
 OPTIM version 22983, Copyright (C) David J. Wales
 OPTIM comes with ABSOLUTELY NO WARRANTY; for details supply WARRANTY as an input keyword.
 This is free software, and you are welcome to redistribute it
 under certain conditions; provide keyword COPYRIGHT to see the details.

 getparams> input coordinates for AMBER9 system will be read from 
start
start               

          -------------------------------------------------------
          Amber 9  SANDER                              2006
          -------------------------------------------------------

| Run on 05/24/2012 at 18:54:00
  [-O]verwriting output

File Assignments:
|  MDIN: min.in                                                                
| MDOUT: min.out                                                               
|INPCRD: coords.inpcrd                                                         
|  PARM: coords.prmtop                                                         
|RESTRT: coords.rst                                                            
|  REFC: refc                                                                  
| MDVEL: mdvel                                                                 
|  MDEN: mden                                                                  
| MDCRD: coords.mdcrd                                                          
|MDINFO: mdinfo                                                                
|INPDIP: inpdip                                                                
|RSTDIP: rstdip                                                                


 Here is the input file:

Minimization                                                                   
&cntrl                                                                         
   imin=1, maxcyc=1, ncyc=1,                                                   
   igb=2, saltcon=0.2,                                                         
   ntpr=1, ntx=1, ntb=0,                                                       
   cut = 999.0                                                                 
 /                                                                             
	                                                                              

--------------------------------------------------------------------------------
   1.  RESOURCE   USE: 
--------------------------------------------------------------------------------

| Flags:                                                                        
| New format PARM file being parsed.
| Version =    1.000 Date = 02/24/09 Time = 08:52:47
 NATOM  =     218 NTYPES =      12 NBONH =     102 MBONA  =     123
 NTHETH =     230 MTHETA =     169 NPHIH =     463 MPHIA  =     323
 NHPARM =       0 NPARM  =       0 NNB   =    1202 NRES   =      12
 NBONA  =     123 NTHETA =     169 NPHIA =     323 NUMBND =      27
 NUMANG =      57 NPTRA  =      40 NATYP =      21 NPHB   =       0
 IFBOX  =       0 NMXRS  =      24 IFCAP =       0 NEXTRA =       0
 NCOPY  =       0

 Implicit solvent radii are modified Bondi radii (mbondi)                                                   

|     Memory Use     Allocated
|     Real               14260
|     Hollerith           1322
|     Integer            31189
|     Max Pairs              1
|     nblistReal             0
|     nblist Int             0
|       Total              238 kbytes
| Duplicated    0 dihedrals
| Duplicated    0 dihedrals

--------------------------------------------------------------------------------
   2.  CONTROL  DATA  FOR  THE  RUN
--------------------------------------------------------------------------------

                                                                                

General flags:
     imin    =       1, nmropt  =       0
     ifswitch=       0, fswitchbeta=  10.000
 mdread> no continuous cutoff will be used for non-bonded terms

Nature and format of input:
     ntx     =       1, irest   =       0, ntrx    =       1

Nature and format of output:
     ntxo    =       1, ntpr    =       1, ntrx    =       1, ntwr    =     500
     iwrap   =       0, ntwx    =       0, ntwv    =       0, ntwe    =       0
     ioutfm  =       0, ntwprt  =       0, idecomp =       0, rbornstat=      0

Potential function:
     ntf     =       1, ntb     =       0, igb     =       2, nsnb    =      25
     ipol    =       0, gbsa    =       0, iesp    =       0
     dielc   =   1.00000, cut     = 999.00000, intdiel =   1.00000
     saltcon =   0.20000, offset  =   0.09000, gbalpha=    0.80000
     gbbeta  =   0.00000, gbgamma =   2.90912, surften =   0.00500
     rdt     =   0.00000, rgbmax  =  25.00000
     alpb  =        0
     scnb    =   2.00000, scee    =   1.20000

Frozen or restrained atoms:
     ibelly  =       0, ntr     =       0

Energy minimization:
     maxcyc  =       1, ncyc    =       1, ntmin   =       1
     dx0     =   0.01000, drms    =   0.00010
|  INFO: Old style inpcrd file read


--------------------------------------------------------------------------------
   3.  ATOMIC COORDINATES AND VELOCITIES
--------------------------------------------------------------------------------

                                                                                
 begin time read from input coords =     0.000 ps

 Number of triangulated 3-point waters found:        0
 getparams> Number of atoms (or variables)  determined as    218
 keyword> Local permutational alignment: alignment threshold=        1.00000
 keyword> Local permutational alignment: alignment cutoff=           5.00000
 keyword> Number of groups of permutable atoms=    25
read argument: coords.prmtop 
Reading parm file (coords.prmtop)
title:
                                                                                
 fetchz> Hybrid EF/BFGS transition state search, maximum steps= 250
         maximum tangent space steps=   5 or  100 when overlap is better than     0.999900
 fetchz> Uphill mode is    0 for initial step and    0 after that
 fetchz> Steps for largest Hessian e/vector= 100, smallest e/vector=2000 convergence at       0.0020%

 fetchz>  654 Cartesian coordinates will be optimised for  218 AMBER atoms

 fetchz> Lowest   1 eigenvalues and eigenvectors will be calculated non-iteratively
 fetchz> Point group checked when RMS force <     0.00100000, highest symmetry axis tested for=  6
 fetchz> Initial distance and eigenvalue tolerances in symmetry determination=     0.00010000     0.00010000
 fetchz> Minimum number of optimization steps=     0
 keywords> Cutoff for identifying atoms in the same orbit=    0.2000000000    
 keywords> lpermdist neighbours, threshold, max sep=    10     1.000000000         3
 fetchz> Convergence criterion for LBFGS optimization: RMS force< 0.10000000E-05 maximum steps= 10000
 fetchz> Maximum energy rise in LBFGS minimization=    0.1000000000E-01
 fetchz> Number of updates in LBFGS=    10000
 fetchz> Number of updates in XLBFGS=   4
 fetchz> Number of updates in mind=   4
 fetchz> Initial guess for diagonal elements in LBFGS=     0.0100
 fetchz> Initial guess for diagonal elements in XLBFGS=    0.1000
 fetchz> Maximum step size in LBFGS energy minimization=     0.1000
 fetchz> Maximum step size in XLBFGS=    0.2000
 fetchz> Maximum step size in LBFGS neb image minimization=                 0.2000
 fetchz> Warnings will be issued if atoms become closer than 0.5 units
 fetchz> Coordinates for intermediate steps will not be dumped to file points


 KeyInt>> Using natural internal coordinates. # of coords =        648
 KeyInt>> Parameter file for internal coordinates is naturals-noH.par                                                                                    
 KeyInt>> KD, NNZ are         74      7440
 KeyInt>> Back transform convergence (for interpolation)     0.1000000000E-07
 KeyInt>> Back transform convergence criterion (except for interpolation)     0.1000000000E-03
 KeyInt>> Using internal coordinates for interpolation.
 KeyInt>> Permuting endpoint atoms to minimise torsion distance
 OPTIM> Using translational/rotational ev shift=     1000000.000    
 OPTIM> Initial energy=    -450.5867733     RMS force=    0.8717231598E-06
 OPTIM> Final energy  =    -448.0973399     RMS force=    0.8545232140E-06
 KeyConnect> Maximum cycles = 50, maximum images = 23
 KeyConnect> Maximum attempts per pair of minima = 3, with increment image density of 2.00
 KeyConnect> Image density = 0.30, iteration density = 35.00
 KeyNEB> Initial and final NEB force constants     10.00000000        10.00000000     factor=    1.010000000    
 KeyNEB> Number of images will vary depending on the separation of the endpoints
 KeyGrad> Overall rotation and translation will NOT be removed
 KeyGrad> Using doubly nudged elastic band gradient
 KeyOutput> Transition state candidates will be optimized
 KeyOutput> Concise printing during transition states optimization
 KeyOutput> Transition state candidates are maxima along NEB
 KeyMin> Maximal number of iterations will vary, depending on the number of images in the band
 KeyMin> RMS convergence criterion is set to 0.001
 KeyMin> L-BFGS minimization
 KeyLBFGS> Maximum step size per image =     0.2000000000    
 KeyLBFGS> 4 Hessian updates per iteration
 KeyLBFGS> Guess for inverse Hessian diagonal elements =     0.1000000000E-02
 KeyTau> Using Henkelman and Jonsson's improved tangent
 KeyDecide> Cost function in Dijkstra algorithm is D^3

 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 1 >>>>>>>>>>>>>>>>>>>>> 2 minima and 0 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      1 steps with      1 missing connections, weight=    0.58687E+06
 decide> The unconnected minima in the chain and their distances are:
     2       83.72     1 
 

 tryconnect> 805-iteration DNEB run for minima 1_S and 2_F using 23 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      146.3563092    
 Double-ended search iterations= 1222 RMS= 0.3935 Dev= 1.15% S= 222.47 time= 210.58
 Following    3 images are candidates for TS:    5   13   19  
 Converged to TS (number of iterations):         83
 Converged to TS (number of iterations):         93
 Converged to TS (number of iterations):        231
 DNEB run yielded 3 true transition state(s) time= 256.75

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                    1254 steps. Energy=    -451.4625761       time=      15.88
 Minus side of path:                    1208 steps. Energy=    -450.0314569       time=      14.59

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -451.4625761  1.5039         -449.9586446 0.72812E-01     -450.0314569   1.752   1.559 175.331   1.243
        *NEW* (Placed in 3)                                     *NEW* (Placed in 4)
 Connection established between members of the U set.

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                    1207 steps. Energy=    -439.0327222       time=      13.66
 Minus side of path:                    1233 steps. Energy=    -439.0327222       time=      12.57

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -439.0327222  1.3380         -437.6947590  1.3380         -439.0327222   4.399   3.100 108.819   2.003
check_cistrans_protein>  WARNING -- cis (or deformed) peptide bond detected between residues      1     2
 tryconnect> MINUS minimum: cis-trans isomerisation of a peptide bond detected involving atom     15
check_cistrans_protein>  WARNING -- cis (or deformed) peptide bond detected between residues      1     2
 tryconnect> PLUS minimum: cis-trans isomerisation of a peptide bond detected involving atom     15
 tryconnect> Cis-trans isomerisation of a peptide bond detected (wrt. the original structure), rejecting
 tryconnect> Transition state with energy     -437.6947590     ignored, cis-trans isomerisation detected in one or more peptide bonds.

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                    1240 steps. Energy=    -441.4262124       time=      12.71
 Minus side of path:                    1268 steps. Energy=    -442.4389925       time=      13.27

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -441.4262124 0.16683         -441.2593864  1.1796         -442.4389925  20.642  19.999   2.153 101.270
check_cistrans_protein>  WARNING -- cis (or deformed) peptide bond detected between residues      1     2
 tryconnect> MINUS minimum: cis-trans isomerisation of a peptide bond detected involving atom     15
check_cistrans_protein>  WARNING -- cis (or deformed) peptide bond detected between residues      1     2
 tryconnect> PLUS minimum: cis-trans isomerisation of a peptide bond detected involving atom     15
 tryconnect> Cis-trans isomerisation of a peptide bond detected (wrt. the original structure), rejecting
 tryconnect> Transition state with energy     -441.2593864     ignored, cis-trans isomerisation detected in one or more peptide bonds.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 2 >>>>>>>>>>>>>>>>>>>>> 4 minima and 3 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      2 steps with      2 missing connections, weight=    0.12426E+07
 decide> The unconnected minima in the chain and their distances are:
     2      104.29     4     4       47.68     1 
 

 tryconnect> 805-iteration DNEB run for minima 2_F and 4_U using 23 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      25.26950195    
 Double-ended search iterations= 1031 RMS= 1.4228 Dev= 2.30% S= 197.95 time= 175.12
 Following    3 images are candidates for TS:    5   14   18  
 Converged to TS (number of iterations):        100
 Converged to TS (number of iterations):        129
 Failed to converge to TS (number of iterations):        251
 DNEB run yielded 2 true transition state(s) time= 278.42

 >>>>>  Path run for ts 4 ...
 Plus  side of path:                    2487 steps. Energy=    -457.8376068       time=      41.08
 Minus side of path:                    1285 steps. Energy=    -450.8743731       time=      13.35

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -457.8376068  10.472         -447.3657524  3.5086         -450.8743731  55.607  45.068   3.001  72.641
        *NEW* (Placed in 5)                                     *NEW* (Placed in 6)
 Connection established between members of the U set.

 >>>>>  Path run for ts 5 ...
 Plus  side of path:                    1250 steps. Energy=    -454.3392437       time=      12.75
 Minus side of path:                    1210 steps. Energy=    -453.1083654       time=      12.14

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -454.3392437  3.7603         -450.5788971  2.5295         -453.1083654  22.957  20.373  12.534  17.393
        *NEW* (Placed in 7)                                     *NEW* (Placed in 8)
 Connection established between members of the U set.

 tryconnect> 490-iteration DNEB run for minima 1_S and 4_U using 14 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.3286616756    
 Double-ended search iterations= 490 RMS= 0.0623 Dev= 3.57% S= 59.53 time= 50.99
 Following    3 images are candidates for TS:    1    5    9  
 Converged to TS (number of iterations):         40
 Failed to converge to TS (number of iterations):        251
 Converged to TS (number of iterations):        146
 DNEB run yielded 2 true transition state(s) time= 229.19

 >>>>>  Path run for ts 6 ...
 Plus  side of path:                    1538 steps. Energy=    -455.3423495       time=      17.29
 Minus side of path:                    1253 steps. Energy=    -450.5867733       time=      12.78

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -455.3423495  5.0946         -450.2477046 0.33907         -450.5867733  31.563  25.532   2.100 103.799
        *NEW* (Placed in 9)                                     Known (#1)
 Unconnected minimum 9 found its way to S set.

 >>>>>  Path run for ts 7 ...
 Plus  side of path:                    1350 steps. Energy=    -450.1626995       time=      14.25
 Minus side of path:                    1854 steps. Energy=    -450.3076155       time=      23.01

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -450.1626995 0.38814         -449.7745588 0.53306         -450.3076155  37.908  24.598   2.376  91.759
        *NEW* (Placed in 10)                                    *NEW* (Placed in 11)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 3 >>>>>>>>>>>>>>>>>>>>> 11 minima and 7 ts are known >>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      2 steps with      1 missing connections, weight=    0.78963E+06
 decide> The unconnected minima in the chain and their distances are:
     2       92.43     9 
 

 tryconnect> 805-iteration DNEB run for minima 2_F and 9_S using 23 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      1030.346764    
 Double-ended search iterations= 865 RMS= 16.9278 Dev= 1.94% S= 195.87 time= 146.91
 Following    4 images are candidates for TS:    7    9   13   18  
 Converged to TS (number of iterations):        109
 Failed to converge to TS (number of iterations):        251
 Converged to TS (number of iterations):         65
 Converged to TS (number of iterations):        133
 DNEB run yielded 3 true transition state(s) time= 331.48

 >>>>>  Path run for ts 8 ...
 Plus  side of path:                    1270 steps. Energy=    -452.5184070       time=      13.57
 Minus side of path:                    1248 steps. Energy=    -452.5494805       time=      12.99

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -452.5184070  2.8608         -449.6575840  2.8919         -452.5494805   7.690   6.861  24.776   8.799
        *NEW* (Placed in 12)                                    *NEW* (Placed in 13)
 Connection established between members of the U set.

 >>>>>  Path run for ts 9 ...
 Plus  side of path:                    1230 steps. Energy=    -447.2250875       time=      12.65
 Minus side of path:                    1225 steps. Energy=    -447.2250875       time=      12.90

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -447.2250875  16.274         -430.9513129  16.274         -447.2250875   6.464   2.493 108.916   2.002
        *NEW* (Placed in 14)                                    Known (#14)
 Connection established between members of the U set.

 >>>>>  Path run for ts 10 ...
 Plus  side of path:                    1142 steps. Energy=    -452.3362042       time=      12.31
 Minus side of path:                    1116 steps. Energy=    -450.9017134       time=      12.73

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -452.3362042  1.4792         -450.8569799 0.44733E-01     -450.9017134   1.313   1.244 182.913   1.192
        *NEW* (Placed in 15)                                    *NEW* (Placed in 16)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 4 >>>>>>>>>>>>>>>>>>>>> 16 minima and 10 ts are known >>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      9 steps with      7 missing connections, weight=    0.69758E+06
 decide> The unconnected minima in the chain and their distances are:
     2       63.40     6     5       23.82    12    12       56.90    14    14       52.43     7     8       33.78     3     3       23.72    10    10       36.60     1 
 

 tryconnect> 665-iteration DNEB run for minima 2_F and 6_U using 19 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.7984714498E-01
 Double-ended search iterations= 665 RMS= 0.0201 Dev= 5.84% S= 80.11 time= 95.69
 Following    1 images are candidates for TS:    5  
 Converged to TS (number of iterations):        120
 DNEB run yielded 1 true transition state(s) time=  63.73

 >>>>>  Path run for ts 11 ...
 Plus  side of path:                    1594 steps. Energy=    -448.3827800       time=      18.43
 Minus side of path:                    1324 steps. Energy=    -448.0973399       time=      14.22

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -448.3827800 0.68095         -447.7018283 0.39551         -448.0973399  40.037  34.884   2.007 108.611
        *NEW* (Placed in 17)                                    Known (#2)
 Unconnected minimum 17 found its way to F set.

 tryconnect> 245-iteration DNEB run for minima 5_U and 12_U using 7 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.9156391332    
 Double-ended search iterations= 245 RMS= 0.0902 Dev= 0.74% S= 25.63 time= 13.14
 Following    1 images are candidates for TS:    5  
 Converged to TS (number of iterations):         43
 DNEB run yielded 1 true transition state(s) time=  37.23

 >>>>>  Path run for ts 12 ...
 Plus  side of path:                    1241 steps. Energy=    -458.2894222       time=      12.75
 Minus side of path:                    1212 steps. Energy=    -456.2229734       time=      12.33

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -458.2894222  2.5289         -455.7605329 0.46244         -456.2229734   5.769   5.356  32.035   6.805
        *NEW* (Placed in 18)                                    *NEW* (Placed in 19)
 Connection established between members of the U set.

 tryconnect> 595-iteration DNEB run for minima 12_U and 14_U using 17 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.3130111196    
 Double-ended search iterations= 595 RMS= 0.0872 Dev= 4.34% S= 79.24 time= 74.63
 Following    5 images are candidates for TS:    7   10   12   15   17  
 Converged to TS (number of iterations):        214
 Converged to TS (number of iterations):         35
 Converged to TS (number of iterations):         38
 Converged to TS (number of iterations):         45
 Converged to TS (number of iterations):         35
 DNEB run yielded 5 true transition state(s) time= 234.85

 >>>>>  Path run for ts 13 ...
 Plus  side of path:                    1303 steps. Energy=    -451.6683452       time=      14.13
 Minus side of path:                    1517 steps. Energy=    -453.5183487       time=      18.54

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -451.6683452 0.41254         -451.2558066  2.2625         -453.5183487  26.118  22.494   2.716  80.276
        *NEW* (Placed in 20)                                    *NEW* (Placed in 21)
 Connection established between members of the U set.

 >>>>>  Path run for ts 14 ...
 Plus  side of path:                    1222 steps. Energy=    -451.6073739       time=      12.87
 Minus side of path:                    1245 steps. Energy=    -453.0911500       time=      13.28

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -451.6073739  2.0277         -449.5797094  3.5114         -453.0911500   7.462   6.405  35.289   6.177
        *NEW* (Placed in 22)                                    *NEW* (Placed in 23)
 Connection established between members of the U set.

 >>>>>  Path run for ts 15 ...
 Plus  side of path:                    1270 steps. Energy=    -451.6507949       time=      13.22
 Minus side of path:                    1244 steps. Energy=    -450.7143223       time=      13.73

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -451.6507949  3.6398         -448.0109518  2.7034         -450.7143223  22.017  20.644  15.098  14.439
        *NEW* (Placed in 24)                                    *NEW* (Placed in 25)
 Connection established between members of the U set.

 >>>>>  Path run for ts 16 ...
 Plus  side of path:                    1282 steps. Energy=    -448.4009816       time=      14.87
 Minus side of path:                    2087 steps. Energy=    -452.5239553       time=      33.63

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -448.4009816  2.0355         -446.3654912  6.1585         -452.5239553  41.829  37.360   1.867 116.735
        *NEW* (Placed in 26)                                    *NEW* (Placed in 27)
 Connection established between members of the U set.

 >>>>>  Path run for ts 17 ...
 Plus  side of path:                    1250 steps. Energy=    -448.4009816       time=      15.62
 Minus side of path:                    1250 steps. Energy=    -447.2250875       time=      13.52

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -448.4009816  1.3462         -447.0547856 0.17030         -447.2250875  18.755  17.442   2.094 104.125
        Known (#26)                                             Known (#14)
 Connection established between members of the U set.

 tryconnect> 525-iteration DNEB run for minima 7_U and 14_U using 15 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      2.678483190    
 Double-ended search iterations= 555 RMS= 0.6299 Dev= 1.92% S= 211.77 time= 62.82
 Following    2 images are candidates for TS:    7    9  
 Converged to TS (number of iterations):         87
 Converged to TS (number of iterations):         87
 DNEB run yielded 2 true transition state(s) time= 117.32

 >>>>>  Path run for ts 18 ...
 Plus  side of path:                    1234 steps. Energy=    -440.4559642       time=      12.78
 Minus side of path:                    1221 steps. Energy=    -439.3182420       time=      12.60

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -440.4559642  2.6831         -437.7728366  1.5454         -439.3182420  10.732   8.811   3.424  63.673
check_cistrans_protein>  WARNING -- cis (or deformed) peptide bond detected between residues      1     2
 tryconnect> MINUS minimum: cis-trans isomerisation of a peptide bond detected involving atom     15
check_cistrans_protein>  WARNING -- cis (or deformed) peptide bond detected between residues      1     2
 tryconnect> PLUS minimum: cis-trans isomerisation of a peptide bond detected involving atom     15
 tryconnect> Cis-trans isomerisation of a peptide bond detected (wrt. the original structure), rejecting
 tryconnect> Transition state with energy     -437.7728366     ignored, cis-trans isomerisation detected in one or more peptide bonds.

 >>>>>  Path run for ts 19 ...
 Plus  side of path:                    1148 steps. Energy=    -437.3723465       time=      11.61
 Minus side of path:                    1060 steps. Energy=    -435.8805547       time=      10.66

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -437.3723465  1.4982         -435.8741831 0.63716E-02     -435.8805547   1.317   1.284 192.871   1.130
check_cistrans_protein>  WARNING -- cis (or deformed) peptide bond detected between residues      1     2
 tryconnect> MINUS minimum: cis-trans isomerisation of a peptide bond detected involving atom     15
check_cistrans_protein>  WARNING -- cis (or deformed) peptide bond detected between residues      1     2
 tryconnect> PLUS minimum: cis-trans isomerisation of a peptide bond detected involving atom     15
 tryconnect> Cis-trans isomerisation of a peptide bond detected (wrt. the original structure), rejecting
 tryconnect> Transition state with energy     -435.8741831     ignored, cis-trans isomerisation detected in one or more peptide bonds.

 tryconnect> 350-iteration DNEB run for minima 3_U and 8_U using 10 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.3286616756    
 Double-ended search iterations= 350 RMS= 0.3035 Dev= 2.26% S= 38.52 time= 26.59
 Following    1 images are candidates for TS:    4  
 Converged to TS (number of iterations):         19
 DNEB run yielded 1 true transition state(s) time=  21.92

 >>>>>  Path run for ts 20 ...
 Plus  side of path:                    1256 steps. Energy=    -451.0259197       time=      12.95
 Minus side of path:                    1222 steps. Energy=    -452.0726728       time=      12.46

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -451.0259197  2.0974         -448.9285382  3.1441         -452.0726728   7.392   6.746  31.206   6.986
        *NEW* (Placed in 28)                                    *NEW* (Placed in 29)
 Connection established between members of the U set.

 tryconnect> 245-iteration DNEB run for minima 3_U and 10_U using 7 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.9156391332    
 Double-ended search iterations= 245 RMS= 0.0780 Dev= 1.19% S= 25.20 time= 13.00
 Following    1 images are candidates for TS:    4  
 Converged to TS (number of iterations):         57
 DNEB run yielded 1 true transition state(s) time=  36.74

 >>>>>  Path run for ts 21 ...
 Plus  side of path:                    1304 steps. Energy=    -451.6693160       time=      13.72
 Minus side of path:                    1369 steps. Energy=    -452.0286912       time=      14.65

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -451.6693160  3.1678         -448.5015207  3.5272         -452.0286912  35.180  24.689   4.111  53.027
        *NEW* (Placed in 30)                                    *NEW* (Placed in 31)
 Connection established between members of the U set.

 tryconnect> 350-iteration DNEB run for minima 1_S and 10_U using 10 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.3286616756    
 Double-ended search iterations= 350 RMS= 0.0781 Dev= 2.96% S= 41.25 time= 26.28
 Following    2 images are candidates for TS:    2    7  
 Converged to TS (number of iterations):         32
 Converged to TS (number of iterations):         42
 DNEB run yielded 2 true transition state(s) time=  57.59
 isnewts> transition state is the same as number        6 energy=     -450.2477046239
 tryconnect> Try the path again for ts      1 with pushoff=    0.1000000000E-01

 >>>>>  Path run for ts 22 ...
 tryconnect> Trying this transition state path again with pushoff=    0.1000000000E-01
 Plus  side of path:                    1538 steps. Energy=    -455.3423495       time=      17.51
 Minus side of path:                    1249 steps. Energy=    -450.5867733       time=      12.99

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -455.3423495  5.0946         -450.2477046 0.33907         -450.5867733  31.563  25.531   2.099 103.879
        Known (#9)                                              Known (#1)
 Alternative path found between members of the S set.

 >>>>>  Path run for ts 23 ...
 Plus  side of path:                    1235 steps. Energy=    -454.2805049       time=      12.63
 Minus side of path:                    1232 steps. Energy=    -453.1956606       time=      12.59

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -454.2805049  3.2321         -451.0484332  2.1472         -453.1956606   8.186   7.004  26.354   8.272
        *NEW* (Placed in 32)                                    *NEW* (Placed in 33)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 5 >>>>>>>>>>>>>>>>>>>>> 33 minima and 23 ts are known >>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has     16 steps with      9 missing connections, weight=    0.50359E+06
 decide> The unconnected minima in the chain and their distances are:
    17       61.57     6     5       44.77    21    20       20.69    23    23       46.73     7     8       31.64    29    28       11.43     4     4       24.09    10    10       27.46    33    32       11.85     9 
 

 tryconnect> 630-iteration DNEB run for minima 6_U and 17_F using 18 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.1365657147    
 Double-ended search iterations= 630 RMS= 0.0454 Dev= 7.16% S= 79.81 time= 85.24
 Following    3 images are candidates for TS:   10   14   16  
 Converged to TS (number of iterations):        195
 Converged to TS (number of iterations):        190
 Converged to TS (number of iterations):        192
 DNEB run yielded 3 true transition state(s) time= 330.26

 >>>>>  Path run for ts 24 ...
 Plus  side of path:                    2682 steps. Energy=    -453.7521424       time=      45.19
 Minus side of path:                    1390 steps. Energy=    -449.8548613       time=      15.28

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -453.7521424  4.4548         -449.2973558 0.55751         -449.8548613  84.295  76.066   1.899 114.800
        *NEW* (Placed in 34)                                    *NEW* (Placed in 35)
 Connection established between members of the U set.

 >>>>>  Path run for ts 25 ...
 Plus  side of path:                    1467 steps. Energy=    -452.9935256       time=      16.39
 Minus side of path:                    1272 steps. Energy=    -449.9096374       time=      13.41

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -452.9935256  3.4095         -449.5840636 0.32557         -449.9096374  54.885  52.670   1.618 134.774
        *NEW* (Placed in 36)                                    *NEW* (Placed in 37)
 Connection established between members of the U set.

 >>>>>  Path run for ts 26 ...
 Plus  side of path:                    1432 steps. Energy=    -452.9935256       time=      15.76
 Minus side of path:                    1329 steps. Energy=    -450.6840424       time=      14.39

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -452.9935256  2.8282         -450.1653271 0.51872         -450.6840424  44.337  37.397   1.758 124.034
        Known (#36)                                             *NEW* (Placed in 38)
 Connection established between members of the U set.

 tryconnect> 455-iteration DNEB run for minima 5_U and 21_U using 13 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.3450947594    
 Double-ended search iterations= 455 RMS= 0.0890 Dev= 3.06% S= 56.32 time= 43.57
 Following    1 images are candidates for TS:    4  
 Converged to TS (number of iterations):        169
 DNEB run yielded 1 true transition state(s) time=  87.65

 >>>>>  Path run for ts 27 ...
 Plus  side of path:                    1964 steps. Energy=    -458.3669285       time=      25.50
 Minus side of path:                    1725 steps. Energy=    -456.9978530       time=      21.14

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -458.3669285  3.7462         -454.6207297  2.3771         -456.9978530  83.506  40.367   3.464  62.925
        *NEW* (Placed in 39)                                    *NEW* (Placed in 40)
 Connection established between members of the U set.

 tryconnect> 210-iteration DNEB run for minima 20_U and 23_U using 6 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      1.288396211    
 Double-ended search iterations= 210 RMS= 0.0862 Dev= 0.11% S= 20.92 time= 9.63
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         44
 DNEB run yielded 1 true transition state(s) time=  30.78

 >>>>>  Path run for ts 28 ...
 Plus  side of path:                    1264 steps. Energy=    -451.6683452       time=      13.08
 Minus side of path:                    1260 steps. Energy=    -453.0911500       time=      13.11

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -451.6683452 0.14264         -451.5257025  1.5654         -453.0911500  23.199  20.694   2.441  89.305
        Known (#20)                                             Known (#23)
 Connection established between members of the U set.

 tryconnect> 490-iteration DNEB run for minima 7_U and 23_U using 14 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      35.55672688    
 Double-ended search iterations= 964 RMS= 0.5440 Dev= 2.19% S= 221.95 time= 101.13
 Following    2 images are candidates for TS:    3    8  
 Converged to TS (number of iterations):         85
 Converged to TS (number of iterations):        157
 DNEB run yielded 2 true transition state(s) time= 151.73

 >>>>>  Path run for ts 29 ...
 Plus  side of path:                    1134 steps. Energy=    -453.5871916       time=      11.24
 Minus side of path:                    1180 steps. Energy=    -454.9741765       time=      11.88

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -453.5871916 0.66033E-01     -453.5211587  1.4530         -454.9741765   1.371   1.296 208.752   1.044
        *NEW* (Placed in 41)                                    *NEW* (Placed in 42)
 Connection established between members of the U set.

 >>>>>  Path run for ts 30 ...
 Plus  side of path:                    1791 steps. Energy=    -444.3973066       time=      21.92
 Minus side of path:                    1236 steps. Energy=    -440.7205145       time=      12.84

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -444.3973066  5.0922         -439.3050702  1.4154         -440.7205145  38.669  33.328   2.223  98.082
check_cistrans_protein>  WARNING -- cis (or deformed) peptide bond detected between residues      1     2
 tryconnect> MINUS minimum: cis-trans isomerisation of a peptide bond detected involving atom     15
check_cistrans_protein>  WARNING -- cis (or deformed) peptide bond detected between residues      1     2
 tryconnect> PLUS minimum: cis-trans isomerisation of a peptide bond detected involving atom     15
 tryconnect> Cis-trans isomerisation of a peptide bond detected (wrt. the original structure), rejecting
 tryconnect> Transition state with energy     -439.3050702     ignored, cis-trans isomerisation detected in one or more peptide bonds.

 tryconnect> 315-iteration DNEB run for minima 8_U and 29_U using 9 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.4624599827    
 Double-ended search iterations= 315 RMS= 0.0222 Dev= 0.47% S= 32.90 time= 21.37
 Following    1 images are candidates for TS:    7  
 Converged to TS (number of iterations):         28
 DNEB run yielded 1 true transition state(s) time=  24.19

 >>>>>  Path run for ts 31 ...
 Plus  side of path:                    1615 steps. Energy=    -453.1083654       time=      19.88
 Minus side of path:                    1211 steps. Energy=    -452.0726728       time=      12.73

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -453.1083654  1.3445         -451.7638988 0.30877         -452.0726728  34.565  31.685   3.524  61.854
        Known (#8)                                              Known (#29)
 Connection established between members of the U set.

 tryconnect> 105-iteration DNEB run for minima 4_U and 28_U using 3 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      4.810170981    
 Double-ended search iterations= 105 RMS= 0.1651 Dev= 1.14% S= 11.87 time= 2.62
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):        106
 DNEB run yielded 1 true transition state(s) time=  62.06

 >>>>>  Path run for ts 32 ...
 Plus  side of path:                    1244 steps. Energy=    -450.7547132       time=      13.68
 Minus side of path:                    1312 steps. Energy=    -451.4625761       time=      14.31

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -450.7547132 0.52267E-01     -450.7024464 0.76013         -451.4625761  18.081  17.620   1.971 110.607
        *NEW* (Placed in 43)                                    Known (#3)
 Connection established between members of the U set.

 tryconnect> 245-iteration DNEB run for minima 4_U and 10_U using 7 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.9156391332    
 Double-ended search iterations= 245 RMS= 0.1077 Dev= 1.20% S= 25.77 time= 13.07
 Following    1 images are candidates for TS:    4  
 Converged to TS (number of iterations):         56
 DNEB run yielded 1 true transition state(s) time=  39.51
 isnewts> transition state is the same as number       21 energy=     -448.5015207249
 tryconnect> Try the path again for ts      1 with pushoff=    0.1000000000E-01

 >>>>>  Path run for ts 33 ...
 tryconnect> Trying this transition state path again with pushoff=    0.1000000000E-01
 Plus  side of path:                    1356 steps. Energy=    -452.0286912       time=      15.70
 Minus side of path:                    1294 steps. Energy=    -451.6693160       time=      14.00

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -452.0286912  3.5272         -448.5015207  3.1678         -451.6693160  35.180  24.689   4.110  53.047
        Known (#31)                                             Known (#30)
 Connection established between members of the U set.

 tryconnect> 280-iteration DNEB run for minima 10_U and 33_U using 8 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.6507276371    
 Double-ended search iterations= 280 RMS= 0.0383 Dev= 0.72% S= 28.25 time= 16.96
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         33
 DNEB run yielded 1 true transition state(s) time=  27.54

 >>>>>  Path run for ts 34 ...
 Plus  side of path:                    1377 steps. Energy=    -453.1956606       time=      15.75
 Minus side of path:                    1259 steps. Energy=    -450.1626995       time=      14.01

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -453.1956606  3.1129         -450.0827763 0.79923E-01     -450.1626995  30.473  27.483   1.724 126.434
        Known (#33)                                             Known (#10)
 Connection established between members of the U set.

 tryconnect> 105-iteration DNEB run for minima 9_S and 32_U using 3 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      3.589423646    
 Double-ended search iterations= 105 RMS= 0.0361 Dev= 0.01% S= 11.88 time= 2.63
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         22
 DNEB run yielded 1 true transition state(s) time=  25.01

 >>>>>  Path run for ts 35 ...
 Plus  side of path:                    1211 steps. Energy=    -454.2805049       time=      13.19
 Minus side of path:                    1244 steps. Energy=    -455.3423495       time=      13.33

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -454.2805049 0.13928         -454.1412277  1.2011         -455.3423495  12.175  11.852   2.707  80.524
        Known (#32)                                             Known (#9)
 Unconnected minimum 32 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 6 >>>>>>>>>>>>>>>>>>>>> 43 minima and 35 ts are known >>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has     10 steps with      2 missing connections, weight=    0.15991E+06
 decide> The unconnected minima in the chain and their distances are:
    17       13.62    37    38       53.99    11 
 

 tryconnect> 140-iteration DNEB run for minima 17_F and 37_U using 4 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      2.550936371    
 Double-ended search iterations= 140 RMS= 0.0442 Dev= 0.25% S= 13.73 time= 4.46
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         29
 DNEB run yielded 1 true transition state(s) time=  26.94

 >>>>>  Path run for ts 36 ...
 Plus  side of path:                    1346 steps. Energy=    -448.3827800       time=      14.44
 Minus side of path:                    1427 steps. Energy=    -449.9096374       time=      15.90

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -448.3827800 0.25773         -448.1250481  1.7846         -449.9096374  35.748  13.712   2.689  81.071
        Known (#17)                                             Known (#37)
 Unconnected minimum 37 found its way to F set.

 tryconnect> 560-iteration DNEB run for minima 11_S and 38_F using 16 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      139.3869611    
 Double-ended search iterations= 870 RMS= 89.2982 Dev= 6.23% S= 176.08 time= 104.52
 Following    3 images are candidates for TS:    2    7   12  
 Converged to TS (number of iterations):         95
 Converged to TS (number of iterations):        128
 Converged to TS (number of iterations):        118
 DNEB run yielded 3 true transition state(s) time= 220.49
 tryconnect> Transition state with energy      2212.435422     ignored

 >>>>>  Path run for ts 37 ...
 Plus  side of path:                    1119 steps. Energy=    -444.2768333       time=      11.28
 Minus side of path:                    1379 steps. Energy=    -445.8884510       time=      15.15

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -444.2768333  1.6648         -442.6120152  3.2764         -445.8884510  14.423  10.569   3.797  57.421
        *NEW* (Placed in 44)                                    *NEW* (Placed in 45)
 Connection established between members of the U set.

 >>>>>  Path run for ts 38 ...
 Plus  side of path:                    1260 steps. Energy=    -447.6183251       time=      13.32
 Minus side of path:                    1258 steps. Energy=    -448.4601421       time=      13.30

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -447.6183251  2.9807         -444.6375845  3.8226         -448.4601421  11.777  10.319  31.940   6.825
        *NEW* (Placed in 46)                                    *NEW* (Placed in 47)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 7 >>>>>>>>>>>>>>>>>>>>> 47 minima and 38 ts are known >>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has     20 steps with      6 missing connections, weight=    0.18250E+06
 decide> The unconnected minima in the chain and their distances are:
    17       30.14    35    34       31.60    39    40       15.11    21    22       46.86     7    28       20.30    30    31       20.69    10 
 

 tryconnect> 315-iteration DNEB run for minima 17_F and 35_U using 9 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.4624599827    
 Double-ended search iterations= 315 RMS= 0.0845 Dev= 1.55% S= 32.55 time= 21.37
 Following    2 images are candidates for TS:    1    4  
 Converged to TS (number of iterations):         33
 Converged to TS (number of iterations):        202
 DNEB run yielded 2 true transition state(s) time= 145.24
 isnewts> transition state is the same as number       36 energy=     -448.1250481453
 tryconnect> Try the path again for ts      1 with pushoff=    0.1000000000E-01
 isnewts> transition state is the same as number       25 energy=     -449.5840636441
 tryconnect> Try the path again for ts      2 with pushoff=    0.1000000000E-01

 >>>>>  Path run for ts 39 ...
 tryconnect> Trying this transition state path again with pushoff=    0.1000000000E-01
 Plus  side of path:                    1418 steps. Energy=    -449.9096374       time=      17.33
 Minus side of path:                    1341 steps. Energy=    -448.3827800       time=      14.79

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -449.9096374  1.7846         -448.1250481 0.25773         -448.3827800  35.748  13.711   2.688  81.109
        Known (#37)                                             Known (#17)
 Alternative path found between members of the F set.

 >>>>>  Path run for ts 40 ...
 tryconnect> Trying this transition state path again with pushoff=    0.1000000000E-01
 Plus  side of path:                    1276 steps. Energy=    -449.9096374       time=      13.38
 Minus side of path:                    1482 steps. Energy=    -452.9935256       time=      17.22

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -449.9096374 0.32557         -449.5840636  3.4095         -452.9935256  54.887  52.673   1.618 134.768
        Known (#37)                                             Known (#36)
 Alternative path found between members of the F set.

 tryconnect> 315-iteration DNEB run for minima 34_U and 39_U using 9 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.4624599827    
 Double-ended search iterations= 315 RMS= 1.0019 Dev= 0.74% S= 38.94 time= 21.47
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):         36
 DNEB run yielded 1 true transition state(s) time=  29.97

 >>>>>  Path run for ts 41 ...
 Plus  side of path:                    1281 steps. Energy=    -453.7521424       time=      14.51
 Minus side of path:                    1463 steps. Energy=    -458.3769930       time=      18.67

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -453.7521424  3.5341         -450.2180219  8.1590         -458.3769930  38.405  32.447  14.416  15.122
        Known (#34)                                             *NEW* (Placed in 48)
 Connection established between members of the U set.

 tryconnect> 140-iteration DNEB run for minima 21_U and 40_U using 4 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      2.550936371    
 Double-ended search iterations= 140 RMS= 0.1172 Dev= 0.16% S= 15.76 time= 4.51
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         34
 DNEB run yielded 1 true transition state(s) time=  28.67

 >>>>>  Path run for ts 42 ...
 Plus  side of path:                    1202 steps. Energy=    -454.4214156       time=      13.37
 Minus side of path:                    1243 steps. Energy=    -456.9978530       time=      14.26

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -454.4214156 0.39058         -454.0308362  2.9670         -456.9978530   6.260   5.759  27.058   8.057
        *NEW* (Placed in 49)                                    Known (#40)
 Connection established between members of the U set.

 tryconnect> 490-iteration DNEB run for minima 7_U and 22_U using 14 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      39.20129138    
 Double-ended search iterations= 915 RMS= 0.7258 Dev= 1.47% S= 219.16 time= 97.09
 Following    1 images are candidates for TS:    9  
 Failed to converge to TS (number of iterations):        251
 DNEB run yielded 0 true transition state(s) time= 124.53

 tryconnect> 210-iteration DNEB run for minima 28_U and 30_U using 6 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      1.288396211    
 Double-ended search iterations= 210 RMS= 0.0709 Dev= 0.73% S= 21.49 time= 9.73
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):         99
 DNEB run yielded 1 true transition state(s) time=  56.47

 >>>>>  Path run for ts 43 ...
 Plus  side of path:                    1279 steps. Energy=    -451.0259197       time=      14.98
 Minus side of path:                    1349 steps. Energy=    -450.7547132       time=      15.58

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -451.0259197 0.54267         -450.4832525 0.27146         -450.7547132  24.636  23.308   1.863 117.043
        Known (#28)                                             Known (#43)
 Connection established between members of the U set.

 tryconnect> 210-iteration DNEB run for minima 10_S and 31_U using 6 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      1.288396211    
 Double-ended search iterations= 210 RMS= 2.1888 Dev= 0.95% S= 21.81 time= 9.75
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         63
 DNEB run yielded 1 true transition state(s) time=  44.13

 >>>>>  Path run for ts 44 ...
 Plus  side of path:                    1327 steps. Energy=    -452.0286912       time=      16.09
 Minus side of path:                    1222 steps. Energy=    -451.0800324       time=      12.61

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -452.0286912  2.1813         -449.8474257  1.2326         -451.0800324  25.607  20.449   2.240  97.337
        Known (#31)                                             *NEW* (Placed in 50)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 8 >>>>>>>>>>>>>>>>>>>>> 50 minima and 44 ts are known >>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has     28 steps with      8 missing connections, weight=    0.17338E+06
 decide> The unconnected minima in the chain and their distances are:
    37       33.67    35    48       17.90    39    49       13.15    21    22       11.42    24    25       10.26    26    26       47.39     7     3       21.41    31    50       20.34    10 
 

 tryconnect> 350-iteration DNEB run for minima 35_U and 37_F using 10 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.3286616756    
 Double-ended search iterations= 350 RMS= 0.1065 Dev= 0.87% S= 35.88 time= 26.26
 Following    1 images are candidates for TS:    7  
 Converged to TS (number of iterations):        157
 DNEB run yielded 1 true transition state(s) time=  94.19
 isnewts> transition state is the same as number       25 energy=     -449.5840636469
 tryconnect> Will not repeat search for TS      1 same as TS     25

 tryconnect> 175-iteration DNEB run for minima 39_U and 48_U using 5 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      1.812902854    
 Double-ended search iterations= 175 RMS= 0.0518 Dev= 0.07% S= 18.21 time= 6.95
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):         51
 DNEB run yielded 1 true transition state(s) time=  36.82

 >>>>>  Path run for ts 45 ...
 Plus  side of path:                    1249 steps. Energy=    -458.3669285       time=      12.95
 Minus side of path:                    1222 steps. Energy=    -458.3769930       time=      12.94

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -458.3669285  1.0331         -457.3338147  1.0432         -458.3769930  22.884  17.898   2.220  98.190
        Known (#39)                                             Known (#48)
 Connection established between members of the U set.

 tryconnect> 105-iteration DNEB run for minima 21_U and 49_U using 3 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      3.589423646    
 Double-ended search iterations= 105 RMS= 0.1811 Dev= 0.14% S= 13.52 time= 2.62
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         81
 DNEB run yielded 1 true transition state(s) time=  49.84

 >>>>>  Path run for ts 46 ...
 Plus  side of path:                    1264 steps. Energy=    -454.8473374       time=      14.06
 Minus side of path:                    1244 steps. Energy=    -453.5183487       time=      14.01

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -454.8473374  1.6071         -453.2402723 0.27808         -453.5183487  26.464  23.761   4.143  52.624
        *NEW* (Placed in 51)                                    Known (#21)
 Connection established between members of the U set.

 tryconnect> 105-iteration DNEB run for minima 22_U and 24_U using 3 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      3.589423646    
 Double-ended search iterations= 105 RMS= 0.0300 Dev= 0.02% S= 11.43 time= 2.62
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         28
 DNEB run yielded 1 true transition state(s) time=  26.35

 >>>>>  Path run for ts 47 ...
 Plus  side of path:                    1232 steps. Energy=    -451.6507949       time=      13.78
 Minus side of path:                    1202 steps. Energy=    -451.6073739       time=      13.27

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -451.6507949 0.14991         -451.5008858 0.10649         -451.6073739  11.575  11.421   4.470  48.764
        Known (#24)                                             Known (#22)
 Connection established between members of the U set.

 tryconnect> 105-iteration DNEB run for minima 25_U and 26_U using 3 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      3.589423646    
 Double-ended search iterations= 105 RMS= 0.1255 Dev= 0.44% S= 11.12 time= 2.64
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         34
 DNEB run yielded 1 true transition state(s) time=  30.68
 isnewts> transition state is the same as number       16 energy=     -446.3654911814
 tryconnect> Try the path again for ts      1 with pushoff=    0.1000000000E-01

 >>>>>  Path run for ts 48 ...
 tryconnect> Trying this transition state path again with pushoff=    0.1000000000E-01
 Plus  side of path:                    2115 steps. Energy=    -452.5239553       time=      32.82
 Minus side of path:                    1269 steps. Energy=    -448.4009816       time=      14.98

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -452.5239553  6.1585         -446.3654912  2.0355         -448.4009816  41.825  37.359   1.864 116.950
        Known (#27)                                             Known (#26)
 Connection established between members of the U set.

 tryconnect> 490-iteration DNEB run for minima 7_U and 26_U using 14 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      3.100679103    
 Double-ended search iterations= 572 RMS= 0.8033 Dev= 1.26% S= 213.43 time= 61.15
 Following    2 images are candidates for TS:    4    8  
 Converged to TS (number of iterations):        120
 Converged to TS (number of iterations):        112
 DNEB run yielded 2 true transition state(s) time= 144.40

 >>>>>  Path run for ts 49 ...
 Plus  side of path:                    1274 steps. Energy=    -448.2008838       time=      15.73
 Minus side of path:                    1254 steps. Energy=    -449.3168057       time=      15.36

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -448.2008838 0.81274         -447.3881408  1.9287         -449.3168057  12.053  10.831   4.060  53.701
        *NEW* (Placed in 52)                                    *NEW* (Placed in 53)
 Connection established between members of the U set.

 >>>>>  Path run for ts 50 ...
 Plus  side of path:                     983 steps. Energy=    -440.9496151       time=      11.53
 Minus side of path:                    1178 steps. Energy=    -442.4189383       time=      12.72

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -440.9496151 0.10138E-01     -440.9394769  1.4795         -442.4189383   1.310   1.271 206.604   1.055
check_cistrans_protein>  WARNING -- cis (or deformed) peptide bond detected between residues      1     2
 tryconnect> MINUS minimum: cis-trans isomerisation of a peptide bond detected involving atom     15
check_cistrans_protein>  WARNING -- cis (or deformed) peptide bond detected between residues      1     2
 tryconnect> PLUS minimum: cis-trans isomerisation of a peptide bond detected involving atom     15
 tryconnect> Cis-trans isomerisation of a peptide bond detected (wrt. the original structure), rejecting
 tryconnect> Transition state with energy     -440.9394769     ignored, cis-trans isomerisation detected in one or more peptide bonds.

 tryconnect> 210-iteration DNEB run for minima 3_U and 31_U using 6 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      1.288396211    
 Double-ended search iterations= 210 RMS= 0.1230 Dev= 0.29% S= 22.73 time= 9.70
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):         70
 DNEB run yielded 1 true transition state(s) time=  46.69

 >>>>>  Path run for ts 51 ...
 Plus  side of path:                    1231 steps. Energy=    -451.4625761       time=      15.11
 Minus side of path:                    1382 steps. Energy=    -452.4204642       time=      17.40

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -451.4625761  1.0203         -450.4422837  1.9782         -452.4204642  26.877  22.455   2.750  79.262
        Known (#3)                                              *NEW* (Placed in 54)
 Connection established between members of the U set.

 tryconnect> 210-iteration DNEB run for minima 10_S and 50_U using 6 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      1.288396211    
 Double-ended search iterations= 210 RMS= 0.0191 Dev= 0.11% S= 20.50 time= 9.80
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         52
 DNEB run yielded 1 true transition state(s) time=  36.24

 >>>>>  Path run for ts 52 ...
 Plus  side of path:                    1288 steps. Energy=    -450.1626995       time=      15.04
 Minus side of path:                    1422 steps. Energy=    -451.0800324       time=      18.94

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -450.1626995 0.48718E-01     -450.1139818 0.96605         -451.0800324  22.000  20.355   2.160 100.928
        Known (#10)                                             Known (#50)
 Unconnected minimum 50 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 9 >>>>>>>>>>>>>>>>>>>>> 54 minima and 52 ts are known >>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has     22 steps with      4 missing connections, weight=    0.17678E+06
 decide> The unconnected minima in the chain and their distances are:
    17       30.14    35    49       16.03    51    51       47.60     7     4       21.59    31 
 

 tryconnect> 805-iteration DNEB run for minima 17_F and 35_U using 23 images  (DNEB attempt #2)  ...
 lbfgs> Final DNEB force constant     0.3804669723    
 Double-ended search iterations= 805 RMS= 0.0157 Dev= 6.64% S= 38.80 time= 139.32
 Following    2 images are candidates for TS:    1    9  
 Converged to TS (number of iterations):         23
 Converged to TS (number of iterations):        159
 DNEB run yielded 2 true transition state(s) time= 118.12
 isnewts> transition state is the same as number       36 energy=     -448.1250481456
 tryconnect> Will not repeat search for TS      1 same as TS     36
 isnewts> transition state is the same as number       25 energy=     -449.5840636444
 tryconnect> Will not repeat search for TS      2 same as TS     25

 tryconnect> 140-iteration DNEB run for minima 49_U and 51_U using 4 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      2.550936371    
 Double-ended search iterations= 140 RMS= 0.0332 Dev= 0.11% S= 16.13 time= 4.44
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         62
 DNEB run yielded 1 true transition state(s) time=  40.47

 >>>>>  Path run for ts 53 ...
 Plus  side of path:                    1215 steps. Energy=    -454.4214156       time=      13.67
 Minus side of path:                    1339 steps. Energy=    -454.8473374       time=      16.26

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -454.4214156 0.14224E-01     -454.4071915 0.44015         -454.8473374  17.023  16.026   6.790  32.106
        Known (#49)                                             Known (#51)
 Connection established between members of the U set.

 tryconnect> 490-iteration DNEB run for minima 7_U and 51_U using 14 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      29.25260720    
 Double-ended search iterations= 834 RMS= 0.5554 Dev= 1.01% S= 216.72 time= 89.27
 Following    2 images are candidates for TS:    4    8  
 Converged to TS (number of iterations):        135
 Converged to TS (number of iterations):         95
 DNEB run yielded 2 true transition state(s) time= 136.12

 >>>>>  Path run for ts 54 ...
 Plus  side of path:                    1278 steps. Energy=    -451.2634759       time=      13.45
 Minus side of path:                    1328 steps. Energy=    -455.5651704       time=      14.18

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -451.2634759  3.0855         -448.1779463  7.3872         -455.5651704  23.461  20.201   5.147  42.358
        *NEW* (Placed in 55)                                    *NEW* (Placed in 56)
 Connection established between members of the U set.

 >>>>>  Path run for ts 55 ...
 Plus  side of path:                    1211 steps. Energy=    -450.7735348       time=      12.44
 Minus side of path:                    1218 steps. Energy=    -452.1774744       time=      12.68

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -450.7735348 0.60758E-01     -450.7127766  1.4647         -452.1774744   1.357   1.286 206.780   1.054
        *NEW* (Placed in 57)                                    *NEW* (Placed in 58)
 Connection established between members of the U set.

 tryconnect> 210-iteration DNEB run for minima 4_U and 31_S using 6 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      1.288396211    
 Double-ended search iterations= 210 RMS= 0.3256 Dev= 0.48% S= 23.13 time= 9.63
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):         63
 DNEB run yielded 1 true transition state(s) time=  39.01
 isnewts> transition state is the same as number       51 energy=     -450.4422837430
 tryconnect> Try the path again for ts      1 with pushoff=    0.1000000000E-01

 >>>>>  Path run for ts 56 ...
 tryconnect> Trying this transition state path again with pushoff=    0.1000000000E-01
 Plus  side of path:                    1242 steps. Energy=    -451.4625761       time=      13.07
 Minus side of path:                    1400 steps. Energy=    -452.4204642       time=      15.44

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -451.4625761  1.0203         -450.4422837  1.9782         -452.4204642  26.877  22.455   2.751  79.249
        Known (#3)                                              Known (#54)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 10 >>>>>>>>>>>>>>>>>>>>> 58 minima and 56 ts are known >>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has     15 steps with      3 missing connections, weight=    0.19075E+06
 decide> The unconnected minima in the chain and their distances are:
    36       41.90    27    26       47.49     8    29       21.60    30 
 

 tryconnect> 420-iteration DNEB run for minima 27_U and 36_F using 12 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.5902291493    
 Double-ended search iterations= 420 RMS= 0.1339 Dev= 5.15% S= 49.47 time= 38.06
 Following    2 images are candidates for TS:    4    8  
 Converged to TS (number of iterations):         24
 Converged to TS (number of iterations):         66
 DNEB run yielded 2 true transition state(s) time=  67.57

 >>>>>  Path run for ts 57 ...
 Plus  side of path:                    1274 steps. Energy=    -451.7981786       time=      13.26
 Minus side of path:                    1266 steps. Energy=    -452.8644269       time=      13.14

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -451.7981786  2.0383         -449.7598934  3.1045         -452.8644269   8.739   8.116  15.062  14.474
        *NEW* (Placed in 59)                                    *NEW* (Placed in 60)
 Connection established between members of the U set.

 >>>>>  Path run for ts 58 ...
 Plus  side of path:                    1573 steps. Energy=    -453.2542217       time=      18.04
 Minus side of path:                    1277 steps. Energy=    -453.1553594       time=      13.32

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -453.2542217 0.84730         -452.4069176 0.74844         -453.1553594  24.153  22.328   3.960  55.055
        *NEW* (Placed in 61)                                    *NEW* (Placed in 62)
 Connection established between members of the U set.

 tryconnect> 490-iteration DNEB run for minima 8_U and 26_U using 14 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      17.95856326    
 Double-ended search iterations= 826 RMS= 0.3863 Dev= 1.10% S= 218.80 time= 87.04
 Following    3 images are candidates for TS:    6    9   13  
 Converged to TS (number of iterations):         78
 Converged to TS (number of iterations):         46
 Converged to TS (number of iterations):         78
 DNEB run yielded 3 true transition state(s) time= 143.55

 >>>>>  Path run for ts 59 ...
 Plus  side of path:                    1275 steps. Energy=    -438.0302702       time=      13.48
 Minus side of path:                    1266 steps. Energy=    -439.4872577       time=      13.32

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -438.0302702  2.2533         -435.7769543  3.7103         -439.4872577  15.846  12.754   3.005  72.550
check_cistrans_protein>  WARNING -- cis (or deformed) peptide bond detected between residues      1     2
 tryconnect> MINUS minimum: cis-trans isomerisation of a peptide bond detected involving atom     15
check_cistrans_protein>  WARNING -- cis (or deformed) peptide bond detected between residues      1     2
 tryconnect> PLUS minimum: cis-trans isomerisation of a peptide bond detected involving atom     15
 tryconnect> Cis-trans isomerisation of a peptide bond detected (wrt. the original structure), rejecting
 tryconnect> Transition state with energy     -435.7769543     ignored, cis-trans isomerisation detected in one or more peptide bonds.

 >>>>>  Path run for ts 60 ...
 Plus  side of path:                    1252 steps. Energy=    -436.3212680       time=      13.20
 Minus side of path:                    1268 steps. Energy=    -437.4286519       time=      13.44

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -436.3212680  2.0759         -434.2454105  3.1832         -437.4286519   7.469   6.710  30.585   7.128
check_cistrans_protein>  WARNING -- cis (or deformed) peptide bond detected between residues      1     2
 tryconnect> MINUS minimum: cis-trans isomerisation of a peptide bond detected involving atom     15
check_cistrans_protein>  WARNING -- cis (or deformed) peptide bond detected between residues      1     2
 tryconnect> PLUS minimum: cis-trans isomerisation of a peptide bond detected involving atom     15
 tryconnect> Cis-trans isomerisation of a peptide bond detected (wrt. the original structure), rejecting
 tryconnect> Transition state with energy     -434.2454105     ignored, cis-trans isomerisation detected in one or more peptide bonds.

 >>>>>  Path run for ts 61 ...
 Plus  side of path:                    1410 steps. Energy=    -438.5823939       time=      15.53
 Minus side of path:                    1429 steps. Energy=    -435.9497068       time=      15.85

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -438.5823939  6.6743         -431.9081133  4.0416         -435.9497068  36.447  22.159   6.127  35.582
check_cistrans_protein>  WARNING -- cis (or deformed) peptide bond detected between residues      1     2
 tryconnect> MINUS minimum: cis-trans isomerisation of a peptide bond detected involving atom     15
check_cistrans_protein>  WARNING -- cis (or deformed) peptide bond detected between residues      1     2
 tryconnect> PLUS minimum: cis-trans isomerisation of a peptide bond detected involving atom     15
 tryconnect> Cis-trans isomerisation of a peptide bond detected (wrt. the original structure), rejecting
 tryconnect> Transition state with energy     -431.9081133     ignored, cis-trans isomerisation detected in one or more peptide bonds.

 tryconnect> 210-iteration DNEB run for minima 29_U and 30_S using 6 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      1.288396211    
 Double-ended search iterations= 210 RMS= 0.1390 Dev= 1.02% S= 23.45 time= 9.64
 Following    1 images are candidates for TS:    4  
 Converged to TS (number of iterations):         35
 DNEB run yielded 1 true transition state(s) time=  27.43

 >>>>>  Path run for ts 62 ...
 Plus  side of path:                    1232 steps. Energy=    -452.6780630       time=      12.92
 Minus side of path:                    1167 steps. Energy=    -451.6693160       time=      11.99

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -452.6780630  3.1250         -449.5530694  2.1162         -451.6693160   7.369   6.657  33.359   6.535
        *NEW* (Placed in 63)                                    Known (#30)
 Unconnected minimum 63 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 11 >>>>>>>>>>>>>>>>>>>>> 63 minima and 62 ts are known >>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has     10 steps with      2 missing connections, weight=    0.12612E+06
 decide> The unconnected minima in the chain and their distances are:
    36       25.33    61    61       47.89    11 
 

 tryconnect> 245-iteration DNEB run for minima 36_F and 61_U using 7 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.9156391332    
 Double-ended search iterations= 245 RMS= 0.8529 Dev= 0.25% S= 25.92 time= 13.13
 Following    1 images are candidates for TS:    4  
 Converged to TS (number of iterations):         45
 DNEB run yielded 1 true transition state(s) time=  33.18

 >>>>>  Path run for ts 63 ...
 Plus  side of path:                    1274 steps. Energy=    -453.2156133       time=      13.36
 Minus side of path:                    1262 steps. Energy=    -453.2542217       time=      13.53

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -453.2156133 0.60730         -452.6083118 0.64591         -453.2542217   9.182   8.865  14.346  15.195
        *NEW* (Placed in 64)                                    Known (#61)
 Connection established between members of the U set.

 tryconnect> 490-iteration DNEB run for minima 11_S and 61_U using 14 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      16.28894627    
 Double-ended search iterations= 750 RMS= 0.6494 Dev= 1.53% S= 237.08 time= 79.22
 Following    3 images are candidates for TS:    5    7    9  
 Converged to TS (number of iterations):         63
 Converged to TS (number of iterations):        166
 Converged to TS (number of iterations):        130
 DNEB run yielded 3 true transition state(s) time= 209.54

 >>>>>  Path run for ts 64 ...
 Plus  side of path:                    1145 steps. Energy=    -454.1151816       time=      13.04
 Minus side of path:                    1228 steps. Energy=    -455.1478121       time=      13.90

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -454.1151816  2.1399         -451.9752990  3.1725         -455.1478121   7.662   6.912  27.469   7.936
        *NEW* (Placed in 65)                                    *NEW* (Placed in 66)
 Connection established between members of the U set.

 >>>>>  Path run for ts 65 ...
 Plus  side of path:                    1318 steps. Energy=    -430.6375390       time=      16.12
 Minus side of path:                    1018 steps. Energy=    -428.1477572       time=      10.46

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -430.6375390  2.5017         -428.1358556 0.11902E-01     -428.1477572  10.279  10.087   8.816  24.728
check_cistrans_protein>  WARNING -- cis (or deformed) peptide bond detected between residues      1     2
check_cistrans_protein>  WARNING -- cis (or deformed) peptide bond detected between residues      3     4
 tryconnect> MINUS minimum: cis-trans isomerisation of a peptide bond detected involving atom     15
 tryconnect> MINUS minimum: cis-trans isomerisation of a peptide bond detected involving atom     53
check_cistrans_protein>  WARNING -- cis (or deformed) peptide bond detected between residues      1     2
check_cistrans_protein>  WARNING -- cis (or deformed) peptide bond detected between residues      3     4
 tryconnect> PLUS minimum: cis-trans isomerisation of a peptide bond detected involving atom     15
 tryconnect> PLUS minimum: cis-trans isomerisation of a peptide bond detected involving atom     53
 tryconnect> Cis-trans isomerisation of a peptide bond detected (wrt. the original structure), rejecting
 tryconnect> Transition state with energy     -428.1358556     ignored, cis-trans isomerisation detected in one or more peptide bonds.

 >>>>>  Path run for ts 66 ...
 Plus  side of path:                    1259 steps. Energy=    -427.0186825       time=      14.77
 Minus side of path:                    1087 steps. Energy=    -425.0374329       time=      11.68

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -427.0186825  1.9820         -425.0366924 0.74051E-03     -425.0374329   4.235   4.208  15.319  14.230
check_cistrans_protein>  WARNING -- cis (or deformed) peptide bond detected between residues      1     2
check_cistrans_protein>  WARNING -- cis (or deformed) peptide bond detected between residues      3     4
 tryconnect> MINUS minimum: cis-trans isomerisation of a peptide bond detected involving atom     15
 tryconnect> MINUS minimum: cis-trans isomerisation of a peptide bond detected involving atom     53
check_cistrans_protein>  WARNING -- cis (or deformed) peptide bond detected between residues      1     2
check_cistrans_protein>  WARNING -- cis (or deformed) peptide bond detected between residues      3     4
 tryconnect> PLUS minimum: cis-trans isomerisation of a peptide bond detected involving atom     15
 tryconnect> PLUS minimum: cis-trans isomerisation of a peptide bond detected involving atom     53
 tryconnect> Cis-trans isomerisation of a peptide bond detected (wrt. the original structure), rejecting
 tryconnect> Transition state with energy     -425.0366924     ignored, cis-trans isomerisation detected in one or more peptide bonds.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 12 >>>>>>>>>>>>>>>>>>>>> 66 minima and 66 ts are known >>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has     10 steps with      2 missing connections, weight=    0.11205E+06
 decide> The unconnected minima in the chain and their distances are:
    36       23.42    64    64       46.29    11 
 

 tryconnect> 245-iteration DNEB run for minima 36_F and 64_U using 7 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.9156391332    
 Double-ended search iterations= 245 RMS= 0.0269 Dev= 0.28% S= 23.77 time= 13.11
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):        102
 DNEB run yielded 1 true transition state(s) time=  54.36

 >>>>>  Path run for ts 67 ...
 Plus  side of path:                    1242 steps. Energy=    -452.9935256       time=      12.89
 Minus side of path:                    1368 steps. Energy=    -453.1553594       time=      14.82

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -452.9935256 0.40613         -452.5873959 0.56796         -453.1553594  27.216  25.510   1.764 123.548
        Known (#36)                                             Known (#62)
 Unconnected minimum 62 found its way to F set.

 tryconnect> 455-iteration DNEB run for minima 11_S and 64_F using 13 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      30.71523756    
 Double-ended search iterations= 763 RMS= 0.9603 Dev= 1.08% S= 229.96 time= 74.81
 Following    2 images are candidates for TS:    5    7  
 Converged to TS (number of iterations):        231
 Converged to TS (number of iterations):        116
 DNEB run yielded 2 true transition state(s) time= 199.28

 >>>>>  Path run for ts 68 ...
 Plus  side of path:                    1208 steps. Energy=    -453.9443735       time=      12.88
 Minus side of path:                    1282 steps. Energy=    -455.9575721       time=      13.82

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -453.9443735 0.39727         -453.5471010  2.4105         -455.9575721  14.577  12.068   2.856  76.338
        *NEW* (Placed in 67)                                    *NEW* (Placed in 68)
 Connection established between members of the U set.

 >>>>>  Path run for ts 69 ...
 Plus  side of path:                    1236 steps. Energy=    -433.1665024       time=      13.13
 Minus side of path:                    1247 steps. Energy=    -434.2725026       time=      12.98

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -433.1665024  2.8138         -430.3526796  3.9198         -434.2725026   4.572   4.012  45.719   4.768
check_cistrans_protein>  WARNING -- cis (or deformed) peptide bond detected between residues      3     4
 tryconnect> MINUS minimum: cis-trans isomerisation of a peptide bond detected involving atom     53
check_cistrans_protein>  WARNING -- cis (or deformed) peptide bond detected between residues      3     4
 tryconnect> PLUS minimum: cis-trans isomerisation of a peptide bond detected involving atom     53
 tryconnect> Cis-trans isomerisation of a peptide bond detected (wrt. the original structure), rejecting
 tryconnect> Transition state with energy     -430.3526796     ignored, cis-trans isomerisation detected in one or more peptide bonds.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 13 >>>>>>>>>>>>>>>>>>>>> 68 minima and 69 ts are known >>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has     10 steps with      1 missing connections, weight=    0.12687E+06
 decide> The unconnected minima in the chain and their distances are:
    62       50.25    11 
 

 tryconnect> 525-iteration DNEB run for minima 11_S and 62_F using 15 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      30.71523756    
 Double-ended search iterations= 836 RMS= 0.7584 Dev= 1.21% S= 227.33 time= 94.50
 Following    3 images are candidates for TS:    5    7   10  
 Converged to TS (number of iterations):         45
 Failed to converge to TS (number of iterations):        251
 Failed to converge to TS (number of iterations):        251
 DNEB run yielded 1 true transition state(s) time= 280.23

 >>>>>  Path run for ts 70 ...
 Plus  side of path:                    1266 steps. Energy=    -457.6032848       time=      13.31
 Minus side of path:                    1226 steps. Energy=    -456.4476456       time=      12.62

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -457.6032848  3.1945         -454.4087568  2.0389         -456.4476456   7.381   6.662  31.198   6.988
        *NEW* (Placed in 69)                                    *NEW* (Placed in 70)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 14 >>>>>>>>>>>>>>>>>>>>> 70 minima and 70 ts are known >>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has     12 steps with      2 missing connections, weight=    0.12966E+06
 decide> The unconnected minima in the chain and their distances are:
    62       24.88    60    59       48.53    11 
 

 tryconnect> 245-iteration DNEB run for minima 60_U and 62_F using 7 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.9156391332    
 Double-ended search iterations= 245 RMS= 0.1767 Dev= 0.87% S= 27.02 time= 13.09
 Following    2 images are candidates for TS:    3    5  
 Converged to TS (number of iterations):         29
 Converged to TS (number of iterations):         72
 DNEB run yielded 2 true transition state(s) time=  69.59

 >>>>>  Path run for ts 71 ...
 Plus  side of path:                    1245 steps. Energy=    -453.6871291       time=      12.83
 Minus side of path:                    1246 steps. Energy=    -452.8644269       time=      12.88

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -453.6871291  2.8972         -450.7899095  2.0745         -452.8644269   8.475   7.675  24.696   8.827
        *NEW* (Placed in 71)                                    Known (#60)
 Connection established between members of the U set.

 >>>>>  Path run for ts 72 ...
 Plus  side of path:                    1384 steps. Energy=    -453.1553594       time=      14.91
 Minus side of path:                    1480 steps. Energy=    -453.8473017       time=      16.47

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -453.1553594  1.1787         -451.9766898  1.8706         -453.8473017  40.693  25.778   1.950 111.777
        Known (#62)                                             *NEW* (Placed in 72)
 Unconnected minimum 72 found its way to F set.

 tryconnect> 490-iteration DNEB run for minima 11_S and 59_U using 14 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      24.06619234    
 Double-ended search iterations= 810 RMS= 0.3640 Dev= 0.94% S= 218.54 time= 85.50
 Following    2 images are candidates for TS:    4    7  
 Converged to TS (number of iterations):        143
 Converged to TS (number of iterations):        117
 DNEB run yielded 2 true transition state(s) time= 161.69

 >>>>>  Path run for ts 73 ...
 Plus  side of path:                    1237 steps. Energy=    -455.6055187       time=      15.62
 Minus side of path:                    1302 steps. Energy=    -457.2028442       time=      14.39

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -455.6055187  2.7283         -452.8772608  4.3256         -457.2028442  29.416  21.902   6.230  34.993
        *NEW* (Placed in 73)                                    *NEW* (Placed in 74)
 Connection established between members of the U set.

 >>>>>  Path run for ts 74 ...
 Plus  side of path:                    1228 steps. Energy=    -448.2659453       time=      12.77
 Minus side of path:                    1175 steps. Energy=    -446.6760990       time=      11.87

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -448.2659453  1.6013         -446.6646371 0.11462E-01     -446.6760990   1.381   1.344 118.596   1.838
check_cistrans_protein>  WARNING -- cis (or deformed) peptide bond detected between residues      1     2
 tryconnect> MINUS minimum: cis-trans isomerisation of a peptide bond detected involving atom     15
check_cistrans_protein>  WARNING -- cis (or deformed) peptide bond detected between residues      1     2
 tryconnect> PLUS minimum: cis-trans isomerisation of a peptide bond detected involving atom     15
 tryconnect> Cis-trans isomerisation of a peptide bond detected (wrt. the original structure), rejecting
 tryconnect> Transition state with energy     -446.6646371     ignored, cis-trans isomerisation detected in one or more peptide bonds.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 15 >>>>>>>>>>>>>>>>>>>>> 74 minima and 74 ts are known >>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has     20 steps with      3 missing connections, weight=    0.12293E+06
 decide> The unconnected minima in the chain and their distances are:
    72        8.10    71    59       48.54     7    29       20.05    63 
 

 tryconnect> 70-iteration DNEB run for minima 71_U and 72_F using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.2252 Dev= 0.19% S= 8.33 time= 1.29
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         21
 DNEB run yielded 1 true transition state(s) time=  21.69

 >>>>>  Path run for ts 75 ...
 Plus  side of path:                    1277 steps. Energy=    -453.6871291       time=      13.33
 Minus side of path:                    1271 steps. Energy=    -453.8473017       time=      13.24

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -453.6871291 0.40802         -453.2791140 0.56819         -453.8473017   8.558   8.098  15.160  14.380
        Known (#71)                                             Known (#72)
 Unconnected minimum 71 found its way to F set.

 tryconnect> 490-iteration DNEB run for minima 7_U and 59_F using 14 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      2.313774487    
 Double-ended search iterations= 518 RMS= 0.7843 Dev= 3.00% S= 224.63 time= 54.70
 Following    1 images are candidates for TS:    8  
 Converged to TS (number of iterations):         43
 DNEB run yielded 1 true transition state(s) time=  38.85

 >>>>>  Path run for ts 76 ...
 Plus  side of path:                    1314 steps. Energy=    -451.6925231       time=      13.96
 Minus side of path:                    1235 steps. Energy=    -450.4975606       time=      12.77

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -451.6925231  3.5283         -448.1642276  2.3333         -450.4975606  13.423  10.942   9.637  22.620
        *NEW* (Placed in 75)                                    *NEW* (Placed in 76)
 Connection established between members of the U set.

 tryconnect> 210-iteration DNEB run for minima 29_U and 63_S using 6 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      1.288396211    
 Double-ended search iterations= 210 RMS= 0.3687 Dev= 0.85% S= 21.37 time= 9.63
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):         67
 DNEB run yielded 1 true transition state(s) time=  41.19

 >>>>>  Path run for ts 77 ...
 Plus  side of path:                    1240 steps. Energy=    -452.4480953       time=      12.81
 Minus side of path:                    1217 steps. Energy=    -451.6340896       time=      12.49

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -452.4480953 0.83607         -451.6120235 0.22066E-01     -451.6340896   8.594   8.375   2.767  78.788
        *NEW* (Placed in 77)                                    *NEW* (Placed in 78)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 16 >>>>>>>>>>>>>>>>>>>>> 78 minima and 77 ts are known >>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has     18 steps with      2 missing connections, weight=    0.13296E+06
 decide> The unconnected minima in the chain and their distances are:
    72       49.86     7    28       20.79    63 
 

 tryconnect> 490-iteration DNEB run for minima 7_U and 72_F using 14 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      2.098661666    
 Double-ended search iterations= 502 RMS= 0.6665 Dev= 2.20% S= 221.45 time= 53.02
 Following    1 images are candidates for TS:    8  
 Converged to TS (number of iterations):        194
 DNEB run yielded 1 true transition state(s) time=  99.74

 >>>>>  Path run for ts 78 ...
 Plus  side of path:                    1412 steps. Energy=    -453.8042026       time=      15.56
 Minus side of path:                    1397 steps. Energy=    -452.2500593       time=      15.34

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -453.8042026  2.2591         -451.5451243 0.70493         -452.2500593  23.688  19.190   2.205  98.878
        *NEW* (Placed in 79)                                    *NEW* (Placed in 80)
 Connection established between members of the U set.

 tryconnect> 210-iteration DNEB run for minima 28_U and 63_S using 6 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      1.288396211    
 Double-ended search iterations= 210 RMS= 0.1090 Dev= 1.23% S= 22.48 time= 9.64
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):         26
 DNEB run yielded 1 true transition state(s) time=  24.22
 isnewts> transition state is the same as number       20 energy=     -448.9285382460
 tryconnect> Try the path again for ts      1 with pushoff=    0.1000000000E-01

 >>>>>  Path run for ts 79 ...
 tryconnect> Trying this transition state path again with pushoff=    0.1000000000E-01
 Plus  side of path:                    1266 steps. Energy=    -452.0726728       time=      13.69
 Minus side of path:                    1245 steps. Energy=    -451.0259197       time=      13.60

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -452.0726728  3.1441         -448.9285382  2.0974         -451.0259197   7.392   6.746  31.177   6.992
        Known (#29)                                             Known (#28)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 17 >>>>>>>>>>>>>>>>>>>>> 80 minima and 79 ts are known >>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has     12 steps with      1 missing connections, weight=    0.13301E+06
 decide> The unconnected minima in the chain and their distances are:
    71       51.05    11 
 

 tryconnect> 525-iteration DNEB run for minima 11_S and 71_F using 15 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      18.85649142    
 Double-ended search iterations= 779 RMS= 0.7240 Dev= 0.83% S= 218.92 time= 88.17
 Following    3 images are candidates for TS:    4    8   13  
 Converged to TS (number of iterations):        159
 Converged to TS (number of iterations):        120
 Converged to TS (number of iterations):         60
 DNEB run yielded 3 true transition state(s) time= 253.51

 >>>>>  Path run for ts 80 ...
 Plus  side of path:                    1316 steps. Energy=    -456.1621855       time=      14.08
 Minus side of path:                    1276 steps. Energy=    -451.5148062       time=      13.50

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -456.1621855  8.1493         -448.0128587  3.5019         -451.5148062  33.515  27.987  14.116  15.443
        *NEW* (Placed in 81)                                    *NEW* (Placed in 82)
 Connection established between members of the U set.

 >>>>>  Path run for ts 81 ...
 Plus  side of path:                    1248 steps. Energy=    -445.0161764       time=      13.12
 Minus side of path:                    1202 steps. Energy=    -445.0161764       time=      12.31

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -445.0161764  3.9255         -441.0906303  3.9255         -445.0161764   5.945   3.102 108.675   2.006
check_cistrans_protein>  WARNING -- cis (or deformed) peptide bond detected between residues      1     2
 tryconnect> MINUS minimum: cis-trans isomerisation of a peptide bond detected involving atom     15
check_cistrans_protein>  WARNING -- cis (or deformed) peptide bond detected between residues      1     2
 tryconnect> PLUS minimum: cis-trans isomerisation of a peptide bond detected involving atom     15
 tryconnect> Cis-trans isomerisation of a peptide bond detected (wrt. the original structure), rejecting
 tryconnect> Transition state with energy     -441.0906303     ignored, cis-trans isomerisation detected in one or more peptide bonds.

 >>>>>  Path run for ts 82 ...
 Plus  side of path:                    1192 steps. Energy=    -450.9980845       time=      12.08
 Minus side of path:                    1174 steps. Energy=    -450.2555892       time=      11.85

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -450.9980845  3.3395         -447.6585636  2.5970         -450.2555892   7.133   6.185  57.011   3.824
check_cistrans_protein>  WARNING -- cis (or deformed) peptide bond detected between residues      1     2
 tryconnect> MINUS minimum: cis-trans isomerisation of a peptide bond detected involving atom     15
check_cistrans_protein>  WARNING -- cis (or deformed) peptide bond detected between residues      1     2
 tryconnect> PLUS minimum: cis-trans isomerisation of a peptide bond detected involving atom     15
 tryconnect> Cis-trans isomerisation of a peptide bond detected (wrt. the original structure), rejecting
 tryconnect> Transition state with energy     -447.6585636     ignored, cis-trans isomerisation detected in one or more peptide bonds.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 18 >>>>>>>>>>>>>>>>>>>>> 82 minima and 82 ts are known >>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has     13 steps with      1 missing connections, weight=    0.13325E+06
 decide> The unconnected minima in the chain and their distances are:
    60       51.08    11 
 

 tryconnect> 525-iteration DNEB run for minima 11_S and 60_F using 15 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      7.835261665    
 Double-ended search iterations= 715 RMS= 0.6680 Dev= 1.60% S= 220.81 time= 80.85
 Following    3 images are candidates for TS:    6    8   12  
 Converged to TS (number of iterations):         83
 Converged to TS (number of iterations):        114
 Converged to TS (number of iterations):        182
 DNEB run yielded 3 true transition state(s) time= 219.39

 >>>>>  Path run for ts 83 ...
 Plus  side of path:                    1275 steps. Energy=    -447.9766437       time=      13.55
 Minus side of path:                    1300 steps. Energy=    -455.1556920       time=      13.79

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -447.9766437  14.201         -433.7754062  21.380         -455.1556920  23.295  16.815  13.293  16.399
check_cistrans_protein>  WARNING -- cis (or deformed) peptide bond detected between residues      1     2
 tryconnect> PLUS minimum: cis-trans isomerisation of a peptide bond detected involving atom     15
 tryconnect> Cis-trans isomerisation of a peptide bond detected (wrt. the original structure), rejecting
 tryconnect> Transition state with energy     -433.7754062     ignored, cis-trans isomerisation detected in one or more peptide bonds.

 >>>>>  Path run for ts 84 ...
 Plus  side of path:                    1118 steps. Energy=    -448.5541927       time=      11.08
 Minus side of path:                    1195 steps. Energy=    -450.1078927       time=      12.19

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -448.5541927 0.15954E-01     -448.5382388  1.5697         -450.1078927   1.325   1.277 180.998   1.204
check_cistrans_protein>  WARNING -- cis (or deformed) peptide bond detected between residues      1     2
 tryconnect> MINUS minimum: cis-trans isomerisation of a peptide bond detected involving atom     15
check_cistrans_protein>  WARNING -- cis (or deformed) peptide bond detected between residues      1     2
 tryconnect> PLUS minimum: cis-trans isomerisation of a peptide bond detected involving atom     15
 tryconnect> Cis-trans isomerisation of a peptide bond detected (wrt. the original structure), rejecting
 tryconnect> Transition state with energy     -448.5382388     ignored, cis-trans isomerisation detected in one or more peptide bonds.

 >>>>>  Path run for ts 85 ...
 Plus  side of path:                    2274 steps. Energy=    -447.3880871       time=      32.39
 Minus side of path:                    2301 steps. Energy=    -446.1808977       time=      34.07

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -447.3880871  6.6849         -440.7032318  5.4777         -446.1808977 112.542  65.275   2.589  84.215
check_cistrans_protein>  WARNING -- cis (or deformed) peptide bond detected between residues      1     2
 tryconnect> MINUS minimum: cis-trans isomerisation of a peptide bond detected involving atom     15
check_cistrans_protein>  WARNING -- cis (or deformed) peptide bond detected between residues      1     2
 tryconnect> PLUS minimum: cis-trans isomerisation of a peptide bond detected involving atom     15
 tryconnect> Cis-trans isomerisation of a peptide bond detected (wrt. the original structure), rejecting
 tryconnect> Transition state with energy     -440.7032318     ignored, cis-trans isomerisation detected in one or more peptide bonds.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 19 >>>>>>>>>>>>>>>>>>>>> 82 minima and 85 ts are known >>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has     21 steps with      2 missing connections, weight=    0.13587E+06
 decide> The unconnected minima in the chain and their distances are:
    71       50.04     7     4       21.92    30 
 

 tryconnect> 525-iteration DNEB run for minima 7_U and 71_F using 15 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      1.491479664    
 Double-ended search iterations= 525 RMS= 0.4319 Dev= 2.23% S= 228.78 time= 59.52
 Following    2 images are candidates for TS:    5    8  
 Converged to TS (number of iterations):         63
 Failed to converge to TS (number of iterations):        251
 DNEB run yielded 1 true transition state(s) time= 171.76

 >>>>>  Path run for ts 86 ...
 Plus  side of path:                    1308 steps. Energy=    -450.6041283       time=      13.78
 Minus side of path:                    1314 steps. Energy=    -450.6041283       time=      13.88

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -450.6041283  2.6181         -447.9860764  2.6181         -450.6041283  22.231   3.101 108.873   2.002
        *NEW* (Placed in 83)                                    Known (#83)
 Connection established between members of the U set.

 tryconnect> 210-iteration DNEB run for minima 4_U and 30_S using 6 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      1.288396211    
 Double-ended search iterations= 210 RMS= 0.0571 Dev= 0.43% S= 22.26 time= 9.63
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):         29
 DNEB run yielded 1 true transition state(s) time=  26.07

 >>>>>  Path run for ts 87 ...
 Plus  side of path:                    1268 steps. Energy=    -451.4625761       time=      13.33
 Minus side of path:                    1302 steps. Energy=    -451.6693160       time=      13.85

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -451.4625761 0.53717         -450.9254038 0.74391         -451.6693160  26.866  22.150   1.817 119.991
        Known (#3)                                              Known (#30)
 Unconnected minimum 3 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 20 >>>>>>>>>>>>>>>>>>>>> 83 minima and 87 ts are known >>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has     21 steps with      1 missing connections, weight=    0.12551E+06
 decide> The unconnected minima in the chain and their distances are:
    60       50.07     7 
 

 tryconnect> 525-iteration DNEB run for minima 7_S and 60_F using 15 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      1.491479664    
 Double-ended search iterations= 525 RMS= 0.4659 Dev= 1.75% S= 225.74 time= 59.51
 Following    1 images are candidates for TS:    8  
 Failed to converge to TS (number of iterations):        251
 DNEB run yielded 0 true transition state(s) time= 119.84
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 21 >>>>>>>>>>>>>>>>>>>>> 83 minima and 87 ts are known >>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has     25 steps with      3 missing connections, weight=    0.13092E+06
 decide> The unconnected minima in the chain and their distances are:
    60       19.97    27    26       10.26    25    24       49.43     7 
 

 tryconnect> 175-iteration DNEB run for minima 27_U and 60_F using 5 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      1.812902854    
 Double-ended search iterations= 175 RMS= 0.0795 Dev= 0.29% S= 20.55 time= 6.82
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):         27
 DNEB run yielded 1 true transition state(s) time=  24.22

 >>>>>  Path run for ts 88 ...
 Plus  side of path:                    1229 steps. Energy=    -453.6216495       time=      12.65
 Minus side of path:                    1221 steps. Energy=    -452.5239553       time=      12.55

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -453.6216495  3.1422         -450.4794358  2.0445         -452.5239553   7.360   6.789  30.158   7.229
        *NEW* (Placed in 84)                                    Known (#27)
 Connection established between members of the U set.

 tryconnect> 805-iteration DNEB run for minima 25_U and 26_U using 23 images  (DNEB attempt #2)  ...
 lbfgs> Final DNEB force constant      1.491479664    
 Double-ended search iterations= 805 RMS= 0.0267 Dev= 6.52% S= 16.11 time= 138.97
 Following    1 images are candidates for TS:   17  
 Converged to TS (number of iterations):         17
 DNEB run yielded 1 true transition state(s) time=  19.28
 isnewts> transition state is the same as number       16 energy=     -446.3654911822
 tryconnect> Will not repeat search for TS      1 same as TS     16

 tryconnect> 490-iteration DNEB run for minima 7_S and 24_U using 14 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      35.55672688    
 Double-ended search iterations= 914 RMS= 0.4676 Dev= 1.98% S= 220.16 time= 96.13
 Following    1 images are candidates for TS:    9  
 Converged to TS (number of iterations):        208
 DNEB run yielded 1 true transition state(s) time= 116.08

 >>>>>  Path run for ts 89 ...
 Plus  side of path:                    1485 steps. Energy=    -443.9357546       time=      17.06
 Minus side of path:                    1245 steps. Energy=    -443.2931083       time=      13.21

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -443.9357546  1.3215         -442.6142198 0.67889         -443.2931083  19.159  15.802   2.076 105.004
check_cistrans_protein>  WARNING -- cis (or deformed) peptide bond detected between residues      1     2
 tryconnect> MINUS minimum: cis-trans isomerisation of a peptide bond detected involving atom     15
check_cistrans_protein>  WARNING -- cis (or deformed) peptide bond detected between residues      1     2
 tryconnect> PLUS minimum: cis-trans isomerisation of a peptide bond detected involving atom     15
 tryconnect> Cis-trans isomerisation of a peptide bond detected (wrt. the original structure), rejecting
 tryconnect> Transition state with energy     -442.6142198     ignored, cis-trans isomerisation detected in one or more peptide bonds.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 22 >>>>>>>>>>>>>>>>>>>>> 84 minima and 89 ts are known >>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has     21 steps with      1 missing connections, weight=    0.13172E+06
 decide> The unconnected minima in the chain and their distances are:
    59       50.88     8 
 

 tryconnect> 525-iteration DNEB run for minima 8_S and 59_F using 15 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      2.203594749    
 Double-ended search iterations= 572 RMS= 0.4467 Dev= 1.74% S= 228.71 time= 64.60
 Following    1 images are candidates for TS:    9  
 Converged to TS (number of iterations):         44
 DNEB run yielded 1 true transition state(s) time=  40.29

 >>>>>  Path run for ts 90 ...
 Plus  side of path:                    1273 steps. Energy=    -449.3533882       time=      13.40
 Minus side of path:                    1249 steps. Energy=    -448.3971421       time=      13.04

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -449.3533882  3.1255         -446.2279120  2.1692         -448.3971421   7.474   6.724  32.564   6.694
        *NEW* (Placed in 85)                                    *NEW* (Placed in 86)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 23 >>>>>>>>>>>>>>>>>>>>> 86 minima and 90 ts are known >>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has     11 steps with      1 missing connections, weight=    0.13807E+06
 decide> The unconnected minima in the chain and their distances are:
    72       51.69    11 
 

 tryconnect> 525-iteration DNEB run for minima 11_S and 72_F using 15 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      89.85007793    
 Double-ended search iterations= 929 RMS= 0.7164 Dev= 1.55% S= 216.04 time= 104.91
 Following    2 images are candidates for TS:    4    7  
 Failed to converge to TS (number of iterations):        251
 Converged to TS (number of iterations):        133
 DNEB run yielded 1 true transition state(s) time= 198.24

 >>>>>  Path run for ts 91 ...
 Plus  side of path:                    1324 steps. Energy=    -437.1608442       time=      14.00
 Minus side of path:                    1237 steps. Energy=    -437.6558665       time=      12.75

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -437.1608442  1.8880         -435.2728051  2.3831         -437.6558665  25.305  21.894   7.823  27.866
check_cistrans_protein>  WARNING -- cis (or deformed) peptide bond detected between residues      3     4
 tryconnect> MINUS minimum: cis-trans isomerisation of a peptide bond detected involving atom     53
check_cistrans_protein>  WARNING -- cis (or deformed) peptide bond detected between residues      3     4
 tryconnect> PLUS minimum: cis-trans isomerisation of a peptide bond detected involving atom     53
 tryconnect> Cis-trans isomerisation of a peptide bond detected (wrt. the original structure), rejecting
 tryconnect> Transition state with energy     -435.2728051     ignored, cis-trans isomerisation detected in one or more peptide bonds.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 24 >>>>>>>>>>>>>>>>>>>>> 86 minima and 91 ts are known >>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has     18 steps with      1 missing connections, weight=    0.14083E+06
 decide> The unconnected minima in the chain and their distances are:
    72       52.03     8 
 

 tryconnect> 525-iteration DNEB run for minima 8_S and 72_F using 15 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      4.362966876    
 Double-ended search iterations= 634 RMS= 0.8409 Dev= 2.79% S= 225.77 time= 71.54
 Following    1 images are candidates for TS:    8  
 Converged to TS (number of iterations):        225
 DNEB run yielded 1 true transition state(s) time= 116.10

 >>>>>  Path run for ts 92 ...
 Plus  side of path:                    1278 steps. Energy=    -448.6913385       time=      13.40
 Minus side of path:                    1280 steps. Energy=    -447.8228573       time=      13.43

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -448.6913385  2.4286         -446.2627160  1.5601         -447.8228573  12.934  11.824   8.531  25.554
        *NEW* (Placed in 87)                                    *NEW* (Placed in 88)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 25 >>>>>>>>>>>>>>>>>>>>> 88 minima and 92 ts are known >>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has     19 steps with      1 missing connections, weight=    0.14199E+06
 decide> The unconnected minima in the chain and their distances are:
    71       52.17     8 
 

 tryconnect> 525-iteration DNEB run for minima 8_S and 71_F using 15 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      2.953027717    
 Double-ended search iterations= 579 RMS= 0.9661 Dev= 2.01% S= 228.65 time= 65.38
 Following    1 images are candidates for TS:    8  
 Failed to converge to TS (number of iterations):        251
 DNEB run yielded 0 true transition state(s) time= 117.14
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 26 >>>>>>>>>>>>>>>>>>>>> 88 minima and 92 ts are known >>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has     11 steps with      1 missing connections, weight=    0.14296E+06
 decide> The unconnected minima in the chain and their distances are:
    64       52.29    10 
 

 tryconnect> 525-iteration DNEB run for minima 10_S and 64_F using 15 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      10.50000000    
 Double-ended search iterations= 525 RMS= 0.1947 Dev= 1.75% S= 54.44 time= 58.55
 Following    1 images are candidates for TS:    8  
 Converged to TS (number of iterations):         58
 DNEB run yielded 1 true transition state(s) time=  42.23

 >>>>>  Path run for ts 93 ...
 Plus  side of path:                    1237 steps. Energy=    -454.2881025       time=      12.71
 Minus side of path:                    1244 steps. Energy=    -455.3753711       time=      12.80

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -454.2881025  2.1479         -452.1402471  3.2351         -455.3753711   8.183   7.001  26.393   8.260
        *NEW* (Placed in 89)                                    *NEW* (Placed in 90)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 27 >>>>>>>>>>>>>>>>>>>>> 90 minima and 93 ts are known >>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has     18 steps with      1 missing connections, weight=    0.14315E+06
 decide> The unconnected minima in the chain and their distances are:
    62       52.31     7 
 

 tryconnect> 525-iteration DNEB run for minima 7_S and 62_F using 15 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      1.491479664    
 Double-ended search iterations= 525 RMS= 0.4919 Dev= 2.35% S= 234.00 time= 59.51
 Following    2 images are candidates for TS:    9   13  
 Converged to TS (number of iterations):        207
 Failed to converge to TS (number of iterations):        251
 DNEB run yielded 1 true transition state(s) time= 227.77

 >>>>>  Path run for ts 94 ...
 Plus  side of path:                    2776 steps. Energy=    -452.4317028       time=      44.49
 Minus side of path:                    1758 steps. Energy=    -450.7276051       time=      21.52

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -452.4317028  5.9711         -446.4606394  4.2670         -450.7276051  77.723  52.711   2.233  97.621
        *NEW* (Placed in 91)                                    *NEW* (Placed in 92)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 28 >>>>>>>>>>>>>>>>>>>>> 92 minima and 94 ts are known >>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has     20 steps with      1 missing connections, weight=    0.14421E+06
 decide> The unconnected minima in the chain and their distances are:
    60       52.44     8 
 

 tryconnect> 525-iteration DNEB run for minima 8_S and 60_F using 15 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      3.255713058    
 Double-ended search iterations= 601 RMS= 0.4930 Dev= 1.81% S= 226.85 time= 67.91
 Following    1 images are candidates for TS:    8  
 Converged to TS (number of iterations):         90
 DNEB run yielded 1 true transition state(s) time=  59.12

 >>>>>  Path run for ts 95 ...
 Plus  side of path:                    1266 steps. Energy=    -450.2199298       time=      13.20
 Minus side of path:                    1274 steps. Energy=    -451.1577619       time=      13.32

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -450.2199298  1.6341         -448.5858008  2.5720         -451.1577619  10.599   7.621   6.362  34.265
        *NEW* (Placed in 93)                                    *NEW* (Placed in 94)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 29 >>>>>>>>>>>>>>>>>>>>> 94 minima and 95 ts are known >>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has     10 steps with      1 missing connections, weight=    0.14740E+06
 decide> The unconnected minima in the chain and their distances are:
    61       52.82    10 
 

 tryconnect> 525-iteration DNEB run for minima 10_S and 61_F using 15 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      12.76281562    
 Double-ended search iterations= 525 RMS= 0.2493 Dev= 0.72% S= 54.94 time= 58.47
 Following    1 images are candidates for TS:    8  
 Converged to TS (number of iterations):         67
 DNEB run yielded 1 true transition state(s) time=  45.71
 isnewts> transition state is the same as number       93 energy=     -452.1402470858
 tryconnect> Try the path again for ts      1 with pushoff=    0.1000000000E-01

 >>>>>  Path run for ts 96 ...
 tryconnect> Trying this transition state path again with pushoff=    0.1000000000E-01
 Plus  side of path:                    1243 steps. Energy=    -454.2881025       time=      12.76
 Minus side of path:                    1237 steps. Energy=    -455.3753711       time=      12.68

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -454.2881025  2.1479         -452.1402471  3.2351         -455.3753711   8.184   7.003  26.279   8.296
        Known (#89)                                             Known (#90)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 30 >>>>>>>>>>>>>>>>>>>>> 94 minima and 96 ts are known >>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has     26 steps with      3 missing connections, weight=    0.14962E+06
 decide> The unconnected minima in the chain and their distances are:
    60       18.89    84    14       18.68    25    25       51.47     7 
 

 tryconnect> 175-iteration DNEB run for minima 60_F and 84_U using 5 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      1.812902854    
 Double-ended search iterations= 175 RMS= 0.0429 Dev= 0.02% S= 18.97 time= 6.82
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         81
 DNEB run yielded 1 true transition state(s) time=  46.38

 >>>>>  Path run for ts 97 ...
 Plus  side of path:                    1234 steps. Energy=    -452.8644269       time=      12.70
 Minus side of path:                    1349 steps. Energy=    -453.6216495       time=      14.44

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -452.8644269 0.72281E-02     -452.8571988 0.76445         -453.6216495  19.556  18.899   2.584  84.379
        Known (#60)                                             Known (#84)
 Unconnected minimum 84 found its way to F set.

 tryconnect> 175-iteration DNEB run for minima 14_F and 25_U using 5 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      1.812902854    
 Double-ended search iterations= 175 RMS= 0.0794 Dev= 0.55% S= 19.50 time= 6.82
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         36
 DNEB run yielded 1 true transition state(s) time=  28.74
 isnewts> transition state is the same as number       16 energy=     -446.3654911826
 tryconnect> Will not repeat search for TS      1 same as TS     16

 tryconnect> 525-iteration DNEB run for minima 7_S and 25_U using 15 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      2.953027717    
 Double-ended search iterations= 623 RMS= 0.8377 Dev= 1.90% S= 215.90 time= 70.43
 Following    2 images are candidates for TS:    5    9  
 Converged to TS (number of iterations):        112
 Converged to TS (number of iterations):         58
 DNEB run yielded 2 true transition state(s) time= 125.43

 >>>>>  Path run for ts 98 ...
 Plus  side of path:                    1268 steps. Energy=    -449.6320123       time=      13.21
 Minus side of path:                    1262 steps. Energy=    -450.6041283       time=      13.22

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -449.6320123 0.82628         -448.8057290  1.7984         -450.6041283  11.501  10.364   4.131  52.767
        *NEW* (Placed in 95)                                    Known (#83)
 Connection established between members of the U set.

 >>>>>  Path run for ts 99 ...
 Plus  side of path:                    1287 steps. Energy=    -442.2222347       time=      13.59
 Minus side of path:                    1236 steps. Energy=    -443.4345561       time=      12.80

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -442.2222347  1.9716         -440.2506657  3.1839         -443.4345561   8.546   7.727  23.787   9.165
check_cistrans_protein>  WARNING -- cis (or deformed) peptide bond detected between residues      1     2
 tryconnect> MINUS minimum: cis-trans isomerisation of a peptide bond detected involving atom     15
check_cistrans_protein>  WARNING -- cis (or deformed) peptide bond detected between residues      1     2
 tryconnect> PLUS minimum: cis-trans isomerisation of a peptide bond detected involving atom     15
 tryconnect> Cis-trans isomerisation of a peptide bond detected (wrt. the original structure), rejecting
 tryconnect> Transition state with energy     -440.2506657     ignored, cis-trans isomerisation detected in one or more peptide bonds.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 31 >>>>>>>>>>>>>>>>>>>>> 95 minima and 99 ts are known >>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has     24 steps with      1 missing connections, weight=    0.14767E+06
 decide> The unconnected minima in the chain and their distances are:
    14       52.86     8 
 

 tryconnect> 525-iteration DNEB run for minima 8_S and 14_F using 15 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      4.362966876    
 Double-ended search iterations= 705 RMS= 0.3418 Dev= 0.78% S= 218.11 time= 79.68
 Following    2 images are candidates for TS:    6    9  
 Converged to TS (number of iterations):         96
 Converged to TS (number of iterations):        181
 DNEB run yielded 2 true transition state(s) time= 141.12
 TS rack redimentioned to hold 200 ts.

 >>>>>  Path run for ts 100 ...
 Plus  side of path:                    1252 steps. Energy=    -448.2818932       time=      12.83
 Minus side of path:                    1271 steps. Energy=    -449.2210221       time=      13.09

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -448.2818932  1.4251         -446.8567813  2.3642         -449.2210221  17.155  15.470  13.636  15.987
        *NEW* (Placed in 96)                                    *NEW* (Placed in 97)
 Connection established between members of the U set.

 >>>>>  Path run for ts 101 ...
 Plus  side of path:                    1332 steps. Energy=    -440.2821970       time=      13.94
 Minus side of path:                    1269 steps. Energy=    -438.3641084       time=      13.02

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -440.2821970  1.9837         -438.2984857 0.65623E-01     -438.3641084  21.288  19.549   3.258  66.917
check_cistrans_protein>  WARNING -- cis (or deformed) peptide bond detected between residues      1     2
 tryconnect> MINUS minimum: cis-trans isomerisation of a peptide bond detected involving atom     15
check_cistrans_protein>  WARNING -- cis (or deformed) peptide bond detected between residues      1     2
 tryconnect> PLUS minimum: cis-trans isomerisation of a peptide bond detected involving atom     15
 tryconnect> Cis-trans isomerisation of a peptide bond detected (wrt. the original structure), rejecting
 tryconnect> Transition state with energy     -438.2984857     ignored, cis-trans isomerisation detected in one or more peptide bonds.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 32 >>>>>>>>>>>>>>>>>>>>> 97 minima and 101 ts are known >>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has     29 steps with      2 missing connections, weight=    0.14961E+06
 decide> The unconnected minima in the chain and their distances are:
    26       23.10    24    51       51.59     8 
 

 tryconnect> 210-iteration DNEB run for minima 24_U and 26_F using 6 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      1.288396211    
 Double-ended search iterations= 210 RMS= 0.4307 Dev= 0.43% S= 25.53 time= 9.69
 Following    1 images are candidates for TS:    5  
 Converged to TS (number of iterations):         36
 DNEB run yielded 1 true transition state(s) time=  27.27
 isnewts> transition state is the same as number       16 energy=     -446.3654911783
 tryconnect> Will not repeat search for TS      1 same as TS     16

 tryconnect> 525-iteration DNEB run for minima 8_S and 51_U using 15 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      14.07100423    
 Double-ended search iterations= 738 RMS= 0.5481 Dev= 1.24% S= 211.81 time= 83.05
 Following    1 images are candidates for TS:    8  
 Converged to TS (number of iterations):         94
 DNEB run yielded 1 true transition state(s) time=  70.65

 >>>>>  Path run for ts 102 ...
 Plus  side of path:                    1256 steps. Energy=    -457.6032848       time=      12.86
 Minus side of path:                    1297 steps. Energy=    -457.3187425       time=      13.42

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -457.6032848  2.5974         -455.0059112  2.3128         -457.3187425  15.346  13.653   2.684  81.233
        Known (#69)                                             *NEW* (Placed in 98)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 33 >>>>>>>>>>>>>>>>>>>>> 98 minima and 102 ts are known >>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has     25 steps with      2 missing connections, weight=    0.15162E+06
 decide> The unconnected minima in the chain and their distances are:
    14       18.68    25    25       51.75     8 
 

 tryconnect> 805-iteration DNEB run for minima 14_F and 25_U using 23 images  (DNEB attempt #2)  ...
 lbfgs> Final DNEB force constant     0.9156391332    
 Double-ended search iterations= 805 RMS= 0.0388 Dev= 7.37% S= 26.13 time= 138.73
 Following    1 images are candidates for TS:    7  
 Converged to TS (number of iterations):         26
 DNEB run yielded 1 true transition state(s) time=  24.01
 isnewts> transition state is the same as number       16 energy=     -446.3654911828
 tryconnect> Will not repeat search for TS      1 same as TS     16

 tryconnect> 525-iteration DNEB run for minima 8_S and 25_U using 15 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      4.362966876    
 Double-ended search iterations= 698 RMS= 0.4289 Dev= 1.50% S= 220.75 time= 78.64
 Following    2 images are candidates for TS:    5    9  
 Converged to TS (number of iterations):         86
 Converged to TS (number of iterations):         71
 DNEB run yielded 2 true transition state(s) time= 120.76

 >>>>>  Path run for ts 103 ...
 Plus  side of path:                    1270 steps. Energy=    -449.9926590       time=      13.03
 Minus side of path:                    1403 steps. Energy=    -451.9119632       time=      15.05

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -449.9926590  3.4492         -446.5434484  5.3685         -451.9119632  28.072  25.206   8.466  25.749
        *NEW* (Placed in 99)                                    *NEW* (Placed in 100)
 Connection established between members of the U set.

 >>>>>  Path run for ts 104 ...
 Plus  side of path:                    1334 steps. Energy=    -438.5454275       time=      14.07
 Minus side of path:                    1264 steps. Energy=    -439.7128294       time=      13.02

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -438.5454275  2.0166         -436.5287917  3.1840         -439.7128294  11.506  10.240  10.889  20.020
check_cistrans_protein>  WARNING -- cis (or deformed) peptide bond detected between residues      1     2
 tryconnect> MINUS minimum: cis-trans isomerisation of a peptide bond detected involving atom     15
check_cistrans_protein>  WARNING -- cis (or deformed) peptide bond detected between residues      1     2
 tryconnect> PLUS minimum: cis-trans isomerisation of a peptide bond detected involving atom     15
 tryconnect> Cis-trans isomerisation of a peptide bond detected (wrt. the original structure), rejecting
 tryconnect> Transition state with energy     -436.5287917     ignored, cis-trans isomerisation detected in one or more peptide bonds.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 34 >>>>>>>>>>>>>>>>>>>>> 100 minima and 104 ts are known >>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has     20 steps with      1 missing connections, weight=    0.15290E+06
 decide> The unconnected minima in the chain and their distances are:
    26       53.47    43 
 

 tryconnect> 560-iteration DNEB run for minima 26_F and 43_S using 16 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.5353552375    
 Double-ended search iterations= 560 RMS= 0.0706 Dev= 4.64% S= 64.38 time= 67.11
 Following    3 images are candidates for TS:    3    7    9  
 Converged to TS (number of iterations):         26
 Converged to TS (number of iterations):        103
 Converged to TS (number of iterations):         64
 DNEB run yielded 3 true transition state(s) time= 118.16

 >>>>>  Path run for ts 105 ...
 Plus  side of path:                    1264 steps. Energy=    -448.7572765       time=      13.01
 Minus side of path:                    2203 steps. Energy=    -452.3534119       time=      29.87

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -448.7572765  1.9532         -446.8041010  5.5493         -452.3534119  45.695  40.393   1.735 125.622
        *NEW* (Placed in 101)                                   *NEW* (Placed in 102)
 Connection established between members of the U set.

 >>>>>  Path run for ts 106 ...
 Plus  side of path:                    1869 steps. Energy=    -451.0800324       time=      23.04
 Minus side of path:                    1458 steps. Energy=    -450.2379114       time=      15.93

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -451.0800324  3.3384         -447.7416780  2.4962         -450.2379114  79.515  73.348   2.043 106.705
        Known (#50)                                             *NEW* (Placed in 103)
 Unconnected minimum 103 found its way to S set.

 >>>>>  Path run for ts 107 ...
 Plus  side of path:                    1347 steps. Energy=    -450.7547132       time=      14.21
 Minus side of path:                    1283 steps. Energy=    -450.1504792       time=      13.36

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -450.7547132  3.4697         -447.2850166  2.8655         -450.1504792  43.202  35.944   2.651  82.228
        Known (#43)                                             *NEW* (Placed in 104)
 Unconnected minimum 104 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 35 >>>>>>>>>>>>>>>>>>>>> 104 minima and 107 ts are known >>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has     12 steps with      1 missing connections, weight=     13823.    
 decide> The unconnected minima in the chain and their distances are:
    72       24.00   103 
 

 tryconnect> 245-iteration DNEB run for minima 72_F and 103_S using 7 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      3.589423646    
 Double-ended search iterations= 245 RMS= 0.1470 Dev= 0.58% S= 25.75 time= 13.15
 Following    1 images are candidates for TS:    5  
 Converged to TS (number of iterations):         54
 DNEB run yielded 1 true transition state(s) time=  39.39

 >>>>>  Path run for ts 108 ...
 Plus  side of path:                    1371 steps. Energy=    -450.2379114       time=      14.88
 Minus side of path:                    1628 steps. Energy=    -452.3534119       time=      18.94

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -450.2379114  5.8259         -444.4120471  7.9414         -452.3534119  51.700  26.794   2.207  98.754
        Known (#103)                                            Known (#102)
 Unconnected minimum 102 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 36 >>>>>>>>>>>>>>>>>>>>> 104 minima and 108 ts are known >>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has     19 steps with      1 missing connections, weight=     449.51    
 decide> The unconnected minima in the chain and their distances are:
    26        7.66   101 
 

 tryconnect> 70-iteration DNEB run for minima 26_F and 101_S using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.9155 Dev= 0.24% S= 7.91 time= 1.30
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         22
 DNEB run yielded 1 true transition state(s) time=  21.90

 >>>>>  Path run for ts 109 ...
 Plus  side of path:                    1234 steps. Energy=    -448.7572765       time=      12.68
 Minus side of path:                    1248 steps. Energy=    -448.4009816       time=      12.78

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -448.7572765 0.65125         -448.1060297 0.29495         -448.4009816   8.012   7.661  12.405  17.574
        Known (#101)                                            Known (#26)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   6     -450.5867733 0.33907        -450.2477046  5.0946        -455.3423495  31.563  25.532   2.100 103.799
  35     -455.3423495  1.2011        -454.1412277 0.13928        -454.2805049  12.175  11.852   2.707  80.524
  23     -454.2805049  3.2321        -451.0484332  2.1472        -453.1956606   8.186   7.004  26.354   8.272
  34     -453.1956606  3.1129        -450.0827763 0.79923E-01    -450.1626995  30.473  27.483   1.724 126.434
  52     -450.1626995 0.48718E-01    -450.1139818 0.96605        -451.0800324  22.000  20.355   2.160 100.928
 106     -451.0800324  3.3384        -447.7416780  2.4962        -450.2379114  79.515  73.348   2.043 106.705
 108     -450.2379114  5.8259        -444.4120471  7.9414        -452.3534119  51.700  26.794   2.207  98.754
 105     -452.3534119  5.5493        -446.8041010  1.9532        -448.7572765  45.695  40.393   1.735 125.622
 109     -448.7572765 0.65125        -448.1060297 0.29495        -448.4009816   8.012   7.661  12.405  17.574
  16     -448.4009816  2.0355        -446.3654912  6.1585        -452.5239553  41.829  37.360   1.867 116.735
  88     -452.5239553  2.0445        -450.4794358  3.1422        -453.6216495   7.360   6.789  30.158   7.229
  97     -453.6216495 0.76445        -452.8571988 0.72281E-02    -452.8644269  19.556  18.899   2.584  84.379
  71     -452.8644269  2.0745        -450.7899095  2.8972        -453.6871291   8.475   7.675  24.696   8.827
  75     -453.6871291 0.40802        -453.2791140 0.56819        -453.8473017   8.558   8.098  15.160  14.380
  72     -453.8473017  1.8706        -451.9766898  1.1787        -453.1553594  40.693  25.778   1.950 111.777
  67     -453.1553594 0.56796        -452.5873959 0.40613        -452.9935256  27.216  25.510   1.764 123.548
  25     -452.9935256  3.4095        -449.5840636 0.32557        -449.9096374  54.885  52.670   1.618 134.774
  36     -449.9096374  1.7846        -448.1250481 0.25773        -448.3827800  35.748  13.712   2.689  81.071
  11     -448.3827800 0.68095        -447.7018283 0.39551        -448.0973399  40.037  34.884   2.007 108.611

 Number of TS in the path       =     19
 Number of cycles               =     36

 Elapsed time=                             15407.78
 OPTIM> # of energy calls=                          0 time=           0.00 %=  0.0
 OPTIM> # of energy+gradient calls=           1046078 time=        7779.02 %= 50.5
 OPTIM> # of energy+gradient+Hessian calls=     13058 time=        3684.66 %= 23.9
