %5d GL score : %5.2f Group : %1d Score_freq : %20.2f Blosum_angle : %5.3f TM score %5.3f Sequence alignment corresponding to structure match: Sum Log MTD Probability protein1 %6.5f protein2 %6.5f @p0 p1 #repeat start0 start1 lg_prot score rms/proba overlap blosum GLscore compat start0 start1 end0 end1 swalign:: not enough memory for RMS computations (pp0,pp1) swalign:: not enough memory for swres! swalign::not enough memory for NewMatrix D C(kn@ocx]8?!e?333333??alignsw:: cc <%c> %f is not s,i or d, this should not append! alignsw:: lastmove <%c> is not s,i or d, this should not append! swalign2: not enough memory for RMS computations %s %s too much overlap (%.3f), restarting... (%4d,%4d) (%4d,%4d) (score=%.2f len=%d) score=%15.2f (minscore=%15.2f) normalized score = %15.2f stop on match: step %d (nmatch=%d): score %.2f (min=%.2f) proba %.4f (lim=%.4f) len %d (minlen=%d) stop on score: step %d (nmatch=%d): score %.2f (min=%.2f) proba %.4f (lim=%.4f) len %d (minlen=%d) stop on proba: step %d (nmatch=%d): score %.2f (min=%.2f) proba %.4f (lim=%.4f) len %d (minlen=%d) stop on length: step %d (nmatch=%d): score %.2f (min=%.2f) proba %.4f (lim=%.4f) len %d (minlen=%d) ?PG{Gz?swalign2.c*plensub*ppp0*ppp1gap_extsIisJjgap_ext[j]sIi[j]sJj[j]best_scoresbest_scores[i]salign pas de match score %f LitPdbProtAlpha:: Error: %s LitProtAlpha:: Empty file pdb.entEnd of file reached End of data file NewProt pb de mallocNO HEADERLitEnTete: Fichier vide PATHNBRESangle non valide: %f (%d) IO error 1 with sequence #%s Fin de ficher Pb in reading PDB file : residu null Problem in residue number reading in header End of file encountered while searching to read next header End of file encountered while reading header LitProtAlpha:: No residue to read in %s LitProtAlpha:: End of file encountered while reading Problem in allocation for pProt in LitProtAlpha Incorrect number of residues: %d read residues over %d Problem with ReadPhipsiLine in LitProtAlpha Maximum number of chains/fragments (%d) exceeded for %s nombre de residus incorrect: %d residus lus sur %d pb avec ReadPhipsiLine ds LitProtAlpha angle %f du residu %d de la proteine %s non valide , ignore Cannot read binary file (is file really in binary format?) BinaryReadProtAlpha: cannot allocate for pProt nb max de chaines/fragments (%d) depasse pour %s angle %f du residu %d de la proteine %s non valide, ignore BinaryReadProtAlpha:: debut frag 0 (frag %d) LitEnTete: pas de HEADER sur ligne [%s] LitEnTete: pas de PATH sur ligne [%s] LitEnTete: Cannot read number of residues LitEnTete: pas de NBRES sur ligne [%s] RecodeAngles:: pb de recodage, angle (%f) recode (%d) est > au maximum (%d) pb dans aa3to1: %s, pos: %s, cases %d indice %d not enought memory for temposeq (fasta) .. IO error 2 with sequence #%s (flag ok 0) sequence non multiple de 3 !!! : %d Too much undefined characters in #%s not enought memory for pProt (fasta) .. IO error 2 with sequence #%s (flag not ok) C44C D 33333f33333f@init_minimier:: Error: Not enough memory for result tree!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! Minimier tree was sorted before all proteins were ranked !!!!!!!!!!!!!!! I think the score hasn't been computed: %f Pas de minimier a desallouer Results impredictable %s%s%s%s%d%d%s PAM %s Proximity %s Distance Matrix used : %s %s Vocabulary : %s %s Threshold : %d %s Values : %s %s %c %3d %s Classes : %s %s %c %d %d %3d%4.2f Matrix file is not symetric bad type matrix MAT%c %c %f Matrix values < minval or > maxval Bad matrix (similarity should be distance) simple_convert: no proper conversion indicated --> Sum %c %f (proba simple %f) B0A?stats.c*t1*t2%d %d %lf lgMot: %d j: %d indxmot %d: %d a %d @ probabilites simples @ %20dHEADER ZZZ %d %f %f %f Set_TableFreq:: can't open %s for statistics ReadTable1Dim:: premature end of frequencies file bad format for number of groups in ReadTable1Dim <%s> ReadTableFreq:: premature end of frequencies file ReadTableFreq:: bad format <%s> ReadTableFreq:: Cannot read line before 2-uple in frequency file ReadTableFreq:: bad format (2) <%s> pb au recodage des angles dans CalculProbaBiAli, angleGroupe: %d, nbGroupes: %d problem in angle recoding in CalculProbaMtd avec %s indx[%d]= %d, max %d, angle %d (%d), : %f %3d %6d %10.2f %8.2f %10.2f %10.2f Ecriture du fichier pour pymol impossibles (un des parametres est null) hide everything, struct1 show ribbon, struct1 color blue, struct1 hide everything, struct2 show ribbon, struct2 color red, struct2 select sel11, struct1 and resi %d-%d select sel12, struct1 and resi %d-%d select sel21, struct2 and resi %d-%d select sel22, struct2 and resi %d-%d fitting struct1, i. %d-%d , struct2, i. %d-%d impossible d'afficher la proteine %d a parameter of EcritEnTeteSet is NULL un des parametres de EcritEnTeteSet est NULL pdbref 0 %d %c-%d %c %d-%d %d-%d pdbref 1 %d %c-%d %c %d-%d %d-%d a parameter of EcritToutDansSet is NULL *-PROTEIN-SET---ASCII-FILE--* Impossible de creer le fichier set load %s.pdb , struct1 load %s.pdb , struct2 color forest, sel11 color yellow, sel12 color purple, sel21 color orange, sel22 run fitting.py name %s%d visible 1 color %d path %s adress %d end name match%d symbol alpha Cannot create "set" file * suite2 * END_PDB_REC END_WORD cant open file %s to readr+*Error* [%d] %s A+i)+>YS??Y4?$tBUG: %s (i >= siz) in DistribRandom(i,j >= siz) in HashRandomstats_sequence.cwater_vingscorebisnbscorebis[i]scores[j]k-uple too big with this alphabetnot enough memory for hash tableswalign:: not enough memory for tempo file stat_sequences.c swalign:: not enough memory for temposeq Error in Shuffling: exit... (%d) wv1: score %f (%4d,%4d) (%4d,%4d) @% @Invalid arguments in routine GAMMQa too large, ITMAX too small in routine GCFv !>x less than 0 in routine GSERa too large, ITMAX too small in routine GSER> Numerical Recipes run-time error... > %s f?[<[<EԘ?J $ԿXp4:p,eM@?\@ԟW?dY+M?|@h @MbX9?%1C4pFk@;->q@ rKa@͋40>yTW @0q@ rKa@͋40>yTW @0 0 : structure analysis -P<0/1/2> 1 : proteique sequence analysis -P<0/1/2> 2 : nucleique sequence analysis ******************** OPTIONS ********************************** -l output on one line per match (several lines output by default) -n number of best subalignments to show (even if they are not statistically significant for sequences) - default for structure: %d - default for sequence: -1, i.e. the algorithm rely on statistical criteria for stopping output) -L minimal length for the repeat %d -m : minimum score for output subalignment -z : use default minimum score for output subalignment(def structure %.0f protein %.0f nucleic %.0f) -N : probability for dna and protein (def:%f) -G -1 : default value for gap open and extension penalty : %5.2f structure, %5.2f protein, %5.2f nucleic) default gap extention penalty : %5.2f structure, %5.2f protein, %5.2f nucleic) gap cost = gap_open + k * gap_ext (k being total gap length) -G : other value for gap open penalty -g : other value for gap extension penalty -r : ratio of tolerated recovering [0,1] (def:%4.2f) -q : output matches are sorted by scores (default: sort is done on RMS) -W : Smith/Waterman algorithm is to be used (default: Huang/Miller algorithm) -F : No sequence/structure size limit, (default:%d when SW is used) ******************** OPTIONS FOR SEQUENCES ONLY ********************************** -x matrix (if amino acid or DNA sequence) -D : number of shuffled sequences used to calculate the statistical significance of the scores, default : %d -p second method of Waterman and Vingron for statistical significance : declumping estimation ******************** OPTIONS FOR STRUCTURES ONLY ********************************** -M : minimum rms for output subalignment(def:%f) -u : normalize minimum rms for output subalignment (Betancourt, Skolnick, 2001) (def:%f) -U use RMSD instead of Relative RMSD -w : value of threshold for angle score (def:%10.2f) note: score is detailed in paper -e : to extend alignment for amino acid distant than less than x Angstrom PrintArbreScan:: No protein returned from the minimier @@ Type of file : 3D amino acid sequences DNA sequences @@ File : %s format PDB fasta binary alpha @@ Minimum score %5.2f @@ Overlap allowed : %2.3f @@ Algorithm : Huang-Miller @@ maximum RRMSD %3.2f @@ P-value %5.2f @@ Declumping method : %d @@ Substitution matrix %s gaps : -i : standard output -j : error output Aư>ףp= ??@zG?)\(?ApA@BError in getrusage -------------------------------------- %s: CPU User Time : %8d sec %4d usec %s: mem size in Ko : ru_minflt:%d ru_majflt:%d %s: mem size in Ko : ru_maxrss:%d ru_ixrss:%d ru_idrss:%d ru_isrss:%d ru_minflt:%d ru_majflt:%d ru_inblock %d ru_oublock %d ru_nswap:%d no_nameprobleme ecriture binaire fin du fichier !!! libfasta.cseq->seqnot enought memory for seq (fasta) .. 1 IO error 1 with sequence #%s 2 IO error 1 with sequence #%s %d /UNK/ALA/CYS/ASP/GLU/PHE/GLY/HIS/ILE/LYS/LEU/MET/ASN/PRO/GLN/ARG/SER/THR/VAL/TRP/TYR/MSE/CSE/ASX/GLX/CEA/HYP/ACD/HSE/HYL/ALB/ARO/PCA/BAS/SAR/BET/TAU/Chain %d %c first res %d%c nbRes %d new_residu:: not enough memoryput_atom_in_res:: not enough memoryset_residue_neighbours:: trop de voisinsget_CA_xyz:%3s %4d has no CA atom get_CA_TFactor:%3s %4d has no CA atom get_distca_1_2:: residue does not existhas no CG(1), OG(1) or SG atomhas no CD(1), OD(1), SD or ND(1) atomhas no CE, CE(1), OE(1), NE or NE(1) atom%s :: residue %s %4d %s residue %s %4d %sget_phi_psi:: residue does not existget_chi:: residue does not existget_alpha_tau:: residue does not existreadPdbResidues: protein %s Cannot read key in line <%s> readPdbResiduesChain: protein %s Cannot read key in line <%s> Reading input file with x y z Reading input file without x y z ReadPhipsiLine:: Bad file format in readBinary: Cannot read header readBinary: Cannot read number of residues readBinary: Not enough memory for binres array ! readBinary: Cannot read residues, %d residues expected, %d residus read! /GLY/ALA//CYS/SER/THR/VAL//ILE/LEU/ASP/ASN/%d chain CAprecedingfollowingerreur distance : trou get_phi_psi get_chi get_alpha_tau get_distca_1_2get_distca_1_3has no CA atomhas no CB atomhas no N atomhas no CO atomat start of chainat end of chain%s :: residue %s %4d %sNCBCGCG1OGOG1SGCDCD1OD1ND1CE1OE1NENE1%hdget_atom: bad atom formatDESCCOMPNDSOURCEREMARK2 RESOLUTION.ATOMHETATMENDMDLENDlibphipsi.c*tChainpb malloc avec %s (%d %s) EXPDTANMRTHEORETICALReadPhipsiLine: no line %3s %hd%c %f %f %f %f %f %f%3s %hd%c %f %f %f<%s> readBinary: Cannot read path !!!!! "">"d"x""O""""""".""""""r3܀@Read errorunZ function: no fileNot enough memory to process %d bitsWrite error failed fwritefailed gzcloseFile is not in compressed format 1.2.2.2%c%c%c%c%c%c%c%c%c%c deflate 1.2.3 Copyright 1995-2005 Jean-loup Gailly yzz z} }} } } }1.2.2.2       L,l\<|B"bR2r J*jZ:zF&fV6vN.n^>~A!aQ1q I)iY9yE%eU5u M-m]=}   S S  3 3  s s    K K  + +  k k     [ [  ; ;  { {     G G  ' '  g g     W W  7 7  w w     O O  / /  o o     _ _  ? ?     @ `P0pH(hX8xD$dT4tC#c         (08@P`p  0@`  0@`uninitialized zip processingnot enough memorybad magic headerEOF while processing headerInvalid compressed dataMore data to process at closebad CRCwrite errorgeneric/internal errorreserved field or compression methoduncompressed size differs from recordedA@!  @a`10  @`Psp0  ` @ X ;x8 h( H T+t4  d$ D \ S|< l,  L R#r2  b" B Z Cz: j*  J V@3v6 f& F  ^ c~> n. N `Qq1  a! A Y ;y9 i)  I U+u5  e% E ] S}= m-  M S#s3  c# C [ C{; k+  K W@3w7 g' G  _ c? o/ O `Psp0  ` @ X ;x8 h( H T+t4  d$ D \ S|< l,  L R#r2  b" B Z Cz: j*  J V@3v6 f& F  ^ c~> n. N `Qq1  a! 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