# Date 2008-01-16 Time 06:26:58 PST -0800 (1200493618.80 s)
#phil __OFF__

Command line arguments: "../1148.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = blackbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 8401
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 1148

-------------------------------------------------------------------------------
  PHENIX: Python-based Hierarchical ENvironment for Integrated Xtallography
  User: phzwart
-------------------------------------------------------------------------------

              phenix.refine: Macromolecular Structure Refinement

-------------------------------------------------------------------------------
Phenix developers include:
  Paul Adams, Pavel Afonine, Vicent Chen, Ian Davis, Kreshna Gopal,
  Ralf Grosse-Kunstleve, Li-Wei Hung, Robert Immormino, Tom Ioerger,
  Airlie McCoy, Erik McKee, Nigel Moriarty, Reetal Pai, Randy Read,
  Jane Richardson, David Richardson, Tod Romo, Jim Sacchettini,
  Nicholas Sauter, Jacob Smith, Laurent Storoni, Tom Terwilliger,
  Peter Zwart
Phenix home page:
  http://www.phenix-online.org/
-------------------------------------------------------------------------------

-------------------------------------------------------------------------------
Phenix components are copyrighted by:
  - Lawrence Berkeley National Laboratory
  - Los Alamos National Laboratory
  - University of Cambridge
  - Duke University
  - Texas Agricultural Experiment Station &
    Texas Engineering Experiment Station
-------------------------------------------------------------------------------

-------------------------------------------------------------------------------
Major third-party components of Phenix include:
    Python, wxwidgets, wxPython, Boost, SCons, Clipper,
    CCP4 Monomer Library, CCP4 I/O libraries, PyCifRW, FFTPACK, L-BFGS
  Enter phenix.acknowledgments for details.
-------------------------------------------------------------------------------

Processing inputs. This may take a minute or two.

Command line parameter definitions:
  refinement.main.number_of_macro_cycles = 5

Working crystal symmetry after inspecting all inputs:
  Unit cell: (71.655, 46.93, 85.9581, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb
  Monomer Library directory:
    "/net/rosie/scratch3/phzwart/CCTBX/Sources/mon_lib"
  Total number of atoms: 2823
  Number of models: 1
  Model: 0
    Number of conformers: 2
    Conformer: "A"
      Number of atoms: 2769
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
        Number of residues, atoms: 436, 436
          Classifications: {'water': 436}
          Link IDs: {None: 435}
    Conformer: "B"
      Number of atoms: 2771
      Common with "A": 2717
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
          bond proxies already assigned to first conformer: 2332
        Number of residues, atoms: 438, 438
          Classifications: {'water': 438}
          Link IDs: {None: 437}
  Time building chain proxies: 2.76, per 1000 atoms: 0.98


================================== X-ray data =================================

F-obs:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA

R-free flags:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (71.655, 46.93, 85.9581, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.1894 1.99104
Completeness in resolution range: 0.958835
Completeness with d_max=infinity: 0.955934

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.1894
                             d_min =   1.9910

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (71.655, 46.93, 85.9581, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.1894 1.99104
Completeness in resolution range: 0.958835
Completeness with d_max=infinity: 0.955934

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.1899 -  4.2610 [2142/2168]  1931   211   9.9%
  bin  2:  4.2610 -  3.3945 [2063/2082]  1855   208  10.1%
  bin  3:  3.3945 -  2.9690 [2032/2051]  1827   205  10.1%
  bin  4:  2.9690 -  2.6992 [2014/2044]  1813   201  10.0%
  bin  5:  2.6992 -  2.5067 [2014/2033]  1817   197   9.8%
  bin  6:  2.5067 -  2.3595 [1984/2009]  1778   206  10.4%
  bin  7:  2.3595 -  2.2417 [1991/2019]  1793   198   9.9%
  bin  8:  2.2417 -  2.1444 [1972/2008]  1780   192   9.7%
  bin  9:  2.1444 -  2.0620 [1972/2014]  1771   201  10.2%
  bin 10:  2.0620 -  1.9910 [1405/2002]  1265   140  10.0%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1148/model_refine_data.mtz


========================== Anomalous scatterer groups =========================

All atoms refined with f_prime=0 and f_double_prime=0.

========================== Set up restraints manager ==========================

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.12 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.81 -     2.42: 11
        2.42 -     3.04: 2188
        3.04 -     3.66: 4634
        3.66 -     4.28: 9002
        4.28 -     4.90: 12260
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z 207 " - " O   HOH Z 341 "  1.851 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 107 " - " O   HOH Z 340 "  2.057 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 208 " - " O   HOH Z 342 "  2.110 3.040 -x+1/2,-y+1,z+1/2
  " CZ BARG A 275 " - " O  BHOH Z 338 "  2.218 3.270
  ... (remaining 28090 not shown)
  Histogram of dihedral angle deviations from ideal:
        0.01 -    17.19: 754
       17.19 -    34.36: 62
       34.36 -    51.54: 27
       51.54 -    68.71: 23
       68.71 -    85.89: 4
  Dihedral angle restraints sorted by residual:
  " CA  PHE A 192 "
  " CB  PHE A 192 "
  " CG  PHE A 192 "
  " CD1 PHE A 192 "
      ideal   model   delta periodicty    weight residual
      90.00    7.91   82.09     2       2.50e-03 1.68e+01
  " N   PRO A  54 "
  " CG  PRO A  54 "
  " CD  PRO A  54 "
  " CB  PRO A  54 "
      ideal   model   delta periodicty    weight residual
      30.00  -27.17   57.17     3       4.44e-03 1.45e+01
  " N   PRO A 280 "
  " CA  PRO A 280 "
  " CB  PRO A 280 "
  " CG  PRO A 280 "
      ideal   model   delta periodicty    weight residual
     -25.00   38.44   56.56     3       4.44e-03 1.42e+01
  ... (remaining 867 not shown)

==================== Fixing bad ADP in input model (if any) ===================


============================== Scattering factors =============================


                ----------X-ray scattering dictionary----------                

Number of scattering types: 4
  Type Number    sf(0)   Gaussians
   S      13     15.96       2
   O     902      7.97       2
   N     437      6.97       2
   C    1471      5.97       2
  sf(0) = scattering factor at diffraction angle 0.


====================== Modifying start model if requested =====================


==================== Fixing bad ADP in input model (if any) ===================


================== Extract refinement strategy and selections =================

individual_sites       = True
rigid_body             = False
individual_adp         = True
group_adp              = False
tls                    = False
individual_occupancies = True
group_occupancies      = False
group_anomalous        = False
size = 2823

n_use            =  2823
n_use_u_iso      =  2823
n_use_u_aniso    =  0
n_grad_site      =  0
n_grad_u_iso     =  0
n_grad_u_aniso   =  0
n_grad_occupancy =  0
n_grad_fp        =  0
n_grad_fdp       =  0
n_anisotropic_flag =  0
total number of scatterers =  2823

==================== Process input NCS or/and find new NCS ====================

Using existing and finding new NCS is disabled.
Use refinement.main.ncs=true to activate it.
Look at refinement.ncs for more NCS related parameters.

=================== Write initial parameters into .eff file ===================

Writing effective parameters to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1148/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1148/model_refine_001.geo

CPU time processing inputs: 7.71


============================ Non-default parameters ===========================

A complete record of all parameters was written to the .eff file above.
Below are only the non-defaults.

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 71.655 46.93 85.95805 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
}
#phil __OFF__


============================= ml refinement start =============================


   ----------structure factors based statistics (before refinement)----------  


                         ----------X-ray data----------                        

|--(resolution: 1.99 - 15.19 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3070   r_free= 0.3070   ksol= 0.00   Bsol= 0.00   scale= 0.969    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.37 A                  |
| x-ray target function (ml) for work reflections: 6.009114                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1899 -  4.7528 0.99   1391  155 0.2829 0.2695       6.336      6.2795|
|  2:  4.7528 -  3.7917 0.99   1343  146 0.2383 0.2407         6.4      6.3696|
|  3:  3.7917 -  3.3181 0.99   1313  147 0.2645 0.2453      6.2886      6.3274|
|  4:  3.3181 -  3.0173 0.99   1316  153 0.2717 0.2844      6.1753      6.1729|
|  5:  3.0173 -  2.8025 0.99   1297  139 0.3047 0.3305      6.0657      6.1973|
|  6:  2.8025 -  2.6382 0.99   1284  143 0.3215 0.3093      6.0091      5.9884|
|  7:  2.6382 -  2.5067 0.99   1299  139 0.3324 0.3342      6.0054      6.0398|
|  8:  2.5067 -  2.3980 0.98   1263  151 0.3393 0.2998      5.9225      5.8541|
|  9:  2.3980 -  2.3060 0.98   1280  144 0.3349 0.3428       5.886      5.9081|
| 10:  2.3060 -  2.2267 0.99   1277  139 0.3429 0.3993      5.8681      5.9964|
| 11:  2.2267 -  2.1573 0.98   1284  138 0.3621 0.3617      5.8529      5.8691|
| 12:  2.1573 -  2.0958 0.97   1246  139 0.3624 0.3434       5.787      5.8261|
| 13:  2.0958 -  2.0407 1.00   1259  140 0.3657 0.3643      5.7104      5.6208|
| 14:  2.0407 -  1.9910 0.59    778   86 0.3227 0.3639      5.5805      5.5767|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.1899 -  4.7528  1391   155  0.80  25.07   0.86     0.82      39510.30|
|  2:  4.7528 -  3.7917  1343   146  0.85  20.95   0.98     0.91      41579.00|
|  3:  3.7917 -  3.3181  1313   147  0.81  25.09   0.99     0.94      41413.52|
|  4:  3.3181 -  3.0173  1316   153  0.79  27.84   0.99     0.93      38037.00|
|  5:  3.0173 -  2.8025  1297   139  0.71  34.45   0.98     0.88      34273.16|
|  6:  2.8025 -  2.6382  1284   143  0.71  34.65   1.01     0.89      29535.84|
|  7:  2.6382 -  2.5067  1299   139  0.73  33.41   1.00     0.90      25823.41|
|  8:  2.5067 -  2.3980  1263   151  0.73  33.46   0.99     0.93      22734.27|
|  9:  2.3980 -  2.3060  1280   144  0.71  34.99   1.03     0.92      22319.26|
| 10:  2.3060 -  2.2267  1277   139  0.68  37.18   1.04     0.90      22614.07|
| 11:  2.2267 -  2.1573  1284   138  0.67  38.72   1.05     0.89      22017.16|
| 12:  2.1573 -  2.0958  1246   139  0.69  36.96   1.03     0.93      19481.30|
| 13:  2.0958 -  2.0407  1259   140  0.69  37.07   1.01     0.94      15675.52|
| 14:  2.0407 -  1.9910   778    86  0.72  34.20   1.07     0.90      11749.74|
|alpha:            min =        0.82 max =            0.94 mean =         0.90|
|beta:             min =    11749.74 max =        41579.00 mean =     28288.92|
|figures of merit: min =        0.00 max =            1.00 mean =         0.74|
|phase err.(work): min =        0.00 max =           89.96 mean =        32.26|
|phase err.(test): min =        0.00 max =           89.98 mean =        31.93|
|-----------------------------------------------------------------------------|

============================== Outliers rejection =============================

basic_wilson_outliers    = 0
extreme_wilson_outliers  = 0
beamstop_shadow_outliers = 0
total                    = 0

====================== Target weights (before refinement) =====================

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 5.250157              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.552   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.636112              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.491   (deg)                 |
|-----------------------------------------------------------------------------|


        ----------Initial model statistics (before refinement)----------       

|-Geometry statistics: start--------------------------------------------------|
|            Histogram of deviations from ideal values for                    |
| Bonds                | Angles                   |  Nonbonded contacts       |
| 0.000 - 0.007:  1367 |   0.001 -   0.989:  1519 |  1.806 -  2.115:        4 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  2.115 -  2.424:        7 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.424 -  2.734:      190 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.734 -  3.043:     1998 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  3.043 -  3.353:     1817 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.353 -  3.662:     2817 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.662 -  3.972:     4640 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.972 -  4.281:     4362 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.281 -  4.591:     5581 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.591 -  4.900:     6679 |
|-----------------------------------------------------------------------------|
|-Geometry statistics: start--------------------------------------------------|
|      Type |    Count |    Deviation from ideal |     Targets | Target (sum) |
|           |          |    rmsd      max    min |             |              |
|      bond |     2439 |   0.010    0.070  0.000 |       0.254 |              |
|     angle |     3299 |   1.822    9.874  0.001 |       1.000 |              |
| chirality |      348 |   0.101    0.314  0.000 |       0.257 |        0.162 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.113    4.900  1.806 |       0.157 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.098)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      5.09    63.06   16.02    None  None   None       |
|    all(noH): 2823   0      5.09    63.06   16.02    None  None   None       |
|    Sol.    : 438    0      6.19    63.06   36.87    None  None   None       |
|    Mac.    : 2385   0      5.09    49.51   12.19    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     5.090 -  10.887: 1254   |   5:    34.075 -  39.872:   81        |
|      1:    10.887 -  16.684:  844   |   6:    39.872 -  45.669:   78        |
|      2:    16.684 -  22.481:  225   |   7:    45.669 -  51.466:   64        |
|      3:    22.481 -  28.278:  122   |   8:    51.466 -  57.263:   37        |
|      4:    28.278 -  34.075:   94   |   9:    57.263 -  63.060:   24        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

|-Occupancies statistics------------------------------------------------------|
| occupancies: max = 1.00   min = 0.30   number of occupancies < 0.1 = 0      |
|-----------------------------------------------------------------------------|

*********************** REFINEMENT MACRO_CYCLE 1 OF 5 *************************

|--(resolution: 1.99 - 15.19 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3070   r_free= 0.3070   ksol= 0.00   Bsol= 0.00   scale= 0.969    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.37 A                  |
| x-ray target function (ml) for work reflections: 6.009114                   |
|-----------------------------------------------------------------------------|

====================== bulk solvent modeling and scaling ======================

|--(resolution: 1.99 - 15.19 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2911   r_free= 0.2925   ksol= 0.32   Bsol= 50.00   scale= 0.975   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.97,-3.05,-1.59,-0.00,-0.00,-0.00); trace/3= -0.89                        |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.37 A                  |
| x-ray target function (ml) for work reflections: 5.983676                   |
|-----------------------------------------------------------------------------|

========================== Target weights: x-ray data =========================

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.667893              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.909   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.338491              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.121   (deg)                 |
|-----------------------------------------------------------------------------|


================================ xyz refinement ===============================

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2911      final r-factor (work) = 0.1705          |
| start r-factor (free) = 0.2925      final r-factor (free) = 0.1935          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 14.1476 = 4.67 * 0.50 * 5.9923 + 1.00 * 0.1619                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 13.3839 = 4.67 * 0.50 * 5.7044 + 1.00 * 0.0701                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

================================ ADP refinement ===============================


                 ----------Individual ADP refinement----------                 

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1705      final r-factor (work) = 0.1578          |
| start r-factor (free) = 0.1935      final r-factor (free) = 0.1960          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.9374 = 0.34 * 1.00 * 5.7044 + 1.00 * 0.0065                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.8697 = 0.34 * 1.00 * 5.4140 + 1.00 * 0.0371                               |
|-----------------------------------------------------------------------------|
| number of iterations = 6       |    number of function evaluations = 8      |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.098)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    67.74   16.70    None  None   None       |
|    all(noH): 2823   0      0.00    67.74   16.70    None  None   None       |
|    Sol.    : 438    0      4.57    63.34   37.66    None  None   None       |
|    Mac.    : 2385   0      0.00    67.74   12.85    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   6.774:  293   |   5:    33.870 -  40.644:  107        |
|      1:     6.774 -  13.548: 1268   |   6:    40.644 -  47.418:   93        |
|      2:    13.548 -  20.322:  642   |   7:    47.418 -  54.192:   80        |
|      3:    20.322 -  27.096:  176   |   8:    54.192 -  60.966:   35        |
|      4:    27.096 -  33.870:  123   |   9:    60.966 -  67.740:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


======================= Individual occupancy refinement =======================

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1578 r_free = 0.1960             target_work(ml) = 5.422         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1573 r_free = 0.1957             target_work(ml) = 5.419         |
| occupancies: max = 1.00  min = 0.06   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

*********************** REFINEMENT MACRO_CYCLE 2 OF 5 *************************

|--(resolution: 1.99 - 15.19 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1573   r_free= 0.1957   ksol= 0.32   Bsol= 50.00   scale= 1.021   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.97,-3.05,-1.59,-0.00,-0.00,-0.00); trace/3= -0.89                        |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.418990                   |
|-----------------------------------------------------------------------------|

====================== bulk solvent modeling and scaling ======================

|--(resolution: 1.99 - 15.19 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1545   r_free= 0.1914   ksol= 0.34   Bsol= 57.26   scale= 0.990   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.31,-3.15,-1.96,-0.00,-0.00,-0.00); trace/3= -2.14                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.406340                   |
|-----------------------------------------------------------------------------|

========================== Target weights: x-ray data =========================

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.190302              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 101.882  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.283182              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 88.926   (deg)                 |
|-----------------------------------------------------------------------------|


================================ xyz refinement ===============================

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1545      final r-factor (work) = 0.1235          |
| start r-factor (free) = 0.1914      final r-factor (free) = 0.1647          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.7200 = 3.19 * 0.50 * 5.4226 + 1.00 * 0.0701                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.5309 = 3.19 * 0.50 * 5.3064 + 1.00 * 0.0664                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

================================ ADP refinement ===============================


                 ----------Individual ADP refinement----------                 

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1235      final r-factor (work) = 0.1172          |
| start r-factor (free) = 0.1647      final r-factor (free) = 0.1604          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.5214 = 0.28 * 1.00 * 5.3064 + 1.00 * 0.0187                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.4777 = 0.28 * 1.00 * 5.1894 + 1.00 * 0.0082                               |
|-----------------------------------------------------------------------------|
| number of iterations = 24      |    number of function evaluations = 24     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.098)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.23    75.03   17.11    None  None   None       |
|    all(noH): 2823   0      1.23    75.03   17.11    None  None   None       |
|    Sol.    : 438    0      4.44    73.38   38.90    None  None   None       |
|    Mac.    : 2385   0      1.23    75.03   13.11    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.227 -   8.607:  601   |   5:    38.127 -  45.506:  109        |
|      1:     8.607 -  15.987: 1313   |   6:    45.506 -  52.886:   85        |
|      2:    15.987 -  23.367:  382   |   7:    52.886 -  60.266:   65        |
|      3:    23.367 -  30.747:  129   |   8:    60.266 -  67.646:   25        |
|      4:    30.747 -  38.127:  105   |   9:    67.646 -  75.026:    9        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


======================= Individual occupancy refinement =======================

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1172 r_free = 0.1604             target_work(ml) = 5.174         |
| occupancies: max = 1.00  min = 0.06   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1171 r_free = 0.1603             target_work(ml) = 5.174         |
| occupancies: max = 1.00  min = 0.04   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

*********************** REFINEMENT MACRO_CYCLE 3 OF 5 *************************

|--(resolution: 1.99 - 15.19 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1171   r_free= 0.1603   ksol= 0.34   Bsol= 57.26   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.31,-3.15,-1.96,-0.00,-0.00,-0.00); trace/3= -2.14                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.174086                   |
|-----------------------------------------------------------------------------|

====================== bulk solvent modeling and scaling ======================

|--(resolution: 1.99 - 15.19 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1171   r_free= 0.1599   ksol= 0.33   Bsol= 57.26   scale= 0.995   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.02,-2.85,-1.81,-0.00,-0.00,-0.00); trace/3= -2.23                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.172417                   |
|-----------------------------------------------------------------------------|

========================== Target weights: x-ray data =========================

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.451923              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 139.984  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.170229              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 145.926  (deg)                 |
|-----------------------------------------------------------------------------|


================================ xyz refinement ===============================

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1171      final r-factor (work) = 0.1121          |
| start r-factor (free) = 0.1599      final r-factor (free) = 0.1584          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.4272 = 2.45 * 0.50 * 5.1884 + 1.00 * 0.0664                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.3847 = 2.45 * 0.50 * 5.1546 + 1.00 * 0.0654                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

================================ ADP refinement ===============================


                 ----------Individual ADP refinement----------                 

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1121      final r-factor (work) = 0.1119          |
| start r-factor (free) = 0.1584      final r-factor (free) = 0.1571          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.8855 = 0.17 * 1.00 * 5.1546 + 1.00 * 0.0081                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.8837 = 0.17 * 1.00 * 5.1485 + 1.00 * 0.0072                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 34     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.098)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.74    75.46   16.82    None  None   None       |
|    all(noH): 2823   0      1.74    75.46   16.82    None  None   None       |
|    Sol.    : 438    0      4.13    74.43   37.70    None  None   None       |
|    Mac.    : 2385   0      1.74    75.46   12.98    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.735 -   9.108:  722   |   5:    38.597 -  45.970:  105        |
|      1:     9.108 -  16.480: 1254   |   6:    45.970 -  53.342:   83        |
|      2:    16.480 -  23.853:  340   |   7:    53.342 -  60.715:   55        |
|      3:    23.853 -  31.225:  128   |   8:    60.715 -  68.087:   15        |
|      4:    31.225 -  38.597:  114   |   9:    68.087 -  75.459:    7        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


======================= Individual occupancy refinement =======================

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1119 r_free = 0.1571             target_work(ml) = 5.144         |
| occupancies: max = 1.00  min = 0.04   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1118 r_free = 0.1571             target_work(ml) = 5.144         |
| occupancies: max = 1.00  min = 0.04   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

*********************** REFINEMENT MACRO_CYCLE 4 OF 5 *************************

|--(resolution: 1.99 - 15.19 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1118   r_free= 0.1571   ksol= 0.33   Bsol= 57.26   scale= 0.993   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.02,-2.85,-1.81,-0.00,-0.00,-0.00); trace/3= -2.23                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.144284                   |
|-----------------------------------------------------------------------------|

====================== bulk solvent modeling and scaling ======================

|--(resolution: 1.99 - 15.19 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1118   r_free= 0.1571   ksol= 0.33   Bsol= 57.26   scale= 0.993   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.21,-2.68,-1.70,-0.00,-0.00,-0.00); trace/3= -2.20                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.143994                   |
|-----------------------------------------------------------------------------|

========================== Target weights: x-ray data =========================

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.514998              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 161.414  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.768653              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 153.996  (deg)                 |
|-----------------------------------------------------------------------------|


================================ xyz refinement ===============================

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1118      final r-factor (work) = 0.1100          |
| start r-factor (free) = 0.1571      final r-factor (free) = 0.1576          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.5392 = 2.51 * 0.50 * 5.1482 + 1.00 * 0.0654                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.5278 = 2.51 * 0.50 * 5.1369 + 1.00 * 0.0682                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

================================ ADP refinement ===============================


                 ----------Individual ADP refinement----------                 

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1100      final r-factor (work) = 0.1089          |
| start r-factor (free) = 0.1576      final r-factor (free) = 0.1583          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.9557 = 0.77 * 1.00 * 5.1369 + 1.00 * 0.0072                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.9531 = 0.77 * 1.00 * 5.1313 + 1.00 * 0.0089                               |
|-----------------------------------------------------------------------------|
| number of iterations = 24      |    number of function evaluations = 25     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.098)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.55    84.40   17.10    None  None   None       |
|    all(noH): 2823   0      0.55    84.40   17.10    None  None   None       |
|    Sol.    : 438    0      5.07    79.11   39.45    None  None   None       |
|    Mac.    : 2385   0      0.55    84.40   13.00    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.549 -   8.934:  749   |   5:    42.475 -  50.861:  101        |
|      1:     8.934 -  17.320: 1294   |   6:    50.861 -  59.246:   82        |
|      2:    17.320 -  25.705:  294   |   7:    59.246 -  67.631:   40        |
|      3:    25.705 -  34.090:  133   |   8:    67.631 -  76.016:   13        |
|      4:    34.090 -  42.475:  111   |   9:    76.016 -  84.402:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


======================= Individual occupancy refinement =======================

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1089 r_free = 0.1583             target_work(ml) = 5.135         |
| occupancies: max = 1.00  min = 0.04   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1088 r_free = 0.1583             target_work(ml) = 5.135         |
| occupancies: max = 1.00  min = 0.03   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

*********************** REFINEMENT MACRO_CYCLE 5 OF 5 *************************

|--(resolution: 1.99 - 15.19 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1088   r_free= 0.1583   ksol= 0.33   Bsol= 57.26   scale= 0.991   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.21,-2.68,-1.70,-0.00,-0.00,-0.00); trace/3= -2.20                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.135228                   |
|-----------------------------------------------------------------------------|

====================== bulk solvent modeling and scaling ======================

|--(resolution: 1.99 - 15.19 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1087   r_free= 0.1583   ksol= 0.33   Bsol= 57.26   scale= 0.996   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.07,-2.45,-1.50,-0.00,-0.00,-0.00); trace/3= -2.00                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.135343                   |
|-----------------------------------------------------------------------------|

========================== Target weights: x-ray data =========================

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.531275              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 159.689  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.128368              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 127.533  (deg)                 |
|-----------------------------------------------------------------------------|


================================ xyz refinement ===============================

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1087      final r-factor (work) = 0.1086          |
| start r-factor (free) = 0.1583      final r-factor (free) = 0.1588          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.5635 = 2.53 * 0.50 * 5.1320 + 1.00 * 0.0682                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.5659 = 2.53 * 0.50 * 5.1348 + 1.00 * 0.0670                               |
|-----------------------------------------------------------------------------|
| number of iterations = 23      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

================================ ADP refinement ===============================


                 ----------Individual ADP refinement----------                 

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1086      final r-factor (work) = 0.1107          |
| start r-factor (free) = 0.1588      final r-factor (free) = 0.1584          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.6680 = 0.13 * 1.00 * 5.1348 + 1.00 * 0.0089                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.6674 = 0.13 * 1.00 * 5.1461 + 1.00 * 0.0068                               |
|-----------------------------------------------------------------------------|
| number of iterations = 19      |    number of function evaluations = 21     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.098)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      2.07    80.18   16.41    None  None   None       |
|    all(noH): 2823   0      2.07    80.18   16.41    None  None   None       |
|    Sol.    : 438    0      6.42    76.70   36.49    None  None   None       |
|    Mac.    : 2385   0      2.07    80.18   12.72    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     2.074 -   9.884:  987   |   5:    41.126 -  48.937:   92        |
|      1:     9.884 -  17.695: 1101   |   6:    48.937 -  56.747:   68        |
|      2:    17.695 -  25.505:  271   |   7:    56.747 -  64.558:   24        |
|      3:    25.505 -  33.316:  130   |   8:    64.558 -  72.368:    8        |
|      4:    33.316 -  41.126:  137   |   9:    72.368 -  80.179:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


======================= Individual occupancy refinement =======================

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1107 r_free = 0.1584             target_work(ml) = 5.144         |
| occupancies: max = 1.00  min = 0.03   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1106 r_free = 0.1583             target_work(ml) = 5.144         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

                         ----------X-ray data----------                        

|--(resolution: 1.99 - 15.19 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1106   r_free= 0.1583   ksol= 0.33   Bsol= 57.26   scale= 0.991   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.07,-2.45,-1.50,-0.00,-0.00,-0.00); trace/3= -2.00                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.143718                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1899 -  4.7528 0.99   1391  155 0.1009 0.1338       5.406      5.5511|
|  2:  4.7528 -  3.7917 0.99   1343  146 0.0873 0.1100      5.4542       5.632|
|  3:  3.7917 -  3.3181 0.99   1313  147 0.1042 0.1547      5.4656      5.8783|
|  4:  3.3181 -  3.0173 0.99   1316  153 0.1182 0.1520      5.4522      5.5721|
|  5:  3.0173 -  2.8025 0.99   1297  139 0.1343 0.1821      5.3375      5.5813|
|  6:  2.8025 -  2.6382 0.99   1284  143 0.1211 0.1816      5.2133      5.4631|
|  7:  2.6382 -  2.5067 0.99   1299  139 0.1220 0.1607        5.17      5.3486|
|  8:  2.5067 -  2.3980 0.98   1263  151 0.1144 0.1772      5.0384      5.3553|
|  9:  2.3980 -  2.3060 0.98   1280  144 0.1133 0.1728      5.0174      5.2943|
| 10:  2.3060 -  2.2267 0.99   1277  139 0.1095 0.1783      4.9405      5.2217|
| 11:  2.2267 -  2.1573 0.98   1284  138 0.1131 0.1822      4.9459       5.293|
| 12:  2.1573 -  2.0958 0.97   1246  139 0.1082 0.1564      4.8794      5.0866|
| 13:  2.0958 -  2.0407 1.00   1259  140 0.1170 0.1788      4.7885      5.0965|
| 14:  2.0407 -  1.9910 0.59    778   86 0.1029 0.1611      4.6287      4.8777|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.1899 -  4.7528  1391   155  0.94   9.33   0.97     0.94       7487.38|
|  2:  4.7528 -  3.7917  1343   146  0.95   8.18   1.00     0.99       9298.30|
|  3:  3.7917 -  3.3181  1313   147  0.93  11.28   1.01     1.01      10347.10|
|  4:  3.3181 -  3.0173  1316   153  0.92  13.66   0.99     0.97      10456.49|
|  5:  3.0173 -  2.8025  1297   139  0.90  16.37   0.99     0.96       8537.87|
|  6:  2.8025 -  2.6382  1284   143  0.90  15.96   0.98     0.95       7197.36|
|  7:  2.6382 -  2.5067  1299   139  0.91  15.35   0.99     0.97       6314.18|
|  8:  2.5067 -  2.3980  1263   151  0.91  15.09   0.98     0.96       5030.33|
|  9:  2.3980 -  2.3060  1280   144  0.91  14.81   0.99     0.96       4802.41|
| 10:  2.3060 -  2.2267  1277   139  0.91  15.21   0.99     0.95       4223.97|
| 11:  2.2267 -  2.1573  1284   138  0.90  16.27   0.99     0.95       4410.77|
| 12:  2.1573 -  2.0958  1246   139  0.91  15.12   1.00     0.99       4064.04|
| 13:  2.0958 -  2.0407  1259   140  0.90  16.26   0.99     0.99       3312.20|
| 14:  2.0407 -  1.9910   778    86  0.92  13.61   0.97     0.93       2295.90|
|alpha:            min =        0.93 max =            1.01 mean =         0.97|
|beta:             min =     2295.90 max =        10456.49 mean =      6429.05|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.68 mean =        13.99|
|phase err.(test): min =        0.00 max =           89.43 mean =        13.48|
|-----------------------------------------------------------------------------|

====================== bulk solvent modeling and scaling ======================

|--(resolution: 1.99 - 15.19 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1106   r_free= 0.1584   ksol= 0.33   Bsol= 57.19   scale= 0.993   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.98,-2.28,-1.33,-0.00,-0.00,-0.00); trace/3= -1.86                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.143772                   |
|-----------------------------------------------------------------------------|

                         ----------X-ray data----------                        

|--(resolution: 1.99 - 15.19 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1106   r_free= 0.1584   ksol= 0.33   Bsol= 57.19   scale= 0.993   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.98,-2.28,-1.33,-0.00,-0.00,-0.00); trace/3= -1.86                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.143772                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1899 -  4.7528 0.99   1391  155 0.1009 0.1338      5.4062      5.5512|
|  2:  4.7528 -  3.7917 0.99   1343  146 0.0873 0.1100      5.4541      5.6317|
|  3:  3.7917 -  3.3181 0.99   1313  147 0.1042 0.1546      5.4654      5.8778|
|  4:  3.3181 -  3.0173 0.99   1316  153 0.1181 0.1519      5.4521      5.5721|
|  5:  3.0173 -  2.8025 0.99   1297  139 0.1343 0.1822      5.3377      5.5816|
|  6:  2.8025 -  2.6382 0.99   1284  143 0.1211 0.1814      5.2134      5.4627|
|  7:  2.6382 -  2.5067 0.99   1299  139 0.1219 0.1606      5.1697      5.3482|
|  8:  2.5067 -  2.3980 0.98   1263  151 0.1143 0.1772      5.0383      5.3556|
|  9:  2.3980 -  2.3060 0.98   1280  144 0.1133 0.1729      5.0176       5.294|
| 10:  2.3060 -  2.2267 0.99   1277  139 0.1095 0.1784      4.9405      5.2218|
| 11:  2.2267 -  2.1573 0.98   1284  138 0.1131 0.1824      4.9461      5.2935|
| 12:  2.1573 -  2.0958 0.97   1246  139 0.1082 0.1565      4.8798       5.087|
| 13:  2.0958 -  2.0407 1.00   1259  140 0.1170 0.1790      4.7886      5.0968|
| 14:  2.0407 -  1.9910 0.59    778   86 0.1029 0.1612      4.6291      4.8776|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.1899 -  4.7528  1391   155  0.94   9.34   0.97     0.94       7489.37|
|  2:  4.7528 -  3.7917  1343   146  0.95   8.18   1.00     0.99       9295.10|
|  3:  3.7917 -  3.3181  1313   147  0.93  11.28   1.01     1.01      10338.17|
|  4:  3.3181 -  3.0173  1316   153  0.92  13.66   1.00     0.97      10457.53|
|  5:  3.0173 -  2.8025  1297   139  0.90  16.37   0.99     0.96       8537.65|
|  6:  2.8025 -  2.6382  1284   143  0.90  15.96   0.98     0.95       7196.39|
|  7:  2.6382 -  2.5067  1299   139  0.91  15.35   0.99     0.97       6311.19|
|  8:  2.5067 -  2.3980  1263   151  0.91  15.09   0.98     0.96       5029.97|
|  9:  2.3980 -  2.3060  1280   144  0.91  14.81   1.00     0.97       4800.77|
| 10:  2.3060 -  2.2267  1277   139  0.91  15.21   0.99     0.96       4224.35|
| 11:  2.2267 -  2.1573  1284   138  0.90  16.28   0.99     0.95       4411.36|
| 12:  2.1573 -  2.0958  1246   139  0.91  15.13   1.00     0.99       4068.24|
| 13:  2.0958 -  2.0407  1259   140  0.90  16.27   0.99     0.99       3314.11|
| 14:  2.0407 -  1.9910   778    86  0.92  13.61   0.97     0.94       2298.00|
|alpha:            min =        0.94 max =            1.01 mean =         0.97|
|beta:             min =     2298.00 max =        10457.53 mean =      6428.52|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.68 mean =        13.99|
|phase err.(test): min =        0.00 max =           89.43 mean =        13.48|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.098)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      2.00    80.10   16.34    None  None   None       |
|    all(noH): 2823   0      2.00    80.10   16.34    None  None   None       |
|    Sol.    : 438    0      6.34    76.63   36.41    None  None   None       |
|    Mac.    : 2385   0      2.00    80.10   12.65    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.999 -   9.809:  987   |   5:    41.051 -  48.862:   92        |
|      1:     9.809 -  17.620: 1101   |   6:    48.862 -  56.672:   68        |
|      2:    17.620 -  25.430:  271   |   7:    56.672 -  64.483:   24        |
|      3:    25.430 -  33.241:  130   |   8:    64.483 -  72.293:    8        |
|      4:    33.241 -  41.051:  137   |   9:    72.293 -  80.104:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


========== residual map mFobs-DFmodel: highest peaks and deepst holes =========


                           ----------peaks----------                           

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 288         
Filter by distance & map next to the model:
   mapped sites are within: 0.609 - 4.716
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 282 from: 288
   mapped sites are within: 0.708 - 4.716

peak=    5.675 closest distance to " O   HOH Z 111 " =    2.167
peak=    5.578 closest distance to " CG  PRO A  54 " =    1.330
peak=    5.419 closest distance to " CB  GLN A 223 " =    1.459
peak=    5.339 closest distance to " O   HOH Z 126 " =    1.843
peak=    5.034 closest distance to " CB  SER A  63 " =    1.255
peak=    5.025 closest distance to " O   HOH Z 232 " =    2.266
peak=    4.763 closest distance to " CG  PRO A 213 " =    1.217
peak=    4.758 closest distance to " CB  ASN A 187 " =    1.310
peak=    4.696 closest distance to " CB  PRO A  54 " =    0.906
peak=    4.689 closest distance to " CB  LEU A 228 " =    1.049
peak=    4.621 closest distance to " CB  ARG A 275 " =    0.908
peak=    4.618 closest distance to " O   HOH Z 298 " =    1.963
peak=    4.607 closest distance to " C   PRO A 198 " =    1.520
peak=    4.540 closest distance to " NE2 GLN A  11 " =    1.140
peak=    4.527 closest distance to " CB  GLU A 152 " =    1.182
peak=    4.510 closest distance to " O   HOH Z 236 " =    1.965
peak=    4.496 closest distance to " CB  GLN A 183 " =    1.164
peak=    4.483 closest distance to " ND2 ASN A 187 " =    1.509
peak=    4.429 closest distance to " O   HOH Z  78 " =    1.679
peak=    4.395 closest distance to " O   HOH Z 369 " =    2.028
peak=    4.371 closest distance to " O   HOH Z  15 " =    2.185
peak=    4.337 closest distance to " CB  ASN A 148 " =    1.402
peak=    4.332 closest distance to " O   HOH Z 193 " =    1.979
peak=    4.324 closest distance to " CB  GLU A 128 " =    1.054
peak=    4.233 closest distance to " CB  ARG A  79 " =    1.361
peak=    4.192 closest distance to " CA  TYR A  30 " =    0.953
peak=    4.183 closest distance to " CG  PRO A  90 " =    1.108
peak=    4.175 closest distance to " CG  PRO A 243 " =    1.098
peak=    4.169 closest distance to " O   HOH Z 234 " =    3.803
peak=    4.156 closest distance to " O   HOH Z 193 " =    1.810
peak=    4.121 closest distance to " CB  TYR A 169 " =    0.708
peak=    4.116 closest distance to " OD1 ASN A  69 " =    2.643
peak=    4.094 closest distance to " CG  PRO A 198 " =    1.239
peak=    4.088 closest distance to " O   HOH Z 272 " =    1.913
peak=    4.081 closest distance to " CB  TRP A 266 " =    0.887
peak=    4.078 closest distance to " NH1AARG A 145 " =    1.227
peak=    4.064 closest distance to " NH2 ARG A 156 " =    1.245
peak=    4.046 closest distance to " O   HOH Z 250 " =    1.550
peak=    4.016 closest distance to " O   HOH Z 303 " =    2.119
peak=    4.006 closest distance to " O   HOH Z 368 " =    1.984
peak=    4.005 closest distance to " O   HOH Z 132 " =    2.611
peak=    3.989 closest distance to " O   HOH Z 144 " =    1.706
peak=    3.988 closest distance to " CB  ARG A 190 " =    1.542
peak=    3.987 closest distance to " CA  THR A 264 " =    0.865
peak=    3.983 closest distance to " CB  SER A   3 " =    1.423
peak=    3.957 closest distance to " CD1 LEU A 300 " =    1.215
peak=    3.946 closest distance to " O   HOH Z 261 " =    2.089
peak=    3.939 closest distance to " O   HOH Z 214 " =    1.980
peak=    3.930 closest distance to " CD  ARG A 159 " =    0.776
peak=    3.899 closest distance to " CZ  PHE A 218 " =    1.059
peak=    3.894 closest distance to " O   HOH Z 213 " =    1.957
peak=    3.876 closest distance to " CA  ALA A  21 " =    1.227
peak=    3.869 closest distance to " O   HOH Z  21 " =    1.742
peak=    3.863 closest distance to " O   HOH Z  78 " =    2.123
peak=    3.854 closest distance to " OD2 ASP A 286 " =    2.916
peak=    3.832 closest distance to " CA  PRO A  54 " =    1.346
peak=    3.828 closest distance to " CB  ASN A  39 " =    0.887
peak=    3.827 closest distance to " CB  VAL A 265 " =    1.281
peak=    3.827 closest distance to " O   HOH Z 346 " =    1.569
peak=    3.820 closest distance to " O   HOH Z 344 " =    3.160
peak=    3.817 closest distance to " CB  SER A 212 " =    1.184
peak=    3.815 closest distance to " O   HOH Z 189 " =    2.506
peak=    3.801 closest distance to " O   HOH Z 158 " =    3.009
peak=    3.799 closest distance to " CB  GLU A 277 " =    3.647
peak=    3.781 closest distance to " ND2 ASN A 249 " =    1.964
peak=    3.776 closest distance to " ND1 HIS A  86 " =    1.643
peak=    3.775 closest distance to " O   HOH Z   1 " =    2.007
peak=    3.772 closest distance to " O   HOH Z  10 " =    1.876
peak=    3.771 closest distance to " O   HOH Z 316 " =    3.132
peak=    3.768 closest distance to " O   HOH Z 427 " =    3.055
peak=    3.765 closest distance to " O   HOH Z  54 " =    2.384
peak=    3.763 closest distance to " O   HOH Z 197 " =    3.055
peak=    3.763 closest distance to " CA  ASN A 215 " =    1.178
peak=    3.754 closest distance to " O   HOH Z 219 " =    2.026
peak=    3.750 closest distance to " O   HOH Z 133 " =    1.718
peak=    3.750 closest distance to " O   HOH Z  68 " =    2.163
peak=    3.747 closest distance to " CA  ALA A  51 " =    0.868
peak=    3.743 closest distance to " CB  SER A 216 " =    0.793
peak=    3.729 closest distance to " CA  MET A  40 " =    1.152
peak=    3.724 closest distance to " ND2 ASN A 110 " =    1.787
peak=    3.714 closest distance to " CB  MET A  40 " =    0.783
peak=    3.711 closest distance to " CB  ASP A 140 " =    0.854
peak=    3.689 closest distance to " O   HOH Z 108 " =    2.470
peak=    3.688 closest distance to " CG2 THR A 221 " =    1.002
peak=    3.684 closest distance to " O   HOH Z  20 " =    1.788
peak=    3.682 closest distance to " O   HOH Z 403 " =    1.718
peak=    3.679 closest distance to " CD  ARG A 269 " =    0.914
peak=    3.677 closest distance to " CD  LYS A 166 " =    1.258
peak=    3.674 closest distance to " O   MET A 105 " =    1.798
peak=    3.665 closest distance to " CB  GLU A  46 " =    0.956
peak=    3.664 closest distance to " CB  TYR A 169 " =    0.721
peak=    3.664 closest distance to " CB  LEU A 143 " =    1.089
peak=    3.653 closest distance to " CE  LYS A  76 " =    0.875
peak=    3.651 closest distance to " CD  ARG A  66 " =    2.237
peak=    3.648 closest distance to " CG2 VAL A 257 " =    0.996
peak=    3.643 closest distance to " O   HOH Z 180 " =    2.088
peak=    3.640 closest distance to " O   HOH Z 368 " =    3.617
peak=    3.636 closest distance to " CD  ARG A 219 " =    1.068
peak=    3.623 closest distance to " CB  ILE A 120 " =    1.161
peak=    3.618 closest distance to " CZ  PHE A 192 " =    0.909
peak=    3.617 closest distance to " O   HOH Z 217 " =    3.154
peak=    3.604 closest distance to " CB  VAL A 202 " =    1.596
peak=    3.604 closest distance to " CG1 ILE A  33 " =    1.286
peak=    3.601 closest distance to " O   HOH Z 147 " =    1.793
peak=    3.599 closest distance to " CB  ASN A 142 " =    0.933
peak=    3.596 closest distance to " O   HOH Z 425 " =    2.041
peak=    3.593 closest distance to " CG  LEU A 167 " =    1.233
peak=    3.592 closest distance to " CB  TRP A 179 " =    1.429
peak=    3.575 closest distance to " CA  THR A 221 " =    0.962
peak=    3.569 closest distance to " CD1 ILE A 106 " =    0.857
peak=    3.568 closest distance to " N   ARG A 156 " =    1.357
peak=    3.566 closest distance to " CD  ARG A  66 " =    2.256
peak=    3.565 closest distance to " O   HOH Z 305 " =    3.717
peak=    3.562 closest distance to " CG2AVAL A  72 " =    1.688
peak=    3.560 closest distance to " O   HOH Z  61 " =    1.598
peak=    3.550 closest distance to " CB  ALA A  34 " =    0.964
peak=    3.550 closest distance to " O   HOH Z 135 " =    1.717
peak=    3.547 closest distance to " CB  GLN A  88 " =    1.265
peak=    3.547 closest distance to " O   HOH Z 203 " =    1.908
peak=    3.544 closest distance to " CA  SER A  87 " =    1.003
peak=    3.539 closest distance to " CA  ALA A 233 " =    1.274
peak=    3.534 closest distance to " O   HOH Z 426 " =    1.558
peak=    3.532 closest distance to " O   HOH Z 273 " =    2.681
peak=    3.532 closest distance to " CA  TYR A  30 " =    1.050
peak=    3.527 closest distance to " O   HOH Z 291 " =    1.671
peak=    3.527 closest distance to " O   HOH Z 133 " =    2.416
peak=    3.525 closest distance to " CA  ASP A 191 " =    0.717
peak=    3.519 closest distance to " N   ASN A 127 " =    1.250
peak=    3.518 closest distance to " NH2BARG A 145 " =    2.141
peak=    3.512 closest distance to " O   SER A  87 " =    2.265
peak=    3.506 closest distance to " CD2 TRP A 179 " =    1.288
peak=    3.484 closest distance to " N   VAL A 126 " =    1.363
peak=    3.476 closest distance to " O   HOH Z  61 " =    1.535
peak=    3.468 closest distance to " CD BLYS A 290 " =    1.043
peak=    3.453 closest distance to " O   HOH Z 334 " =    1.530
peak=    3.450 closest distance to " O   HOH Z 406 " =    1.677
peak=    3.449 closest distance to " O   HOH Z 171 " =    3.912
peak=    3.444 closest distance to " OD1 ASN A 217 " =    1.624
peak=    3.436 closest distance to " O   HOH Z 227 " =    1.692
peak=    3.435 closest distance to " O   HOH Z 402 " =    1.474
peak=    3.431 closest distance to " O   HOH Z 128 " =    2.182
peak=    3.430 closest distance to " O   HOH Z 411 " =    3.853
peak=    3.420 closest distance to " CG1 VAL A 153 " =    0.893
peak=    3.418 closest distance to " CB  ARG A 139 " =    0.966
peak=    3.418 closest distance to " CB  MET A  47 " =    1.044
peak=    3.414 closest distance to " O   HOH Z 313 " =    1.888
peak=    3.413 closest distance to " O   HOH Z 209 " =    2.329
peak=    3.410 closest distance to " O   HOH Z 371 " =    3.049
peak=    3.407 closest distance to " O  BHOH Z 338 " =    2.381
peak=    3.397 closest distance to " O   HOH Z 234 " =    1.716
peak=    3.392 closest distance to " O   HOH Z 193 " =    2.036
peak=    3.390 closest distance to " O   HOH Z  59 " =    2.131
peak=    3.390 closest distance to " CB  ALA A 248 " =    0.961
peak=    3.389 closest distance to " O   HOH Z 280 " =    3.045
peak=    3.387 closest distance to " O   HOH Z  88 " =    3.614
peak=    3.384 closest distance to " CD2 LEU A 255 " =    1.495
peak=    3.384 closest distance to " O   HOH Z 188 " =    2.167
peak=    3.382 closest distance to " O   HOH Z 172 " =    3.475
peak=    3.373 closest distance to " ND1 HIS A  81 " =    1.630
peak=    3.367 closest distance to " CB  ALA A   1 " =    4.716
peak=    3.365 closest distance to " O   HOH Z 423 " =    1.789
peak=    3.364 closest distance to " CZ  PHE A 208 " =    1.138
peak=    3.358 closest distance to " CB  ALA A   9 " =    1.569
peak=    3.356 closest distance to " CB  ALA A 291 " =    1.289
peak=    3.351 closest distance to " CG2 ILE A 120 " =    1.109
peak=    3.351 closest distance to " O   TRP A 274 " =    1.846
peak=    3.348 closest distance to " CB  ASN A 224 " =    1.118
peak=    3.348 closest distance to " CA  ARG A 195 " =    1.205
peak=    3.347 closest distance to " CA  ALA A 154 " =    0.945
peak=    3.345 closest distance to " CA  ALA A 158 " =    1.141
peak=    3.344 closest distance to " O   HOH Z 245 " =    1.343
peak=    3.340 closest distance to " O   HOH Z  49 " =    2.937
peak=    3.339 closest distance to " CB  PHE A  16 " =    1.075
peak=    3.338 closest distance to " O   HOH Z 166 " =    3.590
peak=    3.332 closest distance to " CB  SER A 141 " =    0.957
peak=    3.330 closest distance to " O   HOH Z 425 " =    1.309
peak=    3.329 closest distance to " CA  GLN A 223 " =    0.936
peak=    3.326 closest distance to " O   HOH Z 128 " =    2.234
peak=    3.326 closest distance to " O   HOH Z 327 " =    2.108
peak=    3.325 closest distance to " CB  HIS A 108 " =    0.793
peak=    3.322 closest distance to " O   HOH Z 285 " =    2.998
peak=    3.322 closest distance to " CG  LYS A  76 " =    0.919
peak=    3.320 closest distance to " CA  ILE A  33 " =    1.550
peak=    3.316 closest distance to " O   HOH Z 383 " =    1.921
peak=    3.310 closest distance to " CA  ALA A  84 " =    1.446
peak=    3.309 closest distance to " O   HOH Z 419 " =    1.896
peak=    3.307 closest distance to " OG  SER A  22 " =    2.783
peak=    3.303 closest distance to " O   HOH Z 411 " =    1.828
peak=    3.302 closest distance to " O   HOH Z 287 " =    1.776
peak=    3.298 closest distance to " O   TYR A 116 " =    1.308
peak=    3.296 closest distance to " OD1BASN A 224 " =    2.349
peak=    3.295 closest distance to " O   HOH Z  97 " =    1.903
peak=    3.295 closest distance to " CA  ASP A 140 " =    1.244
peak=    3.294 closest distance to " CA  ALA A 291 " =    0.923
peak=    3.291 closest distance to " OG  SER A  97 " =    3.626
peak=    3.290 closest distance to " N   ASN A  39 " =    1.324
peak=    3.289 closest distance to " O   HOH Z  64 " =    2.119
peak=    3.287 closest distance to " OG  SER A 206 " =    1.285
peak=    3.285 closest distance to " O   HOH Z  40 " =    1.850
peak=    3.283 closest distance to " CB  LYS A 193 " =    0.993
peak=    3.282 closest distance to " CD2 LEU A 297 " =    0.814
peak=    3.270 closest distance to " CB  TYR A 116 " =    0.871
peak=    3.269 closest distance to " O   HOH Z 329 " =    3.786
peak=    3.267 closest distance to " O   HOH Z 388 " =    2.018
peak=    3.267 closest distance to " CG BARG A 275 " =    1.460
peak=    3.267 closest distance to " O   HOH Z 199 " =    1.584
peak=    3.257 closest distance to " O   HOH Z  53 " =    2.575
peak=    3.255 closest distance to " CD  LYS A 119 " =    1.412
peak=    3.254 closest distance to " NE2 HIS A 207 " =    1.390
peak=    3.253 closest distance to " CB  ALA A 248 " =    1.245
peak=    3.248 closest distance to " O   HOH Z 171 " =    2.177
peak=    3.248 closest distance to " O   HOH Z 185 " =    1.804
peak=    3.246 closest distance to " O   HOH Z 281 " =    4.011
peak=    3.244 closest distance to " O   HOH Z 295 " =    1.495
peak=    3.238 closest distance to " CB  TRP A 150 " =    1.413
peak=    3.235 closest distance to " CB  ASN A 110 " =    1.111
peak=    3.232 closest distance to " O   HOH Z 345 " =    1.765
peak=    3.232 closest distance to " O   HOH Z 183 " =    1.476
peak=    3.232 closest distance to " O   HOH Z 148 " =    3.248
peak=    3.230 closest distance to " CG  MET A 185 " =    1.172
peak=    3.230 closest distance to " CG2 THR A 220 " =    0.859
peak=    3.227 closest distance to " CA  TYR A 116 " =    1.416
peak=    3.227 closest distance to " CD  ARG A  14 " =    1.275
peak=    3.223 closest distance to " N   SER A 135 " =    1.349
peak=    3.221 closest distance to " CG  GLN A  11 " =    1.473
peak=    3.220 closest distance to " O   HOH Z 261 " =    2.179
peak=    3.215 closest distance to " CZ3 TRP A 123 " =    1.273
peak=    3.215 closest distance to " CB  ALA A 114 " =    1.221
peak=    3.215 closest distance to " O   HOH Z  93 " =    2.726
peak=    3.214 closest distance to " CB  ALA A 242 " =    0.837
peak=    3.212 closest distance to " O   HOH Z 263 " =    1.734
peak=    3.208 closest distance to " CZ2 TRP A 179 " =    1.747
peak=    3.206 closest distance to " CA  LEU A 282 " =    1.009
peak=    3.206 closest distance to " N   PHE A 130 " =    1.254
peak=    3.205 closest distance to " CB  GLU A 236 " =    0.903
peak=    3.200 closest distance to " CG  MET A 113 " =    1.570
peak=    3.194 closest distance to " O   HOH Z 355 " =    1.625
peak=    3.194 closest distance to " CG1 ILE A 151 " =    0.985
peak=    3.187 closest distance to " O   HOH Z 109 " =    2.679
peak=    3.184 closest distance to " O   HOH Z 302 " =    1.998
peak=    3.183 closest distance to " CG  GLN A  88 " =    1.044
peak=    3.179 closest distance to " CA  ARG A  36 " =    1.165
peak=    3.179 closest distance to " CG AARG A 275 " =    1.211
peak=    3.179 closest distance to " O   ASN A 209 " =    1.318
peak=    3.179 closest distance to " CA  ASN A 217 " =    1.328
peak=    3.173 closest distance to " CA  ASP A 162 " =    1.045
peak=    3.172 closest distance to " O   THR A 251 " =    1.171
peak=    3.170 closest distance to " NH1 ARG A 138 " =    1.105
peak=    3.167 closest distance to " O   HOH Z  88 " =    3.001
peak=    3.166 closest distance to " O   HOH Z  44 " =    3.127
peak=    3.162 closest distance to " O   HOH Z 313 " =    1.778
peak=    3.158 closest distance to " CB  GLN A 103 " =    0.851
peak=    3.154 closest distance to " CG2 ILE A 151 " =    0.725
peak=    3.153 closest distance to " CG BARG A 102 " =    1.851
peak=    3.153 closest distance to " N   ASN A 252 " =    1.388
peak=    3.151 closest distance to " CE3 TRP A 274 " =    2.179
peak=    3.151 closest distance to " CG  MET A 185 " =    1.018
peak=    3.150 closest distance to " CB  ILE A 234 " =    1.024
peak=    3.150 closest distance to " O   HOH Z 152 " =    2.019
peak=    3.145 closest distance to " CB  THR A 157 " =    1.103
peak=    3.144 closest distance to " O   HOH Z 294 " =    1.501
peak=    3.143 closest distance to " CE BLYS A 290 " =    1.024
peak=    3.143 closest distance to " O   HOH Z 258 " =    1.857
peak=    3.142 closest distance to " CD2 HIS A  81 " =    1.216
peak=    3.141 closest distance to " O   PHE A 192 " =    1.444
peak=    3.140 closest distance to " O   HOH Z 353 " =    2.737
peak=    3.139 closest distance to " NH2AARG A 275 " =    3.585
peak=    3.132 closest distance to " CA  GLN A  88 " =    1.463
peak=    3.132 closest distance to " O   HOH Z  49 " =    2.230
peak=    3.130 closest distance to " O   HOH Z 271 " =    2.419
peak=    3.127 closest distance to " CA  MET A 105 " =    0.956
peak=    3.121 closest distance to " N   GLN A 278 " =    0.921
peak=    3.114 closest distance to " CA  ALA A 248 " =    1.265
peak=    3.111 closest distance to " O   ALA A 158 " =    1.299
peak=    3.092 closest distance to " CG  GLN A 278 " =    1.385
peak=    3.079 closest distance to " OG BSER A 164 " =    2.400
peak=    3.073 closest distance to " CA  GLU A  46 " =    0.762
peak=    3.067 closest distance to " O   HOH Z 387 " =    3.186
peak=    3.065 closest distance to " O   HOH Z 391 " =    2.927
peak=    3.047 closest distance to " NH2AARG A 190 " =    1.143
peak=    3.040 closest distance to " O   HOH Z 345 " =    3.533
peak=    3.013 closest distance to " CB  GLU A 152 " =    1.412

                           ----------holes----------                           

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 198         
Filter by distance & map next to the model:
   mapped sites are within: 0.221 - 5.504
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 192 from: 198
   mapped sites are within: 0.746 - 5.504

peak=   -4.601 closest distance to " O   HOH Z 290 " =    1.111
peak=   -4.573 closest distance to " CB  PRO A 243 " =    2.623
peak=   -4.467 closest distance to " O   HOH Z 266 " =    4.942
peak=   -4.352 closest distance to " O   VAL A  67 " =    2.704
peak=   -4.272 closest distance to " CD  ARG A 156 " =    2.047
peak=   -4.213 closest distance to " CD  GLN A 223 " =    1.917
peak=   -4.132 closest distance to " CZ3 TRP A 179 " =    1.095
peak=   -4.112 closest distance to " O   HOH Z 389 " =    1.876
peak=   -4.055 closest distance to " O   ILE A 109 " =    2.634
peak=   -4.014 closest distance to " N   ALA A  43 " =    2.568
peak=   -3.992 closest distance to " CE2 TYR A  30 " =    2.820
peak=   -3.963 closest distance to " O   HOH Z  52 " =    1.257
peak=   -3.953 closest distance to " O   HOH Z  10 " =    1.502
peak=   -3.943 closest distance to " O   HOH Z 126 " =    1.907
peak=   -3.929 closest distance to " O   HOH Z 198 " =    2.166
peak=   -3.925 closest distance to " O   HOH Z 377 " =    2.031
peak=   -3.902 closest distance to " O   HOH Z 353 " =    2.136
peak=   -3.866 closest distance to " CD2 LEU A 300 " =    2.991
peak=   -3.864 closest distance to " ND2 ASN A  45 " =    1.587
peak=   -3.863 closest distance to " SG  CYS A 254 " =    3.626
peak=   -3.858 closest distance to " NH2AARG A 275 " =    5.504
peak=   -3.848 closest distance to " CG1 VAL A 112 " =    2.910
peak=   -3.843 closest distance to " O   HOH Z  38 " =    1.390
peak=   -3.840 closest distance to " O   HOH Z 198 " =    1.095
peak=   -3.836 closest distance to " O   HOH Z 118 " =    3.188
peak=   -3.828 closest distance to " CD  GLN A  58 " =    1.020
peak=   -3.814 closest distance to " O   HOH Z 372 " =    2.469
peak=   -3.785 closest distance to " O   HOH Z 211 " =    1.627
peak=   -3.778 closest distance to " O   GLY A 211 " =    1.537
peak=   -3.763 closest distance to " CD1 PHE A 130 " =    2.250
peak=   -3.751 closest distance to " CD1 PHE A  59 " =    1.856
peak=   -3.737 closest distance to " CB  ALA A 291 " =    2.253
peak=   -3.730 closest distance to " C   ASN A 285 " =    2.491
peak=   -3.725 closest distance to " CG  PHE A 283 " =    2.875
peak=   -3.722 closest distance to " CB  PRO A 163 " =    2.561
peak=   -3.718 closest distance to " O   HOH Z  43 " =    1.542
peak=   -3.715 closest distance to " CB  PHE A 192 " =    2.051
peak=   -3.715 closest distance to " O   HOH Z 435 " =    2.766
peak=   -3.707 closest distance to " CD1 LEU A 228 " =    2.404
peak=   -3.691 closest distance to " CG  ARG A 269 " =    2.417
peak=   -3.687 closest distance to " CG1 VAL A 112 " =    2.578
peak=   -3.685 closest distance to " C   HIS A 108 " =    1.124
peak=   -3.682 closest distance to " CB  ALA A  43 " =    2.524
peak=   -3.660 closest distance to " O   PRO A 198 " =    1.271
peak=   -3.652 closest distance to " O   HOH Z 407 " =    3.374
peak=   -3.649 closest distance to " C   ALA A 158 " =    1.373
peak=   -3.644 closest distance to " CG2 ILE A 263 " =    2.335
peak=   -3.641 closest distance to " ND2 ASN A  45 " =    1.134
peak=   -3.641 closest distance to " CE2 TYR A 186 " =    2.063
peak=   -3.630 closest distance to " NH2 ARG A 159 " =    2.403
peak=   -3.630 closest distance to " O   HOH Z 351 " =    1.463
peak=   -3.623 closest distance to " CG  MET A 105 " =    0.995
peak=   -3.615 closest distance to " CB  ALA A 291 " =    2.249
peak=   -3.606 closest distance to " CG  GLU A 152 " =    0.829
peak=   -3.601 closest distance to " O   HOH Z 185 " =    2.390
peak=   -3.592 closest distance to " O   HOH Z  73 " =    2.162
peak=   -3.587 closest distance to " ND2 ASN A 249 " =    2.347
peak=   -3.587 closest distance to " SG ACYS A 201 " =    1.974
peak=   -3.570 closest distance to " CD1 LEU A 101 " =    2.415
peak=   -3.569 closest distance to " O   VAL A 189 " =    2.567
peak=   -3.565 closest distance to " CG1 VAL A 250 " =    2.695
peak=   -3.563 closest distance to " CA  GLY A 241 " =    2.331
peak=   -3.562 closest distance to " OG  SER A  97 " =    2.209
peak=   -3.557 closest distance to " CG1 VAL A 197 " =    2.297
peak=   -3.556 closest distance to " CG  ASP A 231 " =    0.762
peak=   -3.552 closest distance to " O   HOH Z  60 " =    2.544
peak=   -3.546 closest distance to " OG BSER A 134 " =    1.753
peak=   -3.540 closest distance to " O   HOH Z 241 " =    1.176
peak=   -3.532 closest distance to " CD  ARG A 139 " =    1.620
peak=   -3.517 closest distance to " CD2 LEU A 237 " =    2.814
peak=   -3.513 closest distance to " OD1 ASN A 148 " =    1.633
peak=   -3.509 closest distance to " CD  GLN A  88 " =    0.765
peak=   -3.503 closest distance to " CA  GLY A 241 " =    3.074
peak=   -3.502 closest distance to " OG BSER A 134 " =    1.241
peak=   -3.493 closest distance to " O   HOH Z 311 " =    3.722
peak=   -3.490 closest distance to " CD2 TYR A 293 " =    2.053
peak=   -3.489 closest distance to " CZ  TYR A 169 " =    1.715
peak=   -3.478 closest distance to " CD2 PHE A  61 " =    2.483
peak=   -3.466 closest distance to " CD1 LEU A 297 " =    2.449
peak=   -3.462 closest distance to " CB  ASN A  39 " =    2.265
peak=   -3.461 closest distance to " N   ALA A 226 " =    2.229
peak=   -3.434 closest distance to " CE2 PHE A 218 " =    2.468
peak=   -3.433 closest distance to " OG  SER A  62 " =    1.553
peak=   -3.432 closest distance to " CE  MET A 105 " =    2.282
peak=   -3.430 closest distance to " N   SER A 212 " =    1.939
peak=   -3.429 closest distance to " ND2 ASN A  60 " =    1.359
peak=   -3.424 closest distance to " O   HOH Z 222 " =    1.138
peak=   -3.421 closest distance to " CB  CYS A 201 " =    2.642
peak=   -3.420 closest distance to " CD1 ILE A 239 " =    2.077
peak=   -3.419 closest distance to " O   PRO A 163 " =    2.076
peak=   -3.417 closest distance to " OD1 ASP A 191 " =    1.715
peak=   -3.415 closest distance to " O   HOH Z 176 " =    0.804
peak=   -3.414 closest distance to " CZ  PHE A  59 " =    1.608
peak=   -3.407 closest distance to " OD1 ASP A 171 " =    1.589
peak=   -3.403 closest distance to " NH2 ARG A  79 " =    1.586
peak=   -3.400 closest distance to " O   HOH Z 426 " =    1.665
peak=   -3.399 closest distance to " O   HOH Z 298 " =    2.596
peak=   -3.399 closest distance to " OXT GLY A 302 " =    2.909
peak=   -3.394 closest distance to " NH1 ARG A 195 " =    2.550
peak=   -3.391 closest distance to " O   LEU A 101 " =    2.690
peak=   -3.388 closest distance to " O   VAL A  67 " =    2.578
peak=   -3.379 closest distance to " O   HOH Z 394 " =    1.413
peak=   -3.363 closest distance to " NE2 GLN A  88 " =    1.897
peak=   -3.362 closest distance to " O   PRO A 198 " =    1.268
peak=   -3.362 closest distance to " CD  ARG A 195 " =    5.244
peak=   -3.361 closest distance to " CB  ASP A 286 " =    2.122
peak=   -3.354 closest distance to " CG  ARG A  66 " =    2.314
peak=   -3.353 closest distance to " O   HOH Z  93 " =    2.244
peak=   -3.351 closest distance to " CE  LYS A  76 " =    2.738
peak=   -3.348 closest distance to " O   GLY A 196 " =    1.202
peak=   -3.347 closest distance to " O   HOH Z 196 " =    2.070
peak=   -3.338 closest distance to " O   HOH Z  11 " =    1.790
peak=   -3.337 closest distance to " NH2 ARG A  79 " =    1.913
peak=   -3.337 closest distance to " CA  GLY A 241 " =    2.813
peak=   -3.333 closest distance to " CZ3 TRP A 274 " =    0.976
peak=   -3.314 closest distance to " N   GLN A  58 " =    1.733
peak=   -3.311 closest distance to " NE2 GLN A 103 " =    1.660
peak=   -3.308 closest distance to " CD2 LEU A 300 " =    2.865
peak=   -3.307 closest distance to " C   LEU A 143 " =    1.291
peak=   -3.303 closest distance to " O   HOH Z  76 " =    1.887
peak=   -3.302 closest distance to " CA  GLY A 203 " =    2.328
peak=   -3.301 closest distance to " O   GLN A 240 " =    2.147
peak=   -3.301 closest distance to " CG  TRP A 266 " =    1.776
peak=   -3.299 closest distance to " CB  TRP A  85 " =    2.408
peak=   -3.298 closest distance to " O   HOH Z 111 " =    2.049
peak=   -3.290 closest distance to " CE BMET A  47 " =    2.162
peak=   -3.289 closest distance to " CH2 TRP A 177 " =    2.141
peak=   -3.284 closest distance to " O   HOH Z  51 " =    1.278
peak=   -3.282 closest distance to " CB  ALA A 248 " =    2.532
peak=   -3.281 closest distance to " O   HOH Z 281 " =    2.680
peak=   -3.280 closest distance to " OE1 GLN A  88 " =    1.273
peak=   -3.268 closest distance to " OH  TYR A 247 " =    2.109
peak=   -3.265 closest distance to " O   HOH Z 417 " =    2.499
peak=   -3.264 closest distance to " CG2 THR A 221 " =    2.242
peak=   -3.263 closest distance to " O   HOH Z 393 " =    1.427
peak=   -3.262 closest distance to " N   ASP A 171 " =    2.357
peak=   -3.253 closest distance to " CB  CYS A 254 " =    2.315
peak=   -3.252 closest distance to " C   LEU A 222 " =    0.746
peak=   -3.252 closest distance to " CA  ASP A 298 " =    1.097
peak=   -3.249 closest distance to " CE  MET A  93 " =    1.267
peak=   -3.245 closest distance to " CA  GLY A  98 " =    1.985
peak=   -3.245 closest distance to " CB  ASP A 132 " =    2.340
peak=   -3.233 closest distance to " O   HOH Z 114 " =    1.601
peak=   -3.225 closest distance to " CA  SER A 135 " =    1.344
peak=   -3.222 closest distance to " CE3 TRP A 274 " =    2.526
peak=   -3.220 closest distance to " CE1 TYR A 169 " =    2.595
peak=   -3.218 closest distance to " NE2 GLN A 278 " =    1.778
peak=   -3.217 closest distance to " O   HOH Z 210 " =    1.010
peak=   -3.217 closest distance to " N   THR A 264 " =    1.184
peak=   -3.216 closest distance to " OD2 ASP A 171 " =    1.879
peak=   -3.197 closest distance to " CZ BARG A 275 " =    1.836
peak=   -3.194 closest distance to " NE2 GLN A 194 " =    1.790
peak=   -3.192 closest distance to " O   HOH Z 111 " =    1.233
peak=   -3.190 closest distance to " O   HOH Z  13 " =    1.392
peak=   -3.189 closest distance to " N   THR A 157 " =    1.559
peak=   -3.186 closest distance to " O   ALA A  10 " =    1.655
peak=   -3.176 closest distance to " N   PHE A  59 " =    2.128
peak=   -3.172 closest distance to " CB  ASP A 132 " =    2.285
peak=   -3.171 closest distance to " CD1 ILE A 199 " =    2.660
peak=   -3.170 closest distance to " O   HOH Z 184 " =    1.833
peak=   -3.167 closest distance to " C   ILE A 234 " =    1.254
peak=   -3.163 closest distance to " CA  ASP A  27 " =    2.502
peak=   -3.154 closest distance to " O   HOH Z 417 " =    2.664
peak=   -3.150 closest distance to " O   HOH Z 359 " =    3.149
peak=   -3.139 closest distance to " CG  PRO A 163 " =    2.502
peak=   -3.136 closest distance to " O   HOH Z  70 " =    2.221
peak=   -3.136 closest distance to " O   HOH Z 317 " =    1.526
peak=   -3.134 closest distance to " C   MET A 188 " =    1.452
peak=   -3.132 closest distance to " CD2 PHE A  59 " =    2.550
peak=   -3.124 closest distance to " CB  ALA A 248 " =    1.999
peak=   -3.124 closest distance to " O   HOH Z  88 " =    2.246
peak=   -3.122 closest distance to " CG  ASN A 301 " =    1.930
peak=   -3.120 closest distance to " O   HOH Z 174 " =    3.023
peak=   -3.110 closest distance to " O   HOH Z 390 " =    2.366
peak=   -3.110 closest distance to " CG  GLU A 277 " =    1.158
peak=   -3.109 closest distance to " O   SER A  62 " =    2.148
peak=   -3.108 closest distance to " CD2 TRP A 274 " =    2.481
peak=   -3.102 closest distance to " O   HOH Z 295 " =    1.475
peak=   -3.099 closest distance to " O   HOH Z 282 " =    1.070
peak=   -3.098 closest distance to " CB  TYR A  15 " =    2.138
peak=   -3.088 closest distance to " O   HOH Z 128 " =    2.521
peak=   -3.086 closest distance to " O   HOH Z  22 " =    2.497
peak=   -3.083 closest distance to " N   GLY A  23 " =    2.257
peak=   -3.076 closest distance to " O   HOH Z 166 " =    1.610
peak=   -3.073 closest distance to " O   HOH Z  31 " =    1.739
peak=   -3.067 closest distance to " O   HOH Z 348 " =    2.284
peak=   -3.064 closest distance to " O   HOH Z  51 " =    1.524
peak=   -3.059 closest distance to " CD1 ILE A 239 " =    2.594
peak=   -3.046 closest distance to " O   SER A 164 " =    2.007
peak=   -3.046 closest distance to " CD2 PHE A  61 " =    2.045
peak=   -3.044 closest distance to " O   HOH Z 371 " =    1.794
peak=   -3.044 closest distance to " O   HOH Z 350 " =    2.164

================= overall refinement statistics: step by step =================

****************** REFINEMENT STATISTICS STEP BY STEP ******************
leading digit, like 1_, means number of macro-cycle                     
0    : statistics at the very beginning when nothing is done yet        
1_bss: bulk solvent correction and/or (anisotropic) scaling             
1_xyz: refinement of coordinates                                        
1_adp: refinement of ADPs (Atomic Displacement Parameters)              
1_occ: refinement of individual occupancies                             
------------------------------------------------------------------------
 R-factors, x-ray target values and norm of gradient of x-ray target
 stage     r-work r-free  xray_target_w  xray_target_t
   0    :  0.3070 0.3070   6.009114e+00   6.018211e+00
   1_bss:  0.2911 0.2925   5.983676e+00   5.989538e+00
   1_xyz:  0.1705 0.1935   5.472837e+00   5.583609e+00
   1_adp:  0.1578 0.1960   5.421724e+00   5.602501e+00
   1_occ:  0.1573 0.1957   5.418990e+00   5.600542e+00
   2_bss:  0.1545 0.1914   5.406340e+00   5.587414e+00
   2_xyz:  0.1235 0.1647   5.215712e+00   5.435158e+00
   2_adp:  0.1172 0.1604   5.174204e+00   5.408860e+00
   2_occ:  0.1171 0.1603   5.174086e+00   5.409200e+00
   3_bss:  0.1171 0.1599   5.172417e+00   5.406450e+00
   3_xyz:  0.1121 0.1584   5.148431e+00   5.393651e+00
   3_adp:  0.1119 0.1571   5.144272e+00   5.386111e+00
   3_occ:  0.1118 0.1571   5.144284e+00   5.386530e+00
   4_bss:  0.1118 0.1571   5.143994e+00   5.386132e+00
   4_xyz:  0.1100 0.1576   5.137599e+00   5.388114e+00
   4_adp:  0.1089 0.1583   5.135176e+00   5.392247e+00
   4_occ:  0.1088 0.1583   5.135228e+00   5.392519e+00
   5_bss:  0.1087 0.1583   5.135343e+00   5.392539e+00
   5_xyz:  0.1086 0.1588   5.137450e+00   5.396218e+00
   5_adp:  0.1107 0.1584   5.143712e+00   5.393781e+00
   5_occ:  0.1106 0.1583   5.143718e+00   5.394129e+00
   5_bss:  0.1106 0.1584   5.143772e+00   5.394129e+00
------------------------------------------------------------------------
 stage     k_sol   b_sol     b11     b22     b33     b12     b13     b23
   0    :  0.000   0.000   0.000   0.000   0.000   0.000   0.000   0.000
   1_bss:  0.321  50.000   1.965  -3.049  -1.593  -0.000  -0.000  -0.000
   1_xyz:  0.321  50.000   1.965  -3.049  -1.593  -0.000  -0.000  -0.000
   1_adp:  0.321  50.000   1.965  -3.049  -1.593  -0.000  -0.000  -0.000
   1_occ:  0.321  50.000   1.965  -3.049  -1.593  -0.000  -0.000  -0.000
   2_bss:  0.335  57.263  -1.311  -3.147  -1.964  -0.000  -0.000  -0.000
   2_xyz:  0.335  57.263  -1.311  -3.147  -1.964  -0.000  -0.000  -0.000
   2_adp:  0.335  57.263  -1.311  -3.147  -1.964  -0.000  -0.000  -0.000
   2_occ:  0.335  57.263  -1.311  -3.147  -1.964  -0.000  -0.000  -0.000
   3_bss:  0.328  57.263  -2.015  -2.855  -1.806  -0.000  -0.000  -0.000
   3_xyz:  0.328  57.263  -2.015  -2.855  -1.806  -0.000  -0.000  -0.000
   3_adp:  0.328  57.263  -2.015  -2.855  -1.806  -0.000  -0.000  -0.000
   3_occ:  0.328  57.263  -2.015  -2.855  -1.806  -0.000  -0.000  -0.000
   4_bss:  0.325  57.263  -2.208  -2.678  -1.704  -0.000  -0.000  -0.000
   4_xyz:  0.325  57.263  -2.208  -2.678  -1.704  -0.000  -0.000  -0.000
   4_adp:  0.325  57.263  -2.208  -2.678  -1.704  -0.000  -0.000  -0.000
   4_occ:  0.325  57.263  -2.208  -2.678  -1.704  -0.000  -0.000  -0.000
   5_bss:  0.325  57.263  -2.068  -2.447  -1.499  -0.000  -0.000  -0.000
   5_xyz:  0.325  57.263  -2.068  -2.447  -1.499  -0.000  -0.000  -0.000
   5_adp:  0.325  57.263  -2.068  -2.447  -1.499  -0.000  -0.000  -0.000
   5_occ:  0.325  57.263  -2.068  -2.447  -1.499  -0.000  -0.000  -0.000
   5_bss:  0.325  57.188  -1.979  -2.282  -1.330  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  32.227 0.7365  0.9047    28289.057
   1_bss:  30.988 0.7488  0.8958    25450.510
   1_xyz:  18.068 0.8812  1.0020     9683.774
   1_adp:  18.634 0.8755  1.0020    10026.123
   1_occ:  18.585 0.8758  1.0020     9953.315
   2_bss:  18.213 0.8793  0.9614     9649.356
   2_xyz:  14.886 0.9078  0.9759     7028.435
   2_adp:  14.283 0.9128  0.9764     6602.993
   2_occ:  14.285 0.9128  0.9762     6602.232
   3_bss:  14.240 0.9132  0.9727     6556.841
   3_xyz:  13.975 0.9154  0.9725     6380.560
   3_adp:  13.808 0.9168  0.9696     6316.419
   3_occ:  13.814 0.9168  0.9695     6316.576
   4_bss:  13.810 0.9168  0.9704     6308.305
   4_xyz:  13.844 0.9165  0.9700     6349.449
   4_adp:  13.942 0.9157  0.9645     6372.840
   4_occ:  13.947 0.9157  0.9644     6375.596
   5_bss:  13.950 0.9157  0.9710     6375.830
   5_xyz:  14.014 0.9152  0.9702     6421.774
   5_adp:  13.935 0.9159  0.9668     6428.923
   5_occ:  13.940 0.9158  0.9668     6429.614
   5_bss:  13.941 0.9158  0.9690     6429.085
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.113   1.6191e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.113   1.6191e-01
   1_xyz:   1.089  0.009  0.076 15.169  0.004  4.115   7.0127e-02
   1_adp:   1.089  0.009  0.076 15.169  0.004  4.115   7.0127e-02
   1_occ:   1.089  0.009  0.076 15.169  0.004  4.115   7.0127e-02
   2_bss:   1.089  0.009  0.076 15.169  0.004  4.115   7.0127e-02
   2_xyz:   1.062  0.009  0.078 14.684  0.004  4.128   6.6359e-02
   2_adp:   1.062  0.009  0.078 14.684  0.004  4.128   6.6359e-02
   2_occ:   1.062  0.009  0.078 14.684  0.004  4.128   6.6359e-02
   3_bss:   1.062  0.009  0.078 14.684  0.004  4.128   6.6359e-02
   3_xyz:   1.039  0.009  0.078 14.725  0.004  4.132   6.5386e-02
   3_adp:   1.039  0.009  0.078 14.725  0.004  4.132   6.5386e-02
   3_occ:   1.039  0.009  0.078 14.725  0.004  4.132   6.5386e-02
   4_bss:   1.039  0.009  0.078 14.725  0.004  4.132   6.5386e-02
   4_xyz:   1.067  0.009  0.080 14.699  0.004  4.134   6.8189e-02
   4_adp:   1.067  0.009  0.080 14.699  0.004  4.134   6.8189e-02
   4_occ:   1.067  0.009  0.080 14.699  0.004  4.134   6.8189e-02
   5_bss:   1.067  0.009  0.080 14.699  0.004  4.134   6.8189e-02
   5_xyz:   1.048  0.009  0.079 14.681  0.004  4.113   6.7032e-02
   5_adp:   1.048  0.009  0.079 14.681  0.004  4.113   6.7032e-02
   5_occ:   1.048  0.009  0.079 14.681  0.004  4.113   6.7032e-02
   5_bss:   1.048  0.009  0.079 14.681  0.004  4.113   6.7032e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.806   2.4230e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.806   2.4230e-01
   1_xyz:   9.717  0.039  0.274 84.614  0.036  2.310   7.5013e-02
   1_adp:   9.717  0.039  0.274 84.614  0.036  2.310   7.5013e-02
   1_occ:   9.717  0.039  0.274 84.614  0.036  2.310   7.5013e-02
   2_bss:   9.717  0.039  0.274 84.614  0.036  2.310   7.5013e-02
   2_xyz:   8.120  0.044  0.238 82.906  0.036  2.340   5.0451e-02
   2_adp:   8.120  0.044  0.238 82.906  0.036  2.340   5.0451e-02
   2_occ:   8.120  0.044  0.238 82.906  0.036  2.340   5.0451e-02
   3_bss:   8.120  0.044  0.238 82.906  0.036  2.340   5.0451e-02
   3_xyz:   8.054  0.042  0.239 83.354  0.038  2.306   4.6844e-02
   3_adp:   8.054  0.042  0.239 83.354  0.038  2.306   4.6844e-02
   3_occ:   8.054  0.042  0.239 83.354  0.038  2.306   4.6844e-02
   4_bss:   8.054  0.042  0.239 83.354  0.038  2.306   4.6844e-02
   4_xyz:   7.592  0.043  0.249 83.997  0.037  2.287   5.0288e-02
   4_adp:   7.592  0.043  0.249 83.997  0.037  2.287   5.0288e-02
   4_occ:   7.592  0.043  0.249 83.997  0.037  2.287   5.0288e-02
   5_bss:   7.592  0.043  0.249 83.997  0.037  2.287   5.0288e-02
   5_xyz:   7.581  0.045  0.243 83.709  0.038  2.325   4.8795e-02
   5_adp:   7.581  0.045  0.243 83.709  0.038  2.325   4.8795e-02
   5_occ:   7.581  0.045  0.243 83.709  0.038  2.325   4.8795e-02
   5_bss:   7.581  0.045  0.243 83.709  0.038  2.325   4.8795e-02
------------------------------------------------------------------------
           |-----overall-----|---macromolecule----|------solvent-------|
  stage    b_max  b_min  b_ave  b_max  b_min  b_ave  b_max  b_min  b_ave
   0    :  63.06   5.09  16.02  49.51   5.09  12.19  63.06   6.19  36.87
   1_bss:  63.06   5.09  16.02  49.51   5.09  12.19  63.06   6.19  36.87
   1_xyz:  63.06   5.09  16.02  49.51   5.09  12.19  63.06   6.19  36.87
   1_adp:  67.74   0.00  16.70  67.74   0.00  12.85  63.34   4.57  37.66
   1_occ:  67.74   0.00  16.70  67.74   0.00  12.85  63.34   4.57  37.66
   2_bss:  67.74   0.00  16.70  67.74   0.00  12.85  63.34   4.57  37.66
   2_xyz:  67.74   0.00  16.70  67.74   0.00  12.85  63.34   4.57  37.66
   2_adp:  75.03   1.23  17.11  75.03   1.23  13.11  73.38   4.44  38.90
   2_occ:  75.03   1.23  17.11  75.03   1.23  13.11  73.38   4.44  38.90
   3_bss:  75.03   1.23  17.11  75.03   1.23  13.11  73.38   4.44  38.90
   3_xyz:  75.03   1.23  17.11  75.03   1.23  13.11  73.38   4.44  38.90
   3_adp:  75.46   1.74  16.82  75.46   1.74  12.98  74.43   4.13  37.70
   3_occ:  75.46   1.74  16.82  75.46   1.74  12.98  74.43   4.13  37.70
   4_bss:  75.46   1.74  16.82  75.46   1.74  12.98  74.43   4.13  37.70
   4_xyz:  75.46   1.74  16.82  75.46   1.74  12.98  74.43   4.13  37.70
   4_adp:  84.40   0.55  17.10  84.40   0.55  13.00  79.11   5.07  39.45
   4_occ:  84.40   0.55  17.10  84.40   0.55  13.00  79.11   5.07  39.45
   5_bss:  84.40   0.55  17.10  84.40   0.55  13.00  79.11   5.07  39.45
   5_xyz:  84.40   0.55  17.10  84.40   0.55  13.00  79.11   5.07  39.45
   5_adp:  80.18   2.07  16.41  80.18   2.07  12.72  76.70   6.42  36.49
   5_occ:  80.18   2.07  16.41  80.18   2.07  12.72  76.70   6.42  36.49
   5_bss:  80.10   2.00  16.34  80.10   2.00  12.65  76.63   6.34  36.41
------------------------------------------------------------------------
 stage        Deviation of refined
              model from start model
               max      min     mean
   0    :    0.000    0.000    0.000
   1_bss:    0.000    0.000    0.000
   1_xyz:    0.991    0.010    0.298
   1_adp:    0.991    0.010    0.298
   1_occ:    0.991    0.010    0.298
   2_bss:    0.991    0.010    0.298
   2_xyz:    0.884    0.019    0.347
   2_adp:    0.884    0.019    0.347
   2_occ:    0.884    0.019    0.347
   3_bss:    0.884    0.019    0.347
   3_xyz:    0.884    0.030    0.369
   3_adp:    0.884    0.030    0.369
   3_occ:    0.884    0.030    0.369
   4_bss:    0.884    0.030    0.369
   4_xyz:    0.952    0.020    0.378
   4_adp:    0.952    0.020    0.378
   4_occ:    0.952    0.020    0.378
   5_bss:    0.952    0.020    0.378
   5_xyz:    1.025    0.022    0.381
   5_adp:    1.025    0.022    0.381
   5_occ:    1.025    0.022    0.381
   5_bss:    1.025    0.022    0.381
------------------------------------------------------------------------

CPU time actual refinement: 276.24


============================== Exporting results ==============================

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1148/model_refine_001.pdb
n_use            =  2823
n_use_u_iso      =  2823
n_use_u_aniso    =  0
n_grad_site      =  0
n_grad_u_iso     =  0
n_grad_u_aniso   =  0
n_grad_occupancy =  106
n_grad_fp        =  0
n_grad_fdp       =  0
n_anisotropic_flag =  0
total number of scatterers =  2823

Writing 2mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1148/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1148/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1148/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1148/model_refine_002.def


=============================== Detailed timings ==============================

Pure refinement (no I/O, processing, etc)= 276.12 
  Macro-tasks:
    bulk solvent and scale       = 30.84  
    individual site refinement   = 119.06 
    weights calculation          = 23.85  
    collect and process          = 5.44   
    model show statistics        = 0.08   
    TOTAL for macro-tasks        = 179.27 
  Micro-tasks:
    mask                            = 1.00   
    f_calc                          = 87.82  
    alpha_beta                      = 6.48   
    target                          = 0.94   
    gradients_wrt_atomic_parameters = 97.69  
    fmodel                         = 5.52   
    r_factors                      = 0.19   
    phase_errors                   = 9.34   
    foms                           = 0.34   
    TOTAL for micro-tasks          = 209.32 
NUMBER OF MASK CALCS=  3
Time per interpreted Python bytecode instruction: 3.818 micro seconds
Total CPU time: 4.79 minutes
from_scatterers_fft:    676 calls, 87.50 s
gradients_fft:          621 calls, 85.16 s

=========================== phenix.refine: finished ===========================

# Date 2008-01-16 Time 06:31:46 PST -0800 (1200493906.26 s)
Start R-work = 0.3070, R-free = 0.3070 (no bulk solvent and anisotropic scale)
Final R-work = 0.1347, R-free = 0.1784 (no bulk solvent and anisotropic scale)

Start R-work = 0.2911, R-free = 0.2925
Final R-work = 0.1106, R-free = 0.1584