
 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 10:34:38 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=    -394.1455389     RMS force=    0.9094437648E-06
 OPTIM> Final energy  =    -386.2961324     RMS force=    0.9288106084E-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      31.58071509    
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 1 >>>>>>>>>>>>>>>>>>>>> 2 minima and 0 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      1 steps with      1 missing connections, weight=     31469.    
 decide> The unconnected minima in the chain and their distances are:
     2       31.54     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    264 fraction=    0.990000 images=     3 time=       0.3
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After    289 steps, energy/image=    -374.5412841     RMS=2.596824193     images=   4
 intlbfgs> First  minimum number      1
 intlbfgs> Second minimum number      2
 intlbfgs> DNEB for minima      1     2 dist=   36.61     Attempts, images and iterations=     0    10   350
 lbfgs> Final DNEB force constant     0.3286616756    
 Double-ended search iterations= 350 RMS= 0.0422 Dev= 1.49% S= 36.16 time= 5.26
 Following    1 images are candidates for TS:    9  
 Converged to TS (number of iterations):         20
 DNEB run yielded 1 true transition state(s) time=   3.71

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                     934 steps. Energy=    -386.3634860       time=       2.23
 Minus side of path:                    1164 steps. Energy=    -391.6898575       time=       3.35

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -386.3634860 0.59301         -385.7704785  5.9194         -391.6898575  21.966  19.281   1.996  72.634
        *NEW* (Placed in 3)                                     *NEW* (Placed in 4)
 checkperc> Increasing con cutoff atoms    17   21 from     0.75102E-02 to     0.83623E-02 ref=     2.0782    
 checkperc> Increasing con cutoff atoms    25   27 from     0.44715E-02 to     0.45316E-02 ref=     1.3313    
 checkperc> Increasing con cutoff atoms    33   34 from     0.50956E-01 to     0.52572E-01 ref=     3.8642    
 checkperc> Increasing con cutoff atoms    55   56 from     0.89533E-02 to     0.92335E-02 ref=     1.5287    
 checkperc> Increasing con cutoff atoms    55   57 from     0.44015E-01 to     0.50526E-01 ref=     2.5744    
 checkperc> Increasing con cutoff atoms    13   14 from     0.59010E-02 to     0.62819E-02 ref=     1.5327    
 checkperc> Increasing con cutoff atoms    13   15 from     0.35493E-01 to     0.43427E-01 ref=     2.5780    
 checkperc> Increasing con cutoff atoms    15   17 from     0.35838E-02 to     0.42954E-02 ref=     2.1254    
 checkperc> Increasing con cutoff atoms    18   21 from     0.15673E-01 to     0.17298E-01 ref=     4.4085    
 checkperc> Increasing con cutoff atoms    21   23 from     0.23873E-01 to     0.29097E-01 ref=     4.7212    
 checkperc> Increasing con cutoff atoms    21   24 from     0.28739E-01 to     0.32782E-01 ref=     4.0447    
 checkperc> Increasing con cutoff atoms    27   31 from     0.89783E-01 to     0.10365     ref=     2.6629    
 checkperc> Increasing con cutoff atoms    28   29 from     0.12534E-01 to     0.16551E-01 ref=     2.0958    
 checkperc> Increasing con cutoff atoms    29   36 from     0.38351E-01 to     0.40885E-01 ref=     2.4544    
 checkperc> Increasing con cutoff atoms    30   33 from     0.11477E-02 to     0.15313E-02 ref=     1.5220    
 checkperc> Increasing con cutoff atoms    30   34 from     0.28529E-01 to     0.31399E-01 ref=     2.5469    
 checkperc> Increasing con cutoff atoms    33   34 from     0.52572E-01 to     0.65442E-01 ref=     3.8642    
 checkperc> Increasing con cutoff atoms    35   36 from     0.12757E-01 to     0.18475E-01 ref=     2.2424    
 checkperc> Increasing con cutoff atoms    56   57 from     0.42820E-02 to     0.52142E-02 ref=     1.5236    
 checkperc> Increasing con cutoff atoms    57   58 from     0.34386E-02 to     0.49356E-02 ref=     1.2320    
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 2 >>>>>>>>>>>>>>>>>>>>> 4 minima and 1 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      3 steps with      2 missing connections, weight=     19901.    
 decide> The unconnected minima in the chain and their distances are:
     2        2.24     3     4       27.07     1 
 

 tryconnect> Interpolation for minima 2_F 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=   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=    -382.4507543     RMS=.3309028114E-01 images=   3
 intlbfgs> First  minimum number      2
 intlbfgs> Second minimum number      3
 intlbfgs> DNEB for minima      2     3 dist=   2.419     Attempts, images and iterations=     0     2    70
 lbfgs> Final DNEB force constant      6.139132535    
 Double-ended search iterations= 70 RMS= 0.0172 Dev= 0.48% S= 2.24 time= 0.20
 No maximum in profile - using highest image
 Following    0 images are candidates for TS:    1  
 Converged to TS (number of iterations):         38
 DNEB run yielded 1 true transition state(s) time=   3.93

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                     870 steps. Energy=    -386.2961324       time=       2.23
 Minus side of path:                     922 steps. Energy=    -386.3634860       time=       2.23

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -386.2961324 0.81214E-03     -386.2953203 0.68166E-01     -386.3634860   2.240   2.237   3.563  40.690
        Known (#2)                                              Known (#3)
 Unconnected minimum 3 found its way to F set.

 tryconnect> Interpolation for minima 1_S and 4_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=    51
 intlbfgs> constrained potential finished, time=       0.0
 intlbfgs> switch on true potential at step    205 fraction=    0.990000 images=     3 time=       0.2
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After    230 steps, energy/image=    -370.1426548     RMS=1.273341614     images=   4
 intlbfgs> First  minimum number      1
 intlbfgs> Second minimum number      4
 intlbfgs> DNEB for minima      1     4 dist=   32.13     Attempts, images and iterations=     0     9   315
 lbfgs> Final DNEB force constant     0.4624599827    
 Double-ended search iterations= 315 RMS= 0.0978 Dev= 1.51% S= 32.67 time= 4.24
 Following    1 images are candidates for TS:    6  
 Converged to TS (number of iterations):         55
 DNEB run yielded 1 true transition state(s) time=   5.10

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                     948 steps. Energy=    -393.2137112       time=       2.35
 Minus side of path:                    1012 steps. Energy=    -394.1455389       time=       2.66

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -393.2137112  4.2033         -389.0104323  5.1351         -394.1455389  26.612  17.590   9.162  15.826
        *NEW* (Placed in 5)                                     Known (#1)
 checkperc> Increasing con cutoff atoms    16   19 from     0.42026E-02 to     0.46449E-02 ref=     2.2644    
 checkperc> Increasing con cutoff atoms    17   19 from     0.37473E-02 to     0.43176E-02 ref=     2.1524    
 checkperc> Increasing con cutoff atoms    51   52 from     0.13664E-01 to     0.16311E-01 ref=     2.2480    
 Unconnected minimum 5 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 3 >>>>>>>>>>>>>>>>>>>>> 5 minima and 3 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      4 steps with      1 missing connections, weight=     6331.2    
 decide> The unconnected minima in the chain and their distances are:
     4       18.48     5 
 

 tryconnect> Interpolation for minima 4_F and 5_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=    66
 intlbfgs> constrained potential finished, time=       0.0
 intlbfgs> switch on true potential at step     91 fraction=    0.990000 images=     3 time=       0.1
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After    116 steps, energy/image=    -224.0801478     RMS=41.06089479     images=   3
 intlbfgs> First  minimum number      4
 intlbfgs> Second minimum number      5
 intlbfgs> DNEB for minima      4     5 dist=   23.84     Attempts, images and iterations=     0     7   245
 lbfgs> Final DNEB force constant      1.009492144    
 Double-ended search iterations= 245 RMS= 0.0924 Dev= 1.47% S= 19.20 time= 2.56
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):         34
 DNEB run yielded 1 true transition state(s) time=   4.87

 >>>>>  Path run for ts 4 ...
 Plus  side of path:                     925 steps. Energy=    -393.2137112       time=       2.97
 Minus side of path:                     937 steps. Energy=    -391.6898575       time=       2.42

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -393.2137112  3.1432         -390.0704901  1.6194         -391.6898575  19.696  18.483   3.361  43.142
        Known (#5)                                              Known (#4)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   3     -394.1455389  5.1351        -389.0104323  4.2033        -393.2137112  26.612  17.590   9.162  15.826
   4     -393.2137112  3.1432        -390.0704901  1.6194        -391.6898575  19.696  18.483   3.361  43.142
   1     -391.6898575  5.9194        -385.7704785 0.59301        -386.3634860  21.966  19.281   1.996  72.634
   2     -386.3634860 0.68166E-01    -386.2953203 0.81214E-03    -386.2961324   2.240   2.237   3.563  40.690

 Number of TS in the path       =      4
 Number of cycles               =      3

 Elapsed time=                                51.75
 OPTIM> # of energy calls=                          8 time=           0.01 %=  0.0
 OPTIM> # of energy+gradient calls=             19986 time=          28.68 %= 55.4
 OPTIM> # of energy+gradient+Hessian calls=       147 time=           0.66 %=  1.3
