
 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> 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)@comp34.ch.
                 Created on  5/28/12 at 11:53:25 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
 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


 OPTIM> Using translational/rotational ev shift=     1000000.000    
 OPTIM> Initial energy=    -286.0800001     RMS force=    0.8678044785E-06
 OPTIM> Final energy  =    -296.7298141     RMS force=    0.9865836604E-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=     11535.    
 decide> The unconnected minima in the chain and their distances are:
     2       22.59     1 
 

 tryconnect> 210-iteration DNEB run for minima 1_S and 2_F using 6 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      1.288396211    
 Double-ended search iterations= 210 RMS= 0.7749 Dev= 1.45% S= 27.08 time= 0.69
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         68
 DNEB run yielded 1 true transition state(s) time=   1.16

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                     585 steps. Energy=    -295.1362019       time=       0.52
 Minus side of path:                     604 steps. Energy=    -297.0304022       time=       0.52

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -295.1362019  7.0643         -288.0719227  8.9585         -297.0304022  16.650  10.166   2.882  27.414
        *NEW* (Placed in 3)                                     *NEW* (Placed in 4)
 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=     8520.1    
 decide> The unconnected minima in the chain and their distances are:
     2        7.02     4     3       20.14     1 
 

 tryconnect> 70-iteration DNEB run for minima 2_F and 4_U using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      8.227024748    
 Double-ended search iterations= 70 RMS= 2.4065 Dev= 2.56% S= 9.18 time= 0.08
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         66
 DNEB run yielded 1 true transition state(s) time=   1.14

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                     474 steps. Energy=    -296.7298141       time=       0.37
 Minus side of path:                     468 steps. Energy=    -296.7007597       time=       0.36

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -296.7298141 0.58446         -296.1453556 0.55540         -296.7007597   6.538   6.278   2.224  35.527
        Known (#2)                                              *NEW* (Placed in 5)
 Unconnected minimum 5 found its way to F set.

 tryconnect> 210-iteration DNEB run for minima 1_S and 3_U using 6 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      1.288396211    
 Double-ended search iterations= 210 RMS= 0.7930 Dev= 0.35% S= 22.44 time= 0.70
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):         60
 DNEB run yielded 1 true transition state(s) time=   1.04
 isnewts> transition state is the same as number        1 energy=     -288.0719227289
 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:                     595 steps. Energy=    -297.0304022       time=       0.50
 Minus side of path:                     588 steps. Energy=    -295.1362019       time=       0.49

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -297.0304022  8.9585         -288.0719227  7.0643         -295.1362019  16.650  10.164   2.885  27.386
        Known (#4)                                              Known (#3)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 3 >>>>>>>>>>>>>>>>>>>>> 5 minima and 3 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      2 steps with      1 missing connections, weight=     9009.3    
 decide> The unconnected minima in the chain and their distances are:
     5       20.81     1 
 

 tryconnect> 210-iteration DNEB run for minima 1_S and 5_F using 6 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      1.288396211    
 Double-ended search iterations= 210 RMS= 0.3329 Dev= 1.51% S= 24.91 time= 0.69
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         67
 DNEB run yielded 1 true transition state(s) time=   1.15
 isnewts> transition state is the same as number        1 energy=     -288.0719227289
 tryconnect> Will not repeat search for TS      1 same as TS      1
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 4 >>>>>>>>>>>>>>>>>>>>> 5 minima and 3 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      4 steps with      2 missing connections, weight=     11367.    
 decide> The unconnected minima in the chain and their distances are:
     5        5.58     3     4       22.37     1 
 

 tryconnect> 70-iteration DNEB run for minima 3_U and 5_F using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 7.1939 Dev= 2.10% S= 9.23 time= 0.08
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         34
 DNEB run yielded 1 true transition state(s) time=   0.76

 >>>>>  Path run for ts 4 ...
 Plus  side of path:                     466 steps. Energy=    -294.9521054       time=       0.36
 Minus side of path:                     478 steps. Energy=    -295.1362019       time=       0.37

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -294.9521054 0.56751E-01     -294.8953541 0.24085         -295.1362019   2.988   2.978   4.131  19.124
        *NEW* (Placed in 6)                                     *NEW* (Placed in 7)
 Connection established between members of the U set.

 tryconnect> 210-iteration DNEB run for minima 1_S and 4_U using 6 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      1.288396211    
 Double-ended search iterations= 210 RMS= 0.1637 Dev= 1.31% S= 24.68 time= 0.69
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         40
 DNEB run yielded 1 true transition state(s) time=   0.81

 >>>>>  Path run for ts 5 ...
 Plus  side of path:                     542 steps. Energy=    -286.0800001       time=       0.43
 Minus side of path:                     702 steps. Energy=    -297.0304022       time=       0.63

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -286.0800001  1.3906         -284.6893835  12.341         -297.0304022  24.572  22.566   1.995  39.600
        Known (#1)                                              Known (#4)
 Unconnected minimum 4 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 5 >>>>>>>>>>>>>>>>>>>>> 7 minima and 5 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      5 steps with      2 missing connections, weight=     133.54    
 decide> The unconnected minima in the chain and their distances are:
     5        2.86     7     7        4.79     3 
 

 tryconnect> 70-iteration DNEB run for minima 5_F and 7_U using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.5346 Dev= 2.37% S= 3.68 time= 0.08
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         32
 DNEB run yielded 1 true transition state(s) time=   0.73

 >>>>>  Path run for ts 6 ...
 Plus  side of path:                     482 steps. Energy=    -294.9521054       time=       0.38
 Minus side of path:                     492 steps. Energy=    -298.0373891       time=       0.39

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -294.9521054 0.66476E-01     -294.8856291  3.1518         -298.0373891   6.808   6.434   5.187  15.231
        Known (#6)                                              *NEW* (Placed in 8)
 Connection established between members of the U set.

 checkpair> Energies of the minima in the pair     3    7 are the same - checking distance ...

 tryconnect> 70-iteration DNEB run for minima 3_S and 7_U using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      9.070294785    
 Double-ended search iterations= 70 RMS= 1.5341 Dev= 9.98% S= 7.23 time= 0.08
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         19
 DNEB run yielded 1 true transition state(s) time=   0.64

 >>>>>  Path run for ts 7 ...
 Plus  side of path:                     485 steps. Energy=    -293.5965177       time=       0.38
 Minus side of path:                     497 steps. Energy=    -295.1362019       time=       0.39

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -293.5965177 0.81059         -292.7859266  2.3503         -295.1362019   6.215   5.300   5.846  13.514
        *NEW* (Placed in 9)                                     Known (#3)
 Unconnected minimum 9 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 6 >>>>>>>>>>>>>>>>>>>>> 9 minima and 7 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      6 steps with      2 missing connections, weight=     150.10    
 decide> The unconnected minima in the chain and their distances are:
     5        2.86     7     7        4.69     9 
 

 tryconnect> 210-iteration DNEB run for minima 5_F and 7_U using 6 images  (DNEB attempt #2)  ...
 lbfgs> Final DNEB force constant      2.812407350    
 Double-ended search iterations= 210 RMS= 1.2215 Dev= 2.99% S= 5.79 time= 0.69
 Following    1 images are candidates for TS:    4  
 Converged to TS (number of iterations):         14
 DNEB run yielded 1 true transition state(s) time=   0.53

 >>>>>  Path run for ts 8 ...
 Plus  side of path:                     500 steps. Energy=    -296.7007597       time=       0.40
 Minus side of path:                     501 steps. Energy=    -294.9521054       time=       0.40

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -296.7007597  7.5739         -289.1268423  5.8253         -294.9521054   6.078   3.660   5.783  13.662
        Known (#5)                                              Known (#6)
 Unconnected minimum 6 found its way to F set.

 tryconnect> 70-iteration DNEB run for minima 7_F and 9_S using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.1169 Dev= 0.29% S= 4.85 time= 0.08
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         12
 DNEB run yielded 1 true transition state(s) time=   0.50

 >>>>>  Path run for ts 9 ...
 Plus  side of path:                     431 steps. Energy=    -293.5965177       time=       0.33
 Minus side of path:                     524 steps. Energy=    -295.1362019       time=       0.42

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -293.5965177 0.84481E-01     -293.5120368  1.6242         -295.1362019   4.922   4.693   4.266  18.521
        Known (#9)                                              Known (#7)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   5     -286.0800001  1.3906        -284.6893835  12.341        -297.0304022  24.572  22.566   1.995  39.600
   1     -297.0304022  8.9585        -288.0719227  7.0643        -295.1362019  16.650  10.166   2.882  27.414
   7     -295.1362019  2.3503        -292.7859266 0.81059        -293.5965177   6.215   5.300   5.846  13.514
   9     -293.5965177 0.84481E-01    -293.5120368  1.6242        -295.1362019   4.922   4.693   4.266  18.521
   4     -295.1362019 0.24085        -294.8953541 0.56751E-01    -294.9521054   2.988   2.978   4.131  19.124
   8     -294.9521054  5.8253        -289.1268423  7.5739        -296.7007597   6.078   3.660   5.783  13.662
   2     -296.7007597 0.55540        -296.1453556 0.58446        -296.7298141   6.538   6.278   2.224  35.527

 Number of TS in the path       =      7
 Number of cycles               =      6

 Elapsed time=                                20.37
 OPTIM> # of energy calls=                          0 time=           0.00 %=  0.0
 OPTIM> # of energy+gradient calls=             21863 time=          11.38 %= 55.9
 OPTIM> # of energy+gradient+Hessian calls=       412 time=           0.43 %=  2.1
