
________________________________________________________________________________

______________________ CCP-EM Process | Refmac stats (HM2) _____________________

__ Command _____________________________________________________________________
/Applications/ccp4-7.0/bin/refmac5 xyzin /Users/tom/ccpem_project/Refmac5_171/refined_hm1.pdb hklin /Users/tom/ccpem_project/Refmac5_171/starting_map_hm2.mtz xyzout /Users/tom/ccpem_project/Refmac5_171/fsc_hm2.pdb  << eof
labin FP=Fout0 PHIB=Pout0
make hydr no
solvent no
source EM MB
ncycle 1
weight auto
ncsr global
reso 4.5
ridge dist sigma 0.01
ridge dist dmax 4.2

end
eof
________________________________________________________________________________
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<hr>
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<B><FONT COLOR="#FF0000"><!--SUMMARY_BEGIN-->
<pre>
 
 ###############################################################
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 ### CCP4 7.0.067: Refmac          version 5.8.0238 : 10/15/18##
 ###############################################################
 User: tom  Run date:  4/ 3/2019 Run time: 13:17:44 


 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--- labin FP=Fout0 PHIB=Pout0
  Data line--- make hydr no
  Data line--- solvent no
  Data line--- source EM MB
  Data line--- ncycle 1
  Data line--- weight auto
  Data line--- ncsr global
  Data line--- reso 4.5
  Data line--- ridge dist sigma 0.01
  Data line--- ridge dist dmax 4.2
  Data line--- END

 OPENED INPUT MTZ FILE 
 Logical Name: HKLIN   Filename: /Users/tom/ccpem_project/Refmac5_171/starting_map_hm2.mtz 

===> Warning: Figure of merit of phases has not been assigned
===> Warning: They will be assumed to be equal to 1.0

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


Input coordinate file.  Logical name - XYZIN actual file name  - /Users/tom/ccpem_project/Refmac5_171/refined_hm1.pdb
Output coordinate file. Logical name - XYZOUT actual file name - /Users/tom/ccpem_project/Refmac5_171/fsc_hm2.pdb
Input reflection file.  Logical name - HKLIN actual file name  - /Users/tom/ccpem_project/Refmac5_171/starting_map_hm2.mtz
Output reflection file. Logical name - HKLOUT actual file name - HKLOUT

Cell from mtz :    75.000    75.000    75.000    90.000    90.000    90.000
Space group from mtz: number -    1; name - P 1

  Refinement type                        : Restrained

    ****                           Makecif parameters                           ****

Dictionary files for restraints : /Applications/ccp4-7.0/lib/data/monomers/mon*cif
Parameters for new entry and VDW: /Applications/ccp4-7.0/lib/data/monomers/ener_lib.cif
    Apart from amino acids and DNA/RNA all monomers will be checked to see if atom names and connectivity is correct
    Hydrogens will not be used
    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                               : 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


    ****                 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       0.0025
  Refinement of individual isotropic Bfactors
  Refinement resln        :    75.0000  4.5063
  Estimated number of reflections :      13756
  Auto weighting. An attempt
  Refinement cycles       :     1
  Scaling type                           :
          Wilson scaling type with Guassians

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

  Scaling and SigmaA resln:    75.0000  4.5063

  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
 
 NCS will defined automatically and applied

    ****                          Alignment parameters                          ****

     Alignment leve                   80.000%
     Aligment cut                    2.000A
     Iterative aligment              N

 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

Restraints on changes of interatomic distances is appplied

    ****                    Distance shift penlty parameters                    ****

     Sigma:           0.0100
     Maximum distance 4.2000

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 :/Users/tom/ccpem_project/Refmac5_171/refined_hm1.pdb
  ------------------------------
  ---  LIBRARY OF MONOMERS   ---
 _lib_name         mon_lib
 _lib_version      5.51
 _lib_update       11/07/18
  ------------------------------
  NUMBER OF MONOMERS IN THE LIBRARY          : 24613
                with complete description    : 24613
  NUMBER OF MODIFICATIONS                    :    69
  NUMBER OF LINKS                            :    76
  I am reading libraries. Please wait.
      - energy parameters
      - monomer"s description (links & mod )
  Number of atoms    :    1656
  Number of residues :     214
  Number of chains   :       1
  I am reading library. Please wait.
                mon_lib.cif
  WARNING : CIS peptide bond is found, angle =     16.18
            ch:AAA  res:   3  ILE              -->   4  ILE
  WARNING : TRANS peptide bond (not be changed CIS) angle =     90.29
            ch:AAA  res: 112  PRO              --> 113  ASP
  WARNING : TRANS peptide bond (not be changed CIS) angle =    145.17
            ch:AAA  res: 173  GLN              --> 174  MET
  WARNING : TRANS peptide bond (not be changed CIS) angle =     87.80
            ch:AAA  res: 209  LEU              --> 210  GLU
  --------------------------------
  --- title of input coord file ---
 
  PDB_code:XXXX
  PDB_name:----
  PDB_date:04-MAR-19
  --------------------------------
  ATTENTION: atom:OXT  PHE                19  AAA  is missing in the structure
  ATTENTION: atom:OXT  GLY                32  AAA  is missing in the structure
  ATTENTION: atom:OXT  MET                34  AAA  is missing in the structure
  ATTENTION: atom:OXT  ARG                36  AAA  is missing in the structure
  ATTENTION: atom:OXT  VAL                39  AAA  is missing in the structure
  ATTENTION: atom:OXT  LYS                47  AAA  is missing in the structure
  ATTENTION: atom:OXT  GLN                48  AAA  is missing in the structure
  ATTENTION: atom:OXT  ALA                55  AAA  is missing in the structure
  ATTENTION: atom:OXT  ALA                66  AAA  is missing in the structure
  ATTENTION: atom:OXT  LEU                67  AAA  is missing in the structure
  ATTENTION: atom:OXT  GLU                70  AAA  is missing in the structure
  ATTENTION: atom:OXT  ALA                73  AAA  is missing in the structure
  ATTENTION: atom:OXT  GLN                74  AAA  is missing in the structure
  ATTENTION: atom:OXT  ARG                88  AAA  is missing in the structure
  ATTENTION: atom:OXT  GLN                92  AAA  is missing in the structure
  ATTENTION: atom:OXT  GLU                98  AAA  is missing in the structure
  ATTENTION: atom:OXT  GLY               100  AAA  is missing in the structure
  ATTENTION: atom:OXT  ASN               102  AAA  is missing in the structure
  ATTENTION: atom:OXT  ASP               113  AAA  is missing in the structure
  ATTENTION: atom:OXT  ARG               119  AAA  is missing in the structure
   ... and more ...
  Number of chains                  :       1
  Total number of monomers          :     214
  Number of atoms                   :    1690
  Number of missing atoms           :      34
  Number of rebuilt atoms           :       0
  Number of unknown atoms           :       0
  Number of deleted atoms           :       0
 
  Number of bonds restraints    :    1646
  Number of angles restraints   :    2162
  Number of torsions restraints :    1255
  Number of chiralities         :     219
  Number of planar groups       :     266

_ccp4_form_factor.scat_method    'Mott-Bethe'
_ccp4_form_factor.scat_data_source  electron


 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
  C      2.3103  20.8439   1.0201  10.2075   1.5888   0.5687   0.8651  51.6512   0.2156
  S      6.9054   1.4679   5.2035  22.2151   1.4379   0.2536   1.5863  56.1720   0.8669
  O      3.0487  13.2771   2.2870   5.7011   1.5464   0.3239   0.8671  32.9089   0.2508


 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:      1646         0      1646
               Angles:      2162         0      2162
              Chirals:       219         0       219
               Planes:       266         0       266
             Torsions:      1255         0      1255
            Intervals:         0         0         0
--------------------------------------------------------------------------------
 
 
  Number of harmonic restraints       =            0
  Number of atoms in special position =            0
 -----------------------------------------------------
 

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

FreeR flag                         -999
Number of "free" reflections          0
Number of   all  reflections       9690
 Warning ==>The number of free reflections with flag         -999  is zero
 Warning ==> Switching off use of free R
--------------------------------------------------------------------------------
 Number of reflections in file       9690
 Number of reflections read           9690
 
   Current auto weighting coefficient =    13.76578    
 
 mode : HKRF


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



     CGMAT cycle number =      1

    ****                         Bond distance outliers                         ****

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

A      8 ALA C   . - A      9 PRO N   . mod.= 1.464 id.= 1.352 dev= -0.112 sig.= 0.010
A      9 PRO C   . - A     10 GLY N   . mod.= 1.168 id.= 1.337 dev=  0.169 sig.= 0.011
A     31 THR C   . - A     32 GLY N   . mod.= 1.711 id.= 1.337 dev= -0.374 sig.= 0.011
A     38 ALA C   . - A     39 VAL N   . mod.= 1.644 id.= 1.337 dev= -0.307 sig.= 0.011
A     57 LYS C   . - A     58 LEU N   . mod.= 1.738 id.= 1.337 dev= -0.401 sig.= 0.011
A     58 LEU CG  . - A     58 LEU CD2 . mod.= 1.845 id.= 1.521 dev= -0.324 sig.= 0.015
A     69 LYS C   . - A     70 GLU N   . mod.= 1.642 id.= 1.337 dev= -0.305 sig.= 0.011
A     76 ASP C   . - A     77 CYS N   . mod.= 1.465 id.= 1.337 dev= -0.128 sig.= 0.011
A     77 CYS C   . - A     78 ARG N   . mod.= 1.705 id.= 1.337 dev= -0.368 sig.= 0.011
A     89 THR CB  . - A     89 THR OG1 . mod.= 1.545 id.= 1.428 dev= -0.117 sig.= 0.010
A     89 THR C   . - A     90 ILE N   . mod.= 1.551 id.= 1.337 dev= -0.214 sig.= 0.011
A    104 ASP C   . - A    105 TYR N   . mod.= 1.704 id.= 1.337 dev= -0.367 sig.= 0.011
A    105 TYR C   . - A    106 VAL N   . mod.= 1.499 id.= 1.337 dev= -0.162 sig.= 0.011
A    126 HIS C   . - A    126 HIS O   . mod.= 1.415 id.= 1.229 dev= -0.186 sig.= 0.012
A    126 HIS C   . - A    127 ALA N   . mod.= 1.617 id.= 1.337 dev= -0.280 sig.= 0.011
A    129 SER C   . - A    129 SER O   . mod.= 1.103 id.= 1.229 dev=  0.126 sig.= 0.012
A    138 ASN C   . - A    139 PRO N   . mod.= 1.542 id.= 1.352 dev= -0.190 sig.= 0.010
A    145 LYS C   . - A    146 ASP N   . mod.= 1.623 id.= 1.337 dev= -0.286 sig.= 0.011
A    148 VAL C   . - A    149 THR N   . mod.= 1.697 id.= 1.337 dev= -0.360 sig.= 0.011
A    160 GLN CD  . - A    160 GLN NE2 . mod.= 1.196 id.= 1.323 dev=  0.127 sig.= 0.011
A    163 THR C   . - A    164 VAL N   . mod.= 1.481 id.= 1.337 dev= -0.144 sig.= 0.011
A    179 ILE CG1 . - A    179 ILE CD1 . mod.= 1.719 id.= 1.511 dev= -0.208 sig.= 0.020
A    184 LYS C   . - A    185 GLU N   . mod.= 1.167 id.= 1.337 dev=  0.170 sig.= 0.011
A    187 GLU C   . - A    188 ALA N   . mod.= 1.462 id.= 1.337 dev= -0.125 sig.= 0.011
A    190 ASN C   . - A    191 THR N   . mod.= 1.611 id.= 1.337 dev= -0.274 sig.= 0.011
A    191 THR C   . - A    192 LYS N   . mod.= 1.720 id.= 1.337 dev= -0.383 sig.= 0.011
A    193 TYR C   . - A    194 ALA N   . mod.= 1.529 id.= 1.337 dev= -0.192 sig.= 0.011
A    206 ARG CZ  . - A    206 ARG NH1 . mod.= 1.431 id.= 1.322 dev= -0.109 sig.= 0.010
A    208 ASP C   . - A    209 LEU N   . mod.= 1.620 id.= 1.337 dev= -0.283 sig.= 0.011
A    214 GLY C   . - A    214 GLY O   . mod.= 1.694 id.= 1.231 dev= -0.463 sig.= 0.020
A    214 GLY C   . - A    214 GLY OXT . mod.= 1.662 id.= 1.231 dev= -0.431 sig.= 0.020

    ****                         Torsion angle outliers                         ****

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

A      9 PRO CA    - A     10 GLY CA    mod.= 100.19 id.= 180.00 per.= 1 dev=  79.81 sig.=   5.00
A    112 PRO CA    - A    113 ASP CA    mod.= -90.29 id.=   0.00 per.= 1 dev=  90.29 sig.=   5.00
A    173 GLN CA    - A    174 MET CA    mod.= 145.17 id.=   0.00 per.= 1 dev=-145.17 sig.=   5.00
A    209 LEU CA    - A    210 GLU CA    mod.=  87.80 id.=   0.00 per.= 1 dev= -87.80 sig.=   5.00

    ****                         Chiral volume outliers                         ****

Chiral volume deviations from the ideal >10.000Sigma will be monitored

A      4 ILE CA    mod.=  -1.44 id.=   2.53 dev=  3.968 sig.=  0.200
A     92 GLN CA    mod.=  -0.01 id.=   2.55 dev=  2.554 sig.=  0.200
A    174 MET CA    mod.=   0.09 id.=   2.58 dev=  2.492 sig.=  0.200
A    203 ALA CA    mod.=  -0.72 id.=   2.50 dev=  3.221 sig.=  0.200
A    210 GLU CA    mod.=  -1.41 id.=   2.54 dev=  3.948 sig.=  0.200

    ****                Large deviation of atoms from planarity                 ****

Deviations from the planarity >10.000Sigma will be monitored
Atom: A      3 ILE C     deviation=   0.23 sigma.=   0.02
Atom: A      8 ALA C     deviation=  -0.27 sigma.=   0.02
Atom: A     21 MET C     deviation=   0.33 sigma.=   0.02
Atom: A     31 THR C     deviation=   0.25 sigma.=   0.02
Atom: A     38 ALA C     deviation=  -0.33 sigma.=   0.02
Atom: A     45 LEU C     deviation=  -0.34 sigma.=   0.02
Atom: A     77 CYS C     deviation=  -0.33 sigma.=   0.02
Atom: A     89 THR C     deviation=  -0.38 sigma.=   0.02
Atom: A    104 ASP C     deviation=   0.38 sigma.=   0.02
Atom: A    105 TYR C     deviation=  -0.29 sigma.=   0.02
Atom: A    126 HIS C     deviation=  -0.37 sigma.=   0.02
Atom: A    129 SER C     deviation=  -0.36 sigma.=   0.02
Atom: A    139 PRO N     deviation=   0.39 sigma.=   0.02
Atom: A    145 LYS C     deviation=  -0.35 sigma.=   0.02
Atom: A    163 THR C     deviation=  -0.45 sigma.=   0.02
Atom: A    181 TYR C     deviation=  -0.24 sigma.=   0.02
Atom: A    184 LYS C     deviation=  -0.33 sigma.=   0.02
Atom: A    191 THR C     deviation=   0.47 sigma.=   0.02
Atom: A    191 THR O     deviation=  -0.24 sigma.=   0.02
Atom: A    193 TYR C     deviation=  -0.32 sigma.=   0.02
Atom: A    206 ARG CZ    deviation=  -0.30 sigma.=   0.02
Atom: A    208 ASP C     deviation=  -0.22 sigma.=   0.02

 Limits of asymmetric unit      : 1.00 1.00 1.00
 Grid spacing to be used        :    88   88   88
 Maximuum H,K,L                 :    17   17   17
 Minimum acceptable grid spacing:    58   58   58
 Weight matrix   1.4036139E-02
 Actual weight    13.76578      is applied to the X-ray term
Norm of X_ray positional gradient                286.
Norm of Geom. positional gradient                334.
Norm of X_ray B-factor gradient                  279.
Norm of Geom. B-factor gradient                  48.1
Product of X_ray and Geom posit. gradients      0.558E+08
 Cosine of angle between them                       0.118
Product of X_ray and Geom B-fact gradients      0.473E+07
 Cosine of angle between them                       0.213


Residuals: XRAY=    -0.4876E+07 GEOM=     0.5851E+05 TOTAL=    -0.4818E+07
 function value   -4817772.    

-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1646     0.052     0.012
Bond angles  : refined atoms                   2162     7.063     1.652
Torsion angles, period  1. refined              179    21.396     5.000
Torsion angles, period  2. refined               88    34.488    22.386
Torsion angles, period  3. refined              313    25.359    15.000
Torsion angles, period  4. refined               13    22.265    15.000
Chiral centres: refined atoms                   219     0.578     0.200
Planar groups: refined atoms                   1139     0.061     0.020
VDW repulsions: refined_atoms                  2002     0.508     0.200
VDW; torsion: refined_atoms                    1970     0.397     0.200
HBOND: refined_atoms                            202     0.354     0.200
M. chain bond B values: refined atoms           821    11.179     7.612
M. chain angle B values: refined atoms          965    15.601    11.416
S. chain bond B values: refined atoms           825    11.681     8.132
S. chain angle B values: refined atoms         1197    17.231    12.048
Long range B values: refined atoms             6981    20.355   147.069
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     2.9105, B  =    7.5683
Overall anisotropic scale factors
   B11 =  -0.09 B22 =  -1.22 B33 =   1.31 B12 =   0.19 B13 =   0.45 B23 =  -0.14
-----------------------------------------------------------------------------

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

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


$TABLE: Cycle    1. Rfactor analysis, F distribution v resln  :
$GRAPHS:Cycle    1. M(Rfactor) v. resln :N:1,6,7:
:Cycle    1. M(Fobs) and M(Fc) v. resln :N:1,4,5:
:Cycle    1. % observed v. resln :N:1,3:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used $$
$$
 0.001     125 100.00   475.0   486.9  0.04  0.04
 0.004     184 100.00   181.6   179.5  0.05  0.05
 0.006     285 100.00   145.0   140.2  0.07  0.07
 0.009     301 100.00   122.9   118.3  0.09  0.09
 0.011     351 100.00    97.8    94.9  0.08  0.08
 0.014     361 100.00    85.6    83.8  0.08  0.08
 0.016     384 100.00    75.0    72.8  0.10  0.10
 0.019     493 100.00    67.4    66.3  0.12  0.12
 0.021     471 100.00    63.8    62.6  0.14  0.14
 0.023     486 100.00    57.2    57.2  0.14  0.14
 0.026     511 100.00    54.8    55.6  0.14  0.14
 0.028     582 100.00    52.2    53.0  0.15  0.15
 0.031     543 100.00    52.8    54.5  0.15  0.15
 0.033     616 100.00    53.9    55.4  0.15  0.15
 0.036     589 100.00    54.7    55.8  0.15  0.15
 0.038     636 100.00    55.8    56.6  0.15  0.15
 0.041     699 100.00    54.4    54.0  0.14  0.14
 0.043     658 100.00    55.5    54.5  0.14  0.14
 0.046     663 100.00    54.8    52.7  0.13  0.13
 0.048     749 100.00    54.4    51.0  0.14  0.14
$$

    ****                      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:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCwork CorrFofcWork$$
 $$
  0.0014    125   0.998      0   0.000    125   0.998  0.990  0.9996  0.9996
  0.0039    184   0.997      0   0.000    184   0.997  1.012  0.9972  0.9934
  0.0063    285   0.996      0   0.000    285   0.996  1.030  0.9955  0.9906
  0.0088    301   0.996      0   0.000    301   0.996  1.029  0.9934  0.9831
  0.0112    339   0.995      0   0.000    339   0.995  1.020  0.9938  0.9860
  0.0137    361   0.995      0   0.000    361   0.995  1.013  0.9931  0.9832
  0.0161    384   0.995      0   0.000    384   0.995  1.008  0.9904  0.9761
  0.0186    493   0.994      0   0.000    493   0.994  1.004  0.9852  0.9627
  0.0210    471   0.993      0   0.000    471   0.993  0.995  0.9814  0.9479
  0.0235    486   0.993      0   0.000    486   0.993  0.979  0.9801  0.9507
  0.0259    511   0.993      0   0.000    511   0.993  0.965  0.9803  0.9470
  0.0284    582   0.993      0   0.000    582   0.993  0.955  0.9786  0.9487
  0.0308    543   0.993      0   0.000    543   0.993  0.948  0.9783  0.9451
  0.0333    616   0.993      0   0.000    616   0.993  0.948  0.9787  0.9470
  0.0358    585   0.993      0   0.000    585   0.993  0.951  0.9789  0.9436
  0.0382    636   0.993      0   0.000    636   0.993  0.961  0.9776  0.9381
  0.0407    699   0.993      0   0.000    699   0.993  0.973  0.9776  0.9416
  0.0431    658   0.993      0   0.000    658   0.993  0.995  0.9782  0.9433
  0.0456    663   0.993      0   0.000    663   0.993  1.019  0.9797  0.9486
  0.0480    768   0.993      0   0.000    768   0.993  1.039  0.9778  0.9444
 $$
Resolution limits                    =     75.000     4.506
Number of used reflections           =       9671
Percentage observed                  =   100.0000
Percentage of free reflections       =     0.0000
Overall R factor                     =     0.1124
Average Fourier shell correlation    =     0.9822
Overall weighted R factor            =     0.1124
Overall weighted R2 factor           =     0.0907
Average correlation coefficient      =     0.9543
Overall correlation coefficient      =     0.9935
Cruickshanks DPI for coordinate error=     0.3734
Overall figure of merit              =     0.9934
ML based su of positional parameters =     0.2006
ML based su of thermal parameters    =    17.1600
-----------------------------------------------------------------------------
 Trying gamma equal   0.0000000E+00
 Convergence reached with no gamma cycles 
 fvalues   -354232.4       58514.37      -4817772.      1.0000000E+32

    ****                         Bond distance outliers                         ****

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

A      9 PRO C   . - A     10 GLY N   . mod.= 1.216 id.= 1.337 dev=  0.121 sig.= 0.011
A     31 THR C   . - A     32 GLY N   . mod.= 1.610 id.= 1.337 dev= -0.273 sig.= 0.011
A     38 ALA C   . - A     39 VAL N   . mod.= 1.576 id.= 1.337 dev= -0.239 sig.= 0.011
A     57 LYS C   . - A     58 LEU N   . mod.= 1.593 id.= 1.337 dev= -0.256 sig.= 0.011
A     58 LEU CG  . - A     58 LEU CD2 . mod.= 2.019 id.= 1.521 dev= -0.498 sig.= 0.015
A     69 LYS C   . - A     69 LYS O   . mod.= 1.350 id.= 1.229 dev= -0.121 sig.= 0.012
A     69 LYS C   . - A     70 GLU N   . mod.= 1.580 id.= 1.337 dev= -0.243 sig.= 0.011
A     77 CYS C   . - A     78 ARG N   . mod.= 1.649 id.= 1.337 dev= -0.312 sig.= 0.011
A     89 THR CB  . - A     89 THR OG1 . mod.= 1.530 id.= 1.428 dev= -0.102 sig.= 0.010
A     89 THR C   . - A     90 ILE N   . mod.= 1.486 id.= 1.337 dev= -0.149 sig.= 0.011
A    104 ASP C   . - A    105 TYR N   . mod.= 1.626 id.= 1.337 dev= -0.289 sig.= 0.011
A    105 TYR C   . - A    106 VAL N   . mod.= 1.458 id.= 1.337 dev= -0.121 sig.= 0.011
A    126 HIS C   . - A    127 ALA N   . mod.= 1.586 id.= 1.337 dev= -0.249 sig.= 0.011
A    138 ASN C   . - A    139 PRO N   . mod.= 1.492 id.= 1.352 dev= -0.140 sig.= 0.010
A    145 LYS C   . - A    146 ASP N   . mod.= 1.558 id.= 1.337 dev= -0.221 sig.= 0.011
A    148 VAL C   . - A    149 THR N   . mod.= 1.624 id.= 1.337 dev= -0.287 sig.= 0.011
A    163 THR C   . - A    164 VAL N   . mod.= 1.457 id.= 1.337 dev= -0.120 sig.= 0.011
A    184 LYS C   . - A    185 GLU N   . mod.= 1.183 id.= 1.337 dev=  0.154 sig.= 0.011
A    190 ASN C   . - A    191 THR N   . mod.= 1.559 id.= 1.337 dev= -0.222 sig.= 0.011
A    191 THR C   . - A    192 LYS N   . mod.= 1.612 id.= 1.337 dev= -0.275 sig.= 0.011
A    193 TYR C   . - A    194 ALA N   . mod.= 1.505 id.= 1.337 dev= -0.168 sig.= 0.011
A    208 ASP C   . - A    209 LEU N   . mod.= 1.550 id.= 1.337 dev= -0.213 sig.= 0.011
A    214 GLY C   . - A    214 GLY O   . mod.= 1.651 id.= 1.231 dev= -0.420 sig.= 0.020
A    214 GLY C   . - A    214 GLY OXT . mod.= 1.647 id.= 1.231 dev= -0.416 sig.= 0.020

    ****                         Torsion angle outliers                         ****

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

A      9 PRO CA    - A     10 GLY CA    mod.= 117.31 id.= 180.00 per.= 1 dev=  62.69 sig.=   5.00
A    112 PRO CA    - A    113 ASP CA    mod.= -94.74 id.=   0.00 per.= 1 dev=  94.74 sig.=   5.00
A    173 GLN CA    - A    174 MET CA    mod.= 146.17 id.=   0.00 per.= 1 dev=-146.17 sig.=   5.00
A    209 LEU CA    - A    210 GLU CA    mod.=  87.02 id.=   0.00 per.= 1 dev= -87.02 sig.=   5.00

    ****                         Chiral volume outliers                         ****

Chiral volume deviations from the ideal >10.000Sigma will be monitored

A      4 ILE CA    mod.=  -1.48 id.=   2.53 dev=  4.007 sig.=  0.200
A     92 GLN CA    mod.=   0.11 id.=   2.55 dev=  2.435 sig.=  0.200
A    174 MET CA    mod.=  -0.05 id.=   2.58 dev=  2.630 sig.=  0.200
A    203 ALA CA    mod.=  -0.59 id.=   2.50 dev=  3.093 sig.=  0.200
A    210 GLU CA    mod.=  -1.46 id.=   2.54 dev=  4.000 sig.=  0.200

    ****                Large deviation of atoms from planarity                 ****

Deviations from the planarity >10.000Sigma will be monitored
Atom: A      3 ILE C     deviation=   0.21 sigma.=   0.02
Atom: A      8 ALA C     deviation=  -0.24 sigma.=   0.02
Atom: A     21 MET C     deviation=   0.29 sigma.=   0.02
Atom: A     31 THR C     deviation=   0.23 sigma.=   0.02
Atom: A     38 ALA C     deviation=  -0.32 sigma.=   0.02
Atom: A     45 LEU C     deviation=  -0.32 sigma.=   0.02
Atom: A     77 CYS C     deviation=  -0.32 sigma.=   0.02
Atom: A     89 THR C     deviation=  -0.35 sigma.=   0.02
Atom: A    104 ASP C     deviation=   0.34 sigma.=   0.02
Atom: A    105 TYR C     deviation=  -0.28 sigma.=   0.02
Atom: A    126 HIS C     deviation=  -0.34 sigma.=   0.02
Atom: A    129 SER C     deviation=  -0.32 sigma.=   0.02
Atom: A    139 PRO N     deviation=   0.36 sigma.=   0.02
Atom: A    145 LYS C     deviation=  -0.31 sigma.=   0.02
Atom: A    163 THR C     deviation=  -0.43 sigma.=   0.02
Atom: A    181 TYR C     deviation=  -0.23 sigma.=   0.02
Atom: A    184 LYS C     deviation=  -0.32 sigma.=   0.02
Atom: A    191 THR C     deviation=   0.38 sigma.=   0.02
Atom: A    193 TYR C     deviation=  -0.30 sigma.=   0.02
Atom: A    206 ARG CZ    deviation=  -0.29 sigma.=   0.02
Atom: A    208 ASP C     deviation=  -0.21 sigma.=   0.02

 LABOUT FP=FP SIGFP=SIGFP FC=FC PHIC=PHIC FC_ALL=FC_ALL PHIC_ALL=PHIC_ALL FWT=FW
 T PHWT=PHWT DELFWT=DELFWT PHDELWT=PHDELWT FOM=FOM PHCOMB=PHCOMB FC_ALL_LS=FC_AL
 L_LS PHIC_ALL_LS=PHIC_ALL_LS

 WRITTEN OUTPUT MTZ FILE 
 Logical Name: HKLOUT   Filename: HKLOUT 




-------------------------------------------------------------------------------
             Restraint type              N restraints   Rms Delta   Av(Sigma)
Bond distances: refined atoms                  1646     0.045     0.012
Bond angles  : refined atoms                   2162     6.793     1.652
Torsion angles, period  1. refined              179    21.218     5.000
Torsion angles, period  2. refined               88    34.533    22.386
Torsion angles, period  3. refined              313    25.383    15.000
Torsion angles, period  4. refined               13    21.040    15.000
Chiral centres: refined atoms                   219     0.579     0.200
Planar groups: refined atoms                   1139     0.057     0.020
VDW repulsions: refined_atoms                  2004     0.505     0.200
VDW; torsion: refined_atoms                    1946     0.397     0.200
HBOND: refined_atoms                            196     0.360     0.200
M. chain bond B values: refined atoms           821    10.860     7.908
M. chain angle B values: refined atoms          965    15.771    11.855
S. chain bond B values: refined atoms           825    12.010     8.295
S. chain angle B values: refined atoms         1197    18.078    12.362
Long range B values: refined atoms             6976    22.308   151.709
-------------------------------------------------------------------------------

-----------------------------------------------------------------------------
Overall scale should be multiplied by       1.0000
Overall               : scale =     2.9212, B  =   -2.8249
Overall anisotropic scale factors
   B11 =  -0.25 B22 =  -1.15 B33 =   1.39 B12 =  -0.05 B13 =   0.47 B23 =  -0.06
-----------------------------------------------------------------------------

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

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


$TABLE: Cycle    2. Rfactor analysis, F distribution v resln  :
$GRAPHS:Cycle    2. M(Rfactor) v. resln :N:1,6,7:
:Cycle    2. M(Fobs) and M(Fc) v. resln :N:1,4,5:
:Cycle    2. % observed v. resln :N:1,3:
$$
M(4SSQ/LL) NR_used %_obs M(Fo_used) M(Fc_used) Rf_used WR_used $$
$$
 0.001     125 100.00   473.3   487.5  0.04  0.04
 0.004     184 100.00   180.9   179.3  0.05  0.05
 0.006     285 100.00   144.5   139.8  0.06  0.06
 0.009     301 100.00   122.5   118.2  0.08  0.08
 0.011     351 100.00    97.5    94.7  0.07  0.07
 0.014     361 100.00    85.3    83.4  0.06  0.06
 0.016     384 100.00    74.7    72.6  0.08  0.08
 0.019     493 100.00    67.2    66.2  0.09  0.09
 0.021     471 100.00    63.6    62.7  0.09  0.09
 0.023     486 100.00    56.9    56.9  0.09  0.09
 0.026     511 100.00    54.6    55.6  0.08  0.08
 0.028     582 100.00    52.0    53.3  0.09  0.09
 0.031     543 100.00    52.6    54.0  0.09  0.09
 0.033     616 100.00    53.7    55.2  0.09  0.09
 0.036     589 100.00    54.5    55.1  0.08  0.08
 0.038     636 100.00    55.6    56.3  0.08  0.08
 0.041     699 100.00    54.2    54.4  0.09  0.09
 0.043     658 100.00    55.3    54.5  0.09  0.09
 0.046     663 100.00    54.6    52.8  0.10  0.10
 0.048     749 100.00    54.2    51.1  0.12  0.12
$$

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

 $TABLE: Cycle    2. FSC and  Fom(<cos(DelPhi)>-acentric, centric, overall v resln:
 $GRAPHS:Cycle    2. M(Fom) v. resln :N:1,3,5,7,8,9,10:
 $$
 <4SSQ/LL> NREFa  FOMa  NREFc FOMc NREFall FOMall  SigmaA_Fc1 FSCwork CorrFofcWork$$
 $$
  0.0014    125   0.998      0   0.000    125   0.998  0.987  0.9997  0.9997
  0.0039    184   0.997      0   0.000    184   0.997  1.009  0.9974  0.9941
  0.0063    285   0.996      0   0.000    285   0.996  1.029  0.9959  0.9916
  0.0088    301   0.996      0   0.000    301   0.996  1.028  0.9942  0.9853
  0.0112    339   0.996      0   0.000    339   0.996  1.022  0.9949  0.9888
  0.0137    361   0.996      0   0.000    361   0.996  1.018  0.9950  0.9884
  0.0161    384   0.996      0   0.000    384   0.996  1.014  0.9941  0.9856
  0.0186    493   0.995      0   0.000    493   0.995  1.012  0.9920  0.9812
  0.0210    471   0.995      0   0.000    471   0.995  1.003  0.9911  0.9771
  0.0235    486   0.995      0   0.000    486   0.995  0.988  0.9912  0.9806
  0.0259    511   0.995      0   0.000    511   0.995  0.973  0.9918  0.9800
  0.0284    582   0.995      0   0.000    582   0.995  0.966  0.9918  0.9813
  0.0308    543   0.995      0   0.000    543   0.995  0.965  0.9919  0.9801
  0.0333    616   0.995      0   0.000    616   0.995  0.969  0.9923  0.9822
  0.0358    585   0.995      0   0.000    585   0.995  0.975  0.9928  0.9829
  0.0382    636   0.995      0   0.000    636   0.995  0.979  0.9929  0.9817
  0.0407    699   0.995      0   0.000    699   0.995  0.987  0.9916  0.9793
  0.0431    658   0.995      0   0.000    658   0.995  1.003  0.9910  0.9786
  0.0456    663   0.994      0   0.000    663   0.994  1.019  0.9884  0.9720
  0.0480    768   0.993      0   0.000    768   0.993  1.040  0.9840  0.9590
 $$
Resolution limits                    =     75.000     4.506
Number of used reflections           =       9671
Percentage observed                  =   100.0000
Percentage of free reflections       =     0.0000
Overall R factor                     =     0.0796
Average Fourier shell correlation    =     0.9917
Overall weighted R factor            =     0.0796
Overall weighted R2 factor           =     0.0679
Average correlation coefficient      =     0.9800
Overall correlation coefficient      =     0.9965
Cruickshanks DPI for coordinate error=     0.2643
Overall figure of merit              =     0.9950
ML based su of positional parameters =     0.2006
ML based su of thermal parameters    =    17.1600
-----------------------------------------------------------------------------
  Time in seconds: CPU =         1.03
             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:
$$
    Ncyc    Rfact    Rfree     FOM      -LL     -LLfree  rmsBOND  zBOND rmsANGL  zANGL rmsCHIRAL $$
$$
       0   0.1124   0.0      0.993     -354232.       0.0   0.0518  4.188   7.063  4.262   0.578
       1   0.0796   0.0      0.995     -359998.       0.0   0.0452  3.547   6.793  4.078   0.579
 $$
 $TEXT:Result: $$ Final results $$
                      Initial    Final
           R factor    0.1124   0.0796
     Rms BondLength    0.0518   0.0452
      Rms BondAngle    7.0635   6.7925
     Rms ChirVolume    0.5783   0.5786
 $$
 Harvest: NO PNAME_KEYWRD given - no deposit file created
<B><FONT COLOR="#FF0000"><!--SUMMARY_BEGIN-->
 Refmac:  End of Refmac_5.8.0238  
Times: User:       5.6s System:    0.4s Elapsed:     0:07  
</pre>
</html>
<!--SUMMARY_END--></FONT></B>

CCP-EM version dev 1.2.0-42-g243bc59 ___________________________________________

CCP-EM process finished Monday, 04. March 2019 01:17pm _________________________
________________________________________________________________________________
