
 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)@comp35.ch.
                 Created on  5/28/12 at 12: 5: 8 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=    -297.3202840     RMS force=    0.8095011635E-06
 OPTIM> Final energy  =    -292.7248527     RMS force=    0.9908063110E-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=     51355.    
 decide> The unconnected minima in the chain and their distances are:
     2       37.17     1 
 

 tryconnect> 385-iteration DNEB run for minima 1_S and 2_F using 11 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      89.85007793    
 Double-ended search iterations= 385 RMS= 1.9347 Dev= 0.86% S= 39.82 time= 2.41
 Following    1 images are candidates for TS:    6  
 Converged to TS (number of iterations):        104
 DNEB run yielded 1 true transition state(s) time=   1.80

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                     541 steps. Energy=    -290.6022531       time=       0.45
 Minus side of path:                     545 steps. Energy=    -292.7248527       time=       0.49

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -290.6022531  1.8392         -288.7630372  3.9618         -292.7248527  16.605  15.236   1.662  47.542
        *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=     20505.    
 decide> The unconnected minima in the chain and their distances are:
     2        4.79     4     3       27.32     1 
 

 checkpair> Energies of the minima in the pair     2    4 are the same - checking distance ...

 tryconnect> 70-iteration DNEB run for minima 2_F and 4_U using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      6.768393620    
 Double-ended search iterations= 70 RMS= 0.6623 Dev= 0.31% S= 7.27 time= 0.08
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         27
 DNEB run yielded 1 true transition state(s) time=   0.70

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                     535 steps. Energy=    -291.4152430       time=       0.44
 Minus side of path:                     531 steps. Energy=    -292.7248527       time=       0.44

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -291.4152430  2.8217         -288.5935364  4.1313         -292.7248527  11.075   8.430   9.362   8.438
        *NEW* (Placed in 5)                                     Known (#4)
 Connection established between members of the U set.

 tryconnect> 280-iteration DNEB run for minima 1_S and 3_U using 8 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      12.15506250    
 Double-ended search iterations= 280 RMS= 0.7877 Dev= 0.31% S= 28.88 time= 1.28
 Following    1 images are candidates for TS:    5  
 Converged to TS (number of iterations):         97
 DNEB run yielded 1 true transition state(s) time=   1.62

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                     595 steps. Energy=    -290.6022531       time=       0.52
 Minus side of path:                     590 steps. Energy=    -290.2399057       time=       0.52

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -290.6022531  3.0997         -287.5025243  2.7374         -290.2399057  24.022  18.161   1.764  44.779
        Known (#3)                                              *NEW* (Placed in 6)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 3 >>>>>>>>>>>>>>>>>>>>> 6 minima and 3 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      4 steps with      2 missing connections, weight=     5617.8    
 decide> The unconnected minima in the chain and their distances are:
     2        4.79     4     6       17.54     1 
 

 checkpair> Energies of the minima in the pair     2    4 are the same - checking distance ...

 tryconnect> 385-iteration DNEB run for minima 2_F and 4_U using 11 images  (DNEB attempt #2)  ...
 tryconnect> Changing to an even number of images for possible permutational isomer
 lbfgs> Final DNEB force constant      37.33456322    
 Double-ended search iterations= 385 RMS= 1.0855 Dev= 9.31% S= 10.71 time= 2.66
 Following    2 images are candidates for TS:    4    6  
 Converged to TS (number of iterations):         21
 Converged to TS (number of iterations):         45
 DNEB run yielded 2 true transition state(s) time=   1.56

 >>>>>  Path run for ts 4 ...
 Plus  side of path:                     523 steps. Energy=    -292.7248527       time=       0.43
 Minus side of path:                     530 steps. Energy=    -289.3773078       time=       0.43

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -292.7248527  6.4771         -286.2477587  3.1295         -289.3773078   5.594   4.994   8.694   9.087
        Known (#2)                                              *NEW* (Placed in 7)
 Unconnected minimum 7 found its way to F set.

 >>>>>  Path run for ts 5 ...
 Plus  side of path:                     542 steps. Energy=    -291.4152430       time=       0.44
 Minus side of path:                     577 steps. Energy=    -289.3773078       time=       0.48

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -291.4152430  5.7846         -285.6306227  3.7467         -289.3773078  13.556  11.350   3.489  22.641
        Known (#5)                                              Known (#7)
 Unconnected minimum 5 found its way to F set.

 tryconnect> 175-iteration DNEB run for minima 1_S and 6_F using 5 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      20.78928179    
 Double-ended search iterations= 175 RMS= 0.3756 Dev= 0.18% S= 17.85 time= 0.48
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):         30
 DNEB run yielded 1 true transition state(s) time=   0.71

 >>>>>  Path run for ts 6 ...
 Plus  side of path:                     510 steps. Energy=    -297.3202840       time=       0.40
 Minus side of path:                     523 steps. Energy=    -291.9598839       time=       0.40

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -297.3202840  6.6935         -290.6267752  1.3331         -291.9598839  15.613  13.873   2.970  26.598
        Known (#1)                                              *NEW* (Placed in 8)
 Unconnected minimum 8 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 4 >>>>>>>>>>>>>>>>>>>>> 8 minima and 6 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      7 steps with      1 missing connections, weight=     365.78    
 decide> The unconnected minima in the chain and their distances are:
     6        7.15     8 
 

 tryconnect> 70-iteration DNEB run for minima 6_F and 8_S using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      19.79931599    
 Double-ended search iterations= 70 RMS= 0.9461 Dev= 10.87% S= 7.18 time= 0.07
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         27
 DNEB run yielded 1 true transition state(s) time=   0.69

 >>>>>  Path run for ts 7 ...
 Plus  side of path:                     482 steps. Energy=    -290.2399057       time=       0.38
 Minus side of path:                     528 steps. Energy=    -291.9598839       time=       0.41

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -290.2399057 0.18711E-01     -290.2211944  1.7387         -291.9598839   7.494   7.152   3.797  20.808
        Known (#6)                                              Known (#8)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   6     -297.3202840  6.6935        -290.6267752  1.3331        -291.9598839  15.613  13.873   2.970  26.598
   7     -291.9598839  1.7387        -290.2211944 0.18711E-01    -290.2399057   7.494   7.152   3.797  20.808
   3     -290.2399057  2.7374        -287.5025243  3.0997        -290.6022531  24.022  18.161   1.764  44.779
   1     -290.6022531  1.8392        -288.7630372  3.9618        -292.7248527  16.605  15.236   1.662  47.542
   2     -292.7248527  4.1313        -288.5935364  2.8217        -291.4152430  11.075   8.430   9.362   8.438
   5     -291.4152430  5.7846        -285.6306227  3.7467        -289.3773078  13.556  11.350   3.489  22.641
   4     -289.3773078  3.1295        -286.2477587  6.4771        -292.7248527   5.594   4.994   8.694   9.087

 Number of TS in the path       =      7
 Number of cycles               =      4

 Elapsed time=                                20.63
 OPTIM> # of energy calls=                          0 time=           0.00 %=  0.0
 OPTIM> # of energy+gradient calls=             24059 time=          12.82 %= 62.1
 OPTIM> # of energy+gradient+Hessian calls=       351 time=           0.37 %=  1.8
