################################################################ ### buccaneer-pipeline v1.5 ### ################################################################ ---------------------- INPUT PARAMETERS ---------------------- pdbin-ref /home/jmht/ccp4-6.4.0/lib/data/reference_structures/reference-1tqw.pdb mtzin-ref /home/jmht/ccp4-6.4.0/lib/data/reference_structures/reference-1tqw.mtz colin-ref-fo FP.F_sigF.F,FP.F_sigF.sigF colin-ref-hl FC.ABCD.A,FC.ABCD.B,FC.ABCD.C,FC.ABCD.D seqin /data1/jmht/polya_helices/3PP5/search_polya_15/input/3PP5_1.fasta mtzin /data1/jmht/polya_helices/3PP5/search_polya_15/data/loc0_ALL_polya_15/unmod/mr/phaser/build/shelxe/rebuild/refine/refmacSX_output.mtz colin-fo FP, SIGFP colin-free FREE colin-phifom PHIC, FOM colin-fc FWT, PHWT pdbin /data1/jmht/polya_helices/3PP5/search_polya_15/data/loc0_ALL_polya_15/unmod/mr/phaser/build/shelxe/rebuild/refine/refmacSX_output.pdb pdbout /data1/jmht/polya_helices/3PP5/search_polya_15/data/loc0_ALL_polya_15/unmod/mr/phaser/build/shelxe/rebuild/buccaneer/buccSX_output.pdb cycles 5 buccaneer-anisotropy-correction buccaneer-fast buccaneer-1st-cycles 3 buccaneer-1st-sequence-reliability 0.95 buccaneer-nth-cycles 2 buccaneer-nth-sequence-reliability 0.95 buccaneer-nth-correlation-mode buccaneer-new-residue-name UNK buccaneer-resolution 2.0 refmac-mlhl 1 refmac-twin 0 prefix buccaneer_pipeline/ ---------------------- DEFAULT PARAMETERS ---------------------- title buccaneer auto-build buccaneer-1st-correlation-mode false ----------------------------------------------------------------
 
 ###############################################################
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 ###############################################################
 ### CCP4 6.4: cbuccaneer             version 1.5.2 : 06/10/11##
 ###############################################################
 User: unknown  Run date: 17/ 7/2014 Run time: 18:53:36 


 Please reference: Collaborative Computational Project, Number 4. 1994.
 "The CCP4 Suite: Programs for Protein Crystallography". Acta Cryst. D50, 760-763.
 as well as any specific reference in the program write-up.



Copyright 2002-2010 Kevin Cowtan and University of York.


$TEXT:Reference: $$ Please reference $$

 'Fitting molecular fragments into electron density'
 Cowtan K. (2008) Acta Cryst. D64, 83-89.

$$
$TEXT:Reference: $$ Please reference $$

 'The Buccaneer software for automated model building'
 Cowtan K. (2006) Acta Cryst. D62, 1002-1011.

$$


title 	buccaneer auto-build
pdbin-ref 	/home/jmht/ccp4-6.4.0/lib/data/reference_structures/reference-1tqw.pdb
mtzin-ref 	/home/jmht/ccp4-6.4.0/lib/data/reference_structures/reference-1tqw.mtz
colin-ref-fo 	FP.F_sigF.F,FP.F_sigF.sigF
colin-ref-hl 	FC.ABCD.A,FC.ABCD.B,FC.ABCD.C,FC.ABCD.D
seqin 	/data1/jmht/polya_helices/3PP5/search_polya_15/input/3PP5_1.fasta
mtzin 	/data1/jmht/polya_helices/3PP5/search_polya_15/data/loc0_ALL_polya_15/unmod/mr/phaser/build/shelxe/rebuild/refine/refmacSX_output.mtz
colin-fo 	FP, SIGFP
colin-phifom 	PHIC, FOM
colin-fc 	FWT, PHWT
colin-free 	FREE
pdbin 	/data1/jmht/polya_helices/3PP5/search_polya_15/data/loc0_ALL_polya_15/unmod/mr/phaser/build/shelxe/rebuild/refine/refmacSX_output.pdb
pdbout 	buccaneer_pipeline/build.pdb
anisotropy-correction
fast
cycles 	3
sequence-reliability 	0.95
new-residue-name 	UNK
resolution 	2.0

MTZ file: /data1/jmht/polya_helices/3PP5/search_polya_15/data/loc0_ALL_polya_15/unmod/mr/phaser/build/shelxe/rebuild/refine/refmacSX_output.mtz
  Number of reflections:     16180        Number of columns:  17

Applying anisotropy correction:
| -1.01e-14, 5.538e-17, 6.293e-18|
| 5.538e-17,         0,-1.187e-17|
| 6.293e-18,-1.187e-17,   -0.1121|

PDB file: /data1/jmht/polya_helices/3PP5/search_polya_15/data/loc0_ALL_polya_15/unmod/mr/phaser/build/shelxe/rebuild/refine/refmacSX_output.pdb
  Number of atoms read: 315

Cycle: 1

 C-alphas after finding:    81
 C-alphas after growing:    101
 C-alphas after joining:    69
 C-alphas linked:           0
 C-alphas sequenced:        57
 C-alphas corrected:        0
 C-alphas after filtering:  60
 C-alphas after NCS build:  60
 C-alphas after pruning:    60
 C-alphas after rebuilding: 60


Internal cycle   1
     60 residues were built in   1 fragments, the longest having   60 residues.
     56 residues were sequenced, after pruning.
     60 residues were uniquely allocated to   1 chains.
  Completeness by residues built:   100.0%
  Completeness of chains (number):   82.2%    (1)



Cycle: 2

 C-alphas after finding:    76
 C-alphas after growing:    116
 C-alphas after joining:    76
 C-alphas linked:           0
 C-alphas sequenced:        57
 C-alphas corrected:        0
 C-alphas after filtering:  60
 C-alphas after NCS build:  60
 C-alphas after pruning:    60
 C-alphas after rebuilding: 60


Internal cycle   2
     60 residues were built in   1 fragments, the longest having   60 residues.
     56 residues were sequenced, after pruning.
     60 residues were uniquely allocated to   1 chains.
  Completeness by residues built:   100.0%
  Completeness of chains (number):   82.2%    (1)



Cycle: 3

 C-alphas after finding:    76
 C-alphas after growing:    116
 C-alphas after joining:    76
 C-alphas linked:           0
 C-alphas sequenced:        57
 C-alphas corrected:        0
 C-alphas after filtering:  60
 C-alphas after NCS build:  60
 C-alphas after pruning:    60
 C-alphas after rebuilding: 60


Internal cycle   3
     60 residues were built in   1 fragments, the longest having   60 residues.
     56 residues were sequenced, after pruning.
     60 residues were uniquely allocated to   1 chains.
  Completeness by residues built:   100.0%
  Completeness of chains (number):   82.2%    (1)


$TEXT:Result: $$ $$
     60 residues were built in   1 fragments, the longest having   60 residues.
     56 residues were sequenced, after pruning.
     60 residues were uniquely allocated to   1 chains.
  Completeness by residues built:   100.0%
  Completeness of chains (number):   82.2%    (1)
$$


cbuccaneer: Normal termination
Times: User:      17.9s System:    0.0s Elapsed:     0:17  

 
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 ###############################################################
 ### CCP4 6.4: Refmac_5.8.0049     version 5.8.0049 : 30/06/13##
 ###############################################################
 User: unknown  Run date: 17/ 7/2014 Run time: 18:53:53 


 Please reference: Collaborative Computational Project, Number 4. 1994.
 "The CCP4 Suite: Programs for Protein Crystallography". Acta Cryst. D50, 760-763.
 as well as any specific reference in the program write-up.


 $TEXT:Reference1: $$ Main reference $$ 
   "REFMAC5 for the refinement of macromolecular crystal structures:"
   G.N.Murshudov, P.Skubak, A.A.Lebedev, N.S.Pannu, R.A.Steiner, R.A.Nicholls, M.D.Winn, F.Long and A.A.Vagin,(2011) 
   Acta Crystallogr. D67, 355-367

 $$
 $SUMMARY :Reference1:  $$ Refmac: $$
 :TEXT:Reference1: $$

 $TEXT:Reference2: $$ Secondary reference $$ 
   "Refinement of Macromolecular Structures by the  Maximum-Likelihood Method:"
   G.N. Murshudov, A.A.Vagin and E.J.Dodson,(1997)
   Acta Crystallogr. D53, 240-255
   EU  Validation contract: BIO2CT-92-0524

 $$
 $SUMMARY :Reference2:  $$ Refmac: $$
 :TEXT:Reference2: $$

  Data line--- title  buccaneer auto-build
  Data line--- ncyc 10
  Data line--- labin                    PHIB=PHIC FOM= FOM                FREE=FREE   FP=FP SIGFP= SIGFP
  Data line--- weight AUTO
  Data line--- make check NONE
  Data line--- make hydrogen NO hout NO peptide NO cispeptide YES ssbridge YES symmetry YES sugar YES connectivity NO link NO
  Data line--- refi type REST PHASE resi MLKF meth CGMAT bref ISOT
  Data line--- scal type SIMP LSSC ANISO EXPE
  Data line--- solvent YES VDWProb 1.4 IONProb 0.8 RSHRink 0.8
  Data line--- PHOUT
  Data line--- PNAME buccaneer
  Data line--- DNAME buccaneer
  Data line--- END

 OPENED INPUT MTZ FILE 
 Logical Name: HKLIN   Filename: /data1/jmht/polya_helices/3PP5/search_polya_15/data/loc0_ALL_polya_15/unmod/mr/phaser/build/shelxe/rebuild/refine/refmacSX_output.mtz 


 Spacegroup information obtained from library file: 
 Logical Name: SYMINFO   Filename: /home/jmht/ccp4-6.4.0/lib/data/syminfo.lib


    ****                     Input and Default parameters#                      ****


Input coordinate file.  Logical name - XYZIN actual file name  - buccaneer_pipeline/build.pdb
Output coordinate file. Logical name - XYZOUT actual file name - buccaneer_pipeline/refine.pdb
Input reflection file.  Logical name - HKLIN actual file name  - /data1/jmht/polya_helices/3PP5/search_polya_15/data/loc0_ALL_polya_15/unmod/mr/phaser/build/shelxe/rebuild/refine/refmacSX_outpu
Output reflection file. Logical name - HKLOUT actual file name - buccaneer_pipeline/refine.mtz

Cell from mtz :    39.140    39.140   118.190    90.000    90.000   120.000
Space group from mtz: number -  173; name - P 63

  Refinement type                        : Restrained


    ****                           Makecif parameters                           ****

Dictionary files for restraints : /home/jmht/ccp4-6.4.0/lib/data/monomers/mon*cif
Parameters for new entry and VDW: /home/jmht/ccp4-6.4.0/lib/data/monomers/ener_lib.cif
    Program will rely on residue and atom names. No checking
    If this option is used then monomers should be checked carefully before using
    Hydrogens will not be written to the output file
    Links between monomers will be checked. Only those links present in the coordinate file will be used
    All links to sugar will be analysed and used
    For new ligands "ideal restraint" values will be taken from the energetic libary ener_lib.cif
    Symmetry related links will be analysed and used
    Cis peptides will be found and used automatically


  Residual                               : Phase modified Maximum Likelihood for Fs
 Phase Blurred by  Scale*Exp(-B s**2)    :    1.00    0.00

    ****                    Least-square scaling parameters                     ****

Overall scale
Overall B value
Overall anisotropic B with tr(B) = 0.0
Constant bulk solvent in non protein region
Probe radii for non-ions     1.400
Probe radii for ions         0.800
Shrinkage of the mask  by    0.800


    ****                 Map sharpening parameters and methods                  ****

No map sharpening will be performed

  Method of minimisation                 : Sparse Matrix
  Experimental sigmas used for weighting
  Number of Bins and width:    20       0.0223
  Refinement of individual isotropic Bfactors
  Refinement resln        :    18.5778  1.4990
  Estimated number of reflections :      26875
  Free R exclusion - flag equals:     0
  Auto weighting. An attempt
  Refinement cycles       :    10
  Scaling type                           :
          Wilson using 1 Gaussian

  Estimation of D/Sigma in resolution bins
  using  free set of reflns with experimental sigmas
  Input phases not used in SigmaA estimation

  Scaling and SigmaA resln:    18.5778  1.4990

  Damping factors:     1.0000  1.0000


    ****                    Geometry restraints and weights                     ****


                                              Sigma:
 Bonding distances
          Weight =  1.00

 Bond angles
          Weight =  1.00

 Planar groups (all and main chain)
          WEIGHT= 1.00 1.00

 Chiral centers
          Weight= 1.00

 NON-BONDED CONTACTS
          Overall weight                          =  1.00
          Sigma for simple VDW                    =  0.20
          Sigma for VDW trhough torsion angle     =  0.20
          Sigma for HBOND                         =  0.20
          Sigma for metal-ion                     =  0.20
          Sigma for DUMMY and other atom          =  0.30
          Distance for donor-accepetor = vdw1+vdw2+(-0.30)
          Distance for acceptor - H    = vdw1+     ( 0.10)
          VDW distance through torsion = vdw1+vdw2+(-0.30)
          Distance for DUMMY-others    = vdw1+vdw2+(-0.70)

 TORSION ANGLES
          Weight= 1.00

 THERMAL FACTORS
          Weight= 1.00
     Main chain bond (1-2 neighbour)          1.5A**2
     Main chain angle (1-3 neighbour)         2.0A**2
     Side chain bond                          3.0A**2
     Side chain angle                         4.5A**2

 RESTRAINTS AGAINST EXCESSIVE SHIFTS
     Positional parameters                   0.00A
     Thermal parameters                      0.00A
     Occupancy parameters                    0.00

 RADIUS OF CONFIDENCE
     Positional parameters 0.00A
     Thermal parameters    0.00A**2
     Occupancy parameters  0.00

Monitoring style is "MEDIUM". Complete information will be printed out in the
first and last cycle. In all other cycles minimum information will be printed out
Sigma cutoffs for printing out outliers
If deviation of restraint parameter > alpha*sigma then information will be printed out
Distance outliers      10.000
Angle outliers         10.000
Torsion outliers       10.000
Chiral volume outliers 10.000
Plane outliers         10.000
Non-bonding outliers   10.000
B value  outliers      10.000
---------------------------------------------------------------

 Input file :buccaneer_pipeline/build.pdb
  ------------------------------
  ---  LIBRARY OF MONOMERS   ---
 _lib_name         mon_lib
 _lib_version      5.41
 _lib_update       11/02/13
  ------------------------------
  NUMBER OF MONOMERS IN THE LIBRARY          : 11464
                with complete description    : 11464
  NUMBER OF MODIFICATIONS                    :    56
  NUMBER OF LINKS                            :    68
  I am reading libraries. Please wait.
      - energy parameters
      - monomer"s description (links & mod )

FORMATTED      OLD     file opened on unit  45

Logical name: ATOMSF, Filename: /home/jmht/ccp4-6.4.0/lib/data/atomsf.lib


  Number of atoms    :     483
  Number of residues :      60
  Number of chains   :       1
  I am reading library. Please wait.
                mon_lib.cif
  --------------------------------
  --- title of input coord file ---

  PDB_code:xxxx
  PDB_name:----
  PDB_date:XX-XXX-XX
  --------------------------------
  ATTENTION: atom:CG   UNK                 9  AA   is missing in the structure
  ATTENTION: atom:CG   UNK                10  AA   is missing in the structure
  ATTENTION: atom:CG   PHE                36  AA   is missing in the structure
  ATTENTION: atom:CD1  PHE                36  AA   is missing in the structure
  ATTENTION: atom:CE1  PHE                36  AA   is missing in the structure
  ATTENTION: atom:CZ   PHE                36  AA   is missing in the structure
  ATTENTION: atom:CE2  PHE                36  AA   is missing in the structure
  ATTENTION: atom:CD2  PHE                36  AA   is missing in the structure
  ATTENTION: atom:CG   GLU                41  AA   is missing in the structure
  ATTENTION: atom:CD   GLU                41  AA   is missing in the structure
  ATTENTION: atom:OE1  GLU                41  AA   is missing in the structure
  ATTENTION: atom:OE2  GLU                41  AA   is missing in the structure
  ATTENTION: atom:CG   UNK                63  AA   is missing in the structure
  ATTENTION: atom:CG   UNK                68  AA   is missing in the structure
  Number of chains                  :       1
  Total number of monomers          :      60
  Number of atoms                   :     497
  Number of missing atoms           :      14
  Number of rebuilt atoms           :       0
  Number of unknown atoms           :       0
  Number of deleted atoms           :       0

  Number of bonds restraints    :     486
  Number of angles restraints   :     654
  Number of torsions restraints :     322
  Number of chiralities         :      79
  Number of planar groups       :      84


 loop_
     _atom_type_symbol
     _atom_type_scat_Cromer_Mann_a1
     _atom_type_scat_Cromer_Mann_b1
     _atom_type_scat_Cromer_Mann_a2
     _atom_type_scat_Cromer_Mann_b2
     _atom_type_scat_Cromer_Mann_a3
     _atom_type_scat_Cromer_Mann_b3
     _atom_type_scat_Cromer_Mann_a4
     _atom_type_scat_Cromer_Mann_b4
     _atom_type_scat_Cromer_Mann_c


  N     12.2126   0.0057   3.1322   9.8933   2.0125  28.9975   1.1663   0.5826 -11.5290
  C      2.3100  20.8439   1.0200  10.2075   1.5886   0.5687   0.8650  51.6512   0.2156
  O      3.0485  13.2771   2.2868   5.7011   1.5463   0.3239   0.8670  32.9089   0.2508
  S      6.9053   1.4679   5.2034  22.2151   1.4379   0.2536   1.5863  56.1720   0.8669


 Number of distances         :           0
 Number of angles            :           0
 Number of torsions          :           0
 Number of planes            :           0
 Number of chirals           :           0
 Number of intervals         :           0
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
                        Standard  External       All
                Bonds:       486         0       486
               Angles:       654         0       654
              Chirals:        79         0        79
               Planes:        84         0        84
             Torsions:       322         0       322
            Intervals:         0         0         0
--------------------------------------------------------------------------------


  Number of harmonic restraints       =            0
  Number of atoms in special position =            0
 -----------------------------------------------------


    ****                           Info from mtz file                           ****

FreeR flag                            0
Number of "free" reflections        809
Number of   all  reflections      16180
--------------------------------------------------------------------------------
 Number of reflections in file      16180
 Number of reflections read          16180


     CGMAT cycle number =      1

 Limits of asymmetric unit      : 1.00 1.00 0.50
 Grid spacing to be used        :    96   96  288
 Maximuum H,K,L                 :    27   27   78
 Minimum acceptable grid spacing:    59   59  178
 Limits of asymmetric unit      : 1.00 1.00 0.50
 Grid spacing to be used        :    96   96  288
 Maximuum H,K,L                 :    27   27   78
 Minimum acceptable grid spacing:    59   59  178
 Weight matrix   0.54462564    
 Actual weight    10.000000      is applied to the X-ray term
Norm of X_ray positional gradient                141.
Norm of Geom. positional gradient                30.9
Norm of X_ray B-factor gradient                 0.194E+04
Norm of Geom. B-factor gradient                  0.00
Product of X_ray and Geom posit. gradients      0.130E+06
 Cosine of angle between them                       0.021
Product of X_ray and Geom B-fact gradients       0.00
 Cosine of angle between them                       0.000


Residuals: XRAY=     0.2781E+06 GEOM=      978.0     TOTAL=     0.2791E+06
 function value    279114.66    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                   486     0.011     0.020
Bond angles  : refined atoms                    654     1.169     1.978
Torsion angles, period  1. refined               59     2.730     5.000
Torsion angles, period  2. refined               25    29.835    26.400
Torsion angles, period  3. refined               99    10.676    15.000
Torsion angles, period  4. refined                3     5.427    15.000
Chiral centres: refined atoms                    79     0.074     0.200
Planar groups: refined atoms                    351     0.000     0.020
VDW repulsions: refined_atoms                   208     0.301     0.200
VDW; torsion: refined_atoms                     360     0.302     0.200
HBOND: refined_atoms                              8     0.333     0.200
VDW repulsions: symmetry: refined_atoms          35     0.367     0.200
HBOND: symmetry: refined_atoms                    2     0.098     0.200
M. chain bond B values: refined atoms           239     0.000     3.948
M. chain angle B values: refined atoms          297     0.000     5.922
S. chain bond B values: refined atoms           242     0.000     3.948
S. chain angle B values: refined atoms          356     0.000     5.922
Long range B values: refined atoms              739     0.000    32.630
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall               : scale =    0.776, B  = -22.530
Partial structure    1: scale =    0.443, B  =  53.346
Overall anisotropic scale factors
   B11 = -0.11 B22 = -0.11 B33 =  0.37 B12 = -0.06 B13 = -0.00 B23 = -0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------

    ****                Things for loggraph, R factor and others                ****


$TABLE: Cycle    1. Rfactor analysis, F distribution v resln  :
$GRAPHS:Cycle    1.  v. resln :N:1,6,7,11,12:
:Cycle    1.  and  v. resln :N:1,4,5,9,10:
:Cycle    1. % observed v. resln :N:1,3:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.014     172  83.11   163.9   171.4  0.43  0.65      10   199.0   141.6  0.48  0.58
 0.036     325  96.34   195.0   188.4  0.36  0.48      17   210.5   208.8  0.34  0.40
 0.058     417  97.12   251.2   226.6  0.33  0.41      22   235.1   196.9  0.35  0.47
 0.080     492  99.61   216.0   192.2  0.32  0.38      25   217.7   201.8  0.41  0.58
 0.102     551  99.66   155.1   139.2  0.39  0.45      29   159.7   131.9  0.32  0.34
 0.124     618  99.69   138.4   124.1  0.37  0.42      33   131.9   111.4  0.32  0.36
 0.147     674  99.58   118.6   109.2  0.35  0.39      35   124.4   123.4  0.32  0.33
 0.169     703  99.33   106.7    95.4  0.38  0.41      37    98.0    88.2  0.31  0.33
 0.191     765  99.51    95.6    82.5  0.39  0.40      41   104.9    94.2  0.36  0.37
 0.213     791  99.40    88.6    72.8  0.38  0.38      41    78.0    62.8  0.44  0.41
 0.235     838  99.10    73.3    63.3  0.39  0.38      44    70.9    60.7  0.52  0.51
 0.257     890  99.26    61.8    50.0  0.42  0.41      47    60.7    50.4  0.46  0.43
 0.279     890  99.05    50.7    43.5  0.43  0.41      47    44.9    36.1  0.49  0.48
 0.301     935  99.19    41.3    36.6  0.43  0.40      49    41.8    37.7  0.43  0.40
 0.323     996  98.78    35.3    32.6  0.44  0.41      53    35.4    35.5  0.41  0.34
 0.346    1015  98.89    32.7    30.5  0.45  0.41      53    33.2    31.2  0.38  0.36
 0.368    1029  98.63    29.2    26.4  0.44  0.41      54    25.5    25.0  0.53  0.50
 0.390    1084  98.70    27.4    24.8  0.43  0.40      57    30.4    25.6  0.43  0.44
 0.412    1081  98.36    24.3    21.4  0.43  0.39      57    25.8    24.8  0.41  0.36
 0.434    1105  97.08    21.2    18.5  0.45  0.40      58    23.4    18.0  0.45  0.47
$$

    ****                      Fom and SigmaA vs resolution                      ****

 $TABLE: Cycle    1. FSC and  Fom(-acentric, centric, overall v resln:
 $GRAPHS:Cycle    1. M(Fom) v. resln :N:1,3,5,7,8,9,10:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCwork  FSCfree$$
 $$
  0.0140   164   0.676     8   0.585   172   0.672  0.894  0.4743 *******
  0.0361   312   0.756    13   0.575   325   0.749  0.909  0.4913 *******
  0.0582   402   0.854    15   0.619   417   0.845  0.921  0.6548 *******
  0.0803   478   0.819    14   0.845   492   0.820  0.931  0.7058 *******
  0.1024   535   0.759    16   0.850   551   0.762  0.936  0.6040 *******
  0.1245   605   0.782    13   0.740   618   0.781  0.911  0.6466 *******
  0.1466   659   0.791    15   0.733   674   0.789  0.893  0.6710 *******
  0.1687   691   0.830    12   0.988   703   0.833  0.916  0.6924 *******
  0.1908   748   0.820    17   0.824   765   0.820  0.913  0.6778 *******
  0.2129   778   0.779    13   0.799   791   0.779  0.883  0.6485 *******
  0.2350   823   0.733    15   0.661   838   0.731  0.840  0.6204 *******
  0.2571   875   0.778    15   0.707   890   0.777  0.853  0.6024 *******
  0.2792   877   0.762    13   0.794   890   0.762  0.823  0.5544 *******
  0.3013   923   0.703    12   0.791   935   0.704  0.778  0.4846 *******
  0.3234   978   0.729    18   0.662   996   0.728  0.748  0.5217 *******
  0.3455   998   0.759    17   0.796  1015   0.760  0.739  0.5446 *******
  0.3677  1016   0.769    13   0.858  1029   0.770  0.742  0.5633 *******
  0.3898  1069   0.803    15   0.709  1084   0.801  0.747  0.5979 *******
  0.4119  1066   0.764    15   0.748  1081   0.763  0.774  0.5765 *******
  0.4340  1090   0.752    15   0.611  1105   0.750  0.719  0.5600 *******
 $$
Resolution limits                    =     18.578     1.499
Number of used reflections           =      15371
Percentage observed                  =    98.5504
Percentage of free reflections       =     5.0000
Overall R factor                     =     0.3838
Free R factor                        =     0.3909
Overall Fourier shell correlation    =     0.5926
Free Fourier shell correlation       =     0.0000
Overall weighted R factor            =     0.4105
Free weighted R factor               =     0.4119
Overall weighted R2 factor           =     0.5233
Free weighted R2 factor              =     0.5173
Overall correlation coefficient      =     0.8353
Free correlation coefficient         =     0.8206
Cruickshanks DPI for coordinate error=     0.1115
DPI based on free R factor           =     0.1062
Overall figure of merit              =     0.7697
ML based su of positional parameters =     0.1064
ML based su of thermal parameters    =     2.8725
-----------------------------------------------------------------------------
 Trying gamma equal    0.0000000    
 Convergence reached with no gamma cycles 


 fvalues    34764.660       977.65613       291146.91       348624.25    


     CGMAT cycle number =      2

 Weight matrix   0.77608478    
 Actual weight    10.000000      is applied to the X-ray term


 function value    232578.25    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                   486     0.016     0.020
Bond angles  : refined atoms                    654     1.272     1.978
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall               : scale =    0.804, B  =  -9.773
Partial structure    1: scale =    0.431, B  =  43.536
Overall anisotropic scale factors
   B11 = -0.09 B22 = -0.09 B33 =  0.29 B12 = -0.04 B13 = -0.00 B23 = -0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.3506
Free R factor                        =     0.3643
Overall Fourier shell correlation    =     0.6959
Free Fourier shell correlation       =     0.0000
Overall figure of merit              =     0.7896
-----------------------------------------------------------------------------
 Trying gamma equal    0.0000000    
 Convergence reached with no gamma cycles 


 fvalues    28143.766       1586.5579       219507.02       283024.22    


     CGMAT cycle number =      3

 Weight matrix   0.98679692    
 Actual weight    10.000000      is applied to the X-ray term


 function value    204711.47    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                   486     0.025     0.020
Bond angles  : refined atoms                    654     1.896     1.978
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall               : scale =    0.853, B  =   1.934
Partial structure    1: scale =    0.420, B  =  33.174
Overall anisotropic scale factors
   B11 = -0.04 B22 = -0.04 B33 =  0.12 B12 = -0.02 B13 = -0.00 B23 = -0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.3322
Free R factor                        =     0.3502
Overall Fourier shell correlation    =     0.7362
Free Fourier shell correlation       =     0.0000
Overall figure of merit              =     0.8023
-----------------------------------------------------------------------------
 Trying gamma equal    0.0000000    
 Convergence reached with no gamma cycles 


 fvalues    20136.992       5212.6851       200227.73       206582.61    


     CGMAT cycle number =      4

 Weight matrix   0.99526948    
 Actual weight    9.0909090      is applied to the X-ray term


 function value    177975.42    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                   486     0.025     0.020
Bond angles  : refined atoms                    654     2.031     1.978
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall               : scale =    0.869, B  =   0.730
Partial structure    1: scale =    0.402, B  =  31.887
Overall anisotropic scale factors
   B11 = -0.03 B22 = -0.03 B33 =  0.09 B12 = -0.01 B13 = -0.00 B23 = -0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.3236
Free R factor                        =     0.3462
Overall Fourier shell correlation    =     0.7411
Free Fourier shell correlation       =     0.0000
Overall figure of merit              =     0.8070
-----------------------------------------------------------------------------
 Trying gamma equal    0.0000000    
 Convergence reached with no gamma cycles 


 fvalues    19049.275       4399.4551       176620.42       177574.69    


     CGMAT cycle number =      5

 Weight matrix   0.93920034    
 Actual weight    8.2644625      is applied to the X-ray term


 function value    158267.97    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                   486     0.024     0.020
Bond angles  : refined atoms                    654     2.052     1.978
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall               : scale =    0.884, B  =   0.659
Partial structure    1: scale =    0.400, B  =  31.992
Overall anisotropic scale factors
   B11 = -0.02 B22 = -0.02 B33 =  0.08 B12 = -0.01 B13 = -0.00 B23 = -0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.3205
Free R factor                        =     0.3450
Overall Fourier shell correlation    =     0.7432
Free Fourier shell correlation       =     0.0000
Overall figure of merit              =     0.8091
-----------------------------------------------------------------------------
 Trying gamma equal    0.0000000    
 Convergence reached with no gamma cycles 


 fvalues    18547.285       4621.0625       157590.56       157904.41    


     CGMAT cycle number =      6

 Weight matrix   0.94926268    
 Actual weight    8.2644625      is applied to the X-ray term


 function value    156872.89    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                   486     0.023     0.020
Bond angles  : refined atoms                    654     2.023     1.978
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall               : scale =    0.890, B  =   0.520
Partial structure    1: scale =    0.398, B  =  30.617
Overall anisotropic scale factors
   B11 = -0.02 B22 = -0.02 B33 =  0.08 B12 = -0.01 B13 = -0.00 B23 = -0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.3188
Free R factor                        =     0.3438
Overall Fourier shell correlation    =     0.7432
Free Fourier shell correlation       =     0.0000
Overall figure of merit              =     0.8096
-----------------------------------------------------------------------------
 Trying gamma equal    0.0000000    
 Convergence reached with no gamma cycles 


 fvalues    18396.939       4451.7280       156356.92       156492.55    


     CGMAT cycle number =      7

 Weight matrix   0.95342273    
 Actual weight    8.2644625      is applied to the X-ray term


 function value    156341.17    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                   486     0.023     0.020
Bond angles  : refined atoms                    654     2.041     1.978
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall               : scale =    0.893, B  =   0.503
Partial structure    1: scale =    0.396, B  =  29.534
Overall anisotropic scale factors
   B11 = -0.02 B22 = -0.02 B33 =  0.07 B12 = -0.01 B13 = -0.00 B23 = -0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.3178
Free R factor                        =     0.3434
Overall Fourier shell correlation    =     0.7433
Free Fourier shell correlation       =     0.0000
Overall figure of merit              =     0.8097
-----------------------------------------------------------------------------
 Trying gamma equal    0.0000000    
 Convergence reached with no gamma cycles 


 fvalues    18330.775       4479.4580       155891.14       155973.45    


     CGMAT cycle number =      8

 Weight matrix   0.87491190    
 Actual weight    7.5131474      is applied to the X-ray term


 function value    141948.47    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                   486     0.023     0.020
Bond angles  : refined atoms                    654     2.051     1.978
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall               : scale =    0.896, B  =   0.478
Partial structure    1: scale =    0.395, B  =  29.043
Overall anisotropic scale factors
   B11 = -0.02 B22 = -0.02 B33 =  0.06 B12 = -0.01 B13 = -0.00 B23 = -0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.3172
Free R factor                        =     0.3429
Overall Fourier shell correlation    =     0.7434
Free Fourier shell correlation       =     0.0000
Overall figure of merit              =     0.8101
-----------------------------------------------------------------------------
 Trying gamma equal    0.0000000    
 Convergence reached with no gamma cycles 


 fvalues    18255.480       4465.2666       141575.00       141621.38    


     CGMAT cycle number =      9

 Weight matrix   0.79907840    
 Actual weight    6.8301339      is applied to the X-ray term


 function value    129559.50    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                   486     0.022     0.020
Bond angles  : refined atoms                    654     2.002     1.978
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall               : scale =    0.894, B  =   0.399
Partial structure    1: scale =    0.395, B  =  28.750
Overall anisotropic scale factors
   B11 = -0.02 B22 = -0.02 B33 =  0.07 B12 = -0.01 B13 = -0.00 B23 = -0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.3170
Free R factor                        =     0.3422
Overall Fourier shell correlation    =     0.7429
Free Fourier shell correlation       =     0.0000
Overall figure of merit              =     0.8102
-----------------------------------------------------------------------------
 Trying gamma equal    0.0000000    
 Convergence reached with no gamma cycles 


 fvalues    18300.723       4284.1172       129250.04       129280.50    


     CGMAT cycle number =     10

 Weight matrix   0.80276549    
 Actual weight    6.8301339      is applied to the X-ray term


 function value    129779.46    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                   486     0.021     0.020
Bond angles  : refined atoms                    654     1.943     1.978
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall               : scale =    0.891, B  =   0.383
Partial structure    1: scale =    0.395, B  =  28.552
Overall anisotropic scale factors
   B11 = -0.02 B22 = -0.02 B33 =  0.07 B12 = -0.01 B13 = -0.00 B23 = -0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.3170
Free R factor                        =     0.3418
Overall Fourier shell correlation    =     0.7423
Free Fourier shell correlation       =     0.0000
Overall figure of merit              =     0.8103
-----------------------------------------------------------------------------
 Trying gamma equal    0.0000000    
 Convergence reached with no gamma cycles 


 fvalues    18360.158       4103.9990       129492.20       129506.34    

 Limits of asymmetric unit      : 1.00 1.00 0.50
 Grid spacing to be used        :    96   96  288
 Maximuum H,K,L                 :    27   27   78
 Minimum acceptable grid spacing:    59   59  178
 Limits of asymmetric unit      : 1.00 1.00 0.50
 Grid spacing to be used        :    96   96  288
 Maximuum H,K,L                 :    27   27   78
 Minimum acceptable grid spacing:    59   59  178

 WRITTEN OUTPUT MTZ FILE 
 Logical Name: HKLOUT   Filename: buccaneer_pipeline/refine.mtz 

Norm of X_ray positional gradient                0.00
Norm of Geom. positional gradient                0.00
Norm of X_ray B-factor gradient                  0.00
Norm of Geom. B-factor gradient                  0.00
Product of X_ray and Geom posit. gradients       0.00
 Cosine of angle between them                       0.000
Product of X_ray and Geom B-fact gradients       0.00
 Cosine of angle between them                       0.000


Residuals: XRAY=     0.1259E+06 GEOM=      4100.     TOTAL=     0.1300E+06

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                   486     0.021     0.020
Bond angles  : refined atoms                    654     1.942     1.978
Torsion angles, period  1. refined               59     3.178     5.000
Torsion angles, period  2. refined               25    30.039    26.400
Torsion angles, period  3. refined               99    15.609    15.000
Torsion angles, period  4. refined                3    11.218    15.000
Chiral centres: refined atoms                    79     0.140     0.200
Planar groups: refined atoms                    351     0.010     0.020
VDW repulsions: refined_atoms                   183     0.239     0.200
VDW; torsion: refined_atoms                     351     0.301     0.200
HBOND: refined_atoms                              4     0.219     0.200
VDW repulsions: symmetry: refined_atoms          30     0.250     0.200
HBOND: symmetry: refined_atoms                    2     0.266     0.200
M. chain bond B values: refined atoms           239     1.970     1.739
M. chain angle B values: refined atoms          297     3.026     2.584
S. chain bond B values: refined atoms           245     7.207     2.834
S. chain angle B values: refined atoms          356    10.704     3.830
Long range B values: refined atoms              705    12.029    15.989
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall               : scale =    0.889, B  =   0.407
Partial structure    1: scale =    0.395, B  =  28.783
Overall anisotropic scale factors
   B11 = -0.02 B22 = -0.02 B33 =  0.07 B12 = -0.01 B13 = -0.00 B23 = -0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------

    ****                Things for loggraph, R factor and others                ****


$TABLE: Cycle   11. Rfactor analysis, F distribution v resln  :
$GRAPHS:Cycle   11.  v. resln :N:1,6,7,11,12:
:Cycle   11.  and  v. resln :N:1,4,5,9,10:
:Cycle   11. % observed v. resln :N:1,3:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.014     172  83.11   143.1   163.4  0.45  0.67      10   173.7   126.1  0.40  0.40
 0.036     325  96.34   170.2   168.5  0.32  0.42      17   183.7   176.9  0.32  0.36
 0.058     417  97.12   219.2   203.3  0.27  0.34      22   205.2   185.4  0.30  0.43
 0.080     492  99.61   188.5   173.3  0.26  0.31      25   190.0   172.0  0.31  0.44
 0.102     551  99.66   135.4   126.4  0.33  0.39      29   139.4   126.3  0.29  0.31
 0.124     618  99.69   120.8   113.8  0.31  0.34      33   115.1   114.5  0.41  0.46
 0.147     674  99.58   103.5   101.1  0.28  0.31      35   108.6   100.2  0.27  0.27
 0.169     703  99.33    93.1    87.6  0.30  0.34      37    85.5    80.6  0.32  0.35
 0.191     765  99.51    83.4    74.3  0.30  0.31      41    91.6    79.1  0.30  0.31
 0.213     791  99.40    77.3    63.4  0.32  0.32      41    68.1    58.7  0.40  0.38
 0.235     838  99.10    64.0    51.9  0.34  0.33      44    61.9    45.2  0.43  0.42
 0.257     890  99.26    54.0    43.7  0.34  0.34      47    53.0    42.5  0.37  0.37
 0.279     890  99.05    44.3    37.7  0.36  0.35      47    39.1    34.9  0.41  0.39
 0.301     935  99.19    36.1    31.9  0.37  0.35      49    36.4    34.8  0.34  0.33
 0.323     996  98.78    30.8    29.3  0.38  0.35      53    30.9    30.5  0.37  0.30
 0.346    1015  98.89    28.5    27.3  0.36  0.33      53    29.0    27.3  0.36  0.34
 0.368    1029  98.63    25.5    25.4  0.34  0.31      54    22.3    22.6  0.46  0.42
 0.390    1084  98.70    23.9    23.3  0.32  0.29      57    26.5    25.3  0.30  0.28
 0.412    1081  98.36    21.2    21.2  0.32  0.28      57    22.5    24.3  0.34  0.28
 0.434    1105  97.08    18.5    19.5  0.35  0.31      58    20.4    19.8  0.31  0.29
$$

    ****                      Fom and SigmaA vs resolution                      ****

 $TABLE: Cycle   11. FSC and  Fom(-acentric, centric, overall v resln:
 $GRAPHS:Cycle   11. M(Fom) v. resln :N:1,3,5,7,8,9,10:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCwork  FSCfree$$
 $$
  0.0140   164   0.711     8   0.598   172   0.706  0.896  0.5219 *******
  0.0361   312   0.784    13   0.674   325   0.780  0.913  0.5419 *******
  0.0582   402   0.877    15   0.681   417   0.870  0.926  0.7231 *******
  0.0803   478   0.845    14   0.846   492   0.845  0.938  0.7634 *******
  0.1024   535   0.799    16   0.880   551   0.801  0.942  0.6945 *******
  0.1245   605   0.808    13   0.740   618   0.807  0.902  0.7251 *******
  0.1466   659   0.803    15   0.744   674   0.802  0.876  0.7641 *******
  0.1687   691   0.850    12   0.971   703   0.852  0.917  0.7926 *******
  0.1908   748   0.849    17   0.819   765   0.848  0.962  0.7979 *******
  0.2129   778   0.817    13   0.829   791   0.817  0.983  0.7741 *******
  0.2350   823   0.772    15   0.711   838   0.771  0.972  0.7406 *******
  0.2571   875   0.831    15   0.689   890   0.828  1.016  0.7587 *******
  0.2792   877   0.813    13   0.866   890   0.814  0.955  0.7404 *******
  0.3013   923   0.761    12   0.870   935   0.762  0.861  0.6747 *******
  0.3234   978   0.774    18   0.676   996   0.772  0.808  0.6938 *******
  0.3455   998   0.783    17   0.863  1015   0.784  0.770  0.7361 *******
  0.3677  1016   0.808    13   0.925  1029   0.810  0.793  0.7623 *******
  0.3898  1069   0.853    15   0.758  1084   0.852  0.852  0.7941 *******
  0.4119  1066   0.821    15   0.786  1081   0.821  0.829  0.7723 *******
  0.4340  1090   0.816    15   0.691  1105   0.814  0.770  0.7564 *******
 $$
Resolution limits                    =     18.578     1.499
Number of used reflections           =      15371
Percentage observed                  =    98.5504
Percentage of free reflections       =     5.0000
Overall R factor                     =     0.3168
Free R factor                        =     0.3415
Overall Fourier shell correlation    =     0.7422
Free Fourier shell correlation       =     0.0000
Overall weighted R factor            =     0.3397
Free weighted R factor               =     0.3577
Overall weighted R2 factor           =     0.4450
Free weighted R2 factor              =     0.4539
Overall correlation coefficient      =     0.8854
Free correlation coefficient         =     0.8621
Cruickshanks DPI for coordinate error=     0.0920
DPI based on free R factor           =     0.0928
Overall figure of merit              =     0.8104
ML based su of positional parameters =     0.0725
ML based su of thermal parameters    =     1.8786
-----------------------------------------------------------------------------
  Time in seconds: CPU =        39.68
             Elapsed =         128.00

    ****           Things for loggraph, R factor and others vs cycle            ****


$TABLE: Rfactor analysis, stats vs cycle  :
$GRAPHS: vs cycle :N:1,2,3:
:FOM vs cycle :N:1,4:
:-LL vs cycle :N:1,5:
:-LLfree vs cycle :N:1,6:
:Geometry vs cycle:N:1,7,8,9,10,11:
$$
    Ncyc    Rfact    Rfree     FOM      -LL     -LLfree  rmsBOND  zBOND rmsANGL  zANGL rmsCHIRAL $$
$$
       0   0.3838   0.3909   0.770     27814.    3758.8   0.0113  0.586   1.169  0.562   0.074
       1   0.3506   0.3643   0.790     23099.    3672.0   0.0156  0.784   1.272  0.627   0.081
       2   0.3322   0.3502   0.802     19950.    3590.3   0.0250  1.260   1.896  0.955   0.132
       3   0.3236   0.3462   0.807     19093.    3563.3   0.0250  1.261   2.031  1.027   0.144
       4   0.3205   0.3450   0.809     18591.    3543.6   0.0242  1.219   2.052  1.040   0.147
       5   0.3188   0.3438   0.810     18443.    3536.6   0.0231  1.165   2.023  1.023   0.146
       6   0.3178   0.3434   0.810     18375.    3533.7   0.0232  1.170   2.041  1.031   0.149
       7   0.3172   0.3429   0.810     18299.    3530.5   0.0232  1.172   2.051  1.035   0.151
       8   0.3170   0.3422   0.810     18342.    3531.6   0.0222  1.120   2.002  1.007   0.146
       9   0.3170   0.3418   0.810     18400.    3533.3   0.0211  1.064   1.943  0.974   0.140
      10   0.3168   0.3415   0.810     18429.    3534.7   0.0212  1.067   1.942  0.972   0.140
 $$
 $TEXT:Result: $$ Final results $$
                      Initial    Final
           R factor    0.3838   0.3168
             R free    0.3909   0.3415
     Rms BondLength    0.0113   0.0212
      Rms BondAngle    1.1694   1.9419
     Rms ChirVolume    0.0743   0.1401
 $$

 Refmac_5.8.0049:  End of Refmac_5.8.0049  
Times: User:      39.5s System:    3.2s Elapsed:     0:43  

 
 ###############################################################
 ###############################################################
 ###############################################################
 ### CCP4 6.4: cbuccaneer             version 1.5.2 : 06/10/11##
 ###############################################################
 User: unknown  Run date: 17/ 7/2014 Run time: 18:54:36 


 Please reference: Collaborative Computational Project, Number 4. 1994.
 "The CCP4 Suite: Programs for Protein Crystallography". Acta Cryst. D50, 760-763.
 as well as any specific reference in the program write-up.



Copyright 2002-2010 Kevin Cowtan and University of York.


$TEXT:Reference: $$ Please reference $$

 'Fitting molecular fragments into electron density'
 Cowtan K. (2008) Acta Cryst. D64, 83-89.

$$
$TEXT:Reference: $$ Please reference $$

 'The Buccaneer software for automated model building'
 Cowtan K. (2006) Acta Cryst. D62, 1002-1011.

$$


title 	buccaneer auto-build
pdbin-ref 	/home/jmht/ccp4-6.4.0/lib/data/reference_structures/reference-1tqw.pdb
mtzin-ref 	/home/jmht/ccp4-6.4.0/lib/data/reference_structures/reference-1tqw.mtz
colin-ref-fo 	FP.F_sigF.F,FP.F_sigF.sigF
colin-ref-hl 	FC.ABCD.A,FC.ABCD.B,FC.ABCD.C,FC.ABCD.D
seqin 	/data1/jmht/polya_helices/3PP5/search_polya_15/input/3PP5_1.fasta
mtzin 	buccaneer_pipeline/refine.mtz
colin-fo 	FP, SIGFP
colin-hl 	HLACOMB,HLBCOMB,HLCCOMB,HLDCOMB
colin-fc 	FWT,PHWT
colin-free 	FREE
pdbin 	buccaneer_pipeline/refine.pdb
pdbout 	buccaneer_pipeline/build.pdb
anisotropy-correction
fast
cycles 	2
sequence-reliability 	0.95
correlation-mode
new-residue-name 	UNK
resolution 	2.0

MTZ file: buccaneer_pipeline/refine.mtz
  Number of reflections:     16180        Number of columns:  22

Applying anisotropy correction:
|-9.483e-15, 4.866e-17, 5.728e-17|
| 4.866e-17,         0,-1.927e-17|
| 5.728e-17,-1.927e-17,   -0.1077|

PDB file: buccaneer_pipeline/refine.pdb
  Number of atoms read: 483

Cycle: 1

 C-alphas after finding:    76
 C-alphas after growing:    110
 C-alphas after joining:    76
 C-alphas linked:           0
 C-alphas sequenced:        73
 C-alphas corrected:        0
 C-alphas after filtering:  76
 C-alphas after NCS build:  120
 C-alphas after pruning:    60
 C-alphas after rebuilding: 60


Internal cycle   1
     60 residues were built in   1 fragments, the longest having   60 residues.
     57 residues were sequenced, after pruning.
     60 residues were uniquely allocated to   1 chains.
  Completeness by residues built:   100.0%
  Completeness of chains (number):   82.2%    (1)



Cycle: 2

 C-alphas after finding:    76
 C-alphas after growing:    135
 C-alphas after joining:    76
 C-alphas linked:           0
 C-alphas sequenced:        73
 C-alphas corrected:        0
 C-alphas after filtering:  76
 C-alphas after NCS build:  120
 C-alphas after pruning:    60
 C-alphas after rebuilding: 60


Internal cycle   2
     60 residues were built in   1 fragments, the longest having   60 residues.
     57 residues were sequenced, after pruning.
     60 residues were uniquely allocated to   1 chains.
  Completeness by residues built:   100.0%
  Completeness of chains (number):   82.2%    (1)


$TEXT:Result: $$ $$
     60 residues were built in   1 fragments, the longest having   60 residues.
     57 residues were sequenced, after pruning.
     60 residues were uniquely allocated to   1 chains.
  Completeness by residues built:   100.0%
  Completeness of chains (number):   82.2%    (1)
$$


cbuccaneer: Normal termination
Times: User:      19.8s System:    0.0s Elapsed:     0:20  

 
 ###############################################################
 ###############################################################
 ###############################################################
 ### CCP4 6.4: Refmac_5.8.0049     version 5.8.0049 : 30/06/13##
 ###############################################################
 User: unknown  Run date: 17/ 7/2014 Run time: 18:54:56 


 Please reference: Collaborative Computational Project, Number 4. 1994.
 "The CCP4 Suite: Programs for Protein Crystallography". Acta Cryst. D50, 760-763.
 as well as any specific reference in the program write-up.


 $TEXT:Reference1: $$ Main reference $$ 
   "REFMAC5 for the refinement of macromolecular crystal structures:"
   G.N.Murshudov, P.Skubak, A.A.Lebedev, N.S.Pannu, R.A.Steiner, R.A.Nicholls, M.D.Winn, F.Long and A.A.Vagin,(2011) 
   Acta Crystallogr. D67, 355-367

 $$
 $SUMMARY :Reference1:  $$ Refmac: $$
 :TEXT:Reference1: $$

 $TEXT:Reference2: $$ Secondary reference $$ 
   "Refinement of Macromolecular Structures by the  Maximum-Likelihood Method:"
   G.N. Murshudov, A.A.Vagin and E.J.Dodson,(1997)
   Acta Crystallogr. D53, 240-255
   EU  Validation contract: BIO2CT-92-0524

 $$
 $SUMMARY :Reference2:  $$ Refmac: $$
 :TEXT:Reference2: $$

  Data line--- title  buccaneer auto-build
  Data line--- ncyc 10
  Data line--- labin                    PHIB=PHIC FOM= FOM                FREE=FREE   FP=FP SIGFP= SIGFP
  Data line--- weight AUTO
  Data line--- make check NONE
  Data line--- make hydrogen NO hout NO peptide NO cispeptide YES ssbridge YES symmetry YES sugar YES connectivity NO link NO
  Data line--- refi type REST PHASE resi MLKF meth CGMAT bref ISOT
  Data line--- scal type SIMP LSSC ANISO EXPE
  Data line--- solvent YES VDWProb 1.4 IONProb 0.8 RSHRink 0.8
  Data line--- PHOUT
  Data line--- PNAME buccaneer
  Data line--- DNAME buccaneer
  Data line--- END

 OPENED INPUT MTZ FILE 
 Logical Name: HKLIN   Filename: /data1/jmht/polya_helices/3PP5/search_polya_15/data/loc0_ALL_polya_15/unmod/mr/phaser/build/shelxe/rebuild/refine/refmacSX_output.mtz 


 Spacegroup information obtained from library file: 
 Logical Name: SYMINFO   Filename: /home/jmht/ccp4-6.4.0/lib/data/syminfo.lib


    ****                     Input and Default parameters#                      ****


Input coordinate file.  Logical name - XYZIN actual file name  - buccaneer_pipeline/build.pdb
Output coordinate file. Logical name - XYZOUT actual file name - buccaneer_pipeline/refine.pdb
Input reflection file.  Logical name - HKLIN actual file name  - /data1/jmht/polya_helices/3PP5/search_polya_15/data/loc0_ALL_polya_15/unmod/mr/phaser/build/shelxe/rebuild/refine/refmacSX_outpu
Output reflection file. Logical name - HKLOUT actual file name - buccaneer_pipeline/refine.mtz

Cell from mtz :    39.140    39.140   118.190    90.000    90.000   120.000
Space group from mtz: number -  173; name - P 63

  Refinement type                        : Restrained


    ****                           Makecif parameters                           ****

Dictionary files for restraints : /home/jmht/ccp4-6.4.0/lib/data/monomers/mon*cif
Parameters for new entry and VDW: /home/jmht/ccp4-6.4.0/lib/data/monomers/ener_lib.cif
    Program will rely on residue and atom names. No checking
    If this option is used then monomers should be checked carefully before using
    Hydrogens will not be written to the output file
    Links between monomers will be checked. Only those links present in the coordinate file will be used
    All links to sugar will be analysed and used
    For new ligands "ideal restraint" values will be taken from the energetic libary ener_lib.cif
    Symmetry related links will be analysed and used
    Cis peptides will be found and used automatically


  Residual                               : Phase modified Maximum Likelihood for Fs
 Phase Blurred by  Scale*Exp(-B s**2)    :    1.00    0.00

    ****                    Least-square scaling parameters                     ****

Overall scale
Overall B value
Overall anisotropic B with tr(B) = 0.0
Constant bulk solvent in non protein region
Probe radii for non-ions     1.400
Probe radii for ions         0.800
Shrinkage of the mask  by    0.800


    ****                 Map sharpening parameters and methods                  ****

No map sharpening will be performed

  Method of minimisation                 : Sparse Matrix
  Experimental sigmas used for weighting
  Number of Bins and width:    20       0.0223
  Refinement of individual isotropic Bfactors
  Refinement resln        :    18.5778  1.4990
  Estimated number of reflections :      26875
  Free R exclusion - flag equals:     0
  Auto weighting. An attempt
  Refinement cycles       :    10
  Scaling type                           :
          Wilson using 1 Gaussian

  Estimation of D/Sigma in resolution bins
  using  free set of reflns with experimental sigmas
  Input phases not used in SigmaA estimation

  Scaling and SigmaA resln:    18.5778  1.4990

  Damping factors:     1.0000  1.0000


    ****                    Geometry restraints and weights                     ****


                                              Sigma:
 Bonding distances
          Weight =  1.00

 Bond angles
          Weight =  1.00

 Planar groups (all and main chain)
          WEIGHT= 1.00 1.00

 Chiral centers
          Weight= 1.00

 NON-BONDED CONTACTS
          Overall weight                          =  1.00
          Sigma for simple VDW                    =  0.20
          Sigma for VDW trhough torsion angle     =  0.20
          Sigma for HBOND                         =  0.20
          Sigma for metal-ion                     =  0.20
          Sigma for DUMMY and other atom          =  0.30
          Distance for donor-accepetor = vdw1+vdw2+(-0.30)
          Distance for acceptor - H    = vdw1+     ( 0.10)
          VDW distance through torsion = vdw1+vdw2+(-0.30)
          Distance for DUMMY-others    = vdw1+vdw2+(-0.70)

 TORSION ANGLES
          Weight= 1.00

 THERMAL FACTORS
          Weight= 1.00
     Main chain bond (1-2 neighbour)          1.5A**2
     Main chain angle (1-3 neighbour)         2.0A**2
     Side chain bond                          3.0A**2
     Side chain angle                         4.5A**2

 RESTRAINTS AGAINST EXCESSIVE SHIFTS
     Positional parameters                   0.00A
     Thermal parameters                      0.00A
     Occupancy parameters                    0.00

 RADIUS OF CONFIDENCE
     Positional parameters 0.00A
     Thermal parameters    0.00A**2
     Occupancy parameters  0.00

Monitoring style is "MEDIUM". Complete information will be printed out in the
first and last cycle. In all other cycles minimum information will be printed out
Sigma cutoffs for printing out outliers
If deviation of restraint parameter > alpha*sigma then information will be printed out
Distance outliers      10.000
Angle outliers         10.000
Torsion outliers       10.000
Chiral volume outliers 10.000
Plane outliers         10.000
Non-bonding outliers   10.000
B value  outliers      10.000
---------------------------------------------------------------

 Input file :buccaneer_pipeline/build.pdb
  ------------------------------
  ---  LIBRARY OF MONOMERS   ---
 _lib_name         mon_lib
 _lib_version      5.41
 _lib_update       11/02/13
  ------------------------------
  NUMBER OF MONOMERS IN THE LIBRARY          : 11464
                with complete description    : 11464
  NUMBER OF MODIFICATIONS                    :    56
  NUMBER OF LINKS                            :    68
  I am reading libraries. Please wait.
      - energy parameters
      - monomer"s description (links & mod )

FORMATTED      OLD     file opened on unit  45

Logical name: ATOMSF, Filename: /home/jmht/ccp4-6.4.0/lib/data/atomsf.lib


  Number of atoms    :     501
  Number of residues :      60
  Number of chains   :       1
  I am reading library. Please wait.
                mon_lib.cif
  --------------------------------
  --- title of input coord file ---

  PDB_code:xxxx
  PDB_name:----
  PDB_date:XX-XXX-XX
  --------------------------------
  ATTENTION: atom:CG   UNK                 9  AA   is missing in the structure
  ATTENTION: atom:CG   UNK                10  AA   is missing in the structure
  ATTENTION: atom:CG   UNK                68  AA   is missing in the structure
  Number of chains                  :       1
  Total number of monomers          :      60
  Number of atoms                   :     504
  Number of missing atoms           :       3
  Number of rebuilt atoms           :       0
  Number of unknown atoms           :       0
  Number of deleted atoms           :       0

  Number of bonds restraints    :     506
  Number of angles restraints   :     680
  Number of torsions restraints :     340
  Number of chiralities         :      78
  Number of planar groups       :      88


 loop_
     _atom_type_symbol
     _atom_type_scat_Cromer_Mann_a1
     _atom_type_scat_Cromer_Mann_b1
     _atom_type_scat_Cromer_Mann_a2
     _atom_type_scat_Cromer_Mann_b2
     _atom_type_scat_Cromer_Mann_a3
     _atom_type_scat_Cromer_Mann_b3
     _atom_type_scat_Cromer_Mann_a4
     _atom_type_scat_Cromer_Mann_b4
     _atom_type_scat_Cromer_Mann_c


  N     12.2126   0.0057   3.1322   9.8933   2.0125  28.9975   1.1663   0.5826 -11.5290
  C      2.3100  20.8439   1.0200  10.2075   1.5886   0.5687   0.8650  51.6512   0.2156
  O      3.0485  13.2771   2.2868   5.7011   1.5463   0.3239   0.8670  32.9089   0.2508
  S      6.9053   1.4679   5.2034  22.2151   1.4379   0.2536   1.5863  56.1720   0.8669


 Number of distances         :           0
 Number of angles            :           0
 Number of torsions          :           0
 Number of planes            :           0
 Number of chirals           :           0
 Number of intervals         :           0
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
                        Standard  External       All
                Bonds:       506         0       506
               Angles:       680         0       680
              Chirals:        78         0        78
               Planes:        88         0        88
             Torsions:       340         0       340
            Intervals:         0         0         0
--------------------------------------------------------------------------------


  Number of harmonic restraints       =            0
  Number of atoms in special position =            0
 -----------------------------------------------------


    ****                           Info from mtz file                           ****

FreeR flag                            0
Number of "free" reflections        809
Number of   all  reflections      16180
--------------------------------------------------------------------------------
 Number of reflections in file      16180
 Number of reflections read          16180


     CGMAT cycle number =      1

 Limits of asymmetric unit      : 1.00 1.00 0.50
 Grid spacing to be used        :    96   96  288
 Maximuum H,K,L                 :    27   27   78
 Minimum acceptable grid spacing:    59   59  178
 Limits of asymmetric unit      : 1.00 1.00 0.50
 Grid spacing to be used        :    96   96  288
 Maximuum H,K,L                 :    27   27   78
 Minimum acceptable grid spacing:    59   59  178
 Weight matrix   0.51820004    
 Actual weight    10.000000      is applied to the X-ray term
Norm of X_ray positional gradient                189.
Norm of Geom. positional gradient                39.7
Norm of X_ray B-factor gradient                 0.186E+04
Norm of Geom. B-factor gradient                  0.00
Product of X_ray and Geom posit. gradients      0.462E+06
 Cosine of angle between them                       0.041
Product of X_ray and Geom B-fact gradients       0.00
 Cosine of angle between them                       0.000


Residuals: XRAY=     0.2811E+06 GEOM=      1062.     TOTAL=     0.2822E+06
 function value    282174.66    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                   506     0.011     0.020
Bond angles  : refined atoms                    680     1.303     1.970
Torsion angles, period  1. refined               59     2.214     5.000
Torsion angles, period  2. refined               29    30.763    26.207
Torsion angles, period  3. refined              103    10.504    15.000
Torsion angles, period  4. refined                3    11.394    15.000
Chiral centres: refined atoms                    78     0.070     0.200
Planar groups: refined atoms                    374     0.000     0.020
VDW repulsions: refined_atoms                   224     0.259     0.200
VDW; torsion: refined_atoms                     370     0.310     0.200
HBOND: refined_atoms                              5     0.361     0.200
VDW repulsions: symmetry: refined_atoms          40     0.430     0.200
HBOND: symmetry: refined_atoms                    3     0.489     0.200
M. chain bond B values: refined atoms           239     0.000     3.948
M. chain angle B values: refined atoms          297     0.000     5.922
S. chain bond B values: refined atoms           263     0.000     3.948
S. chain angle B values: refined atoms          382     0.000     5.922
Long range B values: refined atoms              781     0.000    32.710
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall               : scale =    0.774, B  = -22.286
Partial structure    1: scale =    0.464, B  =  45.334
Overall anisotropic scale factors
   B11 = -0.12 B22 = -0.12 B33 =  0.37 B12 = -0.06 B13 = -0.00 B23 = -0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------

    ****                Things for loggraph, R factor and others                ****


$TABLE: Cycle    1. Rfactor analysis, F distribution v resln  :
$GRAPHS:Cycle    1.  v. resln :N:1,6,7,11,12:
:Cycle    1.  and  v. resln :N:1,4,5,9,10:
:Cycle    1. % observed v. resln :N:1,3:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.014     172  83.11   164.4   173.7  0.40  0.57      10   199.6   155.7  0.44  0.47
 0.036     325  96.34   195.6   186.5  0.37  0.47      17   211.2   196.3  0.34  0.49
 0.058     417  97.12   251.9   233.3  0.29  0.37      22   235.8   197.0  0.44  0.60
 0.080     492  99.61   216.6   200.8  0.30  0.38      25   218.3   208.5  0.37  0.47
 0.102     551  99.66   155.6   143.2  0.37  0.43      29   160.2   129.1  0.41  0.44
 0.124     618  99.69   138.8   128.8  0.35  0.40      33   132.3   120.0  0.42  0.50
 0.147     674  99.58   119.0   112.0  0.35  0.39      35   124.8   118.4  0.24  0.26
 0.169     703  99.33   107.0    94.2  0.37  0.40      37    98.3    78.5  0.40  0.42
 0.191     765  99.51    95.9    82.8  0.38  0.39      41   105.3    93.6  0.39  0.38
 0.213     791  99.40    88.9    73.5  0.37  0.38      41    78.3    64.5  0.50  0.51
 0.235     838  99.10    73.5    62.6  0.39  0.38      44    71.1    61.9  0.44  0.42
 0.257     890  99.26    62.0    50.8  0.41  0.40      47    60.9    51.2  0.40  0.37
 0.279     890  99.05    50.9    42.7  0.43  0.40      47    45.0    39.0  0.48  0.44
 0.301     935  99.19    41.4    35.9  0.43  0.41      49    41.9    37.1  0.44  0.39
 0.323     996  98.78    35.4    32.6  0.43  0.40      53    35.5    33.3  0.41  0.33
 0.346    1015  98.89    32.8    30.1  0.46  0.41      53    33.3    32.0  0.42  0.40
 0.368    1029  98.63    29.3    26.8  0.45  0.42      54    25.6    27.5  0.55  0.49
 0.390    1084  98.70    27.5    25.0  0.42  0.38      57    30.5    26.6  0.39  0.41
 0.412    1081  98.36    24.4    21.3  0.44  0.41      57    25.9    23.4  0.40  0.33
 0.434    1105  97.08    21.2    18.4  0.45  0.42      58    23.4    18.5  0.39  0.42
$$

    ****                      Fom and SigmaA vs resolution                      ****

 $TABLE: Cycle    1. FSC and  Fom(-acentric, centric, overall v resln:
 $GRAPHS:Cycle    1. M(Fom) v. resln :N:1,3,5,7,8,9,10:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCwork  FSCfree$$
 $$
  0.0140   164   0.653     8   0.560   172   0.649  0.876  0.4962 *******
  0.0361   312   0.729    13   0.620   325   0.724  0.881  0.4846 *******
  0.0582   402   0.848    15   0.691   417   0.842  0.885  0.6362 *******
  0.0803   478   0.814    14   0.830   492   0.814  0.888  0.6858 *******
  0.1024   535   0.748    16   0.843   551   0.751  0.890  0.6051 *******
  0.1245   605   0.775    13   0.726   618   0.774  0.889  0.6343 *******
  0.1466   659   0.795    15   0.781   674   0.794  0.891  0.6672 *******
  0.1687   691   0.817    12   0.891   703   0.819  0.907  0.6804 *******
  0.1908   748   0.809    17   0.797   765   0.809  0.898  0.6777 *******
  0.2129   778   0.771    13   0.791   791   0.771  0.875  0.6417 *******
  0.2350   823   0.741    15   0.665   838   0.740  0.857  0.6118 *******
  0.2571   875   0.779    15   0.654   890   0.777  0.872  0.5873 *******
  0.2792   877   0.762    13   0.795   890   0.763  0.860  0.5540 *******
  0.3013   923   0.707    12   0.821   935   0.708  0.790  0.4799 *******
  0.3234   978   0.734    18   0.632   996   0.732  0.763  0.4882 *******
  0.3455   998   0.756    17   0.821  1015   0.757  0.724  0.5143 *******
  0.3677  1016   0.764    13   0.844  1029   0.765  0.702  0.5396 *******
  0.3898  1069   0.804    15   0.687  1084   0.803  0.743  0.5857 *******
  0.4119  1066   0.764    15   0.739  1081   0.764  0.777  0.5592 *******
  0.4340  1090   0.753    15   0.637  1105   0.751  0.740  0.5459 *******
 $$
Resolution limits                    =     18.578     1.499
Number of used reflections           =      15371
Percentage observed                  =    98.5504
Percentage of free reflections       =     5.0000
Overall R factor                     =     0.3734
Free R factor                        =     0.4036
Overall Fourier shell correlation    =     0.5796
Free Fourier shell correlation       =     0.0000
Overall weighted R factor            =     0.4017
Free weighted R factor               =     0.4218
Overall weighted R2 factor           =     0.4991
Free weighted R2 factor              =     0.5380
Overall correlation coefficient      =     0.8515
Free correlation coefficient         =     0.8063
Cruickshanks DPI for coordinate error=     0.1108
DPI based on free R factor           =     0.1116
Overall figure of merit              =     0.7673
ML based su of positional parameters =     0.1087
ML based su of thermal parameters    =     2.9113
-----------------------------------------------------------------------------
 Trying gamma equal    0.0000000    
 Convergence reached with no gamma cycles 


 fvalues    34806.355       1061.9855       291370.53       349125.56    


     CGMAT cycle number =      2

 Weight matrix   0.76835871    
 Actual weight    10.000000      is applied to the X-ray term


 function value    231864.56    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                   506     0.016     0.020
Bond angles  : refined atoms                    680     1.365     1.970
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall               : scale =    0.799, B  =  -9.831
Partial structure    1: scale =    0.468, B  =  39.858
Overall anisotropic scale factors
   B11 = -0.08 B22 = -0.08 B33 =  0.26 B12 = -0.04 B13 = -0.00 B23 = -0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.3355
Free R factor                        =     0.3660
Overall Fourier shell correlation    =     0.6931
Free Fourier shell correlation       =     0.0000
Overall figure of merit              =     0.7897
-----------------------------------------------------------------------------
 Trying gamma equal    0.0000000    
 Convergence reached with no gamma cycles 


 fvalues    28199.730       1679.6934       217586.67       283677.00    


     CGMAT cycle number =      3

 Weight matrix    1.0281060    
 Actual weight    10.000000      is applied to the X-ray term


 function value    201279.22    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                   506     0.027     0.020
Bond angles  : refined atoms                    680     2.009     1.970
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall               : scale =    0.846, B  =   1.830
Partial structure    1: scale =    0.429, B  =  26.136
Overall anisotropic scale factors
   B11 = -0.03 B22 = -0.03 B33 =  0.10 B12 = -0.02 B13 = -0.00 B23 = -0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.3150
Free R factor                        =     0.3405
Overall Fourier shell correlation    =     0.7362
Free Fourier shell correlation       =     0.0000
Overall figure of merit              =     0.8057
-----------------------------------------------------------------------------
 Trying gamma equal    0.0000000    
 Convergence reached with no gamma cycles 


 fvalues    19807.445       5255.6235       196534.02       203330.08    


     CGMAT cycle number =      4

 Weight matrix    1.0946236    
 Actual weight    9.0909090      is applied to the X-ray term


 function value    172810.36    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                   506     0.025     0.020
Bond angles  : refined atoms                    680     2.086     1.970
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall               : scale =    0.864, B  =   0.651
Partial structure    1: scale =    0.428, B  =  25.711
Overall anisotropic scale factors
   B11 = -0.02 B22 = -0.02 B33 =  0.08 B12 = -0.01 B13 = -0.00 B23 = -0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.3054
Free R factor                        =     0.3311
Overall Fourier shell correlation    =     0.7412
Free Fourier shell correlation       =     0.0000
Overall figure of merit              =     0.8133
-----------------------------------------------------------------------------
 Trying gamma equal    0.0000000    
 Convergence reached with no gamma cycles 


 fvalues    18492.148       4421.8564       171463.36       172532.30    


     CGMAT cycle number =      5

 Weight matrix    1.1251698    
 Actual weight    9.0909090      is applied to the X-ray term


 function value    169089.33    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                   506     0.025     0.020
Bond angles  : refined atoms                    680     2.135     1.970
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall               : scale =    0.876, B  =   0.591
Partial structure    1: scale =    0.427, B  =  25.205
Overall anisotropic scale factors
   B11 = -0.02 B22 = -0.02 B33 =  0.05 B12 = -0.01 B13 = -0.00 B23 = -0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.3032
Free R factor                        =     0.3305
Overall Fourier shell correlation    =     0.7437
Free Fourier shell correlation       =     0.0000
Overall figure of merit              =     0.8154
-----------------------------------------------------------------------------
 Trying gamma equal    0.0000000    
 Convergence reached with no gamma cycles 


 fvalues    18055.277       4639.7793       168439.86       168778.67    


     CGMAT cycle number =      6

 Weight matrix    1.1316156    
 Actual weight    9.0909090      is applied to the X-ray term


 function value    167553.27    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                   506     0.025     0.020
Bond angles  : refined atoms                    680     2.148     1.970
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall               : scale =    0.883, B  =   0.485
Partial structure    1: scale =    0.426, B  =  25.183
Overall anisotropic scale factors
   B11 = -0.02 B22 = -0.02 B33 =  0.05 B12 = -0.01 B13 = -0.00 B23 = -0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.3016
Free R factor                        =     0.3310
Overall Fourier shell correlation    =     0.7443
Free Fourier shell correlation       =     0.0000
Overall figure of merit              =     0.8159
-----------------------------------------------------------------------------
 Trying gamma equal    0.0000000    
 Convergence reached with no gamma cycles 


 fvalues    17874.797       4692.5469       167091.80       167190.70    


     CGMAT cycle number =      7

 Weight matrix    1.1310663    
 Actual weight    9.0909090      is applied to the X-ray term


 function value    167127.47    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                   506     0.025     0.020
Bond angles  : refined atoms                    680     2.164     1.970
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall               : scale =    0.885, B  =   0.442
Partial structure    1: scale =    0.424, B  =  24.672
Overall anisotropic scale factors
   B11 = -0.02 B22 = -0.02 B33 =  0.05 B12 = -0.01 B13 = -0.00 B23 = -0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.3009
Free R factor                        =     0.3312
Overall Fourier shell correlation    =     0.7445
Free Fourier shell correlation       =     0.0000
Overall figure of merit              =     0.8159
-----------------------------------------------------------------------------
 Trying gamma equal    0.0000000    
 Convergence reached with no gamma cycles 


 fvalues    17822.865       4737.0430       166709.22       166763.09    


     CGMAT cycle number =      8

 Weight matrix    1.1330845    
 Actual weight    9.0909090      is applied to the X-ray term


 function value    166863.34    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                   506     0.024     0.020
Bond angles  : refined atoms                    680     2.169     1.970
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall               : scale =    0.887, B  =   0.424
Partial structure    1: scale =    0.424, B  =  24.829
Overall anisotropic scale factors
   B11 = -0.01 B22 = -0.01 B33 =  0.05 B12 = -0.01 B13 = -0.00 B23 = -0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.3007
Free R factor                        =     0.3316
Overall Fourier shell correlation    =     0.7446
Free Fourier shell correlation       =     0.0000
Overall figure of merit              =     0.8160
-----------------------------------------------------------------------------
 Trying gamma equal    0.0000000    
 Convergence reached with no gamma cycles 


 fvalues    17795.641       4734.8643       166484.92       166513.41    


     CGMAT cycle number =      9

 Weight matrix    1.1330613    
 Actual weight    9.0909090      is applied to the X-ray term


 function value    166952.06    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                   506     0.024     0.020
Bond angles  : refined atoms                    680     2.174     1.970
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall               : scale =    0.886, B  =   0.400
Partial structure    1: scale =    0.427, B  =  25.112
Overall anisotropic scale factors
   B11 = -0.01 B22 = -0.01 B33 =  0.05 B12 = -0.01 B13 = -0.00 B23 = -0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.3005
Free R factor                        =     0.3321
Overall Fourier shell correlation    =     0.7446
Free Fourier shell correlation       =     0.0000
Overall figure of merit              =     0.8160
-----------------------------------------------------------------------------
 Trying gamma equal    0.0000000    
 Convergence reached with no gamma cycles 


 fvalues    17806.213       4740.3647       166600.48       166615.02    


     CGMAT cycle number =     10

 Weight matrix    1.0304188    
 Actual weight    8.2644625      is applied to the X-ray term


 function value    152329.78    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                   506     0.024     0.020
Bond angles  : refined atoms                    680     2.175     1.970
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall               : scale =    0.885, B  =   0.388
Partial structure    1: scale =    0.427, B  =  25.187
Overall anisotropic scale factors
   B11 = -0.02 B22 = -0.02 B33 =  0.05 B12 = -0.01 B13 = -0.00 B23 = -0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.3003
Free R factor                        =     0.3322
Overall Fourier shell correlation    =     0.7446
Free Fourier shell correlation       =     0.0000
Overall figure of merit              =     0.8160
-----------------------------------------------------------------------------
 Trying gamma equal    0.0000000    
 Convergence reached with no gamma cycles 


 fvalues    17821.125       4736.8184       152001.09       152018.83    

 Limits of asymmetric unit      : 1.00 1.00 0.50
 Grid spacing to be used        :    96   96  288
 Maximuum H,K,L                 :    27   27   78
 Minimum acceptable grid spacing:    59   59  178
 Limits of asymmetric unit      : 1.00 1.00 0.50
 Grid spacing to be used        :    96   96  288
 Maximuum H,K,L                 :    27   27   78
 Minimum acceptable grid spacing:    59   59  178

 WRITTEN OUTPUT MTZ FILE 
 Logical Name: HKLOUT   Filename: buccaneer_pipeline/refine.mtz 

Norm of X_ray positional gradient                0.00
Norm of Geom. positional gradient                0.00
Norm of X_ray B-factor gradient                  0.00
Norm of Geom. B-factor gradient                  0.00
Product of X_ray and Geom posit. gradients       0.00
 Cosine of angle between them                       0.000
Product of X_ray and Geom B-fact gradients       0.00
 Cosine of angle between them                       0.000


Residuals: XRAY=     0.1481E+06 GEOM=      4553.     TOTAL=     0.1527E+06

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                   506     0.023     0.020
Bond angles  : refined atoms                    680     2.109     1.970
Torsion angles, period  1. refined               59     3.228     5.000
Torsion angles, period  2. refined               29    28.144    26.207
Torsion angles, period  3. refined              103    14.674    15.000
Torsion angles, period  4. refined                3    18.144    15.000
Chiral centres: refined atoms                    78     0.152     0.200
Planar groups: refined atoms                    374     0.011     0.020
VDW repulsions: refined_atoms                   190     0.223     0.200
VDW; torsion: refined_atoms                     364     0.305     0.200
HBOND: refined_atoms                              5     0.253     0.200
VDW repulsions: symmetry: refined_atoms          33     0.227     0.200
HBOND: symmetry: refined_atoms                    2     0.342     0.200
M. chain bond B values: refined atoms           239     2.041     1.738
M. chain angle B values: refined atoms          297     3.061     2.582
S. chain bond B values: refined atoms           267     7.337     2.872
S. chain angle B values: refined atoms          383    10.844     3.881
Long range B values: refined atoms              744    12.782    16.696
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall               : scale =    0.883, B  =   0.365
Partial structure    1: scale =    0.425, B  =  25.161
Overall anisotropic scale factors
   B11 = -0.02 B22 = -0.02 B33 =  0.06 B12 = -0.01 B13 = -0.00 B23 = -0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------

    ****                Things for loggraph, R factor and others                ****


$TABLE: Cycle   11. Rfactor analysis, F distribution v resln  :
$GRAPHS:Cycle   11.  v. resln :N:1,6,7,11,12:
:Cycle   11.  and  v. resln :N:1,4,5,9,10:
:Cycle   11. % observed v. resln :N:1,3:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.014     172  83.11   144.1   162.1  0.39  0.57      10   174.9   148.1  0.33  0.31
 0.036     325  96.34   171.4   168.6  0.31  0.39      17   185.1   168.5  0.28  0.36
 0.058     417  97.12   220.8   209.2  0.23  0.28      22   206.7   189.0  0.32  0.45
 0.080     492  99.61   189.9   177.9  0.24  0.30      25   191.4   165.7  0.34  0.43
 0.102     551  99.66   136.4   127.9  0.31  0.37      29   140.4   126.9  0.36  0.39
 0.124     618  99.69   121.7   116.9  0.29  0.33      33   115.9   118.9  0.37  0.42
 0.147     674  99.58   104.3   101.9  0.26  0.29      35   109.4   102.6  0.25  0.27
 0.169     703  99.33    93.8    88.8  0.28  0.32      37    86.2    79.6  0.26  0.27
 0.191     765  99.51    84.0    75.4  0.29  0.30      41    92.2    81.6  0.29  0.31
 0.213     791  99.40    77.9    63.7  0.31  0.31      41    68.6    59.0  0.40  0.38
 0.235     838  99.10    64.4    52.7  0.33  0.32      44    62.3    46.1  0.41  0.39
 0.257     890  99.26    54.4    44.0  0.33  0.33      47    53.4    44.1  0.35  0.35
 0.279     890  99.05    44.6    37.8  0.35  0.34      47    39.4    35.8  0.39  0.37
 0.301     935  99.19    36.3    31.9  0.36  0.34      49    36.7    34.4  0.31  0.29
 0.323     996  98.78    31.0    29.6  0.36  0.33      53    31.1    30.1  0.35  0.28
 0.346    1015  98.89    28.7    27.4  0.35  0.32      53    29.2    27.9  0.33  0.32
 0.368    1029  98.63    25.7    25.7  0.33  0.30      54    22.4    22.7  0.43  0.41
 0.390    1084  98.70    24.1    23.5  0.31  0.28      57    26.7    26.2  0.30  0.30
 0.412    1081  98.36    21.3    21.6  0.31  0.28      57    22.7    24.1  0.34  0.28
 0.434    1105  97.08    18.6    19.8  0.35  0.30      58    20.5    20.1  0.31  0.29
$$

    ****                      Fom and SigmaA vs resolution                      ****

 $TABLE: Cycle   11. FSC and  Fom(-acentric, centric, overall v resln:
 $GRAPHS:Cycle   11. M(Fom) v. resln :N:1,3,5,7,8,9,10:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCwork  FSCfree$$
 $$
  0.0140   164   0.712     8   0.585   172   0.706  0.893  0.5392 *******
  0.0361   312   0.777    13   0.646   325   0.772  0.899  0.5370 *******
  0.0582   402   0.876    15   0.673   417   0.868  0.905  0.7069 *******
  0.0803   478   0.843    14   0.848   492   0.843  0.909  0.7514 *******
  0.1024   535   0.786    16   0.877   551   0.789  0.911  0.6932 *******
  0.1245   605   0.812    13   0.762   618   0.811  0.896  0.7173 *******
  0.1466   659   0.823    15   0.786   674   0.822  0.892  0.7605 *******
  0.1687   691   0.866    12   0.987   703   0.868  0.929  0.7973 *******
  0.1908   748   0.857    17   0.812   765   0.856  0.965  0.8016 *******
  0.2129   778   0.820    13   0.807   791   0.820  0.987  0.7790 *******
  0.2350   823   0.779    15   0.723   838   0.778  0.992  0.7436 *******
  0.2571   875   0.836    15   0.722   890   0.834  1.030  0.7639 *******
  0.2792   877   0.821    13   0.892   890   0.822  0.971  0.7458 *******
  0.3013   923   0.770    12   0.876   935   0.772  0.883  0.6819 *******
  0.3234   978   0.787    18   0.700   996   0.786  0.837  0.7015 *******
  0.3455   998   0.793    17   0.874  1015   0.795  0.804  0.7422 *******
  0.3677  1016   0.815    13   0.930  1029   0.817  0.808  0.7661 *******
  0.3898  1069   0.854    15   0.763  1084   0.853  0.850  0.7982 *******
  0.4119  1066   0.824    15   0.783  1081   0.823  0.827  0.7713 *******
  0.4340  1090   0.815    15   0.687  1105   0.813  0.764  0.7563 *******
 $$
Resolution limits                    =     18.578     1.499
Number of used reflections           =      15371
Percentage observed                  =    98.5504
Percentage of free reflections       =     5.0000
Overall R factor                     =     0.3003
Free R factor                        =     0.3319
Overall Fourier shell correlation    =     0.7442
Free Fourier shell correlation       =     0.0000
Overall weighted R factor            =     0.3242
Free weighted R factor               =     0.3470
Overall weighted R2 factor           =     0.4142
Free weighted R2 factor              =     0.4503
Overall correlation coefficient      =     0.9003
Free correlation coefficient         =     0.8684
Cruickshanks DPI for coordinate error=     0.0891
DPI based on free R factor           =     0.0918
Overall figure of merit              =     0.8160
ML based su of positional parameters =     0.0702
ML based su of thermal parameters    =     1.8276
-----------------------------------------------------------------------------
  Time in seconds: CPU =        40.16
             Elapsed =           0.00

    ****           Things for loggraph, R factor and others vs cycle            ****


$TABLE: Rfactor analysis, stats vs cycle  :
$GRAPHS: vs cycle :N:1,2,3:
:FOM vs cycle :N:1,4:
:-LL vs cycle :N:1,5:
:-LLfree vs cycle :N:1,6:
:Geometry vs cycle:N:1,7,8,9,10,11:
$$
    Ncyc    Rfact    Rfree     FOM      -LL     -LLfree  rmsBOND  zBOND rmsANGL  zANGL rmsCHIRAL $$
$$
       0   0.3734   0.4036   0.767     28111.    3756.5   0.0109  0.604   1.303  0.634   0.070
       1   0.3355   0.3660   0.790     23018.    3665.4   0.0162  0.822   1.365  0.664   0.079
       2   0.3150   0.3405   0.806     19602.    3576.3   0.0265  1.345   2.009  0.984   0.137
       3   0.3054   0.3311   0.813     18523.    3540.4   0.0254  1.278   2.086  1.035   0.151
       4   0.3032   0.3305   0.815     18089.    3523.6   0.0248  1.246   2.135  1.064   0.155
       5   0.3016   0.3310   0.816     17915.    3517.1   0.0245  1.235   2.148  1.074   0.157
       6   0.3009   0.3312   0.816     17863.    3515.4   0.0245  1.234   2.164  1.083   0.158
       7   0.3007   0.3316   0.816     17834.    3514.8   0.0245  1.230   2.169  1.086   0.158
       8   0.3005   0.3321   0.816     17843.    3515.7   0.0245  1.230   2.174  1.088   0.159
       9   0.3003   0.3322   0.816     17859.    3516.7   0.0245  1.229   2.175  1.090   0.159
      10   0.3003   0.3319   0.816     17921.    3518.4   0.0233  1.168   2.109  1.055   0.152
 $$
 $TEXT:Result: $$ Final results $$
                      Initial    Final
           R factor    0.3734   0.3003
             R free    0.4036   0.3319
     Rms BondLength    0.0109   0.0233
      Rms BondAngle    1.3032   2.1085
     Rms ChirVolume    0.0700   0.1517
 $$

 Refmac_5.8.0049:  End of Refmac_5.8.0049  
Times: User:      40.2s System:    3.1s Elapsed:     0:43  

 
 ###############################################################
 ###############################################################
 ###############################################################
 ### CCP4 6.4: cbuccaneer             version 1.5.2 : 06/10/11##
 ###############################################################
 User: unknown  Run date: 17/ 7/2014 Run time: 18:55:39 


 Please reference: Collaborative Computational Project, Number 4. 1994.
 "The CCP4 Suite: Programs for Protein Crystallography". Acta Cryst. D50, 760-763.
 as well as any specific reference in the program write-up.



Copyright 2002-2010 Kevin Cowtan and University of York.


$TEXT:Reference: $$ Please reference $$

 'Fitting molecular fragments into electron density'
 Cowtan K. (2008) Acta Cryst. D64, 83-89.

$$
$TEXT:Reference: $$ Please reference $$

 'The Buccaneer software for automated model building'
 Cowtan K. (2006) Acta Cryst. D62, 1002-1011.

$$


title 	buccaneer auto-build
pdbin-ref 	/home/jmht/ccp4-6.4.0/lib/data/reference_structures/reference-1tqw.pdb
mtzin-ref 	/home/jmht/ccp4-6.4.0/lib/data/reference_structures/reference-1tqw.mtz
colin-ref-fo 	FP.F_sigF.F,FP.F_sigF.sigF
colin-ref-hl 	FC.ABCD.A,FC.ABCD.B,FC.ABCD.C,FC.ABCD.D
seqin 	/data1/jmht/polya_helices/3PP5/search_polya_15/input/3PP5_1.fasta
mtzin 	buccaneer_pipeline/refine.mtz
colin-fo 	FP, SIGFP
colin-hl 	HLACOMB,HLBCOMB,HLCCOMB,HLDCOMB
colin-fc 	FWT,PHWT
colin-free 	FREE
pdbin 	buccaneer_pipeline/refine.pdb
pdbout 	buccaneer_pipeline/build.pdb
anisotropy-correction
fast
cycles 	2
sequence-reliability 	0.95
correlation-mode
new-residue-name 	UNK
resolution 	2.0

MTZ file: buccaneer_pipeline/refine.mtz
  Number of reflections:     16180        Number of columns:  22

Applying anisotropy correction:
|-9.168e-15, 1.095e-16,-8.236e-17|
| 1.095e-16,         0,-2.269e-17|
|-8.236e-17,-2.269e-17,   -0.1084|

PDB file: buccaneer_pipeline/refine.pdb
  Number of atoms read: 501

Cycle: 1

 C-alphas after finding:    76
 C-alphas after growing:    118
 C-alphas after joining:    60
 C-alphas linked:           0
 C-alphas sequenced:        57
 C-alphas corrected:        0
 C-alphas after filtering:  60
 C-alphas after NCS build:  60
 C-alphas after pruning:    60
 C-alphas after rebuilding: 60


Internal cycle   1
     60 residues were built in   1 fragments, the longest having   60 residues.
     57 residues were sequenced, after pruning.
     60 residues were uniquely allocated to   1 chains.
  Completeness by residues built:   100.0%
  Completeness of chains (number):   82.2%    (1)



Cycle: 2

 C-alphas after finding:    76
 C-alphas after growing:    141
 C-alphas after joining:    70
 C-alphas linked:           0
 C-alphas sequenced:        67
 C-alphas corrected:        0
 C-alphas after filtering:  70
 C-alphas after NCS build:  70
 C-alphas after pruning:    60
 C-alphas after rebuilding: 60


Internal cycle   2
     60 residues were built in   1 fragments, the longest having   60 residues.
     57 residues were sequenced, after pruning.
     60 residues were uniquely allocated to   1 chains.
  Completeness by residues built:   100.0%
  Completeness of chains (number):   82.2%    (1)


$TEXT:Result: $$ $$
     60 residues were built in   1 fragments, the longest having   60 residues.
     57 residues were sequenced, after pruning.
     60 residues were uniquely allocated to   1 chains.
  Completeness by residues built:   100.0%
  Completeness of chains (number):   82.2%    (1)
$$


cbuccaneer: Normal termination
Times: User:      19.4s System:    0.0s Elapsed:     0:20  

 
 ###############################################################
 ###############################################################
 ###############################################################
 ### CCP4 6.4: Refmac_5.8.0049     version 5.8.0049 : 30/06/13##
 ###############################################################
 User: unknown  Run date: 17/ 7/2014 Run time: 18:55:59 


 Please reference: Collaborative Computational Project, Number 4. 1994.
 "The CCP4 Suite: Programs for Protein Crystallography". Acta Cryst. D50, 760-763.
 as well as any specific reference in the program write-up.


 $TEXT:Reference1: $$ Main reference $$ 
   "REFMAC5 for the refinement of macromolecular crystal structures:"
   G.N.Murshudov, P.Skubak, A.A.Lebedev, N.S.Pannu, R.A.Steiner, R.A.Nicholls, M.D.Winn, F.Long and A.A.Vagin,(2011) 
   Acta Crystallogr. D67, 355-367

 $$
 $SUMMARY :Reference1:  $$ Refmac: $$
 :TEXT:Reference1: $$

 $TEXT:Reference2: $$ Secondary reference $$ 
   "Refinement of Macromolecular Structures by the  Maximum-Likelihood Method:"
   G.N. Murshudov, A.A.Vagin and E.J.Dodson,(1997)
   Acta Crystallogr. D53, 240-255
   EU  Validation contract: BIO2CT-92-0524

 $$
 $SUMMARY :Reference2:  $$ Refmac: $$
 :TEXT:Reference2: $$

  Data line--- title  buccaneer auto-build
  Data line--- ncyc 10
  Data line--- labin                    PHIB=PHIC FOM= FOM                FREE=FREE   FP=FP SIGFP= SIGFP
  Data line--- weight AUTO
  Data line--- make check NONE
  Data line--- make hydrogen NO hout NO peptide NO cispeptide YES ssbridge YES symmetry YES sugar YES connectivity NO link NO
  Data line--- refi type REST PHASE resi MLKF meth CGMAT bref ISOT
  Data line--- scal type SIMP LSSC ANISO EXPE
  Data line--- solvent YES VDWProb 1.4 IONProb 0.8 RSHRink 0.8
  Data line--- PHOUT
  Data line--- PNAME buccaneer
  Data line--- DNAME buccaneer
  Data line--- END

 OPENED INPUT MTZ FILE 
 Logical Name: HKLIN   Filename: /data1/jmht/polya_helices/3PP5/search_polya_15/data/loc0_ALL_polya_15/unmod/mr/phaser/build/shelxe/rebuild/refine/refmacSX_output.mtz 


 Spacegroup information obtained from library file: 
 Logical Name: SYMINFO   Filename: /home/jmht/ccp4-6.4.0/lib/data/syminfo.lib


    ****                     Input and Default parameters#                      ****


Input coordinate file.  Logical name - XYZIN actual file name  - buccaneer_pipeline/build.pdb
Output coordinate file. Logical name - XYZOUT actual file name - buccaneer_pipeline/refine.pdb
Input reflection file.  Logical name - HKLIN actual file name  - /data1/jmht/polya_helices/3PP5/search_polya_15/data/loc0_ALL_polya_15/unmod/mr/phaser/build/shelxe/rebuild/refine/refmacSX_outpu
Output reflection file. Logical name - HKLOUT actual file name - buccaneer_pipeline/refine.mtz

Cell from mtz :    39.140    39.140   118.190    90.000    90.000   120.000
Space group from mtz: number -  173; name - P 63

  Refinement type                        : Restrained


    ****                           Makecif parameters                           ****

Dictionary files for restraints : /home/jmht/ccp4-6.4.0/lib/data/monomers/mon*cif
Parameters for new entry and VDW: /home/jmht/ccp4-6.4.0/lib/data/monomers/ener_lib.cif
    Program will rely on residue and atom names. No checking
    If this option is used then monomers should be checked carefully before using
    Hydrogens will not be written to the output file
    Links between monomers will be checked. Only those links present in the coordinate file will be used
    All links to sugar will be analysed and used
    For new ligands "ideal restraint" values will be taken from the energetic libary ener_lib.cif
    Symmetry related links will be analysed and used
    Cis peptides will be found and used automatically


  Residual                               : Phase modified Maximum Likelihood for Fs
 Phase Blurred by  Scale*Exp(-B s**2)    :    1.00    0.00

    ****                    Least-square scaling parameters                     ****

Overall scale
Overall B value
Overall anisotropic B with tr(B) = 0.0
Constant bulk solvent in non protein region
Probe radii for non-ions     1.400
Probe radii for ions         0.800
Shrinkage of the mask  by    0.800


    ****                 Map sharpening parameters and methods                  ****

No map sharpening will be performed

  Method of minimisation                 : Sparse Matrix
  Experimental sigmas used for weighting
  Number of Bins and width:    20       0.0223
  Refinement of individual isotropic Bfactors
  Refinement resln        :    18.5778  1.4990
  Estimated number of reflections :      26875
  Free R exclusion - flag equals:     0
  Auto weighting. An attempt
  Refinement cycles       :    10
  Scaling type                           :
          Wilson using 1 Gaussian

  Estimation of D/Sigma in resolution bins
  using  free set of reflns with experimental sigmas
  Input phases not used in SigmaA estimation

  Scaling and SigmaA resln:    18.5778  1.4990

  Damping factors:     1.0000  1.0000


    ****                    Geometry restraints and weights                     ****


                                              Sigma:
 Bonding distances
          Weight =  1.00

 Bond angles
          Weight =  1.00

 Planar groups (all and main chain)
          WEIGHT= 1.00 1.00

 Chiral centers
          Weight= 1.00

 NON-BONDED CONTACTS
          Overall weight                          =  1.00
          Sigma for simple VDW                    =  0.20
          Sigma for VDW trhough torsion angle     =  0.20
          Sigma for HBOND                         =  0.20
          Sigma for metal-ion                     =  0.20
          Sigma for DUMMY and other atom          =  0.30
          Distance for donor-accepetor = vdw1+vdw2+(-0.30)
          Distance for acceptor - H    = vdw1+     ( 0.10)
          VDW distance through torsion = vdw1+vdw2+(-0.30)
          Distance for DUMMY-others    = vdw1+vdw2+(-0.70)

 TORSION ANGLES
          Weight= 1.00

 THERMAL FACTORS
          Weight= 1.00
     Main chain bond (1-2 neighbour)          1.5A**2
     Main chain angle (1-3 neighbour)         2.0A**2
     Side chain bond                          3.0A**2
     Side chain angle                         4.5A**2

 RESTRAINTS AGAINST EXCESSIVE SHIFTS
     Positional parameters                   0.00A
     Thermal parameters                      0.00A
     Occupancy parameters                    0.00

 RADIUS OF CONFIDENCE
     Positional parameters 0.00A
     Thermal parameters    0.00A**2
     Occupancy parameters  0.00

Monitoring style is "MEDIUM". Complete information will be printed out in the
first and last cycle. In all other cycles minimum information will be printed out
Sigma cutoffs for printing out outliers
If deviation of restraint parameter > alpha*sigma then information will be printed out
Distance outliers      10.000
Angle outliers         10.000
Torsion outliers       10.000
Chiral volume outliers 10.000
Plane outliers         10.000
Non-bonding outliers   10.000
B value  outliers      10.000
---------------------------------------------------------------

 Input file :buccaneer_pipeline/build.pdb
  ------------------------------
  ---  LIBRARY OF MONOMERS   ---
 _lib_name         mon_lib
 _lib_version      5.41
 _lib_update       11/02/13
  ------------------------------
  NUMBER OF MONOMERS IN THE LIBRARY          : 11464
                with complete description    : 11464
  NUMBER OF MODIFICATIONS                    :    56
  NUMBER OF LINKS                            :    68
  I am reading libraries. Please wait.
      - energy parameters
      - monomer"s description (links & mod )

FORMATTED      OLD     file opened on unit  45

Logical name: ATOMSF, Filename: /home/jmht/ccp4-6.4.0/lib/data/atomsf.lib


  Number of atoms    :     501
  Number of residues :      60
  Number of chains   :       1
  I am reading library. Please wait.
                mon_lib.cif
  --------------------------------
  --- title of input coord file ---

  PDB_code:xxxx
  PDB_name:----
  PDB_date:XX-XXX-XX
  --------------------------------
  ATTENTION: atom:CG   UNK                 9  AA   is missing in the structure
  ATTENTION: atom:CG   UNK                10  AA   is missing in the structure
  ATTENTION: atom:CG   UNK                68  AA   is missing in the structure
  Number of chains                  :       1
  Total number of monomers          :      60
  Number of atoms                   :     504
  Number of missing atoms           :       3
  Number of rebuilt atoms           :       0
  Number of unknown atoms           :       0
  Number of deleted atoms           :       0

  Number of bonds restraints    :     506
  Number of angles restraints   :     680
  Number of torsions restraints :     340
  Number of chiralities         :      78
  Number of planar groups       :      88


 loop_
     _atom_type_symbol
     _atom_type_scat_Cromer_Mann_a1
     _atom_type_scat_Cromer_Mann_b1
     _atom_type_scat_Cromer_Mann_a2
     _atom_type_scat_Cromer_Mann_b2
     _atom_type_scat_Cromer_Mann_a3
     _atom_type_scat_Cromer_Mann_b3
     _atom_type_scat_Cromer_Mann_a4
     _atom_type_scat_Cromer_Mann_b4
     _atom_type_scat_Cromer_Mann_c


  N     12.2126   0.0057   3.1322   9.8933   2.0125  28.9975   1.1663   0.5826 -11.5290
  C      2.3100  20.8439   1.0200  10.2075   1.5886   0.5687   0.8650  51.6512   0.2156
  O      3.0485  13.2771   2.2868   5.7011   1.5463   0.3239   0.8670  32.9089   0.2508
  S      6.9053   1.4679   5.2034  22.2151   1.4379   0.2536   1.5863  56.1720   0.8669


 Number of distances         :           0
 Number of angles            :           0
 Number of torsions          :           0
 Number of planes            :           0
 Number of chirals           :           0
 Number of intervals         :           0
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
                        Standard  External       All
                Bonds:       506         0       506
               Angles:       680         0       680
              Chirals:        78         0        78
               Planes:        88         0        88
             Torsions:       340         0       340
            Intervals:         0         0         0
--------------------------------------------------------------------------------


  Number of harmonic restraints       =            0
  Number of atoms in special position =            0
 -----------------------------------------------------


    ****                           Info from mtz file                           ****

FreeR flag                            0
Number of "free" reflections        809
Number of   all  reflections      16180
--------------------------------------------------------------------------------
 Number of reflections in file      16180
 Number of reflections read          16180


     CGMAT cycle number =      1

    ****                         Bond distance outliers                         ****

Bond distance deviations from the ideal >10.000Sigma will be monitored

A     12 ASN C   . - A     13 ILE N   . mod.= 0.844 id.= 1.329 dev=  0.485 sig.= 0.014
A     68 UNK CA  . - A     68 UNK C   . mod.= 1.042 id.= 1.500 dev=  0.458 sig.= 0.020

    ****                          Bond angle outliers                           ****

Bond angle deviations from the ideal >10.000Sigma will be monitored

A     12 ASN CA    - A     13 ILE N     mod.= 170.77 id.= 116.20 dev=-54.566 sig.=  2.000
A     12 ASN C     - A     13 ILE CA    mod.= 169.61 id.= 121.70 dev=-47.914 sig.=  1.800
A     12 ASN O     - A     13 ILE N     mod.=  68.28 id.= 123.00 dev= 54.717 sig.=  1.600

 Limits of asymmetric unit      : 1.00 1.00 0.50
 Grid spacing to be used        :    96   96  288
 Maximuum H,K,L                 :    27   27   78
 Minimum acceptable grid spacing:    59   59  178
 Limits of asymmetric unit      : 1.00 1.00 0.50
 Grid spacing to be used        :    96   96  288
 Maximuum H,K,L                 :    27   27   78
 Minimum acceptable grid spacing:    59   59  178
 Weight matrix   0.50224590    
 Actual weight    10.000000      is applied to the X-ray term
Norm of X_ray positional gradient                199.
Norm of Geom. positional gradient                176.
Norm of X_ray B-factor gradient                 0.178E+04
Norm of Geom. B-factor gradient                  0.00
Product of X_ray and Geom posit. gradients      0.410E+07
 Cosine of angle between them                       0.078
Product of X_ray and Geom B-fact gradients       0.00
 Cosine of angle between them                       0.000


Residuals: XRAY=     0.2882E+06 GEOM=      4247.     TOTAL=     0.2924E+06
 function value    292449.03    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                   506     0.033     0.020
Bond angles  : refined atoms                    680     3.937     1.970
Torsion angles, period  1. refined               59     2.791     5.000
Torsion angles, period  2. refined               29    30.728    26.207
Torsion angles, period  3. refined              103    11.000    15.000
Torsion angles, period  4. refined                3    11.391    15.000
Chiral centres: refined atoms                    78     0.152     0.200
Planar groups: refined atoms                    374     0.000     0.020
VDW repulsions: refined_atoms                   212     0.265     0.200
VDW; torsion: refined_atoms                     373     0.319     0.200
HBOND: refined_atoms                              7     0.321     0.200
VDW repulsions: symmetry: refined_atoms          28     0.407     0.200
M. chain bond B values: refined atoms           239     0.000     3.948
M. chain angle B values: refined atoms          297     0.000     5.922
S. chain bond B values: refined atoms           263     0.000     3.948
S. chain angle B values: refined atoms          383     0.000     5.922
Long range B values: refined atoms              773     0.000    32.640
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall               : scale =    0.763, B  = -22.434
Partial structure    1: scale =    0.484, B  =  47.099
Overall anisotropic scale factors
   B11 = -0.12 B22 = -0.12 B33 =  0.40 B12 = -0.06 B13 = -0.00 B23 = -0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------

    ****                Things for loggraph, R factor and others                ****


$TABLE: Cycle    1. Rfactor analysis, F distribution v resln  :
$GRAPHS:Cycle    1.  v. resln :N:1,6,7,11,12:
:Cycle    1.  and  v. resln :N:1,4,5,9,10:
:Cycle    1. % observed v. resln :N:1,3:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.014     172  83.11   166.8   166.2  0.39  0.55      10   202.5   139.6  0.49  0.57
 0.036     325  96.34   198.4   195.6  0.36  0.46      17   214.2   198.2  0.34  0.43
 0.058     417  97.12   255.6   237.9  0.29  0.36      22   239.3   214.6  0.34  0.45
 0.080     492  99.61   219.8   198.6  0.32  0.39      25   221.5   196.6  0.31  0.41
 0.102     551  99.66   157.9   143.7  0.39  0.45      29   162.5   129.0  0.37  0.39
 0.124     618  99.69   140.9   131.1  0.35  0.40      33   134.2   113.3  0.43  0.48
 0.147     674  99.58   120.7   112.3  0.36  0.41      35   126.6   126.7  0.25  0.26
 0.169     703  99.33   108.6    93.5  0.37  0.39      37    99.7    92.1  0.42  0.44
 0.191     765  99.51    97.3    81.2  0.39  0.40      41   106.8    87.2  0.35  0.36
 0.213     791  99.40    90.1    74.3  0.39  0.39      41    79.4    67.6  0.43  0.41
 0.235     838  99.10    74.6    63.2  0.40  0.39      44    72.1    58.3  0.42  0.42
 0.257     890  99.26    62.9    52.2  0.42  0.40      47    61.8    46.2  0.41  0.39
 0.279     890  99.05    51.6    43.4  0.42  0.40      47    45.6    39.9  0.43  0.40
 0.301     935  99.19    42.1    36.9  0.44  0.42      49    42.5    39.7  0.45  0.42
 0.323     996  98.78    35.9    33.8  0.45  0.41      53    36.0    36.2  0.41  0.34
 0.346    1015  98.89    33.2    30.8  0.46  0.42      53    33.8    30.1  0.44  0.40
 0.368    1029  98.63    29.7    27.7  0.45  0.41      54    26.0    27.5  0.60  0.53
 0.390    1084  98.70    27.9    24.8  0.44  0.41      57    30.9    24.6  0.46  0.46
 0.412    1081  98.36    24.7    21.3  0.45  0.41      57    26.2    23.6  0.43  0.35
 0.434    1105  97.08    21.5    18.2  0.46  0.43      58    23.8    18.5  0.43  0.45
$$

    ****                      Fom and SigmaA vs resolution                      ****

 $TABLE: Cycle    1. FSC and  Fom(-acentric, centric, overall v resln:
 $GRAPHS:Cycle    1. M(Fom) v. resln :N:1,3,5,7,8,9,10:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCwork  FSCfree$$
 $$
  0.0140   164   0.687     8   0.593   172   0.683  0.908  0.4948 *******
  0.0361   312   0.774    13   0.695   325   0.771  0.911  0.4731 *******
  0.0582   402   0.862    15   0.658   417   0.855  0.914  0.6327 *******
  0.0803   478   0.821    14   0.822   492   0.821  0.916  0.6762 *******
  0.1024   535   0.755    16   0.840   551   0.758  0.915  0.5884 *******
  0.1245   605   0.777    13   0.725   618   0.775  0.886  0.6194 *******
  0.1466   659   0.783    15   0.769   674   0.783  0.875  0.6447 *******
  0.1687   691   0.816    12   0.969   703   0.819  0.927  0.6753 *******
  0.1908   748   0.818    17   0.761   765   0.817  0.942  0.6679 *******
  0.2129   778   0.785    13   0.828   791   0.786  0.924  0.6320 *******
  0.2350   823   0.750    15   0.687   838   0.749  0.884  0.6002 *******
  0.2571   875   0.779    15   0.646   890   0.777  0.866  0.5618 *******
  0.2792   877   0.768    13   0.775   890   0.768  0.862  0.5410 *******
  0.3013   923   0.701    12   0.837   935   0.703  0.772  0.4656 *******
  0.3234   978   0.736    18   0.625   996   0.734  0.747  0.4942 *******
  0.3455   998   0.760    17   0.799  1015   0.761  0.746  0.5150 *******
  0.3677  1016   0.755    13   0.883  1029   0.756  0.641  0.5239 *******
  0.3898  1069   0.790    15   0.690  1084   0.789  0.646  0.5799 *******
  0.4119  1066   0.754    15   0.739  1081   0.754  0.738  0.5343 *******
  0.4340  1090   0.750    15   0.616  1105   0.748  0.734  0.5250 *******
 $$
Resolution limits                    =     18.578     1.499
Number of used reflections           =      15371
Percentage observed                  =    98.5504
Percentage of free reflections       =     5.0000
Overall R factor                     =     0.3801
Free R factor                        =     0.3887
Overall Fourier shell correlation    =     0.5675
Free Fourier shell correlation       =     0.0000
Overall weighted R factor            =     0.4079
Free weighted R factor               =     0.4073
Overall weighted R2 factor           =     0.5079
Free weighted R2 factor              =     0.4970
Overall correlation coefficient      =     0.8454
Free correlation coefficient         =     0.8320
Cruickshanks DPI for coordinate error=     0.1127
DPI based on free R factor           =     0.1075
Overall figure of merit              =     0.7685
ML based su of positional parameters =     0.1102
ML based su of thermal parameters    =     3.0144
-----------------------------------------------------------------------------
 Trying gamma equal    0.0000000    
 Convergence reached with no gamma cycles 


 fvalues    35264.137       4246.6655       297198.41       356888.03    


     CGMAT cycle number =      2

 Weight matrix   0.76097280    
 Actual weight    10.000000      is applied to the X-ray term


 function value    236243.22    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                   506     0.023     0.020
Bond angles  : refined atoms                    680     2.776     1.970
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall               : scale =    0.796, B  =  -9.723
Partial structure    1: scale =    0.478, B  =  37.754
Overall anisotropic scale factors
   B11 = -0.09 B22 = -0.09 B33 =  0.29 B12 = -0.04 B13 = -0.00 B23 = -0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.3390
Free R factor                        =     0.3513
Overall Fourier shell correlation    =     0.6882
Free Fourier shell correlation       =     0.0000
Overall figure of merit              =     0.7913
-----------------------------------------------------------------------------
 Trying gamma equal    0.0000000    
 Convergence reached with no gamma cycles 


 fvalues    28294.482       2767.8269       219519.53       285712.63    


     CGMAT cycle number =      3

 Weight matrix    1.0087540    
 Actual weight    10.000000      is applied to the X-ray term


 function value    201646.70    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                   506     0.027     0.020
Bond angles  : refined atoms                    680     2.217     1.970
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall               : scale =    0.854, B  =   2.053
Partial structure    1: scale =    0.425, B  =  23.952
Overall anisotropic scale factors
   B11 = -0.03 B22 = -0.03 B33 =  0.11 B12 = -0.02 B13 = -0.00 B23 = -0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.3150
Free R factor                        =     0.3366
Overall Fourier shell correlation    =     0.7344
Free Fourier shell correlation       =     0.0000
Overall figure of merit              =     0.8058
-----------------------------------------------------------------------------
 Trying gamma equal    0.0000000    
 Convergence reached with no gamma cycles 


 fvalues    19909.691       5447.2627       196021.61       204544.17    


     CGMAT cycle number =      4

 Weight matrix    1.0611429    
 Actual weight    9.0909090      is applied to the X-ray term


 function value    172815.52    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                   506     0.026     0.020
Bond angles  : refined atoms                    680     2.138     1.970
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall               : scale =    0.871, B  =   0.732
Partial structure    1: scale =    0.421, B  =  24.808
Overall anisotropic scale factors
   B11 = -0.02 B22 = -0.02 B33 =  0.07 B12 = -0.01 B13 = -0.00 B23 = -0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.3038
Free R factor                        =     0.3300
Overall Fourier shell correlation    =     0.7406
Free Fourier shell correlation       =     0.0000
Overall figure of merit              =     0.8126
-----------------------------------------------------------------------------
 Trying gamma equal    0.0000000    
 Convergence reached with no gamma cycles 


 fvalues    18497.369       4432.0400       171196.59       172589.95    


     CGMAT cycle number =      5

 Weight matrix    1.1092039    
 Actual weight    9.0909090      is applied to the X-ray term


 function value    169212.75    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                   506     0.025     0.020
Bond angles  : refined atoms                    680     2.149     1.970
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall               : scale =    0.880, B  =   0.518
Partial structure    1: scale =    0.413, B  =  24.048
Overall anisotropic scale factors
   B11 = -0.02 B22 = -0.02 B33 =  0.06 B12 = -0.01 B13 = -0.00 B23 = -0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.3003
Free R factor                        =     0.3282
Overall Fourier shell correlation    =     0.7433
Free Fourier shell correlation       =     0.0000
Overall figure of merit              =     0.8152
-----------------------------------------------------------------------------
 Trying gamma equal    0.0000000    
 Convergence reached with no gamma cycles 


 fvalues    18072.521       4592.2969       168547.27       168887.94    


     CGMAT cycle number =      6

 Weight matrix    1.1233571    
 Actual weight    9.0909090      is applied to the X-ray term


 function value    167790.30    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                   506     0.025     0.020
Bond angles  : refined atoms                    680     2.170     1.970
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall               : scale =    0.886, B  =   0.480
Partial structure    1: scale =    0.417, B  =  23.968
Overall anisotropic scale factors
   B11 = -0.01 B22 = -0.01 B33 =  0.04 B12 = -0.01 B13 = -0.00 B23 = -0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2989
Free R factor                        =     0.3278
Overall Fourier shell correlation    =     0.7436
Free Fourier shell correlation       =     0.0000
Overall figure of merit              =     0.8160
-----------------------------------------------------------------------------
 Trying gamma equal    0.0000000    
 Convergence reached with no gamma cycles 


 fvalues    17906.881       4688.5566       167345.91       167478.39    


     CGMAT cycle number =      7

 Weight matrix    1.1297624    
 Actual weight    9.0909090      is applied to the X-ray term


 function value    167225.98    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                   506     0.025     0.020
Bond angles  : refined atoms                    680     2.189     1.970
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall               : scale =    0.887, B  =   0.397
Partial structure    1: scale =    0.423, B  =  23.828
Overall anisotropic scale factors
   B11 = -0.01 B22 = -0.01 B33 =  0.03 B12 = -0.00 B13 = -0.00 B23 = -0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2984
Free R factor                        =     0.3285
Overall Fourier shell correlation    =     0.7437
Free Fourier shell correlation       =     0.0000
Overall figure of merit              =     0.8165
-----------------------------------------------------------------------------
 Trying gamma equal    0.0000000    
 Convergence reached with no gamma cycles 


 fvalues    17841.600       4705.5156       166846.20       166901.88    


     CGMAT cycle number =      8

 Weight matrix    1.0263306    
 Actual weight    8.2644625      is applied to the X-ray term


 function value    152295.05    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                   506     0.025     0.020
Bond angles  : refined atoms                    680     2.202     1.970
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall               : scale =    0.888, B  =   0.408
Partial structure    1: scale =    0.427, B  =  23.872
Overall anisotropic scale factors
   B11 = -0.01 B22 = -0.01 B33 =  0.03 B12 = -0.00 B13 = -0.00 B23 = -0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2983
Free R factor                        =     0.3289
Overall Fourier shell correlation    =     0.7438
Free Fourier shell correlation       =     0.0000
Overall figure of merit              =     0.8164
-----------------------------------------------------------------------------
 Trying gamma equal    0.0000000    
 Convergence reached with no gamma cycles 


 fvalues    17817.957       4733.1680       151953.17       151989.02    


     CGMAT cycle number =      9

 Weight matrix   0.93681371    
 Actual weight    7.5131474      is applied to the X-ray term


 function value    139119.30    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                   506     0.024     0.020
Bond angles  : refined atoms                    680     2.138     1.970
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall               : scale =    0.886, B  =   0.354
Partial structure    1: scale =    0.430, B  =  24.044
Overall anisotropic scale factors
   B11 = -0.01 B22 = -0.01 B33 =  0.03 B12 = -0.00 B13 = -0.00 B23 = -0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2985
Free R factor                        =     0.3291
Overall Fourier shell correlation    =     0.7433
Free Fourier shell correlation       =     0.0000
Overall figure of merit              =     0.8165
-----------------------------------------------------------------------------
 Trying gamma equal    0.0000000    
 Convergence reached with no gamma cycles 


 fvalues    17878.715       4539.7930       138837.88       138865.22    


     CGMAT cycle number =     10

 Weight matrix   0.93821031    
 Actual weight    7.5131474      is applied to the X-ray term


 function value    139213.03    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                   506     0.023     0.020
Bond angles  : refined atoms                    680     2.065     1.970
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall               : scale =    0.885, B  =   0.361
Partial structure    1: scale =    0.431, B  =  24.322
Overall anisotropic scale factors
   B11 = -0.01 B22 = -0.01 B33 =  0.03 B12 = -0.00 B13 = -0.00 B23 = -0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2987
Free R factor                        =     0.3289
Overall Fourier shell correlation    =     0.7427
Free Fourier shell correlation       =     0.0000
Overall figure of merit              =     0.8166
-----------------------------------------------------------------------------
 Trying gamma equal    0.0000000    
 Convergence reached with no gamma cycles 


 fvalues    17915.283       4352.3828       138941.33       138952.53    

 Limits of asymmetric unit      : 1.00 1.00 0.50
 Grid spacing to be used        :    96   96  288
 Maximuum H,K,L                 :    27   27   78
 Minimum acceptable grid spacing:    59   59  178
 Limits of asymmetric unit      : 1.00 1.00 0.50
 Grid spacing to be used        :    96   96  288
 Maximuum H,K,L                 :    27   27   78
 Minimum acceptable grid spacing:    59   59  178

 WRITTEN OUTPUT MTZ FILE 
 Logical Name: HKLOUT   Filename: buccaneer_pipeline/refine.mtz 

Norm of X_ray positional gradient                0.00
Norm of Geom. positional gradient                0.00
Norm of X_ray B-factor gradient                  0.00
Norm of Geom. B-factor gradient                  0.00
Product of X_ray and Geom posit. gradients       0.00
 Cosine of angle between them                       0.000
Product of X_ray and Geom B-fact gradients       0.00
 Cosine of angle between them                       0.000


Residuals: XRAY=     0.1347E+06 GEOM=      4343.     TOTAL=     0.1391E+06

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                   506     0.023     0.020
Bond angles  : refined atoms                    680     2.056     1.970
Torsion angles, period  1. refined               59     3.224     5.000
Torsion angles, period  2. refined               29    29.954    26.207
Torsion angles, period  3. refined              103    14.066    15.000
Torsion angles, period  4. refined                3    18.523    15.000
Chiral centres: refined atoms                    78     0.147     0.200
Planar groups: refined atoms                    374     0.010     0.020
VDW repulsions: refined_atoms                   193     0.212     0.200
VDW; torsion: refined_atoms                     357     0.303     0.200
HBOND: refined_atoms                              3     0.346     0.200
VDW repulsions: symmetry: refined_atoms          28     0.282     0.200
M. chain bond B values: refined atoms           239     2.055     1.747
M. chain angle B values: refined atoms          297     3.184     2.592
S. chain bond B values: refined atoms           267     7.108     2.864
S. chain angle B values: refined atoms          383    10.545     3.874
Long range B values: refined atoms              743    12.537    16.501
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall               : scale =    0.886, B  =   0.385
Partial structure    1: scale =    0.432, B  =  24.525
Overall anisotropic scale factors
   B11 = -0.01 B22 = -0.01 B33 =  0.03 B12 = -0.01 B13 = -0.00 B23 = -0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------

    ****                Things for loggraph, R factor and others                ****


$TABLE: Cycle   11. Rfactor analysis, F distribution v resln  :
$GRAPHS:Cycle   11.  v. resln :N:1,6,7,11,12:
:Cycle   11.  and  v. resln :N:1,4,5,9,10:
:Cycle   11. % observed v. resln :N:1,3:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.014     172  83.11   143.6   156.7  0.37  0.53      10   174.4   146.6  0.36  0.37
 0.036     325  96.34   170.9   172.4  0.31  0.40      17   184.5   173.3  0.26  0.27
 0.058     417  97.12   220.1   208.2  0.22  0.28      22   206.0   188.5  0.28  0.39
 0.080     492  99.61   189.3   177.3  0.24  0.30      25   190.7   167.0  0.27  0.35
 0.102     551  99.66   135.9   130.7  0.30  0.35      29   139.9   121.3  0.35  0.37
 0.124     618  99.69   121.3   116.5  0.29  0.33      33   115.5   117.9  0.40  0.44
 0.147     674  99.58   104.0   102.1  0.27  0.30      35   109.0   100.5  0.27  0.30
 0.169     703  99.33    93.5    88.7  0.29  0.33      37    85.9    83.1  0.33  0.35
 0.191     765  99.51    83.7    74.9  0.29  0.31      41    91.9    81.1  0.30  0.32
 0.213     791  99.40    77.6    64.0  0.30  0.31      41    68.4    59.5  0.39  0.37
 0.235     838  99.10    64.2    52.0  0.33  0.32      44    62.1    45.2  0.41  0.39
 0.257     890  99.26    54.2    43.6  0.33  0.33      47    53.2    44.0  0.35  0.35
 0.279     890  99.05    44.4    37.6  0.35  0.34      47    39.3    35.2  0.39  0.37
 0.301     935  99.19    36.2    31.9  0.36  0.34      49    36.6    34.3  0.31  0.29
 0.323     996  98.78    30.9    29.5  0.36  0.33      53    31.0    29.9  0.35  0.28
 0.346    1015  98.89    28.6    27.3  0.34  0.31      53    29.1    27.9  0.33  0.32
 0.368    1029  98.63    25.6    25.6  0.33  0.30      54    22.4    22.7  0.44  0.41
 0.390    1084  98.70    24.0    23.4  0.31  0.28      57    26.6    25.9  0.30  0.30
 0.412    1081  98.36    21.3    21.5  0.31  0.28      57    22.6    24.2  0.33  0.28
 0.434    1105  97.08    18.6    19.7  0.34  0.30      58    20.5    20.1  0.30  0.28
$$

    ****                      Fom and SigmaA vs resolution                      ****

 $TABLE: Cycle   11. FSC and  Fom(-acentric, centric, overall v resln:
 $GRAPHS:Cycle   11. M(Fom) v. resln :N:1,3,5,7,8,9,10:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCwork  FSCfree$$
 $$
  0.0140   164   0.747     8   0.613   172   0.741  0.914  0.5328 *******
  0.0361   312   0.803    13   0.718   325   0.799  0.912  0.5229 *******
  0.0582   402   0.885    15   0.666   417   0.877  0.911  0.7013 *******
  0.0803   478   0.851    14   0.843   492   0.851  0.910  0.7453 *******
  0.1024   535   0.795    16   0.868   551   0.797  0.907  0.6879 *******
  0.1245   605   0.811    13   0.789   618   0.811  0.888  0.7148 *******
  0.1466   659   0.816    15   0.776   674   0.815  0.880  0.7562 *******
  0.1687   691   0.849    12   0.987   703   0.851  0.914  0.7955 *******
  0.1908   748   0.848    17   0.792   765   0.847  0.953  0.8000 *******
  0.2129   778   0.819    13   0.837   791   0.819  0.983  0.7766 *******
  0.2350   823   0.781    15   0.739   838   0.781  1.000  0.7447 *******
  0.2571   875   0.837    15   0.720   890   0.835  1.043  0.7645 *******
  0.2792   877   0.819    13   0.882   890   0.820  0.973  0.7453 *******
  0.3013   923   0.770    12   0.877   935   0.772  0.885  0.6796 *******
  0.3234   978   0.790    18   0.705   996   0.788  0.840  0.7015 *******
  0.3455   998   0.794    17   0.876  1015   0.795  0.802  0.7421 *******
  0.3677  1016   0.814    13   0.934  1029   0.816  0.805  0.7652 *******
  0.3898  1069   0.854    15   0.764  1084   0.852  0.851  0.7970 *******
  0.4119  1066   0.826    15   0.778  1081   0.825  0.832  0.7722 *******
  0.4340  1090   0.818    15   0.692  1105   0.816  0.773  0.7575 *******
 $$
Resolution limits                    =     18.578     1.499
Number of used reflections           =      15371
Percentage observed                  =    98.5504
Percentage of free reflections       =     5.0000
Overall R factor                     =     0.2987
Free R factor                        =     0.3290
Overall Fourier shell correlation    =     0.7426
Free Fourier shell correlation       =     0.0000
Overall weighted R factor            =     0.3235
Free weighted R factor               =     0.3451
Overall weighted R2 factor           =     0.4145
Free weighted R2 factor              =     0.4225
Overall correlation coefficient      =     0.9024
Free correlation coefficient         =     0.8787
Cruickshanks DPI for coordinate error=     0.0886
DPI based on free R factor           =     0.0910
Overall figure of merit              =     0.8167
ML based su of positional parameters =     0.0701
ML based su of thermal parameters    =     1.8197
-----------------------------------------------------------------------------
  Time in seconds: CPU =        39.74
             Elapsed =         128.00

    ****           Things for loggraph, R factor and others vs cycle            ****


$TABLE: Rfactor analysis, stats vs cycle  :
$GRAPHS: vs cycle :N:1,2,3:
:FOM vs cycle :N:1,4:
:-LL vs cycle :N:1,5:
:-LLfree vs cycle :N:1,6:
:Geometry vs cycle:N:1,7,8,9,10,11:
$$
    Ncyc    Rfact    Rfree     FOM      -LL     -LLfree  rmsBOND  zBOND rmsANGL  zANGL rmsCHIRAL $$
$$
       0   0.3801   0.3887   0.769     28820.    3763.1   0.0327  2.009   3.937  2.151   0.152
       1   0.3390   0.3513   0.791     23348.    3660.8   0.0234  1.309   2.776  1.484   0.119
       2   0.3150   0.3366   0.806     19620.    3568.1   0.0272  1.369   2.217  1.107   0.158
       3   0.3038   0.3300   0.813     18522.    3534.6   0.0259  1.305   2.138  1.074   0.165
       4   0.3003   0.3282   0.815     18108.    3521.7   0.0250  1.258   2.149  1.076   0.158
       5   0.2989   0.3278   0.816     17941.    3515.6   0.0250  1.255   2.170  1.086   0.160
       6   0.2984   0.3285   0.816     17877.    3513.9   0.0251  1.262   2.189  1.095   0.161
       7   0.2983   0.3289   0.816     17855.    3513.3   0.0253  1.268   2.202  1.100   0.161
       8   0.2985   0.3291   0.816     17913.    3515.2   0.0241  1.208   2.138  1.067   0.154
       9   0.2987   0.3289   0.817     17950.    3515.2   0.0230  1.151   2.065  1.029   0.148
      10   0.2987   0.3290   0.817     17933.    3514.1   0.0231  1.158   2.056  1.025   0.147
 $$
 $TEXT:Result: $$ Final results $$
                      Initial    Final
           R factor    0.3801   0.2987
             R free    0.3887   0.3290
     Rms BondLength    0.0327   0.0231
      Rms BondAngle    3.9369   2.0556
     Rms ChirVolume    0.1525   0.1473
 $$

 Refmac_5.8.0049:  End of Refmac_5.8.0049  
Times: User:      39.9s System:    3.2s Elapsed:     0:43  

 
 ###############################################################
 ###############################################################
 ###############################################################
 ### CCP4 6.4: cbuccaneer             version 1.5.2 : 06/10/11##
 ###############################################################
 User: unknown  Run date: 17/ 7/2014 Run time: 18:56:42 


 Please reference: Collaborative Computational Project, Number 4. 1994.
 "The CCP4 Suite: Programs for Protein Crystallography". Acta Cryst. D50, 760-763.
 as well as any specific reference in the program write-up.



Copyright 2002-2010 Kevin Cowtan and University of York.


$TEXT:Reference: $$ Please reference $$

 'Fitting molecular fragments into electron density'
 Cowtan K. (2008) Acta Cryst. D64, 83-89.

$$
$TEXT:Reference: $$ Please reference $$

 'The Buccaneer software for automated model building'
 Cowtan K. (2006) Acta Cryst. D62, 1002-1011.

$$


title 	buccaneer auto-build
pdbin-ref 	/home/jmht/ccp4-6.4.0/lib/data/reference_structures/reference-1tqw.pdb
mtzin-ref 	/home/jmht/ccp4-6.4.0/lib/data/reference_structures/reference-1tqw.mtz
colin-ref-fo 	FP.F_sigF.F,FP.F_sigF.sigF
colin-ref-hl 	FC.ABCD.A,FC.ABCD.B,FC.ABCD.C,FC.ABCD.D
seqin 	/data1/jmht/polya_helices/3PP5/search_polya_15/input/3PP5_1.fasta
mtzin 	buccaneer_pipeline/refine.mtz
colin-fo 	FP, SIGFP
colin-hl 	HLACOMB,HLBCOMB,HLCCOMB,HLDCOMB
colin-fc 	FWT,PHWT
colin-free 	FREE
pdbin 	buccaneer_pipeline/refine.pdb
pdbout 	buccaneer_pipeline/build.pdb
anisotropy-correction
fast
cycles 	2
sequence-reliability 	0.95
correlation-mode
new-residue-name 	UNK
resolution 	2.0

MTZ file: buccaneer_pipeline/refine.mtz
  Number of reflections:     16180        Number of columns:  22

Applying anisotropy correction:
|-9.083e-15, 5.552e-17, 1.547e-17|
| 5.552e-17,         0,-1.145e-17|
| 1.547e-17,-1.145e-17,   -0.1098|

PDB file: buccaneer_pipeline/refine.pdb
  Number of atoms read: 501

Cycle: 1

 C-alphas after finding:    76
 C-alphas after growing:    101
 C-alphas after joining:    60
 C-alphas linked:           0
 C-alphas sequenced:        57
 C-alphas corrected:        0
 C-alphas after filtering:  60
 C-alphas after NCS build:  60
 C-alphas after pruning:    60
 C-alphas after rebuilding: 60


Internal cycle   1
     60 residues were built in   1 fragments, the longest having   60 residues.
     57 residues were sequenced, after pruning.
     60 residues were uniquely allocated to   1 chains.
  Completeness by residues built:   100.0%
  Completeness of chains (number):   82.2%    (1)



Cycle: 2

 C-alphas after finding:    76
 C-alphas after growing:    93
 C-alphas after joining:    60
 C-alphas linked:           0
 C-alphas sequenced:        57
 C-alphas corrected:        0
 C-alphas after filtering:  60
 C-alphas after NCS build:  60
 C-alphas after pruning:    60
 C-alphas after rebuilding: 60


Internal cycle   2
     60 residues were built in   1 fragments, the longest having   60 residues.
     57 residues were sequenced, after pruning.
     60 residues were uniquely allocated to   1 chains.
  Completeness by residues built:   100.0%
  Completeness of chains (number):   82.2%    (1)


$TEXT:Result: $$ $$
     60 residues were built in   1 fragments, the longest having   60 residues.
     57 residues were sequenced, after pruning.
     60 residues were uniquely allocated to   1 chains.
  Completeness by residues built:   100.0%
  Completeness of chains (number):   82.2%    (1)
$$


cbuccaneer: Normal termination
Times: User:      16.9s System:    0.0s Elapsed:     0:17  

 
 ###############################################################
 ###############################################################
 ###############################################################
 ### CCP4 6.4: Refmac_5.8.0049     version 5.8.0049 : 30/06/13##
 ###############################################################
 User: unknown  Run date: 17/ 7/2014 Run time: 18:56:59 


 Please reference: Collaborative Computational Project, Number 4. 1994.
 "The CCP4 Suite: Programs for Protein Crystallography". Acta Cryst. D50, 760-763.
 as well as any specific reference in the program write-up.


 $TEXT:Reference1: $$ Main reference $$ 
   "REFMAC5 for the refinement of macromolecular crystal structures:"
   G.N.Murshudov, P.Skubak, A.A.Lebedev, N.S.Pannu, R.A.Steiner, R.A.Nicholls, M.D.Winn, F.Long and A.A.Vagin,(2011) 
   Acta Crystallogr. D67, 355-367

 $$
 $SUMMARY :Reference1:  $$ Refmac: $$
 :TEXT:Reference1: $$

 $TEXT:Reference2: $$ Secondary reference $$ 
   "Refinement of Macromolecular Structures by the  Maximum-Likelihood Method:"
   G.N. Murshudov, A.A.Vagin and E.J.Dodson,(1997)
   Acta Crystallogr. D53, 240-255
   EU  Validation contract: BIO2CT-92-0524

 $$
 $SUMMARY :Reference2:  $$ Refmac: $$
 :TEXT:Reference2: $$

  Data line--- title  buccaneer auto-build
  Data line--- ncyc 10
  Data line--- labin                    PHIB=PHIC FOM= FOM                FREE=FREE   FP=FP SIGFP= SIGFP
  Data line--- weight AUTO
  Data line--- make check NONE
  Data line--- make hydrogen NO hout NO peptide NO cispeptide YES ssbridge YES symmetry YES sugar YES connectivity NO link NO
  Data line--- refi type REST PHASE resi MLKF meth CGMAT bref ISOT
  Data line--- scal type SIMP LSSC ANISO EXPE
  Data line--- solvent YES VDWProb 1.4 IONProb 0.8 RSHRink 0.8
  Data line--- PHOUT
  Data line--- PNAME buccaneer
  Data line--- DNAME buccaneer
  Data line--- END

 OPENED INPUT MTZ FILE 
 Logical Name: HKLIN   Filename: /data1/jmht/polya_helices/3PP5/search_polya_15/data/loc0_ALL_polya_15/unmod/mr/phaser/build/shelxe/rebuild/refine/refmacSX_output.mtz 


 Spacegroup information obtained from library file: 
 Logical Name: SYMINFO   Filename: /home/jmht/ccp4-6.4.0/lib/data/syminfo.lib


    ****                     Input and Default parameters#                      ****


Input coordinate file.  Logical name - XYZIN actual file name  - buccaneer_pipeline/build.pdb
Output coordinate file. Logical name - XYZOUT actual file name - buccaneer_pipeline/refine.pdb
Input reflection file.  Logical name - HKLIN actual file name  - /data1/jmht/polya_helices/3PP5/search_polya_15/data/loc0_ALL_polya_15/unmod/mr/phaser/build/shelxe/rebuild/refine/refmacSX_outpu
Output reflection file. Logical name - HKLOUT actual file name - buccaneer_pipeline/refine.mtz

Cell from mtz :    39.140    39.140   118.190    90.000    90.000   120.000
Space group from mtz: number -  173; name - P 63

  Refinement type                        : Restrained


    ****                           Makecif parameters                           ****

Dictionary files for restraints : /home/jmht/ccp4-6.4.0/lib/data/monomers/mon*cif
Parameters for new entry and VDW: /home/jmht/ccp4-6.4.0/lib/data/monomers/ener_lib.cif
    Program will rely on residue and atom names. No checking
    If this option is used then monomers should be checked carefully before using
    Hydrogens will not be written to the output file
    Links between monomers will be checked. Only those links present in the coordinate file will be used
    All links to sugar will be analysed and used
    For new ligands "ideal restraint" values will be taken from the energetic libary ener_lib.cif
    Symmetry related links will be analysed and used
    Cis peptides will be found and used automatically


  Residual                               : Phase modified Maximum Likelihood for Fs
 Phase Blurred by  Scale*Exp(-B s**2)    :    1.00    0.00

    ****                    Least-square scaling parameters                     ****

Overall scale
Overall B value
Overall anisotropic B with tr(B) = 0.0
Constant bulk solvent in non protein region
Probe radii for non-ions     1.400
Probe radii for ions         0.800
Shrinkage of the mask  by    0.800


    ****                 Map sharpening parameters and methods                  ****

No map sharpening will be performed

  Method of minimisation                 : Sparse Matrix
  Experimental sigmas used for weighting
  Number of Bins and width:    20       0.0223
  Refinement of individual isotropic Bfactors
  Refinement resln        :    18.5778  1.4990
  Estimated number of reflections :      26875
  Free R exclusion - flag equals:     0
  Auto weighting. An attempt
  Refinement cycles       :    10
  Scaling type                           :
          Wilson using 1 Gaussian

  Estimation of D/Sigma in resolution bins
  using  free set of reflns with experimental sigmas
  Input phases not used in SigmaA estimation

  Scaling and SigmaA resln:    18.5778  1.4990

  Damping factors:     1.0000  1.0000


    ****                    Geometry restraints and weights                     ****


                                              Sigma:
 Bonding distances
          Weight =  1.00

 Bond angles
          Weight =  1.00

 Planar groups (all and main chain)
          WEIGHT= 1.00 1.00

 Chiral centers
          Weight= 1.00

 NON-BONDED CONTACTS
          Overall weight                          =  1.00
          Sigma for simple VDW                    =  0.20
          Sigma for VDW trhough torsion angle     =  0.20
          Sigma for HBOND                         =  0.20
          Sigma for metal-ion                     =  0.20
          Sigma for DUMMY and other atom          =  0.30
          Distance for donor-accepetor = vdw1+vdw2+(-0.30)
          Distance for acceptor - H    = vdw1+     ( 0.10)
          VDW distance through torsion = vdw1+vdw2+(-0.30)
          Distance for DUMMY-others    = vdw1+vdw2+(-0.70)

 TORSION ANGLES
          Weight= 1.00

 THERMAL FACTORS
          Weight= 1.00
     Main chain bond (1-2 neighbour)          1.5A**2
     Main chain angle (1-3 neighbour)         2.0A**2
     Side chain bond                          3.0A**2
     Side chain angle                         4.5A**2

 RESTRAINTS AGAINST EXCESSIVE SHIFTS
     Positional parameters                   0.00A
     Thermal parameters                      0.00A
     Occupancy parameters                    0.00

 RADIUS OF CONFIDENCE
     Positional parameters 0.00A
     Thermal parameters    0.00A**2
     Occupancy parameters  0.00

Monitoring style is "MEDIUM". Complete information will be printed out in the
first and last cycle. In all other cycles minimum information will be printed out
Sigma cutoffs for printing out outliers
If deviation of restraint parameter > alpha*sigma then information will be printed out
Distance outliers      10.000
Angle outliers         10.000
Torsion outliers       10.000
Chiral volume outliers 10.000
Plane outliers         10.000
Non-bonding outliers   10.000
B value  outliers      10.000
---------------------------------------------------------------

 Input file :buccaneer_pipeline/build.pdb
  ------------------------------
  ---  LIBRARY OF MONOMERS   ---
 _lib_name         mon_lib
 _lib_version      5.41
 _lib_update       11/02/13
  ------------------------------
  NUMBER OF MONOMERS IN THE LIBRARY          : 11464
                with complete description    : 11464
  NUMBER OF MODIFICATIONS                    :    56
  NUMBER OF LINKS                            :    68
  I am reading libraries. Please wait.
      - energy parameters
      - monomer"s description (links & mod )

FORMATTED      OLD     file opened on unit  45

Logical name: ATOMSF, Filename: /home/jmht/ccp4-6.4.0/lib/data/atomsf.lib


  Number of atoms    :     501
  Number of residues :      60
  Number of chains   :       1
  I am reading library. Please wait.
                mon_lib.cif
  --------------------------------
  --- title of input coord file ---

  PDB_code:xxxx
  PDB_name:----
  PDB_date:XX-XXX-XX
  --------------------------------
  ATTENTION: atom:CG   UNK                 9  AA   is missing in the structure
  ATTENTION: atom:CG   UNK                10  AA   is missing in the structure
  ATTENTION: atom:CG   UNK                68  AA   is missing in the structure
  Number of chains                  :       1
  Total number of monomers          :      60
  Number of atoms                   :     504
  Number of missing atoms           :       3
  Number of rebuilt atoms           :       0
  Number of unknown atoms           :       0
  Number of deleted atoms           :       0

  Number of bonds restraints    :     506
  Number of angles restraints   :     680
  Number of torsions restraints :     340
  Number of chiralities         :      78
  Number of planar groups       :      88


 loop_
     _atom_type_symbol
     _atom_type_scat_Cromer_Mann_a1
     _atom_type_scat_Cromer_Mann_b1
     _atom_type_scat_Cromer_Mann_a2
     _atom_type_scat_Cromer_Mann_b2
     _atom_type_scat_Cromer_Mann_a3
     _atom_type_scat_Cromer_Mann_b3
     _atom_type_scat_Cromer_Mann_a4
     _atom_type_scat_Cromer_Mann_b4
     _atom_type_scat_Cromer_Mann_c


  N     12.2126   0.0057   3.1322   9.8933   2.0125  28.9975   1.1663   0.5826 -11.5290
  C      2.3100  20.8439   1.0200  10.2075   1.5886   0.5687   0.8650  51.6512   0.2156
  O      3.0485  13.2771   2.2868   5.7011   1.5463   0.3239   0.8670  32.9089   0.2508
  S      6.9053   1.4679   5.2034  22.2151   1.4379   0.2536   1.5863  56.1720   0.8669


 Number of distances         :           0
 Number of angles            :           0
 Number of torsions          :           0
 Number of planes            :           0
 Number of chirals           :           0
 Number of intervals         :           0
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
                        Standard  External       All
                Bonds:       506         0       506
               Angles:       680         0       680
              Chirals:        78         0        78
               Planes:        88         0        88
             Torsions:       340         0       340
            Intervals:         0         0         0
--------------------------------------------------------------------------------


  Number of harmonic restraints       =            0
  Number of atoms in special position =            0
 -----------------------------------------------------


    ****                           Info from mtz file                           ****

FreeR flag                            0
Number of "free" reflections        809
Number of   all  reflections      16180
--------------------------------------------------------------------------------
 Number of reflections in file      16180
 Number of reflections read          16180


     CGMAT cycle number =      1

 Limits of asymmetric unit      : 1.00 1.00 0.50
 Grid spacing to be used        :    96   96  288
 Maximuum H,K,L                 :    27   27   78
 Minimum acceptable grid spacing:    59   59  178
 Limits of asymmetric unit      : 1.00 1.00 0.50
 Grid spacing to be used        :    96   96  288
 Maximuum H,K,L                 :    27   27   78
 Minimum acceptable grid spacing:    59   59  178
 Weight matrix   0.52774316    
 Actual weight    10.000000      is applied to the X-ray term
Norm of X_ray positional gradient                152.
Norm of Geom. positional gradient                40.8
Norm of X_ray B-factor gradient                 0.188E+04
Norm of Geom. B-factor gradient                  0.00
Product of X_ray and Geom posit. gradients     -0.336E+06
 Cosine of angle between them                      -0.036
Product of X_ray and Geom B-fact gradients       0.00
 Cosine of angle between them                       0.000


Residuals: XRAY=     0.2776E+06 GEOM=      1085.     TOTAL=     0.2786E+06
 function value    278641.31    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                   506     0.013     0.020
Bond angles  : refined atoms                    680     1.410     1.970
Torsion angles, period  1. refined               59     3.224     5.000
Torsion angles, period  2. refined               29    26.058    26.207
Torsion angles, period  3. refined              103    10.626    15.000
Torsion angles, period  4. refined                3    11.132    15.000
Chiral centres: refined atoms                    78     0.077     0.200
Planar groups: refined atoms                    374     0.000     0.020
VDW repulsions: refined_atoms                   209     0.247     0.200
VDW; torsion: refined_atoms                     368     0.312     0.200
HBOND: refined_atoms                              5     0.383     0.200
VDW repulsions: symmetry: refined_atoms          37     0.454     0.200
HBOND: symmetry: refined_atoms                    2     0.073     0.200
M. chain bond B values: refined atoms           239     0.000     3.948
M. chain angle B values: refined atoms          297     0.000     5.922
S. chain bond B values: refined atoms           264     0.000     3.948
S. chain angle B values: refined atoms          383     0.000     5.922
Long range B values: refined atoms              762     0.000    32.541
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall               : scale =    0.783, B  = -22.082
Partial structure    1: scale =    0.468, B  =  43.156
Overall anisotropic scale factors
   B11 = -0.12 B22 = -0.12 B33 =  0.38 B12 = -0.06 B13 = -0.00 B23 = -0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------

    ****                Things for loggraph, R factor and others                ****


$TABLE: Cycle    1. Rfactor analysis, F distribution v resln  :
$GRAPHS:Cycle    1.  v. resln :N:1,6,7,11,12:
:Cycle    1.  and  v. resln :N:1,4,5,9,10:
:Cycle    1. % observed v. resln :N:1,3:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.014     172  83.11   162.6   166.5  0.38  0.54      10   197.3   152.9  0.42  0.48
 0.036     325  96.34   193.4   190.0  0.36  0.46      17   208.7   204.3  0.29  0.34
 0.058     417  97.12   249.0   235.7  0.29  0.37      22   233.1   199.1  0.34  0.47
 0.080     492  99.61   214.2   199.1  0.29  0.35      25   215.9   193.5  0.35  0.43
 0.102     551  99.66   153.8   144.4  0.35  0.41      29   158.4   129.0  0.32  0.36
 0.124     618  99.69   137.2   129.9  0.34  0.39      33   130.7   111.8  0.39  0.44
 0.147     674  99.58   117.6   110.4  0.36  0.40      35   123.4   113.2  0.28  0.28
 0.169     703  99.33   105.8    95.3  0.36  0.39      37    97.2    87.6  0.40  0.43
 0.191     765  99.51    94.8    80.1  0.38  0.40      41   104.1    95.1  0.38  0.38
 0.213     791  99.40    87.8    73.2  0.38  0.38      41    77.4    59.5  0.45  0.42
 0.235     838  99.10    72.7    61.4  0.39  0.38      44    70.3    60.2  0.39  0.38
 0.257     890  99.26    61.3    49.6  0.41  0.40      47    60.2    49.1  0.41  0.38
 0.279     890  99.05    50.3    41.9  0.43  0.40      47    44.5    36.8  0.48  0.45
 0.301     935  99.19    41.0    36.0  0.44  0.41      49    41.4    35.0  0.47  0.43
 0.323     996  98.78    35.0    32.8  0.45  0.41      53    35.1    36.0  0.43  0.37
 0.346    1015  98.89    32.4    29.6  0.45  0.41      53    32.9    30.8  0.38  0.35
 0.368    1029  98.63    29.0    26.3  0.43  0.40      54    25.3    25.6  0.61  0.57
 0.390    1084  98.70    27.2    24.2  0.43  0.40      57    30.1    24.3  0.44  0.44
 0.412    1081  98.36    24.1    21.1  0.44  0.40      57    25.6    24.6  0.38  0.35
 0.434    1105  97.08    21.0    18.1  0.45  0.41      58    23.2    17.7  0.40  0.41
$$

    ****                      Fom and SigmaA vs resolution                      ****

 $TABLE: Cycle    1. FSC and  Fom(-acentric, centric, overall v resln:
 $GRAPHS:Cycle    1. M(Fom) v. resln :N:1,3,5,7,8,9,10:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCwork  FSCfree$$
 $$
  0.0140   164   0.704     8   0.603   172   0.699  0.911  0.5066 *******
  0.0361   312   0.775    13   0.695   325   0.772  0.915  0.4741 *******
  0.0582   402   0.864    15   0.692   417   0.858  0.919  0.6332 *******
  0.0803   478   0.824    14   0.865   492   0.826  0.922  0.6892 *******
  0.1024   535   0.769    16   0.855   551   0.772  0.921  0.6021 *******
  0.1245   605   0.784    13   0.747   618   0.783  0.895  0.6334 *******
  0.1466   659   0.784    15   0.712   674   0.783  0.877  0.6652 *******
  0.1687   691   0.813    12   0.972   703   0.815  0.898  0.6954 *******
  0.1908   748   0.803    17   0.734   765   0.802  0.881  0.6740 *******
  0.2129   778   0.771    13   0.791   791   0.772  0.870  0.6437 *******
  0.2350   823   0.758    15   0.705   838   0.757  0.908  0.6134 *******
  0.2571   875   0.793    15   0.697   890   0.792  0.927  0.5868 *******
  0.2792   877   0.769    13   0.785   890   0.770  0.868  0.5582 *******
  0.3013   923   0.698    12   0.827   935   0.699  0.755  0.4655 *******
  0.3234   978   0.730    18   0.636   996   0.728  0.742  0.5110 *******
  0.3455   998   0.757    17   0.823  1015   0.758  0.736  0.5361 *******
  0.3677  1016   0.758    13   0.852  1029   0.759  0.681  0.5611 *******
  0.3898  1069   0.797    15   0.713  1084   0.795  0.703  0.5959 *******
  0.4119  1066   0.764    15   0.792  1081   0.764  0.768  0.5650 *******
  0.4340  1090   0.761    15   0.540  1105   0.758  0.798  0.5594 *******
 $$
Resolution limits                    =     18.578     1.499
Number of used reflections           =      15371
Percentage observed                  =    98.5504
Percentage of free reflections       =     5.0000
Overall R factor                     =     0.3691
Free R factor                        =     0.3819
Overall Fourier shell correlation    =     0.5857
Free Fourier shell correlation       =     0.0000
Overall weighted R factor            =     0.3987
Free weighted R factor               =     0.4007
Overall weighted R2 factor           =     0.4973
Free weighted R2 factor              =     0.4828
Overall correlation coefficient      =     0.8565
Free correlation coefficient         =     0.8396
Cruickshanks DPI for coordinate error=     0.1095
DPI based on free R factor           =     0.1057
Overall figure of merit              =     0.7708
ML based su of positional parameters =     0.1078
ML based su of thermal parameters    =     2.9140
-----------------------------------------------------------------------------
 Trying gamma equal    0.0000000    
 Convergence reached with no gamma cycles 


 fvalues    34529.934       1085.4913       288537.72       346384.84    


     CGMAT cycle number =      2

 Weight matrix   0.78682327    
 Actual weight    10.000000      is applied to the X-ray term


 function value    229895.94    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                   506     0.017     0.020
Bond angles  : refined atoms                    680     1.386     1.970
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall               : scale =    0.806, B  =  -9.764
Partial structure    1: scale =    0.460, B  =  34.951
Overall anisotropic scale factors
   B11 = -0.07 B22 = -0.07 B33 =  0.22 B12 = -0.03 B13 = -0.00 B23 = -0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.3330
Free R factor                        =     0.3527
Overall Fourier shell correlation    =     0.6940
Free Fourier shell correlation       =     0.0000
Overall figure of merit              =     0.7930
-----------------------------------------------------------------------------
 Trying gamma equal    0.0000000    
 Convergence reached with no gamma cycles 


 fvalues    27974.477       1654.9310       215876.72       281399.69    


     CGMAT cycle number =      3

 Weight matrix    1.0278270    
 Actual weight    10.000000      is applied to the X-ray term


 function value    200139.89    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                   506     0.026     0.020
Bond angles  : refined atoms                    680     1.931     1.970
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall               : scale =    0.855, B  =   1.832
Partial structure    1: scale =    0.428, B  =  21.350
Overall anisotropic scale factors
   B11 = -0.02 B22 = -0.02 B33 =  0.06 B12 = -0.01 B13 = -0.00 B23 = -0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.3135
Free R factor                        =     0.3329
Overall Fourier shell correlation    =     0.7354
Free Fourier shell correlation       =     0.0000
Overall figure of merit              =     0.8077
-----------------------------------------------------------------------------
 Trying gamma equal    0.0000000    
 Convergence reached with no gamma cycles 


 fvalues    19713.889       5116.4648       195351.48       202255.36    


     CGMAT cycle number =      4

 Weight matrix    1.0670167    
 Actual weight    9.0909090      is applied to the X-ray term


 function value    172716.38    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                   506     0.026     0.020
Bond angles  : refined atoms                    680     2.068     1.970
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall               : scale =    0.870, B  =   0.660
Partial structure    1: scale =    0.422, B  =  23.499
Overall anisotropic scale factors
   B11 = -0.01 B22 = -0.01 B33 =  0.05 B12 = -0.01 B13 = -0.00 B23 = -0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.3041
Free R factor                        =     0.3256
Overall Fourier shell correlation    =     0.7413
Free Fourier shell correlation       =     0.0000
Overall figure of merit              =     0.8139
-----------------------------------------------------------------------------
 Trying gamma equal    0.0000000    
 Convergence reached with no gamma cycles 


 fvalues    18478.828       4431.0298       171270.00       172420.38    


     CGMAT cycle number =      5

 Weight matrix    1.0015640    
 Actual weight    8.2644625      is applied to the X-ray term


 function value    154042.58    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                   506     0.025     0.020
Bond angles  : refined atoms                    680     2.094     1.970
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall               : scale =    0.882, B  =   0.576
Partial structure    1: scale =    0.424, B  =  23.759
Overall anisotropic scale factors
   B11 = -0.01 B22 = -0.01 B33 =  0.04 B12 = -0.01 B13 = -0.00 B23 = -0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.3014
Free R factor                        =     0.3235
Overall Fourier shell correlation    =     0.7435
Free Fourier shell correlation       =     0.0000
Overall figure of merit              =     0.8160
-----------------------------------------------------------------------------
 Trying gamma equal    0.0000000    
 Convergence reached with no gamma cycles 


 fvalues    18034.383       4646.7490       153353.78       153691.23    


     CGMAT cycle number =      6

 Weight matrix    1.0124381    
 Actual weight    8.2644625      is applied to the X-ray term


 function value    152769.27    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                   506     0.024     0.020
Bond angles  : refined atoms                    680     2.061     1.970
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall               : scale =    0.888, B  =   0.486
Partial structure    1: scale =    0.427, B  =  24.544
Overall anisotropic scale factors
   B11 = -0.01 B22 = -0.01 B33 =  0.04 B12 = -0.01 B13 = -0.00 B23 = -0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.3003
Free R factor                        =     0.3257
Overall Fourier shell correlation    =     0.7435
Free Fourier shell correlation       =     0.0000
Overall figure of merit              =     0.8163
-----------------------------------------------------------------------------
 Trying gamma equal    0.0000000    
 Convergence reached with no gamma cycles 


 fvalues    17894.633       4548.7368       152301.81       152438.25    


     CGMAT cycle number =      7

 Weight matrix    1.0203142    
 Actual weight    8.2644625      is applied to the X-ray term


 function value    152014.63    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                   506     0.024     0.020
Bond angles  : refined atoms                    680     2.075     1.970
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall               : scale =    0.891, B  =   0.457
Partial structure    1: scale =    0.431, B  =  24.606
Overall anisotropic scale factors
   B11 = -0.01 B22 = -0.01 B33 =  0.03 B12 = -0.00 B13 = -0.00 B23 = -0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2997
Free R factor                        =     0.3262
Overall Fourier shell correlation    =     0.7436
Free Fourier shell correlation       =     0.0000
Overall figure of merit              =     0.8167
-----------------------------------------------------------------------------
 Trying gamma equal    0.0000000    
 Convergence reached with no gamma cycles 


 fvalues    17804.523       4548.1558       151613.80       151692.97    


     CGMAT cycle number =      8

 Weight matrix   0.93490523    
 Actual weight    7.5131474      is applied to the X-ray term


 function value    138041.03    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                   506     0.024     0.020
Bond angles  : refined atoms                    680     2.092     1.970
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall               : scale =    0.894, B  =   0.439
Partial structure    1: scale =    0.429, B  =  24.687
Overall anisotropic scale factors
   B11 = -0.01 B22 = -0.01 B33 =  0.02 B12 = -0.00 B13 = -0.00 B23 = -0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2993
Free R factor                        =     0.3267
Overall Fourier shell correlation    =     0.7438
Free Fourier shell correlation       =     0.0000
Overall figure of merit              =     0.8170
-----------------------------------------------------------------------------
 Trying gamma equal    0.0000000    
 Convergence reached with no gamma cycles 


 fvalues    17730.350       4559.7769       137701.47       137770.52    


     CGMAT cycle number =      9

 Weight matrix   0.85564077    
 Actual weight    6.8301339      is applied to the X-ray term


 function value    125876.61    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                   506     0.023     0.020
Bond angles  : refined atoms                    680     2.040     1.970
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall               : scale =    0.893, B  =   0.357
Partial structure    1: scale =    0.428, B  =  24.855
Overall anisotropic scale factors
   B11 = -0.01 B22 = -0.01 B33 =  0.02 B12 = -0.00 B13 = -0.00 B23 = -0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2992
Free R factor                        =     0.3270
Overall Fourier shell correlation    =     0.7434
Free Fourier shell correlation       =     0.0000
Overall figure of merit              =     0.8171
-----------------------------------------------------------------------------
 Trying gamma equal    0.0000000    
 Convergence reached with no gamma cycles 


 fvalues    17756.723       4372.2920       125616.48       125653.09    


     CGMAT cycle number =     10

 Weight matrix   0.85951662    
 Actual weight    6.8301339      is applied to the X-ray term


 function value    125962.47    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                   506     0.022     0.020
Bond angles  : refined atoms                    680     1.977     1.970
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall               : scale =    0.891, B  =   0.334
Partial structure    1: scale =    0.432, B  =  25.588
Overall anisotropic scale factors
   B11 = -0.01 B22 = -0.01 B33 =  0.02 B12 = -0.00 B13 = -0.00 B23 = -0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2993
Free R factor                        =     0.3271
Overall Fourier shell correlation    =     0.7427
Free Fourier shell correlation       =     0.0000
Overall figure of merit              =     0.8173
-----------------------------------------------------------------------------
 Trying gamma equal    0.0000000    
 Convergence reached with no gamma cycles 


 fvalues    17797.574       4188.1885       125731.52       125748.00    

 Limits of asymmetric unit      : 1.00 1.00 0.50
 Grid spacing to be used        :    96   96  288
 Maximuum H,K,L                 :    27   27   78
 Minimum acceptable grid spacing:    59   59  178
 Limits of asymmetric unit      : 1.00 1.00 0.50
 Grid spacing to be used        :    96   96  288
 Maximuum H,K,L                 :    27   27   78
 Minimum acceptable grid spacing:    59   59  178

 WRITTEN OUTPUT MTZ FILE 
 Logical Name: HKLOUT   Filename: buccaneer_pipeline/refine.mtz 

Norm of X_ray positional gradient                0.00
Norm of Geom. positional gradient                0.00
Norm of X_ray B-factor gradient                  0.00
Norm of Geom. B-factor gradient                  0.00
Product of X_ray and Geom posit. gradients       0.00
 Cosine of angle between them                       0.000
Product of X_ray and Geom B-fact gradients       0.00
 Cosine of angle between them                       0.000


Residuals: XRAY=     0.1217E+06 GEOM=      4175.     TOTAL=     0.1259E+06

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                   506     0.022     0.020
Bond angles  : refined atoms                    680     1.967     1.970
Torsion angles, period  1. refined               59     3.136     5.000
Torsion angles, period  2. refined               29    28.399    26.207
Torsion angles, period  3. refined              103    15.105    15.000
Torsion angles, period  4. refined                3    23.992    15.000
Chiral centres: refined atoms                    78     0.143     0.200
Planar groups: refined atoms                    374     0.010     0.020
VDW repulsions: refined_atoms                   194     0.215     0.200
VDW; torsion: refined_atoms                     357     0.303     0.200
HBOND: refined_atoms                              4     0.329     0.200
VDW repulsions: symmetry: refined_atoms          26     0.285     0.200
M. chain bond B values: refined atoms           239     2.064     1.766
M. chain angle B values: refined atoms          297     3.213     2.620
S. chain bond B values: refined atoms           267     6.998     2.864
S. chain angle B values: refined atoms          383    10.429     3.884
Long range B values: refined atoms              743    12.274    16.650
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall               : scale =    0.892, B  =   0.346
Partial structure    1: scale =    0.434, B  =  25.485
Overall anisotropic scale factors
   B11 = -0.01 B22 = -0.01 B33 =  0.02 B12 = -0.00 B13 = -0.00 B23 = -0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------

    ****                Things for loggraph, R factor and others                ****


$TABLE: Cycle   11. Rfactor analysis, F distribution v resln  :
$GRAPHS:Cycle   11.  v. resln :N:1,6,7,11,12:
:Cycle   11.  and  v. resln :N:1,4,5,9,10:
:Cycle   11. % observed v. resln :N:1,3:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.014     172  83.11   142.7   158.2  0.38  0.56      10   173.2   150.9  0.30  0.29
 0.036     325  96.34   169.7   170.3  0.30  0.39      17   183.2   177.7  0.25  0.24
 0.058     417  97.12   218.6   208.8  0.22  0.29      22   204.6   186.2  0.29  0.43
 0.080     492  99.61   188.0   176.4  0.25  0.31      25   189.5   165.4  0.31  0.41
 0.102     551  99.66   135.0   129.9  0.30  0.35      29   139.0   126.3  0.32  0.34
 0.124     618  99.69   120.5   116.3  0.29  0.33      33   114.8   116.8  0.40  0.45
 0.147     674  99.58   103.3   101.4  0.27  0.30      35   108.3   101.3  0.29  0.31
 0.169     703  99.33    92.9    88.6  0.29  0.33      37    85.3    82.0  0.31  0.33
 0.191     765  99.51    83.2    74.5  0.29  0.31      41    91.3    81.8  0.29  0.30
 0.213     791  99.40    77.1    63.7  0.30  0.31      41    67.9    59.1  0.39  0.37
 0.235     838  99.10    63.8    51.7  0.33  0.33      44    61.7    45.8  0.40  0.39
 0.257     890  99.26    53.8    43.4  0.33  0.33      47    52.8    43.4  0.35  0.35
 0.279     890  99.05    44.1    37.5  0.35  0.34      47    39.0    34.6  0.40  0.37
 0.301     935  99.19    36.0    31.6  0.36  0.34      49    36.4    34.2  0.31  0.29
 0.323     996  98.78    30.7    29.3  0.37  0.33      53    30.8    29.7  0.35  0.29
 0.346    1015  98.89    28.4    27.1  0.34  0.32      53    28.9    27.7  0.34  0.33
 0.368    1029  98.63    25.4    25.4  0.33  0.30      54    22.2    22.4  0.44  0.42
 0.390    1084  98.70    23.9    23.2  0.31  0.28      57    26.5    25.6  0.30  0.30
 0.412    1081  98.36    21.1    21.3  0.31  0.28      57    22.4    23.9  0.34  0.28
 0.434    1105  97.08    18.4    19.5  0.34  0.30      58    20.3    20.0  0.30  0.29
$$

    ****                      Fom and SigmaA vs resolution                      ****

 $TABLE: Cycle   11. FSC and  Fom(-acentric, centric, overall v resln:
 $GRAPHS:Cycle   11. M(Fom) v. resln :N:1,3,5,7,8,9,10:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCwork  FSCfree$$
 $$
  0.0140   164   0.757     8   0.627   172   0.751  0.921  0.5406 *******
  0.0361   312   0.811    13   0.741   325   0.808  0.919  0.5233 *******
  0.0582   402   0.888    15   0.693   417   0.881  0.918  0.7025 *******
  0.0803   478   0.852    14   0.852   492   0.852  0.917  0.7490 *******
  0.1024   535   0.799    16   0.878   551   0.801  0.913  0.6905 *******
  0.1245   605   0.811    13   0.794   618   0.811  0.888  0.7133 *******
  0.1466   659   0.811    15   0.767   674   0.810  0.876  0.7588 *******
  0.1687   691   0.851    12   0.975   703   0.853  0.914  0.7946 *******
  0.1908   748   0.850    17   0.815   765   0.849  0.957  0.8008 *******
  0.2129   778   0.821    13   0.837   791   0.821  0.984  0.7764 *******
  0.2350   823   0.782    15   0.740   838   0.781  0.993  0.7434 *******
  0.2571   875   0.839    15   0.725   890   0.837  1.039  0.7640 *******
  0.2792   877   0.818    13   0.873   890   0.819  0.968  0.7449 *******
  0.3013   923   0.771    12   0.875   935   0.772  0.886  0.6793 *******
  0.3234   978   0.789    18   0.692   996   0.788  0.838  0.7005 *******
  0.3455   998   0.794    17   0.876  1015   0.795  0.801  0.7419 *******
  0.3677  1016   0.815    13   0.932  1029   0.816  0.809  0.7650 *******
  0.3898  1069   0.853    15   0.759  1084   0.852  0.854  0.7960 *******
  0.4119  1066   0.826    15   0.783  1081   0.825  0.839  0.7717 *******
  0.4340  1090   0.818    15   0.694  1105   0.816  0.779  0.7569 *******
 $$
Resolution limits                    =     18.578     1.499
Number of used reflections           =      15371
Percentage observed                  =    98.5504
Percentage of free reflections       =     5.0000
Overall R factor                     =     0.2993
Free R factor                        =     0.3272
Overall Fourier shell correlation    =     0.7426
Free Fourier shell correlation       =     0.0000
Overall weighted R factor            =     0.3248
Free weighted R factor               =     0.3454
Overall weighted R2 factor           =     0.4174
Free weighted R2 factor              =     0.4328
Overall correlation coefficient      =     0.9020
Free correlation coefficient         =     0.8813
Cruickshanks DPI for coordinate error=     0.0888
DPI based on free R factor           =     0.0905
Overall figure of merit              =     0.8175
ML based su of positional parameters =     0.0699
ML based su of thermal parameters    =     1.8160
-----------------------------------------------------------------------------
  Time in seconds: CPU =        40.10
             Elapsed =           0.00

    ****           Things for loggraph, R factor and others vs cycle            ****


$TABLE: Rfactor analysis, stats vs cycle  :
$GRAPHS: vs cycle :N:1,2,3:
:FOM vs cycle :N:1,4:
:-LL vs cycle :N:1,5:
:-LLfree vs cycle :N:1,6:
:Geometry vs cycle:N:1,7,8,9,10,11:
$$
    Ncyc    Rfact    Rfree     FOM      -LL     -LLfree  rmsBOND  zBOND rmsANGL  zANGL rmsCHIRAL $$
$$
       0   0.3691   0.3819   0.771     27756.    3737.0   0.0130  0.684   1.410  0.697   0.077
       1   0.3330   0.3527   0.793     22824.    3651.5   0.0165  0.833   1.386  0.684   0.088
       2   0.3135   0.3329   0.808     19502.    3563.6   0.0260  1.305   1.931  0.964   0.140
       3   0.3041   0.3256   0.814     18511.    3531.4   0.0264  1.327   2.068  1.035   0.153
       4   0.3014   0.3235   0.816     18077.    3515.4   0.0252  1.265   2.094  1.052   0.158
       5   0.3003   0.3257   0.816     17935.    3510.4   0.0240  1.205   2.061  1.034   0.154
       6   0.2997   0.3262   0.817     17843.    3507.7   0.0241  1.211   2.075  1.040   0.155
       7   0.2993   0.3267   0.817     17766.    3505.0   0.0244  1.226   2.092  1.047   0.155
       8   0.2992   0.3270   0.817     17789.    3505.8   0.0232  1.168   2.040  1.019   0.149
       9   0.2993   0.3271   0.817     17829.    3506.4   0.0220  1.103   1.977  0.985   0.143
      10   0.2993   0.3272   0.817     17823.    3506.2   0.0220  1.104   1.967  0.981   0.143
 $$
 $TEXT:Result: $$ Final results $$
                      Initial    Final
           R factor    0.3691   0.2993
             R free    0.3819   0.3272
     Rms BondLength    0.0130   0.0220
      Rms BondAngle    1.4104   1.9674
     Rms ChirVolume    0.0775   0.1429
 $$

 Refmac_5.8.0049:  End of Refmac_5.8.0049  
Times: User:      40.0s System:    3.2s Elapsed:     0:43  

 
 ###############################################################
 ###############################################################
 ###############################################################
 ### CCP4 6.4: cbuccaneer             version 1.5.2 : 06/10/11##
 ###############################################################
 User: unknown  Run date: 17/ 7/2014 Run time: 18:57:42 


 Please reference: Collaborative Computational Project, Number 4. 1994.
 "The CCP4 Suite: Programs for Protein Crystallography". Acta Cryst. D50, 760-763.
 as well as any specific reference in the program write-up.



Copyright 2002-2010 Kevin Cowtan and University of York.


$TEXT:Reference: $$ Please reference $$

 'Fitting molecular fragments into electron density'
 Cowtan K. (2008) Acta Cryst. D64, 83-89.

$$
$TEXT:Reference: $$ Please reference $$

 'The Buccaneer software for automated model building'
 Cowtan K. (2006) Acta Cryst. D62, 1002-1011.

$$


title 	buccaneer auto-build
pdbin-ref 	/home/jmht/ccp4-6.4.0/lib/data/reference_structures/reference-1tqw.pdb
mtzin-ref 	/home/jmht/ccp4-6.4.0/lib/data/reference_structures/reference-1tqw.mtz
colin-ref-fo 	FP.F_sigF.F,FP.F_sigF.sigF
colin-ref-hl 	FC.ABCD.A,FC.ABCD.B,FC.ABCD.C,FC.ABCD.D
seqin 	/data1/jmht/polya_helices/3PP5/search_polya_15/input/3PP5_1.fasta
mtzin 	buccaneer_pipeline/refine.mtz
colin-fo 	FP, SIGFP
colin-hl 	HLACOMB,HLBCOMB,HLCCOMB,HLDCOMB
colin-fc 	FWT,PHWT
colin-free 	FREE
pdbin 	buccaneer_pipeline/refine.pdb
pdbout 	buccaneer_pipeline/build.pdb
anisotropy-correction
fast
cycles 	2
sequence-reliability 	0.95
correlation-mode
new-residue-name 	UNK
resolution 	2.0

MTZ file: buccaneer_pipeline/refine.mtz
  Number of reflections:     16180        Number of columns:  22

Applying anisotropy correction:
|-9.393e-15, 5.745e-17, 4.529e-18|
| 5.745e-17,         0,-1.019e-17|
| 4.529e-18,-1.019e-17,   -0.1105|

PDB file: buccaneer_pipeline/refine.pdb
  Number of atoms read: 501

Cycle: 1

 C-alphas after finding:    76
 C-alphas after growing:    109
 C-alphas after joining:    60
 C-alphas linked:           0
 C-alphas sequenced:        57
 C-alphas corrected:        0
 C-alphas after filtering:  60
 C-alphas after NCS build:  60
 C-alphas after pruning:    60
 C-alphas after rebuilding: 60


Internal cycle   1
     60 residues were built in   1 fragments, the longest having   60 residues.
     57 residues were sequenced, after pruning.
     60 residues were uniquely allocated to   1 chains.
  Completeness by residues built:   100.0%
  Completeness of chains (number):   82.2%    (1)



Cycle: 2

 C-alphas after finding:    76
 C-alphas after growing:    100
 C-alphas after joining:    60
 C-alphas linked:           0
 C-alphas sequenced:        57
 C-alphas corrected:        0
 C-alphas after filtering:  60
 C-alphas after NCS build:  60
 C-alphas after pruning:    60
 C-alphas after rebuilding: 60


Internal cycle   2
     60 residues were built in   1 fragments, the longest having   60 residues.
     57 residues were sequenced, after pruning.
     60 residues were uniquely allocated to   1 chains.
  Completeness by residues built:   100.0%
  Completeness of chains (number):   82.2%    (1)


$TEXT:Result: $$ $$
     60 residues were built in   1 fragments, the longest having   60 residues.
     57 residues were sequenced, after pruning.
     60 residues were uniquely allocated to   1 chains.
  Completeness by residues built:   100.0%
  Completeness of chains (number):   82.2%    (1)
$$


cbuccaneer: Normal termination
Times: User:      17.5s System:    0.0s Elapsed:     0:18  

 
 ###############################################################
 ###############################################################
 ###############################################################
 ### CCP4 6.4: Refmac_5.8.0049     version 5.8.0049 : 30/06/13##
 ###############################################################
 User: unknown  Run date: 17/ 7/2014 Run time: 18:58:00 


 Please reference: Collaborative Computational Project, Number 4. 1994.
 "The CCP4 Suite: Programs for Protein Crystallography". Acta Cryst. D50, 760-763.
 as well as any specific reference in the program write-up.


 $TEXT:Reference1: $$ Main reference $$ 
   "REFMAC5 for the refinement of macromolecular crystal structures:"
   G.N.Murshudov, P.Skubak, A.A.Lebedev, N.S.Pannu, R.A.Steiner, R.A.Nicholls, M.D.Winn, F.Long and A.A.Vagin,(2011) 
   Acta Crystallogr. D67, 355-367

 $$
 $SUMMARY :Reference1:  $$ Refmac: $$
 :TEXT:Reference1: $$

 $TEXT:Reference2: $$ Secondary reference $$ 
   "Refinement of Macromolecular Structures by the  Maximum-Likelihood Method:"
   G.N. Murshudov, A.A.Vagin and E.J.Dodson,(1997)
   Acta Crystallogr. D53, 240-255
   EU  Validation contract: BIO2CT-92-0524

 $$
 $SUMMARY :Reference2:  $$ Refmac: $$
 :TEXT:Reference2: $$

  Data line--- title  buccaneer auto-build
  Data line--- ncyc 10
  Data line--- labin                    PHIB=PHIC FOM= FOM                FREE=FREE   FP=FP SIGFP= SIGFP
  Data line--- weight AUTO
  Data line--- make check NONE
  Data line--- make hydrogen NO hout NO peptide NO cispeptide YES ssbridge YES symmetry YES sugar YES connectivity NO link NO
  Data line--- refi type REST PHASE resi MLKF meth CGMAT bref ISOT
  Data line--- scal type SIMP LSSC ANISO EXPE
  Data line--- solvent YES VDWProb 1.4 IONProb 0.8 RSHRink 0.8
  Data line--- PHOUT
  Data line--- PNAME buccaneer
  Data line--- DNAME buccaneer
  Data line--- END

 OPENED INPUT MTZ FILE 
 Logical Name: HKLIN   Filename: /data1/jmht/polya_helices/3PP5/search_polya_15/data/loc0_ALL_polya_15/unmod/mr/phaser/build/shelxe/rebuild/refine/refmacSX_output.mtz 


 Spacegroup information obtained from library file: 
 Logical Name: SYMINFO   Filename: /home/jmht/ccp4-6.4.0/lib/data/syminfo.lib


    ****                     Input and Default parameters#                      ****


Input coordinate file.  Logical name - XYZIN actual file name  - buccaneer_pipeline/build.pdb
Output coordinate file. Logical name - XYZOUT actual file name - buccaneer_pipeline/refine.pdb
Input reflection file.  Logical name - HKLIN actual file name  - /data1/jmht/polya_helices/3PP5/search_polya_15/data/loc0_ALL_polya_15/unmod/mr/phaser/build/shelxe/rebuild/refine/refmacSX_outpu
Output reflection file. Logical name - HKLOUT actual file name - buccaneer_pipeline/refine.mtz

Cell from mtz :    39.140    39.140   118.190    90.000    90.000   120.000
Space group from mtz: number -  173; name - P 63

  Refinement type                        : Restrained


    ****                           Makecif parameters                           ****

Dictionary files for restraints : /home/jmht/ccp4-6.4.0/lib/data/monomers/mon*cif
Parameters for new entry and VDW: /home/jmht/ccp4-6.4.0/lib/data/monomers/ener_lib.cif
    Program will rely on residue and atom names. No checking
    If this option is used then monomers should be checked carefully before using
    Hydrogens will not be written to the output file
    Links between monomers will be checked. Only those links present in the coordinate file will be used
    All links to sugar will be analysed and used
    For new ligands "ideal restraint" values will be taken from the energetic libary ener_lib.cif
    Symmetry related links will be analysed and used
    Cis peptides will be found and used automatically


  Residual                               : Phase modified Maximum Likelihood for Fs
 Phase Blurred by  Scale*Exp(-B s**2)    :    1.00    0.00

    ****                    Least-square scaling parameters                     ****

Overall scale
Overall B value
Overall anisotropic B with tr(B) = 0.0
Constant bulk solvent in non protein region
Probe radii for non-ions     1.400
Probe radii for ions         0.800
Shrinkage of the mask  by    0.800


    ****                 Map sharpening parameters and methods                  ****

No map sharpening will be performed

  Method of minimisation                 : Sparse Matrix
  Experimental sigmas used for weighting
  Number of Bins and width:    20       0.0223
  Refinement of individual isotropic Bfactors
  Refinement resln        :    18.5778  1.4990
  Estimated number of reflections :      26875
  Free R exclusion - flag equals:     0
  Auto weighting. An attempt
  Refinement cycles       :    10
  Scaling type                           :
          Wilson using 1 Gaussian

  Estimation of D/Sigma in resolution bins
  using  free set of reflns with experimental sigmas
  Input phases not used in SigmaA estimation

  Scaling and SigmaA resln:    18.5778  1.4990

  Damping factors:     1.0000  1.0000


    ****                    Geometry restraints and weights                     ****


                                              Sigma:
 Bonding distances
          Weight =  1.00

 Bond angles
          Weight =  1.00

 Planar groups (all and main chain)
          WEIGHT= 1.00 1.00

 Chiral centers
          Weight= 1.00

 NON-BONDED CONTACTS
          Overall weight                          =  1.00
          Sigma for simple VDW                    =  0.20
          Sigma for VDW trhough torsion angle     =  0.20
          Sigma for HBOND                         =  0.20
          Sigma for metal-ion                     =  0.20
          Sigma for DUMMY and other atom          =  0.30
          Distance for donor-accepetor = vdw1+vdw2+(-0.30)
          Distance for acceptor - H    = vdw1+     ( 0.10)
          VDW distance through torsion = vdw1+vdw2+(-0.30)
          Distance for DUMMY-others    = vdw1+vdw2+(-0.70)

 TORSION ANGLES
          Weight= 1.00

 THERMAL FACTORS
          Weight= 1.00
     Main chain bond (1-2 neighbour)          1.5A**2
     Main chain angle (1-3 neighbour)         2.0A**2
     Side chain bond                          3.0A**2
     Side chain angle                         4.5A**2

 RESTRAINTS AGAINST EXCESSIVE SHIFTS
     Positional parameters                   0.00A
     Thermal parameters                      0.00A
     Occupancy parameters                    0.00

 RADIUS OF CONFIDENCE
     Positional parameters 0.00A
     Thermal parameters    0.00A**2
     Occupancy parameters  0.00

Monitoring style is "MEDIUM". Complete information will be printed out in the
first and last cycle. In all other cycles minimum information will be printed out
Sigma cutoffs for printing out outliers
If deviation of restraint parameter > alpha*sigma then information will be printed out
Distance outliers      10.000
Angle outliers         10.000
Torsion outliers       10.000
Chiral volume outliers 10.000
Plane outliers         10.000
Non-bonding outliers   10.000
B value  outliers      10.000
---------------------------------------------------------------

 Input file :buccaneer_pipeline/build.pdb
  ------------------------------
  ---  LIBRARY OF MONOMERS   ---
 _lib_name         mon_lib
 _lib_version      5.41
 _lib_update       11/02/13
  ------------------------------
  NUMBER OF MONOMERS IN THE LIBRARY          : 11464
                with complete description    : 11464
  NUMBER OF MODIFICATIONS                    :    56
  NUMBER OF LINKS                            :    68
  I am reading libraries. Please wait.
      - energy parameters
      - monomer"s description (links & mod )

FORMATTED      OLD     file opened on unit  45

Logical name: ATOMSF, Filename: /home/jmht/ccp4-6.4.0/lib/data/atomsf.lib


  Number of atoms    :     501
  Number of residues :      60
  Number of chains   :       1
  I am reading library. Please wait.
                mon_lib.cif
  --------------------------------
  --- title of input coord file ---

  PDB_code:xxxx
  PDB_name:----
  PDB_date:XX-XXX-XX
  --------------------------------
  ATTENTION: atom:CG   UNK                 9  AA   is missing in the structure
  ATTENTION: atom:CG   UNK                10  AA   is missing in the structure
  ATTENTION: atom:CG   UNK                68  AA   is missing in the structure
  Number of chains                  :       1
  Total number of monomers          :      60
  Number of atoms                   :     504
  Number of missing atoms           :       3
  Number of rebuilt atoms           :       0
  Number of unknown atoms           :       0
  Number of deleted atoms           :       0

  Number of bonds restraints    :     506
  Number of angles restraints   :     680
  Number of torsions restraints :     340
  Number of chiralities         :      78
  Number of planar groups       :      88


 loop_
     _atom_type_symbol
     _atom_type_scat_Cromer_Mann_a1
     _atom_type_scat_Cromer_Mann_b1
     _atom_type_scat_Cromer_Mann_a2
     _atom_type_scat_Cromer_Mann_b2
     _atom_type_scat_Cromer_Mann_a3
     _atom_type_scat_Cromer_Mann_b3
     _atom_type_scat_Cromer_Mann_a4
     _atom_type_scat_Cromer_Mann_b4
     _atom_type_scat_Cromer_Mann_c


  N     12.2126   0.0057   3.1322   9.8933   2.0125  28.9975   1.1663   0.5826 -11.5290
  C      2.3100  20.8439   1.0200  10.2075   1.5886   0.5687   0.8650  51.6512   0.2156
  O      3.0485  13.2771   2.2868   5.7011   1.5463   0.3239   0.8670  32.9089   0.2508
  S      6.9053   1.4679   5.2034  22.2151   1.4379   0.2536   1.5863  56.1720   0.8669


 Number of distances         :           0
 Number of angles            :           0
 Number of torsions          :           0
 Number of planes            :           0
 Number of chirals           :           0
 Number of intervals         :           0
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
                        Standard  External       All
                Bonds:       506         0       506
               Angles:       680         0       680
              Chirals:        78         0        78
               Planes:        88         0        88
             Torsions:       340         0       340
            Intervals:         0         0         0
--------------------------------------------------------------------------------


  Number of harmonic restraints       =            0
  Number of atoms in special position =            0
 -----------------------------------------------------


    ****                           Info from mtz file                           ****

FreeR flag                            0
Number of "free" reflections        809
Number of   all  reflections      16180
--------------------------------------------------------------------------------
 Number of reflections in file      16180
 Number of reflections read          16180


     CGMAT cycle number =      1

 Limits of asymmetric unit      : 1.00 1.00 0.50
 Grid spacing to be used        :    96   96  288
 Maximuum H,K,L                 :    27   27   78
 Minimum acceptable grid spacing:    59   59  178
 Limits of asymmetric unit      : 1.00 1.00 0.50
 Grid spacing to be used        :    96   96  288
 Maximuum H,K,L                 :    27   27   78
 Minimum acceptable grid spacing:    59   59  178
 Weight matrix   0.58211029    
 Actual weight    10.000000      is applied to the X-ray term
Norm of X_ray positional gradient                182.
Norm of Geom. positional gradient                43.6
Norm of X_ray B-factor gradient                 0.200E+04
Norm of Geom. B-factor gradient                  0.00
Product of X_ray and Geom posit. gradients     -0.637E+04
 Cosine of angle between them                      -0.001
Product of X_ray and Geom B-fact gradients       0.00
 Cosine of angle between them                       0.000


Residuals: XRAY=     0.2787E+06 GEOM=      1076.     TOTAL=     0.2798E+06
 function value    279757.09    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                   506     0.013     0.020
Bond angles  : refined atoms                    680     1.334     1.970
Torsion angles, period  1. refined               59     2.845     5.000
Torsion angles, period  2. refined               29    30.720    26.207
Torsion angles, period  3. refined              103    12.251    15.000
Torsion angles, period  4. refined                3    11.127    15.000
Chiral centres: refined atoms                    78     0.073     0.200
Planar groups: refined atoms                    374     0.000     0.020
VDW repulsions: refined_atoms                   201     0.254     0.200
VDW; torsion: refined_atoms                     368     0.311     0.200
HBOND: refined_atoms                              6     0.327     0.200
VDW repulsions: symmetry: refined_atoms          36     0.442     0.200
HBOND: symmetry: refined_atoms                    1     0.105     0.200
M. chain bond B values: refined atoms           239     0.000     3.948
M. chain angle B values: refined atoms          297     0.000     5.922
S. chain bond B values: refined atoms           264     0.000     3.948
S. chain angle B values: refined atoms          382     0.000     5.922
Long range B values: refined atoms              758     0.000    32.504
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall               : scale =    0.777, B  = -22.205
Partial structure    1: scale =    0.458, B  =  44.326
Overall anisotropic scale factors
   B11 = -0.12 B22 = -0.12 B33 =  0.37 B12 = -0.06 B13 = -0.00 B23 = -0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------

    ****                Things for loggraph, R factor and others                ****


$TABLE: Cycle    1. Rfactor analysis, F distribution v resln  :
$GRAPHS:Cycle    1.  v. resln :N:1,6,7,11,12:
:Cycle    1.  and  v. resln :N:1,4,5,9,10:
:Cycle    1. % observed v. resln :N:1,3:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.014     172  83.11   163.7   165.7  0.39  0.54      10   198.7   144.8  0.48  0.58
 0.036     325  96.34   194.7   190.0  0.35  0.45      17   210.2   207.2  0.32  0.39
 0.058     417  97.12   250.8   235.0  0.29  0.37      22   234.8   194.4  0.38  0.48
 0.080     492  99.61   215.7   198.3  0.31  0.39      25   217.4   208.7  0.28  0.38
 0.102     551  99.66   154.9   146.5  0.37  0.44      29   159.5   129.1  0.35  0.38
 0.124     618  99.69   138.2   127.7  0.34  0.38      33   131.7   111.3  0.35  0.40
 0.147     674  99.58   118.5   111.2  0.35  0.39      35   124.2   116.6  0.27  0.28
 0.169     703  99.33   106.5    95.6  0.36  0.38      37    97.9    84.3  0.41  0.43
 0.191     765  99.51    95.4    81.2  0.39  0.40      41   104.8    95.9  0.36  0.37
 0.213     791  99.40    88.5    73.6  0.38  0.38      41    77.9    63.1  0.42  0.40
 0.235     838  99.10    73.2    62.2  0.39  0.38      44    70.8    60.8  0.42  0.41
 0.257     890  99.26    61.7    50.7  0.41  0.40      47    60.6    49.8  0.43  0.40
 0.279     890  99.05    50.6    42.3  0.42  0.40      47    44.8    35.7  0.48  0.43
 0.301     935  99.19    41.3    35.9  0.44  0.42      49    41.7    36.2  0.40  0.37
 0.323     996  98.78    35.2    32.8  0.45  0.41      53    35.4    35.7  0.44  0.37
 0.346    1015  98.89    32.6    29.7  0.44  0.40      53    33.2    31.3  0.42  0.37
 0.368    1029  98.63    29.2    26.5  0.42  0.39      54    25.5    26.9  0.55  0.49
 0.390    1084  98.70    27.4    24.6  0.43  0.40      57    30.4    25.5  0.47  0.45
 0.412    1081  98.36    24.2    21.2  0.44  0.40      57    25.7    25.1  0.37  0.32
 0.434    1105  97.08    21.1    18.5  0.45  0.40      58    23.3    17.9  0.36  0.37
$$

    ****                      Fom and SigmaA vs resolution                      ****

 $TABLE: Cycle    1. FSC and  Fom(-acentric, centric, overall v resln:
 $GRAPHS:Cycle    1. M(Fom) v. resln :N:1,3,5,7,8,9,10:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCwork  FSCfree$$
 $$
  0.0140   164   0.697     8   0.602   172   0.692  0.909  0.5058 *******
  0.0361   312   0.771    13   0.722   325   0.769  0.917  0.4722 *******
  0.0582   402   0.868    15   0.678   417   0.861  0.924  0.6334 *******
  0.0803   478   0.838    14   0.879   492   0.840  0.929  0.6792 *******
  0.1024   535   0.787    16   0.853   551   0.789  0.931  0.5962 *******
  0.1245   605   0.800    13   0.784   618   0.799  0.911  0.6262 *******
  0.1466   659   0.798    15   0.727   674   0.797  0.896  0.6694 *******
  0.1687   691   0.821    12   0.970   703   0.824  0.905  0.6877 *******
  0.1908   748   0.808    17   0.756   765   0.807  0.890  0.6785 *******
  0.2129   778   0.774    13   0.757   791   0.774  0.876  0.6418 *******
  0.2350   823   0.748    15   0.676   838   0.747  0.884  0.6090 *******
  0.2571   875   0.783    15   0.661   890   0.781  0.889  0.5777 *******
  0.2792   877   0.767    13   0.824   890   0.767  0.866  0.5501 *******
  0.3013   923   0.707    12   0.811   935   0.708  0.796  0.4691 *******
  0.3234   978   0.735    18   0.653   996   0.733  0.765  0.4968 *******
  0.3455   998   0.760    17   0.861  1015   0.762  0.765  0.5426 *******
  0.3677  1016   0.762    13   0.886  1029   0.764  0.727  0.5599 *******
  0.3898  1069   0.798    15   0.741  1084   0.797  0.730  0.5930 *******
  0.4119  1066   0.770    15   0.776  1081   0.770  0.795  0.5585 *******
  0.4340  1090   0.763    15   0.613  1105   0.761  0.797  0.5521 *******
 $$
Resolution limits                    =     18.578     1.499
Number of used reflections           =      15371
Percentage observed                  =    98.5504
Percentage of free reflections       =     5.0000
Overall R factor                     =     0.3708
Free R factor                        =     0.3781
Overall Fourier shell correlation    =     0.5820
Free Fourier shell correlation       =     0.0000
Overall weighted R factor            =     0.3999
Free weighted R factor               =     0.3946
Overall weighted R2 factor           =     0.5002
Free weighted R2 factor              =     0.4827
Overall correlation coefficient      =     0.8535
Free correlation coefficient         =     0.8413
Cruickshanks DPI for coordinate error=     0.1100
DPI based on free R factor           =     0.1046
Overall figure of merit              =     0.7748
ML based su of positional parameters =     0.1026
ML based su of thermal parameters    =     2.7660
-----------------------------------------------------------------------------
 Trying gamma equal    0.0000000    
 Convergence reached with no gamma cycles 


 fvalues    35057.750       1076.3212       265513.72       351653.81    


     CGMAT cycle number =      2

 Weight matrix   0.80561155    
 Actual weight    10.000000      is applied to the X-ray term


 function value    243312.63    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                   506     0.029     0.020
Bond angles  : refined atoms                    680     1.977     1.970
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall               : scale =    0.789, B  =  -4.219
Partial structure    1: scale =    0.451, B  =  26.479
Overall anisotropic scale factors
   B11 = -0.08 B22 = -0.08 B33 =  0.26 B12 = -0.04 B13 = -0.00 B23 = -0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.3344
Free R factor                        =     0.3488
Overall Fourier shell correlation    =     0.6670
Free Fourier shell correlation       =     0.0000
Overall figure of merit              =     0.7912
-----------------------------------------------------------------------------
 Trying gamma equal    0.0000000    
 Convergence reached with no gamma cycles 


 fvalues    25560.047       2245.9246       222532.33       257846.39    


     CGMAT cycle number =      3

 Weight matrix   0.95866168    
 Actual weight    9.0909090      is applied to the X-ray term


 function value    184896.83    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                   506     0.028     0.020
Bond angles  : refined atoms                    680     2.097     1.970
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall               : scale =    0.844, B  =   2.526
Partial structure    1: scale =    0.420, B  =  20.564
Overall anisotropic scale factors
   B11 = -0.06 B22 = -0.06 B33 =  0.18 B12 = -0.03 B13 = -0.00 B23 = -0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.3119
Free R factor                        =     0.3294
Overall Fourier shell correlation    =     0.7302
Free Fourier shell correlation       =     0.0000
Overall figure of merit              =     0.8098
-----------------------------------------------------------------------------
 Trying gamma equal    0.0000000    
 Convergence reached with no gamma cycles 


 fvalues    20437.078       5054.6719       179213.25       190846.30    


     CGMAT cycle number =      4

 Weight matrix    1.0974079    
 Actual weight    9.0909090      is applied to the X-ray term


 function value    173529.05    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                   506     0.026     0.020
Bond angles  : refined atoms                    680     2.071     1.970
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall               : scale =    0.863, B  =   0.661
Partial structure    1: scale =    0.416, B  =  23.870
Overall anisotropic scale factors
   B11 = -0.02 B22 = -0.02 B33 =  0.08 B12 = -0.01 B13 = -0.00 B23 = -0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.3028
Free R factor                        =     0.3227
Overall Fourier shell correlation    =     0.7388
Free Fourier shell correlation       =     0.0000
Overall figure of merit              =     0.8157
-----------------------------------------------------------------------------
 Trying gamma equal    0.0000000    
 Convergence reached with no gamma cycles 


 fvalues    18611.537       4109.9009       171858.59       173305.70    


     CGMAT cycle number =      5

 Weight matrix    1.1393480    
 Actual weight    9.0909090      is applied to the X-ray term


 function value    168793.09    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                   506     0.026     0.020
Bond angles  : refined atoms                    680     2.141     1.970
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall               : scale =    0.879, B  =   0.626
Partial structure    1: scale =    0.414, B  =  23.316
Overall anisotropic scale factors
   B11 = -0.02 B22 = -0.02 B33 =  0.06 B12 = -0.01 B13 = -0.00 B23 = -0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.3001
Free R factor                        =     0.3219
Overall Fourier shell correlation    =     0.7424
Free Fourier shell correlation       =     0.0000
Overall figure of merit              =     0.8180
-----------------------------------------------------------------------------
 Trying gamma equal    0.0000000    
 Convergence reached with no gamma cycles 


 fvalues    18032.980       4587.2568       168036.73       168523.44    


     CGMAT cycle number =      6

 Weight matrix    1.1538227    
 Actual weight    9.0909090      is applied to the X-ray term


 function value    167488.77    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                   506     0.026     0.020
Bond angles  : refined atoms                    680     2.175     1.970
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall               : scale =    0.883, B  =   0.408
Partial structure    1: scale =    0.415, B  =  23.387
Overall anisotropic scale factors
   B11 = -0.01 B22 = -0.01 B33 =  0.05 B12 = -0.01 B13 = -0.00 B23 = -0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2986
Free R factor                        =     0.3222
Overall Fourier shell correlation    =     0.7435
Free Fourier shell correlation       =     0.0000
Overall figure of merit              =     0.8187
-----------------------------------------------------------------------------
 Trying gamma equal    0.0000000    
 Convergence reached with no gamma cycles 


 fvalues    17871.943       4712.9199       167022.66       167185.13    


     CGMAT cycle number =      7

 Weight matrix    1.0567807    
 Actual weight    8.2644625      is applied to the X-ray term


 function value    151840.92    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                   506     0.026     0.020
Bond angles  : refined atoms                    680     2.202     1.970
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall               : scale =    0.888, B  =   0.433
Partial structure    1: scale =    0.417, B  =  23.326
Overall anisotropic scale factors
   B11 = -0.01 B22 = -0.01 B33 =  0.04 B12 = -0.01 B13 = -0.00 B23 = -0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2982
Free R factor                        =     0.3221
Overall Fourier shell correlation    =     0.7439
Free Fourier shell correlation       =     0.0000
Overall figure of merit              =     0.8192
-----------------------------------------------------------------------------
 Trying gamma equal    0.0000000    
 Convergence reached with no gamma cycles 


 fvalues    17761.590       4788.2773       151480.31       151578.28    


     CGMAT cycle number =      8

 Weight matrix    1.0561959    
 Actual weight    8.2644625      is applied to the X-ray term


 function value    151739.61    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                   506     0.025     0.020
Bond angles  : refined atoms                    680     2.157     1.970
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall               : scale =    0.888, B  =   0.364
Partial structure    1: scale =    0.426, B  =  24.111
Overall anisotropic scale factors
   B11 = -0.01 B22 = -0.01 B33 =  0.03 B12 = -0.01 B13 = -0.00 B23 = -0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2980
Free R factor                        =     0.3222
Overall Fourier shell correlation    =     0.7435
Free Fourier shell correlation       =     0.0000
Overall figure of merit              =     0.8191
-----------------------------------------------------------------------------
 Trying gamma equal    0.0000000    
 Convergence reached with no gamma cycles 


 fvalues    17768.912       4614.5615       151408.91       151465.06    


     CGMAT cycle number =      9

 Weight matrix    1.0586534    
 Actual weight    8.2644625      is applied to the X-ray term


 function value    151559.86    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                   506     0.025     0.020
Bond angles  : refined atoms                    680     2.159     1.970
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall               : scale =    0.889, B  =   0.378
Partial structure    1: scale =    0.427, B  =  23.942
Overall anisotropic scale factors
   B11 = -0.01 B22 = -0.01 B33 =  0.04 B12 = -0.01 B13 = -0.00 B23 = -0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2978
Free R factor                        =     0.3223
Overall Fourier shell correlation    =     0.7435
Free Fourier shell correlation       =     0.0000
Overall figure of merit              =     0.8193
-----------------------------------------------------------------------------
 Trying gamma equal    0.0000000    
 Convergence reached with no gamma cycles 


 fvalues    17746.998       4618.3457       151227.91       151287.75    


     CGMAT cycle number =     10

 Weight matrix   0.96424019    
 Actual weight    7.5131474      is applied to the X-ray term


 function value    137976.36    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                   506     0.025     0.020
Bond angles  : refined atoms                    680     2.164     1.970
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall               : scale =    0.890, B  =   0.375
Partial structure    1: scale =    0.432, B  =  24.385
Overall anisotropic scale factors
   B11 = -0.01 B22 = -0.01 B33 =  0.04 B12 = -0.01 B13 = -0.00 B23 = -0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2977
Free R factor                        =     0.3225
Overall Fourier shell correlation    =     0.7436
Free Fourier shell correlation       =     0.0000
Overall figure of merit              =     0.8194
-----------------------------------------------------------------------------
 Trying gamma equal    0.0000000    
 Convergence reached with no gamma cycles 


 fvalues    17719.627       4597.4883       137691.09       137727.66    

 Limits of asymmetric unit      : 1.00 1.00 0.50
 Grid spacing to be used        :    96   96  288
 Maximuum H,K,L                 :    27   27   78
 Minimum acceptable grid spacing:    59   59  178
 Limits of asymmetric unit      : 1.00 1.00 0.50
 Grid spacing to be used        :    96   96  288
 Maximuum H,K,L                 :    27   27   78
 Minimum acceptable grid spacing:    59   59  178

 WRITTEN OUTPUT MTZ FILE 
 Logical Name: HKLOUT   Filename: buccaneer_pipeline/refine.mtz 

Norm of X_ray positional gradient                0.00
Norm of Geom. positional gradient                0.00
Norm of X_ray B-factor gradient                  0.00
Norm of Geom. B-factor gradient                  0.00
Product of X_ray and Geom posit. gradients       0.00
 Cosine of angle between them                       0.000
Product of X_ray and Geom B-fact gradients       0.00
 Cosine of angle between them                       0.000


Residuals: XRAY=     0.1336E+06 GEOM=      4400.     TOTAL=     0.1380E+06

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                   506     0.023     0.020
Bond angles  : refined atoms                    680     2.099     1.970
Torsion angles, period  1. refined               59     3.200     5.000
Torsion angles, period  2. refined               29    29.664    26.207
Torsion angles, period  3. refined              103    15.344    15.000
Torsion angles, period  4. refined                3    18.698    15.000
Chiral centres: refined atoms                    78     0.151     0.200
Planar groups: refined atoms                    374     0.011     0.020
VDW repulsions: refined_atoms                   194     0.208     0.200
VDW; torsion: refined_atoms                     356     0.305     0.200
HBOND: refined_atoms                              4     0.277     0.200
VDW repulsions: symmetry: refined_atoms          27     0.279     0.200
M. chain bond B values: refined atoms           239     2.125     1.758
M. chain angle B values: refined atoms          297     3.266     2.608
S. chain bond B values: refined atoms           267     7.223     2.884
S. chain angle B values: refined atoms          383    10.744     3.898
Long range B values: refined atoms              744    12.651    16.697
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall               : scale =    0.889, B  =   0.336
Partial structure    1: scale =    0.436, B  =  25.023
Overall anisotropic scale factors
   B11 = -0.01 B22 = -0.01 B33 =  0.04 B12 = -0.01 B13 = -0.00 B23 = -0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------

    ****                Things for loggraph, R factor and others                ****


$TABLE: Cycle   11. Rfactor analysis, F distribution v resln  :
$GRAPHS:Cycle   11.  v. resln :N:1,6,7,11,12:
:Cycle   11.  and  v. resln :N:1,4,5,9,10:
:Cycle   11. % observed v. resln :N:1,3:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.014     172  83.11   143.1   158.1  0.37  0.54      10   173.7   146.3  0.33  0.33
 0.036     325  96.34   170.2   169.6  0.31  0.40      17   183.7   179.7  0.26  0.27
 0.058     417  97.12   219.2   208.8  0.22  0.28      22   205.2   187.2  0.25  0.35
 0.080     492  99.61   188.5   176.8  0.24  0.29      25   190.0   168.6  0.26  0.34
 0.102     551  99.66   135.4   130.5  0.30  0.35      29   139.4   125.4  0.34  0.36
 0.124     618  99.69   120.8   116.0  0.29  0.32      33   115.1   118.1  0.39  0.43
 0.147     674  99.58   103.6   101.6  0.27  0.30      35   108.6   101.6  0.27  0.30
 0.169     703  99.33    93.1    88.5  0.29  0.33      37    85.5    83.5  0.32  0.35
 0.191     765  99.51    83.4    74.9  0.29  0.31      41    91.6    81.0  0.30  0.32
 0.213     791  99.40    77.3    63.8  0.30  0.31      41    68.1    59.5  0.39  0.37
 0.235     838  99.10    64.0    51.8  0.33  0.33      44    61.9    45.5  0.40  0.39
 0.257     890  99.26    54.0    43.6  0.33  0.33      47    53.0    43.9  0.35  0.35
 0.279     890  99.05    44.3    37.6  0.35  0.34      47    39.1    34.9  0.39  0.37
 0.301     935  99.19    36.1    31.9  0.36  0.34      49    36.5    34.2  0.31  0.29
 0.323     996  98.78    30.8    29.4  0.36  0.33      53    30.9    29.9  0.35  0.28
 0.346    1015  98.89    28.5    27.2  0.34  0.31      53    29.0    27.8  0.33  0.33
 0.368    1029  98.63    25.5    25.5  0.33  0.30      54    22.3    22.5  0.44  0.41
 0.390    1084  98.70    23.9    23.3  0.31  0.28      57    26.5    25.8  0.30  0.29
 0.412    1081  98.36    21.2    21.4  0.31  0.28      57    22.5    24.0  0.34  0.28
 0.434    1105  97.08    18.5    19.6  0.34  0.30      58    20.4    20.0  0.30  0.28
$$

    ****                      Fom and SigmaA vs resolution                      ****

 $TABLE: Cycle   11. FSC and  Fom(-acentric, centric, overall v resln:
 $GRAPHS:Cycle   11. M(Fom) v. resln :N:1,3,5,7,8,9,10:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCwork  FSCfree$$
 $$
  0.0140   164   0.768     8   0.633   172   0.762  0.922  0.5427 *******
  0.0361   312   0.822    13   0.738   325   0.819  0.922  0.5255 *******
  0.0582   402   0.895    15   0.683   417   0.887  0.921  0.7031 *******
  0.0803   478   0.861    14   0.833   492   0.861  0.921  0.7480 *******
  0.1024   535   0.813    16   0.875   551   0.814  0.919  0.6884 *******
  0.1245   605   0.821    13   0.809   618   0.820  0.897  0.7160 *******
  0.1466   659   0.818    15   0.779   674   0.817  0.887  0.7576 *******
  0.1687   691   0.853    12   0.984   703   0.855  0.919  0.7955 *******
  0.1908   748   0.849    17   0.802   765   0.848  0.952  0.8017 *******
  0.2129   778   0.819    13   0.834   791   0.819  0.976  0.7755 *******
  0.2350   823   0.781    15   0.739   838   0.780  0.994  0.7441 *******
  0.2571   875   0.837    15   0.725   890   0.836  1.038  0.7643 *******
  0.2792   877   0.820    13   0.878   890   0.821  0.975  0.7452 *******
  0.3013   923   0.770    12   0.877   935   0.772  0.882  0.6794 *******
  0.3234   978   0.791    18   0.703   996   0.789  0.842  0.7017 *******
  0.3455   998   0.796    17   0.878  1015   0.798  0.811  0.7425 *******
  0.3677  1016   0.815    13   0.933  1029   0.817  0.810  0.7653 *******
  0.3898  1069   0.854    15   0.762  1084   0.853  0.851  0.7971 *******
  0.4119  1066   0.826    15   0.779  1081   0.825  0.832  0.7721 *******
  0.4340  1090   0.818    15   0.694  1105   0.816  0.773  0.7571 *******
 $$
Resolution limits                    =     18.578     1.499
Number of used reflections           =      15371
Percentage observed                  =    98.5504
Percentage of free reflections       =     5.0000
Overall R factor                     =     0.2979
Free R factor                        =     0.3222
Overall Fourier shell correlation    =     0.7430
Free Fourier shell correlation       =     0.0000
Overall weighted R factor            =     0.3232
Free weighted R factor               =     0.3390
Overall weighted R2 factor           =     0.4135
Free weighted R2 factor              =     0.4144
Overall correlation coefficient      =     0.9033
Free correlation coefficient         =     0.8868
Cruickshanks DPI for coordinate error=     0.0884
DPI based on free R factor           =     0.0891
Overall figure of merit              =     0.8196
ML based su of positional parameters =     0.0692
ML based su of thermal parameters    =     1.8041
-----------------------------------------------------------------------------
  Time in seconds: CPU =        39.63
             Elapsed =         128.00

    ****           Things for loggraph, R factor and others vs cycle            ****


$TABLE: Rfactor analysis, stats vs cycle  :
$GRAPHS: vs cycle :N:1,2,3:
:FOM vs cycle :N:1,4:
:-LL vs cycle :N:1,5:
:-LLfree vs cycle :N:1,6:
:Geometry vs cycle:N:1,7,8,9,10,11:
$$
    Ncyc    Rfact    Rfree     FOM      -LL     -LLfree  rmsBOND  zBOND rmsANGL  zANGL rmsCHIRAL $$
$$
       0   0.3708   0.3781   0.775     27868.    3733.6   0.0131  0.723   1.334  0.662   0.073
       1   0.3344   0.3488   0.791     24107.    3671.9   0.0289  1.446   1.977  0.994   0.130
       2   0.3119   0.3294   0.810     19783.    3566.8   0.0284  1.425   2.097  1.037   0.136
       3   0.3028   0.3227   0.816     18636.    3535.0   0.0262  1.320   2.071  1.028   0.153
       4   0.3001   0.3219   0.818     18063.    3514.9   0.0261  1.311   2.141  1.069   0.156
       5   0.2986   0.3222   0.819     17905.    3510.9   0.0261  1.314   2.175  1.087   0.161
       6   0.2982   0.3221   0.819     17793.    3506.6   0.0259  1.303   2.202  1.099   0.163
       7   0.2980   0.3222   0.819     17802.    3506.0   0.0248  1.246   2.157  1.074   0.157
       8   0.2978   0.3223   0.819     17780.    3504.9   0.0249  1.255   2.159  1.075   0.157
       9   0.2977   0.3225   0.819     17753.    3504.0   0.0250  1.260   2.164  1.077   0.157
      10   0.2979   0.3222   0.820     17785.    3504.0   0.0235  1.179   2.099  1.044   0.151
 $$
 $TEXT:Result: $$ Final results $$
                      Initial    Final
           R factor    0.3708   0.2979
             R free    0.3781   0.3222
     Rms BondLength    0.0131   0.0235
      Rms BondAngle    1.3339   2.0993
     Rms ChirVolume    0.0727   0.1506
 $$

 Refmac_5.8.0049:  End of Refmac_5.8.0049  
Times: User:      39.6s System:    3.1s Elapsed:     0:43