
 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)@comp28.ch.
                 Created on  5/28/12 at 10:32:26 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=    -385.3045545     RMS force=    0.9414349091E-06
 OPTIM> Final energy  =    -381.3109698     RMS force=    0.9901354532E-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      62.42793834    
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 1 >>>>>>>>>>>>>>>>>>>>> 2 minima and 0 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      1 steps with      1 missing connections, weight=    0.19409E+06
 decide> The unconnected minima in the chain and their distances are:
     2       57.84     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=    11
 intlbfgs> constrained potential finished, time=       0.0
 intlbfgs> switch on true potential at step   1160 fraction=    0.990000 images=     5 time=       0.9
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After   1185 steps, energy/image=    -301.3277287     RMS=1.287221166     images=   6
 intlbfgs> First  minimum number      1
 intlbfgs> Second minimum number      2
 intlbfgs> DNEB for minima      1     2 dist=   61.52     Attempts, images and iterations=     0    18   630
 lbfgs> Final DNEB force constant     0.2703907739    
 Double-ended search iterations= 630 RMS= 0.0418 Dev= 4.00% S= 73.61 time= 12.94
 Following    2 images are candidates for TS:    5   12  
 Converged to TS (number of iterations):         30
 Converged to TS (number of iterations):        121
 DNEB run yielded 2 true transition state(s) time=  14.23

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                    1030 steps. Energy=    -383.7366609       time=       3.15
 Minus side of path:                    1111 steps. Energy=    -385.3045545       time=       2.99

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -383.7366609 0.91399E-01     -383.6452621  1.6593         -385.3045545  31.297  28.154   2.239  64.768
        *NEW* (Placed in 3)                                     Known (#1)
 Unconnected minimum 3 found its way to S set.

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                    1002 steps. Energy=    -377.5175935       time=       2.39
 Minus side of path:                    2059 steps. Energy=    -390.0195607       time=       9.93

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -377.5175935 0.12907E-01     -377.5046865  12.515         -390.0195607  60.304  58.898   1.620  89.510
        *NEW* (Placed in 4)                                     *NEW* (Placed in 5)
 checkperc> Increasing con cutoff atoms    29   38 from     0.28009E-01 to     0.31371E-01 ref=     3.8219    
 checkperc> Increasing con cutoff atoms    36   38 from     0.34052E-02 to     0.41658E-02 ref=     1.4561    
 checkperc> Increasing con cutoff atoms    41   43 from     0.86943E-03 to     0.92490E-03 ref=     1.3744    
 checkperc> Increasing con cutoff atoms    52   53 from     0.39407E-02 to     0.41387E-02 ref=    0.98265    
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 2 >>>>>>>>>>>>>>>>>>>>> 5 minima and 2 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      2 steps with      1 missing connections, weight=     50338.    
 decide> The unconnected minima in the chain and their distances are:
     2       36.89     3 
 

 tryconnect> Interpolation for minima 2_F and 3_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=    10
 intlbfgs> constrained potential finished, time=       0.0
 intlbfgs> switch on true potential at step    286 fraction=    0.990000 images=     3 time=       0.3
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After    311 steps, energy/image=    -367.2422196     RMS=1.413471929     images=   4
 intlbfgs> First  minimum number      2
 intlbfgs> Second minimum number      3
 intlbfgs> DNEB for minima      2     3 dist=   41.28     Attempts, images and iterations=     0    12   420
 lbfgs> Final DNEB force constant     0.2452524026    
 Double-ended search iterations= 420 RMS= 0.0797 Dev= 4.70% S= 47.26 time= 5.70
 Following    2 images are candidates for TS:    3    5  
 Converged to TS (number of iterations):         27
 Converged to TS (number of iterations):         31
 DNEB run yielded 2 true transition state(s) time=   9.09

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                    1325 steps. Energy=    -385.0722818       time=       4.20
 Minus side of path:                     996 steps. Energy=    -381.3109698       time=       2.39

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -385.0722818  6.8547         -378.2175717  3.0934         -381.3109698  52.510  42.468   2.347  61.771
        *NEW* (Placed in 6)                                     Known (#2)
 Unconnected minimum 6 found its way to F set.

 >>>>>  Path run for ts 4 ...
 Plus  side of path:                    1361 steps. Energy=    -383.8347763       time=       4.89
 Minus side of path:                    1565 steps. Energy=    -385.0722818       time=       6.01

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -383.8347763  4.3945         -379.4402855  5.6320         -385.0722818  71.102  48.728   2.088  69.431
        *NEW* (Placed in 7)                                     Known (#6)
 Unconnected minimum 7 found its way to F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 3 >>>>>>>>>>>>>>>>>>>>> 7 minima and 4 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      4 steps with      1 missing connections, weight=     1.1438    
 decide> The unconnected minima in the chain and their distances are:
     7        1.04     3 
 

 tryconnect> Interpolation for minima 3_S and 7_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=   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=    -379.8949093     RMS=.2536455159E-01 images=   3
 intlbfgs> First  minimum number      3
 intlbfgs> Second minimum number      7
 intlbfgs> DNEB for minima      3     7 dist=   1.876     Attempts, images and iterations=     0     2    70
 lbfgs> Final DNEB force constant      9.070294785    
 Double-ended search iterations= 70 RMS= 0.0204 Dev= 0.71% S= 1.05 time= 0.16
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         11
 DNEB run yielded 1 true transition state(s) time=   2.33

 >>>>>  Path run for ts 5 ...
 Plus  side of path:                     994 steps. Energy=    -383.7366609       time=       2.20
 Minus side of path:                     986 steps. Energy=    -383.8347763       time=       2.31

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -383.7366609 0.14941E-01     -383.7217202 0.11306         -383.8347763   1.048   1.045  38.531   3.763
        Known (#3)                                              Known (#7)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   1     -385.3045545  1.6593        -383.6452621 0.91399E-01    -383.7366609  31.297  28.154   2.239  64.768
   5     -383.7366609 0.14941E-01    -383.7217202 0.11306        -383.8347763   1.048   1.045  38.531   3.763
   4     -383.8347763  4.3945        -379.4402855  5.6320        -385.0722818  71.102  48.728   2.088  69.431
   3     -385.0722818  6.8547        -378.2175717  3.0934        -381.3109698  52.510  42.468   2.347  61.771

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

 Elapsed time=                                86.84
 OPTIM> # of energy calls=                          6 time=           0.01 %=  0.0
 OPTIM> # of energy+gradient calls=             34419 time=          38.04 %= 43.8
 OPTIM> # of energy+gradient+Hessian calls=       220 time=           0.95 %=  1.1
