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 ### CCP4 7.0.078: Refmac          version 5.8.0258 : 09/10/19##
 ###############################################################
 User: malyma  Run date: 11/ 3/2021 Run time: 12:39:00 


 Please reference: Collaborative Computational Project, Number 4. 2011.
 "Overview of the CCP4 suite and current developments". Acta Cryst. D67, 235-242.
 as well as any specific reference in the program write-up.

<!--SUMMARY_END--></FONT></B>
 $TEXT:Reference1: $$ Primary reference $$ 
   "Overview of refinement procedures within REFMAC5: utilizing data from different sources"
   O.Kovalevskiy, R.A.Nicholls, F.Long, G.N.Murshudov,(2018) 
   Acta Crystallogr. D74, 492-505

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

 $TEXT:Reference1: $$ Primary reference for EM $$ 
   "Current approaches for the fitting and refinement of atomic models into cryo-EM maps using CCP-EM
   R.A. Nicholls, M. Tykac, O.Kovalevskiy, G.N.Murshudov,(2018) 
   Acta Crystallogr. D74, 215-227

 $$
 $SUMMARY :Reference2:  $$ Refmac: $$
 :TEXT:Reference1: $$

 $TEXT:Reference1: $$ Secondary reference $$ 
   "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

 $$
 $SUMMARY :Reference3:  $$ 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

 $$
 $SUMMARY :Reference4:  $$ Refmac: $$
 :TEXT:Reference2: $$

  Data line--- make     check NONE
  Data line--- refi     type REST reso 47.32 1.90     resi MLKF     meth CGMAT     bref MIXED
  Data line--- scal     type SIMP     LSSC     ANISO     EXPE
  Data line--- solvent YES
  Data line--- bins 5
  Data line--- ncyc 10
  Data line--- monitor MEDIum
  Data line--- free 0
  Data line--- END

 OPENED INPUT MTZ FILE 
 Logical Name: HKLIN   Filename: poli67_1-9A.mtz 

 LABIN FP=F_XDSdataset SIGFP=SIGF_XDSdataset FREE=FreeR_flag

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


Input coordinate file.  Logical name - XYZIN actual file name  - project_R00_2-00A.pdb
Output coordinate file. Logical name - XYZOUT actual file name - project_R00_1-90A.pdb
Input reflection file.  Logical name - HKLIN actual file name  - poli67_1-9A.mtz
Output reflection file. Logical name - HKLOUT actual file name - project_R00_1-90A.mtz

Cell from mtz :    58.265    79.758    94.643    90.000    90.000    90.000
Space group from mtz: number -   19; name - P 21 21 21

  Refinement type                        : Restrained

    ****                           Makecif parameters                           ****

Dictionary files for restraints : /protein2/ccp4/ccp4-7.0/ccp4-7.0/lib/data/monomers/mon*cif
Parameters for new entry and VDW: /protein2/ccp4/ccp4-7.0/ccp4-7.0/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 be restored in their riding positions
    Links between monomers will be checked. Only those links present in the coordinate file will be used
    Standard sugar links 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                               : Rice Maximum Likelihood for Fs

    ****                    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     1.200
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:     5       0.0554
  Refinement of mixed isotropic and anisotropic Bfactors
  Refinement resln        :    47.3245  1.9000
  Estimated number of reflections :      45570
  Free R exclusion - flag equals:     0
  Auto weighting. An attempt
  Refinement cycles       :    10
  Scaling type                           :
          Wilson scaling type with Guassians

  Estimation of D/Sigma in resolution bins
  using  free set of reflns with experimental sigmas
  using  free set of reflns with experimental sigmas

  Scaling and SigmaA resln:    47.3245  1.9000

  Damping factors:     1.0000  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
Rigid bond outliers    10.000
Sphericity outliers    10.000
---------------------------------------------------------------

 Input file :project_R00_2-00A.pdb
  ------------------------------
  ---  LIBRARY OF MONOMERS   ---
 _lib_name         mon_lib
 _lib_version      5.51
 _lib_update       11/07/18
  ------------------------------
  NUMBER OF MONOMERS IN THE LIBRARY          : 24624
                with complete description    : 24624
  NUMBER OF MODIFICATIONS                    :    70
  NUMBER OF LINKS                            :    77
  I am reading libraries. Please wait.
      - energy parameters
      - monomer"s description (links & mod )
  Number of atoms    :    2286
  Number of residues :     307
  Number of chains   :       3
  I am reading library. Please wait.
                mon_lib.cif
  --------------------------------
  --- title of input coord file ---

  PDB_code:xxxx
  PDB_name:----
  PDB_date:24-OCT-17
  --------------------------------
  ATTENTION: atom:OXT  ASN                69  AAA  is missing in the structure
  ATTENTION: atom:OXT  ARG               164  AAA  is missing in the structure
  ATTENTION: atom:OXT  PRO                36  BBB  is missing in the structure
  ATTENTION: atom:OXT  THR                70  BBB  is missing in the structure
  ATTENTION: atom:OXT  ASN               153  BBB  is missing in the structure
  Number of chains                  :       3
  Total number of monomers          :     307
  Number of atoms                   :    4696
  Number of missing atoms           :       5
  Number of rebuilt atoms           :    2331
  Number of unknown atoms           :       0
  Number of deleted atoms           :       0

_ccp4_form_factor.scat_method    'Sum of Gaussians'
_ccp4_form_factor.scat_data_source  X-ray


 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     12.2220   0.0057   3.1346   9.8933   2.0141  28.9975   1.1672   0.5826 -11.5379
  H      0.4930  10.5109   0.3229  26.1257   0.1402   3.1424   0.0408  57.7997   0.0030
  C      2.3103  20.8439   1.0201  10.2075   1.5888   0.5687   0.8651  51.6512   0.2156
  O      3.0487  13.2771   2.2870   5.7011   1.5464   0.3239   0.8671  32.9089   0.2508
  S      6.9054   1.4679   5.2035  22.2151   1.4379   0.2536   1.5863  56.1720   1.0317


 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:      4485         0      4485
               Angles:      8175         0      8175
              Chirals:       284         0       284
               Planes:       646         0       646
             Torsions:      2321         0      2321
            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       1724
Number of   all  reflections      35468
--------------------------------------------------------------------------------
 Number of reflections in file      35470
 Number of reflections read          35468

   Current auto weighting coefficient =    7.2500257    

 mode : HKRF


######  TLS Group Definitions ######


     CGMAT cycle number =      1

 Limits of asymmetric unit      : 1.00 1.00 0.25
 Grid spacing to be used        :   112  160  180
 Maximuum H,K,L                 :    31   42   50
 Minimum acceptable grid spacing:    73  100  119
 Limits of asymmetric unit      : 1.00 1.00 0.25
 Grid spacing to be used        :   112  160  180
 Maximuum H,K,L                 :    31   42   50
 Minimum acceptable grid spacing:    73  100  119
 Weight matrix   1.87927522E-02
 Actual weight    7.2500257      is applied to the X-ray term
Norm of X_ray positional gradient                12.6
Norm of Geom. positional gradient                73.8
Norm of X_ray B-factor gradient                  15.4
Norm of Geom. B-factor gradient                  23.1
Product of X_ray and Geom posit. gradients     -0.306E+07
 Cosine of angle between them                      -0.245
Product of X_ray and Geom B-fact gradients     -0.138E+07
 Cosine of angle between them                      -0.865


Residuals: XRAY=     0.9552E+06 GEOM=     0.1454E+05 TOTAL=     0.9698E+06
 function value    969761.88    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  2284     0.008     0.013
Bond distances: others                         2201     0.034     0.017
Bond angles  : refined atoms                   3054     1.543     1.648
Bond angles  : others                          5121     2.216     1.582
Torsion angles, period  1. refined              265     6.975     5.000
Torsion angles, period  2. refined              135    32.441    22.370
Torsion angles, period  3. refined              475    19.755    15.000
Torsion angles, period  4. refined               19    18.533    15.000
Chiral centres: refined atoms                   284     0.069     0.200
Planar groups: refined atoms                   2462     0.007     0.020
Planar groups: others                           467     0.010     0.020
VDW repulsions: refined_atoms                   515     0.215     0.200
VDW repulsions.others                          1900     0.217     0.200
VDW; torsion: refined_atoms                    1092     0.162     0.200
VDW; torsion.others                            1055     0.073     0.200
HBOND: refined_atoms                             53     0.194     0.200
HBOND.others                                      1     0.020     0.200
VDW repulsions: symmetry: refined_atoms          11     0.193     0.200
VDW repulsions: symmetry: others                 33     0.223     0.200
HBOND: symmetry: refined_atoms                    2     0.120     0.200
M. chain bond B values: refined atoms          1075     6.078     6.962
M. chain bond B values: others                 1074     6.067     6.954
M. chain angle B values: refined atoms         1335     8.423    10.392
M. chain angle B values: others                1336     8.422    10.400
S. chain bond B values: refined atoms          1209     6.838     7.692
S. chain bond B values: others                 1207     6.839     7.685
S. chain angle B values: refined atoms         1719    10.182    11.241
S. chain angle B values: others                1719    10.179    11.241
Long range B values: refined atoms             2595    12.537    79.674
Long range B values: others                    2595    12.545    79.714
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     1.5041, B  =   -1.3519
Partial structure    1: scale =     0.3851, B  =   54.7318
Overall anisotropic scale factors
   B11 =   5.15 B22 =  -1.65 B33 =  -3.50 B12 =   0.00 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. <Rfactor> v. resln :N:1,6,7,11,12:
:Cycle    1. <Fobs> and <Fc> v. resln :N:1,4,5,9,10:
:Cycle    1. % observed v. resln :N:1,3:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.028    3240  99.53   268.7   264.1  0.20  0.21     153   256.0   250.6  0.29  0.29
 0.083    5552  99.88   133.2   123.1  0.21  0.19     305   132.6   123.7  0.28  0.26
 0.139    7124  99.77    44.3    45.4  0.29  0.25     364    46.0    48.8  0.36  0.32
 0.194    8355  99.91    24.1    20.9  0.40  0.39     424    23.9    20.9  0.42  0.40
 0.249    8476  89.91    19.2     9.2  0.57  0.58     428    19.7     9.5  0.56  0.56
$$

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

 $TABLE: Cycle    1. FSC and  Fom(<cos(DelPhi)>-acentric, centric, overall v resln:
 $GRAPHS:Cycle    1. M(Fom) v. resln :N:1,3,5,7,8,9,10,11,12:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0281   2542   0.819    698   0.749   3240   0.804  0.935  0.9118  0.9432  0.8547  0.9252
  0.0834   4838   0.803    714   0.706   5552   0.791  0.986  0.9022  0.9254  0.8564  0.9291
  0.1387   6411   0.658    713   0.610   7124   0.653  0.796  0.8109  0.8311  0.7242  0.8649
  0.1940   7643   0.354    712   0.311   8355   0.351  0.477  0.4814  0.4705  0.7135  0.7005
  0.2493   7833   0.361    643   0.359   8476   0.360  0.792  0.3828  0.3547  0.4201  0.4761
 $$
Resolution limits                    =     47.324     1.900
Number of used reflections           =      32747
Percentage observed                  =    97.0426
Percentage of free reflections       =     4.8633
Overall R factor                     =     0.2607
Free R factor                        =     0.3275
Average Fourier shell correlation    =     0.6429
AverageFree Fourier shell correlation=     0.6438
Overall weighted R factor            =     0.2258
Free weighted R factor               =     0.2951
Overall weighted R2 factor           =     0.2328
Free weighted R2 factor              =     0.3116
Average correlation coefficient      =     0.7392
Overall correlation coefficient      =     0.9599
Free correlation coefficient         =     0.9224
Cruickshanks DPI for coordinate error=     0.1583
DPI based on free R factor           =     0.1689
Overall figure of merit              =     0.5386
ML based su of positional parameters =     0.2746
ML based su of thermal parameters    =    11.4952
-----------------------------------------------------------------------------
 Trying gamma equal    0.0000000    
 Not converging with gamma equal    0.0000000    
 Trying gamma equal   5.24999984E-02
 Gamma decreased to   4.19999994E-02
 fvalues    131754.06       14541.520       969761.88      1.00000003E+32


     CGMAT cycle number =      2

 Weight matrix   1.92819033E-02
 Actual weight    7.2500257      is applied to the X-ray term


 function value    962749.56    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  2284     0.006     0.013
Bond distances: others                         2201     0.002     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     1.4999, B  =   -0.1381
Partial structure    1: scale =     0.3850, B  =   52.5500
Overall anisotropic scale factors
   B11 =   5.18 B22 =  -1.64 B33 =  -3.54 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2637
Free R factor                        =     0.3262
Average Fourier shell correlation    =     0.6310
AverageFree Fourier shell correlation=     0.6341
Average correlation coefficient      =     0.7402
Overall figure of merit              =     0.5265
-----------------------------------------------------------------------------
 Trying gamma equal   4.19999994E-02
 Gamma decreased to   3.24545428E-02
 fvalues    131808.84       7132.0630       962749.56       969761.88    


     CGMAT cycle number =      3

 Weight matrix   1.91049650E-02
 Actual weight    7.2500257      is applied to the X-ray term


 function value    962661.31    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  2284     0.006     0.013
Bond distances: others                         2201     0.001     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     1.5003, B  =    0.0004
Partial structure    1: scale =     0.3849, B  =   52.3678
Overall anisotropic scale factors
   B11 =   5.19 B22 =  -1.64 B33 =  -3.55 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2638
Free R factor                        =     0.3266
Average Fourier shell correlation    =     0.6283
AverageFree Fourier shell correlation=     0.6314
Average correlation coefficient      =     0.7397
Overall figure of merit              =     0.5245
-----------------------------------------------------------------------------
 Trying gamma equal   3.24545428E-02
 Gamma decreased to   2.37768572E-02
 fvalues    131798.73       7117.0996       962661.31       962749.56    


     CGMAT cycle number =      4

 Weight matrix   1.91663206E-02
 Actual weight    7.2500257      is applied to the X-ray term


 function value    962752.94    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  2284     0.006     0.013
Bond distances: others                         2201     0.001     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     1.5003, B  =    0.0002
Partial structure    1: scale =     0.3849, B  =   52.3665
Overall anisotropic scale factors
   B11 =   5.19 B22 =  -1.64 B33 =  -3.55 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2642
Free R factor                        =     0.3271
Average Fourier shell correlation    =     0.6292
AverageFree Fourier shell correlation=     0.6324
Average correlation coefficient      =     0.7394
Overall figure of merit              =     0.5256
-----------------------------------------------------------------------------
 Trying gamma equal   2.37768572E-02
 Gamma decreased to   1.58880539E-02


 fvalues    131827.88       6997.8940       962547.44       962661.31    
 fvalues    131827.88       6997.8940       962547.44       962753.38    


     CGMAT cycle number =      5

 Weight matrix   2.47994959E-02
 Actual weight    9.4250336      is applied to the X-ray term


 function value    1249354.1    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  2284     0.006     0.013
Bond distances: others                         2201     0.001     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     1.5009, B  =   -0.0062
Partial structure    1: scale =     0.3850, B  =   52.2456
Overall anisotropic scale factors
   B11 =   5.20 B22 =  -1.65 B33 =  -3.55 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2644
Free R factor                        =     0.3274
Average Fourier shell correlation    =     0.6288
AverageFree Fourier shell correlation=     0.6319
Average correlation coefficient      =     0.7394
Overall figure of merit              =     0.5253
-----------------------------------------------------------------------------
 Trying gamma equal   1.58880539E-02
 Gamma decreased to   8.71641375E-03


 fvalues    131816.91       6939.9941       1248958.8       962753.38    
 fvalues    131816.91       6939.9941       1248958.8       1249318.8    


     CGMAT cycle number =      6

 Weight matrix   3.22585814E-02
 Actual weight    12.252543      is applied to the X-ray term


 function value    1621614.6    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  2284     0.008     0.013
Bond distances: others                         2201     0.001     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     1.5012, B  =   -0.0058
Partial structure    1: scale =     0.3851, B  =   52.2195
Overall anisotropic scale factors
   B11 =   5.20 B22 =  -1.65 B33 =  -3.55 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2624
Free R factor                        =     0.3272
Average Fourier shell correlation    =     0.6293
AverageFree Fourier shell correlation=     0.6317
Average correlation coefficient      =     0.7406
Overall figure of merit              =     0.5252
-----------------------------------------------------------------------------
 Trying gamma equal   8.71641375E-03
 Gamma decreased to   2.19674082E-03


 fvalues    131717.80       7623.5229       1621044.1       1249318.8    
 fvalues    131717.80       7623.5229       1621044.1       1621501.5    


     CGMAT cycle number =      7

 Weight matrix   3.27008665E-02
 Actual weight    12.252543      is applied to the X-ray term


 function value    1622570.4    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  2284     0.009     0.013
Bond distances: others                         2201     0.001     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     1.4967, B  =   -0.1679
Partial structure    1: scale =     0.3843, B  =   52.8674
Overall anisotropic scale factors
   B11 =   5.16 B22 =  -1.64 B33 =  -3.52 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2611
Free R factor                        =     0.3269
Average Fourier shell correlation    =     0.6313
AverageFree Fourier shell correlation=     0.6332
Average correlation coefficient      =     0.7410
Overall figure of merit              =     0.5263
-----------------------------------------------------------------------------
 Trying gamma equal   2.19674082E-03
 Not converging with gamma equal   2.19674082E-03
 Trying gamma equal   3.33133601E-02
 Gamma decreased to   2.70900354E-02


 fvalues    131755.70       8567.4844       1623053.4       1621501.5    

 fvalues    131755.70       8567.4844       1623086.5       1622910.0    
 fvalues    131755.70       8567.4844       1623086.5       1622910.0    


     CGMAT cycle number =      8

 Weight matrix   3.26249190E-02
 Actual weight    12.252543      is applied to the X-ray term


 function value    1623208.0    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  2284     0.009     0.013
Bond distances: others                         2201     0.001     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     1.4943, B  =   -0.1659
Partial structure    1: scale =     0.3841, B  =   53.1311
Overall anisotropic scale factors
   B11 =   5.14 B22 =  -1.63 B33 =  -3.51 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2610
Free R factor                        =     0.3267
Average Fourier shell correlation    =     0.6314
AverageFree Fourier shell correlation=     0.6332
Average correlation coefficient      =     0.7410
Overall figure of merit              =     0.5260
-----------------------------------------------------------------------------
 Trying gamma equal   2.70900354E-02
 Gamma decreased to   2.14324687E-02


 fvalues    131783.05       8585.2188       1623372.0       1622910.0    

 fvalues    131783.05       8585.2188       1623351.9       1623262.8    
 fvalues    131783.05       8585.2188       1623351.9       1623262.8    


     CGMAT cycle number =      9

 Weight matrix   3.27131636E-02
 Actual weight    12.252543      is applied to the X-ray term


 function value    1623281.0    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  2284     0.009     0.013
Bond distances: others                         2201     0.001     0.017
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     1.4939, B  =   -0.1830
Partial structure    1: scale =     0.3841, B  =   53.1887
Overall anisotropic scale factors
   B11 =   5.13 B22 =  -1.63 B33 =  -3.50 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall R factor                     =     0.2610
Free R factor                        =     0.3268
Average Fourier shell correlation    =     0.6317
AverageFree Fourier shell correlation=     0.6336
Average correlation coefficient      =     0.7409
Overall figure of merit              =     0.5263
-----------------------------------------------------------------------------
 Trying gamma equal   2.14324687E-02
 Gamma decreased to   1.62892267E-02


 fvalues    131785.66       8593.8770       1623363.1       1623262.8    

 fvalues    131785.66       8593.8770       1623352.1       1623303.4    
 fvalues    131785.66       8593.8770       1623352.1       1623303.4    


     CGMAT cycle number =     10

 Limits of asymmetric unit      : 1.00 1.00 0.25
 Grid spacing to be used        :   112  160  180
 Maximuum H,K,L                 :    31   42   50
 Minimum acceptable grid spacing:    73  100  119
 Limits of asymmetric unit      : 1.00 1.00 0.25
 Grid spacing to be used        :   112  160  180
 Maximuum H,K,L                 :    31   42   50
 Minimum acceptable grid spacing:    73  100  119
 Weight matrix   3.26888300E-02
 Actual weight    12.252543      is applied to the X-ray term
Norm of X_ray positional gradient                22.1
Norm of Geom. positional gradient                22.0
Norm of X_ray B-factor gradient                  27.0
Norm of Geom. B-factor gradient                  26.0
Product of X_ray and Geom posit. gradients     -0.652E+07
 Cosine of angle between them                      -0.995
Product of X_ray and Geom B-fact gradients     -0.313E+07
 Cosine of angle between them                      -0.995


Residuals: XRAY=     0.1615E+07 GEOM=      8598.     TOTAL=     0.1623E+07
 function value    1623293.4    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  2284     0.009     0.013
Bond distances: others                         2201     0.001     0.017
Bond angles  : refined atoms                   3054     1.587     1.648
Bond angles  : others                          5121     1.268     1.582
Torsion angles, period  1. refined              265     6.998     5.000
Torsion angles, period  2. refined              135    32.778    22.370
Torsion angles, period  3. refined              475    19.889    15.000
Torsion angles, period  4. refined               19    18.507    15.000
Chiral centres: refined atoms                   284     0.070     0.200
Planar groups: refined atoms                   2462     0.007     0.020
Planar groups: others                           467     0.001     0.020
VDW repulsions: refined_atoms                   524     0.218     0.200
VDW repulsions.others                          2022     0.184     0.200
VDW; torsion: refined_atoms                    1099     0.163     0.200
VDW; torsion.others                            1103     0.085     0.200
HBOND: refined_atoms                             54     0.198     0.200
HBOND.others                                      1     0.087     0.200
VDW repulsions: symmetry: refined_atoms           9     0.207     0.200
VDW repulsions: symmetry: others                 34     0.211     0.200
HBOND: symmetry: refined_atoms                    2     0.131     0.200
M. chain bond B values: refined atoms          1075     6.195     6.820
M. chain bond B values: others                 1074     6.192     6.812
M. chain angle B values: refined atoms         1335     8.502    10.180
M. chain angle B values: others                1336     8.501    10.187
S. chain bond B values: refined atoms          1209     6.911     7.558
S. chain bond B values: others                 1207     6.915     7.551
S. chain angle B values: refined atoms         1719    10.210    11.037
S. chain angle B values: others                1719    10.208    11.037
Long range B values: refined atoms             2607    12.655    78.269
Long range B values: others                    2606    12.660    78.292
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     1.4939, B  =   -0.1647
Partial structure    1: scale =     0.3842, B  =   53.1503
Overall anisotropic scale factors
   B11 =   5.13 B22 =  -1.63 B33 =  -3.50 B12 =   0.00 B13 =   0.00 B23 =   0.00
-----------------------------------------------------------------------------

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

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


$TABLE: Cycle   10. Rfactor analysis, F distribution v resln  :
$GRAPHS:Cycle   10. <Rfactor> v. resln :N:1,6,7,11,12:
:Cycle   10. <Fobs> and <Fc> v. resln :N:1,4,5,9,10:
:Cycle   10. % observed v. resln :N:1,3:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.028    3240  99.53   270.6   265.9  0.20  0.21     153   257.8   251.4  0.29  0.29
 0.083    5552  99.88   134.1   123.7  0.21  0.20     305   133.5   124.2  0.28  0.26
 0.139    7124  99.77    44.7    45.7  0.29  0.25     364    46.3    49.1  0.36  0.32
 0.194    8355  99.91    24.2    21.1  0.40  0.39     424    24.1    21.2  0.41  0.40
 0.249    8476  89.91    19.3     9.2  0.57  0.57     428    19.9     9.6  0.56  0.56
$$

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

 $TABLE: Cycle   10. FSC and  Fom(<cos(DelPhi)>-acentric, centric, overall v resln:
 $GRAPHS:Cycle   10. M(Fom) v. resln :N:1,3,5,7,8,9,10,11,12:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0281   2542   0.830    698   0.760   3240   0.815  0.939  0.9128  0.9448  0.8529  0.9251
  0.0834   4838   0.805    714   0.707   5552   0.793  0.986  0.9025  0.9251  0.8561  0.9276
  0.1387   6411   0.686    713   0.637   7124   0.681  0.808  0.8277  0.8473  0.7224  0.8658
  0.1940   7643   0.276    712   0.243   8355   0.273  0.368  0.4241  0.4086  0.7146  0.6973
  0.2493   7833   0.361    643   0.356   8476   0.361  0.795  0.3844  0.3584  0.4187  0.4860
 $$
Resolution limits                    =     47.324     1.900
Number of used reflections           =      32747
Percentage observed                  =    97.0426
Percentage of free reflections       =     4.8633
Overall R factor                     =     0.2610
Free R factor                        =     0.3268
Average Fourier shell correlation    =     0.6316
AverageFree Fourier shell correlation=     0.6335
Overall weighted R factor            =     0.2265
Free weighted R factor               =     0.2945
Overall weighted R2 factor           =     0.2343
Free weighted R2 factor              =     0.3115
Average correlation coefficient      =     0.7409
Overall correlation coefficient      =     0.9597
Free correlation coefficient         =     0.9216
Cruickshanks DPI for coordinate error=     0.1585
DPI based on free R factor           =     0.1685
Overall figure of merit              =     0.5262
ML based su of positional parameters =     0.2703
ML based su of thermal parameters    =    11.4071
-----------------------------------------------------------------------------
 Trying gamma equal   1.62892267E-02
 Gamma decreased to   1.16135515E-02
 fvalues    131784.52       8597.8594       1623293.4       1623303.4    

 LABOUT FreeR_flag=FreeR_flag F_XDSdataset=F_XDSdataset SIGF_XDSdataset=SIGF_XDSdataset FC=FC PHIC=PHIC FC_ALL=FC_ALL PHIC_ALL=PHIC_ALL FWT=FWT PHWT=PHWT DELFWT=DELFWT PHDELWT=PHDELWT FOM=FOM FC_ALL_LS=FC_ALL_LS PHIC_ALL_LS=PHIC_ALL_LS

 WRITTEN OUTPUT MTZ FILE 
 Logical Name: HKLOUT   Filename: project_R00_1-90A.mtz 


-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  2284     0.009     0.013
Bond distances: others                         2201     0.001     0.017
Bond angles  : refined atoms                   3054     1.588     1.648
Bond angles  : others                          5121     1.268     1.582
Torsion angles, period  1. refined              265     7.001     5.000
Torsion angles, period  2. refined              135    32.787    22.370
Torsion angles, period  3. refined              475    19.892    15.000
Torsion angles, period  4. refined               19    18.531    15.000
Chiral centres: refined atoms                   284     0.070     0.200
Planar groups: refined atoms                   2462     0.007     0.020
Planar groups: others                           467     0.001     0.020
VDW repulsions: refined_atoms                   525     0.218     0.200
VDW repulsions.others                          2024     0.184     0.200
VDW; torsion: refined_atoms                    1099     0.163     0.200
VDW; torsion.others                            1100     0.085     0.200
HBOND: refined_atoms                             54     0.198     0.200
HBOND.others                                      1     0.089     0.200
VDW repulsions: symmetry: refined_atoms           9     0.207     0.200
VDW repulsions: symmetry: others                 34     0.211     0.200
HBOND: symmetry: refined_atoms                    2     0.131     0.200
M. chain bond B values: refined atoms          1075     6.198     6.818
M. chain bond B values: others                 1074     6.195     6.810
M. chain angle B values: refined atoms         1335     8.502    10.177
M. chain angle B values: others                1336     8.501    10.185
S. chain bond B values: refined atoms          1209     6.912     7.556
S. chain bond B values: others                 1207     6.915     7.549
S. chain angle B values: refined atoms         1719    10.210    11.034
S. chain angle B values: others                1719    10.209    11.034
Long range B values: refined atoms             2608    12.666    78.278
Long range B values: others                    2607    12.671    78.301
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     1.4941, B  =   -0.1544
Partial structure    1: scale =     0.3843, B  =   53.0917
Overall anisotropic scale factors
   B11 =   5.14 B22 =  -1.63 B33 =  -3.50 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. <Rfactor> v. resln :N:1,6,7,11,12:
:Cycle   11. <Fobs> and <Fc> v. resln :N:1,4,5,9,10:
:Cycle   11. % observed v. resln :N:1,3:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used
NR_free M(Fo_free) M(Fc_free) Rf_free   WR_free $$
$$
 0.028    3240  99.53   270.5   265.9  0.20  0.21     153   257.8   251.4  0.29  0.29
 0.083    5552  99.88   134.1   123.7  0.21  0.19     305   133.5   124.2  0.28  0.26
 0.139    7124  99.77    44.6    45.7  0.29  0.25     364    46.3    49.1  0.36  0.32
 0.194    8355  99.91    24.2    21.1  0.40  0.39     424    24.1    21.2  0.41  0.40
 0.249    8476  89.91    19.3     9.2  0.57  0.57     428    19.9     9.6  0.56  0.56
$$

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

 $TABLE: Cycle   11. FSC and  Fom(<cos(DelPhi)>-acentric, centric, overall v resln:
 $GRAPHS:Cycle   11. M(Fom) v. resln :N:1,3,5,7,8,9,10,11,12:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCfree  FSCwork CorrFoFcFree CorrFoFcWork$$
 $$
  0.0281   2542   0.831    698   0.760   3240   0.815  0.939  0.9128  0.9448  0.8528  0.9252
  0.0834   4838   0.805    714   0.707   5552   0.793  0.986  0.9026  0.9252  0.8562  0.9276
  0.1387   6411   0.686    713   0.637   7124   0.681  0.808  0.8277  0.8473  0.7222  0.8657
  0.1940   7643   0.276    712   0.243   8355   0.273  0.368  0.4241  0.4086  0.7145  0.6974
  0.2493   7833   0.361    643   0.355   8476   0.361  0.795  0.3844  0.3583  0.4190  0.4860
 $$
Resolution limits                    =     47.324     1.900
Number of used reflections           =      32747
Percentage observed                  =    97.0426
Percentage of free reflections       =     4.8633
Overall R factor                     =     0.2609
Free R factor                        =     0.3267
Average Fourier shell correlation    =     0.6317
AverageFree Fourier shell correlation=     0.6336
Overall weighted R factor            =     0.2265
Free weighted R factor               =     0.2944
Overall weighted R2 factor           =     0.2342
Free weighted R2 factor              =     0.3114
Average correlation coefficient      =     0.7408
Overall correlation coefficient      =     0.9597
Free correlation coefficient         =     0.9216
Cruickshanks DPI for coordinate error=     0.1585
DPI based on free R factor           =     0.1684
Overall figure of merit              =     0.5263
ML based su of positional parameters =     0.2703
ML based su of thermal parameters    =    11.4071
-----------------------------------------------------------------------------
  Time in seconds: CPU =        44.32
             Elapsed =           0.00

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


$TABLE: Rfactor analysis, stats vs cycle  :
$GRAPHS:<Rfactor> 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:
$$
    Ncyc    Rfact    Rfree     FOM      -LL     -LLfree  rmsBOND  zBOND rmsANGL  zANGL rmsCHIRAL $$
$$
       0   0.2607   0.3275   0.539      131754.    6859.8   0.0085  0.587   1.543  0.918   0.069
       1   0.2637   0.3262   0.527      131809.    6863.3   0.0061  0.431   1.441  0.855   0.065
       2   0.2638   0.3266   0.524      131799.    6864.1   0.0064  0.447   1.438  0.854   0.064
       3   0.2642   0.3271   0.526      131828.    6865.6   0.0063  0.439   1.428  0.848   0.063
       4   0.2644   0.3274   0.525      131821.    6864.8   0.0063  0.438   1.420  0.844   0.063
       5   0.2624   0.3272   0.525      131727.    6864.4   0.0075  0.523   1.479  0.879   0.065
       6   0.2611   0.3269   0.526      131728.    6869.5   0.0090  0.625   1.581  0.939   0.070
       7   0.2610   0.3267   0.526      131779.    6871.9   0.0090  0.623   1.585  0.941   0.070
       8   0.2610   0.3268   0.526      131784.    6872.5   0.0090  0.623   1.586  0.942   0.070
       9   0.2610   0.3268   0.526      131785.    6872.4   0.0090  0.623   1.587  0.943   0.070
      10   0.2609   0.3267   0.526      131776.    6872.0   0.0090  0.623   1.588  0.943   0.070
 $$
 $TEXT:Result: $$ Final results $$
                      Initial    Final
           R factor    0.2607   0.2609
             R free    0.3275   0.3267
     Rms BondLength    0.0085   0.0090
      Rms BondAngle    1.5433   1.5882
     Rms ChirVolume    0.0685   0.0702
 $$
 Harvest: NO PNAME_KEYWRD given - no deposit file created
<B><FONT COLOR="#FF0000"><!--SUMMARY_BEGIN-->
 Refmac:  End of Refmac_5.8.0258   
Times: User:      85.4s System:    0.3s Elapsed:     1:28  
</pre>
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