
 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> Number of atoms (or variables)  determined as    145
 keyword> Constraint potential parameters read from file congeom.dat
 keyword> Local permutational alignment: alignment threshold=        1.00000
 keyword> Local permutational alignment: alignment cutoff=           5.00000
 keyword> Number of groups of permutable atoms=     6
CHARMMTYPE set to  2
1
                 Chemistry at HARvard Macromolecular Mechanics
                   (CHARMM) - Developmental Version 35b4   February 15, 2010   
       Copyright(c) 1984-2001  President and Fellows of Harvard College
                              All Rights Reserved
      Current operating system: Linux-2.6.16.54-0.2.5-smp(x86_64)@comp32.ch.
                 Created on  5/28/12 at 10:35:10 by user: wales       

            Maximum number of ATOMS:     25140, and RESidues:       14000
            Current HEAP size:         2048000, and STACK size:    500000

 RDTITL> * INPUT FILE FOR TRYPZIP 1LE1
 RDTITL> *
  
 CHARMM>    BOMLev -2
 Parameter: TOP <- "toph19_eef1_bs360.inp"
 Parameter: PAR <- "param19_eef1_bs360.inp"
  
 CHARMM>    WRNLEV -1
  
 CHARMM>    PRNLEV 1
 NBOND          152
 NTHETA          223
 NPHI           88

chsetdihe> number of internal coordinates for segment    1
 chsetdihe> NPHIPSI           24
 chsetdihe> NOMEGAC           11
 chsetdihe> NSIDECHAIN           27
 chsetdihe> NCHIRAL           13

chsetdihe> total number of internal coordinates
 chsetdihe> NPHIPSITOT=            24
 chsetdihe> NOMEGACTOT=            11
 chsetdihe> NSIDECHAINTOT=            27
 chsetdihe> NCHIRALTOT=            13

 chsetdihe>            51  twistable dihedrals identified
chsetdihe> SEG-NR, NSEGATOMS :    1     145

 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>  435 Cartesian coordinates will be optimised for  145 CHARMM 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
 fetchz> Using constraint potential for initial interpolation in each cycle
         with absolute distance change tolerance         0.30000
         extra distance before turning on constraint potential         0.17500
         constraint spring constant=       10.00000
         image distance spring constant=        1.00000
         repulsion factor between unconstrained atoms=      100.00000
         repulsion cutoff will be the minimum of         1.55000 and the shortest distance in the end points
         fraction for restoring true potential=        0.99000
         maximum separation of atoms in sequence for constraint=   218
         minimum separation of atoms in sequence for repulsion=     0
         maximum optimization steps for constrained potential=  300001
         initial # images for constrained potential, maximum, check interval=       3      75      25
         number of interpolation attempts and initial image increment=       2      12
         RMS gradient per image tolerance for constrained potential=        0.01000
         maximum optimization steps for constrained/real potential=      25
         maximum steps for relaxation after adding a new atom before backtrack=     200
         maximum number of constraints per atom=     6
         maximum energy per image for convergence during constraint potential phase=        0.1000000000
         interval for checking repulsive interactions=    10
         multiple of cutoff for repulsion neighbour list=        2.0000000000
         adding terms for constraint internal minima
         Minimum and Maximum image separations:         0.10000       10.00000
 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> Number of updates in qci=   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


 OPTIM> Using translational/rotational ev shift=     1000000.000    
 OPTIM> Initial energy=    -382.1773825     RMS force=    0.9268464572E-06
 OPTIM> Final energy  =    -395.0112249     RMS force=    0.9702229703E-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 from interp function and dist, power=     3

 initialise> Interpolation metric value for minima 1 and 2 is      146.5820539    
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 1 >>>>>>>>>>>>>>>>>>>>> 2 minima and 0 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      1 steps with      1 missing connections, weight=     90432.    
 decide> The unconnected minima in the chain and their distances are:
     2       44.74     1 
 

 tryconnect> Interpolation for minima 1_S and 2_F using 3 initial images  (interp attempt #1)  ...
 intlbfgs> Maximum number of steps for constraint potential phase is 300001
 intlbfgs> Total number of atoms moving less than threshold=    18
 intlbfgs> constrained potential finished, time=       0.0
 intlbfgs> switch on true potential at step    696 fraction=    0.990000 images=     5 time=       0.5
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After    721 steps, energy/image=     339.5164536     RMS=32.05475109     images=   5
 intlbfgs> First  minimum number      1
 intlbfgs> Second minimum number      2
 intlbfgs> DNEB for minima      1     2 dist=   53.60     Attempts, images and iterations=     0    16   560
 lbfgs> Final DNEB force constant     0.1830111189    
 Double-ended search iterations= 560 RMS= 0.0921 Dev= 6.16% S= 69.23 time= 12.34
 Following    3 images are candidates for TS:    6   11   15  
 Converged to TS (number of iterations):         43
 Converged to TS (number of iterations):         22
 Converged to TS (number of iterations):         28
 DNEB run yielded 3 true transition state(s) time=  12.87

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                    1076 steps. Energy=    -382.5427530       time=       3.69
 Minus side of path:                     910 steps. Energy=    -390.4787888       time=       2.88

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -382.5427530  5.7127         -376.8300957  13.649         -390.4787888  37.663  26.046   7.914  18.323
        *NEW* (Placed in 3)                                     *NEW* (Placed in 4)
 checkperc> Increasing con cutoff atoms    38   40 from     0.20123E-01 to     0.20803E-01 ref=     2.5675    
 checkperc> Increasing con cutoff atoms    38   40 from     0.20803E-01 to     0.22407E-01 ref=     2.5675    
 checkperc> Increasing con cutoff atoms    40   45 from     0.16331E-02 to     0.26267E-02 ref=     2.1596    
 checkperc> Increasing con cutoff atoms    89   92 from     0.16087E-01 to     0.16453E-01 ref=     1.9994    
 checkperc> Increasing con cutoff atoms    91   94 from     0.52970E-01 to     0.55238E-01 ref=     2.4524    
 Connection established between members of the U set.

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                     924 steps. Energy=    -395.3583493       time=       3.04
 Minus side of path:                     873 steps. Energy=    -390.4787888       time=       2.02

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -395.3583493  5.8020         -389.5563691 0.92242         -390.4787888  16.323  14.107  11.480  12.631
        *NEW* (Placed in 5)                                     Known (#4)
 checkperc> Increasing con cutoff atoms    34   38 from     0.11063E-01 to     0.14646E-01 ref=     2.4487    
 checkperc> Increasing con cutoff atoms    36   38 from     0.34052E-02 to     0.37731E-02 ref=     1.4561    
 checkperc> Increasing con cutoff atoms    36   50 from     0.79303E-01 to     0.81363E-01 ref=     2.4679    
 checkperc> Increasing con cutoff atoms    40   44 from     0.74166E-03 to     0.10355E-02 ref=     1.3809    
 checkperc> Increasing con cutoff atoms    40   46 from     0.57500E-02 to     0.89213E-02 ref=     3.1093    
 checkperc> Increasing con cutoff atoms    42   44 from     0.18408E-02 to     0.23688E-02 ref=     2.1533    
 checkperc> Increasing con cutoff atoms    42   45 from     0.10926E-02 to     0.13738E-02 ref=     1.3375    
 checkperc> Increasing con cutoff atoms    42   47 from     0.72034E-03 to     0.84861E-03 ref=     1.3723    
 checkperc> Increasing con cutoff atoms    42   48 from     0.30293E-02 to     0.30672E-02 ref=     2.7037    
 checkperc> Increasing con cutoff atoms    42   49 from     0.30614E-02 to     0.33266E-02 ref=     2.3324    
 checkperc> Increasing con cutoff atoms    44   46 from     0.31757E-02 to     0.65888E-02 ref=     2.0483    
 checkperc> Increasing con cutoff atoms    89   92 from     0.16453E-01 to     0.16695E-01 ref=     1.9994    
 checkperc> Increasing con cutoff atoms    91   94 from     0.55238E-01 to     0.57893E-01 ref=     2.4524    
 Connection established between members of the U set.

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                     925 steps. Energy=    -394.9216256       time=       2.29
 Minus side of path:                     921 steps. Energy=    -395.3198837       time=       2.32

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -394.9216256  1.2371         -393.6845693  1.6353         -395.3198837  14.738  13.526  14.507   9.995
        *NEW* (Placed in 6)                                     *NEW* (Placed in 7)
 checkperc> Increasing con cutoff atoms    38   47 from     0.13393     to     0.15052     ref=     5.6336    
 checkperc> Increasing con cutoff atoms    39   50 from     0.29010E-01 to     0.29129E-01 ref=     2.5089    
 checkperc> Increasing con cutoff atoms    40   45 from     0.26267E-02 to     0.28015E-02 ref=     2.1596    
 checkperc> Increasing con cutoff atoms    40   47 from     0.58663E-02 to     0.81515E-02 ref=     3.4444    
 checkperc> Increasing con cutoff atoms    40   49 from     0.81810E-02 to     0.11089E-01 ref=     4.0174    
 checkperc> Increasing con cutoff atoms    41   42 from     0.14773E-02 to     0.20408E-02 ref=     1.3588    
 checkperc> Increasing con cutoff atoms    41   44 from     0.18040E-02 to     0.21703E-02 ref=     2.2652    
 checkperc> Increasing con cutoff atoms    43   48 from     0.60144E-03 to     0.84491E-03 ref=     1.3869    
 checkperc> Increasing con cutoff atoms    43   49 from     0.21463E-02 to     0.29237E-02 ref=     2.4274    
 checkperc> Increasing con cutoff atoms    44   45 from     0.10193E-02 to     0.12936E-02 ref=     1.3184    
 checkperc> Increasing con cutoff atoms    44   47 from     0.62225E-02 to     0.11053E-01 ref=     3.4540    
 checkperc> Increasing con cutoff atoms    44   48 from     0.10893E-01 to     0.12061E-01 ref=     4.4865    
 checkperc> Increasing con cutoff atoms    44   49 from     0.99759E-02 to     0.14723E-01 ref=     4.4288    
 checkperc> Increasing con cutoff atoms    45   47 from     0.57186E-02 to     0.84258E-02 ref=     2.3784    
 checkperc> Increasing con cutoff atoms    45   48 from     0.82987E-02 to     0.85867E-02 ref=     4.0115    
 checkperc> Increasing con cutoff atoms    45   49 from     0.80318E-02 to     0.10472E-01 ref=     3.5769    
 checkperc> Increasing con cutoff atoms    47   49 from     0.59375E-03 to     0.66815E-03 ref=     1.3864    
 checkperc> Increasing con cutoff atoms    48   49 from     0.10204E-02 to     0.14655E-02 ref=     1.3929    
 checkperc> Increasing con cutoff atoms    34   38 from     0.14646E-01 to     0.15640E-01 ref=     2.4487    
 checkperc> Increasing con cutoff atoms    36   38 from     0.37731E-02 to     0.40637E-02 ref=     1.4561    
 checkperc> Increasing con cutoff atoms    36   50 from     0.81363E-01 to     0.86255E-01 ref=     2.4679    
 checkperc> Increasing con cutoff atoms    40   46 from     0.89213E-02 to     0.89525E-02 ref=     3.1093    
 checkperc> Increasing con cutoff atoms    40   48 from     0.90324E-02 to     0.92790E-02 ref=     3.6642    
 checkperc> Increasing con cutoff atoms    41   43 from     0.86943E-03 to     0.91355E-03 ref=     1.3744    
 checkperc> Increasing con cutoff atoms    42   47 from     0.84861E-03 to     0.10838E-02 ref=     1.3723    
 checkperc> Increasing con cutoff atoms    42   48 from     0.30672E-02 to     0.35152E-02 ref=     2.7037    
 checkperc> Increasing con cutoff atoms    42   49 from     0.33266E-02 to     0.39017E-02 ref=     2.3324    
 checkperc> Increasing con cutoff atoms   122  124 from     0.60793E-02 to     0.61481E-02 ref=     2.1496    
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 2 >>>>>>>>>>>>>>>>>>>>> 7 minima and 3 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      6 steps with      3 missing connections, weight=     2078.4    
 decide> The unconnected minima in the chain and their distances are:
     2        7.53     6     7        1.47     5     3       11.80     1 
 

 tryconnect> Interpolation for minima 2_F and 6_U using 3 initial images  (interp attempt #1)  ...
 intlbfgs> Maximum number of steps for constraint potential phase is 300001
 intlbfgs> Total number of atoms moving less than threshold=   139
 intlbfgs> Freezing    130 atoms
 intlbfgs> constrained potential finished, time=       0.0
 intlbfgs> switch on true potential at step     16 fraction=    0.990000 images=     3 time=       0.0
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After     41 steps, energy/image=    -387.9904565     RMS=2.587086558     images=   3
 intlbfgs> First  minimum number      2
 intlbfgs> Second minimum number      6
 intlbfgs> DNEB for minima      2     6 dist=   14.35     Attempts, images and iterations=     0     4   140
 lbfgs> Final DNEB force constant      7.462153966    
 Double-ended search iterations= 140 RMS= 3.1585 Dev= 2.55% S= 7.71 time= 0.82
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         30
 DNEB run yielded 1 true transition state(s) time=   4.28

 >>>>>  Path run for ts 4 ...
 Plus  side of path:                     892 steps. Energy=    -394.9216256       time=       2.66
 Minus side of path:                     921 steps. Energy=    -395.0968200       time=       3.00

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -394.9216256  1.0226         -393.8989985  1.1978         -395.0968200   6.976   5.912   6.210  23.351
        Known (#6)                                              *NEW* (Placed in 8)
 checkperc> Increasing con cutoff atoms   124  125 from     0.37594E-02 to     0.39467E-02 ref=     1.3171    
 checkperc> Increasing con cutoff atoms   124  126 from     0.14135E-01 to     0.15457E-01 ref=     2.0489    
 Connection established between members of the U set.

 tryconnect> Interpolation for minima 5_U and 7_U using 3 initial images  (interp attempt #1)  ...
 intlbfgs> Maximum number of steps for constraint potential phase is 300001
 intlbfgs> Total number of atoms moving less than threshold=   145
 intlbfgs> Freezing    130 atoms
 intlbfgs> constrained potential finished, time=       0.0
 intlbfgs> switch on true potential at step     16 fraction=    0.990000 images=     3 time=       0.0
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After     41 steps, energy/image=    -391.3650785     RMS=.9907619444E-01 images=   3
 intlbfgs> First  minimum number      5
 intlbfgs> Second minimum number      7
 intlbfgs> DNEB for minima      5     7 dist=   1.922     Attempts, images and iterations=     0     2    70
 lbfgs> Final DNEB force constant      7.462153966    
 Double-ended search iterations= 70 RMS= 0.0268 Dev= 0.60% S= 1.47 time= 0.21
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         12
 DNEB run yielded 1 true transition state(s) time=   3.10

 >>>>>  Path run for ts 5 ...
 Plus  side of path:                     883 steps. Energy=    -395.3198837       time=       2.56
 Minus side of path:                     843 steps. Energy=    -395.3583493       time=       2.50

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -395.3198837 0.23765E-01     -395.2961192 0.62230E-01     -395.3583493   1.472   1.469   3.037  47.744
        Known (#7)                                              Known (#5)
 Connection established between members of the U set.

 tryconnect> Interpolation for minima 1_S and 3_U using 3 initial images  (interp attempt #1)  ...
 intlbfgs> Maximum number of steps for constraint potential phase is 300001
 intlbfgs> Total number of atoms moving less than threshold=    99
 intlbfgs> constrained potential finished, time=       0.0
 intlbfgs> switch on true potential at step     48 fraction=    0.990000 images=     3 time=       0.0
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After     73 steps, energy/image=    -372.9998687     RMS=2.344054139     images=   3
 intlbfgs> First  minimum number      1
 intlbfgs> Second minimum number      3
 intlbfgs> DNEB for minima      1     3 dist=   17.96     Attempts, images and iterations=     0     5   175
 lbfgs> Final DNEB force constant      4.810170981    
 Double-ended search iterations= 175 RMS= 0.0170 Dev= 0.42% S= 11.82 time= 1.16
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):         28
 DNEB run yielded 1 true transition state(s) time=   3.66

 >>>>>  Path run for ts 6 ...
 Plus  side of path:                     952 steps. Energy=    -382.1773825       time=       2.22
 Minus side of path:                     981 steps. Energy=    -382.5427530       time=       2.40

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -382.1773825 0.85218E-01     -382.0921640 0.45059         -382.5427530  12.375  11.799   2.247  64.529
        Known (#1)                                              Known (#3)
 Unconnected minimum 3 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 3 >>>>>>>>>>>>>>>>>>>>> 8 minima and 6 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      7 steps with      1 missing connections, weight=     53.626    
 decide> The unconnected minima in the chain and their distances are:
     2        3.77     8 
 

 tryconnect> Interpolation for minima 2_F and 8_S using 3 initial images  (interp attempt #1)  ...
 intlbfgs> Maximum number of steps for constraint potential phase is 300001
 intlbfgs> Total number of atoms moving less than threshold=   145
 intlbfgs> Freezing    130 atoms
 intlbfgs> constrained potential finished, time=       0.0
 intlbfgs> switch on true potential at step     16 fraction=    0.990000 images=     3 time=       0.0
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After     41 steps, energy/image=    -391.0598023     RMS=.4316520400E-01 images=   3
 intlbfgs> First  minimum number      2
 intlbfgs> Second minimum number      8
 intlbfgs> DNEB for minima      2     8 dist=   3.974     Attempts, images and iterations=     0     2    70
 lbfgs> Final DNEB force constant      5.568374182    
 Double-ended search iterations= 70 RMS= 0.1138 Dev= 0.70% S= 3.77 time= 0.21
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         19
 DNEB run yielded 1 true transition state(s) time=   3.15

 >>>>>  Path run for ts 7 ...
 Plus  side of path:                     912 steps. Energy=    -395.0968200       time=       2.25
 Minus side of path:                     897 steps. Energy=    -395.0112249       time=       2.21

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -395.0968200 0.11704         -394.9797827 0.31442E-01     -395.0112249   3.780   3.767   2.230  65.019
        Known (#8)                                              Known (#2)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   6     -382.1773825 0.85218E-01    -382.0921640 0.45059        -382.5427530  12.375  11.799   2.247  64.529
   1     -382.5427530  5.7127        -376.8300957  13.649        -390.4787888  37.663  26.046   7.914  18.323
   2     -390.4787888 0.92242        -389.5563691  5.8020        -395.3583493  16.323  14.107  11.480  12.631
   5     -395.3583493 0.62230E-01    -395.2961192 0.23765E-01    -395.3198837   1.472   1.469   3.037  47.744
   3     -395.3198837  1.6353        -393.6845693  1.2371        -394.9216256  14.738  13.526  14.507   9.995
   4     -394.9216256  1.0226        -393.8989985  1.1978        -395.0968200   6.976   5.912   6.210  23.351
   7     -395.0968200 0.11704        -394.9797827 0.31442E-01    -395.0112249   3.780   3.767   2.230  65.019

 Number of TS in the path       =      7
 Number of cycles               =      3

 Elapsed time=                                79.79
 OPTIM> # of energy calls=                         10 time=           0.01 %=  0.0
 OPTIM> # of energy+gradient calls=             30447 time=          41.59 %= 52.1
 OPTIM> # of energy+gradient+Hessian calls=       182 time=           0.84 %=  1.0
