
 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     79
 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=     8
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)@comp35.ch.
                 Created on  5/28/12 at 10:24:41 by user: wales       

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

 RDTITL> *
 RDTITL> No title read.

      ***** LEVEL  1 WARNING FROM <RDTITL> *****
      ***** Title expected.
      ******************************************
      BOMLEV (  0) IS NOT REACHED. WRNLEV IS  5

  
 CHARMM>    BOMLev -5
 MISCOM> Setting BOMLev < -2 is NOT a good idea.
 Parameter: TOP <- "toph19_eef1_bs360.inp"
 Parameter: PAR <- "param19_eef1_bs360.inp"
  
 CHARMM>    WRNLEV -1
  
 CHARMM>    PRNLEV 2
 Parameter: 0 <- "/HOME/BS360/C31A2-SAT39/TOPPAR"
 VOPEN> Attempting to open::/home/bs360/c31a2-sat39/toppar/toph19_eef1_bs360.inp::
 OPNLGU> Unit  1 opened for READONLY access to /home/bs360/c31a2-sat39/toppar/toph19_eef1_bs360.inp
 MAINIO> Residue topology file being read from unit   1.
 TITLE> * TOPOLOGY FILE FOR PROTEINS USING EXPLICIT HYDROGEN ATOMS: VERSION 19
 TITLE> * S TRYGUBENKO: ASN, GLN AND TYR DIHEDRALS AND CTER IMPROPER WERE
 TITLE> * SYMMETRIZED TO ENSURE THAT ROTAMERS OF THESE RESIDUES HAVE THE SAME
 TITLE> * ENERGIES AND GEOMETRIES. VISIT HTTP://WWW.TRYGUB.COM/CHARMM/ROTAMERS/
 TITLE> * FOR MORE INFORMATION. UNSUPPORTED. USE THIS FILE AT YOUR OWN RISK.
 TITLE> * MODIFICATIONS ARE MARKED WITH SAT AND DAE.
 TITLE> * ALSO, TOPOLOGY FOR D-PROLINE (DPR) RESIDUE WAS ADDED.
 TITLE> * * T. LAZARIDIS: HERE THE IONIC SIDECHAINS AND TERMINI ARE NEUTRALIZED
 TITLE> * ALSO, A NEW ATOM TYPE HAS BEEN ADDED, CR, FOR 4-BONDED CARBON IN
 TITLE> * AROMATICS AND ARGININE. MODIFICATIONS ARE MARKED BY TL
 TITLE> *
 VCLOSE: Closing unit    1 with status "KEEP"
 VOPEN> Attempting to open::/home/bs360/c31a2-sat39/toppar/param19_eef1_bs360.inp::
 OPNLGU> Unit  2 opened for READONLY access to /home/bs360/c31a2-sat39/toppar/param19_eef1_bs360.inp

          PARAMETER FILE BEING READ FROM UNIT  2
 TITLE> * - PARAMETER FILE PARAM19 * S TRYGUBENKO: ASN, GLN AND TYR DIHEDRALS AND CTER IMPROPER WERE
 TITLE> * SYMMETRIZED TO ENSURE THAT ROTAMERS OF THESE RESIDUES HAVE THE SAME
 TITLE> * ENERGIES AND GEOMETRIES. VISIT HTTP://WWW.TRYGUB.COM/CHARMM/ROTAMERS/
 TITLE> * FOR MORE INFORMATION. UNSUPPORTED. USE THIS FILE AT YOUR OWN RISK.
 TITLE> * MODIFICATIONS ARE MARKED WITH SAT AND DAE.
 TITLE> * * PEPTIDE GEOMETRY FROM RAMACHANDRAN ET AL BBA 359:298 (1974)
 TITLE> * TORSIONS FROM HAGLER ET AL JACS 98:4600 (1976)
 TITLE> * JORGENSEN NONBOND PARAMETERS JACS 103:3976-3985 WITH 1-4 RC=1.80/0.1
 TITLE> *
 VCLOSE: Closing unit    2 with status "KEEP"
 MAINIO> Sequence information being read from unit   5.
 RDTITL> *

          RESIDUE SEQUENCE --     7 RESIDUES
          GLY ASN ASN GLN GLN ASN TYR 
 THE PATCH 'NTER' WILL BE USED FOR THE FIRST RESIDUE
 THE PATCH 'CTER' WILL BE USED FOR THE LAST  RESIDUE
 GENPSF> Segment   1 has been generated. Its identifier is SEG1.
 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared.
 PSFSUM> Summary of the structure file counters :
         Number of segments      =        1   Number of residues   =        7
         Number of atoms         =       79   Number of groups     =       33
         Number of bonds         =       79   Number of angles     =      113
         Number of dihedrals     =       48   Number of impropers  =       37
         Number of cross-terms   =        0
         Number of HB acceptors  =       14   Number of HB donors  =       20
         Number of NB exclusions =        3   Total charge =    0.00000
 VOPEN> Attempting to open::input.crd::
 OPNLGU> Unit 20 opened for READONLY access to input.crd
          SPATIAL COORDINATES BEING READ FROM UNIT 20
 TITLE> 79
 VCLOSE: Closing unit   20 with status "KEEP"

 NONBOND OPTION FLAGS: 
     ELEC     VDW      GROUps   RDIElec  SWITch   VGROup   VSWItch 
     BYGRoup  NOEXtnd  NOEWald 
 CUTNB  = 15.000 CTEXNB =999.000 CTONNB =  7.000 CTOFNB =  9.000
 WMIN   =  1.500 WRNMXD =  0.500 E14FAC =  0.400 EPS    =  1.000
 NBXMOD =      5
 There are        0 atom  pairs and        0 atom  exclusions.
 There are        0 group pairs and        0 group exclusions.
 <MAKINB> with mode   5 found    195 exclusions and    129 interactions(1-4)
 VOPEN> Attempting to open::/home/bs360/c31a2-sat39/toppar/solvpar.inp::
 OPNLGU> Unit 30 opened for READONLY access to /home/bs360/c31a2-sat39/toppar/solvpar.inp
 NBOND           79
 NTHETA          113
 NPHI           48

chsetdihe> number of internal coordinates for segment    1
 chsetdihe> NPHIPSI           14
 chsetdihe> NOMEGAC            6
 chsetdihe> NSIDECHAIN           15
 chsetdihe> NCHIRAL            6

chsetdihe> total number of internal coordinates
 chsetdihe> NPHIPSITOT=            14
 chsetdihe> NOMEGACTOT=             6
 chsetdihe> NSIDECHAINTOT=            15
 chsetdihe> NCHIRALTOT=             6

 chsetdihe>            29  twistable dihedrals identified
chsetdihe> SEG-NR, NSEGATOMS :    1      79

 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>  237 Cartesian coordinates will be optimised for   79 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=    -296.2829535     RMS force=    0.8609684691E-06
 OPTIM> Final energy  =    -294.5394422     RMS force=    0.7861692102E-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      14.17789026    
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 1 >>>>>>>>>>>>>>>>>>>>> 2 minima and 0 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      1 steps with      1 missing connections, weight=     774.93    
 decide> The unconnected minima in the chain and their distances are:
     2        9.17     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=    67
 intlbfgs> Freezing     64 atoms
 intlbfgs> constrained potential finished, time=       0.0
 intlbfgs> switch on true potential at step    118 fraction=    0.990000 images=     3 time=       0.0
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After    143 steps, energy/image=    -282.4538090     RMS=1.529766824     images=   3
 intlbfgs> First  minimum number      1
 intlbfgs> Second minimum number      2
 intlbfgs> DNEB for minima      1     2 dist=   14.94     Attempts, images and iterations=     0     4   140
 lbfgs> Final DNEB force constant      2.812407350    
 Double-ended search iterations= 140 RMS= 0.5690 Dev= 1.49% S= 13.53 time= 0.35
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         42
 DNEB run yielded 1 true transition state(s) time=   0.93

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                     514 steps. Energy=    -296.2829535       time=       0.43
 Minus side of path:                     477 steps. Energy=    -292.9642712       time=       0.39

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -296.2829535  5.8519         -290.4310337  2.5332         -292.9642712   9.323   8.900   3.951  19.993
        *NEW* (Placed in 3)                                     *NEW* (Placed in 4)
 checkperc> Increasing con cutoff atoms    68   72 from     0.31695E-01 to     0.31894E-01 ref=     2.5247    
 checkperc> Increasing con cutoff atoms    68   70 from     0.27439E-01 to     0.34359E-01 ref=     2.5203    
 checkperc> Increasing con cutoff atoms    68   71 from     0.22409E-01 to     0.31418E-01 ref=     3.7873    
 checkperc> Increasing con cutoff atoms    69   70 from     0.33736E-02 to     0.36976E-02 ref=     1.3821    
 checkperc> Increasing con cutoff atoms    69   71 from     0.87994E-02 to     0.96545E-02 ref=     2.3903    
 checkperc> Increasing con cutoff atoms    69   74 from     0.88422E-02 to     0.91915E-02 ref=     2.7496    
 checkperc> Increasing con cutoff atoms    69   75 from     0.12699E-01 to     0.13099E-01 ref=     4.1288    
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 2 >>>>>>>>>>>>>>>>>>>>> 4 minima and 1 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      2 steps with      2 missing connections, weight=     591.56    
 decide> The unconnected minima in the chain and their distances are:
     2        7.83     3     3        4.79     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=    71
 intlbfgs> Freezing     64 atoms
 intlbfgs> constrained potential finished, time=       0.0
 intlbfgs> switch on true potential at step     64 fraction=    0.990000 images=     3 time=       0.0
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After     89 steps, energy/image=    -289.5376812     RMS=.6385240115     images=   3
 intlbfgs> First  minimum number      2
 intlbfgs> Second minimum number      3
 intlbfgs> DNEB for minima      2     3 dist=   11.39     Attempts, images and iterations=     0     3   105
 lbfgs> Final DNEB force constant      7.835261665    
 Double-ended search iterations= 105 RMS= 0.5347 Dev= 0.69% S= 8.54 time= 0.19
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         39
 DNEB run yielded 1 true transition state(s) time=   0.82

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                     445 steps. Energy=    -296.2829535       time=       0.36
 Minus side of path:                     569 steps. Energy=    -294.5394422       time=       0.50

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -296.2829535  3.7754         -292.5076000  2.0318         -294.5394422  10.214   7.848  11.252   7.021
        Known (#3)                                              Known (#2)
 Unconnected minimum 3 found its way to F set.

 checkpair> Energies of the minima in the pair     1    3 are the same - checking distance ...

 tryconnect> Interpolation for minima 1_S and 3_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=    75
 intlbfgs> Freezing     64 atoms
 intlbfgs> constrained potential finished, time=       0.0
 intlbfgs> switch on true potential at step    169 fraction=    0.990000 images=     2 time=       0.0
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After    194 steps, energy/image=    -17.14251288     RMS=193.7778680     images=   2
 intlbfgs> First  minimum number      1
 intlbfgs> Second minimum number      3
 intlbfgs> DNEB for minima      1     3 dist=   13.89     Attempts, images and iterations=     0     4   140
 lbfgs> Final DNEB force constant      8.227024748    
 Double-ended search iterations= 140 RMS= 0.4753 Dev= 0.97% S= 8.45 time= 0.34
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):         43
 DNEB run yielded 1 true transition state(s) time=   0.90
 isnewts> transition state is the same as number        1 energy=     -290.4310336579
 tryconnect> Try the path again for ts      1 with pushoff=    0.1000000000E-01

 >>>>>  Path run for ts 3 ...
 tryconnect> Trying this transition state path again with pushoff=    0.1000000000E-01
 Plus  side of path:                     504 steps. Energy=    -296.2829535       time=       0.42
 Minus side of path:                     489 steps. Energy=    -292.9642712       time=       0.40

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -296.2829535  5.8519         -290.4310337  2.5332         -292.9642712   9.323   8.900   3.931  20.097
        Known (#3)                                              Known (#4)
 Alternative path found between members of the F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 3 >>>>>>>>>>>>>>>>>>>>> 4 minima and 3 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      2 steps with      1 missing connections, weight=     221.44    
 decide> The unconnected minima in the chain and their distances are:
     3        4.79     1 
 

 checkpair> Energies of the minima in the pair     1    3 are the same - checking distance ...

 tryconnect> Interpolation for minima 1_S and 3_F using 15 initial images  (interp attempt #2)  ...
 tryconnect> Changing to an even number of images for possible permutational isomer
 intlbfgs> Maximum number of steps for constraint potential phase is 300001
 intlbfgs> Total number of atoms moving less than threshold=    75
 intlbfgs> Freezing     64 atoms
 intlbfgs> constrained potential finished, time=       0.0
 intlbfgs> switch on true potential at step     93 fraction=    0.990000 images=    12 time=       0.0
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After    118 steps, energy/image=    -291.3227765     RMS=1.516051260     images=  11
 intlbfgs> First  minimum number      1
 intlbfgs> Second minimum number      3
 intlbfgs> DNEB for minima      1     3 dist=   7.407     Attempts, images and iterations=     1    17   595
 lbfgs> Final DNEB force constant     0.6197406068    
 Double-ended search iterations= 595 RMS= 0.1022 Dev= 3.10% S= 21.98 time= 5.98
 Following    2 images are candidates for TS:    8   12  
 Converged to TS (number of iterations):         27
 Converged to TS (number of iterations):         12
 DNEB run yielded 2 true transition state(s) time=   1.16
 isnewts> transition state is the same as number        1 energy=     -290.4310336579
 tryconnect> Will not repeat search for TS      2 same as TS      1

 >>>>>  Path run for ts 4 ...
 Plus  side of path:                     529 steps. Energy=    -295.5387767       time=       0.44
 Minus side of path:                     537 steps. Energy=    -296.2829535       time=       0.46

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -295.5387767  3.3934         -292.1453382  4.1376         -296.2829535  13.605  10.989   4.613  17.126
        *NEW* (Placed in 5)                                     Known (#1)
 Unconnected minimum 5 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 4 >>>>>>>>>>>>>>>>>>>>> 5 minima and 4 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      4 steps with      1 missing connections, weight=     51.674    
 decide> The unconnected minima in the chain and their distances are:
     4        3.72     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=    74
 intlbfgs> Freezing     64 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=    -276.8890775     RMS=16.09866634     images=   3
 intlbfgs> First  minimum number      4
 intlbfgs> Second minimum number      5
 intlbfgs> DNEB for minima      4     5 dist=   11.59     Attempts, images and iterations=     0     3   105
 lbfgs> Final DNEB force constant      11.57625000    
 Double-ended search iterations= 105 RMS= 0.2032 Dev= 0.91% S= 3.83 time= 0.19
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         15
 DNEB run yielded 1 true transition state(s) time=   0.54

 >>>>>  Path run for ts 5 ...
 Plus  side of path:                     432 steps. Energy=    -292.9642712       time=       0.34
 Minus side of path:                     496 steps. Energy=    -295.5387767       time=       0.41

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -292.9642712 0.13841         -292.8258607  2.7129         -295.5387767   4.018   3.721   6.560  12.042
        Known (#4)                                              Known (#5)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   4     -296.2829535  4.1376        -292.1453382  3.3934        -295.5387767  13.605  10.989   4.613  17.126
   5     -295.5387767  2.7129        -292.8258607 0.13841        -292.9642712   4.018   3.721   6.560  12.042
   1     -292.9642712  2.5332        -290.4310337  5.8519        -296.2829535   9.323   8.900   3.951  19.993
   2     -296.2829535  3.7754        -292.5076000  2.0318        -294.5394422  10.214   7.848  11.252   7.021

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

 Elapsed time=                                16.45
 OPTIM> # of energy calls=                         10 time=           0.01 %=  0.0
 OPTIM> # of energy+gradient calls=             20482 time=          11.52 %= 70.0
 OPTIM> # of energy+gradient+Hessian calls=       178 time=           0.21 %=  1.3
